Starting phenix.real_space_refine on Sun Apr 14 09:50:36 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ss2_40741/04_2024/8ss2_40741_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ss2_40741/04_2024/8ss2_40741.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.58 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ss2_40741/04_2024/8ss2_40741.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ss2_40741/04_2024/8ss2_40741.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ss2_40741/04_2024/8ss2_40741_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ss2_40741/04_2024/8ss2_40741_updated.pdb" } resolution = 3.58 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 sd= 0.025 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: 6 Type Number sf(0) Gaussians P 20 5.49 5 S 166 5.16 5 C 20273 2.51 5 N 4965 2.21 5 O 5710 1.98 5 F 12 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 20": "NH1" <-> "NH2" Residue "A ARG 68": "NH1" <-> "NH2" Residue "A TYR 77": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 218": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 300": "NH1" <-> "NH2" Residue "A TYR 356": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 369": "NH1" <-> "NH2" Residue "A PHE 438": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 440": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 545": "NH1" <-> "NH2" Residue "A ARG 594": "NH1" <-> "NH2" Residue "A ARG 599": "NH1" <-> "NH2" Residue "A TYR 647": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 675": "NH1" <-> "NH2" Residue "A ARG 819": "NH1" <-> "NH2" Residue "A ARG 899": "NH1" <-> "NH2" Residue "A ARG 952": "NH1" <-> "NH2" Residue "A ARG 955": "NH1" <-> "NH2" Residue "A ARG 991": "NH1" <-> "NH2" Residue "A ARG 1031": "NH1" <-> "NH2" Residue "B PHE 41": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 77": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 109": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 198": "NH1" <-> "NH2" Residue "B TYR 220": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 356": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 450": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 517": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 594": "NH1" <-> "NH2" Residue "B ARG 628": "NH1" <-> "NH2" Residue "B ARG 660": "NH1" <-> "NH2" Residue "C ARG 20": "NH1" <-> "NH2" Residue "C ARG 68": "NH1" <-> "NH2" Residue "C TYR 77": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 218": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 300": "NH1" <-> "NH2" Residue "C TYR 356": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 369": "NH1" <-> "NH2" Residue "C PHE 438": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 440": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 545": "NH1" <-> "NH2" Residue "C ARG 594": "NH1" <-> "NH2" Residue "C ARG 599": "NH1" <-> "NH2" Residue "C TYR 647": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 675": "NH1" <-> "NH2" Residue "C ARG 819": "NH1" <-> "NH2" Residue "C ARG 899": "NH1" <-> "NH2" Residue "C ARG 952": "NH1" <-> "NH2" Residue "C ARG 955": "NH1" <-> "NH2" Residue "C ARG 991": "NH1" <-> "NH2" Residue "C ARG 1031": "NH1" <-> "NH2" Residue "D PHE 41": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 77": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 109": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 198": "NH1" <-> "NH2" Residue "D TYR 220": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 356": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 450": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 517": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 594": "NH1" <-> "NH2" Residue "D ARG 628": "NH1" <-> "NH2" Residue "D ARG 660": "NH1" <-> "NH2" Residue "E ARG 59": "NH1" <-> "NH2" Residue "E ARG 65": "NH1" <-> "NH2" Residue "F ARG 59": "NH1" <-> "NH2" Residue "F ARG 65": "NH1" <-> "NH2" Time to flip residues: 0.09s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 31146 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 7714 Number of conformers: 1 Conformer: "" Number of residues, atoms: 978, 7714 Classifications: {'peptide': 978} Link IDs: {'PCIS': 3, 'PTRANS': 24, 'TRANS': 950} Chain breaks: 4 Chain: "B" Number of atoms: 6177 Number of conformers: 1 Conformer: "" Number of residues, atoms: 783, 6177 Classifications: {'peptide': 783} Link IDs: {'PCIS': 4, 'PTRANS': 19, 'TRANS': 759} Chain breaks: 2 Chain: "C" Number of atoms: 7714 Number of conformers: 1 Conformer: "" Number of residues, atoms: 978, 7714 Classifications: {'peptide': 978} Link IDs: {'PCIS': 3, 'PTRANS': 24, 'TRANS': 950} Chain breaks: 4 Chain: "D" Number of atoms: 6177 Number of conformers: 1 Conformer: "" Number of residues, atoms: 783, 6177 Classifications: {'peptide': 783} Link IDs: {'PCIS': 4, 'PTRANS': 19, 'TRANS': 759} Chain breaks: 2 Chain: "E" Number of atoms: 1166 Number of conformers: 1 Conformer: "" Number of residues, atoms: 140, 1166 Classifications: {'peptide': 140} Link IDs: {'PTRANS': 3, 'TRANS': 136} Chain breaks: 1 Chain: "F" Number of atoms: 1166 Number of conformers: 1 Conformer: "" Number of residues, atoms: 140, 1166 Classifications: {'peptide': 140} Link IDs: {'PTRANS': 3, 'TRANS': 136} Chain breaks: 1 Chain: "A" Number of atoms: 313 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 313 Unusual residues: {'AJP': 1, 'CLR': 1, 'PCW': 7, 'SPD': 1, 'ZK1': 1} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 219 Unresolved non-hydrogen angles: 270 Unresolved non-hydrogen dihedrals: 263 Unresolved non-hydrogen chiralities: 23 Planarities with less than four sites: {'PCW:plan-1': 3, 'PCW:plan-2': 3, 'PCW:plan-3': 3, 'PCW:plan-4': 3} Unresolved non-hydrogen planarities: 43 Chain: "B" Number of atoms: 154 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 154 Unusual residues: {'PCW': 4, 'ZK1': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 89 Unresolved non-hydrogen angles: 98 Unresolved non-hydrogen dihedrals: 85 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PCW:plan-1': 1, 'PCW:plan-2': 2, 'PCW:plan-3': 1, 'PCW:plan-4': 1} Unresolved non-hydrogen planarities: 17 Chain: "C" Number of atoms: 303 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 303 Unusual residues: {'AJP': 1, 'CLR': 1, 'PCW': 7, 'ZK1': 1} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 219 Unresolved non-hydrogen angles: 270 Unresolved non-hydrogen dihedrals: 263 Unresolved non-hydrogen chiralities: 23 Planarities with less than four sites: {'PCW:plan-1': 3, 'PCW:plan-2': 3, 'PCW:plan-3': 3, 'PCW:plan-4': 3} Unresolved non-hydrogen planarities: 43 Chain: "D" Number of atoms: 154 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 154 Unusual residues: {'PCW': 4, 'ZK1': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 89 Unresolved non-hydrogen angles: 98 Unresolved non-hydrogen dihedrals: 85 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PCW:plan-1': 1, 'PCW:plan-2': 2, 'PCW:plan-3': 1, 'PCW:plan-4': 1} Unresolved non-hydrogen planarities: 17 Chain: "E" Number of atoms: 54 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 54 Unusual residues: {'PCW': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 54 Unresolved non-hydrogen angles: 63 Unresolved non-hydrogen dihedrals: 50 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PCW:plan-1': 1, 'PCW:plan-2': 1, 'PCW:plan-3': 1, 'PCW:plan-4': 1} Unresolved non-hydrogen planarities: 13 Chain: "F" Number of atoms: 54 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 54 Unusual residues: {'PCW': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 54 Unresolved non-hydrogen angles: 63 Unresolved non-hydrogen dihedrals: 50 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PCW:plan-1': 1, 'PCW:plan-2': 1, 'PCW:plan-3': 1, 'PCW:plan-4': 1} Unresolved non-hydrogen planarities: 13 Time building chain proxies: 16.74, per 1000 atoms: 0.54 Number of scatterers: 31146 At special positions: 0 Unit cell: (117.03, 163.51, 197.54, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 166 16.00 P 20 15.00 F 12 9.00 O 5710 8.00 N 4965 7.00 C 20273 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=10, symmetry=0 Simple disulfide: pdb=" SG CYS A 63 " - pdb=" SG CYS A 315 " distance=2.03 Simple disulfide: pdb=" SG CYS A 718 " - pdb=" SG CYS A 773 " distance=2.04 Simple disulfide: pdb=" SG CYS A 890 " - pdb=" SG CYS A 900 " distance=2.04 Simple disulfide: pdb=" SG CYS B 63 " - pdb=" SG CYS B 315 " distance=2.00 Simple disulfide: pdb=" SG CYS B 718 " - pdb=" SG CYS B 773 " distance=2.06 Simple disulfide: pdb=" SG CYS C 63 " - pdb=" SG CYS C 315 " distance=2.03 Simple disulfide: pdb=" SG CYS C 718 " - pdb=" SG CYS C 773 " distance=2.04 Simple disulfide: pdb=" SG CYS C 890 " - pdb=" SG CYS C 900 " distance=2.04 Simple disulfide: pdb=" SG CYS D 63 " - pdb=" SG CYS D 315 " distance=2.00 Simple disulfide: pdb=" SG CYS D 718 " - pdb=" SG CYS D 773 " distance=2.06 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 11.45 Conformation dependent library (CDL) restraints added in 5.6 seconds 7524 Ramachandran restraints generated. 3762 Oldfield, 0 Emsley, 3762 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7020 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 128 helices and 26 sheets defined 41.0% alpha, 4.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 7.51 Creating SS restraints... Processing helix chain 'A' and resid 23 through 33 removed outlier: 3.562A pdb=" N MET A 33 " --> pdb=" O PHE A 29 " (cutoff:3.500A) Processing helix chain 'A' and resid 55 through 66 Processing helix chain 'A' and resid 82 through 91 removed outlier: 3.582A pdb=" N SER A 87 " --> pdb=" O ASN A 83 " (cutoff:3.500A) Processing helix chain 'A' and resid 118 through 128 removed outlier: 3.788A pdb=" N LEU A 122 " --> pdb=" O LYS A 118 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N GLU A 126 " --> pdb=" O LEU A 122 " (cutoff:3.500A) Processing helix chain 'A' and resid 148 through 155 removed outlier: 4.082A pdb=" N ALA A 153 " --> pdb=" O VAL A 149 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N GLU A 155 " --> pdb=" O ASP A 151 " (cutoff:3.500A) Processing helix chain 'A' and resid 173 through 185 removed outlier: 3.926A pdb=" N TYR A 177 " --> pdb=" O LYS A 173 " (cutoff:3.500A) removed outlier: 4.614A pdb=" N ARG A 178 " --> pdb=" O ASP A 174 " (cutoff:3.500A) removed outlier: 4.433A pdb=" N GLN A 182 " --> pdb=" O ARG A 178 " (cutoff:3.500A) Processing helix chain 'A' and resid 198 through 210 removed outlier: 3.736A pdb=" N ASP A 203 " --> pdb=" O ASP A 199 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N THR A 210 " --> pdb=" O ASP A 206 " (cutoff:3.500A) Processing helix chain 'A' and resid 227 through 229 No H-bonds generated for 'chain 'A' and resid 227 through 229' Processing helix chain 'A' and resid 232 through 236 removed outlier: 3.704A pdb=" N GLN A 236 " --> pdb=" O LEU A 233 " (cutoff:3.500A) Processing helix chain 'A' and resid 253 through 263 removed outlier: 3.625A pdb=" N GLU A 260 " --> pdb=" O SER A 256 " (cutoff:3.500A) Processing helix chain 'A' and resid 280 through 299 removed outlier: 3.528A pdb=" N ASP A 287 " --> pdb=" O ALA A 283 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N VAL A 289 " --> pdb=" O THR A 285 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N GLN A 290 " --> pdb=" O TYR A 286 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N VAL A 291 " --> pdb=" O ASP A 287 " (cutoff:3.500A) Processing helix chain 'A' and resid 308 through 310 No H-bonds generated for 'chain 'A' and resid 308 through 310' Processing helix chain 'A' and resid 326 through 334 Processing helix chain 'A' and resid 418 through 420 No H-bonds generated for 'chain 'A' and resid 418 through 420' Processing helix chain 'A' and resid 424 through 433 removed outlier: 3.661A pdb=" N GLU A 431 " --> pdb=" O ASP A 427 " (cutoff:3.500A) Processing helix chain 'A' and resid 462 through 465 No H-bonds generated for 'chain 'A' and resid 462 through 465' Processing helix chain 'A' and resid 485 through 487 No H-bonds generated for 'chain 'A' and resid 485 through 487' Processing helix chain 'A' and resid 523 through 544 removed outlier: 3.659A pdb=" N CYS A 528 " --> pdb=" O GLU A 524 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N VAL A 530 " --> pdb=" O TRP A 526 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N VAL A 539 " --> pdb=" O GLY A 535 " (cutoff:3.500A) Processing helix chain 'A' and resid 573 through 576 No H-bonds generated for 'chain 'A' and resid 573 through 576' Processing helix chain 'A' and resid 581 through 584 No H-bonds generated for 'chain 'A' and resid 581 through 584' Processing helix chain 'A' and resid 601 through 614 removed outlier: 3.642A pdb=" N TRP A 606 " --> pdb=" O GLY A 602 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N ILE A 611 " --> pdb=" O PHE A 607 " (cutoff:3.500A) removed outlier: 4.151A pdb=" N ILE A 613 " --> pdb=" O THR A 609 " (cutoff:3.500A) Processing helix chain 'A' and resid 617 through 623 removed outlier: 4.673A pdb=" N ALA A 622 " --> pdb=" O ALA A 618 " (cutoff:3.500A) Processing helix chain 'A' and resid 637 through 640 No H-bonds generated for 'chain 'A' and resid 637 through 640' Processing helix chain 'A' and resid 654 through 660 removed outlier: 3.771A pdb=" N PHE A 659 " --> pdb=" O THR A 655 " (cutoff:3.500A) Processing helix chain 'A' and resid 666 through 675 removed outlier: 3.500A pdb=" N MET A 674 " --> pdb=" O MET A 670 " (cutoff:3.500A) Processing helix chain 'A' and resid 686 through 695 removed outlier: 3.567A pdb=" N VAL A 693 " --> pdb=" O GLY A 689 " (cutoff:3.500A) Processing helix chain 'A' and resid 706 through 713 removed outlier: 3.893A pdb=" N TYR A 711 " --> pdb=" O THR A 707 " (cutoff:3.500A) Processing helix chain 'A' and resid 744 through 750 Processing helix chain 'A' and resid 752 through 756 Processing helix chain 'A' and resid 758 through 766 removed outlier: 3.798A pdb=" N LYS A 763 " --> pdb=" O LEU A 759 " (cutoff:3.500A) Processing helix chain 'A' and resid 794 through 818 removed outlier: 3.534A pdb=" N LEU A 805 " --> pdb=" O GLY A 801 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N LYS A 817 " --> pdb=" O GLU A 813 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N SER A 818 " --> pdb=" O PHE A 814 " (cutoff:3.500A) Processing helix chain 'A' and resid 834 through 856 removed outlier: 3.788A pdb=" N THR A 838 " --> pdb=" O ARG A 834 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N SER A 842 " --> pdb=" O THR A 838 " (cutoff:3.500A) Processing helix chain 'A' and resid 929 through 951 Proline residue: A 932 - end of helix removed outlier: 3.723A pdb=" N PHE A 938 " --> pdb=" O SER A 935 " (cutoff:3.500A) removed outlier: 4.131A pdb=" N ILE A 941 " --> pdb=" O PHE A 938 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N GLY A 942 " --> pdb=" O MET A 939 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N ILE A 944 " --> pdb=" O ILE A 941 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N ASN A 947 " --> pdb=" O ILE A 944 " (cutoff:3.500A) removed outlier: 4.606A pdb=" N ILE A 948 " --> pdb=" O LEU A 945 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N GLY A 949 " --> pdb=" O SER A 946 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N ILE A 951 " --> pdb=" O ILE A 948 " (cutoff:3.500A) Processing helix chain 'A' and resid 959 through 985 removed outlier: 3.751A pdb=" N PHE A 965 " --> pdb=" O VAL A 961 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N GLY A 970 " --> pdb=" O PHE A 966 " (cutoff:3.500A) Processing helix chain 'A' and resid 1006 through 1034 removed outlier: 3.781A pdb=" N LEU A1015 " --> pdb=" O ALA A1011 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N GLY A1021 " --> pdb=" O THR A1017 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N MET A1029 " --> pdb=" O VAL A1025 " (cutoff:3.500A) removed outlier: 5.353A pdb=" N THR A1033 " --> pdb=" O MET A1029 " (cutoff:3.500A) Processing helix chain 'B' and resid 24 through 34 removed outlier: 4.324A pdb=" N VAL B 34 " --> pdb=" O ARG B 30 " (cutoff:3.500A) Processing helix chain 'B' and resid 55 through 67 removed outlier: 3.512A pdb=" N GLN B 65 " --> pdb=" O ALA B 61 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 91 removed outlier: 3.929A pdb=" N SER B 87 " --> pdb=" O ASN B 83 " (cutoff:3.500A) Processing helix chain 'B' and resid 117 through 128 removed outlier: 4.323A pdb=" N LEU B 121 " --> pdb=" O LYS B 118 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N SER B 123 " --> pdb=" O ALA B 120 " (cutoff:3.500A) removed outlier: 4.058A pdb=" N ILE B 125 " --> pdb=" O LEU B 122 " (cutoff:3.500A) Processing helix chain 'B' and resid 146 through 149 No H-bonds generated for 'chain 'B' and resid 146 through 149' Processing helix chain 'B' and resid 173 through 186 removed outlier: 3.817A pdb=" N ARG B 178 " --> pdb=" O ASP B 174 " (cutoff:3.500A) Processing helix chain 'B' and resid 198 through 209 Processing helix chain 'B' and resid 227 through 229 No H-bonds generated for 'chain 'B' and resid 227 through 229' Processing helix chain 'B' and resid 253 through 264 removed outlier: 3.606A pdb=" N ARG B 261 " --> pdb=" O LYS B 257 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N THR B 264 " --> pdb=" O GLU B 260 " (cutoff:3.500A) Processing helix chain 'B' and resid 280 through 300 removed outlier: 3.561A pdb=" N THR B 285 " --> pdb=" O THR B 281 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N GLN B 290 " --> pdb=" O TYR B 286 " (cutoff:3.500A) removed outlier: 5.117A pdb=" N PHE B 296 " --> pdb=" O MET B 292 " (cutoff:3.500A) Processing helix chain 'B' and resid 326 through 335 removed outlier: 3.592A pdb=" N ILE B 329 " --> pdb=" O GLY B 326 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N ARG B 331 " --> pdb=" O GLU B 328 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N LEU B 333 " --> pdb=" O GLU B 330 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N LYS B 334 " --> pdb=" O ARG B 331 " (cutoff:3.500A) Processing helix chain 'B' and resid 424 through 435 removed outlier: 3.788A pdb=" N LYS B 434 " --> pdb=" O ALA B 430 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N HIS B 435 " --> pdb=" O GLU B 431 " (cutoff:3.500A) Processing helix chain 'B' and resid 463 through 468 Processing helix chain 'B' and resid 483 through 486 No H-bonds generated for 'chain 'B' and resid 483 through 486' Processing helix chain 'B' and resid 526 through 545 removed outlier: 3.707A pdb=" N VAL B 530 " --> pdb=" O TRP B 526 " (cutoff:3.500A) Processing helix chain 'B' and resid 573 through 584 removed outlier: 3.574A pdb=" N LEU B 577 " --> pdb=" O ILE B 573 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N TRP B 578 " --> pdb=" O PHE B 574 " (cutoff:3.500A) Processing helix chain 'B' and resid 596 through 623 removed outlier: 3.633A pdb=" N ILE B 600 " --> pdb=" O LEU B 596 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N VAL B 601 " --> pdb=" O SER B 597 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N TRP B 606 " --> pdb=" O GLY B 602 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N PHE B 607 " --> pdb=" O GLY B 603 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N ILE B 611 " --> pdb=" O PHE B 607 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N SER B 614 " --> pdb=" O LEU B 610 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N ALA B 618 " --> pdb=" O SER B 614 " (cutoff:3.500A) Processing helix chain 'B' and resid 637 through 640 No H-bonds generated for 'chain 'B' and resid 637 through 640' Processing helix chain 'B' and resid 654 through 660 removed outlier: 4.304A pdb=" N PHE B 659 " --> pdb=" O THR B 655 " (cutoff:3.500A) removed outlier: 4.131A pdb=" N ARG B 660 " --> pdb=" O LYS B 656 " (cutoff:3.500A) Processing helix chain 'B' and resid 666 through 676 removed outlier: 3.558A pdb=" N TRP B 671 " --> pdb=" O PHE B 667 " (cutoff:3.500A) removed outlier: 4.114A pdb=" N MET B 674 " --> pdb=" O MET B 670 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N SER B 676 " --> pdb=" O THR B 672 " (cutoff:3.500A) Processing helix chain 'B' and resid 686 through 690 Processing helix chain 'B' and resid 706 through 712 removed outlier: 3.653A pdb=" N GLU B 710 " --> pdb=" O SER B 706 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N TYR B 711 " --> pdb=" O THR B 707 " (cutoff:3.500A) Processing helix chain 'B' and resid 743 through 755 removed outlier: 3.657A pdb=" N ASN B 747 " --> pdb=" O GLY B 743 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N LEU B 751 " --> pdb=" O ASN B 747 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N LYS B 752 " --> pdb=" O LEU B 748 " (cutoff:3.500A) Processing helix chain 'B' and resid 758 through 767 removed outlier: 4.051A pdb=" N LYS B 763 " --> pdb=" O LEU B 759 " (cutoff:3.500A) removed outlier: 4.092A pdb=" N TRP B 766 " --> pdb=" O LEU B 762 " (cutoff:3.500A) Processing helix chain 'B' and resid 793 through 816 removed outlier: 3.534A pdb=" N TYR B 797 " --> pdb=" O ALA B 793 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N ALA B 806 " --> pdb=" O GLY B 802 " (cutoff:3.500A) Processing helix chain 'C' and resid 23 through 33 removed outlier: 3.562A pdb=" N MET C 33 " --> pdb=" O PHE C 29 " (cutoff:3.500A) Processing helix chain 'C' and resid 55 through 66 Processing helix chain 'C' and resid 82 through 91 removed outlier: 3.582A pdb=" N SER C 87 " --> pdb=" O ASN C 83 " (cutoff:3.500A) Processing helix chain 'C' and resid 118 through 128 removed outlier: 3.789A pdb=" N LEU C 122 " --> pdb=" O LYS C 118 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N GLU C 126 " --> pdb=" O LEU C 122 " (cutoff:3.500A) Processing helix chain 'C' and resid 148 through 155 removed outlier: 4.082A pdb=" N ALA C 153 " --> pdb=" O VAL C 149 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N GLU C 155 " --> pdb=" O ASP C 151 " (cutoff:3.500A) Processing helix chain 'C' and resid 173 through 185 removed outlier: 3.926A pdb=" N TYR C 177 " --> pdb=" O LYS C 173 " (cutoff:3.500A) removed outlier: 4.613A pdb=" N ARG C 178 " --> pdb=" O ASP C 174 " (cutoff:3.500A) removed outlier: 4.434A pdb=" N GLN C 182 " --> pdb=" O ARG C 178 " (cutoff:3.500A) Processing helix chain 'C' and resid 198 through 210 removed outlier: 3.735A pdb=" N ASP C 203 " --> pdb=" O ASP C 199 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N THR C 210 " --> pdb=" O ASP C 206 " (cutoff:3.500A) Processing helix chain 'C' and resid 227 through 229 No H-bonds generated for 'chain 'C' and resid 227 through 229' Processing helix chain 'C' and resid 232 through 236 removed outlier: 3.704A pdb=" N GLN C 236 " --> pdb=" O LEU C 233 " (cutoff:3.500A) Processing helix chain 'C' and resid 253 through 263 removed outlier: 3.625A pdb=" N GLU C 260 " --> pdb=" O SER C 256 " (cutoff:3.500A) Processing helix chain 'C' and resid 280 through 299 removed outlier: 3.528A pdb=" N ASP C 287 " --> pdb=" O ALA C 283 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N VAL C 289 " --> pdb=" O THR C 285 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N GLN C 290 " --> pdb=" O TYR C 286 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N VAL C 291 " --> pdb=" O ASP C 287 " (cutoff:3.500A) Processing helix chain 'C' and resid 308 through 310 No H-bonds generated for 'chain 'C' and resid 308 through 310' Processing helix chain 'C' and resid 326 through 334 Processing helix chain 'C' and resid 418 through 420 No H-bonds generated for 'chain 'C' and resid 418 through 420' Processing helix chain 'C' and resid 424 through 433 removed outlier: 3.662A pdb=" N GLU C 431 " --> pdb=" O ASP C 427 " (cutoff:3.500A) Processing helix chain 'C' and resid 462 through 465 No H-bonds generated for 'chain 'C' and resid 462 through 465' Processing helix chain 'C' and resid 485 through 487 No H-bonds generated for 'chain 'C' and resid 485 through 487' Processing helix chain 'C' and resid 523 through 544 removed outlier: 3.660A pdb=" N CYS C 528 " --> pdb=" O GLU C 524 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N VAL C 530 " --> pdb=" O TRP C 526 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N VAL C 539 " --> pdb=" O GLY C 535 " (cutoff:3.500A) Processing helix chain 'C' and resid 573 through 576 No H-bonds generated for 'chain 'C' and resid 573 through 576' Processing helix chain 'C' and resid 581 through 584 No H-bonds generated for 'chain 'C' and resid 581 through 584' Processing helix chain 'C' and resid 601 through 614 removed outlier: 3.642A pdb=" N TRP C 606 " --> pdb=" O GLY C 602 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ILE C 611 " --> pdb=" O PHE C 607 " (cutoff:3.500A) removed outlier: 4.151A pdb=" N ILE C 613 " --> pdb=" O THR C 609 " (cutoff:3.500A) Processing helix chain 'C' and resid 617 through 623 removed outlier: 4.674A pdb=" N ALA C 622 " --> pdb=" O ALA C 618 " (cutoff:3.500A) Processing helix chain 'C' and resid 637 through 640 No H-bonds generated for 'chain 'C' and resid 637 through 640' Processing helix chain 'C' and resid 654 through 660 removed outlier: 3.771A pdb=" N PHE C 659 " --> pdb=" O THR C 655 " (cutoff:3.500A) Processing helix chain 'C' and resid 666 through 675 removed outlier: 3.500A pdb=" N MET C 674 " --> pdb=" O MET C 670 " (cutoff:3.500A) Processing helix chain 'C' and resid 686 through 695 removed outlier: 3.567A pdb=" N VAL C 693 " --> pdb=" O GLY C 689 " (cutoff:3.500A) Processing helix chain 'C' and resid 706 through 713 removed outlier: 3.893A pdb=" N TYR C 711 " --> pdb=" O THR C 707 " (cutoff:3.500A) Processing helix chain 'C' and resid 744 through 750 Processing helix chain 'C' and resid 752 through 756 Processing helix chain 'C' and resid 758 through 766 removed outlier: 3.799A pdb=" N LYS C 763 " --> pdb=" O LEU C 759 " (cutoff:3.500A) Processing helix chain 'C' and resid 794 through 818 removed outlier: 3.534A pdb=" N LEU C 805 " --> pdb=" O GLY C 801 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N LYS C 817 " --> pdb=" O GLU C 813 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N SER C 818 " --> pdb=" O PHE C 814 " (cutoff:3.500A) Processing helix chain 'C' and resid 834 through 856 removed outlier: 3.788A pdb=" N THR C 838 " --> pdb=" O ARG C 834 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N SER C 842 " --> pdb=" O THR C 838 " (cutoff:3.500A) Processing helix chain 'C' and resid 929 through 951 Proline residue: C 932 - end of helix removed outlier: 3.723A pdb=" N PHE C 938 " --> pdb=" O SER C 935 " (cutoff:3.500A) removed outlier: 4.131A pdb=" N ILE C 941 " --> pdb=" O PHE C 938 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N GLY C 942 " --> pdb=" O MET C 939 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N ILE C 944 " --> pdb=" O ILE C 941 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N ASN C 947 " --> pdb=" O ILE C 944 " (cutoff:3.500A) removed outlier: 4.605A pdb=" N ILE C 948 " --> pdb=" O LEU C 945 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N GLY C 949 " --> pdb=" O SER C 946 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N ILE C 951 " --> pdb=" O ILE C 948 " (cutoff:3.500A) Processing helix chain 'C' and resid 959 through 985 removed outlier: 3.750A pdb=" N PHE C 965 " --> pdb=" O VAL C 961 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N GLY C 970 " --> pdb=" O PHE C 966 " (cutoff:3.500A) Processing helix chain 'C' and resid 1006 through 1034 removed outlier: 3.781A pdb=" N LEU C1015 " --> pdb=" O ALA C1011 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N GLY C1021 " --> pdb=" O THR C1017 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N MET C1029 " --> pdb=" O VAL C1025 " (cutoff:3.500A) removed outlier: 5.353A pdb=" N THR C1033 " --> pdb=" O MET C1029 " (cutoff:3.500A) Processing helix chain 'D' and resid 24 through 34 removed outlier: 4.323A pdb=" N VAL D 34 " --> pdb=" O ARG D 30 " (cutoff:3.500A) Processing helix chain 'D' and resid 55 through 67 removed outlier: 3.511A pdb=" N GLN D 65 " --> pdb=" O ALA D 61 " (cutoff:3.500A) Processing helix chain 'D' and resid 82 through 91 removed outlier: 3.929A pdb=" N SER D 87 " --> pdb=" O ASN D 83 " (cutoff:3.500A) Processing helix chain 'D' and resid 117 through 128 removed outlier: 4.323A pdb=" N LEU D 121 " --> pdb=" O LYS D 118 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N SER D 123 " --> pdb=" O ALA D 120 " (cutoff:3.500A) removed outlier: 4.058A pdb=" N ILE D 125 " --> pdb=" O LEU D 122 " (cutoff:3.500A) Processing helix chain 'D' and resid 146 through 149 No H-bonds generated for 'chain 'D' and resid 146 through 149' Processing helix chain 'D' and resid 173 through 186 removed outlier: 3.818A pdb=" N ARG D 178 " --> pdb=" O ASP D 174 " (cutoff:3.500A) Processing helix chain 'D' and resid 198 through 209 Processing helix chain 'D' and resid 227 through 229 No H-bonds generated for 'chain 'D' and resid 227 through 229' Processing helix chain 'D' and resid 253 through 264 removed outlier: 3.605A pdb=" N ARG D 261 " --> pdb=" O LYS D 257 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N THR D 264 " --> pdb=" O GLU D 260 " (cutoff:3.500A) Processing helix chain 'D' and resid 280 through 300 removed outlier: 3.562A pdb=" N THR D 285 " --> pdb=" O THR D 281 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N GLN D 290 " --> pdb=" O TYR D 286 " (cutoff:3.500A) removed outlier: 5.119A pdb=" N PHE D 296 " --> pdb=" O MET D 292 " (cutoff:3.500A) Processing helix chain 'D' and resid 326 through 335 removed outlier: 3.592A pdb=" N ILE D 329 " --> pdb=" O GLY D 326 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N ARG D 331 " --> pdb=" O GLU D 328 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N LEU D 333 " --> pdb=" O GLU D 330 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N LYS D 334 " --> pdb=" O ARG D 331 " (cutoff:3.500A) Processing helix chain 'D' and resid 424 through 435 removed outlier: 3.788A pdb=" N LYS D 434 " --> pdb=" O ALA D 430 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N HIS D 435 " --> pdb=" O GLU D 431 " (cutoff:3.500A) Processing helix chain 'D' and resid 463 through 468 Processing helix chain 'D' and resid 483 through 486 No H-bonds generated for 'chain 'D' and resid 483 through 486' Processing helix chain 'D' and resid 526 through 545 removed outlier: 3.707A pdb=" N VAL D 530 " --> pdb=" O TRP D 526 " (cutoff:3.500A) Processing helix chain 'D' and resid 573 through 584 removed outlier: 3.575A pdb=" N LEU D 577 " --> pdb=" O ILE D 573 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N TRP D 578 " --> pdb=" O PHE D 574 " (cutoff:3.500A) Processing helix chain 'D' and resid 596 through 623 removed outlier: 3.633A pdb=" N ILE D 600 " --> pdb=" O LEU D 596 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N VAL D 601 " --> pdb=" O SER D 597 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N TRP D 606 " --> pdb=" O GLY D 602 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N PHE D 607 " --> pdb=" O GLY D 603 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N ILE D 611 " --> pdb=" O PHE D 607 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N SER D 614 " --> pdb=" O LEU D 610 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N ALA D 618 " --> pdb=" O SER D 614 " (cutoff:3.500A) Processing helix chain 'D' and resid 637 through 640 No H-bonds generated for 'chain 'D' and resid 637 through 640' Processing helix chain 'D' and resid 654 through 660 removed outlier: 4.304A pdb=" N PHE D 659 " --> pdb=" O THR D 655 " (cutoff:3.500A) removed outlier: 4.130A pdb=" N ARG D 660 " --> pdb=" O LYS D 656 " (cutoff:3.500A) Processing helix chain 'D' and resid 666 through 676 removed outlier: 3.558A pdb=" N TRP D 671 " --> pdb=" O PHE D 667 " (cutoff:3.500A) removed outlier: 4.114A pdb=" N MET D 674 " --> pdb=" O MET D 670 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N SER D 676 " --> pdb=" O THR D 672 " (cutoff:3.500A) Processing helix chain 'D' and resid 686 through 690 Processing helix chain 'D' and resid 706 through 712 removed outlier: 3.652A pdb=" N GLU D 710 " --> pdb=" O SER D 706 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N TYR D 711 " --> pdb=" O THR D 707 " (cutoff:3.500A) Processing helix chain 'D' and resid 743 through 755 removed outlier: 3.657A pdb=" N ASN D 747 " --> pdb=" O GLY D 743 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N LEU D 751 " --> pdb=" O ASN D 747 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N LYS D 752 " --> pdb=" O LEU D 748 " (cutoff:3.500A) Processing helix chain 'D' and resid 758 through 767 removed outlier: 4.051A pdb=" N LYS D 763 " --> pdb=" O LEU D 759 " (cutoff:3.500A) removed outlier: 4.092A pdb=" N TRP D 766 " --> pdb=" O LEU D 762 " (cutoff:3.500A) Processing helix chain 'D' and resid 793 through 816 removed outlier: 3.535A pdb=" N TYR D 797 " --> pdb=" O ALA D 793 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N ALA D 806 " --> pdb=" O GLY D 802 " (cutoff:3.500A) Processing helix chain 'E' and resid 5 through 35 removed outlier: 3.661A pdb=" N MET E 11 " --> pdb=" O ALA E 7 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N VAL E 15 " --> pdb=" O MET E 11 " (cutoff:3.500A) removed outlier: 4.074A pdb=" N SER E 19 " --> pdb=" O VAL E 15 " (cutoff:3.500A) removed outlier: 4.146A pdb=" N PHE E 22 " --> pdb=" O ALA E 18 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N ALA E 30 " --> pdb=" O TRP E 26 " (cutoff:3.500A) Processing helix chain 'E' and resid 58 through 84 removed outlier: 3.529A pdb=" N LEU E 64 " --> pdb=" O ILE E 60 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N LYS E 66 " --> pdb=" O CYS E 62 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N LEU E 67 " --> pdb=" O LEU E 63 " (cutoff:3.500A) removed outlier: 4.214A pdb=" N VAL E 68 " --> pdb=" O LEU E 64 " (cutoff:3.500A) removed outlier: 4.471A pdb=" N VAL E 69 " --> pdb=" O ARG E 65 " (cutoff:3.500A) Proline residue: E 70 - end of helix removed outlier: 4.105A pdb=" N HIS E 75 " --> pdb=" O GLU E 71 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N LEU E 80 " --> pdb=" O GLY E 76 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N LEU E 83 " --> pdb=" O CYS E 79 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N CYS E 84 " --> pdb=" O LEU E 80 " (cutoff:3.500A) Processing helix chain 'E' and resid 88 through 104 Proline residue: E 96 - end of helix removed outlier: 3.655A pdb=" N TYR E 100 " --> pdb=" O PRO E 96 " (cutoff:3.500A) Processing helix chain 'E' and resid 126 through 157 removed outlier: 3.811A pdb=" N GLU E 134 " --> pdb=" O TYR E 130 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N TRP E 136 " --> pdb=" O GLN E 132 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N LYS E 138 " --> pdb=" O GLU E 134 " (cutoff:3.500A) removed outlier: 4.548A pdb=" N LEU E 139 " --> pdb=" O SER E 135 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N PHE E 147 " --> pdb=" O LEU E 143 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N LEU E 150 " --> pdb=" O PHE E 146 " (cutoff:3.500A) Processing helix chain 'F' and resid 5 through 35 removed outlier: 3.661A pdb=" N MET F 11 " --> pdb=" O ALA F 7 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N VAL F 15 " --> pdb=" O MET F 11 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N SER F 19 " --> pdb=" O VAL F 15 " (cutoff:3.500A) removed outlier: 4.146A pdb=" N PHE F 22 " --> pdb=" O ALA F 18 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N ALA F 30 " --> pdb=" O TRP F 26 " (cutoff:3.500A) Processing helix chain 'F' and resid 58 through 84 removed outlier: 3.529A pdb=" N LEU F 64 " --> pdb=" O ILE F 60 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N LYS F 66 " --> pdb=" O CYS F 62 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N LEU F 67 " --> pdb=" O LEU F 63 " (cutoff:3.500A) removed outlier: 4.214A pdb=" N VAL F 68 " --> pdb=" O LEU F 64 " (cutoff:3.500A) removed outlier: 4.470A pdb=" N VAL F 69 " --> pdb=" O ARG F 65 " (cutoff:3.500A) Proline residue: F 70 - end of helix removed outlier: 4.105A pdb=" N HIS F 75 " --> pdb=" O GLU F 71 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N LEU F 80 " --> pdb=" O GLY F 76 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N LEU F 83 " --> pdb=" O CYS F 79 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N CYS F 84 " --> pdb=" O LEU F 80 " (cutoff:3.500A) Processing helix chain 'F' and resid 88 through 104 Proline residue: F 96 - end of helix removed outlier: 3.654A pdb=" N TYR F 100 " --> pdb=" O PRO F 96 " (cutoff:3.500A) Processing helix chain 'F' and resid 126 through 157 removed outlier: 3.812A pdb=" N GLU F 134 " --> pdb=" O TYR F 130 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N TRP F 136 " --> pdb=" O GLN F 132 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N LYS F 138 " --> pdb=" O GLU F 134 " (cutoff:3.500A) removed outlier: 4.549A pdb=" N LEU F 139 " --> pdb=" O SER F 135 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N PHE F 147 " --> pdb=" O LEU F 143 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N LEU F 150 " --> pdb=" O PHE F 146 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 42 through 47 removed outlier: 3.770A pdb=" N ILE A 12 " --> pdb=" O ARG A 42 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N HIS A 46 " --> pdb=" O ILE A 14 " (cutoff:3.500A) removed outlier: 6.902A pdb=" N ALA A 72 " --> pdb=" O GLY A 15 " (cutoff:3.500A) removed outlier: 8.357A pdb=" N LEU A 17 " --> pdb=" O ALA A 72 " (cutoff:3.500A) removed outlier: 7.981A pdb=" N PHE A 74 " --> pdb=" O LEU A 17 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 96 through 98 Processing sheet with id= C, first strand: chain 'A' and resid 243 through 246 removed outlier: 3.650A pdb=" N GLY A 244 " --> pdb=" O MET A 361 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N MET A 361 " --> pdb=" O GLY A 244 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N GLY A 367 " --> pdb=" O LYS A 364 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 372 through 374 Processing sheet with id= E, first strand: chain 'A' and resid 703 through 705 removed outlier: 4.143A pdb=" N ILE A 502 " --> pdb=" O VAL A 723 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'A' and resid 997 through 999 Processing sheet with id= G, first strand: chain 'B' and resid 96 through 98 Processing sheet with id= H, first strand: chain 'B' and resid 244 through 246 removed outlier: 3.543A pdb=" N MET B 361 " --> pdb=" O GLY B 244 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'B' and resid 338 through 340 removed outlier: 3.560A pdb=" N VAL B 338 " --> pdb=" O ILE B 345 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'B' and resid 395 through 399 removed outlier: 3.535A pdb=" N VAL B 397 " --> pdb=" O LYS B 441 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'B' and resid 489 through 491 Processing sheet with id= L, first strand: chain 'B' and resid 720 through 723 removed outlier: 3.658A pdb=" N VAL B 723 " --> pdb=" O ILE B 502 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N ILE B 502 " --> pdb=" O VAL B 723 " (cutoff:3.500A) removed outlier: 5.399A pdb=" N LYS B 505 " --> pdb=" O TYR B 700 " (cutoff:3.500A) removed outlier: 8.891A pdb=" N TYR B 700 " --> pdb=" O LYS B 505 " (cutoff:3.500A) removed outlier: 6.827A pdb=" N ALA B 646 " --> pdb=" O ALA B 701 " (cutoff:3.500A) removed outlier: 8.130A pdb=" N LEU B 703 " --> pdb=" O ALA B 646 " (cutoff:3.500A) removed outlier: 7.464A pdb=" N GLY B 648 " --> pdb=" O LEU B 703 " (cutoff:3.500A) removed outlier: 8.980A pdb=" N GLU B 705 " --> pdb=" O GLY B 648 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'B' and resid 373 through 375 removed outlier: 3.540A pdb=" N SER B 375 " --> pdb=" O LYS B 379 " (cutoff:3.500A) removed outlier: 4.298A pdb=" N LYS B 379 " --> pdb=" O SER B 375 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'C' and resid 42 through 47 removed outlier: 3.770A pdb=" N ILE C 12 " --> pdb=" O ARG C 42 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N HIS C 46 " --> pdb=" O ILE C 14 " (cutoff:3.500A) removed outlier: 6.902A pdb=" N ALA C 72 " --> pdb=" O GLY C 15 " (cutoff:3.500A) removed outlier: 8.358A pdb=" N LEU C 17 " --> pdb=" O ALA C 72 " (cutoff:3.500A) removed outlier: 7.980A pdb=" N PHE C 74 " --> pdb=" O LEU C 17 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'C' and resid 96 through 98 Processing sheet with id= P, first strand: chain 'C' and resid 243 through 246 removed outlier: 3.651A pdb=" N GLY C 244 " --> pdb=" O MET C 361 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N MET C 361 " --> pdb=" O GLY C 244 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N GLY C 367 " --> pdb=" O LYS C 364 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'C' and resid 372 through 374 Processing sheet with id= R, first strand: chain 'C' and resid 703 through 705 removed outlier: 4.143A pdb=" N ILE C 502 " --> pdb=" O VAL C 723 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'C' and resid 997 through 999 Processing sheet with id= T, first strand: chain 'D' and resid 96 through 98 Processing sheet with id= U, first strand: chain 'D' and resid 244 through 246 removed outlier: 3.544A pdb=" N MET D 361 " --> pdb=" O GLY D 244 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'D' and resid 338 through 340 removed outlier: 3.560A pdb=" N VAL D 338 " --> pdb=" O ILE D 345 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N ILE D 345 " --> pdb=" O VAL D 338 " (cutoff:3.500A) Processing sheet with id= W, first strand: chain 'D' and resid 395 through 399 removed outlier: 3.534A pdb=" N VAL D 397 " --> pdb=" O LYS D 441 " (cutoff:3.500A) Processing sheet with id= X, first strand: chain 'D' and resid 489 through 491 Processing sheet with id= Y, first strand: chain 'D' and resid 720 through 723 removed outlier: 3.659A pdb=" N VAL D 723 " --> pdb=" O ILE D 502 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N ILE D 502 " --> pdb=" O VAL D 723 " (cutoff:3.500A) removed outlier: 5.399A pdb=" N LYS D 505 " --> pdb=" O TYR D 700 " (cutoff:3.500A) removed outlier: 8.890A pdb=" N TYR D 700 " --> pdb=" O LYS D 505 " (cutoff:3.500A) removed outlier: 6.827A pdb=" N ALA D 646 " --> pdb=" O ALA D 701 " (cutoff:3.500A) removed outlier: 8.131A pdb=" N LEU D 703 " --> pdb=" O ALA D 646 " (cutoff:3.500A) removed outlier: 7.466A pdb=" N GLY D 648 " --> pdb=" O LEU D 703 " (cutoff:3.500A) removed outlier: 8.980A pdb=" N GLU D 705 " --> pdb=" O GLY D 648 " (cutoff:3.500A) Processing sheet with id= Z, first strand: chain 'D' and resid 373 through 375 removed outlier: 3.541A pdb=" N SER D 375 " --> pdb=" O LYS D 379 " (cutoff:3.500A) removed outlier: 4.298A pdb=" N LYS D 379 " --> pdb=" O SER D 375 " (cutoff:3.500A) 905 hydrogen bonds defined for protein. 2571 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: 9.62 Time building geometry restraints manager: 12.50 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.08 - 0.51: 4 0.51 - 0.94: 0 0.94 - 1.36: 10295 1.36 - 1.79: 21401 1.79 - 2.22: 113 Warning: very small bond lengths. Bond restraints: 31813 Sorted by residual: bond pdb=" C27 AJP C1106 " pdb=" O78 AJP C1106 " ideal model delta sigma weight residual 1.406 0.083 1.323 2.00e-02 2.50e+03 4.38e+03 bond pdb=" C27 AJP A1106 " pdb=" O78 AJP A1106 " ideal model delta sigma weight residual 1.406 0.151 1.255 2.00e-02 2.50e+03 3.94e+03 bond pdb=" C23 AJP A1106 " pdb=" O25 AJP A1106 " ideal model delta sigma weight residual 1.423 0.491 0.932 2.00e-02 2.50e+03 2.17e+03 bond pdb=" C23 AJP C1106 " pdb=" O25 AJP C1106 " ideal model delta sigma weight residual 1.423 0.495 0.928 2.00e-02 2.50e+03 2.15e+03 bond pdb=" C26 AJP C1106 " pdb=" O25 AJP C1106 " ideal model delta sigma weight residual 1.375 2.069 -0.694 2.00e-02 2.50e+03 1.21e+03 ... (remaining 31808 not shown) Histogram of bond angle deviations from ideal: 88.31 - 97.88: 18 97.88 - 107.45: 1360 107.45 - 117.02: 20864 117.02 - 126.59: 20211 126.59 - 136.16: 467 Bond angle restraints: 42920 Sorted by residual: angle pdb=" C ALA A 317 " pdb=" N ASN A 318 " pdb=" CA ASN A 318 " ideal model delta sigma weight residual 120.51 132.81 -12.30 1.45e+00 4.76e-01 7.20e+01 angle pdb=" C ALA C 317 " pdb=" N ASN C 318 " pdb=" CA ASN C 318 " ideal model delta sigma weight residual 120.51 132.75 -12.24 1.45e+00 4.76e-01 7.13e+01 angle pdb=" C17 CLR A1105 " pdb=" C13 CLR A1105 " pdb=" C18 CLR A1105 " ideal model delta sigma weight residual 110.18 88.31 21.87 3.00e+00 1.11e-01 5.31e+01 angle pdb=" C28 AJP A1106 " pdb=" C27 AJP A1106 " pdb=" O78 AJP A1106 " ideal model delta sigma weight residual 108.61 129.29 -20.68 3.00e+00 1.11e-01 4.75e+01 angle pdb=" C04 AJP A1106 " pdb=" C05 AJP A1106 " pdb=" C06 AJP A1106 " ideal model delta sigma weight residual 114.54 134.46 -19.92 3.00e+00 1.11e-01 4.41e+01 ... (remaining 42915 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.43: 18529 35.43 - 70.86: 553 70.86 - 106.29: 89 106.29 - 141.73: 47 141.73 - 177.16: 21 Dihedral angle restraints: 19239 sinusoidal: 8259 harmonic: 10980 Sorted by residual: dihedral pdb=" CA MET F 116 " pdb=" C MET F 116 " pdb=" N TYR F 117 " pdb=" CA TYR F 117 " ideal model delta harmonic sigma weight residual 180.00 120.45 59.55 0 5.00e+00 4.00e-02 1.42e+02 dihedral pdb=" CA MET E 116 " pdb=" C MET E 116 " pdb=" N TYR E 117 " pdb=" CA TYR E 117 " ideal model delta harmonic sigma weight residual 180.00 120.51 59.49 0 5.00e+00 4.00e-02 1.42e+02 dihedral pdb=" CA VAL E 115 " pdb=" C VAL E 115 " pdb=" N MET E 116 " pdb=" CA MET E 116 " ideal model delta harmonic sigma weight residual 180.00 124.16 55.84 0 5.00e+00 4.00e-02 1.25e+02 ... (remaining 19236 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 1.112: 4672 1.112 - 2.224: 3 2.224 - 3.336: 3 3.336 - 4.448: 7 4.448 - 5.560: 17 Chirality restraints: 4702 Sorted by residual: chirality pdb=" C02 AJP A1106 " pdb=" C01 AJP A1106 " pdb=" C03 AJP A1106 " pdb=" C85 AJP A1106 " both_signs ideal model delta sigma weight residual False 2.60 -2.96 5.56 2.00e-01 2.50e+01 7.73e+02 chirality pdb=" C15 AJP A1106 " pdb=" C14 AJP A1106 " pdb=" C16 AJP A1106 " pdb=" C20 AJP A1106 " both_signs ideal model delta sigma weight residual False -2.42 3.14 -5.56 2.00e-01 2.50e+01 7.73e+02 chirality pdb=" C02 AJP C1106 " pdb=" C01 AJP C1106 " pdb=" C03 AJP C1106 " pdb=" C85 AJP C1106 " both_signs ideal model delta sigma weight residual False 2.60 -2.96 5.55 2.00e-01 2.50e+01 7.71e+02 ... (remaining 4699 not shown) Planarity restraints: 5286 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA MET F 116 " -0.019 2.00e-02 2.50e+03 3.81e-02 1.45e+01 pdb=" C MET F 116 " 0.066 2.00e-02 2.50e+03 pdb=" O MET F 116 " -0.024 2.00e-02 2.50e+03 pdb=" N TYR F 117 " -0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA MET E 116 " 0.019 2.00e-02 2.50e+03 3.80e-02 1.45e+01 pdb=" C MET E 116 " -0.066 2.00e-02 2.50e+03 pdb=" O MET E 116 " 0.024 2.00e-02 2.50e+03 pdb=" N TYR E 117 " 0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE A 193 " -0.019 2.00e-02 2.50e+03 3.76e-02 1.41e+01 pdb=" C ILE A 193 " 0.065 2.00e-02 2.50e+03 pdb=" O ILE A 193 " -0.024 2.00e-02 2.50e+03 pdb=" N LEU A 194 " -0.022 2.00e-02 2.50e+03 ... (remaining 5283 not shown) Histogram of nonbonded interaction distances: 2.18 - 2.72: 2929 2.72 - 3.27: 30026 3.27 - 3.81: 49988 3.81 - 4.36: 61698 4.36 - 4.90: 102481 Nonbonded interactions: 247122 Sorted by model distance: nonbonded pdb=" O25 AJP A1106 " pdb=" O79 AJP A1106 " model vdw 2.176 2.432 nonbonded pdb=" O25 AJP C1106 " pdb=" O79 AJP C1106 " model vdw 2.176 2.432 nonbonded pdb=" O31 AJP C1106 " pdb=" O78 AJP C1106 " model vdw 2.179 2.432 nonbonded pdb=" OE2 GLU A 755 " pdb=" OG1 THR D 482 " model vdw 2.201 2.440 nonbonded pdb=" OH TYR B 128 " pdb=" OG SER B 243 " model vdw 2.223 2.440 ... (remaining 247117 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 10 through 1035 or resid 1101 through 1110)) selection = chain 'C' } ncs_group { reference = chain 'B' selection = chain 'D' } ncs_group { reference = chain 'E' selection = chain 'F' } 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=1.00 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: 6.250 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.020 Extract box with map and model: 16.660 Check model and map are aligned: 0.470 Set scattering table: 0.290 Process input model: 78.380 Find NCS groups from input model: 1.820 Set up NCS constraints: 0.220 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:2.800 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 106.940 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8034 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 : 0.025 1.323 31813 Z= 1.538 Angle : 1.636 21.867 42920 Z= 0.877 Chirality : 0.360 5.560 4702 Planarity : 0.007 0.064 5286 Dihedral : 18.885 177.158 12189 Min Nonbonded Distance : 2.176 Molprobity Statistics. All-atom Clashscore : 7.42 Ramachandran Plot: Outliers : 0.69 % Allowed : 15.02 % Favored : 84.29 % Rotamer: Outliers : 0.80 % Allowed : 6.36 % Favored : 92.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.21 % Cis-general : 0.00 % Twisted Proline : 3.77 % Twisted General : 0.87 % 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: -5.79 (0.10), residues: 3762 helix: -3.79 (0.07), residues: 1714 sheet: -4.40 (0.21), residues: 370 loop : -3.65 (0.12), residues: 1678 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.004 TRP C 861 HIS 0.012 0.003 HIS C 219 PHE 0.052 0.004 PHE E 99 TYR 0.027 0.004 TYR A 702 ARG 0.009 0.001 ARG B 485 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7524 Ramachandran restraints generated. 3762 Oldfield, 0 Emsley, 3762 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7524 Ramachandran restraints generated. 3762 Oldfield, 0 Emsley, 3762 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 697 residues out of total 3256 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 671 time to evaluate : 3.511 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 414 MET cc_start: 0.8004 (ptm) cc_final: 0.7786 (ptp) REVERT: A 635 SER cc_start: 0.9024 (t) cc_final: 0.8818 (p) REVERT: A 638 ASP cc_start: 0.8386 (m-30) cc_final: 0.7982 (m-30) REVERT: A 879 LYS cc_start: 0.8207 (ttpt) cc_final: 0.7829 (mmmt) REVERT: A 891 PHE cc_start: 0.8381 (m-10) cc_final: 0.7843 (m-10) REVERT: A 907 MET cc_start: 0.2736 (ppp) cc_final: 0.1586 (tpt) REVERT: A 922 LEU cc_start: 0.7924 (OUTLIER) cc_final: 0.7697 (mm) REVERT: A 939 MET cc_start: 0.8371 (ttm) cc_final: 0.7791 (tpt) REVERT: A 966 PHE cc_start: 0.6804 (m-80) cc_final: 0.6580 (m-80) REVERT: B 36 PHE cc_start: 0.6833 (t80) cc_final: 0.6079 (t80) REVERT: B 127 TYR cc_start: 0.8158 (t80) cc_final: 0.7942 (t80) REVERT: B 392 GLN cc_start: 0.7477 (mp10) cc_final: 0.7158 (mp10) REVERT: B 490 ASP cc_start: 0.7680 (m-30) cc_final: 0.7386 (p0) REVERT: B 573 ILE cc_start: 0.8779 (tp) cc_final: 0.8562 (tp) REVERT: B 626 VAL cc_start: 0.9240 (t) cc_final: 0.8655 (m) REVERT: C 414 MET cc_start: 0.8112 (ptm) cc_final: 0.7815 (ptp) REVERT: C 627 GLU cc_start: 0.8037 (pp20) cc_final: 0.7805 (pp20) REVERT: C 816 TYR cc_start: 0.7858 (t80) cc_final: 0.7443 (t80) REVERT: C 863 TYR cc_start: 0.6058 (m-10) cc_final: 0.5583 (m-10) REVERT: C 891 PHE cc_start: 0.8310 (m-10) cc_final: 0.7936 (m-80) REVERT: C 907 MET cc_start: 0.2477 (ppp) cc_final: 0.1857 (tpt) REVERT: C 966 PHE cc_start: 0.6975 (m-80) cc_final: 0.6484 (m-80) REVERT: D 36 PHE cc_start: 0.6737 (t80) cc_final: 0.6405 (t80) REVERT: D 392 GLN cc_start: 0.7302 (mp10) cc_final: 0.6923 (mp10) REVERT: D 440 TYR cc_start: 0.8443 (p90) cc_final: 0.8221 (p90) REVERT: D 490 ASP cc_start: 0.7713 (m-30) cc_final: 0.7477 (p0) REVERT: E 67 LEU cc_start: 0.7897 (mt) cc_final: 0.7696 (mm) REVERT: E 88 TRP cc_start: 0.5912 (m100) cc_final: 0.5264 (t60) REVERT: F 88 TRP cc_start: 0.5698 (m100) cc_final: 0.5161 (t60) outliers start: 26 outliers final: 4 residues processed: 692 average time/residue: 0.4447 time to fit residues: 488.9574 Evaluate side-chains 379 residues out of total 3256 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 374 time to evaluate : 3.755 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 626 VAL Chi-restraints excluded: chain A residue 922 LEU Chi-restraints excluded: chain B residue 591 ILE Chi-restraints excluded: chain E residue 115 VAL Chi-restraints excluded: chain F residue 115 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 378 random chunks: chunk 319 optimal weight: 3.9990 chunk 286 optimal weight: 0.8980 chunk 158 optimal weight: 0.9980 chunk 97 optimal weight: 6.9990 chunk 193 optimal weight: 0.9980 chunk 153 optimal weight: 0.0270 chunk 296 optimal weight: 3.9990 chunk 114 optimal weight: 1.9990 chunk 180 optimal weight: 1.9990 chunk 220 optimal weight: 1.9990 chunk 343 optimal weight: 0.9990 overall best weight: 0.7840 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 46 HIS A 60 ASN A 147 GLN A 167 ASN A 202 ASN A 344 ASN ** A 508 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 575 ASN A 726 ASN A 764 ASN A 950 HIS A 985 ASN B 24 GLN B 46 HIS B 60 ASN B 224 ASN B 311 ASN B 318 ASN B 344 ASN B 461 ASN B 508 GLN C 46 HIS C 60 ASN C 147 GLN C 167 ASN C 202 ASN C 344 ASN ** C 508 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 575 ASN C 726 ASN C 764 ASN C 950 HIS C 985 ASN D 24 GLN D 60 ASN ** D 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 224 ASN D 311 ASN D 318 ASN ** D 325 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 344 ASN D 461 ASN E 129 ASN F 129 ASN Total number of N/Q/H flips: 40 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7953 moved from start: 0.2526 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 31813 Z= 0.216 Angle : 0.947 32.113 42920 Z= 0.430 Chirality : 0.085 2.344 4702 Planarity : 0.005 0.057 5286 Dihedral : 19.471 179.441 5190 Min Nonbonded Distance : 2.056 Molprobity Statistics. All-atom Clashscore : 12.14 Ramachandran Plot: Outliers : 0.48 % Allowed : 11.70 % Favored : 87.83 % Rotamer: Outliers : 2.70 % Allowed : 11.33 % Favored : 85.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.21 % Cis-general : 0.00 % Twisted Proline : 1.89 % Twisted General : 0.52 % 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: -4.26 (0.12), residues: 3762 helix: -2.07 (0.11), residues: 1744 sheet: -4.12 (0.23), residues: 366 loop : -3.31 (0.13), residues: 1652 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 262 HIS 0.005 0.001 HIS E 27 PHE 0.028 0.002 PHE C 517 TYR 0.032 0.002 TYR C1001 ARG 0.008 0.000 ARG D 692 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7524 Ramachandran restraints generated. 3762 Oldfield, 0 Emsley, 3762 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7524 Ramachandran restraints generated. 3762 Oldfield, 0 Emsley, 3762 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 576 residues out of total 3256 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 88 poor density : 488 time to evaluate : 3.436 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 LEU cc_start: 0.8795 (pt) cc_final: 0.8552 (pt) REVERT: A 302 GLN cc_start: 0.7741 (pm20) cc_final: 0.7463 (mp10) REVERT: A 414 MET cc_start: 0.7941 (ptm) cc_final: 0.7681 (ptp) REVERT: A 463 MET cc_start: 0.8439 (OUTLIER) cc_final: 0.8140 (ttp) REVERT: A 678 GLU cc_start: 0.8044 (mm-30) cc_final: 0.7837 (mm-30) REVERT: A 879 LYS cc_start: 0.8154 (ttpt) cc_final: 0.7854 (mmmt) REVERT: A 891 PHE cc_start: 0.8400 (m-10) cc_final: 0.7872 (m-10) REVERT: A 939 MET cc_start: 0.8207 (ttm) cc_final: 0.7884 (tpt) REVERT: A 966 PHE cc_start: 0.7051 (m-80) cc_final: 0.6634 (m-80) REVERT: A 1005 TRP cc_start: 0.7488 (p-90) cc_final: 0.7009 (p-90) REVERT: B 133 PHE cc_start: 0.8531 (m-10) cc_final: 0.8271 (m-10) REVERT: B 361 MET cc_start: 0.8058 (mtp) cc_final: 0.7549 (mtp) REVERT: B 392 GLN cc_start: 0.7600 (mp10) cc_final: 0.7271 (mp10) REVERT: B 408 MET cc_start: 0.6900 (mmm) cc_final: 0.6047 (mmm) REVERT: B 527 MET cc_start: 0.7512 (tpp) cc_final: 0.7236 (mmt) REVERT: B 573 ILE cc_start: 0.8746 (tp) cc_final: 0.8501 (tp) REVERT: B 585 MET cc_start: 0.8532 (mmt) cc_final: 0.8099 (mmt) REVERT: C 50 LEU cc_start: 0.8642 (pt) cc_final: 0.8312 (pt) REVERT: C 414 MET cc_start: 0.7972 (ptm) cc_final: 0.7658 (ptp) REVERT: C 545 ARG cc_start: 0.7511 (ttm-80) cc_final: 0.7129 (ttt180) REVERT: C 627 GLU cc_start: 0.8038 (pp20) cc_final: 0.7739 (tm-30) REVERT: C 674 MET cc_start: 0.9026 (mtp) cc_final: 0.8778 (mtm) REVERT: C 816 TYR cc_start: 0.7782 (t80) cc_final: 0.7414 (t80) REVERT: C 863 TYR cc_start: 0.5435 (m-10) cc_final: 0.5073 (m-10) REVERT: C 891 PHE cc_start: 0.8268 (m-10) cc_final: 0.7926 (m-80) REVERT: C 907 MET cc_start: 0.1951 (ppp) cc_final: 0.1411 (tpt) REVERT: C 966 PHE cc_start: 0.7084 (m-80) cc_final: 0.6426 (m-80) REVERT: D 33 MET cc_start: 0.8741 (ptm) cc_final: 0.8485 (ptt) REVERT: D 269 GLU cc_start: 0.7518 (tp30) cc_final: 0.7075 (tp30) REVERT: D 361 MET cc_start: 0.8003 (mtp) cc_final: 0.7689 (mtt) REVERT: D 373 TYR cc_start: 0.8852 (p90) cc_final: 0.8543 (p90) REVERT: D 390 LEU cc_start: 0.7074 (OUTLIER) cc_final: 0.6820 (pt) REVERT: D 392 GLN cc_start: 0.7403 (mp10) cc_final: 0.7012 (mp10) REVERT: D 408 MET cc_start: 0.7210 (mmm) cc_final: 0.4949 (mmm) REVERT: D 585 MET cc_start: 0.8472 (mmt) cc_final: 0.8089 (mmm) REVERT: D 773 CYS cc_start: 0.7798 (OUTLIER) cc_final: 0.7365 (m) REVERT: E 81 MET cc_start: 0.8237 (OUTLIER) cc_final: 0.7779 (ttt) REVERT: E 88 TRP cc_start: 0.5600 (m100) cc_final: 0.5257 (t60) REVERT: E 116 MET cc_start: 0.1217 (tpp) cc_final: -0.0266 (pmm) REVERT: E 117 TYR cc_start: 0.1331 (m-80) cc_final: -0.1289 (m-80) REVERT: F 88 TRP cc_start: 0.5552 (m100) cc_final: 0.5272 (t60) REVERT: F 115 VAL cc_start: 0.6622 (OUTLIER) cc_final: 0.6265 (m) REVERT: F 116 MET cc_start: 0.0808 (tpp) cc_final: 0.0327 (pmm) outliers start: 88 outliers final: 30 residues processed: 546 average time/residue: 0.4054 time to fit residues: 367.8153 Evaluate side-chains 414 residues out of total 3256 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 379 time to evaluate : 3.633 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 VAL Chi-restraints excluded: chain A residue 116 ASP Chi-restraints excluded: chain A residue 144 SER Chi-restraints excluded: chain A residue 167 ASN Chi-restraints excluded: chain A residue 208 VAL Chi-restraints excluded: chain A residue 350 ASN Chi-restraints excluded: chain A residue 381 VAL Chi-restraints excluded: chain A residue 463 MET Chi-restraints excluded: chain A residue 626 VAL Chi-restraints excluded: chain A residue 720 THR Chi-restraints excluded: chain A residue 974 VAL Chi-restraints excluded: chain A residue 1015 LEU Chi-restraints excluded: chain A residue 1023 MET Chi-restraints excluded: chain B residue 63 CYS Chi-restraints excluded: chain B residue 274 HIS Chi-restraints excluded: chain B residue 400 ILE Chi-restraints excluded: chain B residue 591 ILE Chi-restraints excluded: chain C residue 34 VAL Chi-restraints excluded: chain C residue 167 ASN Chi-restraints excluded: chain C residue 197 GLU Chi-restraints excluded: chain C residue 208 VAL Chi-restraints excluded: chain C residue 350 ASN Chi-restraints excluded: chain C residue 543 VAL Chi-restraints excluded: chain C residue 626 VAL Chi-restraints excluded: chain C residue 750 VAL Chi-restraints excluded: chain D residue 196 CYS Chi-restraints excluded: chain D residue 274 HIS Chi-restraints excluded: chain D residue 390 LEU Chi-restraints excluded: chain D residue 463 MET Chi-restraints excluded: chain D residue 773 CYS Chi-restraints excluded: chain E residue 81 MET Chi-restraints excluded: chain E residue 143 LEU Chi-restraints excluded: chain F residue 67 LEU Chi-restraints excluded: chain F residue 115 VAL Chi-restraints excluded: chain F residue 143 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 378 random chunks: chunk 190 optimal weight: 1.9990 chunk 106 optimal weight: 0.3980 chunk 285 optimal weight: 0.1980 chunk 233 optimal weight: 1.9990 chunk 94 optimal weight: 6.9990 chunk 343 optimal weight: 3.9990 chunk 371 optimal weight: 1.9990 chunk 306 optimal weight: 7.9990 chunk 341 optimal weight: 6.9990 chunk 117 optimal weight: 3.9990 chunk 275 optimal weight: 0.2980 overall best weight: 0.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 112 GLN A 167 ASN B 246 GLN B 350 ASN B 412 HIS C 112 GLN C 167 ASN C 412 HIS C 985 ASN ** D 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 202 ASN D 246 GLN D 412 HIS Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7970 moved from start: 0.3046 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.110 31813 Z= 0.217 Angle : 0.892 32.639 42920 Z= 0.400 Chirality : 0.083 2.264 4702 Planarity : 0.004 0.054 5286 Dihedral : 18.745 177.574 5187 Min Nonbonded Distance : 2.136 Molprobity Statistics. All-atom Clashscore : 10.89 Ramachandran Plot: Outliers : 0.43 % Allowed : 11.80 % Favored : 87.77 % Rotamer: Outliers : 2.95 % Allowed : 12.99 % Favored : 84.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.21 % Cis-general : 0.00 % Twisted Proline : 1.89 % Twisted General : 0.38 % 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: -3.42 (0.13), residues: 3762 helix: -1.21 (0.12), residues: 1740 sheet: -3.87 (0.24), residues: 358 loop : -3.05 (0.14), residues: 1664 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 262 HIS 0.013 0.001 HIS E 27 PHE 0.020 0.001 PHE C 517 TYR 0.029 0.001 TYR F 117 ARG 0.007 0.000 ARG A 545 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7524 Ramachandran restraints generated. 3762 Oldfield, 0 Emsley, 3762 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7524 Ramachandran restraints generated. 3762 Oldfield, 0 Emsley, 3762 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 510 residues out of total 3256 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 96 poor density : 414 time to evaluate : 4.035 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: A 50 LEU cc_start: 0.8752 (pt) cc_final: 0.8506 (pt) REVERT: A 414 MET cc_start: 0.7911 (ptm) cc_final: 0.7693 (ptp) REVERT: A 879 LYS cc_start: 0.8163 (ttpt) cc_final: 0.7868 (mmmt) REVERT: A 891 PHE cc_start: 0.8397 (m-10) cc_final: 0.8077 (m-80) REVERT: A 907 MET cc_start: 0.1573 (OUTLIER) cc_final: 0.0965 (tpt) REVERT: A 939 MET cc_start: 0.8181 (ttm) cc_final: 0.7866 (tpt) REVERT: A 966 PHE cc_start: 0.7078 (m-80) cc_final: 0.6546 (m-80) REVERT: A 988 MET cc_start: 0.8351 (tmm) cc_final: 0.7731 (tmm) REVERT: A 1005 TRP cc_start: 0.7446 (p-90) cc_final: 0.6987 (p-90) REVERT: B 74 PHE cc_start: 0.8079 (t80) cc_final: 0.7827 (t80) REVERT: B 189 GLU cc_start: 0.7206 (mm-30) cc_final: 0.7003 (mm-30) REVERT: B 361 MET cc_start: 0.8073 (mtp) cc_final: 0.7763 (mtp) REVERT: B 392 GLN cc_start: 0.7646 (mp10) cc_final: 0.7301 (mp10) REVERT: B 527 MET cc_start: 0.7496 (tpp) cc_final: 0.7138 (mmt) REVERT: B 573 ILE cc_start: 0.8698 (tp) cc_final: 0.8373 (tp) REVERT: B 585 MET cc_start: 0.8533 (mmt) cc_final: 0.8098 (mmt) REVERT: B 712 ILE cc_start: 0.8957 (mm) cc_final: 0.8749 (mt) REVERT: C 50 LEU cc_start: 0.8580 (pt) cc_final: 0.8271 (pt) REVERT: C 414 MET cc_start: 0.7954 (ptm) cc_final: 0.7626 (ptp) REVERT: C 585 MET cc_start: 0.8045 (mpt) cc_final: 0.7741 (mpt) REVERT: C 627 GLU cc_start: 0.7966 (pp20) cc_final: 0.7746 (tm-30) REVERT: C 635 SER cc_start: 0.9076 (t) cc_final: 0.8812 (p) REVERT: C 816 TYR cc_start: 0.7690 (t80) cc_final: 0.7343 (t80) REVERT: C 863 TYR cc_start: 0.5467 (m-10) cc_final: 0.4988 (m-10) REVERT: C 891 PHE cc_start: 0.8262 (m-10) cc_final: 0.7795 (m-80) REVERT: C 907 MET cc_start: 0.1860 (ppp) cc_final: 0.1101 (tpt) REVERT: C 924 MET cc_start: 0.7293 (ptp) cc_final: 0.6776 (mtm) REVERT: C 966 PHE cc_start: 0.7235 (m-80) cc_final: 0.6480 (m-80) REVERT: C 985 ASN cc_start: 0.7427 (OUTLIER) cc_final: 0.6904 (p0) REVERT: C 1002 LYS cc_start: 0.7034 (ttmp) cc_final: 0.6433 (mtmt) REVERT: D 189 GLU cc_start: 0.7405 (mm-30) cc_final: 0.7170 (mm-30) REVERT: D 361 MET cc_start: 0.8037 (mtp) cc_final: 0.7732 (mtp) REVERT: D 392 GLN cc_start: 0.7419 (mp10) cc_final: 0.7120 (mp10) REVERT: D 585 MET cc_start: 0.8528 (mmt) cc_final: 0.8152 (mmm) REVERT: E 88 TRP cc_start: 0.5635 (m100) cc_final: 0.5365 (t60) REVERT: E 116 MET cc_start: 0.1109 (tpp) cc_final: 0.0141 (pmm) REVERT: E 122 ILE cc_start: 0.6676 (OUTLIER) cc_final: 0.6377 (mm) REVERT: F 115 VAL cc_start: 0.6384 (OUTLIER) cc_final: 0.6150 (m) REVERT: F 116 MET cc_start: 0.0987 (tpp) cc_final: 0.0264 (pmm) outliers start: 96 outliers final: 50 residues processed: 474 average time/residue: 0.4180 time to fit residues: 327.6073 Evaluate side-chains 412 residues out of total 3256 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 358 time to evaluate : 3.667 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 VAL Chi-restraints excluded: chain A residue 34 VAL Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 350 ASN Chi-restraints excluded: chain A residue 447 ASP Chi-restraints excluded: chain A residue 508 GLN Chi-restraints excluded: chain A residue 543 VAL Chi-restraints excluded: chain A residue 626 VAL Chi-restraints excluded: chain A residue 700 TYR Chi-restraints excluded: chain A residue 750 VAL Chi-restraints excluded: chain A residue 907 MET Chi-restraints excluded: chain A residue 974 VAL Chi-restraints excluded: chain A residue 1023 MET Chi-restraints excluded: chain B residue 54 ASN Chi-restraints excluded: chain B residue 63 CYS Chi-restraints excluded: chain B residue 274 HIS Chi-restraints excluded: chain B residue 299 LEU Chi-restraints excluded: chain B residue 341 LEU Chi-restraints excluded: chain B residue 396 VAL Chi-restraints excluded: chain B residue 515 PHE Chi-restraints excluded: chain B residue 538 VAL Chi-restraints excluded: chain B residue 589 CYS Chi-restraints excluded: chain B residue 604 VAL Chi-restraints excluded: chain B residue 683 VAL Chi-restraints excluded: chain B residue 721 MET Chi-restraints excluded: chain B residue 773 CYS Chi-restraints excluded: chain B residue 811 LEU Chi-restraints excluded: chain C residue 10 ASN Chi-restraints excluded: chain C residue 31 VAL Chi-restraints excluded: chain C residue 34 VAL Chi-restraints excluded: chain C residue 197 GLU Chi-restraints excluded: chain C residue 331 ARG Chi-restraints excluded: chain C residue 335 GLN Chi-restraints excluded: chain C residue 350 ASN Chi-restraints excluded: chain C residue 527 MET Chi-restraints excluded: chain C residue 543 VAL Chi-restraints excluded: chain C residue 626 VAL Chi-restraints excluded: chain C residue 720 THR Chi-restraints excluded: chain C residue 748 LEU Chi-restraints excluded: chain C residue 750 VAL Chi-restraints excluded: chain C residue 985 ASN Chi-restraints excluded: chain C residue 1015 LEU Chi-restraints excluded: chain D residue 274 HIS Chi-restraints excluded: chain D residue 299 LEU Chi-restraints excluded: chain D residue 383 THR Chi-restraints excluded: chain D residue 456 ASP Chi-restraints excluded: chain D residue 463 MET Chi-restraints excluded: chain D residue 589 CYS Chi-restraints excluded: chain E residue 122 ILE Chi-restraints excluded: chain E residue 143 LEU Chi-restraints excluded: chain F residue 67 LEU Chi-restraints excluded: chain F residue 71 GLU Chi-restraints excluded: chain F residue 115 VAL Chi-restraints excluded: chain F residue 143 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 378 random chunks: chunk 339 optimal weight: 4.9990 chunk 258 optimal weight: 0.0980 chunk 178 optimal weight: 8.9990 chunk 38 optimal weight: 2.9990 chunk 164 optimal weight: 4.9990 chunk 230 optimal weight: 3.9990 chunk 345 optimal weight: 0.2980 chunk 365 optimal weight: 6.9990 chunk 180 optimal weight: 5.9990 chunk 327 optimal weight: 0.5980 chunk 98 optimal weight: 1.9990 overall best weight: 1.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 167 ASN ** D 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 246 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 107 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 107 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7985 moved from start: 0.3409 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 31813 Z= 0.217 Angle : 0.868 32.797 42920 Z= 0.386 Chirality : 0.082 2.228 4702 Planarity : 0.004 0.043 5286 Dihedral : 18.167 178.685 5185 Min Nonbonded Distance : 2.157 Molprobity Statistics. All-atom Clashscore : 10.83 Ramachandran Plot: Outliers : 0.35 % Allowed : 11.94 % Favored : 87.72 % Rotamer: Outliers : 3.01 % Allowed : 13.91 % Favored : 83.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.21 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.35 % 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: -3.00 (0.13), residues: 3762 helix: -0.81 (0.12), residues: 1766 sheet: -3.69 (0.24), residues: 372 loop : -2.89 (0.14), residues: 1624 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 262 HIS 0.009 0.001 HIS B 412 PHE 0.018 0.001 PHE C 347 TYR 0.028 0.001 TYR C1001 ARG 0.005 0.000 ARG A 545 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7524 Ramachandran restraints generated. 3762 Oldfield, 0 Emsley, 3762 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7524 Ramachandran restraints generated. 3762 Oldfield, 0 Emsley, 3762 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 492 residues out of total 3256 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 98 poor density : 394 time to evaluate : 3.439 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: A 50 LEU cc_start: 0.8664 (pt) cc_final: 0.8421 (pt) REVERT: A 262 TRP cc_start: 0.8379 (t-100) cc_final: 0.8119 (t-100) REVERT: A 414 MET cc_start: 0.7943 (ptm) cc_final: 0.7678 (ptp) REVERT: A 642 GLN cc_start: 0.7746 (mp10) cc_final: 0.7542 (mp10) REVERT: A 879 LYS cc_start: 0.8090 (ttpt) cc_final: 0.7850 (mmmt) REVERT: A 891 PHE cc_start: 0.8353 (m-10) cc_final: 0.8047 (m-80) REVERT: A 907 MET cc_start: 0.1701 (OUTLIER) cc_final: 0.0928 (tpt) REVERT: A 939 MET cc_start: 0.8159 (ttm) cc_final: 0.7887 (tpt) REVERT: A 966 PHE cc_start: 0.7074 (m-80) cc_final: 0.6527 (m-80) REVERT: B 189 GLU cc_start: 0.7139 (mm-30) cc_final: 0.6907 (mm-30) REVERT: B 392 GLN cc_start: 0.7611 (mp10) cc_final: 0.7312 (mp10) REVERT: B 573 ILE cc_start: 0.8593 (tp) cc_final: 0.8347 (tp) REVERT: B 585 MET cc_start: 0.8562 (mmt) cc_final: 0.8157 (mmt) REVERT: B 814 PHE cc_start: 0.7120 (t80) cc_final: 0.6889 (t80) REVERT: C 50 LEU cc_start: 0.8534 (pt) cc_final: 0.8209 (pt) REVERT: C 414 MET cc_start: 0.7954 (ptm) cc_final: 0.7629 (ptp) REVERT: C 635 SER cc_start: 0.9043 (t) cc_final: 0.8817 (p) REVERT: C 863 TYR cc_start: 0.5643 (m-10) cc_final: 0.5406 (m-10) REVERT: C 891 PHE cc_start: 0.8161 (m-10) cc_final: 0.7858 (m-80) REVERT: C 907 MET cc_start: 0.2201 (ppp) cc_final: 0.1253 (tpt) REVERT: C 965 PHE cc_start: 0.8780 (m-80) cc_final: 0.8511 (m-80) REVERT: C 966 PHE cc_start: 0.7260 (m-80) cc_final: 0.6473 (m-80) REVERT: C 1002 LYS cc_start: 0.7161 (ttmp) cc_final: 0.6618 (mtmt) REVERT: C 1009 PHE cc_start: 0.7217 (m-80) cc_final: 0.6819 (t80) REVERT: D 189 GLU cc_start: 0.7397 (mm-30) cc_final: 0.7032 (mm-30) REVERT: D 248 VAL cc_start: 0.7781 (OUTLIER) cc_final: 0.7553 (t) REVERT: D 361 MET cc_start: 0.8038 (mtp) cc_final: 0.7759 (mtp) REVERT: D 392 GLN cc_start: 0.7348 (mp10) cc_final: 0.7007 (mp10) REVERT: D 408 MET cc_start: 0.6989 (OUTLIER) cc_final: 0.6290 (mmp) REVERT: D 527 MET cc_start: 0.7251 (OUTLIER) cc_final: 0.6749 (mmt) REVERT: D 585 MET cc_start: 0.8505 (mmt) cc_final: 0.8232 (mmm) REVERT: E 88 TRP cc_start: 0.5703 (m100) cc_final: 0.5374 (t60) REVERT: E 115 VAL cc_start: 0.6553 (OUTLIER) cc_final: 0.6185 (m) REVERT: E 116 MET cc_start: 0.0777 (tpp) cc_final: -0.0152 (pmm) REVERT: E 122 ILE cc_start: 0.6563 (OUTLIER) cc_final: 0.6195 (mm) REVERT: F 116 MET cc_start: 0.0877 (tpp) cc_final: 0.0304 (pmm) REVERT: F 117 TYR cc_start: 0.4598 (OUTLIER) cc_final: 0.2651 (t80) outliers start: 98 outliers final: 59 residues processed: 460 average time/residue: 0.4155 time to fit residues: 318.2067 Evaluate side-chains 420 residues out of total 3256 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 354 time to evaluate : 4.431 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 VAL Chi-restraints excluded: chain A residue 34 VAL Chi-restraints excluded: chain A residue 144 SER Chi-restraints excluded: chain A residue 180 LEU Chi-restraints excluded: chain A residue 182 GLN Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 278 ILE Chi-restraints excluded: chain A residue 335 GLN Chi-restraints excluded: chain A residue 350 ASN Chi-restraints excluded: chain A residue 447 ASP Chi-restraints excluded: chain A residue 508 GLN Chi-restraints excluded: chain A residue 543 VAL Chi-restraints excluded: chain A residue 626 VAL Chi-restraints excluded: chain A residue 700 TYR Chi-restraints excluded: chain A residue 750 VAL Chi-restraints excluded: chain A residue 907 MET Chi-restraints excluded: chain A residue 972 SER Chi-restraints excluded: chain A residue 974 VAL Chi-restraints excluded: chain A residue 1023 MET Chi-restraints excluded: chain B residue 274 HIS Chi-restraints excluded: chain B residue 299 LEU Chi-restraints excluded: chain B residue 341 LEU Chi-restraints excluded: chain B residue 358 ILE Chi-restraints excluded: chain B residue 400 ILE Chi-restraints excluded: chain B residue 515 PHE Chi-restraints excluded: chain B residue 538 VAL Chi-restraints excluded: chain B residue 589 CYS Chi-restraints excluded: chain B residue 591 ILE Chi-restraints excluded: chain B residue 683 VAL Chi-restraints excluded: chain B residue 721 MET Chi-restraints excluded: chain B residue 773 CYS Chi-restraints excluded: chain C residue 31 VAL Chi-restraints excluded: chain C residue 34 VAL Chi-restraints excluded: chain C residue 144 SER Chi-restraints excluded: chain C residue 208 VAL Chi-restraints excluded: chain C residue 248 VAL Chi-restraints excluded: chain C residue 335 GLN Chi-restraints excluded: chain C residue 350 ASN Chi-restraints excluded: chain C residue 447 ASP Chi-restraints excluded: chain C residue 527 MET Chi-restraints excluded: chain C residue 543 VAL Chi-restraints excluded: chain C residue 626 VAL Chi-restraints excluded: chain C residue 748 LEU Chi-restraints excluded: chain C residue 750 VAL Chi-restraints excluded: chain C residue 890 CYS Chi-restraints excluded: chain C residue 985 ASN Chi-restraints excluded: chain D residue 248 VAL Chi-restraints excluded: chain D residue 274 HIS Chi-restraints excluded: chain D residue 299 LEU Chi-restraints excluded: chain D residue 358 ILE Chi-restraints excluded: chain D residue 408 MET Chi-restraints excluded: chain D residue 456 ASP Chi-restraints excluded: chain D residue 463 MET Chi-restraints excluded: chain D residue 515 PHE Chi-restraints excluded: chain D residue 527 MET Chi-restraints excluded: chain D residue 589 CYS Chi-restraints excluded: chain D residue 683 VAL Chi-restraints excluded: chain D residue 773 CYS Chi-restraints excluded: chain E residue 27 HIS Chi-restraints excluded: chain E residue 115 VAL Chi-restraints excluded: chain E residue 122 ILE Chi-restraints excluded: chain E residue 143 LEU Chi-restraints excluded: chain F residue 67 LEU Chi-restraints excluded: chain F residue 71 GLU Chi-restraints excluded: chain F residue 117 TYR Chi-restraints excluded: chain F residue 143 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 378 random chunks: chunk 304 optimal weight: 3.9990 chunk 207 optimal weight: 2.9990 chunk 5 optimal weight: 8.9990 chunk 272 optimal weight: 10.0000 chunk 150 optimal weight: 5.9990 chunk 311 optimal weight: 5.9990 chunk 252 optimal weight: 9.9990 chunk 0 optimal weight: 10.0000 chunk 186 optimal weight: 1.9990 chunk 327 optimal weight: 3.9990 chunk 92 optimal weight: 5.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 107 HIS A 167 ASN ** A 954 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 202 ASN ** B 337 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 344 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 350 ASN C 107 HIS C 586 GLN C 985 ASN D 107 HIS ** D 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 246 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 337 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 344 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 764 ASN ** E 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 107 HIS ** F 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 107 HIS Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8141 moved from start: 0.3756 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.084 31813 Z= 0.505 Angle : 0.993 34.023 42920 Z= 0.454 Chirality : 0.085 2.263 4702 Planarity : 0.005 0.063 5286 Dihedral : 18.021 178.482 5184 Min Nonbonded Distance : 2.089 Molprobity Statistics. All-atom Clashscore : 13.44 Ramachandran Plot: Outliers : 0.37 % Allowed : 13.82 % Favored : 85.81 % Rotamer: Outliers : 3.44 % Allowed : 15.08 % Favored : 81.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.21 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.38 % 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: -3.10 (0.13), residues: 3762 helix: -0.87 (0.12), residues: 1774 sheet: -3.72 (0.24), residues: 360 loop : -3.01 (0.14), residues: 1628 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A1005 HIS 0.009 0.002 HIS F 107 PHE 0.030 0.002 PHE C 495 TYR 0.031 0.002 TYR C1001 ARG 0.008 0.001 ARG B 331 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7524 Ramachandran restraints generated. 3762 Oldfield, 0 Emsley, 3762 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7524 Ramachandran restraints generated. 3762 Oldfield, 0 Emsley, 3762 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 470 residues out of total 3256 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 112 poor density : 358 time to evaluate : 3.659 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: A 50 LEU cc_start: 0.8988 (pt) cc_final: 0.8760 (pt) REVERT: A 414 MET cc_start: 0.7951 (ptm) cc_final: 0.7685 (ptp) REVERT: A 585 MET cc_start: 0.8490 (mpt) cc_final: 0.7975 (mpt) REVERT: A 642 GLN cc_start: 0.7833 (mp10) cc_final: 0.7474 (mp10) REVERT: A 860 TYR cc_start: 0.7531 (m-80) cc_final: 0.7237 (m-80) REVERT: A 879 LYS cc_start: 0.8092 (ttpt) cc_final: 0.7834 (mmmt) REVERT: A 891 PHE cc_start: 0.8281 (m-10) cc_final: 0.8005 (m-80) REVERT: A 939 MET cc_start: 0.8159 (ttm) cc_final: 0.7871 (tpt) REVERT: A 966 PHE cc_start: 0.7059 (m-80) cc_final: 0.6650 (m-80) REVERT: A 988 MET cc_start: 0.8266 (tmm) cc_final: 0.7970 (tmm) REVERT: B 41 PHE cc_start: 0.4994 (OUTLIER) cc_final: 0.3616 (p90) REVERT: B 357 THR cc_start: 0.7745 (p) cc_final: 0.7500 (t) REVERT: B 392 GLN cc_start: 0.7629 (mp10) cc_final: 0.7309 (mp10) REVERT: B 573 ILE cc_start: 0.8677 (tp) cc_final: 0.8426 (tp) REVERT: B 585 MET cc_start: 0.8733 (mmt) cc_final: 0.8315 (mmt) REVERT: C 50 LEU cc_start: 0.8948 (pt) cc_final: 0.8687 (pt) REVERT: C 414 MET cc_start: 0.8033 (ptm) cc_final: 0.7779 (ptp) REVERT: C 635 SER cc_start: 0.9136 (t) cc_final: 0.8920 (p) REVERT: C 721 MET cc_start: 0.8220 (ptt) cc_final: 0.7971 (ptt) REVERT: C 879 LYS cc_start: 0.8009 (ttpt) cc_final: 0.7772 (mmmt) REVERT: C 891 PHE cc_start: 0.8299 (m-10) cc_final: 0.7989 (m-80) REVERT: C 924 MET cc_start: 0.7566 (ptp) cc_final: 0.6979 (mtm) REVERT: C 925 ILE cc_start: 0.9111 (mt) cc_final: 0.8723 (mt) REVERT: C 965 PHE cc_start: 0.8826 (m-80) cc_final: 0.8573 (m-80) REVERT: C 985 ASN cc_start: 0.7556 (OUTLIER) cc_final: 0.6873 (p0) REVERT: C 1009 PHE cc_start: 0.7371 (m-80) cc_final: 0.7008 (t80) REVERT: D 133 PHE cc_start: 0.8982 (OUTLIER) cc_final: 0.8746 (m-10) REVERT: D 189 GLU cc_start: 0.7409 (mm-30) cc_final: 0.7033 (mm-30) REVERT: D 269 GLU cc_start: 0.7375 (tp30) cc_final: 0.7132 (tp30) REVERT: D 361 MET cc_start: 0.8149 (mtp) cc_final: 0.7846 (mtp) REVERT: D 408 MET cc_start: 0.7072 (OUTLIER) cc_final: 0.6748 (mmt) REVERT: D 527 MET cc_start: 0.7533 (OUTLIER) cc_final: 0.7046 (mmt) REVERT: D 585 MET cc_start: 0.8620 (mmt) cc_final: 0.8272 (mmt) REVERT: E 116 MET cc_start: 0.1136 (tpp) cc_final: -0.0015 (pmm) REVERT: F 116 MET cc_start: 0.0985 (tpp) cc_final: -0.0003 (pmm) REVERT: F 117 TYR cc_start: 0.5350 (OUTLIER) cc_final: 0.3434 (t80) REVERT: F 122 ILE cc_start: 0.6621 (OUTLIER) cc_final: 0.6299 (tp) outliers start: 112 outliers final: 74 residues processed: 435 average time/residue: 0.4200 time to fit residues: 305.1392 Evaluate side-chains 412 residues out of total 3256 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 81 poor density : 331 time to evaluate : 3.471 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 VAL Chi-restraints excluded: chain A residue 34 VAL Chi-restraints excluded: chain A residue 106 THR Chi-restraints excluded: chain A residue 144 SER Chi-restraints excluded: chain A residue 180 LEU Chi-restraints excluded: chain A residue 182 GLN Chi-restraints excluded: chain A residue 208 VAL Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 285 THR Chi-restraints excluded: chain A residue 299 LEU Chi-restraints excluded: chain A residue 335 GLN Chi-restraints excluded: chain A residue 350 ASN Chi-restraints excluded: chain A residue 447 ASP Chi-restraints excluded: chain A residue 508 GLN Chi-restraints excluded: chain A residue 541 PHE Chi-restraints excluded: chain A residue 626 VAL Chi-restraints excluded: chain A residue 645 ILE Chi-restraints excluded: chain A residue 700 TYR Chi-restraints excluded: chain A residue 720 THR Chi-restraints excluded: chain A residue 750 VAL Chi-restraints excluded: chain A residue 922 LEU Chi-restraints excluded: chain A residue 972 SER Chi-restraints excluded: chain A residue 974 VAL Chi-restraints excluded: chain A residue 1015 LEU Chi-restraints excluded: chain A residue 1023 MET Chi-restraints excluded: chain B residue 41 PHE Chi-restraints excluded: chain B residue 225 LEU Chi-restraints excluded: chain B residue 299 LEU Chi-restraints excluded: chain B residue 341 LEU Chi-restraints excluded: chain B residue 358 ILE Chi-restraints excluded: chain B residue 515 PHE Chi-restraints excluded: chain B residue 538 VAL Chi-restraints excluded: chain B residue 589 CYS Chi-restraints excluded: chain B residue 683 VAL Chi-restraints excluded: chain B residue 721 MET Chi-restraints excluded: chain B residue 773 CYS Chi-restraints excluded: chain C residue 31 VAL Chi-restraints excluded: chain C residue 34 VAL Chi-restraints excluded: chain C residue 144 SER Chi-restraints excluded: chain C residue 180 LEU Chi-restraints excluded: chain C residue 182 GLN Chi-restraints excluded: chain C residue 208 VAL Chi-restraints excluded: chain C residue 248 VAL Chi-restraints excluded: chain C residue 299 LEU Chi-restraints excluded: chain C residue 335 GLN Chi-restraints excluded: chain C residue 350 ASN Chi-restraints excluded: chain C residue 447 ASP Chi-restraints excluded: chain C residue 508 GLN Chi-restraints excluded: chain C residue 541 PHE Chi-restraints excluded: chain C residue 543 VAL Chi-restraints excluded: chain C residue 626 VAL Chi-restraints excluded: chain C residue 720 THR Chi-restraints excluded: chain C residue 748 LEU Chi-restraints excluded: chain C residue 750 VAL Chi-restraints excluded: chain C residue 890 CYS Chi-restraints excluded: chain C residue 960 PHE Chi-restraints excluded: chain C residue 985 ASN Chi-restraints excluded: chain C residue 1015 LEU Chi-restraints excluded: chain D residue 133 PHE Chi-restraints excluded: chain D residue 274 HIS Chi-restraints excluded: chain D residue 299 LEU Chi-restraints excluded: chain D residue 358 ILE Chi-restraints excluded: chain D residue 408 MET Chi-restraints excluded: chain D residue 463 MET Chi-restraints excluded: chain D residue 515 PHE Chi-restraints excluded: chain D residue 527 MET Chi-restraints excluded: chain D residue 538 VAL Chi-restraints excluded: chain D residue 589 CYS Chi-restraints excluded: chain D residue 591 ILE Chi-restraints excluded: chain D residue 633 ILE Chi-restraints excluded: chain D residue 683 VAL Chi-restraints excluded: chain D residue 721 MET Chi-restraints excluded: chain D residue 789 LEU Chi-restraints excluded: chain D residue 798 ILE Chi-restraints excluded: chain E residue 27 HIS Chi-restraints excluded: chain E residue 143 LEU Chi-restraints excluded: chain F residue 67 LEU Chi-restraints excluded: chain F residue 95 ILE Chi-restraints excluded: chain F residue 117 TYR Chi-restraints excluded: chain F residue 122 ILE Chi-restraints excluded: chain F residue 143 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 378 random chunks: chunk 122 optimal weight: 7.9990 chunk 329 optimal weight: 0.7980 chunk 72 optimal weight: 3.9990 chunk 214 optimal weight: 0.9980 chunk 90 optimal weight: 6.9990 chunk 365 optimal weight: 0.9990 chunk 303 optimal weight: 0.2980 chunk 169 optimal weight: 0.6980 chunk 30 optimal weight: 30.0000 chunk 120 optimal weight: 2.9990 chunk 192 optimal weight: 0.9980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 412 HIS B 46 HIS ** C 985 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 246 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 107 HIS F 107 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8013 moved from start: 0.4007 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 31813 Z= 0.181 Angle : 0.860 33.380 42920 Z= 0.380 Chirality : 0.081 2.230 4702 Planarity : 0.003 0.049 5286 Dihedral : 17.556 178.853 5184 Min Nonbonded Distance : 2.136 Molprobity Statistics. All-atom Clashscore : 11.20 Ramachandran Plot: Outliers : 0.27 % Allowed : 11.08 % Favored : 88.65 % Rotamer: Outliers : 2.33 % Allowed : 17.32 % Favored : 80.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.21 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.33 % 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: -2.63 (0.14), residues: 3762 helix: -0.42 (0.12), residues: 1790 sheet: -3.46 (0.26), residues: 344 loop : -2.88 (0.14), residues: 1628 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A 262 HIS 0.010 0.001 HIS E 107 PHE 0.022 0.001 PHE F 23 TYR 0.026 0.001 TYR C1001 ARG 0.007 0.000 ARG B 331 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7524 Ramachandran restraints generated. 3762 Oldfield, 0 Emsley, 3762 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7524 Ramachandran restraints generated. 3762 Oldfield, 0 Emsley, 3762 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 451 residues out of total 3256 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 76 poor density : 375 time to evaluate : 3.732 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: A 50 LEU cc_start: 0.8602 (pt) cc_final: 0.8318 (pt) REVERT: A 414 MET cc_start: 0.7932 (ptm) cc_final: 0.7672 (ptp) REVERT: A 585 MET cc_start: 0.8340 (mpt) cc_final: 0.7839 (mpt) REVERT: A 642 GLN cc_start: 0.7760 (mp10) cc_final: 0.7475 (mp10) REVERT: A 879 LYS cc_start: 0.8016 (ttpt) cc_final: 0.7739 (mmmt) REVERT: A 891 PHE cc_start: 0.8275 (m-10) cc_final: 0.7743 (m-10) REVERT: A 966 PHE cc_start: 0.7056 (m-80) cc_final: 0.6509 (m-80) REVERT: A 988 MET cc_start: 0.8172 (tmm) cc_final: 0.7847 (tmm) REVERT: A 1009 PHE cc_start: 0.7633 (m-80) cc_final: 0.7325 (t80) REVERT: B 573 ILE cc_start: 0.8450 (tp) cc_final: 0.8214 (tp) REVERT: B 762 LEU cc_start: 0.9360 (OUTLIER) cc_final: 0.9145 (tt) REVERT: C 50 LEU cc_start: 0.8552 (pt) cc_final: 0.8239 (pt) REVERT: C 414 MET cc_start: 0.7948 (ptm) cc_final: 0.7572 (ptp) REVERT: C 721 MET cc_start: 0.8030 (ptt) cc_final: 0.7782 (ptt) REVERT: C 879 LYS cc_start: 0.7950 (ttpt) cc_final: 0.7723 (mmmt) REVERT: C 891 PHE cc_start: 0.8251 (m-10) cc_final: 0.7946 (m-80) REVERT: C 925 ILE cc_start: 0.9023 (mt) cc_final: 0.8725 (mt) REVERT: C 965 PHE cc_start: 0.8808 (m-80) cc_final: 0.8599 (m-80) REVERT: C 966 PHE cc_start: 0.7376 (m-80) cc_final: 0.6718 (m-80) REVERT: C 985 ASN cc_start: 0.7431 (p0) cc_final: 0.6457 (p0) REVERT: C 1009 PHE cc_start: 0.7211 (m-80) cc_final: 0.6900 (t80) REVERT: D 189 GLU cc_start: 0.7300 (mm-30) cc_final: 0.7059 (mm-30) REVERT: D 269 GLU cc_start: 0.7507 (tp30) cc_final: 0.7247 (tp30) REVERT: D 361 MET cc_start: 0.8172 (mtp) cc_final: 0.7880 (mtp) REVERT: E 115 VAL cc_start: 0.6189 (OUTLIER) cc_final: 0.5983 (m) REVERT: E 116 MET cc_start: 0.0967 (tpp) cc_final: 0.0437 (pmm) REVERT: E 122 ILE cc_start: 0.6688 (OUTLIER) cc_final: 0.6266 (mm) REVERT: F 117 TYR cc_start: 0.5293 (OUTLIER) cc_final: 0.3752 (t80) outliers start: 76 outliers final: 56 residues processed: 425 average time/residue: 0.4107 time to fit residues: 291.7817 Evaluate side-chains 397 residues out of total 3256 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 337 time to evaluate : 3.390 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 VAL Chi-restraints excluded: chain A residue 34 VAL Chi-restraints excluded: chain A residue 182 GLN Chi-restraints excluded: chain A residue 208 VAL Chi-restraints excluded: chain A residue 299 LEU Chi-restraints excluded: chain A residue 335 GLN Chi-restraints excluded: chain A residue 350 ASN Chi-restraints excluded: chain A residue 447 ASP Chi-restraints excluded: chain A residue 508 GLN Chi-restraints excluded: chain A residue 543 VAL Chi-restraints excluded: chain A residue 626 VAL Chi-restraints excluded: chain A residue 639 LEU Chi-restraints excluded: chain A residue 700 TYR Chi-restraints excluded: chain A residue 960 PHE Chi-restraints excluded: chain A residue 974 VAL Chi-restraints excluded: chain A residue 1023 MET Chi-restraints excluded: chain B residue 299 LEU Chi-restraints excluded: chain B residue 341 LEU Chi-restraints excluded: chain B residue 358 ILE Chi-restraints excluded: chain B residue 515 PHE Chi-restraints excluded: chain B residue 721 MET Chi-restraints excluded: chain B residue 762 LEU Chi-restraints excluded: chain B residue 773 CYS Chi-restraints excluded: chain C residue 31 VAL Chi-restraints excluded: chain C residue 34 VAL Chi-restraints excluded: chain C residue 182 GLN Chi-restraints excluded: chain C residue 197 GLU Chi-restraints excluded: chain C residue 208 VAL Chi-restraints excluded: chain C residue 248 VAL Chi-restraints excluded: chain C residue 335 GLN Chi-restraints excluded: chain C residue 350 ASN Chi-restraints excluded: chain C residue 508 GLN Chi-restraints excluded: chain C residue 543 VAL Chi-restraints excluded: chain C residue 626 VAL Chi-restraints excluded: chain C residue 639 LEU Chi-restraints excluded: chain C residue 748 LEU Chi-restraints excluded: chain C residue 750 VAL Chi-restraints excluded: chain C residue 890 CYS Chi-restraints excluded: chain C residue 960 PHE Chi-restraints excluded: chain C residue 972 SER Chi-restraints excluded: chain D residue 225 LEU Chi-restraints excluded: chain D residue 274 HIS Chi-restraints excluded: chain D residue 299 LEU Chi-restraints excluded: chain D residue 358 ILE Chi-restraints excluded: chain D residue 515 PHE Chi-restraints excluded: chain D residue 527 MET Chi-restraints excluded: chain D residue 591 ILE Chi-restraints excluded: chain D residue 647 TYR Chi-restraints excluded: chain D residue 773 CYS Chi-restraints excluded: chain D residue 789 LEU Chi-restraints excluded: chain D residue 811 LEU Chi-restraints excluded: chain E residue 27 HIS Chi-restraints excluded: chain E residue 95 ILE Chi-restraints excluded: chain E residue 115 VAL Chi-restraints excluded: chain E residue 122 ILE Chi-restraints excluded: chain E residue 143 LEU Chi-restraints excluded: chain F residue 67 LEU Chi-restraints excluded: chain F residue 95 ILE Chi-restraints excluded: chain F residue 117 TYR Chi-restraints excluded: chain F residue 143 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 378 random chunks: chunk 352 optimal weight: 6.9990 chunk 41 optimal weight: 0.8980 chunk 208 optimal weight: 0.0050 chunk 267 optimal weight: 0.0060 chunk 206 optimal weight: 0.5980 chunk 307 optimal weight: 0.2980 chunk 204 optimal weight: 7.9990 chunk 364 optimal weight: 2.9990 chunk 228 optimal weight: 8.9990 chunk 222 optimal weight: 0.9980 chunk 168 optimal weight: 0.7980 overall best weight: 0.3410 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 412 HIS C 985 ASN ** D 246 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 107 HIS F 107 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7962 moved from start: 0.4257 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 31813 Z= 0.157 Angle : 0.846 33.020 42920 Z= 0.370 Chirality : 0.080 2.174 4702 Planarity : 0.003 0.041 5286 Dihedral : 17.100 178.486 5184 Min Nonbonded Distance : 2.157 Molprobity Statistics. All-atom Clashscore : 10.60 Ramachandran Plot: Outliers : 0.24 % Allowed : 11.16 % Favored : 88.60 % Rotamer: Outliers : 2.18 % Allowed : 17.54 % Favored : 80.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.21 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.27 % 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: -2.24 (0.14), residues: 3762 helix: -0.03 (0.13), residues: 1774 sheet: -3.25 (0.26), residues: 364 loop : -2.75 (0.15), residues: 1624 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.001 TRP E 103 HIS 0.011 0.001 HIS F 107 PHE 0.019 0.001 PHE A 965 TYR 0.025 0.001 TYR C1001 ARG 0.007 0.000 ARG B 30 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7524 Ramachandran restraints generated. 3762 Oldfield, 0 Emsley, 3762 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7524 Ramachandran restraints generated. 3762 Oldfield, 0 Emsley, 3762 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 436 residues out of total 3256 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 365 time to evaluate : 3.379 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: A 50 LEU cc_start: 0.8323 (pt) cc_final: 0.8043 (pt) REVERT: A 414 MET cc_start: 0.7917 (ptm) cc_final: 0.7656 (ptp) REVERT: A 585 MET cc_start: 0.8245 (mpt) cc_final: 0.7796 (mpt) REVERT: A 638 ASP cc_start: 0.8136 (m-30) cc_final: 0.7536 (t0) REVERT: A 642 GLN cc_start: 0.7706 (mp10) cc_final: 0.7281 (mp10) REVERT: A 879 LYS cc_start: 0.7937 (ttpt) cc_final: 0.7682 (mmmt) REVERT: A 891 PHE cc_start: 0.8279 (m-10) cc_final: 0.7751 (m-10) REVERT: A 966 PHE cc_start: 0.7109 (m-80) cc_final: 0.6701 (m-80) REVERT: A 988 MET cc_start: 0.8043 (tmm) cc_final: 0.7717 (tmm) REVERT: A 1009 PHE cc_start: 0.7591 (m-80) cc_final: 0.7364 (t80) REVERT: B 573 ILE cc_start: 0.8423 (tp) cc_final: 0.8140 (tp) REVERT: B 585 MET cc_start: 0.8369 (mmt) cc_final: 0.8001 (mtt) REVERT: B 762 LEU cc_start: 0.9301 (OUTLIER) cc_final: 0.9076 (tt) REVERT: C 414 MET cc_start: 0.7931 (ptm) cc_final: 0.7550 (ptp) REVERT: C 638 ASP cc_start: 0.8312 (m-30) cc_final: 0.7946 (t0) REVERT: C 721 MET cc_start: 0.7860 (ptt) cc_final: 0.7635 (ptt) REVERT: C 891 PHE cc_start: 0.8251 (m-10) cc_final: 0.7957 (m-80) REVERT: C 924 MET cc_start: 0.7556 (ptp) cc_final: 0.6901 (mtm) REVERT: C 925 ILE cc_start: 0.9017 (mt) cc_final: 0.8662 (mt) REVERT: C 965 PHE cc_start: 0.8801 (m-80) cc_final: 0.8593 (m-80) REVERT: C 966 PHE cc_start: 0.7420 (m-80) cc_final: 0.6725 (m-80) REVERT: C 1009 PHE cc_start: 0.7157 (m-80) cc_final: 0.6919 (t80) REVERT: D 189 GLU cc_start: 0.7303 (mm-30) cc_final: 0.6941 (mm-30) REVERT: D 269 GLU cc_start: 0.7510 (tp30) cc_final: 0.7251 (tp30) REVERT: D 361 MET cc_start: 0.8174 (mtp) cc_final: 0.7880 (mtp) REVERT: D 527 MET cc_start: 0.7274 (OUTLIER) cc_final: 0.6851 (mmt) REVERT: E 115 VAL cc_start: 0.5703 (OUTLIER) cc_final: 0.5372 (m) REVERT: E 116 MET cc_start: 0.1094 (tpp) cc_final: 0.0334 (pmm) REVERT: E 122 ILE cc_start: 0.6338 (OUTLIER) cc_final: 0.5899 (mm) REVERT: F 116 MET cc_start: 0.1055 (tpp) cc_final: -0.0521 (pmm) REVERT: F 117 TYR cc_start: 0.5236 (OUTLIER) cc_final: 0.3346 (t80) outliers start: 71 outliers final: 51 residues processed: 414 average time/residue: 0.3977 time to fit residues: 275.2524 Evaluate side-chains 385 residues out of total 3256 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 329 time to evaluate : 3.507 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 VAL Chi-restraints excluded: chain A residue 34 VAL Chi-restraints excluded: chain A residue 208 VAL Chi-restraints excluded: chain A residue 274 HIS Chi-restraints excluded: chain A residue 278 ILE Chi-restraints excluded: chain A residue 299 LEU Chi-restraints excluded: chain A residue 335 GLN Chi-restraints excluded: chain A residue 350 ASN Chi-restraints excluded: chain A residue 508 GLN Chi-restraints excluded: chain A residue 700 TYR Chi-restraints excluded: chain A residue 907 MET Chi-restraints excluded: chain A residue 960 PHE Chi-restraints excluded: chain A residue 968 LEU Chi-restraints excluded: chain A residue 1023 MET Chi-restraints excluded: chain B residue 63 CYS Chi-restraints excluded: chain B residue 341 LEU Chi-restraints excluded: chain B residue 358 ILE Chi-restraints excluded: chain B residue 515 PHE Chi-restraints excluded: chain B residue 721 MET Chi-restraints excluded: chain B residue 762 LEU Chi-restraints excluded: chain B residue 773 CYS Chi-restraints excluded: chain C residue 31 VAL Chi-restraints excluded: chain C residue 34 VAL Chi-restraints excluded: chain C residue 182 GLN Chi-restraints excluded: chain C residue 197 GLU Chi-restraints excluded: chain C residue 208 VAL Chi-restraints excluded: chain C residue 335 GLN Chi-restraints excluded: chain C residue 350 ASN Chi-restraints excluded: chain C residue 447 ASP Chi-restraints excluded: chain C residue 508 GLN Chi-restraints excluded: chain C residue 543 VAL Chi-restraints excluded: chain C residue 626 VAL Chi-restraints excluded: chain C residue 639 LEU Chi-restraints excluded: chain C residue 645 ILE Chi-restraints excluded: chain C residue 748 LEU Chi-restraints excluded: chain C residue 890 CYS Chi-restraints excluded: chain C residue 960 PHE Chi-restraints excluded: chain C residue 985 ASN Chi-restraints excluded: chain D residue 299 LEU Chi-restraints excluded: chain D residue 341 LEU Chi-restraints excluded: chain D residue 358 ILE Chi-restraints excluded: chain D residue 515 PHE Chi-restraints excluded: chain D residue 527 MET Chi-restraints excluded: chain D residue 577 LEU Chi-restraints excluded: chain D residue 647 TYR Chi-restraints excluded: chain D residue 773 CYS Chi-restraints excluded: chain D residue 789 LEU Chi-restraints excluded: chain E residue 27 HIS Chi-restraints excluded: chain E residue 95 ILE Chi-restraints excluded: chain E residue 115 VAL Chi-restraints excluded: chain E residue 122 ILE Chi-restraints excluded: chain E residue 143 LEU Chi-restraints excluded: chain F residue 67 LEU Chi-restraints excluded: chain F residue 95 ILE Chi-restraints excluded: chain F residue 117 TYR Chi-restraints excluded: chain F residue 143 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 378 random chunks: chunk 225 optimal weight: 0.4980 chunk 145 optimal weight: 4.9990 chunk 217 optimal weight: 0.0570 chunk 109 optimal weight: 1.9990 chunk 71 optimal weight: 3.9990 chunk 70 optimal weight: 8.9990 chunk 231 optimal weight: 0.7980 chunk 248 optimal weight: 4.9990 chunk 180 optimal weight: 0.8980 chunk 33 optimal weight: 4.9990 chunk 286 optimal weight: 1.9990 overall best weight: 0.8500 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 954 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 337 GLN B 344 ASN ** C 985 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 246 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 107 HIS F 107 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7979 moved from start: 0.4383 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 31813 Z= 0.181 Angle : 0.851 33.042 42920 Z= 0.369 Chirality : 0.081 2.165 4702 Planarity : 0.003 0.038 5286 Dihedral : 16.827 178.526 5183 Min Nonbonded Distance : 2.151 Molprobity Statistics. All-atom Clashscore : 10.47 Ramachandran Plot: Outliers : 0.27 % Allowed : 11.14 % Favored : 88.60 % Rotamer: Outliers : 2.24 % Allowed : 17.91 % Favored : 79.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.21 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.27 % 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: -2.09 (0.14), residues: 3762 helix: 0.13 (0.13), residues: 1788 sheet: -3.15 (0.26), residues: 352 loop : -2.77 (0.15), residues: 1622 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP C 262 HIS 0.009 0.001 HIS F 107 PHE 0.031 0.001 PHE D 517 TYR 0.025 0.001 TYR C1001 ARG 0.005 0.000 ARG B 331 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7524 Ramachandran restraints generated. 3762 Oldfield, 0 Emsley, 3762 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7524 Ramachandran restraints generated. 3762 Oldfield, 0 Emsley, 3762 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 423 residues out of total 3256 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 350 time to evaluate : 3.322 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: A 414 MET cc_start: 0.7945 (ptm) cc_final: 0.7674 (ptp) REVERT: A 638 ASP cc_start: 0.8107 (m-30) cc_final: 0.7511 (t0) REVERT: A 642 GLN cc_start: 0.7692 (mp10) cc_final: 0.7209 (mp10) REVERT: A 879 LYS cc_start: 0.7956 (ttpt) cc_final: 0.7746 (mmmt) REVERT: A 891 PHE cc_start: 0.8285 (m-10) cc_final: 0.7727 (m-10) REVERT: A 939 MET cc_start: 0.8241 (tpt) cc_final: 0.7388 (ttt) REVERT: A 966 PHE cc_start: 0.7248 (m-80) cc_final: 0.6560 (m-80) REVERT: A 988 MET cc_start: 0.8020 (tmm) cc_final: 0.7691 (tmm) REVERT: A 1009 PHE cc_start: 0.7616 (m-80) cc_final: 0.7335 (t80) REVERT: B 573 ILE cc_start: 0.8451 (tp) cc_final: 0.8155 (tp) REVERT: B 585 MET cc_start: 0.8441 (mmt) cc_final: 0.8131 (mtt) REVERT: C 414 MET cc_start: 0.7943 (ptm) cc_final: 0.7566 (ptp) REVERT: C 642 GLN cc_start: 0.7587 (mp10) cc_final: 0.7312 (mp10) REVERT: C 721 MET cc_start: 0.7847 (ptt) cc_final: 0.7636 (ptt) REVERT: C 891 PHE cc_start: 0.8260 (m-10) cc_final: 0.7959 (m-80) REVERT: C 924 MET cc_start: 0.7587 (ptp) cc_final: 0.6922 (mtm) REVERT: C 925 ILE cc_start: 0.9078 (mt) cc_final: 0.8713 (mt) REVERT: C 965 PHE cc_start: 0.8794 (m-80) cc_final: 0.8579 (m-80) REVERT: C 966 PHE cc_start: 0.7419 (m-80) cc_final: 0.6804 (m-80) REVERT: C 985 ASN cc_start: 0.7588 (p0) cc_final: 0.6682 (p0) REVERT: D 189 GLU cc_start: 0.7329 (mm-30) cc_final: 0.6953 (mm-30) REVERT: D 269 GLU cc_start: 0.7491 (tp30) cc_final: 0.7220 (tp30) REVERT: D 408 MET cc_start: 0.7201 (mmm) cc_final: 0.6954 (mmp) REVERT: D 527 MET cc_start: 0.7311 (OUTLIER) cc_final: 0.6893 (mmt) REVERT: D 585 MET cc_start: 0.8386 (mmt) cc_final: 0.8067 (mtt) REVERT: E 116 MET cc_start: 0.1528 (tpp) cc_final: 0.0233 (pmm) REVERT: E 130 TYR cc_start: 0.4352 (m-80) cc_final: 0.4117 (m-80) REVERT: F 116 MET cc_start: 0.1170 (tpp) cc_final: -0.0465 (pmm) REVERT: F 117 TYR cc_start: 0.5449 (OUTLIER) cc_final: 0.3474 (t80) outliers start: 73 outliers final: 59 residues processed: 403 average time/residue: 0.3755 time to fit residues: 257.2508 Evaluate side-chains 393 residues out of total 3256 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 332 time to evaluate : 3.716 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 VAL Chi-restraints excluded: chain A residue 34 VAL Chi-restraints excluded: chain A residue 180 LEU Chi-restraints excluded: chain A residue 182 GLN Chi-restraints excluded: chain A residue 208 VAL Chi-restraints excluded: chain A residue 274 HIS Chi-restraints excluded: chain A residue 278 ILE Chi-restraints excluded: chain A residue 299 LEU Chi-restraints excluded: chain A residue 335 GLN Chi-restraints excluded: chain A residue 350 ASN Chi-restraints excluded: chain A residue 447 ASP Chi-restraints excluded: chain A residue 508 GLN Chi-restraints excluded: chain A residue 645 ILE Chi-restraints excluded: chain A residue 700 TYR Chi-restraints excluded: chain A residue 750 VAL Chi-restraints excluded: chain A residue 907 MET Chi-restraints excluded: chain A residue 922 LEU Chi-restraints excluded: chain A residue 960 PHE Chi-restraints excluded: chain A residue 968 LEU Chi-restraints excluded: chain A residue 972 SER Chi-restraints excluded: chain A residue 1023 MET Chi-restraints excluded: chain B residue 63 CYS Chi-restraints excluded: chain B residue 341 LEU Chi-restraints excluded: chain B residue 358 ILE Chi-restraints excluded: chain B residue 515 PHE Chi-restraints excluded: chain B residue 721 MET Chi-restraints excluded: chain B residue 773 CYS Chi-restraints excluded: chain C residue 31 VAL Chi-restraints excluded: chain C residue 34 VAL Chi-restraints excluded: chain C residue 180 LEU Chi-restraints excluded: chain C residue 182 GLN Chi-restraints excluded: chain C residue 197 GLU Chi-restraints excluded: chain C residue 208 VAL Chi-restraints excluded: chain C residue 335 GLN Chi-restraints excluded: chain C residue 350 ASN Chi-restraints excluded: chain C residue 447 ASP Chi-restraints excluded: chain C residue 508 GLN Chi-restraints excluded: chain C residue 639 LEU Chi-restraints excluded: chain C residue 645 ILE Chi-restraints excluded: chain C residue 748 LEU Chi-restraints excluded: chain C residue 890 CYS Chi-restraints excluded: chain C residue 960 PHE Chi-restraints excluded: chain D residue 299 LEU Chi-restraints excluded: chain D residue 341 LEU Chi-restraints excluded: chain D residue 358 ILE Chi-restraints excluded: chain D residue 515 PHE Chi-restraints excluded: chain D residue 527 MET Chi-restraints excluded: chain D residue 577 LEU Chi-restraints excluded: chain D residue 647 TYR Chi-restraints excluded: chain D residue 773 CYS Chi-restraints excluded: chain D residue 789 LEU Chi-restraints excluded: chain D residue 811 LEU Chi-restraints excluded: chain E residue 13 THR Chi-restraints excluded: chain E residue 27 HIS Chi-restraints excluded: chain E residue 61 CYS Chi-restraints excluded: chain E residue 95 ILE Chi-restraints excluded: chain E residue 143 LEU Chi-restraints excluded: chain F residue 67 LEU Chi-restraints excluded: chain F residue 95 ILE Chi-restraints excluded: chain F residue 117 TYR Chi-restraints excluded: chain F residue 143 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 378 random chunks: chunk 331 optimal weight: 2.9990 chunk 349 optimal weight: 9.9990 chunk 318 optimal weight: 4.9990 chunk 339 optimal weight: 5.9990 chunk 348 optimal weight: 0.6980 chunk 204 optimal weight: 5.9990 chunk 147 optimal weight: 0.5980 chunk 266 optimal weight: 0.9980 chunk 104 optimal weight: 2.9990 chunk 306 optimal weight: 0.3980 chunk 321 optimal weight: 0.7980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 182 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 954 HIS B 337 GLN B 344 ASN ** C 182 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 985 ASN ** D 246 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 107 HIS F 107 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7958 moved from start: 0.4560 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 31813 Z= 0.169 Angle : 0.848 32.937 42920 Z= 0.367 Chirality : 0.080 2.153 4702 Planarity : 0.003 0.038 5286 Dihedral : 16.491 178.588 5183 Min Nonbonded Distance : 2.147 Molprobity Statistics. All-atom Clashscore : 10.36 Ramachandran Plot: Outliers : 0.24 % Allowed : 11.03 % Favored : 88.73 % Rotamer: Outliers : 2.15 % Allowed : 18.24 % Favored : 79.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.21 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.24 % 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: -1.90 (0.14), residues: 3762 helix: 0.32 (0.13), residues: 1778 sheet: -3.08 (0.26), residues: 352 loop : -2.68 (0.15), residues: 1632 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP C 262 HIS 0.013 0.001 HIS F 107 PHE 0.027 0.001 PHE B 517 TYR 0.072 0.001 TYR E 117 ARG 0.005 0.000 ARG B 331 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7524 Ramachandran restraints generated. 3762 Oldfield, 0 Emsley, 3762 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7524 Ramachandran restraints generated. 3762 Oldfield, 0 Emsley, 3762 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 414 residues out of total 3256 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 344 time to evaluate : 3.137 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: A 414 MET cc_start: 0.7968 (ptm) cc_final: 0.7581 (ptp) REVERT: A 638 ASP cc_start: 0.8079 (m-30) cc_final: 0.7498 (t0) REVERT: A 642 GLN cc_start: 0.7656 (mp10) cc_final: 0.7180 (mp10) REVERT: A 816 TYR cc_start: 0.7476 (t80) cc_final: 0.6988 (t80) REVERT: A 891 PHE cc_start: 0.8263 (m-10) cc_final: 0.7715 (m-10) REVERT: A 936 LEU cc_start: 0.8300 (tp) cc_final: 0.8099 (tp) REVERT: A 939 MET cc_start: 0.8095 (tpt) cc_final: 0.7125 (ttt) REVERT: A 966 PHE cc_start: 0.7238 (m-80) cc_final: 0.6568 (m-80) REVERT: A 988 MET cc_start: 0.7940 (tmm) cc_final: 0.7627 (tmm) REVERT: A 1009 PHE cc_start: 0.7588 (m-80) cc_final: 0.7328 (t80) REVERT: A 1029 MET cc_start: 0.6883 (tpt) cc_final: 0.6683 (tpt) REVERT: B 337 GLN cc_start: 0.8238 (OUTLIER) cc_final: 0.8016 (tm-30) REVERT: B 573 ILE cc_start: 0.8386 (tp) cc_final: 0.8080 (tp) REVERT: B 585 MET cc_start: 0.8436 (mmt) cc_final: 0.8104 (mtt) REVERT: C 414 MET cc_start: 0.7949 (ptm) cc_final: 0.7577 (ptp) REVERT: C 638 ASP cc_start: 0.8148 (m-30) cc_final: 0.7745 (t0) REVERT: C 891 PHE cc_start: 0.8261 (m-10) cc_final: 0.7967 (m-80) REVERT: C 924 MET cc_start: 0.7595 (ptp) cc_final: 0.6897 (mtm) REVERT: C 925 ILE cc_start: 0.9065 (mt) cc_final: 0.8689 (mt) REVERT: C 939 MET cc_start: 0.7724 (tpt) cc_final: 0.7244 (tpp) REVERT: C 965 PHE cc_start: 0.8782 (m-80) cc_final: 0.8577 (m-80) REVERT: C 966 PHE cc_start: 0.7405 (m-80) cc_final: 0.6728 (m-80) REVERT: D 189 GLU cc_start: 0.7287 (mm-30) cc_final: 0.6926 (mm-30) REVERT: D 269 GLU cc_start: 0.7511 (tp30) cc_final: 0.7250 (tp30) REVERT: D 408 MET cc_start: 0.7325 (mmm) cc_final: 0.7068 (mmp) REVERT: D 527 MET cc_start: 0.7256 (OUTLIER) cc_final: 0.6843 (mmt) REVERT: D 585 MET cc_start: 0.8307 (mmt) cc_final: 0.7990 (mtt) REVERT: E 116 MET cc_start: 0.2006 (tpp) cc_final: 0.0026 (pmm) REVERT: F 116 MET cc_start: 0.1025 (tpp) cc_final: -0.0453 (pmm) REVERT: F 117 TYR cc_start: 0.5429 (OUTLIER) cc_final: 0.3400 (t80) outliers start: 70 outliers final: 54 residues processed: 392 average time/residue: 0.3799 time to fit residues: 254.1115 Evaluate side-chains 388 residues out of total 3256 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 331 time to evaluate : 3.605 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 VAL Chi-restraints excluded: chain A residue 34 VAL Chi-restraints excluded: chain A residue 180 LEU Chi-restraints excluded: chain A residue 208 VAL Chi-restraints excluded: chain A residue 274 HIS Chi-restraints excluded: chain A residue 278 ILE Chi-restraints excluded: chain A residue 335 GLN Chi-restraints excluded: chain A residue 350 ASN Chi-restraints excluded: chain A residue 447 ASP Chi-restraints excluded: chain A residue 508 GLN Chi-restraints excluded: chain A residue 645 ILE Chi-restraints excluded: chain A residue 700 TYR Chi-restraints excluded: chain A residue 907 MET Chi-restraints excluded: chain A residue 960 PHE Chi-restraints excluded: chain A residue 968 LEU Chi-restraints excluded: chain A residue 972 SER Chi-restraints excluded: chain A residue 974 VAL Chi-restraints excluded: chain A residue 1023 MET Chi-restraints excluded: chain B residue 63 CYS Chi-restraints excluded: chain B residue 337 GLN Chi-restraints excluded: chain B residue 341 LEU Chi-restraints excluded: chain B residue 358 ILE Chi-restraints excluded: chain B residue 425 CYS Chi-restraints excluded: chain B residue 515 PHE Chi-restraints excluded: chain B residue 721 MET Chi-restraints excluded: chain B residue 773 CYS Chi-restraints excluded: chain C residue 31 VAL Chi-restraints excluded: chain C residue 34 VAL Chi-restraints excluded: chain C residue 182 GLN Chi-restraints excluded: chain C residue 208 VAL Chi-restraints excluded: chain C residue 335 GLN Chi-restraints excluded: chain C residue 350 ASN Chi-restraints excluded: chain C residue 447 ASP Chi-restraints excluded: chain C residue 508 GLN Chi-restraints excluded: chain C residue 639 LEU Chi-restraints excluded: chain C residue 645 ILE Chi-restraints excluded: chain C residue 748 LEU Chi-restraints excluded: chain C residue 750 VAL Chi-restraints excluded: chain C residue 890 CYS Chi-restraints excluded: chain C residue 960 PHE Chi-restraints excluded: chain C residue 985 ASN Chi-restraints excluded: chain D residue 299 LEU Chi-restraints excluded: chain D residue 341 LEU Chi-restraints excluded: chain D residue 358 ILE Chi-restraints excluded: chain D residue 515 PHE Chi-restraints excluded: chain D residue 527 MET Chi-restraints excluded: chain D residue 577 LEU Chi-restraints excluded: chain D residue 647 TYR Chi-restraints excluded: chain D residue 773 CYS Chi-restraints excluded: chain D residue 789 LEU Chi-restraints excluded: chain D residue 811 LEU Chi-restraints excluded: chain E residue 27 HIS Chi-restraints excluded: chain E residue 143 LEU Chi-restraints excluded: chain F residue 67 LEU Chi-restraints excluded: chain F residue 95 ILE Chi-restraints excluded: chain F residue 117 TYR Chi-restraints excluded: chain F residue 143 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 378 random chunks: chunk 338 optimal weight: 1.9990 chunk 222 optimal weight: 0.9990 chunk 359 optimal weight: 0.0020 chunk 219 optimal weight: 4.9990 chunk 170 optimal weight: 0.4980 chunk 249 optimal weight: 8.9990 chunk 376 optimal weight: 8.9990 chunk 346 optimal weight: 0.9980 chunk 299 optimal weight: 0.9980 chunk 31 optimal weight: 6.9990 chunk 231 optimal weight: 6.9990 overall best weight: 0.6990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 182 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 412 HIS ** C 182 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 985 ASN ** D 246 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 107 HIS F 107 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7956 moved from start: 0.4639 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 31813 Z= 0.168 Angle : 0.853 32.902 42920 Z= 0.367 Chirality : 0.080 2.148 4702 Planarity : 0.003 0.037 5286 Dihedral : 16.372 178.569 5183 Min Nonbonded Distance : 2.135 Molprobity Statistics. All-atom Clashscore : 10.52 Ramachandran Plot: Outliers : 0.24 % Allowed : 10.98 % Favored : 88.78 % Rotamer: Outliers : 1.97 % Allowed : 18.30 % Favored : 79.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.21 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.27 % 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: -1.78 (0.14), residues: 3762 helix: 0.45 (0.13), residues: 1778 sheet: -2.87 (0.28), residues: 316 loop : -2.73 (0.15), residues: 1668 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP C 262 HIS 0.015 0.001 HIS F 107 PHE 0.030 0.001 PHE B 517 TYR 0.024 0.001 TYR F 117 ARG 0.005 0.000 ARG B 331 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7524 Ramachandran restraints generated. 3762 Oldfield, 0 Emsley, 3762 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7524 Ramachandran restraints generated. 3762 Oldfield, 0 Emsley, 3762 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 403 residues out of total 3256 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 339 time to evaluate : 3.361 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: A 408 MET cc_start: 0.7340 (mmm) cc_final: 0.7125 (mmm) REVERT: A 414 MET cc_start: 0.7986 (ptm) cc_final: 0.7705 (ptp) REVERT: A 638 ASP cc_start: 0.8073 (m-30) cc_final: 0.7499 (t0) REVERT: A 642 GLN cc_start: 0.7645 (mp10) cc_final: 0.7166 (mp10) REVERT: A 816 TYR cc_start: 0.7483 (t80) cc_final: 0.6986 (t80) REVERT: A 891 PHE cc_start: 0.8222 (m-10) cc_final: 0.7688 (m-10) REVERT: A 936 LEU cc_start: 0.8314 (tp) cc_final: 0.8111 (tp) REVERT: A 939 MET cc_start: 0.8072 (tpt) cc_final: 0.7128 (ttt) REVERT: A 966 PHE cc_start: 0.7218 (m-80) cc_final: 0.6564 (m-80) REVERT: A 988 MET cc_start: 0.7882 (tmm) cc_final: 0.7579 (tmm) REVERT: A 1009 PHE cc_start: 0.7579 (m-80) cc_final: 0.7359 (t80) REVERT: A 1029 MET cc_start: 0.6855 (tpt) cc_final: 0.6654 (tpt) REVERT: B 573 ILE cc_start: 0.8399 (tp) cc_final: 0.8089 (tp) REVERT: B 585 MET cc_start: 0.8446 (mmt) cc_final: 0.8111 (mtt) REVERT: C 414 MET cc_start: 0.7935 (ptm) cc_final: 0.7574 (ptp) REVERT: C 638 ASP cc_start: 0.8163 (m-30) cc_final: 0.7786 (t0) REVERT: C 864 LEU cc_start: 0.6936 (OUTLIER) cc_final: 0.6605 (tt) REVERT: C 891 PHE cc_start: 0.8255 (m-10) cc_final: 0.7969 (m-80) REVERT: C 924 MET cc_start: 0.7610 (ptp) cc_final: 0.6908 (mtm) REVERT: C 925 ILE cc_start: 0.9066 (mt) cc_final: 0.8683 (mt) REVERT: C 965 PHE cc_start: 0.8798 (m-80) cc_final: 0.8590 (m-80) REVERT: C 966 PHE cc_start: 0.7343 (m-80) cc_final: 0.6753 (m-80) REVERT: C 1009 PHE cc_start: 0.7167 (t80) cc_final: 0.6662 (t80) REVERT: D 189 GLU cc_start: 0.7289 (mm-30) cc_final: 0.6924 (mm-30) REVERT: D 269 GLU cc_start: 0.7524 (tp30) cc_final: 0.7255 (tp30) REVERT: D 527 MET cc_start: 0.7319 (OUTLIER) cc_final: 0.6908 (mmt) REVERT: D 585 MET cc_start: 0.8303 (mmt) cc_final: 0.8003 (mtt) REVERT: E 95 ILE cc_start: 0.8152 (mt) cc_final: 0.7873 (mt) REVERT: E 116 MET cc_start: 0.1944 (tpp) cc_final: -0.0164 (pmm) REVERT: E 117 TYR cc_start: 0.6437 (t80) cc_final: 0.5735 (t80) REVERT: F 116 MET cc_start: 0.0905 (tpp) cc_final: -0.0550 (pmm) REVERT: F 117 TYR cc_start: 0.5485 (OUTLIER) cc_final: 0.3493 (t80) outliers start: 64 outliers final: 53 residues processed: 383 average time/residue: 0.3776 time to fit residues: 247.6835 Evaluate side-chains 384 residues out of total 3256 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 328 time to evaluate : 3.487 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 VAL Chi-restraints excluded: chain A residue 34 VAL Chi-restraints excluded: chain A residue 180 LEU Chi-restraints excluded: chain A residue 182 GLN Chi-restraints excluded: chain A residue 208 VAL Chi-restraints excluded: chain A residue 274 HIS Chi-restraints excluded: chain A residue 278 ILE Chi-restraints excluded: chain A residue 335 GLN Chi-restraints excluded: chain A residue 350 ASN Chi-restraints excluded: chain A residue 447 ASP Chi-restraints excluded: chain A residue 508 GLN Chi-restraints excluded: chain A residue 645 ILE Chi-restraints excluded: chain A residue 700 TYR Chi-restraints excluded: chain A residue 907 MET Chi-restraints excluded: chain A residue 960 PHE Chi-restraints excluded: chain A residue 968 LEU Chi-restraints excluded: chain A residue 972 SER Chi-restraints excluded: chain A residue 974 VAL Chi-restraints excluded: chain A residue 1023 MET Chi-restraints excluded: chain B residue 63 CYS Chi-restraints excluded: chain B residue 341 LEU Chi-restraints excluded: chain B residue 358 ILE Chi-restraints excluded: chain B residue 515 PHE Chi-restraints excluded: chain B residue 721 MET Chi-restraints excluded: chain B residue 773 CYS Chi-restraints excluded: chain C residue 31 VAL Chi-restraints excluded: chain C residue 34 VAL Chi-restraints excluded: chain C residue 180 LEU Chi-restraints excluded: chain C residue 182 GLN Chi-restraints excluded: chain C residue 208 VAL Chi-restraints excluded: chain C residue 335 GLN Chi-restraints excluded: chain C residue 350 ASN Chi-restraints excluded: chain C residue 447 ASP Chi-restraints excluded: chain C residue 508 GLN Chi-restraints excluded: chain C residue 645 ILE Chi-restraints excluded: chain C residue 748 LEU Chi-restraints excluded: chain C residue 750 VAL Chi-restraints excluded: chain C residue 864 LEU Chi-restraints excluded: chain C residue 890 CYS Chi-restraints excluded: chain C residue 985 ASN Chi-restraints excluded: chain D residue 299 LEU Chi-restraints excluded: chain D residue 341 LEU Chi-restraints excluded: chain D residue 358 ILE Chi-restraints excluded: chain D residue 515 PHE Chi-restraints excluded: chain D residue 527 MET Chi-restraints excluded: chain D residue 577 LEU Chi-restraints excluded: chain D residue 591 ILE Chi-restraints excluded: chain D residue 647 TYR Chi-restraints excluded: chain D residue 773 CYS Chi-restraints excluded: chain D residue 789 LEU Chi-restraints excluded: chain D residue 811 LEU Chi-restraints excluded: chain E residue 27 HIS Chi-restraints excluded: chain E residue 143 LEU Chi-restraints excluded: chain F residue 95 ILE Chi-restraints excluded: chain F residue 117 TYR Chi-restraints excluded: chain F residue 143 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 378 random chunks: chunk 183 optimal weight: 5.9990 chunk 238 optimal weight: 1.9990 chunk 319 optimal weight: 0.0270 chunk 91 optimal weight: 1.9990 chunk 276 optimal weight: 5.9990 chunk 44 optimal weight: 4.9990 chunk 83 optimal weight: 8.9990 chunk 300 optimal weight: 2.9990 chunk 125 optimal weight: 0.9980 chunk 308 optimal weight: 1.9990 chunk 38 optimal weight: 0.7980 overall best weight: 1.1642 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 182 GLN ** C 182 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 985 ASN ** D 246 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 107 HIS F 107 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3966 r_free = 0.3966 target = 0.143017 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.107105 restraints weight = 54619.700| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3481 r_free = 0.3481 target = 0.107249 restraints weight = 37053.958| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3482 r_free = 0.3482 target = 0.107649 restraints weight = 40812.673| |-----------------------------------------------------------------------------| r_work (final): 0.3483 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7939 moved from start: 0.4665 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 31813 Z= 0.205 Angle : 0.862 33.028 42920 Z= 0.372 Chirality : 0.081 2.155 4702 Planarity : 0.003 0.037 5286 Dihedral : 16.286 178.736 5183 Min Nonbonded Distance : 2.119 Molprobity Statistics. All-atom Clashscore : 11.03 Ramachandran Plot: Outliers : 0.21 % Allowed : 11.40 % Favored : 88.38 % Rotamer: Outliers : 2.09 % Allowed : 18.34 % Favored : 79.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.21 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.22 % 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: -1.73 (0.14), residues: 3762 helix: 0.48 (0.13), residues: 1780 sheet: -2.86 (0.27), residues: 332 loop : -2.69 (0.15), residues: 1650 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP C 262 HIS 0.014 0.001 HIS F 107 PHE 0.031 0.001 PHE B 517 TYR 0.024 0.001 TYR F 117 ARG 0.005 0.000 ARG B 331 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6784.46 seconds wall clock time: 124 minutes 56.23 seconds (7496.23 seconds total)