Starting phenix.real_space_refine on Tue Feb 20 11:02:03 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5wel_8820/02_2024/5wel_8820_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5wel_8820/02_2024/5wel_8820.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5wel_8820/02_2024/5wel_8820.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5wel_8820/02_2024/5wel_8820.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5wel_8820/02_2024/5wel_8820_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5wel_8820/02_2024/5wel_8820_updated.pdb" } resolution = 4.4 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= 0.001 sd= 0.005 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 4 5.49 5 S 144 5.16 5 C 17760 2.51 5 N 4530 2.21 5 O 5188 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 PHE 41": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 77": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 198": "NH1" <-> "NH2" Residue "A ARG 261": "NH1" <-> "NH2" Residue "A ARG 300": "NH1" <-> "NH2" Residue "A ARG 309": "NH1" <-> "NH2" Residue "A ARG 369": "NH1" <-> "NH2" Residue "A ARG 628": "NH1" <-> "NH2" Residue "A ARG 660": "NH1" <-> "NH2" Residue "A ARG 661": "NH1" <-> "NH2" Residue "A ARG 675": "NH1" <-> "NH2" Residue "A ARG 692": "NH1" <-> "NH2" Residue "A ARG 1005": "NH1" <-> "NH2" Residue "A ARG 1006": "NH1" <-> "NH2" Residue "A ARG 1090": "NH1" <-> "NH2" Residue "B PHE 41": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 77": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 198": "NH1" <-> "NH2" Residue "B ARG 261": "NH1" <-> "NH2" Residue "B ARG 300": "NH1" <-> "NH2" Residue "B ARG 309": "NH1" <-> "NH2" Residue "B ARG 369": "NH1" <-> "NH2" Residue "B ARG 660": "NH1" <-> "NH2" Residue "B ARG 661": "NH1" <-> "NH2" Residue "B ARG 675": "NH1" <-> "NH2" Residue "B ARG 692": "NH1" <-> "NH2" Residue "C PHE 41": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 77": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 198": "NH1" <-> "NH2" Residue "C ARG 261": "NH1" <-> "NH2" Residue "C ARG 300": "NH1" <-> "NH2" Residue "C ARG 309": "NH1" <-> "NH2" Residue "C ARG 369": "NH1" <-> "NH2" Residue "C ARG 628": "NH1" <-> "NH2" Residue "C ARG 660": "NH1" <-> "NH2" Residue "C ARG 661": "NH1" <-> "NH2" Residue "C ARG 675": "NH1" <-> "NH2" Residue "C ARG 692": "NH1" <-> "NH2" Residue "C ARG 1005": "NH1" <-> "NH2" Residue "C ARG 1006": "NH1" <-> "NH2" Residue "C ARG 1090": "NH1" <-> "NH2" Residue "D PHE 41": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 77": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 198": "NH1" <-> "NH2" Residue "D ARG 261": "NH1" <-> "NH2" Residue "D ARG 300": "NH1" <-> "NH2" Residue "D ARG 309": "NH1" <-> "NH2" Residue "D ARG 369": "NH1" <-> "NH2" Residue "D ARG 660": "NH1" <-> "NH2" Residue "D ARG 661": "NH1" <-> "NH2" Residue "D ARG 675": "NH1" <-> "NH2" Residue "D ARG 692": "NH1" <-> "NH2" Time to flip residues: 0.09s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 27638 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 7555 Number of conformers: 1 Conformer: "" Number of residues, atoms: 962, 7555 Classifications: {'peptide': 962} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PCIS': 5, 'PTRANS': 21, 'TRANS': 935} Chain breaks: 5 Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 2} Unresolved non-hydrogen planarities: 10 Chain: "B" Number of atoms: 6125 Number of conformers: 1 Conformer: "" Number of residues, atoms: 780, 6125 Classifications: {'peptide': 780} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PCIS': 4, 'PTRANS': 18, 'TRANS': 757} Chain breaks: 1 Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 2} Unresolved non-hydrogen planarities: 10 Chain: "C" Number of atoms: 7555 Number of conformers: 1 Conformer: "" Number of residues, atoms: 962, 7555 Classifications: {'peptide': 962} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PCIS': 5, 'PTRANS': 21, 'TRANS': 935} Chain breaks: 5 Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 2} Unresolved non-hydrogen planarities: 10 Chain: "D" Number of atoms: 6125 Number of conformers: 1 Conformer: "" Number of residues, atoms: 780, 6125 Classifications: {'peptide': 780} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PCIS': 4, 'PTRANS': 18, 'TRANS': 757} Chain breaks: 1 Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 2} Unresolved non-hydrogen planarities: 10 Chain: "A" Number of atoms: 112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 112 Unusual residues: {'AJP': 1, 'ZK1': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ZK1': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 112 Unusual residues: {'AJP': 1, 'ZK1': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ZK1': 1} Classifications: {'undetermined': 1} Time building chain proxies: 16.79, per 1000 atoms: 0.61 Number of scatterers: 27638 At special positions: 0 Unit cell: (120.54, 157.78, 189.14, 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 144 16.00 P 4 15.00 F 12 9.00 O 5188 8.00 N 4530 7.00 C 17760 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=2.02 Simple disulfide: pdb=" SG CYS A1099 " - pdb=" SG CYS A1110 " distance=2.03 Simple disulfide: pdb=" SG CYS B 63 " - pdb=" SG CYS B 315 " distance=2.03 Simple disulfide: pdb=" SG CYS B 718 " - pdb=" SG CYS B 773 " distance=2.02 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=2.02 Simple disulfide: pdb=" SG CYS C1099 " - pdb=" SG CYS C1110 " distance=2.03 Simple disulfide: pdb=" SG CYS D 63 " - pdb=" SG CYS D 315 " distance=2.03 Simple disulfide: pdb=" SG CYS D 718 " - pdb=" SG CYS D 773 " distance=2.02 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=2, symmetry=0 Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 11.85 Conformation dependent library (CDL) restraints added in 7.1 seconds 6904 Ramachandran restraints generated. 3452 Oldfield, 0 Emsley, 3452 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6408 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 122 helices and 34 sheets defined 43.1% alpha, 11.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 8.10 Creating SS restraints... Processing helix chain 'A' and resid 23 through 35 Processing helix chain 'A' and resid 55 through 68 Processing helix chain 'A' and resid 82 through 92 Processing helix chain 'A' and resid 118 through 128 Processing helix chain 'A' and resid 144 through 155 removed outlier: 3.598A pdb=" N GLU A 155 " --> pdb=" O ASP A 151 " (cutoff:3.500A) Processing helix chain 'A' and resid 175 through 187 removed outlier: 3.505A pdb=" N GLN A 182 " --> pdb=" O ARG A 178 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N LYS A 187 " --> pdb=" O ASP A 183 " (cutoff:3.500A) Processing helix chain 'A' and resid 198 through 211 Processing helix chain 'A' and resid 253 through 262 removed outlier: 3.528A pdb=" N PHE A 258 " --> pdb=" O LEU A 254 " (cutoff:3.500A) Processing helix chain 'A' and resid 280 through 302 removed outlier: 3.526A pdb=" N GLN A 290 " --> pdb=" O TYR A 286 " (cutoff:3.500A) Processing helix chain 'A' and resid 324 through 334 removed outlier: 3.513A pdb=" N ALA A 332 " --> pdb=" O ILE A 329 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N LEU A 333 " --> pdb=" O GLU A 330 " (cutoff:3.500A) Processing helix chain 'A' and resid 417 through 420 Processing helix chain 'A' and resid 424 through 436 Processing helix chain 'A' and resid 462 through 468 Processing helix chain 'A' and resid 483 through 486 No H-bonds generated for 'chain 'A' and resid 483 through 486' Processing helix chain 'A' and resid 517 through 519 No H-bonds generated for 'chain 'A' and resid 517 through 519' Processing helix chain 'A' and resid 523 through 537 removed outlier: 3.930A pdb=" N VAL A 530 " --> pdb=" O TRP A 526 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N TYR A 533 " --> pdb=" O ILE A 529 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N ILE A 534 " --> pdb=" O VAL A 530 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N GLY A 535 " --> pdb=" O PHE A 531 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N VAL A 536 " --> pdb=" O ALA A 532 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N SER A 537 " --> pdb=" O TYR A 533 " (cutoff:3.500A) Processing helix chain 'A' and resid 540 through 542 No H-bonds generated for 'chain 'A' and resid 540 through 542' Processing helix chain 'A' and resid 576 through 582 removed outlier: 3.530A pdb=" N LEU A 581 " --> pdb=" O LEU A 577 " (cutoff:3.500A) Processing helix chain 'A' and resid 597 through 629 removed outlier: 3.803A pdb=" N TRP A 605 " --> pdb=" O VAL A 601 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N TRP A 606 " --> pdb=" O GLY A 602 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N LEU A 610 " --> pdb=" O TRP A 606 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N ILE A 611 " --> pdb=" O PHE A 607 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N ILE A 612 " --> pdb=" O PHE A 608 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N VAL A 626 " --> pdb=" O ALA A 622 " (cutoff:3.500A) Processing helix chain 'A' and resid 637 through 641 Processing helix chain 'A' and resid 654 through 661 Processing helix chain 'A' and resid 665 through 675 Processing helix chain 'A' and resid 686 through 696 Processing helix chain 'A' and resid 706 through 714 Processing helix chain 'A' and resid 741 through 756 removed outlier: 4.096A pdb=" N THR A 744 " --> pdb=" O SER A 741 " (cutoff:3.500A) Proline residue: A 745 - end of helix removed outlier: 3.507A pdb=" N VAL A 750 " --> pdb=" O ASN A 747 " (cutoff:3.500A) removed outlier: 4.527A pdb=" N SER A 754 " --> pdb=" O LEU A 751 " (cutoff:3.500A) Processing helix chain 'A' and resid 758 through 767 Processing helix chain 'A' and resid 777 through 780 Processing helix chain 'A' and resid 790 through 792 No H-bonds generated for 'chain 'A' and resid 790 through 792' Processing helix chain 'A' and resid 796 through 818 removed outlier: 3.599A pdb=" N LEU A 808 " --> pdb=" O GLY A 804 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N VAL A 809 " --> pdb=" O LEU A 805 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N LEU A 811 " --> pdb=" O MET A 807 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N CYS A 815 " --> pdb=" O LEU A 811 " (cutoff:3.500A) removed outlier: 4.861A pdb=" N SER A 818 " --> pdb=" O PHE A 814 " (cutoff:3.500A) Processing helix chain 'A' and resid 1003 through 1028 removed outlier: 3.769A pdb=" N LEU A1028 " --> pdb=" O THR A1024 " (cutoff:3.500A) Processing helix chain 'A' and resid 1119 through 1152 removed outlier: 3.504A pdb=" N VAL A1130 " --> pdb=" O TRP A1126 " (cutoff:3.500A) Processing helix chain 'A' and resid 1160 through 1193 removed outlier: 3.600A pdb=" N VAL A1168 " --> pdb=" O ALA A1164 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N PHE A1169 " --> pdb=" O PHE A1165 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N VAL A1171 " --> pdb=" O ALA A1167 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N LEU A1176 " --> pdb=" O LEU A1172 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N MET A1182 " --> pdb=" O MET A1178 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N THR A1185 " --> pdb=" O HIS A1181 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N GLN A1186 " --> pdb=" O MET A1182 " (cutoff:3.500A) Processing helix chain 'A' and resid 1209 through 1227 removed outlier: 3.636A pdb=" N GLY A1215 " --> pdb=" O CYS A1211 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N PHE A1217 " --> pdb=" O ALA A1213 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N THR A1218 " --> pdb=" O TRP A1214 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N SER A1224 " --> pdb=" O CYS A1220 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N THR A1226 " --> pdb=" O ALA A1222 " (cutoff:3.500A) Processing helix chain 'B' and resid 23 through 35 Processing helix chain 'B' and resid 55 through 68 Processing helix chain 'B' and resid 82 through 92 Processing helix chain 'B' and resid 118 through 128 Processing helix chain 'B' and resid 144 through 155 removed outlier: 3.599A pdb=" N GLU B 155 " --> pdb=" O ASP B 151 " (cutoff:3.500A) Processing helix chain 'B' and resid 175 through 187 removed outlier: 3.504A pdb=" N GLN B 182 " --> pdb=" O ARG B 178 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N LYS B 187 " --> pdb=" O ASP B 183 " (cutoff:3.500A) Processing helix chain 'B' and resid 198 through 211 Processing helix chain 'B' and resid 253 through 262 removed outlier: 3.528A pdb=" N PHE B 258 " --> pdb=" O LEU B 254 " (cutoff:3.500A) Processing helix chain 'B' and resid 280 through 302 removed outlier: 3.526A pdb=" N GLN B 290 " --> pdb=" O TYR B 286 " (cutoff:3.500A) Processing helix chain 'B' and resid 324 through 334 removed outlier: 3.513A pdb=" N ALA B 332 " --> pdb=" O ILE B 329 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N LEU B 333 " --> pdb=" O GLU B 330 " (cutoff:3.500A) Processing helix chain 'B' and resid 417 through 420 Processing helix chain 'B' and resid 424 through 436 Processing helix chain 'B' and resid 462 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 517 through 519 No H-bonds generated for 'chain 'B' and resid 517 through 519' Processing helix chain 'B' and resid 523 through 537 removed outlier: 3.930A pdb=" N VAL B 530 " --> pdb=" O TRP B 526 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N TYR B 533 " --> pdb=" O ILE B 529 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N ILE B 534 " --> pdb=" O VAL B 530 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N GLY B 535 " --> pdb=" O PHE B 531 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N VAL B 536 " --> pdb=" O ALA B 532 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N SER B 537 " --> pdb=" O TYR B 533 " (cutoff:3.500A) Processing helix chain 'B' and resid 540 through 542 No H-bonds generated for 'chain 'B' and resid 540 through 542' Processing helix chain 'B' and resid 576 through 582 removed outlier: 3.530A pdb=" N LEU B 581 " --> pdb=" O LEU B 577 " (cutoff:3.500A) Processing helix chain 'B' and resid 597 through 623 removed outlier: 3.804A pdb=" N TRP B 605 " --> pdb=" O VAL B 601 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N TRP B 606 " --> pdb=" O GLY B 602 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N LEU B 610 " --> pdb=" O TRP B 606 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N ILE B 611 " --> pdb=" O PHE B 607 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N ILE B 612 " --> pdb=" O PHE B 608 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N ILE B 613 " --> pdb=" O THR B 609 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N SER B 614 " --> pdb=" O LEU B 610 " (cutoff:3.500A) Processing helix chain 'B' and resid 637 through 641 Processing helix chain 'B' and resid 654 through 661 Processing helix chain 'B' and resid 665 through 675 Processing helix chain 'B' and resid 686 through 696 Processing helix chain 'B' and resid 706 through 714 Processing helix chain 'B' and resid 741 through 756 removed outlier: 4.095A pdb=" N THR B 744 " --> pdb=" O SER B 741 " (cutoff:3.500A) Proline residue: B 745 - end of helix removed outlier: 3.506A pdb=" N VAL B 750 " --> pdb=" O ASN B 747 " (cutoff:3.500A) removed outlier: 4.527A pdb=" N SER B 754 " --> pdb=" O LEU B 751 " (cutoff:3.500A) Processing helix chain 'B' and resid 758 through 767 Processing helix chain 'B' and resid 775 through 779 Processing helix chain 'B' and resid 790 through 816 removed outlier: 3.523A pdb=" N GLY B 794 " --> pdb=" O SER B 790 " (cutoff:3.500A) removed outlier: 4.590A pdb=" N VAL B 795 " --> pdb=" O ASN B 791 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N TYR B 797 " --> pdb=" O ALA B 793 " (cutoff:3.500A) removed outlier: 4.258A pdb=" N ILE B 798 " --> pdb=" O GLY B 794 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N LEU B 808 " --> pdb=" O GLY B 804 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N VAL B 809 " --> pdb=" O LEU B 805 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N LEU B 811 " --> pdb=" O MET B 807 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N CYS B 815 " --> pdb=" O LEU B 811 " (cutoff:3.500A) Processing helix chain 'C' and resid 23 through 35 Processing helix chain 'C' and resid 55 through 68 Processing helix chain 'C' and resid 82 through 92 Processing helix chain 'C' and resid 118 through 128 Processing helix chain 'C' and resid 144 through 155 removed outlier: 3.600A pdb=" N GLU C 155 " --> pdb=" O ASP C 151 " (cutoff:3.500A) Processing helix chain 'C' and resid 175 through 187 removed outlier: 3.505A pdb=" N GLN C 182 " --> pdb=" O ARG C 178 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N LYS C 187 " --> pdb=" O ASP C 183 " (cutoff:3.500A) Processing helix chain 'C' and resid 198 through 211 Processing helix chain 'C' and resid 253 through 262 removed outlier: 3.527A pdb=" N PHE C 258 " --> pdb=" O LEU C 254 " (cutoff:3.500A) Processing helix chain 'C' and resid 280 through 302 removed outlier: 3.526A pdb=" N GLN C 290 " --> pdb=" O TYR C 286 " (cutoff:3.500A) Processing helix chain 'C' and resid 324 through 334 removed outlier: 3.513A pdb=" N ALA C 332 " --> pdb=" O ILE C 329 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N LEU C 333 " --> pdb=" O GLU C 330 " (cutoff:3.500A) Processing helix chain 'C' and resid 417 through 420 Processing helix chain 'C' and resid 424 through 436 Processing helix chain 'C' and resid 462 through 468 Processing helix chain 'C' and resid 483 through 486 No H-bonds generated for 'chain 'C' and resid 483 through 486' Processing helix chain 'C' and resid 517 through 519 No H-bonds generated for 'chain 'C' and resid 517 through 519' Processing helix chain 'C' and resid 523 through 537 removed outlier: 3.931A pdb=" N VAL C 530 " --> pdb=" O TRP C 526 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N TYR C 533 " --> pdb=" O ILE C 529 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N ILE C 534 " --> pdb=" O VAL C 530 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N GLY C 535 " --> pdb=" O PHE C 531 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N VAL C 536 " --> pdb=" O ALA C 532 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N SER C 537 " --> pdb=" O TYR C 533 " (cutoff:3.500A) Processing helix chain 'C' and resid 540 through 542 No H-bonds generated for 'chain 'C' and resid 540 through 542' Processing helix chain 'C' and resid 576 through 582 removed outlier: 3.530A pdb=" N LEU C 581 " --> pdb=" O LEU C 577 " (cutoff:3.500A) Processing helix chain 'C' and resid 597 through 629 removed outlier: 3.804A pdb=" N TRP C 605 " --> pdb=" O VAL C 601 " (cutoff:3.500A) removed outlier: 4.038A pdb=" N TRP C 606 " --> pdb=" O GLY C 602 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N LEU C 610 " --> pdb=" O TRP C 606 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N ILE C 611 " --> pdb=" O PHE C 607 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N ILE C 612 " --> pdb=" O PHE C 608 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N ILE C 613 " --> pdb=" O THR C 609 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N SER C 614 " --> pdb=" O LEU C 610 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N VAL C 626 " --> pdb=" O ALA C 622 " (cutoff:3.500A) Processing helix chain 'C' and resid 637 through 641 Processing helix chain 'C' and resid 654 through 661 Processing helix chain 'C' and resid 665 through 675 Processing helix chain 'C' and resid 686 through 696 Processing helix chain 'C' and resid 706 through 714 Processing helix chain 'C' and resid 741 through 756 removed outlier: 4.096A pdb=" N THR C 744 " --> pdb=" O SER C 741 " (cutoff:3.500A) Proline residue: C 745 - end of helix removed outlier: 3.507A pdb=" N VAL C 750 " --> pdb=" O ASN C 747 " (cutoff:3.500A) removed outlier: 4.527A pdb=" N SER C 754 " --> pdb=" O LEU C 751 " (cutoff:3.500A) Processing helix chain 'C' and resid 758 through 767 Processing helix chain 'C' and resid 777 through 780 Processing helix chain 'C' and resid 790 through 792 No H-bonds generated for 'chain 'C' and resid 790 through 792' Processing helix chain 'C' and resid 796 through 816 removed outlier: 3.599A pdb=" N LEU C 808 " --> pdb=" O GLY C 804 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N VAL C 809 " --> pdb=" O LEU C 805 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N LEU C 811 " --> pdb=" O MET C 807 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N CYS C 815 " --> pdb=" O LEU C 811 " (cutoff:3.500A) Processing helix chain 'C' and resid 1003 through 1028 removed outlier: 3.769A pdb=" N LEU C1028 " --> pdb=" O THR C1024 " (cutoff:3.500A) Processing helix chain 'C' and resid 1119 through 1152 removed outlier: 3.504A pdb=" N VAL C1130 " --> pdb=" O TRP C1126 " (cutoff:3.500A) Processing helix chain 'C' and resid 1160 through 1193 removed outlier: 3.600A pdb=" N VAL C1168 " --> pdb=" O ALA C1164 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N PHE C1169 " --> pdb=" O PHE C1165 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N VAL C1171 " --> pdb=" O ALA C1167 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N LEU C1176 " --> pdb=" O LEU C1172 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N MET C1182 " --> pdb=" O MET C1178 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N THR C1185 " --> pdb=" O HIS C1181 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N GLN C1186 " --> pdb=" O MET C1182 " (cutoff:3.500A) Processing helix chain 'C' and resid 1209 through 1227 removed outlier: 3.637A pdb=" N GLY C1215 " --> pdb=" O CYS C1211 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N PHE C1217 " --> pdb=" O ALA C1213 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N THR C1218 " --> pdb=" O TRP C1214 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N SER C1224 " --> pdb=" O CYS C1220 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N THR C1226 " --> pdb=" O ALA C1222 " (cutoff:3.500A) Processing helix chain 'D' and resid 23 through 35 Processing helix chain 'D' and resid 55 through 68 Processing helix chain 'D' and resid 82 through 92 Processing helix chain 'D' and resid 118 through 128 Processing helix chain 'D' and resid 144 through 155 removed outlier: 3.600A pdb=" N GLU D 155 " --> pdb=" O ASP D 151 " (cutoff:3.500A) Processing helix chain 'D' and resid 175 through 187 removed outlier: 3.505A pdb=" N GLN D 182 " --> pdb=" O ARG D 178 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N LYS D 187 " --> pdb=" O ASP D 183 " (cutoff:3.500A) Processing helix chain 'D' and resid 198 through 211 Processing helix chain 'D' and resid 253 through 262 removed outlier: 3.528A pdb=" N PHE D 258 " --> pdb=" O LEU D 254 " (cutoff:3.500A) Processing helix chain 'D' and resid 280 through 302 removed outlier: 3.526A pdb=" N GLN D 290 " --> pdb=" O TYR D 286 " (cutoff:3.500A) Processing helix chain 'D' and resid 324 through 334 removed outlier: 3.513A pdb=" N ALA D 332 " --> pdb=" O ILE D 329 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N LEU D 333 " --> pdb=" O GLU D 330 " (cutoff:3.500A) Processing helix chain 'D' and resid 417 through 420 Processing helix chain 'D' and resid 424 through 436 Processing helix chain 'D' and resid 462 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 517 through 519 No H-bonds generated for 'chain 'D' and resid 517 through 519' Processing helix chain 'D' and resid 523 through 537 removed outlier: 3.930A pdb=" N VAL D 530 " --> pdb=" O TRP D 526 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N TYR D 533 " --> pdb=" O ILE D 529 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N ILE D 534 " --> pdb=" O VAL D 530 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N GLY D 535 " --> pdb=" O PHE D 531 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N VAL D 536 " --> pdb=" O ALA D 532 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N SER D 537 " --> pdb=" O TYR D 533 " (cutoff:3.500A) Processing helix chain 'D' and resid 540 through 542 No H-bonds generated for 'chain 'D' and resid 540 through 542' Processing helix chain 'D' and resid 576 through 582 removed outlier: 3.529A pdb=" N LEU D 581 " --> pdb=" O LEU D 577 " (cutoff:3.500A) Processing helix chain 'D' and resid 597 through 623 removed outlier: 3.804A pdb=" N TRP D 605 " --> pdb=" O VAL D 601 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N TRP D 606 " --> pdb=" O GLY D 602 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N LEU D 610 " --> pdb=" O TRP D 606 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N ILE D 611 " --> pdb=" O PHE D 607 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N ILE D 612 " --> pdb=" O PHE D 608 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N ILE D 613 " --> pdb=" O THR D 609 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N SER D 614 " --> pdb=" O LEU D 610 " (cutoff:3.500A) Processing helix chain 'D' and resid 637 through 641 Processing helix chain 'D' and resid 654 through 661 Processing helix chain 'D' and resid 665 through 675 Processing helix chain 'D' and resid 686 through 696 Processing helix chain 'D' and resid 706 through 714 Processing helix chain 'D' and resid 741 through 756 removed outlier: 4.096A pdb=" N THR D 744 " --> pdb=" O SER D 741 " (cutoff:3.500A) Proline residue: D 745 - end of helix removed outlier: 3.508A pdb=" N VAL D 750 " --> pdb=" O ASN D 747 " (cutoff:3.500A) removed outlier: 4.527A pdb=" N SER D 754 " --> pdb=" O LEU D 751 " (cutoff:3.500A) Processing helix chain 'D' and resid 758 through 767 Processing helix chain 'D' and resid 775 through 779 Processing helix chain 'D' and resid 790 through 816 removed outlier: 3.525A pdb=" N GLY D 794 " --> pdb=" O SER D 790 " (cutoff:3.500A) removed outlier: 4.589A pdb=" N VAL D 795 " --> pdb=" O ASN D 791 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N TYR D 797 " --> pdb=" O ALA D 793 " (cutoff:3.500A) removed outlier: 4.257A pdb=" N ILE D 798 " --> pdb=" O GLY D 794 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N LEU D 808 " --> pdb=" O GLY D 804 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N VAL D 809 " --> pdb=" O LEU D 805 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N LEU D 811 " --> pdb=" O MET D 807 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N CYS D 815 " --> pdb=" O LEU D 811 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 12 through 19 Processing sheet with id= B, first strand: chain 'A' and resid 72 through 75 removed outlier: 6.842A pdb=" N SER A 95 " --> pdb=" O ILE A 73 " (cutoff:3.500A) removed outlier: 8.291A pdb=" N GLY A 75 " --> pdb=" O SER A 95 " (cutoff:3.500A) removed outlier: 6.034A pdb=" N ILE A 97 " --> pdb=" O GLY A 75 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 159 through 164 removed outlier: 3.607A pdb=" N PHE A 133 " --> pdb=" O GLN A 159 " (cutoff:3.500A) removed outlier: 5.552A pdb=" N ARG A 191 " --> pdb=" O LYS A 132 " (cutoff:3.500A) removed outlier: 6.208A pdb=" N HIS A 219 " --> pdb=" O VAL A 192 " (cutoff:3.500A) removed outlier: 7.221A pdb=" N LEU A 194 " --> pdb=" O HIS A 219 " (cutoff:3.500A) removed outlier: 6.086A pdb=" N ILE A 221 " --> pdb=" O LEU A 194 " (cutoff:3.500A) removed outlier: 6.299A pdb=" N GLU A 241 " --> pdb=" O TYR A 220 " (cutoff:3.500A) removed outlier: 7.678A pdb=" N ILE A 222 " --> pdb=" O GLU A 241 " (cutoff:3.500A) removed outlier: 6.977A pdb=" N SER A 243 " --> pdb=" O ILE A 222 " (cutoff:3.500A) removed outlier: 4.547A pdb=" N VAL A 242 " --> pdb=" O LEU A 363 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N GLY A 372 " --> pdb=" O ILE A 360 " (cutoff:3.500A) removed outlier: 6.346A pdb=" N GLU A 362 " --> pdb=" O LYS A 370 " (cutoff:3.500A) removed outlier: 5.121A pdb=" N LYS A 370 " --> pdb=" O GLU A 362 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 338 through 340 Processing sheet with id= E, first strand: chain 'A' and resid 395 through 399 Processing sheet with id= F, first strand: chain 'A' and resid 489 through 491 Processing sheet with id= G, first strand: chain 'A' and resid 720 through 723 removed outlier: 3.886A pdb=" N ILE A 502 " --> pdb=" O VAL A 723 " (cutoff:3.500A) removed outlier: 5.206A pdb=" N LYS A 505 " --> pdb=" O TYR A 700 " (cutoff:3.500A) removed outlier: 8.937A pdb=" N TYR A 700 " --> pdb=" O LYS A 505 " (cutoff:3.500A) removed outlier: 6.332A pdb=" N ALA A 646 " --> pdb=" O ALA A 701 " (cutoff:3.500A) removed outlier: 7.879A pdb=" N LEU A 703 " --> pdb=" O ALA A 646 " (cutoff:3.500A) removed outlier: 6.822A pdb=" N GLY A 648 " --> pdb=" O LEU A 703 " (cutoff:3.500A) removed outlier: 9.116A pdb=" N GLU A 705 " --> pdb=" O GLY A 648 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'A' and resid 1033 through 1036 removed outlier: 3.510A pdb=" N THR A1093 " --> pdb=" O CYS A1033 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'A' and resid 494 through 498 removed outlier: 6.765A pdb=" N TYR A 732 " --> pdb=" O PHE A 495 " (cutoff:3.500A) removed outlier: 4.465A pdb=" N SER A 497 " --> pdb=" O LYS A 730 " (cutoff:3.500A) removed outlier: 6.493A pdb=" N LYS A 730 " --> pdb=" O SER A 497 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'B' and resid 12 through 19 Processing sheet with id= K, first strand: chain 'B' and resid 72 through 75 removed outlier: 6.842A pdb=" N SER B 95 " --> pdb=" O ILE B 73 " (cutoff:3.500A) removed outlier: 8.290A pdb=" N GLY B 75 " --> pdb=" O SER B 95 " (cutoff:3.500A) removed outlier: 6.034A pdb=" N ILE B 97 " --> pdb=" O GLY B 75 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'B' and resid 159 through 164 removed outlier: 3.607A pdb=" N PHE B 133 " --> pdb=" O GLN B 159 " (cutoff:3.500A) removed outlier: 5.552A pdb=" N ARG B 191 " --> pdb=" O LYS B 132 " (cutoff:3.500A) removed outlier: 6.209A pdb=" N HIS B 219 " --> pdb=" O VAL B 192 " (cutoff:3.500A) removed outlier: 7.220A pdb=" N LEU B 194 " --> pdb=" O HIS B 219 " (cutoff:3.500A) removed outlier: 6.086A pdb=" N ILE B 221 " --> pdb=" O LEU B 194 " (cutoff:3.500A) removed outlier: 6.298A pdb=" N GLU B 241 " --> pdb=" O TYR B 220 " (cutoff:3.500A) removed outlier: 7.677A pdb=" N ILE B 222 " --> pdb=" O GLU B 241 " (cutoff:3.500A) removed outlier: 6.978A pdb=" N SER B 243 " --> pdb=" O ILE B 222 " (cutoff:3.500A) removed outlier: 4.547A pdb=" N VAL B 242 " --> pdb=" O LEU B 363 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N GLY B 372 " --> pdb=" O ILE B 360 " (cutoff:3.500A) removed outlier: 6.346A pdb=" N GLU B 362 " --> pdb=" O LYS B 370 " (cutoff:3.500A) removed outlier: 5.121A pdb=" N LYS B 370 " --> pdb=" O GLU B 362 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'B' and resid 338 through 340 Processing sheet with id= N, first strand: chain 'B' and resid 395 through 399 Processing sheet with id= O, first strand: chain 'B' and resid 489 through 491 Processing sheet with id= P, first strand: chain 'B' and resid 720 through 723 removed outlier: 3.887A pdb=" N ILE B 502 " --> pdb=" O VAL B 723 " (cutoff:3.500A) removed outlier: 5.206A pdb=" N LYS B 505 " --> pdb=" O TYR B 700 " (cutoff:3.500A) removed outlier: 8.937A pdb=" N TYR B 700 " --> pdb=" O LYS B 505 " (cutoff:3.500A) removed outlier: 6.331A pdb=" N ALA B 646 " --> pdb=" O ALA B 701 " (cutoff:3.500A) removed outlier: 7.878A pdb=" N LEU B 703 " --> pdb=" O ALA B 646 " (cutoff:3.500A) removed outlier: 6.822A pdb=" N GLY B 648 " --> pdb=" O LEU B 703 " (cutoff:3.500A) removed outlier: 9.117A pdb=" N GLU B 705 " --> pdb=" O GLY B 648 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'B' and resid 494 through 498 removed outlier: 6.765A pdb=" N TYR B 732 " --> pdb=" O PHE B 495 " (cutoff:3.500A) removed outlier: 4.464A pdb=" N SER B 497 " --> pdb=" O LYS B 730 " (cutoff:3.500A) removed outlier: 6.493A pdb=" N LYS B 730 " --> pdb=" O SER B 497 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'C' and resid 12 through 19 Processing sheet with id= S, first strand: chain 'C' and resid 72 through 75 removed outlier: 6.842A pdb=" N SER C 95 " --> pdb=" O ILE C 73 " (cutoff:3.500A) removed outlier: 8.290A pdb=" N GLY C 75 " --> pdb=" O SER C 95 " (cutoff:3.500A) removed outlier: 6.034A pdb=" N ILE C 97 " --> pdb=" O GLY C 75 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'C' and resid 159 through 164 removed outlier: 3.606A pdb=" N PHE C 133 " --> pdb=" O GLN C 159 " (cutoff:3.500A) removed outlier: 5.552A pdb=" N ARG C 191 " --> pdb=" O LYS C 132 " (cutoff:3.500A) removed outlier: 6.209A pdb=" N HIS C 219 " --> pdb=" O VAL C 192 " (cutoff:3.500A) removed outlier: 7.221A pdb=" N LEU C 194 " --> pdb=" O HIS C 219 " (cutoff:3.500A) removed outlier: 6.086A pdb=" N ILE C 221 " --> pdb=" O LEU C 194 " (cutoff:3.500A) removed outlier: 6.298A pdb=" N GLU C 241 " --> pdb=" O TYR C 220 " (cutoff:3.500A) removed outlier: 7.677A pdb=" N ILE C 222 " --> pdb=" O GLU C 241 " (cutoff:3.500A) removed outlier: 6.977A pdb=" N SER C 243 " --> pdb=" O ILE C 222 " (cutoff:3.500A) removed outlier: 4.547A pdb=" N VAL C 242 " --> pdb=" O LEU C 363 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N GLY C 372 " --> pdb=" O ILE C 360 " (cutoff:3.500A) removed outlier: 6.346A pdb=" N GLU C 362 " --> pdb=" O LYS C 370 " (cutoff:3.500A) removed outlier: 5.120A pdb=" N LYS C 370 " --> pdb=" O GLU C 362 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'C' and resid 338 through 340 Processing sheet with id= V, first strand: chain 'C' and resid 395 through 399 Processing sheet with id= W, first strand: chain 'C' and resid 489 through 491 Processing sheet with id= X, first strand: chain 'C' and resid 720 through 723 removed outlier: 3.887A pdb=" N ILE C 502 " --> pdb=" O VAL C 723 " (cutoff:3.500A) removed outlier: 5.206A pdb=" N LYS C 505 " --> pdb=" O TYR C 700 " (cutoff:3.500A) removed outlier: 8.937A pdb=" N TYR C 700 " --> pdb=" O LYS C 505 " (cutoff:3.500A) removed outlier: 6.332A pdb=" N ALA C 646 " --> pdb=" O ALA C 701 " (cutoff:3.500A) removed outlier: 7.878A pdb=" N LEU C 703 " --> pdb=" O ALA C 646 " (cutoff:3.500A) removed outlier: 6.822A pdb=" N GLY C 648 " --> pdb=" O LEU C 703 " (cutoff:3.500A) removed outlier: 9.116A pdb=" N GLU C 705 " --> pdb=" O GLY C 648 " (cutoff:3.500A) Processing sheet with id= Y, first strand: chain 'C' and resid 1033 through 1036 removed outlier: 3.510A pdb=" N THR C1093 " --> pdb=" O CYS C1033 " (cutoff:3.500A) Processing sheet with id= Z, first strand: chain 'C' and resid 494 through 498 removed outlier: 6.765A pdb=" N TYR C 732 " --> pdb=" O PHE C 495 " (cutoff:3.500A) removed outlier: 4.465A pdb=" N SER C 497 " --> pdb=" O LYS C 730 " (cutoff:3.500A) removed outlier: 6.492A pdb=" N LYS C 730 " --> pdb=" O SER C 497 " (cutoff:3.500A) Processing sheet with id= AA, first strand: chain 'D' and resid 12 through 19 Processing sheet with id= AB, first strand: chain 'D' and resid 72 through 75 removed outlier: 6.842A pdb=" N SER D 95 " --> pdb=" O ILE D 73 " (cutoff:3.500A) removed outlier: 8.290A pdb=" N GLY D 75 " --> pdb=" O SER D 95 " (cutoff:3.500A) removed outlier: 6.034A pdb=" N ILE D 97 " --> pdb=" O GLY D 75 " (cutoff:3.500A) Processing sheet with id= AC, first strand: chain 'D' and resid 159 through 164 removed outlier: 3.607A pdb=" N PHE D 133 " --> pdb=" O GLN D 159 " (cutoff:3.500A) removed outlier: 5.552A pdb=" N ARG D 191 " --> pdb=" O LYS D 132 " (cutoff:3.500A) removed outlier: 6.209A pdb=" N HIS D 219 " --> pdb=" O VAL D 192 " (cutoff:3.500A) removed outlier: 7.221A pdb=" N LEU D 194 " --> pdb=" O HIS D 219 " (cutoff:3.500A) removed outlier: 6.087A pdb=" N ILE D 221 " --> pdb=" O LEU D 194 " (cutoff:3.500A) removed outlier: 6.298A pdb=" N GLU D 241 " --> pdb=" O TYR D 220 " (cutoff:3.500A) removed outlier: 7.678A pdb=" N ILE D 222 " --> pdb=" O GLU D 241 " (cutoff:3.500A) removed outlier: 6.977A pdb=" N SER D 243 " --> pdb=" O ILE D 222 " (cutoff:3.500A) removed outlier: 4.548A pdb=" N VAL D 242 " --> pdb=" O LEU D 363 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N GLY D 372 " --> pdb=" O ILE D 360 " (cutoff:3.500A) removed outlier: 6.345A pdb=" N GLU D 362 " --> pdb=" O LYS D 370 " (cutoff:3.500A) removed outlier: 5.121A pdb=" N LYS D 370 " --> pdb=" O GLU D 362 " (cutoff:3.500A) Processing sheet with id= AD, first strand: chain 'D' and resid 338 through 340 Processing sheet with id= AE, first strand: chain 'D' and resid 395 through 399 Processing sheet with id= AF, first strand: chain 'D' and resid 489 through 491 Processing sheet with id= AG, first strand: chain 'D' and resid 720 through 723 removed outlier: 3.886A pdb=" N ILE D 502 " --> pdb=" O VAL D 723 " (cutoff:3.500A) removed outlier: 5.206A pdb=" N LYS D 505 " --> pdb=" O TYR D 700 " (cutoff:3.500A) removed outlier: 8.937A pdb=" N TYR D 700 " --> pdb=" O LYS D 505 " (cutoff:3.500A) removed outlier: 6.331A pdb=" N ALA D 646 " --> pdb=" O ALA D 701 " (cutoff:3.500A) removed outlier: 7.878A pdb=" N LEU D 703 " --> pdb=" O ALA D 646 " (cutoff:3.500A) removed outlier: 6.821A pdb=" N GLY D 648 " --> pdb=" O LEU D 703 " (cutoff:3.500A) removed outlier: 9.116A pdb=" N GLU D 705 " --> pdb=" O GLY D 648 " (cutoff:3.500A) Processing sheet with id= AH, first strand: chain 'D' and resid 494 through 498 removed outlier: 6.764A pdb=" N TYR D 732 " --> pdb=" O PHE D 495 " (cutoff:3.500A) removed outlier: 4.465A pdb=" N SER D 497 " --> pdb=" O LYS D 730 " (cutoff:3.500A) removed outlier: 6.493A pdb=" N LYS D 730 " --> pdb=" O SER D 497 " (cutoff:3.500A) 1053 hydrogen bonds defined for protein. 2955 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: 10.28 Time building geometry restraints manager: 12.70 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.35: 8660 1.35 - 1.48: 7325 1.48 - 1.61: 12021 1.61 - 1.73: 8 1.73 - 1.86: 234 Bond restraints: 28248 Sorted by residual: bond pdb=" CAT ZK1 D1301 " pdb=" OAA ZK1 D1301 " ideal model delta sigma weight residual 1.214 1.407 -0.193 2.00e-02 2.50e+03 9.29e+01 bond pdb=" CAT ZK1 C1301 " pdb=" OAA ZK1 C1301 " ideal model delta sigma weight residual 1.214 1.407 -0.193 2.00e-02 2.50e+03 9.28e+01 bond pdb=" CAT ZK1 A1301 " pdb=" OAA ZK1 A1301 " ideal model delta sigma weight residual 1.214 1.406 -0.192 2.00e-02 2.50e+03 9.24e+01 bond pdb=" CAT ZK1 B1301 " pdb=" OAA ZK1 B1301 " ideal model delta sigma weight residual 1.214 1.404 -0.190 2.00e-02 2.50e+03 9.01e+01 bond pdb=" CAU ZK1 D1301 " pdb=" OAB ZK1 D1301 " ideal model delta sigma weight residual 1.215 1.403 -0.188 2.00e-02 2.50e+03 8.87e+01 ... (remaining 28243 not shown) Histogram of bond angle deviations from ideal: 95.07 - 103.39: 275 103.39 - 111.71: 13109 111.71 - 120.03: 12210 120.03 - 128.35: 12443 128.35 - 136.67: 217 Bond angle restraints: 38254 Sorted by residual: angle pdb=" CA ILE A 612 " pdb=" C ILE A 612 " pdb=" N ILE A 613 " ideal model delta sigma weight residual 117.69 105.49 12.20 1.27e+00 6.20e-01 9.23e+01 angle pdb=" O ILE C 612 " pdb=" C ILE C 612 " pdb=" N ILE C 613 " ideal model delta sigma weight residual 121.83 112.44 9.39 1.03e+00 9.43e-01 8.31e+01 angle pdb=" O ILE A 612 " pdb=" C ILE A 612 " pdb=" N ILE A 613 " ideal model delta sigma weight residual 121.80 131.60 -9.80 1.13e+00 7.83e-01 7.51e+01 angle pdb=" CA GLU D 634 " pdb=" C GLU D 634 " pdb=" N SER D 635 " ideal model delta sigma weight residual 118.04 106.73 11.31 1.32e+00 5.74e-01 7.34e+01 angle pdb=" CA ILE C 612 " pdb=" C ILE C 612 " pdb=" N ILE C 613 " ideal model delta sigma weight residual 117.28 126.87 -9.59 1.16e+00 7.43e-01 6.83e+01 ... (remaining 38249 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.37: 16720 35.37 - 70.74: 140 70.74 - 106.11: 78 106.11 - 141.48: 116 141.48 - 176.86: 26 Dihedral angle restraints: 17080 sinusoidal: 7056 harmonic: 10024 Sorted by residual: dihedral pdb=" CA GLY A1207 " pdb=" C GLY A1207 " pdb=" N TRP A1208 " pdb=" CA TRP A1208 " ideal model delta harmonic sigma weight residual 180.00 -86.19 -93.81 0 5.00e+00 4.00e-02 3.52e+02 dihedral pdb=" CA GLY C1207 " pdb=" C GLY C1207 " pdb=" N TRP C1208 " pdb=" CA TRP C1208 " ideal model delta harmonic sigma weight residual -180.00 -86.20 -93.80 0 5.00e+00 4.00e-02 3.52e+02 dihedral pdb=" CA GLU A 384 " pdb=" C GLU A 384 " pdb=" N ASP A 385 " pdb=" CA ASP A 385 " ideal model delta harmonic sigma weight residual -180.00 -127.33 -52.67 0 5.00e+00 4.00e-02 1.11e+02 ... (remaining 17077 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 1.166: 4228 1.166 - 2.333: 0 2.333 - 3.499: 0 3.499 - 4.666: 2 4.666 - 5.832: 66 Chirality restraints: 4296 Sorted by residual: chirality pdb=" C12 AJP C1302 " pdb=" C07 AJP C1302 " pdb=" C11 AJP C1302 " pdb=" C13 AJP C1302 " both_signs ideal model delta sigma weight residual False 3.01 -2.82 5.83 2.00e-01 2.50e+01 8.50e+02 chirality pdb=" C12 AJP A1302 " pdb=" C07 AJP A1302 " pdb=" C11 AJP A1302 " pdb=" C13 AJP A1302 " both_signs ideal model delta sigma weight residual False 3.01 -2.82 5.82 2.00e-01 2.50e+01 8.48e+02 chirality pdb=" C20 AJP C1302 " pdb=" C15 AJP C1302 " pdb=" C19 AJP C1302 " pdb=" C21 AJP C1302 " both_signs ideal model delta sigma weight residual False 2.96 -2.71 5.67 2.00e-01 2.50e+01 8.02e+02 ... (remaining 4293 not shown) Planarity restraints: 4756 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA THR D 383 " 0.033 2.00e-02 2.50e+03 6.84e-02 4.67e+01 pdb=" C THR D 383 " -0.118 2.00e-02 2.50e+03 pdb=" O THR D 383 " 0.045 2.00e-02 2.50e+03 pdb=" N GLU D 384 " 0.040 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR C 383 " -0.033 2.00e-02 2.50e+03 6.57e-02 4.31e+01 pdb=" C THR C 383 " 0.114 2.00e-02 2.50e+03 pdb=" O THR C 383 " -0.042 2.00e-02 2.50e+03 pdb=" N GLU C 384 " -0.038 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA CYS A 773 " 0.030 2.00e-02 2.50e+03 6.03e-02 3.64e+01 pdb=" C CYS A 773 " -0.104 2.00e-02 2.50e+03 pdb=" O CYS A 773 " 0.039 2.00e-02 2.50e+03 pdb=" N GLY A 774 " 0.035 2.00e-02 2.50e+03 ... (remaining 4753 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.74: 3072 2.74 - 3.28: 27627 3.28 - 3.82: 47084 3.82 - 4.36: 56835 4.36 - 4.90: 91601 Nonbonded interactions: 226219 Sorted by model distance: nonbonded pdb=" O33 AJP C1302 " pdb=" O76 AJP C1302 " model vdw 2.206 2.440 nonbonded pdb=" O33 AJP A1302 " pdb=" O76 AJP A1302 " model vdw 2.206 2.440 nonbonded pdb=" O62 AJP A1302 " pdb=" O75 AJP A1302 " model vdw 2.220 2.440 nonbonded pdb=" O62 AJP C1302 " pdb=" O75 AJP C1302 " model vdw 2.220 2.440 nonbonded pdb=" NE2 GLN C 129 " pdb=" O78 AJP C1302 " model vdw 2.225 2.520 ... (remaining 226214 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' selection = chain 'C' } ncs_group { reference = chain 'B' selection = chain 'D' } 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: 2.100 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 7.410 Check model and map are aligned: 0.450 Set scattering table: 0.280 Process input model: 80.670 Find NCS groups from input model: 1.490 Set up NCS constraints: 0.180 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: 0.010 Load rotamer database and sin/cos tables:2.720 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 95.330 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6890 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.193 28248 Z= 0.420 Angle : 0.981 17.140 38254 Z= 0.549 Chirality : 0.641 5.832 4296 Planarity : 0.007 0.091 4756 Dihedral : 19.467 176.856 10642 Min Nonbonded Distance : 2.206 Molprobity Statistics. All-atom Clashscore : 6.86 Ramachandran Plot: Outliers : 0.14 % Allowed : 6.46 % Favored : 93.40 % Rotamer: Outliers : 0.61 % Allowed : 0.88 % Favored : 98.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 18.75 % 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: -4.07 (0.11), residues: 3452 helix: -3.36 (0.07), residues: 1566 sheet: -1.94 (0.25), residues: 380 loop : -1.93 (0.14), residues: 1506 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.003 TRP A1199 HIS 0.010 0.002 HIS A1152 PHE 0.030 0.002 PHE C1143 TYR 0.019 0.002 TYR C 816 ARG 0.007 0.001 ARG C1038 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6904 Ramachandran restraints generated. 3452 Oldfield, 0 Emsley, 3452 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6904 Ramachandran restraints generated. 3452 Oldfield, 0 Emsley, 3452 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 900 residues out of total 2968 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 882 time to evaluate : 3.252 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 18 PHE cc_start: 0.8155 (m-80) cc_final: 0.7902 (m-80) REVERT: A 170 ASN cc_start: 0.8820 (m-40) cc_final: 0.8595 (m-40) REVERT: A 188 LYS cc_start: 0.9350 (mttt) cc_final: 0.8997 (mmmm) REVERT: A 235 ILE cc_start: 0.9010 (OUTLIER) cc_final: 0.8541 (mm) REVERT: A 331 ARG cc_start: 0.9110 (mtt180) cc_final: 0.8745 (tpt90) REVERT: A 378 ASP cc_start: 0.8869 (m-30) cc_final: 0.8579 (t0) REVERT: A 400 ILE cc_start: 0.7937 (tt) cc_final: 0.7412 (tp) REVERT: A 414 MET cc_start: 0.8175 (mmm) cc_final: 0.7869 (tmm) REVERT: A 424 TYR cc_start: 0.8512 (t80) cc_final: 0.8236 (t80) REVERT: A 458 LYS cc_start: 0.8560 (mttt) cc_final: 0.8008 (mmmt) REVERT: A 471 LYS cc_start: 0.8902 (tptt) cc_final: 0.8569 (mtmt) REVERT: A 491 PHE cc_start: 0.8060 (m-80) cc_final: 0.7191 (m-80) REVERT: A 503 MET cc_start: 0.7918 (ttm) cc_final: 0.7352 (tmm) REVERT: A 657 GLU cc_start: 0.9161 (tt0) cc_final: 0.8961 (tm-30) REVERT: A 693 VAL cc_start: 0.7822 (t) cc_final: 0.6901 (p) REVERT: A 710 GLU cc_start: 0.8057 (mt-10) cc_final: 0.7361 (mm-30) REVERT: A 720 THR cc_start: 0.9211 (p) cc_final: 0.8843 (t) REVERT: A 721 MET cc_start: 0.7783 (ptm) cc_final: 0.7108 (ptp) REVERT: A 1028 LEU cc_start: 0.7697 (OUTLIER) cc_final: 0.7276 (tt) REVERT: A 1181 HIS cc_start: 0.7423 (m-70) cc_final: 0.7139 (m170) REVERT: B 26 TYR cc_start: 0.8844 (t80) cc_final: 0.8482 (t80) REVERT: B 83 ASN cc_start: 0.8646 (m-40) cc_final: 0.8399 (m-40) REVERT: B 111 ILE cc_start: 0.8096 (mm) cc_final: 0.7864 (mm) REVERT: B 113 MET cc_start: 0.8830 (mmp) cc_final: 0.8018 (mmp) REVERT: B 143 LEU cc_start: 0.8958 (mp) cc_final: 0.8275 (mt) REVERT: B 158 TRP cc_start: 0.7164 (m-10) cc_final: 0.6844 (m-10) REVERT: B 189 GLU cc_start: 0.7994 (mm-30) cc_final: 0.7220 (mm-30) REVERT: B 210 THR cc_start: 0.7854 (m) cc_final: 0.7528 (m) REVERT: B 303 ARG cc_start: 0.8980 (mtt180) cc_final: 0.8514 (ptp90) REVERT: B 361 MET cc_start: 0.7547 (mmm) cc_final: 0.7315 (mtt) REVERT: B 386 ASP cc_start: 0.5782 (t0) cc_final: 0.5254 (p0) REVERT: B 432 ILE cc_start: 0.7946 (mm) cc_final: 0.7578 (tp) REVERT: B 491 PHE cc_start: 0.7849 (m-80) cc_final: 0.7119 (m-80) REVERT: B 503 MET cc_start: 0.8047 (ttm) cc_final: 0.7735 (tpp) REVERT: B 508 GLN cc_start: 0.8900 (pt0) cc_final: 0.8210 (pm20) REVERT: B 524 GLU cc_start: 0.8619 (mp0) cc_final: 0.8382 (tt0) REVERT: B 541 PHE cc_start: 0.6978 (t80) cc_final: 0.6758 (t80) REVERT: B 578 TRP cc_start: 0.5463 (t60) cc_final: 0.5034 (t60) REVERT: B 625 THR cc_start: 0.8739 (m) cc_final: 0.8469 (p) REVERT: B 647 TYR cc_start: 0.6798 (p90) cc_final: 0.6378 (p90) REVERT: B 657 GLU cc_start: 0.9361 (tt0) cc_final: 0.8969 (tp30) REVERT: B 684 ARG cc_start: 0.8804 (mtt180) cc_final: 0.8422 (tpp-160) REVERT: B 708 MET cc_start: 0.9328 (tpt) cc_final: 0.9099 (tpt) REVERT: B 709 ASN cc_start: 0.8255 (t0) cc_final: 0.8003 (t0) REVERT: B 732 TYR cc_start: 0.7362 (m-10) cc_final: 0.6553 (m-80) REVERT: B 755 GLU cc_start: 0.8371 (tt0) cc_final: 0.7769 (tm-30) REVERT: B 797 TYR cc_start: 0.8613 (m-80) cc_final: 0.8194 (m-10) REVERT: C 78 ASP cc_start: 0.8536 (t0) cc_final: 0.8279 (t0) REVERT: C 80 LYS cc_start: 0.8405 (mttt) cc_final: 0.7994 (mtmt) REVERT: C 170 ASN cc_start: 0.8829 (m-40) cc_final: 0.8623 (m-40) REVERT: C 188 LYS cc_start: 0.9263 (mttt) cc_final: 0.8839 (mmmm) REVERT: C 235 ILE cc_start: 0.9064 (OUTLIER) cc_final: 0.8544 (mm) REVERT: C 243 SER cc_start: 0.8822 (m) cc_final: 0.8331 (t) REVERT: C 378 ASP cc_start: 0.8806 (m-30) cc_final: 0.8490 (t0) REVERT: C 415 LEU cc_start: 0.6862 (mt) cc_final: 0.6636 (mt) REVERT: C 424 TYR cc_start: 0.8576 (t80) cc_final: 0.8196 (t80) REVERT: C 458 LYS cc_start: 0.8812 (mttt) cc_final: 0.8378 (mmmt) REVERT: C 471 LYS cc_start: 0.9018 (tptt) cc_final: 0.8759 (mttp) REVERT: C 483 LEU cc_start: 0.8449 (tp) cc_final: 0.8043 (mt) REVERT: C 491 PHE cc_start: 0.7372 (m-80) cc_final: 0.7071 (m-80) REVERT: C 533 TYR cc_start: 0.7027 (t80) cc_final: 0.6659 (t80) REVERT: C 606 TRP cc_start: 0.6620 (t60) cc_final: 0.6028 (t60) REVERT: C 611 ILE cc_start: 0.8684 (mm) cc_final: 0.8309 (mm) REVERT: C 612 ILE cc_start: 0.8324 (mt) cc_final: 0.8085 (mt) REVERT: C 627 GLU cc_start: 0.9047 (tp30) cc_final: 0.8847 (tm-30) REVERT: C 637 GLU cc_start: 0.8994 (mt-10) cc_final: 0.8247 (tm-30) REVERT: C 639 LEU cc_start: 0.8265 (mt) cc_final: 0.7801 (mp) REVERT: C 710 GLU cc_start: 0.8381 (mt-10) cc_final: 0.8039 (mm-30) REVERT: C 713 GLU cc_start: 0.8481 (tt0) cc_final: 0.8225 (tm-30) REVERT: C 720 THR cc_start: 0.8798 (p) cc_final: 0.8213 (p) REVERT: C 721 MET cc_start: 0.7643 (ptm) cc_final: 0.6723 (ptp) REVERT: C 738 LYS cc_start: 0.9155 (tttm) cc_final: 0.8765 (tptp) REVERT: C 807 MET cc_start: 0.5077 (mmm) cc_final: 0.4745 (ppp) REVERT: C 1088 LEU cc_start: 0.7380 (mt) cc_final: 0.7047 (pt) REVERT: C 1181 HIS cc_start: 0.8954 (m-70) cc_final: 0.8034 (m90) REVERT: C 1184 TYR cc_start: 0.8033 (t80) cc_final: 0.7525 (t80) REVERT: C 1216 SER cc_start: 0.8868 (p) cc_final: 0.8313 (t) REVERT: D 26 TYR cc_start: 0.8736 (t80) cc_final: 0.8380 (t80) REVERT: D 111 ILE cc_start: 0.7997 (mm) cc_final: 0.7706 (mm) REVERT: D 113 MET cc_start: 0.8788 (mmp) cc_final: 0.8006 (mmp) REVERT: D 116 ASP cc_start: 0.8314 (t0) cc_final: 0.7915 (t0) REVERT: D 158 TRP cc_start: 0.7289 (m-10) cc_final: 0.7040 (m-10) REVERT: D 189 GLU cc_start: 0.8080 (mm-30) cc_final: 0.7314 (mm-30) REVERT: D 231 ASP cc_start: 0.7981 (t0) cc_final: 0.7542 (t0) REVERT: D 303 ARG cc_start: 0.9035 (mtt180) cc_final: 0.8462 (ptp90) REVERT: D 386 ASP cc_start: 0.5888 (t0) cc_final: 0.5520 (p0) REVERT: D 407 MET cc_start: 0.7079 (mtm) cc_final: 0.6576 (mtm) REVERT: D 432 ILE cc_start: 0.7938 (mm) cc_final: 0.7530 (tp) REVERT: D 466 GLU cc_start: 0.8216 (mt-10) cc_final: 0.7821 (mt-10) REVERT: D 473 ASP cc_start: 0.7978 (m-30) cc_final: 0.7040 (t0) REVERT: D 491 PHE cc_start: 0.7075 (m-80) cc_final: 0.6767 (m-80) REVERT: D 498 LEU cc_start: 0.7930 (pp) cc_final: 0.7670 (pp) REVERT: D 503 MET cc_start: 0.8190 (ttm) cc_final: 0.7854 (tpp) REVERT: D 639 LEU cc_start: 0.7485 (mt) cc_final: 0.7092 (mp) REVERT: D 657 GLU cc_start: 0.9224 (tt0) cc_final: 0.8731 (tp30) REVERT: D 668 ASP cc_start: 0.8510 (t0) cc_final: 0.8289 (m-30) REVERT: D 708 MET cc_start: 0.9259 (tpt) cc_final: 0.9026 (tpt) REVERT: D 732 TYR cc_start: 0.6964 (m-10) cc_final: 0.5947 (m-80) REVERT: D 768 TYR cc_start: 0.7746 (m-80) cc_final: 0.7496 (m-10) outliers start: 18 outliers final: 2 residues processed: 895 average time/residue: 0.4520 time to fit residues: 603.2394 Evaluate side-chains 473 residues out of total 2968 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 468 time to evaluate : 3.254 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 348 random chunks: chunk 293 optimal weight: 6.9990 chunk 263 optimal weight: 10.0000 chunk 146 optimal weight: 3.9990 chunk 90 optimal weight: 1.9990 chunk 177 optimal weight: 20.0000 chunk 140 optimal weight: 2.9990 chunk 272 optimal weight: 10.0000 chunk 105 optimal weight: 8.9990 chunk 165 optimal weight: 5.9990 chunk 203 optimal weight: 6.9990 chunk 316 optimal weight: 6.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 35 GLN A 83 ASN ** A 236 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 246 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 290 GLN ** A 337 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 412 HIS ** A 586 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 587 GLN ** A 642 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 756 GLN A 791 ASN A1034 GLN A1037 GLN ** A1181 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 60 ASN ** B 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 219 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 337 GLN ** B 392 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 619 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 35 GLN C 65 GLN ** C 246 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 290 GLN ** C 337 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 587 GLN ** C 642 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 756 GLN C 791 ASN C1034 GLN ** C1037 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1092 HIS ** C1163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1181 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 60 ASN ** D 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 147 GLN ** D 219 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 337 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 392 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 412 HIS D 756 GLN Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7148 moved from start: 0.4395 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.080 28248 Z= 0.374 Angle : 1.067 39.068 38254 Z= 0.467 Chirality : 0.089 2.508 4296 Planarity : 0.006 0.076 4756 Dihedral : 17.016 179.858 4282 Min Nonbonded Distance : 2.068 Molprobity Statistics. All-atom Clashscore : 18.39 Ramachandran Plot: Outliers : 0.12 % Allowed : 5.94 % Favored : 93.95 % Rotamer: Outliers : 0.03 % Allowed : 3.11 % Favored : 96.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 18.75 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % 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: -2.21 (0.13), residues: 3452 helix: -1.20 (0.11), residues: 1592 sheet: -1.36 (0.27), residues: 376 loop : -1.65 (0.16), residues: 1484 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP D 158 HIS 0.010 0.002 HIS A1181 PHE 0.022 0.002 PHE A 517 TYR 0.030 0.003 TYR A 421 ARG 0.006 0.001 ARG C1008 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6904 Ramachandran restraints generated. 3452 Oldfield, 0 Emsley, 3452 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6904 Ramachandran restraints generated. 3452 Oldfield, 0 Emsley, 3452 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 511 residues out of total 2968 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 510 time to evaluate : 3.426 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 188 LYS cc_start: 0.9246 (mttt) cc_final: 0.8979 (mmmm) REVERT: A 378 ASP cc_start: 0.8867 (m-30) cc_final: 0.8551 (t0) REVERT: A 400 ILE cc_start: 0.8225 (tt) cc_final: 0.7942 (tp) REVERT: A 415 LEU cc_start: 0.7549 (mt) cc_final: 0.7346 (mt) REVERT: A 440 TYR cc_start: 0.9145 (p90) cc_final: 0.8705 (p90) REVERT: A 458 LYS cc_start: 0.8970 (mttt) cc_final: 0.8614 (mmmt) REVERT: A 471 LYS cc_start: 0.9101 (tptt) cc_final: 0.8712 (mtmm) REVERT: A 496 MET cc_start: 0.7903 (tpp) cc_final: 0.7379 (tmm) REVERT: A 503 MET cc_start: 0.8132 (ttm) cc_final: 0.7665 (tmm) REVERT: A 705 GLU cc_start: 0.9107 (mp0) cc_final: 0.8803 (mp0) REVERT: A 708 MET cc_start: 0.8039 (tmm) cc_final: 0.7693 (ppp) REVERT: A 1183 MET cc_start: 0.9002 (mmp) cc_final: 0.8788 (mmm) REVERT: B 113 MET cc_start: 0.9090 (mmp) cc_final: 0.8425 (mmm) REVERT: B 170 ASN cc_start: 0.8961 (p0) cc_final: 0.8719 (p0) REVERT: B 189 GLU cc_start: 0.7895 (mm-30) cc_final: 0.7225 (mm-30) REVERT: B 231 ASP cc_start: 0.8109 (t0) cc_final: 0.7776 (t0) REVERT: B 248 VAL cc_start: 0.8379 (t) cc_final: 0.7994 (t) REVERT: B 508 GLN cc_start: 0.8966 (pt0) cc_final: 0.8325 (pm20) REVERT: B 524 GLU cc_start: 0.8155 (mp0) cc_final: 0.7831 (tt0) REVERT: B 585 MET cc_start: 0.7251 (ptt) cc_final: 0.7014 (ppp) REVERT: B 670 MET cc_start: 0.8962 (mtt) cc_final: 0.8737 (mmp) REVERT: B 684 ARG cc_start: 0.8751 (mtt180) cc_final: 0.8342 (ttm110) REVERT: B 783 LYS cc_start: 0.7670 (mttt) cc_final: 0.7470 (mmtm) REVERT: C 79 LYS cc_start: 0.8657 (pttp) cc_final: 0.8349 (tppt) REVERT: C 80 LYS cc_start: 0.8902 (mttt) cc_final: 0.8281 (mtmt) REVERT: C 113 MET cc_start: 0.9570 (mmt) cc_final: 0.9338 (mmm) REVERT: C 188 LYS cc_start: 0.9203 (mttt) cc_final: 0.8895 (mmmm) REVERT: C 378 ASP cc_start: 0.8819 (m-30) cc_final: 0.8422 (t0) REVERT: C 440 TYR cc_start: 0.9093 (p90) cc_final: 0.8739 (p90) REVERT: C 458 LYS cc_start: 0.9003 (mttt) cc_final: 0.8588 (mmmt) REVERT: C 471 LYS cc_start: 0.9218 (tptt) cc_final: 0.8761 (mtmm) REVERT: C 491 PHE cc_start: 0.8156 (m-80) cc_final: 0.7949 (m-10) REVERT: C 503 MET cc_start: 0.8121 (ttt) cc_final: 0.7537 (tmm) REVERT: C 521 LEU cc_start: 0.6269 (tt) cc_final: 0.5999 (tt) REVERT: C 611 ILE cc_start: 0.8798 (mm) cc_final: 0.8554 (mm) REVERT: C 627 GLU cc_start: 0.9167 (tp30) cc_final: 0.8830 (tm-30) REVERT: C 637 GLU cc_start: 0.9014 (mt-10) cc_final: 0.8639 (tm-30) REVERT: C 645 ILE cc_start: 0.7764 (mp) cc_final: 0.7502 (mt) REVERT: C 700 TYR cc_start: 0.6395 (t80) cc_final: 0.6047 (t80) REVERT: C 708 MET cc_start: 0.8421 (tmm) cc_final: 0.8135 (tmm) REVERT: C 710 GLU cc_start: 0.8540 (mt-10) cc_final: 0.8181 (mm-30) REVERT: C 721 MET cc_start: 0.8057 (ptm) cc_final: 0.6930 (ptp) REVERT: C 738 LYS cc_start: 0.9052 (tttm) cc_final: 0.8761 (tptp) REVERT: C 1034 GLN cc_start: 0.7286 (tt0) cc_final: 0.6899 (tp40) REVERT: C 1129 VAL cc_start: 0.8359 (m) cc_final: 0.8158 (p) REVERT: C 1182 MET cc_start: 0.8774 (ptt) cc_final: 0.8450 (ptt) REVERT: C 1183 MET cc_start: 0.9320 (mmp) cc_final: 0.9060 (mmm) REVERT: D 113 MET cc_start: 0.9007 (mmp) cc_final: 0.8295 (mmm) REVERT: D 170 ASN cc_start: 0.8872 (p0) cc_final: 0.8626 (p0) REVERT: D 189 GLU cc_start: 0.7925 (mm-30) cc_final: 0.7210 (mm-30) REVERT: D 231 ASP cc_start: 0.8040 (t0) cc_final: 0.7656 (t0) REVERT: D 248 VAL cc_start: 0.8475 (t) cc_final: 0.8173 (t) REVERT: D 361 MET cc_start: 0.8553 (mtt) cc_final: 0.8184 (mtt) REVERT: D 408 MET cc_start: 0.8535 (mmm) cc_final: 0.8241 (mmm) REVERT: D 491 PHE cc_start: 0.7571 (m-80) cc_final: 0.7346 (m-80) REVERT: D 496 MET cc_start: 0.8708 (tpt) cc_final: 0.8326 (tpp) REVERT: D 503 MET cc_start: 0.8182 (ttm) cc_final: 0.7508 (tmm) REVERT: D 639 LEU cc_start: 0.7766 (mt) cc_final: 0.7265 (mp) REVERT: D 647 TYR cc_start: 0.7306 (p90) cc_final: 0.6899 (p90) REVERT: D 657 GLU cc_start: 0.9329 (tt0) cc_final: 0.8511 (tp30) REVERT: D 668 ASP cc_start: 0.8643 (t0) cc_final: 0.8386 (m-30) REVERT: D 684 ARG cc_start: 0.8774 (mtt180) cc_final: 0.8375 (ttm110) REVERT: D 708 MET cc_start: 0.9207 (tpt) cc_final: 0.8965 (tpt) REVERT: D 711 TYR cc_start: 0.8716 (t80) cc_final: 0.8196 (t80) REVERT: D 732 TYR cc_start: 0.6448 (m-10) cc_final: 0.6080 (m-80) outliers start: 1 outliers final: 1 residues processed: 511 average time/residue: 0.3956 time to fit residues: 316.6702 Evaluate side-chains 331 residues out of total 2968 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 330 time to evaluate : 3.231 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 348 random chunks: chunk 175 optimal weight: 10.0000 chunk 98 optimal weight: 6.9990 chunk 263 optimal weight: 8.9990 chunk 215 optimal weight: 0.8980 chunk 87 optimal weight: 7.9990 chunk 316 optimal weight: 0.9980 chunk 342 optimal weight: 0.9980 chunk 281 optimal weight: 2.9990 chunk 313 optimal weight: 10.0000 chunk 107 optimal weight: 0.7980 chunk 253 optimal weight: 20.0000 overall best weight: 1.3382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 65 GLN ** A 246 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 290 GLN A 337 GLN A 586 GLN ** A 642 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1181 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 60 ASN ** B 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 392 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 170 ASN C 337 GLN C 412 HIS ** C 586 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 642 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1037 GLN D 60 ASN ** D 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 83 ASN D 337 GLN ** D 392 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7119 moved from start: 0.5005 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 28248 Z= 0.177 Angle : 0.857 37.236 38254 Z= 0.365 Chirality : 0.084 2.451 4296 Planarity : 0.005 0.074 4756 Dihedral : 15.471 174.949 4282 Min Nonbonded Distance : 2.082 Molprobity Statistics. All-atom Clashscore : 13.02 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.66 % Favored : 95.25 % Rotamer: Outliers : 0.03 % Allowed : 1.96 % Favored : 98.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 18.75 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: -1.23 (0.14), residues: 3452 helix: -0.11 (0.13), residues: 1568 sheet: -1.30 (0.26), residues: 406 loop : -1.36 (0.16), residues: 1478 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.001 TRP C 766 HIS 0.007 0.001 HIS A1181 PHE 0.034 0.001 PHE C 623 TYR 0.021 0.001 TYR A 421 ARG 0.005 0.000 ARG B 420 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6904 Ramachandran restraints generated. 3452 Oldfield, 0 Emsley, 3452 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6904 Ramachandran restraints generated. 3452 Oldfield, 0 Emsley, 3452 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 498 residues out of total 2968 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 497 time to evaluate : 3.364 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 89 CYS cc_start: 0.8784 (m) cc_final: 0.8323 (p) REVERT: A 112 GLN cc_start: 0.9059 (pt0) cc_final: 0.8803 (pm20) REVERT: A 378 ASP cc_start: 0.8827 (m-30) cc_final: 0.8550 (t0) REVERT: A 400 ILE cc_start: 0.8135 (tt) cc_final: 0.7760 (tp) REVERT: A 440 TYR cc_start: 0.9175 (p90) cc_final: 0.8731 (p90) REVERT: A 471 LYS cc_start: 0.9080 (tptt) cc_final: 0.8683 (mtmm) REVERT: A 496 MET cc_start: 0.7858 (tpp) cc_final: 0.7484 (tmm) REVERT: A 503 MET cc_start: 0.8055 (ttm) cc_final: 0.7786 (ppp) REVERT: A 705 GLU cc_start: 0.9137 (mp0) cc_final: 0.8797 (mp0) REVERT: A 708 MET cc_start: 0.8028 (tmm) cc_final: 0.7707 (tmm) REVERT: A 710 GLU cc_start: 0.8038 (mt-10) cc_final: 0.7727 (mm-30) REVERT: A 1129 VAL cc_start: 0.8458 (m) cc_final: 0.8209 (p) REVERT: A 1183 MET cc_start: 0.9201 (mmp) cc_final: 0.8882 (mmm) REVERT: B 113 MET cc_start: 0.8960 (mmp) cc_final: 0.8258 (mmm) REVERT: B 170 ASN cc_start: 0.8911 (p0) cc_final: 0.8614 (p0) REVERT: B 189 GLU cc_start: 0.7778 (mm-30) cc_final: 0.7184 (mm-30) REVERT: B 231 ASP cc_start: 0.8073 (t0) cc_final: 0.7466 (t0) REVERT: B 248 VAL cc_start: 0.8464 (t) cc_final: 0.8181 (t) REVERT: B 361 MET cc_start: 0.8445 (mtt) cc_final: 0.7887 (mtt) REVERT: B 491 PHE cc_start: 0.7960 (m-80) cc_final: 0.7134 (m-80) REVERT: B 508 GLN cc_start: 0.8970 (pt0) cc_final: 0.8354 (pm20) REVERT: B 524 GLU cc_start: 0.8184 (mp0) cc_final: 0.7935 (tt0) REVERT: B 585 MET cc_start: 0.7336 (ptt) cc_final: 0.6493 (ppp) REVERT: B 684 ARG cc_start: 0.8696 (mtt180) cc_final: 0.8301 (ttm110) REVERT: B 787 LEU cc_start: 0.8304 (tp) cc_final: 0.7806 (pp) REVERT: C 80 LYS cc_start: 0.8503 (mttt) cc_final: 0.8256 (mtmt) REVERT: C 89 CYS cc_start: 0.8799 (m) cc_final: 0.8247 (p) REVERT: C 113 MET cc_start: 0.9524 (mmt) cc_final: 0.9302 (mmm) REVERT: C 378 ASP cc_start: 0.8784 (m-30) cc_final: 0.8435 (t0) REVERT: C 440 TYR cc_start: 0.9115 (p90) cc_final: 0.8824 (p90) REVERT: C 458 LYS cc_start: 0.8931 (mttt) cc_final: 0.8634 (mmmt) REVERT: C 471 LYS cc_start: 0.9258 (tptt) cc_final: 0.8781 (mtmm) REVERT: C 496 MET cc_start: 0.7720 (tpp) cc_final: 0.7090 (tmm) REVERT: C 503 MET cc_start: 0.8526 (ttt) cc_final: 0.8057 (tmm) REVERT: C 526 TRP cc_start: 0.5829 (m100) cc_final: 0.5249 (m100) REVERT: C 627 GLU cc_start: 0.9180 (tp30) cc_final: 0.8875 (tm-30) REVERT: C 705 GLU cc_start: 0.8980 (mp0) cc_final: 0.8767 (mp0) REVERT: C 708 MET cc_start: 0.8237 (tmm) cc_final: 0.7910 (tmm) REVERT: C 795 VAL cc_start: 0.7076 (p) cc_final: 0.6486 (p) REVERT: C 1182 MET cc_start: 0.8763 (ptt) cc_final: 0.8382 (ptt) REVERT: C 1183 MET cc_start: 0.9411 (mmp) cc_final: 0.9195 (mmm) REVERT: D 23 ASP cc_start: 0.9306 (p0) cc_final: 0.9030 (p0) REVERT: D 73 ILE cc_start: 0.8399 (mt) cc_final: 0.8029 (tt) REVERT: D 113 MET cc_start: 0.8817 (mmp) cc_final: 0.8079 (mmm) REVERT: D 167 ASN cc_start: 0.8640 (t0) cc_final: 0.8106 (p0) REVERT: D 170 ASN cc_start: 0.8843 (p0) cc_final: 0.8582 (p0) REVERT: D 187 LYS cc_start: 0.8929 (mmtt) cc_final: 0.8563 (mmtm) REVERT: D 189 GLU cc_start: 0.7803 (mm-30) cc_final: 0.7174 (mm-30) REVERT: D 195 ASP cc_start: 0.8090 (t0) cc_final: 0.7706 (t0) REVERT: D 248 VAL cc_start: 0.8459 (t) cc_final: 0.8099 (t) REVERT: D 361 MET cc_start: 0.8481 (mtt) cc_final: 0.8159 (mtt) REVERT: D 473 ASP cc_start: 0.8059 (m-30) cc_final: 0.7051 (t0) REVERT: D 491 PHE cc_start: 0.7650 (m-80) cc_final: 0.7016 (m-80) REVERT: D 496 MET cc_start: 0.8749 (tpt) cc_final: 0.8433 (tpp) REVERT: D 503 MET cc_start: 0.8269 (ttm) cc_final: 0.7518 (tmm) REVERT: D 521 LEU cc_start: 0.8060 (tt) cc_final: 0.7807 (mt) REVERT: D 525 ILE cc_start: 0.6207 (mm) cc_final: 0.5861 (mm) REVERT: D 526 TRP cc_start: 0.3929 (m100) cc_final: 0.3305 (m100) REVERT: D 684 ARG cc_start: 0.8709 (mtt180) cc_final: 0.8274 (ttm110) REVERT: D 695 LYS cc_start: 0.8814 (mmmt) cc_final: 0.8544 (mmmm) REVERT: D 708 MET cc_start: 0.9225 (tpt) cc_final: 0.8884 (tpp) REVERT: D 711 TYR cc_start: 0.8720 (t80) cc_final: 0.8186 (t80) REVERT: D 732 TYR cc_start: 0.6020 (m-10) cc_final: 0.5621 (m-80) outliers start: 1 outliers final: 1 residues processed: 498 average time/residue: 0.3968 time to fit residues: 310.1368 Evaluate side-chains 346 residues out of total 2968 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 345 time to evaluate : 3.156 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 348 random chunks: chunk 312 optimal weight: 2.9990 chunk 238 optimal weight: 0.0980 chunk 164 optimal weight: 2.9990 chunk 35 optimal weight: 7.9990 chunk 151 optimal weight: 20.0000 chunk 212 optimal weight: 0.9990 chunk 317 optimal weight: 0.9990 chunk 336 optimal weight: 10.0000 chunk 165 optimal weight: 3.9990 chunk 301 optimal weight: 0.6980 chunk 90 optimal weight: 7.9990 overall best weight: 1.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 246 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 337 GLN ** A 642 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1181 HIS B 60 ASN ** B 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 202 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 392 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 619 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 83 ASN ** C 246 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 337 GLN ** C1037 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 60 ASN ** D 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 83 ASN ** D 392 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7138 moved from start: 0.5526 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 28248 Z= 0.165 Angle : 0.837 36.703 38254 Z= 0.352 Chirality : 0.083 2.292 4296 Planarity : 0.004 0.066 4756 Dihedral : 15.087 176.576 4282 Min Nonbonded Distance : 2.134 Molprobity Statistics. All-atom Clashscore : 12.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.98 % Favored : 95.02 % Rotamer: Outliers : 0.00 % Allowed : 1.59 % Favored : 98.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 18.75 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.79 (0.14), residues: 3452 helix: 0.39 (0.13), residues: 1570 sheet: -1.30 (0.26), residues: 410 loop : -1.23 (0.16), residues: 1472 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 262 HIS 0.005 0.001 HIS C 412 PHE 0.019 0.001 PHE A1027 TYR 0.019 0.001 TYR B 797 ARG 0.003 0.000 ARG B 30 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6904 Ramachandran restraints generated. 3452 Oldfield, 0 Emsley, 3452 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6904 Ramachandran restraints generated. 3452 Oldfield, 0 Emsley, 3452 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 480 residues out of total 2968 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 480 time to evaluate : 3.197 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 70 VAL cc_start: 0.8109 (m) cc_final: 0.7830 (m) REVERT: A 89 CYS cc_start: 0.8808 (m) cc_final: 0.8325 (p) REVERT: A 361 MET cc_start: 0.8802 (tpp) cc_final: 0.8599 (tpp) REVERT: A 400 ILE cc_start: 0.8025 (tt) cc_final: 0.7680 (tp) REVERT: A 408 MET cc_start: 0.8475 (pmm) cc_final: 0.8169 (tpp) REVERT: A 440 TYR cc_start: 0.9133 (p90) cc_final: 0.8737 (p90) REVERT: A 471 LYS cc_start: 0.9063 (tptt) cc_final: 0.8651 (mtmm) REVERT: A 496 MET cc_start: 0.7927 (tpp) cc_final: 0.7248 (tmm) REVERT: A 503 MET cc_start: 0.8086 (ttm) cc_final: 0.7839 (ppp) REVERT: A 705 GLU cc_start: 0.9115 (mp0) cc_final: 0.8866 (mp0) REVERT: A 1183 MET cc_start: 0.9309 (mmp) cc_final: 0.9000 (mmm) REVERT: B 73 ILE cc_start: 0.8291 (mt) cc_final: 0.7950 (tt) REVERT: B 113 MET cc_start: 0.9033 (mmp) cc_final: 0.8381 (mmp) REVERT: B 170 ASN cc_start: 0.9004 (p0) cc_final: 0.8641 (p0) REVERT: B 189 GLU cc_start: 0.7725 (mm-30) cc_final: 0.7181 (mm-30) REVERT: B 231 ASP cc_start: 0.7796 (t0) cc_final: 0.7389 (t0) REVERT: B 248 VAL cc_start: 0.8453 (t) cc_final: 0.8161 (t) REVERT: B 407 MET cc_start: 0.7732 (ptp) cc_final: 0.7397 (pmm) REVERT: B 491 PHE cc_start: 0.7888 (m-80) cc_final: 0.7035 (m-80) REVERT: B 508 GLN cc_start: 0.8955 (pt0) cc_final: 0.8351 (pm20) REVERT: B 524 GLU cc_start: 0.8029 (mp0) cc_final: 0.7765 (tt0) REVERT: B 585 MET cc_start: 0.7546 (ptt) cc_final: 0.5909 (ppp) REVERT: B 684 ARG cc_start: 0.8741 (mtt180) cc_final: 0.8321 (ttm110) REVERT: B 732 TYR cc_start: 0.5545 (m-80) cc_final: 0.5199 (m-80) REVERT: C 74 PHE cc_start: 0.8584 (t80) cc_final: 0.7819 (t80) REVERT: C 80 LYS cc_start: 0.8490 (mttt) cc_final: 0.8267 (mtmt) REVERT: C 89 CYS cc_start: 0.8731 (m) cc_final: 0.8207 (p) REVERT: C 140 ASP cc_start: 0.8362 (t0) cc_final: 0.8082 (p0) REVERT: C 378 ASP cc_start: 0.8698 (m-30) cc_final: 0.8389 (t0) REVERT: C 440 TYR cc_start: 0.9218 (p90) cc_final: 0.8873 (p90) REVERT: C 458 LYS cc_start: 0.8913 (mttt) cc_final: 0.8627 (mmmt) REVERT: C 471 LYS cc_start: 0.9222 (tptt) cc_final: 0.8768 (mtmm) REVERT: C 503 MET cc_start: 0.8706 (ttt) cc_final: 0.8202 (tmm) REVERT: C 526 TRP cc_start: 0.6375 (m100) cc_final: 0.5694 (m100) REVERT: C 627 GLU cc_start: 0.9234 (tp30) cc_final: 0.8924 (tm-30) REVERT: C 708 MET cc_start: 0.8254 (tmm) cc_final: 0.7952 (tmm) REVERT: C 795 VAL cc_start: 0.7244 (p) cc_final: 0.6712 (p) REVERT: C 1088 LEU cc_start: 0.6653 (mp) cc_final: 0.6283 (pt) REVERT: C 1182 MET cc_start: 0.8702 (ptt) cc_final: 0.8397 (ppp) REVERT: C 1221 MET cc_start: 0.6897 (mmp) cc_final: 0.6601 (mmp) REVERT: D 23 ASP cc_start: 0.9364 (p0) cc_final: 0.9026 (p0) REVERT: D 73 ILE cc_start: 0.8306 (mt) cc_final: 0.7971 (tt) REVERT: D 113 MET cc_start: 0.8935 (mmp) cc_final: 0.8257 (mmp) REVERT: D 170 ASN cc_start: 0.8966 (p0) cc_final: 0.8637 (p0) REVERT: D 187 LYS cc_start: 0.9036 (mmtt) cc_final: 0.8569 (mmtm) REVERT: D 189 GLU cc_start: 0.7771 (mm-30) cc_final: 0.7203 (mm-30) REVERT: D 248 VAL cc_start: 0.8498 (t) cc_final: 0.8161 (t) REVERT: D 361 MET cc_start: 0.8425 (mtt) cc_final: 0.8094 (mtt) REVERT: D 407 MET cc_start: 0.8254 (ptp) cc_final: 0.7971 (ptp) REVERT: D 491 PHE cc_start: 0.7594 (m-80) cc_final: 0.6856 (m-80) REVERT: D 503 MET cc_start: 0.8160 (ttm) cc_final: 0.7384 (tmm) REVERT: D 521 LEU cc_start: 0.8044 (tt) cc_final: 0.7719 (mt) REVERT: D 525 ILE cc_start: 0.6399 (mm) cc_final: 0.6056 (mm) REVERT: D 526 TRP cc_start: 0.4237 (m100) cc_final: 0.3533 (m100) REVERT: D 684 ARG cc_start: 0.8722 (mtt180) cc_final: 0.8201 (ttm110) REVERT: D 708 MET cc_start: 0.9180 (tpt) cc_final: 0.8828 (tpp) REVERT: D 711 TYR cc_start: 0.8731 (t80) cc_final: 0.8258 (t80) outliers start: 0 outliers final: 0 residues processed: 480 average time/residue: 0.3886 time to fit residues: 295.6419 Evaluate side-chains 339 residues out of total 2968 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 339 time to evaluate : 3.180 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 348 random chunks: chunk 280 optimal weight: 3.9990 chunk 190 optimal weight: 5.9990 chunk 4 optimal weight: 0.9990 chunk 250 optimal weight: 9.9990 chunk 138 optimal weight: 9.9990 chunk 287 optimal weight: 1.9990 chunk 232 optimal weight: 1.9990 chunk 0 optimal weight: 10.0000 chunk 171 optimal weight: 8.9990 chunk 301 optimal weight: 30.0000 chunk 84 optimal weight: 10.0000 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 246 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 337 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 359 ASN ** A 642 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 60 ASN ** B 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 182 GLN B 246 GLN ** B 392 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 246 GLN C 290 GLN ** C 337 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 60 ASN ** D 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 83 ASN ** D 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 246 GLN ** D 392 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 642 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7210 moved from start: 0.6312 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 28248 Z= 0.264 Angle : 0.889 36.857 38254 Z= 0.386 Chirality : 0.083 2.260 4296 Planarity : 0.005 0.070 4756 Dihedral : 14.779 175.717 4282 Min Nonbonded Distance : 2.055 Molprobity Statistics. All-atom Clashscore : 16.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.40 % Favored : 93.60 % Rotamer: Outliers : 0.07 % Allowed : 2.10 % Favored : 97.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 18.75 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.76 (0.14), residues: 3452 helix: 0.39 (0.13), residues: 1578 sheet: -1.36 (0.25), residues: 410 loop : -1.15 (0.17), residues: 1464 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP C1032 HIS 0.005 0.001 HIS A1202 PHE 0.022 0.002 PHE A 517 TYR 0.017 0.002 TYR A 405 ARG 0.006 0.000 ARG D 628 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6904 Ramachandran restraints generated. 3452 Oldfield, 0 Emsley, 3452 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6904 Ramachandran restraints generated. 3452 Oldfield, 0 Emsley, 3452 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 437 residues out of total 2968 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 435 time to evaluate : 3.211 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 74 PHE cc_start: 0.8316 (t80) cc_final: 0.7702 (t80) REVERT: A 89 CYS cc_start: 0.8789 (m) cc_final: 0.8227 (p) REVERT: A 361 MET cc_start: 0.8989 (tpp) cc_final: 0.8764 (tpp) REVERT: A 400 ILE cc_start: 0.8086 (tt) cc_final: 0.7783 (tp) REVERT: A 408 MET cc_start: 0.8569 (pmm) cc_final: 0.8167 (tpp) REVERT: A 471 LYS cc_start: 0.9091 (tptt) cc_final: 0.8610 (mtmm) REVERT: A 496 MET cc_start: 0.7823 (tpp) cc_final: 0.7326 (tmm) REVERT: A 503 MET cc_start: 0.8122 (ttm) cc_final: 0.7860 (tmm) REVERT: A 619 ASN cc_start: 0.7223 (t0) cc_final: 0.6922 (t0) REVERT: A 620 LEU cc_start: 0.8936 (tp) cc_final: 0.8727 (tp) REVERT: A 663 LYS cc_start: 0.8589 (mtmt) cc_final: 0.8298 (pttm) REVERT: A 705 GLU cc_start: 0.9197 (mp0) cc_final: 0.8672 (mp0) REVERT: A 708 MET cc_start: 0.8064 (tmm) cc_final: 0.7834 (tmm) REVERT: A 796 PHE cc_start: 0.7979 (m-10) cc_final: 0.7615 (m-80) REVERT: B 23 ASP cc_start: 0.9388 (p0) cc_final: 0.9132 (p0) REVERT: B 78 ASP cc_start: 0.7290 (t70) cc_final: 0.6616 (m-30) REVERT: B 80 LYS cc_start: 0.8606 (pttm) cc_final: 0.8266 (pttp) REVERT: B 89 CYS cc_start: 0.8734 (m) cc_final: 0.8272 (p) REVERT: B 113 MET cc_start: 0.9143 (mmp) cc_final: 0.8539 (mmp) REVERT: B 170 ASN cc_start: 0.9077 (p0) cc_final: 0.8723 (p0) REVERT: B 189 GLU cc_start: 0.7647 (mm-30) cc_final: 0.7053 (mm-30) REVERT: B 248 VAL cc_start: 0.8434 (t) cc_final: 0.8107 (t) REVERT: B 361 MET cc_start: 0.8650 (mtt) cc_final: 0.8241 (mtt) REVERT: B 503 MET cc_start: 0.8110 (ttm) cc_final: 0.7901 (ttt) REVERT: B 508 GLN cc_start: 0.8809 (pt0) cc_final: 0.8278 (pm20) REVERT: B 657 GLU cc_start: 0.9508 (mt-10) cc_final: 0.9308 (mp0) REVERT: B 670 MET cc_start: 0.9148 (mtt) cc_final: 0.8763 (mmp) REVERT: B 684 ARG cc_start: 0.8779 (mtt180) cc_final: 0.8368 (ttm110) REVERT: C 74 PHE cc_start: 0.8534 (t80) cc_final: 0.7811 (t80) REVERT: C 80 LYS cc_start: 0.8718 (mttt) cc_final: 0.8459 (mtpt) REVERT: C 440 TYR cc_start: 0.9216 (p90) cc_final: 0.8909 (p90) REVERT: C 458 LYS cc_start: 0.9012 (mttt) cc_final: 0.8728 (mmmt) REVERT: C 466 GLU cc_start: 0.9019 (mt-10) cc_final: 0.8739 (mt-10) REVERT: C 471 LYS cc_start: 0.9195 (tptt) cc_final: 0.8805 (mtmm) REVERT: C 503 MET cc_start: 0.8689 (ttt) cc_final: 0.8316 (tmm) REVERT: C 609 THR cc_start: 0.8298 (t) cc_final: 0.7792 (t) REVERT: C 708 MET cc_start: 0.8298 (tmm) cc_final: 0.8013 (tmm) REVERT: C 795 VAL cc_start: 0.7418 (p) cc_final: 0.6952 (p) REVERT: C 1034 GLN cc_start: 0.7282 (tt0) cc_final: 0.7040 (tt0) REVERT: C 1179 VAL cc_start: 0.9261 (t) cc_final: 0.8689 (t) REVERT: C 1182 MET cc_start: 0.8660 (ptt) cc_final: 0.8196 (ppp) REVERT: C 1183 MET cc_start: 0.9473 (mmp) cc_final: 0.8470 (mpp) REVERT: D 23 ASP cc_start: 0.9449 (p0) cc_final: 0.9143 (p0) REVERT: D 89 CYS cc_start: 0.8751 (m) cc_final: 0.8333 (p) REVERT: D 113 MET cc_start: 0.9075 (mmp) cc_final: 0.8499 (mmp) REVERT: D 170 ASN cc_start: 0.9040 (p0) cc_final: 0.8699 (p0) REVERT: D 189 GLU cc_start: 0.7669 (mm-30) cc_final: 0.7035 (mm-30) REVERT: D 248 VAL cc_start: 0.8387 (t) cc_final: 0.8040 (t) REVERT: D 361 MET cc_start: 0.8656 (mtt) cc_final: 0.8277 (mtt) REVERT: D 407 MET cc_start: 0.8300 (ptp) cc_final: 0.7889 (ptp) REVERT: D 441 LYS cc_start: 0.8931 (pttt) cc_final: 0.8687 (mmtm) REVERT: D 496 MET cc_start: 0.9197 (tpp) cc_final: 0.8775 (tpp) REVERT: D 503 MET cc_start: 0.8140 (ttm) cc_final: 0.7412 (tmm) REVERT: D 684 ARG cc_start: 0.8790 (mtt180) cc_final: 0.8241 (ttm110) REVERT: D 708 MET cc_start: 0.9239 (tpt) cc_final: 0.8947 (tpp) outliers start: 2 outliers final: 1 residues processed: 437 average time/residue: 0.4200 time to fit residues: 294.6464 Evaluate side-chains 324 residues out of total 2968 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 323 time to evaluate : 3.088 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 348 random chunks: chunk 113 optimal weight: 0.8980 chunk 302 optimal weight: 7.9990 chunk 66 optimal weight: 0.0030 chunk 197 optimal weight: 10.0000 chunk 83 optimal weight: 20.0000 chunk 336 optimal weight: 10.0000 chunk 279 optimal weight: 10.0000 chunk 155 optimal weight: 9.9990 chunk 27 optimal weight: 10.0000 chunk 111 optimal weight: 8.9990 chunk 176 optimal weight: 9.9990 overall best weight: 5.5796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 246 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 302 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 337 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 586 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 642 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1016 ASN ** A1092 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 60 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 337 GLN ** B 392 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 619 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 236 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 302 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 337 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 60 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 83 ASN D 147 GLN D 337 GLN ** D 392 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 619 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 642 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7277 moved from start: 0.7464 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.069 28248 Z= 0.426 Angle : 1.006 37.188 38254 Z= 0.458 Chirality : 0.085 2.268 4296 Planarity : 0.005 0.059 4756 Dihedral : 14.781 176.710 4282 Min Nonbonded Distance : 2.047 Molprobity Statistics. All-atom Clashscore : 23.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.62 % Favored : 92.38 % Rotamer: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 18.75 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.36 (0.14), residues: 3452 helix: -0.19 (0.12), residues: 1576 sheet: -1.62 (0.25), residues: 410 loop : -1.36 (0.17), residues: 1466 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.003 TRP C1032 HIS 0.009 0.002 HIS C1202 PHE 0.029 0.003 PHE C1091 TYR 0.033 0.003 TYR B 450 ARG 0.009 0.001 ARG B 715 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6904 Ramachandran restraints generated. 3452 Oldfield, 0 Emsley, 3452 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6904 Ramachandran restraints generated. 3452 Oldfield, 0 Emsley, 3452 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 405 residues out of total 2968 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 405 time to evaluate : 3.196 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 74 PHE cc_start: 0.8391 (t80) cc_final: 0.7762 (t80) REVERT: A 79 LYS cc_start: 0.8820 (pttp) cc_final: 0.8329 (tppt) REVERT: A 126 GLU cc_start: 0.9014 (mt-10) cc_final: 0.8712 (mm-30) REVERT: A 361 MET cc_start: 0.9089 (tpp) cc_final: 0.8653 (tpp) REVERT: A 400 ILE cc_start: 0.8218 (tt) cc_final: 0.7951 (tp) REVERT: A 408 MET cc_start: 0.8728 (pmm) cc_final: 0.8270 (pmm) REVERT: A 414 MET cc_start: 0.7411 (tmm) cc_final: 0.7132 (tmm) REVERT: A 503 MET cc_start: 0.8283 (ttm) cc_final: 0.8010 (ppp) REVERT: A 611 ILE cc_start: 0.7885 (mm) cc_final: 0.7562 (mm) REVERT: A 700 TYR cc_start: 0.6677 (t80) cc_final: 0.6349 (t80) REVERT: A 705 GLU cc_start: 0.9224 (mp0) cc_final: 0.8923 (mp0) REVERT: A 796 PHE cc_start: 0.8079 (m-10) cc_final: 0.7711 (m-80) REVERT: A 1183 MET cc_start: 0.9221 (mmm) cc_final: 0.8961 (mmm) REVERT: B 89 CYS cc_start: 0.8841 (m) cc_final: 0.8362 (p) REVERT: B 96 PHE cc_start: 0.7697 (t80) cc_final: 0.7442 (t80) REVERT: B 113 MET cc_start: 0.9111 (mmp) cc_final: 0.8534 (mmp) REVERT: B 170 ASN cc_start: 0.9170 (p0) cc_final: 0.8915 (p0) REVERT: B 248 VAL cc_start: 0.8444 (t) cc_final: 0.8192 (t) REVERT: B 405 TYR cc_start: 0.7775 (m-80) cc_final: 0.7535 (m-80) REVERT: B 508 GLN cc_start: 0.9005 (pt0) cc_final: 0.8359 (pm20) REVERT: B 657 GLU cc_start: 0.9533 (mt-10) cc_final: 0.9234 (mt-10) REVERT: B 670 MET cc_start: 0.9178 (mtt) cc_final: 0.8788 (mmp) REVERT: B 684 ARG cc_start: 0.8742 (mtt180) cc_final: 0.8331 (ttm110) REVERT: C 74 PHE cc_start: 0.8424 (t80) cc_final: 0.7768 (t80) REVERT: C 79 LYS cc_start: 0.8752 (pttp) cc_final: 0.8170 (tptm) REVERT: C 80 LYS cc_start: 0.8648 (mttt) cc_final: 0.8130 (mtmm) REVERT: C 113 MET cc_start: 0.9624 (mmp) cc_final: 0.9415 (mmt) REVERT: C 414 MET cc_start: 0.7903 (tmm) cc_final: 0.7668 (tmm) REVERT: C 466 GLU cc_start: 0.9115 (mt-10) cc_final: 0.8805 (mt-10) REVERT: C 471 LYS cc_start: 0.9154 (tptt) cc_final: 0.8792 (mtmm) REVERT: C 483 LEU cc_start: 0.8925 (tt) cc_final: 0.8555 (tp) REVERT: C 490 ASP cc_start: 0.7887 (m-30) cc_final: 0.7365 (m-30) REVERT: C 496 MET cc_start: 0.7879 (tpp) cc_final: 0.7565 (ttm) REVERT: C 498 LEU cc_start: 0.8721 (pp) cc_final: 0.8426 (pp) REVERT: C 619 ASN cc_start: 0.8058 (t0) cc_final: 0.7699 (t0) REVERT: C 660 ARG cc_start: 0.9443 (ttt180) cc_final: 0.8929 (ttp-110) REVERT: C 705 GLU cc_start: 0.9100 (mp0) cc_final: 0.8841 (mp0) REVERT: C 708 MET cc_start: 0.8454 (tmm) cc_final: 0.8092 (tmm) REVERT: C 1179 VAL cc_start: 0.9261 (t) cc_final: 0.8728 (t) REVERT: C 1182 MET cc_start: 0.8687 (ptt) cc_final: 0.8205 (ppp) REVERT: C 1183 MET cc_start: 0.9429 (mmp) cc_final: 0.8462 (mpp) REVERT: D 89 CYS cc_start: 0.8785 (m) cc_final: 0.8390 (p) REVERT: D 113 MET cc_start: 0.8932 (mmp) cc_final: 0.8276 (mpp) REVERT: D 170 ASN cc_start: 0.9099 (p0) cc_final: 0.8842 (p0) REVERT: D 188 LYS cc_start: 0.9304 (mtmm) cc_final: 0.9006 (mmtt) REVERT: D 189 GLU cc_start: 0.7664 (mm-30) cc_final: 0.7249 (mm-30) REVERT: D 248 VAL cc_start: 0.8459 (t) cc_final: 0.8152 (t) REVERT: D 361 MET cc_start: 0.8792 (mtt) cc_final: 0.8445 (mtt) REVERT: D 435 HIS cc_start: 0.8529 (t-90) cc_final: 0.8229 (t-90) REVERT: D 503 MET cc_start: 0.8125 (ttm) cc_final: 0.7408 (tmm) REVERT: D 517 PHE cc_start: 0.6517 (t80) cc_final: 0.6297 (t80) REVERT: D 684 ARG cc_start: 0.8848 (mtt180) cc_final: 0.8475 (ttm110) REVERT: D 708 MET cc_start: 0.9282 (tpt) cc_final: 0.9024 (tpt) REVERT: D 721 MET cc_start: 0.7838 (ptm) cc_final: 0.7636 (ptm) outliers start: 0 outliers final: 0 residues processed: 405 average time/residue: 0.3698 time to fit residues: 241.3617 Evaluate side-chains 301 residues out of total 2968 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 301 time to evaluate : 3.198 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 348 random chunks: chunk 324 optimal weight: 6.9990 chunk 37 optimal weight: 3.9990 chunk 191 optimal weight: 0.4980 chunk 245 optimal weight: 1.9990 chunk 190 optimal weight: 2.9990 chunk 283 optimal weight: 0.9980 chunk 188 optimal weight: 2.9990 chunk 335 optimal weight: 9.9990 chunk 209 optimal weight: 4.9990 chunk 204 optimal weight: 0.9990 chunk 154 optimal weight: 4.9990 overall best weight: 1.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 246 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 337 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 586 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 642 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 60 ASN ** B 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 392 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 619 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 337 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 60 ASN ** D 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 83 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 392 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 619 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 642 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7226 moved from start: 0.7450 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.081 28248 Z= 0.202 Angle : 0.865 36.301 38254 Z= 0.371 Chirality : 0.082 2.213 4296 Planarity : 0.004 0.070 4756 Dihedral : 14.521 176.632 4282 Min Nonbonded Distance : 2.108 Molprobity Statistics. All-atom Clashscore : 15.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.30 % Favored : 94.70 % Rotamer: Outliers : 0.00 % Allowed : 1.01 % Favored : 98.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 18.75 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.82 (0.14), residues: 3452 helix: 0.41 (0.13), residues: 1564 sheet: -1.64 (0.25), residues: 410 loop : -1.19 (0.17), residues: 1478 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP A 606 HIS 0.004 0.001 HIS A1092 PHE 0.025 0.002 PHE A1210 TYR 0.020 0.001 TYR D 450 ARG 0.005 0.000 ARG B 178 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6904 Ramachandran restraints generated. 3452 Oldfield, 0 Emsley, 3452 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6904 Ramachandran restraints generated. 3452 Oldfield, 0 Emsley, 3452 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 431 residues out of total 2968 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 431 time to evaluate : 3.313 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 89 CYS cc_start: 0.8846 (m) cc_final: 0.8303 (p) REVERT: A 126 GLU cc_start: 0.8866 (mt-10) cc_final: 0.8604 (mm-30) REVERT: A 361 MET cc_start: 0.9106 (tpp) cc_final: 0.8663 (tpp) REVERT: A 400 ILE cc_start: 0.8197 (tt) cc_final: 0.7859 (tp) REVERT: A 408 MET cc_start: 0.8671 (pmm) cc_final: 0.8186 (pmm) REVERT: A 414 MET cc_start: 0.7351 (tmm) cc_final: 0.7099 (tmm) REVERT: A 471 LYS cc_start: 0.9044 (tptt) cc_final: 0.8625 (mtmm) REVERT: A 503 MET cc_start: 0.8290 (ttm) cc_final: 0.8032 (ppp) REVERT: A 611 ILE cc_start: 0.7674 (mm) cc_final: 0.7471 (mm) REVERT: A 619 ASN cc_start: 0.7775 (t0) cc_final: 0.7482 (t0) REVERT: A 705 GLU cc_start: 0.9119 (mp0) cc_final: 0.8789 (mp0) REVERT: A 708 MET cc_start: 0.7870 (tmm) cc_final: 0.7548 (ppp) REVERT: A 721 MET cc_start: 0.7497 (pmm) cc_final: 0.7258 (pmm) REVERT: A 796 PHE cc_start: 0.8010 (m-10) cc_final: 0.7690 (m-80) REVERT: A 1183 MET cc_start: 0.9146 (mmm) cc_final: 0.8839 (mmm) REVERT: A 1189 GLN cc_start: 0.9456 (mp10) cc_final: 0.9200 (mp10) REVERT: B 23 ASP cc_start: 0.9384 (p0) cc_final: 0.9013 (p0) REVERT: B 96 PHE cc_start: 0.7776 (t80) cc_final: 0.7487 (t80) REVERT: B 113 MET cc_start: 0.9030 (mmp) cc_final: 0.8496 (mmp) REVERT: B 170 ASN cc_start: 0.9131 (p0) cc_final: 0.8844 (p0) REVERT: B 231 ASP cc_start: 0.8439 (m-30) cc_final: 0.7858 (m-30) REVERT: B 435 HIS cc_start: 0.8476 (t-90) cc_final: 0.8270 (t-90) REVERT: B 541 PHE cc_start: 0.6930 (t80) cc_final: 0.6504 (t80) REVERT: B 585 MET cc_start: 0.6609 (pmm) cc_final: 0.5935 (pmm) REVERT: B 608 PHE cc_start: 0.8691 (t80) cc_final: 0.8468 (t80) REVERT: B 657 GLU cc_start: 0.9510 (mt-10) cc_final: 0.9286 (mp0) REVERT: B 684 ARG cc_start: 0.8726 (mtt180) cc_final: 0.8210 (ttm110) REVERT: B 708 MET cc_start: 0.9262 (mmm) cc_final: 0.8970 (tpp) REVERT: C 74 PHE cc_start: 0.8492 (t80) cc_final: 0.7705 (t80) REVERT: C 79 LYS cc_start: 0.8651 (pttp) cc_final: 0.8270 (tppt) REVERT: C 89 CYS cc_start: 0.8788 (m) cc_final: 0.8221 (p) REVERT: C 113 MET cc_start: 0.9520 (mmp) cc_final: 0.9254 (mmt) REVERT: C 292 MET cc_start: 0.8851 (ptm) cc_final: 0.8637 (ptt) REVERT: C 414 MET cc_start: 0.8032 (tmm) cc_final: 0.7774 (tmm) REVERT: C 471 LYS cc_start: 0.9053 (tptt) cc_final: 0.8663 (mtmm) REVERT: C 483 LEU cc_start: 0.8880 (tt) cc_final: 0.8475 (mt) REVERT: C 490 ASP cc_start: 0.7457 (m-30) cc_final: 0.7014 (m-30) REVERT: C 527 MET cc_start: 0.7766 (mtm) cc_final: 0.7470 (ptm) REVERT: C 609 THR cc_start: 0.8231 (t) cc_final: 0.7647 (t) REVERT: C 700 TYR cc_start: 0.5842 (t80) cc_final: 0.5640 (t80) REVERT: C 708 MET cc_start: 0.8311 (tmm) cc_final: 0.7964 (tmm) REVERT: C 789 LEU cc_start: 0.8881 (tp) cc_final: 0.8540 (tp) REVERT: C 1179 VAL cc_start: 0.9148 (t) cc_final: 0.8560 (t) REVERT: C 1182 MET cc_start: 0.8669 (ptt) cc_final: 0.8095 (ppp) REVERT: C 1183 MET cc_start: 0.9379 (mmp) cc_final: 0.8337 (mpp) REVERT: D 23 ASP cc_start: 0.9327 (p0) cc_final: 0.8988 (p0) REVERT: D 78 ASP cc_start: 0.8377 (t70) cc_final: 0.7843 (p0) REVERT: D 113 MET cc_start: 0.8850 (mmp) cc_final: 0.8415 (mmp) REVERT: D 170 ASN cc_start: 0.9113 (p0) cc_final: 0.8817 (p0) REVERT: D 188 LYS cc_start: 0.9362 (mtmm) cc_final: 0.9062 (mmtt) REVERT: D 189 GLU cc_start: 0.7682 (mm-30) cc_final: 0.7283 (mm-30) REVERT: D 361 MET cc_start: 0.8706 (mtt) cc_final: 0.8335 (mtt) REVERT: D 405 TYR cc_start: 0.7685 (m-80) cc_final: 0.7385 (m-10) REVERT: D 435 HIS cc_start: 0.8501 (t-90) cc_final: 0.8230 (t-90) REVERT: D 503 MET cc_start: 0.8017 (ttm) cc_final: 0.7301 (tmm) REVERT: D 684 ARG cc_start: 0.8785 (mtt180) cc_final: 0.8284 (ttm110) REVERT: D 708 MET cc_start: 0.9285 (tpt) cc_final: 0.9032 (tpp) REVERT: D 711 TYR cc_start: 0.8762 (t80) cc_final: 0.8300 (t80) REVERT: D 787 LEU cc_start: 0.8038 (mm) cc_final: 0.7822 (mt) REVERT: D 790 SER cc_start: 0.7489 (m) cc_final: 0.6947 (t) outliers start: 0 outliers final: 0 residues processed: 431 average time/residue: 0.3900 time to fit residues: 271.3010 Evaluate side-chains 316 residues out of total 2968 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 316 time to evaluate : 3.197 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 348 random chunks: chunk 207 optimal weight: 0.7980 chunk 133 optimal weight: 6.9990 chunk 200 optimal weight: 10.0000 chunk 101 optimal weight: 0.7980 chunk 65 optimal weight: 10.0000 chunk 64 optimal weight: 3.9990 chunk 213 optimal weight: 8.9990 chunk 228 optimal weight: 2.9990 chunk 165 optimal weight: 0.6980 chunk 31 optimal weight: 2.9990 chunk 263 optimal weight: 5.9990 overall best weight: 1.6584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 246 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 337 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 586 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 642 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 246 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 392 GLN ** B 619 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 337 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 246 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 392 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 619 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 642 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7226 moved from start: 0.7633 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.067 28248 Z= 0.197 Angle : 0.852 36.240 38254 Z= 0.363 Chirality : 0.082 2.195 4296 Planarity : 0.004 0.059 4756 Dihedral : 14.406 175.998 4282 Min Nonbonded Distance : 2.117 Molprobity Statistics. All-atom Clashscore : 14.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.68 % Favored : 94.32 % Rotamer: Outliers : 0.00 % Allowed : 0.58 % Favored : 99.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 18.75 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.64 (0.15), residues: 3452 helix: 0.58 (0.13), residues: 1562 sheet: -1.60 (0.25), residues: 410 loop : -1.10 (0.17), residues: 1480 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP C1032 HIS 0.003 0.001 HIS A1202 PHE 0.020 0.002 PHE A1210 TYR 0.019 0.001 TYR D 450 ARG 0.010 0.000 ARG D 660 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6904 Ramachandran restraints generated. 3452 Oldfield, 0 Emsley, 3452 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6904 Ramachandran restraints generated. 3452 Oldfield, 0 Emsley, 3452 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 405 residues out of total 2968 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 405 time to evaluate : 3.478 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 89 CYS cc_start: 0.8851 (m) cc_final: 0.8289 (p) REVERT: A 400 ILE cc_start: 0.8176 (tt) cc_final: 0.7814 (tp) REVERT: A 408 MET cc_start: 0.8655 (pmm) cc_final: 0.8183 (pmm) REVERT: A 414 MET cc_start: 0.7363 (tmm) cc_final: 0.7097 (tmm) REVERT: A 471 LYS cc_start: 0.9048 (tptt) cc_final: 0.8624 (mtmm) REVERT: A 496 MET cc_start: 0.7268 (tmm) cc_final: 0.6565 (tmm) REVERT: A 503 MET cc_start: 0.8213 (ttm) cc_final: 0.7965 (ppp) REVERT: A 619 ASN cc_start: 0.7718 (t0) cc_final: 0.7369 (t0) REVERT: A 628 ARG cc_start: 0.7547 (mtp85) cc_final: 0.7305 (mtt-85) REVERT: A 705 GLU cc_start: 0.9038 (mp0) cc_final: 0.8703 (mp0) REVERT: A 708 MET cc_start: 0.7885 (tmm) cc_final: 0.7601 (ppp) REVERT: A 721 MET cc_start: 0.7474 (pmm) cc_final: 0.7214 (pmm) REVERT: A 796 PHE cc_start: 0.8002 (m-10) cc_final: 0.7711 (m-80) REVERT: A 1183 MET cc_start: 0.9059 (mmm) cc_final: 0.8813 (mmm) REVERT: B 96 PHE cc_start: 0.7719 (t80) cc_final: 0.7459 (t80) REVERT: B 113 MET cc_start: 0.9033 (mmp) cc_final: 0.8474 (mmp) REVERT: B 170 ASN cc_start: 0.9131 (p0) cc_final: 0.8815 (p0) REVERT: B 189 GLU cc_start: 0.7688 (mm-30) cc_final: 0.7155 (mm-30) REVERT: B 231 ASP cc_start: 0.8492 (m-30) cc_final: 0.7911 (m-30) REVERT: B 266 GLU cc_start: 0.8638 (tm-30) cc_final: 0.8436 (pm20) REVERT: B 361 MET cc_start: 0.8676 (mtt) cc_final: 0.8162 (mtt) REVERT: B 509 LYS cc_start: 0.9334 (mmmm) cc_final: 0.9061 (mmmt) REVERT: B 584 PHE cc_start: 0.6703 (t80) cc_final: 0.6483 (t80) REVERT: B 585 MET cc_start: 0.6794 (pmm) cc_final: 0.5850 (pmm) REVERT: B 657 GLU cc_start: 0.9506 (mt-10) cc_final: 0.9293 (mp0) REVERT: B 684 ARG cc_start: 0.8726 (mtt180) cc_final: 0.8216 (ttm110) REVERT: C 74 PHE cc_start: 0.8441 (t80) cc_final: 0.7662 (t80) REVERT: C 79 LYS cc_start: 0.8678 (pttp) cc_final: 0.8320 (tppt) REVERT: C 89 CYS cc_start: 0.8782 (m) cc_final: 0.8190 (p) REVERT: C 113 MET cc_start: 0.9549 (mmp) cc_final: 0.9292 (mmt) REVERT: C 292 MET cc_start: 0.8849 (ptm) cc_final: 0.8648 (ptt) REVERT: C 414 MET cc_start: 0.7963 (tmm) cc_final: 0.7690 (tmm) REVERT: C 466 GLU cc_start: 0.9085 (mt-10) cc_final: 0.8786 (mt-10) REVERT: C 471 LYS cc_start: 0.9055 (tptt) cc_final: 0.8639 (mtmm) REVERT: C 483 LEU cc_start: 0.8881 (tt) cc_final: 0.8465 (mt) REVERT: C 490 ASP cc_start: 0.7397 (m-30) cc_final: 0.6971 (m-30) REVERT: C 496 MET cc_start: 0.8339 (ttp) cc_final: 0.7879 (tmm) REVERT: C 503 MET cc_start: 0.8072 (ppp) cc_final: 0.7785 (ppp) REVERT: C 609 THR cc_start: 0.8205 (t) cc_final: 0.7414 (t) REVERT: C 700 TYR cc_start: 0.5855 (t80) cc_final: 0.5605 (t80) REVERT: C 708 MET cc_start: 0.8326 (tmm) cc_final: 0.7999 (tmm) REVERT: C 1179 VAL cc_start: 0.9135 (t) cc_final: 0.8659 (t) REVERT: C 1182 MET cc_start: 0.8729 (ptt) cc_final: 0.8269 (ppp) REVERT: C 1183 MET cc_start: 0.9339 (mmp) cc_final: 0.8375 (mpp) REVERT: D 23 ASP cc_start: 0.9359 (p0) cc_final: 0.9005 (p0) REVERT: D 78 ASP cc_start: 0.8280 (t70) cc_final: 0.7799 (p0) REVERT: D 96 PHE cc_start: 0.7632 (t80) cc_final: 0.7310 (t80) REVERT: D 113 MET cc_start: 0.8857 (mmp) cc_final: 0.8400 (mmp) REVERT: D 170 ASN cc_start: 0.9117 (p0) cc_final: 0.8806 (p0) REVERT: D 188 LYS cc_start: 0.9364 (mtmm) cc_final: 0.9062 (mmtt) REVERT: D 189 GLU cc_start: 0.7692 (mm-30) cc_final: 0.7273 (mm-30) REVERT: D 361 MET cc_start: 0.8599 (mtt) cc_final: 0.8228 (mtt) REVERT: D 435 HIS cc_start: 0.8558 (t-90) cc_final: 0.8293 (t-90) REVERT: D 503 MET cc_start: 0.8098 (ttm) cc_final: 0.7430 (tmm) REVERT: D 657 GLU cc_start: 0.9217 (pt0) cc_final: 0.8540 (tp30) REVERT: D 684 ARG cc_start: 0.8743 (mtt180) cc_final: 0.8262 (ttm110) REVERT: D 708 MET cc_start: 0.9217 (tpt) cc_final: 0.8866 (tpp) REVERT: D 711 TYR cc_start: 0.8790 (t80) cc_final: 0.8353 (t80) REVERT: D 712 ILE cc_start: 0.9045 (pt) cc_final: 0.8789 (pt) REVERT: D 787 LEU cc_start: 0.7973 (mm) cc_final: 0.7664 (mt) outliers start: 0 outliers final: 0 residues processed: 405 average time/residue: 0.3700 time to fit residues: 242.6088 Evaluate side-chains 310 residues out of total 2968 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 310 time to evaluate : 3.004 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 348 random chunks: chunk 305 optimal weight: 10.0000 chunk 321 optimal weight: 0.4980 chunk 293 optimal weight: 4.9990 chunk 312 optimal weight: 0.0010 chunk 188 optimal weight: 0.0770 chunk 136 optimal weight: 10.0000 chunk 245 optimal weight: 1.9990 chunk 95 optimal weight: 20.0000 chunk 282 optimal weight: 0.8980 chunk 295 optimal weight: 5.9990 chunk 311 optimal weight: 5.9990 overall best weight: 0.6946 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 246 GLN ** A 337 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 359 ASN ** A 586 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 619 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 642 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1163 ASN B 60 ASN ** B 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 246 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 412 HIS ** B 619 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 337 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 619 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 60 ASN ** D 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 83 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 246 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 392 GLN D 619 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7197 moved from start: 0.7738 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 28248 Z= 0.156 Angle : 0.834 35.776 38254 Z= 0.351 Chirality : 0.081 2.178 4296 Planarity : 0.004 0.060 4756 Dihedral : 14.380 175.805 4282 Min Nonbonded Distance : 2.140 Molprobity Statistics. All-atom Clashscore : 12.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.10 % Favored : 94.90 % Rotamer: Outliers : 0.00 % Allowed : 0.27 % Favored : 99.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 18.75 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.39 (0.15), residues: 3452 helix: 0.86 (0.14), residues: 1556 sheet: -1.49 (0.24), residues: 410 loop : -1.03 (0.17), residues: 1486 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP A 526 HIS 0.004 0.000 HIS A1092 PHE 0.029 0.001 PHE A1210 TYR 0.020 0.001 TYR B 711 ARG 0.003 0.000 ARG A1089 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6904 Ramachandran restraints generated. 3452 Oldfield, 0 Emsley, 3452 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6904 Ramachandran restraints generated. 3452 Oldfield, 0 Emsley, 3452 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 419 residues out of total 2968 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 419 time to evaluate : 3.162 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 78 ASP cc_start: 0.8388 (t0) cc_final: 0.8051 (m-30) REVERT: A 89 CYS cc_start: 0.8716 (m) cc_final: 0.8214 (p) REVERT: A 400 ILE cc_start: 0.8110 (tt) cc_final: 0.7738 (tp) REVERT: A 408 MET cc_start: 0.8596 (pmm) cc_final: 0.8124 (pmm) REVERT: A 414 MET cc_start: 0.7403 (tmm) cc_final: 0.7134 (tmm) REVERT: A 471 LYS cc_start: 0.9009 (tptt) cc_final: 0.8585 (mtmm) REVERT: A 476 ILE cc_start: 0.8055 (tt) cc_final: 0.7846 (tt) REVERT: A 491 PHE cc_start: 0.7538 (m-80) cc_final: 0.6881 (m-80) REVERT: A 496 MET cc_start: 0.7363 (tmm) cc_final: 0.7094 (tmm) REVERT: A 503 MET cc_start: 0.8265 (ttm) cc_final: 0.7892 (ppp) REVERT: A 521 LEU cc_start: 0.5453 (tt) cc_final: 0.5200 (tp) REVERT: A 526 TRP cc_start: 0.6004 (m100) cc_final: 0.5249 (m100) REVERT: A 619 ASN cc_start: 0.7433 (t0) cc_final: 0.7089 (t0) REVERT: A 721 MET cc_start: 0.7470 (pmm) cc_final: 0.7180 (pmm) REVERT: A 796 PHE cc_start: 0.7924 (m-10) cc_final: 0.7556 (m-80) REVERT: A 1146 MET cc_start: 0.2584 (mmt) cc_final: 0.2252 (mmt) REVERT: A 1183 MET cc_start: 0.9089 (mmm) cc_final: 0.8742 (mmm) REVERT: A 1184 TYR cc_start: 0.8070 (t80) cc_final: 0.7697 (t80) REVERT: A 1221 MET cc_start: 0.6622 (mmp) cc_final: 0.6312 (mmp) REVERT: B 83 ASN cc_start: 0.8201 (m-40) cc_final: 0.7765 (p0) REVERT: B 97 ILE cc_start: 0.9203 (mp) cc_final: 0.8990 (mp) REVERT: B 113 MET cc_start: 0.8889 (mmp) cc_final: 0.8199 (mpp) REVERT: B 170 ASN cc_start: 0.9129 (p0) cc_final: 0.8805 (p0) REVERT: B 189 GLU cc_start: 0.7621 (mm-30) cc_final: 0.7150 (mm-30) REVERT: B 231 ASP cc_start: 0.8381 (m-30) cc_final: 0.7843 (m-30) REVERT: B 241 GLU cc_start: 0.9034 (mt-10) cc_final: 0.8517 (mp0) REVERT: B 407 MET cc_start: 0.7905 (ptp) cc_final: 0.7419 (pmm) REVERT: B 408 MET cc_start: 0.8046 (mmm) cc_final: 0.7758 (mmp) REVERT: B 434 LYS cc_start: 0.9145 (tptm) cc_final: 0.8900 (tmtt) REVERT: B 509 LYS cc_start: 0.9323 (mmmm) cc_final: 0.9109 (mmmt) REVERT: B 584 PHE cc_start: 0.6667 (t80) cc_final: 0.6332 (t80) REVERT: B 585 MET cc_start: 0.6760 (pmm) cc_final: 0.5816 (pmm) REVERT: B 684 ARG cc_start: 0.8658 (mtt180) cc_final: 0.8147 (ttm110) REVERT: C 74 PHE cc_start: 0.8400 (t80) cc_final: 0.7598 (t80) REVERT: C 79 LYS cc_start: 0.8689 (pttp) cc_final: 0.8420 (tptt) REVERT: C 89 CYS cc_start: 0.8681 (m) cc_final: 0.8179 (p) REVERT: C 292 MET cc_start: 0.8853 (ptm) cc_final: 0.8635 (ptt) REVERT: C 414 MET cc_start: 0.7991 (tmm) cc_final: 0.7714 (tmm) REVERT: C 471 LYS cc_start: 0.9017 (tptt) cc_final: 0.8693 (mtmm) REVERT: C 483 LEU cc_start: 0.8897 (tt) cc_final: 0.8472 (mt) REVERT: C 496 MET cc_start: 0.8340 (ttp) cc_final: 0.7870 (tmm) REVERT: C 527 MET cc_start: 0.7707 (mtm) cc_final: 0.7455 (ptm) REVERT: C 609 THR cc_start: 0.8190 (t) cc_final: 0.7436 (t) REVERT: C 619 ASN cc_start: 0.7880 (t0) cc_final: 0.7462 (t0) REVERT: C 708 MET cc_start: 0.8279 (tmm) cc_final: 0.7922 (tmm) REVERT: C 1088 LEU cc_start: 0.6693 (mp) cc_final: 0.6215 (pt) REVERT: C 1179 VAL cc_start: 0.9099 (t) cc_final: 0.8618 (t) REVERT: C 1182 MET cc_start: 0.8626 (ptt) cc_final: 0.8205 (ppp) REVERT: C 1183 MET cc_start: 0.9242 (mmp) cc_final: 0.8295 (mpp) REVERT: C 1221 MET cc_start: 0.6949 (mmp) cc_final: 0.6612 (mmp) REVERT: D 23 ASP cc_start: 0.9306 (p0) cc_final: 0.8908 (p0) REVERT: D 78 ASP cc_start: 0.8288 (t70) cc_final: 0.7653 (p0) REVERT: D 96 PHE cc_start: 0.7655 (t80) cc_final: 0.7345 (t80) REVERT: D 113 MET cc_start: 0.8758 (mmp) cc_final: 0.8269 (mmp) REVERT: D 170 ASN cc_start: 0.9195 (p0) cc_final: 0.8854 (p0) REVERT: D 188 LYS cc_start: 0.9334 (mtmm) cc_final: 0.9028 (mmtt) REVERT: D 189 GLU cc_start: 0.7664 (mm-30) cc_final: 0.7218 (mm-30) REVERT: D 303 ARG cc_start: 0.8950 (mtt180) cc_final: 0.8743 (ttm-80) REVERT: D 407 MET cc_start: 0.7713 (ptp) cc_final: 0.7095 (pmm) REVERT: D 435 HIS cc_start: 0.8596 (t-90) cc_final: 0.8386 (t-90) REVERT: D 491 PHE cc_start: 0.7845 (m-80) cc_final: 0.7521 (m-80) REVERT: D 503 MET cc_start: 0.8067 (ttt) cc_final: 0.7823 (tmm) REVERT: D 657 GLU cc_start: 0.9201 (pt0) cc_final: 0.8767 (mp0) REVERT: D 684 ARG cc_start: 0.8746 (mtt180) cc_final: 0.8169 (ttm110) REVERT: D 708 MET cc_start: 0.9154 (tpt) cc_final: 0.8846 (tpp) REVERT: D 711 TYR cc_start: 0.8744 (t80) cc_final: 0.8383 (t80) outliers start: 0 outliers final: 0 residues processed: 419 average time/residue: 0.3745 time to fit residues: 251.0243 Evaluate side-chains 318 residues out of total 2968 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 318 time to evaluate : 3.184 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 348 random chunks: chunk 205 optimal weight: 0.8980 chunk 330 optimal weight: 9.9990 chunk 201 optimal weight: 6.9990 chunk 156 optimal weight: 5.9990 chunk 229 optimal weight: 10.0000 chunk 346 optimal weight: 10.0000 chunk 319 optimal weight: 1.9990 chunk 276 optimal weight: 8.9990 chunk 28 optimal weight: 0.8980 chunk 213 optimal weight: 6.9990 chunk 169 optimal weight: 0.0270 overall best weight: 1.9642 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 337 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 586 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 619 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 642 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 60 ASN ** B 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 246 GLN ** C 337 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 60 ASN ** D 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 83 ASN ** D 246 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 709 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7230 moved from start: 0.7941 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 28248 Z= 0.203 Angle : 0.849 36.116 38254 Z= 0.362 Chirality : 0.081 2.173 4296 Planarity : 0.004 0.056 4756 Dihedral : 14.306 175.267 4282 Min Nonbonded Distance : 2.128 Molprobity Statistics. All-atom Clashscore : 14.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.68 % Favored : 94.32 % Rotamer: Outliers : 0.00 % Allowed : 0.14 % Favored : 99.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 18.75 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.42 (0.15), residues: 3452 helix: 0.83 (0.14), residues: 1548 sheet: -1.47 (0.24), residues: 426 loop : -1.04 (0.17), residues: 1478 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP C1032 HIS 0.003 0.001 HIS A1202 PHE 0.028 0.002 PHE B 541 TYR 0.016 0.001 TYR D 450 ARG 0.003 0.000 ARG A1089 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6904 Ramachandran restraints generated. 3452 Oldfield, 0 Emsley, 3452 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6904 Ramachandran restraints generated. 3452 Oldfield, 0 Emsley, 3452 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 385 residues out of total 2968 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 385 time to evaluate : 3.298 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 78 ASP cc_start: 0.8441 (t0) cc_final: 0.8079 (m-30) REVERT: A 89 CYS cc_start: 0.8744 (m) cc_final: 0.8236 (p) REVERT: A 400 ILE cc_start: 0.8152 (tt) cc_final: 0.7799 (tp) REVERT: A 408 MET cc_start: 0.8643 (pmm) cc_final: 0.8177 (pmm) REVERT: A 471 LYS cc_start: 0.9034 (tptt) cc_final: 0.8599 (mtmm) REVERT: A 491 PHE cc_start: 0.7587 (m-80) cc_final: 0.6959 (m-80) REVERT: A 503 MET cc_start: 0.8265 (ttm) cc_final: 0.8001 (ppp) REVERT: A 721 MET cc_start: 0.7435 (pmm) cc_final: 0.7141 (pmm) REVERT: A 796 PHE cc_start: 0.7990 (m-10) cc_final: 0.7624 (m-80) REVERT: A 1112 SER cc_start: 0.8521 (m) cc_final: 0.8245 (t) REVERT: A 1146 MET cc_start: 0.2534 (mmt) cc_final: 0.2155 (mmt) REVERT: A 1183 MET cc_start: 0.9043 (mmm) cc_final: 0.8807 (mmt) REVERT: A 1221 MET cc_start: 0.6784 (mmp) cc_final: 0.4740 (ppp) REVERT: B 96 PHE cc_start: 0.7771 (t80) cc_final: 0.7143 (t80) REVERT: B 97 ILE cc_start: 0.9138 (mp) cc_final: 0.8704 (tp) REVERT: B 113 MET cc_start: 0.8979 (mmp) cc_final: 0.8445 (mmm) REVERT: B 170 ASN cc_start: 0.9153 (p0) cc_final: 0.8829 (p0) REVERT: B 189 GLU cc_start: 0.7491 (mm-30) cc_final: 0.6992 (mm-30) REVERT: B 231 ASP cc_start: 0.8390 (m-30) cc_final: 0.7868 (m-30) REVERT: B 241 GLU cc_start: 0.9000 (mt-10) cc_final: 0.8592 (mp0) REVERT: B 503 MET cc_start: 0.8164 (ttp) cc_final: 0.7380 (ppp) REVERT: B 509 LYS cc_start: 0.9335 (mmmm) cc_final: 0.9070 (mmmt) REVERT: B 527 MET cc_start: 0.8969 (mmp) cc_final: 0.8628 (mtt) REVERT: B 585 MET cc_start: 0.7028 (pmm) cc_final: 0.6123 (pmm) REVERT: B 608 PHE cc_start: 0.8832 (t80) cc_final: 0.8593 (t80) REVERT: B 670 MET cc_start: 0.8712 (mmt) cc_final: 0.8434 (mmp) REVERT: B 684 ARG cc_start: 0.8729 (mtt180) cc_final: 0.8220 (ttm110) REVERT: C 74 PHE cc_start: 0.8429 (t80) cc_final: 0.7754 (t80) REVERT: C 79 LYS cc_start: 0.8606 (pttp) cc_final: 0.8376 (tptt) REVERT: C 89 CYS cc_start: 0.8711 (m) cc_final: 0.8207 (p) REVERT: C 113 MET cc_start: 0.9473 (mmp) cc_final: 0.9240 (mmt) REVERT: C 292 MET cc_start: 0.8894 (ptm) cc_final: 0.8654 (ptt) REVERT: C 414 MET cc_start: 0.7943 (tmm) cc_final: 0.7709 (tmm) REVERT: C 471 LYS cc_start: 0.9010 (tptt) cc_final: 0.8679 (mtmm) REVERT: C 483 LEU cc_start: 0.8879 (tt) cc_final: 0.8448 (mt) REVERT: C 496 MET cc_start: 0.8277 (ttp) cc_final: 0.7813 (tmm) REVERT: C 503 MET cc_start: 0.8029 (ppp) cc_final: 0.7746 (ppp) REVERT: C 527 MET cc_start: 0.7772 (mtm) cc_final: 0.7541 (ptm) REVERT: C 609 THR cc_start: 0.8220 (t) cc_final: 0.7169 (t) REVERT: C 656 LYS cc_start: 0.8748 (tmtt) cc_final: 0.8546 (tmtt) REVERT: C 708 MET cc_start: 0.8269 (tmm) cc_final: 0.7929 (tmm) REVERT: C 1088 LEU cc_start: 0.6784 (mp) cc_final: 0.6269 (pt) REVERT: C 1179 VAL cc_start: 0.9064 (t) cc_final: 0.8577 (t) REVERT: C 1182 MET cc_start: 0.8692 (ptt) cc_final: 0.8297 (ppp) REVERT: C 1183 MET cc_start: 0.9238 (mmp) cc_final: 0.8234 (mpp) REVERT: D 23 ASP cc_start: 0.9344 (p0) cc_final: 0.8922 (p0) REVERT: D 78 ASP cc_start: 0.8288 (t70) cc_final: 0.7500 (p0) REVERT: D 96 PHE cc_start: 0.7641 (t80) cc_final: 0.7325 (t80) REVERT: D 113 MET cc_start: 0.8738 (mmp) cc_final: 0.8174 (mmp) REVERT: D 170 ASN cc_start: 0.9197 (p0) cc_final: 0.8866 (p0) REVERT: D 188 LYS cc_start: 0.9319 (mtmm) cc_final: 0.9001 (mmtt) REVERT: D 189 GLU cc_start: 0.7667 (mm-30) cc_final: 0.7252 (mm-30) REVERT: D 303 ARG cc_start: 0.8950 (mtt180) cc_final: 0.8746 (ttm-80) REVERT: D 361 MET cc_start: 0.8665 (mtt) cc_final: 0.8237 (mtt) REVERT: D 435 HIS cc_start: 0.8628 (t-90) cc_final: 0.8362 (t-90) REVERT: D 503 MET cc_start: 0.8086 (ttt) cc_final: 0.7700 (tmm) REVERT: D 684 ARG cc_start: 0.8761 (mtt180) cc_final: 0.8246 (ttm110) REVERT: D 705 GLU cc_start: 0.9164 (mp0) cc_final: 0.8837 (mp0) REVERT: D 708 MET cc_start: 0.9129 (tpt) cc_final: 0.8832 (tpp) REVERT: D 711 TYR cc_start: 0.8820 (t80) cc_final: 0.8412 (t80) outliers start: 0 outliers final: 0 residues processed: 385 average time/residue: 0.3773 time to fit residues: 234.5478 Evaluate side-chains 304 residues out of total 2968 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 304 time to evaluate : 3.251 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 348 random chunks: chunk 219 optimal weight: 7.9990 chunk 294 optimal weight: 9.9990 chunk 84 optimal weight: 3.9990 chunk 254 optimal weight: 9.9990 chunk 40 optimal weight: 0.1980 chunk 76 optimal weight: 9.9990 chunk 276 optimal weight: 8.9990 chunk 115 optimal weight: 0.9990 chunk 283 optimal weight: 0.3980 chunk 35 optimal weight: 0.9990 chunk 50 optimal weight: 0.9990 overall best weight: 0.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 337 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 619 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 642 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 60 ASN ** B 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 337 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 60 ASN ** D 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 246 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3761 r_free = 0.3761 target = 0.102868 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3397 r_free = 0.3397 target = 0.083428 restraints weight = 100934.596| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 50)----------------| | r_work = 0.3430 r_free = 0.3430 target = 0.085023 restraints weight = 69651.292| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 54)----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.086148 restraints weight = 53576.442| |-----------------------------------------------------------------------------| r_work (final): 0.3445 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7819 moved from start: 0.8011 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 28248 Z= 0.153 Angle : 0.831 35.618 38254 Z= 0.348 Chirality : 0.081 2.161 4296 Planarity : 0.004 0.058 4756 Dihedral : 14.341 175.603 4282 Min Nonbonded Distance : 2.157 Molprobity Statistics. All-atom Clashscore : 12.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.21 % Favored : 94.79 % Rotamer: Outliers : 0.00 % Allowed : 0.20 % Favored : 99.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 18.75 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.25 (0.15), residues: 3452 helix: 0.96 (0.14), residues: 1546 sheet: -1.41 (0.25), residues: 412 loop : -0.93 (0.17), residues: 1494 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 526 HIS 0.003 0.000 HIS A1092 PHE 0.020 0.001 PHE A1210 TYR 0.013 0.001 TYR D 450 ARG 0.006 0.000 ARG D 628 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6318.68 seconds wall clock time: 115 minutes 36.14 seconds (6936.14 seconds total)