Starting phenix.real_space_refine on Mon Feb 19 09:37:43 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ear_27983/02_2024/8ear_27983_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ear_27983/02_2024/8ear_27983.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ear_27983/02_2024/8ear_27983_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ear_27983/02_2024/8ear_27983_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ear_27983/02_2024/8ear_27983_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ear_27983/02_2024/8ear_27983.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ear_27983/02_2024/8ear_27983.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ear_27983/02_2024/8ear_27983_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ear_27983/02_2024/8ear_27983_updated.pdb" } resolution = 3.5 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= 0.000 sd= 0.003 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: 7 Type Number sf(0) Gaussians Ca 16 9.91 5 Zn 4 6.06 5 P 52 5.49 5 S 468 5.16 5 C 49924 2.51 5 N 13384 2.21 5 O 14664 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ASP 379": "OD1" <-> "OD2" Residue "A TYR 387": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 988": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1084": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1244": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1622": "OE1" <-> "OE2" Residue "A PHE 1844": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1958": "OE1" <-> "OE2" Residue "A PHE 1987": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 2101": "OE1" <-> "OE2" Residue "A PHE 2418": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 2453": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 2470": "OE1" <-> "OE2" Residue "A PHE 2573": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 2619": "OD1" <-> "OD2" Residue "A PHE 2621": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 2628": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 2689": "OE1" <-> "OE2" Residue "A GLU 2691": "OE1" <-> "OE2" Residue "B ASP 379": "OD1" <-> "OD2" Residue "B TYR 387": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 988": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 1084": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 1244": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 1622": "OE1" <-> "OE2" Residue "B PHE 1844": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 1958": "OE1" <-> "OE2" Residue "B PHE 1987": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 2101": "OE1" <-> "OE2" Residue "B PHE 2418": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 2453": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 2470": "OE1" <-> "OE2" Residue "B PHE 2573": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 2619": "OD1" <-> "OD2" Residue "B PHE 2621": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 2628": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 2689": "OE1" <-> "OE2" Residue "B GLU 2691": "OE1" <-> "OE2" Residue "C ASP 379": "OD1" <-> "OD2" Residue "C TYR 387": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 988": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 1084": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 1244": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 1622": "OE1" <-> "OE2" Residue "C PHE 1844": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 1958": "OE1" <-> "OE2" Residue "C PHE 1987": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 2101": "OE1" <-> "OE2" Residue "C PHE 2418": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 2453": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 2470": "OE1" <-> "OE2" Residue "C PHE 2573": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 2619": "OD1" <-> "OD2" Residue "C PHE 2621": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 2628": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 2689": "OE1" <-> "OE2" Residue "C GLU 2691": "OE1" <-> "OE2" Residue "D ASP 379": "OD1" <-> "OD2" Residue "D TYR 387": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 988": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 1084": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 1244": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 1622": "OE1" <-> "OE2" Residue "D PHE 1844": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 1958": "OE1" <-> "OE2" Residue "D PHE 1987": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 2101": "OE1" <-> "OE2" Residue "D PHE 2418": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 2453": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 2470": "OE1" <-> "OE2" Residue "D PHE 2573": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 2619": "OD1" <-> "OD2" Residue "D PHE 2621": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 2628": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 2689": "OE1" <-> "OE2" Residue "D GLU 2691": "OE1" <-> "OE2" Time to flip residues: 0.20s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 78512 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 19296 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 2389, 19280 Classifications: {'peptide': 2389} Link IDs: {'PCIS': 3, 'PTRANS': 70, 'TRANS': 2315} Chain breaks: 10 Conformer: "B" Number of residues, atoms: 2389, 19280 Classifications: {'peptide': 2389} Link IDs: {'PCIS': 3, 'PTRANS': 70, 'TRANS': 2315} Chain breaks: 10 bond proxies already assigned to first conformer: 19614 Chain: "B" Number of atoms: 19296 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 2389, 19280 Classifications: {'peptide': 2389} Link IDs: {'PCIS': 3, 'PTRANS': 70, 'TRANS': 2315} Chain breaks: 10 Conformer: "B" Number of residues, atoms: 2389, 19280 Classifications: {'peptide': 2389} Link IDs: {'PCIS': 3, 'PTRANS': 70, 'TRANS': 2315} Chain breaks: 10 bond proxies already assigned to first conformer: 19614 Chain: "C" Number of atoms: 19296 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 2389, 19280 Classifications: {'peptide': 2389} Link IDs: {'PCIS': 3, 'PTRANS': 70, 'TRANS': 2315} Chain breaks: 10 Conformer: "B" Number of residues, atoms: 2389, 19280 Classifications: {'peptide': 2389} Link IDs: {'PCIS': 3, 'PTRANS': 70, 'TRANS': 2315} Chain breaks: 10 bond proxies already assigned to first conformer: 19614 Chain: "D" Number of atoms: 19296 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 2389, 19280 Classifications: {'peptide': 2389} Link IDs: {'PCIS': 3, 'PTRANS': 70, 'TRANS': 2315} Chain breaks: 10 Conformer: "B" Number of residues, atoms: 2389, 19280 Classifications: {'peptide': 2389} Link IDs: {'PCIS': 3, 'PTRANS': 70, 'TRANS': 2315} Chain breaks: 10 bond proxies already assigned to first conformer: 19614 Chain: "A" Number of atoms: 332 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 332 Unusual residues: {' CA': 4, ' ZN': 1, 'ATP': 1, 'I3P': 1, 'PLX': 7} Classifications: {'undetermined': 14} Link IDs: {None: 13} Unresolved non-hydrogen bonds: 92 Unresolved non-hydrogen angles: 92 Unresolved non-hydrogen dihedrals: 92 Chain: "B" Number of atoms: 332 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 332 Unusual residues: {' CA': 4, ' ZN': 1, 'ATP': 1, 'I3P': 1, 'PLX': 7} Classifications: {'undetermined': 14} Link IDs: {None: 13} Unresolved non-hydrogen bonds: 92 Unresolved non-hydrogen angles: 92 Unresolved non-hydrogen dihedrals: 92 Chain: "C" Number of atoms: 332 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 332 Unusual residues: {' CA': 4, ' ZN': 1, 'ATP': 1, 'I3P': 1, 'PLX': 7} Classifications: {'undetermined': 14} Link IDs: {None: 13} Unresolved non-hydrogen bonds: 92 Unresolved non-hydrogen angles: 92 Unresolved non-hydrogen dihedrals: 92 Chain: "D" Number of atoms: 332 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 332 Unusual residues: {' CA': 4, ' ZN': 1, 'ATP': 1, 'I3P': 1, 'PLX': 7} Classifications: {'undetermined': 14} Link IDs: {None: 13} Unresolved non-hydrogen bonds: 92 Unresolved non-hydrogen angles: 92 Unresolved non-hydrogen dihedrals: 92 List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 18220 SG CYS A2611 136.742 147.293 107.186 1.00 82.54 S ATOM 18245 SG CYS A2614 135.459 145.901 104.840 1.00 85.00 S ATOM 37516 SG CYS B2611 109.519 136.748 107.181 1.00 82.54 S ATOM 37541 SG CYS B2614 110.911 135.465 104.835 1.00 85.00 S ATOM 56812 SG CYS C2611 120.050 109.512 107.185 1.00 82.54 S ATOM 56837 SG CYS C2614 121.333 110.904 104.839 1.00 85.00 S ATOM 76108 SG CYS D2611 147.286 120.048 107.180 1.00 82.54 S ATOM 76133 SG CYS D2614 145.894 121.331 104.834 1.00 85.00 S Residues with excluded nonbonded symmetry interactions: 4 residue: pdb=" N AASN A2583 " occ=0.50 ... (14 atoms not shown) pdb=" ND2BASN A2583 " occ=0.50 residue: pdb=" N AASN B2583 " occ=0.50 ... (14 atoms not shown) pdb=" ND2BASN B2583 " occ=0.50 residue: pdb=" N AASN C2583 " occ=0.50 ... (14 atoms not shown) pdb=" ND2BASN C2583 " occ=0.50 residue: pdb=" N AASN D2583 " occ=0.50 ... (14 atoms not shown) pdb=" ND2BASN D2583 " occ=0.50 Time building chain proxies: 56.37, per 1000 atoms: 0.72 Number of scatterers: 78512 At special positions: 0 Unit cell: (257.87, 257.87, 196.88, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 4 29.99 Ca 16 19.99 S 468 16.00 P 52 15.00 O 14664 8.00 N 13384 7.00 C 49924 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS A2528 " - pdb=" SG CYS A2534 " distance=2.04 Simple disulfide: pdb=" SG CYS B2528 " - pdb=" SG CYS B2534 " distance=2.04 Simple disulfide: pdb=" SG CYS C2528 " - pdb=" SG CYS C2534 " distance=2.04 Simple disulfide: pdb=" SG CYS D2528 " - pdb=" SG CYS D2534 " 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=16, symmetry=0 Number of additional bonds: simple=16, symmetry=0 Coordination: Other bonds: Time building additional restraints: 24.58 Conformation dependent library (CDL) restraints added in 21.4 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A2801 " pdb="ZN ZN A2801 " - pdb=" SG CYS A2614 " pdb="ZN ZN A2801 " - pdb=" NE2 HIS A2631 " pdb="ZN ZN A2801 " - pdb=" SG CYS A2611 " pdb=" ZN B2801 " pdb="ZN ZN B2801 " - pdb=" SG CYS B2614 " pdb="ZN ZN B2801 " - pdb=" NE2 HIS B2631 " pdb="ZN ZN B2801 " - pdb=" SG CYS B2611 " pdb=" ZN C2801 " pdb="ZN ZN C2801 " - pdb=" SG CYS C2614 " pdb="ZN ZN C2801 " - pdb=" NE2 HIS C2631 " pdb="ZN ZN C2801 " - pdb=" SG CYS C2611 " pdb=" ZN D2801 " pdb="ZN ZN D2801 " - pdb=" SG CYS D2614 " pdb="ZN ZN D2801 " - pdb=" NE2 HIS D2631 " pdb="ZN ZN D2801 " - pdb=" SG CYS D2611 " 18968 Ramachandran restraints generated. 9484 Oldfield, 0 Emsley, 9484 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 18264 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 432 helices and 52 sheets defined 58.3% alpha, 4.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 23.83 Creating SS restraints... Processing helix chain 'A' and resid 67 through 76 Processing helix chain 'A' and resid 84 through 109 Processing helix chain 'A' and resid 157 through 159 No H-bonds generated for 'chain 'A' and resid 157 through 159' Processing helix chain 'A' and resid 364 through 366 No H-bonds generated for 'chain 'A' and resid 364 through 366' Processing helix chain 'A' and resid 437 through 458 removed outlier: 3.648A pdb=" N ARG A 441 " --> pdb=" O PRO A 437 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N LEU A 453 " --> pdb=" O ALA A 449 " (cutoff:3.500A) Processing helix chain 'A' and resid 467 through 474 removed outlier: 3.981A pdb=" N VAL A 473 " --> pdb=" O GLU A 469 " (cutoff:3.500A) Processing helix chain 'A' and resid 476 through 485 removed outlier: 3.738A pdb=" N LEU A 480 " --> pdb=" O LEU A 476 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N VAL A 481 " --> pdb=" O LEU A 477 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N TYR A 482 " --> pdb=" O GLU A 478 " (cutoff:3.500A) Processing helix chain 'A' and resid 506 through 512 Processing helix chain 'A' and resid 515 through 528 removed outlier: 4.074A pdb=" N PHE A 520 " --> pdb=" O LEU A 516 " (cutoff:3.500A) removed outlier: 4.213A pdb=" N LYS A 521 " --> pdb=" O LYS A 517 " (cutoff:3.500A) removed outlier: 4.079A pdb=" N LEU A 523 " --> pdb=" O ILE A 519 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N GLN A 524 " --> pdb=" O PHE A 520 " (cutoff:3.500A) Proline residue: A 526 - end of helix Processing helix chain 'A' and resid 548 through 564 removed outlier: 3.906A pdb=" N LEU A 555 " --> pdb=" O HIS A 551 " (cutoff:3.500A) removed outlier: 4.118A pdb=" N CYS A 556 " --> pdb=" O ILE A 552 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N TYR A 557 " --> pdb=" O CYS A 553 " (cutoff:3.500A) Processing helix chain 'A' and resid 568 through 577 removed outlier: 3.641A pdb=" N LYS A 576 " --> pdb=" O GLU A 572 " (cutoff:3.500A) removed outlier: 4.865A pdb=" N GLN A 577 " --> pdb=" O TYR A 573 " (cutoff:3.500A) Processing helix chain 'A' and resid 580 through 584 removed outlier: 4.511A pdb=" N GLN A 584 " --> pdb=" O PHE A 580 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 580 through 584' Processing helix chain 'A' and resid 591 through 600 Processing helix chain 'A' and resid 603 through 609 removed outlier: 3.844A pdb=" N LYS A 608 " --> pdb=" O LYS A 604 " (cutoff:3.500A) Processing helix chain 'A' and resid 612 through 625 removed outlier: 3.632A pdb=" N VAL A 622 " --> pdb=" O PHE A 618 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N ARG A 623 " --> pdb=" O VAL A 619 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N LYS A 624 " --> pdb=" O SER A 620 " (cutoff:3.500A) Processing helix chain 'A' and resid 629 through 638 removed outlier: 3.632A pdb=" N ASP A 632 " --> pdb=" O ARG A 629 " (cutoff:3.500A) Processing helix chain 'A' and resid 646 through 663 removed outlier: 4.092A pdb=" N LYS A 654 " --> pdb=" O GLU A 650 " (cutoff:3.500A) removed outlier: 4.183A pdb=" N ALA A 655 " --> pdb=" O LEU A 651 " (cutoff:3.500A) Proline residue: A 659 - end of helix removed outlier: 4.616A pdb=" N ALA A 662 " --> pdb=" O ASN A 658 " (cutoff:3.500A) removed outlier: 4.577A pdb=" N ASP A 663 " --> pdb=" O PRO A 659 " (cutoff:3.500A) Processing helix chain 'A' and resid 712 through 721 removed outlier: 3.534A pdb=" N LYS A 720 " --> pdb=" O ALA A 716 " (cutoff:3.500A) Processing helix chain 'A' and resid 724 through 740 Processing helix chain 'A' and resid 745 through 747 No H-bonds generated for 'chain 'A' and resid 745 through 747' Processing helix chain 'A' and resid 752 through 757 Processing helix chain 'A' and resid 761 through 767 removed outlier: 4.037A pdb=" N CYS A 767 " --> pdb=" O LEU A 763 " (cutoff:3.500A) Processing helix chain 'A' and resid 775 through 789 Processing helix chain 'A' and resid 816 through 818 No H-bonds generated for 'chain 'A' and resid 816 through 818' Processing helix chain 'A' and resid 825 through 848 removed outlier: 4.215A pdb=" N GLU A 828 " --> pdb=" O SER A 825 " (cutoff:3.500A) removed outlier: 5.590A pdb=" N GLN A 835 " --> pdb=" O ARG A 832 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N GLU A 842 " --> pdb=" O PHE A 839 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N TYR A 843 " --> pdb=" O VAL A 840 " (cutoff:3.500A) Processing helix chain 'A' and resid 857 through 875 removed outlier: 4.322A pdb=" N GLU A 865 " --> pdb=" O LYS A 861 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N VAL A 866 " --> pdb=" O LEU A 862 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N TYR A 875 " --> pdb=" O ARG A 871 " (cutoff:3.500A) Processing helix chain 'A' and resid 881 through 899 removed outlier: 3.657A pdb=" N LEU A 885 " --> pdb=" O PHE A 881 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N ARG A 886 " --> pdb=" O SER A 882 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N ILE A 890 " --> pdb=" O ARG A 886 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N LEU A 895 " --> pdb=" O LEU A 891 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N HIS A 899 " --> pdb=" O LEU A 895 " (cutoff:3.500A) Processing helix chain 'A' and resid 965 through 1005 removed outlier: 4.470A pdb=" N THR A 970 " --> pdb=" O MET A 966 " (cutoff:3.500A) removed outlier: 4.664A pdb=" N LYS A 971 " --> pdb=" O VAL A 967 " (cutoff:3.500A) removed outlier: 4.225A pdb=" N LEU A 972 " --> pdb=" O MET A 968 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N GLU A 976 " --> pdb=" O LEU A 972 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N ILE A 977 " --> pdb=" O LYS A 973 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N ARG A 985 " --> pdb=" O ILE A 981 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N LEU A 986 " --> pdb=" O LEU A 982 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N ASP A 987 " --> pdb=" O ASN A 983 " (cutoff:3.500A) Processing helix chain 'A' and resid 1030 through 1039 removed outlier: 4.629A pdb=" N GLU A1035 " --> pdb=" O GLU A1031 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N GLN A1036 " --> pdb=" O HIS A1032 " (cutoff:3.500A) Processing helix chain 'A' and resid 1045 through 1047 No H-bonds generated for 'chain 'A' and resid 1045 through 1047' Processing helix chain 'A' and resid 1058 through 1069 removed outlier: 4.289A pdb=" N ARG A1062 " --> pdb=" O ARG A1058 " (cutoff:3.500A) removed outlier: 4.118A pdb=" N VAL A1063 " --> pdb=" O THR A1059 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N LEU A1064 " --> pdb=" O PHE A1060 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N MET A1069 " --> pdb=" O LEU A1065 " (cutoff:3.500A) Processing helix chain 'A' and resid 1073 through 1087 removed outlier: 3.544A pdb=" N LEU A1083 " --> pdb=" O ALA A1079 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N PHE A1084 " --> pdb=" O LEU A1080 " (cutoff:3.500A) Processing helix chain 'A' and resid 1089 through 1098 removed outlier: 3.684A pdb=" N ALA A1096 " --> pdb=" O GLU A1092 " (cutoff:3.500A) Processing helix chain 'A' and resid 1106 through 1127 Processing helix chain 'A' and resid 1129 through 1131 No H-bonds generated for 'chain 'A' and resid 1129 through 1131' Processing helix chain 'A' and resid 1168 through 1187 removed outlier: 3.502A pdb=" N ARG A1174 " --> pdb=" O SER A1170 " (cutoff:3.500A) removed outlier: 4.242A pdb=" N LYS A1177 " --> pdb=" O TYR A1173 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N GLU A1178 " --> pdb=" O ARG A1174 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N ILE A1179 " --> pdb=" O VAL A1175 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N CYS A1187 " --> pdb=" O LEU A1183 " (cutoff:3.500A) Processing helix chain 'A' and resid 1201 through 1208 Processing helix chain 'A' and resid 1210 through 1219 Processing helix chain 'A' and resid 1228 through 1245 Processing helix chain 'A' and resid 1250 through 1262 removed outlier: 3.932A pdb=" N LYS A1257 " --> pdb=" O ALA A1253 " (cutoff:3.500A) removed outlier: 5.037A pdb=" N HIS A1258 " --> pdb=" O LEU A1254 " (cutoff:3.500A) removed outlier: 4.278A pdb=" N ILE A1259 " --> pdb=" O LEU A1255 " (cutoff:3.500A) removed outlier: 5.651A pdb=" N ASN A1260 " --> pdb=" O HIS A1256 " (cutoff:3.500A) removed outlier: 6.588A pdb=" N LEU A1261 " --> pdb=" O LYS A1257 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N PHE A1262 " --> pdb=" O HIS A1258 " (cutoff:3.500A) Processing helix chain 'A' and resid 1268 through 1276 removed outlier: 3.696A pdb=" N MET A1273 " --> pdb=" O GLU A1269 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N GLN A1274 " --> pdb=" O ALA A1270 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N HIS A1275 " --> pdb=" O VAL A1271 " (cutoff:3.500A) Processing helix chain 'A' and resid 1281 through 1286 removed outlier: 3.966A pdb=" N GLU A1286 " --> pdb=" O GLN A1282 " (cutoff:3.500A) Processing helix chain 'A' and resid 1289 through 1301 Processing helix chain 'A' and resid 1306 through 1316 removed outlier: 3.706A pdb=" N PHE A1311 " --> pdb=" O GLN A1307 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N LEU A1312 " --> pdb=" O TYR A1308 " (cutoff:3.500A) Processing helix chain 'A' and resid 1324 through 1341 removed outlier: 3.848A pdb=" N MET A1331 " --> pdb=" O GLN A1327 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N VAL A1335 " --> pdb=" O MET A1331 " (cutoff:3.500A) removed outlier: 5.101A pdb=" N ASN A1336 " --> pdb=" O ALA A1332 " (cutoff:3.500A) removed outlier: 4.111A pdb=" N GLY A1338 " --> pdb=" O LEU A1334 " (cutoff:3.500A) removed outlier: 6.288A pdb=" N GLU A1339 " --> pdb=" O VAL A1335 " (cutoff:3.500A) removed outlier: 7.948A pdb=" N ASP A1340 " --> pdb=" O ASN A1336 " (cutoff:3.500A) removed outlier: 4.337A pdb=" N VAL A1341 " --> pdb=" O SER A1337 " (cutoff:3.500A) Processing helix chain 'A' and resid 1348 through 1363 removed outlier: 3.598A pdb=" N SER A1360 " --> pdb=" O GLN A1356 " (cutoff:3.500A) Processing helix chain 'A' and resid 1369 through 1386 removed outlier: 3.710A pdb=" N TYR A1374 " --> pdb=" O PRO A1370 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N HIS A1375 " --> pdb=" O LEU A1371 " (cutoff:3.500A) Processing helix chain 'A' and resid 1391 through 1400 removed outlier: 4.024A pdb=" N SER A1399 " --> pdb=" O ILE A1395 " (cutoff:3.500A) removed outlier: 4.226A pdb=" N LEU A1400 " --> pdb=" O LYS A1396 " (cutoff:3.500A) Processing helix chain 'A' and resid 1403 through 1411 Processing helix chain 'A' and resid 1417 through 1431 removed outlier: 3.660A pdb=" N PHE A1426 " --> pdb=" O ALA A1422 " (cutoff:3.500A) Processing helix chain 'A' and resid 1439 through 1442 No H-bonds generated for 'chain 'A' and resid 1439 through 1442' Processing helix chain 'A' and resid 1446 through 1462 Processing helix chain 'A' and resid 1473 through 1492 removed outlier: 4.568A pdb=" N VAL A1483 " --> pdb=" O VAL A1479 " (cutoff:3.500A) removed outlier: 5.016A pdb=" N MET A1484 " --> pdb=" O THR A1480 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N PHE A1490 " --> pdb=" O ILE A1486 " (cutoff:3.500A) Processing helix chain 'A' and resid 1495 through 1498 Processing helix chain 'A' and resid 1506 through 1521 removed outlier: 3.669A pdb=" N TYR A1520 " --> pdb=" O VAL A1516 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N HIS A1521 " --> pdb=" O PHE A1517 " (cutoff:3.500A) Processing helix chain 'A' and resid 1527 through 1547 removed outlier: 3.874A pdb=" N ALA A1531 " --> pdb=" O PRO A1527 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N SER A1532 " --> pdb=" O SER A1528 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N CYS A1536 " --> pdb=" O SER A1532 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ILE A1537 " --> pdb=" O VAL A1533 " (cutoff:3.500A) Processing helix chain 'A' and resid 1553 through 1565 Processing helix chain 'A' and resid 1590 through 1631 removed outlier: 3.677A pdb=" N TYR A1597 " --> pdb=" O ALA A1593 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N GLN A1605 " --> pdb=" O ILE A1601 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N ASP A1606 " --> pdb=" O GLU A1602 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N ARG A1616 " --> pdb=" O GLU A1612 " (cutoff:3.500A) Proline residue: A1617 - end of helix removed outlier: 3.577A pdb=" N GLN A1620 " --> pdb=" O ARG A1616 " (cutoff:3.500A) removed outlier: 4.438A pdb=" N ALA A1621 " --> pdb=" O PRO A1617 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N GLU A1622 " --> pdb=" O LEU A1618 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N VAL A1627 " --> pdb=" O LEU A1623 " (cutoff:3.500A) Processing helix chain 'A' and resid 1642 through 1648 Processing helix chain 'A' and resid 1651 through 1663 Processing helix chain 'A' and resid 1669 through 1682 removed outlier: 3.648A pdb=" N GLU A1681 " --> pdb=" O GLN A1677 " (cutoff:3.500A) removed outlier: 4.354A pdb=" N MET A1682 " --> pdb=" O THR A1678 " (cutoff:3.500A) Processing helix chain 'A' and resid 1723 through 1745 Processing helix chain 'A' and resid 1792 through 1801 removed outlier: 3.775A pdb=" N GLN A1796 " --> pdb=" O LEU A1792 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N CYS A1797 " --> pdb=" O ALA A1793 " (cutoff:3.500A) Processing helix chain 'A' and resid 1804 through 1813 removed outlier: 3.544A pdb=" N VAL A1808 " --> pdb=" O ALA A1804 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N ILE A1809 " --> pdb=" O SER A1805 " (cutoff:3.500A) Processing helix chain 'A' and resid 1818 through 1831 Processing helix chain 'A' and resid 1837 through 1849 Processing helix chain 'A' and resid 1853 through 1874 removed outlier: 3.977A pdb=" N ALA A1867 " --> pdb=" O ARG A1863 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N ALA A1873 " --> pdb=" O GLN A1869 " (cutoff:3.500A) Processing helix chain 'A' and resid 1961 through 1980 removed outlier: 3.779A pdb=" N MET A1966 " --> pdb=" O VAL A1962 " (cutoff:3.500A) removed outlier: 4.094A pdb=" N GLN A1967 " --> pdb=" O ILE A1963 " (cutoff:3.500A) Proline residue: A1968 - end of helix removed outlier: 3.589A pdb=" N CYS A1977 " --> pdb=" O LEU A1973 " (cutoff:3.500A) removed outlier: 5.676A pdb=" N ASN A1979 " --> pdb=" O LEU A1975 " (cutoff:3.500A) removed outlier: 6.280A pdb=" N HIS A1980 " --> pdb=" O LEU A1976 " (cutoff:3.500A) Processing helix chain 'A' and resid 1982 through 1989 removed outlier: 4.013A pdb=" N ASN A1986 " --> pdb=" O ARG A1982 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N PHE A1987 " --> pdb=" O ASP A1983 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N ARG A1989 " --> pdb=" O GLN A1985 " (cutoff:3.500A) Processing helix chain 'A' and resid 1999 through 2010 removed outlier: 3.522A pdb=" N LEU A2007 " --> pdb=" O THR A2003 " (cutoff:3.500A) Processing helix chain 'A' and resid 2016 through 2018 No H-bonds generated for 'chain 'A' and resid 2016 through 2018' Processing helix chain 'A' and resid 2021 through 2024 No H-bonds generated for 'chain 'A' and resid 2021 through 2024' Processing helix chain 'A' and resid 2030 through 2043 removed outlier: 3.563A pdb=" N GLU A2042 " --> pdb=" O GLU A2038 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N TYR A2043 " --> pdb=" O SER A2039 " (cutoff:3.500A) Processing helix chain 'A' and resid 2049 through 2056 Processing helix chain 'A' and resid 2062 through 2069 removed outlier: 3.647A pdb=" N ILE A2066 " --> pdb=" O GLY A2062 " (cutoff:3.500A) Processing helix chain 'A' and resid 2077 through 2080 No H-bonds generated for 'chain 'A' and resid 2077 through 2080' Processing helix chain 'A' and resid 2082 through 2100 removed outlier: 3.708A pdb=" N MET A2100 " --> pdb=" O LEU A2096 " (cutoff:3.500A) Processing helix chain 'A' and resid 2107 through 2114 Processing helix chain 'A' and resid 2118 through 2127 removed outlier: 3.557A pdb=" N VAL A2122 " --> pdb=" O PRO A2118 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N LYS A2126 " --> pdb=" O VAL A2122 " (cutoff:3.500A) Processing helix chain 'A' and resid 2130 through 2138 removed outlier: 4.030A pdb=" N ASP A2138 " --> pdb=" O VAL A2134 " (cutoff:3.500A) Processing helix chain 'A' and resid 2149 through 2166 removed outlier: 4.303A pdb=" N ARG A2165 " --> pdb=" O HIS A2161 " (cutoff:3.500A) removed outlier: 4.819A pdb=" N HIS A2166 " --> pdb=" O GLN A2162 " (cutoff:3.500A) Processing helix chain 'A' and resid 2170 through 2174 removed outlier: 3.715A pdb=" N LEU A2174 " --> pdb=" O LEU A2170 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 2170 through 2174' Processing helix chain 'A' and resid 2184 through 2191 Processing helix chain 'A' and resid 2215 through 2218 Processing helix chain 'A' and resid 2221 through 2230 Processing helix chain 'A' and resid 2240 through 2245 Processing helix chain 'A' and resid 2247 through 2261 removed outlier: 3.784A pdb=" N LYS A2259 " --> pdb=" O ASN A2255 " (cutoff:3.500A) Processing helix chain 'A' and resid 2266 through 2294 removed outlier: 3.709A pdb=" N ASN A2272 " --> pdb=" O TRP A2268 " (cutoff:3.500A) removed outlier: 4.146A pdb=" N MET A2273 " --> pdb=" O CYS A2269 " (cutoff:3.500A) removed outlier: 6.348A pdb=" N SER A2274 " --> pdb=" O ALA A2270 " (cutoff:3.500A) removed outlier: 6.099A pdb=" N PHE A2275 " --> pdb=" O ARG A2271 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N LEU A2286 " --> pdb=" O ASN A2282 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N LEU A2290 " --> pdb=" O LEU A2286 " (cutoff:3.500A) removed outlier: 4.099A pdb=" N VAL A2291 " --> pdb=" O MET A2287 " (cutoff:3.500A) Processing helix chain 'A' and resid 2309 through 2325 removed outlier: 3.793A pdb=" N TRP A2314 " --> pdb=" O SER A2310 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N THR A2315 " --> pdb=" O GLY A2311 " (cutoff:3.500A) removed outlier: 4.213A pdb=" N SER A2320 " --> pdb=" O ALA A2316 " (cutoff:3.500A) removed outlier: 4.464A pdb=" N LEU A2321 " --> pdb=" O MET A2317 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N ALA A2322 " --> pdb=" O LEU A2318 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N ILE A2323 " --> pdb=" O ILE A2319 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N VAL A2324 " --> pdb=" O SER A2320 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N ILE A2325 " --> pdb=" O LEU A2321 " (cutoff:3.500A) Processing helix chain 'A' and resid 2329 through 2345 removed outlier: 3.652A pdb=" N LEU A2344 " --> pdb=" O THR A2340 " (cutoff:3.500A) Processing helix chain 'A' and resid 2350 through 2376 Processing helix chain 'A' and resid 2378 through 2381 Processing helix chain 'A' and resid 2383 through 2388 Processing helix chain 'A' and resid 2390 through 2407 removed outlier: 3.799A pdb=" N TYR A2398 " --> pdb=" O TYR A2394 " (cutoff:3.500A) Processing helix chain 'A' and resid 2410 through 2423 removed outlier: 3.562A pdb=" N TYR A2413 " --> pdb=" O GLU A2410 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N VAL A2421 " --> pdb=" O PHE A2418 " (cutoff:3.500A) Processing helix chain 'A' and resid 2426 through 2436 removed outlier: 3.623A pdb=" N SER A2433 " --> pdb=" O ASN A2429 " (cutoff:3.500A) removed outlier: 4.410A pdb=" N VAL A2434 " --> pdb=" O VAL A2430 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N THR A2435 " --> pdb=" O ILE A2431 " (cutoff:3.500A) Processing helix chain 'A' and resid 2438 through 2462 Processing helix chain 'A' and resid 2464 through 2466 No H-bonds generated for 'chain 'A' and resid 2464 through 2466' Processing helix chain 'A' and resid 2531 through 2541 removed outlier: 3.639A pdb=" N VAL A2538 " --> pdb=" O CYS A2534 " (cutoff:3.500A) Processing helix chain 'A' and resid 2549 through 2551 No H-bonds generated for 'chain 'A' and resid 2549 through 2551' Processing helix chain 'A' and resid 2563 through 2577 Processing helix chain 'A' and resid 2581 through 2609 removed outlier: 4.163A pdb=" N PHE A2586 " --> pdb=" O LEU A2582 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N VAL A2588 " --> pdb=" O LEU A2584 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N ILE A2589 " --> pdb=" O ILE A2585 " (cutoff:3.500A) Processing helix chain 'A' and resid 2628 through 2631 No H-bonds generated for 'chain 'A' and resid 2628 through 2631' Processing helix chain 'A' and resid 2638 through 2649 removed outlier: 3.789A pdb=" N LEU A2642 " --> pdb=" O MET A2638 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N LYS A2649 " --> pdb=" O ILE A2645 " (cutoff:3.500A) Processing helix chain 'A' and resid 2653 through 2655 No H-bonds generated for 'chain 'A' and resid 2653 through 2655' Processing helix chain 'A' and resid 2658 through 2668 removed outlier: 3.567A pdb=" N TYR A2662 " --> pdb=" O GLY A2658 " (cutoff:3.500A) Processing helix chain 'A' and resid 2681 through 2684 No H-bonds generated for 'chain 'A' and resid 2681 through 2684' Processing helix chain 'A' and resid 2692 through 2738 removed outlier: 4.116A pdb=" N LYS A2707 " --> pdb=" O GLU A2703 " (cutoff:3.500A) removed outlier: 4.635A pdb=" N LEU A2708 " --> pdb=" O SER A2704 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N LEU A2712 " --> pdb=" O LEU A2708 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N SER A2713 " --> pdb=" O VAL A2709 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N LYS A2720 " --> pdb=" O LEU A2716 " (cutoff:3.500A) removed outlier: 4.205A pdb=" N LEU A2735 " --> pdb=" O GLN A2731 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N GLY A2737 " --> pdb=" O ILE A2733 " (cutoff:3.500A) Processing helix chain 'B' and resid 67 through 76 Processing helix chain 'B' and resid 84 through 109 Processing helix chain 'B' and resid 157 through 159 No H-bonds generated for 'chain 'B' and resid 157 through 159' Processing helix chain 'B' and resid 364 through 366 No H-bonds generated for 'chain 'B' and resid 364 through 366' Processing helix chain 'B' and resid 437 through 458 removed outlier: 3.649A pdb=" N ARG B 441 " --> pdb=" O PRO B 437 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N LEU B 453 " --> pdb=" O ALA B 449 " (cutoff:3.500A) Processing helix chain 'B' and resid 467 through 474 removed outlier: 3.981A pdb=" N VAL B 473 " --> pdb=" O GLU B 469 " (cutoff:3.500A) Processing helix chain 'B' and resid 476 through 485 removed outlier: 3.738A pdb=" N LEU B 480 " --> pdb=" O LEU B 476 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N VAL B 481 " --> pdb=" O LEU B 477 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N TYR B 482 " --> pdb=" O GLU B 478 " (cutoff:3.500A) Processing helix chain 'B' and resid 506 through 512 Processing helix chain 'B' and resid 515 through 528 removed outlier: 4.074A pdb=" N PHE B 520 " --> pdb=" O LEU B 516 " (cutoff:3.500A) removed outlier: 4.213A pdb=" N LYS B 521 " --> pdb=" O LYS B 517 " (cutoff:3.500A) removed outlier: 4.079A pdb=" N LEU B 523 " --> pdb=" O ILE B 519 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N GLN B 524 " --> pdb=" O PHE B 520 " (cutoff:3.500A) Proline residue: B 526 - end of helix Processing helix chain 'B' and resid 548 through 564 removed outlier: 3.906A pdb=" N LEU B 555 " --> pdb=" O HIS B 551 " (cutoff:3.500A) removed outlier: 4.118A pdb=" N CYS B 556 " --> pdb=" O ILE B 552 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N TYR B 557 " --> pdb=" O CYS B 553 " (cutoff:3.500A) Processing helix chain 'B' and resid 568 through 577 removed outlier: 3.642A pdb=" N LYS B 576 " --> pdb=" O GLU B 572 " (cutoff:3.500A) removed outlier: 4.865A pdb=" N GLN B 577 " --> pdb=" O TYR B 573 " (cutoff:3.500A) Processing helix chain 'B' and resid 580 through 584 removed outlier: 4.511A pdb=" N GLN B 584 " --> pdb=" O PHE B 580 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 580 through 584' Processing helix chain 'B' and resid 591 through 600 Processing helix chain 'B' and resid 603 through 609 removed outlier: 3.844A pdb=" N LYS B 608 " --> pdb=" O LYS B 604 " (cutoff:3.500A) Processing helix chain 'B' and resid 612 through 625 removed outlier: 3.632A pdb=" N VAL B 622 " --> pdb=" O PHE B 618 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N ARG B 623 " --> pdb=" O VAL B 619 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N LYS B 624 " --> pdb=" O SER B 620 " (cutoff:3.500A) Processing helix chain 'B' and resid 629 through 638 removed outlier: 3.632A pdb=" N ASP B 632 " --> pdb=" O ARG B 629 " (cutoff:3.500A) Processing helix chain 'B' and resid 646 through 663 removed outlier: 4.092A pdb=" N LYS B 654 " --> pdb=" O GLU B 650 " (cutoff:3.500A) removed outlier: 4.183A pdb=" N ALA B 655 " --> pdb=" O LEU B 651 " (cutoff:3.500A) Proline residue: B 659 - end of helix removed outlier: 4.616A pdb=" N ALA B 662 " --> pdb=" O ASN B 658 " (cutoff:3.500A) removed outlier: 4.577A pdb=" N ASP B 663 " --> pdb=" O PRO B 659 " (cutoff:3.500A) Processing helix chain 'B' and resid 712 through 721 removed outlier: 3.534A pdb=" N LYS B 720 " --> pdb=" O ALA B 716 " (cutoff:3.500A) Processing helix chain 'B' and resid 724 through 740 Processing helix chain 'B' and resid 745 through 747 No H-bonds generated for 'chain 'B' and resid 745 through 747' Processing helix chain 'B' and resid 752 through 757 Processing helix chain 'B' and resid 761 through 767 removed outlier: 4.037A pdb=" N CYS B 767 " --> pdb=" O LEU B 763 " (cutoff:3.500A) Processing helix chain 'B' and resid 775 through 789 Processing helix chain 'B' and resid 816 through 818 No H-bonds generated for 'chain 'B' and resid 816 through 818' Processing helix chain 'B' and resid 825 through 848 removed outlier: 4.215A pdb=" N GLU B 828 " --> pdb=" O SER B 825 " (cutoff:3.500A) removed outlier: 5.590A pdb=" N GLN B 835 " --> pdb=" O ARG B 832 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N GLU B 842 " --> pdb=" O PHE B 839 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N TYR B 843 " --> pdb=" O VAL B 840 " (cutoff:3.500A) Processing helix chain 'B' and resid 857 through 875 removed outlier: 4.322A pdb=" N GLU B 865 " --> pdb=" O LYS B 861 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N VAL B 866 " --> pdb=" O LEU B 862 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N TYR B 875 " --> pdb=" O ARG B 871 " (cutoff:3.500A) Processing helix chain 'B' and resid 881 through 899 removed outlier: 3.656A pdb=" N LEU B 885 " --> pdb=" O PHE B 881 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N ARG B 886 " --> pdb=" O SER B 882 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N ILE B 890 " --> pdb=" O ARG B 886 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N LEU B 895 " --> pdb=" O LEU B 891 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N HIS B 899 " --> pdb=" O LEU B 895 " (cutoff:3.500A) Processing helix chain 'B' and resid 965 through 1005 removed outlier: 4.470A pdb=" N THR B 970 " --> pdb=" O MET B 966 " (cutoff:3.500A) removed outlier: 4.664A pdb=" N LYS B 971 " --> pdb=" O VAL B 967 " (cutoff:3.500A) removed outlier: 4.225A pdb=" N LEU B 972 " --> pdb=" O MET B 968 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N GLU B 976 " --> pdb=" O LEU B 972 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N ILE B 977 " --> pdb=" O LYS B 973 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N ARG B 985 " --> pdb=" O ILE B 981 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N LEU B 986 " --> pdb=" O LEU B 982 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N ASP B 987 " --> pdb=" O ASN B 983 " (cutoff:3.500A) Processing helix chain 'B' and resid 1030 through 1039 removed outlier: 4.630A pdb=" N GLU B1035 " --> pdb=" O GLU B1031 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N GLN B1036 " --> pdb=" O HIS B1032 " (cutoff:3.500A) Processing helix chain 'B' and resid 1045 through 1047 No H-bonds generated for 'chain 'B' and resid 1045 through 1047' Processing helix chain 'B' and resid 1058 through 1069 removed outlier: 4.289A pdb=" N ARG B1062 " --> pdb=" O ARG B1058 " (cutoff:3.500A) removed outlier: 4.118A pdb=" N VAL B1063 " --> pdb=" O THR B1059 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N LEU B1064 " --> pdb=" O PHE B1060 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N MET B1069 " --> pdb=" O LEU B1065 " (cutoff:3.500A) Processing helix chain 'B' and resid 1073 through 1087 removed outlier: 3.544A pdb=" N LEU B1083 " --> pdb=" O ALA B1079 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N PHE B1084 " --> pdb=" O LEU B1080 " (cutoff:3.500A) Processing helix chain 'B' and resid 1089 through 1098 removed outlier: 3.684A pdb=" N ALA B1096 " --> pdb=" O GLU B1092 " (cutoff:3.500A) Processing helix chain 'B' and resid 1106 through 1127 Processing helix chain 'B' and resid 1129 through 1131 No H-bonds generated for 'chain 'B' and resid 1129 through 1131' Processing helix chain 'B' and resid 1168 through 1187 removed outlier: 3.502A pdb=" N ARG B1174 " --> pdb=" O SER B1170 " (cutoff:3.500A) removed outlier: 4.242A pdb=" N LYS B1177 " --> pdb=" O TYR B1173 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N GLU B1178 " --> pdb=" O ARG B1174 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N ILE B1179 " --> pdb=" O VAL B1175 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N CYS B1187 " --> pdb=" O LEU B1183 " (cutoff:3.500A) Processing helix chain 'B' and resid 1201 through 1208 Processing helix chain 'B' and resid 1210 through 1219 Processing helix chain 'B' and resid 1228 through 1245 Processing helix chain 'B' and resid 1250 through 1262 removed outlier: 3.932A pdb=" N LYS B1257 " --> pdb=" O ALA B1253 " (cutoff:3.500A) removed outlier: 5.038A pdb=" N HIS B1258 " --> pdb=" O LEU B1254 " (cutoff:3.500A) removed outlier: 4.278A pdb=" N ILE B1259 " --> pdb=" O LEU B1255 " (cutoff:3.500A) removed outlier: 5.651A pdb=" N ASN B1260 " --> pdb=" O HIS B1256 " (cutoff:3.500A) removed outlier: 6.588A pdb=" N LEU B1261 " --> pdb=" O LYS B1257 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N PHE B1262 " --> pdb=" O HIS B1258 " (cutoff:3.500A) Processing helix chain 'B' and resid 1268 through 1276 removed outlier: 3.697A pdb=" N MET B1273 " --> pdb=" O GLU B1269 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N GLN B1274 " --> pdb=" O ALA B1270 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N HIS B1275 " --> pdb=" O VAL B1271 " (cutoff:3.500A) Processing helix chain 'B' and resid 1281 through 1286 removed outlier: 3.966A pdb=" N GLU B1286 " --> pdb=" O GLN B1282 " (cutoff:3.500A) Processing helix chain 'B' and resid 1289 through 1301 Processing helix chain 'B' and resid 1306 through 1316 removed outlier: 3.706A pdb=" N PHE B1311 " --> pdb=" O GLN B1307 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N LEU B1312 " --> pdb=" O TYR B1308 " (cutoff:3.500A) Processing helix chain 'B' and resid 1324 through 1341 removed outlier: 3.848A pdb=" N MET B1331 " --> pdb=" O GLN B1327 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N VAL B1335 " --> pdb=" O MET B1331 " (cutoff:3.500A) removed outlier: 5.101A pdb=" N ASN B1336 " --> pdb=" O ALA B1332 " (cutoff:3.500A) removed outlier: 4.111A pdb=" N GLY B1338 " --> pdb=" O LEU B1334 " (cutoff:3.500A) removed outlier: 6.288A pdb=" N GLU B1339 " --> pdb=" O VAL B1335 " (cutoff:3.500A) removed outlier: 7.947A pdb=" N ASP B1340 " --> pdb=" O ASN B1336 " (cutoff:3.500A) removed outlier: 4.337A pdb=" N VAL B1341 " --> pdb=" O SER B1337 " (cutoff:3.500A) Processing helix chain 'B' and resid 1348 through 1363 removed outlier: 3.598A pdb=" N SER B1360 " --> pdb=" O GLN B1356 " (cutoff:3.500A) Processing helix chain 'B' and resid 1369 through 1386 removed outlier: 3.710A pdb=" N TYR B1374 " --> pdb=" O PRO B1370 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N HIS B1375 " --> pdb=" O LEU B1371 " (cutoff:3.500A) Processing helix chain 'B' and resid 1391 through 1400 removed outlier: 4.024A pdb=" N SER B1399 " --> pdb=" O ILE B1395 " (cutoff:3.500A) removed outlier: 4.226A pdb=" N LEU B1400 " --> pdb=" O LYS B1396 " (cutoff:3.500A) Processing helix chain 'B' and resid 1403 through 1411 Processing helix chain 'B' and resid 1417 through 1431 removed outlier: 3.660A pdb=" N PHE B1426 " --> pdb=" O ALA B1422 " (cutoff:3.500A) Processing helix chain 'B' and resid 1439 through 1442 No H-bonds generated for 'chain 'B' and resid 1439 through 1442' Processing helix chain 'B' and resid 1446 through 1462 Processing helix chain 'B' and resid 1473 through 1492 removed outlier: 4.569A pdb=" N VAL B1483 " --> pdb=" O VAL B1479 " (cutoff:3.500A) removed outlier: 5.016A pdb=" N MET B1484 " --> pdb=" O THR B1480 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N PHE B1490 " --> pdb=" O ILE B1486 " (cutoff:3.500A) Processing helix chain 'B' and resid 1495 through 1498 Processing helix chain 'B' and resid 1506 through 1521 removed outlier: 3.669A pdb=" N TYR B1520 " --> pdb=" O VAL B1516 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N HIS B1521 " --> pdb=" O PHE B1517 " (cutoff:3.500A) Processing helix chain 'B' and resid 1527 through 1547 removed outlier: 3.875A pdb=" N ALA B1531 " --> pdb=" O PRO B1527 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N SER B1532 " --> pdb=" O SER B1528 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N CYS B1536 " --> pdb=" O SER B1532 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ILE B1537 " --> pdb=" O VAL B1533 " (cutoff:3.500A) Processing helix chain 'B' and resid 1553 through 1565 Processing helix chain 'B' and resid 1590 through 1631 removed outlier: 3.676A pdb=" N TYR B1597 " --> pdb=" O ALA B1593 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N GLN B1605 " --> pdb=" O ILE B1601 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N ASP B1606 " --> pdb=" O GLU B1602 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N ARG B1616 " --> pdb=" O GLU B1612 " (cutoff:3.500A) Proline residue: B1617 - end of helix removed outlier: 3.577A pdb=" N GLN B1620 " --> pdb=" O ARG B1616 " (cutoff:3.500A) removed outlier: 4.438A pdb=" N ALA B1621 " --> pdb=" O PRO B1617 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N GLU B1622 " --> pdb=" O LEU B1618 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N VAL B1627 " --> pdb=" O LEU B1623 " (cutoff:3.500A) Processing helix chain 'B' and resid 1642 through 1648 Processing helix chain 'B' and resid 1651 through 1663 Processing helix chain 'B' and resid 1669 through 1682 removed outlier: 3.648A pdb=" N GLU B1681 " --> pdb=" O GLN B1677 " (cutoff:3.500A) removed outlier: 4.354A pdb=" N MET B1682 " --> pdb=" O THR B1678 " (cutoff:3.500A) Processing helix chain 'B' and resid 1723 through 1745 Processing helix chain 'B' and resid 1792 through 1801 removed outlier: 3.775A pdb=" N GLN B1796 " --> pdb=" O LEU B1792 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N CYS B1797 " --> pdb=" O ALA B1793 " (cutoff:3.500A) Processing helix chain 'B' and resid 1804 through 1813 removed outlier: 3.544A pdb=" N VAL B1808 " --> pdb=" O ALA B1804 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N ILE B1809 " --> pdb=" O SER B1805 " (cutoff:3.500A) Processing helix chain 'B' and resid 1818 through 1831 Processing helix chain 'B' and resid 1837 through 1849 Processing helix chain 'B' and resid 1853 through 1874 removed outlier: 3.978A pdb=" N ALA B1867 " --> pdb=" O ARG B1863 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N ALA B1873 " --> pdb=" O GLN B1869 " (cutoff:3.500A) Processing helix chain 'B' and resid 1961 through 1980 removed outlier: 3.779A pdb=" N MET B1966 " --> pdb=" O VAL B1962 " (cutoff:3.500A) removed outlier: 4.094A pdb=" N GLN B1967 " --> pdb=" O ILE B1963 " (cutoff:3.500A) Proline residue: B1968 - end of helix removed outlier: 3.589A pdb=" N CYS B1977 " --> pdb=" O LEU B1973 " (cutoff:3.500A) removed outlier: 5.676A pdb=" N ASN B1979 " --> pdb=" O LEU B1975 " (cutoff:3.500A) removed outlier: 6.280A pdb=" N HIS B1980 " --> pdb=" O LEU B1976 " (cutoff:3.500A) Processing helix chain 'B' and resid 1982 through 1989 removed outlier: 4.013A pdb=" N ASN B1986 " --> pdb=" O ARG B1982 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N PHE B1987 " --> pdb=" O ASP B1983 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N ARG B1989 " --> pdb=" O GLN B1985 " (cutoff:3.500A) Processing helix chain 'B' and resid 1999 through 2010 removed outlier: 3.522A pdb=" N LEU B2007 " --> pdb=" O THR B2003 " (cutoff:3.500A) Processing helix chain 'B' and resid 2016 through 2018 No H-bonds generated for 'chain 'B' and resid 2016 through 2018' Processing helix chain 'B' and resid 2021 through 2024 No H-bonds generated for 'chain 'B' and resid 2021 through 2024' Processing helix chain 'B' and resid 2030 through 2043 removed outlier: 3.563A pdb=" N GLU B2042 " --> pdb=" O GLU B2038 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N TYR B2043 " --> pdb=" O SER B2039 " (cutoff:3.500A) Processing helix chain 'B' and resid 2049 through 2056 Processing helix chain 'B' and resid 2062 through 2069 removed outlier: 3.647A pdb=" N ILE B2066 " --> pdb=" O GLY B2062 " (cutoff:3.500A) Processing helix chain 'B' and resid 2077 through 2080 No H-bonds generated for 'chain 'B' and resid 2077 through 2080' Processing helix chain 'B' and resid 2082 through 2100 removed outlier: 3.708A pdb=" N MET B2100 " --> pdb=" O LEU B2096 " (cutoff:3.500A) Processing helix chain 'B' and resid 2107 through 2114 Processing helix chain 'B' and resid 2118 through 2127 removed outlier: 3.556A pdb=" N VAL B2122 " --> pdb=" O PRO B2118 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N LYS B2126 " --> pdb=" O VAL B2122 " (cutoff:3.500A) Processing helix chain 'B' and resid 2130 through 2138 removed outlier: 4.030A pdb=" N ASP B2138 " --> pdb=" O VAL B2134 " (cutoff:3.500A) Processing helix chain 'B' and resid 2149 through 2166 removed outlier: 4.303A pdb=" N ARG B2165 " --> pdb=" O HIS B2161 " (cutoff:3.500A) removed outlier: 4.819A pdb=" N HIS B2166 " --> pdb=" O GLN B2162 " (cutoff:3.500A) Processing helix chain 'B' and resid 2170 through 2174 removed outlier: 3.715A pdb=" N LEU B2174 " --> pdb=" O LEU B2170 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 2170 through 2174' Processing helix chain 'B' and resid 2184 through 2191 Processing helix chain 'B' and resid 2215 through 2218 Processing helix chain 'B' and resid 2221 through 2230 Processing helix chain 'B' and resid 2240 through 2245 Processing helix chain 'B' and resid 2247 through 2261 removed outlier: 3.784A pdb=" N LYS B2259 " --> pdb=" O ASN B2255 " (cutoff:3.500A) Processing helix chain 'B' and resid 2266 through 2294 removed outlier: 3.709A pdb=" N ASN B2272 " --> pdb=" O TRP B2268 " (cutoff:3.500A) removed outlier: 4.146A pdb=" N MET B2273 " --> pdb=" O CYS B2269 " (cutoff:3.500A) removed outlier: 6.348A pdb=" N SER B2274 " --> pdb=" O ALA B2270 " (cutoff:3.500A) removed outlier: 6.099A pdb=" N PHE B2275 " --> pdb=" O ARG B2271 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N LEU B2286 " --> pdb=" O ASN B2282 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N LEU B2290 " --> pdb=" O LEU B2286 " (cutoff:3.500A) removed outlier: 4.099A pdb=" N VAL B2291 " --> pdb=" O MET B2287 " (cutoff:3.500A) Processing helix chain 'B' and resid 2309 through 2325 removed outlier: 3.793A pdb=" N TRP B2314 " --> pdb=" O SER B2310 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N THR B2315 " --> pdb=" O GLY B2311 " (cutoff:3.500A) removed outlier: 4.213A pdb=" N SER B2320 " --> pdb=" O ALA B2316 " (cutoff:3.500A) removed outlier: 4.463A pdb=" N LEU B2321 " --> pdb=" O MET B2317 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N ALA B2322 " --> pdb=" O LEU B2318 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N ILE B2323 " --> pdb=" O ILE B2319 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N VAL B2324 " --> pdb=" O SER B2320 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N ILE B2325 " --> pdb=" O LEU B2321 " (cutoff:3.500A) Processing helix chain 'B' and resid 2329 through 2345 removed outlier: 3.653A pdb=" N LEU B2344 " --> pdb=" O THR B2340 " (cutoff:3.500A) Processing helix chain 'B' and resid 2350 through 2376 Processing helix chain 'B' and resid 2378 through 2381 Processing helix chain 'B' and resid 2383 through 2388 Processing helix chain 'B' and resid 2390 through 2407 removed outlier: 3.799A pdb=" N TYR B2398 " --> pdb=" O TYR B2394 " (cutoff:3.500A) Processing helix chain 'B' and resid 2410 through 2423 removed outlier: 3.562A pdb=" N TYR B2413 " --> pdb=" O GLU B2410 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N VAL B2421 " --> pdb=" O PHE B2418 " (cutoff:3.500A) Processing helix chain 'B' and resid 2426 through 2436 removed outlier: 3.623A pdb=" N SER B2433 " --> pdb=" O ASN B2429 " (cutoff:3.500A) removed outlier: 4.410A pdb=" N VAL B2434 " --> pdb=" O VAL B2430 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N THR B2435 " --> pdb=" O ILE B2431 " (cutoff:3.500A) Processing helix chain 'B' and resid 2438 through 2462 Processing helix chain 'B' and resid 2464 through 2466 No H-bonds generated for 'chain 'B' and resid 2464 through 2466' Processing helix chain 'B' and resid 2531 through 2541 removed outlier: 3.638A pdb=" N VAL B2538 " --> pdb=" O CYS B2534 " (cutoff:3.500A) Processing helix chain 'B' and resid 2549 through 2551 No H-bonds generated for 'chain 'B' and resid 2549 through 2551' Processing helix chain 'B' and resid 2563 through 2577 Processing helix chain 'B' and resid 2581 through 2609 removed outlier: 4.162A pdb=" N PHE B2586 " --> pdb=" O LEU B2582 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N VAL B2588 " --> pdb=" O LEU B2584 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N ILE B2589 " --> pdb=" O ILE B2585 " (cutoff:3.500A) Processing helix chain 'B' and resid 2628 through 2631 No H-bonds generated for 'chain 'B' and resid 2628 through 2631' Processing helix chain 'B' and resid 2638 through 2649 removed outlier: 3.789A pdb=" N LEU B2642 " --> pdb=" O MET B2638 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N LYS B2649 " --> pdb=" O ILE B2645 " (cutoff:3.500A) Processing helix chain 'B' and resid 2653 through 2655 No H-bonds generated for 'chain 'B' and resid 2653 through 2655' Processing helix chain 'B' and resid 2658 through 2668 removed outlier: 3.567A pdb=" N TYR B2662 " --> pdb=" O GLY B2658 " (cutoff:3.500A) Processing helix chain 'B' and resid 2681 through 2684 No H-bonds generated for 'chain 'B' and resid 2681 through 2684' Processing helix chain 'B' and resid 2692 through 2738 removed outlier: 4.116A pdb=" N LYS B2707 " --> pdb=" O GLU B2703 " (cutoff:3.500A) removed outlier: 4.636A pdb=" N LEU B2708 " --> pdb=" O SER B2704 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N LEU B2712 " --> pdb=" O LEU B2708 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N SER B2713 " --> pdb=" O VAL B2709 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N LYS B2720 " --> pdb=" O LEU B2716 " (cutoff:3.500A) removed outlier: 4.205A pdb=" N LEU B2735 " --> pdb=" O GLN B2731 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N GLY B2737 " --> pdb=" O ILE B2733 " (cutoff:3.500A) Processing helix chain 'C' and resid 67 through 76 Processing helix chain 'C' and resid 84 through 109 Processing helix chain 'C' and resid 157 through 159 No H-bonds generated for 'chain 'C' and resid 157 through 159' Processing helix chain 'C' and resid 364 through 366 No H-bonds generated for 'chain 'C' and resid 364 through 366' Processing helix chain 'C' and resid 437 through 458 removed outlier: 3.649A pdb=" N ARG C 441 " --> pdb=" O PRO C 437 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N LEU C 453 " --> pdb=" O ALA C 449 " (cutoff:3.500A) Processing helix chain 'C' and resid 467 through 474 removed outlier: 3.981A pdb=" N VAL C 473 " --> pdb=" O GLU C 469 " (cutoff:3.500A) Processing helix chain 'C' and resid 476 through 485 removed outlier: 3.738A pdb=" N LEU C 480 " --> pdb=" O LEU C 476 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N VAL C 481 " --> pdb=" O LEU C 477 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N TYR C 482 " --> pdb=" O GLU C 478 " (cutoff:3.500A) Processing helix chain 'C' and resid 506 through 512 Processing helix chain 'C' and resid 515 through 528 removed outlier: 4.074A pdb=" N PHE C 520 " --> pdb=" O LEU C 516 " (cutoff:3.500A) removed outlier: 4.213A pdb=" N LYS C 521 " --> pdb=" O LYS C 517 " (cutoff:3.500A) removed outlier: 4.079A pdb=" N LEU C 523 " --> pdb=" O ILE C 519 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N GLN C 524 " --> pdb=" O PHE C 520 " (cutoff:3.500A) Proline residue: C 526 - end of helix Processing helix chain 'C' and resid 548 through 564 removed outlier: 3.906A pdb=" N LEU C 555 " --> pdb=" O HIS C 551 " (cutoff:3.500A) removed outlier: 4.118A pdb=" N CYS C 556 " --> pdb=" O ILE C 552 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N TYR C 557 " --> pdb=" O CYS C 553 " (cutoff:3.500A) Processing helix chain 'C' and resid 568 through 577 removed outlier: 3.641A pdb=" N LYS C 576 " --> pdb=" O GLU C 572 " (cutoff:3.500A) removed outlier: 4.866A pdb=" N GLN C 577 " --> pdb=" O TYR C 573 " (cutoff:3.500A) Processing helix chain 'C' and resid 580 through 584 removed outlier: 4.511A pdb=" N GLN C 584 " --> pdb=" O PHE C 580 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 580 through 584' Processing helix chain 'C' and resid 591 through 600 Processing helix chain 'C' and resid 603 through 609 removed outlier: 3.844A pdb=" N LYS C 608 " --> pdb=" O LYS C 604 " (cutoff:3.500A) Processing helix chain 'C' and resid 612 through 625 removed outlier: 3.632A pdb=" N VAL C 622 " --> pdb=" O PHE C 618 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N ARG C 623 " --> pdb=" O VAL C 619 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N LYS C 624 " --> pdb=" O SER C 620 " (cutoff:3.500A) Processing helix chain 'C' and resid 629 through 638 removed outlier: 3.632A pdb=" N ASP C 632 " --> pdb=" O ARG C 629 " (cutoff:3.500A) Processing helix chain 'C' and resid 646 through 663 removed outlier: 4.092A pdb=" N LYS C 654 " --> pdb=" O GLU C 650 " (cutoff:3.500A) removed outlier: 4.183A pdb=" N ALA C 655 " --> pdb=" O LEU C 651 " (cutoff:3.500A) Proline residue: C 659 - end of helix removed outlier: 4.617A pdb=" N ALA C 662 " --> pdb=" O ASN C 658 " (cutoff:3.500A) removed outlier: 4.577A pdb=" N ASP C 663 " --> pdb=" O PRO C 659 " (cutoff:3.500A) Processing helix chain 'C' and resid 712 through 721 removed outlier: 3.534A pdb=" N LYS C 720 " --> pdb=" O ALA C 716 " (cutoff:3.500A) Processing helix chain 'C' and resid 724 through 740 Processing helix chain 'C' and resid 745 through 747 No H-bonds generated for 'chain 'C' and resid 745 through 747' Processing helix chain 'C' and resid 752 through 757 Processing helix chain 'C' and resid 761 through 767 removed outlier: 4.037A pdb=" N CYS C 767 " --> pdb=" O LEU C 763 " (cutoff:3.500A) Processing helix chain 'C' and resid 775 through 789 Processing helix chain 'C' and resid 816 through 818 No H-bonds generated for 'chain 'C' and resid 816 through 818' Processing helix chain 'C' and resid 825 through 848 removed outlier: 4.215A pdb=" N GLU C 828 " --> pdb=" O SER C 825 " (cutoff:3.500A) removed outlier: 5.590A pdb=" N GLN C 835 " --> pdb=" O ARG C 832 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N GLU C 842 " --> pdb=" O PHE C 839 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N TYR C 843 " --> pdb=" O VAL C 840 " (cutoff:3.500A) Processing helix chain 'C' and resid 857 through 875 removed outlier: 4.322A pdb=" N GLU C 865 " --> pdb=" O LYS C 861 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N VAL C 866 " --> pdb=" O LEU C 862 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N TYR C 875 " --> pdb=" O ARG C 871 " (cutoff:3.500A) Processing helix chain 'C' and resid 881 through 899 removed outlier: 3.656A pdb=" N LEU C 885 " --> pdb=" O PHE C 881 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N ARG C 886 " --> pdb=" O SER C 882 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N ILE C 890 " --> pdb=" O ARG C 886 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N LEU C 895 " --> pdb=" O LEU C 891 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N HIS C 899 " --> pdb=" O LEU C 895 " (cutoff:3.500A) Processing helix chain 'C' and resid 965 through 1005 removed outlier: 4.470A pdb=" N THR C 970 " --> pdb=" O MET C 966 " (cutoff:3.500A) removed outlier: 4.664A pdb=" N LYS C 971 " --> pdb=" O VAL C 967 " (cutoff:3.500A) removed outlier: 4.225A pdb=" N LEU C 972 " --> pdb=" O MET C 968 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N GLU C 976 " --> pdb=" O LEU C 972 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N ILE C 977 " --> pdb=" O LYS C 973 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N ARG C 985 " --> pdb=" O ILE C 981 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N LEU C 986 " --> pdb=" O LEU C 982 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N ASP C 987 " --> pdb=" O ASN C 983 " (cutoff:3.500A) Processing helix chain 'C' and resid 1030 through 1039 removed outlier: 4.630A pdb=" N GLU C1035 " --> pdb=" O GLU C1031 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N GLN C1036 " --> pdb=" O HIS C1032 " (cutoff:3.500A) Processing helix chain 'C' and resid 1045 through 1047 No H-bonds generated for 'chain 'C' and resid 1045 through 1047' Processing helix chain 'C' and resid 1058 through 1069 removed outlier: 4.289A pdb=" N ARG C1062 " --> pdb=" O ARG C1058 " (cutoff:3.500A) removed outlier: 4.118A pdb=" N VAL C1063 " --> pdb=" O THR C1059 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N LEU C1064 " --> pdb=" O PHE C1060 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N MET C1069 " --> pdb=" O LEU C1065 " (cutoff:3.500A) Processing helix chain 'C' and resid 1073 through 1087 removed outlier: 3.544A pdb=" N LEU C1083 " --> pdb=" O ALA C1079 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N PHE C1084 " --> pdb=" O LEU C1080 " (cutoff:3.500A) Processing helix chain 'C' and resid 1089 through 1098 removed outlier: 3.684A pdb=" N ALA C1096 " --> pdb=" O GLU C1092 " (cutoff:3.500A) Processing helix chain 'C' and resid 1106 through 1127 Processing helix chain 'C' and resid 1129 through 1131 No H-bonds generated for 'chain 'C' and resid 1129 through 1131' Processing helix chain 'C' and resid 1168 through 1187 removed outlier: 3.502A pdb=" N ARG C1174 " --> pdb=" O SER C1170 " (cutoff:3.500A) removed outlier: 4.242A pdb=" N LYS C1177 " --> pdb=" O TYR C1173 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N GLU C1178 " --> pdb=" O ARG C1174 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N ILE C1179 " --> pdb=" O VAL C1175 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N CYS C1187 " --> pdb=" O LEU C1183 " (cutoff:3.500A) Processing helix chain 'C' and resid 1201 through 1208 Processing helix chain 'C' and resid 1210 through 1219 Processing helix chain 'C' and resid 1228 through 1245 Processing helix chain 'C' and resid 1250 through 1262 removed outlier: 3.932A pdb=" N LYS C1257 " --> pdb=" O ALA C1253 " (cutoff:3.500A) removed outlier: 5.037A pdb=" N HIS C1258 " --> pdb=" O LEU C1254 " (cutoff:3.500A) removed outlier: 4.278A pdb=" N ILE C1259 " --> pdb=" O LEU C1255 " (cutoff:3.500A) removed outlier: 5.651A pdb=" N ASN C1260 " --> pdb=" O HIS C1256 " (cutoff:3.500A) removed outlier: 6.588A pdb=" N LEU C1261 " --> pdb=" O LYS C1257 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N PHE C1262 " --> pdb=" O HIS C1258 " (cutoff:3.500A) Processing helix chain 'C' and resid 1268 through 1276 removed outlier: 3.696A pdb=" N MET C1273 " --> pdb=" O GLU C1269 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N GLN C1274 " --> pdb=" O ALA C1270 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N HIS C1275 " --> pdb=" O VAL C1271 " (cutoff:3.500A) Processing helix chain 'C' and resid 1281 through 1286 removed outlier: 3.966A pdb=" N GLU C1286 " --> pdb=" O GLN C1282 " (cutoff:3.500A) Processing helix chain 'C' and resid 1289 through 1301 Processing helix chain 'C' and resid 1306 through 1316 removed outlier: 3.705A pdb=" N PHE C1311 " --> pdb=" O GLN C1307 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N LEU C1312 " --> pdb=" O TYR C1308 " (cutoff:3.500A) Processing helix chain 'C' and resid 1324 through 1341 removed outlier: 3.848A pdb=" N MET C1331 " --> pdb=" O GLN C1327 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N VAL C1335 " --> pdb=" O MET C1331 " (cutoff:3.500A) removed outlier: 5.101A pdb=" N ASN C1336 " --> pdb=" O ALA C1332 " (cutoff:3.500A) removed outlier: 4.111A pdb=" N GLY C1338 " --> pdb=" O LEU C1334 " (cutoff:3.500A) removed outlier: 6.288A pdb=" N GLU C1339 " --> pdb=" O VAL C1335 " (cutoff:3.500A) removed outlier: 7.948A pdb=" N ASP C1340 " --> pdb=" O ASN C1336 " (cutoff:3.500A) removed outlier: 4.337A pdb=" N VAL C1341 " --> pdb=" O SER C1337 " (cutoff:3.500A) Processing helix chain 'C' and resid 1348 through 1363 removed outlier: 3.598A pdb=" N SER C1360 " --> pdb=" O GLN C1356 " (cutoff:3.500A) Processing helix chain 'C' and resid 1369 through 1386 removed outlier: 3.710A pdb=" N TYR C1374 " --> pdb=" O PRO C1370 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N HIS C1375 " --> pdb=" O LEU C1371 " (cutoff:3.500A) Processing helix chain 'C' and resid 1391 through 1400 removed outlier: 4.023A pdb=" N SER C1399 " --> pdb=" O ILE C1395 " (cutoff:3.500A) removed outlier: 4.226A pdb=" N LEU C1400 " --> pdb=" O LYS C1396 " (cutoff:3.500A) Processing helix chain 'C' and resid 1403 through 1411 Processing helix chain 'C' and resid 1417 through 1431 removed outlier: 3.660A pdb=" N PHE C1426 " --> pdb=" O ALA C1422 " (cutoff:3.500A) Processing helix chain 'C' and resid 1439 through 1442 No H-bonds generated for 'chain 'C' and resid 1439 through 1442' Processing helix chain 'C' and resid 1446 through 1462 Processing helix chain 'C' and resid 1473 through 1492 removed outlier: 4.568A pdb=" N VAL C1483 " --> pdb=" O VAL C1479 " (cutoff:3.500A) removed outlier: 5.016A pdb=" N MET C1484 " --> pdb=" O THR C1480 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N PHE C1490 " --> pdb=" O ILE C1486 " (cutoff:3.500A) Processing helix chain 'C' and resid 1495 through 1498 Processing helix chain 'C' and resid 1506 through 1521 removed outlier: 3.669A pdb=" N TYR C1520 " --> pdb=" O VAL C1516 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N HIS C1521 " --> pdb=" O PHE C1517 " (cutoff:3.500A) Processing helix chain 'C' and resid 1527 through 1547 removed outlier: 3.875A pdb=" N ALA C1531 " --> pdb=" O PRO C1527 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N SER C1532 " --> pdb=" O SER C1528 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N CYS C1536 " --> pdb=" O SER C1532 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ILE C1537 " --> pdb=" O VAL C1533 " (cutoff:3.500A) Processing helix chain 'C' and resid 1553 through 1565 Processing helix chain 'C' and resid 1590 through 1631 removed outlier: 3.677A pdb=" N TYR C1597 " --> pdb=" O ALA C1593 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N GLN C1605 " --> pdb=" O ILE C1601 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N ASP C1606 " --> pdb=" O GLU C1602 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N ARG C1616 " --> pdb=" O GLU C1612 " (cutoff:3.500A) Proline residue: C1617 - end of helix removed outlier: 3.577A pdb=" N GLN C1620 " --> pdb=" O ARG C1616 " (cutoff:3.500A) removed outlier: 4.438A pdb=" N ALA C1621 " --> pdb=" O PRO C1617 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N GLU C1622 " --> pdb=" O LEU C1618 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N VAL C1627 " --> pdb=" O LEU C1623 " (cutoff:3.500A) Processing helix chain 'C' and resid 1642 through 1648 Processing helix chain 'C' and resid 1651 through 1663 Processing helix chain 'C' and resid 1669 through 1682 removed outlier: 3.648A pdb=" N GLU C1681 " --> pdb=" O GLN C1677 " (cutoff:3.500A) removed outlier: 4.354A pdb=" N MET C1682 " --> pdb=" O THR C1678 " (cutoff:3.500A) Processing helix chain 'C' and resid 1723 through 1745 Processing helix chain 'C' and resid 1792 through 1801 removed outlier: 3.775A pdb=" N GLN C1796 " --> pdb=" O LEU C1792 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N CYS C1797 " --> pdb=" O ALA C1793 " (cutoff:3.500A) Processing helix chain 'C' and resid 1804 through 1813 removed outlier: 3.544A pdb=" N VAL C1808 " --> pdb=" O ALA C1804 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N ILE C1809 " --> pdb=" O SER C1805 " (cutoff:3.500A) Processing helix chain 'C' and resid 1818 through 1831 Processing helix chain 'C' and resid 1837 through 1849 Processing helix chain 'C' and resid 1853 through 1874 removed outlier: 3.977A pdb=" N ALA C1867 " --> pdb=" O ARG C1863 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N ALA C1873 " --> pdb=" O GLN C1869 " (cutoff:3.500A) Processing helix chain 'C' and resid 1961 through 1980 removed outlier: 3.778A pdb=" N MET C1966 " --> pdb=" O VAL C1962 " (cutoff:3.500A) removed outlier: 4.094A pdb=" N GLN C1967 " --> pdb=" O ILE C1963 " (cutoff:3.500A) Proline residue: C1968 - end of helix removed outlier: 3.589A pdb=" N CYS C1977 " --> pdb=" O LEU C1973 " (cutoff:3.500A) removed outlier: 5.676A pdb=" N ASN C1979 " --> pdb=" O LEU C1975 " (cutoff:3.500A) removed outlier: 6.280A pdb=" N HIS C1980 " --> pdb=" O LEU C1976 " (cutoff:3.500A) Processing helix chain 'C' and resid 1982 through 1989 removed outlier: 4.013A pdb=" N ASN C1986 " --> pdb=" O ARG C1982 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N PHE C1987 " --> pdb=" O ASP C1983 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N ARG C1989 " --> pdb=" O GLN C1985 " (cutoff:3.500A) Processing helix chain 'C' and resid 1999 through 2010 removed outlier: 3.522A pdb=" N LEU C2007 " --> pdb=" O THR C2003 " (cutoff:3.500A) Processing helix chain 'C' and resid 2016 through 2018 No H-bonds generated for 'chain 'C' and resid 2016 through 2018' Processing helix chain 'C' and resid 2021 through 2024 No H-bonds generated for 'chain 'C' and resid 2021 through 2024' Processing helix chain 'C' and resid 2030 through 2043 removed outlier: 3.564A pdb=" N GLU C2042 " --> pdb=" O GLU C2038 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N TYR C2043 " --> pdb=" O SER C2039 " (cutoff:3.500A) Processing helix chain 'C' and resid 2049 through 2056 Processing helix chain 'C' and resid 2062 through 2069 removed outlier: 3.648A pdb=" N ILE C2066 " --> pdb=" O GLY C2062 " (cutoff:3.500A) Processing helix chain 'C' and resid 2077 through 2080 No H-bonds generated for 'chain 'C' and resid 2077 through 2080' Processing helix chain 'C' and resid 2082 through 2100 removed outlier: 3.708A pdb=" N MET C2100 " --> pdb=" O LEU C2096 " (cutoff:3.500A) Processing helix chain 'C' and resid 2107 through 2114 Processing helix chain 'C' and resid 2118 through 2127 removed outlier: 3.558A pdb=" N VAL C2122 " --> pdb=" O PRO C2118 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N LYS C2126 " --> pdb=" O VAL C2122 " (cutoff:3.500A) Processing helix chain 'C' and resid 2130 through 2138 removed outlier: 4.030A pdb=" N ASP C2138 " --> pdb=" O VAL C2134 " (cutoff:3.500A) Processing helix chain 'C' and resid 2149 through 2166 removed outlier: 4.303A pdb=" N ARG C2165 " --> pdb=" O HIS C2161 " (cutoff:3.500A) removed outlier: 4.819A pdb=" N HIS C2166 " --> pdb=" O GLN C2162 " (cutoff:3.500A) Processing helix chain 'C' and resid 2170 through 2174 removed outlier: 3.715A pdb=" N LEU C2174 " --> pdb=" O LEU C2170 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 2170 through 2174' Processing helix chain 'C' and resid 2184 through 2191 Processing helix chain 'C' and resid 2215 through 2218 Processing helix chain 'C' and resid 2221 through 2230 Processing helix chain 'C' and resid 2240 through 2245 Processing helix chain 'C' and resid 2247 through 2261 removed outlier: 3.784A pdb=" N LYS C2259 " --> pdb=" O ASN C2255 " (cutoff:3.500A) Processing helix chain 'C' and resid 2266 through 2294 removed outlier: 3.709A pdb=" N ASN C2272 " --> pdb=" O TRP C2268 " (cutoff:3.500A) removed outlier: 4.146A pdb=" N MET C2273 " --> pdb=" O CYS C2269 " (cutoff:3.500A) removed outlier: 6.348A pdb=" N SER C2274 " --> pdb=" O ALA C2270 " (cutoff:3.500A) removed outlier: 6.099A pdb=" N PHE C2275 " --> pdb=" O ARG C2271 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N LEU C2286 " --> pdb=" O ASN C2282 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N LEU C2290 " --> pdb=" O LEU C2286 " (cutoff:3.500A) removed outlier: 4.099A pdb=" N VAL C2291 " --> pdb=" O MET C2287 " (cutoff:3.500A) Processing helix chain 'C' and resid 2309 through 2325 removed outlier: 3.792A pdb=" N TRP C2314 " --> pdb=" O SER C2310 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N THR C2315 " --> pdb=" O GLY C2311 " (cutoff:3.500A) removed outlier: 4.213A pdb=" N SER C2320 " --> pdb=" O ALA C2316 " (cutoff:3.500A) removed outlier: 4.463A pdb=" N LEU C2321 " --> pdb=" O MET C2317 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N ALA C2322 " --> pdb=" O LEU C2318 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N ILE C2323 " --> pdb=" O ILE C2319 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N VAL C2324 " --> pdb=" O SER C2320 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N ILE C2325 " --> pdb=" O LEU C2321 " (cutoff:3.500A) Processing helix chain 'C' and resid 2329 through 2345 removed outlier: 3.652A pdb=" N LEU C2344 " --> pdb=" O THR C2340 " (cutoff:3.500A) Processing helix chain 'C' and resid 2350 through 2376 Processing helix chain 'C' and resid 2378 through 2381 Processing helix chain 'C' and resid 2383 through 2388 Processing helix chain 'C' and resid 2390 through 2407 removed outlier: 3.799A pdb=" N TYR C2398 " --> pdb=" O TYR C2394 " (cutoff:3.500A) Processing helix chain 'C' and resid 2410 through 2423 removed outlier: 3.562A pdb=" N TYR C2413 " --> pdb=" O GLU C2410 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N VAL C2421 " --> pdb=" O PHE C2418 " (cutoff:3.500A) Processing helix chain 'C' and resid 2426 through 2436 removed outlier: 3.623A pdb=" N SER C2433 " --> pdb=" O ASN C2429 " (cutoff:3.500A) removed outlier: 4.410A pdb=" N VAL C2434 " --> pdb=" O VAL C2430 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N THR C2435 " --> pdb=" O ILE C2431 " (cutoff:3.500A) Processing helix chain 'C' and resid 2438 through 2462 Processing helix chain 'C' and resid 2464 through 2466 No H-bonds generated for 'chain 'C' and resid 2464 through 2466' Processing helix chain 'C' and resid 2531 through 2541 removed outlier: 3.639A pdb=" N VAL C2538 " --> pdb=" O CYS C2534 " (cutoff:3.500A) Processing helix chain 'C' and resid 2549 through 2551 No H-bonds generated for 'chain 'C' and resid 2549 through 2551' Processing helix chain 'C' and resid 2563 through 2577 Processing helix chain 'C' and resid 2581 through 2609 removed outlier: 4.163A pdb=" N PHE C2586 " --> pdb=" O LEU C2582 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N VAL C2588 " --> pdb=" O LEU C2584 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N ILE C2589 " --> pdb=" O ILE C2585 " (cutoff:3.500A) Processing helix chain 'C' and resid 2628 through 2631 No H-bonds generated for 'chain 'C' and resid 2628 through 2631' Processing helix chain 'C' and resid 2638 through 2649 removed outlier: 3.789A pdb=" N LEU C2642 " --> pdb=" O MET C2638 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N LYS C2649 " --> pdb=" O ILE C2645 " (cutoff:3.500A) Processing helix chain 'C' and resid 2653 through 2655 No H-bonds generated for 'chain 'C' and resid 2653 through 2655' Processing helix chain 'C' and resid 2658 through 2668 removed outlier: 3.567A pdb=" N TYR C2662 " --> pdb=" O GLY C2658 " (cutoff:3.500A) Processing helix chain 'C' and resid 2681 through 2684 No H-bonds generated for 'chain 'C' and resid 2681 through 2684' Processing helix chain 'C' and resid 2692 through 2738 removed outlier: 4.116A pdb=" N LYS C2707 " --> pdb=" O GLU C2703 " (cutoff:3.500A) removed outlier: 4.636A pdb=" N LEU C2708 " --> pdb=" O SER C2704 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N LEU C2712 " --> pdb=" O LEU C2708 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N SER C2713 " --> pdb=" O VAL C2709 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N LYS C2720 " --> pdb=" O LEU C2716 " (cutoff:3.500A) removed outlier: 4.205A pdb=" N LEU C2735 " --> pdb=" O GLN C2731 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N GLY C2737 " --> pdb=" O ILE C2733 " (cutoff:3.500A) Processing helix chain 'D' and resid 67 through 76 Processing helix chain 'D' and resid 84 through 109 Processing helix chain 'D' and resid 157 through 159 No H-bonds generated for 'chain 'D' and resid 157 through 159' Processing helix chain 'D' and resid 364 through 366 No H-bonds generated for 'chain 'D' and resid 364 through 366' Processing helix chain 'D' and resid 437 through 458 removed outlier: 3.648A pdb=" N ARG D 441 " --> pdb=" O PRO D 437 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N LEU D 453 " --> pdb=" O ALA D 449 " (cutoff:3.500A) Processing helix chain 'D' and resid 467 through 474 removed outlier: 3.981A pdb=" N VAL D 473 " --> pdb=" O GLU D 469 " (cutoff:3.500A) Processing helix chain 'D' and resid 476 through 485 removed outlier: 3.738A pdb=" N LEU D 480 " --> pdb=" O LEU D 476 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N VAL D 481 " --> pdb=" O LEU D 477 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N TYR D 482 " --> pdb=" O GLU D 478 " (cutoff:3.500A) Processing helix chain 'D' and resid 506 through 512 Processing helix chain 'D' and resid 515 through 528 removed outlier: 4.074A pdb=" N PHE D 520 " --> pdb=" O LEU D 516 " (cutoff:3.500A) removed outlier: 4.213A pdb=" N LYS D 521 " --> pdb=" O LYS D 517 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N LEU D 523 " --> pdb=" O ILE D 519 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N GLN D 524 " --> pdb=" O PHE D 520 " (cutoff:3.500A) Proline residue: D 526 - end of helix Processing helix chain 'D' and resid 548 through 564 removed outlier: 3.906A pdb=" N LEU D 555 " --> pdb=" O HIS D 551 " (cutoff:3.500A) removed outlier: 4.117A pdb=" N CYS D 556 " --> pdb=" O ILE D 552 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N TYR D 557 " --> pdb=" O CYS D 553 " (cutoff:3.500A) Processing helix chain 'D' and resid 568 through 577 removed outlier: 3.641A pdb=" N LYS D 576 " --> pdb=" O GLU D 572 " (cutoff:3.500A) removed outlier: 4.865A pdb=" N GLN D 577 " --> pdb=" O TYR D 573 " (cutoff:3.500A) Processing helix chain 'D' and resid 580 through 584 removed outlier: 4.512A pdb=" N GLN D 584 " --> pdb=" O PHE D 580 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 580 through 584' Processing helix chain 'D' and resid 591 through 600 Processing helix chain 'D' and resid 603 through 609 removed outlier: 3.844A pdb=" N LYS D 608 " --> pdb=" O LYS D 604 " (cutoff:3.500A) Processing helix chain 'D' and resid 612 through 625 removed outlier: 3.632A pdb=" N VAL D 622 " --> pdb=" O PHE D 618 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N ARG D 623 " --> pdb=" O VAL D 619 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N LYS D 624 " --> pdb=" O SER D 620 " (cutoff:3.500A) Processing helix chain 'D' and resid 629 through 638 removed outlier: 3.631A pdb=" N ASP D 632 " --> pdb=" O ARG D 629 " (cutoff:3.500A) Processing helix chain 'D' and resid 646 through 663 removed outlier: 4.092A pdb=" N LYS D 654 " --> pdb=" O GLU D 650 " (cutoff:3.500A) removed outlier: 4.183A pdb=" N ALA D 655 " --> pdb=" O LEU D 651 " (cutoff:3.500A) Proline residue: D 659 - end of helix removed outlier: 4.616A pdb=" N ALA D 662 " --> pdb=" O ASN D 658 " (cutoff:3.500A) removed outlier: 4.577A pdb=" N ASP D 663 " --> pdb=" O PRO D 659 " (cutoff:3.500A) Processing helix chain 'D' and resid 712 through 721 removed outlier: 3.535A pdb=" N LYS D 720 " --> pdb=" O ALA D 716 " (cutoff:3.500A) Processing helix chain 'D' and resid 724 through 740 Processing helix chain 'D' and resid 745 through 747 No H-bonds generated for 'chain 'D' and resid 745 through 747' Processing helix chain 'D' and resid 752 through 757 Processing helix chain 'D' and resid 761 through 767 removed outlier: 4.038A pdb=" N CYS D 767 " --> pdb=" O LEU D 763 " (cutoff:3.500A) Processing helix chain 'D' and resid 775 through 789 Processing helix chain 'D' and resid 816 through 818 No H-bonds generated for 'chain 'D' and resid 816 through 818' Processing helix chain 'D' and resid 825 through 848 removed outlier: 4.215A pdb=" N GLU D 828 " --> pdb=" O SER D 825 " (cutoff:3.500A) removed outlier: 5.590A pdb=" N GLN D 835 " --> pdb=" O ARG D 832 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N GLU D 842 " --> pdb=" O PHE D 839 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N TYR D 843 " --> pdb=" O VAL D 840 " (cutoff:3.500A) Processing helix chain 'D' and resid 857 through 875 removed outlier: 4.322A pdb=" N GLU D 865 " --> pdb=" O LYS D 861 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N VAL D 866 " --> pdb=" O LEU D 862 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N TYR D 875 " --> pdb=" O ARG D 871 " (cutoff:3.500A) Processing helix chain 'D' and resid 881 through 899 removed outlier: 3.657A pdb=" N LEU D 885 " --> pdb=" O PHE D 881 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N ARG D 886 " --> pdb=" O SER D 882 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N ILE D 890 " --> pdb=" O ARG D 886 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N LEU D 895 " --> pdb=" O LEU D 891 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N HIS D 899 " --> pdb=" O LEU D 895 " (cutoff:3.500A) Processing helix chain 'D' and resid 965 through 1005 removed outlier: 4.469A pdb=" N THR D 970 " --> pdb=" O MET D 966 " (cutoff:3.500A) removed outlier: 4.663A pdb=" N LYS D 971 " --> pdb=" O VAL D 967 " (cutoff:3.500A) removed outlier: 4.224A pdb=" N LEU D 972 " --> pdb=" O MET D 968 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N GLU D 976 " --> pdb=" O LEU D 972 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N ILE D 977 " --> pdb=" O LYS D 973 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N ARG D 985 " --> pdb=" O ILE D 981 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N LEU D 986 " --> pdb=" O LEU D 982 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N ASP D 987 " --> pdb=" O ASN D 983 " (cutoff:3.500A) Processing helix chain 'D' and resid 1030 through 1039 removed outlier: 4.629A pdb=" N GLU D1035 " --> pdb=" O GLU D1031 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N GLN D1036 " --> pdb=" O HIS D1032 " (cutoff:3.500A) Processing helix chain 'D' and resid 1045 through 1047 No H-bonds generated for 'chain 'D' and resid 1045 through 1047' Processing helix chain 'D' and resid 1058 through 1069 removed outlier: 4.290A pdb=" N ARG D1062 " --> pdb=" O ARG D1058 " (cutoff:3.500A) removed outlier: 4.118A pdb=" N VAL D1063 " --> pdb=" O THR D1059 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N LEU D1064 " --> pdb=" O PHE D1060 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N MET D1069 " --> pdb=" O LEU D1065 " (cutoff:3.500A) Processing helix chain 'D' and resid 1073 through 1087 removed outlier: 3.544A pdb=" N LEU D1083 " --> pdb=" O ALA D1079 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N PHE D1084 " --> pdb=" O LEU D1080 " (cutoff:3.500A) Processing helix chain 'D' and resid 1089 through 1098 removed outlier: 3.684A pdb=" N ALA D1096 " --> pdb=" O GLU D1092 " (cutoff:3.500A) Processing helix chain 'D' and resid 1106 through 1127 Processing helix chain 'D' and resid 1129 through 1131 No H-bonds generated for 'chain 'D' and resid 1129 through 1131' Processing helix chain 'D' and resid 1168 through 1187 removed outlier: 3.502A pdb=" N ARG D1174 " --> pdb=" O SER D1170 " (cutoff:3.500A) removed outlier: 4.242A pdb=" N LYS D1177 " --> pdb=" O TYR D1173 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N GLU D1178 " --> pdb=" O ARG D1174 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N ILE D1179 " --> pdb=" O VAL D1175 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N CYS D1187 " --> pdb=" O LEU D1183 " (cutoff:3.500A) Processing helix chain 'D' and resid 1201 through 1208 Processing helix chain 'D' and resid 1210 through 1219 Processing helix chain 'D' and resid 1228 through 1245 Processing helix chain 'D' and resid 1250 through 1262 removed outlier: 3.932A pdb=" N LYS D1257 " --> pdb=" O ALA D1253 " (cutoff:3.500A) removed outlier: 5.038A pdb=" N HIS D1258 " --> pdb=" O LEU D1254 " (cutoff:3.500A) removed outlier: 4.279A pdb=" N ILE D1259 " --> pdb=" O LEU D1255 " (cutoff:3.500A) removed outlier: 5.651A pdb=" N ASN D1260 " --> pdb=" O HIS D1256 " (cutoff:3.500A) removed outlier: 6.588A pdb=" N LEU D1261 " --> pdb=" O LYS D1257 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N PHE D1262 " --> pdb=" O HIS D1258 " (cutoff:3.500A) Processing helix chain 'D' and resid 1268 through 1276 removed outlier: 3.696A pdb=" N MET D1273 " --> pdb=" O GLU D1269 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N GLN D1274 " --> pdb=" O ALA D1270 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N HIS D1275 " --> pdb=" O VAL D1271 " (cutoff:3.500A) Processing helix chain 'D' and resid 1281 through 1286 removed outlier: 3.966A pdb=" N GLU D1286 " --> pdb=" O GLN D1282 " (cutoff:3.500A) Processing helix chain 'D' and resid 1289 through 1301 Processing helix chain 'D' and resid 1306 through 1316 removed outlier: 3.705A pdb=" N PHE D1311 " --> pdb=" O GLN D1307 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N LEU D1312 " --> pdb=" O TYR D1308 " (cutoff:3.500A) Processing helix chain 'D' and resid 1324 through 1341 removed outlier: 3.848A pdb=" N MET D1331 " --> pdb=" O GLN D1327 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N VAL D1335 " --> pdb=" O MET D1331 " (cutoff:3.500A) removed outlier: 5.101A pdb=" N ASN D1336 " --> pdb=" O ALA D1332 " (cutoff:3.500A) removed outlier: 4.112A pdb=" N GLY D1338 " --> pdb=" O LEU D1334 " (cutoff:3.500A) removed outlier: 6.288A pdb=" N GLU D1339 " --> pdb=" O VAL D1335 " (cutoff:3.500A) removed outlier: 7.947A pdb=" N ASP D1340 " --> pdb=" O ASN D1336 " (cutoff:3.500A) removed outlier: 4.336A pdb=" N VAL D1341 " --> pdb=" O SER D1337 " (cutoff:3.500A) Processing helix chain 'D' and resid 1348 through 1363 removed outlier: 3.599A pdb=" N SER D1360 " --> pdb=" O GLN D1356 " (cutoff:3.500A) Processing helix chain 'D' and resid 1369 through 1386 removed outlier: 3.710A pdb=" N TYR D1374 " --> pdb=" O PRO D1370 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N HIS D1375 " --> pdb=" O LEU D1371 " (cutoff:3.500A) Processing helix chain 'D' and resid 1391 through 1400 removed outlier: 4.024A pdb=" N SER D1399 " --> pdb=" O ILE D1395 " (cutoff:3.500A) removed outlier: 4.226A pdb=" N LEU D1400 " --> pdb=" O LYS D1396 " (cutoff:3.500A) Processing helix chain 'D' and resid 1403 through 1411 Processing helix chain 'D' and resid 1417 through 1431 removed outlier: 3.660A pdb=" N PHE D1426 " --> pdb=" O ALA D1422 " (cutoff:3.500A) Processing helix chain 'D' and resid 1439 through 1442 No H-bonds generated for 'chain 'D' and resid 1439 through 1442' Processing helix chain 'D' and resid 1446 through 1462 Processing helix chain 'D' and resid 1473 through 1492 removed outlier: 4.568A pdb=" N VAL D1483 " --> pdb=" O VAL D1479 " (cutoff:3.500A) removed outlier: 5.016A pdb=" N MET D1484 " --> pdb=" O THR D1480 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N PHE D1490 " --> pdb=" O ILE D1486 " (cutoff:3.500A) Processing helix chain 'D' and resid 1495 through 1498 Processing helix chain 'D' and resid 1506 through 1521 removed outlier: 3.669A pdb=" N TYR D1520 " --> pdb=" O VAL D1516 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N HIS D1521 " --> pdb=" O PHE D1517 " (cutoff:3.500A) Processing helix chain 'D' and resid 1527 through 1547 removed outlier: 3.874A pdb=" N ALA D1531 " --> pdb=" O PRO D1527 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N SER D1532 " --> pdb=" O SER D1528 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N CYS D1536 " --> pdb=" O SER D1532 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ILE D1537 " --> pdb=" O VAL D1533 " (cutoff:3.500A) Processing helix chain 'D' and resid 1553 through 1565 Processing helix chain 'D' and resid 1590 through 1631 removed outlier: 3.677A pdb=" N TYR D1597 " --> pdb=" O ALA D1593 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N GLN D1605 " --> pdb=" O ILE D1601 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N ASP D1606 " --> pdb=" O GLU D1602 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N ARG D1616 " --> pdb=" O GLU D1612 " (cutoff:3.500A) Proline residue: D1617 - end of helix removed outlier: 3.577A pdb=" N GLN D1620 " --> pdb=" O ARG D1616 " (cutoff:3.500A) removed outlier: 4.438A pdb=" N ALA D1621 " --> pdb=" O PRO D1617 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N GLU D1622 " --> pdb=" O LEU D1618 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N VAL D1627 " --> pdb=" O LEU D1623 " (cutoff:3.500A) Processing helix chain 'D' and resid 1642 through 1648 Processing helix chain 'D' and resid 1651 through 1663 Processing helix chain 'D' and resid 1669 through 1682 removed outlier: 3.648A pdb=" N GLU D1681 " --> pdb=" O GLN D1677 " (cutoff:3.500A) removed outlier: 4.354A pdb=" N MET D1682 " --> pdb=" O THR D1678 " (cutoff:3.500A) Processing helix chain 'D' and resid 1723 through 1745 Processing helix chain 'D' and resid 1792 through 1801 removed outlier: 3.775A pdb=" N GLN D1796 " --> pdb=" O LEU D1792 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N CYS D1797 " --> pdb=" O ALA D1793 " (cutoff:3.500A) Processing helix chain 'D' and resid 1804 through 1813 removed outlier: 3.544A pdb=" N VAL D1808 " --> pdb=" O ALA D1804 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N ILE D1809 " --> pdb=" O SER D1805 " (cutoff:3.500A) Processing helix chain 'D' and resid 1818 through 1831 Processing helix chain 'D' and resid 1837 through 1849 Processing helix chain 'D' and resid 1853 through 1874 removed outlier: 3.977A pdb=" N ALA D1867 " --> pdb=" O ARG D1863 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N ALA D1873 " --> pdb=" O GLN D1869 " (cutoff:3.500A) Processing helix chain 'D' and resid 1961 through 1980 removed outlier: 3.779A pdb=" N MET D1966 " --> pdb=" O VAL D1962 " (cutoff:3.500A) removed outlier: 4.094A pdb=" N GLN D1967 " --> pdb=" O ILE D1963 " (cutoff:3.500A) Proline residue: D1968 - end of helix removed outlier: 3.589A pdb=" N CYS D1977 " --> pdb=" O LEU D1973 " (cutoff:3.500A) removed outlier: 5.676A pdb=" N ASN D1979 " --> pdb=" O LEU D1975 " (cutoff:3.500A) removed outlier: 6.280A pdb=" N HIS D1980 " --> pdb=" O LEU D1976 " (cutoff:3.500A) Processing helix chain 'D' and resid 1982 through 1989 removed outlier: 4.013A pdb=" N ASN D1986 " --> pdb=" O ARG D1982 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N PHE D1987 " --> pdb=" O ASP D1983 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N ARG D1989 " --> pdb=" O GLN D1985 " (cutoff:3.500A) Processing helix chain 'D' and resid 1999 through 2010 removed outlier: 3.523A pdb=" N LEU D2007 " --> pdb=" O THR D2003 " (cutoff:3.500A) Processing helix chain 'D' and resid 2016 through 2018 No H-bonds generated for 'chain 'D' and resid 2016 through 2018' Processing helix chain 'D' and resid 2021 through 2024 No H-bonds generated for 'chain 'D' and resid 2021 through 2024' Processing helix chain 'D' and resid 2030 through 2043 removed outlier: 3.563A pdb=" N GLU D2042 " --> pdb=" O GLU D2038 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N TYR D2043 " --> pdb=" O SER D2039 " (cutoff:3.500A) Processing helix chain 'D' and resid 2049 through 2056 Processing helix chain 'D' and resid 2062 through 2069 removed outlier: 3.647A pdb=" N ILE D2066 " --> pdb=" O GLY D2062 " (cutoff:3.500A) Processing helix chain 'D' and resid 2077 through 2080 No H-bonds generated for 'chain 'D' and resid 2077 through 2080' Processing helix chain 'D' and resid 2082 through 2100 removed outlier: 3.708A pdb=" N MET D2100 " --> pdb=" O LEU D2096 " (cutoff:3.500A) Processing helix chain 'D' and resid 2107 through 2114 Processing helix chain 'D' and resid 2118 through 2127 removed outlier: 3.557A pdb=" N VAL D2122 " --> pdb=" O PRO D2118 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N LYS D2126 " --> pdb=" O VAL D2122 " (cutoff:3.500A) Processing helix chain 'D' and resid 2130 through 2138 removed outlier: 4.030A pdb=" N ASP D2138 " --> pdb=" O VAL D2134 " (cutoff:3.500A) Processing helix chain 'D' and resid 2149 through 2166 removed outlier: 4.303A pdb=" N ARG D2165 " --> pdb=" O HIS D2161 " (cutoff:3.500A) removed outlier: 4.818A pdb=" N HIS D2166 " --> pdb=" O GLN D2162 " (cutoff:3.500A) Processing helix chain 'D' and resid 2170 through 2174 removed outlier: 3.714A pdb=" N LEU D2174 " --> pdb=" O LEU D2170 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 2170 through 2174' Processing helix chain 'D' and resid 2184 through 2191 Processing helix chain 'D' and resid 2215 through 2218 Processing helix chain 'D' and resid 2221 through 2230 Processing helix chain 'D' and resid 2240 through 2245 Processing helix chain 'D' and resid 2247 through 2261 removed outlier: 3.785A pdb=" N LYS D2259 " --> pdb=" O ASN D2255 " (cutoff:3.500A) Processing helix chain 'D' and resid 2266 through 2294 removed outlier: 3.709A pdb=" N ASN D2272 " --> pdb=" O TRP D2268 " (cutoff:3.500A) removed outlier: 4.146A pdb=" N MET D2273 " --> pdb=" O CYS D2269 " (cutoff:3.500A) removed outlier: 6.348A pdb=" N SER D2274 " --> pdb=" O ALA D2270 " (cutoff:3.500A) removed outlier: 6.100A pdb=" N PHE D2275 " --> pdb=" O ARG D2271 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N LEU D2286 " --> pdb=" O ASN D2282 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N LEU D2290 " --> pdb=" O LEU D2286 " (cutoff:3.500A) removed outlier: 4.098A pdb=" N VAL D2291 " --> pdb=" O MET D2287 " (cutoff:3.500A) Processing helix chain 'D' and resid 2309 through 2325 removed outlier: 3.792A pdb=" N TRP D2314 " --> pdb=" O SER D2310 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N THR D2315 " --> pdb=" O GLY D2311 " (cutoff:3.500A) removed outlier: 4.213A pdb=" N SER D2320 " --> pdb=" O ALA D2316 " (cutoff:3.500A) removed outlier: 4.464A pdb=" N LEU D2321 " --> pdb=" O MET D2317 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N ALA D2322 " --> pdb=" O LEU D2318 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N ILE D2323 " --> pdb=" O ILE D2319 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N VAL D2324 " --> pdb=" O SER D2320 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N ILE D2325 " --> pdb=" O LEU D2321 " (cutoff:3.500A) Processing helix chain 'D' and resid 2329 through 2345 removed outlier: 3.652A pdb=" N LEU D2344 " --> pdb=" O THR D2340 " (cutoff:3.500A) Processing helix chain 'D' and resid 2350 through 2376 Processing helix chain 'D' and resid 2378 through 2381 Processing helix chain 'D' and resid 2383 through 2388 Processing helix chain 'D' and resid 2390 through 2407 removed outlier: 3.799A pdb=" N TYR D2398 " --> pdb=" O TYR D2394 " (cutoff:3.500A) Processing helix chain 'D' and resid 2410 through 2423 removed outlier: 3.562A pdb=" N TYR D2413 " --> pdb=" O GLU D2410 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N VAL D2421 " --> pdb=" O PHE D2418 " (cutoff:3.500A) Processing helix chain 'D' and resid 2426 through 2436 removed outlier: 3.623A pdb=" N SER D2433 " --> pdb=" O ASN D2429 " (cutoff:3.500A) removed outlier: 4.410A pdb=" N VAL D2434 " --> pdb=" O VAL D2430 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N THR D2435 " --> pdb=" O ILE D2431 " (cutoff:3.500A) Processing helix chain 'D' and resid 2438 through 2462 Processing helix chain 'D' and resid 2464 through 2466 No H-bonds generated for 'chain 'D' and resid 2464 through 2466' Processing helix chain 'D' and resid 2531 through 2541 removed outlier: 3.640A pdb=" N VAL D2538 " --> pdb=" O CYS D2534 " (cutoff:3.500A) Processing helix chain 'D' and resid 2549 through 2551 No H-bonds generated for 'chain 'D' and resid 2549 through 2551' Processing helix chain 'D' and resid 2563 through 2577 Processing helix chain 'D' and resid 2581 through 2609 removed outlier: 4.163A pdb=" N PHE D2586 " --> pdb=" O LEU D2582 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N VAL D2588 " --> pdb=" O LEU D2584 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N ILE D2589 " --> pdb=" O ILE D2585 " (cutoff:3.500A) Processing helix chain 'D' and resid 2628 through 2631 No H-bonds generated for 'chain 'D' and resid 2628 through 2631' Processing helix chain 'D' and resid 2638 through 2649 removed outlier: 3.789A pdb=" N LEU D2642 " --> pdb=" O MET D2638 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N LYS D2649 " --> pdb=" O ILE D2645 " (cutoff:3.500A) Processing helix chain 'D' and resid 2653 through 2655 No H-bonds generated for 'chain 'D' and resid 2653 through 2655' Processing helix chain 'D' and resid 2658 through 2668 removed outlier: 3.567A pdb=" N TYR D2662 " --> pdb=" O GLY D2658 " (cutoff:3.500A) Processing helix chain 'D' and resid 2681 through 2684 No H-bonds generated for 'chain 'D' and resid 2681 through 2684' Processing helix chain 'D' and resid 2692 through 2738 removed outlier: 4.116A pdb=" N LYS D2707 " --> pdb=" O GLU D2703 " (cutoff:3.500A) removed outlier: 4.635A pdb=" N LEU D2708 " --> pdb=" O SER D2704 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N LEU D2712 " --> pdb=" O LEU D2708 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N SER D2713 " --> pdb=" O VAL D2709 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N LYS D2720 " --> pdb=" O LEU D2716 " (cutoff:3.500A) removed outlier: 4.205A pdb=" N LEU D2735 " --> pdb=" O GLN D2731 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N GLY D2737 " --> pdb=" O ILE D2733 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 121 through 125 removed outlier: 5.909A pdb=" N SER A 16 " --> pdb=" O LEU A 222 " (cutoff:3.500A) removed outlier: 5.492A pdb=" N LEU A 222 " --> pdb=" O SER A 16 " (cutoff:3.500A) removed outlier: 6.583A pdb=" N TYR A 18 " --> pdb=" O ILE A 220 " (cutoff:3.500A) removed outlier: 5.435A pdb=" N ILE A 220 " --> pdb=" O TYR A 18 " (cutoff:3.500A) removed outlier: 7.342A pdb=" N GLU A 20 " --> pdb=" O TRP A 218 " (cutoff:3.500A) removed outlier: 6.144A pdb=" N TRP A 218 " --> pdb=" O GLU A 20 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 26 through 28 removed outlier: 4.184A pdb=" N PHE A 26 " --> pdb=" O GLN A 40 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N GLN A 40 " --> pdb=" O PHE A 26 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 131 through 134 Processing sheet with id= D, first strand: chain 'A' and resid 161 through 165 Processing sheet with id= E, first strand: chain 'A' and resid 193 through 195 Processing sheet with id= F, first strand: chain 'A' and resid 430 through 434 Processing sheet with id= G, first strand: chain 'A' and resid 250 through 256 removed outlier: 3.896A pdb=" N PHE A 250 " --> pdb=" O ARG A 265 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'A' and resid 313 through 318 Processing sheet with id= I, first strand: chain 'A' and resid 368 through 372 Processing sheet with id= J, first strand: chain 'A' and resid 398 through 401 Processing sheet with id= K, first strand: chain 'A' and resid 1188 through 1190 removed outlier: 3.776A pdb=" N GLN A1189 " --> pdb=" O LYS A1196 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N LYS A1196 " --> pdb=" O GLN A1189 " (cutoff:3.500A) No H-bonds generated for sheet with id= K Processing sheet with id= L, first strand: chain 'A' and resid 2196 through 2199 Processing sheet with id= M, first strand: chain 'A' and resid 2468 through 2470 Processing sheet with id= N, first strand: chain 'B' and resid 121 through 125 removed outlier: 5.909A pdb=" N SER B 16 " --> pdb=" O LEU B 222 " (cutoff:3.500A) removed outlier: 5.491A pdb=" N LEU B 222 " --> pdb=" O SER B 16 " (cutoff:3.500A) removed outlier: 6.583A pdb=" N TYR B 18 " --> pdb=" O ILE B 220 " (cutoff:3.500A) removed outlier: 5.436A pdb=" N ILE B 220 " --> pdb=" O TYR B 18 " (cutoff:3.500A) removed outlier: 7.342A pdb=" N GLU B 20 " --> pdb=" O TRP B 218 " (cutoff:3.500A) removed outlier: 6.144A pdb=" N TRP B 218 " --> pdb=" O GLU B 20 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'B' and resid 26 through 28 removed outlier: 4.184A pdb=" N PHE B 26 " --> pdb=" O GLN B 40 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N GLN B 40 " --> pdb=" O PHE B 26 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'B' and resid 131 through 134 Processing sheet with id= Q, first strand: chain 'B' and resid 161 through 165 Processing sheet with id= R, first strand: chain 'B' and resid 193 through 195 Processing sheet with id= S, first strand: chain 'B' and resid 430 through 434 Processing sheet with id= T, first strand: chain 'B' and resid 250 through 256 removed outlier: 3.895A pdb=" N PHE B 250 " --> pdb=" O ARG B 265 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'B' and resid 313 through 318 Processing sheet with id= V, first strand: chain 'B' and resid 368 through 372 Processing sheet with id= W, first strand: chain 'B' and resid 398 through 401 Processing sheet with id= X, first strand: chain 'B' and resid 1188 through 1190 removed outlier: 3.776A pdb=" N GLN B1189 " --> pdb=" O LYS B1196 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N LYS B1196 " --> pdb=" O GLN B1189 " (cutoff:3.500A) No H-bonds generated for sheet with id= X Processing sheet with id= Y, first strand: chain 'B' and resid 2196 through 2199 Processing sheet with id= Z, first strand: chain 'B' and resid 2468 through 2470 Processing sheet with id= AA, first strand: chain 'C' and resid 121 through 125 removed outlier: 5.909A pdb=" N SER C 16 " --> pdb=" O LEU C 222 " (cutoff:3.500A) removed outlier: 5.492A pdb=" N LEU C 222 " --> pdb=" O SER C 16 " (cutoff:3.500A) removed outlier: 6.583A pdb=" N TYR C 18 " --> pdb=" O ILE C 220 " (cutoff:3.500A) removed outlier: 5.435A pdb=" N ILE C 220 " --> pdb=" O TYR C 18 " (cutoff:3.500A) removed outlier: 7.341A pdb=" N GLU C 20 " --> pdb=" O TRP C 218 " (cutoff:3.500A) removed outlier: 6.143A pdb=" N TRP C 218 " --> pdb=" O GLU C 20 " (cutoff:3.500A) Processing sheet with id= AB, first strand: chain 'C' and resid 26 through 28 removed outlier: 4.184A pdb=" N PHE C 26 " --> pdb=" O GLN C 40 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N GLN C 40 " --> pdb=" O PHE C 26 " (cutoff:3.500A) Processing sheet with id= AC, first strand: chain 'C' and resid 131 through 134 Processing sheet with id= AD, first strand: chain 'C' and resid 161 through 165 Processing sheet with id= AE, first strand: chain 'C' and resid 193 through 195 Processing sheet with id= AF, first strand: chain 'C' and resid 430 through 434 Processing sheet with id= AG, first strand: chain 'C' and resid 250 through 256 removed outlier: 3.896A pdb=" N PHE C 250 " --> pdb=" O ARG C 265 " (cutoff:3.500A) Processing sheet with id= AH, first strand: chain 'C' and resid 313 through 318 Processing sheet with id= AI, first strand: chain 'C' and resid 368 through 372 Processing sheet with id= AJ, first strand: chain 'C' and resid 398 through 401 Processing sheet with id= AK, first strand: chain 'C' and resid 1188 through 1190 removed outlier: 3.776A pdb=" N GLN C1189 " --> pdb=" O LYS C1196 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N LYS C1196 " --> pdb=" O GLN C1189 " (cutoff:3.500A) No H-bonds generated for sheet with id= AK Processing sheet with id= AL, first strand: chain 'C' and resid 2196 through 2199 Processing sheet with id= AM, first strand: chain 'C' and resid 2468 through 2470 Processing sheet with id= AN, first strand: chain 'D' and resid 121 through 125 removed outlier: 5.909A pdb=" N SER D 16 " --> pdb=" O LEU D 222 " (cutoff:3.500A) removed outlier: 5.491A pdb=" N LEU D 222 " --> pdb=" O SER D 16 " (cutoff:3.500A) removed outlier: 6.583A pdb=" N TYR D 18 " --> pdb=" O ILE D 220 " (cutoff:3.500A) removed outlier: 5.435A pdb=" N ILE D 220 " --> pdb=" O TYR D 18 " (cutoff:3.500A) removed outlier: 7.342A pdb=" N GLU D 20 " --> pdb=" O TRP D 218 " (cutoff:3.500A) removed outlier: 6.144A pdb=" N TRP D 218 " --> pdb=" O GLU D 20 " (cutoff:3.500A) Processing sheet with id= AO, first strand: chain 'D' and resid 26 through 28 removed outlier: 4.184A pdb=" N PHE D 26 " --> pdb=" O GLN D 40 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N GLN D 40 " --> pdb=" O PHE D 26 " (cutoff:3.500A) Processing sheet with id= AP, first strand: chain 'D' and resid 131 through 134 Processing sheet with id= AQ, first strand: chain 'D' and resid 161 through 165 Processing sheet with id= AR, first strand: chain 'D' and resid 193 through 195 Processing sheet with id= AS, first strand: chain 'D' and resid 430 through 434 Processing sheet with id= AT, first strand: chain 'D' and resid 250 through 256 removed outlier: 3.895A pdb=" N PHE D 250 " --> pdb=" O ARG D 265 " (cutoff:3.500A) Processing sheet with id= AU, first strand: chain 'D' and resid 313 through 318 Processing sheet with id= AV, first strand: chain 'D' and resid 368 through 372 Processing sheet with id= AW, first strand: chain 'D' and resid 398 through 401 Processing sheet with id= AX, first strand: chain 'D' and resid 1188 through 1190 removed outlier: 3.776A pdb=" N GLN D1189 " --> pdb=" O LYS D1196 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N LYS D1196 " --> pdb=" O GLN D1189 " (cutoff:3.500A) No H-bonds generated for sheet with id= AX Processing sheet with id= AY, first strand: chain 'D' and resid 2196 through 2199 Processing sheet with id= AZ, first strand: chain 'D' and resid 2468 through 2470 3436 hydrogen bonds defined for protein. 9528 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: 35.24 Time building geometry restraints manager: 27.07 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 19762 1.33 - 1.46: 17648 1.46 - 1.58: 41702 1.58 - 1.71: 76 1.71 - 1.83: 708 Bond restraints: 79896 Sorted by residual: bond pdb=" N VAL D1100 " pdb=" CA VAL D1100 " ideal model delta sigma weight residual 1.459 1.501 -0.042 1.25e-02 6.40e+03 1.14e+01 bond pdb=" N VAL A1100 " pdb=" CA VAL A1100 " ideal model delta sigma weight residual 1.459 1.500 -0.041 1.25e-02 6.40e+03 1.09e+01 bond pdb=" N VAL C1100 " pdb=" CA VAL C1100 " ideal model delta sigma weight residual 1.459 1.500 -0.041 1.25e-02 6.40e+03 1.08e+01 bond pdb=" N VAL B1100 " pdb=" CA VAL B1100 " ideal model delta sigma weight residual 1.459 1.500 -0.041 1.25e-02 6.40e+03 1.08e+01 bond pdb=" N LEU D1102 " pdb=" CA LEU D1102 " ideal model delta sigma weight residual 1.456 1.488 -0.031 1.16e-02 7.43e+03 7.34e+00 ... (remaining 79891 not shown) Histogram of bond angle deviations from ideal: 98.10 - 106.43: 1728 106.43 - 114.77: 48978 114.77 - 123.10: 53894 123.10 - 131.43: 3068 131.43 - 139.77: 108 Bond angle restraints: 107776 Sorted by residual: angle pdb=" N GLU C2630 " pdb=" CA GLU C2630 " pdb=" C GLU C2630 " ideal model delta sigma weight residual 114.31 105.83 8.48 1.29e+00 6.01e-01 4.32e+01 angle pdb=" N GLU A2630 " pdb=" CA GLU A2630 " pdb=" C GLU A2630 " ideal model delta sigma weight residual 114.31 105.83 8.48 1.29e+00 6.01e-01 4.32e+01 angle pdb=" N GLU B2630 " pdb=" CA GLU B2630 " pdb=" C GLU B2630 " ideal model delta sigma weight residual 114.31 105.83 8.48 1.29e+00 6.01e-01 4.32e+01 angle pdb=" N GLU D2630 " pdb=" CA GLU D2630 " pdb=" C GLU D2630 " ideal model delta sigma weight residual 114.31 105.86 8.45 1.29e+00 6.01e-01 4.29e+01 angle pdb=" CB MET B 147 " pdb=" CG MET B 147 " pdb=" SD MET B 147 " ideal model delta sigma weight residual 112.70 99.27 13.43 3.00e+00 1.11e-01 2.00e+01 ... (remaining 107771 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 30.83: 47446 30.83 - 61.67: 1798 61.67 - 92.50: 96 92.50 - 123.34: 16 123.34 - 154.17: 24 Dihedral angle restraints: 49380 sinusoidal: 21316 harmonic: 28064 Sorted by residual: dihedral pdb=" C5 PLX A2810 " pdb=" C3 PLX A2810 " pdb=" C4 PLX A2810 " pdb=" O4 PLX A2810 " ideal model delta sinusoidal sigma weight residual 216.95 62.78 154.17 1 3.00e+01 1.11e-03 2.03e+01 dihedral pdb=" C5 PLX B2811 " pdb=" C3 PLX B2811 " pdb=" C4 PLX B2811 " pdb=" O4 PLX B2811 " ideal model delta sinusoidal sigma weight residual 216.95 62.78 154.17 1 3.00e+01 1.11e-03 2.03e+01 dihedral pdb=" C5 PLX C2803 " pdb=" C3 PLX C2803 " pdb=" C4 PLX C2803 " pdb=" O4 PLX C2803 " ideal model delta sinusoidal sigma weight residual 216.95 62.80 154.15 1 3.00e+01 1.11e-03 2.03e+01 ... (remaining 49377 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.052: 9815 0.052 - 0.104: 1957 0.104 - 0.155: 252 0.155 - 0.207: 18 0.207 - 0.259: 14 Chirality restraints: 12056 Sorted by residual: chirality pdb=" CA GLU A2630 " pdb=" N GLU A2630 " pdb=" C GLU A2630 " pdb=" CB GLU A2630 " both_signs ideal model delta sigma weight residual False 2.51 2.77 -0.26 2.00e-01 2.50e+01 1.68e+00 chirality pdb=" CA GLU B2630 " pdb=" N GLU B2630 " pdb=" C GLU B2630 " pdb=" CB GLU B2630 " both_signs ideal model delta sigma weight residual False 2.51 2.77 -0.26 2.00e-01 2.50e+01 1.66e+00 chirality pdb=" CA GLU C2630 " pdb=" N GLU C2630 " pdb=" C GLU C2630 " pdb=" CB GLU C2630 " both_signs ideal model delta sigma weight residual False 2.51 2.77 -0.26 2.00e-01 2.50e+01 1.63e+00 ... (remaining 12053 not shown) Planarity restraints: 13652 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLN B1099 " -0.030 2.00e-02 2.50e+03 5.93e-02 3.51e+01 pdb=" C GLN B1099 " 0.102 2.00e-02 2.50e+03 pdb=" O GLN B1099 " -0.038 2.00e-02 2.50e+03 pdb=" N VAL B1100 " -0.035 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLN D1099 " 0.029 2.00e-02 2.50e+03 5.91e-02 3.50e+01 pdb=" C GLN D1099 " -0.102 2.00e-02 2.50e+03 pdb=" O GLN D1099 " 0.038 2.00e-02 2.50e+03 pdb=" N VAL D1100 " 0.034 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLN C1099 " 0.029 2.00e-02 2.50e+03 5.91e-02 3.49e+01 pdb=" C GLN C1099 " -0.102 2.00e-02 2.50e+03 pdb=" O GLN C1099 " 0.038 2.00e-02 2.50e+03 pdb=" N VAL C1100 " 0.034 2.00e-02 2.50e+03 ... (remaining 13649 not shown) Histogram of nonbonded interaction distances: 2.09 - 2.65: 1104 2.65 - 3.21: 75407 3.21 - 3.78: 120868 3.78 - 4.34: 161804 4.34 - 4.90: 259373 Nonbonded interactions: 618556 Sorted by model distance: nonbonded pdb=" OG1 THR C2527 " pdb=" OG1 THR C2537 " model vdw 2.089 2.440 nonbonded pdb=" OG1 THR B2527 " pdb=" OG1 THR B2537 " model vdw 2.089 2.440 nonbonded pdb=" OG1 THR A2527 " pdb=" OG1 THR A2537 " model vdw 2.089 2.440 nonbonded pdb=" OG1 THR D2527 " pdb=" OG1 THR D2537 " model vdw 2.089 2.440 nonbonded pdb=" OG SER B1791 " pdb=" OE1 GLU B1794 " model vdw 2.152 2.440 ... (remaining 618551 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 6 through 2582 or resid 2584 through 2585 or resid 2587 th \ rough 2741 or resid 2801 or (resid 2813 and (name C1 or name C10 or name C11 or \ name C12 or name C13 or name C14 or name C1A or name C1B or name C1C or name C2 \ or name C24 or name C25 or name C26 or name C27 or name C28 or name C29 or name \ C3 or name C30 or name C31 or name C32 or name C4 or name C5 or name C6 or name \ C7 or name C8 or name C9 or name N1 or name O1 or name O2 or name O3 or name O4 \ or name O6 or name O7 or name O8 or name O9 or name P1 )) or resid 2814)) selection = (chain 'B' and (resid 6 through 2582 or resid 2584 through 2585 or resid 2587 th \ rough 2741 or resid 2801 or (resid 2813 and (name C1 or name C10 or name C11 or \ name C12 or name C13 or name C14 or name C1A or name C1B or name C1C or name C2 \ or name C24 or name C25 or name C26 or name C27 or name C28 or name C29 or name \ C3 or name C30 or name C31 or name C32 or name C4 or name C5 or name C6 or name \ C7 or name C8 or name C9 or name N1 or name O1 or name O2 or name O3 or name O4 \ or name O6 or name O7 or name O8 or name O9 or name P1 )) or (resid 2814 and (na \ me C1 or name C10 or name C11 or name C12 or name C13 or name C14 or name C1A or \ name C1B or name C1C or name C2 or name C24 or name C25 or name C26 or name C27 \ or name C28 or name C29 or name C3 or name C30 or name C31 or name C32 or name \ C33 or name C4 or name C5 or name C6 or name C7 or name C8 or name C9 or name N1 \ or name O1 or name O2 or name O3 or name O4 or name O6 or name O7 or name O8 or \ name O9 or name P1 )))) selection = (chain 'C' and (resid 6 through 2582 or resid 2584 through 2585 or resid 2587 th \ rough 2741 or resid 2801 or (resid 2813 and (name C1 or name C10 or name C11 or \ name C12 or name C13 or name C14 or name C1A or name C1B or name C1C or name C2 \ or name C24 or name C25 or name C26 or name C27 or name C28 or name C29 or name \ C3 or name C30 or name C31 or name C32 or name C4 or name C5 or name C6 or name \ C7 or name C8 or name C9 or name N1 or name O1 or name O2 or name O3 or name O4 \ or name O6 or name O7 or name O8 or name O9 or name P1 )) or (resid 2814 and (na \ me C1 or name C10 or name C11 or name C12 or name C13 or name C14 or name C1A or \ name C1B or name C1C or name C2 or name C24 or name C25 or name C26 or name C27 \ or name C28 or name C29 or name C3 or name C30 or name C31 or name C32 or name \ C33 or name C4 or name C5 or name C6 or name C7 or name C8 or name C9 or name N1 \ or name O1 or name O2 or name O3 or name O4 or name O6 or name O7 or name O8 or \ name O9 or name P1 )))) selection = (chain 'D' and (resid 6 through 2582 or resid 2584 through 2585 or resid 2587 th \ rough 2741 or resid 2801 or (resid 2813 and (name C1 or name C10 or name C11 or \ name C12 or name C13 or name C14 or name C1A or name C1B or name C1C or name C2 \ or name C24 or name C25 or name C26 or name C27 or name C28 or name C29 or name \ C3 or name C30 or name C31 or name C32 or name C4 or name C5 or name C6 or name \ C7 or name C8 or name C9 or name N1 or name O1 or name O2 or name O3 or name O4 \ or name O6 or name O7 or name O8 or name O9 or name P1 )) or resid 2814)) } 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: 3.260 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.120 Extract box with map and model: 11.550 Check model and map are aligned: 0.930 Set scattering table: 0.580 Process input model: 221.580 Find NCS groups from input model: 6.390 Set up NCS constraints: 0.570 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: 0.020 Load rotamer database and sin/cos tables:2.590 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 247.590 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6746 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 : 0.004 0.061 79896 Z= 0.232 Angle : 0.642 13.429 107776 Z= 0.345 Chirality : 0.042 0.259 12056 Planarity : 0.004 0.069 13652 Dihedral : 15.895 154.171 31104 Min Nonbonded Distance : 2.089 Molprobity Statistics. All-atom Clashscore : 11.65 Ramachandran Plot: Outliers : 0.30 % Allowed : 4.12 % Favored : 95.59 % Rotamer: Outliers : 0.18 % Allowed : 0.37 % Favored : 99.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.29 % 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: 0.42 (0.09), residues: 9484 helix: 0.86 (0.07), residues: 5424 sheet: -0.30 (0.23), residues: 576 loop : -0.40 (0.11), residues: 3484 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP B2639 HIS 0.006 0.001 HIS D2331 PHE 0.027 0.002 PHE B2210 TYR 0.032 0.001 TYR A 875 ARG 0.006 0.000 ARG A 871 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 18968 Ramachandran restraints generated. 9484 Oldfield, 0 Emsley, 9484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 18968 Ramachandran restraints generated. 9484 Oldfield, 0 Emsley, 9484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1089 residues out of total 8636 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 1077 time to evaluate : 6.821 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: A 481 VAL cc_start: 0.7480 (t) cc_final: 0.7249 (m) REVERT: A 641 MET cc_start: 0.6276 (mmp) cc_final: 0.5843 (mtp) REVERT: A 765 LEU cc_start: 0.4351 (tt) cc_final: 0.4071 (mm) REVERT: A 966 MET cc_start: 0.7677 (ttt) cc_final: 0.7347 (ttp) REVERT: A 968 MET cc_start: 0.7553 (ttt) cc_final: 0.6766 (mmp) REVERT: A 1273 MET cc_start: 0.6688 (tpp) cc_final: 0.6313 (tpp) REVERT: A 1331 MET cc_start: 0.2218 (mpp) cc_final: 0.0120 (tpt) REVERT: A 1484 MET cc_start: 0.5572 (mmt) cc_final: 0.5222 (mmm) REVERT: A 1630 LEU cc_start: 0.8477 (tt) cc_final: 0.8149 (mm) REVERT: A 1852 LYS cc_start: 0.8526 (pttp) cc_final: 0.8229 (ptmt) REVERT: A 1862 ASP cc_start: 0.8579 (m-30) cc_final: 0.8361 (m-30) REVERT: A 2064 ASP cc_start: 0.7764 (m-30) cc_final: 0.7521 (m-30) REVERT: A 2234 ASP cc_start: 0.8720 (m-30) cc_final: 0.8278 (m-30) REVERT: A 2533 MET cc_start: 0.8076 (tpp) cc_final: 0.7643 (tpp) REVERT: A 2666 MET cc_start: 0.8339 (mmm) cc_final: 0.8129 (mmt) REVERT: B 259 LYS cc_start: 0.8752 (mptt) cc_final: 0.8533 (mmtm) REVERT: B 481 VAL cc_start: 0.7482 (t) cc_final: 0.7249 (m) REVERT: B 641 MET cc_start: 0.6277 (mmp) cc_final: 0.5849 (mtp) REVERT: B 765 LEU cc_start: 0.4345 (tt) cc_final: 0.4061 (mm) REVERT: B 966 MET cc_start: 0.7687 (ttt) cc_final: 0.7148 (tmm) REVERT: B 968 MET cc_start: 0.7581 (ttt) cc_final: 0.6773 (mmp) REVERT: B 1273 MET cc_start: 0.6690 (tpp) cc_final: 0.6314 (tpp) REVERT: B 1331 MET cc_start: 0.2220 (mpp) cc_final: 0.0118 (tpt) REVERT: B 1484 MET cc_start: 0.5572 (mmt) cc_final: 0.5222 (mmm) REVERT: B 1630 LEU cc_start: 0.8471 (tt) cc_final: 0.8155 (mm) REVERT: B 1852 LYS cc_start: 0.8527 (pttp) cc_final: 0.8227 (ptmt) REVERT: B 1862 ASP cc_start: 0.8582 (m-30) cc_final: 0.8358 (m-30) REVERT: B 2064 ASP cc_start: 0.7763 (m-30) cc_final: 0.7522 (m-30) REVERT: B 2196 ILE cc_start: 0.8032 (pt) cc_final: 0.7819 (pt) REVERT: B 2234 ASP cc_start: 0.8738 (m-30) cc_final: 0.8275 (m-30) REVERT: B 2666 MET cc_start: 0.8316 (mmm) cc_final: 0.8093 (mmt) REVERT: C 481 VAL cc_start: 0.7480 (t) cc_final: 0.7250 (m) REVERT: C 641 MET cc_start: 0.6276 (mmp) cc_final: 0.5849 (mtp) REVERT: C 765 LEU cc_start: 0.4358 (tt) cc_final: 0.4076 (mm) REVERT: C 966 MET cc_start: 0.7659 (ttt) cc_final: 0.7127 (tmm) REVERT: C 968 MET cc_start: 0.7550 (ttt) cc_final: 0.6756 (mmp) REVERT: C 1273 MET cc_start: 0.6684 (tpp) cc_final: 0.6311 (tpp) REVERT: C 1331 MET cc_start: 0.2221 (mpp) cc_final: 0.0115 (tpt) REVERT: C 1484 MET cc_start: 0.5568 (mmt) cc_final: 0.5218 (mmm) REVERT: C 1630 LEU cc_start: 0.8473 (tt) cc_final: 0.8157 (mm) REVERT: C 1852 LYS cc_start: 0.8524 (pttp) cc_final: 0.8228 (ptmt) REVERT: C 1862 ASP cc_start: 0.8580 (m-30) cc_final: 0.8364 (m-30) REVERT: C 2064 ASP cc_start: 0.7759 (m-30) cc_final: 0.7518 (m-30) REVERT: C 2234 ASP cc_start: 0.8741 (m-30) cc_final: 0.8281 (m-30) REVERT: C 2533 MET cc_start: 0.7996 (tpp) cc_final: 0.7595 (tpp) REVERT: C 2666 MET cc_start: 0.8344 (mmm) cc_final: 0.8129 (mmt) REVERT: D 481 VAL cc_start: 0.7481 (t) cc_final: 0.7252 (m) REVERT: D 641 MET cc_start: 0.6268 (mmp) cc_final: 0.5846 (mtp) REVERT: D 765 LEU cc_start: 0.4358 (tt) cc_final: 0.4074 (mm) REVERT: D 966 MET cc_start: 0.7676 (ttt) cc_final: 0.7144 (tmm) REVERT: D 968 MET cc_start: 0.7556 (ttt) cc_final: 0.6755 (mmp) REVERT: D 1273 MET cc_start: 0.6684 (tpp) cc_final: 0.6310 (tpp) REVERT: D 1331 MET cc_start: 0.2244 (mpp) cc_final: 0.0089 (tpp) REVERT: D 1484 MET cc_start: 0.5566 (mmt) cc_final: 0.5219 (mmm) REVERT: D 1630 LEU cc_start: 0.8472 (tt) cc_final: 0.8158 (mm) REVERT: D 1852 LYS cc_start: 0.8528 (pttp) cc_final: 0.8227 (ptmt) REVERT: D 1862 ASP cc_start: 0.8565 (m-30) cc_final: 0.8337 (m-30) REVERT: D 2064 ASP cc_start: 0.7752 (m-30) cc_final: 0.7511 (m-30) REVERT: D 2196 ILE cc_start: 0.7992 (pt) cc_final: 0.7775 (pt) REVERT: D 2234 ASP cc_start: 0.8716 (m-30) cc_final: 0.8265 (m-30) REVERT: D 2666 MET cc_start: 0.8343 (mmm) cc_final: 0.8134 (mmt) outliers start: 12 outliers final: 4 residues processed: 1085 average time/residue: 0.7662 time to fit residues: 1388.9110 Evaluate side-chains 777 residues out of total 8636 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 773 time to evaluate : 6.637 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1103 LEU Chi-restraints excluded: chain B residue 1103 LEU Chi-restraints excluded: chain C residue 1103 LEU Chi-restraints excluded: chain D residue 1103 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 952 random chunks: chunk 803 optimal weight: 10.0000 chunk 721 optimal weight: 20.0000 chunk 400 optimal weight: 3.9990 chunk 246 optimal weight: 7.9990 chunk 486 optimal weight: 9.9990 chunk 385 optimal weight: 4.9990 chunk 746 optimal weight: 6.9990 chunk 288 optimal weight: 6.9990 chunk 453 optimal weight: 0.9990 chunk 555 optimal weight: 0.9990 chunk 864 optimal weight: 9.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 544 GLN A1066 HIS A1101 GLN A1238 HIS ** A1280 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1375 HIS A1605 GLN A1667 ASN A1868 GLN ** A1981 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2207 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2409 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A2623 ASN ** A2715 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A2731 GLN ** B 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 544 GLN B1066 HIS B1101 GLN B1238 HIS ** B1280 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1375 HIS B1605 GLN B1667 ASN B1868 GLN ** B1981 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2207 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2409 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2583 ASN A ** both conformations clash, **PLEASE CHECK MANUALLY** B2623 ASN ** B2715 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B2731 GLN ** C 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 544 GLN C 600 HIS C1066 HIS C1101 GLN C1238 HIS C1252 GLN ** C1280 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1375 HIS C1605 GLN C1667 ASN C1868 GLN ** C1981 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2207 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2409 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C2623 ASN ** C2715 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C2731 GLN ** D 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 544 GLN D1066 HIS D1101 GLN D1238 HIS D1252 GLN ** D1280 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D1375 HIS D1605 GLN D1667 ASN D1868 GLN ** D1981 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2207 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2409 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D2623 ASN ** D2715 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D2731 GLN Total number of N/Q/H flips: 43 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6829 moved from start: 0.1483 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 79896 Z= 0.306 Angle : 0.653 13.290 107776 Z= 0.334 Chirality : 0.043 0.234 12056 Planarity : 0.004 0.067 13652 Dihedral : 13.055 165.234 11788 Min Nonbonded Distance : 2.116 Molprobity Statistics. All-atom Clashscore : 13.25 Ramachandran Plot: Outliers : 0.17 % Allowed : 4.08 % Favored : 95.75 % Rotamer: Outliers : 0.82 % Allowed : 7.85 % Favored : 91.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.29 % 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: -0.01 (0.09), residues: 9484 helix: 0.50 (0.07), residues: 5500 sheet: -0.32 (0.23), residues: 564 loop : -0.62 (0.11), residues: 3420 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP A2639 HIS 0.009 0.001 HIS C 600 PHE 0.037 0.002 PHE B2210 TYR 0.016 0.002 TYR C 875 ARG 0.007 0.001 ARG D2670 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 18968 Ramachandran restraints generated. 9484 Oldfield, 0 Emsley, 9484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 18968 Ramachandran restraints generated. 9484 Oldfield, 0 Emsley, 9484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 905 residues out of total 8636 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 838 time to evaluate : 6.811 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: A 765 LEU cc_start: 0.4895 (tt) cc_final: 0.4326 (mm) REVERT: A 968 MET cc_start: 0.7850 (ttt) cc_final: 0.6773 (tpp) REVERT: A 1084 PHE cc_start: 0.8149 (m-80) cc_final: 0.7949 (m-80) REVERT: A 1208 MET cc_start: 0.5336 (mmp) cc_final: 0.5128 (mmm) REVERT: A 1245 CYS cc_start: 0.8715 (OUTLIER) cc_final: 0.8448 (t) REVERT: A 1331 MET cc_start: 0.2272 (mpp) cc_final: 0.0202 (tpp) REVERT: A 1423 TYR cc_start: 0.6582 (m-80) cc_final: 0.6143 (m-80) REVERT: A 1484 MET cc_start: 0.5439 (mmt) cc_final: 0.5155 (mmm) REVERT: A 1683 MET cc_start: 0.7470 (OUTLIER) cc_final: 0.7240 (mmm) REVERT: A 1852 LYS cc_start: 0.8429 (pttp) cc_final: 0.8050 (ptmt) REVERT: A 1862 ASP cc_start: 0.8626 (m-30) cc_final: 0.8274 (m-30) REVERT: A 1958 GLU cc_start: 0.6654 (tm-30) cc_final: 0.6314 (tm-30) REVERT: A 2082 MET cc_start: 0.7736 (tpp) cc_final: 0.7310 (tpp) REVERT: A 2234 ASP cc_start: 0.8766 (m-30) cc_final: 0.8254 (m-30) REVERT: A 2419 ASP cc_start: 0.7783 (t70) cc_final: 0.6957 (p0) REVERT: A 2533 MET cc_start: 0.8234 (tpp) cc_final: 0.7965 (tpp) REVERT: B 765 LEU cc_start: 0.4892 (tt) cc_final: 0.4320 (mm) REVERT: B 1084 PHE cc_start: 0.8145 (m-80) cc_final: 0.7943 (m-80) REVERT: B 1331 MET cc_start: 0.2271 (mpp) cc_final: 0.0195 (tpp) REVERT: B 1423 TYR cc_start: 0.6532 (m-80) cc_final: 0.6103 (m-80) REVERT: B 1484 MET cc_start: 0.5438 (mmt) cc_final: 0.5154 (mmm) REVERT: B 1683 MET cc_start: 0.7470 (OUTLIER) cc_final: 0.7244 (mmm) REVERT: B 1852 LYS cc_start: 0.8442 (pttp) cc_final: 0.8143 (ptmt) REVERT: B 1862 ASP cc_start: 0.8646 (m-30) cc_final: 0.8302 (m-30) REVERT: B 1958 GLU cc_start: 0.6658 (tm-30) cc_final: 0.6318 (tm-30) REVERT: B 2082 MET cc_start: 0.7728 (tpp) cc_final: 0.7304 (tpp) REVERT: B 2234 ASP cc_start: 0.8767 (m-30) cc_final: 0.8254 (m-30) REVERT: B 2419 ASP cc_start: 0.7791 (t70) cc_final: 0.6958 (p0) REVERT: B 2533 MET cc_start: 0.8125 (tpp) cc_final: 0.7808 (tpp) REVERT: C 765 LEU cc_start: 0.4897 (tt) cc_final: 0.4327 (mm) REVERT: C 968 MET cc_start: 0.7845 (ttt) cc_final: 0.6769 (tpp) REVERT: C 1084 PHE cc_start: 0.8147 (m-80) cc_final: 0.7945 (m-80) REVERT: C 1208 MET cc_start: 0.5342 (mmp) cc_final: 0.5135 (mmm) REVERT: C 1245 CYS cc_start: 0.8722 (OUTLIER) cc_final: 0.8441 (t) REVERT: C 1331 MET cc_start: 0.2277 (mpp) cc_final: 0.0203 (tpp) REVERT: C 1423 TYR cc_start: 0.6584 (m-80) cc_final: 0.6147 (m-80) REVERT: C 1484 MET cc_start: 0.5432 (mmt) cc_final: 0.5153 (mmm) REVERT: C 1683 MET cc_start: 0.7508 (OUTLIER) cc_final: 0.7281 (mmm) REVERT: C 1852 LYS cc_start: 0.8415 (pttp) cc_final: 0.8040 (ptmt) REVERT: C 1862 ASP cc_start: 0.8628 (m-30) cc_final: 0.8277 (m-30) REVERT: C 1958 GLU cc_start: 0.6656 (tm-30) cc_final: 0.6317 (tm-30) REVERT: C 2082 MET cc_start: 0.7733 (tpp) cc_final: 0.7309 (tpp) REVERT: C 2234 ASP cc_start: 0.8767 (m-30) cc_final: 0.8253 (m-30) REVERT: C 2419 ASP cc_start: 0.7783 (t70) cc_final: 0.6955 (p0) REVERT: C 2533 MET cc_start: 0.8235 (tpp) cc_final: 0.7968 (tpp) REVERT: D 765 LEU cc_start: 0.4897 (tt) cc_final: 0.4327 (mm) REVERT: D 1084 PHE cc_start: 0.8146 (m-80) cc_final: 0.7943 (m-80) REVERT: D 1208 MET cc_start: 0.5339 (mmp) cc_final: 0.5134 (mmm) REVERT: D 1245 CYS cc_start: 0.8722 (OUTLIER) cc_final: 0.8440 (t) REVERT: D 1331 MET cc_start: 0.2275 (mpp) cc_final: 0.0205 (tpp) REVERT: D 1423 TYR cc_start: 0.6582 (m-80) cc_final: 0.6138 (m-80) REVERT: D 1484 MET cc_start: 0.5432 (mmt) cc_final: 0.5150 (mmm) REVERT: D 1683 MET cc_start: 0.7506 (OUTLIER) cc_final: 0.7281 (mmm) REVERT: D 1852 LYS cc_start: 0.8416 (pttp) cc_final: 0.8045 (ptmt) REVERT: D 1862 ASP cc_start: 0.8629 (m-30) cc_final: 0.8278 (m-30) REVERT: D 1958 GLU cc_start: 0.6653 (tm-30) cc_final: 0.6316 (tm-30) REVERT: D 2082 MET cc_start: 0.7733 (tpp) cc_final: 0.7310 (tpp) REVERT: D 2234 ASP cc_start: 0.8765 (m-30) cc_final: 0.8253 (m-30) REVERT: D 2419 ASP cc_start: 0.7785 (t70) cc_final: 0.6957 (p0) REVERT: D 2533 MET cc_start: 0.8119 (tpp) cc_final: 0.7804 (tpp) outliers start: 67 outliers final: 40 residues processed: 861 average time/residue: 0.7239 time to fit residues: 1069.0535 Evaluate side-chains 834 residues out of total 8636 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 787 time to evaluate : 6.682 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 CYS Chi-restraints excluded: chain A residue 115 ILE Chi-restraints excluded: chain A residue 394 CYS Chi-restraints excluded: chain A residue 544 GLN Chi-restraints excluded: chain A residue 768 MET Chi-restraints excluded: chain A residue 773 LEU Chi-restraints excluded: chain A residue 1103 LEU Chi-restraints excluded: chain A residue 1245 CYS Chi-restraints excluded: chain A residue 1683 MET Chi-restraints excluded: chain A residue 2033 ILE Chi-restraints excluded: chain A residue 2723 MET Chi-restraints excluded: chain B residue 61 CYS Chi-restraints excluded: chain B residue 115 ILE Chi-restraints excluded: chain B residue 394 CYS Chi-restraints excluded: chain B residue 544 GLN Chi-restraints excluded: chain B residue 768 MET Chi-restraints excluded: chain B residue 773 LEU Chi-restraints excluded: chain B residue 1103 LEU Chi-restraints excluded: chain B residue 1245 CYS Chi-restraints excluded: chain B residue 1683 MET Chi-restraints excluded: chain B residue 2033 ILE Chi-restraints excluded: chain B residue 2723 MET Chi-restraints excluded: chain C residue 20 GLU Chi-restraints excluded: chain C residue 61 CYS Chi-restraints excluded: chain C residue 115 ILE Chi-restraints excluded: chain C residue 394 CYS Chi-restraints excluded: chain C residue 544 GLN Chi-restraints excluded: chain C residue 768 MET Chi-restraints excluded: chain C residue 773 LEU Chi-restraints excluded: chain C residue 1103 LEU Chi-restraints excluded: chain C residue 1245 CYS Chi-restraints excluded: chain C residue 1252 GLN Chi-restraints excluded: chain C residue 1683 MET Chi-restraints excluded: chain C residue 2033 ILE Chi-restraints excluded: chain C residue 2723 MET Chi-restraints excluded: chain D residue 61 CYS Chi-restraints excluded: chain D residue 115 ILE Chi-restraints excluded: chain D residue 394 CYS Chi-restraints excluded: chain D residue 544 GLN Chi-restraints excluded: chain D residue 768 MET Chi-restraints excluded: chain D residue 773 LEU Chi-restraints excluded: chain D residue 1103 LEU Chi-restraints excluded: chain D residue 1245 CYS Chi-restraints excluded: chain D residue 1252 GLN Chi-restraints excluded: chain D residue 1683 MET Chi-restraints excluded: chain D residue 2033 ILE Chi-restraints excluded: chain D residue 2723 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 952 random chunks: chunk 480 optimal weight: 0.9990 chunk 268 optimal weight: 7.9990 chunk 719 optimal weight: 6.9990 chunk 588 optimal weight: 9.9990 chunk 238 optimal weight: 10.0000 chunk 866 optimal weight: 5.9990 chunk 935 optimal weight: 2.9990 chunk 771 optimal weight: 3.9990 chunk 858 optimal weight: 2.9990 chunk 295 optimal weight: 2.9990 chunk 694 optimal weight: 0.8980 overall best weight: 2.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 584 GLN A 649 GLN A1099 GLN A1238 HIS ** A1280 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1375 HIS A1868 GLN ** A1981 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2207 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2409 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2583 ASN A ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2715 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 584 GLN B 649 GLN B1099 GLN B1238 HIS ** B1280 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1375 HIS B1868 GLN ** B1981 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B2104 HIS ** B2207 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2409 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2583 ASN A ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2715 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 584 GLN C 649 GLN C1099 GLN C1238 HIS ** C1252 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1280 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1375 HIS C1868 GLN ** C1981 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2207 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2409 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2583 ASN A ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2715 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 649 GLN D1099 GLN D1238 HIS ** D1252 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1280 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D1375 HIS D1868 GLN ** D1981 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D2104 HIS ** D2207 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2409 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2583 ASN A ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2715 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 25 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6809 moved from start: 0.1705 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 79896 Z= 0.214 Angle : 0.588 12.806 107776 Z= 0.296 Chirality : 0.041 0.278 12056 Planarity : 0.004 0.065 13652 Dihedral : 12.613 173.655 11788 Min Nonbonded Distance : 2.143 Molprobity Statistics. All-atom Clashscore : 12.27 Ramachandran Plot: Outliers : 0.17 % Allowed : 4.00 % Favored : 95.83 % Rotamer: Outliers : 0.87 % Allowed : 9.69 % Favored : 89.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.29 % 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: 0.09 (0.09), residues: 9484 helix: 0.60 (0.07), residues: 5460 sheet: -0.38 (0.23), residues: 564 loop : -0.59 (0.11), residues: 3460 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A2639 HIS 0.004 0.001 HIS D2331 PHE 0.043 0.002 PHE D1372 TYR 0.016 0.001 TYR A2453 ARG 0.003 0.000 ARG A 108 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 18968 Ramachandran restraints generated. 9484 Oldfield, 0 Emsley, 9484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 18968 Ramachandran restraints generated. 9484 Oldfield, 0 Emsley, 9484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 909 residues out of total 8636 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 838 time to evaluate : 6.869 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: A 174 ASP cc_start: 0.7986 (m-30) cc_final: 0.7188 (t0) REVERT: A 481 VAL cc_start: 0.7497 (t) cc_final: 0.7296 (m) REVERT: A 604 LYS cc_start: 0.8314 (mmtm) cc_final: 0.8097 (mmmt) REVERT: A 765 LEU cc_start: 0.4914 (tt) cc_final: 0.4325 (mm) REVERT: A 968 MET cc_start: 0.7815 (ttt) cc_final: 0.6830 (mmp) REVERT: A 1084 PHE cc_start: 0.8114 (m-80) cc_final: 0.7865 (m-80) REVERT: A 1245 CYS cc_start: 0.8694 (OUTLIER) cc_final: 0.8472 (t) REVERT: A 1331 MET cc_start: 0.2063 (mpp) cc_final: -0.0014 (tpp) REVERT: A 1661 LYS cc_start: 0.8593 (tppp) cc_final: 0.8249 (tptm) REVERT: A 1682 MET cc_start: 0.6910 (mmm) cc_final: 0.6675 (mmm) REVERT: A 1862 ASP cc_start: 0.8513 (m-30) cc_final: 0.8190 (m-30) REVERT: A 1958 GLU cc_start: 0.6504 (tm-30) cc_final: 0.6117 (tm-30) REVERT: A 2234 ASP cc_start: 0.8749 (m-30) cc_final: 0.8253 (m-30) REVERT: A 2419 ASP cc_start: 0.7930 (t70) cc_final: 0.7044 (p0) REVERT: A 2669 GLU cc_start: 0.7757 (tt0) cc_final: 0.7154 (tm-30) REVERT: B 174 ASP cc_start: 0.7992 (m-30) cc_final: 0.7192 (t0) REVERT: B 481 VAL cc_start: 0.7498 (t) cc_final: 0.7296 (m) REVERT: B 604 LYS cc_start: 0.8318 (mmtm) cc_final: 0.8099 (mmmt) REVERT: B 765 LEU cc_start: 0.4911 (tt) cc_final: 0.4319 (mm) REVERT: B 968 MET cc_start: 0.7510 (ttt) cc_final: 0.6427 (mmp) REVERT: B 969 ASP cc_start: 0.7824 (t70) cc_final: 0.7422 (t0) REVERT: B 1084 PHE cc_start: 0.8014 (m-80) cc_final: 0.7751 (m-80) REVERT: B 1103 LEU cc_start: 0.5781 (OUTLIER) cc_final: 0.4745 (mt) REVERT: B 1245 CYS cc_start: 0.8696 (OUTLIER) cc_final: 0.8478 (t) REVERT: B 1331 MET cc_start: 0.2061 (mpp) cc_final: -0.0020 (tpp) REVERT: B 1661 LYS cc_start: 0.8560 (tppp) cc_final: 0.8229 (tptm) REVERT: B 1682 MET cc_start: 0.6907 (mmm) cc_final: 0.6594 (mmm) REVERT: B 1683 MET cc_start: 0.7534 (OUTLIER) cc_final: 0.7267 (mmm) REVERT: B 1862 ASP cc_start: 0.8516 (m-30) cc_final: 0.8191 (m-30) REVERT: B 1958 GLU cc_start: 0.6447 (tm-30) cc_final: 0.6108 (tm-30) REVERT: B 2234 ASP cc_start: 0.8749 (m-30) cc_final: 0.8253 (m-30) REVERT: B 2419 ASP cc_start: 0.7935 (t70) cc_final: 0.7062 (p0) REVERT: B 2669 GLU cc_start: 0.7753 (tt0) cc_final: 0.7147 (tm-30) REVERT: C 174 ASP cc_start: 0.7988 (m-30) cc_final: 0.7194 (t0) REVERT: C 604 LYS cc_start: 0.8317 (mmtm) cc_final: 0.8098 (mmmt) REVERT: C 765 LEU cc_start: 0.4917 (tt) cc_final: 0.4326 (mm) REVERT: C 968 MET cc_start: 0.7846 (ttt) cc_final: 0.6840 (mmp) REVERT: C 1084 PHE cc_start: 0.8109 (m-80) cc_final: 0.7860 (m-80) REVERT: C 1103 LEU cc_start: 0.5782 (OUTLIER) cc_final: 0.4744 (mt) REVERT: C 1245 CYS cc_start: 0.8694 (OUTLIER) cc_final: 0.8435 (t) REVERT: C 1331 MET cc_start: 0.2074 (mpp) cc_final: -0.0019 (tpp) REVERT: C 1661 LYS cc_start: 0.8594 (tppp) cc_final: 0.8246 (tptm) REVERT: C 1682 MET cc_start: 0.6925 (mmm) cc_final: 0.6616 (mmm) REVERT: C 1683 MET cc_start: 0.7513 (OUTLIER) cc_final: 0.7240 (mmm) REVERT: C 1862 ASP cc_start: 0.8513 (m-30) cc_final: 0.8189 (m-30) REVERT: C 1958 GLU cc_start: 0.6504 (tm-30) cc_final: 0.6119 (tm-30) REVERT: C 2234 ASP cc_start: 0.8749 (m-30) cc_final: 0.8252 (m-30) REVERT: C 2419 ASP cc_start: 0.7927 (t70) cc_final: 0.7060 (p0) REVERT: C 2669 GLU cc_start: 0.7757 (tt0) cc_final: 0.7153 (tm-30) REVERT: D 174 ASP cc_start: 0.8000 (m-30) cc_final: 0.7196 (t0) REVERT: D 481 VAL cc_start: 0.7498 (t) cc_final: 0.7297 (m) REVERT: D 604 LYS cc_start: 0.8316 (mmtm) cc_final: 0.8096 (mmmt) REVERT: D 765 LEU cc_start: 0.4908 (tt) cc_final: 0.4321 (mm) REVERT: D 968 MET cc_start: 0.7510 (ttt) cc_final: 0.6424 (mmp) REVERT: D 969 ASP cc_start: 0.7820 (t70) cc_final: 0.7418 (t0) REVERT: D 1084 PHE cc_start: 0.8108 (m-80) cc_final: 0.7857 (m-80) REVERT: D 1103 LEU cc_start: 0.5789 (OUTLIER) cc_final: 0.4751 (mt) REVERT: D 1245 CYS cc_start: 0.8697 (OUTLIER) cc_final: 0.8436 (t) REVERT: D 1331 MET cc_start: 0.2060 (mpp) cc_final: -0.0013 (tpp) REVERT: D 1661 LYS cc_start: 0.8561 (tppp) cc_final: 0.8228 (tptm) REVERT: D 1682 MET cc_start: 0.6916 (mmm) cc_final: 0.6608 (mmm) REVERT: D 1683 MET cc_start: 0.7512 (OUTLIER) cc_final: 0.7240 (mmm) REVERT: D 1862 ASP cc_start: 0.8516 (m-30) cc_final: 0.8192 (m-30) REVERT: D 1958 GLU cc_start: 0.6502 (tm-30) cc_final: 0.6117 (tm-30) REVERT: D 2234 ASP cc_start: 0.8747 (m-30) cc_final: 0.8252 (m-30) REVERT: D 2419 ASP cc_start: 0.7931 (t70) cc_final: 0.7063 (p0) REVERT: D 2669 GLU cc_start: 0.7749 (tt0) cc_final: 0.7151 (tm-30) outliers start: 71 outliers final: 36 residues processed: 882 average time/residue: 0.7501 time to fit residues: 1131.0153 Evaluate side-chains 831 residues out of total 8636 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 785 time to evaluate : 6.795 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 CYS Chi-restraints excluded: chain A residue 394 CYS Chi-restraints excluded: chain A residue 773 LEU Chi-restraints excluded: chain A residue 842 GLU Chi-restraints excluded: chain A residue 994 LEU Chi-restraints excluded: chain A residue 1103 LEU Chi-restraints excluded: chain A residue 1245 CYS Chi-restraints excluded: chain A residue 1631 HIS Chi-restraints excluded: chain A residue 2033 ILE Chi-restraints excluded: chain A residue 2673 ASP Chi-restraints excluded: chain B residue 61 CYS Chi-restraints excluded: chain B residue 394 CYS Chi-restraints excluded: chain B residue 773 LEU Chi-restraints excluded: chain B residue 842 GLU Chi-restraints excluded: chain B residue 994 LEU Chi-restraints excluded: chain B residue 1103 LEU Chi-restraints excluded: chain B residue 1245 CYS Chi-restraints excluded: chain B residue 1627 VAL Chi-restraints excluded: chain B residue 1631 HIS Chi-restraints excluded: chain B residue 1683 MET Chi-restraints excluded: chain B residue 2033 ILE Chi-restraints excluded: chain C residue 61 CYS Chi-restraints excluded: chain C residue 394 CYS Chi-restraints excluded: chain C residue 773 LEU Chi-restraints excluded: chain C residue 842 GLU Chi-restraints excluded: chain C residue 994 LEU Chi-restraints excluded: chain C residue 1103 LEU Chi-restraints excluded: chain C residue 1245 CYS Chi-restraints excluded: chain C residue 1252 GLN Chi-restraints excluded: chain C residue 1627 VAL Chi-restraints excluded: chain C residue 1631 HIS Chi-restraints excluded: chain C residue 1683 MET Chi-restraints excluded: chain C residue 2033 ILE Chi-restraints excluded: chain C residue 2673 ASP Chi-restraints excluded: chain D residue 61 CYS Chi-restraints excluded: chain D residue 394 CYS Chi-restraints excluded: chain D residue 773 LEU Chi-restraints excluded: chain D residue 842 GLU Chi-restraints excluded: chain D residue 994 LEU Chi-restraints excluded: chain D residue 1103 LEU Chi-restraints excluded: chain D residue 1245 CYS Chi-restraints excluded: chain D residue 1252 GLN Chi-restraints excluded: chain D residue 1627 VAL Chi-restraints excluded: chain D residue 1631 HIS Chi-restraints excluded: chain D residue 1683 MET Chi-restraints excluded: chain D residue 2033 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 952 random chunks: chunk 855 optimal weight: 30.0000 chunk 651 optimal weight: 5.9990 chunk 449 optimal weight: 2.9990 chunk 95 optimal weight: 6.9990 chunk 413 optimal weight: 3.9990 chunk 581 optimal weight: 0.9990 chunk 869 optimal weight: 5.9990 chunk 920 optimal weight: 9.9990 chunk 454 optimal weight: 6.9990 chunk 823 optimal weight: 8.9990 chunk 247 optimal weight: 6.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 544 GLN A 600 HIS A1066 HIS ** A1202 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1238 HIS ** A1280 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1412 HIS ** A1868 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1981 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2207 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2409 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2583 ASN A ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2715 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 544 GLN B 600 HIS B1066 HIS B1238 HIS ** B1280 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1412 HIS ** B1981 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2035 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B2104 HIS ** B2207 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2409 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2583 ASN A ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2715 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 544 GLN C 600 HIS C1066 HIS ** C1202 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1238 HIS C1252 GLN ** C1280 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1412 HIS ** C1981 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2035 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2207 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2409 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2583 ASN A ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2715 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 69 GLN D 544 GLN D 600 HIS D1066 HIS D1238 HIS D1252 GLN ** D1280 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D1412 HIS ** D1981 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2035 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D2104 HIS ** D2207 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2409 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2583 ASN A ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2715 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 25 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6869 moved from start: 0.2337 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 79896 Z= 0.331 Angle : 0.669 12.920 107776 Z= 0.341 Chirality : 0.043 0.279 12056 Planarity : 0.005 0.064 13652 Dihedral : 12.453 179.285 11788 Min Nonbonded Distance : 2.085 Molprobity Statistics. All-atom Clashscore : 15.14 Ramachandran Plot: Outliers : 0.17 % Allowed : 4.78 % Favored : 95.05 % Rotamer: Outliers : 1.54 % Allowed : 11.53 % Favored : 86.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.29 % 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: -0.38 (0.09), residues: 9484 helix: 0.25 (0.07), residues: 5472 sheet: -0.75 (0.23), residues: 540 loop : -0.80 (0.11), residues: 3472 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP B 218 HIS 0.009 0.001 HIS A 600 PHE 0.045 0.002 PHE A1372 TYR 0.021 0.002 TYR B1374 ARG 0.007 0.001 ARG D2670 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 18968 Ramachandran restraints generated. 9484 Oldfield, 0 Emsley, 9484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 18968 Ramachandran restraints generated. 9484 Oldfield, 0 Emsley, 9484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 937 residues out of total 8636 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 129 poor density : 808 time to evaluate : 6.919 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: A 481 VAL cc_start: 0.7529 (t) cc_final: 0.7315 (m) REVERT: A 600 HIS cc_start: 0.6747 (OUTLIER) cc_final: 0.6105 (t70) REVERT: A 604 LYS cc_start: 0.8409 (mmtm) cc_final: 0.8177 (mmmt) REVERT: A 968 MET cc_start: 0.7865 (ttt) cc_final: 0.6766 (mmp) REVERT: A 1423 TYR cc_start: 0.6695 (m-80) cc_final: 0.6216 (m-80) REVERT: A 1682 MET cc_start: 0.6969 (mmm) cc_final: 0.6675 (mmm) REVERT: A 1862 ASP cc_start: 0.8608 (m-30) cc_final: 0.8254 (m-30) REVERT: A 1958 GLU cc_start: 0.6527 (tm-30) cc_final: 0.6133 (tm-30) REVERT: A 2232 GLU cc_start: 0.7869 (pm20) cc_final: 0.7604 (pm20) REVERT: A 2234 ASP cc_start: 0.8753 (m-30) cc_final: 0.8283 (m-30) REVERT: A 2242 ASP cc_start: 0.7514 (t0) cc_final: 0.7273 (t0) REVERT: A 2260 LEU cc_start: 0.7363 (OUTLIER) cc_final: 0.7121 (mm) REVERT: A 2533 MET cc_start: 0.8240 (tpp) cc_final: 0.7971 (tpt) REVERT: A 2665 GLU cc_start: 0.7827 (mp0) cc_final: 0.7210 (mp0) REVERT: B 481 VAL cc_start: 0.7621 (t) cc_final: 0.7402 (m) REVERT: B 600 HIS cc_start: 0.6748 (OUTLIER) cc_final: 0.6107 (t70) REVERT: B 604 LYS cc_start: 0.8410 (mmtm) cc_final: 0.8178 (mmmt) REVERT: B 968 MET cc_start: 0.7490 (ttt) cc_final: 0.6353 (tpp) REVERT: B 973 LYS cc_start: 0.8370 (mmmt) cc_final: 0.8160 (mmtp) REVERT: B 1245 CYS cc_start: 0.8631 (OUTLIER) cc_final: 0.8416 (t) REVERT: B 1423 TYR cc_start: 0.6696 (m-80) cc_final: 0.6218 (m-80) REVERT: B 1682 MET cc_start: 0.7037 (mmm) cc_final: 0.6539 (mmm) REVERT: B 1862 ASP cc_start: 0.8607 (m-30) cc_final: 0.8254 (m-30) REVERT: B 1958 GLU cc_start: 0.6530 (tm-30) cc_final: 0.6137 (tm-30) REVERT: B 2234 ASP cc_start: 0.8750 (m-30) cc_final: 0.8283 (m-30) REVERT: B 2260 LEU cc_start: 0.7368 (OUTLIER) cc_final: 0.7136 (mm) REVERT: B 2665 GLU cc_start: 0.7831 (mp0) cc_final: 0.7214 (mp0) REVERT: C 600 HIS cc_start: 0.6675 (OUTLIER) cc_final: 0.6051 (t70) REVERT: C 604 LYS cc_start: 0.8410 (mmtm) cc_final: 0.8177 (mmmt) REVERT: C 968 MET cc_start: 0.7846 (ttt) cc_final: 0.6734 (mmp) REVERT: C 1423 TYR cc_start: 0.6697 (m-80) cc_final: 0.6217 (m-80) REVERT: C 1682 MET cc_start: 0.7047 (mmm) cc_final: 0.6643 (mmm) REVERT: C 1862 ASP cc_start: 0.8614 (m-30) cc_final: 0.8291 (m-30) REVERT: C 1958 GLU cc_start: 0.6529 (tm-30) cc_final: 0.6137 (tm-30) REVERT: C 2234 ASP cc_start: 0.8747 (m-30) cc_final: 0.8278 (m-30) REVERT: C 2242 ASP cc_start: 0.7512 (t0) cc_final: 0.7121 (t0) REVERT: C 2260 LEU cc_start: 0.7368 (OUTLIER) cc_final: 0.7136 (mm) REVERT: C 2533 MET cc_start: 0.8238 (tpp) cc_final: 0.7973 (tpt) REVERT: C 2665 GLU cc_start: 0.7832 (mp0) cc_final: 0.7215 (mp0) REVERT: D 481 VAL cc_start: 0.7528 (t) cc_final: 0.7317 (m) REVERT: D 600 HIS cc_start: 0.6747 (OUTLIER) cc_final: 0.6104 (t70) REVERT: D 604 LYS cc_start: 0.8408 (mmtm) cc_final: 0.8177 (mmmt) REVERT: D 968 MET cc_start: 0.7503 (ttt) cc_final: 0.6345 (mmm) REVERT: D 973 LYS cc_start: 0.8366 (mmmt) cc_final: 0.8147 (mmtp) REVERT: D 1423 TYR cc_start: 0.6694 (m-80) cc_final: 0.6214 (m-80) REVERT: D 1682 MET cc_start: 0.7029 (mmm) cc_final: 0.6536 (mmm) REVERT: D 1862 ASP cc_start: 0.8614 (m-30) cc_final: 0.8291 (m-30) REVERT: D 1958 GLU cc_start: 0.6528 (tm-30) cc_final: 0.6135 (tm-30) REVERT: D 2234 ASP cc_start: 0.8748 (m-30) cc_final: 0.8284 (m-30) REVERT: D 2260 LEU cc_start: 0.7368 (OUTLIER) cc_final: 0.7125 (mm) REVERT: D 2665 GLU cc_start: 0.7826 (mp0) cc_final: 0.7210 (mp0) outliers start: 129 outliers final: 87 residues processed: 883 average time/residue: 0.7073 time to fit residues: 1083.4758 Evaluate side-chains 877 residues out of total 8636 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 96 poor density : 781 time to evaluate : 6.723 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 CYS Chi-restraints excluded: chain A residue 115 ILE Chi-restraints excluded: chain A residue 152 ASP Chi-restraints excluded: chain A residue 289 HIS Chi-restraints excluded: chain A residue 381 LEU Chi-restraints excluded: chain A residue 394 CYS Chi-restraints excluded: chain A residue 544 GLN Chi-restraints excluded: chain A residue 600 HIS Chi-restraints excluded: chain A residue 773 LEU Chi-restraints excluded: chain A residue 842 GLU Chi-restraints excluded: chain A residue 994 LEU Chi-restraints excluded: chain A residue 1100 VAL Chi-restraints excluded: chain A residue 1103 LEU Chi-restraints excluded: chain A residue 1245 CYS Chi-restraints excluded: chain A residue 1627 VAL Chi-restraints excluded: chain A residue 1631 HIS Chi-restraints excluded: chain A residue 1683 MET Chi-restraints excluded: chain A residue 1959 MET Chi-restraints excluded: chain A residue 2023 LEU Chi-restraints excluded: chain A residue 2033 ILE Chi-restraints excluded: chain A residue 2087 GLU Chi-restraints excluded: chain A residue 2260 LEU Chi-restraints excluded: chain A residue 2286 LEU Chi-restraints excluded: chain A residue 2552 VAL Chi-restraints excluded: chain A residue 2723 MET Chi-restraints excluded: chain B residue 20 GLU Chi-restraints excluded: chain B residue 61 CYS Chi-restraints excluded: chain B residue 115 ILE Chi-restraints excluded: chain B residue 289 HIS Chi-restraints excluded: chain B residue 381 LEU Chi-restraints excluded: chain B residue 394 CYS Chi-restraints excluded: chain B residue 544 GLN Chi-restraints excluded: chain B residue 600 HIS Chi-restraints excluded: chain B residue 773 LEU Chi-restraints excluded: chain B residue 842 GLU Chi-restraints excluded: chain B residue 994 LEU Chi-restraints excluded: chain B residue 1100 VAL Chi-restraints excluded: chain B residue 1103 LEU Chi-restraints excluded: chain B residue 1245 CYS Chi-restraints excluded: chain B residue 1627 VAL Chi-restraints excluded: chain B residue 1631 HIS Chi-restraints excluded: chain B residue 1959 MET Chi-restraints excluded: chain B residue 2023 LEU Chi-restraints excluded: chain B residue 2033 ILE Chi-restraints excluded: chain B residue 2087 GLU Chi-restraints excluded: chain B residue 2260 LEU Chi-restraints excluded: chain B residue 2286 LEU Chi-restraints excluded: chain B residue 2552 VAL Chi-restraints excluded: chain B residue 2673 ASP Chi-restraints excluded: chain B residue 2723 MET Chi-restraints excluded: chain C residue 61 CYS Chi-restraints excluded: chain C residue 115 ILE Chi-restraints excluded: chain C residue 152 ASP Chi-restraints excluded: chain C residue 289 HIS Chi-restraints excluded: chain C residue 381 LEU Chi-restraints excluded: chain C residue 394 CYS Chi-restraints excluded: chain C residue 544 GLN Chi-restraints excluded: chain C residue 600 HIS Chi-restraints excluded: chain C residue 773 LEU Chi-restraints excluded: chain C residue 842 GLU Chi-restraints excluded: chain C residue 994 LEU Chi-restraints excluded: chain C residue 1100 VAL Chi-restraints excluded: chain C residue 1103 LEU Chi-restraints excluded: chain C residue 1627 VAL Chi-restraints excluded: chain C residue 1631 HIS Chi-restraints excluded: chain C residue 1959 MET Chi-restraints excluded: chain C residue 2023 LEU Chi-restraints excluded: chain C residue 2033 ILE Chi-restraints excluded: chain C residue 2087 GLU Chi-restraints excluded: chain C residue 2260 LEU Chi-restraints excluded: chain C residue 2286 LEU Chi-restraints excluded: chain C residue 2552 VAL Chi-restraints excluded: chain C residue 2723 MET Chi-restraints excluded: chain D residue 61 CYS Chi-restraints excluded: chain D residue 115 ILE Chi-restraints excluded: chain D residue 289 HIS Chi-restraints excluded: chain D residue 381 LEU Chi-restraints excluded: chain D residue 394 CYS Chi-restraints excluded: chain D residue 544 GLN Chi-restraints excluded: chain D residue 600 HIS Chi-restraints excluded: chain D residue 773 LEU Chi-restraints excluded: chain D residue 842 GLU Chi-restraints excluded: chain D residue 994 LEU Chi-restraints excluded: chain D residue 1100 VAL Chi-restraints excluded: chain D residue 1103 LEU Chi-restraints excluded: chain D residue 1627 VAL Chi-restraints excluded: chain D residue 1631 HIS Chi-restraints excluded: chain D residue 1959 MET Chi-restraints excluded: chain D residue 2023 LEU Chi-restraints excluded: chain D residue 2033 ILE Chi-restraints excluded: chain D residue 2087 GLU Chi-restraints excluded: chain D residue 2260 LEU Chi-restraints excluded: chain D residue 2286 LEU Chi-restraints excluded: chain D residue 2552 VAL Chi-restraints excluded: chain D residue 2673 ASP Chi-restraints excluded: chain D residue 2723 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 952 random chunks: chunk 766 optimal weight: 6.9990 chunk 522 optimal weight: 10.0000 chunk 13 optimal weight: 7.9990 chunk 685 optimal weight: 0.9980 chunk 379 optimal weight: 40.0000 chunk 785 optimal weight: 1.9990 chunk 636 optimal weight: 0.9980 chunk 1 optimal weight: 10.0000 chunk 469 optimal weight: 2.9990 chunk 825 optimal weight: 8.9990 chunk 232 optimal weight: 2.9990 overall best weight: 1.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 40 GLN A 544 GLN A 868 ASN A1238 HIS ** A1280 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1412 HIS ** A1981 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2035 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2207 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2409 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2583 ASN A ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2715 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 40 GLN B 544 GLN B1238 HIS ** B1280 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2035 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B2104 HIS ** B2207 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2409 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2583 ASN A ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2715 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 40 GLN C 544 GLN C 868 ASN C1238 HIS ** C1280 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1412 HIS ** C2035 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2207 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2409 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2583 ASN A ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2715 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 40 GLN ** D 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 544 GLN D1238 HIS ** D1280 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D1412 HIS ** D2035 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D2104 HIS ** D2207 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2409 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2583 ASN A ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2715 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6827 moved from start: 0.2327 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 79896 Z= 0.203 Angle : 0.601 13.155 107776 Z= 0.300 Chirality : 0.040 0.258 12056 Planarity : 0.004 0.063 13652 Dihedral : 11.830 174.451 11788 Min Nonbonded Distance : 2.153 Molprobity Statistics. All-atom Clashscore : 12.52 Ramachandran Plot: Outliers : 0.21 % Allowed : 3.96 % Favored : 95.83 % Rotamer: Outliers : 1.13 % Allowed : 13.58 % Favored : 85.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.29 % 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: -0.22 (0.09), residues: 9484 helix: 0.42 (0.07), residues: 5496 sheet: -0.67 (0.23), residues: 572 loop : -0.83 (0.11), residues: 3416 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A2256 HIS 0.017 0.001 HIS A 600 PHE 0.045 0.002 PHE B1372 TYR 0.019 0.001 TYR C2453 ARG 0.006 0.000 ARG A2670 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 18968 Ramachandran restraints generated. 9484 Oldfield, 0 Emsley, 9484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 18968 Ramachandran restraints generated. 9484 Oldfield, 0 Emsley, 9484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 922 residues out of total 8636 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 94 poor density : 828 time to evaluate : 6.908 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: A 481 VAL cc_start: 0.7790 (t) cc_final: 0.7546 (m) REVERT: A 535 MET cc_start: 0.5729 (mmm) cc_final: 0.4165 (mtp) REVERT: A 604 LYS cc_start: 0.8418 (mmtm) cc_final: 0.8179 (mmmt) REVERT: A 667 GLU cc_start: 0.4573 (OUTLIER) cc_final: 0.4244 (mt-10) REVERT: A 968 MET cc_start: 0.7560 (ttt) cc_final: 0.6884 (mmp) REVERT: A 1103 LEU cc_start: 0.6110 (OUTLIER) cc_final: 0.4892 (mt) REVERT: A 1245 CYS cc_start: 0.8606 (OUTLIER) cc_final: 0.8396 (t) REVERT: A 1331 MET cc_start: 0.2913 (mpp) cc_final: 0.0298 (tpp) REVERT: A 1423 TYR cc_start: 0.6662 (m-80) cc_final: 0.6207 (m-80) REVERT: A 1484 MET cc_start: 0.4977 (mtt) cc_final: 0.4666 (mtp) REVERT: A 1682 MET cc_start: 0.6927 (mmm) cc_final: 0.6604 (mmm) REVERT: A 1862 ASP cc_start: 0.8575 (m-30) cc_final: 0.8228 (m-30) REVERT: A 1958 GLU cc_start: 0.6396 (tm-30) cc_final: 0.6005 (tm-30) REVERT: A 2042 GLU cc_start: 0.7373 (mp0) cc_final: 0.7107 (mp0) REVERT: A 2234 ASP cc_start: 0.8755 (m-30) cc_final: 0.8303 (m-30) REVERT: A 2533 MET cc_start: 0.8127 (tpp) cc_final: 0.7736 (tpp) REVERT: B 481 VAL cc_start: 0.7818 (t) cc_final: 0.7610 (m) REVERT: B 535 MET cc_start: 0.5708 (mmm) cc_final: 0.4119 (mtp) REVERT: B 604 LYS cc_start: 0.8420 (mmtm) cc_final: 0.8181 (mmmt) REVERT: B 667 GLU cc_start: 0.4569 (OUTLIER) cc_final: 0.4217 (mm-30) REVERT: B 968 MET cc_start: 0.7574 (ttt) cc_final: 0.6389 (mmm) REVERT: B 1103 LEU cc_start: 0.6112 (OUTLIER) cc_final: 0.4875 (mt) REVERT: B 1245 CYS cc_start: 0.8662 (OUTLIER) cc_final: 0.8456 (t) REVERT: B 1331 MET cc_start: 0.2906 (mpp) cc_final: 0.0291 (tpp) REVERT: B 1423 TYR cc_start: 0.6664 (m-80) cc_final: 0.6208 (m-80) REVERT: B 1484 MET cc_start: 0.4979 (mtt) cc_final: 0.4667 (mtp) REVERT: B 1862 ASP cc_start: 0.8577 (m-30) cc_final: 0.8232 (m-30) REVERT: B 1958 GLU cc_start: 0.6412 (tm-30) cc_final: 0.5996 (tm-30) REVERT: B 2042 GLU cc_start: 0.7369 (mp0) cc_final: 0.7103 (mp0) REVERT: B 2234 ASP cc_start: 0.8741 (m-30) cc_final: 0.8271 (m-30) REVERT: B 2533 MET cc_start: 0.8077 (tpp) cc_final: 0.7840 (tpp) REVERT: C 535 MET cc_start: 0.5706 (mmm) cc_final: 0.4118 (mtp) REVERT: C 604 LYS cc_start: 0.8416 (mmtm) cc_final: 0.8176 (mmmt) REVERT: C 667 GLU cc_start: 0.4565 (OUTLIER) cc_final: 0.4240 (mt-10) REVERT: C 968 MET cc_start: 0.7510 (ttt) cc_final: 0.6886 (mmp) REVERT: C 1103 LEU cc_start: 0.6036 (OUTLIER) cc_final: 0.4763 (mt) REVERT: C 1331 MET cc_start: 0.2917 (mpp) cc_final: 0.0298 (tpp) REVERT: C 1423 TYR cc_start: 0.6663 (m-80) cc_final: 0.6206 (m-80) REVERT: C 1484 MET cc_start: 0.4978 (mtt) cc_final: 0.4667 (mtp) REVERT: C 1682 MET cc_start: 0.6913 (mmm) cc_final: 0.6610 (mmm) REVERT: C 1862 ASP cc_start: 0.8577 (m-30) cc_final: 0.8229 (m-30) REVERT: C 1958 GLU cc_start: 0.6394 (tm-30) cc_final: 0.5994 (tm-30) REVERT: C 2042 GLU cc_start: 0.7369 (mp0) cc_final: 0.7103 (mp0) REVERT: C 2234 ASP cc_start: 0.8742 (m-30) cc_final: 0.8273 (m-30) REVERT: C 2533 MET cc_start: 0.8128 (tpp) cc_final: 0.7734 (tpp) REVERT: D 481 VAL cc_start: 0.7806 (t) cc_final: 0.7571 (m) REVERT: D 535 MET cc_start: 0.5736 (mmm) cc_final: 0.4177 (mtp) REVERT: D 604 LYS cc_start: 0.8417 (mmtm) cc_final: 0.8181 (mmmt) REVERT: D 667 GLU cc_start: 0.4570 (OUTLIER) cc_final: 0.4243 (mt-10) REVERT: D 968 MET cc_start: 0.7533 (ttt) cc_final: 0.6379 (mmm) REVERT: D 1103 LEU cc_start: 0.6094 (OUTLIER) cc_final: 0.4835 (mt) REVERT: D 1331 MET cc_start: 0.2910 (mpp) cc_final: 0.0299 (tpp) REVERT: D 1423 TYR cc_start: 0.6663 (m-80) cc_final: 0.6237 (m-80) REVERT: D 1484 MET cc_start: 0.4975 (mtt) cc_final: 0.4664 (mtp) REVERT: D 1862 ASP cc_start: 0.8574 (m-30) cc_final: 0.8226 (m-30) REVERT: D 1958 GLU cc_start: 0.6391 (tm-30) cc_final: 0.5991 (tm-30) REVERT: D 2042 GLU cc_start: 0.7370 (mp0) cc_final: 0.7101 (mp0) REVERT: D 2234 ASP cc_start: 0.8741 (m-30) cc_final: 0.8275 (m-30) REVERT: D 2533 MET cc_start: 0.8078 (tpp) cc_final: 0.7839 (tpp) outliers start: 94 outliers final: 72 residues processed: 886 average time/residue: 0.7183 time to fit residues: 1105.0335 Evaluate side-chains 879 residues out of total 8636 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 82 poor density : 797 time to evaluate : 6.820 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 CYS Chi-restraints excluded: chain A residue 289 HIS Chi-restraints excluded: chain A residue 394 CYS Chi-restraints excluded: chain A residue 415 MET Chi-restraints excluded: chain A residue 544 GLN Chi-restraints excluded: chain A residue 666 ILE Chi-restraints excluded: chain A residue 667 GLU Chi-restraints excluded: chain A residue 765 LEU Chi-restraints excluded: chain A residue 773 LEU Chi-restraints excluded: chain A residue 842 GLU Chi-restraints excluded: chain A residue 994 LEU Chi-restraints excluded: chain A residue 1053 ASP Chi-restraints excluded: chain A residue 1100 VAL Chi-restraints excluded: chain A residue 1103 LEU Chi-restraints excluded: chain A residue 1245 CYS Chi-restraints excluded: chain A residue 1627 VAL Chi-restraints excluded: chain A residue 1631 HIS Chi-restraints excluded: chain A residue 2033 ILE Chi-restraints excluded: chain A residue 2087 GLU Chi-restraints excluded: chain A residue 2286 LEU Chi-restraints excluded: chain A residue 2419 ASP Chi-restraints excluded: chain B residue 20 GLU Chi-restraints excluded: chain B residue 61 CYS Chi-restraints excluded: chain B residue 289 HIS Chi-restraints excluded: chain B residue 394 CYS Chi-restraints excluded: chain B residue 415 MET Chi-restraints excluded: chain B residue 544 GLN Chi-restraints excluded: chain B residue 666 ILE Chi-restraints excluded: chain B residue 667 GLU Chi-restraints excluded: chain B residue 765 LEU Chi-restraints excluded: chain B residue 773 LEU Chi-restraints excluded: chain B residue 842 GLU Chi-restraints excluded: chain B residue 994 LEU Chi-restraints excluded: chain B residue 1053 ASP Chi-restraints excluded: chain B residue 1100 VAL Chi-restraints excluded: chain B residue 1103 LEU Chi-restraints excluded: chain B residue 1245 CYS Chi-restraints excluded: chain B residue 1627 VAL Chi-restraints excluded: chain B residue 2023 LEU Chi-restraints excluded: chain B residue 2087 GLU Chi-restraints excluded: chain B residue 2116 MET Chi-restraints excluded: chain B residue 2286 LEU Chi-restraints excluded: chain B residue 2673 ASP Chi-restraints excluded: chain C residue 61 CYS Chi-restraints excluded: chain C residue 289 HIS Chi-restraints excluded: chain C residue 394 CYS Chi-restraints excluded: chain C residue 415 MET Chi-restraints excluded: chain C residue 544 GLN Chi-restraints excluded: chain C residue 666 ILE Chi-restraints excluded: chain C residue 667 GLU Chi-restraints excluded: chain C residue 765 LEU Chi-restraints excluded: chain C residue 773 LEU Chi-restraints excluded: chain C residue 842 GLU Chi-restraints excluded: chain C residue 994 LEU Chi-restraints excluded: chain C residue 1053 ASP Chi-restraints excluded: chain C residue 1100 VAL Chi-restraints excluded: chain C residue 1103 LEU Chi-restraints excluded: chain C residue 1631 HIS Chi-restraints excluded: chain C residue 2023 LEU Chi-restraints excluded: chain C residue 2033 ILE Chi-restraints excluded: chain C residue 2087 GLU Chi-restraints excluded: chain C residue 2286 LEU Chi-restraints excluded: chain C residue 2419 ASP Chi-restraints excluded: chain D residue 61 CYS Chi-restraints excluded: chain D residue 289 HIS Chi-restraints excluded: chain D residue 394 CYS Chi-restraints excluded: chain D residue 415 MET Chi-restraints excluded: chain D residue 544 GLN Chi-restraints excluded: chain D residue 666 ILE Chi-restraints excluded: chain D residue 667 GLU Chi-restraints excluded: chain D residue 765 LEU Chi-restraints excluded: chain D residue 773 LEU Chi-restraints excluded: chain D residue 842 GLU Chi-restraints excluded: chain D residue 994 LEU Chi-restraints excluded: chain D residue 1053 ASP Chi-restraints excluded: chain D residue 1100 VAL Chi-restraints excluded: chain D residue 1103 LEU Chi-restraints excluded: chain D residue 2023 LEU Chi-restraints excluded: chain D residue 2033 ILE Chi-restraints excluded: chain D residue 2087 GLU Chi-restraints excluded: chain D residue 2286 LEU Chi-restraints excluded: chain D residue 2673 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 952 random chunks: chunk 309 optimal weight: 0.0170 chunk 828 optimal weight: 7.9990 chunk 181 optimal weight: 4.9990 chunk 540 optimal weight: 8.9990 chunk 227 optimal weight: 9.9990 chunk 921 optimal weight: 3.9990 chunk 764 optimal weight: 2.9990 chunk 426 optimal weight: 7.9990 chunk 76 optimal weight: 0.1980 chunk 304 optimal weight: 5.9990 chunk 483 optimal weight: 20.0000 overall best weight: 2.4424 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 544 GLN ** A1202 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1238 HIS ** A1280 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1412 HIS ** A1981 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2035 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A2104 HIS ** A2207 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2409 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2583 ASN A ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2715 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 69 GLN B 544 GLN B 868 ASN ** B1202 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1238 HIS ** B1280 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1412 HIS ** B1981 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2035 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B2104 HIS ** B2207 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2409 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2583 ASN A ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2715 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 544 GLN C1238 HIS ** C1280 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1981 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2035 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C2104 HIS ** C2207 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2409 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2583 ASN A ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2715 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 544 GLN D 584 GLN D 868 ASN D1238 HIS ** D1280 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D1412 HIS ** D1981 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2035 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D2104 HIS ** D2207 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2409 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2583 ASN A ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2715 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6835 moved from start: 0.2470 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 79896 Z= 0.227 Angle : 0.601 13.198 107776 Z= 0.302 Chirality : 0.041 0.254 12056 Planarity : 0.004 0.063 13652 Dihedral : 11.520 171.643 11788 Min Nonbonded Distance : 2.140 Molprobity Statistics. All-atom Clashscore : 13.01 Ramachandran Plot: Outliers : 0.21 % Allowed : 4.33 % Favored : 95.46 % Rotamer: Outliers : 1.43 % Allowed : 13.81 % Favored : 84.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.29 % 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: -0.24 (0.09), residues: 9484 helix: 0.41 (0.07), residues: 5504 sheet: -0.67 (0.22), residues: 572 loop : -0.86 (0.11), residues: 3408 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D2256 HIS 0.006 0.001 HIS B1659 PHE 0.045 0.002 PHE C1372 TYR 0.021 0.001 TYR B2453 ARG 0.005 0.000 ARG A2670 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 18968 Ramachandran restraints generated. 9484 Oldfield, 0 Emsley, 9484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 18968 Ramachandran restraints generated. 9484 Oldfield, 0 Emsley, 9484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 933 residues out of total 8636 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 120 poor density : 813 time to evaluate : 6.792 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: A 481 VAL cc_start: 0.7815 (t) cc_final: 0.7586 (m) REVERT: A 604 LYS cc_start: 0.8418 (mmtm) cc_final: 0.8196 (mmmt) REVERT: A 765 LEU cc_start: 0.4244 (OUTLIER) cc_final: 0.3888 (tp) REVERT: A 968 MET cc_start: 0.7613 (ttt) cc_final: 0.6929 (mmp) REVERT: A 1103 LEU cc_start: 0.6236 (OUTLIER) cc_final: 0.5045 (mt) REVERT: A 1331 MET cc_start: 0.2948 (mpp) cc_final: 0.0283 (tpt) REVERT: A 1423 TYR cc_start: 0.6708 (m-80) cc_final: 0.6272 (m-80) REVERT: A 1484 MET cc_start: 0.5148 (mtt) cc_final: 0.4814 (mtp) REVERT: A 1682 MET cc_start: 0.7187 (mmm) cc_final: 0.6728 (mmm) REVERT: A 1862 ASP cc_start: 0.8569 (m-30) cc_final: 0.8231 (m-30) REVERT: A 1958 GLU cc_start: 0.6286 (tm-30) cc_final: 0.5809 (tm-30) REVERT: A 2042 GLU cc_start: 0.7441 (mp0) cc_final: 0.7205 (mp0) REVERT: A 2234 ASP cc_start: 0.8742 (m-30) cc_final: 0.8279 (m-30) REVERT: A 2260 LEU cc_start: 0.7358 (OUTLIER) cc_final: 0.7094 (mm) REVERT: A 2533 MET cc_start: 0.8151 (tpp) cc_final: 0.7784 (tpp) REVERT: B 481 VAL cc_start: 0.7805 (t) cc_final: 0.7604 (m) REVERT: B 604 LYS cc_start: 0.8419 (mmtm) cc_final: 0.8197 (mmmt) REVERT: B 667 GLU cc_start: 0.4571 (OUTLIER) cc_final: 0.4237 (mt-10) REVERT: B 968 MET cc_start: 0.7562 (ttt) cc_final: 0.6450 (tpp) REVERT: B 1103 LEU cc_start: 0.6226 (OUTLIER) cc_final: 0.5041 (mt) REVERT: B 1331 MET cc_start: 0.2950 (mpp) cc_final: 0.0271 (tpt) REVERT: B 1423 TYR cc_start: 0.6710 (m-80) cc_final: 0.6273 (m-80) REVERT: B 1484 MET cc_start: 0.5169 (mtt) cc_final: 0.4844 (mtp) REVERT: B 1862 ASP cc_start: 0.8570 (m-30) cc_final: 0.8233 (m-30) REVERT: B 1958 GLU cc_start: 0.6289 (tm-30) cc_final: 0.5812 (tm-30) REVERT: B 2042 GLU cc_start: 0.7436 (mp0) cc_final: 0.7195 (mp0) REVERT: B 2234 ASP cc_start: 0.8746 (m-30) cc_final: 0.8275 (m-30) REVERT: B 2260 LEU cc_start: 0.7363 (OUTLIER) cc_final: 0.7097 (mm) REVERT: B 2533 MET cc_start: 0.8091 (tpp) cc_final: 0.7831 (tpp) REVERT: C 604 LYS cc_start: 0.8423 (mmtm) cc_final: 0.8196 (mmmt) REVERT: C 765 LEU cc_start: 0.4248 (OUTLIER) cc_final: 0.3893 (tp) REVERT: C 968 MET cc_start: 0.7908 (ttt) cc_final: 0.7044 (mmp) REVERT: C 1103 LEU cc_start: 0.6231 (OUTLIER) cc_final: 0.5042 (mt) REVERT: C 1331 MET cc_start: 0.2948 (mpp) cc_final: 0.0281 (tpt) REVERT: C 1423 TYR cc_start: 0.6707 (m-80) cc_final: 0.6272 (m-80) REVERT: C 1484 MET cc_start: 0.5166 (mtt) cc_final: 0.4842 (mtp) REVERT: C 1682 MET cc_start: 0.7114 (mmm) cc_final: 0.6664 (mmm) REVERT: C 1862 ASP cc_start: 0.8569 (m-30) cc_final: 0.8231 (m-30) REVERT: C 1958 GLU cc_start: 0.6286 (tm-30) cc_final: 0.5812 (tm-30) REVERT: C 2042 GLU cc_start: 0.7429 (mp0) cc_final: 0.7192 (mp0) REVERT: C 2234 ASP cc_start: 0.8744 (m-30) cc_final: 0.8275 (m-30) REVERT: C 2260 LEU cc_start: 0.7359 (OUTLIER) cc_final: 0.7095 (mm) REVERT: C 2533 MET cc_start: 0.8155 (tpp) cc_final: 0.7784 (tpp) REVERT: D 481 VAL cc_start: 0.7816 (t) cc_final: 0.7595 (m) REVERT: D 604 LYS cc_start: 0.8416 (mmtm) cc_final: 0.8196 (mmmt) REVERT: D 667 GLU cc_start: 0.4650 (OUTLIER) cc_final: 0.4311 (mt-10) REVERT: D 968 MET cc_start: 0.7590 (ttt) cc_final: 0.6453 (tpp) REVERT: D 1331 MET cc_start: 0.2945 (mpp) cc_final: 0.0286 (tpt) REVERT: D 1423 TYR cc_start: 0.6707 (m-80) cc_final: 0.6269 (m-80) REVERT: D 1484 MET cc_start: 0.5162 (mtt) cc_final: 0.4839 (mtp) REVERT: D 1862 ASP cc_start: 0.8569 (m-30) cc_final: 0.8230 (m-30) REVERT: D 1958 GLU cc_start: 0.6283 (tm-30) cc_final: 0.5810 (tm-30) REVERT: D 2042 GLU cc_start: 0.7432 (mp0) cc_final: 0.7190 (mp0) REVERT: D 2234 ASP cc_start: 0.8746 (m-30) cc_final: 0.8275 (m-30) REVERT: D 2260 LEU cc_start: 0.7362 (OUTLIER) cc_final: 0.7096 (mm) REVERT: D 2533 MET cc_start: 0.8089 (tpp) cc_final: 0.7828 (tpp) outliers start: 120 outliers final: 92 residues processed: 893 average time/residue: 0.7062 time to fit residues: 1094.4281 Evaluate side-chains 898 residues out of total 8636 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 103 poor density : 795 time to evaluate : 6.775 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 CYS Chi-restraints excluded: chain A residue 289 HIS Chi-restraints excluded: chain A residue 394 CYS Chi-restraints excluded: chain A residue 415 MET Chi-restraints excluded: chain A residue 544 GLN Chi-restraints excluded: chain A residue 666 ILE Chi-restraints excluded: chain A residue 765 LEU Chi-restraints excluded: chain A residue 767 CYS Chi-restraints excluded: chain A residue 773 LEU Chi-restraints excluded: chain A residue 842 GLU Chi-restraints excluded: chain A residue 994 LEU Chi-restraints excluded: chain A residue 1053 ASP Chi-restraints excluded: chain A residue 1100 VAL Chi-restraints excluded: chain A residue 1103 LEU Chi-restraints excluded: chain A residue 1627 VAL Chi-restraints excluded: chain A residue 1631 HIS Chi-restraints excluded: chain A residue 1959 MET Chi-restraints excluded: chain A residue 2023 LEU Chi-restraints excluded: chain A residue 2033 ILE Chi-restraints excluded: chain A residue 2087 GLU Chi-restraints excluded: chain A residue 2260 LEU Chi-restraints excluded: chain A residue 2286 LEU Chi-restraints excluded: chain A residue 2345 ILE Chi-restraints excluded: chain A residue 2419 ASP Chi-restraints excluded: chain A residue 2552 VAL Chi-restraints excluded: chain B residue 20 GLU Chi-restraints excluded: chain B residue 61 CYS Chi-restraints excluded: chain B residue 289 HIS Chi-restraints excluded: chain B residue 394 CYS Chi-restraints excluded: chain B residue 415 MET Chi-restraints excluded: chain B residue 544 GLN Chi-restraints excluded: chain B residue 666 ILE Chi-restraints excluded: chain B residue 667 GLU Chi-restraints excluded: chain B residue 765 LEU Chi-restraints excluded: chain B residue 767 CYS Chi-restraints excluded: chain B residue 773 LEU Chi-restraints excluded: chain B residue 842 GLU Chi-restraints excluded: chain B residue 994 LEU Chi-restraints excluded: chain B residue 1053 ASP Chi-restraints excluded: chain B residue 1100 VAL Chi-restraints excluded: chain B residue 1103 LEU Chi-restraints excluded: chain B residue 1627 VAL Chi-restraints excluded: chain B residue 1631 HIS Chi-restraints excluded: chain B residue 1959 MET Chi-restraints excluded: chain B residue 2023 LEU Chi-restraints excluded: chain B residue 2033 ILE Chi-restraints excluded: chain B residue 2087 GLU Chi-restraints excluded: chain B residue 2116 MET Chi-restraints excluded: chain B residue 2260 LEU Chi-restraints excluded: chain B residue 2286 LEU Chi-restraints excluded: chain B residue 2345 ILE Chi-restraints excluded: chain B residue 2419 ASP Chi-restraints excluded: chain B residue 2552 VAL Chi-restraints excluded: chain B residue 2673 ASP Chi-restraints excluded: chain C residue 61 CYS Chi-restraints excluded: chain C residue 289 HIS Chi-restraints excluded: chain C residue 394 CYS Chi-restraints excluded: chain C residue 415 MET Chi-restraints excluded: chain C residue 544 GLN Chi-restraints excluded: chain C residue 666 ILE Chi-restraints excluded: chain C residue 765 LEU Chi-restraints excluded: chain C residue 767 CYS Chi-restraints excluded: chain C residue 773 LEU Chi-restraints excluded: chain C residue 842 GLU Chi-restraints excluded: chain C residue 994 LEU Chi-restraints excluded: chain C residue 1053 ASP Chi-restraints excluded: chain C residue 1100 VAL Chi-restraints excluded: chain C residue 1103 LEU Chi-restraints excluded: chain C residue 1627 VAL Chi-restraints excluded: chain C residue 1631 HIS Chi-restraints excluded: chain C residue 2023 LEU Chi-restraints excluded: chain C residue 2033 ILE Chi-restraints excluded: chain C residue 2087 GLU Chi-restraints excluded: chain C residue 2260 LEU Chi-restraints excluded: chain C residue 2286 LEU Chi-restraints excluded: chain C residue 2345 ILE Chi-restraints excluded: chain C residue 2419 ASP Chi-restraints excluded: chain C residue 2552 VAL Chi-restraints excluded: chain D residue 61 CYS Chi-restraints excluded: chain D residue 289 HIS Chi-restraints excluded: chain D residue 394 CYS Chi-restraints excluded: chain D residue 415 MET Chi-restraints excluded: chain D residue 544 GLN Chi-restraints excluded: chain D residue 666 ILE Chi-restraints excluded: chain D residue 667 GLU Chi-restraints excluded: chain D residue 765 LEU Chi-restraints excluded: chain D residue 767 CYS Chi-restraints excluded: chain D residue 773 LEU Chi-restraints excluded: chain D residue 842 GLU Chi-restraints excluded: chain D residue 994 LEU Chi-restraints excluded: chain D residue 1053 ASP Chi-restraints excluded: chain D residue 1100 VAL Chi-restraints excluded: chain D residue 1627 VAL Chi-restraints excluded: chain D residue 1631 HIS Chi-restraints excluded: chain D residue 2023 LEU Chi-restraints excluded: chain D residue 2033 ILE Chi-restraints excluded: chain D residue 2087 GLU Chi-restraints excluded: chain D residue 2260 LEU Chi-restraints excluded: chain D residue 2286 LEU Chi-restraints excluded: chain D residue 2345 ILE Chi-restraints excluded: chain D residue 2419 ASP Chi-restraints excluded: chain D residue 2552 VAL Chi-restraints excluded: chain D residue 2673 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 952 random chunks: chunk 888 optimal weight: 2.9990 chunk 103 optimal weight: 20.0000 chunk 524 optimal weight: 8.9990 chunk 672 optimal weight: 7.9990 chunk 521 optimal weight: 10.0000 chunk 775 optimal weight: 0.7980 chunk 514 optimal weight: 6.9990 chunk 917 optimal weight: 10.0000 chunk 574 optimal weight: 6.9990 chunk 559 optimal weight: 1.9990 chunk 423 optimal weight: 9.9990 overall best weight: 3.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 717 GLN ** A1202 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1238 HIS ** A1280 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1375 HIS ** A1981 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2035 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A2104 HIS ** A2207 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2409 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2583 ASN A ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2715 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 524 GLN B 717 GLN ** B 850 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 868 ASN ** B1202 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1238 HIS ** B1280 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1375 HIS ** B1981 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2035 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2207 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2409 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2583 ASN A ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2715 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 69 GLN C 600 HIS C 717 GLN C 868 ASN ** C1202 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1238 HIS ** C1280 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1375 HIS ** C1981 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2035 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C2104 HIS ** C2207 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2409 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2583 ASN A ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2715 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 717 GLN ** D 850 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 868 ASN ** D1202 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1238 HIS ** D1280 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D1375 HIS D1412 HIS ** D1981 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2035 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2207 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2409 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2583 ASN A ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2715 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6874 moved from start: 0.2803 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.061 79896 Z= 0.326 Angle : 0.664 12.979 107776 Z= 0.338 Chirality : 0.043 0.262 12056 Planarity : 0.004 0.060 13652 Dihedral : 11.562 166.128 11786 Min Nonbonded Distance : 2.099 Molprobity Statistics. All-atom Clashscore : 15.50 Ramachandran Plot: Outliers : 0.23 % Allowed : 5.02 % Favored : 94.75 % Rotamer: Outliers : 1.48 % Allowed : 14.51 % Favored : 84.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.29 % 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: -0.60 (0.09), residues: 9484 helix: 0.12 (0.07), residues: 5516 sheet: -0.88 (0.22), residues: 568 loop : -1.00 (0.11), residues: 3400 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP C2256 HIS 0.007 0.001 HIS C 600 PHE 0.044 0.002 PHE B1372 TYR 0.025 0.002 TYR C2398 ARG 0.004 0.001 ARG C 626 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 18968 Ramachandran restraints generated. 9484 Oldfield, 0 Emsley, 9484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 18968 Ramachandran restraints generated. 9484 Oldfield, 0 Emsley, 9484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 922 residues out of total 8636 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 124 poor density : 798 time to evaluate : 6.886 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: A 481 VAL cc_start: 0.7556 (t) cc_final: 0.7353 (m) REVERT: A 535 MET cc_start: 0.5955 (mmm) cc_final: 0.4423 (mtp) REVERT: A 604 LYS cc_start: 0.8435 (mmtm) cc_final: 0.8214 (mmmt) REVERT: A 968 MET cc_start: 0.7910 (ttt) cc_final: 0.7248 (mmp) REVERT: A 973 LYS cc_start: 0.8426 (mmmt) cc_final: 0.8082 (mmtp) REVERT: A 1331 MET cc_start: 0.3306 (mpp) cc_final: 0.0634 (tpt) REVERT: A 1423 TYR cc_start: 0.6662 (m-80) cc_final: 0.6420 (m-80) REVERT: A 1484 MET cc_start: 0.5142 (mtt) cc_final: 0.4839 (mtp) REVERT: A 1862 ASP cc_start: 0.8544 (m-30) cc_final: 0.8237 (m-30) REVERT: A 1958 GLU cc_start: 0.6332 (tm-30) cc_final: 0.5835 (tm-30) REVERT: A 2042 GLU cc_start: 0.7597 (mp0) cc_final: 0.7296 (mp0) REVERT: A 2082 MET cc_start: 0.7744 (tpp) cc_final: 0.7363 (tpp) REVERT: A 2232 GLU cc_start: 0.7891 (pm20) cc_final: 0.7644 (pm20) REVERT: A 2234 ASP cc_start: 0.8765 (m-30) cc_final: 0.8326 (m-30) REVERT: A 2242 ASP cc_start: 0.7521 (t0) cc_final: 0.7291 (t0) REVERT: A 2260 LEU cc_start: 0.7293 (OUTLIER) cc_final: 0.7059 (mm) REVERT: A 2638 MET cc_start: 0.7615 (OUTLIER) cc_final: 0.7345 (ptt) REVERT: B 535 MET cc_start: 0.5926 (mmm) cc_final: 0.4414 (mtp) REVERT: B 604 LYS cc_start: 0.8438 (mmtm) cc_final: 0.8216 (mmmt) REVERT: B 968 MET cc_start: 0.7647 (ttt) cc_final: 0.6642 (tpp) REVERT: B 1331 MET cc_start: 0.3260 (mpp) cc_final: 0.0652 (tpt) REVERT: B 1423 TYR cc_start: 0.6665 (m-80) cc_final: 0.6424 (m-80) REVERT: B 1484 MET cc_start: 0.5189 (mtt) cc_final: 0.4892 (mtp) REVERT: B 1862 ASP cc_start: 0.8544 (m-30) cc_final: 0.8237 (m-30) REVERT: B 1958 GLU cc_start: 0.6336 (tm-30) cc_final: 0.5837 (tm-30) REVERT: B 2042 GLU cc_start: 0.7577 (mp0) cc_final: 0.7262 (mp0) REVERT: B 2082 MET cc_start: 0.7719 (tpp) cc_final: 0.7336 (tpp) REVERT: B 2234 ASP cc_start: 0.8744 (m-30) cc_final: 0.8298 (m-30) REVERT: B 2260 LEU cc_start: 0.7295 (OUTLIER) cc_final: 0.7064 (mm) REVERT: C 535 MET cc_start: 0.5927 (mmm) cc_final: 0.4424 (mtp) REVERT: C 600 HIS cc_start: 0.6760 (OUTLIER) cc_final: 0.6176 (t70) REVERT: C 604 LYS cc_start: 0.8450 (mmtm) cc_final: 0.8227 (mmmt) REVERT: C 968 MET cc_start: 0.7971 (ttt) cc_final: 0.6980 (mmm) REVERT: C 1329 MET cc_start: 0.2723 (ttt) cc_final: 0.2494 (ttp) REVERT: C 1331 MET cc_start: 0.3250 (mpp) cc_final: 0.0580 (tpt) REVERT: C 1423 TYR cc_start: 0.6662 (m-80) cc_final: 0.6420 (m-80) REVERT: C 1484 MET cc_start: 0.5185 (mtt) cc_final: 0.4888 (mtp) REVERT: C 1862 ASP cc_start: 0.8544 (m-30) cc_final: 0.8236 (m-30) REVERT: C 1958 GLU cc_start: 0.6341 (tm-30) cc_final: 0.5845 (tm-30) REVERT: C 2042 GLU cc_start: 0.7592 (mp0) cc_final: 0.7296 (mp0) REVERT: C 2082 MET cc_start: 0.7719 (tpp) cc_final: 0.7340 (tpp) REVERT: C 2234 ASP cc_start: 0.8742 (m-30) cc_final: 0.8295 (m-30) REVERT: C 2260 LEU cc_start: 0.7296 (OUTLIER) cc_final: 0.7061 (mm) REVERT: C 2638 MET cc_start: 0.7617 (OUTLIER) cc_final: 0.7347 (ptt) REVERT: D 535 MET cc_start: 0.5923 (mmm) cc_final: 0.4425 (mtp) REVERT: D 604 LYS cc_start: 0.8434 (mmtm) cc_final: 0.8215 (mmmt) REVERT: D 968 MET cc_start: 0.7627 (ttt) cc_final: 0.6635 (tpp) REVERT: D 1331 MET cc_start: 0.3252 (mpp) cc_final: 0.0636 (tpt) REVERT: D 1423 TYR cc_start: 0.6663 (m-80) cc_final: 0.6435 (m-80) REVERT: D 1484 MET cc_start: 0.5184 (mtt) cc_final: 0.4889 (mtp) REVERT: D 1862 ASP cc_start: 0.8561 (m-30) cc_final: 0.8252 (m-30) REVERT: D 1958 GLU cc_start: 0.6337 (tm-30) cc_final: 0.5844 (tm-30) REVERT: D 2042 GLU cc_start: 0.7596 (mp0) cc_final: 0.7295 (mp0) REVERT: D 2082 MET cc_start: 0.7719 (tpp) cc_final: 0.7338 (tpp) REVERT: D 2234 ASP cc_start: 0.8745 (m-30) cc_final: 0.8300 (m-30) REVERT: D 2260 LEU cc_start: 0.7298 (OUTLIER) cc_final: 0.7064 (mm) outliers start: 124 outliers final: 92 residues processed: 876 average time/residue: 0.7161 time to fit residues: 1085.2929 Evaluate side-chains 863 residues out of total 8636 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 99 poor density : 764 time to evaluate : 6.726 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 CYS Chi-restraints excluded: chain A residue 115 ILE Chi-restraints excluded: chain A residue 289 HIS Chi-restraints excluded: chain A residue 394 CYS Chi-restraints excluded: chain A residue 666 ILE Chi-restraints excluded: chain A residue 765 LEU Chi-restraints excluded: chain A residue 767 CYS Chi-restraints excluded: chain A residue 842 GLU Chi-restraints excluded: chain A residue 994 LEU Chi-restraints excluded: chain A residue 1053 ASP Chi-restraints excluded: chain A residue 1100 VAL Chi-restraints excluded: chain A residue 1627 VAL Chi-restraints excluded: chain A residue 1631 HIS Chi-restraints excluded: chain A residue 1959 MET Chi-restraints excluded: chain A residue 2023 LEU Chi-restraints excluded: chain A residue 2033 ILE Chi-restraints excluded: chain A residue 2087 GLU Chi-restraints excluded: chain A residue 2260 LEU Chi-restraints excluded: chain A residue 2286 LEU Chi-restraints excluded: chain A residue 2419 ASP Chi-restraints excluded: chain A residue 2426 THR Chi-restraints excluded: chain A residue 2552 VAL Chi-restraints excluded: chain A residue 2638 MET Chi-restraints excluded: chain A residue 2723 MET Chi-restraints excluded: chain B residue 61 CYS Chi-restraints excluded: chain B residue 115 ILE Chi-restraints excluded: chain B residue 133 THR Chi-restraints excluded: chain B residue 394 CYS Chi-restraints excluded: chain B residue 666 ILE Chi-restraints excluded: chain B residue 765 LEU Chi-restraints excluded: chain B residue 767 CYS Chi-restraints excluded: chain B residue 803 TYR Chi-restraints excluded: chain B residue 842 GLU Chi-restraints excluded: chain B residue 994 LEU Chi-restraints excluded: chain B residue 1053 ASP Chi-restraints excluded: chain B residue 1100 VAL Chi-restraints excluded: chain B residue 1627 VAL Chi-restraints excluded: chain B residue 1631 HIS Chi-restraints excluded: chain B residue 1959 MET Chi-restraints excluded: chain B residue 2023 LEU Chi-restraints excluded: chain B residue 2033 ILE Chi-restraints excluded: chain B residue 2087 GLU Chi-restraints excluded: chain B residue 2260 LEU Chi-restraints excluded: chain B residue 2286 LEU Chi-restraints excluded: chain B residue 2419 ASP Chi-restraints excluded: chain B residue 2426 THR Chi-restraints excluded: chain B residue 2552 VAL Chi-restraints excluded: chain B residue 2673 ASP Chi-restraints excluded: chain B residue 2723 MET Chi-restraints excluded: chain C residue 61 CYS Chi-restraints excluded: chain C residue 115 ILE Chi-restraints excluded: chain C residue 289 HIS Chi-restraints excluded: chain C residue 394 CYS Chi-restraints excluded: chain C residue 600 HIS Chi-restraints excluded: chain C residue 666 ILE Chi-restraints excluded: chain C residue 765 LEU Chi-restraints excluded: chain C residue 767 CYS Chi-restraints excluded: chain C residue 842 GLU Chi-restraints excluded: chain C residue 994 LEU Chi-restraints excluded: chain C residue 1053 ASP Chi-restraints excluded: chain C residue 1100 VAL Chi-restraints excluded: chain C residue 1627 VAL Chi-restraints excluded: chain C residue 1631 HIS Chi-restraints excluded: chain C residue 1959 MET Chi-restraints excluded: chain C residue 2023 LEU Chi-restraints excluded: chain C residue 2033 ILE Chi-restraints excluded: chain C residue 2087 GLU Chi-restraints excluded: chain C residue 2260 LEU Chi-restraints excluded: chain C residue 2286 LEU Chi-restraints excluded: chain C residue 2419 ASP Chi-restraints excluded: chain C residue 2426 THR Chi-restraints excluded: chain C residue 2552 VAL Chi-restraints excluded: chain C residue 2638 MET Chi-restraints excluded: chain C residue 2723 MET Chi-restraints excluded: chain D residue 61 CYS Chi-restraints excluded: chain D residue 115 ILE Chi-restraints excluded: chain D residue 133 THR Chi-restraints excluded: chain D residue 289 HIS Chi-restraints excluded: chain D residue 394 CYS Chi-restraints excluded: chain D residue 666 ILE Chi-restraints excluded: chain D residue 765 LEU Chi-restraints excluded: chain D residue 767 CYS Chi-restraints excluded: chain D residue 842 GLU Chi-restraints excluded: chain D residue 994 LEU Chi-restraints excluded: chain D residue 1053 ASP Chi-restraints excluded: chain D residue 1100 VAL Chi-restraints excluded: chain D residue 1375 HIS Chi-restraints excluded: chain D residue 1627 VAL Chi-restraints excluded: chain D residue 1631 HIS Chi-restraints excluded: chain D residue 1959 MET Chi-restraints excluded: chain D residue 2023 LEU Chi-restraints excluded: chain D residue 2033 ILE Chi-restraints excluded: chain D residue 2087 GLU Chi-restraints excluded: chain D residue 2260 LEU Chi-restraints excluded: chain D residue 2286 LEU Chi-restraints excluded: chain D residue 2419 ASP Chi-restraints excluded: chain D residue 2426 THR Chi-restraints excluded: chain D residue 2552 VAL Chi-restraints excluded: chain D residue 2723 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 952 random chunks: chunk 567 optimal weight: 3.9990 chunk 366 optimal weight: 30.0000 chunk 548 optimal weight: 0.0030 chunk 276 optimal weight: 3.9990 chunk 180 optimal weight: 2.9990 chunk 177 optimal weight: 4.9990 chunk 583 optimal weight: 5.9990 chunk 625 optimal weight: 5.9990 chunk 453 optimal weight: 4.9990 chunk 85 optimal weight: 7.9990 chunk 721 optimal weight: 20.0000 overall best weight: 3.1998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 69 GLN A 544 GLN ** A 850 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 868 ASN ** A1202 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1238 HIS ** A1280 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1375 HIS ** A1981 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2035 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2207 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2409 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2583 ASN A ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2715 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 524 GLN B 544 GLN ** B 850 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 868 ASN ** B1202 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1238 HIS ** B1280 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1375 HIS ** B1981 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2035 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2207 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2409 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2583 ASN A ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2715 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 544 GLN C 600 HIS ** C 850 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1202 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1238 HIS ** C1280 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1375 HIS ** C1981 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2035 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2207 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2409 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2583 ASN A ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2715 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 544 GLN ** D 850 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1202 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1238 HIS ** D1280 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D1375 HIS D1412 HIS ** D1981 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2035 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2207 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2409 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2583 ASN A ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2715 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6859 moved from start: 0.2858 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 79896 Z= 0.274 Angle : 0.632 13.104 107776 Z= 0.319 Chirality : 0.042 0.248 12056 Planarity : 0.004 0.058 13652 Dihedral : 11.304 162.167 11780 Min Nonbonded Distance : 2.119 Molprobity Statistics. All-atom Clashscore : 14.59 Ramachandran Plot: Outliers : 0.24 % Allowed : 4.89 % Favored : 94.87 % Rotamer: Outliers : 1.34 % Allowed : 15.33 % Favored : 83.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.29 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: -0.55 (0.09), residues: 9484 helix: 0.18 (0.07), residues: 5488 sheet: -0.86 (0.22), residues: 568 loop : -1.00 (0.11), residues: 3428 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C2256 HIS 0.010 0.001 HIS D1375 PHE 0.044 0.002 PHE B1372 TYR 0.024 0.002 TYR D2398 ARG 0.004 0.000 ARG A2670 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 18968 Ramachandran restraints generated. 9484 Oldfield, 0 Emsley, 9484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 18968 Ramachandran restraints generated. 9484 Oldfield, 0 Emsley, 9484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 889 residues out of total 8636 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 112 poor density : 777 time to evaluate : 6.996 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: A 481 VAL cc_start: 0.7785 (t) cc_final: 0.7572 (m) REVERT: A 535 MET cc_start: 0.5613 (mmm) cc_final: 0.4231 (mtp) REVERT: A 572 GLU cc_start: 0.5800 (OUTLIER) cc_final: 0.5222 (mt-10) REVERT: A 604 LYS cc_start: 0.8439 (mmtm) cc_final: 0.8230 (mmmt) REVERT: A 842 GLU cc_start: 0.7666 (OUTLIER) cc_final: 0.7403 (pm20) REVERT: A 968 MET cc_start: 0.7962 (ttt) cc_final: 0.7324 (mmp) REVERT: A 1331 MET cc_start: 0.3473 (mpp) cc_final: 0.0865 (tpp) REVERT: A 1423 TYR cc_start: 0.6665 (m-80) cc_final: 0.6418 (m-80) REVERT: A 1484 MET cc_start: 0.5161 (mtt) cc_final: 0.4872 (mtp) REVERT: A 1862 ASP cc_start: 0.8557 (m-30) cc_final: 0.8234 (m-30) REVERT: A 1958 GLU cc_start: 0.6330 (tm-30) cc_final: 0.5835 (tm-30) REVERT: A 2042 GLU cc_start: 0.7515 (mp0) cc_final: 0.7251 (mp0) REVERT: A 2210 PHE cc_start: 0.6518 (OUTLIER) cc_final: 0.6130 (p90) REVERT: A 2234 ASP cc_start: 0.8744 (m-30) cc_final: 0.8313 (m-30) REVERT: A 2260 LEU cc_start: 0.7405 (OUTLIER) cc_final: 0.7175 (mm) REVERT: B 535 MET cc_start: 0.5615 (mmm) cc_final: 0.4232 (mtp) REVERT: B 572 GLU cc_start: 0.5799 (OUTLIER) cc_final: 0.5211 (mt-10) REVERT: B 604 LYS cc_start: 0.8444 (mmtm) cc_final: 0.8233 (mmmt) REVERT: B 968 MET cc_start: 0.7714 (ttt) cc_final: 0.6706 (tpp) REVERT: B 1329 MET cc_start: 0.2628 (ttt) cc_final: 0.2418 (ttp) REVERT: B 1331 MET cc_start: 0.3233 (mpp) cc_final: 0.0701 (tpp) REVERT: B 1423 TYR cc_start: 0.6665 (m-80) cc_final: 0.6419 (m-80) REVERT: B 1484 MET cc_start: 0.5163 (mtt) cc_final: 0.4874 (mtp) REVERT: B 1862 ASP cc_start: 0.8557 (m-30) cc_final: 0.8234 (m-30) REVERT: B 1958 GLU cc_start: 0.6343 (tm-30) cc_final: 0.5842 (tm-30) REVERT: B 2042 GLU cc_start: 0.7514 (mp0) cc_final: 0.7251 (mp0) REVERT: B 2210 PHE cc_start: 0.6563 (OUTLIER) cc_final: 0.6150 (p90) REVERT: B 2234 ASP cc_start: 0.8726 (m-30) cc_final: 0.8284 (m-30) REVERT: B 2260 LEU cc_start: 0.7387 (OUTLIER) cc_final: 0.7165 (mm) REVERT: C 535 MET cc_start: 0.5615 (mmm) cc_final: 0.4233 (mtp) REVERT: C 572 GLU cc_start: 0.5802 (OUTLIER) cc_final: 0.5209 (mt-10) REVERT: C 604 LYS cc_start: 0.8466 (mmtm) cc_final: 0.8255 (mmmt) REVERT: C 842 GLU cc_start: 0.7673 (OUTLIER) cc_final: 0.7401 (pm20) REVERT: C 968 MET cc_start: 0.7996 (ttt) cc_final: 0.6987 (mmm) REVERT: C 1329 MET cc_start: 0.2695 (ttt) cc_final: 0.2478 (ttp) REVERT: C 1331 MET cc_start: 0.3217 (mpp) cc_final: 0.0696 (tpp) REVERT: C 1423 TYR cc_start: 0.6664 (m-80) cc_final: 0.6419 (m-80) REVERT: C 1484 MET cc_start: 0.5164 (mtt) cc_final: 0.4873 (mtp) REVERT: C 1862 ASP cc_start: 0.8555 (m-30) cc_final: 0.8233 (m-30) REVERT: C 1958 GLU cc_start: 0.6342 (tm-30) cc_final: 0.5842 (tm-30) REVERT: C 2042 GLU cc_start: 0.7510 (mp0) cc_final: 0.7248 (mp0) REVERT: C 2210 PHE cc_start: 0.6523 (OUTLIER) cc_final: 0.6134 (p90) REVERT: C 2234 ASP cc_start: 0.8729 (m-30) cc_final: 0.8289 (m-30) REVERT: C 2260 LEU cc_start: 0.7386 (OUTLIER) cc_final: 0.7163 (mm) REVERT: D 535 MET cc_start: 0.5616 (mmm) cc_final: 0.4236 (mtp) REVERT: D 604 LYS cc_start: 0.8440 (mmtm) cc_final: 0.8225 (mmmt) REVERT: D 968 MET cc_start: 0.7690 (ttt) cc_final: 0.6718 (tpp) REVERT: D 1329 MET cc_start: 0.2692 (ttt) cc_final: 0.2473 (ttp) REVERT: D 1331 MET cc_start: 0.3486 (mpp) cc_final: 0.0779 (tpt) REVERT: D 1423 TYR cc_start: 0.6641 (m-80) cc_final: 0.6153 (m-80) REVERT: D 1484 MET cc_start: 0.5164 (mtt) cc_final: 0.4874 (mtp) REVERT: D 1862 ASP cc_start: 0.8558 (m-30) cc_final: 0.8235 (m-30) REVERT: D 1958 GLU cc_start: 0.6362 (tm-30) cc_final: 0.5862 (tm-30) REVERT: D 2042 GLU cc_start: 0.7517 (mp0) cc_final: 0.7251 (mp0) REVERT: D 2210 PHE cc_start: 0.6565 (OUTLIER) cc_final: 0.6153 (p90) REVERT: D 2234 ASP cc_start: 0.8725 (m-30) cc_final: 0.8284 (m-30) REVERT: D 2260 LEU cc_start: 0.7386 (OUTLIER) cc_final: 0.7163 (mm) outliers start: 112 outliers final: 95 residues processed: 851 average time/residue: 0.7234 time to fit residues: 1069.5702 Evaluate side-chains 865 residues out of total 8636 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 108 poor density : 757 time to evaluate : 7.018 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 CYS Chi-restraints excluded: chain A residue 115 ILE Chi-restraints excluded: chain A residue 133 THR Chi-restraints excluded: chain A residue 289 HIS Chi-restraints excluded: chain A residue 394 CYS Chi-restraints excluded: chain A residue 415 MET Chi-restraints excluded: chain A residue 544 GLN Chi-restraints excluded: chain A residue 572 GLU Chi-restraints excluded: chain A residue 666 ILE Chi-restraints excluded: chain A residue 765 LEU Chi-restraints excluded: chain A residue 767 CYS Chi-restraints excluded: chain A residue 842 GLU Chi-restraints excluded: chain A residue 994 LEU Chi-restraints excluded: chain A residue 1053 ASP Chi-restraints excluded: chain A residue 1100 VAL Chi-restraints excluded: chain A residue 1627 VAL Chi-restraints excluded: chain A residue 1631 HIS Chi-restraints excluded: chain A residue 1959 MET Chi-restraints excluded: chain A residue 2023 LEU Chi-restraints excluded: chain A residue 2033 ILE Chi-restraints excluded: chain A residue 2087 GLU Chi-restraints excluded: chain A residue 2210 PHE Chi-restraints excluded: chain A residue 2260 LEU Chi-restraints excluded: chain A residue 2286 LEU Chi-restraints excluded: chain A residue 2419 ASP Chi-restraints excluded: chain A residue 2552 VAL Chi-restraints excluded: chain A residue 2723 MET Chi-restraints excluded: chain B residue 61 CYS Chi-restraints excluded: chain B residue 115 ILE Chi-restraints excluded: chain B residue 133 THR Chi-restraints excluded: chain B residue 289 HIS Chi-restraints excluded: chain B residue 394 CYS Chi-restraints excluded: chain B residue 415 MET Chi-restraints excluded: chain B residue 544 GLN Chi-restraints excluded: chain B residue 572 GLU Chi-restraints excluded: chain B residue 666 ILE Chi-restraints excluded: chain B residue 765 LEU Chi-restraints excluded: chain B residue 767 CYS Chi-restraints excluded: chain B residue 803 TYR Chi-restraints excluded: chain B residue 842 GLU Chi-restraints excluded: chain B residue 994 LEU Chi-restraints excluded: chain B residue 1053 ASP Chi-restraints excluded: chain B residue 1100 VAL Chi-restraints excluded: chain B residue 1627 VAL Chi-restraints excluded: chain B residue 1631 HIS Chi-restraints excluded: chain B residue 1959 MET Chi-restraints excluded: chain B residue 2023 LEU Chi-restraints excluded: chain B residue 2033 ILE Chi-restraints excluded: chain B residue 2087 GLU Chi-restraints excluded: chain B residue 2116 MET Chi-restraints excluded: chain B residue 2210 PHE Chi-restraints excluded: chain B residue 2260 LEU Chi-restraints excluded: chain B residue 2286 LEU Chi-restraints excluded: chain B residue 2419 ASP Chi-restraints excluded: chain B residue 2552 VAL Chi-restraints excluded: chain B residue 2673 ASP Chi-restraints excluded: chain C residue 61 CYS Chi-restraints excluded: chain C residue 115 ILE Chi-restraints excluded: chain C residue 133 THR Chi-restraints excluded: chain C residue 289 HIS Chi-restraints excluded: chain C residue 394 CYS Chi-restraints excluded: chain C residue 415 MET Chi-restraints excluded: chain C residue 544 GLN Chi-restraints excluded: chain C residue 572 GLU Chi-restraints excluded: chain C residue 666 ILE Chi-restraints excluded: chain C residue 765 LEU Chi-restraints excluded: chain C residue 767 CYS Chi-restraints excluded: chain C residue 842 GLU Chi-restraints excluded: chain C residue 994 LEU Chi-restraints excluded: chain C residue 1053 ASP Chi-restraints excluded: chain C residue 1100 VAL Chi-restraints excluded: chain C residue 1627 VAL Chi-restraints excluded: chain C residue 1631 HIS Chi-restraints excluded: chain C residue 1959 MET Chi-restraints excluded: chain C residue 2023 LEU Chi-restraints excluded: chain C residue 2033 ILE Chi-restraints excluded: chain C residue 2087 GLU Chi-restraints excluded: chain C residue 2210 PHE Chi-restraints excluded: chain C residue 2260 LEU Chi-restraints excluded: chain C residue 2286 LEU Chi-restraints excluded: chain C residue 2419 ASP Chi-restraints excluded: chain C residue 2552 VAL Chi-restraints excluded: chain C residue 2723 MET Chi-restraints excluded: chain D residue 61 CYS Chi-restraints excluded: chain D residue 115 ILE Chi-restraints excluded: chain D residue 133 THR Chi-restraints excluded: chain D residue 289 HIS Chi-restraints excluded: chain D residue 394 CYS Chi-restraints excluded: chain D residue 415 MET Chi-restraints excluded: chain D residue 544 GLN Chi-restraints excluded: chain D residue 666 ILE Chi-restraints excluded: chain D residue 765 LEU Chi-restraints excluded: chain D residue 767 CYS Chi-restraints excluded: chain D residue 842 GLU Chi-restraints excluded: chain D residue 994 LEU Chi-restraints excluded: chain D residue 1053 ASP Chi-restraints excluded: chain D residue 1100 VAL Chi-restraints excluded: chain D residue 1627 VAL Chi-restraints excluded: chain D residue 1631 HIS Chi-restraints excluded: chain D residue 1959 MET Chi-restraints excluded: chain D residue 2023 LEU Chi-restraints excluded: chain D residue 2033 ILE Chi-restraints excluded: chain D residue 2087 GLU Chi-restraints excluded: chain D residue 2210 PHE Chi-restraints excluded: chain D residue 2260 LEU Chi-restraints excluded: chain D residue 2286 LEU Chi-restraints excluded: chain D residue 2419 ASP Chi-restraints excluded: chain D residue 2552 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 952 random chunks: chunk 834 optimal weight: 1.9990 chunk 879 optimal weight: 0.9990 chunk 802 optimal weight: 7.9990 chunk 855 optimal weight: 40.0000 chunk 878 optimal weight: 9.9990 chunk 514 optimal weight: 0.0060 chunk 372 optimal weight: 0.0010 chunk 671 optimal weight: 5.9990 chunk 262 optimal weight: 3.9990 chunk 772 optimal weight: 7.9990 chunk 808 optimal weight: 2.9990 overall best weight: 1.2008 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 850 GLN A1238 HIS ** A1280 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1375 HIS ** A2035 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2207 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2409 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2583 ASN A ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2715 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 850 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 868 ASN ** B1202 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1238 HIS ** B1280 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1375 HIS ** B2035 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2207 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2409 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2583 ASN A ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2715 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 850 GLN C1238 HIS ** C1280 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1375 HIS ** C2035 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2207 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2409 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2583 ASN A ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2715 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 850 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1202 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1238 HIS ** D1280 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D1375 HIS D1412 HIS ** D2035 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2207 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2409 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2583 ASN A ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2715 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6805 moved from start: 0.2755 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 79896 Z= 0.168 Angle : 0.586 13.870 107776 Z= 0.291 Chirality : 0.040 0.225 12056 Planarity : 0.004 0.058 13652 Dihedral : 10.797 167.856 11780 Min Nonbonded Distance : 2.164 Molprobity Statistics. All-atom Clashscore : 12.59 Ramachandran Plot: Outliers : 0.23 % Allowed : 3.92 % Favored : 95.85 % Rotamer: Outliers : 0.98 % Allowed : 15.80 % Favored : 83.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.29 % 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: -0.17 (0.09), residues: 9484 helix: 0.52 (0.07), residues: 5496 sheet: -0.73 (0.22), residues: 564 loop : -0.92 (0.11), residues: 3424 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A2256 HIS 0.006 0.001 HIS D1659 PHE 0.041 0.001 PHE B1372 TYR 0.025 0.001 TYR A2453 ARG 0.006 0.000 ARG A 545 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 18968 Ramachandran restraints generated. 9484 Oldfield, 0 Emsley, 9484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 18968 Ramachandran restraints generated. 9484 Oldfield, 0 Emsley, 9484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 913 residues out of total 8636 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 81 poor density : 832 time to evaluate : 6.947 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: A 351 MET cc_start: 0.4204 (mmt) cc_final: 0.3904 (mmt) REVERT: A 572 GLU cc_start: 0.5838 (OUTLIER) cc_final: 0.5197 (mp0) REVERT: A 807 TRP cc_start: 0.4383 (t-100) cc_final: 0.3616 (t60) REVERT: A 842 GLU cc_start: 0.7671 (OUTLIER) cc_final: 0.7441 (pm20) REVERT: A 968 MET cc_start: 0.7935 (ttt) cc_final: 0.7248 (mmp) REVERT: A 1331 MET cc_start: 0.3916 (mpp) cc_final: 0.1247 (tpt) REVERT: A 1365 MET cc_start: 0.3160 (mmp) cc_final: 0.2177 (ttp) REVERT: A 1423 TYR cc_start: 0.6629 (m-80) cc_final: 0.6388 (m-80) REVERT: A 1484 MET cc_start: 0.5055 (mtt) cc_final: 0.4771 (mtp) REVERT: A 1862 ASP cc_start: 0.8380 (m-30) cc_final: 0.8046 (m-30) REVERT: A 1958 GLU cc_start: 0.6235 (tm-30) cc_final: 0.5750 (tm-30) REVERT: A 2042 GLU cc_start: 0.7316 (mp0) cc_final: 0.7036 (mp0) REVERT: A 2234 ASP cc_start: 0.8703 (m-30) cc_final: 0.8262 (m-30) REVERT: A 2260 LEU cc_start: 0.7430 (OUTLIER) cc_final: 0.7176 (mm) REVERT: A 2732 ARG cc_start: 0.7236 (tpm170) cc_final: 0.6726 (ttp-170) REVERT: B 572 GLU cc_start: 0.5841 (OUTLIER) cc_final: 0.5202 (mp0) REVERT: B 807 TRP cc_start: 0.4349 (t-100) cc_final: 0.3602 (t60) REVERT: B 842 GLU cc_start: 0.7584 (OUTLIER) cc_final: 0.7313 (pm20) REVERT: B 968 MET cc_start: 0.7795 (ttt) cc_final: 0.6755 (mmp) REVERT: B 1329 MET cc_start: 0.2333 (ttt) cc_final: 0.2111 (ttp) REVERT: B 1331 MET cc_start: 0.3438 (mpp) cc_final: 0.0898 (tpt) REVERT: B 1423 TYR cc_start: 0.6644 (m-80) cc_final: 0.6362 (m-80) REVERT: B 1484 MET cc_start: 0.5063 (mtt) cc_final: 0.4777 (mtp) REVERT: B 1682 MET cc_start: 0.6981 (mmm) cc_final: 0.6545 (mmm) REVERT: B 1683 MET cc_start: 0.7681 (OUTLIER) cc_final: 0.7376 (mmm) REVERT: B 1862 ASP cc_start: 0.8509 (m-30) cc_final: 0.8162 (m-30) REVERT: B 1958 GLU cc_start: 0.6241 (tm-30) cc_final: 0.5757 (tm-30) REVERT: B 2042 GLU cc_start: 0.7313 (mp0) cc_final: 0.7035 (mp0) REVERT: B 2234 ASP cc_start: 0.8722 (m-30) cc_final: 0.8263 (m-30) REVERT: B 2260 LEU cc_start: 0.7430 (OUTLIER) cc_final: 0.7178 (mm) REVERT: B 2732 ARG cc_start: 0.7238 (tpm170) cc_final: 0.6733 (ttp-170) REVERT: C 572 GLU cc_start: 0.5837 (OUTLIER) cc_final: 0.5198 (mp0) REVERT: C 604 LYS cc_start: 0.8515 (mmtm) cc_final: 0.8313 (mmmt) REVERT: C 842 GLU cc_start: 0.7719 (OUTLIER) cc_final: 0.7476 (pm20) REVERT: C 968 MET cc_start: 0.7850 (ttt) cc_final: 0.6979 (tpp) REVERT: C 1329 MET cc_start: 0.2530 (ttt) cc_final: 0.2321 (ttp) REVERT: C 1331 MET cc_start: 0.3932 (mpp) cc_final: 0.1261 (tpt) REVERT: C 1423 TYR cc_start: 0.6629 (m-80) cc_final: 0.6348 (m-80) REVERT: C 1484 MET cc_start: 0.5056 (mtt) cc_final: 0.4769 (mtp) REVERT: C 1682 MET cc_start: 0.7060 (mmm) cc_final: 0.6784 (mmm) REVERT: C 1862 ASP cc_start: 0.8507 (m-30) cc_final: 0.8163 (m-30) REVERT: C 1958 GLU cc_start: 0.6268 (tm-30) cc_final: 0.5761 (tm-30) REVERT: C 2042 GLU cc_start: 0.7311 (mp0) cc_final: 0.7035 (mp0) REVERT: C 2234 ASP cc_start: 0.8725 (m-30) cc_final: 0.8265 (m-30) REVERT: C 2260 LEU cc_start: 0.7430 (OUTLIER) cc_final: 0.7177 (mm) REVERT: C 2732 ARG cc_start: 0.7236 (tpm170) cc_final: 0.6723 (ttp-170) REVERT: D 842 GLU cc_start: 0.7580 (OUTLIER) cc_final: 0.7311 (pm20) REVERT: D 968 MET cc_start: 0.7782 (ttt) cc_final: 0.6753 (mmp) REVERT: D 1329 MET cc_start: 0.2545 (ttt) cc_final: 0.2326 (ttp) REVERT: D 1331 MET cc_start: 0.3927 (mpp) cc_final: 0.1257 (tpt) REVERT: D 1423 TYR cc_start: 0.6596 (m-80) cc_final: 0.6337 (m-80) REVERT: D 1484 MET cc_start: 0.5055 (mtt) cc_final: 0.4771 (mtp) REVERT: D 1655 LYS cc_start: 0.7876 (tptm) cc_final: 0.7676 (tptm) REVERT: D 1683 MET cc_start: 0.7670 (OUTLIER) cc_final: 0.7377 (mmm) REVERT: D 1862 ASP cc_start: 0.8382 (m-30) cc_final: 0.8046 (m-30) REVERT: D 1958 GLU cc_start: 0.6265 (tm-30) cc_final: 0.5758 (tm-30) REVERT: D 2042 GLU cc_start: 0.7312 (mp0) cc_final: 0.7033 (mp0) REVERT: D 2234 ASP cc_start: 0.8722 (m-30) cc_final: 0.8262 (m-30) REVERT: D 2260 LEU cc_start: 0.7430 (OUTLIER) cc_final: 0.7177 (mm) REVERT: D 2732 ARG cc_start: 0.7226 (tpm170) cc_final: 0.6737 (ttp-170) outliers start: 81 outliers final: 61 residues processed: 882 average time/residue: 0.7112 time to fit residues: 1084.8831 Evaluate side-chains 845 residues out of total 8636 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 74 poor density : 771 time to evaluate : 6.769 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 CYS Chi-restraints excluded: chain A residue 115 ILE Chi-restraints excluded: chain A residue 133 THR Chi-restraints excluded: chain A residue 289 HIS Chi-restraints excluded: chain A residue 394 CYS Chi-restraints excluded: chain A residue 415 MET Chi-restraints excluded: chain A residue 572 GLU Chi-restraints excluded: chain A residue 666 ILE Chi-restraints excluded: chain A residue 765 LEU Chi-restraints excluded: chain A residue 767 CYS Chi-restraints excluded: chain A residue 842 GLU Chi-restraints excluded: chain A residue 1053 ASP Chi-restraints excluded: chain A residue 1100 VAL Chi-restraints excluded: chain A residue 1627 VAL Chi-restraints excluded: chain A residue 2023 LEU Chi-restraints excluded: chain A residue 2087 GLU Chi-restraints excluded: chain A residue 2260 LEU Chi-restraints excluded: chain A residue 2426 THR Chi-restraints excluded: chain A residue 2552 VAL Chi-restraints excluded: chain B residue 61 CYS Chi-restraints excluded: chain B residue 289 HIS Chi-restraints excluded: chain B residue 394 CYS Chi-restraints excluded: chain B residue 415 MET Chi-restraints excluded: chain B residue 572 GLU Chi-restraints excluded: chain B residue 666 ILE Chi-restraints excluded: chain B residue 765 LEU Chi-restraints excluded: chain B residue 767 CYS Chi-restraints excluded: chain B residue 842 GLU Chi-restraints excluded: chain B residue 1053 ASP Chi-restraints excluded: chain B residue 1100 VAL Chi-restraints excluded: chain B residue 1627 VAL Chi-restraints excluded: chain B residue 1683 MET Chi-restraints excluded: chain B residue 2023 LEU Chi-restraints excluded: chain B residue 2087 GLU Chi-restraints excluded: chain B residue 2260 LEU Chi-restraints excluded: chain B residue 2419 ASP Chi-restraints excluded: chain B residue 2426 THR Chi-restraints excluded: chain B residue 2552 VAL Chi-restraints excluded: chain B residue 2673 ASP Chi-restraints excluded: chain C residue 61 CYS Chi-restraints excluded: chain C residue 115 ILE Chi-restraints excluded: chain C residue 289 HIS Chi-restraints excluded: chain C residue 394 CYS Chi-restraints excluded: chain C residue 415 MET Chi-restraints excluded: chain C residue 572 GLU Chi-restraints excluded: chain C residue 666 ILE Chi-restraints excluded: chain C residue 765 LEU Chi-restraints excluded: chain C residue 767 CYS Chi-restraints excluded: chain C residue 842 GLU Chi-restraints excluded: chain C residue 1053 ASP Chi-restraints excluded: chain C residue 1100 VAL Chi-restraints excluded: chain C residue 1627 VAL Chi-restraints excluded: chain C residue 2087 GLU Chi-restraints excluded: chain C residue 2260 LEU Chi-restraints excluded: chain C residue 2426 THR Chi-restraints excluded: chain C residue 2552 VAL Chi-restraints excluded: chain D residue 61 CYS Chi-restraints excluded: chain D residue 289 HIS Chi-restraints excluded: chain D residue 394 CYS Chi-restraints excluded: chain D residue 415 MET Chi-restraints excluded: chain D residue 666 ILE Chi-restraints excluded: chain D residue 765 LEU Chi-restraints excluded: chain D residue 767 CYS Chi-restraints excluded: chain D residue 842 GLU Chi-restraints excluded: chain D residue 994 LEU Chi-restraints excluded: chain D residue 1053 ASP Chi-restraints excluded: chain D residue 1100 VAL Chi-restraints excluded: chain D residue 1627 VAL Chi-restraints excluded: chain D residue 1683 MET Chi-restraints excluded: chain D residue 2087 GLU Chi-restraints excluded: chain D residue 2260 LEU Chi-restraints excluded: chain D residue 2419 ASP Chi-restraints excluded: chain D residue 2426 THR Chi-restraints excluded: chain D residue 2552 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 952 random chunks: chunk 852 optimal weight: 8.9990 chunk 561 optimal weight: 6.9990 chunk 904 optimal weight: 0.5980 chunk 551 optimal weight: 8.9990 chunk 428 optimal weight: 0.0370 chunk 628 optimal weight: 7.9990 chunk 948 optimal weight: 4.9990 chunk 872 optimal weight: 6.9990 chunk 755 optimal weight: 7.9990 chunk 78 optimal weight: 0.7980 chunk 583 optimal weight: 0.0050 overall best weight: 1.2874 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 518 GLN A 600 HIS A1032 HIS A1238 HIS ** A1280 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1375 HIS ** A2035 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2207 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2409 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2583 ASN A ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2715 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 518 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 600 HIS B 850 GLN B1032 HIS ** B1202 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1238 HIS ** B1280 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1368 ASN B1375 HIS ** B2035 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B2104 HIS ** B2207 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2409 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2583 ASN A ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2715 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 518 GLN C1238 HIS ** C1280 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1368 ASN C1375 HIS ** C2035 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2207 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2409 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2583 ASN A ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2715 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 518 GLN D 850 GLN ** D1202 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1238 HIS ** D1280 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D1375 HIS D1412 HIS ** D2035 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D2104 HIS ** D2207 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2409 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2583 ASN A ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2715 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6804 moved from start: 0.2787 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 79896 Z= 0.173 Angle : 0.597 14.920 107776 Z= 0.296 Chirality : 0.040 0.355 12056 Planarity : 0.004 0.058 13652 Dihedral : 10.648 169.398 11780 Min Nonbonded Distance : 2.162 Molprobity Statistics. All-atom Clashscore : 12.84 Ramachandran Plot: Outliers : 0.23 % Allowed : 4.07 % Favored : 95.70 % Rotamer: Outliers : 1.04 % Allowed : 16.02 % Favored : 82.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.29 % 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: -0.05 (0.09), residues: 9484 helix: 0.61 (0.07), residues: 5480 sheet: -0.68 (0.22), residues: 564 loop : -0.83 (0.11), residues: 3440 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.002 TRP C 218 HIS 0.011 0.001 HIS A 600 PHE 0.040 0.001 PHE C1372 TYR 0.026 0.001 TYR D2453 ARG 0.006 0.000 ARG A1206 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 18968 Ramachandran restraints generated. 9484 Oldfield, 0 Emsley, 9484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 18968 Ramachandran restraints generated. 9484 Oldfield, 0 Emsley, 9484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 880 residues out of total 8636 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 86 poor density : 794 time to evaluate : 7.040 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: A 351 MET cc_start: 0.4605 (mmt) cc_final: 0.4316 (mmt) REVERT: A 535 MET cc_start: 0.5727 (mmm) cc_final: 0.4343 (mtp) REVERT: A 572 GLU cc_start: 0.5795 (OUTLIER) cc_final: 0.5174 (mp0) REVERT: A 600 HIS cc_start: 0.6711 (OUTLIER) cc_final: 0.5989 (t70) REVERT: A 807 TRP cc_start: 0.4227 (t-100) cc_final: 0.3559 (t60) REVERT: A 838 GLU cc_start: 0.8492 (mt-10) cc_final: 0.7915 (mm-30) REVERT: A 842 GLU cc_start: 0.7523 (OUTLIER) cc_final: 0.7313 (pm20) REVERT: A 968 MET cc_start: 0.7929 (ttt) cc_final: 0.7239 (mmp) REVERT: A 1331 MET cc_start: 0.3898 (mpp) cc_final: 0.1256 (tpt) REVERT: A 1365 MET cc_start: 0.3419 (mmp) cc_final: 0.2409 (ttp) REVERT: A 1423 TYR cc_start: 0.6645 (m-80) cc_final: 0.6432 (m-80) REVERT: A 1484 MET cc_start: 0.4847 (mtt) cc_final: 0.4570 (mtp) REVERT: A 1862 ASP cc_start: 0.8400 (m-30) cc_final: 0.8096 (m-30) REVERT: A 1958 GLU cc_start: 0.6209 (tm-30) cc_final: 0.5727 (tm-30) REVERT: A 2042 GLU cc_start: 0.7319 (mp0) cc_final: 0.7052 (mp0) REVERT: A 2234 ASP cc_start: 0.8692 (m-30) cc_final: 0.8233 (m-30) REVERT: A 2242 ASP cc_start: 0.7103 (t0) cc_final: 0.6836 (t0) REVERT: A 2260 LEU cc_start: 0.7373 (OUTLIER) cc_final: 0.7151 (mm) REVERT: A 2555 LYS cc_start: 0.8638 (mptt) cc_final: 0.8410 (mmmt) REVERT: B 535 MET cc_start: 0.5840 (mmm) cc_final: 0.4432 (mtp) REVERT: B 572 GLU cc_start: 0.5802 (OUTLIER) cc_final: 0.5150 (mp0) REVERT: B 600 HIS cc_start: 0.6671 (OUTLIER) cc_final: 0.5957 (t70) REVERT: B 807 TRP cc_start: 0.4226 (t-100) cc_final: 0.3558 (t60) REVERT: B 842 GLU cc_start: 0.7612 (OUTLIER) cc_final: 0.7368 (pm20) REVERT: B 968 MET cc_start: 0.7835 (ttt) cc_final: 0.6630 (tpp) REVERT: B 1329 MET cc_start: 0.2405 (ttt) cc_final: 0.2203 (ttp) REVERT: B 1331 MET cc_start: 0.4017 (mpp) cc_final: 0.1412 (tpt) REVERT: B 1365 MET cc_start: 0.3418 (mmp) cc_final: 0.2417 (ttp) REVERT: B 1423 TYR cc_start: 0.6617 (m-80) cc_final: 0.6355 (m-80) REVERT: B 1484 MET cc_start: 0.4850 (mtt) cc_final: 0.4573 (mtp) REVERT: B 1682 MET cc_start: 0.6982 (mmm) cc_final: 0.6704 (mmm) REVERT: B 1683 MET cc_start: 0.7604 (OUTLIER) cc_final: 0.7284 (mmm) REVERT: B 1862 ASP cc_start: 0.8401 (m-30) cc_final: 0.8096 (m-30) REVERT: B 1958 GLU cc_start: 0.6229 (tm-30) cc_final: 0.5734 (tm-30) REVERT: B 2042 GLU cc_start: 0.7316 (mp0) cc_final: 0.7056 (mp0) REVERT: B 2234 ASP cc_start: 0.8713 (m-30) cc_final: 0.8242 (m-30) REVERT: B 2260 LEU cc_start: 0.7372 (OUTLIER) cc_final: 0.7153 (mm) REVERT: B 2555 LYS cc_start: 0.8621 (mptt) cc_final: 0.8375 (mmmt) REVERT: C 535 MET cc_start: 0.5842 (mmm) cc_final: 0.4441 (mtp) REVERT: C 572 GLU cc_start: 0.5796 (OUTLIER) cc_final: 0.5174 (mp0) REVERT: C 842 GLU cc_start: 0.7544 (OUTLIER) cc_final: 0.7327 (pm20) REVERT: C 968 MET cc_start: 0.7891 (ttt) cc_final: 0.7097 (mmp) REVERT: C 1329 MET cc_start: 0.2270 (ttt) cc_final: 0.2052 (ttp) REVERT: C 1331 MET cc_start: 0.3913 (mpp) cc_final: 0.1260 (tpt) REVERT: C 1365 MET cc_start: 0.3305 (mmp) cc_final: 0.2356 (ttp) REVERT: C 1423 TYR cc_start: 0.6616 (m-80) cc_final: 0.6355 (m-80) REVERT: C 1484 MET cc_start: 0.4847 (mtt) cc_final: 0.4570 (mtp) REVERT: C 1655 LYS cc_start: 0.7828 (tptm) cc_final: 0.7626 (tptm) REVERT: C 1682 MET cc_start: 0.7115 (mmm) cc_final: 0.6751 (mmm) REVERT: C 1862 ASP cc_start: 0.8402 (m-30) cc_final: 0.8097 (m-30) REVERT: C 1958 GLU cc_start: 0.6237 (tm-30) cc_final: 0.5746 (tm-30) REVERT: C 2042 GLU cc_start: 0.7312 (mp0) cc_final: 0.7046 (mp0) REVERT: C 2234 ASP cc_start: 0.8715 (m-30) cc_final: 0.8246 (m-30) REVERT: C 2260 LEU cc_start: 0.7372 (OUTLIER) cc_final: 0.7152 (mm) REVERT: C 2555 LYS cc_start: 0.8638 (mptt) cc_final: 0.8412 (mmmt) REVERT: D 535 MET cc_start: 0.5724 (mmm) cc_final: 0.4343 (mtp) REVERT: D 572 GLU cc_start: 0.5801 (OUTLIER) cc_final: 0.5220 (mt-10) REVERT: D 842 GLU cc_start: 0.7631 (OUTLIER) cc_final: 0.7375 (pm20) REVERT: D 968 MET cc_start: 0.7819 (ttt) cc_final: 0.6632 (tpp) REVERT: D 1329 MET cc_start: 0.2344 (ttt) cc_final: 0.2127 (ttp) REVERT: D 1331 MET cc_start: 0.3905 (mpp) cc_final: 0.1264 (tpt) REVERT: D 1365 MET cc_start: 0.3314 (mmp) cc_final: 0.2361 (ttp) REVERT: D 1423 TYR cc_start: 0.6623 (m-80) cc_final: 0.6338 (m-80) REVERT: D 1484 MET cc_start: 0.4848 (mtt) cc_final: 0.4571 (mtp) REVERT: D 1683 MET cc_start: 0.7592 (OUTLIER) cc_final: 0.7321 (mmm) REVERT: D 1862 ASP cc_start: 0.8401 (m-30) cc_final: 0.8093 (m-30) REVERT: D 1958 GLU cc_start: 0.6234 (tm-30) cc_final: 0.5742 (tm-30) REVERT: D 2042 GLU cc_start: 0.7316 (mp0) cc_final: 0.7054 (mp0) REVERT: D 2234 ASP cc_start: 0.8714 (m-30) cc_final: 0.8245 (m-30) REVERT: D 2260 LEU cc_start: 0.7373 (OUTLIER) cc_final: 0.7153 (mm) REVERT: D 2555 LYS cc_start: 0.8607 (mptt) cc_final: 0.8353 (mmmt) outliers start: 86 outliers final: 59 residues processed: 845 average time/residue: 0.7259 time to fit residues: 1065.2167 Evaluate side-chains 848 residues out of total 8636 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 75 poor density : 773 time to evaluate : 6.781 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 CYS Chi-restraints excluded: chain A residue 289 HIS Chi-restraints excluded: chain A residue 394 CYS Chi-restraints excluded: chain A residue 415 MET Chi-restraints excluded: chain A residue 572 GLU Chi-restraints excluded: chain A residue 600 HIS Chi-restraints excluded: chain A residue 666 ILE Chi-restraints excluded: chain A residue 765 LEU Chi-restraints excluded: chain A residue 767 CYS Chi-restraints excluded: chain A residue 842 GLU Chi-restraints excluded: chain A residue 1053 ASP Chi-restraints excluded: chain A residue 1100 VAL Chi-restraints excluded: chain A residue 1627 VAL Chi-restraints excluded: chain A residue 2023 LEU Chi-restraints excluded: chain A residue 2087 GLU Chi-restraints excluded: chain A residue 2260 LEU Chi-restraints excluded: chain A residue 2426 THR Chi-restraints excluded: chain A residue 2552 VAL Chi-restraints excluded: chain B residue 61 CYS Chi-restraints excluded: chain B residue 289 HIS Chi-restraints excluded: chain B residue 394 CYS Chi-restraints excluded: chain B residue 415 MET Chi-restraints excluded: chain B residue 572 GLU Chi-restraints excluded: chain B residue 600 HIS Chi-restraints excluded: chain B residue 666 ILE Chi-restraints excluded: chain B residue 765 LEU Chi-restraints excluded: chain B residue 767 CYS Chi-restraints excluded: chain B residue 842 GLU Chi-restraints excluded: chain B residue 1053 ASP Chi-restraints excluded: chain B residue 1100 VAL Chi-restraints excluded: chain B residue 1627 VAL Chi-restraints excluded: chain B residue 1683 MET Chi-restraints excluded: chain B residue 2023 LEU Chi-restraints excluded: chain B residue 2087 GLU Chi-restraints excluded: chain B residue 2260 LEU Chi-restraints excluded: chain B residue 2419 ASP Chi-restraints excluded: chain B residue 2426 THR Chi-restraints excluded: chain B residue 2552 VAL Chi-restraints excluded: chain B residue 2673 ASP Chi-restraints excluded: chain C residue 61 CYS Chi-restraints excluded: chain C residue 289 HIS Chi-restraints excluded: chain C residue 394 CYS Chi-restraints excluded: chain C residue 415 MET Chi-restraints excluded: chain C residue 572 GLU Chi-restraints excluded: chain C residue 666 ILE Chi-restraints excluded: chain C residue 765 LEU Chi-restraints excluded: chain C residue 767 CYS Chi-restraints excluded: chain C residue 842 GLU Chi-restraints excluded: chain C residue 1053 ASP Chi-restraints excluded: chain C residue 1100 VAL Chi-restraints excluded: chain C residue 1627 VAL Chi-restraints excluded: chain C residue 2087 GLU Chi-restraints excluded: chain C residue 2260 LEU Chi-restraints excluded: chain C residue 2426 THR Chi-restraints excluded: chain C residue 2552 VAL Chi-restraints excluded: chain D residue 61 CYS Chi-restraints excluded: chain D residue 289 HIS Chi-restraints excluded: chain D residue 394 CYS Chi-restraints excluded: chain D residue 415 MET Chi-restraints excluded: chain D residue 572 GLU Chi-restraints excluded: chain D residue 666 ILE Chi-restraints excluded: chain D residue 765 LEU Chi-restraints excluded: chain D residue 767 CYS Chi-restraints excluded: chain D residue 842 GLU Chi-restraints excluded: chain D residue 994 LEU Chi-restraints excluded: chain D residue 1053 ASP Chi-restraints excluded: chain D residue 1100 VAL Chi-restraints excluded: chain D residue 1627 VAL Chi-restraints excluded: chain D residue 1683 MET Chi-restraints excluded: chain D residue 2023 LEU Chi-restraints excluded: chain D residue 2087 GLU Chi-restraints excluded: chain D residue 2260 LEU Chi-restraints excluded: chain D residue 2419 ASP Chi-restraints excluded: chain D residue 2426 THR Chi-restraints excluded: chain D residue 2552 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 952 random chunks: chunk 463 optimal weight: 4.9990 chunk 599 optimal weight: 0.9980 chunk 804 optimal weight: 0.0970 chunk 231 optimal weight: 7.9990 chunk 696 optimal weight: 0.6980 chunk 111 optimal weight: 0.8980 chunk 209 optimal weight: 0.9980 chunk 756 optimal weight: 0.0470 chunk 316 optimal weight: 0.3980 chunk 776 optimal weight: 6.9990 chunk 95 optimal weight: 1.9990 overall best weight: 0.4276 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 600 HIS A1238 HIS ** A1280 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1368 ASN A1375 HIS ** A1398 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2035 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A2161 HIS ** A2207 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2409 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2583 ASN A ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2715 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 518 GLN B 600 HIS ** B1202 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1238 HIS ** B1280 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1375 HIS ** B2035 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B2161 HIS ** B2207 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2409 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2583 ASN A ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2715 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1238 HIS ** C1280 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1375 HIS ** C2035 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C2161 HIS ** C2207 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2409 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2583 ASN A ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2715 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 600 HIS ** D1202 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1238 HIS ** D1280 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D1368 ASN D1375 HIS D1412 HIS ** D2035 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2207 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2409 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2583 ASN A ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2715 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4428 r_free = 0.4428 target = 0.173599 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4129 r_free = 0.4129 target = 0.148871 restraints weight = 258251.323| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.4073 r_free = 0.4073 target = 0.145096 restraints weight = 284503.754| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.4058 r_free = 0.4058 target = 0.145082 restraints weight = 166305.338| |-----------------------------------------------------------------------------| r_work (final): 0.4085 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4084 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4084 r_free = 0.4084 target_work(ls_wunit_k1) = 0.145 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4084 r_free = 0.4084 target_work(ls_wunit_k1) = 0.145 | | occupancies: max = 1.00 min = 0.32 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.4084 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7019 moved from start: 0.2792 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.046 79896 Z= 0.149 Angle : 0.598 15.579 107776 Z= 0.293 Chirality : 0.039 0.341 12056 Planarity : 0.004 0.058 13652 Dihedral : 10.357 165.301 11780 Min Nonbonded Distance : 2.179 Molprobity Statistics. All-atom Clashscore : 12.02 Ramachandran Plot: Outliers : 0.19 % Allowed : 3.46 % Favored : 96.35 % Rotamer: Outliers : 0.72 % Allowed : 16.56 % Favored : 82.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.29 % 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: 0.12 (0.09), residues: 9484 helix: 0.79 (0.07), residues: 5440 sheet: -0.66 (0.24), residues: 488 loop : -0.81 (0.11), residues: 3556 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.001 TRP C 218 HIS 0.011 0.001 HIS D 600 PHE 0.040 0.001 PHE B1372 TYR 0.025 0.001 TYR C2453 ARG 0.005 0.000 ARG D1090 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 18581.66 seconds wall clock time: 328 minutes 13.90 seconds (19693.90 seconds total)