Starting phenix.real_space_refine on Wed Mar 20 19:42:15 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ses_40427/03_2024/8ses_40427.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ses_40427/03_2024/8ses_40427.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.98 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ses_40427/03_2024/8ses_40427.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ses_40427/03_2024/8ses_40427.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ses_40427/03_2024/8ses_40427.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ses_40427/03_2024/8ses_40427.pdb" } resolution = 3.98 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.002 sd= 0.065 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians Zn 4 6.06 5 S 960 5.16 5 C 90916 2.51 5 N 24692 2.21 5 O 26368 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 1089": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 2973": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 3757": "OE1" <-> "OE2" Residue "A PHE 4789": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 5021": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 5032": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 1089": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 2973": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 3757": "OE1" <-> "OE2" Residue "B PHE 4789": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 5021": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 5032": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 1089": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 2973": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 3757": "OE1" <-> "OE2" Residue "C PHE 4789": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 5021": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 5032": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 1089": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 2973": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 3757": "OE1" <-> "OE2" Residue "D PHE 4789": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 5021": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 5032": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 1.79s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 142940 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 34906 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 4377, 34843 Classifications: {'peptide': 4377} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PCIS': 1, 'PTRANS': 215, 'TRANS': 4160} Chain breaks: 15 Unresolved chain link angles: 2 Unresolved chain link dihedrals: 4 Unresolved non-hydrogen bonds: 54 Unresolved non-hydrogen angles: 63 Unresolved non-hydrogen dihedrals: 46 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'TYR:plan': 1, 'GLU:plan': 2, 'ARG:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 28 Conformer: "B" Number of residues, atoms: 4377, 34849 Classifications: {'peptide': 4377} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PCIS': 1, 'PTRANS': 215, 'TRANS': 4160} Chain breaks: 15 Unresolved non-hydrogen bonds: 47 Unresolved non-hydrogen angles: 54 Unresolved non-hydrogen dihedrals: 43 Planarities with less than four sites: {'TYR:plan': 1, 'GLU:plan': 1, 'ARG:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 24 bond proxies already assigned to first conformer: 35561 Chain: "B" Number of atoms: 34906 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 4377, 34843 Classifications: {'peptide': 4377} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PCIS': 1, 'PTRANS': 215, 'TRANS': 4160} Chain breaks: 15 Unresolved chain link angles: 2 Unresolved chain link dihedrals: 4 Unresolved non-hydrogen bonds: 54 Unresolved non-hydrogen angles: 63 Unresolved non-hydrogen dihedrals: 46 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'TYR:plan': 1, 'GLU:plan': 2, 'ARG:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 28 Conformer: "B" Number of residues, atoms: 4377, 34849 Classifications: {'peptide': 4377} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PCIS': 1, 'PTRANS': 215, 'TRANS': 4160} Chain breaks: 15 Unresolved non-hydrogen bonds: 47 Unresolved non-hydrogen angles: 54 Unresolved non-hydrogen dihedrals: 43 Planarities with less than four sites: {'TYR:plan': 1, 'GLU:plan': 1, 'ARG:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 24 bond proxies already assigned to first conformer: 35561 Chain: "C" Number of atoms: 34906 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 4377, 34843 Classifications: {'peptide': 4377} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PCIS': 1, 'PTRANS': 215, 'TRANS': 4160} Chain breaks: 15 Unresolved chain link angles: 2 Unresolved chain link dihedrals: 4 Unresolved non-hydrogen bonds: 54 Unresolved non-hydrogen angles: 63 Unresolved non-hydrogen dihedrals: 46 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'TYR:plan': 1, 'GLU:plan': 2, 'ARG:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 28 Conformer: "B" Number of residues, atoms: 4377, 34849 Classifications: {'peptide': 4377} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PCIS': 1, 'PTRANS': 215, 'TRANS': 4160} Chain breaks: 15 Unresolved non-hydrogen bonds: 47 Unresolved non-hydrogen angles: 54 Unresolved non-hydrogen dihedrals: 43 Planarities with less than four sites: {'TYR:plan': 1, 'GLU:plan': 1, 'ARG:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 24 bond proxies already assigned to first conformer: 35561 Chain: "D" Number of atoms: 34906 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 4377, 34843 Classifications: {'peptide': 4377} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PCIS': 1, 'PTRANS': 215, 'TRANS': 4160} Chain breaks: 15 Unresolved chain link angles: 2 Unresolved chain link dihedrals: 4 Unresolved non-hydrogen bonds: 54 Unresolved non-hydrogen angles: 63 Unresolved non-hydrogen dihedrals: 46 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'TYR:plan': 1, 'GLU:plan': 2, 'ARG:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 28 Conformer: "B" Number of residues, atoms: 4377, 34849 Classifications: {'peptide': 4377} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PCIS': 1, 'PTRANS': 215, 'TRANS': 4160} Chain breaks: 15 Unresolved non-hydrogen bonds: 47 Unresolved non-hydrogen angles: 54 Unresolved non-hydrogen dihedrals: 43 Planarities with less than four sites: {'TYR:plan': 1, 'GLU:plan': 1, 'ARG:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 24 bond proxies already assigned to first conformer: 35561 Chain: "E" Number of atoms: 818 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 818 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 7, 'TRANS': 99} Chain: "F" Number of atoms: 818 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 818 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 7, 'TRANS': 99} Chain: "G" Number of atoms: 818 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 818 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 7, 'TRANS': 99} Chain: "H" Number of atoms: 818 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 818 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 7, 'TRANS': 99} Chain: "A" Number of atoms: 11 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 11 Unusual residues: {' ZN': 1} Classifications: {'DNA': 1, 'undetermined': 1} Modifications used: {'5*END': 1} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 11 Unresolved non-hydrogen chiralities: 3 Unresolved non-hydrogen planarities: 1 Chain: "B" Number of atoms: 11 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 11 Unusual residues: {' ZN': 1} Classifications: {'DNA': 1, 'undetermined': 1} Modifications used: {'5*END': 1} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 11 Unresolved non-hydrogen chiralities: 3 Unresolved non-hydrogen planarities: 1 Chain: "C" Number of atoms: 11 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 11 Unusual residues: {' ZN': 1} Classifications: {'DNA': 1, 'undetermined': 1} Modifications used: {'5*END': 1} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 11 Unresolved non-hydrogen chiralities: 3 Unresolved non-hydrogen planarities: 1 Chain: "D" Number of atoms: 11 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 11 Unusual residues: {' ZN': 1} Classifications: {'DNA': 1, 'undetermined': 1} Modifications used: {'5*END': 1} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 11 Unresolved non-hydrogen chiralities: 3 Unresolved non-hydrogen planarities: 1 List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 34232 SG CYS A4958 175.761 201.246 87.477 1.00176.19 S ATOM 34257 SG CYS A4961 178.432 201.788 89.752 1.00170.06 S ATOM 69138 SG CYS B4958 179.961 175.762 87.463 1.00176.19 S ATOM 69163 SG CYS B4961 179.421 178.433 89.740 1.00170.06 S ATOM A034C SG CYS C4958 205.486 179.961 87.463 1.00176.19 S ATOM A0351 SG CYS C4961 202.815 179.421 89.739 1.00170.06 S ATOM A0U1Y SG CYS D4958 201.287 205.485 87.463 1.00176.19 S ATOM A0U2N SG CYS D4961 201.827 202.815 89.740 1.00170.06 S Time building chain proxies: 102.22, per 1000 atoms: 0.72 Number of scatterers: 142940 At special positions: 0 Unit cell: (382.536, 382.536, 212.52, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Zn 4 29.99 S 960 16.00 O 26368 8.00 N 24692 7.00 C 90916 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=12, symmetry=0 Simple disulfide: pdb=" SG CYS A 230 " - pdb=" SG CYS A 253 " distance=2.03 Simple disulfide: pdb=" SG CYS A3170 " - pdb=" SG CYS A3240 " distance=2.03 Simple disulfide: pdb=" SG CYS A4876 " - pdb=" SG CYS A4882 " distance=2.04 Simple disulfide: pdb=" SG CYS B 230 " - pdb=" SG CYS B 253 " distance=2.04 Simple disulfide: pdb=" SG CYS B3170 " - pdb=" SG CYS B3240 " distance=2.03 Simple disulfide: pdb=" SG CYS B4876 " - pdb=" SG CYS B4882 " distance=2.04 Simple disulfide: pdb=" SG CYS C 230 " - pdb=" SG CYS C 253 " distance=2.03 Simple disulfide: pdb=" SG CYS C3170 " - pdb=" SG CYS C3240 " distance=2.03 Simple disulfide: pdb=" SG CYS C4876 " - pdb=" SG CYS C4882 " distance=2.04 Simple disulfide: pdb=" SG CYS D 230 " - pdb=" SG CYS D 253 " distance=2.03 Simple disulfide: pdb=" SG CYS D3170 " - pdb=" SG CYS D3240 " distance=2.03 Simple disulfide: pdb=" SG CYS D4876 " - pdb=" SG CYS D4882 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 44.12 Conformation dependent library (CDL) restraints added in 38.8 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A5101 " pdb="ZN ZN A5101 " - pdb=" NE2 HIS A4978 " pdb="ZN ZN A5101 " - pdb=" ND1 HIS A4983 " pdb="ZN ZN A5101 " - pdb=" SG CYS A4961 " pdb="ZN ZN A5101 " - pdb=" SG CYS A4958 " pdb=" ZN B5101 " pdb="ZN ZN B5101 " - pdb=" NE2 HIS B4978 " pdb="ZN ZN B5101 " - pdb=" ND1 HIS B4983 " pdb="ZN ZN B5101 " - pdb=" SG CYS B4961 " pdb="ZN ZN B5101 " - pdb=" SG CYS B4958 " pdb=" ZN C5101 " pdb="ZN ZN C5101 " - pdb=" NE2 HIS C4978 " pdb="ZN ZN C5101 " - pdb=" ND1 HIS C4983 " pdb="ZN ZN C5101 " - pdb=" SG CYS C4961 " pdb="ZN ZN C5101 " - pdb=" SG CYS C4958 " pdb=" ZN D5101 " pdb="ZN ZN D5101 " - pdb=" NE2 HIS D4978 " pdb="ZN ZN D5101 " - pdb=" ND1 HIS D4983 " pdb="ZN ZN D5101 " - pdb=" SG CYS D4961 " pdb="ZN ZN D5101 " - pdb=" SG CYS D4958 " Number of angles added : 4 35664 Ramachandran restraints generated. 17832 Oldfield, 0 Emsley, 17832 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 33672 Finding SS restraints... Secondary structure from input PDB file: 780 helices and 100 sheets defined 55.8% alpha, 9.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 19.29 Creating SS restraints... Processing helix chain 'A' and resid 74 through 84 Processing helix chain 'A' and resid 251 through 258 removed outlier: 3.684A pdb=" N THR A 254 " --> pdb=" O ALA A 251 " (cutoff:3.500A) removed outlier: 6.072A pdb=" N ALA A 256 " --> pdb=" O CYS A 253 " (cutoff:3.500A) removed outlier: 6.666A pdb=" N ARG A 257 " --> pdb=" O THR A 254 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N SER A 258 " --> pdb=" O HIS A 255 " (cutoff:3.500A) Processing helix chain 'A' and resid 305 through 307 No H-bonds generated for 'chain 'A' and resid 305 through 307' Processing helix chain 'A' and resid 365 through 370 removed outlier: 4.315A pdb=" N LEU A 369 " --> pdb=" O LYS A 365 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N GLY A 370 " --> pdb=" O ALA A 366 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 365 through 370' Processing helix chain 'A' and resid 394 through 421 removed outlier: 3.902A pdb=" N ARG A 402 " --> pdb=" O SER A 398 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N MET A 403 " --> pdb=" O GLN A 399 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N ILE A 404 " --> pdb=" O ALA A 400 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N HIS A 405 " --> pdb=" O ALA A 401 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N GLY A 409 " --> pdb=" O HIS A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 437 through 452 removed outlier: 3.557A pdb=" N GLY A 450 " --> pdb=" O GLN A 446 " (cutoff:3.500A) Processing helix chain 'A' and resid 460 through 481 Processing helix chain 'A' and resid 482 through 495 Processing helix chain 'A' and resid 499 through 505 Processing helix chain 'A' and resid 508 through 513 removed outlier: 4.130A pdb=" N GLU A 513 " --> pdb=" O GLU A 509 " (cutoff:3.500A) Processing helix chain 'A' and resid 513 through 531 removed outlier: 4.561A pdb=" N GLU A 517 " --> pdb=" O GLU A 513 " (cutoff:3.500A) Processing helix chain 'A' and resid 533 through 538 Processing helix chain 'A' and resid 539 through 542 removed outlier: 3.826A pdb=" N THR A 542 " --> pdb=" O LEU A 539 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 539 through 542' Processing helix chain 'A' and resid 543 through 549 removed outlier: 4.166A pdb=" N VAL A 547 " --> pdb=" O ASN A 543 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N VAL A 548 " --> pdb=" O LEU A 544 " (cutoff:3.500A) Processing helix chain 'A' and resid 557 through 569 Processing helix chain 'A' and resid 571 through 578 removed outlier: 3.935A pdb=" N LEU A 575 " --> pdb=" O SER A 571 " (cutoff:3.500A) Processing helix chain 'A' and resid 579 through 593 removed outlier: 3.630A pdb=" N ILE A 583 " --> pdb=" O GLN A 579 " (cutoff:3.500A) Processing helix chain 'A' and resid 596 through 607 removed outlier: 4.169A pdb=" N LEU A 600 " --> pdb=" O ASN A 596 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N ASP A 601 " --> pdb=" O HIS A 597 " (cutoff:3.500A) Processing helix chain 'A' and resid 614 through 626 removed outlier: 3.554A pdb=" N ASP A 619 " --> pdb=" O ARG A 615 " (cutoff:3.500A) removed outlier: 4.428A pdb=" N LEU A 620 " --> pdb=" O SER A 616 " (cutoff:3.500A) Processing helix chain 'A' and resid 794 through 798 removed outlier: 3.978A pdb=" N GLY A 798 " --> pdb=" O GLY A 795 " (cutoff:3.500A) Processing helix chain 'A' and resid 812 through 814 No H-bonds generated for 'chain 'A' and resid 812 through 814' Processing helix chain 'A' and resid 847 through 851 Processing helix chain 'A' and resid 864 through 869 Processing helix chain 'A' and resid 872 through 877 Processing helix chain 'A' and resid 880 through 885 removed outlier: 4.365A pdb=" N THR A 885 " --> pdb=" O LEU A 881 " (cutoff:3.500A) Processing helix chain 'A' and resid 914 through 936 Processing helix chain 'A' and resid 978 through 1003 removed outlier: 3.508A pdb=" N VAL A 995 " --> pdb=" O ASN A 991 " (cutoff:3.500A) Processing helix chain 'A' and resid 1023 through 1027 Processing helix chain 'A' and resid 1028 through 1049 removed outlier: 4.080A pdb=" N SER A1038 " --> pdb=" O SER A1034 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N LEU A1039 " --> pdb=" O ASN A1035 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N TYR A1049 " --> pdb=" O THR A1045 " (cutoff:3.500A) Processing helix chain 'A' and resid 1068 through 1072 removed outlier: 3.771A pdb=" N ARG A1071 " --> pdb=" O ARG A1068 " (cutoff:3.500A) removed outlier: 4.416A pdb=" N VAL A1072 " --> pdb=" O TRP A1069 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1068 through 1072' Processing helix chain 'A' and resid 1079 through 1082 Processing helix chain 'A' and resid 1423 through 1430 Processing helix chain 'A' and resid 1444 through 1446 No H-bonds generated for 'chain 'A' and resid 1444 through 1446' Processing helix chain 'A' and resid 1465 through 1469 removed outlier: 3.583A pdb=" N VAL A1469 " --> pdb=" O LEU A1466 " (cutoff:3.500A) Processing helix chain 'A' and resid 1498 through 1500 No H-bonds generated for 'chain 'A' and resid 1498 through 1500' Processing helix chain 'A' and resid 1574 through 1580 removed outlier: 3.780A pdb=" N ALA A1578 " --> pdb=" O PRO A1574 " (cutoff:3.500A) Processing helix chain 'A' and resid 1581 through 1584 removed outlier: 4.074A pdb=" N ARG A1584 " --> pdb=" O LEU A1581 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1581 through 1584' Processing helix chain 'A' and resid 1651 through 1655 Processing helix chain 'A' and resid 1656 through 1674 removed outlier: 4.119A pdb=" N PHE A1662 " --> pdb=" O ASP A1658 " (cutoff:3.500A) Processing helix chain 'A' and resid 1678 through 1689 removed outlier: 3.614A pdb=" N ALA A1684 " --> pdb=" O ARG A1680 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N CYS A1686 " --> pdb=" O ALA A1682 " (cutoff:3.500A) removed outlier: 4.153A pdb=" N SER A1687 " --> pdb=" O HIS A1683 " (cutoff:3.500A) removed outlier: 4.331A pdb=" N HIS A1688 " --> pdb=" O ALA A1684 " (cutoff:3.500A) Processing helix chain 'A' and resid 1690 through 1699 removed outlier: 4.169A pdb=" N GLU A1699 " --> pdb=" O LEU A1695 " (cutoff:3.500A) Processing helix chain 'A' and resid 1704 through 1720 Processing helix chain 'A' and resid 1720 through 1731 Processing helix chain 'A' and resid 1739 through 1744 Processing helix chain 'A' and resid 1803 through 1824 removed outlier: 3.674A pdb=" N GLY A1823 " --> pdb=" O VAL A1819 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N GLN A1824 " --> pdb=" O ARG A1820 " (cutoff:3.500A) Processing helix chain 'A' and resid 1833 through 1852 Proline residue: A1840 - end of helix Processing helix chain 'A' and resid 1855 through 1867 Processing helix chain 'A' and resid 1925 through 1929 removed outlier: 4.098A pdb=" N GLN A1928 " --> pdb=" O GLY A1925 " (cutoff:3.500A) Processing helix chain 'A' and resid 1932 through 1982 removed outlier: 3.823A pdb=" N GLN A1938 " --> pdb=" O SER A1934 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N PHE A1946 " --> pdb=" O LEU A1942 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N GLN A1949 " --> pdb=" O TYR A1945 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N GLU A1950 " --> pdb=" O PHE A1946 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N LEU A1951 " --> pdb=" O CYS A1947 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N ASP A1967 " --> pdb=" O GLU A1963 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N LYS A1968 " --> pdb=" O ARG A1964 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N ARG A1982 " --> pdb=" O ALA A1978 " (cutoff:3.500A) Processing helix chain 'A' and resid 1983 through 1986 Processing helix chain 'A' and resid 1990 through 1995 Processing helix chain 'A' and resid 2001 through 2011 Processing helix chain 'A' and resid 2024 through 2042 removed outlier: 3.669A pdb=" N GLN A2032 " --> pdb=" O ARG A2028 " (cutoff:3.500A) Processing helix chain 'A' and resid 2093 through 2109 removed outlier: 3.762A pdb=" N ASP A2109 " --> pdb=" O TRP A2105 " (cutoff:3.500A) Processing helix chain 'A' and resid 2113 through 2129 Processing helix chain 'A' and resid 2129 through 2136 removed outlier: 3.606A pdb=" N GLU A2133 " --> pdb=" O ASP A2129 " (cutoff:3.500A) Processing helix chain 'A' and resid 2137 through 2139 No H-bonds generated for 'chain 'A' and resid 2137 through 2139' Processing helix chain 'A' and resid 2145 through 2147 No H-bonds generated for 'chain 'A' and resid 2145 through 2147' Processing helix chain 'A' and resid 2148 through 2165 removed outlier: 3.672A pdb=" N CYS A2158 " --> pdb=" O SER A2154 " (cutoff:3.500A) Processing helix chain 'A' and resid 2166 through 2168 No H-bonds generated for 'chain 'A' and resid 2166 through 2168' Processing helix chain 'A' and resid 2171 through 2188 removed outlier: 3.515A pdb=" N ILE A2185 " --> pdb=" O SER A2181 " (cutoff:3.500A) Processing helix chain 'A' and resid 2189 through 2194 Processing helix chain 'A' and resid 2194 through 2202 removed outlier: 3.540A pdb=" N MET A2198 " --> pdb=" O HIS A2194 " (cutoff:3.500A) Processing helix chain 'A' and resid 2202 through 2217 removed outlier: 3.531A pdb=" N VAL A2210 " --> pdb=" O THR A2206 " (cutoff:3.500A) Processing helix chain 'A' and resid 2225 through 2243 removed outlier: 3.850A pdb=" N VAL A2229 " --> pdb=" O PHE A2225 " (cutoff:3.500A) removed outlier: 4.512A pdb=" N SER A2243 " --> pdb=" O PHE A2239 " (cutoff:3.500A) Processing helix chain 'A' and resid 2243 through 2252 Processing helix chain 'A' and resid 2253 through 2261 removed outlier: 3.569A pdb=" N LEU A2258 " --> pdb=" O LEU A2254 " (cutoff:3.500A) removed outlier: 4.131A pdb=" N GLU A2259 " --> pdb=" O SER A2255 " (cutoff:3.500A) removed outlier: 4.451A pdb=" N ASN A2260 " --> pdb=" O TYR A2256 " (cutoff:3.500A) Processing helix chain 'A' and resid 2262 through 2267 removed outlier: 5.414A pdb=" N LEU A2265 " --> pdb=" O GLY A2262 " (cutoff:3.500A) Processing helix chain 'A' and resid 2271 through 2279 Processing helix chain 'A' and resid 2283 through 2290 Processing helix chain 'A' and resid 2291 through 2306 Processing helix chain 'A' and resid 2310 through 2316 Processing helix chain 'A' and resid 2324 through 2339 Processing helix chain 'A' and resid 2346 through 2360 Processing helix chain 'A' and resid 2361 through 2365 Processing helix chain 'A' and resid 2375 through 2389 removed outlier: 4.110A pdb=" N GLU A2381 " --> pdb=" O LEU A2377 " (cutoff:3.500A) removed outlier: 4.410A pdb=" N GLU A2382 " --> pdb=" O ALA A2378 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N ALA A2383 " --> pdb=" O ALA A2379 " (cutoff:3.500A) Processing helix chain 'A' and resid 2417 through 2437 Processing helix chain 'A' and resid 2439 through 2446 Processing helix chain 'A' and resid 2447 through 2461 removed outlier: 3.701A pdb=" N ARG A2452 " --> pdb=" O GLY A2448 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ARG A2454 " --> pdb=" O ALA A2450 " (cutoff:3.500A) Processing helix chain 'A' and resid 2462 through 2471 Processing helix chain 'A' and resid 2489 through 2493 removed outlier: 4.246A pdb=" N SER A2493 " --> pdb=" O MET A2490 " (cutoff:3.500A) Processing helix chain 'A' and resid 2495 through 2510 removed outlier: 4.133A pdb=" N LYS A2499 " --> pdb=" O VAL A2495 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N MET A2502 " --> pdb=" O HIS A2498 " (cutoff:3.500A) Processing helix chain 'A' and resid 2514 through 2526 removed outlier: 4.325A pdb=" N VAL A2524 " --> pdb=" O HIS A2520 " (cutoff:3.500A) Processing helix chain 'A' and resid 2526 through 2537 Processing helix chain 'A' and resid 2544 through 2557 Processing helix chain 'A' and resid 2557 through 2565 removed outlier: 3.512A pdb=" N LYS A2564 " --> pdb=" O PRO A2560 " (cutoff:3.500A) Processing helix chain 'A' and resid 2566 through 2574 removed outlier: 4.325A pdb=" N GLY A2571 " --> pdb=" O LEU A2568 " (cutoff:3.500A) removed outlier: 4.135A pdb=" N THR A2572 " --> pdb=" O PHE A2569 " (cutoff:3.500A) removed outlier: 5.381A pdb=" N GLU A2573 " --> pdb=" O ALA A2570 " (cutoff:3.500A) removed outlier: 4.491A pdb=" N HIS A2574 " --> pdb=" O GLY A2571 " (cutoff:3.500A) Processing helix chain 'A' and resid 2575 through 2591 removed outlier: 4.034A pdb=" N VAL A2579 " --> pdb=" O ARG A2575 " (cutoff:3.500A) Processing helix chain 'A' and resid 2596 through 2613 removed outlier: 3.532A pdb=" N ARG A2612 " --> pdb=" O MET A2608 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N TYR A2613 " --> pdb=" O ALA A2609 " (cutoff:3.500A) Processing helix chain 'A' and resid 2615 through 2630 removed outlier: 4.974A pdb=" N HIS A2621 " --> pdb=" O SER A2617 " (cutoff:3.500A) removed outlier: 4.287A pdb=" N LEU A2622 " --> pdb=" O MET A2618 " (cutoff:3.500A) Processing helix chain 'A' and resid 2631 through 2633 No H-bonds generated for 'chain 'A' and resid 2631 through 2633' Processing helix chain 'A' and resid 2634 through 2636 No H-bonds generated for 'chain 'A' and resid 2634 through 2636' Processing helix chain 'A' and resid 2637 through 2651 removed outlier: 3.910A pdb=" N LYS A2642 " --> pdb=" O LYS A2638 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N HIS A2647 " --> pdb=" O LEU A2643 " (cutoff:3.500A) Processing helix chain 'A' and resid 2651 through 2657 removed outlier: 3.839A pdb=" N TYR A2655 " --> pdb=" O CYS A2651 " (cutoff:3.500A) Processing helix chain 'A' and resid 2670 through 2689 removed outlier: 3.648A pdb=" N ALA A2687 " --> pdb=" O PHE A2683 " (cutoff:3.500A) Processing helix chain 'A' and resid 2692 through 2710 removed outlier: 3.579A pdb=" N MET A2698 " --> pdb=" O GLU A2694 " (cutoff:3.500A) Proline residue: A2701 - end of helix Processing helix chain 'A' and resid 2748 through 2750 No H-bonds generated for 'chain 'A' and resid 2748 through 2750' Processing helix chain 'A' and resid 2751 through 2773 removed outlier: 3.730A pdb=" N LYS A2757 " --> pdb=" O SER A2753 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N HIS A2763 " --> pdb=" O ALA A2759 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N GLU A2764 " --> pdb=" O GLU A2760 " (cutoff:3.500A) Processing helix chain 'A' and resid 2806 through 2819 removed outlier: 3.877A pdb=" N LEU A2813 " --> pdb=" O ILE A2809 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N LYS A2814 " --> pdb=" O LYS A2810 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N TRP A2819 " --> pdb=" O ALA A2815 " (cutoff:3.500A) Processing helix chain 'A' and resid 2868 through 2895 removed outlier: 4.109A pdb=" N GLU A2893 " --> pdb=" O LYS A2889 " (cutoff:3.500A) Processing helix chain 'A' and resid 2912 through 2932 removed outlier: 5.535A pdb=" N ARG A2918 " --> pdb=" O LYS A2914 " (cutoff:3.500A) removed outlier: 4.415A pdb=" N ASP A2919 " --> pdb=" O GLU A2915 " (cutoff:3.500A) Processing helix chain 'A' and resid 2954 through 2983 removed outlier: 3.778A pdb=" N ILE A2969 " --> pdb=" O ARG A2965 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N ALA A2975 " --> pdb=" O GLN A2971 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N HIS A2976 " --> pdb=" O GLU A2972 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N SER A2983 " --> pdb=" O ALA A2979 " (cutoff:3.500A) Processing helix chain 'A' and resid 2991 through 3013 removed outlier: 5.459A pdb=" N LEU A3003 " --> pdb=" O ALA A2999 " (cutoff:3.500A) Proline residue: A3004 - end of helix removed outlier: 3.514A pdb=" N PHE A3010 " --> pdb=" O ILE A3006 " (cutoff:3.500A) removed outlier: 4.156A pdb=" N THR A3011 " --> pdb=" O ASN A3007 " (cutoff:3.500A) Processing helix chain 'A' and resid 3013 through 3018 Processing helix chain 'A' and resid 3032 through 3051 removed outlier: 3.791A pdb=" N GLU A3037 " --> pdb=" O ASN A3033 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N ALA A3047 " --> pdb=" O PHE A3043 " (cutoff:3.500A) Processing helix chain 'A' and resid 3053 through 3058 Processing helix chain 'A' and resid 3060 through 3074 removed outlier: 3.501A pdb=" N ASN A3066 " --> pdb=" O PRO A3062 " (cutoff:3.500A) Processing helix chain 'A' and resid 3076 through 3083 removed outlier: 3.972A pdb=" N VAL A3080 " --> pdb=" O ASP A3076 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N MET A3081 " --> pdb=" O ALA A3077 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N LYS A3082 " --> pdb=" O ARG A3078 " (cutoff:3.500A) Processing helix chain 'A' and resid 3085 through 3111 Processing helix chain 'A' and resid 3124 through 3136 removed outlier: 3.883A pdb=" N ASN A3128 " --> pdb=" O GLY A3124 " (cutoff:3.500A) Processing helix chain 'A' and resid 3136 through 3151 Processing helix chain 'A' and resid 3152 through 3157 Processing helix chain 'A' and resid 3160 through 3174 removed outlier: 3.843A pdb=" N ARG A3167 " --> pdb=" O VAL A3163 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N THR A3168 " --> pdb=" O SER A3164 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N TYR A3173 " --> pdb=" O LEU A3169 " (cutoff:3.500A) Processing helix chain 'A' and resid 3175 through 3178 Processing helix chain 'A' and resid 3180 through 3201 Proline residue: A3188 - end of helix Processing helix chain 'A' and resid 3207 through 3214 removed outlier: 5.176A pdb=" N GLU A3212 " --> pdb=" O GLN A3209 " (cutoff:3.500A) Processing helix chain 'A' and resid 3217 through 3222 Processing helix chain 'A' and resid 3245 through 3260 removed outlier: 3.676A pdb=" N ALA A3251 " --> pdb=" O ASP A3247 " (cutoff:3.500A) Processing helix chain 'A' and resid 3266 through 3272 Processing helix chain 'A' and resid 3272 through 3279 Processing helix chain 'A' and resid 3280 through 3286 removed outlier: 4.075A pdb=" N GLU A3286 " --> pdb=" O PRO A3282 " (cutoff:3.500A) Processing helix chain 'A' and resid 3308 through 3326 removed outlier: 3.615A pdb=" N LEU A3315 " --> pdb=" O HIS A3311 " (cutoff:3.500A) Processing helix chain 'A' and resid 3334 through 3343 Processing helix chain 'A' and resid 3344 through 3350 removed outlier: 3.829A pdb=" N SER A3347 " --> pdb=" O PRO A3344 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N ARG A3348 " --> pdb=" O ILE A3345 " (cutoff:3.500A) removed outlier: 6.741A pdb=" N ARG A3350 " --> pdb=" O SER A3347 " (cutoff:3.500A) Processing helix chain 'A' and resid 3351 through 3357 removed outlier: 4.160A pdb=" N HIS A3355 " --> pdb=" O PRO A3351 " (cutoff:3.500A) Processing helix chain 'A' and resid 3357 through 3382 removed outlier: 3.709A pdb=" N GLU A3382 " --> pdb=" O GLN A3378 " (cutoff:3.500A) Processing helix chain 'A' and resid 3384 through 3386 No H-bonds generated for 'chain 'A' and resid 3384 through 3386' Processing helix chain 'A' and resid 3387 through 3419 removed outlier: 3.670A pdb=" N LEU A3392 " --> pdb=" O GLU A3388 " (cutoff:3.500A) removed outlier: 7.011A pdb=" N LEU A3393 " --> pdb=" O GLU A3389 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N VAL A3394 " --> pdb=" O GLY A3390 " (cutoff:3.500A) Proline residue: A3410 - end of helix removed outlier: 3.617A pdb=" N ARG A3414 " --> pdb=" O PRO A3410 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N ASN A3419 " --> pdb=" O TYR A3415 " (cutoff:3.500A) Processing helix chain 'A' and resid 3419 through 3426 Processing helix chain 'A' and resid 3428 through 3448 Processing helix chain 'A' and resid 3448 through 3463 Processing helix chain 'A' and resid 3471 through 3477 Processing helix chain 'A' and resid 3504 through 3507 Processing helix chain 'A' and resid 3508 through 3522 Proline residue: A3519 - end of helix Processing helix chain 'A' and resid 3526 through 3528 No H-bonds generated for 'chain 'A' and resid 3526 through 3528' Processing helix chain 'A' and resid 3529 through 3542 Processing helix chain 'A' and resid 3545 through 3556 Processing helix chain 'A' and resid 3566 through 3578 removed outlier: 3.863A pdb=" N ARG A3570 " --> pdb=" O SER A3566 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N TRP A3571 " --> pdb=" O PRO A3567 " (cutoff:3.500A) Processing helix chain 'A' and resid 3588 through 3611 Processing helix chain 'A' and resid 3624 through 3638 removed outlier: 6.727A pdb=" N ARG A3630 " --> pdb=" O LYS A3626 " (cutoff:3.500A) removed outlier: 6.366A pdb=" N ALA A3631 " --> pdb=" O GLN A3627 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N VAL A3632 " --> pdb=" O ARG A3628 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N VAL A3633 " --> pdb=" O ARG A3629 " (cutoff:3.500A) Processing helix chain 'A' and resid 3640 through 3644 Processing helix chain 'A' and resid 3645 through 3661 removed outlier: 3.556A pdb=" N GLU A3655 " --> pdb=" O ASN A3651 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N ALA A3659 " --> pdb=" O GLU A3655 " (cutoff:3.500A) Processing helix chain 'A' and resid 3669 through 3678 Processing helix chain 'A' and resid 3696 through 3710 Processing helix chain 'A' and resid 3719 through 3735 removed outlier: 4.101A pdb=" N CYS A3733 " --> pdb=" O MET A3729 " (cutoff:3.500A) removed outlier: 4.571A pdb=" N HIS A3734 " --> pdb=" O ALA A3730 " (cutoff:3.500A) removed outlier: 4.361A pdb=" N LEU A3735 " --> pdb=" O LYS A3731 " (cutoff:3.500A) Processing helix chain 'A' and resid 3752 through 3772 removed outlier: 4.268A pdb=" N MET A3758 " --> pdb=" O GLU A3754 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N GLU A3759 " --> pdb=" O GLU A3755 " (cutoff:3.500A) Processing helix chain 'A' and resid 3774 through 3786 removed outlier: 3.522A pdb=" N LEU A3780 " --> pdb=" O ALA A3776 " (cutoff:3.500A) Processing helix chain 'A' and resid 3791 through 3806 Processing helix chain 'A' and resid 3809 through 3824 Processing helix chain 'A' and resid 3826 through 3838 Processing helix chain 'A' and resid 3843 through 3857 removed outlier: 3.802A pdb=" N PHE A3847 " --> pdb=" O ASP A3843 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N GLY A3857 " --> pdb=" O ALA A3853 " (cutoff:3.500A) Processing helix chain 'A' and resid 3877 through 3892 removed outlier: 3.549A pdb=" N PHE A3885 " --> pdb=" O THR A3881 " (cutoff:3.500A) Processing helix chain 'A' and resid 3896 through 3905 removed outlier: 3.660A pdb=" N TYR A3902 " --> pdb=" O ASP A3898 " (cutoff:3.500A) Processing helix chain 'A' and resid 3914 through 3935 Processing helix chain 'A' and resid 3944 through 3970 removed outlier: 3.764A pdb=" N SER A3956 " --> pdb=" O SER A3952 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N VAL A3957 " --> pdb=" O LYS A3953 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N ALA A3958 " --> pdb=" O ALA A3954 " (cutoff:3.500A) Processing helix chain 'A' and resid 3973 through 3982 Processing helix chain 'A' and resid 3984 through 4005 removed outlier: 3.824A pdb=" N MET A4001 " --> pdb=" O ALA A3997 " (cutoff:3.500A) Processing helix chain 'A' and resid 4009 through 4032 Processing helix chain 'A' and resid 4038 through 4051 removed outlier: 3.667A pdb=" N GLU A4050 " --> pdb=" O ASP A4046 " (cutoff:3.500A) Processing helix chain 'A' and resid 4051 through 4072 removed outlier: 3.933A pdb=" N MET A4057 " --> pdb=" O SER A4053 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N MET A4064 " --> pdb=" O LYS A4060 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N PHE A4065 " --> pdb=" O PHE A4061 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N ASP A4070 " --> pdb=" O LEU A4066 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N ILE A4071 " --> pdb=" O LYS A4067 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N VAL A4072 " --> pdb=" O LEU A4068 " (cutoff:3.500A) Processing helix chain 'A' and resid 4074 through 4079 Processing helix chain 'A' and resid 4090 through 4098 removed outlier: 3.787A pdb=" N ALA A4096 " --> pdb=" O ASP A4092 " (cutoff:3.500A) removed outlier: 4.114A pdb=" N ASP A4098 " --> pdb=" O GLN A4094 " (cutoff:3.500A) Processing helix chain 'A' and resid 4099 through 4101 No H-bonds generated for 'chain 'A' and resid 4099 through 4101' Processing helix chain 'A' and resid 4104 through 4115 Processing helix chain 'A' and resid 4128 through 4131 Processing helix chain 'A' and resid 4132 through 4154 removed outlier: 4.338A pdb=" N ASP A4138 " --> pdb=" O GLU A4134 " (cutoff:3.500A) removed outlier: 4.305A pdb=" N ILE A4139 " --> pdb=" O PRO A4135 " (cutoff:3.500A) Processing helix chain 'A' and resid 4157 through 4166 removed outlier: 3.809A pdb=" N ARG A4161 " --> pdb=" O ASP A4157 " (cutoff:3.500A) Processing helix chain 'A' and resid 4167 through 4175 removed outlier: 4.090A pdb=" N LEU A4171 " --> pdb=" O ALA A4167 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N GLU A4172 " --> pdb=" O GLU A4168 " (cutoff:3.500A) removed outlier: 4.335A pdb=" N TYR A4173 " --> pdb=" O SER A4169 " (cutoff:3.500A) Processing helix chain 'A' and resid 4198 through 4207 Processing helix chain 'A' and resid 4207 through 4225 Processing helix chain 'A' and resid 4226 through 4252 removed outlier: 4.188A pdb=" N MET A4231 " --> pdb=" O GLU A4227 " (cutoff:3.500A) removed outlier: 5.066A pdb=" N GLU A4232 " --> pdb=" O ALA A4228 " (cutoff:3.500A) Processing helix chain 'A' and resid 4541 through 4558 Processing helix chain 'A' and resid 4558 through 4578 Processing helix chain 'A' and resid 4638 through 4665 Processing helix chain 'A' and resid 4665 through 4683 Processing helix chain 'A' and resid 4696 through 4706 removed outlier: 3.549A pdb=" N GLN A4700 " --> pdb=" O ASP A4696 " (cutoff:3.500A) removed outlier: 4.157A pdb=" N LEU A4704 " --> pdb=" O GLN A4700 " (cutoff:3.500A) removed outlier: 4.412A pdb=" N VAL A4705 " --> pdb=" O TRP A4701 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N LEU A4706 " --> pdb=" O ASP A4702 " (cutoff:3.500A) Processing helix chain 'A' and resid 4719 through 4733 removed outlier: 4.981A pdb=" N ASP A4730 " --> pdb=" O ASP A4726 " (cutoff:3.500A) removed outlier: 5.933A pdb=" N ILE A4731 " --> pdb=" O LYS A4727 " (cutoff:3.500A) Processing helix chain 'A' and resid 4733 through 4742 Processing helix chain 'A' and resid 4773 through 4786 Processing helix chain 'A' and resid 4786 through 4805 removed outlier: 3.783A pdb=" N HIS A4803 " --> pdb=" O SER A4799 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N TYR A4804 " --> pdb=" O LEU A4800 " (cutoff:3.500A) Processing helix chain 'A' and resid 4806 through 4814 removed outlier: 3.892A pdb=" N HIS A4812 " --> pdb=" O PHE A4809 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N LEU A4813 " --> pdb=" O ALA A4810 " (cutoff:3.500A) removed outlier: 4.117A pdb=" N LEU A4814 " --> pdb=" O ALA A4811 " (cutoff:3.500A) Processing helix chain 'A' and resid 4815 through 4820 Processing helix chain 'A' and resid 4820 through 4832 removed outlier: 3.566A pdb=" N VAL A4830 " --> pdb=" O ILE A4826 " (cutoff:3.500A) Processing helix chain 'A' and resid 4833 through 4859 Processing helix chain 'A' and resid 4878 through 4890 Processing helix chain 'A' and resid 4895 through 4901 removed outlier: 4.193A pdb=" N ASP A4899 " --> pdb=" O GLY A4895 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N GLU A4900 " --> pdb=" O GLY A4896 " (cutoff:3.500A) Processing helix chain 'A' and resid 4910 through 4923 Processing helix chain 'A' and resid 4930 through 4957 Processing helix chain 'A' and resid 4964 through 4969 removed outlier: 4.186A pdb=" N PHE A4968 " --> pdb=" O GLY A4964 " (cutoff:3.500A) Processing helix chain 'A' and resid 4973 through 4979 Processing helix chain 'A' and resid 4984 through 4998 Processing helix chain 'A' and resid 5004 through 5016 Processing helix chain 'A' and resid 5027 through 5032 Processing helix chain 'A' and resid 5032 through 5037 removed outlier: 3.655A pdb=" N SER A5037 " --> pdb=" O GLU A5033 " (cutoff:3.500A) Processing helix chain 'B' and resid 74 through 84 Processing helix chain 'B' and resid 251 through 258 removed outlier: 3.684A pdb=" N THR B 254 " --> pdb=" O ALA B 251 " (cutoff:3.500A) removed outlier: 6.072A pdb=" N ALA B 256 " --> pdb=" O CYS B 253 " (cutoff:3.500A) removed outlier: 6.666A pdb=" N ARG B 257 " --> pdb=" O THR B 254 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N SER B 258 " --> pdb=" O HIS B 255 " (cutoff:3.500A) Processing helix chain 'B' and resid 305 through 307 No H-bonds generated for 'chain 'B' and resid 305 through 307' Processing helix chain 'B' and resid 365 through 370 removed outlier: 4.315A pdb=" N LEU B 369 " --> pdb=" O LYS B 365 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N GLY B 370 " --> pdb=" O ALA B 366 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 365 through 370' Processing helix chain 'B' and resid 394 through 421 removed outlier: 3.902A pdb=" N ARG B 402 " --> pdb=" O SER B 398 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N MET B 403 " --> pdb=" O GLN B 399 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N ILE B 404 " --> pdb=" O ALA B 400 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N HIS B 405 " --> pdb=" O ALA B 401 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N GLY B 409 " --> pdb=" O HIS B 405 " (cutoff:3.500A) Processing helix chain 'B' and resid 437 through 452 removed outlier: 3.556A pdb=" N GLY B 450 " --> pdb=" O GLN B 446 " (cutoff:3.500A) Processing helix chain 'B' and resid 460 through 481 Processing helix chain 'B' and resid 482 through 495 Processing helix chain 'B' and resid 499 through 505 Processing helix chain 'B' and resid 508 through 513 removed outlier: 4.130A pdb=" N GLU B 513 " --> pdb=" O GLU B 509 " (cutoff:3.500A) Processing helix chain 'B' and resid 513 through 531 removed outlier: 4.562A pdb=" N GLU B 517 " --> pdb=" O GLU B 513 " (cutoff:3.500A) Processing helix chain 'B' and resid 533 through 538 Processing helix chain 'B' and resid 539 through 542 removed outlier: 3.826A pdb=" N THR B 542 " --> pdb=" O LEU B 539 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 539 through 542' Processing helix chain 'B' and resid 543 through 549 removed outlier: 4.166A pdb=" N VAL B 547 " --> pdb=" O ASN B 543 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N VAL B 548 " --> pdb=" O LEU B 544 " (cutoff:3.500A) Processing helix chain 'B' and resid 557 through 569 Processing helix chain 'B' and resid 571 through 578 removed outlier: 3.936A pdb=" N LEU B 575 " --> pdb=" O SER B 571 " (cutoff:3.500A) Processing helix chain 'B' and resid 579 through 593 removed outlier: 3.630A pdb=" N ILE B 583 " --> pdb=" O GLN B 579 " (cutoff:3.500A) Processing helix chain 'B' and resid 596 through 607 removed outlier: 4.169A pdb=" N LEU B 600 " --> pdb=" O ASN B 596 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N ASP B 601 " --> pdb=" O HIS B 597 " (cutoff:3.500A) Processing helix chain 'B' and resid 614 through 626 removed outlier: 3.554A pdb=" N ASP B 619 " --> pdb=" O ARG B 615 " (cutoff:3.500A) removed outlier: 4.429A pdb=" N LEU B 620 " --> pdb=" O SER B 616 " (cutoff:3.500A) Processing helix chain 'B' and resid 794 through 798 removed outlier: 3.978A pdb=" N GLY B 798 " --> pdb=" O GLY B 795 " (cutoff:3.500A) Processing helix chain 'B' and resid 812 through 814 No H-bonds generated for 'chain 'B' and resid 812 through 814' Processing helix chain 'B' and resid 847 through 851 Processing helix chain 'B' and resid 864 through 869 Processing helix chain 'B' and resid 872 through 877 Processing helix chain 'B' and resid 880 through 885 removed outlier: 4.364A pdb=" N THR B 885 " --> pdb=" O LEU B 881 " (cutoff:3.500A) Processing helix chain 'B' and resid 914 through 936 Processing helix chain 'B' and resid 978 through 1003 removed outlier: 3.508A pdb=" N VAL B 995 " --> pdb=" O ASN B 991 " (cutoff:3.500A) Processing helix chain 'B' and resid 1023 through 1027 Processing helix chain 'B' and resid 1028 through 1049 removed outlier: 4.081A pdb=" N SER B1038 " --> pdb=" O SER B1034 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N LEU B1039 " --> pdb=" O ASN B1035 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N TYR B1049 " --> pdb=" O THR B1045 " (cutoff:3.500A) Processing helix chain 'B' and resid 1068 through 1072 removed outlier: 3.772A pdb=" N ARG B1071 " --> pdb=" O ARG B1068 " (cutoff:3.500A) removed outlier: 4.417A pdb=" N VAL B1072 " --> pdb=" O TRP B1069 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 1068 through 1072' Processing helix chain 'B' and resid 1079 through 1082 Processing helix chain 'B' and resid 1423 through 1430 Processing helix chain 'B' and resid 1444 through 1446 No H-bonds generated for 'chain 'B' and resid 1444 through 1446' Processing helix chain 'B' and resid 1465 through 1469 removed outlier: 3.583A pdb=" N VAL B1469 " --> pdb=" O LEU B1466 " (cutoff:3.500A) Processing helix chain 'B' and resid 1498 through 1500 No H-bonds generated for 'chain 'B' and resid 1498 through 1500' Processing helix chain 'B' and resid 1574 through 1580 removed outlier: 3.779A pdb=" N ALA B1578 " --> pdb=" O PRO B1574 " (cutoff:3.500A) Processing helix chain 'B' and resid 1581 through 1584 removed outlier: 4.074A pdb=" N ARG B1584 " --> pdb=" O LEU B1581 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 1581 through 1584' Processing helix chain 'B' and resid 1651 through 1655 Processing helix chain 'B' and resid 1656 through 1674 removed outlier: 4.120A pdb=" N PHE B1662 " --> pdb=" O ASP B1658 " (cutoff:3.500A) Processing helix chain 'B' and resid 1678 through 1689 removed outlier: 3.614A pdb=" N ALA B1684 " --> pdb=" O ARG B1680 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N CYS B1686 " --> pdb=" O ALA B1682 " (cutoff:3.500A) removed outlier: 4.152A pdb=" N SER B1687 " --> pdb=" O HIS B1683 " (cutoff:3.500A) removed outlier: 4.330A pdb=" N HIS B1688 " --> pdb=" O ALA B1684 " (cutoff:3.500A) Processing helix chain 'B' and resid 1690 through 1699 removed outlier: 4.169A pdb=" N GLU B1699 " --> pdb=" O LEU B1695 " (cutoff:3.500A) Processing helix chain 'B' and resid 1704 through 1720 Processing helix chain 'B' and resid 1720 through 1731 Processing helix chain 'B' and resid 1739 through 1744 Processing helix chain 'B' and resid 1803 through 1824 removed outlier: 3.674A pdb=" N GLY B1823 " --> pdb=" O VAL B1819 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N GLN B1824 " --> pdb=" O ARG B1820 " (cutoff:3.500A) Processing helix chain 'B' and resid 1833 through 1852 Proline residue: B1840 - end of helix Processing helix chain 'B' and resid 1855 through 1867 Processing helix chain 'B' and resid 1925 through 1929 removed outlier: 4.098A pdb=" N GLN B1928 " --> pdb=" O GLY B1925 " (cutoff:3.500A) Processing helix chain 'B' and resid 1932 through 1982 removed outlier: 3.823A pdb=" N GLN B1938 " --> pdb=" O SER B1934 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N PHE B1946 " --> pdb=" O LEU B1942 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N GLN B1949 " --> pdb=" O TYR B1945 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N GLU B1950 " --> pdb=" O PHE B1946 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N LEU B1951 " --> pdb=" O CYS B1947 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N ASP B1967 " --> pdb=" O GLU B1963 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N LYS B1968 " --> pdb=" O ARG B1964 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N ARG B1982 " --> pdb=" O ALA B1978 " (cutoff:3.500A) Processing helix chain 'B' and resid 1983 through 1986 Processing helix chain 'B' and resid 1990 through 1995 Processing helix chain 'B' and resid 2001 through 2011 Processing helix chain 'B' and resid 2024 through 2042 removed outlier: 3.669A pdb=" N GLN B2032 " --> pdb=" O ARG B2028 " (cutoff:3.500A) Processing helix chain 'B' and resid 2093 through 2109 removed outlier: 3.760A pdb=" N ASP B2109 " --> pdb=" O TRP B2105 " (cutoff:3.500A) Processing helix chain 'B' and resid 2113 through 2129 Processing helix chain 'B' and resid 2129 through 2136 removed outlier: 3.607A pdb=" N GLU B2133 " --> pdb=" O ASP B2129 " (cutoff:3.500A) Processing helix chain 'B' and resid 2137 through 2139 No H-bonds generated for 'chain 'B' and resid 2137 through 2139' Processing helix chain 'B' and resid 2145 through 2147 No H-bonds generated for 'chain 'B' and resid 2145 through 2147' Processing helix chain 'B' and resid 2148 through 2165 removed outlier: 3.673A pdb=" N CYS B2158 " --> pdb=" O SER B2154 " (cutoff:3.500A) Processing helix chain 'B' and resid 2166 through 2168 No H-bonds generated for 'chain 'B' and resid 2166 through 2168' Processing helix chain 'B' and resid 2171 through 2188 removed outlier: 3.515A pdb=" N ILE B2185 " --> pdb=" O SER B2181 " (cutoff:3.500A) Processing helix chain 'B' and resid 2189 through 2194 Processing helix chain 'B' and resid 2194 through 2202 removed outlier: 3.541A pdb=" N MET B2198 " --> pdb=" O HIS B2194 " (cutoff:3.500A) Processing helix chain 'B' and resid 2202 through 2217 removed outlier: 3.530A pdb=" N VAL B2210 " --> pdb=" O THR B2206 " (cutoff:3.500A) Processing helix chain 'B' and resid 2225 through 2243 removed outlier: 3.851A pdb=" N VAL B2229 " --> pdb=" O PHE B2225 " (cutoff:3.500A) removed outlier: 4.511A pdb=" N SER B2243 " --> pdb=" O PHE B2239 " (cutoff:3.500A) Processing helix chain 'B' and resid 2243 through 2252 Processing helix chain 'B' and resid 2253 through 2261 removed outlier: 3.569A pdb=" N LEU B2258 " --> pdb=" O LEU B2254 " (cutoff:3.500A) removed outlier: 4.133A pdb=" N GLU B2259 " --> pdb=" O SER B2255 " (cutoff:3.500A) removed outlier: 4.451A pdb=" N ASN B2260 " --> pdb=" O TYR B2256 " (cutoff:3.500A) Processing helix chain 'B' and resid 2262 through 2267 removed outlier: 5.413A pdb=" N LEU B2265 " --> pdb=" O GLY B2262 " (cutoff:3.500A) Processing helix chain 'B' and resid 2271 through 2279 Processing helix chain 'B' and resid 2283 through 2290 Processing helix chain 'B' and resid 2291 through 2306 Processing helix chain 'B' and resid 2310 through 2316 Processing helix chain 'B' and resid 2324 through 2339 Processing helix chain 'B' and resid 2346 through 2360 Processing helix chain 'B' and resid 2361 through 2365 Processing helix chain 'B' and resid 2375 through 2389 removed outlier: 4.110A pdb=" N GLU B2381 " --> pdb=" O LEU B2377 " (cutoff:3.500A) removed outlier: 4.411A pdb=" N GLU B2382 " --> pdb=" O ALA B2378 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N ALA B2383 " --> pdb=" O ALA B2379 " (cutoff:3.500A) Processing helix chain 'B' and resid 2417 through 2437 Processing helix chain 'B' and resid 2439 through 2446 Processing helix chain 'B' and resid 2447 through 2461 removed outlier: 3.702A pdb=" N ARG B2452 " --> pdb=" O GLY B2448 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ARG B2454 " --> pdb=" O ALA B2450 " (cutoff:3.500A) Processing helix chain 'B' and resid 2462 through 2471 Processing helix chain 'B' and resid 2489 through 2493 removed outlier: 4.245A pdb=" N SER B2493 " --> pdb=" O MET B2490 " (cutoff:3.500A) Processing helix chain 'B' and resid 2495 through 2510 removed outlier: 4.133A pdb=" N LYS B2499 " --> pdb=" O VAL B2495 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N MET B2502 " --> pdb=" O HIS B2498 " (cutoff:3.500A) Processing helix chain 'B' and resid 2514 through 2526 removed outlier: 4.325A pdb=" N VAL B2524 " --> pdb=" O HIS B2520 " (cutoff:3.500A) Processing helix chain 'B' and resid 2526 through 2537 Processing helix chain 'B' and resid 2544 through 2557 Processing helix chain 'B' and resid 2557 through 2565 removed outlier: 3.512A pdb=" N LYS B2564 " --> pdb=" O PRO B2560 " (cutoff:3.500A) Processing helix chain 'B' and resid 2566 through 2574 removed outlier: 4.325A pdb=" N GLY B2571 " --> pdb=" O LEU B2568 " (cutoff:3.500A) removed outlier: 4.135A pdb=" N THR B2572 " --> pdb=" O PHE B2569 " (cutoff:3.500A) removed outlier: 5.381A pdb=" N GLU B2573 " --> pdb=" O ALA B2570 " (cutoff:3.500A) removed outlier: 4.491A pdb=" N HIS B2574 " --> pdb=" O GLY B2571 " (cutoff:3.500A) Processing helix chain 'B' and resid 2575 through 2591 removed outlier: 4.033A pdb=" N VAL B2579 " --> pdb=" O ARG B2575 " (cutoff:3.500A) Processing helix chain 'B' and resid 2596 through 2613 removed outlier: 3.532A pdb=" N ARG B2612 " --> pdb=" O MET B2608 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N TYR B2613 " --> pdb=" O ALA B2609 " (cutoff:3.500A) Processing helix chain 'B' and resid 2615 through 2630 removed outlier: 4.974A pdb=" N HIS B2621 " --> pdb=" O SER B2617 " (cutoff:3.500A) removed outlier: 4.286A pdb=" N LEU B2622 " --> pdb=" O MET B2618 " (cutoff:3.500A) Processing helix chain 'B' and resid 2631 through 2633 No H-bonds generated for 'chain 'B' and resid 2631 through 2633' Processing helix chain 'B' and resid 2634 through 2636 No H-bonds generated for 'chain 'B' and resid 2634 through 2636' Processing helix chain 'B' and resid 2637 through 2651 removed outlier: 3.910A pdb=" N LYS B2642 " --> pdb=" O LYS B2638 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N HIS B2647 " --> pdb=" O LEU B2643 " (cutoff:3.500A) Processing helix chain 'B' and resid 2651 through 2657 removed outlier: 3.838A pdb=" N TYR B2655 " --> pdb=" O CYS B2651 " (cutoff:3.500A) Processing helix chain 'B' and resid 2670 through 2689 removed outlier: 3.647A pdb=" N ALA B2687 " --> pdb=" O PHE B2683 " (cutoff:3.500A) Processing helix chain 'B' and resid 2692 through 2710 removed outlier: 3.579A pdb=" N MET B2698 " --> pdb=" O GLU B2694 " (cutoff:3.500A) Proline residue: B2701 - end of helix Processing helix chain 'B' and resid 2748 through 2750 No H-bonds generated for 'chain 'B' and resid 2748 through 2750' Processing helix chain 'B' and resid 2751 through 2773 removed outlier: 3.730A pdb=" N LYS B2757 " --> pdb=" O SER B2753 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N HIS B2763 " --> pdb=" O ALA B2759 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N GLU B2764 " --> pdb=" O GLU B2760 " (cutoff:3.500A) Processing helix chain 'B' and resid 2806 through 2819 removed outlier: 3.877A pdb=" N LEU B2813 " --> pdb=" O ILE B2809 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N LYS B2814 " --> pdb=" O LYS B2810 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N TRP B2819 " --> pdb=" O ALA B2815 " (cutoff:3.500A) Processing helix chain 'B' and resid 2868 through 2895 removed outlier: 4.109A pdb=" N GLU B2893 " --> pdb=" O LYS B2889 " (cutoff:3.500A) Processing helix chain 'B' and resid 2912 through 2932 removed outlier: 5.535A pdb=" N ARG B2918 " --> pdb=" O LYS B2914 " (cutoff:3.500A) removed outlier: 4.416A pdb=" N ASP B2919 " --> pdb=" O GLU B2915 " (cutoff:3.500A) Processing helix chain 'B' and resid 2954 through 2983 removed outlier: 3.778A pdb=" N ILE B2969 " --> pdb=" O ARG B2965 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N ALA B2975 " --> pdb=" O GLN B2971 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N HIS B2976 " --> pdb=" O GLU B2972 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N SER B2983 " --> pdb=" O ALA B2979 " (cutoff:3.500A) Processing helix chain 'B' and resid 2991 through 3013 removed outlier: 5.458A pdb=" N LEU B3003 " --> pdb=" O ALA B2999 " (cutoff:3.500A) Proline residue: B3004 - end of helix removed outlier: 3.514A pdb=" N PHE B3010 " --> pdb=" O ILE B3006 " (cutoff:3.500A) removed outlier: 4.157A pdb=" N THR B3011 " --> pdb=" O ASN B3007 " (cutoff:3.500A) Processing helix chain 'B' and resid 3013 through 3018 Processing helix chain 'B' and resid 3032 through 3051 removed outlier: 3.791A pdb=" N GLU B3037 " --> pdb=" O ASN B3033 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N ALA B3047 " --> pdb=" O PHE B3043 " (cutoff:3.500A) Processing helix chain 'B' and resid 3053 through 3058 Processing helix chain 'B' and resid 3060 through 3074 removed outlier: 3.501A pdb=" N ASN B3066 " --> pdb=" O PRO B3062 " (cutoff:3.500A) Processing helix chain 'B' and resid 3076 through 3083 removed outlier: 3.972A pdb=" N VAL B3080 " --> pdb=" O ASP B3076 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N MET B3081 " --> pdb=" O ALA B3077 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N LYS B3082 " --> pdb=" O ARG B3078 " (cutoff:3.500A) Processing helix chain 'B' and resid 3085 through 3111 Processing helix chain 'B' and resid 3124 through 3136 removed outlier: 3.883A pdb=" N ASN B3128 " --> pdb=" O GLY B3124 " (cutoff:3.500A) Processing helix chain 'B' and resid 3136 through 3151 Processing helix chain 'B' and resid 3152 through 3157 Processing helix chain 'B' and resid 3160 through 3174 removed outlier: 3.842A pdb=" N ARG B3167 " --> pdb=" O VAL B3163 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N THR B3168 " --> pdb=" O SER B3164 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N TYR B3173 " --> pdb=" O LEU B3169 " (cutoff:3.500A) Processing helix chain 'B' and resid 3175 through 3178 Processing helix chain 'B' and resid 3180 through 3201 Proline residue: B3188 - end of helix Processing helix chain 'B' and resid 3207 through 3214 removed outlier: 5.176A pdb=" N GLU B3212 " --> pdb=" O GLN B3209 " (cutoff:3.500A) Processing helix chain 'B' and resid 3217 through 3222 Processing helix chain 'B' and resid 3245 through 3260 removed outlier: 3.676A pdb=" N ALA B3251 " --> pdb=" O ASP B3247 " (cutoff:3.500A) Processing helix chain 'B' and resid 3266 through 3272 Processing helix chain 'B' and resid 3272 through 3279 Processing helix chain 'B' and resid 3280 through 3286 removed outlier: 4.075A pdb=" N GLU B3286 " --> pdb=" O PRO B3282 " (cutoff:3.500A) Processing helix chain 'B' and resid 3308 through 3326 removed outlier: 3.614A pdb=" N LEU B3315 " --> pdb=" O HIS B3311 " (cutoff:3.500A) Processing helix chain 'B' and resid 3334 through 3343 Processing helix chain 'B' and resid 3344 through 3350 removed outlier: 3.829A pdb=" N SER B3347 " --> pdb=" O PRO B3344 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N ARG B3348 " --> pdb=" O ILE B3345 " (cutoff:3.500A) removed outlier: 6.740A pdb=" N ARG B3350 " --> pdb=" O SER B3347 " (cutoff:3.500A) Processing helix chain 'B' and resid 3351 through 3357 removed outlier: 4.161A pdb=" N HIS B3355 " --> pdb=" O PRO B3351 " (cutoff:3.500A) Processing helix chain 'B' and resid 3357 through 3382 removed outlier: 3.710A pdb=" N GLU B3382 " --> pdb=" O GLN B3378 " (cutoff:3.500A) Processing helix chain 'B' and resid 3384 through 3386 No H-bonds generated for 'chain 'B' and resid 3384 through 3386' Processing helix chain 'B' and resid 3387 through 3419 removed outlier: 3.670A pdb=" N LEU B3392 " --> pdb=" O GLU B3388 " (cutoff:3.500A) removed outlier: 7.010A pdb=" N LEU B3393 " --> pdb=" O GLU B3389 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N VAL B3394 " --> pdb=" O GLY B3390 " (cutoff:3.500A) Proline residue: B3410 - end of helix removed outlier: 3.616A pdb=" N ARG B3414 " --> pdb=" O PRO B3410 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N ASN B3419 " --> pdb=" O TYR B3415 " (cutoff:3.500A) Processing helix chain 'B' and resid 3419 through 3426 Processing helix chain 'B' and resid 3428 through 3448 Processing helix chain 'B' and resid 3448 through 3463 Processing helix chain 'B' and resid 3471 through 3477 Processing helix chain 'B' and resid 3504 through 3507 Processing helix chain 'B' and resid 3508 through 3522 Proline residue: B3519 - end of helix Processing helix chain 'B' and resid 3526 through 3528 No H-bonds generated for 'chain 'B' and resid 3526 through 3528' Processing helix chain 'B' and resid 3529 through 3542 Processing helix chain 'B' and resid 3545 through 3556 Processing helix chain 'B' and resid 3566 through 3578 removed outlier: 3.863A pdb=" N ARG B3570 " --> pdb=" O SER B3566 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N TRP B3571 " --> pdb=" O PRO B3567 " (cutoff:3.500A) Processing helix chain 'B' and resid 3588 through 3611 Processing helix chain 'B' and resid 3624 through 3638 removed outlier: 6.726A pdb=" N ARG B3630 " --> pdb=" O LYS B3626 " (cutoff:3.500A) removed outlier: 6.366A pdb=" N ALA B3631 " --> pdb=" O GLN B3627 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N VAL B3632 " --> pdb=" O ARG B3628 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N VAL B3633 " --> pdb=" O ARG B3629 " (cutoff:3.500A) Processing helix chain 'B' and resid 3640 through 3644 Processing helix chain 'B' and resid 3645 through 3661 removed outlier: 3.556A pdb=" N GLU B3655 " --> pdb=" O ASN B3651 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N ALA B3659 " --> pdb=" O GLU B3655 " (cutoff:3.500A) Processing helix chain 'B' and resid 3669 through 3678 Processing helix chain 'B' and resid 3696 through 3710 Processing helix chain 'B' and resid 3719 through 3735 removed outlier: 4.102A pdb=" N CYS B3733 " --> pdb=" O MET B3729 " (cutoff:3.500A) removed outlier: 4.571A pdb=" N HIS B3734 " --> pdb=" O ALA B3730 " (cutoff:3.500A) removed outlier: 4.362A pdb=" N LEU B3735 " --> pdb=" O LYS B3731 " (cutoff:3.500A) Processing helix chain 'B' and resid 3752 through 3772 removed outlier: 4.269A pdb=" N MET B3758 " --> pdb=" O GLU B3754 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N GLU B3759 " --> pdb=" O GLU B3755 " (cutoff:3.500A) Processing helix chain 'B' and resid 3774 through 3786 removed outlier: 3.522A pdb=" N LEU B3780 " --> pdb=" O ALA B3776 " (cutoff:3.500A) Processing helix chain 'B' and resid 3791 through 3806 Processing helix chain 'B' and resid 3809 through 3824 Processing helix chain 'B' and resid 3826 through 3838 Processing helix chain 'B' and resid 3843 through 3857 removed outlier: 3.802A pdb=" N PHE B3847 " --> pdb=" O ASP B3843 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N GLY B3857 " --> pdb=" O ALA B3853 " (cutoff:3.500A) Processing helix chain 'B' and resid 3877 through 3892 removed outlier: 3.549A pdb=" N PHE B3885 " --> pdb=" O THR B3881 " (cutoff:3.500A) Processing helix chain 'B' and resid 3896 through 3905 removed outlier: 3.660A pdb=" N TYR B3902 " --> pdb=" O ASP B3898 " (cutoff:3.500A) Processing helix chain 'B' and resid 3914 through 3935 Processing helix chain 'B' and resid 3944 through 3970 removed outlier: 3.763A pdb=" N SER B3956 " --> pdb=" O SER B3952 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N VAL B3957 " --> pdb=" O LYS B3953 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N ALA B3958 " --> pdb=" O ALA B3954 " (cutoff:3.500A) Processing helix chain 'B' and resid 3973 through 3982 Processing helix chain 'B' and resid 3984 through 4005 removed outlier: 3.824A pdb=" N MET B4001 " --> pdb=" O ALA B3997 " (cutoff:3.500A) Processing helix chain 'B' and resid 4009 through 4032 Processing helix chain 'B' and resid 4038 through 4051 removed outlier: 3.666A pdb=" N GLU B4050 " --> pdb=" O ASP B4046 " (cutoff:3.500A) Processing helix chain 'B' and resid 4051 through 4072 removed outlier: 3.933A pdb=" N MET B4057 " --> pdb=" O SER B4053 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N MET B4064 " --> pdb=" O LYS B4060 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N PHE B4065 " --> pdb=" O PHE B4061 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N ASP B4070 " --> pdb=" O LEU B4066 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N ILE B4071 " --> pdb=" O LYS B4067 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N VAL B4072 " --> pdb=" O LEU B4068 " (cutoff:3.500A) Processing helix chain 'B' and resid 4074 through 4079 Processing helix chain 'B' and resid 4090 through 4098 removed outlier: 3.787A pdb=" N ALA B4096 " --> pdb=" O ASP B4092 " (cutoff:3.500A) removed outlier: 4.113A pdb=" N ASP B4098 " --> pdb=" O GLN B4094 " (cutoff:3.500A) Processing helix chain 'B' and resid 4099 through 4101 No H-bonds generated for 'chain 'B' and resid 4099 through 4101' Processing helix chain 'B' and resid 4104 through 4115 Processing helix chain 'B' and resid 4128 through 4131 Processing helix chain 'B' and resid 4132 through 4154 removed outlier: 4.339A pdb=" N ASP B4138 " --> pdb=" O GLU B4134 " (cutoff:3.500A) removed outlier: 4.305A pdb=" N ILE B4139 " --> pdb=" O PRO B4135 " (cutoff:3.500A) Processing helix chain 'B' and resid 4157 through 4166 removed outlier: 3.810A pdb=" N ARG B4161 " --> pdb=" O ASP B4157 " (cutoff:3.500A) Processing helix chain 'B' and resid 4167 through 4175 removed outlier: 4.091A pdb=" N LEU B4171 " --> pdb=" O ALA B4167 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N GLU B4172 " --> pdb=" O GLU B4168 " (cutoff:3.500A) removed outlier: 4.336A pdb=" N TYR B4173 " --> pdb=" O SER B4169 " (cutoff:3.500A) Processing helix chain 'B' and resid 4198 through 4207 Processing helix chain 'B' and resid 4207 through 4225 Processing helix chain 'B' and resid 4226 through 4252 removed outlier: 4.189A pdb=" N MET B4231 " --> pdb=" O GLU B4227 " (cutoff:3.500A) removed outlier: 5.067A pdb=" N GLU B4232 " --> pdb=" O ALA B4228 " (cutoff:3.500A) Processing helix chain 'B' and resid 4541 through 4558 Processing helix chain 'B' and resid 4558 through 4578 Processing helix chain 'B' and resid 4638 through 4665 Processing helix chain 'B' and resid 4665 through 4683 Processing helix chain 'B' and resid 4696 through 4706 removed outlier: 3.549A pdb=" N GLN B4700 " --> pdb=" O ASP B4696 " (cutoff:3.500A) removed outlier: 4.159A pdb=" N LEU B4704 " --> pdb=" O GLN B4700 " (cutoff:3.500A) removed outlier: 4.412A pdb=" N VAL B4705 " --> pdb=" O TRP B4701 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N LEU B4706 " --> pdb=" O ASP B4702 " (cutoff:3.500A) Processing helix chain 'B' and resid 4719 through 4733 removed outlier: 4.982A pdb=" N ASP B4730 " --> pdb=" O ASP B4726 " (cutoff:3.500A) removed outlier: 5.933A pdb=" N ILE B4731 " --> pdb=" O LYS B4727 " (cutoff:3.500A) Processing helix chain 'B' and resid 4733 through 4742 Processing helix chain 'B' and resid 4773 through 4786 Processing helix chain 'B' and resid 4786 through 4805 removed outlier: 3.784A pdb=" N HIS B4803 " --> pdb=" O SER B4799 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N TYR B4804 " --> pdb=" O LEU B4800 " (cutoff:3.500A) Processing helix chain 'B' and resid 4806 through 4814 removed outlier: 3.892A pdb=" N HIS B4812 " --> pdb=" O PHE B4809 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N LEU B4813 " --> pdb=" O ALA B4810 " (cutoff:3.500A) removed outlier: 4.118A pdb=" N LEU B4814 " --> pdb=" O ALA B4811 " (cutoff:3.500A) Processing helix chain 'B' and resid 4815 through 4820 Processing helix chain 'B' and resid 4820 through 4832 removed outlier: 3.567A pdb=" N VAL B4830 " --> pdb=" O ILE B4826 " (cutoff:3.500A) Processing helix chain 'B' and resid 4833 through 4859 Processing helix chain 'B' and resid 4878 through 4890 Processing helix chain 'B' and resid 4895 through 4901 removed outlier: 4.192A pdb=" N ASP B4899 " --> pdb=" O GLY B4895 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N GLU B4900 " --> pdb=" O GLY B4896 " (cutoff:3.500A) Processing helix chain 'B' and resid 4910 through 4923 Processing helix chain 'B' and resid 4930 through 4957 Processing helix chain 'B' and resid 4964 through 4969 removed outlier: 4.186A pdb=" N PHE B4968 " --> pdb=" O GLY B4964 " (cutoff:3.500A) Processing helix chain 'B' and resid 4973 through 4979 Processing helix chain 'B' and resid 4984 through 4998 Processing helix chain 'B' and resid 5004 through 5016 Processing helix chain 'B' and resid 5027 through 5032 Processing helix chain 'B' and resid 5032 through 5037 removed outlier: 3.654A pdb=" N SER B5037 " --> pdb=" O GLU B5033 " (cutoff:3.500A) Processing helix chain 'C' and resid 74 through 84 Processing helix chain 'C' and resid 251 through 258 removed outlier: 3.684A pdb=" N THR C 254 " --> pdb=" O ALA C 251 " (cutoff:3.500A) removed outlier: 6.072A pdb=" N ALA C 256 " --> pdb=" O CYS C 253 " (cutoff:3.500A) removed outlier: 6.666A pdb=" N ARG C 257 " --> pdb=" O THR C 254 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N SER C 258 " --> pdb=" O HIS C 255 " (cutoff:3.500A) Processing helix chain 'C' and resid 305 through 307 No H-bonds generated for 'chain 'C' and resid 305 through 307' Processing helix chain 'C' and resid 365 through 370 removed outlier: 4.315A pdb=" N LEU C 369 " --> pdb=" O LYS C 365 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N GLY C 370 " --> pdb=" O ALA C 366 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 365 through 370' Processing helix chain 'C' and resid 394 through 421 removed outlier: 3.902A pdb=" N ARG C 402 " --> pdb=" O SER C 398 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N MET C 403 " --> pdb=" O GLN C 399 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N ILE C 404 " --> pdb=" O ALA C 400 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N HIS C 405 " --> pdb=" O ALA C 401 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N GLY C 409 " --> pdb=" O HIS C 405 " (cutoff:3.500A) Processing helix chain 'C' and resid 437 through 452 removed outlier: 3.556A pdb=" N GLY C 450 " --> pdb=" O GLN C 446 " (cutoff:3.500A) Processing helix chain 'C' and resid 460 through 481 Processing helix chain 'C' and resid 482 through 495 Processing helix chain 'C' and resid 499 through 505 Processing helix chain 'C' and resid 508 through 513 removed outlier: 4.130A pdb=" N GLU C 513 " --> pdb=" O GLU C 509 " (cutoff:3.500A) Processing helix chain 'C' and resid 513 through 531 removed outlier: 4.561A pdb=" N GLU C 517 " --> pdb=" O GLU C 513 " (cutoff:3.500A) Processing helix chain 'C' and resid 533 through 538 Processing helix chain 'C' and resid 539 through 542 removed outlier: 3.826A pdb=" N THR C 542 " --> pdb=" O LEU C 539 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 539 through 542' Processing helix chain 'C' and resid 543 through 549 removed outlier: 4.166A pdb=" N VAL C 547 " --> pdb=" O ASN C 543 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N VAL C 548 " --> pdb=" O LEU C 544 " (cutoff:3.500A) Processing helix chain 'C' and resid 557 through 569 Processing helix chain 'C' and resid 571 through 578 removed outlier: 3.936A pdb=" N LEU C 575 " --> pdb=" O SER C 571 " (cutoff:3.500A) Processing helix chain 'C' and resid 579 through 593 removed outlier: 3.630A pdb=" N ILE C 583 " --> pdb=" O GLN C 579 " (cutoff:3.500A) Processing helix chain 'C' and resid 596 through 607 removed outlier: 4.169A pdb=" N LEU C 600 " --> pdb=" O ASN C 596 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N ASP C 601 " --> pdb=" O HIS C 597 " (cutoff:3.500A) Processing helix chain 'C' and resid 614 through 626 removed outlier: 3.554A pdb=" N ASP C 619 " --> pdb=" O ARG C 615 " (cutoff:3.500A) removed outlier: 4.429A pdb=" N LEU C 620 " --> pdb=" O SER C 616 " (cutoff:3.500A) Processing helix chain 'C' and resid 794 through 798 removed outlier: 3.978A pdb=" N GLY C 798 " --> pdb=" O GLY C 795 " (cutoff:3.500A) Processing helix chain 'C' and resid 812 through 814 No H-bonds generated for 'chain 'C' and resid 812 through 814' Processing helix chain 'C' and resid 847 through 851 Processing helix chain 'C' and resid 864 through 869 Processing helix chain 'C' and resid 872 through 877 Processing helix chain 'C' and resid 880 through 885 removed outlier: 4.364A pdb=" N THR C 885 " --> pdb=" O LEU C 881 " (cutoff:3.500A) Processing helix chain 'C' and resid 914 through 936 Processing helix chain 'C' and resid 978 through 1003 removed outlier: 3.508A pdb=" N VAL C 995 " --> pdb=" O ASN C 991 " (cutoff:3.500A) Processing helix chain 'C' and resid 1023 through 1027 Processing helix chain 'C' and resid 1028 through 1049 removed outlier: 4.080A pdb=" N SER C1038 " --> pdb=" O SER C1034 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N LEU C1039 " --> pdb=" O ASN C1035 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N TYR C1049 " --> pdb=" O THR C1045 " (cutoff:3.500A) Processing helix chain 'C' and resid 1068 through 1072 removed outlier: 3.772A pdb=" N ARG C1071 " --> pdb=" O ARG C1068 " (cutoff:3.500A) removed outlier: 4.418A pdb=" N VAL C1072 " --> pdb=" O TRP C1069 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 1068 through 1072' Processing helix chain 'C' and resid 1079 through 1082 Processing helix chain 'C' and resid 1423 through 1430 Processing helix chain 'C' and resid 1444 through 1446 No H-bonds generated for 'chain 'C' and resid 1444 through 1446' Processing helix chain 'C' and resid 1465 through 1469 removed outlier: 3.583A pdb=" N VAL C1469 " --> pdb=" O LEU C1466 " (cutoff:3.500A) Processing helix chain 'C' and resid 1498 through 1500 No H-bonds generated for 'chain 'C' and resid 1498 through 1500' Processing helix chain 'C' and resid 1574 through 1580 removed outlier: 3.779A pdb=" N ALA C1578 " --> pdb=" O PRO C1574 " (cutoff:3.500A) Processing helix chain 'C' and resid 1581 through 1584 removed outlier: 4.073A pdb=" N ARG C1584 " --> pdb=" O LEU C1581 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 1581 through 1584' Processing helix chain 'C' and resid 1651 through 1655 Processing helix chain 'C' and resid 1656 through 1674 removed outlier: 4.119A pdb=" N PHE C1662 " --> pdb=" O ASP C1658 " (cutoff:3.500A) Processing helix chain 'C' and resid 1678 through 1689 removed outlier: 3.614A pdb=" N ALA C1684 " --> pdb=" O ARG C1680 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N CYS C1686 " --> pdb=" O ALA C1682 " (cutoff:3.500A) removed outlier: 4.152A pdb=" N SER C1687 " --> pdb=" O HIS C1683 " (cutoff:3.500A) removed outlier: 4.330A pdb=" N HIS C1688 " --> pdb=" O ALA C1684 " (cutoff:3.500A) Processing helix chain 'C' and resid 1690 through 1699 removed outlier: 4.170A pdb=" N GLU C1699 " --> pdb=" O LEU C1695 " (cutoff:3.500A) Processing helix chain 'C' and resid 1704 through 1720 Processing helix chain 'C' and resid 1720 through 1731 Processing helix chain 'C' and resid 1739 through 1744 Processing helix chain 'C' and resid 1803 through 1824 removed outlier: 3.674A pdb=" N GLY C1823 " --> pdb=" O VAL C1819 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N GLN C1824 " --> pdb=" O ARG C1820 " (cutoff:3.500A) Processing helix chain 'C' and resid 1833 through 1852 Proline residue: C1840 - end of helix Processing helix chain 'C' and resid 1855 through 1867 Processing helix chain 'C' and resid 1925 through 1929 removed outlier: 4.098A pdb=" N GLN C1928 " --> pdb=" O GLY C1925 " (cutoff:3.500A) Processing helix chain 'C' and resid 1932 through 1982 removed outlier: 3.823A pdb=" N GLN C1938 " --> pdb=" O SER C1934 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N PHE C1946 " --> pdb=" O LEU C1942 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N GLN C1949 " --> pdb=" O TYR C1945 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N GLU C1950 " --> pdb=" O PHE C1946 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N LEU C1951 " --> pdb=" O CYS C1947 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N ASP C1967 " --> pdb=" O GLU C1963 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N LYS C1968 " --> pdb=" O ARG C1964 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N ARG C1982 " --> pdb=" O ALA C1978 " (cutoff:3.500A) Processing helix chain 'C' and resid 1983 through 1986 Processing helix chain 'C' and resid 1990 through 1995 Processing helix chain 'C' and resid 2001 through 2011 Processing helix chain 'C' and resid 2024 through 2042 removed outlier: 3.669A pdb=" N GLN C2032 " --> pdb=" O ARG C2028 " (cutoff:3.500A) Processing helix chain 'C' and resid 2093 through 2109 removed outlier: 3.761A pdb=" N ASP C2109 " --> pdb=" O TRP C2105 " (cutoff:3.500A) Processing helix chain 'C' and resid 2113 through 2129 Processing helix chain 'C' and resid 2129 through 2136 removed outlier: 3.606A pdb=" N GLU C2133 " --> pdb=" O ASP C2129 " (cutoff:3.500A) Processing helix chain 'C' and resid 2137 through 2139 No H-bonds generated for 'chain 'C' and resid 2137 through 2139' Processing helix chain 'C' and resid 2145 through 2147 No H-bonds generated for 'chain 'C' and resid 2145 through 2147' Processing helix chain 'C' and resid 2148 through 2165 removed outlier: 3.673A pdb=" N CYS C2158 " --> pdb=" O SER C2154 " (cutoff:3.500A) Processing helix chain 'C' and resid 2166 through 2168 No H-bonds generated for 'chain 'C' and resid 2166 through 2168' Processing helix chain 'C' and resid 2171 through 2188 removed outlier: 3.515A pdb=" N ILE C2185 " --> pdb=" O SER C2181 " (cutoff:3.500A) Processing helix chain 'C' and resid 2189 through 2194 Processing helix chain 'C' and resid 2194 through 2202 removed outlier: 3.540A pdb=" N MET C2198 " --> pdb=" O HIS C2194 " (cutoff:3.500A) Processing helix chain 'C' and resid 2202 through 2217 removed outlier: 3.530A pdb=" N VAL C2210 " --> pdb=" O THR C2206 " (cutoff:3.500A) Processing helix chain 'C' and resid 2225 through 2243 removed outlier: 3.851A pdb=" N VAL C2229 " --> pdb=" O PHE C2225 " (cutoff:3.500A) removed outlier: 4.511A pdb=" N SER C2243 " --> pdb=" O PHE C2239 " (cutoff:3.500A) Processing helix chain 'C' and resid 2243 through 2252 Processing helix chain 'C' and resid 2253 through 2261 removed outlier: 3.569A pdb=" N LEU C2258 " --> pdb=" O LEU C2254 " (cutoff:3.500A) removed outlier: 4.132A pdb=" N GLU C2259 " --> pdb=" O SER C2255 " (cutoff:3.500A) removed outlier: 4.450A pdb=" N ASN C2260 " --> pdb=" O TYR C2256 " (cutoff:3.500A) Processing helix chain 'C' and resid 2262 through 2267 removed outlier: 5.413A pdb=" N LEU C2265 " --> pdb=" O GLY C2262 " (cutoff:3.500A) Processing helix chain 'C' and resid 2271 through 2279 Processing helix chain 'C' and resid 2283 through 2290 Processing helix chain 'C' and resid 2291 through 2306 Processing helix chain 'C' and resid 2310 through 2316 Processing helix chain 'C' and resid 2324 through 2339 Processing helix chain 'C' and resid 2346 through 2360 Processing helix chain 'C' and resid 2361 through 2365 Processing helix chain 'C' and resid 2375 through 2389 removed outlier: 4.110A pdb=" N GLU C2381 " --> pdb=" O LEU C2377 " (cutoff:3.500A) removed outlier: 4.411A pdb=" N GLU C2382 " --> pdb=" O ALA C2378 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N ALA C2383 " --> pdb=" O ALA C2379 " (cutoff:3.500A) Processing helix chain 'C' and resid 2417 through 2437 Processing helix chain 'C' and resid 2439 through 2446 Processing helix chain 'C' and resid 2447 through 2461 removed outlier: 3.702A pdb=" N ARG C2452 " --> pdb=" O GLY C2448 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ARG C2454 " --> pdb=" O ALA C2450 " (cutoff:3.500A) Processing helix chain 'C' and resid 2462 through 2471 Processing helix chain 'C' and resid 2489 through 2493 removed outlier: 4.245A pdb=" N SER C2493 " --> pdb=" O MET C2490 " (cutoff:3.500A) Processing helix chain 'C' and resid 2495 through 2510 removed outlier: 4.133A pdb=" N LYS C2499 " --> pdb=" O VAL C2495 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N MET C2502 " --> pdb=" O HIS C2498 " (cutoff:3.500A) Processing helix chain 'C' and resid 2514 through 2526 removed outlier: 4.324A pdb=" N VAL C2524 " --> pdb=" O HIS C2520 " (cutoff:3.500A) Processing helix chain 'C' and resid 2526 through 2537 Processing helix chain 'C' and resid 2544 through 2557 Processing helix chain 'C' and resid 2557 through 2565 removed outlier: 3.512A pdb=" N LYS C2564 " --> pdb=" O PRO C2560 " (cutoff:3.500A) Processing helix chain 'C' and resid 2566 through 2574 removed outlier: 4.325A pdb=" N GLY C2571 " --> pdb=" O LEU C2568 " (cutoff:3.500A) removed outlier: 4.135A pdb=" N THR C2572 " --> pdb=" O PHE C2569 " (cutoff:3.500A) removed outlier: 5.381A pdb=" N GLU C2573 " --> pdb=" O ALA C2570 " (cutoff:3.500A) removed outlier: 4.491A pdb=" N HIS C2574 " --> pdb=" O GLY C2571 " (cutoff:3.500A) Processing helix chain 'C' and resid 2575 through 2591 removed outlier: 4.033A pdb=" N VAL C2579 " --> pdb=" O ARG C2575 " (cutoff:3.500A) Processing helix chain 'C' and resid 2596 through 2613 removed outlier: 3.532A pdb=" N ARG C2612 " --> pdb=" O MET C2608 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N TYR C2613 " --> pdb=" O ALA C2609 " (cutoff:3.500A) Processing helix chain 'C' and resid 2615 through 2630 removed outlier: 4.974A pdb=" N HIS C2621 " --> pdb=" O SER C2617 " (cutoff:3.500A) removed outlier: 4.286A pdb=" N LEU C2622 " --> pdb=" O MET C2618 " (cutoff:3.500A) Processing helix chain 'C' and resid 2631 through 2633 No H-bonds generated for 'chain 'C' and resid 2631 through 2633' Processing helix chain 'C' and resid 2634 through 2636 No H-bonds generated for 'chain 'C' and resid 2634 through 2636' Processing helix chain 'C' and resid 2637 through 2651 removed outlier: 3.910A pdb=" N LYS C2642 " --> pdb=" O LYS C2638 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N HIS C2647 " --> pdb=" O LEU C2643 " (cutoff:3.500A) Processing helix chain 'C' and resid 2651 through 2657 removed outlier: 3.838A pdb=" N TYR C2655 " --> pdb=" O CYS C2651 " (cutoff:3.500A) Processing helix chain 'C' and resid 2670 through 2689 removed outlier: 3.647A pdb=" N ALA C2687 " --> pdb=" O PHE C2683 " (cutoff:3.500A) Processing helix chain 'C' and resid 2692 through 2710 removed outlier: 3.580A pdb=" N MET C2698 " --> pdb=" O GLU C2694 " (cutoff:3.500A) Proline residue: C2701 - end of helix Processing helix chain 'C' and resid 2748 through 2750 No H-bonds generated for 'chain 'C' and resid 2748 through 2750' Processing helix chain 'C' and resid 2751 through 2773 removed outlier: 3.730A pdb=" N LYS C2757 " --> pdb=" O SER C2753 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N HIS C2763 " --> pdb=" O ALA C2759 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N GLU C2764 " --> pdb=" O GLU C2760 " (cutoff:3.500A) Processing helix chain 'C' and resid 2806 through 2819 removed outlier: 3.877A pdb=" N LEU C2813 " --> pdb=" O ILE C2809 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N LYS C2814 " --> pdb=" O LYS C2810 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N TRP C2819 " --> pdb=" O ALA C2815 " (cutoff:3.500A) Processing helix chain 'C' and resid 2868 through 2895 removed outlier: 4.110A pdb=" N GLU C2893 " --> pdb=" O LYS C2889 " (cutoff:3.500A) Processing helix chain 'C' and resid 2912 through 2932 removed outlier: 5.534A pdb=" N ARG C2918 " --> pdb=" O LYS C2914 " (cutoff:3.500A) removed outlier: 4.416A pdb=" N ASP C2919 " --> pdb=" O GLU C2915 " (cutoff:3.500A) Processing helix chain 'C' and resid 2954 through 2983 removed outlier: 3.779A pdb=" N ILE C2969 " --> pdb=" O ARG C2965 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N ALA C2975 " --> pdb=" O GLN C2971 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N HIS C2976 " --> pdb=" O GLU C2972 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N SER C2983 " --> pdb=" O ALA C2979 " (cutoff:3.500A) Processing helix chain 'C' and resid 2991 through 3013 removed outlier: 5.458A pdb=" N LEU C3003 " --> pdb=" O ALA C2999 " (cutoff:3.500A) Proline residue: C3004 - end of helix removed outlier: 3.514A pdb=" N PHE C3010 " --> pdb=" O ILE C3006 " (cutoff:3.500A) removed outlier: 4.157A pdb=" N THR C3011 " --> pdb=" O ASN C3007 " (cutoff:3.500A) Processing helix chain 'C' and resid 3013 through 3018 Processing helix chain 'C' and resid 3032 through 3051 removed outlier: 3.791A pdb=" N GLU C3037 " --> pdb=" O ASN C3033 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N ALA C3047 " --> pdb=" O PHE C3043 " (cutoff:3.500A) Processing helix chain 'C' and resid 3053 through 3058 Processing helix chain 'C' and resid 3060 through 3074 removed outlier: 3.501A pdb=" N ASN C3066 " --> pdb=" O PRO C3062 " (cutoff:3.500A) Processing helix chain 'C' and resid 3076 through 3083 removed outlier: 3.972A pdb=" N VAL C3080 " --> pdb=" O ASP C3076 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N MET C3081 " --> pdb=" O ALA C3077 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N LYS C3082 " --> pdb=" O ARG C3078 " (cutoff:3.500A) Processing helix chain 'C' and resid 3085 through 3111 Processing helix chain 'C' and resid 3124 through 3136 removed outlier: 3.883A pdb=" N ASN C3128 " --> pdb=" O GLY C3124 " (cutoff:3.500A) Processing helix chain 'C' and resid 3136 through 3151 Processing helix chain 'C' and resid 3152 through 3157 Processing helix chain 'C' and resid 3160 through 3174 removed outlier: 3.842A pdb=" N ARG C3167 " --> pdb=" O VAL C3163 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N THR C3168 " --> pdb=" O SER C3164 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N TYR C3173 " --> pdb=" O LEU C3169 " (cutoff:3.500A) Processing helix chain 'C' and resid 3175 through 3178 Processing helix chain 'C' and resid 3180 through 3201 Proline residue: C3188 - end of helix Processing helix chain 'C' and resid 3207 through 3214 removed outlier: 5.176A pdb=" N GLU C3212 " --> pdb=" O GLN C3209 " (cutoff:3.500A) Processing helix chain 'C' and resid 3217 through 3222 Processing helix chain 'C' and resid 3245 through 3260 removed outlier: 3.676A pdb=" N ALA C3251 " --> pdb=" O ASP C3247 " (cutoff:3.500A) Processing helix chain 'C' and resid 3266 through 3272 Processing helix chain 'C' and resid 3272 through 3279 Processing helix chain 'C' and resid 3280 through 3286 removed outlier: 4.076A pdb=" N GLU C3286 " --> pdb=" O PRO C3282 " (cutoff:3.500A) Processing helix chain 'C' and resid 3308 through 3326 removed outlier: 3.614A pdb=" N LEU C3315 " --> pdb=" O HIS C3311 " (cutoff:3.500A) Processing helix chain 'C' and resid 3334 through 3343 Processing helix chain 'C' and resid 3344 through 3350 removed outlier: 3.828A pdb=" N SER C3347 " --> pdb=" O PRO C3344 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N ARG C3348 " --> pdb=" O ILE C3345 " (cutoff:3.500A) removed outlier: 6.741A pdb=" N ARG C3350 " --> pdb=" O SER C3347 " (cutoff:3.500A) Processing helix chain 'C' and resid 3351 through 3357 removed outlier: 4.161A pdb=" N HIS C3355 " --> pdb=" O PRO C3351 " (cutoff:3.500A) Processing helix chain 'C' and resid 3357 through 3382 removed outlier: 3.710A pdb=" N GLU C3382 " --> pdb=" O GLN C3378 " (cutoff:3.500A) Processing helix chain 'C' and resid 3384 through 3386 No H-bonds generated for 'chain 'C' and resid 3384 through 3386' Processing helix chain 'C' and resid 3387 through 3419 removed outlier: 3.670A pdb=" N LEU C3392 " --> pdb=" O GLU C3388 " (cutoff:3.500A) removed outlier: 7.010A pdb=" N LEU C3393 " --> pdb=" O GLU C3389 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N VAL C3394 " --> pdb=" O GLY C3390 " (cutoff:3.500A) Proline residue: C3410 - end of helix removed outlier: 3.617A pdb=" N ARG C3414 " --> pdb=" O PRO C3410 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N ASN C3419 " --> pdb=" O TYR C3415 " (cutoff:3.500A) Processing helix chain 'C' and resid 3419 through 3426 Processing helix chain 'C' and resid 3428 through 3448 Processing helix chain 'C' and resid 3448 through 3463 Processing helix chain 'C' and resid 3471 through 3477 Processing helix chain 'C' and resid 3504 through 3507 Processing helix chain 'C' and resid 3508 through 3522 Proline residue: C3519 - end of helix Processing helix chain 'C' and resid 3526 through 3528 No H-bonds generated for 'chain 'C' and resid 3526 through 3528' Processing helix chain 'C' and resid 3529 through 3542 Processing helix chain 'C' and resid 3545 through 3556 Processing helix chain 'C' and resid 3566 through 3578 removed outlier: 3.863A pdb=" N ARG C3570 " --> pdb=" O SER C3566 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N TRP C3571 " --> pdb=" O PRO C3567 " (cutoff:3.500A) Processing helix chain 'C' and resid 3588 through 3611 Processing helix chain 'C' and resid 3624 through 3638 removed outlier: 6.726A pdb=" N ARG C3630 " --> pdb=" O LYS C3626 " (cutoff:3.500A) removed outlier: 6.366A pdb=" N ALA C3631 " --> pdb=" O GLN C3627 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N VAL C3632 " --> pdb=" O ARG C3628 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N VAL C3633 " --> pdb=" O ARG C3629 " (cutoff:3.500A) Processing helix chain 'C' and resid 3640 through 3644 Processing helix chain 'C' and resid 3645 through 3661 removed outlier: 3.556A pdb=" N GLU C3655 " --> pdb=" O ASN C3651 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N ALA C3659 " --> pdb=" O GLU C3655 " (cutoff:3.500A) Processing helix chain 'C' and resid 3669 through 3678 Processing helix chain 'C' and resid 3696 through 3710 Processing helix chain 'C' and resid 3719 through 3735 removed outlier: 4.102A pdb=" N CYS C3733 " --> pdb=" O MET C3729 " (cutoff:3.500A) removed outlier: 4.571A pdb=" N HIS C3734 " --> pdb=" O ALA C3730 " (cutoff:3.500A) removed outlier: 4.360A pdb=" N LEU C3735 " --> pdb=" O LYS C3731 " (cutoff:3.500A) Processing helix chain 'C' and resid 3752 through 3772 removed outlier: 4.269A pdb=" N MET C3758 " --> pdb=" O GLU C3754 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N GLU C3759 " --> pdb=" O GLU C3755 " (cutoff:3.500A) Processing helix chain 'C' and resid 3774 through 3786 removed outlier: 3.523A pdb=" N LEU C3780 " --> pdb=" O ALA C3776 " (cutoff:3.500A) Processing helix chain 'C' and resid 3791 through 3806 Processing helix chain 'C' and resid 3809 through 3824 Processing helix chain 'C' and resid 3826 through 3838 Processing helix chain 'C' and resid 3843 through 3857 removed outlier: 3.802A pdb=" N PHE C3847 " --> pdb=" O ASP C3843 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N GLY C3857 " --> pdb=" O ALA C3853 " (cutoff:3.500A) Processing helix chain 'C' and resid 3877 through 3892 removed outlier: 3.549A pdb=" N PHE C3885 " --> pdb=" O THR C3881 " (cutoff:3.500A) Processing helix chain 'C' and resid 3896 through 3905 removed outlier: 3.660A pdb=" N TYR C3902 " --> pdb=" O ASP C3898 " (cutoff:3.500A) Processing helix chain 'C' and resid 3914 through 3935 Processing helix chain 'C' and resid 3944 through 3970 removed outlier: 3.763A pdb=" N SER C3956 " --> pdb=" O SER C3952 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N VAL C3957 " --> pdb=" O LYS C3953 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N ALA C3958 " --> pdb=" O ALA C3954 " (cutoff:3.500A) Processing helix chain 'C' and resid 3973 through 3982 Processing helix chain 'C' and resid 3984 through 4005 removed outlier: 3.824A pdb=" N MET C4001 " --> pdb=" O ALA C3997 " (cutoff:3.500A) Processing helix chain 'C' and resid 4009 through 4032 Processing helix chain 'C' and resid 4038 through 4051 removed outlier: 3.667A pdb=" N GLU C4050 " --> pdb=" O ASP C4046 " (cutoff:3.500A) Processing helix chain 'C' and resid 4051 through 4072 removed outlier: 3.933A pdb=" N MET C4057 " --> pdb=" O SER C4053 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N MET C4064 " --> pdb=" O LYS C4060 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N PHE C4065 " --> pdb=" O PHE C4061 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N ASP C4070 " --> pdb=" O LEU C4066 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N ILE C4071 " --> pdb=" O LYS C4067 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N VAL C4072 " --> pdb=" O LEU C4068 " (cutoff:3.500A) Processing helix chain 'C' and resid 4074 through 4079 Processing helix chain 'C' and resid 4090 through 4098 removed outlier: 3.787A pdb=" N ALA C4096 " --> pdb=" O ASP C4092 " (cutoff:3.500A) removed outlier: 4.113A pdb=" N ASP C4098 " --> pdb=" O GLN C4094 " (cutoff:3.500A) Processing helix chain 'C' and resid 4099 through 4101 No H-bonds generated for 'chain 'C' and resid 4099 through 4101' Processing helix chain 'C' and resid 4104 through 4115 Processing helix chain 'C' and resid 4128 through 4131 Processing helix chain 'C' and resid 4132 through 4154 removed outlier: 4.338A pdb=" N ASP C4138 " --> pdb=" O GLU C4134 " (cutoff:3.500A) removed outlier: 4.305A pdb=" N ILE C4139 " --> pdb=" O PRO C4135 " (cutoff:3.500A) Processing helix chain 'C' and resid 4157 through 4166 removed outlier: 3.810A pdb=" N ARG C4161 " --> pdb=" O ASP C4157 " (cutoff:3.500A) Processing helix chain 'C' and resid 4167 through 4175 removed outlier: 4.091A pdb=" N LEU C4171 " --> pdb=" O ALA C4167 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N GLU C4172 " --> pdb=" O GLU C4168 " (cutoff:3.500A) removed outlier: 4.335A pdb=" N TYR C4173 " --> pdb=" O SER C4169 " (cutoff:3.500A) Processing helix chain 'C' and resid 4198 through 4207 Processing helix chain 'C' and resid 4207 through 4225 Processing helix chain 'C' and resid 4226 through 4252 removed outlier: 4.188A pdb=" N MET C4231 " --> pdb=" O GLU C4227 " (cutoff:3.500A) removed outlier: 5.066A pdb=" N GLU C4232 " --> pdb=" O ALA C4228 " (cutoff:3.500A) Processing helix chain 'C' and resid 4541 through 4558 Processing helix chain 'C' and resid 4558 through 4578 Processing helix chain 'C' and resid 4638 through 4665 Processing helix chain 'C' and resid 4665 through 4683 Processing helix chain 'C' and resid 4696 through 4706 removed outlier: 3.550A pdb=" N GLN C4700 " --> pdb=" O ASP C4696 " (cutoff:3.500A) removed outlier: 4.158A pdb=" N LEU C4704 " --> pdb=" O GLN C4700 " (cutoff:3.500A) removed outlier: 4.411A pdb=" N VAL C4705 " --> pdb=" O TRP C4701 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N LEU C4706 " --> pdb=" O ASP C4702 " (cutoff:3.500A) Processing helix chain 'C' and resid 4719 through 4733 removed outlier: 4.983A pdb=" N ASP C4730 " --> pdb=" O ASP C4726 " (cutoff:3.500A) removed outlier: 5.933A pdb=" N ILE C4731 " --> pdb=" O LYS C4727 " (cutoff:3.500A) Processing helix chain 'C' and resid 4733 through 4742 Processing helix chain 'C' and resid 4773 through 4786 Processing helix chain 'C' and resid 4786 through 4805 removed outlier: 3.783A pdb=" N HIS C4803 " --> pdb=" O SER C4799 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N TYR C4804 " --> pdb=" O LEU C4800 " (cutoff:3.500A) Processing helix chain 'C' and resid 4806 through 4814 removed outlier: 3.892A pdb=" N HIS C4812 " --> pdb=" O PHE C4809 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N LEU C4813 " --> pdb=" O ALA C4810 " (cutoff:3.500A) removed outlier: 4.118A pdb=" N LEU C4814 " --> pdb=" O ALA C4811 " (cutoff:3.500A) Processing helix chain 'C' and resid 4815 through 4820 Processing helix chain 'C' and resid 4820 through 4832 removed outlier: 3.567A pdb=" N VAL C4830 " --> pdb=" O ILE C4826 " (cutoff:3.500A) Processing helix chain 'C' and resid 4833 through 4859 Processing helix chain 'C' and resid 4878 through 4890 Processing helix chain 'C' and resid 4895 through 4901 removed outlier: 4.193A pdb=" N ASP C4899 " --> pdb=" O GLY C4895 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N GLU C4900 " --> pdb=" O GLY C4896 " (cutoff:3.500A) Processing helix chain 'C' and resid 4910 through 4923 Processing helix chain 'C' and resid 4930 through 4957 Processing helix chain 'C' and resid 4964 through 4969 removed outlier: 4.187A pdb=" N PHE C4968 " --> pdb=" O GLY C4964 " (cutoff:3.500A) Processing helix chain 'C' and resid 4973 through 4979 Processing helix chain 'C' and resid 4984 through 4998 Processing helix chain 'C' and resid 5004 through 5016 Processing helix chain 'C' and resid 5027 through 5032 Processing helix chain 'C' and resid 5032 through 5037 removed outlier: 3.654A pdb=" N SER C5037 " --> pdb=" O GLU C5033 " (cutoff:3.500A) Processing helix chain 'D' and resid 74 through 84 Processing helix chain 'D' and resid 251 through 258 removed outlier: 3.684A pdb=" N THR D 254 " --> pdb=" O ALA D 251 " (cutoff:3.500A) removed outlier: 6.072A pdb=" N ALA D 256 " --> pdb=" O CYS D 253 " (cutoff:3.500A) removed outlier: 6.665A pdb=" N ARG D 257 " --> pdb=" O THR D 254 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N SER D 258 " --> pdb=" O HIS D 255 " (cutoff:3.500A) Processing helix chain 'D' and resid 305 through 307 No H-bonds generated for 'chain 'D' and resid 305 through 307' Processing helix chain 'D' and resid 365 through 370 removed outlier: 4.315A pdb=" N LEU D 369 " --> pdb=" O LYS D 365 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N GLY D 370 " --> pdb=" O ALA D 366 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 365 through 370' Processing helix chain 'D' and resid 394 through 421 removed outlier: 3.902A pdb=" N ARG D 402 " --> pdb=" O SER D 398 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N MET D 403 " --> pdb=" O GLN D 399 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N ILE D 404 " --> pdb=" O ALA D 400 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N HIS D 405 " --> pdb=" O ALA D 401 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N GLY D 409 " --> pdb=" O HIS D 405 " (cutoff:3.500A) Processing helix chain 'D' and resid 437 through 452 removed outlier: 3.557A pdb=" N GLY D 450 " --> pdb=" O GLN D 446 " (cutoff:3.500A) Processing helix chain 'D' and resid 460 through 481 Processing helix chain 'D' and resid 482 through 495 Processing helix chain 'D' and resid 499 through 505 Processing helix chain 'D' and resid 508 through 513 removed outlier: 4.130A pdb=" N GLU D 513 " --> pdb=" O GLU D 509 " (cutoff:3.500A) Processing helix chain 'D' and resid 513 through 531 removed outlier: 4.561A pdb=" N GLU D 517 " --> pdb=" O GLU D 513 " (cutoff:3.500A) Processing helix chain 'D' and resid 533 through 538 Processing helix chain 'D' and resid 539 through 542 removed outlier: 3.826A pdb=" N THR D 542 " --> pdb=" O LEU D 539 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 539 through 542' Processing helix chain 'D' and resid 543 through 549 removed outlier: 4.166A pdb=" N VAL D 547 " --> pdb=" O ASN D 543 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N VAL D 548 " --> pdb=" O LEU D 544 " (cutoff:3.500A) Processing helix chain 'D' and resid 557 through 569 Processing helix chain 'D' and resid 571 through 578 removed outlier: 3.936A pdb=" N LEU D 575 " --> pdb=" O SER D 571 " (cutoff:3.500A) Processing helix chain 'D' and resid 579 through 593 removed outlier: 3.630A pdb=" N ILE D 583 " --> pdb=" O GLN D 579 " (cutoff:3.500A) Processing helix chain 'D' and resid 596 through 607 removed outlier: 4.169A pdb=" N LEU D 600 " --> pdb=" O ASN D 596 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N ASP D 601 " --> pdb=" O HIS D 597 " (cutoff:3.500A) Processing helix chain 'D' and resid 614 through 626 removed outlier: 3.554A pdb=" N ASP D 619 " --> pdb=" O ARG D 615 " (cutoff:3.500A) removed outlier: 4.429A pdb=" N LEU D 620 " --> pdb=" O SER D 616 " (cutoff:3.500A) Processing helix chain 'D' and resid 794 through 798 removed outlier: 3.978A pdb=" N GLY D 798 " --> pdb=" O GLY D 795 " (cutoff:3.500A) Processing helix chain 'D' and resid 812 through 814 No H-bonds generated for 'chain 'D' and resid 812 through 814' Processing helix chain 'D' and resid 847 through 851 Processing helix chain 'D' and resid 864 through 869 Processing helix chain 'D' and resid 872 through 877 Processing helix chain 'D' and resid 880 through 885 removed outlier: 4.364A pdb=" N THR D 885 " --> pdb=" O LEU D 881 " (cutoff:3.500A) Processing helix chain 'D' and resid 914 through 936 Processing helix chain 'D' and resid 978 through 1003 removed outlier: 3.507A pdb=" N VAL D 995 " --> pdb=" O ASN D 991 " (cutoff:3.500A) Processing helix chain 'D' and resid 1023 through 1027 Processing helix chain 'D' and resid 1028 through 1049 removed outlier: 4.080A pdb=" N SER D1038 " --> pdb=" O SER D1034 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N LEU D1039 " --> pdb=" O ASN D1035 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N TYR D1049 " --> pdb=" O THR D1045 " (cutoff:3.500A) Processing helix chain 'D' and resid 1068 through 1072 removed outlier: 3.772A pdb=" N ARG D1071 " --> pdb=" O ARG D1068 " (cutoff:3.500A) removed outlier: 4.417A pdb=" N VAL D1072 " --> pdb=" O TRP D1069 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 1068 through 1072' Processing helix chain 'D' and resid 1079 through 1082 Processing helix chain 'D' and resid 1423 through 1430 Processing helix chain 'D' and resid 1444 through 1446 No H-bonds generated for 'chain 'D' and resid 1444 through 1446' Processing helix chain 'D' and resid 1465 through 1469 removed outlier: 3.583A pdb=" N VAL D1469 " --> pdb=" O LEU D1466 " (cutoff:3.500A) Processing helix chain 'D' and resid 1498 through 1500 No H-bonds generated for 'chain 'D' and resid 1498 through 1500' Processing helix chain 'D' and resid 1574 through 1580 removed outlier: 3.779A pdb=" N ALA D1578 " --> pdb=" O PRO D1574 " (cutoff:3.500A) Processing helix chain 'D' and resid 1581 through 1584 removed outlier: 4.074A pdb=" N ARG D1584 " --> pdb=" O LEU D1581 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 1581 through 1584' Processing helix chain 'D' and resid 1651 through 1655 Processing helix chain 'D' and resid 1656 through 1674 removed outlier: 4.120A pdb=" N PHE D1662 " --> pdb=" O ASP D1658 " (cutoff:3.500A) Processing helix chain 'D' and resid 1678 through 1689 removed outlier: 3.615A pdb=" N ALA D1684 " --> pdb=" O ARG D1680 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N CYS D1686 " --> pdb=" O ALA D1682 " (cutoff:3.500A) removed outlier: 4.152A pdb=" N SER D1687 " --> pdb=" O HIS D1683 " (cutoff:3.500A) removed outlier: 4.330A pdb=" N HIS D1688 " --> pdb=" O ALA D1684 " (cutoff:3.500A) Processing helix chain 'D' and resid 1690 through 1699 removed outlier: 4.170A pdb=" N GLU D1699 " --> pdb=" O LEU D1695 " (cutoff:3.500A) Processing helix chain 'D' and resid 1704 through 1720 Processing helix chain 'D' and resid 1720 through 1731 Processing helix chain 'D' and resid 1739 through 1744 Processing helix chain 'D' and resid 1803 through 1824 removed outlier: 3.674A pdb=" N GLY D1823 " --> pdb=" O VAL D1819 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N GLN D1824 " --> pdb=" O ARG D1820 " (cutoff:3.500A) Processing helix chain 'D' and resid 1833 through 1852 Proline residue: D1840 - end of helix Processing helix chain 'D' and resid 1855 through 1867 Processing helix chain 'D' and resid 1925 through 1929 removed outlier: 4.099A pdb=" N GLN D1928 " --> pdb=" O GLY D1925 " (cutoff:3.500A) Processing helix chain 'D' and resid 1932 through 1982 removed outlier: 3.823A pdb=" N GLN D1938 " --> pdb=" O SER D1934 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N PHE D1946 " --> pdb=" O LEU D1942 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N GLN D1949 " --> pdb=" O TYR D1945 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N GLU D1950 " --> pdb=" O PHE D1946 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N LEU D1951 " --> pdb=" O CYS D1947 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N ASP D1967 " --> pdb=" O GLU D1963 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N LYS D1968 " --> pdb=" O ARG D1964 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N ARG D1982 " --> pdb=" O ALA D1978 " (cutoff:3.500A) Processing helix chain 'D' and resid 1983 through 1986 Processing helix chain 'D' and resid 1990 through 1995 Processing helix chain 'D' and resid 2001 through 2011 Processing helix chain 'D' and resid 2024 through 2042 removed outlier: 3.669A pdb=" N GLN D2032 " --> pdb=" O ARG D2028 " (cutoff:3.500A) Processing helix chain 'D' and resid 2093 through 2109 removed outlier: 3.760A pdb=" N ASP D2109 " --> pdb=" O TRP D2105 " (cutoff:3.500A) Processing helix chain 'D' and resid 2113 through 2129 Processing helix chain 'D' and resid 2129 through 2136 removed outlier: 3.606A pdb=" N GLU D2133 " --> pdb=" O ASP D2129 " (cutoff:3.500A) Processing helix chain 'D' and resid 2137 through 2139 No H-bonds generated for 'chain 'D' and resid 2137 through 2139' Processing helix chain 'D' and resid 2145 through 2147 No H-bonds generated for 'chain 'D' and resid 2145 through 2147' Processing helix chain 'D' and resid 2148 through 2165 removed outlier: 3.673A pdb=" N CYS D2158 " --> pdb=" O SER D2154 " (cutoff:3.500A) Processing helix chain 'D' and resid 2166 through 2168 No H-bonds generated for 'chain 'D' and resid 2166 through 2168' Processing helix chain 'D' and resid 2171 through 2188 removed outlier: 3.515A pdb=" N ILE D2185 " --> pdb=" O SER D2181 " (cutoff:3.500A) Processing helix chain 'D' and resid 2189 through 2194 Processing helix chain 'D' and resid 2194 through 2202 removed outlier: 3.540A pdb=" N MET D2198 " --> pdb=" O HIS D2194 " (cutoff:3.500A) Processing helix chain 'D' and resid 2202 through 2217 removed outlier: 3.529A pdb=" N VAL D2210 " --> pdb=" O THR D2206 " (cutoff:3.500A) Processing helix chain 'D' and resid 2225 through 2243 removed outlier: 3.850A pdb=" N VAL D2229 " --> pdb=" O PHE D2225 " (cutoff:3.500A) removed outlier: 4.511A pdb=" N SER D2243 " --> pdb=" O PHE D2239 " (cutoff:3.500A) Processing helix chain 'D' and resid 2243 through 2252 Processing helix chain 'D' and resid 2253 through 2261 removed outlier: 3.569A pdb=" N LEU D2258 " --> pdb=" O LEU D2254 " (cutoff:3.500A) removed outlier: 4.132A pdb=" N GLU D2259 " --> pdb=" O SER D2255 " (cutoff:3.500A) removed outlier: 4.451A pdb=" N ASN D2260 " --> pdb=" O TYR D2256 " (cutoff:3.500A) Processing helix chain 'D' and resid 2262 through 2267 removed outlier: 5.414A pdb=" N LEU D2265 " --> pdb=" O GLY D2262 " (cutoff:3.500A) Processing helix chain 'D' and resid 2271 through 2279 Processing helix chain 'D' and resid 2283 through 2290 Processing helix chain 'D' and resid 2291 through 2306 Processing helix chain 'D' and resid 2310 through 2316 Processing helix chain 'D' and resid 2324 through 2339 Processing helix chain 'D' and resid 2346 through 2360 Processing helix chain 'D' and resid 2361 through 2365 Processing helix chain 'D' and resid 2375 through 2389 removed outlier: 4.110A pdb=" N GLU D2381 " --> pdb=" O LEU D2377 " (cutoff:3.500A) removed outlier: 4.410A pdb=" N GLU D2382 " --> pdb=" O ALA D2378 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N ALA D2383 " --> pdb=" O ALA D2379 " (cutoff:3.500A) Processing helix chain 'D' and resid 2417 through 2437 Processing helix chain 'D' and resid 2439 through 2446 Processing helix chain 'D' and resid 2447 through 2461 removed outlier: 3.702A pdb=" N ARG D2452 " --> pdb=" O GLY D2448 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ARG D2454 " --> pdb=" O ALA D2450 " (cutoff:3.500A) Processing helix chain 'D' and resid 2462 through 2471 Processing helix chain 'D' and resid 2489 through 2493 removed outlier: 4.245A pdb=" N SER D2493 " --> pdb=" O MET D2490 " (cutoff:3.500A) Processing helix chain 'D' and resid 2495 through 2510 removed outlier: 4.133A pdb=" N LYS D2499 " --> pdb=" O VAL D2495 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N MET D2502 " --> pdb=" O HIS D2498 " (cutoff:3.500A) Processing helix chain 'D' and resid 2514 through 2526 removed outlier: 4.325A pdb=" N VAL D2524 " --> pdb=" O HIS D2520 " (cutoff:3.500A) Processing helix chain 'D' and resid 2526 through 2537 Processing helix chain 'D' and resid 2544 through 2557 Processing helix chain 'D' and resid 2557 through 2565 removed outlier: 3.513A pdb=" N LYS D2564 " --> pdb=" O PRO D2560 " (cutoff:3.500A) Processing helix chain 'D' and resid 2566 through 2574 removed outlier: 4.326A pdb=" N GLY D2571 " --> pdb=" O LEU D2568 " (cutoff:3.500A) removed outlier: 4.135A pdb=" N THR D2572 " --> pdb=" O PHE D2569 " (cutoff:3.500A) removed outlier: 5.381A pdb=" N GLU D2573 " --> pdb=" O ALA D2570 " (cutoff:3.500A) removed outlier: 4.491A pdb=" N HIS D2574 " --> pdb=" O GLY D2571 " (cutoff:3.500A) Processing helix chain 'D' and resid 2575 through 2591 removed outlier: 4.033A pdb=" N VAL D2579 " --> pdb=" O ARG D2575 " (cutoff:3.500A) Processing helix chain 'D' and resid 2596 through 2613 removed outlier: 3.531A pdb=" N ARG D2612 " --> pdb=" O MET D2608 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N TYR D2613 " --> pdb=" O ALA D2609 " (cutoff:3.500A) Processing helix chain 'D' and resid 2615 through 2630 removed outlier: 4.974A pdb=" N HIS D2621 " --> pdb=" O SER D2617 " (cutoff:3.500A) removed outlier: 4.286A pdb=" N LEU D2622 " --> pdb=" O MET D2618 " (cutoff:3.500A) Processing helix chain 'D' and resid 2631 through 2633 No H-bonds generated for 'chain 'D' and resid 2631 through 2633' Processing helix chain 'D' and resid 2634 through 2636 No H-bonds generated for 'chain 'D' and resid 2634 through 2636' Processing helix chain 'D' and resid 2637 through 2651 removed outlier: 3.910A pdb=" N LYS D2642 " --> pdb=" O LYS D2638 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N HIS D2647 " --> pdb=" O LEU D2643 " (cutoff:3.500A) Processing helix chain 'D' and resid 2651 through 2657 removed outlier: 3.838A pdb=" N TYR D2655 " --> pdb=" O CYS D2651 " (cutoff:3.500A) Processing helix chain 'D' and resid 2670 through 2689 removed outlier: 3.648A pdb=" N ALA D2687 " --> pdb=" O PHE D2683 " (cutoff:3.500A) Processing helix chain 'D' and resid 2692 through 2710 removed outlier: 3.580A pdb=" N MET D2698 " --> pdb=" O GLU D2694 " (cutoff:3.500A) Proline residue: D2701 - end of helix Processing helix chain 'D' and resid 2748 through 2750 No H-bonds generated for 'chain 'D' and resid 2748 through 2750' Processing helix chain 'D' and resid 2751 through 2773 removed outlier: 3.729A pdb=" N LYS D2757 " --> pdb=" O SER D2753 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N HIS D2763 " --> pdb=" O ALA D2759 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N GLU D2764 " --> pdb=" O GLU D2760 " (cutoff:3.500A) Processing helix chain 'D' and resid 2806 through 2819 removed outlier: 3.877A pdb=" N LEU D2813 " --> pdb=" O ILE D2809 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N LYS D2814 " --> pdb=" O LYS D2810 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N TRP D2819 " --> pdb=" O ALA D2815 " (cutoff:3.500A) Processing helix chain 'D' and resid 2868 through 2895 removed outlier: 4.110A pdb=" N GLU D2893 " --> pdb=" O LYS D2889 " (cutoff:3.500A) Processing helix chain 'D' and resid 2912 through 2932 removed outlier: 5.534A pdb=" N ARG D2918 " --> pdb=" O LYS D2914 " (cutoff:3.500A) removed outlier: 4.415A pdb=" N ASP D2919 " --> pdb=" O GLU D2915 " (cutoff:3.500A) Processing helix chain 'D' and resid 2954 through 2983 removed outlier: 3.779A pdb=" N ILE D2969 " --> pdb=" O ARG D2965 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N ALA D2975 " --> pdb=" O GLN D2971 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N HIS D2976 " --> pdb=" O GLU D2972 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N SER D2983 " --> pdb=" O ALA D2979 " (cutoff:3.500A) Processing helix chain 'D' and resid 2991 through 3013 removed outlier: 5.458A pdb=" N LEU D3003 " --> pdb=" O ALA D2999 " (cutoff:3.500A) Proline residue: D3004 - end of helix removed outlier: 3.513A pdb=" N PHE D3010 " --> pdb=" O ILE D3006 " (cutoff:3.500A) removed outlier: 4.156A pdb=" N THR D3011 " --> pdb=" O ASN D3007 " (cutoff:3.500A) Processing helix chain 'D' and resid 3013 through 3018 Processing helix chain 'D' and resid 3032 through 3051 removed outlier: 3.792A pdb=" N GLU D3037 " --> pdb=" O ASN D3033 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N ALA D3047 " --> pdb=" O PHE D3043 " (cutoff:3.500A) Processing helix chain 'D' and resid 3053 through 3058 Processing helix chain 'D' and resid 3060 through 3074 removed outlier: 3.501A pdb=" N ASN D3066 " --> pdb=" O PRO D3062 " (cutoff:3.500A) Processing helix chain 'D' and resid 3076 through 3083 removed outlier: 3.973A pdb=" N VAL D3080 " --> pdb=" O ASP D3076 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N MET D3081 " --> pdb=" O ALA D3077 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N LYS D3082 " --> pdb=" O ARG D3078 " (cutoff:3.500A) Processing helix chain 'D' and resid 3085 through 3111 Processing helix chain 'D' and resid 3124 through 3136 removed outlier: 3.882A pdb=" N ASN D3128 " --> pdb=" O GLY D3124 " (cutoff:3.500A) Processing helix chain 'D' and resid 3136 through 3151 Processing helix chain 'D' and resid 3152 through 3157 Processing helix chain 'D' and resid 3160 through 3174 removed outlier: 3.842A pdb=" N ARG D3167 " --> pdb=" O VAL D3163 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N THR D3168 " --> pdb=" O SER D3164 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N TYR D3173 " --> pdb=" O LEU D3169 " (cutoff:3.500A) Processing helix chain 'D' and resid 3175 through 3178 Processing helix chain 'D' and resid 3180 through 3201 Proline residue: D3188 - end of helix Processing helix chain 'D' and resid 3207 through 3214 removed outlier: 5.176A pdb=" N GLU D3212 " --> pdb=" O GLN D3209 " (cutoff:3.500A) Processing helix chain 'D' and resid 3217 through 3222 Processing helix chain 'D' and resid 3245 through 3260 removed outlier: 3.676A pdb=" N ALA D3251 " --> pdb=" O ASP D3247 " (cutoff:3.500A) Processing helix chain 'D' and resid 3266 through 3272 Processing helix chain 'D' and resid 3272 through 3279 Processing helix chain 'D' and resid 3280 through 3286 removed outlier: 4.075A pdb=" N GLU D3286 " --> pdb=" O PRO D3282 " (cutoff:3.500A) Processing helix chain 'D' and resid 3308 through 3326 removed outlier: 3.615A pdb=" N LEU D3315 " --> pdb=" O HIS D3311 " (cutoff:3.500A) Processing helix chain 'D' and resid 3334 through 3343 Processing helix chain 'D' and resid 3344 through 3350 removed outlier: 3.829A pdb=" N SER D3347 " --> pdb=" O PRO D3344 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N ARG D3348 " --> pdb=" O ILE D3345 " (cutoff:3.500A) removed outlier: 6.740A pdb=" N ARG D3350 " --> pdb=" O SER D3347 " (cutoff:3.500A) Processing helix chain 'D' and resid 3351 through 3357 removed outlier: 4.160A pdb=" N HIS D3355 " --> pdb=" O PRO D3351 " (cutoff:3.500A) Processing helix chain 'D' and resid 3357 through 3382 removed outlier: 3.710A pdb=" N GLU D3382 " --> pdb=" O GLN D3378 " (cutoff:3.500A) Processing helix chain 'D' and resid 3384 through 3386 No H-bonds generated for 'chain 'D' and resid 3384 through 3386' Processing helix chain 'D' and resid 3387 through 3419 removed outlier: 3.670A pdb=" N LEU D3392 " --> pdb=" O GLU D3388 " (cutoff:3.500A) removed outlier: 7.011A pdb=" N LEU D3393 " --> pdb=" O GLU D3389 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N VAL D3394 " --> pdb=" O GLY D3390 " (cutoff:3.500A) Proline residue: D3410 - end of helix removed outlier: 3.616A pdb=" N ARG D3414 " --> pdb=" O PRO D3410 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N ASN D3419 " --> pdb=" O TYR D3415 " (cutoff:3.500A) Processing helix chain 'D' and resid 3419 through 3426 Processing helix chain 'D' and resid 3428 through 3448 Processing helix chain 'D' and resid 3448 through 3463 Processing helix chain 'D' and resid 3471 through 3477 Processing helix chain 'D' and resid 3504 through 3507 Processing helix chain 'D' and resid 3508 through 3522 Proline residue: D3519 - end of helix Processing helix chain 'D' and resid 3526 through 3528 No H-bonds generated for 'chain 'D' and resid 3526 through 3528' Processing helix chain 'D' and resid 3529 through 3542 Processing helix chain 'D' and resid 3545 through 3556 Processing helix chain 'D' and resid 3566 through 3578 removed outlier: 3.863A pdb=" N ARG D3570 " --> pdb=" O SER D3566 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N TRP D3571 " --> pdb=" O PRO D3567 " (cutoff:3.500A) Processing helix chain 'D' and resid 3588 through 3611 Processing helix chain 'D' and resid 3624 through 3638 removed outlier: 6.726A pdb=" N ARG D3630 " --> pdb=" O LYS D3626 " (cutoff:3.500A) removed outlier: 6.365A pdb=" N ALA D3631 " --> pdb=" O GLN D3627 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N VAL D3632 " --> pdb=" O ARG D3628 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N VAL D3633 " --> pdb=" O ARG D3629 " (cutoff:3.500A) Processing helix chain 'D' and resid 3640 through 3644 Processing helix chain 'D' and resid 3645 through 3661 removed outlier: 3.556A pdb=" N GLU D3655 " --> pdb=" O ASN D3651 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N ALA D3659 " --> pdb=" O GLU D3655 " (cutoff:3.500A) Processing helix chain 'D' and resid 3669 through 3678 Processing helix chain 'D' and resid 3696 through 3710 Processing helix chain 'D' and resid 3719 through 3735 removed outlier: 4.101A pdb=" N CYS D3733 " --> pdb=" O MET D3729 " (cutoff:3.500A) removed outlier: 4.571A pdb=" N HIS D3734 " --> pdb=" O ALA D3730 " (cutoff:3.500A) removed outlier: 4.362A pdb=" N LEU D3735 " --> pdb=" O LYS D3731 " (cutoff:3.500A) Processing helix chain 'D' and resid 3752 through 3772 removed outlier: 4.269A pdb=" N MET D3758 " --> pdb=" O GLU D3754 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N GLU D3759 " --> pdb=" O GLU D3755 " (cutoff:3.500A) Processing helix chain 'D' and resid 3774 through 3786 removed outlier: 3.522A pdb=" N LEU D3780 " --> pdb=" O ALA D3776 " (cutoff:3.500A) Processing helix chain 'D' and resid 3791 through 3806 Processing helix chain 'D' and resid 3809 through 3824 Processing helix chain 'D' and resid 3826 through 3838 Processing helix chain 'D' and resid 3843 through 3857 removed outlier: 3.802A pdb=" N PHE D3847 " --> pdb=" O ASP D3843 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N GLY D3857 " --> pdb=" O ALA D3853 " (cutoff:3.500A) Processing helix chain 'D' and resid 3877 through 3892 removed outlier: 3.549A pdb=" N PHE D3885 " --> pdb=" O THR D3881 " (cutoff:3.500A) Processing helix chain 'D' and resid 3896 through 3905 removed outlier: 3.660A pdb=" N TYR D3902 " --> pdb=" O ASP D3898 " (cutoff:3.500A) Processing helix chain 'D' and resid 3914 through 3935 Processing helix chain 'D' and resid 3944 through 3970 removed outlier: 3.764A pdb=" N SER D3956 " --> pdb=" O SER D3952 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N VAL D3957 " --> pdb=" O LYS D3953 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N ALA D3958 " --> pdb=" O ALA D3954 " (cutoff:3.500A) Processing helix chain 'D' and resid 3973 through 3982 Processing helix chain 'D' and resid 3984 through 4005 removed outlier: 3.825A pdb=" N MET D4001 " --> pdb=" O ALA D3997 " (cutoff:3.500A) Processing helix chain 'D' and resid 4009 through 4032 Processing helix chain 'D' and resid 4038 through 4051 removed outlier: 3.667A pdb=" N GLU D4050 " --> pdb=" O ASP D4046 " (cutoff:3.500A) Processing helix chain 'D' and resid 4051 through 4072 removed outlier: 3.934A pdb=" N MET D4057 " --> pdb=" O SER D4053 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N MET D4064 " --> pdb=" O LYS D4060 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N PHE D4065 " --> pdb=" O PHE D4061 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N ASP D4070 " --> pdb=" O LEU D4066 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N ILE D4071 " --> pdb=" O LYS D4067 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N VAL D4072 " --> pdb=" O LEU D4068 " (cutoff:3.500A) Processing helix chain 'D' and resid 4074 through 4079 Processing helix chain 'D' and resid 4090 through 4098 removed outlier: 3.787A pdb=" N ALA D4096 " --> pdb=" O ASP D4092 " (cutoff:3.500A) removed outlier: 4.114A pdb=" N ASP D4098 " --> pdb=" O GLN D4094 " (cutoff:3.500A) Processing helix chain 'D' and resid 4099 through 4101 No H-bonds generated for 'chain 'D' and resid 4099 through 4101' Processing helix chain 'D' and resid 4104 through 4115 Processing helix chain 'D' and resid 4128 through 4131 Processing helix chain 'D' and resid 4132 through 4154 removed outlier: 4.338A pdb=" N ASP D4138 " --> pdb=" O GLU D4134 " (cutoff:3.500A) removed outlier: 4.305A pdb=" N ILE D4139 " --> pdb=" O PRO D4135 " (cutoff:3.500A) Processing helix chain 'D' and resid 4157 through 4166 removed outlier: 3.810A pdb=" N ARG D4161 " --> pdb=" O ASP D4157 " (cutoff:3.500A) Processing helix chain 'D' and resid 4167 through 4175 removed outlier: 4.091A pdb=" N LEU D4171 " --> pdb=" O ALA D4167 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N GLU D4172 " --> pdb=" O GLU D4168 " (cutoff:3.500A) removed outlier: 4.336A pdb=" N TYR D4173 " --> pdb=" O SER D4169 " (cutoff:3.500A) Processing helix chain 'D' and resid 4198 through 4207 Processing helix chain 'D' and resid 4207 through 4225 Processing helix chain 'D' and resid 4226 through 4252 removed outlier: 4.188A pdb=" N MET D4231 " --> pdb=" O GLU D4227 " (cutoff:3.500A) removed outlier: 5.066A pdb=" N GLU D4232 " --> pdb=" O ALA D4228 " (cutoff:3.500A) Processing helix chain 'D' and resid 4541 through 4558 Processing helix chain 'D' and resid 4558 through 4578 Processing helix chain 'D' and resid 4638 through 4665 Processing helix chain 'D' and resid 4665 through 4683 Processing helix chain 'D' and resid 4696 through 4706 removed outlier: 3.549A pdb=" N GLN D4700 " --> pdb=" O ASP D4696 " (cutoff:3.500A) removed outlier: 4.158A pdb=" N LEU D4704 " --> pdb=" O GLN D4700 " (cutoff:3.500A) removed outlier: 4.411A pdb=" N VAL D4705 " --> pdb=" O TRP D4701 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N LEU D4706 " --> pdb=" O ASP D4702 " (cutoff:3.500A) Processing helix chain 'D' and resid 4719 through 4733 removed outlier: 4.982A pdb=" N ASP D4730 " --> pdb=" O ASP D4726 " (cutoff:3.500A) removed outlier: 5.933A pdb=" N ILE D4731 " --> pdb=" O LYS D4727 " (cutoff:3.500A) Processing helix chain 'D' and resid 4733 through 4742 Processing helix chain 'D' and resid 4773 through 4786 Processing helix chain 'D' and resid 4786 through 4805 removed outlier: 3.783A pdb=" N HIS D4803 " --> pdb=" O SER D4799 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N TYR D4804 " --> pdb=" O LEU D4800 " (cutoff:3.500A) Processing helix chain 'D' and resid 4806 through 4814 removed outlier: 3.892A pdb=" N HIS D4812 " --> pdb=" O PHE D4809 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N LEU D4813 " --> pdb=" O ALA D4810 " (cutoff:3.500A) removed outlier: 4.118A pdb=" N LEU D4814 " --> pdb=" O ALA D4811 " (cutoff:3.500A) Processing helix chain 'D' and resid 4815 through 4820 Processing helix chain 'D' and resid 4820 through 4832 removed outlier: 3.566A pdb=" N VAL D4830 " --> pdb=" O ILE D4826 " (cutoff:3.500A) Processing helix chain 'D' and resid 4833 through 4859 Processing helix chain 'D' and resid 4878 through 4890 Processing helix chain 'D' and resid 4895 through 4901 removed outlier: 4.192A pdb=" N ASP D4899 " --> pdb=" O GLY D4895 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N GLU D4900 " --> pdb=" O GLY D4896 " (cutoff:3.500A) Processing helix chain 'D' and resid 4910 through 4923 Processing helix chain 'D' and resid 4930 through 4957 Processing helix chain 'D' and resid 4964 through 4969 removed outlier: 4.187A pdb=" N PHE D4968 " --> pdb=" O GLY D4964 " (cutoff:3.500A) Processing helix chain 'D' and resid 4973 through 4979 Processing helix chain 'D' and resid 4984 through 4998 Processing helix chain 'D' and resid 5004 through 5016 Processing helix chain 'D' and resid 5027 through 5032 Processing helix chain 'D' and resid 5032 through 5037 removed outlier: 3.654A pdb=" N SER D5037 " --> pdb=" O GLU D5033 " (cutoff:3.500A) Processing helix chain 'E' and resid 56 through 65 Processing helix chain 'F' and resid 56 through 65 Processing helix chain 'G' and resid 56 through 65 Processing helix chain 'H' and resid 56 through 65 Processing sheet with id=AA1, first strand: chain 'A' and resid 48 through 51 removed outlier: 3.601A pdb=" N VAL A 28 " --> pdb=" O GLU A 31 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N LEU A 35 " --> pdb=" O CYS A 24 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N LEU A 37 " --> pdb=" O LEU A 22 " (cutoff:3.500A) removed outlier: 6.148A pdb=" N LEU A 22 " --> pdb=" O LEU A 37 " (cutoff:3.500A) removed outlier: 6.896A pdb=" N GLU A 19 " --> pdb=" O ILE A 205 " (cutoff:3.500A) removed outlier: 4.301A pdb=" N GLN A 71 " --> pdb=" O LEU A 108 " (cutoff:3.500A) removed outlier: 7.749A pdb=" N ARG A 110 " --> pdb=" O LEU A 69 " (cutoff:3.500A) removed outlier: 5.641A pdb=" N LEU A 69 " --> pdb=" O ARG A 110 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N ASP A 18 " --> pdb=" O LEU A 69 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 117 through 120 Processing sheet with id=AA3, first strand: chain 'A' and resid 179 through 183 removed outlier: 3.677A pdb=" N GLN A 190 " --> pdb=" O SER A 183 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 299 through 303 removed outlier: 3.692A pdb=" N ARG A 289 " --> pdb=" O HIS A 284 " (cutoff:3.500A) removed outlier: 5.847A pdb=" N ILE A 282 " --> pdb=" O LEU A 291 " (cutoff:3.500A) removed outlier: 11.286A pdb=" N LEU A 293 " --> pdb=" O LEU A 280 " (cutoff:3.500A) removed outlier: 15.193A pdb=" N LEU A 280 " --> pdb=" O LEU A 293 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 230 through 232 Processing sheet with id=AA6, first strand: chain 'A' and resid 608 through 609 Processing sheet with id=AA7, first strand: chain 'A' and resid 634 through 639 removed outlier: 3.535A pdb=" N GLN A 634 " --> pdb=" O HIS A1640 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 721 through 722 removed outlier: 3.650A pdb=" N TRP A 686 " --> pdb=" O TYR A 714 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 762 through 764 removed outlier: 4.177A pdb=" N PHE A 757 " --> pdb=" O VAL A 764 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N SER A 754 " --> pdb=" O ASP A 749 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 762 through 764 removed outlier: 4.177A pdb=" N PHE A 757 " --> pdb=" O VAL A 764 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N SER A 754 " --> pdb=" O ASP A 749 " (cutoff:3.500A) removed outlier: 6.996A pdb=" N LYS A 788 " --> pdb=" O ASP A 669 " (cutoff:3.500A) removed outlier: 7.139A pdb=" N GLY A1625 " --> pdb=" O ALA A1620 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N ALA A1620 " --> pdb=" O GLY A1625 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 766 through 769 removed outlier: 3.514A pdb=" N VAL A 767 " --> pdb=" O THR A1475 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 830 through 831 removed outlier: 3.594A pdb=" N PHE A1090 " --> pdb=" O CYS A1151 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N ASP A1147 " --> pdb=" O ALA A1094 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 830 through 831 removed outlier: 3.594A pdb=" N PHE A1090 " --> pdb=" O CYS A1151 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N ASP A1147 " --> pdb=" O ALA A1094 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N PHE A1179 " --> pdb=" O ILE A1160 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 1006 through 1007 removed outlier: 6.395A pdb=" N SER A1006 " --> pdb=" O ASN A1018 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB5 Processing sheet with id=AB6, first strand: chain 'A' and resid 1136 through 1138 removed outlier: 3.642A pdb=" N ALA A1077 " --> pdb=" O PRO A1190 " (cutoff:3.500A) removed outlier: 4.988A pdb=" N ILE A1074 " --> pdb=" O SER A1239 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 1244 through 1247 removed outlier: 6.043A pdb=" N PHE A1288 " --> pdb=" O LEU A1600 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 1244 through 1247 removed outlier: 6.043A pdb=" N PHE A1288 " --> pdb=" O LEU A1600 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'A' and resid 1255 through 1260 removed outlier: 3.551A pdb=" N ILE A1562 " --> pdb=" O LEU A1272 " (cutoff:3.500A) removed outlier: 6.735A pdb=" N HIS A1274 " --> pdb=" O ASN A1560 " (cutoff:3.500A) removed outlier: 6.201A pdb=" N ASN A1560 " --> pdb=" O HIS A1274 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N SER A1436 " --> pdb=" O GLU A1565 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N LEU A1526 " --> pdb=" O ASP A1521 " (cutoff:3.500A) removed outlier: 4.572A pdb=" N PHE A1529 " --> pdb=" O THR A1538 " (cutoff:3.500A) removed outlier: 6.754A pdb=" N THR A1538 " --> pdb=" O PHE A1529 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'A' and resid 1734 through 1737 removed outlier: 6.611A pdb=" N TYR A1734 " --> pdb=" O TYR A2142 " (cutoff:3.500A) removed outlier: 7.583A pdb=" N ILE A2144 " --> pdb=" O TYR A1734 " (cutoff:3.500A) removed outlier: 6.135A pdb=" N VAL A1736 " --> pdb=" O ILE A2144 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC1 Processing sheet with id=AC2, first strand: chain 'A' and resid 1777 through 1778 Processing sheet with id=AC3, first strand: chain 'A' and resid 2340 through 2341 Processing sheet with id=AC4, first strand: chain 'A' and resid 4088 through 4089 Processing sheet with id=AC5, first strand: chain 'A' and resid 4178 through 4184 Processing sheet with id=AC6, first strand: chain 'A' and resid 4580 through 4583 removed outlier: 4.134A pdb=" N SER A4583 " --> pdb=" O TYR A4629 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N TYR A4629 " --> pdb=" O SER A4583 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 48 through 51 removed outlier: 3.600A pdb=" N VAL B 28 " --> pdb=" O GLU B 31 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N LEU B 35 " --> pdb=" O CYS B 24 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N LEU B 37 " --> pdb=" O LEU B 22 " (cutoff:3.500A) removed outlier: 6.148A pdb=" N LEU B 22 " --> pdb=" O LEU B 37 " (cutoff:3.500A) removed outlier: 6.897A pdb=" N GLU B 19 " --> pdb=" O ILE B 205 " (cutoff:3.500A) removed outlier: 4.300A pdb=" N GLN B 71 " --> pdb=" O LEU B 108 " (cutoff:3.500A) removed outlier: 7.749A pdb=" N ARG B 110 " --> pdb=" O LEU B 69 " (cutoff:3.500A) removed outlier: 5.641A pdb=" N LEU B 69 " --> pdb=" O ARG B 110 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N ASP B 18 " --> pdb=" O LEU B 69 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 117 through 120 Processing sheet with id=AC9, first strand: chain 'B' and resid 179 through 183 removed outlier: 3.676A pdb=" N GLN B 190 " --> pdb=" O SER B 183 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 299 through 303 removed outlier: 3.693A pdb=" N ARG B 289 " --> pdb=" O HIS B 284 " (cutoff:3.500A) removed outlier: 5.847A pdb=" N ILE B 282 " --> pdb=" O LEU B 291 " (cutoff:3.500A) removed outlier: 11.286A pdb=" N LEU B 293 " --> pdb=" O LEU B 280 " (cutoff:3.500A) removed outlier: 15.192A pdb=" N LEU B 280 " --> pdb=" O LEU B 293 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 230 through 232 Processing sheet with id=AD3, first strand: chain 'B' and resid 608 through 609 Processing sheet with id=AD4, first strand: chain 'B' and resid 634 through 639 removed outlier: 3.535A pdb=" N GLN B 634 " --> pdb=" O HIS B1640 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'B' and resid 721 through 722 removed outlier: 3.650A pdb=" N TRP B 686 " --> pdb=" O TYR B 714 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'B' and resid 762 through 764 removed outlier: 4.177A pdb=" N PHE B 757 " --> pdb=" O VAL B 764 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N SER B 754 " --> pdb=" O ASP B 749 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'B' and resid 762 through 764 removed outlier: 4.177A pdb=" N PHE B 757 " --> pdb=" O VAL B 764 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N SER B 754 " --> pdb=" O ASP B 749 " (cutoff:3.500A) removed outlier: 6.996A pdb=" N LYS B 788 " --> pdb=" O ASP B 669 " (cutoff:3.500A) removed outlier: 7.140A pdb=" N GLY B1625 " --> pdb=" O ALA B1620 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N ALA B1620 " --> pdb=" O GLY B1625 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'B' and resid 766 through 769 removed outlier: 3.515A pdb=" N VAL B 767 " --> pdb=" O THR B1475 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'B' and resid 830 through 831 removed outlier: 3.594A pdb=" N PHE B1090 " --> pdb=" O CYS B1151 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N ASP B1147 " --> pdb=" O ALA B1094 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'B' and resid 830 through 831 removed outlier: 3.594A pdb=" N PHE B1090 " --> pdb=" O CYS B1151 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N ASP B1147 " --> pdb=" O ALA B1094 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N PHE B1179 " --> pdb=" O ILE B1160 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'B' and resid 1006 through 1007 removed outlier: 6.395A pdb=" N SER B1006 " --> pdb=" O ASN B1018 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE2 Processing sheet with id=AE3, first strand: chain 'B' and resid 1136 through 1138 removed outlier: 3.642A pdb=" N ALA B1077 " --> pdb=" O PRO B1190 " (cutoff:3.500A) removed outlier: 4.989A pdb=" N ILE B1074 " --> pdb=" O SER B1239 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'B' and resid 1244 through 1247 removed outlier: 6.043A pdb=" N PHE B1288 " --> pdb=" O LEU B1600 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'B' and resid 1244 through 1247 removed outlier: 6.043A pdb=" N PHE B1288 " --> pdb=" O LEU B1600 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'B' and resid 1255 through 1260 removed outlier: 3.551A pdb=" N ILE B1562 " --> pdb=" O LEU B1272 " (cutoff:3.500A) removed outlier: 6.735A pdb=" N HIS B1274 " --> pdb=" O ASN B1560 " (cutoff:3.500A) removed outlier: 6.200A pdb=" N ASN B1560 " --> pdb=" O HIS B1274 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N SER B1436 " --> pdb=" O GLU B1565 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N LEU B1526 " --> pdb=" O ASP B1521 " (cutoff:3.500A) removed outlier: 4.572A pdb=" N PHE B1529 " --> pdb=" O THR B1538 " (cutoff:3.500A) removed outlier: 6.754A pdb=" N THR B1538 " --> pdb=" O PHE B1529 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'B' and resid 1734 through 1737 removed outlier: 6.611A pdb=" N TYR B1734 " --> pdb=" O TYR B2142 " (cutoff:3.500A) removed outlier: 7.583A pdb=" N ILE B2144 " --> pdb=" O TYR B1734 " (cutoff:3.500A) removed outlier: 6.135A pdb=" N VAL B1736 " --> pdb=" O ILE B2144 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE7 Processing sheet with id=AE8, first strand: chain 'B' and resid 1777 through 1778 Processing sheet with id=AE9, first strand: chain 'B' and resid 2340 through 2341 Processing sheet with id=AF1, first strand: chain 'B' and resid 4088 through 4089 Processing sheet with id=AF2, first strand: chain 'B' and resid 4178 through 4184 Processing sheet with id=AF3, first strand: chain 'B' and resid 4580 through 4583 removed outlier: 4.134A pdb=" N SER B4583 " --> pdb=" O TYR B4629 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N TYR B4629 " --> pdb=" O SER B4583 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'C' and resid 48 through 51 removed outlier: 3.600A pdb=" N VAL C 28 " --> pdb=" O GLU C 31 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N LEU C 35 " --> pdb=" O CYS C 24 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N LEU C 37 " --> pdb=" O LEU C 22 " (cutoff:3.500A) removed outlier: 6.149A pdb=" N LEU C 22 " --> pdb=" O LEU C 37 " (cutoff:3.500A) removed outlier: 6.896A pdb=" N GLU C 19 " --> pdb=" O ILE C 205 " (cutoff:3.500A) removed outlier: 4.301A pdb=" N GLN C 71 " --> pdb=" O LEU C 108 " (cutoff:3.500A) removed outlier: 7.750A pdb=" N ARG C 110 " --> pdb=" O LEU C 69 " (cutoff:3.500A) removed outlier: 5.641A pdb=" N LEU C 69 " --> pdb=" O ARG C 110 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N ASP C 18 " --> pdb=" O LEU C 69 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'C' and resid 117 through 120 Processing sheet with id=AF6, first strand: chain 'C' and resid 179 through 183 removed outlier: 3.677A pdb=" N GLN C 190 " --> pdb=" O SER C 183 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'C' and resid 299 through 303 removed outlier: 3.692A pdb=" N ARG C 289 " --> pdb=" O HIS C 284 " (cutoff:3.500A) removed outlier: 5.847A pdb=" N ILE C 282 " --> pdb=" O LEU C 291 " (cutoff:3.500A) removed outlier: 11.286A pdb=" N LEU C 293 " --> pdb=" O LEU C 280 " (cutoff:3.500A) removed outlier: 15.193A pdb=" N LEU C 280 " --> pdb=" O LEU C 293 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'C' and resid 230 through 232 Processing sheet with id=AF9, first strand: chain 'C' and resid 608 through 609 Processing sheet with id=AG1, first strand: chain 'C' and resid 634 through 639 removed outlier: 3.536A pdb=" N GLN C 634 " --> pdb=" O HIS C1640 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'C' and resid 721 through 722 removed outlier: 3.651A pdb=" N TRP C 686 " --> pdb=" O TYR C 714 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'C' and resid 762 through 764 removed outlier: 4.178A pdb=" N PHE C 757 " --> pdb=" O VAL C 764 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N SER C 754 " --> pdb=" O ASP C 749 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'C' and resid 762 through 764 removed outlier: 4.178A pdb=" N PHE C 757 " --> pdb=" O VAL C 764 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N SER C 754 " --> pdb=" O ASP C 749 " (cutoff:3.500A) removed outlier: 6.995A pdb=" N LYS C 788 " --> pdb=" O ASP C 669 " (cutoff:3.500A) removed outlier: 7.140A pdb=" N GLY C1625 " --> pdb=" O ALA C1620 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N ALA C1620 " --> pdb=" O GLY C1625 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'C' and resid 766 through 769 removed outlier: 3.514A pdb=" N VAL C 767 " --> pdb=" O THR C1475 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'C' and resid 830 through 831 removed outlier: 3.595A pdb=" N PHE C1090 " --> pdb=" O CYS C1151 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N ASP C1147 " --> pdb=" O ALA C1094 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'C' and resid 830 through 831 removed outlier: 3.595A pdb=" N PHE C1090 " --> pdb=" O CYS C1151 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N ASP C1147 " --> pdb=" O ALA C1094 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N PHE C1179 " --> pdb=" O ILE C1160 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'C' and resid 1006 through 1007 removed outlier: 6.395A pdb=" N SER C1006 " --> pdb=" O ASN C1018 " (cutoff:3.500A) No H-bonds generated for sheet with id=AG8 Processing sheet with id=AG9, first strand: chain 'C' and resid 1136 through 1138 removed outlier: 3.642A pdb=" N ALA C1077 " --> pdb=" O PRO C1190 " (cutoff:3.500A) removed outlier: 4.989A pdb=" N ILE C1074 " --> pdb=" O SER C1239 " (cutoff:3.500A) Processing sheet with id=AH1, first strand: chain 'C' and resid 1244 through 1247 removed outlier: 6.043A pdb=" N PHE C1288 " --> pdb=" O LEU C1600 " (cutoff:3.500A) Processing sheet with id=AH2, first strand: chain 'C' and resid 1244 through 1247 removed outlier: 6.043A pdb=" N PHE C1288 " --> pdb=" O LEU C1600 " (cutoff:3.500A) Processing sheet with id=AH3, first strand: chain 'C' and resid 1255 through 1260 removed outlier: 3.551A pdb=" N ILE C1562 " --> pdb=" O LEU C1272 " (cutoff:3.500A) removed outlier: 6.735A pdb=" N HIS C1274 " --> pdb=" O ASN C1560 " (cutoff:3.500A) removed outlier: 6.200A pdb=" N ASN C1560 " --> pdb=" O HIS C1274 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N SER C1436 " --> pdb=" O GLU C1565 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N LEU C1526 " --> pdb=" O ASP C1521 " (cutoff:3.500A) removed outlier: 4.572A pdb=" N PHE C1529 " --> pdb=" O THR C1538 " (cutoff:3.500A) removed outlier: 6.754A pdb=" N THR C1538 " --> pdb=" O PHE C1529 " (cutoff:3.500A) Processing sheet with id=AH4, first strand: chain 'C' and resid 1734 through 1737 removed outlier: 6.611A pdb=" N TYR C1734 " --> pdb=" O TYR C2142 " (cutoff:3.500A) removed outlier: 7.583A pdb=" N ILE C2144 " --> pdb=" O TYR C1734 " (cutoff:3.500A) removed outlier: 6.135A pdb=" N VAL C1736 " --> pdb=" O ILE C2144 " (cutoff:3.500A) No H-bonds generated for sheet with id=AH4 Processing sheet with id=AH5, first strand: chain 'C' and resid 1777 through 1778 Processing sheet with id=AH6, first strand: chain 'C' and resid 2340 through 2341 Processing sheet with id=AH7, first strand: chain 'C' and resid 4088 through 4089 Processing sheet with id=AH8, first strand: chain 'C' and resid 4178 through 4184 Processing sheet with id=AH9, first strand: chain 'C' and resid 4580 through 4583 removed outlier: 4.134A pdb=" N SER C4583 " --> pdb=" O TYR C4629 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N TYR C4629 " --> pdb=" O SER C4583 " (cutoff:3.500A) Processing sheet with id=AI1, first strand: chain 'D' and resid 48 through 51 removed outlier: 3.601A pdb=" N VAL D 28 " --> pdb=" O GLU D 31 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N LEU D 35 " --> pdb=" O CYS D 24 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N LEU D 37 " --> pdb=" O LEU D 22 " (cutoff:3.500A) removed outlier: 6.148A pdb=" N LEU D 22 " --> pdb=" O LEU D 37 " (cutoff:3.500A) removed outlier: 6.896A pdb=" N GLU D 19 " --> pdb=" O ILE D 205 " (cutoff:3.500A) removed outlier: 4.300A pdb=" N GLN D 71 " --> pdb=" O LEU D 108 " (cutoff:3.500A) removed outlier: 7.750A pdb=" N ARG D 110 " --> pdb=" O LEU D 69 " (cutoff:3.500A) removed outlier: 5.641A pdb=" N LEU D 69 " --> pdb=" O ARG D 110 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N ASP D 18 " --> pdb=" O LEU D 69 " (cutoff:3.500A) Processing sheet with id=AI2, first strand: chain 'D' and resid 117 through 120 Processing sheet with id=AI3, first strand: chain 'D' and resid 179 through 183 removed outlier: 3.676A pdb=" N GLN D 190 " --> pdb=" O SER D 183 " (cutoff:3.500A) Processing sheet with id=AI4, first strand: chain 'D' and resid 299 through 303 removed outlier: 3.693A pdb=" N ARG D 289 " --> pdb=" O HIS D 284 " (cutoff:3.500A) removed outlier: 5.847A pdb=" N ILE D 282 " --> pdb=" O LEU D 291 " (cutoff:3.500A) removed outlier: 11.286A pdb=" N LEU D 293 " --> pdb=" O LEU D 280 " (cutoff:3.500A) removed outlier: 15.192A pdb=" N LEU D 280 " --> pdb=" O LEU D 293 " (cutoff:3.500A) Processing sheet with id=AI5, first strand: chain 'D' and resid 230 through 232 Processing sheet with id=AI6, first strand: chain 'D' and resid 608 through 609 Processing sheet with id=AI7, first strand: chain 'D' and resid 634 through 639 removed outlier: 3.535A pdb=" N GLN D 634 " --> pdb=" O HIS D1640 " (cutoff:3.500A) Processing sheet with id=AI8, first strand: chain 'D' and resid 721 through 722 removed outlier: 3.651A pdb=" N TRP D 686 " --> pdb=" O TYR D 714 " (cutoff:3.500A) Processing sheet with id=AI9, first strand: chain 'D' and resid 762 through 764 removed outlier: 4.178A pdb=" N PHE D 757 " --> pdb=" O VAL D 764 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N SER D 754 " --> pdb=" O ASP D 749 " (cutoff:3.500A) Processing sheet with id=AJ1, first strand: chain 'D' and resid 762 through 764 removed outlier: 4.178A pdb=" N PHE D 757 " --> pdb=" O VAL D 764 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N SER D 754 " --> pdb=" O ASP D 749 " (cutoff:3.500A) removed outlier: 6.995A pdb=" N LYS D 788 " --> pdb=" O ASP D 669 " (cutoff:3.500A) removed outlier: 7.140A pdb=" N GLY D1625 " --> pdb=" O ALA D1620 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N ALA D1620 " --> pdb=" O GLY D1625 " (cutoff:3.500A) Processing sheet with id=AJ2, first strand: chain 'D' and resid 766 through 769 removed outlier: 3.514A pdb=" N VAL D 767 " --> pdb=" O THR D1475 " (cutoff:3.500A) Processing sheet with id=AJ3, first strand: chain 'D' and resid 830 through 831 removed outlier: 3.595A pdb=" N PHE D1090 " --> pdb=" O CYS D1151 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N ASP D1147 " --> pdb=" O ALA D1094 " (cutoff:3.500A) Processing sheet with id=AJ4, first strand: chain 'D' and resid 830 through 831 removed outlier: 3.595A pdb=" N PHE D1090 " --> pdb=" O CYS D1151 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N ASP D1147 " --> pdb=" O ALA D1094 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N PHE D1179 " --> pdb=" O ILE D1160 " (cutoff:3.500A) Processing sheet with id=AJ5, first strand: chain 'D' and resid 1006 through 1007 removed outlier: 6.396A pdb=" N SER D1006 " --> pdb=" O ASN D1018 " (cutoff:3.500A) No H-bonds generated for sheet with id=AJ5 Processing sheet with id=AJ6, first strand: chain 'D' and resid 1136 through 1138 removed outlier: 3.642A pdb=" N ALA D1077 " --> pdb=" O PRO D1190 " (cutoff:3.500A) removed outlier: 4.989A pdb=" N ILE D1074 " --> pdb=" O SER D1239 " (cutoff:3.500A) Processing sheet with id=AJ7, first strand: chain 'D' and resid 1244 through 1247 removed outlier: 6.043A pdb=" N PHE D1288 " --> pdb=" O LEU D1600 " (cutoff:3.500A) Processing sheet with id=AJ8, first strand: chain 'D' and resid 1244 through 1247 removed outlier: 6.043A pdb=" N PHE D1288 " --> pdb=" O LEU D1600 " (cutoff:3.500A) Processing sheet with id=AJ9, first strand: chain 'D' and resid 1255 through 1260 removed outlier: 3.551A pdb=" N ILE D1562 " --> pdb=" O LEU D1272 " (cutoff:3.500A) removed outlier: 6.735A pdb=" N HIS D1274 " --> pdb=" O ASN D1560 " (cutoff:3.500A) removed outlier: 6.200A pdb=" N ASN D1560 " --> pdb=" O HIS D1274 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N SER D1436 " --> pdb=" O GLU D1565 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N LEU D1526 " --> pdb=" O ASP D1521 " (cutoff:3.500A) removed outlier: 4.572A pdb=" N PHE D1529 " --> pdb=" O THR D1538 " (cutoff:3.500A) removed outlier: 6.754A pdb=" N THR D1538 " --> pdb=" O PHE D1529 " (cutoff:3.500A) Processing sheet with id=AK1, first strand: chain 'D' and resid 1734 through 1737 removed outlier: 6.611A pdb=" N TYR D1734 " --> pdb=" O TYR D2142 " (cutoff:3.500A) removed outlier: 7.582A pdb=" N ILE D2144 " --> pdb=" O TYR D1734 " (cutoff:3.500A) removed outlier: 6.135A pdb=" N VAL D1736 " --> pdb=" O ILE D2144 " (cutoff:3.500A) No H-bonds generated for sheet with id=AK1 Processing sheet with id=AK2, first strand: chain 'D' and resid 1777 through 1778 Processing sheet with id=AK3, first strand: chain 'D' and resid 2340 through 2341 Processing sheet with id=AK4, first strand: chain 'D' and resid 4088 through 4089 Processing sheet with id=AK5, first strand: chain 'D' and resid 4178 through 4184 Processing sheet with id=AK6, first strand: chain 'D' and resid 4580 through 4583 removed outlier: 4.134A pdb=" N SER D4583 " --> pdb=" O TYR D4629 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N TYR D4629 " --> pdb=" O SER D4583 " (cutoff:3.500A) Processing sheet with id=AK7, first strand: chain 'E' and resid 5 through 8 removed outlier: 6.331A pdb=" N ARG E 71 " --> pdb=" O ILE E 7 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N LEU E 104 " --> pdb=" O VAL E 23 " (cutoff:3.500A) removed outlier: 7.764A pdb=" N VAL E 23 " --> pdb=" O LEU E 104 " (cutoff:3.500A) Processing sheet with id=AK8, first strand: chain 'F' and resid 5 through 8 removed outlier: 6.331A pdb=" N ARG F 71 " --> pdb=" O ILE F 7 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N LEU F 104 " --> pdb=" O VAL F 23 " (cutoff:3.500A) removed outlier: 7.764A pdb=" N VAL F 23 " --> pdb=" O LEU F 104 " (cutoff:3.500A) Processing sheet with id=AK9, first strand: chain 'G' and resid 5 through 8 removed outlier: 6.331A pdb=" N ARG G 71 " --> pdb=" O ILE G 7 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N LEU G 104 " --> pdb=" O VAL G 23 " (cutoff:3.500A) removed outlier: 7.764A pdb=" N VAL G 23 " --> pdb=" O LEU G 104 " (cutoff:3.500A) Processing sheet with id=AL1, first strand: chain 'H' and resid 5 through 8 removed outlier: 6.331A pdb=" N ARG H 71 " --> pdb=" O ILE H 7 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N LEU H 104 " --> pdb=" O VAL H 23 " (cutoff:3.500A) removed outlier: 7.764A pdb=" N VAL H 23 " --> pdb=" O LEU H 104 " (cutoff:3.500A) 7412 hydrogen bonds defined for protein. 21348 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 148.56 Time building geometry restraints manager: 48.73 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 44862 1.34 - 1.47: 35283 1.47 - 1.59: 64527 1.59 - 1.72: 12 1.72 - 1.84: 1512 Bond restraints: 146196 Sorted by residual: bond pdb=" C HIS B 904 " pdb=" N PRO B 905 " ideal model delta sigma weight residual 1.334 1.427 -0.093 2.34e-02 1.83e+03 1.58e+01 bond pdb=" C HIS C 904 " pdb=" N PRO C 905 " ideal model delta sigma weight residual 1.334 1.427 -0.093 2.34e-02 1.83e+03 1.58e+01 bond pdb=" C HIS D 904 " pdb=" N PRO D 905 " ideal model delta sigma weight residual 1.334 1.427 -0.093 2.34e-02 1.83e+03 1.58e+01 bond pdb=" C HIS A 904 " pdb=" N PRO A 905 " ideal model delta sigma weight residual 1.334 1.427 -0.093 2.34e-02 1.83e+03 1.58e+01 bond pdb=" CG1 ILE A2453 " pdb=" CD1 ILE A2453 " ideal model delta sigma weight residual 1.513 1.392 0.121 3.90e-02 6.57e+02 9.55e+00 ... (remaining 146191 not shown) Histogram of bond angle deviations from ideal: 94.34 - 102.39: 586 102.39 - 110.44: 35891 110.44 - 118.49: 78181 118.49 - 126.54: 80905 126.54 - 134.59: 2453 Bond angle restraints: 198016 Sorted by residual: angle pdb=" CA ARG C 844 " pdb=" CB ARG C 844 " pdb=" CG ARG C 844 " ideal model delta sigma weight residual 114.10 128.78 -14.68 2.00e+00 2.50e-01 5.39e+01 angle pdb=" CA ARG D 844 " pdb=" CB ARG D 844 " pdb=" CG ARG D 844 " ideal model delta sigma weight residual 114.10 128.78 -14.68 2.00e+00 2.50e-01 5.39e+01 angle pdb=" CA ARG A 844 " pdb=" CB ARG A 844 " pdb=" CG ARG A 844 " ideal model delta sigma weight residual 114.10 128.77 -14.67 2.00e+00 2.50e-01 5.38e+01 angle pdb=" CA ARG B 844 " pdb=" CB ARG B 844 " pdb=" CG ARG B 844 " ideal model delta sigma weight residual 114.10 128.75 -14.65 2.00e+00 2.50e-01 5.36e+01 angle pdb=" CG ARG A 76 " pdb=" CD ARG A 76 " pdb=" NE ARG A 76 " ideal model delta sigma weight residual 112.00 126.51 -14.51 2.20e+00 2.07e-01 4.35e+01 ... (remaining 198011 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.97: 79323 17.97 - 35.94: 6903 35.94 - 53.92: 1514 53.92 - 71.89: 383 71.89 - 89.86: 133 Dihedral angle restraints: 88256 sinusoidal: 36092 harmonic: 52164 Sorted by residual: dihedral pdb=" CA HIS A 904 " pdb=" C HIS A 904 " pdb=" N PRO A 905 " pdb=" CA PRO A 905 " ideal model delta harmonic sigma weight residual -180.00 -151.55 -28.45 0 5.00e+00 4.00e-02 3.24e+01 dihedral pdb=" CA HIS C 904 " pdb=" C HIS C 904 " pdb=" N PRO C 905 " pdb=" CA PRO C 905 " ideal model delta harmonic sigma weight residual 180.00 -151.57 -28.43 0 5.00e+00 4.00e-02 3.23e+01 dihedral pdb=" CA HIS D 904 " pdb=" C HIS D 904 " pdb=" N PRO D 905 " pdb=" CA PRO D 905 " ideal model delta harmonic sigma weight residual -180.00 -151.57 -28.43 0 5.00e+00 4.00e-02 3.23e+01 ... (remaining 88253 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.066: 16453 0.066 - 0.132: 4316 0.132 - 0.198: 803 0.198 - 0.264: 136 0.264 - 0.331: 52 Chirality restraints: 21760 Sorted by residual: chirality pdb=" CB VAL B1123 " pdb=" CA VAL B1123 " pdb=" CG1 VAL B1123 " pdb=" CG2 VAL B1123 " both_signs ideal model delta sigma weight residual False -2.63 -2.30 -0.33 2.00e-01 2.50e+01 2.73e+00 chirality pdb=" CB VAL C1123 " pdb=" CA VAL C1123 " pdb=" CG1 VAL C1123 " pdb=" CG2 VAL C1123 " both_signs ideal model delta sigma weight residual False -2.63 -2.30 -0.33 2.00e-01 2.50e+01 2.71e+00 chirality pdb=" CB VAL A1123 " pdb=" CA VAL A1123 " pdb=" CG1 VAL A1123 " pdb=" CG2 VAL A1123 " both_signs ideal model delta sigma weight residual False -2.63 -2.30 -0.33 2.00e-01 2.50e+01 2.71e+00 ... (remaining 21757 not shown) Planarity restraints: 25752 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA MET A4064 " 0.023 2.00e-02 2.50e+03 4.61e-02 2.12e+01 pdb=" C MET A4064 " -0.080 2.00e-02 2.50e+03 pdb=" O MET A4064 " 0.030 2.00e-02 2.50e+03 pdb=" N PHE A4065 " 0.027 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA MET C4064 " -0.023 2.00e-02 2.50e+03 4.59e-02 2.11e+01 pdb=" C MET C4064 " 0.079 2.00e-02 2.50e+03 pdb=" O MET C4064 " -0.030 2.00e-02 2.50e+03 pdb=" N PHE C4065 " -0.027 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA MET D4064 " -0.023 2.00e-02 2.50e+03 4.59e-02 2.10e+01 pdb=" C MET D4064 " 0.079 2.00e-02 2.50e+03 pdb=" O MET D4064 " -0.030 2.00e-02 2.50e+03 pdb=" N PHE D4065 " -0.027 2.00e-02 2.50e+03 ... (remaining 25749 not shown) Histogram of nonbonded interaction distances: 2.18 - 2.72: 6274 2.72 - 3.27: 149097 3.27 - 3.81: 245620 3.81 - 4.36: 296856 4.36 - 4.90: 482253 Nonbonded interactions: 1180100 Sorted by model distance: nonbonded pdb=" OG1 THR D 978 " pdb=" OE1 GLN D 981 " model vdw 2.179 2.440 nonbonded pdb=" OG1 THR B 978 " pdb=" OE1 GLN B 981 " model vdw 2.179 2.440 nonbonded pdb=" OG1 THR C 978 " pdb=" OE1 GLN C 981 " model vdw 2.179 2.440 nonbonded pdb=" OG1 THR A 978 " pdb=" OE1 GLN A 981 " model vdw 2.180 2.440 nonbonded pdb=" O MET B 403 " pdb=" OG1 THR B 407 " model vdw 2.186 2.440 ... (remaining 1180095 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 11 through 1230 or resid 1232 through 1742 or resid 1744 t \ hrough 2099 or resid 2101 through 2267 or resid 2269 through 2368 or resid 2370 \ through 2583 or resid 2585 through 2611 or resid 2613 through 2869 or resid 2871 \ through 3421 or resid 3423 through 5037 or resid 5101 through 5102)) selection = (chain 'B' and (resid 11 through 1230 or resid 1232 through 1742 or resid 1744 t \ hrough 2099 or resid 2101 through 2267 or resid 2269 through 2368 or resid 2370 \ through 2583 or resid 2585 through 2611 or resid 2613 through 2869 or resid 2871 \ through 3421 or resid 3423 through 5037 or resid 5101 through 5102)) selection = (chain 'C' and (resid 11 through 1230 or resid 1232 through 1742 or resid 1744 t \ hrough 2099 or resid 2101 through 2267 or resid 2269 through 2368 or resid 2370 \ through 2583 or resid 2585 through 2611 or resid 2613 through 2869 or resid 2871 \ through 3421 or resid 3423 through 5037 or resid 5101 through 5102)) selection = (chain 'D' and (resid 11 through 1230 or resid 1232 through 1742 or resid 1744 t \ hrough 2099 or resid 2101 through 2267 or resid 2269 through 2368 or resid 2370 \ through 2583 or resid 2585 through 2611 or resid 2613 through 2869 or resid 2871 \ through 3421 or resid 3423 through 5037 or resid 5101 through 5102)) } ncs_group { reference = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.50 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.970 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.190 Extract box with map and model: 18.940 Check model and map are aligned: 1.650 Set scattering table: 1.020 Process input model: 494.490 Find NCS groups from input model: 8.070 Set up NCS constraints: 1.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.030 Load rotamer database and sin/cos tables:2.430 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 531.880 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8402 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.121 146196 Z= 0.398 Angle : 1.142 14.677 198016 Z= 0.622 Chirality : 0.063 0.331 21760 Planarity : 0.008 0.129 25752 Dihedral : 14.828 89.860 54548 Min Nonbonded Distance : 2.179 Molprobity Statistics. All-atom Clashscore : 7.41 Ramachandran Plot: Outliers : 0.16 % Allowed : 5.07 % Favored : 94.77 % Rotamer: Outliers : 3.51 % Allowed : 2.53 % Favored : 93.96 % Cbeta Deviations : 0.02 % Peptide Plane: Cis-proline : 0.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.30 (0.06), residues: 17832 helix: 0.48 (0.06), residues: 8592 sheet: -0.60 (0.13), residues: 1608 loop : -0.79 (0.07), residues: 7632 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.063 0.003 TRP B1143 HIS 0.021 0.002 HIS B 224 PHE 0.053 0.003 PHE D4110 TYR 0.068 0.003 TYR A3968 ARG 0.028 0.001 ARG C4913 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 35664 Ramachandran restraints generated. 17832 Oldfield, 0 Emsley, 17832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 35664 Ramachandran restraints generated. 17832 Oldfield, 0 Emsley, 17832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2170 residues out of total 15548 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 530 poor density : 1640 time to evaluate : 12.469 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 155 LYS cc_start: 0.9354 (mmtt) cc_final: 0.9071 (tppt) REVERT: A 196 MET cc_start: 0.8970 (mpp) cc_final: 0.8724 (mpp) REVERT: A 211 GLU cc_start: 0.8933 (tp30) cc_final: 0.8696 (tp30) REVERT: A 384 MET cc_start: 0.7136 (tmm) cc_final: 0.6757 (tmm) REVERT: A 561 LEU cc_start: 0.9741 (tt) cc_final: 0.9374 (pp) REVERT: A 565 TYR cc_start: 0.9254 (t80) cc_final: 0.8984 (t80) REVERT: A 625 LEU cc_start: 0.9625 (tp) cc_final: 0.9412 (tp) REVERT: A 667 MET cc_start: 0.9418 (tpp) cc_final: 0.9025 (tpp) REVERT: A 859 VAL cc_start: 0.7941 (t) cc_final: 0.7640 (t) REVERT: A 941 MET cc_start: 0.5390 (tmm) cc_final: 0.5072 (mmm) REVERT: A 948 ASP cc_start: 0.8673 (m-30) cc_final: 0.8333 (t0) REVERT: A 960 MET cc_start: 0.4380 (mmm) cc_final: 0.2298 (ptp) REVERT: A 961 MET cc_start: 0.6786 (pmm) cc_final: 0.6422 (pmm) REVERT: A 1260 MET cc_start: 0.9089 (mtm) cc_final: 0.8654 (mtm) REVERT: A 1494 MET cc_start: 0.8588 (mmp) cc_final: 0.8103 (mmp) REVERT: A 1601 MET cc_start: 0.9569 (tpt) cc_final: 0.9367 (tpp) REVERT: A 1865 MET cc_start: 0.9324 (mpp) cc_final: 0.9035 (mpp) REVERT: A 1986 MET cc_start: 0.7779 (ppp) cc_final: 0.7517 (pmm) REVERT: A 2153 MET cc_start: 0.9486 (mmp) cc_final: 0.9066 (mmm) REVERT: A 2211 MET cc_start: 0.9453 (mpp) cc_final: 0.9000 (mpp) REVERT: A 2293 GLN cc_start: 0.9319 (mm-40) cc_final: 0.9004 (tm-30) REVERT: A 2294 ASP cc_start: 0.9451 (m-30) cc_final: 0.8670 (m-30) REVERT: A 2360 LYS cc_start: 0.9728 (mmpt) cc_final: 0.9417 (mtmt) REVERT: A 2698 MET cc_start: 0.8554 (ppp) cc_final: 0.8318 (ppp) REVERT: A 2932 MET cc_start: 0.7087 (tpt) cc_final: 0.6673 (ptt) REVERT: A 3081 MET cc_start: 0.6330 (ptp) cc_final: 0.5778 (pmm) REVERT: A 3335 MET cc_start: 0.7969 (pmm) cc_final: 0.7721 (pmm) REVERT: A 3411 LEU cc_start: 0.9680 (pp) cc_final: 0.9303 (mt) REVERT: A 3675 ASP cc_start: 0.9308 (m-30) cc_final: 0.9095 (m-30) REVERT: A 3723 MET cc_start: 0.9261 (mmm) cc_final: 0.9040 (mmm) REVERT: A 3758 MET cc_start: 0.9275 (tmm) cc_final: 0.8943 (tmm) REVERT: A 3780 LEU cc_start: 0.9660 (mt) cc_final: 0.9261 (mt) REVERT: A 4023 MET cc_start: 0.8909 (ttt) cc_final: 0.8516 (tmm) REVERT: A 4026 MET cc_start: 0.9551 (tmm) cc_final: 0.9231 (tmm) REVERT: A 4175 ARG cc_start: 0.9235 (ttp80) cc_final: 0.9027 (ttp80) REVERT: A 4181 ILE cc_start: 0.9304 (OUTLIER) cc_final: 0.8294 (pt) REVERT: A 4182 GLU cc_start: 0.9081 (OUTLIER) cc_final: 0.7583 (mm-30) REVERT: A 4188 ARG cc_start: 0.9217 (mmm160) cc_final: 0.8964 (mmm160) REVERT: A 4190 ILE cc_start: 0.9379 (OUTLIER) cc_final: 0.9092 (mm) REVERT: A 4571 PHE cc_start: 0.8930 (m-80) cc_final: 0.8692 (m-80) REVERT: A 4634 GLU cc_start: 0.5736 (OUTLIER) cc_final: 0.5106 (pm20) REVERT: A 4639 MET cc_start: 0.9272 (mtp) cc_final: 0.9035 (mtp) REVERT: A 4779 LYS cc_start: 0.9656 (OUTLIER) cc_final: 0.9388 (ptpp) REVERT: A 4874 MET cc_start: 0.8652 (OUTLIER) cc_final: 0.8335 (mmm) REVERT: A 4879 MET cc_start: 0.8852 (mmm) cc_final: 0.8248 (tpp) REVERT: A 4886 HIS cc_start: 0.7568 (OUTLIER) cc_final: 0.7172 (m90) REVERT: A 4918 ILE cc_start: 0.9512 (OUTLIER) cc_final: 0.8860 (pt) REVERT: A 4920 PHE cc_start: 0.8711 (t80) cc_final: 0.8433 (t80) REVERT: A 4942 GLU cc_start: 0.8701 (OUTLIER) cc_final: 0.8096 (mm-30) REVERT: A 4946 GLN cc_start: 0.8969 (mt0) cc_final: 0.8741 (mp10) REVERT: A 4949 GLN cc_start: 0.9455 (OUTLIER) cc_final: 0.9008 (tp40) REVERT: A 4968 PHE cc_start: 0.8153 (m-80) cc_final: 0.7841 (m-80) REVERT: A 4973 HIS cc_start: 0.9210 (OUTLIER) cc_final: 0.8950 (m90) REVERT: A 4982 GLU cc_start: 0.8832 (OUTLIER) cc_final: 0.8105 (pt0) REVERT: A 5013 MET cc_start: 0.9562 (mmm) cc_final: 0.9204 (mmm) REVERT: A 5016 GLU cc_start: 0.9551 (mt-10) cc_final: 0.9243 (mp0) REVERT: B 155 LYS cc_start: 0.9318 (mmtt) cc_final: 0.9047 (tppt) REVERT: B 196 MET cc_start: 0.9055 (mpp) cc_final: 0.8762 (mpp) REVERT: B 211 GLU cc_start: 0.8930 (tp30) cc_final: 0.8662 (tp30) REVERT: B 384 MET cc_start: 0.7175 (tmm) cc_final: 0.6807 (tmm) REVERT: B 561 LEU cc_start: 0.9756 (tt) cc_final: 0.9390 (pp) REVERT: B 565 TYR cc_start: 0.9269 (t80) cc_final: 0.9030 (t80) REVERT: B 625 LEU cc_start: 0.9643 (tp) cc_final: 0.9430 (mp) REVERT: B 667 MET cc_start: 0.9453 (tpp) cc_final: 0.9143 (tpp) REVERT: B 859 VAL cc_start: 0.7813 (t) cc_final: 0.7451 (t) REVERT: B 960 MET cc_start: 0.4157 (mmm) cc_final: 0.2007 (ptp) REVERT: B 961 MET cc_start: 0.6822 (pmm) cc_final: 0.6519 (mpp) REVERT: B 1025 ARG cc_start: 0.9296 (mtp-110) cc_final: 0.8999 (ptm-80) REVERT: B 1186 ASP cc_start: 0.9516 (m-30) cc_final: 0.9306 (m-30) REVERT: B 1494 MET cc_start: 0.8698 (mmp) cc_final: 0.8184 (mmp) REVERT: B 1865 MET cc_start: 0.9398 (mpp) cc_final: 0.9027 (mpp) REVERT: B 1929 MET cc_start: 0.8572 (mtm) cc_final: 0.8363 (mtt) REVERT: B 1986 MET cc_start: 0.7730 (ppp) cc_final: 0.7481 (pmm) REVERT: B 2153 MET cc_start: 0.9498 (mmp) cc_final: 0.9059 (mmm) REVERT: B 2211 MET cc_start: 0.9460 (mpp) cc_final: 0.9183 (mpp) REVERT: B 2293 GLN cc_start: 0.9343 (mm-40) cc_final: 0.9138 (tm-30) REVERT: B 2294 ASP cc_start: 0.9448 (m-30) cc_final: 0.8680 (m-30) REVERT: B 2360 LYS cc_start: 0.9724 (mmpt) cc_final: 0.9468 (mtmt) REVERT: B 2490 MET cc_start: 0.8765 (tpp) cc_final: 0.8397 (mtt) REVERT: B 2618 MET cc_start: 0.8714 (mpp) cc_final: 0.8405 (mpp) REVERT: B 2698 MET cc_start: 0.8558 (ppp) cc_final: 0.8339 (ppp) REVERT: B 2932 MET cc_start: 0.7166 (tpt) cc_final: 0.6775 (ptt) REVERT: B 3081 MET cc_start: 0.6560 (ptp) cc_final: 0.5964 (pmm) REVERT: B 3239 MET cc_start: 0.6273 (tmm) cc_final: 0.5282 (mmm) REVERT: B 3335 MET cc_start: 0.8039 (pmm) cc_final: 0.7834 (pmm) REVERT: B 3411 LEU cc_start: 0.9665 (pp) cc_final: 0.9271 (mt) REVERT: B 3675 ASP cc_start: 0.9367 (m-30) cc_final: 0.9121 (m-30) REVERT: B 3723 MET cc_start: 0.9252 (mmm) cc_final: 0.9014 (mmm) REVERT: B 3758 MET cc_start: 0.9199 (tmm) cc_final: 0.8893 (tmm) REVERT: B 3780 LEU cc_start: 0.9645 (mt) cc_final: 0.9215 (mt) REVERT: B 3798 LEU cc_start: 0.9865 (mp) cc_final: 0.9351 (tt) REVERT: B 4175 ARG cc_start: 0.9243 (ttp80) cc_final: 0.9036 (ttp80) REVERT: B 4181 ILE cc_start: 0.9300 (OUTLIER) cc_final: 0.8341 (pt) REVERT: B 4182 GLU cc_start: 0.9078 (OUTLIER) cc_final: 0.7556 (mm-30) REVERT: B 4188 ARG cc_start: 0.9217 (mmm160) cc_final: 0.8959 (mmm160) REVERT: B 4190 ILE cc_start: 0.9400 (OUTLIER) cc_final: 0.9073 (mm) REVERT: B 4571 PHE cc_start: 0.8843 (m-80) cc_final: 0.8604 (m-80) REVERT: B 4634 GLU cc_start: 0.6010 (OUTLIER) cc_final: 0.5333 (pm20) REVERT: B 4639 MET cc_start: 0.9229 (mtp) cc_final: 0.9007 (mtp) REVERT: B 4779 LYS cc_start: 0.9655 (OUTLIER) cc_final: 0.9347 (ptpp) REVERT: B 4865 LYS cc_start: 0.9133 (OUTLIER) cc_final: 0.8812 (mmtm) REVERT: B 4874 MET cc_start: 0.8487 (OUTLIER) cc_final: 0.8049 (mmm) REVERT: B 4879 MET cc_start: 0.8828 (mmm) cc_final: 0.8277 (tpp) REVERT: B 4886 HIS cc_start: 0.7535 (OUTLIER) cc_final: 0.7134 (m90) REVERT: B 4918 ILE cc_start: 0.9504 (OUTLIER) cc_final: 0.8885 (pt) REVERT: B 4920 PHE cc_start: 0.8627 (t80) cc_final: 0.8377 (t80) REVERT: B 4942 GLU cc_start: 0.8687 (OUTLIER) cc_final: 0.8023 (mm-30) REVERT: B 4946 GLN cc_start: 0.8908 (mt0) cc_final: 0.8666 (mp10) REVERT: B 4949 GLN cc_start: 0.9461 (OUTLIER) cc_final: 0.8994 (mm110) REVERT: B 4968 PHE cc_start: 0.8237 (m-80) cc_final: 0.7919 (m-80) REVERT: B 4973 HIS cc_start: 0.9236 (OUTLIER) cc_final: 0.8947 (m90) REVERT: B 4982 GLU cc_start: 0.8828 (OUTLIER) cc_final: 0.8119 (pt0) REVERT: B 5013 MET cc_start: 0.9579 (mmm) cc_final: 0.9199 (mmm) REVERT: B 5016 GLU cc_start: 0.9561 (mt-10) cc_final: 0.9257 (mp0) REVERT: C 155 LYS cc_start: 0.9317 (mmtt) cc_final: 0.8975 (tppt) REVERT: C 196 MET cc_start: 0.9059 (mpp) cc_final: 0.8763 (mpp) REVERT: C 211 GLU cc_start: 0.8931 (tp30) cc_final: 0.8663 (tp30) REVERT: C 384 MET cc_start: 0.7175 (tmm) cc_final: 0.6805 (tmm) REVERT: C 561 LEU cc_start: 0.9756 (tt) cc_final: 0.9389 (pp) REVERT: C 565 TYR cc_start: 0.9270 (t80) cc_final: 0.9030 (t80) REVERT: C 625 LEU cc_start: 0.9642 (tp) cc_final: 0.9429 (mp) REVERT: C 667 MET cc_start: 0.9452 (tpp) cc_final: 0.9145 (tpp) REVERT: C 859 VAL cc_start: 0.7814 (t) cc_final: 0.7451 (t) REVERT: C 960 MET cc_start: 0.4165 (mmm) cc_final: 0.2014 (ptp) REVERT: C 961 MET cc_start: 0.6821 (pmm) cc_final: 0.6518 (mpp) REVERT: C 1025 ARG cc_start: 0.9297 (mtp-110) cc_final: 0.8998 (ptm-80) REVERT: C 1186 ASP cc_start: 0.9516 (m-30) cc_final: 0.9306 (m-30) REVERT: C 1494 MET cc_start: 0.8699 (mmp) cc_final: 0.8186 (mmp) REVERT: C 1865 MET cc_start: 0.9398 (mpp) cc_final: 0.9026 (mpp) REVERT: C 1929 MET cc_start: 0.8572 (mtm) cc_final: 0.8366 (mtt) REVERT: C 1986 MET cc_start: 0.7729 (ppp) cc_final: 0.7479 (pmm) REVERT: C 2153 MET cc_start: 0.9500 (mmp) cc_final: 0.9060 (mmm) REVERT: C 2211 MET cc_start: 0.9461 (mpp) cc_final: 0.9227 (mpp) REVERT: C 2293 GLN cc_start: 0.9345 (mm-40) cc_final: 0.9137 (tm-30) REVERT: C 2294 ASP cc_start: 0.9448 (m-30) cc_final: 0.8681 (m-30) REVERT: C 2360 LYS cc_start: 0.9724 (mmpt) cc_final: 0.9468 (mtmt) REVERT: C 2490 MET cc_start: 0.8766 (tpp) cc_final: 0.8397 (mtt) REVERT: C 2618 MET cc_start: 0.8715 (mpp) cc_final: 0.8406 (mpp) REVERT: C 2698 MET cc_start: 0.8556 (ppp) cc_final: 0.8337 (ppp) REVERT: C 2932 MET cc_start: 0.7165 (tpt) cc_final: 0.6775 (ptt) REVERT: C 3081 MET cc_start: 0.6561 (ptp) cc_final: 0.5965 (pmm) REVERT: C 3239 MET cc_start: 0.6277 (tmm) cc_final: 0.5284 (mmm) REVERT: C 3335 MET cc_start: 0.8039 (pmm) cc_final: 0.7834 (pmm) REVERT: C 3411 LEU cc_start: 0.9665 (pp) cc_final: 0.9271 (mt) REVERT: C 3675 ASP cc_start: 0.9367 (m-30) cc_final: 0.9122 (m-30) REVERT: C 3723 MET cc_start: 0.9251 (mmm) cc_final: 0.9014 (mmm) REVERT: C 3758 MET cc_start: 0.9199 (tmm) cc_final: 0.8893 (tmm) REVERT: C 3780 LEU cc_start: 0.9645 (mt) cc_final: 0.9215 (mt) REVERT: C 3798 LEU cc_start: 0.9865 (mp) cc_final: 0.9352 (tt) REVERT: C 4175 ARG cc_start: 0.9243 (ttp80) cc_final: 0.9035 (ttp80) REVERT: C 4181 ILE cc_start: 0.9300 (OUTLIER) cc_final: 0.8337 (pt) REVERT: C 4182 GLU cc_start: 0.9077 (OUTLIER) cc_final: 0.7552 (mm-30) REVERT: C 4188 ARG cc_start: 0.9216 (mmm160) cc_final: 0.8959 (mmm160) REVERT: C 4190 ILE cc_start: 0.9399 (OUTLIER) cc_final: 0.9079 (mm) REVERT: C 4571 PHE cc_start: 0.8842 (m-80) cc_final: 0.8603 (m-80) REVERT: C 4634 GLU cc_start: 0.6009 (OUTLIER) cc_final: 0.5332 (pm20) REVERT: C 4639 MET cc_start: 0.9229 (mtp) cc_final: 0.9007 (mtp) REVERT: C 4779 LYS cc_start: 0.9655 (OUTLIER) cc_final: 0.9346 (ptpp) REVERT: C 4865 LYS cc_start: 0.9134 (OUTLIER) cc_final: 0.8813 (mmtm) REVERT: C 4874 MET cc_start: 0.8488 (OUTLIER) cc_final: 0.8053 (mmm) REVERT: C 4879 MET cc_start: 0.8845 (mmm) cc_final: 0.8248 (tpp) REVERT: C 4886 HIS cc_start: 0.7536 (OUTLIER) cc_final: 0.7136 (m90) REVERT: C 4918 ILE cc_start: 0.9504 (OUTLIER) cc_final: 0.8902 (pt) REVERT: C 4920 PHE cc_start: 0.8624 (t80) cc_final: 0.8376 (t80) REVERT: C 4942 GLU cc_start: 0.8667 (OUTLIER) cc_final: 0.8007 (mm-30) REVERT: C 4946 GLN cc_start: 0.8907 (mt0) cc_final: 0.8668 (mp10) REVERT: C 4949 GLN cc_start: 0.9461 (OUTLIER) cc_final: 0.8997 (mm110) REVERT: C 4968 PHE cc_start: 0.8236 (m-80) cc_final: 0.7963 (m-80) REVERT: C 4973 HIS cc_start: 0.9237 (OUTLIER) cc_final: 0.8946 (m90) REVERT: C 4982 GLU cc_start: 0.8827 (OUTLIER) cc_final: 0.8121 (pt0) REVERT: C 5013 MET cc_start: 0.9579 (mmm) cc_final: 0.9201 (mmm) REVERT: C 5016 GLU cc_start: 0.9561 (mt-10) cc_final: 0.9256 (mp0) REVERT: D 155 LYS cc_start: 0.9317 (mmtt) cc_final: 0.8974 (tppt) REVERT: D 196 MET cc_start: 0.9058 (mpp) cc_final: 0.8763 (mpp) REVERT: D 211 GLU cc_start: 0.8931 (tp30) cc_final: 0.8663 (tp30) REVERT: D 384 MET cc_start: 0.7172 (tmm) cc_final: 0.6807 (tmm) REVERT: D 561 LEU cc_start: 0.9756 (tt) cc_final: 0.9389 (pp) REVERT: D 565 TYR cc_start: 0.9270 (t80) cc_final: 0.9030 (t80) REVERT: D 625 LEU cc_start: 0.9643 (tp) cc_final: 0.9430 (mp) REVERT: D 667 MET cc_start: 0.9453 (tpp) cc_final: 0.9145 (tpp) REVERT: D 859 VAL cc_start: 0.7813 (t) cc_final: 0.7450 (t) REVERT: D 960 MET cc_start: 0.4162 (mmm) cc_final: 0.2013 (ptp) REVERT: D 961 MET cc_start: 0.6822 (pmm) cc_final: 0.6520 (mpp) REVERT: D 1025 ARG cc_start: 0.9297 (mtp-110) cc_final: 0.8997 (ptm-80) REVERT: D 1186 ASP cc_start: 0.9516 (m-30) cc_final: 0.9306 (m-30) REVERT: D 1494 MET cc_start: 0.8701 (mmp) cc_final: 0.8187 (mmp) REVERT: D 1865 MET cc_start: 0.9397 (mpp) cc_final: 0.9025 (mpp) REVERT: D 1986 MET cc_start: 0.7730 (ppp) cc_final: 0.7481 (pmm) REVERT: D 2153 MET cc_start: 0.9498 (mmp) cc_final: 0.9060 (mmm) REVERT: D 2211 MET cc_start: 0.9460 (mpp) cc_final: 0.9183 (mpp) REVERT: D 2293 GLN cc_start: 0.9343 (mm-40) cc_final: 0.9138 (tm-30) REVERT: D 2294 ASP cc_start: 0.9448 (m-30) cc_final: 0.8681 (m-30) REVERT: D 2360 LYS cc_start: 0.9724 (mmpt) cc_final: 0.9468 (mtmt) REVERT: D 2618 MET cc_start: 0.8716 (mpp) cc_final: 0.8405 (mpp) REVERT: D 2698 MET cc_start: 0.8555 (ppp) cc_final: 0.8338 (ppp) REVERT: D 2932 MET cc_start: 0.7166 (tpt) cc_final: 0.6775 (ptt) REVERT: D 3081 MET cc_start: 0.6561 (ptp) cc_final: 0.5966 (pmm) REVERT: D 3239 MET cc_start: 0.6277 (tmm) cc_final: 0.5283 (mmm) REVERT: D 3335 MET cc_start: 0.8037 (pmm) cc_final: 0.7832 (pmm) REVERT: D 3411 LEU cc_start: 0.9666 (pp) cc_final: 0.9272 (mt) REVERT: D 3675 ASP cc_start: 0.9368 (m-30) cc_final: 0.9121 (m-30) REVERT: D 3723 MET cc_start: 0.9252 (mmm) cc_final: 0.9016 (mmm) REVERT: D 3758 MET cc_start: 0.9199 (tmm) cc_final: 0.8893 (tmm) REVERT: D 3780 LEU cc_start: 0.9645 (mt) cc_final: 0.9216 (mt) REVERT: D 3798 LEU cc_start: 0.9865 (mp) cc_final: 0.9352 (tt) REVERT: D 4175 ARG cc_start: 0.9243 (ttp80) cc_final: 0.9034 (ttp80) REVERT: D 4181 ILE cc_start: 0.9301 (OUTLIER) cc_final: 0.8339 (pt) REVERT: D 4182 GLU cc_start: 0.9076 (OUTLIER) cc_final: 0.7553 (mm-30) REVERT: D 4188 ARG cc_start: 0.9218 (mmm160) cc_final: 0.8959 (mmm160) REVERT: D 4190 ILE cc_start: 0.9400 (OUTLIER) cc_final: 0.9074 (mm) REVERT: D 4571 PHE cc_start: 0.8840 (m-80) cc_final: 0.8599 (m-80) REVERT: D 4634 GLU cc_start: 0.6013 (OUTLIER) cc_final: 0.5338 (pm20) REVERT: D 4639 MET cc_start: 0.9228 (mtp) cc_final: 0.9009 (mtp) REVERT: D 4779 LYS cc_start: 0.9655 (OUTLIER) cc_final: 0.9347 (ptpp) REVERT: D 4865 LYS cc_start: 0.9134 (OUTLIER) cc_final: 0.8812 (mmtm) REVERT: D 4874 MET cc_start: 0.8487 (OUTLIER) cc_final: 0.8049 (mmm) REVERT: D 4879 MET cc_start: 0.8845 (mmm) cc_final: 0.8246 (tpp) REVERT: D 4886 HIS cc_start: 0.7539 (OUTLIER) cc_final: 0.7136 (m90) REVERT: D 4918 ILE cc_start: 0.9504 (OUTLIER) cc_final: 0.8901 (pt) REVERT: D 4920 PHE cc_start: 0.8624 (t80) cc_final: 0.8378 (t80) REVERT: D 4942 GLU cc_start: 0.8666 (OUTLIER) cc_final: 0.8003 (mm-30) REVERT: D 4946 GLN cc_start: 0.8908 (mt0) cc_final: 0.8667 (mp10) REVERT: D 4949 GLN cc_start: 0.9461 (OUTLIER) cc_final: 0.8997 (mm110) REVERT: D 4968 PHE cc_start: 0.8236 (m-80) cc_final: 0.7924 (m-80) REVERT: D 4973 HIS cc_start: 0.9233 (OUTLIER) cc_final: 0.8947 (m90) REVERT: D 4982 GLU cc_start: 0.8825 (OUTLIER) cc_final: 0.8108 (pt0) REVERT: D 5013 MET cc_start: 0.9579 (mmm) cc_final: 0.9200 (mmm) REVERT: D 5016 GLU cc_start: 0.9561 (mt-10) cc_final: 0.9255 (mp0) REVERT: E 73 LYS cc_start: 0.9370 (tmtt) cc_final: 0.9031 (tppt) REVERT: F 73 LYS cc_start: 0.9370 (tmtt) cc_final: 0.9032 (tppt) REVERT: G 73 LYS cc_start: 0.9370 (tmtt) cc_final: 0.9031 (tppt) REVERT: H 73 LYS cc_start: 0.9370 (tmtt) cc_final: 0.9031 (tppt) outliers start: 530 outliers final: 96 residues processed: 2000 average time/residue: 1.1892 time to fit residues: 4210.8314 Evaluate side-chains 1325 residues out of total 15548 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 147 poor density : 1178 time to evaluate : 12.401 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4181 ILE Chi-restraints excluded: chain A residue 4182 GLU Chi-restraints excluded: chain A residue 4190 ILE Chi-restraints excluded: chain A residue 4200 THR Chi-restraints excluded: chain A residue 4207 MET Chi-restraints excluded: chain A residue 4222 VAL Chi-restraints excluded: chain A residue 4544 LEU Chi-restraints excluded: chain A residue 4561 THR Chi-restraints excluded: chain A residue 4581 LYS Chi-restraints excluded: chain A residue 4583 SER Chi-restraints excluded: chain A residue 4585 SER Chi-restraints excluded: chain A residue 4634 GLU Chi-restraints excluded: chain A residue 4697 VAL Chi-restraints excluded: chain A residue 4700 GLN Chi-restraints excluded: chain A residue 4720 VAL Chi-restraints excluded: chain A residue 4731 ILE Chi-restraints excluded: chain A residue 4734 ARG Chi-restraints excluded: chain A residue 4779 LYS Chi-restraints excluded: chain A residue 4785 THR Chi-restraints excluded: chain A residue 4788 SER Chi-restraints excluded: chain A residue 4843 LEU Chi-restraints excluded: chain A residue 4852 THR Chi-restraints excluded: chain A residue 4870 ASP Chi-restraints excluded: chain A residue 4874 MET Chi-restraints excluded: chain A residue 4886 HIS Chi-restraints excluded: chain A residue 4914 VAL Chi-restraints excluded: chain A residue 4918 ILE Chi-restraints excluded: chain A residue 4924 VAL Chi-restraints excluded: chain A residue 4926 VAL Chi-restraints excluded: chain A residue 4942 GLU Chi-restraints excluded: chain A residue 4949 GLN Chi-restraints excluded: chain A residue 4950 VAL Chi-restraints excluded: chain A residue 4971 THR Chi-restraints excluded: chain A residue 4973 HIS Chi-restraints excluded: chain A residue 4982 GLU Chi-restraints excluded: chain B residue 4181 ILE Chi-restraints excluded: chain B residue 4182 GLU Chi-restraints excluded: chain B residue 4190 ILE Chi-restraints excluded: chain B residue 4200 THR Chi-restraints excluded: chain B residue 4207 MET Chi-restraints excluded: chain B residue 4222 VAL Chi-restraints excluded: chain B residue 4544 LEU Chi-restraints excluded: chain B residue 4550 LYS Chi-restraints excluded: chain B residue 4561 THR Chi-restraints excluded: chain B residue 4581 LYS Chi-restraints excluded: chain B residue 4583 SER Chi-restraints excluded: chain B residue 4585 SER Chi-restraints excluded: chain B residue 4634 GLU Chi-restraints excluded: chain B residue 4697 VAL Chi-restraints excluded: chain B residue 4700 GLN Chi-restraints excluded: chain B residue 4720 VAL Chi-restraints excluded: chain B residue 4731 ILE Chi-restraints excluded: chain B residue 4734 ARG Chi-restraints excluded: chain B residue 4779 LYS Chi-restraints excluded: chain B residue 4785 THR Chi-restraints excluded: chain B residue 4788 SER Chi-restraints excluded: chain B residue 4843 LEU Chi-restraints excluded: chain B residue 4852 THR Chi-restraints excluded: chain B residue 4865 LYS Chi-restraints excluded: chain B residue 4870 ASP Chi-restraints excluded: chain B residue 4874 MET Chi-restraints excluded: chain B residue 4886 HIS Chi-restraints excluded: chain B residue 4914 VAL Chi-restraints excluded: chain B residue 4918 ILE Chi-restraints excluded: chain B residue 4924 VAL Chi-restraints excluded: chain B residue 4926 VAL Chi-restraints excluded: chain B residue 4942 GLU Chi-restraints excluded: chain B residue 4949 GLN Chi-restraints excluded: chain B residue 4950 VAL Chi-restraints excluded: chain B residue 4971 THR Chi-restraints excluded: chain B residue 4973 HIS Chi-restraints excluded: chain B residue 4982 GLU Chi-restraints excluded: chain C residue 4181 ILE Chi-restraints excluded: chain C residue 4182 GLU Chi-restraints excluded: chain C residue 4190 ILE Chi-restraints excluded: chain C residue 4200 THR Chi-restraints excluded: chain C residue 4207 MET Chi-restraints excluded: chain C residue 4222 VAL Chi-restraints excluded: chain C residue 4544 LEU Chi-restraints excluded: chain C residue 4550 LYS Chi-restraints excluded: chain C residue 4561 THR Chi-restraints excluded: chain C residue 4581 LYS Chi-restraints excluded: chain C residue 4583 SER Chi-restraints excluded: chain C residue 4585 SER Chi-restraints excluded: chain C residue 4634 GLU Chi-restraints excluded: chain C residue 4697 VAL Chi-restraints excluded: chain C residue 4700 GLN Chi-restraints excluded: chain C residue 4720 VAL Chi-restraints excluded: chain C residue 4731 ILE Chi-restraints excluded: chain C residue 4734 ARG Chi-restraints excluded: chain C residue 4779 LYS Chi-restraints excluded: chain C residue 4785 THR Chi-restraints excluded: chain C residue 4788 SER Chi-restraints excluded: chain C residue 4843 LEU Chi-restraints excluded: chain C residue 4852 THR Chi-restraints excluded: chain C residue 4865 LYS Chi-restraints excluded: chain C residue 4870 ASP Chi-restraints excluded: chain C residue 4874 MET Chi-restraints excluded: chain C residue 4886 HIS Chi-restraints excluded: chain C residue 4914 VAL Chi-restraints excluded: chain C residue 4918 ILE Chi-restraints excluded: chain C residue 4924 VAL Chi-restraints excluded: chain C residue 4926 VAL Chi-restraints excluded: chain C residue 4942 GLU Chi-restraints excluded: chain C residue 4949 GLN Chi-restraints excluded: chain C residue 4950 VAL Chi-restraints excluded: chain C residue 4971 THR Chi-restraints excluded: chain C residue 4973 HIS Chi-restraints excluded: chain C residue 4982 GLU Chi-restraints excluded: chain D residue 4181 ILE Chi-restraints excluded: chain D residue 4182 GLU Chi-restraints excluded: chain D residue 4190 ILE Chi-restraints excluded: chain D residue 4200 THR Chi-restraints excluded: chain D residue 4207 MET Chi-restraints excluded: chain D residue 4222 VAL Chi-restraints excluded: chain D residue 4544 LEU Chi-restraints excluded: chain D residue 4550 LYS Chi-restraints excluded: chain D residue 4561 THR Chi-restraints excluded: chain D residue 4581 LYS Chi-restraints excluded: chain D residue 4583 SER Chi-restraints excluded: chain D residue 4585 SER Chi-restraints excluded: chain D residue 4634 GLU Chi-restraints excluded: chain D residue 4697 VAL Chi-restraints excluded: chain D residue 4700 GLN Chi-restraints excluded: chain D residue 4720 VAL Chi-restraints excluded: chain D residue 4731 ILE Chi-restraints excluded: chain D residue 4734 ARG Chi-restraints excluded: chain D residue 4779 LYS Chi-restraints excluded: chain D residue 4785 THR Chi-restraints excluded: chain D residue 4788 SER Chi-restraints excluded: chain D residue 4822 THR Chi-restraints excluded: chain D residue 4843 LEU Chi-restraints excluded: chain D residue 4852 THR Chi-restraints excluded: chain D residue 4865 LYS Chi-restraints excluded: chain D residue 4870 ASP Chi-restraints excluded: chain D residue 4874 MET Chi-restraints excluded: chain D residue 4886 HIS Chi-restraints excluded: chain D residue 4914 VAL Chi-restraints excluded: chain D residue 4918 ILE Chi-restraints excluded: chain D residue 4924 VAL Chi-restraints excluded: chain D residue 4926 VAL Chi-restraints excluded: chain D residue 4942 GLU Chi-restraints excluded: chain D residue 4949 GLN Chi-restraints excluded: chain D residue 4950 VAL Chi-restraints excluded: chain D residue 4971 THR Chi-restraints excluded: chain D residue 4973 HIS Chi-restraints excluded: chain D residue 4982 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1788 random chunks: chunk 1509 optimal weight: 10.0000 chunk 1355 optimal weight: 1.9990 chunk 751 optimal weight: 20.0000 chunk 462 optimal weight: 0.9990 chunk 914 optimal weight: 30.0000 chunk 724 optimal weight: 20.0000 chunk 1401 optimal weight: 8.9990 chunk 542 optimal weight: 9.9990 chunk 852 optimal weight: 9.9990 chunk 1043 optimal weight: 2.9990 chunk 1623 optimal weight: 20.0000 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 203 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 226 HIS A 278 GLN ** A 475 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 533 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 576 ASN A 624 ASN ** A 838 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 877 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1252 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1299 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1300 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1545 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1610 ASN ** A2213 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2931 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2933 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A3214 ASN ** A3318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A3457 ASN A3608 GLN A3667 HIS A4223 ASN A4547 GLN A4728 HIS A4806 ASN A4832 HIS A4836 GLN ** A4864 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A4886 HIS A5003 HIS ** B 203 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 226 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 278 GLN ** B 475 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 533 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 576 ASN ** B 838 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 877 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1252 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1299 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1300 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1545 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1563 GLN B1610 ASN ** B2931 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2933 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B3214 ASN ** B3318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B3457 ASN B3608 GLN B3667 HIS B4223 ASN B4728 HIS B4806 ASN B4836 GLN ** B4864 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B4886 HIS B5003 HIS ** C 203 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 226 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 278 GLN ** C 475 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 533 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 576 ASN ** C 838 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 877 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1252 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1299 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1300 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1545 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1610 ASN ** C2213 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2931 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2933 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C3214 ASN ** C3318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C3457 ASN C3608 GLN C3667 HIS C4223 ASN C4728 HIS C4806 ASN C4836 GLN ** C4864 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C4886 HIS C5003 HIS ** D 203 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 226 HIS D 278 GLN ** D 475 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 533 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 576 ASN ** D 838 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 877 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1252 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1299 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1300 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D1563 GLN D1610 ASN ** D2931 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2933 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D3214 ASN ** D3318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D3457 ASN D3608 GLN D3667 HIS ** D4133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D4201 ASN D4223 ASN D4728 HIS D4806 ASN D4836 GLN ** D4864 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D4886 HIS D5003 HIS ** E 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 60 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8460 moved from start: 0.1674 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.072 146196 Z= 0.283 Angle : 0.735 14.588 198016 Z= 0.376 Chirality : 0.044 0.271 21760 Planarity : 0.005 0.079 25752 Dihedral : 6.177 76.436 19865 Min Nonbonded Distance : 2.063 Molprobity Statistics. All-atom Clashscore : 18.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.42 % Favored : 95.58 % Rotamer: Outliers : 1.62 % Allowed : 9.33 % Favored : 89.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.45 % Cis-general : 0.00 % Twisted Proline : 0.45 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.18 (0.06), residues: 17832 helix: 0.70 (0.05), residues: 8804 sheet: -0.66 (0.13), residues: 1728 loop : -0.90 (0.07), residues: 7300 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP C1143 HIS 0.015 0.001 HIS D1298 PHE 0.046 0.002 PHE A4922 TYR 0.029 0.002 TYR A 411 ARG 0.009 0.001 ARG A 844 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 35664 Ramachandran restraints generated. 17832 Oldfield, 0 Emsley, 17832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 35664 Ramachandran restraints generated. 17832 Oldfield, 0 Emsley, 17832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1449 residues out of total 15548 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 236 poor density : 1213 time to evaluate : 11.373 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 155 LYS cc_start: 0.9500 (mmtt) cc_final: 0.9112 (tppt) REVERT: A 196 MET cc_start: 0.8889 (mpp) cc_final: 0.8611 (mpp) REVERT: A 228 ASP cc_start: 0.9610 (m-30) cc_final: 0.9171 (p0) REVERT: A 384 MET cc_start: 0.7105 (tmm) cc_final: 0.6749 (tmm) REVERT: A 407 THR cc_start: 0.9258 (OUTLIER) cc_final: 0.8863 (t) REVERT: A 565 TYR cc_start: 0.9307 (t80) cc_final: 0.9065 (t80) REVERT: A 601 ASP cc_start: 0.9172 (m-30) cc_final: 0.8881 (m-30) REVERT: A 667 MET cc_start: 0.9363 (tpp) cc_final: 0.9007 (tpp) REVERT: A 960 MET cc_start: 0.4807 (mmm) cc_final: 0.3275 (mtm) REVERT: A 961 MET cc_start: 0.7062 (pmm) cc_final: 0.6684 (pmm) REVERT: A 1260 MET cc_start: 0.9103 (mtm) cc_final: 0.8565 (mtm) REVERT: A 1601 MET cc_start: 0.9664 (tpt) cc_final: 0.9415 (tpp) REVERT: A 1670 TYR cc_start: 0.9204 (m-10) cc_final: 0.8968 (m-80) REVERT: A 2170 MET cc_start: 0.8596 (tpp) cc_final: 0.8263 (tpp) REVERT: A 2267 MET cc_start: 0.8309 (tpt) cc_final: 0.8109 (tpt) REVERT: A 2293 GLN cc_start: 0.9424 (mm-40) cc_final: 0.9066 (tm-30) REVERT: A 2294 ASP cc_start: 0.9458 (m-30) cc_final: 0.8655 (m-30) REVERT: A 2440 MET cc_start: 0.9156 (mmp) cc_final: 0.8891 (mmp) REVERT: A 2618 MET cc_start: 0.8789 (mpp) cc_final: 0.8440 (mpp) REVERT: A 2698 MET cc_start: 0.8549 (ppp) cc_final: 0.8291 (ppp) REVERT: A 2932 MET cc_start: 0.7219 (tpt) cc_final: 0.6827 (ptt) REVERT: A 3106 MET cc_start: 0.9255 (mmp) cc_final: 0.9055 (mmp) REVERT: A 3276 MET cc_start: 0.8124 (mmp) cc_final: 0.7511 (mmm) REVERT: A 3411 LEU cc_start: 0.9753 (pp) cc_final: 0.9296 (mm) REVERT: A 3515 LYS cc_start: 0.9489 (mmmm) cc_final: 0.9268 (ptpt) REVERT: A 3675 ASP cc_start: 0.9486 (m-30) cc_final: 0.9239 (m-30) REVERT: A 3758 MET cc_start: 0.9122 (tmm) cc_final: 0.8807 (tmm) REVERT: A 3778 MET cc_start: 0.9548 (tmm) cc_final: 0.9330 (tmm) REVERT: A 3816 MET cc_start: 0.9634 (mmt) cc_final: 0.9152 (mmp) REVERT: A 3999 MET cc_start: 0.9558 (mmm) cc_final: 0.9329 (mmm) REVERT: A 4023 MET cc_start: 0.8992 (ttt) cc_final: 0.8725 (tmm) REVERT: A 4026 MET cc_start: 0.9603 (tmm) cc_final: 0.9322 (tmm) REVERT: A 4182 GLU cc_start: 0.9089 (OUTLIER) cc_final: 0.7713 (mm-30) REVERT: A 4571 PHE cc_start: 0.9011 (m-80) cc_final: 0.8760 (m-80) REVERT: A 4639 MET cc_start: 0.9295 (mtp) cc_final: 0.9093 (mtp) REVERT: A 4779 LYS cc_start: 0.9657 (OUTLIER) cc_final: 0.9352 (ptpp) REVERT: A 4874 MET cc_start: 0.8375 (mmm) cc_final: 0.8074 (mmm) REVERT: A 4879 MET cc_start: 0.8878 (mmm) cc_final: 0.8499 (tpp) REVERT: A 4942 GLU cc_start: 0.9164 (OUTLIER) cc_final: 0.8111 (mm-30) REVERT: A 4949 GLN cc_start: 0.9396 (OUTLIER) cc_final: 0.9193 (mm-40) REVERT: A 4967 TYR cc_start: 0.7552 (t80) cc_final: 0.7336 (t80) REVERT: A 4969 ASP cc_start: 0.9529 (m-30) cc_final: 0.9299 (m-30) REVERT: A 5013 MET cc_start: 0.9644 (mmm) cc_final: 0.9171 (mmm) REVERT: B 155 LYS cc_start: 0.9493 (mmtt) cc_final: 0.9114 (tppt) REVERT: B 196 MET cc_start: 0.8980 (mpp) cc_final: 0.8644 (mpp) REVERT: B 340 LYS cc_start: 0.8987 (mmmt) cc_final: 0.8724 (mmmt) REVERT: B 343 GLU cc_start: 0.8791 (mt-10) cc_final: 0.8211 (mp0) REVERT: B 384 MET cc_start: 0.7130 (tmm) cc_final: 0.6770 (tmm) REVERT: B 667 MET cc_start: 0.9395 (tpp) cc_final: 0.9014 (tpp) REVERT: B 941 MET cc_start: 0.5244 (OUTLIER) cc_final: 0.4814 (mmm) REVERT: B 960 MET cc_start: 0.4276 (mmm) cc_final: 0.2574 (mtm) REVERT: B 961 MET cc_start: 0.7001 (pmm) cc_final: 0.6708 (pmm) REVERT: B 1186 ASP cc_start: 0.9429 (m-30) cc_final: 0.9223 (m-30) REVERT: B 1601 MET cc_start: 0.9574 (tpp) cc_final: 0.9266 (tpp) REVERT: B 1670 TYR cc_start: 0.9194 (m-10) cc_final: 0.8915 (m-80) REVERT: B 1986 MET cc_start: 0.7805 (ppp) cc_final: 0.7494 (pmm) REVERT: B 2170 MET cc_start: 0.8619 (tpp) cc_final: 0.8259 (tpp) REVERT: B 2267 MET cc_start: 0.8358 (tpt) cc_final: 0.8108 (tpt) REVERT: B 2293 GLN cc_start: 0.9463 (mm-40) cc_final: 0.9080 (tm-30) REVERT: B 2294 ASP cc_start: 0.9460 (m-30) cc_final: 0.8677 (m-30) REVERT: B 2440 MET cc_start: 0.9152 (mmp) cc_final: 0.8894 (mmp) REVERT: B 2618 MET cc_start: 0.8844 (mpp) cc_final: 0.8512 (mpp) REVERT: B 2698 MET cc_start: 0.8539 (ppp) cc_final: 0.8282 (ppp) REVERT: B 2932 MET cc_start: 0.7179 (tpt) cc_final: 0.6795 (ptt) REVERT: B 3106 MET cc_start: 0.9099 (mmm) cc_final: 0.8886 (mmp) REVERT: B 3276 MET cc_start: 0.8151 (mmp) cc_final: 0.7538 (mmm) REVERT: B 3411 LEU cc_start: 0.9751 (pp) cc_final: 0.9336 (mm) REVERT: B 3515 LYS cc_start: 0.9487 (mmmm) cc_final: 0.9279 (ptpt) REVERT: B 3675 ASP cc_start: 0.9484 (m-30) cc_final: 0.9259 (m-30) REVERT: B 3758 MET cc_start: 0.9111 (tmm) cc_final: 0.8792 (tmm) REVERT: B 3778 MET cc_start: 0.9525 (tmm) cc_final: 0.9311 (tmm) REVERT: B 3816 MET cc_start: 0.9645 (mmt) cc_final: 0.9153 (mmp) REVERT: B 3999 MET cc_start: 0.9561 (mmm) cc_final: 0.9328 (mmm) REVERT: B 4182 GLU cc_start: 0.9086 (OUTLIER) cc_final: 0.7893 (mp0) REVERT: B 4571 PHE cc_start: 0.8960 (m-80) cc_final: 0.8674 (m-80) REVERT: B 4639 MET cc_start: 0.9263 (mtp) cc_final: 0.9020 (mtp) REVERT: B 4779 LYS cc_start: 0.9661 (OUTLIER) cc_final: 0.9348 (ptpp) REVERT: B 4874 MET cc_start: 0.8141 (mmm) cc_final: 0.7740 (mmm) REVERT: B 4879 MET cc_start: 0.8886 (mmm) cc_final: 0.8571 (tpp) REVERT: B 4880 MET cc_start: 0.8810 (ptp) cc_final: 0.8576 (ptp) REVERT: B 4942 GLU cc_start: 0.9074 (OUTLIER) cc_final: 0.8057 (mm-30) REVERT: B 4954 MET cc_start: 0.9445 (tpp) cc_final: 0.9155 (tpp) REVERT: B 4967 TYR cc_start: 0.7588 (t80) cc_final: 0.7289 (t80) REVERT: B 4969 ASP cc_start: 0.9519 (m-30) cc_final: 0.9297 (m-30) REVERT: B 4989 MET cc_start: 0.9276 (ppp) cc_final: 0.8933 (tpt) REVERT: B 5013 MET cc_start: 0.9648 (mmm) cc_final: 0.9247 (mmm) REVERT: C 155 LYS cc_start: 0.9529 (mmtt) cc_final: 0.9095 (tppt) REVERT: C 196 MET cc_start: 0.8984 (mpp) cc_final: 0.8647 (mpp) REVERT: C 340 LYS cc_start: 0.8981 (mmmt) cc_final: 0.8719 (mmmt) REVERT: C 343 GLU cc_start: 0.8789 (mt-10) cc_final: 0.8208 (mp0) REVERT: C 384 MET cc_start: 0.7130 (tmm) cc_final: 0.6769 (tmm) REVERT: C 565 TYR cc_start: 0.9296 (t80) cc_final: 0.9082 (t80) REVERT: C 667 MET cc_start: 0.9397 (tpp) cc_final: 0.9018 (tpp) REVERT: C 941 MET cc_start: 0.5246 (OUTLIER) cc_final: 0.4816 (mmm) REVERT: C 960 MET cc_start: 0.4277 (mmm) cc_final: 0.2576 (mtm) REVERT: C 961 MET cc_start: 0.6999 (pmm) cc_final: 0.6706 (pmm) REVERT: C 1186 ASP cc_start: 0.9429 (m-30) cc_final: 0.9224 (m-30) REVERT: C 1601 MET cc_start: 0.9575 (tpp) cc_final: 0.9268 (tpp) REVERT: C 1670 TYR cc_start: 0.9195 (m-10) cc_final: 0.8916 (m-80) REVERT: C 1986 MET cc_start: 0.7804 (ppp) cc_final: 0.7492 (pmm) REVERT: C 2170 MET cc_start: 0.8623 (tpp) cc_final: 0.8265 (tpp) REVERT: C 2267 MET cc_start: 0.8362 (tpt) cc_final: 0.8110 (tpt) REVERT: C 2293 GLN cc_start: 0.9463 (mm-40) cc_final: 0.9080 (tm-30) REVERT: C 2294 ASP cc_start: 0.9459 (m-30) cc_final: 0.8678 (m-30) REVERT: C 2440 MET cc_start: 0.9142 (mmp) cc_final: 0.8877 (mmp) REVERT: C 2502 MET cc_start: 0.9166 (mtp) cc_final: 0.8598 (ttp) REVERT: C 2618 MET cc_start: 0.8845 (mpp) cc_final: 0.8512 (mpp) REVERT: C 2698 MET cc_start: 0.8540 (ppp) cc_final: 0.8285 (ppp) REVERT: C 2932 MET cc_start: 0.7179 (tpt) cc_final: 0.6795 (ptt) REVERT: C 3106 MET cc_start: 0.9099 (mmm) cc_final: 0.8886 (mmp) REVERT: C 3276 MET cc_start: 0.8151 (mmp) cc_final: 0.7539 (mmm) REVERT: C 3411 LEU cc_start: 0.9751 (pp) cc_final: 0.9336 (mm) REVERT: C 3515 LYS cc_start: 0.9486 (mmmm) cc_final: 0.9278 (ptpt) REVERT: C 3675 ASP cc_start: 0.9484 (m-30) cc_final: 0.9259 (m-30) REVERT: C 3758 MET cc_start: 0.9111 (tmm) cc_final: 0.8791 (tmm) REVERT: C 3778 MET cc_start: 0.9522 (tmm) cc_final: 0.9308 (tmm) REVERT: C 3798 LEU cc_start: 0.9818 (mp) cc_final: 0.9371 (tt) REVERT: C 3816 MET cc_start: 0.9645 (mmt) cc_final: 0.9159 (mmp) REVERT: C 3999 MET cc_start: 0.9561 (mmm) cc_final: 0.9324 (mmm) REVERT: C 4182 GLU cc_start: 0.9076 (OUTLIER) cc_final: 0.7882 (mp0) REVERT: C 4571 PHE cc_start: 0.8956 (m-80) cc_final: 0.8674 (m-80) REVERT: C 4639 MET cc_start: 0.9263 (mtp) cc_final: 0.9020 (mtp) REVERT: C 4779 LYS cc_start: 0.9661 (OUTLIER) cc_final: 0.9348 (ptpp) REVERT: C 4874 MET cc_start: 0.8144 (mmm) cc_final: 0.7743 (mmm) REVERT: C 4879 MET cc_start: 0.8905 (mmm) cc_final: 0.8566 (tpp) REVERT: C 4880 MET cc_start: 0.8819 (ptp) cc_final: 0.8584 (ptp) REVERT: C 4942 GLU cc_start: 0.9076 (OUTLIER) cc_final: 0.8062 (mm-30) REVERT: C 4954 MET cc_start: 0.9447 (tpp) cc_final: 0.9168 (tpp) REVERT: C 4967 TYR cc_start: 0.7749 (t80) cc_final: 0.7446 (t80) REVERT: C 4969 ASP cc_start: 0.9496 (m-30) cc_final: 0.9283 (m-30) REVERT: C 4989 MET cc_start: 0.9274 (ppp) cc_final: 0.8934 (tpt) REVERT: C 5013 MET cc_start: 0.9649 (mmm) cc_final: 0.9253 (mmm) REVERT: D 155 LYS cc_start: 0.9528 (mmtt) cc_final: 0.9096 (tppt) REVERT: D 196 MET cc_start: 0.8985 (mpp) cc_final: 0.8647 (mpp) REVERT: D 228 ASP cc_start: 0.9596 (m-30) cc_final: 0.9129 (p0) REVERT: D 340 LYS cc_start: 0.8986 (mmmt) cc_final: 0.8725 (mmmt) REVERT: D 343 GLU cc_start: 0.8791 (mt-10) cc_final: 0.8210 (mp0) REVERT: D 384 MET cc_start: 0.7130 (tmm) cc_final: 0.6770 (tmm) REVERT: D 565 TYR cc_start: 0.9296 (t80) cc_final: 0.9082 (t80) REVERT: D 667 MET cc_start: 0.9397 (tpp) cc_final: 0.9018 (tpp) REVERT: D 941 MET cc_start: 0.5245 (OUTLIER) cc_final: 0.4817 (mmm) REVERT: D 960 MET cc_start: 0.4272 (mmm) cc_final: 0.2571 (mtm) REVERT: D 961 MET cc_start: 0.6997 (pmm) cc_final: 0.6705 (pmm) REVERT: D 1186 ASP cc_start: 0.9428 (m-30) cc_final: 0.9223 (m-30) REVERT: D 1601 MET cc_start: 0.9574 (tpp) cc_final: 0.9267 (tpp) REVERT: D 1670 TYR cc_start: 0.9195 (m-10) cc_final: 0.8915 (m-80) REVERT: D 1986 MET cc_start: 0.7805 (ppp) cc_final: 0.7493 (pmm) REVERT: D 2170 MET cc_start: 0.8619 (tpp) cc_final: 0.8260 (tpp) REVERT: D 2267 MET cc_start: 0.8358 (tpt) cc_final: 0.8107 (tpt) REVERT: D 2293 GLN cc_start: 0.9463 (mm-40) cc_final: 0.9079 (tm-30) REVERT: D 2294 ASP cc_start: 0.9459 (m-30) cc_final: 0.8677 (m-30) REVERT: D 2440 MET cc_start: 0.9143 (mmp) cc_final: 0.8877 (mmp) REVERT: D 2618 MET cc_start: 0.8844 (mpp) cc_final: 0.8512 (mpp) REVERT: D 2698 MET cc_start: 0.8540 (ppp) cc_final: 0.8283 (ppp) REVERT: D 2932 MET cc_start: 0.7179 (tpt) cc_final: 0.6795 (ptt) REVERT: D 3106 MET cc_start: 0.9099 (mmm) cc_final: 0.8885 (mmp) REVERT: D 3276 MET cc_start: 0.8150 (mmp) cc_final: 0.7539 (mmm) REVERT: D 3411 LEU cc_start: 0.9752 (pp) cc_final: 0.9336 (mm) REVERT: D 3515 LYS cc_start: 0.9486 (mmmm) cc_final: 0.9279 (ptpt) REVERT: D 3675 ASP cc_start: 0.9484 (m-30) cc_final: 0.9259 (m-30) REVERT: D 3758 MET cc_start: 0.9112 (tmm) cc_final: 0.8792 (tmm) REVERT: D 3778 MET cc_start: 0.9523 (tmm) cc_final: 0.9309 (tmm) REVERT: D 3798 LEU cc_start: 0.9818 (mp) cc_final: 0.9371 (tt) REVERT: D 3816 MET cc_start: 0.9646 (mmt) cc_final: 0.9159 (mmp) REVERT: D 3999 MET cc_start: 0.9561 (mmm) cc_final: 0.9324 (mmm) REVERT: D 4182 GLU cc_start: 0.9084 (OUTLIER) cc_final: 0.7885 (mp0) REVERT: D 4571 PHE cc_start: 0.8943 (m-80) cc_final: 0.8659 (m-80) REVERT: D 4639 MET cc_start: 0.9250 (mtp) cc_final: 0.8943 (mtp) REVERT: D 4779 LYS cc_start: 0.9661 (OUTLIER) cc_final: 0.9348 (ptpp) REVERT: D 4874 MET cc_start: 0.8144 (mmm) cc_final: 0.7744 (mmm) REVERT: D 4879 MET cc_start: 0.8906 (mmm) cc_final: 0.8569 (tpp) REVERT: D 4880 MET cc_start: 0.8825 (ptp) cc_final: 0.8584 (ptp) REVERT: D 4942 GLU cc_start: 0.9074 (OUTLIER) cc_final: 0.8061 (mm-30) REVERT: D 4954 MET cc_start: 0.9445 (tpp) cc_final: 0.9168 (tpp) REVERT: D 4967 TYR cc_start: 0.7326 (t80) cc_final: 0.6921 (t80) REVERT: D 4969 ASP cc_start: 0.9478 (m-30) cc_final: 0.9267 (m-30) REVERT: D 4989 MET cc_start: 0.9278 (ppp) cc_final: 0.8815 (tpt) REVERT: D 5013 MET cc_start: 0.9649 (mmm) cc_final: 0.9249 (mmm) REVERT: E 73 LYS cc_start: 0.9404 (tmtt) cc_final: 0.9121 (tppt) REVERT: F 73 LYS cc_start: 0.9403 (tmtt) cc_final: 0.9121 (tppt) REVERT: G 73 LYS cc_start: 0.9404 (tmtt) cc_final: 0.9122 (tppt) REVERT: H 73 LYS cc_start: 0.9404 (tmtt) cc_final: 0.9123 (tppt) outliers start: 236 outliers final: 126 residues processed: 1382 average time/residue: 1.1648 time to fit residues: 2903.5128 Evaluate side-chains 1244 residues out of total 15548 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 143 poor density : 1101 time to evaluate : 11.275 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 199 LEU Chi-restraints excluded: chain A residue 207 SER Chi-restraints excluded: chain A residue 334 MET Chi-restraints excluded: chain A residue 407 THR Chi-restraints excluded: chain A residue 605 SER Chi-restraints excluded: chain A residue 1658 ASP Chi-restraints excluded: chain A residue 3898 ASP Chi-restraints excluded: chain A residue 4059 LEU Chi-restraints excluded: chain A residue 4170 ILE Chi-restraints excluded: chain A residue 4182 GLU Chi-restraints excluded: chain A residue 4198 SER Chi-restraints excluded: chain A residue 4200 THR Chi-restraints excluded: chain A residue 4585 SER Chi-restraints excluded: chain A residue 4656 LEU Chi-restraints excluded: chain A residue 4697 VAL Chi-restraints excluded: chain A residue 4720 VAL Chi-restraints excluded: chain A residue 4731 ILE Chi-restraints excluded: chain A residue 4779 LYS Chi-restraints excluded: chain A residue 4785 THR Chi-restraints excluded: chain A residue 4800 LEU Chi-restraints excluded: chain A residue 4822 THR Chi-restraints excluded: chain A residue 4830 VAL Chi-restraints excluded: chain A residue 4852 THR Chi-restraints excluded: chain A residue 4882 CYS Chi-restraints excluded: chain A residue 4891 VAL Chi-restraints excluded: chain A residue 4911 LEU Chi-restraints excluded: chain A residue 4924 VAL Chi-restraints excluded: chain A residue 4929 LEU Chi-restraints excluded: chain A residue 4942 GLU Chi-restraints excluded: chain A residue 4949 GLN Chi-restraints excluded: chain A residue 4965 SER Chi-restraints excluded: chain A residue 4971 THR Chi-restraints excluded: chain B residue 199 LEU Chi-restraints excluded: chain B residue 207 SER Chi-restraints excluded: chain B residue 334 MET Chi-restraints excluded: chain B residue 407 THR Chi-restraints excluded: chain B residue 605 SER Chi-restraints excluded: chain B residue 891 TRP Chi-restraints excluded: chain B residue 941 MET Chi-restraints excluded: chain B residue 1608 MET Chi-restraints excluded: chain B residue 1658 ASP Chi-restraints excluded: chain B residue 3898 ASP Chi-restraints excluded: chain B residue 4059 LEU Chi-restraints excluded: chain B residue 4165 GLU Chi-restraints excluded: chain B residue 4170 ILE Chi-restraints excluded: chain B residue 4182 GLU Chi-restraints excluded: chain B residue 4198 SER Chi-restraints excluded: chain B residue 4200 THR Chi-restraints excluded: chain B residue 4585 SER Chi-restraints excluded: chain B residue 4656 LEU Chi-restraints excluded: chain B residue 4697 VAL Chi-restraints excluded: chain B residue 4720 VAL Chi-restraints excluded: chain B residue 4731 ILE Chi-restraints excluded: chain B residue 4779 LYS Chi-restraints excluded: chain B residue 4785 THR Chi-restraints excluded: chain B residue 4800 LEU Chi-restraints excluded: chain B residue 4822 THR Chi-restraints excluded: chain B residue 4830 VAL Chi-restraints excluded: chain B residue 4852 THR Chi-restraints excluded: chain B residue 4882 CYS Chi-restraints excluded: chain B residue 4911 LEU Chi-restraints excluded: chain B residue 4914 VAL Chi-restraints excluded: chain B residue 4924 VAL Chi-restraints excluded: chain B residue 4926 VAL Chi-restraints excluded: chain B residue 4929 LEU Chi-restraints excluded: chain B residue 4942 GLU Chi-restraints excluded: chain B residue 4965 SER Chi-restraints excluded: chain B residue 4971 THR Chi-restraints excluded: chain C residue 199 LEU Chi-restraints excluded: chain C residue 207 SER Chi-restraints excluded: chain C residue 334 MET Chi-restraints excluded: chain C residue 407 THR Chi-restraints excluded: chain C residue 605 SER Chi-restraints excluded: chain C residue 891 TRP Chi-restraints excluded: chain C residue 941 MET Chi-restraints excluded: chain C residue 1658 ASP Chi-restraints excluded: chain C residue 3898 ASP Chi-restraints excluded: chain C residue 4059 LEU Chi-restraints excluded: chain C residue 4165 GLU Chi-restraints excluded: chain C residue 4170 ILE Chi-restraints excluded: chain C residue 4182 GLU Chi-restraints excluded: chain C residue 4198 SER Chi-restraints excluded: chain C residue 4200 THR Chi-restraints excluded: chain C residue 4585 SER Chi-restraints excluded: chain C residue 4656 LEU Chi-restraints excluded: chain C residue 4697 VAL Chi-restraints excluded: chain C residue 4720 VAL Chi-restraints excluded: chain C residue 4731 ILE Chi-restraints excluded: chain C residue 4779 LYS Chi-restraints excluded: chain C residue 4785 THR Chi-restraints excluded: chain C residue 4800 LEU Chi-restraints excluded: chain C residue 4822 THR Chi-restraints excluded: chain C residue 4830 VAL Chi-restraints excluded: chain C residue 4852 THR Chi-restraints excluded: chain C residue 4882 CYS Chi-restraints excluded: chain C residue 4911 LEU Chi-restraints excluded: chain C residue 4914 VAL Chi-restraints excluded: chain C residue 4924 VAL Chi-restraints excluded: chain C residue 4926 VAL Chi-restraints excluded: chain C residue 4929 LEU Chi-restraints excluded: chain C residue 4942 GLU Chi-restraints excluded: chain C residue 4965 SER Chi-restraints excluded: chain C residue 4971 THR Chi-restraints excluded: chain D residue 199 LEU Chi-restraints excluded: chain D residue 207 SER Chi-restraints excluded: chain D residue 334 MET Chi-restraints excluded: chain D residue 407 THR Chi-restraints excluded: chain D residue 605 SER Chi-restraints excluded: chain D residue 891 TRP Chi-restraints excluded: chain D residue 941 MET Chi-restraints excluded: chain D residue 1608 MET Chi-restraints excluded: chain D residue 1658 ASP Chi-restraints excluded: chain D residue 3898 ASP Chi-restraints excluded: chain D residue 4059 LEU Chi-restraints excluded: chain D residue 4165 GLU Chi-restraints excluded: chain D residue 4170 ILE Chi-restraints excluded: chain D residue 4182 GLU Chi-restraints excluded: chain D residue 4198 SER Chi-restraints excluded: chain D residue 4200 THR Chi-restraints excluded: chain D residue 4585 SER Chi-restraints excluded: chain D residue 4634 GLU Chi-restraints excluded: chain D residue 4656 LEU Chi-restraints excluded: chain D residue 4697 VAL Chi-restraints excluded: chain D residue 4720 VAL Chi-restraints excluded: chain D residue 4731 ILE Chi-restraints excluded: chain D residue 4779 LYS Chi-restraints excluded: chain D residue 4785 THR Chi-restraints excluded: chain D residue 4800 LEU Chi-restraints excluded: chain D residue 4830 VAL Chi-restraints excluded: chain D residue 4852 THR Chi-restraints excluded: chain D residue 4882 CYS Chi-restraints excluded: chain D residue 4911 LEU Chi-restraints excluded: chain D residue 4914 VAL Chi-restraints excluded: chain D residue 4924 VAL Chi-restraints excluded: chain D residue 4926 VAL Chi-restraints excluded: chain D residue 4929 LEU Chi-restraints excluded: chain D residue 4942 GLU Chi-restraints excluded: chain D residue 4965 SER Chi-restraints excluded: chain D residue 4971 THR Chi-restraints excluded: chain E residue 79 ASP Chi-restraints excluded: chain F residue 79 ASP Chi-restraints excluded: chain G residue 79 ASP Chi-restraints excluded: chain H residue 79 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1788 random chunks: chunk 902 optimal weight: 0.0470 chunk 503 optimal weight: 8.9990 chunk 1351 optimal weight: 30.0000 chunk 1105 optimal weight: 8.9990 chunk 447 optimal weight: 7.9990 chunk 1626 optimal weight: 40.0000 chunk 1757 optimal weight: 4.9990 chunk 1448 optimal weight: 20.0000 chunk 1613 optimal weight: 30.0000 chunk 554 optimal weight: 20.0000 chunk 1304 optimal weight: 0.7980 overall best weight: 4.5684 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 226 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 284 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 412 ASN ** A 475 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 533 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 838 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 877 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1299 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1300 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2213 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2247 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2931 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2933 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A3994 HIS A4223 ASN ** A4933 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 98 HIS ** B 226 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 284 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 412 ASN ** B 475 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 533 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 838 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 877 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1299 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1300 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2247 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2931 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2933 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B3994 HIS B4223 ASN ** B4864 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 98 HIS ** C 226 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 284 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 412 ASN ** C 475 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 533 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 838 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 877 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1299 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1300 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2213 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2247 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2931 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2933 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C3318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C3994 HIS C4223 ASN ** C4864 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C4933 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 98 HIS ** D 226 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 284 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 412 ASN ** D 475 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 533 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 838 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 877 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1299 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1300 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2247 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2931 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2933 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D3318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D3994 HIS D4223 ASN ** D4864 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8468 moved from start: 0.2021 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.113 146196 Z= 0.257 Angle : 0.691 12.939 198016 Z= 0.351 Chirality : 0.043 0.228 21760 Planarity : 0.005 0.085 25752 Dihedral : 5.326 75.284 19656 Min Nonbonded Distance : 2.076 Molprobity Statistics. All-atom Clashscore : 18.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.39 % Favored : 95.61 % Rotamer: Outliers : 1.52 % Allowed : 11.61 % Favored : 86.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.45 % Cis-general : 0.00 % Twisted Proline : 0.45 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.13 (0.06), residues: 17832 helix: 0.74 (0.05), residues: 8824 sheet: -0.75 (0.13), residues: 1720 loop : -0.86 (0.07), residues: 7288 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRP C3935 HIS 0.009 0.001 HIS B3771 PHE 0.036 0.002 PHE D4234 TYR 0.027 0.002 TYR A 411 ARG 0.017 0.000 ARG B1180 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 35664 Ramachandran restraints generated. 17832 Oldfield, 0 Emsley, 17832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 35664 Ramachandran restraints generated. 17832 Oldfield, 0 Emsley, 17832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1402 residues out of total 15548 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 217 poor density : 1185 time to evaluate : 12.760 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 155 LYS cc_start: 0.9505 (mmtt) cc_final: 0.9094 (tppt) REVERT: A 196 MET cc_start: 0.8769 (mpp) cc_final: 0.8497 (mpp) REVERT: A 343 GLU cc_start: 0.8703 (mt-10) cc_final: 0.8162 (mp0) REVERT: A 565 TYR cc_start: 0.9283 (t80) cc_final: 0.9014 (t80) REVERT: A 601 ASP cc_start: 0.9159 (m-30) cc_final: 0.8959 (m-30) REVERT: A 667 MET cc_start: 0.9297 (tpp) cc_final: 0.8916 (tpp) REVERT: A 941 MET cc_start: 0.5862 (tpt) cc_final: 0.4933 (mmm) REVERT: A 960 MET cc_start: 0.5020 (mmm) cc_final: 0.3405 (mtm) REVERT: A 961 MET cc_start: 0.6907 (pmm) cc_final: 0.6502 (pmm) REVERT: A 1100 MET cc_start: 0.8151 (mpp) cc_final: 0.7927 (mpp) REVERT: A 1260 MET cc_start: 0.9114 (mtm) cc_final: 0.8579 (mtm) REVERT: A 1601 MET cc_start: 0.9645 (tpt) cc_final: 0.9217 (tpt) REVERT: A 1865 MET cc_start: 0.9435 (mpp) cc_final: 0.9069 (mpp) REVERT: A 2228 MET cc_start: 0.9634 (ppp) cc_final: 0.9195 (ppp) REVERT: A 2293 GLN cc_start: 0.9471 (mm-40) cc_final: 0.9151 (tm-30) REVERT: A 2294 ASP cc_start: 0.9446 (m-30) cc_final: 0.8694 (m-30) REVERT: A 2440 MET cc_start: 0.9093 (OUTLIER) cc_final: 0.8830 (mmp) REVERT: A 2618 MET cc_start: 0.8721 (mpp) cc_final: 0.8307 (mpp) REVERT: A 2698 MET cc_start: 0.8589 (ppp) cc_final: 0.8356 (ppp) REVERT: A 2932 MET cc_start: 0.7257 (tpt) cc_final: 0.6873 (ptt) REVERT: A 3038 MET cc_start: 0.5770 (mpp) cc_final: 0.5264 (mpp) REVERT: A 3276 MET cc_start: 0.8072 (mmp) cc_final: 0.7514 (mmm) REVERT: A 3335 MET cc_start: 0.7930 (pmm) cc_final: 0.6978 (pmm) REVERT: A 3411 LEU cc_start: 0.9754 (pp) cc_final: 0.9316 (mm) REVERT: A 3673 MET cc_start: 0.9801 (mmm) cc_final: 0.9453 (tpt) REVERT: A 3675 ASP cc_start: 0.9502 (m-30) cc_final: 0.9253 (m-30) REVERT: A 3723 MET cc_start: 0.9389 (mmm) cc_final: 0.9187 (mmm) REVERT: A 3758 MET cc_start: 0.9075 (tmm) cc_final: 0.8834 (tmm) REVERT: A 3778 MET cc_start: 0.9539 (tmm) cc_final: 0.9321 (tmm) REVERT: A 3816 MET cc_start: 0.9631 (mmt) cc_final: 0.9140 (mmp) REVERT: A 4639 MET cc_start: 0.9337 (mtp) cc_final: 0.9081 (mtp) REVERT: A 4704 LEU cc_start: 0.8668 (OUTLIER) cc_final: 0.8135 (pp) REVERT: A 4779 LYS cc_start: 0.9634 (OUTLIER) cc_final: 0.9213 (ptpp) REVERT: A 4874 MET cc_start: 0.8305 (mmm) cc_final: 0.7978 (mmm) REVERT: A 4879 MET cc_start: 0.8855 (mmm) cc_final: 0.8326 (tpp) REVERT: A 4942 GLU cc_start: 0.9095 (OUTLIER) cc_final: 0.8158 (mm-30) REVERT: A 4949 GLN cc_start: 0.9419 (OUTLIER) cc_final: 0.9139 (mm-40) REVERT: A 4967 TYR cc_start: 0.7666 (t80) cc_final: 0.7220 (t80) REVERT: A 4969 ASP cc_start: 0.9547 (m-30) cc_final: 0.9302 (m-30) REVERT: A 5013 MET cc_start: 0.9610 (mmm) cc_final: 0.9265 (mmm) REVERT: B 155 LYS cc_start: 0.9503 (mmtt) cc_final: 0.9110 (tppt) REVERT: B 196 MET cc_start: 0.8907 (mpp) cc_final: 0.8552 (mpp) REVERT: B 228 ASP cc_start: 0.9606 (m-30) cc_final: 0.9403 (m-30) REVERT: B 340 LYS cc_start: 0.9071 (mmmt) cc_final: 0.8791 (mmmt) REVERT: B 343 GLU cc_start: 0.8839 (mt-10) cc_final: 0.8261 (mp0) REVERT: B 384 MET cc_start: 0.7117 (tmm) cc_final: 0.6740 (tmm) REVERT: B 667 MET cc_start: 0.9357 (tpp) cc_final: 0.8998 (tpp) REVERT: B 960 MET cc_start: 0.4374 (mmm) cc_final: 0.2766 (mtm) REVERT: B 961 MET cc_start: 0.7125 (pmm) cc_final: 0.6809 (pmm) REVERT: B 1108 GLU cc_start: 0.8353 (pm20) cc_final: 0.8116 (pm20) REVERT: B 1601 MET cc_start: 0.9590 (tpp) cc_final: 0.9243 (tpp) REVERT: B 1865 MET cc_start: 0.9440 (mpp) cc_final: 0.9101 (mpp) REVERT: B 1986 MET cc_start: 0.7818 (ppp) cc_final: 0.7509 (pmm) REVERT: B 2170 MET cc_start: 0.8655 (tpp) cc_final: 0.8450 (tpp) REVERT: B 2203 MET cc_start: 0.9440 (pmm) cc_final: 0.9218 (pmm) REVERT: B 2228 MET cc_start: 0.9618 (ppp) cc_final: 0.9102 (ppp) REVERT: B 2293 GLN cc_start: 0.9477 (mm-40) cc_final: 0.9163 (tm-30) REVERT: B 2294 ASP cc_start: 0.9444 (m-30) cc_final: 0.8702 (m-30) REVERT: B 2440 MET cc_start: 0.9088 (OUTLIER) cc_final: 0.8833 (mmp) REVERT: B 2698 MET cc_start: 0.8429 (ppp) cc_final: 0.8203 (ppp) REVERT: B 2932 MET cc_start: 0.7163 (tpt) cc_final: 0.6774 (ptt) REVERT: B 3038 MET cc_start: 0.5891 (mpp) cc_final: 0.5471 (mpp) REVERT: B 3106 MET cc_start: 0.8996 (mmm) cc_final: 0.8711 (mmp) REVERT: B 3276 MET cc_start: 0.8093 (mmp) cc_final: 0.7493 (mmm) REVERT: B 3335 MET cc_start: 0.7940 (pmm) cc_final: 0.6948 (pmm) REVERT: B 3411 LEU cc_start: 0.9761 (pp) cc_final: 0.9336 (mm) REVERT: B 3675 ASP cc_start: 0.9489 (m-30) cc_final: 0.9253 (m-30) REVERT: B 3723 MET cc_start: 0.9381 (mmm) cc_final: 0.9174 (mmm) REVERT: B 3778 MET cc_start: 0.9526 (tmm) cc_final: 0.9316 (tmm) REVERT: B 3798 LEU cc_start: 0.9847 (mp) cc_final: 0.9392 (tt) REVERT: B 3816 MET cc_start: 0.9640 (mmt) cc_final: 0.9149 (mmp) REVERT: B 4571 PHE cc_start: 0.9022 (m-80) cc_final: 0.8772 (m-80) REVERT: B 4639 MET cc_start: 0.9317 (mtp) cc_final: 0.9054 (mtp) REVERT: B 4704 LEU cc_start: 0.8718 (OUTLIER) cc_final: 0.8123 (pp) REVERT: B 4779 LYS cc_start: 0.9639 (OUTLIER) cc_final: 0.9252 (ptpp) REVERT: B 4874 MET cc_start: 0.8074 (mmm) cc_final: 0.7629 (mmm) REVERT: B 4879 MET cc_start: 0.8831 (mmm) cc_final: 0.8557 (tpp) REVERT: B 4880 MET cc_start: 0.8778 (ptp) cc_final: 0.8435 (ptp) REVERT: B 4887 MET cc_start: 0.8452 (mtp) cc_final: 0.8103 (mtm) REVERT: B 4954 MET cc_start: 0.9457 (tpp) cc_final: 0.9190 (tpp) REVERT: B 4967 TYR cc_start: 0.7702 (t80) cc_final: 0.7178 (t80) REVERT: B 4969 ASP cc_start: 0.9552 (m-30) cc_final: 0.9312 (m-30) REVERT: B 5013 MET cc_start: 0.9616 (mmm) cc_final: 0.9270 (mmm) REVERT: C 155 LYS cc_start: 0.9537 (mmtt) cc_final: 0.9031 (tppt) REVERT: C 196 MET cc_start: 0.8848 (mpp) cc_final: 0.8560 (mpp) REVERT: C 228 ASP cc_start: 0.9606 (m-30) cc_final: 0.9403 (m-30) REVERT: C 340 LYS cc_start: 0.9066 (mmmt) cc_final: 0.8787 (mmmt) REVERT: C 343 GLU cc_start: 0.8837 (mt-10) cc_final: 0.8260 (mp0) REVERT: C 384 MET cc_start: 0.7116 (tmm) cc_final: 0.6737 (tmm) REVERT: C 565 TYR cc_start: 0.9284 (t80) cc_final: 0.9051 (t80) REVERT: C 667 MET cc_start: 0.9358 (tpp) cc_final: 0.9001 (tpp) REVERT: C 960 MET cc_start: 0.4367 (mmm) cc_final: 0.2762 (mtm) REVERT: C 961 MET cc_start: 0.7122 (pmm) cc_final: 0.6808 (pmm) REVERT: C 1108 GLU cc_start: 0.8353 (pm20) cc_final: 0.8115 (pm20) REVERT: C 1260 MET cc_start: 0.8398 (mtm) cc_final: 0.7973 (mtm) REVERT: C 1601 MET cc_start: 0.9592 (tpp) cc_final: 0.9244 (tpp) REVERT: C 1865 MET cc_start: 0.9439 (mpp) cc_final: 0.9100 (mpp) REVERT: C 1986 MET cc_start: 0.7817 (ppp) cc_final: 0.7508 (pmm) REVERT: C 2170 MET cc_start: 0.8662 (tpp) cc_final: 0.8458 (tpp) REVERT: C 2203 MET cc_start: 0.9441 (pmm) cc_final: 0.9219 (pmm) REVERT: C 2228 MET cc_start: 0.9627 (ppp) cc_final: 0.9115 (ppp) REVERT: C 2293 GLN cc_start: 0.9477 (mm-40) cc_final: 0.9162 (tm-30) REVERT: C 2294 ASP cc_start: 0.9444 (m-30) cc_final: 0.8701 (m-30) REVERT: C 2440 MET cc_start: 0.9082 (mmp) cc_final: 0.8821 (mmp) REVERT: C 2698 MET cc_start: 0.8429 (ppp) cc_final: 0.8203 (ppp) REVERT: C 2932 MET cc_start: 0.7163 (tpt) cc_final: 0.6774 (ptt) REVERT: C 3038 MET cc_start: 0.5895 (mpp) cc_final: 0.5474 (mpp) REVERT: C 3106 MET cc_start: 0.8998 (mmm) cc_final: 0.8712 (mmp) REVERT: C 3276 MET cc_start: 0.8095 (mmp) cc_final: 0.7493 (mmm) REVERT: C 3335 MET cc_start: 0.7941 (pmm) cc_final: 0.6948 (pmm) REVERT: C 3411 LEU cc_start: 0.9761 (pp) cc_final: 0.9337 (mm) REVERT: C 3675 ASP cc_start: 0.9488 (m-30) cc_final: 0.9254 (m-30) REVERT: C 3723 MET cc_start: 0.9381 (mmm) cc_final: 0.9176 (mmm) REVERT: C 3778 MET cc_start: 0.9528 (tmm) cc_final: 0.9313 (tmm) REVERT: C 3816 MET cc_start: 0.9640 (mmt) cc_final: 0.9144 (mmp) REVERT: C 3999 MET cc_start: 0.9541 (mmm) cc_final: 0.9340 (mmm) REVERT: C 4571 PHE cc_start: 0.9019 (m-80) cc_final: 0.8771 (m-80) REVERT: C 4639 MET cc_start: 0.9318 (mtp) cc_final: 0.9053 (mtp) REVERT: C 4704 LEU cc_start: 0.8719 (OUTLIER) cc_final: 0.8123 (pp) REVERT: C 4779 LYS cc_start: 0.9639 (OUTLIER) cc_final: 0.9251 (ptpp) REVERT: C 4874 MET cc_start: 0.8071 (mmm) cc_final: 0.7627 (mmm) REVERT: C 4879 MET cc_start: 0.8887 (mmm) cc_final: 0.8530 (tpp) REVERT: C 4880 MET cc_start: 0.8776 (ptp) cc_final: 0.8448 (ptp) REVERT: C 4887 MET cc_start: 0.8451 (mtp) cc_final: 0.8098 (mtm) REVERT: C 4942 GLU cc_start: 0.8986 (OUTLIER) cc_final: 0.7810 (mm-30) REVERT: C 4954 MET cc_start: 0.9455 (tpp) cc_final: 0.9188 (tpp) REVERT: C 4969 ASP cc_start: 0.9524 (m-30) cc_final: 0.9286 (m-30) REVERT: C 5013 MET cc_start: 0.9619 (mmm) cc_final: 0.9284 (mmm) REVERT: D 155 LYS cc_start: 0.9537 (mmtt) cc_final: 0.9030 (tppt) REVERT: D 196 MET cc_start: 0.8914 (mpp) cc_final: 0.8559 (mpp) REVERT: D 228 ASP cc_start: 0.9603 (m-30) cc_final: 0.9394 (m-30) REVERT: D 340 LYS cc_start: 0.9070 (mmmt) cc_final: 0.8790 (mmmt) REVERT: D 343 GLU cc_start: 0.8838 (mt-10) cc_final: 0.8260 (mp0) REVERT: D 384 MET cc_start: 0.7118 (tmm) cc_final: 0.6740 (tmm) REVERT: D 565 TYR cc_start: 0.9285 (t80) cc_final: 0.9051 (t80) REVERT: D 667 MET cc_start: 0.9358 (tpp) cc_final: 0.9001 (tpp) REVERT: D 960 MET cc_start: 0.4379 (mmm) cc_final: 0.2772 (mtm) REVERT: D 961 MET cc_start: 0.7127 (pmm) cc_final: 0.6812 (pmm) REVERT: D 1108 GLU cc_start: 0.8349 (pm20) cc_final: 0.8113 (pm20) REVERT: D 1601 MET cc_start: 0.9590 (tpp) cc_final: 0.9244 (tpp) REVERT: D 1865 MET cc_start: 0.9464 (mpp) cc_final: 0.9120 (mpp) REVERT: D 1986 MET cc_start: 0.7818 (ppp) cc_final: 0.7509 (pmm) REVERT: D 2170 MET cc_start: 0.8658 (tpp) cc_final: 0.8452 (tpp) REVERT: D 2203 MET cc_start: 0.9438 (pmm) cc_final: 0.9213 (pmm) REVERT: D 2228 MET cc_start: 0.9619 (ppp) cc_final: 0.9103 (ppp) REVERT: D 2293 GLN cc_start: 0.9476 (mm-40) cc_final: 0.9163 (tm-30) REVERT: D 2294 ASP cc_start: 0.9445 (m-30) cc_final: 0.8702 (m-30) REVERT: D 2440 MET cc_start: 0.9082 (mmp) cc_final: 0.8821 (mmp) REVERT: D 2618 MET cc_start: 0.8741 (mpp) cc_final: 0.8335 (mpp) REVERT: D 2698 MET cc_start: 0.8428 (ppp) cc_final: 0.8202 (ppp) REVERT: D 2932 MET cc_start: 0.7163 (tpt) cc_final: 0.6775 (ptt) REVERT: D 3038 MET cc_start: 0.5893 (mpp) cc_final: 0.5472 (mpp) REVERT: D 3081 MET cc_start: 0.6548 (ptp) cc_final: 0.6275 (ptp) REVERT: D 3106 MET cc_start: 0.8997 (mmm) cc_final: 0.8712 (mmp) REVERT: D 3266 MET cc_start: 0.9361 (OUTLIER) cc_final: 0.9098 (ppp) REVERT: D 3276 MET cc_start: 0.8095 (mmp) cc_final: 0.7484 (mmm) REVERT: D 3335 MET cc_start: 0.7939 (pmm) cc_final: 0.6945 (pmm) REVERT: D 3411 LEU cc_start: 0.9761 (pp) cc_final: 0.9338 (mm) REVERT: D 3675 ASP cc_start: 0.9489 (m-30) cc_final: 0.9254 (m-30) REVERT: D 3723 MET cc_start: 0.9381 (mmm) cc_final: 0.9175 (mmm) REVERT: D 3778 MET cc_start: 0.9529 (tmm) cc_final: 0.9314 (tmm) REVERT: D 3816 MET cc_start: 0.9641 (mmt) cc_final: 0.9143 (mmp) REVERT: D 3999 MET cc_start: 0.9540 (mmm) cc_final: 0.9337 (mmm) REVERT: D 4571 PHE cc_start: 0.9014 (m-80) cc_final: 0.8762 (m-80) REVERT: D 4639 MET cc_start: 0.9303 (mtp) cc_final: 0.9042 (mtp) REVERT: D 4704 LEU cc_start: 0.8720 (OUTLIER) cc_final: 0.8126 (pp) REVERT: D 4779 LYS cc_start: 0.9639 (OUTLIER) cc_final: 0.9252 (ptpp) REVERT: D 4874 MET cc_start: 0.8072 (mmm) cc_final: 0.7628 (mmm) REVERT: D 4879 MET cc_start: 0.8881 (mmm) cc_final: 0.8516 (tpp) REVERT: D 4880 MET cc_start: 0.8759 (ptp) cc_final: 0.8435 (ptp) REVERT: D 4887 MET cc_start: 0.8406 (mtp) cc_final: 0.8048 (mtm) REVERT: D 4942 GLU cc_start: 0.8985 (OUTLIER) cc_final: 0.7803 (mm-30) REVERT: D 4954 MET cc_start: 0.9454 (tpp) cc_final: 0.9185 (tpp) REVERT: D 4969 ASP cc_start: 0.9512 (m-30) cc_final: 0.9278 (m-30) REVERT: D 5013 MET cc_start: 0.9616 (mmm) cc_final: 0.9268 (mmm) REVERT: E 73 LYS cc_start: 0.9371 (tmtt) cc_final: 0.9077 (tppt) REVERT: E 74 LEU cc_start: 0.9239 (OUTLIER) cc_final: 0.9038 (mp) REVERT: F 73 LYS cc_start: 0.9372 (tmtt) cc_final: 0.9078 (tppt) REVERT: F 74 LEU cc_start: 0.9237 (OUTLIER) cc_final: 0.9037 (mp) REVERT: G 73 LYS cc_start: 0.9372 (tmtt) cc_final: 0.9078 (tppt) REVERT: G 74 LEU cc_start: 0.9238 (OUTLIER) cc_final: 0.9037 (mp) REVERT: H 73 LYS cc_start: 0.9371 (tmtt) cc_final: 0.9078 (tppt) outliers start: 217 outliers final: 119 residues processed: 1333 average time/residue: 1.1524 time to fit residues: 2783.0890 Evaluate side-chains 1219 residues out of total 15548 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 137 poor density : 1082 time to evaluate : 12.410 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 CYS Chi-restraints excluded: chain A residue 199 LEU Chi-restraints excluded: chain A residue 207 SER Chi-restraints excluded: chain A residue 334 MET Chi-restraints excluded: chain A residue 605 SER Chi-restraints excluded: chain A residue 1658 ASP Chi-restraints excluded: chain A residue 2440 MET Chi-restraints excluded: chain A residue 2602 VAL Chi-restraints excluded: chain A residue 3192 GLU Chi-restraints excluded: chain A residue 3456 GLN Chi-restraints excluded: chain A residue 3715 LYS Chi-restraints excluded: chain A residue 3898 ASP Chi-restraints excluded: chain A residue 3990 VAL Chi-restraints excluded: chain A residue 4015 GLU Chi-restraints excluded: chain A residue 4170 ILE Chi-restraints excluded: chain A residue 4198 SER Chi-restraints excluded: chain A residue 4200 THR Chi-restraints excluded: chain A residue 4697 VAL Chi-restraints excluded: chain A residue 4704 LEU Chi-restraints excluded: chain A residue 4720 VAL Chi-restraints excluded: chain A residue 4731 ILE Chi-restraints excluded: chain A residue 4779 LYS Chi-restraints excluded: chain A residue 4795 TYR Chi-restraints excluded: chain A residue 4800 LEU Chi-restraints excluded: chain A residue 4830 VAL Chi-restraints excluded: chain A residue 4837 LEU Chi-restraints excluded: chain A residue 4852 THR Chi-restraints excluded: chain A residue 4882 CYS Chi-restraints excluded: chain A residue 4942 GLU Chi-restraints excluded: chain A residue 4949 GLN Chi-restraints excluded: chain A residue 4971 THR Chi-restraints excluded: chain B residue 66 CYS Chi-restraints excluded: chain B residue 199 LEU Chi-restraints excluded: chain B residue 207 SER Chi-restraints excluded: chain B residue 334 MET Chi-restraints excluded: chain B residue 605 SER Chi-restraints excluded: chain B residue 891 TRP Chi-restraints excluded: chain B residue 1608 MET Chi-restraints excluded: chain B residue 1658 ASP Chi-restraints excluded: chain B residue 2440 MET Chi-restraints excluded: chain B residue 2602 VAL Chi-restraints excluded: chain B residue 3192 GLU Chi-restraints excluded: chain B residue 3456 GLN Chi-restraints excluded: chain B residue 3715 LYS Chi-restraints excluded: chain B residue 3898 ASP Chi-restraints excluded: chain B residue 3990 VAL Chi-restraints excluded: chain B residue 4015 GLU Chi-restraints excluded: chain B residue 4170 ILE Chi-restraints excluded: chain B residue 4198 SER Chi-restraints excluded: chain B residue 4200 THR Chi-restraints excluded: chain B residue 4697 VAL Chi-restraints excluded: chain B residue 4704 LEU Chi-restraints excluded: chain B residue 4720 VAL Chi-restraints excluded: chain B residue 4731 ILE Chi-restraints excluded: chain B residue 4779 LYS Chi-restraints excluded: chain B residue 4800 LEU Chi-restraints excluded: chain B residue 4837 LEU Chi-restraints excluded: chain B residue 4852 THR Chi-restraints excluded: chain B residue 4882 CYS Chi-restraints excluded: chain B residue 4924 VAL Chi-restraints excluded: chain B residue 4926 VAL Chi-restraints excluded: chain B residue 4929 LEU Chi-restraints excluded: chain B residue 4942 GLU Chi-restraints excluded: chain B residue 4971 THR Chi-restraints excluded: chain C residue 66 CYS Chi-restraints excluded: chain C residue 199 LEU Chi-restraints excluded: chain C residue 207 SER Chi-restraints excluded: chain C residue 334 MET Chi-restraints excluded: chain C residue 605 SER Chi-restraints excluded: chain C residue 891 TRP Chi-restraints excluded: chain C residue 1658 ASP Chi-restraints excluded: chain C residue 2602 VAL Chi-restraints excluded: chain C residue 3192 GLU Chi-restraints excluded: chain C residue 3456 GLN Chi-restraints excluded: chain C residue 3715 LYS Chi-restraints excluded: chain C residue 3898 ASP Chi-restraints excluded: chain C residue 3990 VAL Chi-restraints excluded: chain C residue 4015 GLU Chi-restraints excluded: chain C residue 4170 ILE Chi-restraints excluded: chain C residue 4190 ILE Chi-restraints excluded: chain C residue 4198 SER Chi-restraints excluded: chain C residue 4200 THR Chi-restraints excluded: chain C residue 4697 VAL Chi-restraints excluded: chain C residue 4704 LEU Chi-restraints excluded: chain C residue 4720 VAL Chi-restraints excluded: chain C residue 4731 ILE Chi-restraints excluded: chain C residue 4779 LYS Chi-restraints excluded: chain C residue 4800 LEU Chi-restraints excluded: chain C residue 4837 LEU Chi-restraints excluded: chain C residue 4852 THR Chi-restraints excluded: chain C residue 4882 CYS Chi-restraints excluded: chain C residue 4924 VAL Chi-restraints excluded: chain C residue 4926 VAL Chi-restraints excluded: chain C residue 4929 LEU Chi-restraints excluded: chain C residue 4942 GLU Chi-restraints excluded: chain C residue 4971 THR Chi-restraints excluded: chain D residue 66 CYS Chi-restraints excluded: chain D residue 199 LEU Chi-restraints excluded: chain D residue 207 SER Chi-restraints excluded: chain D residue 334 MET Chi-restraints excluded: chain D residue 605 SER Chi-restraints excluded: chain D residue 891 TRP Chi-restraints excluded: chain D residue 1608 MET Chi-restraints excluded: chain D residue 1658 ASP Chi-restraints excluded: chain D residue 2602 VAL Chi-restraints excluded: chain D residue 3192 GLU Chi-restraints excluded: chain D residue 3266 MET Chi-restraints excluded: chain D residue 3456 GLN Chi-restraints excluded: chain D residue 3715 LYS Chi-restraints excluded: chain D residue 3898 ASP Chi-restraints excluded: chain D residue 3990 VAL Chi-restraints excluded: chain D residue 4015 GLU Chi-restraints excluded: chain D residue 4170 ILE Chi-restraints excluded: chain D residue 4198 SER Chi-restraints excluded: chain D residue 4200 THR Chi-restraints excluded: chain D residue 4634 GLU Chi-restraints excluded: chain D residue 4697 VAL Chi-restraints excluded: chain D residue 4704 LEU Chi-restraints excluded: chain D residue 4720 VAL Chi-restraints excluded: chain D residue 4731 ILE Chi-restraints excluded: chain D residue 4779 LYS Chi-restraints excluded: chain D residue 4800 LEU Chi-restraints excluded: chain D residue 4837 LEU Chi-restraints excluded: chain D residue 4852 THR Chi-restraints excluded: chain D residue 4882 CYS Chi-restraints excluded: chain D residue 4924 VAL Chi-restraints excluded: chain D residue 4926 VAL Chi-restraints excluded: chain D residue 4929 LEU Chi-restraints excluded: chain D residue 4942 GLU Chi-restraints excluded: chain D residue 4971 THR Chi-restraints excluded: chain E residue 74 LEU Chi-restraints excluded: chain E residue 79 ASP Chi-restraints excluded: chain F residue 74 LEU Chi-restraints excluded: chain F residue 79 ASP Chi-restraints excluded: chain G residue 74 LEU Chi-restraints excluded: chain G residue 79 ASP Chi-restraints excluded: chain H residue 79 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1788 random chunks: chunk 1607 optimal weight: 7.9990 chunk 1222 optimal weight: 10.0000 chunk 844 optimal weight: 0.7980 chunk 180 optimal weight: 4.9990 chunk 776 optimal weight: 7.9990 chunk 1092 optimal weight: 9.9990 chunk 1632 optimal weight: 1.9990 chunk 1728 optimal weight: 10.0000 chunk 852 optimal weight: 10.0000 chunk 1547 optimal weight: 10.0000 chunk 465 optimal weight: 0.4980 overall best weight: 3.2586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 284 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 475 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 533 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 597 HIS ** A 838 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 877 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1299 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1300 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1569 GLN ** A2213 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2247 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2931 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2933 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4201 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4933 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 98 HIS ** B 226 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 475 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 533 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 597 HIS ** B 838 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 877 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1299 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1300 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1569 GLN B1614 GLN ** B2247 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2931 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2933 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B3318 ASN B4201 ASN ** B4864 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 98 HIS ** C 226 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 284 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 475 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 489 ASN ** C 533 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 597 HIS ** C 838 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 877 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1299 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1300 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C1569 GLN ** C2213 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2247 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2931 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2933 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C3318 ASN C4201 ASN ** C4864 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 98 HIS ** D 284 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 475 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 533 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 597 HIS ** D 838 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 877 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1299 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1300 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D1569 GLN ** D2247 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2931 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2933 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D3318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D4864 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8461 moved from start: 0.2227 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 146196 Z= 0.216 Angle : 0.672 13.198 198016 Z= 0.336 Chirality : 0.042 0.345 21760 Planarity : 0.005 0.074 25752 Dihedral : 5.110 78.962 19632 Min Nonbonded Distance : 2.079 Molprobity Statistics. All-atom Clashscore : 17.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.39 % Favored : 95.61 % Rotamer: Outliers : 1.26 % Allowed : 12.78 % Favored : 85.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.45 % Cis-general : 0.00 % Twisted Proline : 0.45 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.02 (0.06), residues: 17832 helix: 0.82 (0.06), residues: 8796 sheet: -0.68 (0.12), residues: 1736 loop : -0.79 (0.07), residues: 7300 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP C1143 HIS 0.008 0.001 HIS B3771 PHE 0.046 0.002 PHE A4571 TYR 0.019 0.002 TYR D5032 ARG 0.014 0.000 ARG D1180 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 35664 Ramachandran restraints generated. 17832 Oldfield, 0 Emsley, 17832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 35664 Ramachandran restraints generated. 17832 Oldfield, 0 Emsley, 17832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1319 residues out of total 15548 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 176 poor density : 1143 time to evaluate : 12.684 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 155 LYS cc_start: 0.9539 (mmtt) cc_final: 0.9121 (tppt) REVERT: A 196 MET cc_start: 0.8739 (mpp) cc_final: 0.8444 (mpp) REVERT: A 228 ASP cc_start: 0.9423 (m-30) cc_final: 0.9153 (m-30) REVERT: A 343 GLU cc_start: 0.8759 (mt-10) cc_final: 0.8217 (mp0) REVERT: A 483 MET cc_start: 0.9000 (mmt) cc_final: 0.8788 (mmp) REVERT: A 565 TYR cc_start: 0.9259 (t80) cc_final: 0.8968 (t80) REVERT: A 667 MET cc_start: 0.9338 (tpp) cc_final: 0.8803 (tpp) REVERT: A 960 MET cc_start: 0.5171 (mmm) cc_final: 0.3486 (mtm) REVERT: A 961 MET cc_start: 0.6929 (pmm) cc_final: 0.6529 (pmm) REVERT: A 1100 MET cc_start: 0.7983 (mpp) cc_final: 0.7568 (mpp) REVERT: A 1260 MET cc_start: 0.9120 (mtm) cc_final: 0.8878 (mtm) REVERT: A 1573 MET cc_start: 0.8407 (tpt) cc_final: 0.8186 (tpt) REVERT: A 1601 MET cc_start: 0.9611 (tpt) cc_final: 0.9245 (tpp) REVERT: A 1865 MET cc_start: 0.9411 (mpp) cc_final: 0.9185 (mtp) REVERT: A 2228 MET cc_start: 0.9622 (ppp) cc_final: 0.9177 (ppp) REVERT: A 2293 GLN cc_start: 0.9468 (mm-40) cc_final: 0.9150 (tm-30) REVERT: A 2294 ASP cc_start: 0.9431 (m-30) cc_final: 0.8680 (m-30) REVERT: A 2440 MET cc_start: 0.9074 (OUTLIER) cc_final: 0.8830 (mmp) REVERT: A 2698 MET cc_start: 0.8459 (ppp) cc_final: 0.8234 (ppp) REVERT: A 2932 MET cc_start: 0.7179 (tpt) cc_final: 0.6800 (ptt) REVERT: A 3081 MET cc_start: 0.6319 (ptp) cc_final: 0.6098 (ptp) REVERT: A 3276 MET cc_start: 0.8040 (mmp) cc_final: 0.7463 (mmm) REVERT: A 3335 MET cc_start: 0.7960 (pmm) cc_final: 0.6861 (pmm) REVERT: A 3411 LEU cc_start: 0.9756 (pp) cc_final: 0.9295 (mm) REVERT: A 3673 MET cc_start: 0.9817 (mmm) cc_final: 0.9483 (tpt) REVERT: A 3675 ASP cc_start: 0.9525 (m-30) cc_final: 0.9323 (m-30) REVERT: A 3723 MET cc_start: 0.9359 (mmm) cc_final: 0.9052 (mmm) REVERT: A 3778 MET cc_start: 0.9572 (tmm) cc_final: 0.9329 (tmm) REVERT: A 3798 LEU cc_start: 0.9822 (mp) cc_final: 0.9323 (tt) REVERT: A 3816 MET cc_start: 0.9620 (mmt) cc_final: 0.9096 (mmp) REVERT: A 4184 MET cc_start: 0.8936 (tpp) cc_final: 0.8236 (tpp) REVERT: A 4244 GLU cc_start: 0.9090 (tm-30) cc_final: 0.8860 (tm-30) REVERT: A 4639 MET cc_start: 0.9339 (mtp) cc_final: 0.9085 (mtp) REVERT: A 4704 LEU cc_start: 0.8683 (OUTLIER) cc_final: 0.8059 (pp) REVERT: A 4779 LYS cc_start: 0.9628 (OUTLIER) cc_final: 0.9233 (ptpp) REVERT: A 4798 MET cc_start: 0.9584 (tpp) cc_final: 0.9362 (mmm) REVERT: A 4818 MET cc_start: 0.8872 (tmm) cc_final: 0.8491 (tpp) REVERT: A 4874 MET cc_start: 0.8329 (mmm) cc_final: 0.8012 (mmm) REVERT: A 4879 MET cc_start: 0.8831 (mmm) cc_final: 0.8287 (tpp) REVERT: A 4949 GLN cc_start: 0.9367 (OUTLIER) cc_final: 0.9089 (mm-40) REVERT: A 4954 MET cc_start: 0.9440 (tpp) cc_final: 0.9151 (tpp) REVERT: A 4967 TYR cc_start: 0.7822 (t80) cc_final: 0.7147 (t80) REVERT: A 4969 ASP cc_start: 0.9549 (m-30) cc_final: 0.9293 (m-30) REVERT: A 5013 MET cc_start: 0.9583 (mmm) cc_final: 0.9285 (mmm) REVERT: A 5032 TYR cc_start: 0.9260 (m-80) cc_final: 0.8979 (m-10) REVERT: B 155 LYS cc_start: 0.9536 (mmtt) cc_final: 0.9102 (tppt) REVERT: B 196 MET cc_start: 0.8738 (mpp) cc_final: 0.8459 (mpp) REVERT: B 228 ASP cc_start: 0.9605 (m-30) cc_final: 0.9399 (m-30) REVERT: B 343 GLU cc_start: 0.8846 (mt-10) cc_final: 0.8259 (mp0) REVERT: B 384 MET cc_start: 0.7093 (tmm) cc_final: 0.6721 (tmm) REVERT: B 667 MET cc_start: 0.9389 (tpp) cc_final: 0.8972 (tpp) REVERT: B 846 LEU cc_start: 0.8797 (OUTLIER) cc_final: 0.8568 (mp) REVERT: B 960 MET cc_start: 0.4596 (mmm) cc_final: 0.3066 (mtm) REVERT: B 961 MET cc_start: 0.7185 (pmm) cc_final: 0.6836 (pmm) REVERT: B 1260 MET cc_start: 0.8405 (mtm) cc_final: 0.7974 (mtm) REVERT: B 1573 MET cc_start: 0.8549 (tpt) cc_final: 0.8303 (tpt) REVERT: B 1601 MET cc_start: 0.9545 (tpp) cc_final: 0.9147 (tpp) REVERT: B 1986 MET cc_start: 0.7871 (ppp) cc_final: 0.7548 (pmm) REVERT: B 2198 MET cc_start: 0.9208 (mpp) cc_final: 0.8706 (mpp) REVERT: B 2203 MET cc_start: 0.9412 (pmm) cc_final: 0.9117 (pmm) REVERT: B 2228 MET cc_start: 0.9613 (ppp) cc_final: 0.9181 (ppp) REVERT: B 2293 GLN cc_start: 0.9471 (mm-40) cc_final: 0.9158 (tm-30) REVERT: B 2294 ASP cc_start: 0.9429 (m-30) cc_final: 0.8718 (m-30) REVERT: B 2440 MET cc_start: 0.9054 (OUTLIER) cc_final: 0.8807 (mmp) REVERT: B 2698 MET cc_start: 0.8438 (ppp) cc_final: 0.8212 (ppp) REVERT: B 2932 MET cc_start: 0.7138 (tpt) cc_final: 0.6756 (ptt) REVERT: B 3081 MET cc_start: 0.6127 (ptp) cc_final: 0.5499 (pmm) REVERT: B 3106 MET cc_start: 0.9020 (mmm) cc_final: 0.8697 (mmp) REVERT: B 3276 MET cc_start: 0.8062 (mmp) cc_final: 0.7477 (mmm) REVERT: B 3335 MET cc_start: 0.7966 (pmm) cc_final: 0.7762 (pmm) REVERT: B 3411 LEU cc_start: 0.9763 (pp) cc_final: 0.9338 (mm) REVERT: B 3675 ASP cc_start: 0.9510 (m-30) cc_final: 0.9305 (m-30) REVERT: B 3723 MET cc_start: 0.9358 (mmm) cc_final: 0.9050 (mmm) REVERT: B 3778 MET cc_start: 0.9564 (tmm) cc_final: 0.9326 (tmm) REVERT: B 3798 LEU cc_start: 0.9839 (mp) cc_final: 0.9386 (tt) REVERT: B 4047 MET cc_start: 0.9417 (tmm) cc_final: 0.9063 (ppp) REVERT: B 4184 MET cc_start: 0.9003 (tpp) cc_final: 0.8242 (tpp) REVERT: B 4244 GLU cc_start: 0.9168 (tm-30) cc_final: 0.8916 (tm-30) REVERT: B 4571 PHE cc_start: 0.9039 (m-80) cc_final: 0.8798 (m-80) REVERT: B 4639 MET cc_start: 0.9305 (mtp) cc_final: 0.9052 (mtp) REVERT: B 4704 LEU cc_start: 0.8752 (OUTLIER) cc_final: 0.8088 (pp) REVERT: B 4779 LYS cc_start: 0.9629 (OUTLIER) cc_final: 0.9249 (ptpp) REVERT: B 4818 MET cc_start: 0.8873 (tmm) cc_final: 0.8480 (tpp) REVERT: B 4874 MET cc_start: 0.8176 (mmm) cc_final: 0.7793 (mmm) REVERT: B 4879 MET cc_start: 0.8855 (mmm) cc_final: 0.8429 (tpp) REVERT: B 4880 MET cc_start: 0.8705 (ptp) cc_final: 0.8371 (ptp) REVERT: B 4887 MET cc_start: 0.8433 (mtp) cc_final: 0.8038 (mtm) REVERT: B 4954 MET cc_start: 0.9443 (tpp) cc_final: 0.9171 (tpp) REVERT: B 4967 TYR cc_start: 0.7763 (t80) cc_final: 0.7070 (t80) REVERT: B 4969 ASP cc_start: 0.9542 (m-30) cc_final: 0.9294 (m-30) REVERT: B 5013 MET cc_start: 0.9590 (mmm) cc_final: 0.9267 (mmm) REVERT: B 5032 TYR cc_start: 0.9232 (m-80) cc_final: 0.8940 (m-10) REVERT: C 155 LYS cc_start: 0.9539 (mmtt) cc_final: 0.9021 (tppt) REVERT: C 196 MET cc_start: 0.8742 (mpp) cc_final: 0.8461 (mpp) REVERT: C 228 ASP cc_start: 0.9605 (m-30) cc_final: 0.9400 (m-30) REVERT: C 343 GLU cc_start: 0.8844 (mt-10) cc_final: 0.8258 (mp0) REVERT: C 384 MET cc_start: 0.7091 (tmm) cc_final: 0.6720 (tmm) REVERT: C 565 TYR cc_start: 0.9293 (t80) cc_final: 0.9062 (t80) REVERT: C 601 ASP cc_start: 0.9111 (m-30) cc_final: 0.8877 (m-30) REVERT: C 667 MET cc_start: 0.9391 (tpp) cc_final: 0.8978 (tpp) REVERT: C 960 MET cc_start: 0.4582 (mmm) cc_final: 0.3059 (mtm) REVERT: C 961 MET cc_start: 0.7181 (pmm) cc_final: 0.6834 (pmm) REVERT: C 1260 MET cc_start: 0.8395 (mtm) cc_final: 0.7943 (mtm) REVERT: C 1573 MET cc_start: 0.8551 (tpt) cc_final: 0.8306 (tpt) REVERT: C 1601 MET cc_start: 0.9546 (tpp) cc_final: 0.9148 (tpp) REVERT: C 1986 MET cc_start: 0.7871 (ppp) cc_final: 0.7548 (pmm) REVERT: C 2198 MET cc_start: 0.9209 (mpp) cc_final: 0.8709 (mpp) REVERT: C 2203 MET cc_start: 0.9411 (pmm) cc_final: 0.9115 (pmm) REVERT: C 2228 MET cc_start: 0.9624 (ppp) cc_final: 0.9170 (ppp) REVERT: C 2293 GLN cc_start: 0.9472 (mm-40) cc_final: 0.9157 (tm-30) REVERT: C 2294 ASP cc_start: 0.9427 (m-30) cc_final: 0.8716 (m-30) REVERT: C 2440 MET cc_start: 0.9054 (OUTLIER) cc_final: 0.8812 (mmp) REVERT: C 2698 MET cc_start: 0.8437 (ppp) cc_final: 0.8210 (ppp) REVERT: C 2932 MET cc_start: 0.7138 (tpt) cc_final: 0.6756 (ptt) REVERT: C 3081 MET cc_start: 0.6128 (ptp) cc_final: 0.5502 (pmm) REVERT: C 3106 MET cc_start: 0.9021 (mmm) cc_final: 0.8698 (mmp) REVERT: C 3276 MET cc_start: 0.8062 (mmp) cc_final: 0.7477 (mmm) REVERT: C 3335 MET cc_start: 0.7966 (pmm) cc_final: 0.7762 (pmm) REVERT: C 3411 LEU cc_start: 0.9763 (pp) cc_final: 0.9339 (mm) REVERT: C 3675 ASP cc_start: 0.9511 (m-30) cc_final: 0.9305 (m-30) REVERT: C 3723 MET cc_start: 0.9358 (mmm) cc_final: 0.9048 (mmm) REVERT: C 3778 MET cc_start: 0.9565 (tmm) cc_final: 0.9326 (tmm) REVERT: C 3798 LEU cc_start: 0.9846 (mp) cc_final: 0.9389 (tt) REVERT: C 4047 MET cc_start: 0.9410 (tmm) cc_final: 0.9097 (ppp) REVERT: C 4190 ILE cc_start: 0.8973 (OUTLIER) cc_final: 0.8771 (mt) REVERT: C 4244 GLU cc_start: 0.9128 (tm-30) cc_final: 0.8918 (tm-30) REVERT: C 4571 PHE cc_start: 0.9037 (m-80) cc_final: 0.8798 (m-80) REVERT: C 4639 MET cc_start: 0.9305 (mtp) cc_final: 0.9053 (mtp) REVERT: C 4704 LEU cc_start: 0.8750 (OUTLIER) cc_final: 0.8085 (pp) REVERT: C 4779 LYS cc_start: 0.9628 (OUTLIER) cc_final: 0.9249 (ptpp) REVERT: C 4818 MET cc_start: 0.8873 (tmm) cc_final: 0.8473 (tpp) REVERT: C 4874 MET cc_start: 0.8175 (mmm) cc_final: 0.7794 (mmm) REVERT: C 4879 MET cc_start: 0.8845 (mmm) cc_final: 0.8451 (tpp) REVERT: C 4880 MET cc_start: 0.8687 (ptp) cc_final: 0.8343 (ptp) REVERT: C 4887 MET cc_start: 0.8457 (mtp) cc_final: 0.8080 (mtm) REVERT: C 4942 GLU cc_start: 0.8877 (OUTLIER) cc_final: 0.8219 (mm-30) REVERT: C 4954 MET cc_start: 0.9440 (tpp) cc_final: 0.9178 (tpp) REVERT: C 4969 ASP cc_start: 0.9515 (m-30) cc_final: 0.9268 (m-30) REVERT: C 4993 MET cc_start: 0.9096 (ptm) cc_final: 0.8887 (ppp) REVERT: C 5013 MET cc_start: 0.9592 (mmm) cc_final: 0.9276 (mmm) REVERT: D 155 LYS cc_start: 0.9538 (mmtt) cc_final: 0.9021 (tppt) REVERT: D 196 MET cc_start: 0.8742 (mpp) cc_final: 0.8461 (mpp) REVERT: D 228 ASP cc_start: 0.9610 (m-30) cc_final: 0.9402 (m-30) REVERT: D 343 GLU cc_start: 0.8845 (mt-10) cc_final: 0.8258 (mp0) REVERT: D 384 MET cc_start: 0.7094 (tmm) cc_final: 0.6724 (tmm) REVERT: D 565 TYR cc_start: 0.9294 (t80) cc_final: 0.9061 (t80) REVERT: D 601 ASP cc_start: 0.9111 (m-30) cc_final: 0.8877 (m-30) REVERT: D 667 MET cc_start: 0.9391 (tpp) cc_final: 0.8978 (tpp) REVERT: D 846 LEU cc_start: 0.8782 (OUTLIER) cc_final: 0.8555 (mp) REVERT: D 960 MET cc_start: 0.4593 (mmm) cc_final: 0.3063 (mtm) REVERT: D 961 MET cc_start: 0.7173 (pmm) cc_final: 0.6837 (pmm) REVERT: D 1260 MET cc_start: 0.8405 (mtm) cc_final: 0.7974 (mtm) REVERT: D 1573 MET cc_start: 0.8549 (tpt) cc_final: 0.8303 (tpt) REVERT: D 1601 MET cc_start: 0.9547 (tpp) cc_final: 0.9150 (tpp) REVERT: D 1986 MET cc_start: 0.7871 (ppp) cc_final: 0.7548 (pmm) REVERT: D 2198 MET cc_start: 0.9209 (mpp) cc_final: 0.8708 (mpp) REVERT: D 2203 MET cc_start: 0.9412 (pmm) cc_final: 0.9117 (pmm) REVERT: D 2228 MET cc_start: 0.9615 (ppp) cc_final: 0.9183 (ppp) REVERT: D 2293 GLN cc_start: 0.9472 (mm-40) cc_final: 0.9158 (tm-30) REVERT: D 2294 ASP cc_start: 0.9428 (m-30) cc_final: 0.8716 (m-30) REVERT: D 2440 MET cc_start: 0.9055 (OUTLIER) cc_final: 0.8814 (mmp) REVERT: D 2698 MET cc_start: 0.8437 (ppp) cc_final: 0.8211 (ppp) REVERT: D 2932 MET cc_start: 0.7138 (tpt) cc_final: 0.6755 (ptt) REVERT: D 3081 MET cc_start: 0.6534 (ptp) cc_final: 0.6262 (ptp) REVERT: D 3106 MET cc_start: 0.9021 (mmm) cc_final: 0.8698 (mmp) REVERT: D 3266 MET cc_start: 0.9335 (OUTLIER) cc_final: 0.9066 (ppp) REVERT: D 3276 MET cc_start: 0.8065 (mmp) cc_final: 0.7477 (mmm) REVERT: D 3411 LEU cc_start: 0.9764 (pp) cc_final: 0.9339 (mm) REVERT: D 3675 ASP cc_start: 0.9511 (m-30) cc_final: 0.9305 (m-30) REVERT: D 3723 MET cc_start: 0.9359 (mmm) cc_final: 0.9049 (mmm) REVERT: D 3778 MET cc_start: 0.9566 (tmm) cc_final: 0.9328 (tmm) REVERT: D 3798 LEU cc_start: 0.9847 (mp) cc_final: 0.9388 (tt) REVERT: D 4047 MET cc_start: 0.9418 (tmm) cc_final: 0.9063 (ppp) REVERT: D 4184 MET cc_start: 0.8963 (tpp) cc_final: 0.8185 (tpp) REVERT: D 4244 GLU cc_start: 0.9173 (tm-30) cc_final: 0.8914 (tm-30) REVERT: D 4571 PHE cc_start: 0.9031 (m-80) cc_final: 0.8792 (m-80) REVERT: D 4634 GLU cc_start: 0.5092 (OUTLIER) cc_final: 0.2893 (pt0) REVERT: D 4639 MET cc_start: 0.9320 (mtp) cc_final: 0.8743 (mtp) REVERT: D 4704 LEU cc_start: 0.8754 (OUTLIER) cc_final: 0.8087 (pp) REVERT: D 4779 LYS cc_start: 0.9629 (OUTLIER) cc_final: 0.9250 (ptpp) REVERT: D 4818 MET cc_start: 0.8877 (tmm) cc_final: 0.8487 (tpp) REVERT: D 4874 MET cc_start: 0.8174 (mmm) cc_final: 0.7793 (mmm) REVERT: D 4879 MET cc_start: 0.8836 (mmm) cc_final: 0.8445 (tpp) REVERT: D 4880 MET cc_start: 0.8686 (ptp) cc_final: 0.8345 (ptp) REVERT: D 4887 MET cc_start: 0.8460 (mtp) cc_final: 0.8088 (mtm) REVERT: D 4942 GLU cc_start: 0.8873 (OUTLIER) cc_final: 0.8211 (mm-30) REVERT: D 4954 MET cc_start: 0.9441 (tpp) cc_final: 0.9168 (tpp) REVERT: D 4969 ASP cc_start: 0.9516 (m-30) cc_final: 0.9262 (m-30) REVERT: D 5013 MET cc_start: 0.9591 (mmm) cc_final: 0.9268 (mmm) REVERT: D 5032 TYR cc_start: 0.9211 (m-80) cc_final: 0.8937 (m-10) REVERT: E 73 LYS cc_start: 0.9360 (tmtt) cc_final: 0.9096 (tppt) REVERT: F 73 LYS cc_start: 0.9360 (tmtt) cc_final: 0.9096 (tppt) REVERT: G 73 LYS cc_start: 0.9359 (tmtt) cc_final: 0.9097 (tppt) REVERT: H 73 LYS cc_start: 0.9345 (tmtt) cc_final: 0.9065 (tppt) outliers start: 176 outliers final: 122 residues processed: 1264 average time/residue: 1.1982 time to fit residues: 2755.9664 Evaluate side-chains 1234 residues out of total 15548 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 142 poor density : 1092 time to evaluate : 12.647 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 163 VAL Chi-restraints excluded: chain A residue 199 LEU Chi-restraints excluded: chain A residue 207 SER Chi-restraints excluded: chain A residue 334 MET Chi-restraints excluded: chain A residue 605 SER Chi-restraints excluded: chain A residue 845 CYS Chi-restraints excluded: chain A residue 1658 ASP Chi-restraints excluded: chain A residue 2440 MET Chi-restraints excluded: chain A residue 3192 GLU Chi-restraints excluded: chain A residue 3203 VAL Chi-restraints excluded: chain A residue 3456 GLN Chi-restraints excluded: chain A residue 3715 LYS Chi-restraints excluded: chain A residue 3782 MET Chi-restraints excluded: chain A residue 3898 ASP Chi-restraints excluded: chain A residue 4015 GLU Chi-restraints excluded: chain A residue 4059 LEU Chi-restraints excluded: chain A residue 4170 ILE Chi-restraints excluded: chain A residue 4198 SER Chi-restraints excluded: chain A residue 4200 THR Chi-restraints excluded: chain A residue 4580 TYR Chi-restraints excluded: chain A residue 4697 VAL Chi-restraints excluded: chain A residue 4704 LEU Chi-restraints excluded: chain A residue 4720 VAL Chi-restraints excluded: chain A residue 4731 ILE Chi-restraints excluded: chain A residue 4779 LYS Chi-restraints excluded: chain A residue 4837 LEU Chi-restraints excluded: chain A residue 4882 CYS Chi-restraints excluded: chain A residue 4891 VAL Chi-restraints excluded: chain A residue 4926 VAL Chi-restraints excluded: chain A residue 4942 GLU Chi-restraints excluded: chain A residue 4946 GLN Chi-restraints excluded: chain A residue 4949 GLN Chi-restraints excluded: chain A residue 4971 THR Chi-restraints excluded: chain B residue 163 VAL Chi-restraints excluded: chain B residue 199 LEU Chi-restraints excluded: chain B residue 207 SER Chi-restraints excluded: chain B residue 334 MET Chi-restraints excluded: chain B residue 605 SER Chi-restraints excluded: chain B residue 846 LEU Chi-restraints excluded: chain B residue 891 TRP Chi-restraints excluded: chain B residue 1658 ASP Chi-restraints excluded: chain B residue 2440 MET Chi-restraints excluded: chain B residue 3192 GLU Chi-restraints excluded: chain B residue 3203 VAL Chi-restraints excluded: chain B residue 3456 GLN Chi-restraints excluded: chain B residue 3715 LYS Chi-restraints excluded: chain B residue 3782 MET Chi-restraints excluded: chain B residue 3898 ASP Chi-restraints excluded: chain B residue 4015 GLU Chi-restraints excluded: chain B residue 4059 LEU Chi-restraints excluded: chain B residue 4170 ILE Chi-restraints excluded: chain B residue 4198 SER Chi-restraints excluded: chain B residue 4200 THR Chi-restraints excluded: chain B residue 4580 TYR Chi-restraints excluded: chain B residue 4697 VAL Chi-restraints excluded: chain B residue 4704 LEU Chi-restraints excluded: chain B residue 4720 VAL Chi-restraints excluded: chain B residue 4731 ILE Chi-restraints excluded: chain B residue 4779 LYS Chi-restraints excluded: chain B residue 4800 LEU Chi-restraints excluded: chain B residue 4882 CYS Chi-restraints excluded: chain B residue 4924 VAL Chi-restraints excluded: chain B residue 4926 VAL Chi-restraints excluded: chain B residue 4929 LEU Chi-restraints excluded: chain B residue 4942 GLU Chi-restraints excluded: chain B residue 4971 THR Chi-restraints excluded: chain C residue 163 VAL Chi-restraints excluded: chain C residue 199 LEU Chi-restraints excluded: chain C residue 207 SER Chi-restraints excluded: chain C residue 334 MET Chi-restraints excluded: chain C residue 605 SER Chi-restraints excluded: chain C residue 846 LEU Chi-restraints excluded: chain C residue 891 TRP Chi-restraints excluded: chain C residue 1658 ASP Chi-restraints excluded: chain C residue 2440 MET Chi-restraints excluded: chain C residue 3192 GLU Chi-restraints excluded: chain C residue 3203 VAL Chi-restraints excluded: chain C residue 3456 GLN Chi-restraints excluded: chain C residue 3715 LYS Chi-restraints excluded: chain C residue 3782 MET Chi-restraints excluded: chain C residue 3898 ASP Chi-restraints excluded: chain C residue 4015 GLU Chi-restraints excluded: chain C residue 4059 LEU Chi-restraints excluded: chain C residue 4170 ILE Chi-restraints excluded: chain C residue 4190 ILE Chi-restraints excluded: chain C residue 4198 SER Chi-restraints excluded: chain C residue 4200 THR Chi-restraints excluded: chain C residue 4580 TYR Chi-restraints excluded: chain C residue 4697 VAL Chi-restraints excluded: chain C residue 4704 LEU Chi-restraints excluded: chain C residue 4720 VAL Chi-restraints excluded: chain C residue 4731 ILE Chi-restraints excluded: chain C residue 4779 LYS Chi-restraints excluded: chain C residue 4800 LEU Chi-restraints excluded: chain C residue 4837 LEU Chi-restraints excluded: chain C residue 4882 CYS Chi-restraints excluded: chain C residue 4924 VAL Chi-restraints excluded: chain C residue 4926 VAL Chi-restraints excluded: chain C residue 4929 LEU Chi-restraints excluded: chain C residue 4942 GLU Chi-restraints excluded: chain C residue 4971 THR Chi-restraints excluded: chain D residue 163 VAL Chi-restraints excluded: chain D residue 199 LEU Chi-restraints excluded: chain D residue 207 SER Chi-restraints excluded: chain D residue 334 MET Chi-restraints excluded: chain D residue 605 SER Chi-restraints excluded: chain D residue 846 LEU Chi-restraints excluded: chain D residue 891 TRP Chi-restraints excluded: chain D residue 1658 ASP Chi-restraints excluded: chain D residue 2440 MET Chi-restraints excluded: chain D residue 3192 GLU Chi-restraints excluded: chain D residue 3203 VAL Chi-restraints excluded: chain D residue 3266 MET Chi-restraints excluded: chain D residue 3456 GLN Chi-restraints excluded: chain D residue 3715 LYS Chi-restraints excluded: chain D residue 3782 MET Chi-restraints excluded: chain D residue 3898 ASP Chi-restraints excluded: chain D residue 4015 GLU Chi-restraints excluded: chain D residue 4059 LEU Chi-restraints excluded: chain D residue 4170 ILE Chi-restraints excluded: chain D residue 4198 SER Chi-restraints excluded: chain D residue 4200 THR Chi-restraints excluded: chain D residue 4555 LEU Chi-restraints excluded: chain D residue 4580 TYR Chi-restraints excluded: chain D residue 4634 GLU Chi-restraints excluded: chain D residue 4697 VAL Chi-restraints excluded: chain D residue 4704 LEU Chi-restraints excluded: chain D residue 4720 VAL Chi-restraints excluded: chain D residue 4731 ILE Chi-restraints excluded: chain D residue 4779 LYS Chi-restraints excluded: chain D residue 4800 LEU Chi-restraints excluded: chain D residue 4837 LEU Chi-restraints excluded: chain D residue 4882 CYS Chi-restraints excluded: chain D residue 4924 VAL Chi-restraints excluded: chain D residue 4926 VAL Chi-restraints excluded: chain D residue 4929 LEU Chi-restraints excluded: chain D residue 4942 GLU Chi-restraints excluded: chain D residue 4971 THR Chi-restraints excluded: chain E residue 79 ASP Chi-restraints excluded: chain F residue 79 ASP Chi-restraints excluded: chain G residue 79 ASP Chi-restraints excluded: chain H residue 79 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1788 random chunks: chunk 1439 optimal weight: 0.0270 chunk 981 optimal weight: 8.9990 chunk 25 optimal weight: 1.9990 chunk 1286 optimal weight: 6.9990 chunk 713 optimal weight: 30.0000 chunk 1474 optimal weight: 7.9990 chunk 1194 optimal weight: 20.0000 chunk 2 optimal weight: 7.9990 chunk 882 optimal weight: 10.0000 chunk 1551 optimal weight: 6.9990 chunk 436 optimal weight: 5.9990 overall best weight: 4.4046 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 226 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 284 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 475 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 533 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 838 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 877 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1299 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1300 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2213 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2247 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2931 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2933 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4201 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 226 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 284 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 475 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 533 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 838 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 877 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1299 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1300 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2247 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2931 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2933 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 226 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 284 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 838 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 877 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1299 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1300 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C1614 GLN ** C2213 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2247 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2931 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2933 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C4864 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C4933 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 226 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 284 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 475 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 533 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 877 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1299 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1300 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2247 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2931 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2933 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D3318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D4864 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D4933 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8477 moved from start: 0.2480 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 146196 Z= 0.253 Angle : 0.682 16.137 198016 Z= 0.342 Chirality : 0.042 0.329 21760 Planarity : 0.005 0.072 25752 Dihedral : 5.089 80.415 19628 Min Nonbonded Distance : 2.064 Molprobity Statistics. All-atom Clashscore : 19.96 Ramachandran Plot: Outliers : 0.01 % Allowed : 4.79 % Favored : 95.20 % Rotamer: Outliers : 1.56 % Allowed : 13.40 % Favored : 85.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.45 % Cis-general : 0.00 % Twisted Proline : 0.34 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.06 (0.06), residues: 17832 helix: 0.80 (0.06), residues: 8824 sheet: -0.76 (0.12), residues: 1776 loop : -0.80 (0.07), residues: 7232 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B1143 HIS 0.007 0.001 HIS D3771 PHE 0.046 0.002 PHE A4571 TYR 0.019 0.002 TYR C4967 ARG 0.012 0.000 ARG A1180 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 35664 Ramachandran restraints generated. 17832 Oldfield, 0 Emsley, 17832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 35664 Ramachandran restraints generated. 17832 Oldfield, 0 Emsley, 17832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1338 residues out of total 15548 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 223 poor density : 1115 time to evaluate : 12.626 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 155 LYS cc_start: 0.9548 (mmtt) cc_final: 0.9088 (tppt) REVERT: A 196 MET cc_start: 0.8742 (mpp) cc_final: 0.8411 (mpp) REVERT: A 213 TYR cc_start: 0.8300 (m-80) cc_final: 0.7374 (m-80) REVERT: A 228 ASP cc_start: 0.9424 (m-30) cc_final: 0.9156 (m-30) REVERT: A 340 LYS cc_start: 0.9240 (mmmm) cc_final: 0.9001 (mmmt) REVERT: A 343 GLU cc_start: 0.8758 (OUTLIER) cc_final: 0.8293 (mp0) REVERT: A 565 TYR cc_start: 0.9258 (t80) cc_final: 0.8964 (t80) REVERT: A 667 MET cc_start: 0.9326 (tpp) cc_final: 0.8816 (tpp) REVERT: A 960 MET cc_start: 0.5558 (mmm) cc_final: 0.3715 (mtm) REVERT: A 961 MET cc_start: 0.6900 (pmm) cc_final: 0.6448 (pmm) REVERT: A 1260 MET cc_start: 0.9132 (mtm) cc_final: 0.8876 (mtm) REVERT: A 1573 MET cc_start: 0.8486 (tpt) cc_final: 0.8047 (tpt) REVERT: A 1601 MET cc_start: 0.9638 (tpt) cc_final: 0.9216 (tpp) REVERT: A 2228 MET cc_start: 0.9631 (ppp) cc_final: 0.9172 (ppp) REVERT: A 2355 ARG cc_start: 0.9707 (ttm-80) cc_final: 0.9305 (ttm110) REVERT: A 2440 MET cc_start: 0.9084 (OUTLIER) cc_final: 0.8851 (mmp) REVERT: A 2698 MET cc_start: 0.8459 (ppp) cc_final: 0.8246 (ppp) REVERT: A 2932 MET cc_start: 0.7182 (tpt) cc_final: 0.6796 (ptt) REVERT: A 3276 MET cc_start: 0.8082 (mmp) cc_final: 0.7549 (mmm) REVERT: A 3411 LEU cc_start: 0.9758 (pp) cc_final: 0.9298 (mm) REVERT: A 3675 ASP cc_start: 0.9532 (m-30) cc_final: 0.9332 (m-30) REVERT: A 3778 MET cc_start: 0.9579 (tmm) cc_final: 0.9350 (tmm) REVERT: A 3798 LEU cc_start: 0.9815 (mp) cc_final: 0.9334 (tt) REVERT: A 3816 MET cc_start: 0.9625 (mmt) cc_final: 0.9142 (mmp) REVERT: A 4184 MET cc_start: 0.9046 (tpp) cc_final: 0.8401 (tpp) REVERT: A 4627 MET cc_start: 0.8937 (pmm) cc_final: 0.8616 (pmm) REVERT: A 4639 MET cc_start: 0.9338 (mtp) cc_final: 0.9078 (mtp) REVERT: A 4704 LEU cc_start: 0.8775 (OUTLIER) cc_final: 0.8093 (pp) REVERT: A 4779 LYS cc_start: 0.9617 (OUTLIER) cc_final: 0.9225 (ptpp) REVERT: A 4798 MET cc_start: 0.9565 (tpp) cc_final: 0.9270 (mmm) REVERT: A 4818 MET cc_start: 0.8963 (tmm) cc_final: 0.8477 (tpp) REVERT: A 4839 MET cc_start: 0.8954 (ppp) cc_final: 0.8695 (ppp) REVERT: A 4874 MET cc_start: 0.8301 (mmm) cc_final: 0.8035 (mmm) REVERT: A 4879 MET cc_start: 0.8866 (mmm) cc_final: 0.8266 (tpp) REVERT: A 4880 MET cc_start: 0.8628 (ptp) cc_final: 0.8275 (mpp) REVERT: A 4911 LEU cc_start: 0.9315 (OUTLIER) cc_final: 0.8960 (pt) REVERT: A 4949 GLN cc_start: 0.9433 (OUTLIER) cc_final: 0.9191 (tp40) REVERT: A 4954 MET cc_start: 0.9420 (tpp) cc_final: 0.9152 (tpp) REVERT: A 4967 TYR cc_start: 0.7987 (t80) cc_final: 0.7211 (t80) REVERT: A 4969 ASP cc_start: 0.9532 (m-30) cc_final: 0.9265 (m-30) REVERT: A 4993 MET cc_start: 0.9151 (ptm) cc_final: 0.8831 (ppp) REVERT: A 5013 MET cc_start: 0.9590 (mmm) cc_final: 0.9320 (mmm) REVERT: B 155 LYS cc_start: 0.9543 (mmtt) cc_final: 0.9071 (tppt) REVERT: B 196 MET cc_start: 0.8718 (mpp) cc_final: 0.8368 (mpp) REVERT: B 228 ASP cc_start: 0.9604 (m-30) cc_final: 0.9205 (m-30) REVERT: B 343 GLU cc_start: 0.8876 (mt-10) cc_final: 0.8329 (mp0) REVERT: B 384 MET cc_start: 0.7117 (tmm) cc_final: 0.6804 (tmm) REVERT: B 667 MET cc_start: 0.9356 (tpp) cc_final: 0.8885 (tpp) REVERT: B 941 MET cc_start: 0.5456 (tpt) cc_final: 0.3989 (mmp) REVERT: B 960 MET cc_start: 0.4996 (mmm) cc_final: 0.3429 (mtm) REVERT: B 961 MET cc_start: 0.6779 (pmm) cc_final: 0.6392 (pmm) REVERT: B 1100 MET cc_start: 0.8351 (mpp) cc_final: 0.7950 (mpp) REVERT: B 1573 MET cc_start: 0.8502 (tpt) cc_final: 0.8100 (tpt) REVERT: B 1601 MET cc_start: 0.9570 (tpp) cc_final: 0.9139 (tpp) REVERT: B 2198 MET cc_start: 0.9167 (mpp) cc_final: 0.8941 (mpp) REVERT: B 2228 MET cc_start: 0.9604 (ppp) cc_final: 0.9169 (ppp) REVERT: B 2293 GLN cc_start: 0.9488 (mm-40) cc_final: 0.9153 (tm-30) REVERT: B 2294 ASP cc_start: 0.9434 (m-30) cc_final: 0.8751 (m-30) REVERT: B 2355 ARG cc_start: 0.9710 (ttm-80) cc_final: 0.9305 (ttm110) REVERT: B 2440 MET cc_start: 0.9081 (OUTLIER) cc_final: 0.8852 (mmp) REVERT: B 2618 MET cc_start: 0.8744 (mpp) cc_final: 0.8439 (mpp) REVERT: B 2639 MET cc_start: 0.9388 (ppp) cc_final: 0.8848 (pmm) REVERT: B 2698 MET cc_start: 0.8468 (ppp) cc_final: 0.8241 (ppp) REVERT: B 2932 MET cc_start: 0.7142 (tpt) cc_final: 0.6762 (ptt) REVERT: B 3081 MET cc_start: 0.6578 (ptp) cc_final: 0.5933 (pmm) REVERT: B 3106 MET cc_start: 0.9048 (mmm) cc_final: 0.8674 (mmp) REVERT: B 3276 MET cc_start: 0.8081 (mmp) cc_final: 0.7511 (mmm) REVERT: B 3411 LEU cc_start: 0.9766 (pp) cc_final: 0.9339 (mm) REVERT: B 3778 MET cc_start: 0.9590 (tmm) cc_final: 0.9342 (tmm) REVERT: B 3798 LEU cc_start: 0.9822 (mp) cc_final: 0.9430 (tt) REVERT: B 4023 MET cc_start: 0.9392 (tmm) cc_final: 0.8825 (tmm) REVERT: B 4047 MET cc_start: 0.9461 (tmm) cc_final: 0.9111 (ppp) REVERT: B 4184 MET cc_start: 0.9060 (tpp) cc_final: 0.8360 (tpp) REVERT: B 4244 GLU cc_start: 0.9225 (tm-30) cc_final: 0.8958 (tm-30) REVERT: B 4245 MET cc_start: 0.9198 (mmm) cc_final: 0.8840 (mmm) REVERT: B 4571 PHE cc_start: 0.9068 (m-80) cc_final: 0.8809 (m-80) REVERT: B 4639 MET cc_start: 0.9334 (mtp) cc_final: 0.9060 (mtp) REVERT: B 4779 LYS cc_start: 0.9623 (OUTLIER) cc_final: 0.9252 (ptpp) REVERT: B 4818 MET cc_start: 0.8987 (tmm) cc_final: 0.8550 (tpp) REVERT: B 4874 MET cc_start: 0.8194 (mmm) cc_final: 0.7737 (mmm) REVERT: B 4879 MET cc_start: 0.8809 (mmm) cc_final: 0.8379 (tpp) REVERT: B 4880 MET cc_start: 0.8591 (ptp) cc_final: 0.8254 (ptp) REVERT: B 4911 LEU cc_start: 0.9272 (OUTLIER) cc_final: 0.8965 (pt) REVERT: B 4954 MET cc_start: 0.9439 (tpp) cc_final: 0.9188 (tpp) REVERT: B 4967 TYR cc_start: 0.8006 (t80) cc_final: 0.7213 (t80) REVERT: B 4969 ASP cc_start: 0.9524 (m-30) cc_final: 0.9241 (m-30) REVERT: B 5013 MET cc_start: 0.9588 (mmm) cc_final: 0.9294 (mmm) REVERT: C 155 LYS cc_start: 0.9567 (mmtt) cc_final: 0.9026 (tppt) REVERT: C 196 MET cc_start: 0.8721 (mpp) cc_final: 0.8367 (mpp) REVERT: C 228 ASP cc_start: 0.9604 (m-30) cc_final: 0.9206 (m-30) REVERT: C 343 GLU cc_start: 0.8881 (mt-10) cc_final: 0.8320 (mp0) REVERT: C 384 MET cc_start: 0.7117 (tmm) cc_final: 0.6805 (tmm) REVERT: C 565 TYR cc_start: 0.9274 (t80) cc_final: 0.9029 (t80) REVERT: C 667 MET cc_start: 0.9356 (tpp) cc_final: 0.8886 (tpp) REVERT: C 941 MET cc_start: 0.5456 (tpt) cc_final: 0.3992 (mmp) REVERT: C 960 MET cc_start: 0.4961 (mmm) cc_final: 0.3408 (mtm) REVERT: C 961 MET cc_start: 0.6773 (pmm) cc_final: 0.6386 (pmm) REVERT: C 1100 MET cc_start: 0.8355 (mpp) cc_final: 0.7954 (mpp) REVERT: C 1260 MET cc_start: 0.8346 (mtm) cc_final: 0.7872 (mtm) REVERT: C 1573 MET cc_start: 0.8499 (tpt) cc_final: 0.8098 (tpt) REVERT: C 1601 MET cc_start: 0.9571 (tpp) cc_final: 0.9139 (tpp) REVERT: C 2198 MET cc_start: 0.9166 (mpp) cc_final: 0.8943 (mpp) REVERT: C 2228 MET cc_start: 0.9624 (ppp) cc_final: 0.9182 (ppp) REVERT: C 2293 GLN cc_start: 0.9489 (mm-40) cc_final: 0.9153 (tm-30) REVERT: C 2294 ASP cc_start: 0.9433 (m-30) cc_final: 0.8750 (m-30) REVERT: C 2355 ARG cc_start: 0.9710 (ttm-80) cc_final: 0.9305 (ttm110) REVERT: C 2440 MET cc_start: 0.9083 (OUTLIER) cc_final: 0.8858 (mmp) REVERT: C 2618 MET cc_start: 0.8745 (mpp) cc_final: 0.8439 (mpp) REVERT: C 2639 MET cc_start: 0.9387 (ppp) cc_final: 0.8847 (pmm) REVERT: C 2698 MET cc_start: 0.8467 (ppp) cc_final: 0.8240 (ppp) REVERT: C 2932 MET cc_start: 0.7143 (tpt) cc_final: 0.6764 (ptt) REVERT: C 3081 MET cc_start: 0.6579 (ptp) cc_final: 0.5932 (pmm) REVERT: C 3106 MET cc_start: 0.9050 (mmm) cc_final: 0.8676 (mmp) REVERT: C 3276 MET cc_start: 0.8082 (mmp) cc_final: 0.7513 (mmm) REVERT: C 3411 LEU cc_start: 0.9766 (pp) cc_final: 0.9340 (mm) REVERT: C 3778 MET cc_start: 0.9591 (tmm) cc_final: 0.9342 (tmm) REVERT: C 3798 LEU cc_start: 0.9832 (mp) cc_final: 0.9436 (tt) REVERT: C 4047 MET cc_start: 0.9459 (tmm) cc_final: 0.9114 (ppp) REVERT: C 4184 MET cc_start: 0.8990 (tpp) cc_final: 0.8175 (tpp) REVERT: C 4190 ILE cc_start: 0.9051 (OUTLIER) cc_final: 0.8743 (mt) REVERT: C 4244 GLU cc_start: 0.9168 (tm-30) cc_final: 0.8965 (tm-30) REVERT: C 4571 PHE cc_start: 0.9065 (m-80) cc_final: 0.8807 (m-80) REVERT: C 4639 MET cc_start: 0.9334 (mtp) cc_final: 0.9061 (mtp) REVERT: C 4779 LYS cc_start: 0.9624 (OUTLIER) cc_final: 0.9250 (ptpp) REVERT: C 4818 MET cc_start: 0.8990 (tmm) cc_final: 0.8544 (tpp) REVERT: C 4874 MET cc_start: 0.8191 (mmm) cc_final: 0.7736 (mmm) REVERT: C 4879 MET cc_start: 0.8809 (mmm) cc_final: 0.8345 (tpp) REVERT: C 4880 MET cc_start: 0.8657 (ptp) cc_final: 0.8362 (ptp) REVERT: C 4911 LEU cc_start: 0.9277 (OUTLIER) cc_final: 0.8971 (pt) REVERT: C 4954 MET cc_start: 0.9442 (tpp) cc_final: 0.9176 (tpp) REVERT: C 4969 ASP cc_start: 0.9521 (m-30) cc_final: 0.9236 (m-30) REVERT: C 5013 MET cc_start: 0.9590 (mmm) cc_final: 0.9293 (mmm) REVERT: D 155 LYS cc_start: 0.9566 (mmtt) cc_final: 0.9026 (tppt) REVERT: D 196 MET cc_start: 0.8722 (mpp) cc_final: 0.8369 (mpp) REVERT: D 228 ASP cc_start: 0.9606 (m-30) cc_final: 0.9204 (m-30) REVERT: D 343 GLU cc_start: 0.8881 (mt-10) cc_final: 0.8320 (mp0) REVERT: D 384 MET cc_start: 0.7118 (tmm) cc_final: 0.6805 (tmm) REVERT: D 565 TYR cc_start: 0.9275 (t80) cc_final: 0.9029 (t80) REVERT: D 667 MET cc_start: 0.9356 (tpp) cc_final: 0.8887 (tpp) REVERT: D 941 MET cc_start: 0.5457 (tpt) cc_final: 0.3992 (mmp) REVERT: D 960 MET cc_start: 0.4959 (mmm) cc_final: 0.3406 (mtm) REVERT: D 961 MET cc_start: 0.6775 (pmm) cc_final: 0.6386 (pmm) REVERT: D 1100 MET cc_start: 0.8284 (mpp) cc_final: 0.7851 (mpp) REVERT: D 1573 MET cc_start: 0.8500 (tpt) cc_final: 0.8101 (tpt) REVERT: D 1601 MET cc_start: 0.9571 (tpp) cc_final: 0.9140 (tpp) REVERT: D 2198 MET cc_start: 0.9166 (mpp) cc_final: 0.8943 (mpp) REVERT: D 2228 MET cc_start: 0.9605 (ppp) cc_final: 0.9171 (ppp) REVERT: D 2293 GLN cc_start: 0.9489 (mm-40) cc_final: 0.9153 (tm-30) REVERT: D 2294 ASP cc_start: 0.9433 (m-30) cc_final: 0.8750 (m-30) REVERT: D 2355 ARG cc_start: 0.9710 (ttm-80) cc_final: 0.9305 (ttm110) REVERT: D 2440 MET cc_start: 0.9085 (OUTLIER) cc_final: 0.8858 (mmp) REVERT: D 2639 MET cc_start: 0.9387 (ppp) cc_final: 0.8846 (pmm) REVERT: D 2698 MET cc_start: 0.8469 (ppp) cc_final: 0.8240 (ppp) REVERT: D 2932 MET cc_start: 0.7141 (tpt) cc_final: 0.6762 (ptt) REVERT: D 3106 MET cc_start: 0.9049 (mmm) cc_final: 0.8674 (mmp) REVERT: D 3266 MET cc_start: 0.9340 (OUTLIER) cc_final: 0.9028 (ppp) REVERT: D 3276 MET cc_start: 0.8097 (mmp) cc_final: 0.7528 (mmm) REVERT: D 3335 MET cc_start: 0.7566 (pmm) cc_final: 0.6368 (pmm) REVERT: D 3411 LEU cc_start: 0.9766 (pp) cc_final: 0.9340 (mm) REVERT: D 3778 MET cc_start: 0.9591 (tmm) cc_final: 0.9342 (tmm) REVERT: D 3798 LEU cc_start: 0.9832 (mp) cc_final: 0.9435 (tt) REVERT: D 4023 MET cc_start: 0.9391 (tmm) cc_final: 0.8824 (tmm) REVERT: D 4047 MET cc_start: 0.9461 (tmm) cc_final: 0.9111 (ppp) REVERT: D 4184 MET cc_start: 0.9056 (tpp) cc_final: 0.8351 (tpp) REVERT: D 4245 MET cc_start: 0.9199 (mmm) cc_final: 0.8842 (mmm) REVERT: D 4571 PHE cc_start: 0.9061 (m-80) cc_final: 0.8802 (m-80) REVERT: D 4639 MET cc_start: 0.9357 (mtp) cc_final: 0.8877 (mtp) REVERT: D 4779 LYS cc_start: 0.9623 (OUTLIER) cc_final: 0.9250 (ptpp) REVERT: D 4818 MET cc_start: 0.9045 (tmm) cc_final: 0.8612 (tpp) REVERT: D 4874 MET cc_start: 0.8190 (mmm) cc_final: 0.7733 (mmm) REVERT: D 4879 MET cc_start: 0.8802 (mmm) cc_final: 0.8342 (tpp) REVERT: D 4880 MET cc_start: 0.8576 (ptp) cc_final: 0.8312 (ptp) REVERT: D 4911 LEU cc_start: 0.9276 (OUTLIER) cc_final: 0.8970 (pt) REVERT: D 4942 GLU cc_start: 0.8913 (OUTLIER) cc_final: 0.8213 (mm-30) REVERT: D 4954 MET cc_start: 0.9438 (tpp) cc_final: 0.9173 (tpp) REVERT: D 4969 ASP cc_start: 0.9522 (m-30) cc_final: 0.9220 (m-30) REVERT: D 5013 MET cc_start: 0.9589 (mmm) cc_final: 0.9295 (mmm) REVERT: E 73 LYS cc_start: 0.9369 (tmtt) cc_final: 0.9118 (tppt) REVERT: F 73 LYS cc_start: 0.9368 (tmtt) cc_final: 0.9119 (tppt) REVERT: G 73 LYS cc_start: 0.9369 (tmtt) cc_final: 0.9119 (tppt) outliers start: 223 outliers final: 153 residues processed: 1264 average time/residue: 1.1701 time to fit residues: 2681.9034 Evaluate side-chains 1253 residues out of total 15548 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 171 poor density : 1082 time to evaluate : 12.583 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 199 LEU Chi-restraints excluded: chain A residue 207 SER Chi-restraints excluded: chain A residue 334 MET Chi-restraints excluded: chain A residue 343 GLU Chi-restraints excluded: chain A residue 605 SER Chi-restraints excluded: chain A residue 845 CYS Chi-restraints excluded: chain A residue 1248 VAL Chi-restraints excluded: chain A residue 1289 LEU Chi-restraints excluded: chain A residue 1608 MET Chi-restraints excluded: chain A residue 1658 ASP Chi-restraints excluded: chain A residue 2440 MET Chi-restraints excluded: chain A residue 3192 GLU Chi-restraints excluded: chain A residue 3203 VAL Chi-restraints excluded: chain A residue 3456 GLN Chi-restraints excluded: chain A residue 3606 LEU Chi-restraints excluded: chain A residue 3715 LYS Chi-restraints excluded: chain A residue 3782 MET Chi-restraints excluded: chain A residue 3898 ASP Chi-restraints excluded: chain A residue 4059 LEU Chi-restraints excluded: chain A residue 4170 ILE Chi-restraints excluded: chain A residue 4198 SER Chi-restraints excluded: chain A residue 4200 THR Chi-restraints excluded: chain A residue 4555 LEU Chi-restraints excluded: chain A residue 4580 TYR Chi-restraints excluded: chain A residue 4656 LEU Chi-restraints excluded: chain A residue 4697 VAL Chi-restraints excluded: chain A residue 4704 LEU Chi-restraints excluded: chain A residue 4717 ASP Chi-restraints excluded: chain A residue 4720 VAL Chi-restraints excluded: chain A residue 4731 ILE Chi-restraints excluded: chain A residue 4779 LYS Chi-restraints excluded: chain A residue 4837 LEU Chi-restraints excluded: chain A residue 4882 CYS Chi-restraints excluded: chain A residue 4891 VAL Chi-restraints excluded: chain A residue 4911 LEU Chi-restraints excluded: chain A residue 4926 VAL Chi-restraints excluded: chain A residue 4929 LEU Chi-restraints excluded: chain A residue 4942 GLU Chi-restraints excluded: chain A residue 4946 GLN Chi-restraints excluded: chain A residue 4949 GLN Chi-restraints excluded: chain A residue 4960 ILE Chi-restraints excluded: chain A residue 4971 THR Chi-restraints excluded: chain B residue 199 LEU Chi-restraints excluded: chain B residue 207 SER Chi-restraints excluded: chain B residue 334 MET Chi-restraints excluded: chain B residue 605 SER Chi-restraints excluded: chain B residue 845 CYS Chi-restraints excluded: chain B residue 846 LEU Chi-restraints excluded: chain B residue 891 TRP Chi-restraints excluded: chain B residue 1248 VAL Chi-restraints excluded: chain B residue 1289 LEU Chi-restraints excluded: chain B residue 1658 ASP Chi-restraints excluded: chain B residue 2377 LEU Chi-restraints excluded: chain B residue 2440 MET Chi-restraints excluded: chain B residue 3192 GLU Chi-restraints excluded: chain B residue 3203 VAL Chi-restraints excluded: chain B residue 3456 GLN Chi-restraints excluded: chain B residue 3606 LEU Chi-restraints excluded: chain B residue 3715 LYS Chi-restraints excluded: chain B residue 3782 MET Chi-restraints excluded: chain B residue 3898 ASP Chi-restraints excluded: chain B residue 4059 LEU Chi-restraints excluded: chain B residue 4170 ILE Chi-restraints excluded: chain B residue 4198 SER Chi-restraints excluded: chain B residue 4200 THR Chi-restraints excluded: chain B residue 4555 LEU Chi-restraints excluded: chain B residue 4561 THR Chi-restraints excluded: chain B residue 4580 TYR Chi-restraints excluded: chain B residue 4656 LEU Chi-restraints excluded: chain B residue 4697 VAL Chi-restraints excluded: chain B residue 4704 LEU Chi-restraints excluded: chain B residue 4717 ASP Chi-restraints excluded: chain B residue 4720 VAL Chi-restraints excluded: chain B residue 4731 ILE Chi-restraints excluded: chain B residue 4779 LYS Chi-restraints excluded: chain B residue 4800 LEU Chi-restraints excluded: chain B residue 4882 CYS Chi-restraints excluded: chain B residue 4911 LEU Chi-restraints excluded: chain B residue 4924 VAL Chi-restraints excluded: chain B residue 4929 LEU Chi-restraints excluded: chain B residue 4942 GLU Chi-restraints excluded: chain B residue 4960 ILE Chi-restraints excluded: chain B residue 4971 THR Chi-restraints excluded: chain C residue 199 LEU Chi-restraints excluded: chain C residue 207 SER Chi-restraints excluded: chain C residue 334 MET Chi-restraints excluded: chain C residue 605 SER Chi-restraints excluded: chain C residue 845 CYS Chi-restraints excluded: chain C residue 846 LEU Chi-restraints excluded: chain C residue 891 TRP Chi-restraints excluded: chain C residue 1248 VAL Chi-restraints excluded: chain C residue 1289 LEU Chi-restraints excluded: chain C residue 1658 ASP Chi-restraints excluded: chain C residue 2440 MET Chi-restraints excluded: chain C residue 3192 GLU Chi-restraints excluded: chain C residue 3203 VAL Chi-restraints excluded: chain C residue 3456 GLN Chi-restraints excluded: chain C residue 3606 LEU Chi-restraints excluded: chain C residue 3715 LYS Chi-restraints excluded: chain C residue 3782 MET Chi-restraints excluded: chain C residue 3898 ASP Chi-restraints excluded: chain C residue 4015 GLU Chi-restraints excluded: chain C residue 4059 LEU Chi-restraints excluded: chain C residue 4170 ILE Chi-restraints excluded: chain C residue 4190 ILE Chi-restraints excluded: chain C residue 4198 SER Chi-restraints excluded: chain C residue 4200 THR Chi-restraints excluded: chain C residue 4555 LEU Chi-restraints excluded: chain C residue 4561 THR Chi-restraints excluded: chain C residue 4580 TYR Chi-restraints excluded: chain C residue 4656 LEU Chi-restraints excluded: chain C residue 4697 VAL Chi-restraints excluded: chain C residue 4704 LEU Chi-restraints excluded: chain C residue 4717 ASP Chi-restraints excluded: chain C residue 4720 VAL Chi-restraints excluded: chain C residue 4731 ILE Chi-restraints excluded: chain C residue 4779 LYS Chi-restraints excluded: chain C residue 4800 LEU Chi-restraints excluded: chain C residue 4882 CYS Chi-restraints excluded: chain C residue 4911 LEU Chi-restraints excluded: chain C residue 4924 VAL Chi-restraints excluded: chain C residue 4929 LEU Chi-restraints excluded: chain C residue 4942 GLU Chi-restraints excluded: chain C residue 4960 ILE Chi-restraints excluded: chain C residue 4971 THR Chi-restraints excluded: chain D residue 199 LEU Chi-restraints excluded: chain D residue 207 SER Chi-restraints excluded: chain D residue 334 MET Chi-restraints excluded: chain D residue 605 SER Chi-restraints excluded: chain D residue 845 CYS Chi-restraints excluded: chain D residue 846 LEU Chi-restraints excluded: chain D residue 891 TRP Chi-restraints excluded: chain D residue 1248 VAL Chi-restraints excluded: chain D residue 1289 LEU Chi-restraints excluded: chain D residue 1658 ASP Chi-restraints excluded: chain D residue 2301 TYR Chi-restraints excluded: chain D residue 2377 LEU Chi-restraints excluded: chain D residue 2440 MET Chi-restraints excluded: chain D residue 3192 GLU Chi-restraints excluded: chain D residue 3203 VAL Chi-restraints excluded: chain D residue 3266 MET Chi-restraints excluded: chain D residue 3456 GLN Chi-restraints excluded: chain D residue 3606 LEU Chi-restraints excluded: chain D residue 3715 LYS Chi-restraints excluded: chain D residue 3782 MET Chi-restraints excluded: chain D residue 3898 ASP Chi-restraints excluded: chain D residue 4059 LEU Chi-restraints excluded: chain D residue 4170 ILE Chi-restraints excluded: chain D residue 4198 SER Chi-restraints excluded: chain D residue 4200 THR Chi-restraints excluded: chain D residue 4561 THR Chi-restraints excluded: chain D residue 4580 TYR Chi-restraints excluded: chain D residue 4656 LEU Chi-restraints excluded: chain D residue 4697 VAL Chi-restraints excluded: chain D residue 4704 LEU Chi-restraints excluded: chain D residue 4717 ASP Chi-restraints excluded: chain D residue 4720 VAL Chi-restraints excluded: chain D residue 4731 ILE Chi-restraints excluded: chain D residue 4779 LYS Chi-restraints excluded: chain D residue 4800 LEU Chi-restraints excluded: chain D residue 4882 CYS Chi-restraints excluded: chain D residue 4911 LEU Chi-restraints excluded: chain D residue 4924 VAL Chi-restraints excluded: chain D residue 4929 LEU Chi-restraints excluded: chain D residue 4942 GLU Chi-restraints excluded: chain D residue 4960 ILE Chi-restraints excluded: chain D residue 4971 THR Chi-restraints excluded: chain E residue 79 ASP Chi-restraints excluded: chain F residue 79 ASP Chi-restraints excluded: chain G residue 79 ASP Chi-restraints excluded: chain H residue 79 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1788 random chunks: chunk 581 optimal weight: 4.9990 chunk 1556 optimal weight: 10.0000 chunk 341 optimal weight: 9.9990 chunk 1014 optimal weight: 9.9990 chunk 426 optimal weight: 9.9990 chunk 1729 optimal weight: 7.9990 chunk 1436 optimal weight: 20.0000 chunk 800 optimal weight: 7.9990 chunk 143 optimal weight: 9.9990 chunk 572 optimal weight: 3.9990 chunk 908 optimal weight: 0.2980 overall best weight: 5.0588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 284 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 475 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 533 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 877 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1299 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1300 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1614 GLN ** A2213 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2247 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2931 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2933 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4020 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4201 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 226 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 838 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 877 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1299 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1300 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1645 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2931 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2933 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B4020 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B4933 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 226 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 284 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 838 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 877 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1299 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1300 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1645 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2213 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2931 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2933 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C4020 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C4864 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C4933 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 284 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 475 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 533 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 877 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1299 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1300 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D1614 GLN ** D2931 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2933 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D3318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D4020 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D4864 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D4933 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8488 moved from start: 0.2719 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.071 146196 Z= 0.275 Angle : 0.694 18.437 198016 Z= 0.350 Chirality : 0.042 0.347 21760 Planarity : 0.005 0.071 25752 Dihedral : 5.125 83.157 19622 Min Nonbonded Distance : 2.067 Molprobity Statistics. All-atom Clashscore : 21.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.92 % Favored : 95.08 % Rotamer: Outliers : 1.68 % Allowed : 13.99 % Favored : 84.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.45 % Cis-general : 0.00 % Twisted Proline : 0.34 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.08 (0.06), residues: 17832 helix: 0.78 (0.06), residues: 8800 sheet: -0.83 (0.12), residues: 1744 loop : -0.79 (0.08), residues: 7288 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP C1143 HIS 0.007 0.001 HIS B3771 PHE 0.045 0.002 PHE A4571 TYR 0.029 0.002 TYR B5032 ARG 0.009 0.000 ARG D 76 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 35664 Ramachandran restraints generated. 17832 Oldfield, 0 Emsley, 17832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 35664 Ramachandran restraints generated. 17832 Oldfield, 0 Emsley, 17832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1346 residues out of total 15548 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 237 poor density : 1109 time to evaluate : 12.596 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 155 LYS cc_start: 0.9568 (mmtt) cc_final: 0.9110 (tppt) REVERT: A 196 MET cc_start: 0.8670 (mpp) cc_final: 0.8391 (mpp) REVERT: A 228 ASP cc_start: 0.9441 (m-30) cc_final: 0.9183 (m-30) REVERT: A 343 GLU cc_start: 0.8857 (mt-10) cc_final: 0.8350 (mp0) REVERT: A 565 TYR cc_start: 0.9258 (t80) cc_final: 0.8962 (t80) REVERT: A 667 MET cc_start: 0.9331 (tpp) cc_final: 0.8908 (tpp) REVERT: A 960 MET cc_start: 0.5461 (mmm) cc_final: 0.3771 (mtm) REVERT: A 961 MET cc_start: 0.6910 (pmm) cc_final: 0.6399 (pmm) REVERT: A 1100 MET cc_start: 0.8301 (mmm) cc_final: 0.7965 (mmt) REVERT: A 1573 MET cc_start: 0.8585 (tpt) cc_final: 0.8105 (tpt) REVERT: A 1601 MET cc_start: 0.9659 (tpt) cc_final: 0.9244 (tpp) REVERT: A 2228 MET cc_start: 0.9636 (ppp) cc_final: 0.9188 (ppp) REVERT: A 2355 ARG cc_start: 0.9716 (ttm-80) cc_final: 0.9392 (ttm110) REVERT: A 2440 MET cc_start: 0.9093 (OUTLIER) cc_final: 0.8877 (mmp) REVERT: A 2698 MET cc_start: 0.8496 (ppp) cc_final: 0.8261 (ppp) REVERT: A 2932 MET cc_start: 0.7255 (tpt) cc_final: 0.6881 (ptt) REVERT: A 3081 MET cc_start: 0.6511 (ptp) cc_final: 0.5966 (pmm) REVERT: A 3266 MET cc_start: 0.9451 (ppp) cc_final: 0.9230 (ppp) REVERT: A 3276 MET cc_start: 0.8181 (mmp) cc_final: 0.7614 (mmm) REVERT: A 3335 MET cc_start: 0.7973 (pmm) cc_final: 0.7708 (pmm) REVERT: A 3411 LEU cc_start: 0.9748 (pp) cc_final: 0.9269 (mm) REVERT: A 3675 ASP cc_start: 0.9493 (m-30) cc_final: 0.9290 (m-30) REVERT: A 3723 MET cc_start: 0.9361 (mmm) cc_final: 0.9107 (mmm) REVERT: A 3778 MET cc_start: 0.9586 (tmm) cc_final: 0.9377 (tmm) REVERT: A 3798 LEU cc_start: 0.9812 (mp) cc_final: 0.9395 (tt) REVERT: A 3816 MET cc_start: 0.9640 (mmt) cc_final: 0.9158 (mmp) REVERT: A 4184 MET cc_start: 0.9092 (tpp) cc_final: 0.8389 (tpp) REVERT: A 4639 MET cc_start: 0.9355 (mtp) cc_final: 0.9085 (mtp) REVERT: A 4652 LEU cc_start: 0.9500 (pp) cc_final: 0.9289 (mm) REVERT: A 4779 LYS cc_start: 0.9635 (OUTLIER) cc_final: 0.9253 (ptpp) REVERT: A 4798 MET cc_start: 0.9550 (tpp) cc_final: 0.9236 (mmm) REVERT: A 4818 MET cc_start: 0.8998 (tmm) cc_final: 0.8465 (tpp) REVERT: A 4839 MET cc_start: 0.8956 (ppp) cc_final: 0.8693 (ppp) REVERT: A 4874 MET cc_start: 0.8362 (mmm) cc_final: 0.8134 (mmm) REVERT: A 4879 MET cc_start: 0.8889 (mmm) cc_final: 0.8319 (tpp) REVERT: A 4911 LEU cc_start: 0.9340 (OUTLIER) cc_final: 0.8981 (pt) REVERT: A 4933 GLN cc_start: 0.9210 (mt0) cc_final: 0.8936 (mp10) REVERT: A 4949 GLN cc_start: 0.9343 (OUTLIER) cc_final: 0.9127 (tp40) REVERT: A 4954 MET cc_start: 0.9404 (tpp) cc_final: 0.9157 (tpp) REVERT: A 4967 TYR cc_start: 0.8122 (t80) cc_final: 0.7516 (t80) REVERT: A 4969 ASP cc_start: 0.9527 (m-30) cc_final: 0.9226 (m-30) REVERT: A 4993 MET cc_start: 0.9188 (ptm) cc_final: 0.8823 (ppp) REVERT: A 5013 MET cc_start: 0.9518 (mmm) cc_final: 0.9240 (mmm) REVERT: B 155 LYS cc_start: 0.9574 (mmtt) cc_final: 0.9108 (tppt) REVERT: B 196 MET cc_start: 0.8739 (mpp) cc_final: 0.8375 (mpp) REVERT: B 228 ASP cc_start: 0.9616 (m-30) cc_final: 0.9221 (m-30) REVERT: B 343 GLU cc_start: 0.8905 (mt-10) cc_final: 0.8367 (mp0) REVERT: B 384 MET cc_start: 0.7159 (tmm) cc_final: 0.6836 (tmm) REVERT: B 667 MET cc_start: 0.9357 (tpp) cc_final: 0.8922 (tpp) REVERT: B 941 MET cc_start: 0.5625 (tpt) cc_final: 0.4409 (mmm) REVERT: B 960 MET cc_start: 0.5416 (mmm) cc_final: 0.3802 (mtm) REVERT: B 961 MET cc_start: 0.6725 (pmm) cc_final: 0.6256 (pmm) REVERT: B 1100 MET cc_start: 0.8275 (mpp) cc_final: 0.7778 (mpp) REVERT: B 1573 MET cc_start: 0.8535 (tpt) cc_final: 0.8071 (tpt) REVERT: B 1601 MET cc_start: 0.9519 (tpp) cc_final: 0.9083 (tpp) REVERT: B 1865 MET cc_start: 0.9409 (mtp) cc_final: 0.9154 (mpp) REVERT: B 2153 MET cc_start: 0.9524 (mmp) cc_final: 0.9039 (mmm) REVERT: B 2198 MET cc_start: 0.9355 (mpp) cc_final: 0.8862 (mpp) REVERT: B 2228 MET cc_start: 0.9600 (ppp) cc_final: 0.9239 (ppp) REVERT: B 2293 GLN cc_start: 0.9489 (mm-40) cc_final: 0.9165 (tm-30) REVERT: B 2294 ASP cc_start: 0.9439 (m-30) cc_final: 0.8793 (m-30) REVERT: B 2355 ARG cc_start: 0.9720 (ttm-80) cc_final: 0.9354 (ttm110) REVERT: B 2440 MET cc_start: 0.9095 (OUTLIER) cc_final: 0.8875 (mmp) REVERT: B 2618 MET cc_start: 0.8726 (mpp) cc_final: 0.8430 (mpp) REVERT: B 2639 MET cc_start: 0.9289 (ppp) cc_final: 0.8863 (pmm) REVERT: B 2698 MET cc_start: 0.8415 (ppp) cc_final: 0.8185 (ppp) REVERT: B 2932 MET cc_start: 0.7238 (tpt) cc_final: 0.6881 (ptt) REVERT: B 3081 MET cc_start: 0.6925 (ptp) cc_final: 0.6298 (pmm) REVERT: B 3106 MET cc_start: 0.9049 (mmm) cc_final: 0.8658 (mmp) REVERT: B 3266 MET cc_start: 0.9449 (ppp) cc_final: 0.9193 (ppp) REVERT: B 3276 MET cc_start: 0.8162 (mmp) cc_final: 0.7581 (mmm) REVERT: B 3411 LEU cc_start: 0.9757 (pp) cc_final: 0.9310 (mm) REVERT: B 3723 MET cc_start: 0.9357 (mmm) cc_final: 0.9113 (mmm) REVERT: B 3778 MET cc_start: 0.9598 (tmm) cc_final: 0.9370 (tmm) REVERT: B 3798 LEU cc_start: 0.9816 (mp) cc_final: 0.9430 (tt) REVERT: B 4000 MET cc_start: 0.8858 (ptt) cc_final: 0.8639 (ptt) REVERT: B 4044 MET cc_start: 0.9658 (OUTLIER) cc_final: 0.9363 (tpp) REVERT: B 4184 MET cc_start: 0.9064 (tpp) cc_final: 0.8384 (tpp) REVERT: B 4571 PHE cc_start: 0.9074 (m-80) cc_final: 0.8806 (m-80) REVERT: B 4627 MET cc_start: 0.8926 (pmm) cc_final: 0.8609 (pmm) REVERT: B 4639 MET cc_start: 0.9393 (mtp) cc_final: 0.9101 (mtp) REVERT: B 4779 LYS cc_start: 0.9645 (OUTLIER) cc_final: 0.9227 (ptpp) REVERT: B 4818 MET cc_start: 0.8976 (tmm) cc_final: 0.8555 (tpp) REVERT: B 4874 MET cc_start: 0.8150 (mmm) cc_final: 0.7515 (mmm) REVERT: B 4879 MET cc_start: 0.8788 (mmm) cc_final: 0.8353 (tpp) REVERT: B 4880 MET cc_start: 0.8590 (ptp) cc_final: 0.8294 (ptp) REVERT: B 4911 LEU cc_start: 0.9284 (OUTLIER) cc_final: 0.8973 (pt) REVERT: B 4954 MET cc_start: 0.9433 (tpp) cc_final: 0.9182 (tpp) REVERT: B 4967 TYR cc_start: 0.8137 (t80) cc_final: 0.7517 (t80) REVERT: B 4969 ASP cc_start: 0.9506 (m-30) cc_final: 0.9201 (m-30) REVERT: B 5013 MET cc_start: 0.9589 (mmm) cc_final: 0.9337 (mmm) REVERT: C 155 LYS cc_start: 0.9588 (mmtt) cc_final: 0.9068 (tppt) REVERT: C 196 MET cc_start: 0.8739 (mpp) cc_final: 0.8372 (mpp) REVERT: C 228 ASP cc_start: 0.9616 (m-30) cc_final: 0.9220 (m-30) REVERT: C 343 GLU cc_start: 0.8903 (mt-10) cc_final: 0.8365 (mp0) REVERT: C 384 MET cc_start: 0.7159 (tmm) cc_final: 0.6834 (tmm) REVERT: C 565 TYR cc_start: 0.9281 (t80) cc_final: 0.9022 (t80) REVERT: C 667 MET cc_start: 0.9358 (tpp) cc_final: 0.8922 (tpp) REVERT: C 941 MET cc_start: 0.5632 (tpt) cc_final: 0.4419 (mmm) REVERT: C 960 MET cc_start: 0.5407 (mmm) cc_final: 0.3797 (mtm) REVERT: C 961 MET cc_start: 0.6721 (pmm) cc_final: 0.6253 (pmm) REVERT: C 1100 MET cc_start: 0.8285 (mpp) cc_final: 0.7788 (mpp) REVERT: C 1573 MET cc_start: 0.8536 (tpt) cc_final: 0.8071 (tpt) REVERT: C 1601 MET cc_start: 0.9522 (tpp) cc_final: 0.9087 (tpp) REVERT: C 1865 MET cc_start: 0.9408 (mtp) cc_final: 0.9154 (mpp) REVERT: C 2153 MET cc_start: 0.9524 (mmp) cc_final: 0.9038 (mmm) REVERT: C 2198 MET cc_start: 0.9356 (mpp) cc_final: 0.8867 (mpp) REVERT: C 2228 MET cc_start: 0.9611 (ppp) cc_final: 0.9189 (ppp) REVERT: C 2293 GLN cc_start: 0.9490 (mm-40) cc_final: 0.9164 (tm-30) REVERT: C 2294 ASP cc_start: 0.9438 (m-30) cc_final: 0.8791 (m-30) REVERT: C 2355 ARG cc_start: 0.9720 (ttm-80) cc_final: 0.9355 (ttm110) REVERT: C 2440 MET cc_start: 0.9097 (OUTLIER) cc_final: 0.8887 (mmp) REVERT: C 2618 MET cc_start: 0.8726 (mpp) cc_final: 0.8429 (mpp) REVERT: C 2639 MET cc_start: 0.9289 (ppp) cc_final: 0.8863 (pmm) REVERT: C 2698 MET cc_start: 0.8416 (ppp) cc_final: 0.8188 (ppp) REVERT: C 2932 MET cc_start: 0.7237 (tpt) cc_final: 0.6880 (ptt) REVERT: C 3081 MET cc_start: 0.6926 (ptp) cc_final: 0.6299 (pmm) REVERT: C 3106 MET cc_start: 0.9050 (mmm) cc_final: 0.8660 (mmp) REVERT: C 3266 MET cc_start: 0.9449 (ppp) cc_final: 0.9192 (ppp) REVERT: C 3276 MET cc_start: 0.8162 (mmp) cc_final: 0.7580 (mmm) REVERT: C 3411 LEU cc_start: 0.9757 (pp) cc_final: 0.9311 (mm) REVERT: C 3723 MET cc_start: 0.9360 (mmm) cc_final: 0.9110 (mmm) REVERT: C 3778 MET cc_start: 0.9599 (tmm) cc_final: 0.9371 (tmm) REVERT: C 3798 LEU cc_start: 0.9823 (mp) cc_final: 0.9433 (tt) REVERT: C 4000 MET cc_start: 0.8893 (ptt) cc_final: 0.8685 (ptt) REVERT: C 4044 MET cc_start: 0.9659 (OUTLIER) cc_final: 0.9360 (tpp) REVERT: C 4184 MET cc_start: 0.9056 (tpp) cc_final: 0.8268 (tpp) REVERT: C 4190 ILE cc_start: 0.9157 (OUTLIER) cc_final: 0.8691 (mt) REVERT: C 4571 PHE cc_start: 0.9071 (m-80) cc_final: 0.8804 (m-80) REVERT: C 4627 MET cc_start: 0.8946 (pmm) cc_final: 0.8619 (pmm) REVERT: C 4639 MET cc_start: 0.9393 (mtp) cc_final: 0.9101 (mtp) REVERT: C 4779 LYS cc_start: 0.9645 (OUTLIER) cc_final: 0.9227 (ptpp) REVERT: C 4818 MET cc_start: 0.8890 (tmm) cc_final: 0.8459 (tpp) REVERT: C 4874 MET cc_start: 0.8140 (mmm) cc_final: 0.7505 (mmm) REVERT: C 4879 MET cc_start: 0.8716 (mmm) cc_final: 0.8303 (tpp) REVERT: C 4880 MET cc_start: 0.8604 (ptp) cc_final: 0.8299 (ptp) REVERT: C 4911 LEU cc_start: 0.9279 (OUTLIER) cc_final: 0.8969 (pt) REVERT: C 4954 MET cc_start: 0.9433 (tpp) cc_final: 0.9182 (tpp) REVERT: C 4969 ASP cc_start: 0.9513 (m-30) cc_final: 0.9197 (m-30) REVERT: C 5013 MET cc_start: 0.9591 (mmm) cc_final: 0.9342 (mmm) REVERT: C 5029 ARG cc_start: 0.8500 (OUTLIER) cc_final: 0.7992 (ttp80) REVERT: D 155 LYS cc_start: 0.9588 (mmtt) cc_final: 0.9069 (tppt) REVERT: D 196 MET cc_start: 0.8748 (mpp) cc_final: 0.8377 (mpp) REVERT: D 228 ASP cc_start: 0.9617 (m-30) cc_final: 0.9219 (m-30) REVERT: D 343 GLU cc_start: 0.8902 (mt-10) cc_final: 0.8365 (mp0) REVERT: D 384 MET cc_start: 0.7162 (tmm) cc_final: 0.6836 (tmm) REVERT: D 565 TYR cc_start: 0.9282 (t80) cc_final: 0.9022 (t80) REVERT: D 667 MET cc_start: 0.9358 (tpp) cc_final: 0.8923 (tpp) REVERT: D 941 MET cc_start: 0.5631 (tpt) cc_final: 0.4419 (mmm) REVERT: D 960 MET cc_start: 0.5405 (mmm) cc_final: 0.3795 (mtm) REVERT: D 961 MET cc_start: 0.6719 (pmm) cc_final: 0.6252 (pmm) REVERT: D 1100 MET cc_start: 0.8281 (mpp) cc_final: 0.7787 (mpp) REVERT: D 1573 MET cc_start: 0.8537 (tpt) cc_final: 0.8072 (tpt) REVERT: D 1601 MET cc_start: 0.9519 (tpp) cc_final: 0.9083 (tpp) REVERT: D 1865 MET cc_start: 0.9415 (mtp) cc_final: 0.9176 (mpp) REVERT: D 2198 MET cc_start: 0.9380 (mpp) cc_final: 0.8914 (mpp) REVERT: D 2228 MET cc_start: 0.9601 (ppp) cc_final: 0.9242 (ppp) REVERT: D 2293 GLN cc_start: 0.9491 (mm-40) cc_final: 0.9164 (tm-30) REVERT: D 2294 ASP cc_start: 0.9438 (m-30) cc_final: 0.8793 (m-30) REVERT: D 2355 ARG cc_start: 0.9720 (ttm-80) cc_final: 0.9355 (ttm110) REVERT: D 2440 MET cc_start: 0.9098 (OUTLIER) cc_final: 0.8889 (mmp) REVERT: D 2639 MET cc_start: 0.9289 (ppp) cc_final: 0.8858 (pmm) REVERT: D 2698 MET cc_start: 0.8492 (ppp) cc_final: 0.8259 (ppp) REVERT: D 2932 MET cc_start: 0.7238 (tpt) cc_final: 0.6882 (ptt) REVERT: D 3081 MET cc_start: 0.6495 (ptp) cc_final: 0.5945 (pmm) REVERT: D 3106 MET cc_start: 0.9051 (mmm) cc_final: 0.8659 (mmp) REVERT: D 3276 MET cc_start: 0.8164 (mmp) cc_final: 0.7495 (mmp) REVERT: D 3411 LEU cc_start: 0.9759 (pp) cc_final: 0.9311 (mm) REVERT: D 3723 MET cc_start: 0.9360 (mmm) cc_final: 0.9111 (mmm) REVERT: D 3778 MET cc_start: 0.9600 (tmm) cc_final: 0.9372 (tmm) REVERT: D 3798 LEU cc_start: 0.9823 (mp) cc_final: 0.9433 (tt) REVERT: D 4000 MET cc_start: 0.8894 (ptt) cc_final: 0.8687 (ptt) REVERT: D 4044 MET cc_start: 0.9658 (OUTLIER) cc_final: 0.9365 (tpp) REVERT: D 4184 MET cc_start: 0.9061 (tpp) cc_final: 0.8330 (tpp) REVERT: D 4571 PHE cc_start: 0.9073 (m-80) cc_final: 0.8805 (m-80) REVERT: D 4627 MET cc_start: 0.8930 (pmm) cc_final: 0.8613 (pmm) REVERT: D 4639 MET cc_start: 0.9412 (mtp) cc_final: 0.9118 (mtp) REVERT: D 4779 LYS cc_start: 0.9645 (OUTLIER) cc_final: 0.9228 (ptpp) REVERT: D 4818 MET cc_start: 0.8887 (tmm) cc_final: 0.8457 (tpp) REVERT: D 4874 MET cc_start: 0.8143 (mmm) cc_final: 0.7513 (mmm) REVERT: D 4879 MET cc_start: 0.8778 (mmm) cc_final: 0.8329 (tpp) REVERT: D 4880 MET cc_start: 0.8602 (ptp) cc_final: 0.8301 (ptp) REVERT: D 4911 LEU cc_start: 0.9279 (OUTLIER) cc_final: 0.8969 (pt) REVERT: D 4954 MET cc_start: 0.9435 (tpp) cc_final: 0.9184 (tpp) REVERT: D 4969 ASP cc_start: 0.9528 (m-30) cc_final: 0.9226 (m-30) REVERT: D 5013 MET cc_start: 0.9590 (mmm) cc_final: 0.9341 (mmm) REVERT: E 73 LYS cc_start: 0.9370 (tmtt) cc_final: 0.9166 (tppt) REVERT: F 73 LYS cc_start: 0.9369 (tmtt) cc_final: 0.9167 (tppt) REVERT: G 73 LYS cc_start: 0.9369 (tmtt) cc_final: 0.9167 (tppt) outliers start: 237 outliers final: 181 residues processed: 1270 average time/residue: 1.1472 time to fit residues: 2642.6180 Evaluate side-chains 1271 residues out of total 15548 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 199 poor density : 1072 time to evaluate : 12.622 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 CYS Chi-restraints excluded: chain A residue 163 VAL Chi-restraints excluded: chain A residue 199 LEU Chi-restraints excluded: chain A residue 207 SER Chi-restraints excluded: chain A residue 334 MET Chi-restraints excluded: chain A residue 605 SER Chi-restraints excluded: chain A residue 845 CYS Chi-restraints excluded: chain A residue 1248 VAL Chi-restraints excluded: chain A residue 1608 MET Chi-restraints excluded: chain A residue 1658 ASP Chi-restraints excluded: chain A residue 2440 MET Chi-restraints excluded: chain A residue 3192 GLU Chi-restraints excluded: chain A residue 3203 VAL Chi-restraints excluded: chain A residue 3456 GLN Chi-restraints excluded: chain A residue 3715 LYS Chi-restraints excluded: chain A residue 3898 ASP Chi-restraints excluded: chain A residue 3990 VAL Chi-restraints excluded: chain A residue 4015 GLU Chi-restraints excluded: chain A residue 4059 LEU Chi-restraints excluded: chain A residue 4170 ILE Chi-restraints excluded: chain A residue 4198 SER Chi-restraints excluded: chain A residue 4200 THR Chi-restraints excluded: chain A residue 4555 LEU Chi-restraints excluded: chain A residue 4561 THR Chi-restraints excluded: chain A residue 4580 TYR Chi-restraints excluded: chain A residue 4656 LEU Chi-restraints excluded: chain A residue 4697 VAL Chi-restraints excluded: chain A residue 4704 LEU Chi-restraints excluded: chain A residue 4717 ASP Chi-restraints excluded: chain A residue 4720 VAL Chi-restraints excluded: chain A residue 4731 ILE Chi-restraints excluded: chain A residue 4779 LYS Chi-restraints excluded: chain A residue 4852 THR Chi-restraints excluded: chain A residue 4882 CYS Chi-restraints excluded: chain A residue 4891 VAL Chi-restraints excluded: chain A residue 4911 LEU Chi-restraints excluded: chain A residue 4924 VAL Chi-restraints excluded: chain A residue 4926 VAL Chi-restraints excluded: chain A residue 4942 GLU Chi-restraints excluded: chain A residue 4946 GLN Chi-restraints excluded: chain A residue 4949 GLN Chi-restraints excluded: chain A residue 4960 ILE Chi-restraints excluded: chain A residue 4971 THR Chi-restraints excluded: chain B residue 66 CYS Chi-restraints excluded: chain B residue 163 VAL Chi-restraints excluded: chain B residue 199 LEU Chi-restraints excluded: chain B residue 207 SER Chi-restraints excluded: chain B residue 334 MET Chi-restraints excluded: chain B residue 605 SER Chi-restraints excluded: chain B residue 710 ASP Chi-restraints excluded: chain B residue 845 CYS Chi-restraints excluded: chain B residue 846 LEU Chi-restraints excluded: chain B residue 891 TRP Chi-restraints excluded: chain B residue 1248 VAL Chi-restraints excluded: chain B residue 1599 MET Chi-restraints excluded: chain B residue 1658 ASP Chi-restraints excluded: chain B residue 2301 TYR Chi-restraints excluded: chain B residue 2377 LEU Chi-restraints excluded: chain B residue 2440 MET Chi-restraints excluded: chain B residue 3192 GLU Chi-restraints excluded: chain B residue 3203 VAL Chi-restraints excluded: chain B residue 3454 GLU Chi-restraints excluded: chain B residue 3456 GLN Chi-restraints excluded: chain B residue 3606 LEU Chi-restraints excluded: chain B residue 3715 LYS Chi-restraints excluded: chain B residue 3782 MET Chi-restraints excluded: chain B residue 3898 ASP Chi-restraints excluded: chain B residue 3990 VAL Chi-restraints excluded: chain B residue 4015 GLU Chi-restraints excluded: chain B residue 4044 MET Chi-restraints excluded: chain B residue 4059 LEU Chi-restraints excluded: chain B residue 4170 ILE Chi-restraints excluded: chain B residue 4198 SER Chi-restraints excluded: chain B residue 4200 THR Chi-restraints excluded: chain B residue 4555 LEU Chi-restraints excluded: chain B residue 4561 THR Chi-restraints excluded: chain B residue 4569 LEU Chi-restraints excluded: chain B residue 4580 TYR Chi-restraints excluded: chain B residue 4656 LEU Chi-restraints excluded: chain B residue 4697 VAL Chi-restraints excluded: chain B residue 4704 LEU Chi-restraints excluded: chain B residue 4717 ASP Chi-restraints excluded: chain B residue 4720 VAL Chi-restraints excluded: chain B residue 4723 LYS Chi-restraints excluded: chain B residue 4731 ILE Chi-restraints excluded: chain B residue 4779 LYS Chi-restraints excluded: chain B residue 4800 LEU Chi-restraints excluded: chain B residue 4837 LEU Chi-restraints excluded: chain B residue 4882 CYS Chi-restraints excluded: chain B residue 4911 LEU Chi-restraints excluded: chain B residue 4929 LEU Chi-restraints excluded: chain B residue 4942 GLU Chi-restraints excluded: chain B residue 4946 GLN Chi-restraints excluded: chain B residue 4960 ILE Chi-restraints excluded: chain B residue 4971 THR Chi-restraints excluded: chain C residue 66 CYS Chi-restraints excluded: chain C residue 163 VAL Chi-restraints excluded: chain C residue 199 LEU Chi-restraints excluded: chain C residue 207 SER Chi-restraints excluded: chain C residue 334 MET Chi-restraints excluded: chain C residue 605 SER Chi-restraints excluded: chain C residue 710 ASP Chi-restraints excluded: chain C residue 845 CYS Chi-restraints excluded: chain C residue 846 LEU Chi-restraints excluded: chain C residue 891 TRP Chi-restraints excluded: chain C residue 1248 VAL Chi-restraints excluded: chain C residue 1599 MET Chi-restraints excluded: chain C residue 1658 ASP Chi-restraints excluded: chain C residue 2301 TYR Chi-restraints excluded: chain C residue 2377 LEU Chi-restraints excluded: chain C residue 2440 MET Chi-restraints excluded: chain C residue 3192 GLU Chi-restraints excluded: chain C residue 3203 VAL Chi-restraints excluded: chain C residue 3454 GLU Chi-restraints excluded: chain C residue 3456 GLN Chi-restraints excluded: chain C residue 3606 LEU Chi-restraints excluded: chain C residue 3715 LYS Chi-restraints excluded: chain C residue 3782 MET Chi-restraints excluded: chain C residue 3898 ASP Chi-restraints excluded: chain C residue 3990 VAL Chi-restraints excluded: chain C residue 4044 MET Chi-restraints excluded: chain C residue 4059 LEU Chi-restraints excluded: chain C residue 4170 ILE Chi-restraints excluded: chain C residue 4190 ILE Chi-restraints excluded: chain C residue 4198 SER Chi-restraints excluded: chain C residue 4200 THR Chi-restraints excluded: chain C residue 4555 LEU Chi-restraints excluded: chain C residue 4561 THR Chi-restraints excluded: chain C residue 4569 LEU Chi-restraints excluded: chain C residue 4580 TYR Chi-restraints excluded: chain C residue 4656 LEU Chi-restraints excluded: chain C residue 4697 VAL Chi-restraints excluded: chain C residue 4704 LEU Chi-restraints excluded: chain C residue 4717 ASP Chi-restraints excluded: chain C residue 4720 VAL Chi-restraints excluded: chain C residue 4731 ILE Chi-restraints excluded: chain C residue 4779 LYS Chi-restraints excluded: chain C residue 4800 LEU Chi-restraints excluded: chain C residue 4882 CYS Chi-restraints excluded: chain C residue 4911 LEU Chi-restraints excluded: chain C residue 4929 LEU Chi-restraints excluded: chain C residue 4942 GLU Chi-restraints excluded: chain C residue 4946 GLN Chi-restraints excluded: chain C residue 4960 ILE Chi-restraints excluded: chain C residue 4971 THR Chi-restraints excluded: chain C residue 5029 ARG Chi-restraints excluded: chain D residue 66 CYS Chi-restraints excluded: chain D residue 163 VAL Chi-restraints excluded: chain D residue 199 LEU Chi-restraints excluded: chain D residue 207 SER Chi-restraints excluded: chain D residue 334 MET Chi-restraints excluded: chain D residue 605 SER Chi-restraints excluded: chain D residue 710 ASP Chi-restraints excluded: chain D residue 845 CYS Chi-restraints excluded: chain D residue 846 LEU Chi-restraints excluded: chain D residue 891 TRP Chi-restraints excluded: chain D residue 1248 VAL Chi-restraints excluded: chain D residue 1599 MET Chi-restraints excluded: chain D residue 1658 ASP Chi-restraints excluded: chain D residue 2301 TYR Chi-restraints excluded: chain D residue 2377 LEU Chi-restraints excluded: chain D residue 2440 MET Chi-restraints excluded: chain D residue 3192 GLU Chi-restraints excluded: chain D residue 3203 VAL Chi-restraints excluded: chain D residue 3454 GLU Chi-restraints excluded: chain D residue 3456 GLN Chi-restraints excluded: chain D residue 3606 LEU Chi-restraints excluded: chain D residue 3715 LYS Chi-restraints excluded: chain D residue 3782 MET Chi-restraints excluded: chain D residue 3898 ASP Chi-restraints excluded: chain D residue 3990 VAL Chi-restraints excluded: chain D residue 4015 GLU Chi-restraints excluded: chain D residue 4044 MET Chi-restraints excluded: chain D residue 4059 LEU Chi-restraints excluded: chain D residue 4170 ILE Chi-restraints excluded: chain D residue 4198 SER Chi-restraints excluded: chain D residue 4200 THR Chi-restraints excluded: chain D residue 4561 THR Chi-restraints excluded: chain D residue 4569 LEU Chi-restraints excluded: chain D residue 4580 TYR Chi-restraints excluded: chain D residue 4656 LEU Chi-restraints excluded: chain D residue 4697 VAL Chi-restraints excluded: chain D residue 4704 LEU Chi-restraints excluded: chain D residue 4717 ASP Chi-restraints excluded: chain D residue 4720 VAL Chi-restraints excluded: chain D residue 4731 ILE Chi-restraints excluded: chain D residue 4779 LYS Chi-restraints excluded: chain D residue 4800 LEU Chi-restraints excluded: chain D residue 4882 CYS Chi-restraints excluded: chain D residue 4911 LEU Chi-restraints excluded: chain D residue 4929 LEU Chi-restraints excluded: chain D residue 4942 GLU Chi-restraints excluded: chain D residue 4946 GLN Chi-restraints excluded: chain D residue 4960 ILE Chi-restraints excluded: chain D residue 4971 THR Chi-restraints excluded: chain E residue 79 ASP Chi-restraints excluded: chain F residue 79 ASP Chi-restraints excluded: chain G residue 79 ASP Chi-restraints excluded: chain H residue 79 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1788 random chunks: chunk 1667 optimal weight: 8.9990 chunk 194 optimal weight: 8.9990 chunk 985 optimal weight: 7.9990 chunk 1263 optimal weight: 2.9990 chunk 978 optimal weight: 20.0000 chunk 1456 optimal weight: 10.0000 chunk 966 optimal weight: 3.9990 chunk 1723 optimal weight: 6.9990 chunk 1078 optimal weight: 5.9990 chunk 1050 optimal weight: 10.0000 chunk 795 optimal weight: 10.0000 overall best weight: 5.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 226 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 284 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 475 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 533 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 797 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 877 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1299 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1300 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1645 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2213 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2247 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2931 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2933 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A3457 ASN ** A4020 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A4109 GLN ** A4201 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4803 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 226 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 284 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 838 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 877 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1299 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1300 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1645 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2931 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2933 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3211 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3214 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B4020 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B4109 GLN ** B4864 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B4933 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 98 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 226 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 284 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 838 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 877 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1299 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1300 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1645 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2213 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2931 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2933 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C3211 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C3214 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C4020 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C4109 GLN ** C4864 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C4933 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 226 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 284 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 877 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1299 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1300 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1645 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2283 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2931 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2933 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D3211 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D3214 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D3318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D4020 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D4109 GLN ** D4864 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D4933 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8498 moved from start: 0.2943 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.078 146196 Z= 0.295 Angle : 0.716 19.312 198016 Z= 0.360 Chirality : 0.043 0.359 21760 Planarity : 0.005 0.071 25752 Dihedral : 5.182 85.230 19619 Min Nonbonded Distance : 2.060 Molprobity Statistics. All-atom Clashscore : 22.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.24 % Favored : 94.76 % Rotamer: Outliers : 1.73 % Allowed : 14.52 % Favored : 83.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.45 % Cis-general : 0.00 % Twisted Proline : 0.34 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.17 (0.06), residues: 17832 helix: 0.69 (0.05), residues: 8816 sheet: -1.00 (0.12), residues: 1812 loop : -0.79 (0.08), residues: 7204 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP C1143 HIS 0.007 0.001 HIS B 597 PHE 0.043 0.002 PHE A4571 TYR 0.028 0.002 TYR D5032 ARG 0.012 0.001 ARG C 76 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 35664 Ramachandran restraints generated. 17832 Oldfield, 0 Emsley, 17832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 35664 Ramachandran restraints generated. 17832 Oldfield, 0 Emsley, 17832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1342 residues out of total 15548 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 246 poor density : 1096 time to evaluate : 12.573 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 155 LYS cc_start: 0.9573 (mmtt) cc_final: 0.9056 (tppt) REVERT: A 196 MET cc_start: 0.8683 (mpp) cc_final: 0.8311 (mpp) REVERT: A 213 TYR cc_start: 0.8204 (m-80) cc_final: 0.7055 (m-80) REVERT: A 228 ASP cc_start: 0.9456 (m-30) cc_final: 0.9204 (m-30) REVERT: A 340 LYS cc_start: 0.9251 (mmmm) cc_final: 0.9032 (mmmt) REVERT: A 343 GLU cc_start: 0.8873 (mt-10) cc_final: 0.8429 (mp0) REVERT: A 565 TYR cc_start: 0.9264 (t80) cc_final: 0.8969 (t80) REVERT: A 960 MET cc_start: 0.5961 (mmm) cc_final: 0.4143 (mtm) REVERT: A 961 MET cc_start: 0.7060 (pmm) cc_final: 0.6536 (pmm) REVERT: A 1100 MET cc_start: 0.8416 (mmm) cc_final: 0.8019 (mmt) REVERT: A 1260 MET cc_start: 0.8398 (mtm) cc_final: 0.7338 (mpp) REVERT: A 1573 MET cc_start: 0.8604 (tpt) cc_final: 0.8108 (tpt) REVERT: A 1601 MET cc_start: 0.9653 (tpt) cc_final: 0.9255 (tpp) REVERT: A 1939 MET cc_start: 0.9645 (mmm) cc_final: 0.9365 (mmm) REVERT: A 2228 MET cc_start: 0.9621 (ppp) cc_final: 0.9194 (ppp) REVERT: A 2293 GLN cc_start: 0.9350 (mm110) cc_final: 0.8891 (mm110) REVERT: A 2355 ARG cc_start: 0.9729 (ttm-80) cc_final: 0.9396 (ttm110) REVERT: A 2440 MET cc_start: 0.9135 (OUTLIER) cc_final: 0.8919 (mmp) REVERT: A 2490 MET cc_start: 0.8750 (tpp) cc_final: 0.8362 (mtt) REVERT: A 2618 MET cc_start: 0.8791 (mpp) cc_final: 0.8516 (mpp) REVERT: A 2639 MET cc_start: 0.9293 (ppp) cc_final: 0.8782 (pmm) REVERT: A 2698 MET cc_start: 0.8487 (ppp) cc_final: 0.8256 (ppp) REVERT: A 2932 MET cc_start: 0.7208 (tpt) cc_final: 0.6889 (ptp) REVERT: A 3038 MET cc_start: 0.5885 (mpp) cc_final: 0.5644 (mpp) REVERT: A 3081 MET cc_start: 0.6677 (ptp) cc_final: 0.6071 (pmm) REVERT: A 3276 MET cc_start: 0.8241 (mmp) cc_final: 0.7569 (mmp) REVERT: A 3411 LEU cc_start: 0.9759 (pp) cc_final: 0.9295 (mm) REVERT: A 3723 MET cc_start: 0.9318 (mmm) cc_final: 0.9064 (mmm) REVERT: A 3778 MET cc_start: 0.9613 (tmm) cc_final: 0.9291 (tmm) REVERT: A 3798 LEU cc_start: 0.9805 (mp) cc_final: 0.9401 (tt) REVERT: A 3816 MET cc_start: 0.9665 (mmt) cc_final: 0.9132 (mmp) REVERT: A 4000 MET cc_start: 0.8794 (ptt) cc_final: 0.8593 (ptt) REVERT: A 4023 MET cc_start: 0.9477 (tmm) cc_final: 0.8808 (tmm) REVERT: A 4184 MET cc_start: 0.9113 (tpp) cc_final: 0.8547 (tpp) REVERT: A 4639 MET cc_start: 0.9362 (mtp) cc_final: 0.9087 (mtp) REVERT: A 4652 LEU cc_start: 0.9486 (pp) cc_final: 0.9277 (mm) REVERT: A 4779 LYS cc_start: 0.9650 (OUTLIER) cc_final: 0.9192 (ptpp) REVERT: A 4796 MET cc_start: 0.8364 (mmm) cc_final: 0.8033 (mmm) REVERT: A 4818 MET cc_start: 0.8986 (tmm) cc_final: 0.8477 (tpp) REVERT: A 4839 MET cc_start: 0.8906 (ppp) cc_final: 0.8655 (ppp) REVERT: A 4879 MET cc_start: 0.8934 (mmm) cc_final: 0.8225 (tpp) REVERT: A 4911 LEU cc_start: 0.9351 (OUTLIER) cc_final: 0.8954 (pt) REVERT: A 4933 GLN cc_start: 0.9210 (mt0) cc_final: 0.8891 (mp10) REVERT: A 4954 MET cc_start: 0.9377 (tpp) cc_final: 0.8803 (tmm) REVERT: A 4967 TYR cc_start: 0.8183 (t80) cc_final: 0.7268 (t80) REVERT: A 4969 ASP cc_start: 0.9526 (m-30) cc_final: 0.9198 (m-30) REVERT: A 4993 MET cc_start: 0.9208 (ptm) cc_final: 0.8920 (ppp) REVERT: A 5013 MET cc_start: 0.9523 (mmm) cc_final: 0.9243 (mmm) REVERT: B 155 LYS cc_start: 0.9576 (mmtt) cc_final: 0.9082 (tppt) REVERT: B 196 MET cc_start: 0.8727 (mpp) cc_final: 0.8316 (mpp) REVERT: B 213 TYR cc_start: 0.8394 (m-80) cc_final: 0.7319 (m-80) REVERT: B 228 ASP cc_start: 0.9624 (m-30) cc_final: 0.9234 (m-30) REVERT: B 340 LYS cc_start: 0.9281 (mmmm) cc_final: 0.9011 (mmmt) REVERT: B 343 GLU cc_start: 0.8841 (mt-10) cc_final: 0.8285 (mp0) REVERT: B 384 MET cc_start: 0.7175 (tmm) cc_final: 0.6878 (tmm) REVERT: B 667 MET cc_start: 0.9322 (tpp) cc_final: 0.9001 (tpp) REVERT: B 941 MET cc_start: 0.5882 (tpt) cc_final: 0.4993 (mmm) REVERT: B 960 MET cc_start: 0.5807 (mmm) cc_final: 0.3938 (mtm) REVERT: B 961 MET cc_start: 0.6965 (pmm) cc_final: 0.6500 (pmm) REVERT: B 1100 MET cc_start: 0.8347 (mpp) cc_final: 0.8133 (mmm) REVERT: B 1260 MET cc_start: 0.8249 (mtm) cc_final: 0.7441 (mpp) REVERT: B 1573 MET cc_start: 0.8597 (tpt) cc_final: 0.8118 (tpt) REVERT: B 1601 MET cc_start: 0.9514 (tpp) cc_final: 0.9092 (tpp) REVERT: B 1865 MET cc_start: 0.9418 (mtp) cc_final: 0.9162 (mpp) REVERT: B 1939 MET cc_start: 0.9634 (mmm) cc_final: 0.9392 (mmm) REVERT: B 1986 MET cc_start: 0.7904 (ppp) cc_final: 0.7439 (pmm) REVERT: B 2165 LEU cc_start: 0.9424 (OUTLIER) cc_final: 0.9195 (mm) REVERT: B 2178 MET cc_start: 0.8957 (mmp) cc_final: 0.8473 (mmp) REVERT: B 2198 MET cc_start: 0.9443 (mpp) cc_final: 0.8921 (mpp) REVERT: B 2213 ASN cc_start: 0.9504 (OUTLIER) cc_final: 0.9216 (p0) REVERT: B 2228 MET cc_start: 0.9606 (ppp) cc_final: 0.9250 (ppp) REVERT: B 2293 GLN cc_start: 0.9497 (mm-40) cc_final: 0.9205 (tm-30) REVERT: B 2294 ASP cc_start: 0.9467 (m-30) cc_final: 0.8819 (m-30) REVERT: B 2355 ARG cc_start: 0.9717 (ttm-80) cc_final: 0.9390 (ttm110) REVERT: B 2440 MET cc_start: 0.9134 (OUTLIER) cc_final: 0.8922 (mmp) REVERT: B 2490 MET cc_start: 0.8675 (tpp) cc_final: 0.8298 (mtt) REVERT: B 2618 MET cc_start: 0.8755 (mpp) cc_final: 0.8428 (mpp) REVERT: B 2698 MET cc_start: 0.8440 (ppp) cc_final: 0.8200 (ppp) REVERT: B 2932 MET cc_start: 0.7366 (tpt) cc_final: 0.7052 (ptp) REVERT: B 3038 MET cc_start: 0.5916 (mpp) cc_final: 0.5673 (mpp) REVERT: B 3081 MET cc_start: 0.6982 (ptp) cc_final: 0.6330 (pmm) REVERT: B 3106 MET cc_start: 0.8967 (mmm) cc_final: 0.8567 (mmp) REVERT: B 3276 MET cc_start: 0.8273 (mmp) cc_final: 0.7563 (mmp) REVERT: B 3411 LEU cc_start: 0.9757 (pp) cc_final: 0.9287 (mm) REVERT: B 3723 MET cc_start: 0.9294 (mmm) cc_final: 0.9045 (mmm) REVERT: B 3778 MET cc_start: 0.9582 (tmm) cc_final: 0.9343 (tmm) REVERT: B 3798 LEU cc_start: 0.9814 (mp) cc_final: 0.9383 (tt) REVERT: B 4023 MET cc_start: 0.9394 (tmm) cc_final: 0.8778 (tmm) REVERT: B 4184 MET cc_start: 0.9122 (tpp) cc_final: 0.8537 (tpp) REVERT: B 4639 MET cc_start: 0.9401 (mtp) cc_final: 0.9105 (mtp) REVERT: B 4665 LYS cc_start: 0.9457 (mmtp) cc_final: 0.9239 (mmtp) REVERT: B 4779 LYS cc_start: 0.9654 (OUTLIER) cc_final: 0.9213 (ptpp) REVERT: B 4818 MET cc_start: 0.8966 (tmm) cc_final: 0.8566 (tpp) REVERT: B 4874 MET cc_start: 0.8240 (mmm) cc_final: 0.7716 (mmm) REVERT: B 4879 MET cc_start: 0.8636 (mmm) cc_final: 0.8235 (tpp) REVERT: B 4880 MET cc_start: 0.8573 (ptp) cc_final: 0.8287 (ptp) REVERT: B 4911 LEU cc_start: 0.9259 (OUTLIER) cc_final: 0.8905 (pt) REVERT: B 4954 MET cc_start: 0.9432 (tpp) cc_final: 0.9176 (tpp) REVERT: B 4967 TYR cc_start: 0.8203 (t80) cc_final: 0.7313 (t80) REVERT: B 4969 ASP cc_start: 0.9536 (m-30) cc_final: 0.9188 (m-30) REVERT: B 5013 MET cc_start: 0.9586 (mmm) cc_final: 0.9330 (mmm) REVERT: C 155 LYS cc_start: 0.9584 (mmtt) cc_final: 0.9097 (tppt) REVERT: C 196 MET cc_start: 0.8730 (mpp) cc_final: 0.8318 (mpp) REVERT: C 213 TYR cc_start: 0.8389 (m-80) cc_final: 0.7311 (m-80) REVERT: C 228 ASP cc_start: 0.9624 (m-30) cc_final: 0.9234 (m-30) REVERT: C 340 LYS cc_start: 0.9278 (mmmm) cc_final: 0.9008 (mmmt) REVERT: C 343 GLU cc_start: 0.8837 (mt-10) cc_final: 0.8284 (mp0) REVERT: C 384 MET cc_start: 0.7174 (tmm) cc_final: 0.6877 (tmm) REVERT: C 565 TYR cc_start: 0.9314 (t80) cc_final: 0.9038 (t80) REVERT: C 667 MET cc_start: 0.9321 (tpp) cc_final: 0.9001 (tpp) REVERT: C 941 MET cc_start: 0.5887 (tpt) cc_final: 0.4998 (mmm) REVERT: C 960 MET cc_start: 0.5797 (mmm) cc_final: 0.3932 (mtm) REVERT: C 961 MET cc_start: 0.6964 (pmm) cc_final: 0.6500 (pmm) REVERT: C 1100 MET cc_start: 0.8359 (mpp) cc_final: 0.8137 (mmm) REVERT: C 1260 MET cc_start: 0.8298 (mtm) cc_final: 0.7473 (mpp) REVERT: C 1573 MET cc_start: 0.8599 (tpt) cc_final: 0.8119 (tpt) REVERT: C 1601 MET cc_start: 0.9517 (tpp) cc_final: 0.9095 (tpp) REVERT: C 1865 MET cc_start: 0.9419 (mtp) cc_final: 0.9163 (mpp) REVERT: C 1939 MET cc_start: 0.9633 (mmm) cc_final: 0.9393 (mmm) REVERT: C 1986 MET cc_start: 0.7903 (ppp) cc_final: 0.7439 (pmm) REVERT: C 2165 LEU cc_start: 0.9422 (OUTLIER) cc_final: 0.9195 (mm) REVERT: C 2178 MET cc_start: 0.8954 (mmp) cc_final: 0.8473 (mmp) REVERT: C 2198 MET cc_start: 0.9421 (mpp) cc_final: 0.8873 (mpp) REVERT: C 2228 MET cc_start: 0.9614 (ppp) cc_final: 0.9143 (ppp) REVERT: C 2293 GLN cc_start: 0.9498 (mm-40) cc_final: 0.9204 (tm-30) REVERT: C 2294 ASP cc_start: 0.9466 (m-30) cc_final: 0.8819 (m-30) REVERT: C 2355 ARG cc_start: 0.9717 (ttm-80) cc_final: 0.9389 (ttm110) REVERT: C 2440 MET cc_start: 0.9141 (OUTLIER) cc_final: 0.8930 (mmp) REVERT: C 2490 MET cc_start: 0.8676 (tpp) cc_final: 0.8298 (mtt) REVERT: C 2618 MET cc_start: 0.8757 (mpp) cc_final: 0.8429 (mpp) REVERT: C 2698 MET cc_start: 0.8439 (ppp) cc_final: 0.8199 (ppp) REVERT: C 2932 MET cc_start: 0.7365 (tpt) cc_final: 0.7051 (ptp) REVERT: C 3038 MET cc_start: 0.5917 (mpp) cc_final: 0.5674 (mpp) REVERT: C 3081 MET cc_start: 0.6984 (ptp) cc_final: 0.6331 (pmm) REVERT: C 3106 MET cc_start: 0.8969 (mmm) cc_final: 0.8569 (mmp) REVERT: C 3276 MET cc_start: 0.8274 (mmp) cc_final: 0.7564 (mmp) REVERT: C 3411 LEU cc_start: 0.9757 (pp) cc_final: 0.9288 (mm) REVERT: C 3723 MET cc_start: 0.9291 (mmm) cc_final: 0.9041 (mmm) REVERT: C 3778 MET cc_start: 0.9584 (tmm) cc_final: 0.9343 (tmm) REVERT: C 3798 LEU cc_start: 0.9819 (mp) cc_final: 0.9437 (tt) REVERT: C 4023 MET cc_start: 0.9406 (tmm) cc_final: 0.8827 (tmm) REVERT: C 4184 MET cc_start: 0.9040 (tpp) cc_final: 0.8429 (tpp) REVERT: C 4639 MET cc_start: 0.9400 (mtp) cc_final: 0.9093 (mtp) REVERT: C 4665 LYS cc_start: 0.9458 (mmtp) cc_final: 0.9242 (mmtp) REVERT: C 4779 LYS cc_start: 0.9653 (OUTLIER) cc_final: 0.9213 (ptpp) REVERT: C 4818 MET cc_start: 0.8909 (tmm) cc_final: 0.8478 (tpp) REVERT: C 4874 MET cc_start: 0.8168 (mmm) cc_final: 0.7661 (mmm) REVERT: C 4879 MET cc_start: 0.8623 (mmm) cc_final: 0.8236 (tpp) REVERT: C 4880 MET cc_start: 0.8576 (ptp) cc_final: 0.8297 (ptp) REVERT: C 4911 LEU cc_start: 0.9269 (OUTLIER) cc_final: 0.8939 (pt) REVERT: C 4954 MET cc_start: 0.9428 (tpp) cc_final: 0.9171 (tpp) REVERT: C 4969 ASP cc_start: 0.9527 (m-30) cc_final: 0.9207 (m-30) REVERT: C 5013 MET cc_start: 0.9586 (mmm) cc_final: 0.9330 (mmm) REVERT: C 5029 ARG cc_start: 0.8584 (OUTLIER) cc_final: 0.8272 (ttp-170) REVERT: D 155 LYS cc_start: 0.9583 (mmtt) cc_final: 0.9098 (tppt) REVERT: D 196 MET cc_start: 0.8733 (mpp) cc_final: 0.8325 (mpp) REVERT: D 213 TYR cc_start: 0.8390 (m-80) cc_final: 0.7314 (m-80) REVERT: D 228 ASP cc_start: 0.9624 (m-30) cc_final: 0.9232 (m-30) REVERT: D 340 LYS cc_start: 0.9281 (mmmm) cc_final: 0.9012 (mmmt) REVERT: D 343 GLU cc_start: 0.8838 (mt-10) cc_final: 0.8284 (mp0) REVERT: D 384 MET cc_start: 0.7176 (tmm) cc_final: 0.6878 (tmm) REVERT: D 565 TYR cc_start: 0.9313 (t80) cc_final: 0.9038 (t80) REVERT: D 667 MET cc_start: 0.9321 (tpp) cc_final: 0.9001 (tpp) REVERT: D 941 MET cc_start: 0.5887 (tpt) cc_final: 0.4998 (mmm) REVERT: D 960 MET cc_start: 0.5794 (mmm) cc_final: 0.3927 (mtm) REVERT: D 961 MET cc_start: 0.6966 (pmm) cc_final: 0.6501 (pmm) REVERT: D 1100 MET cc_start: 0.8356 (mpp) cc_final: 0.8132 (mmm) REVERT: D 1260 MET cc_start: 0.8250 (mtm) cc_final: 0.7443 (mpp) REVERT: D 1573 MET cc_start: 0.8597 (tpt) cc_final: 0.8118 (tpt) REVERT: D 1601 MET cc_start: 0.9515 (tpp) cc_final: 0.9093 (tpp) REVERT: D 1865 MET cc_start: 0.9443 (mtp) cc_final: 0.9179 (mpp) REVERT: D 1939 MET cc_start: 0.9632 (mmm) cc_final: 0.9369 (mmm) REVERT: D 1986 MET cc_start: 0.7904 (ppp) cc_final: 0.7441 (pmm) REVERT: D 2153 MET cc_start: 0.9508 (mmp) cc_final: 0.9029 (mmm) REVERT: D 2165 LEU cc_start: 0.9424 (OUTLIER) cc_final: 0.9194 (mm) REVERT: D 2178 MET cc_start: 0.8955 (mmp) cc_final: 0.8475 (mmp) REVERT: D 2198 MET cc_start: 0.9427 (mpp) cc_final: 0.8876 (mpp) REVERT: D 2213 ASN cc_start: 0.9503 (OUTLIER) cc_final: 0.9216 (p0) REVERT: D 2228 MET cc_start: 0.9608 (ppp) cc_final: 0.9249 (ppp) REVERT: D 2293 GLN cc_start: 0.9497 (mm-40) cc_final: 0.9205 (tm-30) REVERT: D 2294 ASP cc_start: 0.9466 (m-30) cc_final: 0.8819 (m-30) REVERT: D 2355 ARG cc_start: 0.9723 (ttm-80) cc_final: 0.9392 (ttm110) REVERT: D 2440 MET cc_start: 0.9141 (OUTLIER) cc_final: 0.8931 (mmp) REVERT: D 2618 MET cc_start: 0.8756 (mpp) cc_final: 0.8448 (mpp) REVERT: D 2698 MET cc_start: 0.8442 (ppp) cc_final: 0.8201 (ppp) REVERT: D 2932 MET cc_start: 0.7367 (tpt) cc_final: 0.7053 (ptp) REVERT: D 3038 MET cc_start: 0.5915 (mpp) cc_final: 0.5671 (mpp) REVERT: D 3081 MET cc_start: 0.6824 (ptp) cc_final: 0.6219 (pmm) REVERT: D 3106 MET cc_start: 0.8969 (mmm) cc_final: 0.8568 (mmp) REVERT: D 3276 MET cc_start: 0.8268 (mmp) cc_final: 0.7565 (mmp) REVERT: D 3335 MET cc_start: 0.7876 (pmm) cc_final: 0.7253 (pmm) REVERT: D 3411 LEU cc_start: 0.9757 (pp) cc_final: 0.9290 (mm) REVERT: D 3723 MET cc_start: 0.9291 (mmm) cc_final: 0.9040 (mmm) REVERT: D 3778 MET cc_start: 0.9584 (tmm) cc_final: 0.9343 (tmm) REVERT: D 3798 LEU cc_start: 0.9819 (mp) cc_final: 0.9438 (tt) REVERT: D 4023 MET cc_start: 0.9390 (tmm) cc_final: 0.8777 (tmm) REVERT: D 4184 MET cc_start: 0.9123 (tpp) cc_final: 0.8536 (tpp) REVERT: D 4639 MET cc_start: 0.9397 (mtp) cc_final: 0.9178 (mtp) REVERT: D 4665 LYS cc_start: 0.9457 (mmtp) cc_final: 0.9241 (mmtp) REVERT: D 4779 LYS cc_start: 0.9654 (OUTLIER) cc_final: 0.9213 (ptpp) REVERT: D 4818 MET cc_start: 0.8991 (tmm) cc_final: 0.8559 (tpp) REVERT: D 4874 MET cc_start: 0.8172 (mmm) cc_final: 0.7667 (mmm) REVERT: D 4879 MET cc_start: 0.8612 (mmm) cc_final: 0.8242 (tpp) REVERT: D 4880 MET cc_start: 0.8573 (ptp) cc_final: 0.8288 (ptp) REVERT: D 4911 LEU cc_start: 0.9267 (OUTLIER) cc_final: 0.8937 (pt) REVERT: D 4954 MET cc_start: 0.9430 (tpp) cc_final: 0.9176 (tpp) REVERT: D 4969 ASP cc_start: 0.9533 (m-30) cc_final: 0.9195 (m-30) REVERT: D 5013 MET cc_start: 0.9587 (mmm) cc_final: 0.9332 (mmm) outliers start: 246 outliers final: 186 residues processed: 1257 average time/residue: 1.1540 time to fit residues: 2634.3234 Evaluate side-chains 1262 residues out of total 15548 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 204 poor density : 1058 time to evaluate : 12.495 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 LEU Chi-restraints excluded: chain A residue 163 VAL Chi-restraints excluded: chain A residue 199 LEU Chi-restraints excluded: chain A residue 207 SER Chi-restraints excluded: chain A residue 334 MET Chi-restraints excluded: chain A residue 605 SER Chi-restraints excluded: chain A residue 845 CYS Chi-restraints excluded: chain A residue 1248 VAL Chi-restraints excluded: chain A residue 1608 MET Chi-restraints excluded: chain A residue 1658 ASP Chi-restraints excluded: chain A residue 2440 MET Chi-restraints excluded: chain A residue 2602 VAL Chi-restraints excluded: chain A residue 3192 GLU Chi-restraints excluded: chain A residue 3203 VAL Chi-restraints excluded: chain A residue 3529 ASP Chi-restraints excluded: chain A residue 3606 LEU Chi-restraints excluded: chain A residue 3715 LYS Chi-restraints excluded: chain A residue 3898 ASP Chi-restraints excluded: chain A residue 3990 VAL Chi-restraints excluded: chain A residue 4015 GLU Chi-restraints excluded: chain A residue 4059 LEU Chi-restraints excluded: chain A residue 4170 ILE Chi-restraints excluded: chain A residue 4198 SER Chi-restraints excluded: chain A residue 4200 THR Chi-restraints excluded: chain A residue 4561 THR Chi-restraints excluded: chain A residue 4580 TYR Chi-restraints excluded: chain A residue 4656 LEU Chi-restraints excluded: chain A residue 4697 VAL Chi-restraints excluded: chain A residue 4704 LEU Chi-restraints excluded: chain A residue 4717 ASP Chi-restraints excluded: chain A residue 4720 VAL Chi-restraints excluded: chain A residue 4731 ILE Chi-restraints excluded: chain A residue 4779 LYS Chi-restraints excluded: chain A residue 4843 LEU Chi-restraints excluded: chain A residue 4852 THR Chi-restraints excluded: chain A residue 4882 CYS Chi-restraints excluded: chain A residue 4891 VAL Chi-restraints excluded: chain A residue 4911 LEU Chi-restraints excluded: chain A residue 4924 VAL Chi-restraints excluded: chain A residue 4926 VAL Chi-restraints excluded: chain A residue 4929 LEU Chi-restraints excluded: chain A residue 4942 GLU Chi-restraints excluded: chain A residue 4946 GLN Chi-restraints excluded: chain A residue 4960 ILE Chi-restraints excluded: chain B residue 37 LEU Chi-restraints excluded: chain B residue 66 CYS Chi-restraints excluded: chain B residue 163 VAL Chi-restraints excluded: chain B residue 199 LEU Chi-restraints excluded: chain B residue 207 SER Chi-restraints excluded: chain B residue 334 MET Chi-restraints excluded: chain B residue 605 SER Chi-restraints excluded: chain B residue 710 ASP Chi-restraints excluded: chain B residue 845 CYS Chi-restraints excluded: chain B residue 846 LEU Chi-restraints excluded: chain B residue 891 TRP Chi-restraints excluded: chain B residue 1248 VAL Chi-restraints excluded: chain B residue 1599 MET Chi-restraints excluded: chain B residue 1658 ASP Chi-restraints excluded: chain B residue 2165 LEU Chi-restraints excluded: chain B residue 2213 ASN Chi-restraints excluded: chain B residue 2377 LEU Chi-restraints excluded: chain B residue 2440 MET Chi-restraints excluded: chain B residue 2602 VAL Chi-restraints excluded: chain B residue 3192 GLU Chi-restraints excluded: chain B residue 3203 VAL Chi-restraints excluded: chain B residue 3454 GLU Chi-restraints excluded: chain B residue 3456 GLN Chi-restraints excluded: chain B residue 3529 ASP Chi-restraints excluded: chain B residue 3606 LEU Chi-restraints excluded: chain B residue 3715 LYS Chi-restraints excluded: chain B residue 3898 ASP Chi-restraints excluded: chain B residue 3990 VAL Chi-restraints excluded: chain B residue 4015 GLU Chi-restraints excluded: chain B residue 4059 LEU Chi-restraints excluded: chain B residue 4170 ILE Chi-restraints excluded: chain B residue 4198 SER Chi-restraints excluded: chain B residue 4200 THR Chi-restraints excluded: chain B residue 4555 LEU Chi-restraints excluded: chain B residue 4561 THR Chi-restraints excluded: chain B residue 4569 LEU Chi-restraints excluded: chain B residue 4580 TYR Chi-restraints excluded: chain B residue 4656 LEU Chi-restraints excluded: chain B residue 4697 VAL Chi-restraints excluded: chain B residue 4704 LEU Chi-restraints excluded: chain B residue 4717 ASP Chi-restraints excluded: chain B residue 4720 VAL Chi-restraints excluded: chain B residue 4723 LYS Chi-restraints excluded: chain B residue 4731 ILE Chi-restraints excluded: chain B residue 4779 LYS Chi-restraints excluded: chain B residue 4800 LEU Chi-restraints excluded: chain B residue 4837 LEU Chi-restraints excluded: chain B residue 4882 CYS Chi-restraints excluded: chain B residue 4911 LEU Chi-restraints excluded: chain B residue 4929 LEU Chi-restraints excluded: chain B residue 4946 GLN Chi-restraints excluded: chain B residue 4960 ILE Chi-restraints excluded: chain C residue 37 LEU Chi-restraints excluded: chain C residue 66 CYS Chi-restraints excluded: chain C residue 163 VAL Chi-restraints excluded: chain C residue 199 LEU Chi-restraints excluded: chain C residue 207 SER Chi-restraints excluded: chain C residue 334 MET Chi-restraints excluded: chain C residue 605 SER Chi-restraints excluded: chain C residue 710 ASP Chi-restraints excluded: chain C residue 845 CYS Chi-restraints excluded: chain C residue 846 LEU Chi-restraints excluded: chain C residue 891 TRP Chi-restraints excluded: chain C residue 1248 VAL Chi-restraints excluded: chain C residue 1599 MET Chi-restraints excluded: chain C residue 1658 ASP Chi-restraints excluded: chain C residue 2165 LEU Chi-restraints excluded: chain C residue 2440 MET Chi-restraints excluded: chain C residue 2602 VAL Chi-restraints excluded: chain C residue 3192 GLU Chi-restraints excluded: chain C residue 3203 VAL Chi-restraints excluded: chain C residue 3456 GLN Chi-restraints excluded: chain C residue 3529 ASP Chi-restraints excluded: chain C residue 3606 LEU Chi-restraints excluded: chain C residue 3715 LYS Chi-restraints excluded: chain C residue 3898 ASP Chi-restraints excluded: chain C residue 3990 VAL Chi-restraints excluded: chain C residue 4015 GLU Chi-restraints excluded: chain C residue 4059 LEU Chi-restraints excluded: chain C residue 4170 ILE Chi-restraints excluded: chain C residue 4198 SER Chi-restraints excluded: chain C residue 4200 THR Chi-restraints excluded: chain C residue 4555 LEU Chi-restraints excluded: chain C residue 4561 THR Chi-restraints excluded: chain C residue 4569 LEU Chi-restraints excluded: chain C residue 4580 TYR Chi-restraints excluded: chain C residue 4656 LEU Chi-restraints excluded: chain C residue 4697 VAL Chi-restraints excluded: chain C residue 4704 LEU Chi-restraints excluded: chain C residue 4717 ASP Chi-restraints excluded: chain C residue 4720 VAL Chi-restraints excluded: chain C residue 4723 LYS Chi-restraints excluded: chain C residue 4731 ILE Chi-restraints excluded: chain C residue 4779 LYS Chi-restraints excluded: chain C residue 4800 LEU Chi-restraints excluded: chain C residue 4837 LEU Chi-restraints excluded: chain C residue 4843 LEU Chi-restraints excluded: chain C residue 4882 CYS Chi-restraints excluded: chain C residue 4911 LEU Chi-restraints excluded: chain C residue 4929 LEU Chi-restraints excluded: chain C residue 4942 GLU Chi-restraints excluded: chain C residue 4946 GLN Chi-restraints excluded: chain C residue 4960 ILE Chi-restraints excluded: chain C residue 5029 ARG Chi-restraints excluded: chain D residue 37 LEU Chi-restraints excluded: chain D residue 66 CYS Chi-restraints excluded: chain D residue 163 VAL Chi-restraints excluded: chain D residue 199 LEU Chi-restraints excluded: chain D residue 207 SER Chi-restraints excluded: chain D residue 334 MET Chi-restraints excluded: chain D residue 605 SER Chi-restraints excluded: chain D residue 710 ASP Chi-restraints excluded: chain D residue 845 CYS Chi-restraints excluded: chain D residue 846 LEU Chi-restraints excluded: chain D residue 891 TRP Chi-restraints excluded: chain D residue 1248 VAL Chi-restraints excluded: chain D residue 1599 MET Chi-restraints excluded: chain D residue 1658 ASP Chi-restraints excluded: chain D residue 2165 LEU Chi-restraints excluded: chain D residue 2213 ASN Chi-restraints excluded: chain D residue 2377 LEU Chi-restraints excluded: chain D residue 2440 MET Chi-restraints excluded: chain D residue 2602 VAL Chi-restraints excluded: chain D residue 3192 GLU Chi-restraints excluded: chain D residue 3203 VAL Chi-restraints excluded: chain D residue 3454 GLU Chi-restraints excluded: chain D residue 3456 GLN Chi-restraints excluded: chain D residue 3529 ASP Chi-restraints excluded: chain D residue 3606 LEU Chi-restraints excluded: chain D residue 3715 LYS Chi-restraints excluded: chain D residue 3898 ASP Chi-restraints excluded: chain D residue 3990 VAL Chi-restraints excluded: chain D residue 4015 GLU Chi-restraints excluded: chain D residue 4059 LEU Chi-restraints excluded: chain D residue 4170 ILE Chi-restraints excluded: chain D residue 4198 SER Chi-restraints excluded: chain D residue 4200 THR Chi-restraints excluded: chain D residue 4555 LEU Chi-restraints excluded: chain D residue 4561 THR Chi-restraints excluded: chain D residue 4569 LEU Chi-restraints excluded: chain D residue 4580 TYR Chi-restraints excluded: chain D residue 4656 LEU Chi-restraints excluded: chain D residue 4697 VAL Chi-restraints excluded: chain D residue 4704 LEU Chi-restraints excluded: chain D residue 4717 ASP Chi-restraints excluded: chain D residue 4720 VAL Chi-restraints excluded: chain D residue 4723 LYS Chi-restraints excluded: chain D residue 4731 ILE Chi-restraints excluded: chain D residue 4779 LYS Chi-restraints excluded: chain D residue 4800 LEU Chi-restraints excluded: chain D residue 4882 CYS Chi-restraints excluded: chain D residue 4911 LEU Chi-restraints excluded: chain D residue 4929 LEU Chi-restraints excluded: chain D residue 4942 GLU Chi-restraints excluded: chain D residue 4946 GLN Chi-restraints excluded: chain D residue 4960 ILE Chi-restraints excluded: chain E residue 79 ASP Chi-restraints excluded: chain F residue 79 ASP Chi-restraints excluded: chain G residue 79 ASP Chi-restraints excluded: chain H residue 79 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1788 random chunks: chunk 1066 optimal weight: 10.0000 chunk 688 optimal weight: 40.0000 chunk 1029 optimal weight: 4.9990 chunk 519 optimal weight: 20.0000 chunk 338 optimal weight: 20.0000 chunk 333 optimal weight: 0.8980 chunk 1095 optimal weight: 0.8980 chunk 1174 optimal weight: 0.0040 chunk 852 optimal weight: 9.9990 chunk 160 optimal weight: 0.8980 chunk 1354 optimal weight: 8.9990 overall best weight: 1.5394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 284 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 475 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 533 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 877 ASN ** A1299 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1300 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2213 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2247 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2931 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4020 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A4201 ASN ** B 284 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 412 ASN ** B 475 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 533 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 838 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 877 ASN ** B1299 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1300 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2247 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2931 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B4020 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B4864 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B4933 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 284 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 412 ASN ** C 475 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 533 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 838 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 877 ASN ** C1299 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1300 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2213 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2247 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2931 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C4020 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C4864 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C4933 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 284 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 475 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 489 ASN ** D 533 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 838 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 877 ASN ** D1299 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1300 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2247 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2931 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D3318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D4020 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D4864 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D4933 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8453 moved from start: 0.2899 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 146196 Z= 0.185 Angle : 0.703 20.107 198016 Z= 0.340 Chirality : 0.043 0.333 21760 Planarity : 0.004 0.070 25752 Dihedral : 4.935 85.670 19609 Min Nonbonded Distance : 2.104 Molprobity Statistics. All-atom Clashscore : 17.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.34 % Favored : 95.66 % Rotamer: Outliers : 1.38 % Allowed : 15.10 % Favored : 83.52 % Cbeta Deviations : 0.01 % Peptide Plane: Cis-proline : 0.45 % Cis-general : 0.00 % Twisted Proline : 0.34 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.10 (0.06), residues: 17832 helix: 0.93 (0.06), residues: 8824 sheet: -0.81 (0.12), residues: 1776 loop : -0.69 (0.08), residues: 7232 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B1143 HIS 0.006 0.001 HIS A3771 PHE 0.043 0.002 PHE A4571 TYR 0.022 0.001 TYR B5032 ARG 0.007 0.000 ARG D1180 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 35664 Ramachandran restraints generated. 17832 Oldfield, 0 Emsley, 17832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 35664 Ramachandran restraints generated. 17832 Oldfield, 0 Emsley, 17832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1353 residues out of total 15548 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 191 poor density : 1162 time to evaluate : 12.774 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 155 LYS cc_start: 0.9557 (mmtt) cc_final: 0.9061 (tppt) REVERT: A 196 MET cc_start: 0.8740 (mpp) cc_final: 0.8384 (mpp) REVERT: A 213 TYR cc_start: 0.8243 (m-80) cc_final: 0.7077 (m-80) REVERT: A 340 LYS cc_start: 0.9234 (mmmm) cc_final: 0.8990 (mmmt) REVERT: A 343 GLU cc_start: 0.8841 (mt-10) cc_final: 0.8386 (mp0) REVERT: A 565 TYR cc_start: 0.9247 (t80) cc_final: 0.8959 (t80) REVERT: A 667 MET cc_start: 0.9240 (mmm) cc_final: 0.8428 (tpp) REVERT: A 960 MET cc_start: 0.5676 (mmm) cc_final: 0.4185 (mtm) REVERT: A 961 MET cc_start: 0.7030 (pmm) cc_final: 0.6537 (pmm) REVERT: A 1100 MET cc_start: 0.8196 (mmm) cc_final: 0.7800 (mmt) REVERT: A 1260 MET cc_start: 0.8322 (mtm) cc_final: 0.7369 (mpp) REVERT: A 1562 ILE cc_start: 0.9492 (pt) cc_final: 0.9146 (mp) REVERT: A 1573 MET cc_start: 0.8506 (tpt) cc_final: 0.7982 (tpt) REVERT: A 1601 MET cc_start: 0.9615 (tpt) cc_final: 0.9201 (tpp) REVERT: A 1939 MET cc_start: 0.9637 (mmm) cc_final: 0.9332 (mmm) REVERT: A 2153 MET cc_start: 0.9486 (mmp) cc_final: 0.9002 (mmm) REVERT: A 2228 MET cc_start: 0.9597 (ppp) cc_final: 0.9258 (ppp) REVERT: A 2440 MET cc_start: 0.9057 (OUTLIER) cc_final: 0.8854 (mmp) REVERT: A 2698 MET cc_start: 0.8377 (ppp) cc_final: 0.8172 (ppp) REVERT: A 2932 MET cc_start: 0.6976 (tpt) cc_final: 0.6617 (ptt) REVERT: A 3038 MET cc_start: 0.5879 (mpp) cc_final: 0.5660 (mpp) REVERT: A 3081 MET cc_start: 0.6738 (ptp) cc_final: 0.6234 (pmm) REVERT: A 3276 MET cc_start: 0.8194 (mmp) cc_final: 0.7630 (mmm) REVERT: A 3335 MET cc_start: 0.7616 (pmm) cc_final: 0.7311 (pmm) REVERT: A 3411 LEU cc_start: 0.9755 (pp) cc_final: 0.9288 (mm) REVERT: A 3723 MET cc_start: 0.9332 (mmm) cc_final: 0.9055 (mmm) REVERT: A 3778 MET cc_start: 0.9634 (tmm) cc_final: 0.9397 (tmm) REVERT: A 3798 LEU cc_start: 0.9784 (mp) cc_final: 0.9387 (tt) REVERT: A 4026 MET cc_start: 0.9634 (tmm) cc_final: 0.9327 (tmm) REVERT: A 4184 MET cc_start: 0.9119 (tpp) cc_final: 0.8502 (tpp) REVERT: A 4639 MET cc_start: 0.9326 (mtp) cc_final: 0.9017 (mtp) REVERT: A 4652 LEU cc_start: 0.9492 (pp) cc_final: 0.9281 (mm) REVERT: A 4779 LYS cc_start: 0.9663 (OUTLIER) cc_final: 0.9212 (ptpp) REVERT: A 4798 MET cc_start: 0.9399 (tpp) cc_final: 0.8967 (mmm) REVERT: A 4818 MET cc_start: 0.9041 (tmm) cc_final: 0.8523 (tpp) REVERT: A 4839 MET cc_start: 0.8855 (ppp) cc_final: 0.8590 (ppp) REVERT: A 4879 MET cc_start: 0.8891 (mmm) cc_final: 0.8111 (tpp) REVERT: A 4911 LEU cc_start: 0.9328 (OUTLIER) cc_final: 0.8939 (pt) REVERT: A 4922 PHE cc_start: 0.8782 (m-80) cc_final: 0.8191 (m-80) REVERT: A 4942 GLU cc_start: 0.9036 (OUTLIER) cc_final: 0.8257 (mm-30) REVERT: A 4954 MET cc_start: 0.9366 (tpp) cc_final: 0.9093 (tpp) REVERT: A 4967 TYR cc_start: 0.8249 (t80) cc_final: 0.7422 (t80) REVERT: A 4969 ASP cc_start: 0.9449 (m-30) cc_final: 0.8910 (p0) REVERT: A 4993 MET cc_start: 0.9181 (ptm) cc_final: 0.8964 (ppp) REVERT: A 5013 MET cc_start: 0.9450 (mmm) cc_final: 0.9165 (mmm) REVERT: B 155 LYS cc_start: 0.9545 (mmtt) cc_final: 0.8990 (tppt) REVERT: B 196 MET cc_start: 0.8700 (mpp) cc_final: 0.8346 (mpp) REVERT: B 213 TYR cc_start: 0.8228 (m-80) cc_final: 0.7039 (m-80) REVERT: B 228 ASP cc_start: 0.9617 (m-30) cc_final: 0.9236 (m-30) REVERT: B 340 LYS cc_start: 0.9242 (mmmm) cc_final: 0.8974 (mmmt) REVERT: B 343 GLU cc_start: 0.8935 (mt-10) cc_final: 0.8378 (mp0) REVERT: B 384 MET cc_start: 0.7168 (tmm) cc_final: 0.6851 (tmm) REVERT: B 667 MET cc_start: 0.9329 (tpp) cc_final: 0.8945 (tpp) REVERT: B 941 MET cc_start: 0.5857 (tpt) cc_final: 0.4860 (mmm) REVERT: B 960 MET cc_start: 0.5689 (mmm) cc_final: 0.3920 (mtm) REVERT: B 961 MET cc_start: 0.6855 (pmm) cc_final: 0.6392 (pmm) REVERT: B 1260 MET cc_start: 0.8376 (mtm) cc_final: 0.7615 (mpp) REVERT: B 1562 ILE cc_start: 0.9493 (pt) cc_final: 0.9123 (mp) REVERT: B 1573 MET cc_start: 0.8545 (tpt) cc_final: 0.8027 (tpt) REVERT: B 1601 MET cc_start: 0.9485 (tpp) cc_final: 0.9037 (tpp) REVERT: B 1865 MET cc_start: 0.9428 (mtp) cc_final: 0.9164 (mpp) REVERT: B 1939 MET cc_start: 0.9616 (mmm) cc_final: 0.9356 (mmm) REVERT: B 1986 MET cc_start: 0.7886 (ppp) cc_final: 0.7428 (pmm) REVERT: B 2153 MET cc_start: 0.9486 (mmp) cc_final: 0.9023 (mmm) REVERT: B 2198 MET cc_start: 0.9313 (mpp) cc_final: 0.8940 (mpp) REVERT: B 2228 MET cc_start: 0.9571 (ppp) cc_final: 0.9220 (ppp) REVERT: B 2293 GLN cc_start: 0.9440 (mm-40) cc_final: 0.9166 (tm-30) REVERT: B 2294 ASP cc_start: 0.9445 (m-30) cc_final: 0.8751 (m-30) REVERT: B 2440 MET cc_start: 0.9015 (OUTLIER) cc_final: 0.8811 (mmp) REVERT: B 2530 MET cc_start: 0.9593 (mpp) cc_final: 0.8494 (pmm) REVERT: B 2639 MET cc_start: 0.9262 (ppp) cc_final: 0.8705 (pmm) REVERT: B 2698 MET cc_start: 0.8368 (ppp) cc_final: 0.8165 (ppp) REVERT: B 2932 MET cc_start: 0.7171 (tpt) cc_final: 0.6841 (ptt) REVERT: B 3038 MET cc_start: 0.5791 (mpp) cc_final: 0.5568 (mpp) REVERT: B 3081 MET cc_start: 0.6692 (ptp) cc_final: 0.6078 (pmm) REVERT: B 3106 MET cc_start: 0.8836 (mmm) cc_final: 0.8432 (mmp) REVERT: B 3276 MET cc_start: 0.8209 (mmp) cc_final: 0.7611 (mmm) REVERT: B 3411 LEU cc_start: 0.9752 (pp) cc_final: 0.9280 (mm) REVERT: B 3723 MET cc_start: 0.9324 (mmm) cc_final: 0.9045 (mmm) REVERT: B 3798 LEU cc_start: 0.9798 (mp) cc_final: 0.9374 (tt) REVERT: B 3816 MET cc_start: 0.9329 (mmp) cc_final: 0.8425 (mmp) REVERT: B 4026 MET cc_start: 0.9609 (tmm) cc_final: 0.9402 (tmm) REVERT: B 4184 MET cc_start: 0.9153 (tpp) cc_final: 0.8546 (tpp) REVERT: B 4244 GLU cc_start: 0.9224 (tm-30) cc_final: 0.8862 (pp20) REVERT: B 4245 MET cc_start: 0.9377 (mmm) cc_final: 0.8812 (mmm) REVERT: B 4639 MET cc_start: 0.9344 (mtp) cc_final: 0.9045 (mtp) REVERT: B 4652 LEU cc_start: 0.9502 (pp) cc_final: 0.9217 (mm) REVERT: B 4779 LYS cc_start: 0.9645 (OUTLIER) cc_final: 0.9175 (ptpp) REVERT: B 4874 MET cc_start: 0.8251 (mmm) cc_final: 0.8044 (mmm) REVERT: B 4879 MET cc_start: 0.8708 (mmm) cc_final: 0.8339 (tpp) REVERT: B 4880 MET cc_start: 0.8520 (ptp) cc_final: 0.8218 (ptp) REVERT: B 4911 LEU cc_start: 0.9317 (OUTLIER) cc_final: 0.8947 (pt) REVERT: B 4954 MET cc_start: 0.9409 (tpp) cc_final: 0.9128 (tpp) REVERT: B 4967 TYR cc_start: 0.8257 (t80) cc_final: 0.7419 (t80) REVERT: B 4969 ASP cc_start: 0.9464 (m-30) cc_final: 0.8932 (p0) REVERT: B 5013 MET cc_start: 0.9539 (mmm) cc_final: 0.9238 (mmm) REVERT: C 155 LYS cc_start: 0.9554 (mmtt) cc_final: 0.9001 (tppt) REVERT: C 196 MET cc_start: 0.8702 (mpp) cc_final: 0.8345 (mpp) REVERT: C 213 TYR cc_start: 0.8223 (m-80) cc_final: 0.7038 (m-80) REVERT: C 228 ASP cc_start: 0.9618 (m-30) cc_final: 0.9234 (m-30) REVERT: C 340 LYS cc_start: 0.9239 (mmmm) cc_final: 0.8980 (mmmt) REVERT: C 343 GLU cc_start: 0.8930 (mt-10) cc_final: 0.8377 (mp0) REVERT: C 384 MET cc_start: 0.7169 (tmm) cc_final: 0.6853 (tmm) REVERT: C 565 TYR cc_start: 0.9317 (t80) cc_final: 0.9041 (t80) REVERT: C 667 MET cc_start: 0.9327 (tpp) cc_final: 0.8945 (tpp) REVERT: C 941 MET cc_start: 0.5860 (tpt) cc_final: 0.4863 (mmm) REVERT: C 960 MET cc_start: 0.5663 (mmm) cc_final: 0.3900 (mtm) REVERT: C 961 MET cc_start: 0.6850 (pmm) cc_final: 0.6387 (pmm) REVERT: C 1260 MET cc_start: 0.8362 (mtm) cc_final: 0.7604 (mpp) REVERT: C 1573 MET cc_start: 0.8544 (tpt) cc_final: 0.8027 (tpt) REVERT: C 1601 MET cc_start: 0.9487 (tpp) cc_final: 0.9040 (tpp) REVERT: C 1865 MET cc_start: 0.9428 (mtp) cc_final: 0.9163 (mpp) REVERT: C 1939 MET cc_start: 0.9616 (mmm) cc_final: 0.9356 (mmm) REVERT: C 1986 MET cc_start: 0.7887 (ppp) cc_final: 0.7428 (pmm) REVERT: C 2153 MET cc_start: 0.9486 (mmp) cc_final: 0.9022 (mmm) REVERT: C 2198 MET cc_start: 0.9309 (mpp) cc_final: 0.8951 (mpp) REVERT: C 2228 MET cc_start: 0.9587 (ppp) cc_final: 0.9225 (ppp) REVERT: C 2293 GLN cc_start: 0.9439 (mm-40) cc_final: 0.9166 (tm-30) REVERT: C 2294 ASP cc_start: 0.9447 (m-30) cc_final: 0.8746 (m-30) REVERT: C 2530 MET cc_start: 0.9593 (mpp) cc_final: 0.8494 (pmm) REVERT: C 2639 MET cc_start: 0.9260 (ppp) cc_final: 0.8705 (pmm) REVERT: C 2698 MET cc_start: 0.8368 (ppp) cc_final: 0.8165 (ppp) REVERT: C 2932 MET cc_start: 0.7171 (tpt) cc_final: 0.6840 (ptt) REVERT: C 3038 MET cc_start: 0.5795 (mpp) cc_final: 0.5573 (mpp) REVERT: C 3081 MET cc_start: 0.6692 (ptp) cc_final: 0.6078 (pmm) REVERT: C 3106 MET cc_start: 0.8838 (mmm) cc_final: 0.8435 (mmp) REVERT: C 3276 MET cc_start: 0.8208 (mmp) cc_final: 0.7609 (mmm) REVERT: C 3411 LEU cc_start: 0.9753 (pp) cc_final: 0.9281 (mm) REVERT: C 3723 MET cc_start: 0.9322 (mmm) cc_final: 0.9042 (mmm) REVERT: C 3798 LEU cc_start: 0.9801 (mp) cc_final: 0.9380 (tt) REVERT: C 3816 MET cc_start: 0.9330 (mmp) cc_final: 0.8425 (mmp) REVERT: C 4026 MET cc_start: 0.9614 (tmm) cc_final: 0.9295 (tmm) REVERT: C 4047 MET cc_start: 0.9385 (tmm) cc_final: 0.9179 (ppp) REVERT: C 4184 MET cc_start: 0.9097 (tpp) cc_final: 0.8467 (tpp) REVERT: C 4639 MET cc_start: 0.9344 (mtp) cc_final: 0.9047 (mtp) REVERT: C 4652 LEU cc_start: 0.9502 (pp) cc_final: 0.9217 (mm) REVERT: C 4779 LYS cc_start: 0.9644 (OUTLIER) cc_final: 0.9174 (ptpp) REVERT: C 4818 MET cc_start: 0.8916 (tmm) cc_final: 0.8513 (tpp) REVERT: C 4874 MET cc_start: 0.8241 (mmm) cc_final: 0.8033 (mmm) REVERT: C 4879 MET cc_start: 0.8711 (mmm) cc_final: 0.8333 (tpp) REVERT: C 4880 MET cc_start: 0.8480 (ptp) cc_final: 0.8198 (ptp) REVERT: C 4911 LEU cc_start: 0.9300 (OUTLIER) cc_final: 0.8949 (pt) REVERT: C 4954 MET cc_start: 0.9403 (tpp) cc_final: 0.9133 (tpp) REVERT: C 4969 ASP cc_start: 0.9493 (m-30) cc_final: 0.9143 (m-30) REVERT: C 5013 MET cc_start: 0.9536 (mmm) cc_final: 0.9237 (mmm) REVERT: D 155 LYS cc_start: 0.9554 (mmtt) cc_final: 0.9002 (tppt) REVERT: D 196 MET cc_start: 0.8731 (mpp) cc_final: 0.8364 (mpp) REVERT: D 213 TYR cc_start: 0.8229 (m-80) cc_final: 0.7036 (m-80) REVERT: D 228 ASP cc_start: 0.9608 (m-30) cc_final: 0.9203 (m-30) REVERT: D 340 LYS cc_start: 0.9242 (mmmm) cc_final: 0.8974 (mmmt) REVERT: D 343 GLU cc_start: 0.8932 (mt-10) cc_final: 0.8376 (mp0) REVERT: D 384 MET cc_start: 0.7171 (tmm) cc_final: 0.6856 (tmm) REVERT: D 565 TYR cc_start: 0.9317 (t80) cc_final: 0.9040 (t80) REVERT: D 667 MET cc_start: 0.9327 (tpp) cc_final: 0.8945 (tpp) REVERT: D 941 MET cc_start: 0.5862 (tpt) cc_final: 0.4866 (mmm) REVERT: D 960 MET cc_start: 0.5659 (mmm) cc_final: 0.3896 (mtm) REVERT: D 961 MET cc_start: 0.6848 (pmm) cc_final: 0.6386 (pmm) REVERT: D 1260 MET cc_start: 0.8378 (mtm) cc_final: 0.7617 (mpp) REVERT: D 1562 ILE cc_start: 0.9494 (pt) cc_final: 0.9123 (mp) REVERT: D 1573 MET cc_start: 0.8544 (tpt) cc_final: 0.8027 (tpt) REVERT: D 1601 MET cc_start: 0.9486 (tpp) cc_final: 0.9040 (tpp) REVERT: D 1865 MET cc_start: 0.9405 (mtp) cc_final: 0.9146 (mpp) REVERT: D 1986 MET cc_start: 0.7887 (ppp) cc_final: 0.7429 (pmm) REVERT: D 2153 MET cc_start: 0.9487 (mmp) cc_final: 0.9021 (mmm) REVERT: D 2198 MET cc_start: 0.9317 (mpp) cc_final: 0.8943 (mpp) REVERT: D 2228 MET cc_start: 0.9537 (ppp) cc_final: 0.9225 (ppp) REVERT: D 2293 GLN cc_start: 0.9439 (mm-40) cc_final: 0.9165 (tm-30) REVERT: D 2294 ASP cc_start: 0.9446 (m-30) cc_final: 0.8750 (m-30) REVERT: D 2530 MET cc_start: 0.9593 (mpp) cc_final: 0.8495 (pmm) REVERT: D 2639 MET cc_start: 0.9257 (ppp) cc_final: 0.8703 (pmm) REVERT: D 2698 MET cc_start: 0.8371 (ppp) cc_final: 0.8165 (ppp) REVERT: D 2932 MET cc_start: 0.7176 (tpt) cc_final: 0.6844 (ptt) REVERT: D 3038 MET cc_start: 0.5794 (mpp) cc_final: 0.5570 (mpp) REVERT: D 3081 MET cc_start: 0.6740 (ptp) cc_final: 0.6237 (pmm) REVERT: D 3106 MET cc_start: 0.8838 (mmm) cc_final: 0.8433 (mmp) REVERT: D 3276 MET cc_start: 0.8266 (mmp) cc_final: 0.7696 (mmm) REVERT: D 3411 LEU cc_start: 0.9754 (pp) cc_final: 0.9284 (mm) REVERT: D 3723 MET cc_start: 0.9323 (mmm) cc_final: 0.9043 (mmm) REVERT: D 3798 LEU cc_start: 0.9801 (mp) cc_final: 0.9379 (tt) REVERT: D 3816 MET cc_start: 0.9332 (mmp) cc_final: 0.8428 (mmp) REVERT: D 4026 MET cc_start: 0.9610 (tmm) cc_final: 0.9404 (tmm) REVERT: D 4184 MET cc_start: 0.9152 (tpp) cc_final: 0.8540 (tpp) REVERT: D 4244 GLU cc_start: 0.9167 (tm-30) cc_final: 0.8723 (pp20) REVERT: D 4245 MET cc_start: 0.9349 (mmm) cc_final: 0.8794 (mmm) REVERT: D 4639 MET cc_start: 0.9398 (mtp) cc_final: 0.9176 (mtp) REVERT: D 4652 LEU cc_start: 0.9501 (pp) cc_final: 0.9214 (mm) REVERT: D 4779 LYS cc_start: 0.9644 (OUTLIER) cc_final: 0.9177 (ptpp) REVERT: D 4874 MET cc_start: 0.8244 (mmm) cc_final: 0.8035 (mmm) REVERT: D 4879 MET cc_start: 0.8708 (mmm) cc_final: 0.8328 (tpp) REVERT: D 4880 MET cc_start: 0.8479 (ptp) cc_final: 0.8205 (ptp) REVERT: D 4911 LEU cc_start: 0.9299 (OUTLIER) cc_final: 0.8948 (pt) REVERT: D 4942 GLU cc_start: 0.8920 (OUTLIER) cc_final: 0.8125 (mm-30) REVERT: D 4954 MET cc_start: 0.9405 (tpp) cc_final: 0.9135 (tpp) REVERT: D 4969 ASP cc_start: 0.9530 (m-30) cc_final: 0.9172 (m-30) REVERT: D 5013 MET cc_start: 0.9539 (mmm) cc_final: 0.9239 (mmm) outliers start: 191 outliers final: 144 residues processed: 1289 average time/residue: 1.1522 time to fit residues: 2694.2671 Evaluate side-chains 1240 residues out of total 15548 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 156 poor density : 1084 time to evaluate : 12.120 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 163 VAL Chi-restraints excluded: chain A residue 199 LEU Chi-restraints excluded: chain A residue 334 MET Chi-restraints excluded: chain A residue 605 SER Chi-restraints excluded: chain A residue 1248 VAL Chi-restraints excluded: chain A residue 1608 MET Chi-restraints excluded: chain A residue 1658 ASP Chi-restraints excluded: chain A residue 2440 MET Chi-restraints excluded: chain A residue 2602 VAL Chi-restraints excluded: chain A residue 3192 GLU Chi-restraints excluded: chain A residue 3203 VAL Chi-restraints excluded: chain A residue 3456 GLN Chi-restraints excluded: chain A residue 3715 LYS Chi-restraints excluded: chain A residue 3782 MET Chi-restraints excluded: chain A residue 3898 ASP Chi-restraints excluded: chain A residue 3899 PHE Chi-restraints excluded: chain A residue 4015 GLU Chi-restraints excluded: chain A residue 4059 LEU Chi-restraints excluded: chain A residue 4198 SER Chi-restraints excluded: chain A residue 4200 THR Chi-restraints excluded: chain A residue 4555 LEU Chi-restraints excluded: chain A residue 4580 TYR Chi-restraints excluded: chain A residue 4656 LEU Chi-restraints excluded: chain A residue 4697 VAL Chi-restraints excluded: chain A residue 4704 LEU Chi-restraints excluded: chain A residue 4720 VAL Chi-restraints excluded: chain A residue 4731 ILE Chi-restraints excluded: chain A residue 4779 LYS Chi-restraints excluded: chain A residue 4882 CYS Chi-restraints excluded: chain A residue 4911 LEU Chi-restraints excluded: chain A residue 4924 VAL Chi-restraints excluded: chain A residue 4929 LEU Chi-restraints excluded: chain A residue 4942 GLU Chi-restraints excluded: chain A residue 4946 GLN Chi-restraints excluded: chain A residue 4960 ILE Chi-restraints excluded: chain B residue 66 CYS Chi-restraints excluded: chain B residue 163 VAL Chi-restraints excluded: chain B residue 197 GLN Chi-restraints excluded: chain B residue 199 LEU Chi-restraints excluded: chain B residue 334 MET Chi-restraints excluded: chain B residue 605 SER Chi-restraints excluded: chain B residue 845 CYS Chi-restraints excluded: chain B residue 846 LEU Chi-restraints excluded: chain B residue 891 TRP Chi-restraints excluded: chain B residue 1248 VAL Chi-restraints excluded: chain B residue 1658 ASP Chi-restraints excluded: chain B residue 2440 MET Chi-restraints excluded: chain B residue 3192 GLU Chi-restraints excluded: chain B residue 3203 VAL Chi-restraints excluded: chain B residue 3454 GLU Chi-restraints excluded: chain B residue 3456 GLN Chi-restraints excluded: chain B residue 3715 LYS Chi-restraints excluded: chain B residue 3782 MET Chi-restraints excluded: chain B residue 3898 ASP Chi-restraints excluded: chain B residue 3990 VAL Chi-restraints excluded: chain B residue 4015 GLU Chi-restraints excluded: chain B residue 4059 LEU Chi-restraints excluded: chain B residue 4170 ILE Chi-restraints excluded: chain B residue 4198 SER Chi-restraints excluded: chain B residue 4200 THR Chi-restraints excluded: chain B residue 4555 LEU Chi-restraints excluded: chain B residue 4580 TYR Chi-restraints excluded: chain B residue 4656 LEU Chi-restraints excluded: chain B residue 4697 VAL Chi-restraints excluded: chain B residue 4704 LEU Chi-restraints excluded: chain B residue 4720 VAL Chi-restraints excluded: chain B residue 4723 LYS Chi-restraints excluded: chain B residue 4731 ILE Chi-restraints excluded: chain B residue 4779 LYS Chi-restraints excluded: chain B residue 4800 LEU Chi-restraints excluded: chain B residue 4837 LEU Chi-restraints excluded: chain B residue 4882 CYS Chi-restraints excluded: chain B residue 4911 LEU Chi-restraints excluded: chain B residue 4929 LEU Chi-restraints excluded: chain B residue 4946 GLN Chi-restraints excluded: chain C residue 66 CYS Chi-restraints excluded: chain C residue 163 VAL Chi-restraints excluded: chain C residue 197 GLN Chi-restraints excluded: chain C residue 199 LEU Chi-restraints excluded: chain C residue 334 MET Chi-restraints excluded: chain C residue 605 SER Chi-restraints excluded: chain C residue 845 CYS Chi-restraints excluded: chain C residue 846 LEU Chi-restraints excluded: chain C residue 891 TRP Chi-restraints excluded: chain C residue 1248 VAL Chi-restraints excluded: chain C residue 1658 ASP Chi-restraints excluded: chain C residue 3192 GLU Chi-restraints excluded: chain C residue 3203 VAL Chi-restraints excluded: chain C residue 3454 GLU Chi-restraints excluded: chain C residue 3456 GLN Chi-restraints excluded: chain C residue 3715 LYS Chi-restraints excluded: chain C residue 3782 MET Chi-restraints excluded: chain C residue 3898 ASP Chi-restraints excluded: chain C residue 3990 VAL Chi-restraints excluded: chain C residue 4015 GLU Chi-restraints excluded: chain C residue 4059 LEU Chi-restraints excluded: chain C residue 4170 ILE Chi-restraints excluded: chain C residue 4198 SER Chi-restraints excluded: chain C residue 4200 THR Chi-restraints excluded: chain C residue 4555 LEU Chi-restraints excluded: chain C residue 4580 TYR Chi-restraints excluded: chain C residue 4656 LEU Chi-restraints excluded: chain C residue 4697 VAL Chi-restraints excluded: chain C residue 4704 LEU Chi-restraints excluded: chain C residue 4720 VAL Chi-restraints excluded: chain C residue 4723 LYS Chi-restraints excluded: chain C residue 4731 ILE Chi-restraints excluded: chain C residue 4779 LYS Chi-restraints excluded: chain C residue 4800 LEU Chi-restraints excluded: chain C residue 4882 CYS Chi-restraints excluded: chain C residue 4911 LEU Chi-restraints excluded: chain C residue 4929 LEU Chi-restraints excluded: chain C residue 4942 GLU Chi-restraints excluded: chain C residue 4946 GLN Chi-restraints excluded: chain D residue 66 CYS Chi-restraints excluded: chain D residue 163 VAL Chi-restraints excluded: chain D residue 199 LEU Chi-restraints excluded: chain D residue 334 MET Chi-restraints excluded: chain D residue 605 SER Chi-restraints excluded: chain D residue 845 CYS Chi-restraints excluded: chain D residue 846 LEU Chi-restraints excluded: chain D residue 891 TRP Chi-restraints excluded: chain D residue 1248 VAL Chi-restraints excluded: chain D residue 1658 ASP Chi-restraints excluded: chain D residue 3192 GLU Chi-restraints excluded: chain D residue 3203 VAL Chi-restraints excluded: chain D residue 3454 GLU Chi-restraints excluded: chain D residue 3456 GLN Chi-restraints excluded: chain D residue 3715 LYS Chi-restraints excluded: chain D residue 3782 MET Chi-restraints excluded: chain D residue 3898 ASP Chi-restraints excluded: chain D residue 3990 VAL Chi-restraints excluded: chain D residue 4015 GLU Chi-restraints excluded: chain D residue 4059 LEU Chi-restraints excluded: chain D residue 4170 ILE Chi-restraints excluded: chain D residue 4198 SER Chi-restraints excluded: chain D residue 4200 THR Chi-restraints excluded: chain D residue 4555 LEU Chi-restraints excluded: chain D residue 4580 TYR Chi-restraints excluded: chain D residue 4656 LEU Chi-restraints excluded: chain D residue 4697 VAL Chi-restraints excluded: chain D residue 4704 LEU Chi-restraints excluded: chain D residue 4720 VAL Chi-restraints excluded: chain D residue 4723 LYS Chi-restraints excluded: chain D residue 4731 ILE Chi-restraints excluded: chain D residue 4779 LYS Chi-restraints excluded: chain D residue 4800 LEU Chi-restraints excluded: chain D residue 4882 CYS Chi-restraints excluded: chain D residue 4911 LEU Chi-restraints excluded: chain D residue 4929 LEU Chi-restraints excluded: chain D residue 4942 GLU Chi-restraints excluded: chain D residue 4946 GLN Chi-restraints excluded: chain E residue 79 ASP Chi-restraints excluded: chain F residue 79 ASP Chi-restraints excluded: chain G residue 79 ASP Chi-restraints excluded: chain H residue 79 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1788 random chunks: chunk 1567 optimal weight: 6.9990 chunk 1651 optimal weight: 9.9990 chunk 1506 optimal weight: 9.9990 chunk 1605 optimal weight: 7.9990 chunk 1650 optimal weight: 4.9990 chunk 966 optimal weight: 0.0050 chunk 699 optimal weight: 20.0000 chunk 1261 optimal weight: 9.9990 chunk 492 optimal weight: 5.9990 chunk 1451 optimal weight: 7.9990 chunk 1518 optimal weight: 2.9990 overall best weight: 4.2002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 284 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 475 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 533 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 797 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 877 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1299 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1300 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2213 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2247 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2931 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3211 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3214 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4020 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4803 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A4933 GLN ** B 284 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 412 ASN ** B 475 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 533 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 838 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 877 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1299 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1300 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2247 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2931 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3211 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3214 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B4020 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B4864 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 98 HIS ** C 284 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 412 ASN ** C 838 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 877 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1299 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1300 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2007 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2213 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2247 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2931 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C3211 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C3214 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C4020 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C4864 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C4933 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C5006 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 284 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 475 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 533 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 877 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1299 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1300 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2007 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2247 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2931 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D3211 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D3214 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D3318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D4020 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D4864 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D4933 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8480 moved from start: 0.3052 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 146196 Z= 0.249 Angle : 0.715 18.284 198016 Z= 0.351 Chirality : 0.043 0.375 21760 Planarity : 0.005 0.069 25752 Dihedral : 4.937 88.703 19609 Min Nonbonded Distance : 2.063 Molprobity Statistics. All-atom Clashscore : 21.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.88 % Favored : 95.12 % Rotamer: Outliers : 1.32 % Allowed : 15.64 % Favored : 83.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.45 % Cis-general : 0.00 % Twisted Proline : 0.34 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.04 (0.06), residues: 17832 helix: 0.88 (0.06), residues: 8804 sheet: -0.94 (0.12), residues: 1760 loop : -0.68 (0.08), residues: 7268 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 882 HIS 0.007 0.001 HIS B3771 PHE 0.050 0.002 PHE A4234 TYR 0.026 0.002 TYR B3968 ARG 0.011 0.000 ARG A1180 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 35664 Ramachandran restraints generated. 17832 Oldfield, 0 Emsley, 17832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 35664 Ramachandran restraints generated. 17832 Oldfield, 0 Emsley, 17832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1275 residues out of total 15548 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 182 poor density : 1093 time to evaluate : 12.624 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 155 LYS cc_start: 0.9571 (mmtt) cc_final: 0.9069 (tppt) REVERT: A 196 MET cc_start: 0.8691 (mpp) cc_final: 0.8320 (mpp) REVERT: A 213 TYR cc_start: 0.8347 (m-80) cc_final: 0.7311 (m-80) REVERT: A 228 ASP cc_start: 0.9438 (m-30) cc_final: 0.9177 (m-30) REVERT: A 340 LYS cc_start: 0.9259 (mmmm) cc_final: 0.9050 (mmmt) REVERT: A 343 GLU cc_start: 0.8846 (mt-10) cc_final: 0.8382 (mp0) REVERT: A 565 TYR cc_start: 0.9265 (t80) cc_final: 0.8957 (t80) REVERT: A 667 MET cc_start: 0.9206 (mmm) cc_final: 0.8501 (tpp) REVERT: A 960 MET cc_start: 0.5917 (mmm) cc_final: 0.4194 (mtm) REVERT: A 961 MET cc_start: 0.7003 (pmm) cc_final: 0.6456 (pmm) REVERT: A 1100 MET cc_start: 0.8272 (mmm) cc_final: 0.7767 (mmt) REVERT: A 1260 MET cc_start: 0.8352 (mtm) cc_final: 0.7441 (mpp) REVERT: A 1601 MET cc_start: 0.9622 (tpt) cc_final: 0.9218 (tpp) REVERT: A 1939 MET cc_start: 0.9651 (mmm) cc_final: 0.9353 (mmm) REVERT: A 1986 MET cc_start: 0.7921 (ppp) cc_final: 0.7461 (pmm) REVERT: A 2120 MET cc_start: 0.9314 (ttt) cc_final: 0.9074 (tpp) REVERT: A 2228 MET cc_start: 0.9610 (ppp) cc_final: 0.9170 (ppp) REVERT: A 2355 ARG cc_start: 0.9700 (ttm-80) cc_final: 0.9307 (ttm110) REVERT: A 2440 MET cc_start: 0.9102 (OUTLIER) cc_final: 0.8897 (mmp) REVERT: A 2618 MET cc_start: 0.8752 (mpp) cc_final: 0.8475 (mpp) REVERT: A 2932 MET cc_start: 0.7001 (tpt) cc_final: 0.6642 (ptt) REVERT: A 3038 MET cc_start: 0.5928 (mpp) cc_final: 0.5710 (mpp) REVERT: A 3081 MET cc_start: 0.6777 (ptp) cc_final: 0.6167 (pmm) REVERT: A 3276 MET cc_start: 0.8302 (mmp) cc_final: 0.7725 (mmp) REVERT: A 3411 LEU cc_start: 0.9756 (pp) cc_final: 0.9291 (mm) REVERT: A 3723 MET cc_start: 0.9305 (mmm) cc_final: 0.9039 (mmm) REVERT: A 3778 MET cc_start: 0.9652 (tmm) cc_final: 0.9406 (tmm) REVERT: A 3798 LEU cc_start: 0.9801 (mp) cc_final: 0.9415 (tt) REVERT: A 4023 MET cc_start: 0.9174 (tpp) cc_final: 0.8967 (tmm) REVERT: A 4184 MET cc_start: 0.9060 (tpp) cc_final: 0.8570 (tpp) REVERT: A 4639 MET cc_start: 0.9351 (mtp) cc_final: 0.9055 (mtp) REVERT: A 4779 LYS cc_start: 0.9645 (OUTLIER) cc_final: 0.9195 (ptpp) REVERT: A 4798 MET cc_start: 0.9415 (tpp) cc_final: 0.8795 (mmm) REVERT: A 4818 MET cc_start: 0.9010 (tmm) cc_final: 0.8479 (tpp) REVERT: A 4839 MET cc_start: 0.8843 (ppp) cc_final: 0.8600 (ppp) REVERT: A 4879 MET cc_start: 0.8921 (mmm) cc_final: 0.8136 (tpp) REVERT: A 4911 LEU cc_start: 0.9329 (OUTLIER) cc_final: 0.8935 (pt) REVERT: A 4954 MET cc_start: 0.9368 (tpp) cc_final: 0.9120 (tpp) REVERT: A 4967 TYR cc_start: 0.8350 (t80) cc_final: 0.7922 (t80) REVERT: A 4969 ASP cc_start: 0.9450 (m-30) cc_final: 0.8892 (p0) REVERT: A 4993 MET cc_start: 0.9215 (ptm) cc_final: 0.8993 (ppp) REVERT: A 5013 MET cc_start: 0.9359 (mmm) cc_final: 0.8987 (mmm) REVERT: B 155 LYS cc_start: 0.9557 (mmtt) cc_final: 0.9052 (tppt) REVERT: B 196 MET cc_start: 0.8648 (mpp) cc_final: 0.8248 (mpp) REVERT: B 213 TYR cc_start: 0.8374 (m-80) cc_final: 0.7396 (m-80) REVERT: B 228 ASP cc_start: 0.9618 (m-30) cc_final: 0.9217 (m-30) REVERT: B 340 LYS cc_start: 0.9272 (mmmm) cc_final: 0.9047 (mmmt) REVERT: B 343 GLU cc_start: 0.8973 (mt-10) cc_final: 0.8395 (mp0) REVERT: B 384 MET cc_start: 0.7184 (tmm) cc_final: 0.6904 (tmm) REVERT: B 483 MET cc_start: 0.8873 (mmt) cc_final: 0.8607 (mmp) REVERT: B 667 MET cc_start: 0.9322 (tpp) cc_final: 0.8989 (tpp) REVERT: B 941 MET cc_start: 0.5921 (tpt) cc_final: 0.4924 (mmm) REVERT: B 960 MET cc_start: 0.5822 (mmm) cc_final: 0.3990 (mtm) REVERT: B 961 MET cc_start: 0.6925 (pmm) cc_final: 0.6445 (pmm) REVERT: B 1100 MET cc_start: 0.8077 (mmm) cc_final: 0.7855 (mmt) REVERT: B 1260 MET cc_start: 0.8346 (mtm) cc_final: 0.7626 (mpp) REVERT: B 1601 MET cc_start: 0.9494 (tpp) cc_final: 0.9040 (tpp) REVERT: B 1865 MET cc_start: 0.9425 (mtp) cc_final: 0.9218 (mpp) REVERT: B 1939 MET cc_start: 0.9630 (mmm) cc_final: 0.9379 (mmm) REVERT: B 1986 MET cc_start: 0.7836 (ppp) cc_final: 0.7385 (pmm) REVERT: B 2120 MET cc_start: 0.9295 (ttt) cc_final: 0.9074 (tpp) REVERT: B 2153 MET cc_start: 0.9501 (mmp) cc_final: 0.8998 (mmm) REVERT: B 2198 MET cc_start: 0.9383 (mpp) cc_final: 0.8911 (mpp) REVERT: B 2293 GLN cc_start: 0.9473 (mm-40) cc_final: 0.9184 (tm-30) REVERT: B 2294 ASP cc_start: 0.9471 (m-30) cc_final: 0.8784 (m-30) REVERT: B 2355 ARG cc_start: 0.9697 (ttm-80) cc_final: 0.9304 (ttm110) REVERT: B 2440 MET cc_start: 0.9103 (OUTLIER) cc_final: 0.8901 (mmp) REVERT: B 2618 MET cc_start: 0.8760 (mpp) cc_final: 0.8491 (mpp) REVERT: B 2639 MET cc_start: 0.9221 (ppp) cc_final: 0.8658 (pmm) REVERT: B 2932 MET cc_start: 0.7193 (tpt) cc_final: 0.6904 (ptp) REVERT: B 3038 MET cc_start: 0.5907 (mpp) cc_final: 0.5688 (mpp) REVERT: B 3081 MET cc_start: 0.6896 (ptp) cc_final: 0.6261 (pmm) REVERT: B 3106 MET cc_start: 0.8860 (mmm) cc_final: 0.8458 (mmp) REVERT: B 3276 MET cc_start: 0.8238 (mmp) cc_final: 0.7606 (mmm) REVERT: B 3411 LEU cc_start: 0.9753 (pp) cc_final: 0.9283 (mm) REVERT: B 3723 MET cc_start: 0.9311 (mmm) cc_final: 0.9043 (mmm) REVERT: B 3798 LEU cc_start: 0.9804 (mp) cc_final: 0.9383 (tt) REVERT: B 4184 MET cc_start: 0.9061 (tpp) cc_final: 0.8567 (tpp) REVERT: B 4244 GLU cc_start: 0.9214 (tm-30) cc_final: 0.8690 (pp20) REVERT: B 4245 MET cc_start: 0.9389 (mmm) cc_final: 0.8867 (mmm) REVERT: B 4639 MET cc_start: 0.9371 (mtp) cc_final: 0.9071 (mtp) REVERT: B 4652 LEU cc_start: 0.9502 (pp) cc_final: 0.9221 (mm) REVERT: B 4779 LYS cc_start: 0.9650 (OUTLIER) cc_final: 0.9150 (ptpp) REVERT: B 4874 MET cc_start: 0.8327 (mmm) cc_final: 0.7884 (mmm) REVERT: B 4879 MET cc_start: 0.8763 (mmm) cc_final: 0.8384 (tpp) REVERT: B 4880 MET cc_start: 0.8517 (ptp) cc_final: 0.8255 (ptp) REVERT: B 4911 LEU cc_start: 0.9307 (OUTLIER) cc_final: 0.8949 (pt) REVERT: B 4954 MET cc_start: 0.9429 (tpp) cc_final: 0.9166 (tpp) REVERT: B 4967 TYR cc_start: 0.8354 (t80) cc_final: 0.7916 (t80) REVERT: B 4969 ASP cc_start: 0.9452 (m-30) cc_final: 0.8901 (p0) REVERT: B 5013 MET cc_start: 0.9573 (mmm) cc_final: 0.9298 (mmm) REVERT: C 155 LYS cc_start: 0.9562 (mmtt) cc_final: 0.9079 (tppt) REVERT: C 196 MET cc_start: 0.8652 (mpp) cc_final: 0.8258 (mpp) REVERT: C 213 TYR cc_start: 0.8330 (m-80) cc_final: 0.7300 (m-80) REVERT: C 228 ASP cc_start: 0.9618 (m-30) cc_final: 0.9218 (m-30) REVERT: C 340 LYS cc_start: 0.9269 (mmmm) cc_final: 0.9045 (mmmt) REVERT: C 343 GLU cc_start: 0.8969 (mt-10) cc_final: 0.8393 (mp0) REVERT: C 384 MET cc_start: 0.7195 (tmm) cc_final: 0.6910 (tmm) REVERT: C 565 TYR cc_start: 0.9310 (t80) cc_final: 0.9022 (t80) REVERT: C 667 MET cc_start: 0.9323 (tpp) cc_final: 0.8989 (tpp) REVERT: C 941 MET cc_start: 0.5924 (tpt) cc_final: 0.4929 (mmm) REVERT: C 960 MET cc_start: 0.5795 (mmm) cc_final: 0.3971 (mtm) REVERT: C 961 MET cc_start: 0.6919 (pmm) cc_final: 0.6437 (pmm) REVERT: C 1100 MET cc_start: 0.8092 (mmm) cc_final: 0.7869 (mmt) REVERT: C 1260 MET cc_start: 0.8530 (mtm) cc_final: 0.7713 (mpp) REVERT: C 1601 MET cc_start: 0.9496 (tpp) cc_final: 0.9049 (tpp) REVERT: C 1865 MET cc_start: 0.9425 (mtp) cc_final: 0.9218 (mpp) REVERT: C 1939 MET cc_start: 0.9630 (mmm) cc_final: 0.9378 (mmm) REVERT: C 1986 MET cc_start: 0.7836 (ppp) cc_final: 0.7384 (pmm) REVERT: C 2120 MET cc_start: 0.9296 (ttt) cc_final: 0.9075 (tpp) REVERT: C 2153 MET cc_start: 0.9501 (mmp) cc_final: 0.8998 (mmm) REVERT: C 2198 MET cc_start: 0.9381 (mpp) cc_final: 0.8889 (mpp) REVERT: C 2228 MET cc_start: 0.9603 (ppp) cc_final: 0.9188 (ppp) REVERT: C 2293 GLN cc_start: 0.9473 (mm-40) cc_final: 0.9184 (tm-30) REVERT: C 2294 ASP cc_start: 0.9466 (m-30) cc_final: 0.8781 (m-30) REVERT: C 2355 ARG cc_start: 0.9697 (ttm-80) cc_final: 0.9301 (ttm110) REVERT: C 2618 MET cc_start: 0.8761 (mpp) cc_final: 0.8490 (mpp) REVERT: C 2639 MET cc_start: 0.9221 (ppp) cc_final: 0.8658 (pmm) REVERT: C 2932 MET cc_start: 0.7192 (tpt) cc_final: 0.6903 (ptp) REVERT: C 3038 MET cc_start: 0.5908 (mpp) cc_final: 0.5689 (mpp) REVERT: C 3081 MET cc_start: 0.6898 (ptp) cc_final: 0.6262 (pmm) REVERT: C 3106 MET cc_start: 0.8861 (mmm) cc_final: 0.8461 (mmp) REVERT: C 3276 MET cc_start: 0.8239 (mmp) cc_final: 0.7590 (mmp) REVERT: C 3411 LEU cc_start: 0.9753 (pp) cc_final: 0.9284 (mm) REVERT: C 3723 MET cc_start: 0.9311 (mmm) cc_final: 0.9040 (mmm) REVERT: C 3798 LEU cc_start: 0.9803 (mp) cc_final: 0.9387 (tt) REVERT: C 4184 MET cc_start: 0.9041 (tpp) cc_final: 0.8471 (tpp) REVERT: C 4639 MET cc_start: 0.9371 (mtp) cc_final: 0.9072 (mtp) REVERT: C 4652 LEU cc_start: 0.9502 (pp) cc_final: 0.9221 (mm) REVERT: C 4779 LYS cc_start: 0.9649 (OUTLIER) cc_final: 0.9149 (ptpp) REVERT: C 4874 MET cc_start: 0.8313 (mmm) cc_final: 0.7871 (mmm) REVERT: C 4879 MET cc_start: 0.8761 (mmm) cc_final: 0.8368 (tpp) REVERT: C 4880 MET cc_start: 0.8479 (ptp) cc_final: 0.8240 (ptp) REVERT: C 4911 LEU cc_start: 0.9310 (OUTLIER) cc_final: 0.8947 (pt) REVERT: C 4954 MET cc_start: 0.9421 (tpp) cc_final: 0.9157 (tpp) REVERT: C 5013 MET cc_start: 0.9576 (mmm) cc_final: 0.9301 (mmm) REVERT: D 155 LYS cc_start: 0.9562 (mmtt) cc_final: 0.9079 (tppt) REVERT: D 196 MET cc_start: 0.8654 (mpp) cc_final: 0.8257 (mpp) REVERT: D 213 TYR cc_start: 0.8333 (m-80) cc_final: 0.7302 (m-80) REVERT: D 228 ASP cc_start: 0.9618 (m-30) cc_final: 0.9216 (m-30) REVERT: D 340 LYS cc_start: 0.9260 (mmmm) cc_final: 0.9039 (mmmt) REVERT: D 343 GLU cc_start: 0.8968 (mt-10) cc_final: 0.8390 (mp0) REVERT: D 384 MET cc_start: 0.7198 (tmm) cc_final: 0.6910 (tmm) REVERT: D 565 TYR cc_start: 0.9310 (t80) cc_final: 0.9021 (t80) REVERT: D 667 MET cc_start: 0.9323 (tpp) cc_final: 0.8989 (tpp) REVERT: D 941 MET cc_start: 0.5925 (tpt) cc_final: 0.4929 (mmm) REVERT: D 960 MET cc_start: 0.5790 (mmm) cc_final: 0.3968 (mtm) REVERT: D 961 MET cc_start: 0.6917 (pmm) cc_final: 0.6437 (pmm) REVERT: D 1100 MET cc_start: 0.8083 (mmm) cc_final: 0.7860 (mmt) REVERT: D 1260 MET cc_start: 0.8349 (mtm) cc_final: 0.7628 (mpp) REVERT: D 1601 MET cc_start: 0.9495 (tpp) cc_final: 0.9040 (tpp) REVERT: D 1865 MET cc_start: 0.9409 (mtp) cc_final: 0.9204 (mpp) REVERT: D 1939 MET cc_start: 0.9624 (mmm) cc_final: 0.9282 (mmm) REVERT: D 1986 MET cc_start: 0.7836 (ppp) cc_final: 0.7386 (pmm) REVERT: D 2120 MET cc_start: 0.9289 (ttt) cc_final: 0.9070 (tpp) REVERT: D 2153 MET cc_start: 0.9499 (mmp) cc_final: 0.9001 (mmm) REVERT: D 2198 MET cc_start: 0.9384 (mpp) cc_final: 0.8913 (mpp) REVERT: D 2293 GLN cc_start: 0.9474 (mm-40) cc_final: 0.9184 (tm-30) REVERT: D 2294 ASP cc_start: 0.9471 (m-30) cc_final: 0.8785 (m-30) REVERT: D 2355 ARG cc_start: 0.9697 (ttm-80) cc_final: 0.9301 (ttm110) REVERT: D 2618 MET cc_start: 0.8760 (mpp) cc_final: 0.8490 (mpp) REVERT: D 2639 MET cc_start: 0.9216 (ppp) cc_final: 0.8656 (pmm) REVERT: D 2932 MET cc_start: 0.7195 (tpt) cc_final: 0.6907 (ptp) REVERT: D 3038 MET cc_start: 0.5910 (mpp) cc_final: 0.5690 (mpp) REVERT: D 3081 MET cc_start: 0.6774 (ptp) cc_final: 0.6165 (pmm) REVERT: D 3106 MET cc_start: 0.8860 (mmm) cc_final: 0.8458 (mmp) REVERT: D 3276 MET cc_start: 0.8256 (mmp) cc_final: 0.7627 (mmm) REVERT: D 3411 LEU cc_start: 0.9754 (pp) cc_final: 0.9287 (mm) REVERT: D 3723 MET cc_start: 0.9311 (mmm) cc_final: 0.9041 (mmm) REVERT: D 3798 LEU cc_start: 0.9803 (mp) cc_final: 0.9387 (tt) REVERT: D 4184 MET cc_start: 0.9054 (tpp) cc_final: 0.8562 (tpp) REVERT: D 4207 MET cc_start: 0.9068 (ttp) cc_final: 0.8620 (tmm) REVERT: D 4244 GLU cc_start: 0.9198 (tm-30) cc_final: 0.8734 (pp20) REVERT: D 4245 MET cc_start: 0.9367 (mmm) cc_final: 0.8870 (mmm) REVERT: D 4652 LEU cc_start: 0.9495 (pp) cc_final: 0.9207 (mm) REVERT: D 4779 LYS cc_start: 0.9651 (OUTLIER) cc_final: 0.9152 (ptpp) REVERT: D 4874 MET cc_start: 0.8319 (mmm) cc_final: 0.7875 (mmm) REVERT: D 4879 MET cc_start: 0.8751 (mmm) cc_final: 0.8365 (tpp) REVERT: D 4880 MET cc_start: 0.8478 (ptp) cc_final: 0.8243 (ptp) REVERT: D 4911 LEU cc_start: 0.9309 (OUTLIER) cc_final: 0.8947 (pt) REVERT: D 4954 MET cc_start: 0.9420 (tpp) cc_final: 0.9156 (tpp) REVERT: D 4969 ASP cc_start: 0.9491 (m-30) cc_final: 0.9111 (m-30) REVERT: D 5013 MET cc_start: 0.9572 (mmm) cc_final: 0.9299 (mmm) REVERT: E 98 ILE cc_start: 0.8434 (OUTLIER) cc_final: 0.8232 (mp) REVERT: F 98 ILE cc_start: 0.8447 (OUTLIER) cc_final: 0.8241 (mp) REVERT: G 98 ILE cc_start: 0.8446 (OUTLIER) cc_final: 0.8241 (mp) outliers start: 182 outliers final: 154 residues processed: 1223 average time/residue: 1.1642 time to fit residues: 2588.1901 Evaluate side-chains 1241 residues out of total 15548 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 167 poor density : 1074 time to evaluate : 12.625 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 163 VAL Chi-restraints excluded: chain A residue 199 LEU Chi-restraints excluded: chain A residue 334 MET Chi-restraints excluded: chain A residue 605 SER Chi-restraints excluded: chain A residue 1248 VAL Chi-restraints excluded: chain A residue 1608 MET Chi-restraints excluded: chain A residue 1658 ASP Chi-restraints excluded: chain A residue 2440 MET Chi-restraints excluded: chain A residue 2602 VAL Chi-restraints excluded: chain A residue 3192 GLU Chi-restraints excluded: chain A residue 3203 VAL Chi-restraints excluded: chain A residue 3456 GLN Chi-restraints excluded: chain A residue 3529 ASP Chi-restraints excluded: chain A residue 3534 MET Chi-restraints excluded: chain A residue 3606 LEU Chi-restraints excluded: chain A residue 3715 LYS Chi-restraints excluded: chain A residue 3782 MET Chi-restraints excluded: chain A residue 3898 ASP Chi-restraints excluded: chain A residue 3899 PHE Chi-restraints excluded: chain A residue 4015 GLU Chi-restraints excluded: chain A residue 4059 LEU Chi-restraints excluded: chain A residue 4170 ILE Chi-restraints excluded: chain A residue 4198 SER Chi-restraints excluded: chain A residue 4200 THR Chi-restraints excluded: chain A residue 4555 LEU Chi-restraints excluded: chain A residue 4561 THR Chi-restraints excluded: chain A residue 4580 TYR Chi-restraints excluded: chain A residue 4656 LEU Chi-restraints excluded: chain A residue 4662 ASN Chi-restraints excluded: chain A residue 4697 VAL Chi-restraints excluded: chain A residue 4704 LEU Chi-restraints excluded: chain A residue 4720 VAL Chi-restraints excluded: chain A residue 4731 ILE Chi-restraints excluded: chain A residue 4779 LYS Chi-restraints excluded: chain A residue 4837 LEU Chi-restraints excluded: chain A residue 4852 THR Chi-restraints excluded: chain A residue 4882 CYS Chi-restraints excluded: chain A residue 4911 LEU Chi-restraints excluded: chain A residue 4924 VAL Chi-restraints excluded: chain A residue 4933 GLN Chi-restraints excluded: chain A residue 4942 GLU Chi-restraints excluded: chain A residue 4946 GLN Chi-restraints excluded: chain B residue 163 VAL Chi-restraints excluded: chain B residue 199 LEU Chi-restraints excluded: chain B residue 334 MET Chi-restraints excluded: chain B residue 605 SER Chi-restraints excluded: chain B residue 845 CYS Chi-restraints excluded: chain B residue 846 LEU Chi-restraints excluded: chain B residue 891 TRP Chi-restraints excluded: chain B residue 1248 VAL Chi-restraints excluded: chain B residue 1658 ASP Chi-restraints excluded: chain B residue 2440 MET Chi-restraints excluded: chain B residue 3192 GLU Chi-restraints excluded: chain B residue 3203 VAL Chi-restraints excluded: chain B residue 3454 GLU Chi-restraints excluded: chain B residue 3456 GLN Chi-restraints excluded: chain B residue 3534 MET Chi-restraints excluded: chain B residue 3715 LYS Chi-restraints excluded: chain B residue 3782 MET Chi-restraints excluded: chain B residue 3898 ASP Chi-restraints excluded: chain B residue 3990 VAL Chi-restraints excluded: chain B residue 4015 GLU Chi-restraints excluded: chain B residue 4059 LEU Chi-restraints excluded: chain B residue 4170 ILE Chi-restraints excluded: chain B residue 4198 SER Chi-restraints excluded: chain B residue 4200 THR Chi-restraints excluded: chain B residue 4555 LEU Chi-restraints excluded: chain B residue 4580 TYR Chi-restraints excluded: chain B residue 4656 LEU Chi-restraints excluded: chain B residue 4662 ASN Chi-restraints excluded: chain B residue 4697 VAL Chi-restraints excluded: chain B residue 4704 LEU Chi-restraints excluded: chain B residue 4717 ASP Chi-restraints excluded: chain B residue 4720 VAL Chi-restraints excluded: chain B residue 4723 LYS Chi-restraints excluded: chain B residue 4731 ILE Chi-restraints excluded: chain B residue 4779 LYS Chi-restraints excluded: chain B residue 4800 LEU Chi-restraints excluded: chain B residue 4882 CYS Chi-restraints excluded: chain B residue 4911 LEU Chi-restraints excluded: chain B residue 4929 LEU Chi-restraints excluded: chain B residue 4946 GLN Chi-restraints excluded: chain C residue 163 VAL Chi-restraints excluded: chain C residue 199 LEU Chi-restraints excluded: chain C residue 334 MET Chi-restraints excluded: chain C residue 605 SER Chi-restraints excluded: chain C residue 845 CYS Chi-restraints excluded: chain C residue 846 LEU Chi-restraints excluded: chain C residue 891 TRP Chi-restraints excluded: chain C residue 1248 VAL Chi-restraints excluded: chain C residue 1658 ASP Chi-restraints excluded: chain C residue 3192 GLU Chi-restraints excluded: chain C residue 3203 VAL Chi-restraints excluded: chain C residue 3454 GLU Chi-restraints excluded: chain C residue 3456 GLN Chi-restraints excluded: chain C residue 3534 MET Chi-restraints excluded: chain C residue 3715 LYS Chi-restraints excluded: chain C residue 3782 MET Chi-restraints excluded: chain C residue 3898 ASP Chi-restraints excluded: chain C residue 3990 VAL Chi-restraints excluded: chain C residue 4015 GLU Chi-restraints excluded: chain C residue 4059 LEU Chi-restraints excluded: chain C residue 4170 ILE Chi-restraints excluded: chain C residue 4198 SER Chi-restraints excluded: chain C residue 4200 THR Chi-restraints excluded: chain C residue 4555 LEU Chi-restraints excluded: chain C residue 4580 TYR Chi-restraints excluded: chain C residue 4656 LEU Chi-restraints excluded: chain C residue 4662 ASN Chi-restraints excluded: chain C residue 4697 VAL Chi-restraints excluded: chain C residue 4704 LEU Chi-restraints excluded: chain C residue 4717 ASP Chi-restraints excluded: chain C residue 4720 VAL Chi-restraints excluded: chain C residue 4731 ILE Chi-restraints excluded: chain C residue 4779 LYS Chi-restraints excluded: chain C residue 4800 LEU Chi-restraints excluded: chain C residue 4882 CYS Chi-restraints excluded: chain C residue 4911 LEU Chi-restraints excluded: chain C residue 4929 LEU Chi-restraints excluded: chain C residue 4942 GLU Chi-restraints excluded: chain C residue 4946 GLN Chi-restraints excluded: chain D residue 66 CYS Chi-restraints excluded: chain D residue 163 VAL Chi-restraints excluded: chain D residue 199 LEU Chi-restraints excluded: chain D residue 334 MET Chi-restraints excluded: chain D residue 605 SER Chi-restraints excluded: chain D residue 845 CYS Chi-restraints excluded: chain D residue 846 LEU Chi-restraints excluded: chain D residue 891 TRP Chi-restraints excluded: chain D residue 1248 VAL Chi-restraints excluded: chain D residue 1658 ASP Chi-restraints excluded: chain D residue 3192 GLU Chi-restraints excluded: chain D residue 3203 VAL Chi-restraints excluded: chain D residue 3454 GLU Chi-restraints excluded: chain D residue 3456 GLN Chi-restraints excluded: chain D residue 3534 MET Chi-restraints excluded: chain D residue 3715 LYS Chi-restraints excluded: chain D residue 3782 MET Chi-restraints excluded: chain D residue 3898 ASP Chi-restraints excluded: chain D residue 3990 VAL Chi-restraints excluded: chain D residue 4015 GLU Chi-restraints excluded: chain D residue 4059 LEU Chi-restraints excluded: chain D residue 4170 ILE Chi-restraints excluded: chain D residue 4198 SER Chi-restraints excluded: chain D residue 4200 THR Chi-restraints excluded: chain D residue 4555 LEU Chi-restraints excluded: chain D residue 4580 TYR Chi-restraints excluded: chain D residue 4656 LEU Chi-restraints excluded: chain D residue 4697 VAL Chi-restraints excluded: chain D residue 4704 LEU Chi-restraints excluded: chain D residue 4717 ASP Chi-restraints excluded: chain D residue 4720 VAL Chi-restraints excluded: chain D residue 4731 ILE Chi-restraints excluded: chain D residue 4779 LYS Chi-restraints excluded: chain D residue 4800 LEU Chi-restraints excluded: chain D residue 4882 CYS Chi-restraints excluded: chain D residue 4911 LEU Chi-restraints excluded: chain D residue 4929 LEU Chi-restraints excluded: chain D residue 4942 GLU Chi-restraints excluded: chain D residue 4946 GLN Chi-restraints excluded: chain E residue 79 ASP Chi-restraints excluded: chain E residue 98 ILE Chi-restraints excluded: chain F residue 79 ASP Chi-restraints excluded: chain F residue 98 ILE Chi-restraints excluded: chain G residue 79 ASP Chi-restraints excluded: chain G residue 98 ILE Chi-restraints excluded: chain H residue 79 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1788 random chunks: chunk 1600 optimal weight: 2.9990 chunk 1054 optimal weight: 0.0020 chunk 1698 optimal weight: 4.9990 chunk 1036 optimal weight: 3.9990 chunk 805 optimal weight: 2.9990 chunk 1180 optimal weight: 4.9990 chunk 1781 optimal weight: 10.0000 chunk 1639 optimal weight: 3.9990 chunk 1418 optimal weight: 20.0000 chunk 147 optimal weight: 20.0000 chunk 1095 optimal weight: 4.9990 overall best weight: 2.7996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 284 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 475 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 533 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1299 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1300 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2213 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2247 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2931 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3211 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3214 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4020 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 284 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 475 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 533 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 838 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1299 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1300 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2247 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2931 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3211 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3214 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B4020 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B4864 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 98 HIS ** C 284 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 412 ASN ** C 475 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 533 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 838 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1299 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1300 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2213 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2247 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2931 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C3211 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C3214 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C4020 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C4864 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C4933 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 284 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 412 ASN ** D 475 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 533 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1299 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1300 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2247 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2931 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D3211 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D3214 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D3318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D4020 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D4864 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D4933 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8464 moved from start: 0.3087 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.074 146196 Z= 0.208 Angle : 0.719 19.235 198016 Z= 0.348 Chirality : 0.043 0.374 21760 Planarity : 0.004 0.070 25752 Dihedral : 4.902 89.547 19609 Min Nonbonded Distance : 2.081 Molprobity Statistics. All-atom Clashscore : 19.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.59 % Favored : 95.41 % Rotamer: Outliers : 1.30 % Allowed : 15.78 % Favored : 82.92 % Cbeta Deviations : 0.01 % Peptide Plane: Cis-proline : 0.45 % Cis-general : 0.00 % Twisted Proline : 0.34 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.09 (0.06), residues: 17832 helix: 0.91 (0.06), residues: 8816 sheet: -0.89 (0.12), residues: 1760 loop : -0.66 (0.08), residues: 7256 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A1143 HIS 0.006 0.001 HIS A3771 PHE 0.051 0.002 PHE A4234 TYR 0.032 0.001 TYR A3968 ARG 0.011 0.000 ARG A1180 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 35664 Ramachandran restraints generated. 17832 Oldfield, 0 Emsley, 17832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 35664 Ramachandran restraints generated. 17832 Oldfield, 0 Emsley, 17832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1286 residues out of total 15548 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 178 poor density : 1108 time to evaluate : 11.678 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 155 LYS cc_start: 0.9568 (mmtt) cc_final: 0.9096 (tppt) REVERT: A 196 MET cc_start: 0.8668 (mpp) cc_final: 0.8363 (mpp) REVERT: A 213 TYR cc_start: 0.8299 (m-80) cc_final: 0.7348 (m-80) REVERT: A 228 ASP cc_start: 0.9446 (m-30) cc_final: 0.9192 (m-30) REVERT: A 340 LYS cc_start: 0.9247 (mmmm) cc_final: 0.9014 (mmmt) REVERT: A 343 GLU cc_start: 0.8868 (mt-10) cc_final: 0.8423 (mp0) REVERT: A 565 TYR cc_start: 0.9257 (t80) cc_final: 0.8975 (t80) REVERT: A 667 MET cc_start: 0.9166 (mmm) cc_final: 0.8471 (tpp) REVERT: A 960 MET cc_start: 0.5909 (mmm) cc_final: 0.4389 (mtm) REVERT: A 961 MET cc_start: 0.6908 (pmm) cc_final: 0.6387 (pmm) REVERT: A 1100 MET cc_start: 0.8239 (mmm) cc_final: 0.7800 (mmt) REVERT: A 1230 MET cc_start: 0.8617 (mmm) cc_final: 0.8294 (mmm) REVERT: A 1260 MET cc_start: 0.8454 (mtm) cc_final: 0.7562 (mpp) REVERT: A 1601 MET cc_start: 0.9601 (tpt) cc_final: 0.9191 (tpp) REVERT: A 1939 MET cc_start: 0.9626 (mmm) cc_final: 0.9333 (mmm) REVERT: A 1986 MET cc_start: 0.7913 (ppp) cc_final: 0.7458 (pmm) REVERT: A 2198 MET cc_start: 0.8877 (mmp) cc_final: 0.7918 (mpp) REVERT: A 2228 MET cc_start: 0.9592 (ppp) cc_final: 0.9240 (ppp) REVERT: A 2490 MET cc_start: 0.8534 (mtp) cc_final: 0.7931 (mtt) REVERT: A 2618 MET cc_start: 0.8783 (mpp) cc_final: 0.8513 (mpp) REVERT: A 2932 MET cc_start: 0.7061 (tpt) cc_final: 0.6717 (ptt) REVERT: A 3038 MET cc_start: 0.5909 (mpp) cc_final: 0.5697 (mpp) REVERT: A 3081 MET cc_start: 0.6912 (ptp) cc_final: 0.6382 (pmm) REVERT: A 3276 MET cc_start: 0.8289 (mmp) cc_final: 0.7763 (mmm) REVERT: A 3411 LEU cc_start: 0.9754 (pp) cc_final: 0.9288 (mm) REVERT: A 3652 MET cc_start: 0.9537 (mpp) cc_final: 0.9168 (pmm) REVERT: A 3723 MET cc_start: 0.9307 (mmm) cc_final: 0.9036 (mmm) REVERT: A 3778 MET cc_start: 0.9650 (tmm) cc_final: 0.9422 (tmm) REVERT: A 3798 LEU cc_start: 0.9786 (mp) cc_final: 0.9384 (tt) REVERT: A 4023 MET cc_start: 0.9131 (tpp) cc_final: 0.8880 (tmm) REVERT: A 4026 MET cc_start: 0.9626 (tmm) cc_final: 0.9392 (tmm) REVERT: A 4184 MET cc_start: 0.9061 (tpp) cc_final: 0.8583 (tpp) REVERT: A 4639 MET cc_start: 0.9343 (mtp) cc_final: 0.9039 (mtp) REVERT: A 4779 LYS cc_start: 0.9658 (OUTLIER) cc_final: 0.9201 (ptpp) REVERT: A 4798 MET cc_start: 0.9371 (tpp) cc_final: 0.8869 (mmm) REVERT: A 4818 MET cc_start: 0.9036 (tmm) cc_final: 0.8488 (tpp) REVERT: A 4839 MET cc_start: 0.8816 (ppp) cc_final: 0.8590 (ppp) REVERT: A 4879 MET cc_start: 0.8888 (mmm) cc_final: 0.8167 (tpp) REVERT: A 4911 LEU cc_start: 0.9318 (OUTLIER) cc_final: 0.8947 (pt) REVERT: A 4922 PHE cc_start: 0.8960 (m-80) cc_final: 0.8499 (m-80) REVERT: A 4954 MET cc_start: 0.9336 (tpp) cc_final: 0.9087 (tpp) REVERT: A 4967 TYR cc_start: 0.8337 (t80) cc_final: 0.7914 (t80) REVERT: A 4969 ASP cc_start: 0.9420 (m-30) cc_final: 0.8863 (p0) REVERT: A 4993 MET cc_start: 0.9216 (ptm) cc_final: 0.8979 (ppp) REVERT: A 5013 MET cc_start: 0.9335 (mmm) cc_final: 0.8921 (mmm) REVERT: B 155 LYS cc_start: 0.9552 (mmtt) cc_final: 0.9012 (tppt) REVERT: B 196 MET cc_start: 0.8655 (mpp) cc_final: 0.8346 (mpp) REVERT: B 213 TYR cc_start: 0.8282 (m-80) cc_final: 0.7322 (m-80) REVERT: B 228 ASP cc_start: 0.9616 (m-30) cc_final: 0.9215 (m-30) REVERT: B 340 LYS cc_start: 0.9243 (mmmm) cc_final: 0.8995 (mmmt) REVERT: B 343 GLU cc_start: 0.8942 (mt-10) cc_final: 0.8377 (mp0) REVERT: B 384 MET cc_start: 0.7162 (tmm) cc_final: 0.6876 (tmm) REVERT: B 667 MET cc_start: 0.9296 (tpp) cc_final: 0.8912 (tpp) REVERT: B 941 MET cc_start: 0.6079 (tpt) cc_final: 0.5134 (mmm) REVERT: B 960 MET cc_start: 0.5870 (mmm) cc_final: 0.4072 (mtm) REVERT: B 961 MET cc_start: 0.6876 (pmm) cc_final: 0.6366 (pmm) REVERT: B 1100 MET cc_start: 0.8021 (mmm) cc_final: 0.7805 (mmt) REVERT: B 1260 MET cc_start: 0.8314 (mtm) cc_final: 0.7623 (mpp) REVERT: B 1601 MET cc_start: 0.9477 (tpp) cc_final: 0.9030 (tpp) REVERT: B 1865 MET cc_start: 0.9435 (mtp) cc_final: 0.9203 (mpp) REVERT: B 1939 MET cc_start: 0.9621 (mmm) cc_final: 0.9369 (mmm) REVERT: B 1986 MET cc_start: 0.7822 (ppp) cc_final: 0.7375 (pmm) REVERT: B 2153 MET cc_start: 0.9498 (mmp) cc_final: 0.9024 (mmm) REVERT: B 2198 MET cc_start: 0.9345 (mpp) cc_final: 0.8914 (mpp) REVERT: B 2293 GLN cc_start: 0.9451 (mm-40) cc_final: 0.9173 (tm-30) REVERT: B 2294 ASP cc_start: 0.9463 (m-30) cc_final: 0.8759 (m-30) REVERT: B 2490 MET cc_start: 0.8505 (mtp) cc_final: 0.7902 (mtt) REVERT: B 2530 MET cc_start: 0.9595 (mpp) cc_final: 0.8500 (pmm) REVERT: B 2618 MET cc_start: 0.8746 (mpp) cc_final: 0.8470 (mpp) REVERT: B 2639 MET cc_start: 0.9160 (ppp) cc_final: 0.8683 (pmm) REVERT: B 2932 MET cc_start: 0.7172 (tpt) cc_final: 0.6847 (ptt) REVERT: B 3038 MET cc_start: 0.5889 (mpp) cc_final: 0.5675 (mpp) REVERT: B 3081 MET cc_start: 0.6879 (ptp) cc_final: 0.6252 (pmm) REVERT: B 3106 MET cc_start: 0.8855 (mmm) cc_final: 0.8443 (mmp) REVERT: B 3276 MET cc_start: 0.8243 (mmp) cc_final: 0.7649 (mmm) REVERT: B 3411 LEU cc_start: 0.9751 (pp) cc_final: 0.9280 (mm) REVERT: B 3652 MET cc_start: 0.9552 (mpp) cc_final: 0.9181 (pmm) REVERT: B 3723 MET cc_start: 0.9316 (mmm) cc_final: 0.9052 (mmm) REVERT: B 3798 LEU cc_start: 0.9800 (mp) cc_final: 0.9371 (tt) REVERT: B 3816 MET cc_start: 0.9409 (mmp) cc_final: 0.8532 (mmp) REVERT: B 4026 MET cc_start: 0.9606 (tmm) cc_final: 0.9382 (tmm) REVERT: B 4184 MET cc_start: 0.9058 (tpp) cc_final: 0.8596 (tpp) REVERT: B 4245 MET cc_start: 0.9388 (mmm) cc_final: 0.9050 (mmm) REVERT: B 4639 MET cc_start: 0.9363 (mtp) cc_final: 0.9066 (mtp) REVERT: B 4652 LEU cc_start: 0.9498 (pp) cc_final: 0.9224 (mm) REVERT: B 4779 LYS cc_start: 0.9660 (OUTLIER) cc_final: 0.9152 (ptpp) REVERT: B 4818 MET cc_start: 0.8903 (tpp) cc_final: 0.8669 (tpp) REVERT: B 4874 MET cc_start: 0.8346 (mmm) cc_final: 0.8145 (mmm) REVERT: B 4879 MET cc_start: 0.8734 (mmm) cc_final: 0.8307 (tpp) REVERT: B 4880 MET cc_start: 0.8497 (ptp) cc_final: 0.8206 (ptp) REVERT: B 4911 LEU cc_start: 0.9293 (OUTLIER) cc_final: 0.8932 (pt) REVERT: B 4954 MET cc_start: 0.9411 (tpp) cc_final: 0.9138 (tpp) REVERT: B 4967 TYR cc_start: 0.8336 (t80) cc_final: 0.7905 (t80) REVERT: B 4969 ASP cc_start: 0.9423 (m-30) cc_final: 0.8870 (p0) REVERT: B 5013 MET cc_start: 0.9553 (mmm) cc_final: 0.9255 (mmm) REVERT: C 155 LYS cc_start: 0.9552 (mmtt) cc_final: 0.9000 (tppt) REVERT: C 196 MET cc_start: 0.8660 (mpp) cc_final: 0.8353 (mpp) REVERT: C 213 TYR cc_start: 0.8278 (m-80) cc_final: 0.7318 (m-80) REVERT: C 228 ASP cc_start: 0.9616 (m-30) cc_final: 0.9216 (m-30) REVERT: C 340 LYS cc_start: 0.9239 (mmmm) cc_final: 0.8992 (mmmt) REVERT: C 343 GLU cc_start: 0.8937 (mt-10) cc_final: 0.8375 (mp0) REVERT: C 384 MET cc_start: 0.7163 (tmm) cc_final: 0.6879 (tmm) REVERT: C 565 TYR cc_start: 0.9332 (t80) cc_final: 0.9020 (t80) REVERT: C 667 MET cc_start: 0.9298 (tpp) cc_final: 0.8913 (tpp) REVERT: C 941 MET cc_start: 0.6080 (tpt) cc_final: 0.5136 (mmm) REVERT: C 960 MET cc_start: 0.5840 (mmm) cc_final: 0.4050 (mtm) REVERT: C 961 MET cc_start: 0.6870 (pmm) cc_final: 0.6360 (pmm) REVERT: C 1100 MET cc_start: 0.8026 (mmm) cc_final: 0.7811 (mmt) REVERT: C 1260 MET cc_start: 0.8306 (mtm) cc_final: 0.7619 (mpp) REVERT: C 1601 MET cc_start: 0.9482 (tpp) cc_final: 0.9034 (tpp) REVERT: C 1865 MET cc_start: 0.9435 (mtp) cc_final: 0.9203 (mpp) REVERT: C 1939 MET cc_start: 0.9621 (mmm) cc_final: 0.9370 (mmm) REVERT: C 1986 MET cc_start: 0.7821 (ppp) cc_final: 0.7375 (pmm) REVERT: C 2153 MET cc_start: 0.9497 (mmp) cc_final: 0.9022 (mmm) REVERT: C 2198 MET cc_start: 0.9343 (mpp) cc_final: 0.8886 (mpp) REVERT: C 2228 MET cc_start: 0.9580 (ppp) cc_final: 0.9236 (ppp) REVERT: C 2293 GLN cc_start: 0.9450 (mm-40) cc_final: 0.9173 (tm-30) REVERT: C 2294 ASP cc_start: 0.9462 (m-30) cc_final: 0.8757 (m-30) REVERT: C 2490 MET cc_start: 0.8506 (mtp) cc_final: 0.7903 (mtt) REVERT: C 2530 MET cc_start: 0.9593 (mpp) cc_final: 0.8500 (pmm) REVERT: C 2618 MET cc_start: 0.8746 (mpp) cc_final: 0.8470 (mpp) REVERT: C 2639 MET cc_start: 0.9159 (ppp) cc_final: 0.8682 (pmm) REVERT: C 2932 MET cc_start: 0.7172 (tpt) cc_final: 0.6846 (ptt) REVERT: C 3038 MET cc_start: 0.5890 (mpp) cc_final: 0.5677 (mpp) REVERT: C 3081 MET cc_start: 0.6880 (ptp) cc_final: 0.6253 (pmm) REVERT: C 3106 MET cc_start: 0.8855 (mmm) cc_final: 0.8444 (mmp) REVERT: C 3276 MET cc_start: 0.8249 (mmp) cc_final: 0.7653 (mmm) REVERT: C 3411 LEU cc_start: 0.9751 (pp) cc_final: 0.9281 (mm) REVERT: C 3652 MET cc_start: 0.9553 (mpp) cc_final: 0.9183 (pmm) REVERT: C 3723 MET cc_start: 0.9313 (mmm) cc_final: 0.9051 (mmm) REVERT: C 3798 LEU cc_start: 0.9801 (mp) cc_final: 0.9377 (tt) REVERT: C 3816 MET cc_start: 0.9408 (mmp) cc_final: 0.8532 (mmp) REVERT: C 4000 MET cc_start: 0.8855 (tpp) cc_final: 0.8369 (tpp) REVERT: C 4026 MET cc_start: 0.9641 (tmm) cc_final: 0.9408 (tmm) REVERT: C 4184 MET cc_start: 0.9043 (tpp) cc_final: 0.8520 (tpp) REVERT: C 4639 MET cc_start: 0.9365 (mtp) cc_final: 0.9067 (mtp) REVERT: C 4652 LEU cc_start: 0.9499 (pp) cc_final: 0.9224 (mm) REVERT: C 4779 LYS cc_start: 0.9660 (OUTLIER) cc_final: 0.9152 (ptpp) REVERT: C 4818 MET cc_start: 0.8845 (tpp) cc_final: 0.8586 (tpp) REVERT: C 4874 MET cc_start: 0.8373 (mmm) cc_final: 0.8166 (mmm) REVERT: C 4879 MET cc_start: 0.8742 (mmm) cc_final: 0.8280 (tpp) REVERT: C 4880 MET cc_start: 0.8465 (ptp) cc_final: 0.8196 (ptp) REVERT: C 4911 LEU cc_start: 0.9295 (OUTLIER) cc_final: 0.8930 (pt) REVERT: C 4954 MET cc_start: 0.9403 (tpp) cc_final: 0.9125 (tpp) REVERT: C 5013 MET cc_start: 0.9557 (mmm) cc_final: 0.9256 (mmm) REVERT: D 155 LYS cc_start: 0.9551 (mmtt) cc_final: 0.9001 (tppt) REVERT: D 196 MET cc_start: 0.8659 (mpp) cc_final: 0.8353 (mpp) REVERT: D 213 TYR cc_start: 0.8280 (m-80) cc_final: 0.7325 (m-80) REVERT: D 228 ASP cc_start: 0.9614 (m-30) cc_final: 0.9210 (m-30) REVERT: D 340 LYS cc_start: 0.9232 (mmmm) cc_final: 0.8988 (mmmt) REVERT: D 343 GLU cc_start: 0.8937 (mt-10) cc_final: 0.8373 (mp0) REVERT: D 384 MET cc_start: 0.7171 (tmm) cc_final: 0.6883 (tmm) REVERT: D 565 TYR cc_start: 0.9331 (t80) cc_final: 0.9020 (t80) REVERT: D 667 MET cc_start: 0.9299 (tpp) cc_final: 0.8914 (tpp) REVERT: D 941 MET cc_start: 0.6082 (tpt) cc_final: 0.5139 (mmm) REVERT: D 960 MET cc_start: 0.5831 (mmm) cc_final: 0.4046 (mtm) REVERT: D 961 MET cc_start: 0.6868 (pmm) cc_final: 0.6358 (pmm) REVERT: D 1100 MET cc_start: 0.8021 (mmm) cc_final: 0.7808 (mmt) REVERT: D 1260 MET cc_start: 0.8314 (mtm) cc_final: 0.7622 (mpp) REVERT: D 1601 MET cc_start: 0.9480 (tpp) cc_final: 0.9032 (tpp) REVERT: D 1865 MET cc_start: 0.9420 (mtp) cc_final: 0.9215 (mpp) REVERT: D 1939 MET cc_start: 0.9620 (mmm) cc_final: 0.9269 (mmm) REVERT: D 1986 MET cc_start: 0.7822 (ppp) cc_final: 0.7376 (pmm) REVERT: D 2153 MET cc_start: 0.9496 (mmp) cc_final: 0.9024 (mmm) REVERT: D 2198 MET cc_start: 0.9346 (mpp) cc_final: 0.8917 (mpp) REVERT: D 2293 GLN cc_start: 0.9451 (mm-40) cc_final: 0.9174 (tm-30) REVERT: D 2294 ASP cc_start: 0.9463 (m-30) cc_final: 0.8759 (m-30) REVERT: D 2530 MET cc_start: 0.9592 (mpp) cc_final: 0.8499 (pmm) REVERT: D 2618 MET cc_start: 0.8748 (mpp) cc_final: 0.8472 (mpp) REVERT: D 2639 MET cc_start: 0.9152 (ppp) cc_final: 0.8655 (pmm) REVERT: D 2932 MET cc_start: 0.7179 (tpt) cc_final: 0.6853 (ptt) REVERT: D 3038 MET cc_start: 0.5890 (mpp) cc_final: 0.5677 (mpp) REVERT: D 3081 MET cc_start: 0.6900 (ptp) cc_final: 0.6322 (pmm) REVERT: D 3106 MET cc_start: 0.8854 (mmm) cc_final: 0.8444 (mmp) REVERT: D 3276 MET cc_start: 0.8247 (mmp) cc_final: 0.7653 (mmm) REVERT: D 3411 LEU cc_start: 0.9752 (pp) cc_final: 0.9284 (mm) REVERT: D 3652 MET cc_start: 0.9551 (mpp) cc_final: 0.9180 (pmm) REVERT: D 3723 MET cc_start: 0.9313 (mmm) cc_final: 0.9052 (mmm) REVERT: D 3798 LEU cc_start: 0.9801 (mp) cc_final: 0.9376 (tt) REVERT: D 3816 MET cc_start: 0.9411 (mmp) cc_final: 0.8532 (mmp) REVERT: D 4000 MET cc_start: 0.8813 (tpp) cc_final: 0.8334 (tpp) REVERT: D 4026 MET cc_start: 0.9606 (tmm) cc_final: 0.9380 (tmm) REVERT: D 4184 MET cc_start: 0.9048 (tpp) cc_final: 0.8586 (tpp) REVERT: D 4205 TRP cc_start: 0.9496 (t-100) cc_final: 0.9283 (t60) REVERT: D 4207 MET cc_start: 0.9107 (ttp) cc_final: 0.8675 (tmm) REVERT: D 4245 MET cc_start: 0.9358 (mmm) cc_final: 0.9008 (mmm) REVERT: D 4639 MET cc_start: 0.9378 (mtp) cc_final: 0.8739 (mpp) REVERT: D 4652 LEU cc_start: 0.9498 (pp) cc_final: 0.9218 (mm) REVERT: D 4779 LYS cc_start: 0.9660 (OUTLIER) cc_final: 0.9153 (ptpp) REVERT: D 4818 MET cc_start: 0.8933 (tpp) cc_final: 0.8639 (tpp) REVERT: D 4879 MET cc_start: 0.8714 (mmm) cc_final: 0.8269 (tpp) REVERT: D 4880 MET cc_start: 0.8464 (ptp) cc_final: 0.8187 (ptp) REVERT: D 4911 LEU cc_start: 0.9313 (OUTLIER) cc_final: 0.8955 (pt) REVERT: D 4954 MET cc_start: 0.9406 (tpp) cc_final: 0.9129 (tpp) REVERT: D 4969 ASP cc_start: 0.9475 (m-30) cc_final: 0.9075 (m-30) REVERT: D 5013 MET cc_start: 0.9553 (mmm) cc_final: 0.9256 (mmm) REVERT: F 98 ILE cc_start: 0.8391 (OUTLIER) cc_final: 0.8189 (mp) REVERT: G 98 ILE cc_start: 0.8390 (OUTLIER) cc_final: 0.8189 (mp) outliers start: 178 outliers final: 149 residues processed: 1233 average time/residue: 1.1920 time to fit residues: 2682.0077 Evaluate side-chains 1248 residues out of total 15548 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 159 poor density : 1089 time to evaluate : 11.326 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 163 VAL Chi-restraints excluded: chain A residue 197 GLN Chi-restraints excluded: chain A residue 199 LEU Chi-restraints excluded: chain A residue 334 MET Chi-restraints excluded: chain A residue 605 SER Chi-restraints excluded: chain A residue 1248 VAL Chi-restraints excluded: chain A residue 1608 MET Chi-restraints excluded: chain A residue 1658 ASP Chi-restraints excluded: chain A residue 2602 VAL Chi-restraints excluded: chain A residue 3192 GLU Chi-restraints excluded: chain A residue 3203 VAL Chi-restraints excluded: chain A residue 3456 GLN Chi-restraints excluded: chain A residue 3529 ASP Chi-restraints excluded: chain A residue 3534 MET Chi-restraints excluded: chain A residue 3606 LEU Chi-restraints excluded: chain A residue 3715 LYS Chi-restraints excluded: chain A residue 3782 MET Chi-restraints excluded: chain A residue 3898 ASP Chi-restraints excluded: chain A residue 3899 PHE Chi-restraints excluded: chain A residue 4015 GLU Chi-restraints excluded: chain A residue 4059 LEU Chi-restraints excluded: chain A residue 4170 ILE Chi-restraints excluded: chain A residue 4198 SER Chi-restraints excluded: chain A residue 4200 THR Chi-restraints excluded: chain A residue 4555 LEU Chi-restraints excluded: chain A residue 4580 TYR Chi-restraints excluded: chain A residue 4656 LEU Chi-restraints excluded: chain A residue 4662 ASN Chi-restraints excluded: chain A residue 4697 VAL Chi-restraints excluded: chain A residue 4704 LEU Chi-restraints excluded: chain A residue 4720 VAL Chi-restraints excluded: chain A residue 4731 ILE Chi-restraints excluded: chain A residue 4779 LYS Chi-restraints excluded: chain A residue 4837 LEU Chi-restraints excluded: chain A residue 4882 CYS Chi-restraints excluded: chain A residue 4911 LEU Chi-restraints excluded: chain A residue 4942 GLU Chi-restraints excluded: chain A residue 4946 GLN Chi-restraints excluded: chain B residue 66 CYS Chi-restraints excluded: chain B residue 197 GLN Chi-restraints excluded: chain B residue 199 LEU Chi-restraints excluded: chain B residue 334 MET Chi-restraints excluded: chain B residue 605 SER Chi-restraints excluded: chain B residue 845 CYS Chi-restraints excluded: chain B residue 846 LEU Chi-restraints excluded: chain B residue 891 TRP Chi-restraints excluded: chain B residue 1248 VAL Chi-restraints excluded: chain B residue 1658 ASP Chi-restraints excluded: chain B residue 3192 GLU Chi-restraints excluded: chain B residue 3203 VAL Chi-restraints excluded: chain B residue 3454 GLU Chi-restraints excluded: chain B residue 3456 GLN Chi-restraints excluded: chain B residue 3534 MET Chi-restraints excluded: chain B residue 3715 LYS Chi-restraints excluded: chain B residue 3782 MET Chi-restraints excluded: chain B residue 3898 ASP Chi-restraints excluded: chain B residue 4015 GLU Chi-restraints excluded: chain B residue 4059 LEU Chi-restraints excluded: chain B residue 4170 ILE Chi-restraints excluded: chain B residue 4198 SER Chi-restraints excluded: chain B residue 4200 THR Chi-restraints excluded: chain B residue 4555 LEU Chi-restraints excluded: chain B residue 4580 TYR Chi-restraints excluded: chain B residue 4656 LEU Chi-restraints excluded: chain B residue 4662 ASN Chi-restraints excluded: chain B residue 4697 VAL Chi-restraints excluded: chain B residue 4704 LEU Chi-restraints excluded: chain B residue 4717 ASP Chi-restraints excluded: chain B residue 4720 VAL Chi-restraints excluded: chain B residue 4723 LYS Chi-restraints excluded: chain B residue 4731 ILE Chi-restraints excluded: chain B residue 4779 LYS Chi-restraints excluded: chain B residue 4800 LEU Chi-restraints excluded: chain B residue 4882 CYS Chi-restraints excluded: chain B residue 4911 LEU Chi-restraints excluded: chain B residue 4929 LEU Chi-restraints excluded: chain B residue 4946 GLN Chi-restraints excluded: chain C residue 66 CYS Chi-restraints excluded: chain C residue 197 GLN Chi-restraints excluded: chain C residue 199 LEU Chi-restraints excluded: chain C residue 334 MET Chi-restraints excluded: chain C residue 605 SER Chi-restraints excluded: chain C residue 845 CYS Chi-restraints excluded: chain C residue 846 LEU Chi-restraints excluded: chain C residue 891 TRP Chi-restraints excluded: chain C residue 1248 VAL Chi-restraints excluded: chain C residue 1658 ASP Chi-restraints excluded: chain C residue 3192 GLU Chi-restraints excluded: chain C residue 3203 VAL Chi-restraints excluded: chain C residue 3454 GLU Chi-restraints excluded: chain C residue 3456 GLN Chi-restraints excluded: chain C residue 3715 LYS Chi-restraints excluded: chain C residue 3782 MET Chi-restraints excluded: chain C residue 3898 ASP Chi-restraints excluded: chain C residue 3990 VAL Chi-restraints excluded: chain C residue 4015 GLU Chi-restraints excluded: chain C residue 4059 LEU Chi-restraints excluded: chain C residue 4170 ILE Chi-restraints excluded: chain C residue 4200 THR Chi-restraints excluded: chain C residue 4555 LEU Chi-restraints excluded: chain C residue 4580 TYR Chi-restraints excluded: chain C residue 4656 LEU Chi-restraints excluded: chain C residue 4662 ASN Chi-restraints excluded: chain C residue 4697 VAL Chi-restraints excluded: chain C residue 4704 LEU Chi-restraints excluded: chain C residue 4717 ASP Chi-restraints excluded: chain C residue 4720 VAL Chi-restraints excluded: chain C residue 4731 ILE Chi-restraints excluded: chain C residue 4779 LYS Chi-restraints excluded: chain C residue 4800 LEU Chi-restraints excluded: chain C residue 4882 CYS Chi-restraints excluded: chain C residue 4911 LEU Chi-restraints excluded: chain C residue 4929 LEU Chi-restraints excluded: chain C residue 4942 GLU Chi-restraints excluded: chain C residue 4946 GLN Chi-restraints excluded: chain C residue 4971 THR Chi-restraints excluded: chain D residue 66 CYS Chi-restraints excluded: chain D residue 199 LEU Chi-restraints excluded: chain D residue 334 MET Chi-restraints excluded: chain D residue 605 SER Chi-restraints excluded: chain D residue 845 CYS Chi-restraints excluded: chain D residue 846 LEU Chi-restraints excluded: chain D residue 891 TRP Chi-restraints excluded: chain D residue 1248 VAL Chi-restraints excluded: chain D residue 1658 ASP Chi-restraints excluded: chain D residue 3192 GLU Chi-restraints excluded: chain D residue 3203 VAL Chi-restraints excluded: chain D residue 3454 GLU Chi-restraints excluded: chain D residue 3456 GLN Chi-restraints excluded: chain D residue 3534 MET Chi-restraints excluded: chain D residue 3715 LYS Chi-restraints excluded: chain D residue 3782 MET Chi-restraints excluded: chain D residue 3898 ASP Chi-restraints excluded: chain D residue 4015 GLU Chi-restraints excluded: chain D residue 4059 LEU Chi-restraints excluded: chain D residue 4170 ILE Chi-restraints excluded: chain D residue 4198 SER Chi-restraints excluded: chain D residue 4200 THR Chi-restraints excluded: chain D residue 4555 LEU Chi-restraints excluded: chain D residue 4580 TYR Chi-restraints excluded: chain D residue 4656 LEU Chi-restraints excluded: chain D residue 4697 VAL Chi-restraints excluded: chain D residue 4704 LEU Chi-restraints excluded: chain D residue 4717 ASP Chi-restraints excluded: chain D residue 4720 VAL Chi-restraints excluded: chain D residue 4731 ILE Chi-restraints excluded: chain D residue 4779 LYS Chi-restraints excluded: chain D residue 4800 LEU Chi-restraints excluded: chain D residue 4882 CYS Chi-restraints excluded: chain D residue 4911 LEU Chi-restraints excluded: chain D residue 4929 LEU Chi-restraints excluded: chain D residue 4942 GLU Chi-restraints excluded: chain D residue 4946 GLN Chi-restraints excluded: chain E residue 79 ASP Chi-restraints excluded: chain F residue 79 ASP Chi-restraints excluded: chain F residue 98 ILE Chi-restraints excluded: chain G residue 79 ASP Chi-restraints excluded: chain G residue 98 ILE Chi-restraints excluded: chain H residue 79 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1788 random chunks: chunk 869 optimal weight: 6.9990 chunk 1126 optimal weight: 40.0000 chunk 1510 optimal weight: 5.9990 chunk 434 optimal weight: 10.0000 chunk 1307 optimal weight: 2.9990 chunk 209 optimal weight: 6.9990 chunk 394 optimal weight: 8.9990 chunk 1420 optimal weight: 20.0000 chunk 594 optimal weight: 9.9990 chunk 1458 optimal weight: 20.0000 chunk 179 optimal weight: 7.9990 overall best weight: 6.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 226 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 284 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 475 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 533 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 797 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 877 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1299 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1300 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1645 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2213 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2247 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2931 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3211 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3214 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3734 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4020 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4803 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A4933 GLN ** B 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 226 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 284 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 838 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 877 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1299 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1300 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1645 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2283 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2931 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3211 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3214 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3734 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B4020 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B4803 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B4933 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 226 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 284 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 412 ASN C 489 ASN ** C 838 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 877 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1299 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1300 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1645 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2213 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2931 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C3211 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C3214 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C3734 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C4020 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C4803 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C4933 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C5006 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 226 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 284 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 412 ASN ** D 877 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1299 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1300 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1645 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2283 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2931 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D3211 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D3214 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D3318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D3734 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D4020 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D4803 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D4933 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3579 r_free = 0.3579 target = 0.053542 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3112 r_free = 0.3112 target = 0.037026 restraints weight = 2252552.668| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3151 r_free = 0.3151 target = 0.038376 restraints weight = 1165445.135| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3177 r_free = 0.3177 target = 0.039272 restraints weight = 761034.724| |-----------------------------------------------------------------------------| r_work (final): 0.3122 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3122 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3122 r_free = 0.3122 target_work(ls_wunit_k1) = 0.038 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3121 r_free = 0.3121 target_work(ls_wunit_k1) = 0.038 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 24 | |-----------------------------------------------------------------------------| r_final: 0.3121 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8529 moved from start: 0.3305 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.127 146196 Z= 0.315 Angle : 0.756 20.827 198016 Z= 0.376 Chirality : 0.044 0.479 21760 Planarity : 0.005 0.069 25752 Dihedral : 5.037 90.559 19609 Min Nonbonded Distance : 2.042 Molprobity Statistics. All-atom Clashscore : 24.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.50 % Favored : 94.50 % Rotamer: Outliers : 1.24 % Allowed : 15.99 % Favored : 82.77 % Cbeta Deviations : 0.01 % Peptide Plane: Cis-proline : 0.45 % Cis-general : 0.00 % Twisted Proline : 0.34 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.13 (0.06), residues: 17832 helix: 0.71 (0.06), residues: 8800 sheet: -1.03 (0.12), residues: 1776 loop : -0.73 (0.08), residues: 7256 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP B4205 HIS 0.007 0.001 HIS A 597 PHE 0.051 0.002 PHE A4571 TYR 0.035 0.002 TYR A3968 ARG 0.015 0.001 ARG A1180 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 41168.30 seconds wall clock time: 718 minutes 22.13 seconds (43102.13 seconds total)