Starting phenix.real_space_refine on Mon Sep 14 04:47:29 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/5wel_8820/09_2026/5wel_8820.cif Found real_map, /net/cci-nas-00/data/ceres_data/5wel_8820/09_2026/5wel_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/cci-nas-00/data/ceres_data/5wel_8820/09_2026/5wel_8820.map" default_real_map = "/net/cci-nas-00/data/ceres_data/5wel_8820/09_2026/5wel_8820.map" model { file = "/net/cci-nas-00/data/ceres_data/5wel_8820/09_2026/5wel_8820.cif" } default_model = "/net/cci-nas-00/data/ceres_data/5wel_8820/09_2026/5wel_8820.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/5wel_8820/09_2026/5wel_8820.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/5wel_8820/09_2026/5wel_8820.cif" } resolution = 4.4 write_initial_geo_file = False refinement { macro_cycles = 10 } 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. Time to flip 52 residue(s): 0.26s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/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: 6.14, per 1000 atoms: 0.22 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 - 3.00 Amino acid : True - 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: 2.52 Conformation dependent library (CDL) restraints added in 1.5 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... Secondary structure from input PDB file: 126 helices and 34 sheets defined 49.1% alpha, 12.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.10 Creating SS restraints... Processing helix chain 'A' and resid 22 through 36 Processing helix chain 'A' and resid 54 through 69 Processing helix chain 'A' and resid 81 through 93 Processing helix chain 'A' and resid 117 through 129 Processing helix chain 'A' and resid 143 through 156 removed outlier: 3.598A pdb=" N GLU A 155 " --> pdb=" O ASP A 151 " (cutoff:3.500A) Processing helix chain 'A' and resid 174 through 185 removed outlier: 3.943A pdb=" N ARG A 178 " --> pdb=" O ASP A 174 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N GLN A 182 " --> pdb=" O ARG A 178 " (cutoff:3.500A) Processing helix chain 'A' and resid 197 through 212 Processing helix chain 'A' and resid 232 through 236 removed outlier: 3.637A pdb=" N ILE A 235 " --> pdb=" O LEU A 232 " (cutoff:3.500A) Processing helix chain 'A' and resid 252 through 263 removed outlier: 3.528A pdb=" N PHE A 258 " --> pdb=" O LEU A 254 " (cutoff:3.500A) Processing helix chain 'A' and resid 279 through 303 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 335 removed outlier: 4.347A pdb=" N GLU A 328 " --> pdb=" O GLY A 324 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 419 Processing helix chain 'A' and resid 423 through 437 Processing helix chain 'A' and resid 461 through 469 Processing helix chain 'A' and resid 482 through 487 removed outlier: 3.637A pdb=" N GLU A 486 " --> pdb=" O THR A 482 " (cutoff:3.500A) Processing helix chain 'A' and resid 522 through 538 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) removed outlier: 4.056A pdb=" N VAL A 538 " --> pdb=" O ILE A 534 " (cutoff:3.500A) Processing helix chain 'A' and resid 539 through 543 Processing helix chain 'A' and resid 575 through 583 removed outlier: 3.666A pdb=" N PHE A 579 " --> pdb=" O ASN A 575 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N LEU A 581 " --> pdb=" O LEU A 577 " (cutoff:3.500A) Processing helix chain 'A' and resid 596 through 630 removed outlier: 3.843A pdb=" N ILE A 600 " --> pdb=" O LEU A 596 " (cutoff:3.500A) 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 636 through 642 Processing helix chain 'A' and resid 653 through 662 Processing helix chain 'A' and resid 664 through 676 Processing helix chain 'A' and resid 685 through 697 Processing helix chain 'A' and resid 706 through 715 Processing helix chain 'A' and resid 742 through 754 removed outlier: 3.515A pdb=" N LEU A 751 " --> pdb=" O ASN A 747 " (cutoff:3.500A) Processing helix chain 'A' and resid 757 through 769 Processing helix chain 'A' and resid 776 through 781 removed outlier: 3.896A pdb=" N LYS A 781 " --> pdb=" O SER A 778 " (cutoff:3.500A) Processing helix chain 'A' and resid 788 through 793 Processing helix chain 'A' and resid 795 through 817 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) Processing helix chain 'A' and resid 1003 through 1026 Processing helix chain 'A' and resid 1027 through 1029 No H-bonds generated for 'chain 'A' and resid 1027 through 1029' Processing helix chain 'A' and resid 1118 through 1153 removed outlier: 3.504A pdb=" N VAL A1130 " --> pdb=" O TRP A1126 " (cutoff:3.500A) Processing helix chain 'A' and resid 1159 through 1195 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 1208 through 1228 removed outlier: 3.740A pdb=" N LEU A1212 " --> pdb=" O TRP A1208 " (cutoff:3.500A) 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 'A' and resid 1229 through 1233 removed outlier: 3.588A pdb=" N THR A1232 " --> pdb=" O ASN A1229 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N LYS A1233 " --> pdb=" O SER A1230 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1229 through 1233' Processing helix chain 'B' and resid 22 through 36 Processing helix chain 'B' and resid 54 through 69 Processing helix chain 'B' and resid 81 through 93 Processing helix chain 'B' and resid 117 through 129 Processing helix chain 'B' and resid 143 through 156 removed outlier: 3.599A pdb=" N GLU B 155 " --> pdb=" O ASP B 151 " (cutoff:3.500A) Processing helix chain 'B' and resid 174 through 185 removed outlier: 3.943A pdb=" N ARG B 178 " --> pdb=" O ASP B 174 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N GLN B 182 " --> pdb=" O ARG B 178 " (cutoff:3.500A) Processing helix chain 'B' and resid 197 through 212 Processing helix chain 'B' and resid 232 through 236 removed outlier: 3.637A pdb=" N ILE B 235 " --> pdb=" O LEU B 232 " (cutoff:3.500A) Processing helix chain 'B' and resid 252 through 263 removed outlier: 3.528A pdb=" N PHE B 258 " --> pdb=" O LEU B 254 " (cutoff:3.500A) Processing helix chain 'B' and resid 279 through 303 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 335 removed outlier: 4.347A pdb=" N GLU B 328 " --> pdb=" O GLY B 324 " (cutoff:3.500A) Processing helix chain 'B' and resid 416 through 419 Processing helix chain 'B' and resid 423 through 437 Processing helix chain 'B' and resid 461 through 469 Processing helix chain 'B' and resid 482 through 487 removed outlier: 3.638A pdb=" N GLU B 486 " --> pdb=" O THR B 482 " (cutoff:3.500A) Processing helix chain 'B' and resid 522 through 538 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) removed outlier: 4.056A pdb=" N VAL B 538 " --> pdb=" O ILE B 534 " (cutoff:3.500A) Processing helix chain 'B' and resid 539 through 543 Processing helix chain 'B' and resid 575 through 583 removed outlier: 3.665A pdb=" N PHE B 579 " --> pdb=" O ASN B 575 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N LEU B 581 " --> pdb=" O LEU B 577 " (cutoff:3.500A) Processing helix chain 'B' and resid 596 through 624 removed outlier: 3.843A pdb=" N ILE B 600 " --> pdb=" O LEU B 596 " (cutoff:3.500A) 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 636 through 642 Processing helix chain 'B' and resid 653 through 662 Processing helix chain 'B' and resid 664 through 676 Processing helix chain 'B' and resid 685 through 697 Processing helix chain 'B' and resid 706 through 715 Processing helix chain 'B' and resid 742 through 754 removed outlier: 3.514A pdb=" N LEU B 751 " --> pdb=" O ASN B 747 " (cutoff:3.500A) Processing helix chain 'B' and resid 757 through 769 Processing helix chain 'B' and resid 774 through 780 removed outlier: 3.601A pdb=" N SER B 780 " --> pdb=" O LYS B 776 " (cutoff:3.500A) Processing helix chain 'B' and resid 789 through 817 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 22 through 36 Processing helix chain 'C' and resid 54 through 69 Processing helix chain 'C' and resid 81 through 93 Processing helix chain 'C' and resid 117 through 129 Processing helix chain 'C' and resid 143 through 156 removed outlier: 3.600A pdb=" N GLU C 155 " --> pdb=" O ASP C 151 " (cutoff:3.500A) Processing helix chain 'C' and resid 174 through 185 removed outlier: 3.943A pdb=" N ARG C 178 " --> pdb=" O ASP C 174 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N GLN C 182 " --> pdb=" O ARG C 178 " (cutoff:3.500A) Processing helix chain 'C' and resid 197 through 212 Processing helix chain 'C' and resid 232 through 236 removed outlier: 3.636A pdb=" N ILE C 235 " --> pdb=" O LEU C 232 " (cutoff:3.500A) Processing helix chain 'C' and resid 252 through 263 removed outlier: 3.527A pdb=" N PHE C 258 " --> pdb=" O LEU C 254 " (cutoff:3.500A) Processing helix chain 'C' and resid 279 through 303 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 335 removed outlier: 4.347A pdb=" N GLU C 328 " --> pdb=" O GLY C 324 " (cutoff:3.500A) Processing helix chain 'C' and resid 416 through 419 Processing helix chain 'C' and resid 423 through 437 Processing helix chain 'C' and resid 461 through 469 Processing helix chain 'C' and resid 482 through 487 removed outlier: 3.638A pdb=" N GLU C 486 " --> pdb=" O THR C 482 " (cutoff:3.500A) Processing helix chain 'C' and resid 522 through 538 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) removed outlier: 4.056A pdb=" N VAL C 538 " --> pdb=" O ILE C 534 " (cutoff:3.500A) Processing helix chain 'C' and resid 539 through 543 Processing helix chain 'C' and resid 575 through 583 removed outlier: 3.666A pdb=" N PHE C 579 " --> pdb=" O ASN C 575 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N LEU C 581 " --> pdb=" O LEU C 577 " (cutoff:3.500A) Processing helix chain 'C' and resid 596 through 630 removed outlier: 3.843A pdb=" N ILE C 600 " --> pdb=" O LEU C 596 " (cutoff:3.500A) 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 636 through 642 Processing helix chain 'C' and resid 653 through 662 Processing helix chain 'C' and resid 664 through 676 Processing helix chain 'C' and resid 685 through 697 Processing helix chain 'C' and resid 706 through 715 Processing helix chain 'C' and resid 742 through 754 removed outlier: 3.514A pdb=" N LEU C 751 " --> pdb=" O ASN C 747 " (cutoff:3.500A) Processing helix chain 'C' and resid 757 through 769 Processing helix chain 'C' and resid 776 through 781 removed outlier: 3.896A pdb=" N LYS C 781 " --> pdb=" O SER C 778 " (cutoff:3.500A) Processing helix chain 'C' and resid 788 through 793 Processing helix chain 'C' and resid 795 through 817 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 1026 Processing helix chain 'C' and resid 1027 through 1029 No H-bonds generated for 'chain 'C' and resid 1027 through 1029' Processing helix chain 'C' and resid 1118 through 1153 removed outlier: 3.504A pdb=" N VAL C1130 " --> pdb=" O TRP C1126 " (cutoff:3.500A) Processing helix chain 'C' and resid 1159 through 1195 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 1208 through 1228 removed outlier: 3.742A pdb=" N LEU C1212 " --> pdb=" O TRP C1208 " (cutoff:3.500A) 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 'C' and resid 1229 through 1233 removed outlier: 3.588A pdb=" N THR C1232 " --> pdb=" O ASN C1229 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N LYS C1233 " --> pdb=" O SER C1230 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 1229 through 1233' Processing helix chain 'D' and resid 22 through 36 Processing helix chain 'D' and resid 54 through 69 Processing helix chain 'D' and resid 81 through 93 Processing helix chain 'D' and resid 117 through 129 Processing helix chain 'D' and resid 143 through 156 removed outlier: 3.600A pdb=" N GLU D 155 " --> pdb=" O ASP D 151 " (cutoff:3.500A) Processing helix chain 'D' and resid 174 through 185 removed outlier: 3.943A pdb=" N ARG D 178 " --> pdb=" O ASP D 174 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N GLN D 182 " --> pdb=" O ARG D 178 " (cutoff:3.500A) Processing helix chain 'D' and resid 197 through 212 Processing helix chain 'D' and resid 232 through 236 removed outlier: 3.637A pdb=" N ILE D 235 " --> pdb=" O LEU D 232 " (cutoff:3.500A) Processing helix chain 'D' and resid 252 through 263 removed outlier: 3.528A pdb=" N PHE D 258 " --> pdb=" O LEU D 254 " (cutoff:3.500A) Processing helix chain 'D' and resid 279 through 303 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 335 removed outlier: 4.348A pdb=" N GLU D 328 " --> pdb=" O GLY D 324 " (cutoff:3.500A) Processing helix chain 'D' and resid 416 through 419 Processing helix chain 'D' and resid 423 through 437 Processing helix chain 'D' and resid 461 through 469 Processing helix chain 'D' and resid 482 through 487 removed outlier: 3.638A pdb=" N GLU D 486 " --> pdb=" O THR D 482 " (cutoff:3.500A) Processing helix chain 'D' and resid 522 through 538 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) removed outlier: 4.056A pdb=" N VAL D 538 " --> pdb=" O ILE D 534 " (cutoff:3.500A) Processing helix chain 'D' and resid 539 through 543 Processing helix chain 'D' and resid 575 through 583 removed outlier: 3.666A pdb=" N PHE D 579 " --> pdb=" O ASN D 575 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N LEU D 581 " --> pdb=" O LEU D 577 " (cutoff:3.500A) Processing helix chain 'D' and resid 596 through 624 removed outlier: 3.843A pdb=" N ILE D 600 " --> pdb=" O LEU D 596 " (cutoff:3.500A) 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 636 through 642 Processing helix chain 'D' and resid 653 through 662 Processing helix chain 'D' and resid 664 through 676 Processing helix chain 'D' and resid 685 through 697 Processing helix chain 'D' and resid 706 through 715 Processing helix chain 'D' and resid 742 through 754 removed outlier: 3.514A pdb=" N LEU D 751 " --> pdb=" O ASN D 747 " (cutoff:3.500A) Processing helix chain 'D' and resid 757 through 769 Processing helix chain 'D' and resid 774 through 780 removed outlier: 3.601A pdb=" N SER D 780 " --> pdb=" O LYS D 776 " (cutoff:3.500A) Processing helix chain 'D' and resid 789 through 817 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=AA1, first strand: chain 'A' and resid 12 through 19 removed outlier: 6.218A pdb=" N ILE A 12 " --> pdb=" O THR A 44 " (cutoff:3.500A) removed outlier: 7.338A pdb=" N HIS A 46 " --> pdb=" O ILE A 12 " (cutoff:3.500A) removed outlier: 7.616A pdb=" N ILE A 14 " --> pdb=" O HIS A 46 " (cutoff:3.500A) removed outlier: 8.192A pdb=" N ASP A 48 " --> pdb=" O ILE A 14 " (cutoff:3.500A) removed outlier: 6.825A pdb=" N GLY A 16 " --> pdb=" O ASP A 48 " (cutoff:3.500A) removed outlier: 6.889A pdb=" N LEU A 50 " --> pdb=" O GLY A 16 " (cutoff:3.500A) removed outlier: 5.680A pdb=" N PHE A 18 " --> pdb=" O LEU A 50 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 72 through 74 removed outlier: 6.303A pdb=" N ILE A 73 " --> pdb=" O ILE A 97 " (cutoff:3.500A) removed outlier: 5.693A pdb=" N PHE A 96 " --> pdb=" O ILE A 111 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, 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: 4.012A pdb=" N PHE A 245 " --> 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=AA4, first strand: chain 'A' and resid 338 through 340 Processing sheet with id=AA5, first strand: chain 'A' and resid 440 through 444 Processing sheet with id=AA6, first strand: chain 'A' and resid 407 through 408 Processing sheet with id=AA7, first strand: chain 'A' and resid 489 through 498 removed outlier: 7.054A pdb=" N SER A 492 " --> pdb=" O THR A 736 " (cutoff:3.500A) removed outlier: 8.052A pdb=" N THR A 736 " --> pdb=" O SER A 492 " (cutoff:3.500A) removed outlier: 7.132A pdb=" N ILE A 734 " --> pdb=" O PRO A 494 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 646 through 648 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) removed outlier: 8.937A pdb=" N TYR A 700 " --> pdb=" O LYS A 505 " (cutoff:3.500A) removed outlier: 5.206A pdb=" N LYS A 505 " --> pdb=" O TYR A 700 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N ILE A 502 " --> pdb=" O VAL A 723 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 1033 through 1036 removed outlier: 3.510A pdb=" N THR A1093 " --> pdb=" O CYS A1033 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N ARG A1090 " --> pdb=" O GLU A1101 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N CYS A1099 " --> pdb=" O HIS A1092 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 12 through 19 removed outlier: 6.219A pdb=" N ILE B 12 " --> pdb=" O THR B 44 " (cutoff:3.500A) removed outlier: 7.338A pdb=" N HIS B 46 " --> pdb=" O ILE B 12 " (cutoff:3.500A) removed outlier: 7.616A pdb=" N ILE B 14 " --> pdb=" O HIS B 46 " (cutoff:3.500A) removed outlier: 8.192A pdb=" N ASP B 48 " --> pdb=" O ILE B 14 " (cutoff:3.500A) removed outlier: 6.825A pdb=" N GLY B 16 " --> pdb=" O ASP B 48 " (cutoff:3.500A) removed outlier: 6.888A pdb=" N LEU B 50 " --> pdb=" O GLY B 16 " (cutoff:3.500A) removed outlier: 5.680A pdb=" N PHE B 18 " --> pdb=" O LEU B 50 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'B' and resid 72 through 74 removed outlier: 6.303A pdb=" N ILE B 73 " --> pdb=" O ILE B 97 " (cutoff:3.500A) removed outlier: 5.694A pdb=" N PHE B 96 " --> pdb=" O ILE B 111 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, 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: 4.013A pdb=" N PHE B 245 " --> 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=AB4, first strand: chain 'B' and resid 338 through 340 Processing sheet with id=AB5, first strand: chain 'B' and resid 440 through 444 Processing sheet with id=AB6, first strand: chain 'B' and resid 407 through 408 Processing sheet with id=AB7, first strand: chain 'B' and resid 489 through 498 removed outlier: 7.053A pdb=" N SER B 492 " --> pdb=" O THR B 736 " (cutoff:3.500A) removed outlier: 8.052A pdb=" N THR B 736 " --> pdb=" O SER B 492 " (cutoff:3.500A) removed outlier: 7.132A pdb=" N ILE B 734 " --> pdb=" O PRO B 494 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 646 through 648 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) removed outlier: 8.937A pdb=" N TYR B 700 " --> pdb=" O LYS B 505 " (cutoff:3.500A) removed outlier: 5.206A pdb=" N LYS B 505 " --> pdb=" O TYR B 700 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N ILE B 502 " --> pdb=" O VAL B 723 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 12 through 19 removed outlier: 6.219A pdb=" N ILE C 12 " --> pdb=" O THR C 44 " (cutoff:3.500A) removed outlier: 7.338A pdb=" N HIS C 46 " --> pdb=" O ILE C 12 " (cutoff:3.500A) removed outlier: 7.616A pdb=" N ILE C 14 " --> pdb=" O HIS C 46 " (cutoff:3.500A) removed outlier: 8.191A pdb=" N ASP C 48 " --> pdb=" O ILE C 14 " (cutoff:3.500A) removed outlier: 6.825A pdb=" N GLY C 16 " --> pdb=" O ASP C 48 " (cutoff:3.500A) removed outlier: 6.887A pdb=" N LEU C 50 " --> pdb=" O GLY C 16 " (cutoff:3.500A) removed outlier: 5.680A pdb=" N PHE C 18 " --> pdb=" O LEU C 50 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB9 Processing sheet with id=AC1, first strand: chain 'C' and resid 72 through 74 removed outlier: 6.303A pdb=" N ILE C 73 " --> pdb=" O ILE C 97 " (cutoff:3.500A) removed outlier: 5.695A pdb=" N PHE C 96 " --> pdb=" O ILE C 111 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC1 Processing sheet with id=AC2, 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: 4.013A pdb=" N PHE C 245 " --> 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=AC3, first strand: chain 'C' and resid 338 through 340 Processing sheet with id=AC4, first strand: chain 'C' and resid 440 through 444 Processing sheet with id=AC5, first strand: chain 'C' and resid 407 through 408 Processing sheet with id=AC6, first strand: chain 'C' and resid 489 through 498 removed outlier: 7.054A pdb=" N SER C 492 " --> pdb=" O THR C 736 " (cutoff:3.500A) removed outlier: 8.052A pdb=" N THR C 736 " --> pdb=" O SER C 492 " (cutoff:3.500A) removed outlier: 7.132A pdb=" N ILE C 734 " --> pdb=" O PRO C 494 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'C' and resid 646 through 648 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) removed outlier: 8.937A pdb=" N TYR C 700 " --> pdb=" O LYS C 505 " (cutoff:3.500A) removed outlier: 5.206A pdb=" N LYS C 505 " --> pdb=" O TYR C 700 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N ILE C 502 " --> pdb=" O VAL C 723 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'C' and resid 1033 through 1036 removed outlier: 3.510A pdb=" N THR C1093 " --> pdb=" O CYS C1033 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N ARG C1090 " --> pdb=" O GLU C1101 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N CYS C1099 " --> pdb=" O HIS C1092 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'D' and resid 12 through 19 removed outlier: 6.219A pdb=" N ILE D 12 " --> pdb=" O THR D 44 " (cutoff:3.500A) removed outlier: 7.338A pdb=" N HIS D 46 " --> pdb=" O ILE D 12 " (cutoff:3.500A) removed outlier: 7.616A pdb=" N ILE D 14 " --> pdb=" O HIS D 46 " (cutoff:3.500A) removed outlier: 8.192A pdb=" N ASP D 48 " --> pdb=" O ILE D 14 " (cutoff:3.500A) removed outlier: 6.825A pdb=" N GLY D 16 " --> pdb=" O ASP D 48 " (cutoff:3.500A) removed outlier: 6.888A pdb=" N LEU D 50 " --> pdb=" O GLY D 16 " (cutoff:3.500A) removed outlier: 5.680A pdb=" N PHE D 18 " --> pdb=" O LEU D 50 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC9 Processing sheet with id=AD1, first strand: chain 'D' and resid 72 through 74 removed outlier: 6.304A pdb=" N ILE D 73 " --> pdb=" O ILE D 97 " (cutoff:3.500A) removed outlier: 5.694A pdb=" N PHE D 96 " --> pdb=" O ILE D 111 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD1 Processing sheet with id=AD2, 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: 4.012A pdb=" N PHE D 245 " --> 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=AD3, first strand: chain 'D' and resid 338 through 340 Processing sheet with id=AD4, first strand: chain 'D' and resid 440 through 444 Processing sheet with id=AD5, first strand: chain 'D' and resid 407 through 408 Processing sheet with id=AD6, first strand: chain 'D' and resid 489 through 498 removed outlier: 7.053A pdb=" N SER D 492 " --> pdb=" O THR D 736 " (cutoff:3.500A) removed outlier: 8.052A pdb=" N THR D 736 " --> pdb=" O SER D 492 " (cutoff:3.500A) removed outlier: 7.132A pdb=" N ILE D 734 " --> pdb=" O PRO D 494 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'D' and resid 646 through 648 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) removed outlier: 8.937A pdb=" N TYR D 700 " --> pdb=" O LYS D 505 " (cutoff:3.500A) removed outlier: 5.206A pdb=" N LYS D 505 " --> pdb=" O TYR D 700 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N ILE D 502 " --> pdb=" O VAL D 723 " (cutoff:3.500A) 1268 hydrogen bonds defined for protein. 3639 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: 5.94 Time building geometry restraints manager: 3.31 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: 0.00 - 3.43: 37788 3.43 - 6.86: 382 6.86 - 10.28: 68 10.28 - 13.71: 12 13.71 - 17.14: 4 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 - 22.72: 16309 22.72 - 45.44: 238 45.44 - 68.16: 30 68.16 - 90.88: 9 90.88 - 113.61: 8 Dihedral angle restraints: 16594 sinusoidal: 6570 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 16591 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: 3025 2.74 - 3.28: 27462 3.28 - 3.82: 46813 3.82 - 4.36: 56483 4.36 - 4.90: 91576 Nonbonded interactions: 225359 Sorted by model distance: nonbonded pdb=" O33 AJP C1302 " pdb=" O76 AJP C1302 " model vdw 2.206 3.040 nonbonded pdb=" O33 AJP A1302 " pdb=" O76 AJP A1302 " model vdw 2.206 3.040 nonbonded pdb=" O62 AJP A1302 " pdb=" O75 AJP A1302 " model vdw 2.220 3.040 nonbonded pdb=" O62 AJP C1302 " pdb=" O75 AJP C1302 " model vdw 2.220 3.040 nonbonded pdb=" NE2 GLN C 129 " pdb=" O78 AJP C1302 " model vdw 2.225 3.120 ... (remaining 225354 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.03 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: 2.700 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: 0.040 Extract box with map and model: 0.500 Check model and map are aligned: 0.080 Set scattering table: 0.060 Process input model: 27.100 Find NCS groups from input model: 0.490 Set up NCS constraints: 0.100 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:1.440 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.520 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6834 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 : 0.009 0.753 28260 Z= 0.653 Angle : 0.982 17.140 38274 Z= 0.549 Chirality : 0.641 5.832 4296 Planarity : 0.007 0.091 4756 Dihedral : 9.593 113.606 10156 Min Nonbonded Distance : 2.206 Molprobity Statistics. All-atom Clashscore : 8.16 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. 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 ARG 0.007 0.001 ARG C1038 TYR 0.019 0.002 TYR C 816 PHE 0.030 0.002 PHE C1143 TRP 0.026 0.003 TRP A1199 HIS 0.010 0.002 HIS A1152 Details of bonding type rmsd/Z covalent geometry : bond 0.00646 / 0.33 (28248) covalent geometry : angle 0.98143 / 0.55 (38254) SS BOND : bond 0.00887 / 0.53 ( 10) SS BOND : angle 1.47622 / 0.97 ( 20) hydrogen bonds : bond 0.27287 / 18.00 ( 1268) hydrogen bonds : angle 10.15644 / 7.17 ( 3639) Misc. bond : bond 0.66821 / 33.98 ( 2) *********************** 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 to be fit. rotamer outliers: 18 poor density : 882 time to evaluate : 1.010 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: 0.7901 (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: 0.9011 (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: 0.5781 (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: 0.6799 (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: 0.6552 (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: 0.8246 (tm-30) REVERT: C 639 LEU cc_start: 0.8265 (mt) cc_final: 0.7801 (mp) REVERT: C 710 GLU cc_start: 0.8382 (mt-10) cc_final: 0.8039 (mm-30) REVERT: C 713 GLU cc_start: 0.8482 (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: 0.8867 (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: 0.7041 (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: 0.7855 (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: 0.2034 time to fit residues: 276.6904 Evaluate side-chains 473 residues out of total 2968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 468 time to evaluate : 1.012 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 348 random chunks: chunk 197 optimal weight: 0.8980 chunk 215 optimal weight: 2.9990 chunk 20 optimal weight: 8.9990 chunk 132 optimal weight: 6.9990 chunk 261 optimal weight: 5.9990 chunk 248 optimal weight: 5.9990 chunk 207 optimal weight: 0.7980 chunk 155 optimal weight: 4.9990 chunk 244 optimal weight: 0.5980 chunk 183 optimal weight: 7.9990 chunk 298 optimal weight: 7.9990 overall best weight: 2.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 35 GLN A 65 GLN A 412 HIS ** A 586 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 642 GLN A 756 GLN A 791 ASN A1034 GLN ** A1092 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 167 ASN 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 147 GLN ** C 246 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 586 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 C1037 GLN ** D 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 83 ASN D 147 GLN D 167 ASN D 337 GLN D 392 GLN D 412 HIS D 756 GLN Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3902 r_free = 0.3902 target = 0.109953 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3533 r_free = 0.3533 target = 0.089639 restraints weight = 100159.578| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3566 r_free = 0.3566 target = 0.091306 restraints weight = 68546.276| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3582 r_free = 0.3582 target = 0.092000 restraints weight = 51445.689| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3591 r_free = 0.3591 target = 0.092498 restraints weight = 42823.502| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3596 r_free = 0.3596 target = 0.092696 restraints weight = 39472.276| |-----------------------------------------------------------------------------| r_work (final): 0.3588 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7555 moved from start: 0.3782 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 28260 Z= 0.176 Angle : 0.966 38.373 38274 Z= 0.415 Chirality : 0.090 2.425 4296 Planarity : 0.005 0.070 4756 Dihedral : 6.505 75.623 3796 Min Nonbonded Distance : 2.011 Molprobity Statistics. All-atom Clashscore : 12.40 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.10 % Favored : 94.84 % Rotamer: Outliers : 0.03 % Allowed : 2.23 % Favored : 97.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 18.75 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.12 (0.13), residues: 3452 helix: -1.08 (0.11), residues: 1612 sheet: -1.67 (0.26), residues: 380 loop : -1.56 (0.16), residues: 1460 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG D 715 TYR 0.026 0.002 TYR A 732 PHE 0.023 0.002 PHE C 623 TRP 0.019 0.002 TRP A 262 HIS 0.007 0.001 HIS A1181 Details of bonding type rmsd/Z covalent geometry : bond 0.00371 / 0.18 (28248) covalent geometry : angle 0.96639 / 0.42 (38254) SS BOND : bond 0.01060 / 0.70 ( 10) SS BOND : angle 1.03514 / 0.66 ( 20) hydrogen bonds : bond 0.04259 / 2.75 ( 1268) hydrogen bonds : angle 5.65127 / 4.07 ( 3639) Misc. bond : bond 0.00602 / 0.30 ( 2) *********************** 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 577 residues out of total 2968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 576 time to evaluate : 1.065 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 113 MET cc_start: 0.8852 (mmp) cc_final: 0.8623 (mmt) REVERT: A 170 ASN cc_start: 0.8478 (m-40) cc_final: 0.8217 (m110) REVERT: A 400 ILE cc_start: 0.9026 (tt) cc_final: 0.8776 (tp) REVERT: A 415 LEU cc_start: 0.7010 (mt) cc_final: 0.6671 (mt) REVERT: A 463 MET cc_start: 0.8499 (mpp) cc_final: 0.7896 (mpp) REVERT: A 476 ILE cc_start: 0.9247 (tt) cc_final: 0.9023 (tt) REVERT: A 498 LEU cc_start: 0.9023 (pp) cc_final: 0.8647 (pp) REVERT: A 650 LEU cc_start: 0.9461 (tp) cc_final: 0.8960 (tp) REVERT: A 700 TYR cc_start: 0.6610 (t80) cc_final: 0.6271 (t80) REVERT: A 710 GLU cc_start: 0.8226 (mt-10) cc_final: 0.7942 (mm-30) REVERT: A 816 TYR cc_start: 0.6561 (m-80) cc_final: 0.6301 (m-80) REVERT: A 1093 THR cc_start: 0.7551 (p) cc_final: 0.7342 (t) REVERT: B 25 GLU cc_start: 0.9238 (mp0) cc_final: 0.8929 (mp0) REVERT: B 189 GLU cc_start: 0.7669 (mm-30) cc_final: 0.7324 (mm-30) REVERT: B 248 VAL cc_start: 0.8841 (t) cc_final: 0.8631 (t) REVERT: B 491 PHE cc_start: 0.8227 (m-80) cc_final: 0.7963 (m-80) REVERT: B 508 GLN cc_start: 0.8342 (pt0) cc_final: 0.7901 (pm20) REVERT: B 721 MET cc_start: 0.8410 (ptm) cc_final: 0.7937 (ptm) REVERT: B 787 LEU cc_start: 0.8020 (tp) cc_final: 0.7306 (pp) REVERT: B 797 TYR cc_start: 0.8271 (m-80) cc_final: 0.8009 (m-10) REVERT: C 440 TYR cc_start: 0.8388 (p90) cc_final: 0.8086 (p90) REVERT: C 463 MET cc_start: 0.8135 (mtp) cc_final: 0.7439 (mtt) REVERT: C 488 VAL cc_start: 0.9430 (m) cc_final: 0.9211 (t) REVERT: C 498 LEU cc_start: 0.8926 (pp) cc_final: 0.8708 (pp) REVERT: C 526 TRP cc_start: 0.5702 (m100) cc_final: 0.5032 (m100) REVERT: C 527 MET cc_start: 0.7280 (mmm) cc_final: 0.6996 (mtt) REVERT: C 650 LEU cc_start: 0.9338 (tp) cc_final: 0.8819 (tp) REVERT: C 700 TYR cc_start: 0.6943 (t80) cc_final: 0.6611 (t80) REVERT: C 721 MET cc_start: 0.8657 (ptm) cc_final: 0.8007 (ptp) REVERT: C 807 MET cc_start: 0.4714 (mmm) cc_final: 0.4430 (ppp) REVERT: C 1034 GLN cc_start: 0.7028 (tt0) cc_final: 0.6560 (tp40) REVERT: C 1088 LEU cc_start: 0.7098 (mt) cc_final: 0.6362 (pt) REVERT: C 1089 ARG cc_start: 0.5756 (mtt90) cc_final: 0.5425 (ttm-80) REVERT: C 1093 THR cc_start: 0.7549 (p) cc_final: 0.6909 (t) REVERT: C 1178 MET cc_start: 0.8949 (tpp) cc_final: 0.8747 (tpp) REVERT: C 1181 HIS cc_start: 0.8707 (m-70) cc_final: 0.7834 (m90) REVERT: D 25 GLU cc_start: 0.9176 (mp0) cc_final: 0.8643 (mp0) REVERT: D 187 LYS cc_start: 0.8390 (mmtt) cc_final: 0.8035 (mmtm) REVERT: D 189 GLU cc_start: 0.7637 (mm-30) cc_final: 0.7040 (mm-30) REVERT: D 432 ILE cc_start: 0.8973 (mm) cc_final: 0.8706 (tp) REVERT: D 491 PHE cc_start: 0.7518 (m-80) cc_final: 0.7253 (m-80) REVERT: D 521 LEU cc_start: 0.8170 (tt) cc_final: 0.7332 (mt) REVERT: D 526 TRP cc_start: 0.3100 (m100) cc_final: 0.2555 (m100) REVERT: D 639 LEU cc_start: 0.8317 (mt) cc_final: 0.7803 (mp) REVERT: D 647 TYR cc_start: 0.6445 (p90) cc_final: 0.6099 (p90) REVERT: D 657 GLU cc_start: 0.8703 (tt0) cc_final: 0.8419 (tp30) REVERT: D 721 MET cc_start: 0.8017 (ptm) cc_final: 0.7613 (ptm) REVERT: D 728 ASP cc_start: 0.6961 (p0) cc_final: 0.6719 (p0) outliers start: 1 outliers final: 0 residues processed: 577 average time/residue: 0.1861 time to fit residues: 169.9175 Evaluate side-chains 364 residues out of total 2968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 364 time to evaluate : 0.878 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 348 random chunks: chunk 334 optimal weight: 5.9990 chunk 174 optimal weight: 20.0000 chunk 24 optimal weight: 6.9990 chunk 305 optimal weight: 10.0000 chunk 80 optimal weight: 10.0000 chunk 223 optimal weight: 2.9990 chunk 191 optimal weight: 3.9990 chunk 91 optimal weight: 0.9980 chunk 177 optimal weight: 7.9990 chunk 154 optimal weight: 4.9990 chunk 73 optimal weight: 3.9990 overall best weight: 3.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 83 ASN A 159 GLN ** A 214 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 246 GLN A 290 GLN A 586 GLN ** A 642 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 791 ASN ** A1092 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1181 HIS ** B 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 219 HIS B 246 GLN ** B 392 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 83 ASN C 170 ASN ** C 246 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 290 GLN C1034 GLN C1181 HIS ** D 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 83 ASN D 219 HIS D 246 GLN ** D 642 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 709 ASN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3807 r_free = 0.3807 target = 0.104512 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.083894 restraints weight = 101705.703| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3455 r_free = 0.3455 target = 0.085766 restraints weight = 72361.336| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3466 r_free = 0.3466 target = 0.086352 restraints weight = 51766.692| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3472 r_free = 0.3472 target = 0.086614 restraints weight = 46748.981| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3476 r_free = 0.3476 target = 0.086804 restraints weight = 45168.772| |-----------------------------------------------------------------------------| r_work (final): 0.3468 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7761 moved from start: 0.5341 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 28260 Z= 0.226 Angle : 0.937 36.820 38274 Z= 0.418 Chirality : 0.088 2.469 4296 Planarity : 0.005 0.073 4756 Dihedral : 6.210 64.355 3796 Min Nonbonded Distance : 2.190 Molprobity Statistics. All-atom Clashscore : 14.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.94 % Favored : 94.06 % Rotamer: Outliers : 0.00 % Allowed : 3.15 % Favored : 96.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 18.75 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.23 (0.14), residues: 3452 helix: -0.04 (0.12), residues: 1616 sheet: -1.50 (0.25), residues: 406 loop : -1.41 (0.17), residues: 1430 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 141 TYR 0.023 0.002 TYR B 450 PHE 0.026 0.002 PHE A 517 TRP 0.022 0.002 TRP B 606 HIS 0.006 0.001 HIS A1202 Details of bonding type rmsd/Z covalent geometry : bond 0.00484 / 0.23 (28248) covalent geometry : angle 0.93694 / 0.42 (38254) SS BOND : bond 0.00462 / 0.28 ( 10) SS BOND : angle 1.14689 / 0.70 ( 20) hydrogen bonds : bond 0.04142 / 2.71 ( 1268) hydrogen bonds : angle 5.37966 / 3.87 ( 3639) Misc. bond : bond 0.00101 / 0.05 ( 2) *********************** 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 467 residues out of total 2968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 467 time to evaluate : 0.766 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 400 ILE cc_start: 0.9181 (tt) cc_final: 0.8907 (tp) REVERT: A 491 PHE cc_start: 0.7755 (m-80) cc_final: 0.7457 (m-10) REVERT: A 498 LEU cc_start: 0.9268 (pp) cc_final: 0.8700 (pp) REVERT: A 650 LEU cc_start: 0.9376 (tp) cc_final: 0.8956 (tp) REVERT: A 700 TYR cc_start: 0.6881 (t80) cc_final: 0.6652 (t80) REVERT: A 705 GLU cc_start: 0.7620 (mp0) cc_final: 0.7196 (mp0) REVERT: A 711 TYR cc_start: 0.7766 (t80) cc_final: 0.7544 (t80) REVERT: A 732 TYR cc_start: 0.8237 (m-10) cc_final: 0.7784 (m-80) REVERT: A 1152 HIS cc_start: 0.4507 (m-70) cc_final: 0.4214 (t70) REVERT: B 25 GLU cc_start: 0.9245 (mp0) cc_final: 0.8462 (mp0) REVERT: B 96 PHE cc_start: 0.7519 (t80) cc_final: 0.7175 (t80) REVERT: B 189 GLU cc_start: 0.7384 (mm-30) cc_final: 0.6889 (mm-30) REVERT: B 248 VAL cc_start: 0.8993 (t) cc_final: 0.8756 (t) REVERT: B 380 MET cc_start: 0.7768 (tmm) cc_final: 0.7256 (ttt) REVERT: B 491 PHE cc_start: 0.8295 (m-80) cc_final: 0.8080 (m-80) REVERT: B 508 GLN cc_start: 0.8547 (pt0) cc_final: 0.8102 (pm20) REVERT: B 585 MET cc_start: 0.7466 (pmm) cc_final: 0.6117 (ppp) REVERT: B 695 LYS cc_start: 0.8855 (pttm) cc_final: 0.8319 (mmmm) REVERT: B 720 THR cc_start: 0.8550 (p) cc_final: 0.8282 (p) REVERT: B 721 MET cc_start: 0.8277 (ptm) cc_final: 0.7955 (ptm) REVERT: B 787 LEU cc_start: 0.8207 (tp) cc_final: 0.7738 (pp) REVERT: B 797 TYR cc_start: 0.8252 (m-80) cc_final: 0.8052 (m-10) REVERT: B 803 LEU cc_start: 0.8359 (mt) cc_final: 0.8142 (mt) REVERT: B 807 MET cc_start: 0.8683 (mmm) cc_final: 0.8069 (mmm) REVERT: C 74 PHE cc_start: 0.7949 (t80) cc_final: 0.7641 (t80) REVERT: C 78 ASP cc_start: 0.8620 (t0) cc_final: 0.8247 (m-30) REVERT: C 414 MET cc_start: 0.8054 (tmm) cc_final: 0.7836 (tmm) REVERT: C 488 VAL cc_start: 0.9535 (m) cc_final: 0.9293 (t) REVERT: C 503 MET cc_start: 0.7972 (tmm) cc_final: 0.7517 (tmm) REVERT: C 526 TRP cc_start: 0.6641 (m100) cc_final: 0.5066 (m100) REVERT: C 527 MET cc_start: 0.8032 (mmm) cc_final: 0.7821 (mtt) REVERT: C 577 LEU cc_start: 0.6324 (tp) cc_final: 0.6024 (pt) REVERT: C 611 ILE cc_start: 0.9046 (mm) cc_final: 0.8834 (mm) REVERT: C 650 LEU cc_start: 0.9351 (tp) cc_final: 0.8916 (tp) REVERT: C 670 MET cc_start: 0.8770 (mtp) cc_final: 0.8469 (mtp) REVERT: C 1034 GLN cc_start: 0.6909 (tt0) cc_final: 0.6431 (tp40) REVERT: C 1088 LEU cc_start: 0.7182 (mt) cc_final: 0.6366 (pt) REVERT: C 1129 VAL cc_start: 0.8359 (m) cc_final: 0.8147 (p) REVERT: C 1182 MET cc_start: 0.8244 (ptt) cc_final: 0.7703 (ppp) REVERT: C 1183 MET cc_start: 0.9181 (mmp) cc_final: 0.8668 (mmm) REVERT: D 25 GLU cc_start: 0.9165 (mp0) cc_final: 0.8309 (mp0) REVERT: D 96 PHE cc_start: 0.7534 (t80) cc_final: 0.7191 (t80) REVERT: D 189 GLU cc_start: 0.7533 (mm-30) cc_final: 0.6984 (mm-30) REVERT: D 473 ASP cc_start: 0.7222 (m-30) cc_final: 0.6339 (t0) REVERT: D 521 LEU cc_start: 0.8046 (tt) cc_final: 0.7736 (mt) REVERT: D 526 TRP cc_start: 0.4139 (m100) cc_final: 0.3315 (m100) REVERT: D 639 LEU cc_start: 0.8884 (mt) cc_final: 0.8493 (mp) REVERT: D 657 GLU cc_start: 0.8568 (tt0) cc_final: 0.8277 (tp30) REVERT: D 700 TYR cc_start: 0.6790 (t80) cc_final: 0.6575 (t80) REVERT: D 721 MET cc_start: 0.8206 (ptm) cc_final: 0.7722 (ptm) outliers start: 0 outliers final: 0 residues processed: 467 average time/residue: 0.1739 time to fit residues: 131.7719 Evaluate side-chains 322 residues out of total 2968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 322 time to evaluate : 1.176 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 348 random chunks: chunk 135 optimal weight: 4.9990 chunk 196 optimal weight: 0.6980 chunk 188 optimal weight: 0.8980 chunk 220 optimal weight: 5.9990 chunk 226 optimal weight: 0.8980 chunk 85 optimal weight: 3.9990 chunk 28 optimal weight: 0.9990 chunk 294 optimal weight: 9.9990 chunk 313 optimal weight: 3.9990 chunk 16 optimal weight: 7.9990 chunk 136 optimal weight: 3.9990 overall best weight: 1.4984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 65 GLN A 159 GLN ** A 214 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 202 ASN B 246 GLN ** B 392 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 586 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 709 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 65 GLN ** C 246 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 290 GLN C 412 HIS C 619 ASN C1092 HIS ** D 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 83 ASN D 246 GLN D 337 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3833 r_free = 0.3833 target = 0.106126 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3456 r_free = 0.3456 target = 0.085692 restraints weight = 100342.584| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3490 r_free = 0.3490 target = 0.087371 restraints weight = 68958.947| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.088525 restraints weight = 53070.574| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 59)----------------| | r_work = 0.3529 r_free = 0.3529 target = 0.089341 restraints weight = 43930.705| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3538 r_free = 0.3538 target = 0.089773 restraints weight = 38509.290| |-----------------------------------------------------------------------------| r_work (final): 0.3529 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7689 moved from start: 0.5766 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 28260 Z= 0.129 Angle : 0.850 35.755 38274 Z= 0.366 Chirality : 0.086 2.354 4296 Planarity : 0.004 0.063 4756 Dihedral : 5.910 73.061 3796 Min Nonbonded Distance : 2.257 Molprobity Statistics. All-atom Clashscore : 11.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.87 % Favored : 95.13 % Rotamer: Outliers : 0.00 % Allowed : 2.03 % Favored : 97.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 18.75 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.80 (0.14), residues: 3452 helix: 0.44 (0.13), residues: 1616 sheet: -1.44 (0.25), residues: 408 loop : -1.30 (0.17), residues: 1428 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 303 TYR 0.018 0.001 TYR B 700 PHE 0.015 0.001 PHE C 623 TRP 0.018 0.001 TRP C1032 HIS 0.005 0.001 HIS A1092 Details of bonding type rmsd/Z covalent geometry : bond 0.00286 / 0.13 (28248) covalent geometry : angle 0.85017 / 0.37 (38254) SS BOND : bond 0.00228 / 0.14 ( 10) SS BOND : angle 0.69021 / 0.44 ( 20) hydrogen bonds : bond 0.03323 / 2.17 ( 1268) hydrogen bonds : angle 4.98558 / 3.57 ( 3639) Misc. bond : bond 0.00076 / 0.04 ( 2) *********************** 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 455 residues out of total 2968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 455 time to evaluate : 1.104 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 400 ILE cc_start: 0.9024 (tt) cc_final: 0.8804 (tp) REVERT: A 498 LEU cc_start: 0.9251 (pp) cc_final: 0.8456 (pp) REVERT: A 619 ASN cc_start: 0.7631 (t0) cc_final: 0.7303 (t0) REVERT: A 634 GLU cc_start: 0.8951 (pm20) cc_final: 0.8731 (pm20) REVERT: A 650 LEU cc_start: 0.9340 (tp) cc_final: 0.8900 (tp) REVERT: A 705 GLU cc_start: 0.7627 (mp0) cc_final: 0.7330 (mp0) REVERT: A 732 TYR cc_start: 0.8309 (m-10) cc_final: 0.7825 (m-10) REVERT: A 1022 PHE cc_start: 0.7840 (m-80) cc_final: 0.7562 (m-80) REVERT: A 1146 MET cc_start: 0.3631 (mmt) cc_final: 0.3320 (mmt) REVERT: A 1152 HIS cc_start: 0.4577 (m-70) cc_final: 0.4348 (t70) REVERT: A 1181 HIS cc_start: 0.8315 (m90) cc_final: 0.7991 (m170) REVERT: B 25 GLU cc_start: 0.9217 (mp0) cc_final: 0.8433 (mp0) REVERT: B 78 ASP cc_start: 0.8920 (t0) cc_final: 0.8021 (m-30) REVERT: B 187 LYS cc_start: 0.8677 (mmtt) cc_final: 0.8365 (mmtt) REVERT: B 189 GLU cc_start: 0.7539 (mm-30) cc_final: 0.6960 (mm-30) REVERT: B 248 VAL cc_start: 0.8995 (t) cc_final: 0.8769 (t) REVERT: B 508 GLN cc_start: 0.8585 (pt0) cc_final: 0.8152 (pm20) REVERT: B 527 MET cc_start: 0.8279 (mmp) cc_final: 0.7866 (mtt) REVERT: B 695 LYS cc_start: 0.8761 (pttm) cc_final: 0.8215 (mmmm) REVERT: B 721 MET cc_start: 0.8385 (ptm) cc_final: 0.7953 (ptm) REVERT: B 797 TYR cc_start: 0.8199 (m-80) cc_final: 0.7830 (m-10) REVERT: B 803 LEU cc_start: 0.8374 (mt) cc_final: 0.8131 (mt) REVERT: C 414 MET cc_start: 0.8115 (tmm) cc_final: 0.7805 (tmm) REVERT: C 526 TRP cc_start: 0.6967 (m100) cc_final: 0.5806 (m100) REVERT: C 527 MET cc_start: 0.8181 (mmm) cc_final: 0.7843 (mtt) REVERT: C 577 LEU cc_start: 0.6142 (tp) cc_final: 0.5892 (pt) REVERT: C 650 LEU cc_start: 0.9372 (tp) cc_final: 0.9044 (tp) REVERT: C 700 TYR cc_start: 0.6920 (t80) cc_final: 0.6595 (t80) REVERT: C 1088 LEU cc_start: 0.7049 (mt) cc_final: 0.6351 (pt) REVERT: C 1182 MET cc_start: 0.8238 (ptt) cc_final: 0.7898 (ppp) REVERT: C 1183 MET cc_start: 0.9203 (mmp) cc_final: 0.8655 (mpp) REVERT: D 25 GLU cc_start: 0.9125 (mp0) cc_final: 0.8547 (mp0) REVERT: D 187 LYS cc_start: 0.8540 (mmtt) cc_final: 0.8138 (mmtt) REVERT: D 189 GLU cc_start: 0.7504 (mm-30) cc_final: 0.6888 (mm-30) REVERT: D 231 ASP cc_start: 0.7687 (m-30) cc_final: 0.7372 (m-30) REVERT: D 248 VAL cc_start: 0.8941 (t) cc_final: 0.8741 (t) REVERT: D 639 LEU cc_start: 0.8953 (mt) cc_final: 0.8275 (mp) REVERT: D 721 MET cc_start: 0.8449 (ptm) cc_final: 0.8115 (ptm) REVERT: D 755 GLU cc_start: 0.8417 (tp30) cc_final: 0.8110 (tp30) outliers start: 0 outliers final: 0 residues processed: 455 average time/residue: 0.1764 time to fit residues: 129.3486 Evaluate side-chains 344 residues out of total 2968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 344 time to evaluate : 1.022 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 348 random chunks: chunk 142 optimal weight: 0.0060 chunk 236 optimal weight: 0.0980 chunk 176 optimal weight: 10.0000 chunk 173 optimal weight: 6.9990 chunk 335 optimal weight: 8.9990 chunk 324 optimal weight: 8.9990 chunk 163 optimal weight: 0.9990 chunk 244 optimal weight: 0.4980 chunk 76 optimal weight: 0.9980 chunk 178 optimal weight: 0.0870 chunk 198 optimal weight: 0.9990 overall best weight: 0.3374 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 214 HIS ** B 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 246 GLN B 337 GLN ** B 392 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 586 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 709 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 246 GLN C 587 GLN C1037 GLN ** D 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 83 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 619 ASN D 642 GLN D 756 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3872 r_free = 0.3872 target = 0.108392 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3486 r_free = 0.3486 target = 0.087170 restraints weight = 100339.790| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 50)----------------| | r_work = 0.3523 r_free = 0.3523 target = 0.089071 restraints weight = 66624.438| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3549 r_free = 0.3549 target = 0.090358 restraints weight = 49847.851| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 51)----------------| | r_work = 0.3566 r_free = 0.3566 target = 0.091296 restraints weight = 40606.717| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3576 r_free = 0.3576 target = 0.091824 restraints weight = 35119.529| |-----------------------------------------------------------------------------| r_work (final): 0.3570 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7623 moved from start: 0.6001 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 28260 Z= 0.105 Angle : 0.825 35.469 38274 Z= 0.349 Chirality : 0.085 2.299 4296 Planarity : 0.004 0.063 4756 Dihedral : 5.675 76.497 3796 Min Nonbonded Distance : 2.255 Molprobity Statistics. All-atom Clashscore : 9.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.90 % Favored : 95.10 % Rotamer: Outliers : 0.00 % Allowed : 1.45 % Favored : 98.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 18.75 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.48 (0.15), residues: 3452 helix: 0.77 (0.13), residues: 1620 sheet: -1.36 (0.25), residues: 412 loop : -1.22 (0.17), residues: 1420 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 300 TYR 0.022 0.001 TYR B 732 PHE 0.015 0.001 PHE A1022 TRP 0.018 0.001 TRP C 262 HIS 0.005 0.001 HIS A1092 Details of bonding type rmsd/Z covalent geometry : bond 0.00225 / 0.11 (28248) covalent geometry : angle 0.82513 / 0.35 (38254) SS BOND : bond 0.00160 / 0.09 ( 10) SS BOND : angle 0.60522 / 0.39 ( 20) hydrogen bonds : bond 0.02951 / 1.93 ( 1268) hydrogen bonds : angle 4.70372 / 3.36 ( 3639) Misc. bond : bond 0.00059 / 0.03 ( 2) *********************** 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 474 residues out of total 2968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 474 time to evaluate : 1.026 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: A 400 ILE cc_start: 0.8954 (tt) cc_final: 0.8690 (tp) REVERT: A 463 MET cc_start: 0.8181 (mpp) cc_final: 0.7950 (mpp) REVERT: A 498 LEU cc_start: 0.9162 (pp) cc_final: 0.8723 (pp) REVERT: A 634 GLU cc_start: 0.8983 (pm20) cc_final: 0.8583 (pm20) REVERT: A 663 LYS cc_start: 0.8045 (pttm) cc_final: 0.7542 (mttt) REVERT: A 732 TYR cc_start: 0.8266 (m-10) cc_final: 0.7802 (m-10) REVERT: A 1022 PHE cc_start: 0.7806 (m-80) cc_final: 0.7568 (m-10) REVERT: A 1112 SER cc_start: 0.8232 (m) cc_final: 0.7967 (t) REVERT: A 1146 MET cc_start: 0.3367 (mmt) cc_final: 0.3073 (mmt) REVERT: B 25 GLU cc_start: 0.9172 (mp0) cc_final: 0.8654 (mp0) REVERT: B 170 ASN cc_start: 0.7892 (p0) cc_final: 0.7650 (p0) REVERT: B 188 LYS cc_start: 0.8871 (ptpp) cc_final: 0.8646 (ptpp) REVERT: B 189 GLU cc_start: 0.7484 (mm-30) cc_final: 0.6998 (mm-30) REVERT: B 380 MET cc_start: 0.7511 (tmm) cc_final: 0.6832 (ttt) REVERT: B 503 MET cc_start: 0.7322 (tpp) cc_final: 0.6956 (tpp) REVERT: B 521 LEU cc_start: 0.8998 (tt) cc_final: 0.8796 (tt) REVERT: B 616 TYR cc_start: 0.9079 (t80) cc_final: 0.8877 (t80) REVERT: B 721 MET cc_start: 0.8344 (ptm) cc_final: 0.7491 (ptm) REVERT: B 797 TYR cc_start: 0.8156 (m-80) cc_final: 0.7697 (m-10) REVERT: B 803 LEU cc_start: 0.8280 (mt) cc_final: 0.8065 (mt) REVERT: B 807 MET cc_start: 0.8774 (mmm) cc_final: 0.8540 (tpp) REVERT: C 361 MET cc_start: 0.8051 (tpp) cc_final: 0.7570 (tpp) REVERT: C 414 MET cc_start: 0.8108 (tmm) cc_final: 0.7753 (tmm) REVERT: C 498 LEU cc_start: 0.8998 (pp) cc_final: 0.8793 (pp) REVERT: C 526 TRP cc_start: 0.7229 (m100) cc_final: 0.6054 (m100) REVERT: C 527 MET cc_start: 0.8123 (mmm) cc_final: 0.7794 (mtt) REVERT: C 577 LEU cc_start: 0.6155 (tp) cc_final: 0.5913 (pt) REVERT: C 1088 LEU cc_start: 0.6964 (mt) cc_final: 0.6300 (pt) REVERT: C 1093 THR cc_start: 0.7333 (p) cc_final: 0.6632 (t) REVERT: C 1181 HIS cc_start: 0.8331 (m90) cc_final: 0.7224 (m90) REVERT: C 1183 MET cc_start: 0.9133 (mmp) cc_final: 0.8574 (mpp) REVERT: C 1221 MET cc_start: 0.7529 (mmp) cc_final: 0.7279 (mmp) REVERT: D 25 GLU cc_start: 0.9081 (mp0) cc_final: 0.8499 (mp0) REVERT: D 188 LYS cc_start: 0.8823 (ptpp) cc_final: 0.8526 (ptpp) REVERT: D 189 GLU cc_start: 0.7414 (mm-30) cc_final: 0.6856 (mm-30) REVERT: D 199 ASP cc_start: 0.8703 (t70) cc_final: 0.8470 (t0) REVERT: D 380 MET cc_start: 0.7634 (tmm) cc_final: 0.6897 (ttt) REVERT: D 491 PHE cc_start: 0.7800 (m-80) cc_final: 0.7342 (m-80) REVERT: D 503 MET cc_start: 0.7721 (tpp) cc_final: 0.7353 (tpp) REVERT: D 585 MET cc_start: 0.8139 (mmt) cc_final: 0.7873 (mmm) REVERT: D 639 LEU cc_start: 0.8994 (mt) cc_final: 0.8356 (mp) REVERT: D 721 MET cc_start: 0.8398 (ptm) cc_final: 0.7389 (ptm) outliers start: 0 outliers final: 0 residues processed: 474 average time/residue: 0.1806 time to fit residues: 138.7464 Evaluate side-chains 344 residues out of total 2968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 344 time to evaluate : 1.064 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 348 random chunks: chunk 5 optimal weight: 2.9990 chunk 62 optimal weight: 0.0170 chunk 193 optimal weight: 0.9990 chunk 222 optimal weight: 0.7980 chunk 118 optimal weight: 0.0040 chunk 159 optimal weight: 0.6980 chunk 130 optimal weight: 5.9990 chunk 242 optimal weight: 6.9990 chunk 199 optimal weight: 0.4980 chunk 146 optimal weight: 9.9990 chunk 343 optimal weight: 0.0570 overall best weight: 0.2548 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 586 GLN A 642 GLN A 791 ASN A1034 GLN A1181 HIS ** B 246 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 392 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 586 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 246 GLN C 619 ASN C1186 GLN ** D 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 83 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 642 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3885 r_free = 0.3885 target = 0.109161 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3516 r_free = 0.3516 target = 0.088529 restraints weight = 99446.270| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3550 r_free = 0.3550 target = 0.090254 restraints weight = 68167.177| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3575 r_free = 0.3575 target = 0.091493 restraints weight = 52199.135| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3593 r_free = 0.3593 target = 0.092389 restraints weight = 43009.252| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 56)----------------| | r_work = 0.3603 r_free = 0.3603 target = 0.092971 restraints weight = 37429.466| |-----------------------------------------------------------------------------| r_work (final): 0.3599 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7592 moved from start: 0.6317 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 28260 Z= 0.107 Angle : 0.826 35.308 38274 Z= 0.349 Chirality : 0.085 2.256 4296 Planarity : 0.004 0.056 4756 Dihedral : 5.581 80.307 3796 Min Nonbonded Distance : 2.258 Molprobity Statistics. All-atom Clashscore : 9.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.63 % Favored : 95.37 % Rotamer: Outliers : 0.00 % Allowed : 1.49 % Favored : 98.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 18.75 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.26 (0.15), residues: 3452 helix: 1.00 (0.13), residues: 1608 sheet: -1.48 (0.24), residues: 424 loop : -1.05 (0.17), residues: 1420 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 300 TYR 0.028 0.001 TYR B 732 PHE 0.027 0.001 PHE A1210 TRP 0.017 0.001 TRP A 606 HIS 0.006 0.001 HIS A1181 Details of bonding type rmsd/Z covalent geometry : bond 0.00233 / 0.11 (28248) covalent geometry : angle 0.82633 / 0.35 (38254) SS BOND : bond 0.00166 / 0.09 ( 10) SS BOND : angle 0.58602 / 0.38 ( 20) hydrogen bonds : bond 0.02839 / 1.87 ( 1268) hydrogen bonds : angle 4.55366 / 3.26 ( 3639) Misc. bond : bond 0.00054 / 0.03 ( 2) *********************** 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 455 residues out of total 2968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 455 time to evaluate : 1.030 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: A 400 ILE cc_start: 0.8923 (tt) cc_final: 0.8661 (tp) REVERT: A 498 LEU cc_start: 0.9251 (pp) cc_final: 0.8473 (pp) REVERT: A 619 ASN cc_start: 0.7674 (t0) cc_final: 0.7290 (t0) REVERT: A 634 GLU cc_start: 0.8940 (pm20) cc_final: 0.8513 (pm20) REVERT: A 663 LYS cc_start: 0.8047 (pttm) cc_final: 0.7444 (mttt) REVERT: A 732 TYR cc_start: 0.8322 (m-10) cc_final: 0.7974 (m-10) REVERT: A 1022 PHE cc_start: 0.7832 (m-80) cc_final: 0.7574 (m-10) REVERT: A 1112 SER cc_start: 0.8573 (m) cc_final: 0.8309 (t) REVERT: A 1221 MET cc_start: 0.6816 (mmp) cc_final: 0.5172 (ppp) REVERT: B 25 GLU cc_start: 0.9119 (mp0) cc_final: 0.8633 (mp0) REVERT: B 170 ASN cc_start: 0.7781 (p0) cc_final: 0.7574 (p0) REVERT: B 189 GLU cc_start: 0.7455 (mm-30) cc_final: 0.6974 (mm-30) REVERT: B 380 MET cc_start: 0.7475 (tmm) cc_final: 0.6759 (ttt) REVERT: B 527 MET cc_start: 0.8333 (mmp) cc_final: 0.7961 (mtt) REVERT: B 616 TYR cc_start: 0.9113 (t80) cc_final: 0.8910 (t80) REVERT: B 720 THR cc_start: 0.8450 (p) cc_final: 0.8241 (p) REVERT: B 796 PHE cc_start: 0.6664 (m-10) cc_final: 0.6427 (m-80) REVERT: B 797 TYR cc_start: 0.8121 (m-80) cc_final: 0.7673 (m-10) REVERT: B 803 LEU cc_start: 0.8284 (mt) cc_final: 0.8037 (mt) REVERT: C 415 LEU cc_start: 0.6578 (mt) cc_final: 0.6348 (mt) REVERT: C 526 TRP cc_start: 0.7311 (m100) cc_final: 0.6037 (m100) REVERT: C 527 MET cc_start: 0.8167 (mmm) cc_final: 0.7803 (mtt) REVERT: C 577 LEU cc_start: 0.6178 (tp) cc_final: 0.5891 (pt) REVERT: C 700 TYR cc_start: 0.6717 (t80) cc_final: 0.6378 (t80) REVERT: C 1088 LEU cc_start: 0.6415 (mt) cc_final: 0.5941 (pt) REVERT: C 1093 THR cc_start: 0.7420 (p) cc_final: 0.6831 (t) REVERT: C 1178 MET cc_start: 0.8947 (tpp) cc_final: 0.8494 (tpp) REVERT: C 1181 HIS cc_start: 0.8335 (m90) cc_final: 0.7215 (m90) REVERT: C 1182 MET cc_start: 0.8407 (ppp) cc_final: 0.7504 (ppp) REVERT: C 1183 MET cc_start: 0.9080 (mmp) cc_final: 0.8798 (mmt) REVERT: C 1221 MET cc_start: 0.7346 (mmp) cc_final: 0.7127 (mmp) REVERT: D 25 GLU cc_start: 0.9047 (mp0) cc_final: 0.8485 (mp0) REVERT: D 188 LYS cc_start: 0.8765 (ptpp) cc_final: 0.8463 (ptpp) REVERT: D 189 GLU cc_start: 0.7307 (mm-30) cc_final: 0.6794 (mm-30) REVERT: D 195 ASP cc_start: 0.8221 (p0) cc_final: 0.7772 (t70) REVERT: D 199 ASP cc_start: 0.8646 (t70) cc_final: 0.8432 (t0) REVERT: D 247 ILE cc_start: 0.8675 (pt) cc_final: 0.8470 (mt) REVERT: D 380 MET cc_start: 0.7597 (tmm) cc_final: 0.6841 (ttt) REVERT: D 491 PHE cc_start: 0.7636 (m-80) cc_final: 0.7202 (m-80) REVERT: D 697 LYS cc_start: 0.8609 (pttm) cc_final: 0.8031 (tptt) REVERT: D 708 MET cc_start: 0.7966 (tpt) cc_final: 0.7630 (tpp) REVERT: D 721 MET cc_start: 0.8393 (ptm) cc_final: 0.7510 (ptm) outliers start: 0 outliers final: 0 residues processed: 455 average time/residue: 0.1715 time to fit residues: 126.6044 Evaluate side-chains 328 residues out of total 2968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 328 time to evaluate : 1.068 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 348 random chunks: chunk 345 optimal weight: 0.9990 chunk 207 optimal weight: 8.9990 chunk 152 optimal weight: 9.9990 chunk 112 optimal weight: 0.0870 chunk 180 optimal weight: 1.9990 chunk 169 optimal weight: 4.9990 chunk 32 optimal weight: 9.9990 chunk 139 optimal weight: 8.9990 chunk 329 optimal weight: 5.9990 chunk 76 optimal weight: 7.9990 chunk 327 optimal weight: 0.9990 overall best weight: 1.8166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 642 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1034 GLN B 246 GLN B 337 GLN ** B 392 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 586 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 619 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 246 GLN C 619 ASN ** D 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 246 GLN D 337 GLN D 756 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3839 r_free = 0.3839 target = 0.106259 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3455 r_free = 0.3455 target = 0.085528 restraints weight = 101016.065| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3489 r_free = 0.3489 target = 0.087204 restraints weight = 70503.388| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 55)----------------| | r_work = 0.3512 r_free = 0.3512 target = 0.088358 restraints weight = 54478.074| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3529 r_free = 0.3529 target = 0.089174 restraints weight = 45481.996| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3539 r_free = 0.3539 target = 0.089699 restraints weight = 39997.297| |-----------------------------------------------------------------------------| r_work (final): 0.3534 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7689 moved from start: 0.6657 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 28260 Z= 0.135 Angle : 0.836 35.396 38274 Z= 0.358 Chirality : 0.084 2.225 4296 Planarity : 0.004 0.060 4756 Dihedral : 5.590 80.834 3796 Min Nonbonded Distance : 2.195 Molprobity Statistics. All-atom Clashscore : 11.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.33 % Favored : 94.67 % Rotamer: Outliers : 0.00 % Allowed : 1.15 % Favored : 98.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 18.75 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.22 (0.15), residues: 3452 helix: 1.02 (0.13), residues: 1604 sheet: -1.55 (0.24), residues: 416 loop : -0.98 (0.17), residues: 1432 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 300 TYR 0.024 0.001 TYR B 732 PHE 0.024 0.002 PHE B 541 TRP 0.018 0.001 TRP C1032 HIS 0.004 0.001 HIS B 219 Details of bonding type rmsd/Z covalent geometry : bond 0.00305 / 0.14 (28248) covalent geometry : angle 0.83597 / 0.36 (38254) SS BOND : bond 0.00311 / 0.19 ( 10) SS BOND : angle 0.75881 / 0.49 ( 20) hydrogen bonds : bond 0.03006 / 1.97 ( 1268) hydrogen bonds : angle 4.59286 / 3.29 ( 3639) Misc. bond : bond 0.00076 / 0.04 ( 2) *********************** 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 421 residues out of total 2968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 421 time to evaluate : 0.954 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 400 ILE cc_start: 0.8964 (tt) cc_final: 0.8697 (tp) REVERT: A 414 MET cc_start: 0.7520 (tmm) cc_final: 0.7296 (tmm) REVERT: A 498 LEU cc_start: 0.9227 (pp) cc_final: 0.8162 (pp) REVERT: A 619 ASN cc_start: 0.7864 (t0) cc_final: 0.7452 (t0) REVERT: A 663 LYS cc_start: 0.8109 (pttm) cc_final: 0.7596 (mttt) REVERT: A 732 TYR cc_start: 0.8430 (m-10) cc_final: 0.8029 (m-80) REVERT: A 1022 PHE cc_start: 0.7971 (m-80) cc_final: 0.7738 (m-10) REVERT: A 1112 SER cc_start: 0.8427 (m) cc_final: 0.8194 (t) REVERT: A 1146 MET cc_start: 0.2642 (mmt) cc_final: 0.2133 (mmt) REVERT: A 1186 GLN cc_start: 0.8756 (tm-30) cc_final: 0.8550 (tm-30) REVERT: B 25 GLU cc_start: 0.9133 (mp0) cc_final: 0.8300 (mp0) REVERT: B 170 ASN cc_start: 0.7966 (p0) cc_final: 0.7766 (p0) REVERT: B 189 GLU cc_start: 0.7411 (mm-30) cc_final: 0.6944 (mm-30) REVERT: B 380 MET cc_start: 0.7575 (tmm) cc_final: 0.7097 (ttt) REVERT: B 695 LYS cc_start: 0.8788 (pttp) cc_final: 0.8105 (mtmm) REVERT: B 716 LYS cc_start: 0.8490 (tppt) cc_final: 0.7929 (mmmt) REVERT: B 797 TYR cc_start: 0.8178 (m-80) cc_final: 0.7737 (m-10) REVERT: B 803 LEU cc_start: 0.8269 (mt) cc_final: 0.8034 (mt) REVERT: C 361 MET cc_start: 0.7751 (tpp) cc_final: 0.7355 (tpp) REVERT: C 414 MET cc_start: 0.8118 (tmm) cc_final: 0.7901 (tmm) REVERT: C 498 LEU cc_start: 0.9112 (pp) cc_final: 0.8050 (pp) REVERT: C 526 TRP cc_start: 0.7742 (m100) cc_final: 0.6382 (m100) REVERT: C 527 MET cc_start: 0.8416 (mmm) cc_final: 0.7965 (mtt) REVERT: C 577 LEU cc_start: 0.6050 (tp) cc_final: 0.5731 (pt) REVERT: C 619 ASN cc_start: 0.9149 (t160) cc_final: 0.8761 (t0) REVERT: C 705 GLU cc_start: 0.7434 (mp0) cc_final: 0.7174 (mp0) REVERT: C 732 TYR cc_start: 0.8231 (m-10) cc_final: 0.7816 (m-10) REVERT: C 1088 LEU cc_start: 0.6515 (mt) cc_final: 0.5936 (pt) REVERT: C 1093 THR cc_start: 0.7407 (p) cc_final: 0.6874 (t) REVERT: C 1179 VAL cc_start: 0.9261 (t) cc_final: 0.8435 (t) REVERT: C 1182 MET cc_start: 0.8316 (ppp) cc_final: 0.7750 (ppp) REVERT: C 1221 MET cc_start: 0.7610 (mmp) cc_final: 0.7302 (mmp) REVERT: D 25 GLU cc_start: 0.9143 (mp0) cc_final: 0.8544 (mp0) REVERT: D 188 LYS cc_start: 0.8802 (ptpp) cc_final: 0.8474 (ptpp) REVERT: D 189 GLU cc_start: 0.7213 (mm-30) cc_final: 0.6582 (mm-30) REVERT: D 195 ASP cc_start: 0.8284 (p0) cc_final: 0.7910 (t70) REVERT: D 473 ASP cc_start: 0.6774 (m-30) cc_final: 0.6319 (t0) REVERT: D 491 PHE cc_start: 0.7769 (m-80) cc_final: 0.7465 (m-80) REVERT: D 697 LYS cc_start: 0.8570 (pttm) cc_final: 0.8072 (tptt) REVERT: D 721 MET cc_start: 0.8644 (ptm) cc_final: 0.7713 (ptm) REVERT: D 807 MET cc_start: 0.8217 (mmm) cc_final: 0.7828 (mmt) outliers start: 0 outliers final: 0 residues processed: 421 average time/residue: 0.1719 time to fit residues: 117.4216 Evaluate side-chains 319 residues out of total 2968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 319 time to evaluate : 1.034 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 348 random chunks: chunk 297 optimal weight: 3.9990 chunk 311 optimal weight: 1.9990 chunk 208 optimal weight: 7.9990 chunk 139 optimal weight: 5.9990 chunk 160 optimal weight: 0.9990 chunk 262 optimal weight: 20.0000 chunk 118 optimal weight: 0.9990 chunk 137 optimal weight: 7.9990 chunk 280 optimal weight: 9.9990 chunk 188 optimal weight: 0.5980 chunk 26 optimal weight: 9.9990 overall best weight: 1.7188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 642 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 791 ASN ** B 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 392 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 586 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 619 ASN C 619 ASN ** D 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 337 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3832 r_free = 0.3832 target = 0.105949 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.085438 restraints weight = 101441.706| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3483 r_free = 0.3483 target = 0.087051 restraints weight = 70498.963| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3506 r_free = 0.3506 target = 0.088173 restraints weight = 54715.619| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 58)----------------| | r_work = 0.3522 r_free = 0.3522 target = 0.089007 restraints weight = 45681.684| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3531 r_free = 0.3531 target = 0.089458 restraints weight = 40203.510| |-----------------------------------------------------------------------------| r_work (final): 0.3524 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7702 moved from start: 0.6936 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 28260 Z= 0.133 Angle : 0.839 35.228 38274 Z= 0.359 Chirality : 0.084 2.203 4296 Planarity : 0.004 0.059 4756 Dihedral : 5.608 82.745 3796 Min Nonbonded Distance : 2.183 Molprobity Statistics. All-atom Clashscore : 11.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.84 % Favored : 95.16 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.17 (0.15), residues: 3452 helix: 1.10 (0.13), residues: 1604 sheet: -1.59 (0.24), residues: 418 loop : -0.99 (0.17), residues: 1430 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A1038 TYR 0.027 0.001 TYR D 732 PHE 0.023 0.002 PHE A1210 TRP 0.021 0.001 TRP C1032 HIS 0.005 0.001 HIS A1202 Details of bonding type rmsd/Z covalent geometry : bond 0.00300 / 0.13 (28248) covalent geometry : angle 0.83886 / 0.36 (38254) SS BOND : bond 0.00279 / 0.16 ( 10) SS BOND : angle 0.70830 / 0.45 ( 20) hydrogen bonds : bond 0.02976 / 1.95 ( 1268) hydrogen bonds : angle 4.58825 / 3.28 ( 3639) Misc. bond : bond 0.00075 / 0.04 ( 2) *********************** 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 412 residues out of total 2968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 412 time to evaluate : 0.823 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 400 ILE cc_start: 0.8959 (tt) cc_final: 0.8714 (tp) REVERT: A 414 MET cc_start: 0.7436 (tmm) cc_final: 0.7170 (tmm) REVERT: A 415 LEU cc_start: 0.6524 (mt) cc_final: 0.6300 (mt) REVERT: A 498 LEU cc_start: 0.9163 (pp) cc_final: 0.7832 (pp) REVERT: A 619 ASN cc_start: 0.8055 (t0) cc_final: 0.7631 (t0) REVERT: A 663 LYS cc_start: 0.8082 (pttm) cc_final: 0.7586 (mttt) REVERT: A 707 THR cc_start: 0.7426 (p) cc_final: 0.7143 (t) REVERT: A 732 TYR cc_start: 0.8422 (m-10) cc_final: 0.7982 (m-80) REVERT: A 1112 SER cc_start: 0.8462 (m) cc_final: 0.8242 (t) REVERT: A 1146 MET cc_start: 0.2870 (mmt) cc_final: 0.2449 (mmt) REVERT: A 1186 GLN cc_start: 0.8769 (tm-30) cc_final: 0.8518 (tm-30) REVERT: B 25 GLU cc_start: 0.9165 (mp0) cc_final: 0.8351 (mp0) REVERT: B 96 PHE cc_start: 0.7284 (t80) cc_final: 0.7058 (t80) REVERT: B 170 ASN cc_start: 0.8008 (p0) cc_final: 0.7801 (p0) REVERT: B 189 GLU cc_start: 0.7371 (mm-30) cc_final: 0.6925 (mm-30) REVERT: B 232 LEU cc_start: 0.8377 (mp) cc_final: 0.8061 (mp) REVERT: B 380 MET cc_start: 0.7524 (tmm) cc_final: 0.7155 (ttt) REVERT: B 716 LYS cc_start: 0.8521 (tppt) cc_final: 0.7960 (mmmt) REVERT: B 797 TYR cc_start: 0.8162 (m-80) cc_final: 0.7738 (m-10) REVERT: B 803 LEU cc_start: 0.8254 (mt) cc_final: 0.8027 (mt) REVERT: C 361 MET cc_start: 0.7840 (tpp) cc_final: 0.7461 (tpp) REVERT: C 414 MET cc_start: 0.8176 (tmm) cc_final: 0.7925 (tmm) REVERT: C 491 PHE cc_start: 0.7874 (m-80) cc_final: 0.7307 (m-10) REVERT: C 498 LEU cc_start: 0.9122 (pp) cc_final: 0.8001 (pp) REVERT: C 527 MET cc_start: 0.8428 (mmm) cc_final: 0.8218 (mtt) REVERT: C 577 LEU cc_start: 0.5964 (tp) cc_final: 0.5616 (pt) REVERT: C 619 ASN cc_start: 0.9104 (t160) cc_final: 0.8727 (t0) REVERT: C 705 GLU cc_start: 0.7256 (mp0) cc_final: 0.6950 (mp0) REVERT: C 732 TYR cc_start: 0.8206 (m-10) cc_final: 0.7789 (m-10) REVERT: C 1088 LEU cc_start: 0.6442 (mt) cc_final: 0.5818 (pt) REVERT: C 1093 THR cc_start: 0.7390 (p) cc_final: 0.6900 (t) REVERT: C 1181 HIS cc_start: 0.8750 (m90) cc_final: 0.7520 (m90) REVERT: C 1182 MET cc_start: 0.8341 (ppp) cc_final: 0.7624 (ppp) REVERT: C 1183 MET cc_start: 0.9100 (mmp) cc_final: 0.8888 (mmt) REVERT: D 25 GLU cc_start: 0.9088 (mp0) cc_final: 0.8557 (mp0) REVERT: D 96 PHE cc_start: 0.7445 (t80) cc_final: 0.7168 (t80) REVERT: D 188 LYS cc_start: 0.8788 (ptpp) cc_final: 0.8448 (ptpp) REVERT: D 189 GLU cc_start: 0.7091 (mm-30) cc_final: 0.6480 (mm-30) REVERT: D 195 ASP cc_start: 0.8256 (p0) cc_final: 0.7905 (t0) REVERT: D 231 ASP cc_start: 0.7456 (m-30) cc_final: 0.7055 (m-30) REVERT: D 380 MET cc_start: 0.7519 (tmm) cc_final: 0.6921 (ttt) REVERT: D 473 ASP cc_start: 0.6722 (m-30) cc_final: 0.6382 (t0) REVERT: D 491 PHE cc_start: 0.7889 (m-80) cc_final: 0.7520 (m-80) REVERT: D 697 LYS cc_start: 0.8512 (pttm) cc_final: 0.8056 (tptt) REVERT: D 721 MET cc_start: 0.8720 (ptm) cc_final: 0.8017 (ptm) REVERT: D 789 LEU cc_start: 0.7388 (mp) cc_final: 0.6626 (tp) REVERT: D 807 MET cc_start: 0.8399 (mmm) cc_final: 0.8036 (mmt) outliers start: 0 outliers final: 0 residues processed: 412 average time/residue: 0.1745 time to fit residues: 117.4554 Evaluate side-chains 310 residues out of total 2968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 310 time to evaluate : 1.054 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 348 random chunks: chunk 215 optimal weight: 2.9990 chunk 222 optimal weight: 2.9990 chunk 61 optimal weight: 5.9990 chunk 262 optimal weight: 20.0000 chunk 195 optimal weight: 0.8980 chunk 275 optimal weight: 0.7980 chunk 115 optimal weight: 0.7980 chunk 232 optimal weight: 4.9990 chunk 301 optimal weight: 0.9990 chunk 139 optimal weight: 7.9990 chunk 169 optimal weight: 4.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 619 ASN ** A 642 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 791 ASN A1034 GLN ** B 392 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 586 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 214 HIS C 619 ASN ** D 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 337 GLN ** D 619 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 709 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3837 r_free = 0.3837 target = 0.106194 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3460 r_free = 0.3460 target = 0.085774 restraints weight = 101093.333| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 51)----------------| | r_work = 0.3493 r_free = 0.3493 target = 0.087423 restraints weight = 70344.762| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3517 r_free = 0.3517 target = 0.088564 restraints weight = 54394.465| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3534 r_free = 0.3534 target = 0.089411 restraints weight = 45301.550| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 57)----------------| | r_work = 0.3544 r_free = 0.3544 target = 0.089989 restraints weight = 39726.813| |-----------------------------------------------------------------------------| r_work (final): 0.3537 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7688 moved from start: 0.7151 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 28260 Z= 0.119 Angle : 0.832 34.980 38274 Z= 0.355 Chirality : 0.084 2.180 4296 Planarity : 0.004 0.055 4756 Dihedral : 5.592 84.416 3796 Min Nonbonded Distance : 2.190 Molprobity Statistics. All-atom Clashscore : 10.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.07 % Favored : 94.93 % Rotamer: Outliers : 0.00 % Allowed : 0.44 % Favored : 99.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 18.75 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.08 (0.15), residues: 3452 helix: 1.18 (0.13), residues: 1620 sheet: -1.68 (0.24), residues: 410 loop : -0.92 (0.17), residues: 1422 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 694 TYR 0.020 0.001 TYR D 732 PHE 0.030 0.001 PHE B 541 TRP 0.022 0.001 TRP C1032 HIS 0.004 0.001 HIS A1092 Details of bonding type rmsd/Z covalent geometry : bond 0.00269 / 0.12 (28248) covalent geometry : angle 0.83221 / 0.35 (38254) SS BOND : bond 0.00241 / 0.14 ( 10) SS BOND : angle 0.65794 / 0.42 ( 20) hydrogen bonds : bond 0.02951 / 1.95 ( 1268) hydrogen bonds : angle 4.53797 / 3.23 ( 3639) Misc. bond : bond 0.00061 / 0.03 ( 2) *********************** 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 407 residues out of total 2968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 407 time to evaluate : 1.111 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 361 MET cc_start: 0.7616 (tpp) cc_final: 0.7188 (tpp) REVERT: A 400 ILE cc_start: 0.8960 (tt) cc_final: 0.8757 (tp) REVERT: A 414 MET cc_start: 0.7364 (tmm) cc_final: 0.7079 (tmm) REVERT: A 415 LEU cc_start: 0.6476 (mt) cc_final: 0.6267 (mt) REVERT: A 498 LEU cc_start: 0.9164 (pp) cc_final: 0.7924 (pp) REVERT: A 619 ASN cc_start: 0.8348 (t0) cc_final: 0.7877 (t0) REVERT: A 663 LYS cc_start: 0.8030 (pttm) cc_final: 0.7605 (mttt) REVERT: A 700 TYR cc_start: 0.7165 (t80) cc_final: 0.6688 (t80) REVERT: A 732 TYR cc_start: 0.8384 (m-10) cc_final: 0.8022 (m-80) REVERT: A 1112 SER cc_start: 0.8439 (m) cc_final: 0.8226 (t) REVERT: A 1146 MET cc_start: 0.2865 (mmt) cc_final: 0.2430 (mmt) REVERT: A 1184 TYR cc_start: 0.8035 (t80) cc_final: 0.7727 (t80) REVERT: A 1186 GLN cc_start: 0.8775 (tm-30) cc_final: 0.8557 (tm-30) REVERT: A 1221 MET cc_start: 0.7401 (mmp) cc_final: 0.5602 (ppp) REVERT: B 25 GLU cc_start: 0.9151 (mp0) cc_final: 0.8339 (mp0) REVERT: B 170 ASN cc_start: 0.7952 (p0) cc_final: 0.7723 (p0) REVERT: B 189 GLU cc_start: 0.7327 (mm-30) cc_final: 0.6911 (mm-30) REVERT: B 232 LEU cc_start: 0.8361 (mp) cc_final: 0.8042 (mp) REVERT: B 380 MET cc_start: 0.7524 (tmm) cc_final: 0.7167 (ttt) REVERT: B 503 MET cc_start: 0.7740 (tmm) cc_final: 0.6913 (tmm) REVERT: B 616 TYR cc_start: 0.9250 (t80) cc_final: 0.8993 (t80) REVERT: B 695 LYS cc_start: 0.8867 (pttm) cc_final: 0.8118 (mtmm) REVERT: B 716 LYS cc_start: 0.8539 (tppt) cc_final: 0.8064 (mmmt) REVERT: B 797 TYR cc_start: 0.8180 (m-80) cc_final: 0.7736 (m-10) REVERT: B 803 LEU cc_start: 0.8229 (mt) cc_final: 0.8016 (mt) REVERT: C 361 MET cc_start: 0.7796 (tpp) cc_final: 0.7430 (tpp) REVERT: C 414 MET cc_start: 0.8169 (tmm) cc_final: 0.7952 (tmm) REVERT: C 491 PHE cc_start: 0.7803 (m-80) cc_final: 0.7354 (m-80) REVERT: C 498 LEU cc_start: 0.9113 (pp) cc_final: 0.8015 (pp) REVERT: C 527 MET cc_start: 0.8533 (mmm) cc_final: 0.8294 (mtt) REVERT: C 577 LEU cc_start: 0.5806 (tp) cc_final: 0.5509 (pt) REVERT: C 611 ILE cc_start: 0.8831 (mm) cc_final: 0.8628 (mm) REVERT: C 619 ASN cc_start: 0.9098 (t160) cc_final: 0.8786 (t0) REVERT: C 705 GLU cc_start: 0.7202 (mp0) cc_final: 0.6931 (mp0) REVERT: C 732 TYR cc_start: 0.8268 (m-10) cc_final: 0.7795 (m-10) REVERT: C 1088 LEU cc_start: 0.6385 (mt) cc_final: 0.5774 (pt) REVERT: C 1093 THR cc_start: 0.7365 (p) cc_final: 0.6849 (t) REVERT: C 1181 HIS cc_start: 0.8534 (m90) cc_final: 0.7479 (m90) REVERT: C 1182 MET cc_start: 0.8395 (ppp) cc_final: 0.7593 (ppp) REVERT: C 1186 GLN cc_start: 0.8995 (mm-40) cc_final: 0.8600 (mp10) REVERT: D 25 GLU cc_start: 0.9073 (mp0) cc_final: 0.8525 (mp0) REVERT: D 188 LYS cc_start: 0.8741 (ptpp) cc_final: 0.8422 (ptpp) REVERT: D 189 GLU cc_start: 0.7069 (mm-30) cc_final: 0.6455 (mm-30) REVERT: D 231 ASP cc_start: 0.7377 (m-30) cc_final: 0.7015 (m-30) REVERT: D 380 MET cc_start: 0.7498 (tmm) cc_final: 0.6872 (ttt) REVERT: D 491 PHE cc_start: 0.7902 (m-80) cc_final: 0.7273 (m-80) REVERT: D 697 LYS cc_start: 0.8420 (pttm) cc_final: 0.7970 (tptt) REVERT: D 721 MET cc_start: 0.8752 (ptm) cc_final: 0.8534 (ptm) REVERT: D 807 MET cc_start: 0.8410 (mmm) cc_final: 0.8043 (mmt) outliers start: 0 outliers final: 0 residues processed: 407 average time/residue: 0.1760 time to fit residues: 117.0280 Evaluate side-chains 309 residues out of total 2968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 309 time to evaluate : 1.136 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 348 random chunks: chunk 122 optimal weight: 0.9990 chunk 31 optimal weight: 0.1980 chunk 11 optimal weight: 6.9990 chunk 65 optimal weight: 3.9990 chunk 154 optimal weight: 0.7980 chunk 215 optimal weight: 0.8980 chunk 207 optimal weight: 0.6980 chunk 57 optimal weight: 0.9980 chunk 241 optimal weight: 3.9990 chunk 225 optimal weight: 6.9990 chunk 137 optimal weight: 0.9980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 619 ASN ** A 642 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 791 ASN ** B 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 337 GLN ** B 392 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 619 ASN ** D 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 246 GLN D 337 GLN ** D 619 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3857 r_free = 0.3857 target = 0.107384 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3478 r_free = 0.3478 target = 0.086823 restraints weight = 100930.133| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3512 r_free = 0.3512 target = 0.088468 restraints weight = 70952.594| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3535 r_free = 0.3535 target = 0.089629 restraints weight = 55145.353| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.090421 restraints weight = 46064.762| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 57)----------------| | r_work = 0.3562 r_free = 0.3562 target = 0.091020 restraints weight = 40539.150| |-----------------------------------------------------------------------------| r_work (final): 0.3556 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7659 moved from start: 0.7296 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 28260 Z= 0.107 Angle : 0.832 34.700 38274 Z= 0.353 Chirality : 0.084 2.164 4296 Planarity : 0.004 0.056 4756 Dihedral : 5.563 85.850 3796 Min Nonbonded Distance : 2.205 Molprobity Statistics. All-atom Clashscore : 10.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.95 % Favored : 95.05 % Rotamer: Outliers : 0.00 % Allowed : 0.24 % Favored : 99.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 18.75 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.01 (0.15), residues: 3452 helix: 1.26 (0.13), residues: 1626 sheet: -1.64 (0.24), residues: 412 loop : -0.89 (0.17), residues: 1414 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 485 TYR 0.017 0.001 TYR B 673 PHE 0.026 0.001 PHE A1022 TRP 0.020 0.001 TRP C1032 HIS 0.004 0.000 HIS A1092 Details of bonding type rmsd/Z covalent geometry : bond 0.00238 / 0.11 (28248) covalent geometry : angle 0.83186 / 0.35 (38254) SS BOND : bond 0.00197 / 0.12 ( 10) SS BOND : angle 0.63737 / 0.41 ( 20) hydrogen bonds : bond 0.02827 / 1.85 ( 1268) hydrogen bonds : angle 4.49607 / 3.20 ( 3639) Misc. bond : bond 0.00049 / 0.02 ( 2) ********************** 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 414 residues out of total 2968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 414 time to evaluate : 1.122 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 116 ASP cc_start: 0.8839 (m-30) cc_final: 0.8586 (m-30) REVERT: A 361 MET cc_start: 0.7547 (tpp) cc_final: 0.7174 (tpp) REVERT: A 414 MET cc_start: 0.7399 (tmm) cc_final: 0.7120 (tmm) REVERT: A 498 LEU cc_start: 0.9115 (pp) cc_final: 0.8207 (pp) REVERT: A 619 ASN cc_start: 0.8299 (t160) cc_final: 0.7880 (t0) REVERT: A 700 TYR cc_start: 0.7249 (t80) cc_final: 0.6687 (t80) REVERT: A 732 TYR cc_start: 0.8352 (m-10) cc_final: 0.8031 (m-10) REVERT: A 1112 SER cc_start: 0.8530 (m) cc_final: 0.8328 (t) REVERT: A 1146 MET cc_start: 0.2832 (mmt) cc_final: 0.2404 (mmt) REVERT: A 1186 GLN cc_start: 0.8748 (tm-30) cc_final: 0.8399 (tm-30) REVERT: A 1189 GLN cc_start: 0.9646 (mp10) cc_final: 0.9345 (mp10) REVERT: A 1221 MET cc_start: 0.7332 (mmp) cc_final: 0.5708 (ppp) REVERT: B 25 GLU cc_start: 0.9065 (mp0) cc_final: 0.8561 (mp0) REVERT: B 96 PHE cc_start: 0.7172 (t80) cc_final: 0.6895 (t80) REVERT: B 170 ASN cc_start: 0.7859 (p0) cc_final: 0.7623 (p0) REVERT: B 189 GLU cc_start: 0.7300 (mm-30) cc_final: 0.6890 (mm-30) REVERT: B 232 LEU cc_start: 0.8321 (mp) cc_final: 0.8013 (mp) REVERT: B 380 MET cc_start: 0.7457 (tmm) cc_final: 0.7197 (ttt) REVERT: B 503 MET cc_start: 0.7792 (tmm) cc_final: 0.7018 (tmm) REVERT: B 616 TYR cc_start: 0.9200 (t80) cc_final: 0.8963 (t80) REVERT: B 697 LYS cc_start: 0.7920 (pttm) cc_final: 0.7441 (ttmt) REVERT: B 716 LYS cc_start: 0.8669 (tppt) cc_final: 0.8211 (mmmt) REVERT: B 797 TYR cc_start: 0.8281 (m-80) cc_final: 0.7802 (m-10) REVERT: C 361 MET cc_start: 0.7781 (tpp) cc_final: 0.7423 (tpp) REVERT: C 414 MET cc_start: 0.8191 (tmm) cc_final: 0.7969 (tmm) REVERT: C 491 PHE cc_start: 0.7796 (m-80) cc_final: 0.7406 (m-80) REVERT: C 577 LEU cc_start: 0.5836 (tp) cc_final: 0.5526 (pt) REVERT: C 609 THR cc_start: 0.8672 (t) cc_final: 0.7876 (m) REVERT: C 705 GLU cc_start: 0.7166 (mp0) cc_final: 0.6950 (mp0) REVERT: C 721 MET cc_start: 0.8095 (pmm) cc_final: 0.7764 (ptp) REVERT: C 732 TYR cc_start: 0.8178 (m-10) cc_final: 0.7703 (m-10) REVERT: C 1088 LEU cc_start: 0.6231 (mt) cc_final: 0.5620 (pt) REVERT: C 1093 THR cc_start: 0.7378 (p) cc_final: 0.6883 (t) REVERT: C 1178 MET cc_start: 0.8783 (tpp) cc_final: 0.8493 (tpp) REVERT: C 1181 HIS cc_start: 0.8419 (m90) cc_final: 0.7519 (m90) REVERT: C 1182 MET cc_start: 0.8322 (ppp) cc_final: 0.7777 (ppp) REVERT: C 1183 MET cc_start: 0.8720 (mmt) cc_final: 0.8253 (mmm) REVERT: D 25 GLU cc_start: 0.9046 (mp0) cc_final: 0.8508 (mp0) REVERT: D 96 PHE cc_start: 0.7195 (t80) cc_final: 0.6972 (t80) REVERT: D 188 LYS cc_start: 0.8667 (ptpp) cc_final: 0.8374 (ptpp) REVERT: D 189 GLU cc_start: 0.7043 (mm-30) cc_final: 0.6501 (mm-30) REVERT: D 231 ASP cc_start: 0.7249 (m-30) cc_final: 0.6922 (m-30) REVERT: D 380 MET cc_start: 0.7491 (tmm) cc_final: 0.6860 (ttt) REVERT: D 473 ASP cc_start: 0.6601 (m-30) cc_final: 0.6372 (t0) REVERT: D 491 PHE cc_start: 0.7802 (m-80) cc_final: 0.7242 (m-80) REVERT: D 697 LYS cc_start: 0.8209 (pttm) cc_final: 0.7857 (tptt) REVERT: D 711 TYR cc_start: 0.8023 (t80) cc_final: 0.7789 (t80) REVERT: D 807 MET cc_start: 0.8403 (mmm) cc_final: 0.8109 (mmt) outliers start: 0 outliers final: 0 residues processed: 414 average time/residue: 0.1759 time to fit residues: 118.9908 Evaluate side-chains 310 residues out of total 2968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 310 time to evaluate : 0.996 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 348 random chunks: chunk 156 optimal weight: 4.9990 chunk 129 optimal weight: 10.0000 chunk 326 optimal weight: 3.9990 chunk 264 optimal weight: 2.9990 chunk 47 optimal weight: 1.9990 chunk 232 optimal weight: 6.9990 chunk 66 optimal weight: 0.0060 chunk 138 optimal weight: 0.9980 chunk 347 optimal weight: 7.9990 chunk 84 optimal weight: 20.0000 chunk 207 optimal weight: 0.9980 overall best weight: 1.4000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 586 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 619 ASN A 791 ASN A1034 GLN B 337 GLN ** B 392 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 412 HIS ** B 586 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 246 GLN D 337 GLN ** D 619 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 709 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3838 r_free = 0.3838 target = 0.106417 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3458 r_free = 0.3458 target = 0.085937 restraints weight = 101340.972| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 55)----------------| | r_work = 0.3491 r_free = 0.3491 target = 0.087550 restraints weight = 70737.584| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.088680 restraints weight = 54867.659| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3531 r_free = 0.3531 target = 0.089518 restraints weight = 45746.003| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 43)----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.090091 restraints weight = 40159.858| |-----------------------------------------------------------------------------| r_work (final): 0.3534 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7691 moved from start: 0.7470 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 28260 Z= 0.123 Angle : 0.843 34.823 38274 Z= 0.360 Chirality : 0.084 2.162 4296 Planarity : 0.004 0.056 4756 Dihedral : 5.583 85.909 3796 Min Nonbonded Distance : 2.191 Molprobity Statistics. All-atom Clashscore : 11.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.13 % Favored : 94.87 % Rotamer: Outliers : 0.00 % Allowed : 0.30 % Favored : 99.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 18.75 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.03 (0.15), residues: 3452 helix: 1.29 (0.13), residues: 1618 sheet: -1.61 (0.24), residues: 424 loop : -0.90 (0.17), residues: 1410 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 42 TYR 0.023 0.001 TYR B 673 PHE 0.030 0.002 PHE B 541 TRP 0.022 0.002 TRP C1032 HIS 0.004 0.001 HIS B 219 Details of bonding type rmsd/Z covalent geometry : bond 0.00278 / 0.12 (28248) covalent geometry : angle 0.84259 / 0.36 (38254) SS BOND : bond 0.00268 / 0.16 ( 10) SS BOND : angle 0.67289 / 0.43 ( 20) hydrogen bonds : bond 0.02945 / 1.94 ( 1268) hydrogen bonds : angle 4.52093 / 3.22 ( 3639) Misc. bond : bond 0.00053 / 0.03 ( 2) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4861.74 seconds wall clock time: 85 minutes 0.21 seconds (5100.21 seconds total)