Starting phenix.real_space_refine on Tue Jun 24 16:43:37 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8cyd_27075/06_2025/8cyd_27075.cif Found real_map, /net/cci-nas-00/data/ceres_data/8cyd_27075/06_2025/8cyd_27075.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8cyd_27075/06_2025/8cyd_27075.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8cyd_27075/06_2025/8cyd_27075.map" model { file = "/net/cci-nas-00/data/ceres_data/8cyd_27075/06_2025/8cyd_27075.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8cyd_27075/06_2025/8cyd_27075.cif" } resolution = 2.6 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.022 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: 4 Type Number sf(0) Gaussians S 129 5.16 5 C 18097 2.51 5 N 4769 2.21 5 O 5459 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 6 residue(s): 1.44s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 28454 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 8581 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1100, 8581 Classifications: {'peptide': 1100} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'CIS': 1, 'PTRANS': 55, 'TRANS': 1043} Chain breaks: 2 Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 5 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "B" Number of atoms: 8585 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1100, 8585 Classifications: {'peptide': 1100} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 55, 'TRANS': 1044} Chain breaks: 2 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Chain: "C" Number of atoms: 8585 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1100, 8585 Classifications: {'peptide': 1100} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 55, 'TRANS': 1044} Chain breaks: 2 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Chain: "D" Number of atoms: 901 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 901 Classifications: {'peptide': 121} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 117} Chain: "E" Number of atoms: 901 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 901 Classifications: {'peptide': 121} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 117} Chain: "F" Number of atoms: 901 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 901 Classifications: {'peptide': 121} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 117} Time building chain proxies: 17.29, per 1000 atoms: 0.61 Number of scatterers: 28454 At special positions: 0 Unit cell: (170.13, 179.76, 200.09, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 129 16.00 O 5459 8.00 N 4769 7.00 C 18097 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=38, symmetry=0 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.03 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.02 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.03 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.03 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.03 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 590 " distance=2.03 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=2.03 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.03 Simple disulfide: pdb=" SG CYS A 738 " - pdb=" SG CYS A 760 " distance=2.03 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.03 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.03 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.03 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=2.03 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.03 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.03 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.03 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.03 Simple disulfide: pdb=" SG CYS B 538 " - pdb=" SG CYS B 590 " distance=2.03 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 649 " distance=2.03 Simple disulfide: pdb=" SG CYS B 662 " - pdb=" SG CYS B 671 " distance=2.03 Simple disulfide: pdb=" SG CYS B 738 " - pdb=" SG CYS B 760 " distance=2.03 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=2.03 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.03 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.03 Simple disulfide: pdb=" SG CYS C 291 " - pdb=" SG CYS C 301 " distance=2.03 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.03 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.03 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.03 Simple disulfide: pdb=" SG CYS C 480 " - pdb=" SG CYS C 488 " distance=2.03 Simple disulfide: pdb=" SG CYS C 617 " - pdb=" SG CYS C 649 " distance=2.03 Simple disulfide: pdb=" SG CYS C 662 " - pdb=" SG CYS C 671 " distance=2.03 Simple disulfide: pdb=" SG CYS C 738 " - pdb=" SG CYS C 760 " distance=2.03 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.03 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=2.03 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.03 Simple disulfide: pdb=" SG CYS D 22 " - pdb=" SG CYS D 95 " distance=2.03 Simple disulfide: pdb=" SG CYS E 22 " - pdb=" SG CYS E 95 " distance=2.03 Simple disulfide: pdb=" SG CYS F 22 " - pdb=" SG CYS F 95 " distance=2.03 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=0, symmetry=0 Time building additional restraints: 7.03 Conformation dependent library (CDL) restraints added in 3.7 seconds 7278 Ramachandran restraints generated. 3639 Oldfield, 0 Emsley, 3639 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6816 Finding SS restraints... Secondary structure from input PDB file: 76 helices and 58 sheets defined 22.7% alpha, 27.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 5.36 Creating SS restraints... Processing helix chain 'A' and resid 248 through 250 No H-bonds generated for 'chain 'A' and resid 248 through 250' Processing helix chain 'A' and resid 294 through 303 Processing helix chain 'A' and resid 337 through 343 removed outlier: 3.887A pdb=" N VAL A 341 " --> pdb=" O PRO A 337 " (cutoff:3.500A) Processing helix chain 'A' and resid 365 through 370 Processing helix chain 'A' and resid 385 through 389 Processing helix chain 'A' and resid 405 through 410 removed outlier: 4.093A pdb=" N ARG A 408 " --> pdb=" O ASP A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 438 through 443 Processing helix chain 'A' and resid 502 through 505 Processing helix chain 'A' and resid 619 through 623 Processing helix chain 'A' and resid 629 through 634 Processing helix chain 'A' and resid 737 through 743 Processing helix chain 'A' and resid 746 through 755 removed outlier: 3.757A pdb=" N GLN A 755 " --> pdb=" O ASN A 751 " (cutoff:3.500A) Processing helix chain 'A' and resid 758 through 783 Processing helix chain 'A' and resid 816 through 826 Processing helix chain 'A' and resid 849 through 854 removed outlier: 3.504A pdb=" N GLN A 853 " --> pdb=" O ILE A 850 " (cutoff:3.500A) Processing helix chain 'A' and resid 866 through 885 Processing helix chain 'A' and resid 886 through 890 Processing helix chain 'A' and resid 897 through 909 Processing helix chain 'A' and resid 912 through 919 removed outlier: 4.410A pdb=" N LEU A 916 " --> pdb=" O THR A 912 " (cutoff:3.500A) Processing helix chain 'A' and resid 919 through 941 Processing helix chain 'A' and resid 945 through 965 Processing helix chain 'A' and resid 966 through 968 No H-bonds generated for 'chain 'A' and resid 966 through 968' Processing helix chain 'A' and resid 976 through 984 Processing helix chain 'A' and resid 985 through 1033 removed outlier: 4.265A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) Processing helix chain 'A' and resid 1140 through 1147 removed outlier: 3.616A pdb=" N GLU A1144 " --> pdb=" O PRO A1140 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 304 Processing helix chain 'B' and resid 337 through 343 removed outlier: 3.740A pdb=" N VAL B 341 " --> pdb=" O PRO B 337 " (cutoff:3.500A) Processing helix chain 'B' and resid 365 through 370 Processing helix chain 'B' and resid 385 through 389 Processing helix chain 'B' and resid 405 through 410 removed outlier: 4.157A pdb=" N ARG B 408 " --> pdb=" O ASP B 405 " (cutoff:3.500A) Processing helix chain 'B' and resid 438 through 443 Processing helix chain 'B' and resid 502 through 505 Processing helix chain 'B' and resid 616 through 620 Processing helix chain 'B' and resid 634 through 638 removed outlier: 3.838A pdb=" N THR B 638 " --> pdb=" O VAL B 635 " (cutoff:3.500A) Processing helix chain 'B' and resid 737 through 743 Processing helix chain 'B' and resid 746 through 755 removed outlier: 3.794A pdb=" N GLN B 755 " --> pdb=" O ASN B 751 " (cutoff:3.500A) Processing helix chain 'B' and resid 758 through 783 Processing helix chain 'B' and resid 816 through 826 Processing helix chain 'B' and resid 850 through 854 removed outlier: 3.699A pdb=" N GLN B 853 " --> pdb=" O ILE B 850 " (cutoff:3.500A) removed outlier: 4.060A pdb=" N LYS B 854 " --> pdb=" O CYS B 851 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 850 through 854' Processing helix chain 'B' and resid 866 through 885 Processing helix chain 'B' and resid 886 through 890 Processing helix chain 'B' and resid 897 through 909 Processing helix chain 'B' and resid 913 through 918 removed outlier: 3.508A pdb=" N TYR B 917 " --> pdb=" O GLN B 913 " (cutoff:3.500A) Processing helix chain 'B' and resid 919 through 940 Processing helix chain 'B' and resid 945 through 965 Processing helix chain 'B' and resid 966 through 968 No H-bonds generated for 'chain 'B' and resid 966 through 968' Processing helix chain 'B' and resid 976 through 984 Processing helix chain 'B' and resid 985 through 1033 removed outlier: 4.500A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) Processing helix chain 'B' and resid 1141 through 1147 Processing helix chain 'C' and resid 294 through 304 Processing helix chain 'C' and resid 337 through 341 removed outlier: 3.797A pdb=" N GLU C 340 " --> pdb=" O PRO C 337 " (cutoff:3.500A) Processing helix chain 'C' and resid 365 through 370 Processing helix chain 'C' and resid 385 through 389 Processing helix chain 'C' and resid 405 through 410 removed outlier: 4.006A pdb=" N ARG C 408 " --> pdb=" O ASP C 405 " (cutoff:3.500A) Processing helix chain 'C' and resid 438 through 443 removed outlier: 3.625A pdb=" N SER C 443 " --> pdb=" O ASN C 439 " (cutoff:3.500A) Processing helix chain 'C' and resid 502 through 505 Processing helix chain 'C' and resid 633 through 638 Processing helix chain 'C' and resid 737 through 743 Processing helix chain 'C' and resid 746 through 755 removed outlier: 3.790A pdb=" N GLN C 755 " --> pdb=" O ASN C 751 " (cutoff:3.500A) Processing helix chain 'C' and resid 758 through 783 Processing helix chain 'C' and resid 816 through 826 Processing helix chain 'C' and resid 866 through 885 Processing helix chain 'C' and resid 886 through 890 Processing helix chain 'C' and resid 897 through 909 Processing helix chain 'C' and resid 912 through 919 removed outlier: 4.477A pdb=" N LEU C 916 " --> pdb=" O THR C 912 " (cutoff:3.500A) Processing helix chain 'C' and resid 919 through 941 Processing helix chain 'C' and resid 945 through 965 Processing helix chain 'C' and resid 966 through 968 No H-bonds generated for 'chain 'C' and resid 966 through 968' Processing helix chain 'C' and resid 976 through 984 Processing helix chain 'C' and resid 985 through 1032 removed outlier: 4.232A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) Processing helix chain 'C' and resid 1141 through 1147 removed outlier: 4.197A pdb=" N ASP C1146 " --> pdb=" O PRO C1143 " (cutoff:3.500A) Processing helix chain 'D' and resid 28 through 32 removed outlier: 3.811A pdb=" N ILE D 31 " --> pdb=" O ASP D 28 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N LEU D 32 " --> pdb=" O PHE D 29 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 28 through 32' Processing helix chain 'D' and resid 86 through 90 Processing helix chain 'E' and resid 86 through 90 Processing helix chain 'F' and resid 28 through 32 removed outlier: 3.785A pdb=" N ILE F 31 " --> pdb=" O ASP F 28 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N LEU F 32 " --> pdb=" O PHE F 29 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 28 through 32' Processing helix chain 'F' and resid 86 through 90 Processing sheet with id=AA1, first strand: chain 'A' and resid 27 through 30 removed outlier: 4.255A pdb=" N ALA A 27 " --> pdb=" O TRP A 64 " (cutoff:3.500A) removed outlier: 7.910A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 5.419A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ASN A 188 " --> pdb=" O GLU A 96 " (cutoff:3.500A) removed outlier: 6.673A pdb=" N PHE A 201 " --> pdb=" O ASP A 228 " (cutoff:3.500A) removed outlier: 4.382A pdb=" N ASP A 228 " --> pdb=" O PHE A 201 " (cutoff:3.500A) removed outlier: 6.731A pdb=" N ILE A 203 " --> pdb=" O LEU A 226 " (cutoff:3.500A) removed outlier: 6.348A pdb=" N HIS A 207 " --> pdb=" O ALA A 222 " (cutoff:3.500A) removed outlier: 8.370A pdb=" N ALA A 222 " --> pdb=" O HIS A 207 " (cutoff:3.500A) removed outlier: 7.184A pdb=" N VAL A 36 " --> pdb=" O LEU A 223 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 47 through 55 removed outlier: 3.835A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 84 through 85 removed outlier: 3.566A pdb=" N GLY A 107 " --> pdb=" O ARG A 237 " (cutoff:3.500A) removed outlier: 5.768A pdb=" N ARG A 102 " --> pdb=" O ASN A 121 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N VAL A 126 " --> pdb=" O SER A 172 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N SER A 172 " --> pdb=" O VAL A 126 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 84 through 85 removed outlier: 3.566A pdb=" N GLY A 107 " --> pdb=" O ARG A 237 " (cutoff:3.500A) removed outlier: 6.835A pdb=" N LEU A 241 " --> pdb=" O ARG A 102 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 153 through 154 removed outlier: 7.376A pdb=" N VAL A 143 " --> pdb=" O ARG A 246 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 311 through 317 removed outlier: 6.736A pdb=" N VAL A 595 " --> pdb=" O THR A 315 " (cutoff:3.500A) removed outlier: 4.127A pdb=" N GLY A 594 " --> pdb=" O GLN A 613 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 327 through 328 removed outlier: 4.849A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) removed outlier: 6.558A pdb=" N GLY A 566 " --> pdb=" O ASP A 574 " (cutoff:3.500A) removed outlier: 6.552A pdb=" N PHE A 565 " --> pdb=" O PHE C 43 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 354 through 358 Processing sheet with id=AA9, first strand: chain 'A' and resid 448 through 454 removed outlier: 3.944A pdb=" N ASN A 450 " --> pdb=" O TYR A 495 " (cutoff:3.500A) removed outlier: 7.075A pdb=" N TYR A 495 " --> pdb=" O ASN A 450 " (cutoff:3.500A) removed outlier: 4.531A pdb=" N LEU A 452 " --> pdb=" O GLN A 493 " (cutoff:3.500A) removed outlier: 6.371A pdb=" N GLN A 493 " --> pdb=" O LEU A 452 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 473 through 474 Processing sheet with id=AB2, first strand: chain 'A' and resid 654 through 655 removed outlier: 5.962A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 8.488A pdb=" N THR A 696 " --> pdb=" O GLU A 654 " (cutoff:3.500A) removed outlier: 6.387A pdb=" N ALA A 672 " --> pdb=" O PRO A 665 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 701 through 704 Processing sheet with id=AB4, first strand: chain 'A' and resid 711 through 715 removed outlier: 3.730A pdb=" N ALA A1078 " --> pdb=" O PHE A1095 " (cutoff:3.500A) removed outlier: 4.604A pdb=" N PHE A1095 " --> pdb=" O ALA A1078 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 718 through 728 removed outlier: 7.023A pdb=" N GLY A1059 " --> pdb=" O SER A1055 " (cutoff:3.500A) removed outlier: 5.167A pdb=" N SER A1055 " --> pdb=" O GLY A1059 " (cutoff:3.500A) removed outlier: 6.656A pdb=" N VAL A1061 " --> pdb=" O PRO A1053 " (cutoff:3.500A) removed outlier: 6.459A pdb=" N LEU A1063 " --> pdb=" O SER A1051 " (cutoff:3.500A) removed outlier: 4.347A pdb=" N SER A1051 " --> pdb=" O LEU A1063 " (cutoff:3.500A) removed outlier: 6.861A pdb=" N VAL A1065 " --> pdb=" O LEU A1049 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 735 through 736 removed outlier: 3.532A pdb=" N SER A 735 " --> pdb=" O THR A 859 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 787 through 790 Processing sheet with id=AB8, first strand: chain 'A' and resid 1120 through 1125 removed outlier: 4.509A pdb=" N ALA A1087 " --> pdb=" O SER A1123 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 27 through 30 removed outlier: 4.293A pdb=" N ALA B 27 " --> pdb=" O TRP B 64 " (cutoff:3.500A) removed outlier: 7.640A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 5.299A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N ALA B 264 " --> pdb=" O THR B 95 " (cutoff:3.500A) removed outlier: 6.714A pdb=" N PHE B 201 " --> pdb=" O ASP B 228 " (cutoff:3.500A) removed outlier: 4.419A pdb=" N ASP B 228 " --> pdb=" O PHE B 201 " (cutoff:3.500A) removed outlier: 6.762A pdb=" N ILE B 203 " --> pdb=" O LEU B 226 " (cutoff:3.500A) removed outlier: 7.014A pdb=" N HIS B 207 " --> pdb=" O ALA B 222 " (cutoff:3.500A) removed outlier: 8.423A pdb=" N ALA B 222 " --> pdb=" O HIS B 207 " (cutoff:3.500A) removed outlier: 6.877A pdb=" N VAL B 36 " --> pdb=" O LEU B 223 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 27 through 30 removed outlier: 4.293A pdb=" N ALA B 27 " --> pdb=" O TRP B 64 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 42 through 43 removed outlier: 6.622A pdb=" N GLY C 566 " --> pdb=" O ASP C 574 " (cutoff:3.500A) removed outlier: 5.323A pdb=" N ASP C 574 " --> pdb=" O ILE C 587 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 47 through 55 removed outlier: 3.850A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 84 through 85 removed outlier: 5.705A pdb=" N ALA B 243 " --> pdb=" O ILE B 101 " (cutoff:3.500A) removed outlier: 6.800A pdb=" N ILE B 101 " --> pdb=" O ALA B 243 " (cutoff:3.500A) removed outlier: 5.913A pdb=" N ARG B 102 " --> pdb=" O ASN B 121 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N PHE B 168 " --> pdb=" O VAL B 130 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 153 through 156 removed outlier: 3.963A pdb=" N MET B 153 " --> pdb=" O TYR B 144 " (cutoff:3.500A) removed outlier: 6.568A pdb=" N GLY B 142 " --> pdb=" O SER B 155 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N ARG B 246 " --> pdb=" O VAL B 143 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 311 through 318 removed outlier: 5.305A pdb=" N ILE B 312 " --> pdb=" O THR B 599 " (cutoff:3.500A) removed outlier: 7.219A pdb=" N THR B 599 " --> pdb=" O ILE B 312 " (cutoff:3.500A) removed outlier: 5.827A pdb=" N GLN B 314 " --> pdb=" O VAL B 597 " (cutoff:3.500A) removed outlier: 6.566A pdb=" N VAL B 597 " --> pdb=" O GLN B 314 " (cutoff:3.500A) removed outlier: 4.868A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 326 through 328 removed outlier: 4.499A pdb=" N GLU B 583 " --> pdb=" O ASP B 578 " (cutoff:3.500A) removed outlier: 5.376A pdb=" N ASP B 574 " --> pdb=" O ILE B 587 " (cutoff:3.500A) removed outlier: 6.820A pdb=" N GLY B 566 " --> pdb=" O ASP B 574 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 354 through 358 Processing sheet with id=AC9, first strand: chain 'B' and resid 361 through 362 removed outlier: 6.869A pdb=" N CYS B 361 " --> pdb=" O CYS B 525 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC9 Processing sheet with id=AD1, first strand: chain 'B' and resid 448 through 454 removed outlier: 3.991A pdb=" N ASN B 450 " --> pdb=" O TYR B 495 " (cutoff:3.500A) removed outlier: 7.015A pdb=" N TYR B 495 " --> pdb=" O ASN B 450 " (cutoff:3.500A) removed outlier: 4.553A pdb=" N LEU B 452 " --> pdb=" O GLN B 493 " (cutoff:3.500A) removed outlier: 6.389A pdb=" N GLN B 493 " --> pdb=" O LEU B 452 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 473 through 474 Processing sheet with id=AD3, first strand: chain 'B' and resid 654 through 655 removed outlier: 6.054A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 8.701A pdb=" N THR B 696 " --> pdb=" O GLU B 654 " (cutoff:3.500A) removed outlier: 6.539A pdb=" N ILE B 670 " --> pdb=" O ILE B 666 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 711 through 715 removed outlier: 3.719A pdb=" N ALA B1078 " --> pdb=" O PHE B1095 " (cutoff:3.500A) removed outlier: 4.549A pdb=" N PHE B1095 " --> pdb=" O ALA B1078 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'B' and resid 718 through 728 removed outlier: 7.049A pdb=" N GLY B1059 " --> pdb=" O SER B1055 " (cutoff:3.500A) removed outlier: 5.182A pdb=" N SER B1055 " --> pdb=" O GLY B1059 " (cutoff:3.500A) removed outlier: 6.620A pdb=" N VAL B1061 " --> pdb=" O PRO B1053 " (cutoff:3.500A) removed outlier: 6.378A pdb=" N LEU B1063 " --> pdb=" O SER B1051 " (cutoff:3.500A) removed outlier: 4.331A pdb=" N SER B1051 " --> pdb=" O LEU B1063 " (cutoff:3.500A) removed outlier: 6.837A pdb=" N VAL B1065 " --> pdb=" O LEU B1049 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'B' and resid 735 through 736 removed outlier: 3.744A pdb=" N SER B 735 " --> pdb=" O THR B 859 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N THR B 859 " --> pdb=" O SER B 735 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD6 Processing sheet with id=AD7, first strand: chain 'B' and resid 788 through 789 removed outlier: 5.490A pdb=" N ILE B 788 " --> pdb=" O ASN C 703 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD7 Processing sheet with id=AD8, first strand: chain 'B' and resid 1120 through 1122 Processing sheet with id=AD9, first strand: chain 'C' and resid 27 through 30 removed outlier: 4.387A pdb=" N ALA C 27 " --> pdb=" O TRP C 64 " (cutoff:3.500A) removed outlier: 8.567A pdb=" N ASN C 61 " --> pdb=" O TYR C 269 " (cutoff:3.500A) removed outlier: 6.389A pdb=" N TYR C 269 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N ALA C 264 " --> pdb=" O THR C 95 " (cutoff:3.500A) removed outlier: 6.781A pdb=" N PHE C 201 " --> pdb=" O ASP C 228 " (cutoff:3.500A) removed outlier: 4.505A pdb=" N ASP C 228 " --> pdb=" O PHE C 201 " (cutoff:3.500A) removed outlier: 6.836A pdb=" N ILE C 203 " --> pdb=" O LEU C 226 " (cutoff:3.500A) removed outlier: 6.589A pdb=" N HIS C 207 " --> pdb=" O ALA C 222 " (cutoff:3.500A) removed outlier: 8.803A pdb=" N ALA C 222 " --> pdb=" O HIS C 207 " (cutoff:3.500A) removed outlier: 6.871A pdb=" N VAL C 36 " --> pdb=" O LEU C 223 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 47 through 55 removed outlier: 3.954A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 84 through 85 removed outlier: 4.084A pdb=" N GLY C 103 " --> pdb=" O LEU C 241 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N PHE C 168 " --> pdb=" O VAL C 130 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 153 through 157 removed outlier: 3.587A pdb=" N SER C 155 " --> pdb=" O GLY C 142 " (cutoff:3.500A) removed outlier: 6.885A pdb=" N GLY C 142 " --> pdb=" O SER C 155 " (cutoff:3.500A) removed outlier: 6.356A pdb=" N LEU C 141 " --> pdb=" O LEU C 244 " (cutoff:3.500A) removed outlier: 7.328A pdb=" N ARG C 246 " --> pdb=" O LEU C 141 " (cutoff:3.500A) removed outlier: 7.440A pdb=" N VAL C 143 " --> pdb=" O ARG C 246 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 311 through 317 removed outlier: 5.378A pdb=" N ILE C 312 " --> pdb=" O THR C 599 " (cutoff:3.500A) removed outlier: 7.296A pdb=" N THR C 599 " --> pdb=" O ILE C 312 " (cutoff:3.500A) removed outlier: 5.698A pdb=" N GLN C 314 " --> pdb=" O VAL C 597 " (cutoff:3.500A) removed outlier: 6.482A pdb=" N VAL C 597 " --> pdb=" O GLN C 314 " (cutoff:3.500A) removed outlier: 4.219A pdb=" N GLY C 594 " --> pdb=" O GLN C 613 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 354 through 358 Processing sheet with id=AE6, first strand: chain 'C' and resid 361 through 362 removed outlier: 6.286A pdb=" N CYS C 361 " --> pdb=" O CYS C 525 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'C' and resid 448 through 454 removed outlier: 3.940A pdb=" N ASN C 450 " --> pdb=" O TYR C 495 " (cutoff:3.500A) removed outlier: 7.078A pdb=" N TYR C 495 " --> pdb=" O ASN C 450 " (cutoff:3.500A) removed outlier: 4.533A pdb=" N LEU C 452 " --> pdb=" O GLN C 493 " (cutoff:3.500A) removed outlier: 6.387A pdb=" N GLN C 493 " --> pdb=" O LEU C 452 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'C' and resid 473 through 474 Processing sheet with id=AE9, first strand: chain 'C' and resid 654 through 655 removed outlier: 6.014A pdb=" N GLU C 654 " --> pdb=" O ALA C 694 " (cutoff:3.500A) removed outlier: 8.635A pdb=" N THR C 696 " --> pdb=" O GLU C 654 " (cutoff:3.500A) removed outlier: 6.494A pdb=" N ALA C 672 " --> pdb=" O PRO C 665 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'C' and resid 711 through 715 removed outlier: 3.881A pdb=" N ALA C1078 " --> pdb=" O PHE C1095 " (cutoff:3.500A) removed outlier: 4.655A pdb=" N PHE C1095 " --> pdb=" O ALA C1078 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'C' and resid 718 through 728 removed outlier: 7.101A pdb=" N GLY C1059 " --> pdb=" O SER C1055 " (cutoff:3.500A) removed outlier: 5.167A pdb=" N SER C1055 " --> pdb=" O GLY C1059 " (cutoff:3.500A) removed outlier: 6.576A pdb=" N VAL C1061 " --> pdb=" O PRO C1053 " (cutoff:3.500A) removed outlier: 6.427A pdb=" N LEU C1063 " --> pdb=" O SER C1051 " (cutoff:3.500A) removed outlier: 4.327A pdb=" N SER C1051 " --> pdb=" O LEU C1063 " (cutoff:3.500A) removed outlier: 6.831A pdb=" N VAL C1065 " --> pdb=" O LEU C1049 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'C' and resid 735 through 736 removed outlier: 3.507A pdb=" N SER C 735 " --> pdb=" O THR C 859 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'C' and resid 1120 through 1125 removed outlier: 4.472A pdb=" N ALA C1087 " --> pdb=" O SER C1123 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'D' and resid 3 through 8 Processing sheet with id=AF6, first strand: chain 'D' and resid 10 through 13 removed outlier: 6.170A pdb=" N GLY D 10 " --> pdb=" O THR D 118 " (cutoff:3.500A) removed outlier: 7.707A pdb=" N SER D 120 " --> pdb=" O GLY D 10 " (cutoff:3.500A) removed outlier: 7.254A pdb=" N VAL D 12 " --> pdb=" O SER D 120 " (cutoff:3.500A) removed outlier: 6.977A pdb=" N ILE D 34 " --> pdb=" O ALA D 50 " (cutoff:3.500A) removed outlier: 4.824A pdb=" N ALA D 50 " --> pdb=" O ILE D 34 " (cutoff:3.500A) removed outlier: 6.546A pdb=" N TRP D 36 " --> pdb=" O VAL D 48 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'D' and resid 10 through 13 removed outlier: 6.170A pdb=" N GLY D 10 " --> pdb=" O THR D 118 " (cutoff:3.500A) removed outlier: 7.707A pdb=" N SER D 120 " --> pdb=" O GLY D 10 " (cutoff:3.500A) removed outlier: 7.254A pdb=" N VAL D 12 " --> pdb=" O SER D 120 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'E' and resid 3 through 8 Processing sheet with id=AF9, first strand: chain 'E' and resid 10 through 13 removed outlier: 6.128A pdb=" N GLY E 10 " --> pdb=" O THR E 118 " (cutoff:3.500A) removed outlier: 7.610A pdb=" N SER E 120 " --> pdb=" O GLY E 10 " (cutoff:3.500A) removed outlier: 7.043A pdb=" N VAL E 12 " --> pdb=" O SER E 120 " (cutoff:3.500A) removed outlier: 6.077A pdb=" N ARG E 38 " --> pdb=" O LEU E 47 " (cutoff:3.500A) removed outlier: 5.544A pdb=" N LEU E 47 " --> pdb=" O ARG E 38 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'E' and resid 10 through 13 removed outlier: 6.128A pdb=" N GLY E 10 " --> pdb=" O THR E 118 " (cutoff:3.500A) removed outlier: 7.610A pdb=" N SER E 120 " --> pdb=" O GLY E 10 " (cutoff:3.500A) removed outlier: 7.043A pdb=" N VAL E 12 " --> pdb=" O SER E 120 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'F' and resid 3 through 8 Processing sheet with id=AG3, first strand: chain 'F' and resid 10 through 13 removed outlier: 6.202A pdb=" N GLY F 10 " --> pdb=" O THR F 118 " (cutoff:3.500A) removed outlier: 7.789A pdb=" N SER F 120 " --> pdb=" O GLY F 10 " (cutoff:3.500A) removed outlier: 7.134A pdb=" N VAL F 12 " --> pdb=" O SER F 120 " (cutoff:3.500A) removed outlier: 5.923A pdb=" N ARG F 38 " --> pdb=" O LEU F 47 " (cutoff:3.500A) removed outlier: 5.374A pdb=" N LEU F 47 " --> pdb=" O ARG F 38 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'F' and resid 10 through 13 removed outlier: 6.202A pdb=" N GLY F 10 " --> pdb=" O THR F 118 " (cutoff:3.500A) removed outlier: 7.789A pdb=" N SER F 120 " --> pdb=" O GLY F 10 " (cutoff:3.500A) removed outlier: 7.134A pdb=" N VAL F 12 " --> pdb=" O SER F 120 " (cutoff:3.500A) 1184 hydrogen bonds defined for protein. 3126 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: 17.27 Time building geometry restraints manager: 8.35 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 9045 1.34 - 1.46: 5204 1.46 - 1.58: 14691 1.58 - 1.70: 0 1.70 - 1.82: 165 Bond restraints: 29105 Sorted by residual: bond pdb=" CE1 HIS C 625 " pdb=" NE2 HIS C 625 " ideal model delta sigma weight residual 1.321 1.363 -0.042 1.00e-02 1.00e+04 1.75e+01 bond pdb=" N PHE A 329 " pdb=" CA PHE A 329 " ideal model delta sigma weight residual 1.456 1.487 -0.031 8.70e-03 1.32e+04 1.28e+01 bond pdb=" N ILE A 332 " pdb=" CA ILE A 332 " ideal model delta sigma weight residual 1.459 1.498 -0.039 1.25e-02 6.40e+03 9.93e+00 bond pdb=" N ILE C 624 " pdb=" CA ILE C 624 " ideal model delta sigma weight residual 1.459 1.496 -0.037 1.25e-02 6.40e+03 8.69e+00 bond pdb=" N LEU A 335 " pdb=" CA LEU A 335 " ideal model delta sigma weight residual 1.453 1.492 -0.039 1.37e-02 5.33e+03 8.09e+00 ... (remaining 29100 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.35: 38661 1.35 - 2.69: 699 2.69 - 4.04: 232 4.04 - 5.39: 25 5.39 - 6.73: 8 Bond angle restraints: 39625 Sorted by residual: angle pdb=" N PRO C 621 " pdb=" CA PRO C 621 " pdb=" CB PRO C 621 " ideal model delta sigma weight residual 103.25 96.87 6.38 1.05e+00 9.07e-01 3.69e+01 angle pdb=" CA PRO C 621 " pdb=" N PRO C 621 " pdb=" CD PRO C 621 " ideal model delta sigma weight residual 112.00 105.42 6.58 1.40e+00 5.10e-01 2.21e+01 angle pdb=" CA ASN A 334 " pdb=" C ASN A 334 " pdb=" O ASN A 334 " ideal model delta sigma weight residual 122.01 117.46 4.55 1.05e+00 9.07e-01 1.88e+01 angle pdb=" N VAL C 860 " pdb=" CA VAL C 860 " pdb=" C VAL C 860 " ideal model delta sigma weight residual 106.42 112.31 -5.89 1.51e+00 4.39e-01 1.52e+01 angle pdb=" N GLU C 619 " pdb=" CA GLU C 619 " pdb=" C GLU C 619 " ideal model delta sigma weight residual 113.20 108.59 4.61 1.21e+00 6.83e-01 1.45e+01 ... (remaining 39620 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.95: 16032 17.95 - 35.90: 1066 35.90 - 53.85: 155 53.85 - 71.79: 42 71.79 - 89.74: 24 Dihedral angle restraints: 17319 sinusoidal: 6693 harmonic: 10626 Sorted by residual: dihedral pdb=" CB CYS A 291 " pdb=" SG CYS A 291 " pdb=" SG CYS A 301 " pdb=" CB CYS A 301 " ideal model delta sinusoidal sigma weight residual 93.00 -177.64 -89.36 1 1.00e+01 1.00e-02 9.49e+01 dihedral pdb=" CB CYS B 291 " pdb=" SG CYS B 291 " pdb=" SG CYS B 301 " pdb=" CB CYS B 301 " ideal model delta sinusoidal sigma weight residual 93.00 174.29 -81.29 1 1.00e+01 1.00e-02 8.15e+01 dihedral pdb=" CB CYS C 291 " pdb=" SG CYS C 291 " pdb=" SG CYS C 301 " pdb=" CB CYS C 301 " ideal model delta sinusoidal sigma weight residual 93.00 171.20 -78.20 1 1.00e+01 1.00e-02 7.64e+01 ... (remaining 17316 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.039: 3354 0.039 - 0.079: 721 0.079 - 0.118: 337 0.118 - 0.158: 82 0.158 - 0.197: 3 Chirality restraints: 4497 Sorted by residual: chirality pdb=" CA VAL C 622 " pdb=" N VAL C 622 " pdb=" C VAL C 622 " pdb=" CB VAL C 622 " both_signs ideal model delta sigma weight residual False 2.44 2.64 -0.20 2.00e-01 2.50e+01 9.70e-01 chirality pdb=" CA VAL C 635 " pdb=" N VAL C 635 " pdb=" C VAL C 635 " pdb=" CB VAL C 635 " both_signs ideal model delta sigma weight residual False 2.44 2.63 -0.19 2.00e-01 2.50e+01 9.08e-01 chirality pdb=" CA ILE B 203 " pdb=" N ILE B 203 " pdb=" C ILE B 203 " pdb=" CB ILE B 203 " both_signs ideal model delta sigma weight residual False 2.43 2.61 -0.18 2.00e-01 2.50e+01 8.21e-01 ... (remaining 4494 not shown) Planarity restraints: 5147 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG C 634 " -1.064 9.50e-02 1.11e+02 4.77e-01 1.37e+02 pdb=" NE ARG C 634 " 0.063 2.00e-02 2.50e+03 pdb=" CZ ARG C 634 " 0.015 2.00e-02 2.50e+03 pdb=" NH1 ARG C 634 " -0.009 2.00e-02 2.50e+03 pdb=" NH2 ARG C 634 " -0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LEU C 229 " 0.052 5.00e-02 4.00e+02 7.91e-02 1.00e+01 pdb=" N PRO C 230 " -0.137 5.00e-02 4.00e+02 pdb=" CA PRO C 230 " 0.042 5.00e-02 4.00e+02 pdb=" CD PRO C 230 " 0.044 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO B 862 " -0.042 5.00e-02 4.00e+02 6.37e-02 6.49e+00 pdb=" N PRO B 863 " 0.110 5.00e-02 4.00e+02 pdb=" CA PRO B 863 " -0.032 5.00e-02 4.00e+02 pdb=" CD PRO B 863 " -0.036 5.00e-02 4.00e+02 ... (remaining 5144 not shown) Histogram of nonbonded interaction distances: 1.93 - 2.52: 192 2.52 - 3.12: 22348 3.12 - 3.71: 43430 3.71 - 4.31: 62738 4.31 - 4.90: 105977 Nonbonded interactions: 234685 Sorted by model distance: nonbonded pdb=" OE1 GLN B 52 " pdb=" OG1 THR B 274 " model vdw 1.930 3.040 nonbonded pdb=" OG1 THR C1116 " pdb=" OD1 ASP C1118 " model vdw 1.958 3.040 nonbonded pdb=" O ARG C 246 " pdb=" OG1 THR C 250 " model vdw 1.991 3.040 nonbonded pdb=" OG1 THR A 618 " pdb=" OE1 GLU A 619 " model vdw 2.026 3.040 nonbonded pdb=" OG1 THR A 109 " pdb=" OD1 ASP A 111 " model vdw 2.051 3.040 ... (remaining 234680 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: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = (chain 'B' and (resid 15 through 320 or (resid 321 and (name N or name CA or nam \ e C or name O or name CB )) or resid 322 through 1147)) selection = (chain 'C' and (resid 15 through 320 or (resid 321 and (name N or name CA or nam \ e C or name O or name CB )) or resid 322 through 1147)) } ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'F' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic 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: 4.650 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 1.030 Check model and map are aligned: 0.210 Set scattering table: 0.300 Process input model: 72.860 Find NCS groups from input model: 1.350 Set up NCS constraints: 0.170 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:15.040 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 95.640 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7746 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 : 0.002 0.042 29143 Z= 0.138 Angle : 0.508 6.732 39701 Z= 0.295 Chirality : 0.043 0.197 4497 Planarity : 0.008 0.477 5147 Dihedral : 12.525 89.743 10389 Min Nonbonded Distance : 1.930 Molprobity Statistics. All-atom Clashscore : 6.47 Ramachandran Plot: Outliers : 0.41 % Allowed : 4.86 % Favored : 94.72 % Rotamer: Outliers : 0.32 % Allowed : 0.22 % Favored : 99.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.03 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.04 (0.14), residues: 3639 helix: 2.08 (0.21), residues: 711 sheet: 0.16 (0.17), residues: 872 loop : -0.78 (0.14), residues: 2056 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 64 HIS 0.004 0.000 HIS C 146 PHE 0.015 0.001 PHE C 342 TYR 0.021 0.001 TYR B 200 ARG 0.004 0.000 ARG C 634 Details of bonding type rmsd hydrogen bonds : bond 0.11628 ( 1166) hydrogen bonds : angle 6.57996 ( 3126) SS BOND : bond 0.00192 ( 38) SS BOND : angle 0.64164 ( 76) covalent geometry : bond 0.00236 (29105) covalent geometry : angle 0.50770 (39625) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7278 Ramachandran restraints generated. 3639 Oldfield, 0 Emsley, 3639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7278 Ramachandran restraints generated. 3639 Oldfield, 0 Emsley, 3639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 3171 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 172 time to evaluate : 3.263 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 330 PRO cc_start: 0.7346 (OUTLIER) cc_final: 0.7131 (Cg_endo) REVERT: A 902 MET cc_start: 0.9416 (tpp) cc_final: 0.9171 (mmt) REVERT: B 237 ARG cc_start: 0.8614 (mtp-110) cc_final: 0.7964 (ttp-110) REVERT: C 118 LEU cc_start: 0.7356 (tt) cc_final: 0.7072 (pt) REVERT: C 565 PHE cc_start: 0.7328 (m-80) cc_final: 0.6877 (m-10) REVERT: D 82 MET cc_start: 0.0216 (mpp) cc_final: -0.0045 (mpt) REVERT: F 101 MET cc_start: 0.2569 (mtt) cc_final: -0.0827 (ptp) outliers start: 10 outliers final: 2 residues processed: 182 average time/residue: 1.1253 time to fit residues: 250.8367 Evaluate side-chains 125 residues out of total 3171 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 122 time to evaluate : 3.088 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 330 PRO Chi-restraints excluded: chain C residue 632 THR Chi-restraints excluded: chain C residue 638 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 366 random chunks: chunk 309 optimal weight: 4.9990 chunk 277 optimal weight: 0.8980 chunk 153 optimal weight: 0.8980 chunk 94 optimal weight: 2.9990 chunk 187 optimal weight: 2.9990 chunk 148 optimal weight: 20.0000 chunk 286 optimal weight: 3.9990 chunk 111 optimal weight: 5.9990 chunk 174 optimal weight: 4.9990 chunk 213 optimal weight: 1.9990 chunk 332 optimal weight: 30.0000 overall best weight: 1.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 61 ASN ** A 992 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1119 ASN ** B 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 207 HIS ** B 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 616 ASN B 625 HIS ** B 675 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 717 ASN B1005 GLN C 61 ASN C 804 GLN C 969 ASN ** C1142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4477 r_free = 0.4477 target = 0.172368 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3477 r_free = 0.3477 target = 0.097141 restraints weight = 57856.265| |-----------------------------------------------------------------------------| r_work (start): 0.3199 rms_B_bonded: 3.33 r_work: 0.3024 rms_B_bonded: 3.42 restraints_weight: 0.5000 r_work: 0.2891 rms_B_bonded: 4.71 restraints_weight: 0.2500 r_work (final): 0.2891 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8308 moved from start: 0.1277 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.055 29143 Z= 0.262 Angle : 0.630 10.850 39701 Z= 0.334 Chirality : 0.048 0.255 4497 Planarity : 0.005 0.147 5147 Dihedral : 4.567 41.447 3947 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 4.29 Ramachandran Plot: Outliers : 0.27 % Allowed : 5.00 % Favored : 94.72 % Rotamer: Outliers : 1.17 % Allowed : 5.37 % Favored : 93.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.03 % Twisted Proline : 0.57 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.12 (0.14), residues: 3639 helix: 1.80 (0.20), residues: 709 sheet: 0.19 (0.17), residues: 861 loop : -0.88 (0.13), residues: 2069 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP B 258 HIS 0.012 0.001 HIS B 207 PHE 0.024 0.002 PHE C 906 TYR 0.024 0.002 TYR C1067 ARG 0.007 0.001 ARG C 190 Details of bonding type rmsd hydrogen bonds : bond 0.04706 ( 1166) hydrogen bonds : angle 5.73612 ( 3126) SS BOND : bond 0.00364 ( 38) SS BOND : angle 1.04463 ( 76) covalent geometry : bond 0.00614 (29105) covalent geometry : angle 0.62896 (39625) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7278 Ramachandran restraints generated. 3639 Oldfield, 0 Emsley, 3639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7278 Ramachandran restraints generated. 3639 Oldfield, 0 Emsley, 3639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 3171 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 137 time to evaluate : 2.826 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 200 TYR cc_start: 0.8523 (OUTLIER) cc_final: 0.8245 (t80) REVERT: B 237 ARG cc_start: 0.8884 (mtp-110) cc_final: 0.8209 (ttp-110) REVERT: C 153 MET cc_start: 0.7941 (pp-130) cc_final: 0.7658 (ppp) REVERT: C 189 LEU cc_start: 0.9155 (mt) cc_final: 0.8780 (mt) REVERT: C 565 PHE cc_start: 0.8024 (m-80) cc_final: 0.7731 (m-10) REVERT: C 634 ARG cc_start: 0.8149 (tpt170) cc_final: 0.7735 (tmt-80) REVERT: C 907 ASN cc_start: 0.9253 (OUTLIER) cc_final: 0.8697 (m-40) REVERT: C 985 ASP cc_start: 0.8109 (OUTLIER) cc_final: 0.7844 (p0) REVERT: D 82 MET cc_start: 0.0439 (mpp) cc_final: -0.0331 (pmm) outliers start: 37 outliers final: 14 residues processed: 163 average time/residue: 1.1672 time to fit residues: 232.9527 Evaluate side-chains 135 residues out of total 3171 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 118 time to evaluate : 2.842 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 200 TYR Chi-restraints excluded: chain A residue 216 LEU Chi-restraints excluded: chain A residue 957 GLN Chi-restraints excluded: chain A residue 964 LYS Chi-restraints excluded: chain B residue 200 TYR Chi-restraints excluded: chain B residue 216 LEU Chi-restraints excluded: chain C residue 45 SER Chi-restraints excluded: chain C residue 48 LEU Chi-restraints excluded: chain C residue 533 LEU Chi-restraints excluded: chain C residue 582 LEU Chi-restraints excluded: chain C residue 632 THR Chi-restraints excluded: chain C residue 638 THR Chi-restraints excluded: chain C residue 860 VAL Chi-restraints excluded: chain C residue 907 ASN Chi-restraints excluded: chain C residue 915 VAL Chi-restraints excluded: chain C residue 985 ASP Chi-restraints excluded: chain C residue 1092 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 366 random chunks: chunk 10 optimal weight: 10.0000 chunk 38 optimal weight: 9.9990 chunk 94 optimal weight: 0.6980 chunk 329 optimal weight: 0.9990 chunk 358 optimal weight: 0.2980 chunk 60 optimal weight: 3.9990 chunk 364 optimal weight: 20.0000 chunk 54 optimal weight: 0.8980 chunk 6 optimal weight: 7.9990 chunk 28 optimal weight: 0.8980 chunk 142 optimal weight: 0.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 188 ASN ** B 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 675 GLN B 955 ASN C 762 GLN C1142 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4498 r_free = 0.4498 target = 0.173414 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3573 r_free = 0.3573 target = 0.104221 restraints weight = 58841.923| |-----------------------------------------------------------------------------| r_work (start): 0.3283 rms_B_bonded: 3.08 r_work: 0.3123 rms_B_bonded: 3.49 restraints_weight: 0.5000 r_work: 0.2993 rms_B_bonded: 4.87 restraints_weight: 0.2500 r_work (final): 0.2993 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8027 moved from start: 0.1464 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 29143 Z= 0.137 Angle : 0.549 9.474 39701 Z= 0.291 Chirality : 0.044 0.195 4497 Planarity : 0.004 0.133 5147 Dihedral : 4.401 41.265 3944 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 4.36 Ramachandran Plot: Outliers : 0.27 % Allowed : 4.37 % Favored : 95.36 % Rotamer: Outliers : 1.11 % Allowed : 7.67 % Favored : 91.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.03 % Twisted Proline : 0.57 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.09 (0.14), residues: 3639 helix: 1.95 (0.20), residues: 712 sheet: 0.25 (0.17), residues: 873 loop : -0.94 (0.13), residues: 2054 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 258 HIS 0.004 0.001 HIS B 146 PHE 0.021 0.001 PHE B 133 TYR 0.020 0.001 TYR A 170 ARG 0.004 0.000 ARG C 634 Details of bonding type rmsd hydrogen bonds : bond 0.04048 ( 1166) hydrogen bonds : angle 5.46640 ( 3126) SS BOND : bond 0.00233 ( 38) SS BOND : angle 0.80610 ( 76) covalent geometry : bond 0.00308 (29105) covalent geometry : angle 0.54863 (39625) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7278 Ramachandran restraints generated. 3639 Oldfield, 0 Emsley, 3639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7278 Ramachandran restraints generated. 3639 Oldfield, 0 Emsley, 3639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 3171 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 131 time to evaluate : 2.930 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 200 TYR cc_start: 0.8401 (OUTLIER) cc_final: 0.8094 (t80) REVERT: A 855 PHE cc_start: 0.7703 (OUTLIER) cc_final: 0.7361 (m-80) REVERT: B 675 GLN cc_start: 0.8229 (OUTLIER) cc_final: 0.7883 (pp30) REVERT: C 189 LEU cc_start: 0.9194 (mt) cc_final: 0.8819 (mt) REVERT: C 565 PHE cc_start: 0.7938 (m-80) cc_final: 0.7715 (m-10) REVERT: C 634 ARG cc_start: 0.8354 (tpt170) cc_final: 0.7967 (tmt-80) REVERT: C 985 ASP cc_start: 0.7824 (OUTLIER) cc_final: 0.7602 (p0) REVERT: D 82 MET cc_start: 0.0287 (mpp) cc_final: -0.0182 (pmm) outliers start: 35 outliers final: 10 residues processed: 157 average time/residue: 1.0716 time to fit residues: 208.4628 Evaluate side-chains 133 residues out of total 3171 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 119 time to evaluate : 2.870 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 200 TYR Chi-restraints excluded: chain A residue 590 CYS Chi-restraints excluded: chain A residue 855 PHE Chi-restraints excluded: chain B residue 200 TYR Chi-restraints excluded: chain B residue 582 LEU Chi-restraints excluded: chain B residue 675 GLN Chi-restraints excluded: chain B residue 915 VAL Chi-restraints excluded: chain C residue 48 LEU Chi-restraints excluded: chain C residue 533 LEU Chi-restraints excluded: chain C residue 632 THR Chi-restraints excluded: chain C residue 638 THR Chi-restraints excluded: chain C residue 860 VAL Chi-restraints excluded: chain C residue 985 ASP Chi-restraints excluded: chain C residue 1092 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 366 random chunks: chunk 152 optimal weight: 8.9990 chunk 171 optimal weight: 3.9990 chunk 140 optimal weight: 1.9990 chunk 0 optimal weight: 20.0000 chunk 300 optimal weight: 4.9990 chunk 130 optimal weight: 6.9990 chunk 222 optimal weight: 6.9990 chunk 98 optimal weight: 0.7980 chunk 285 optimal weight: 1.9990 chunk 204 optimal weight: 0.9980 chunk 319 optimal weight: 2.9990 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 30 ASN A 282 ASN A 675 GLN A 690 GLN A 907 ASN ** A 992 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 196 ASN ** B 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 148 ASN C 935 GLN C 969 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4470 r_free = 0.4470 target = 0.171314 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.3453 r_free = 0.3453 target = 0.095567 restraints weight = 58125.516| |-----------------------------------------------------------------------------| r_work (start): 0.3177 rms_B_bonded: 3.37 r_work: 0.3009 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work: 0.2893 rms_B_bonded: 4.41 restraints_weight: 0.2500 r_work (final): 0.2893 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8259 moved from start: 0.1823 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.060 29143 Z= 0.237 Angle : 0.596 12.575 39701 Z= 0.315 Chirality : 0.046 0.233 4497 Planarity : 0.005 0.134 5147 Dihedral : 4.569 51.827 3944 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 5.53 Ramachandran Plot: Outliers : 0.25 % Allowed : 4.73 % Favored : 95.03 % Rotamer: Outliers : 1.74 % Allowed : 8.90 % Favored : 89.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.03 % Twisted Proline : 0.57 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.14 (0.14), residues: 3639 helix: 1.84 (0.20), residues: 700 sheet: 0.23 (0.17), residues: 859 loop : -0.93 (0.13), residues: 2080 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 152 HIS 0.004 0.001 HIS A 49 PHE 0.025 0.002 PHE A 168 TYR 0.021 0.001 TYR A1067 ARG 0.010 0.000 ARG A 237 Details of bonding type rmsd hydrogen bonds : bond 0.04452 ( 1166) hydrogen bonds : angle 5.52253 ( 3126) SS BOND : bond 0.00307 ( 38) SS BOND : angle 1.01086 ( 76) covalent geometry : bond 0.00550 (29105) covalent geometry : angle 0.59491 (39625) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7278 Ramachandran restraints generated. 3639 Oldfield, 0 Emsley, 3639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7278 Ramachandran restraints generated. 3639 Oldfield, 0 Emsley, 3639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 3171 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 126 time to evaluate : 3.021 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 200 TYR cc_start: 0.8484 (OUTLIER) cc_final: 0.8214 (t80) REVERT: A 239 GLN cc_start: 0.7470 (mm110) cc_final: 0.6866 (mm110) REVERT: B 237 ARG cc_start: 0.8878 (mtp-110) cc_final: 0.8612 (ptm160) REVERT: B 675 GLN cc_start: 0.8164 (pp30) cc_final: 0.7942 (pp30) REVERT: C 55 PHE cc_start: 0.7995 (m-80) cc_final: 0.7719 (m-80) REVERT: C 189 LEU cc_start: 0.9153 (mt) cc_final: 0.8882 (mt) REVERT: C 273 ARG cc_start: 0.6498 (mmt90) cc_final: 0.6140 (mmt90) REVERT: C 634 ARG cc_start: 0.8377 (tpt170) cc_final: 0.8061 (tmt-80) REVERT: C 740 MET cc_start: 0.9145 (ttp) cc_final: 0.8910 (ttm) REVERT: C 786 LYS cc_start: 0.8993 (OUTLIER) cc_final: 0.8783 (pmtt) REVERT: D 82 MET cc_start: 0.0088 (mpp) cc_final: -0.0464 (pmm) REVERT: E 101 MET cc_start: 0.2374 (ptm) cc_final: 0.1996 (ptp) REVERT: F 101 MET cc_start: 0.3422 (mtt) cc_final: 0.0147 (ptp) outliers start: 55 outliers final: 17 residues processed: 171 average time/residue: 1.0240 time to fit residues: 220.1215 Evaluate side-chains 140 residues out of total 3171 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 121 time to evaluate : 3.158 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 200 TYR Chi-restraints excluded: chain A residue 307 THR Chi-restraints excluded: chain A residue 590 CYS Chi-restraints excluded: chain A residue 632 THR Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 915 VAL Chi-restraints excluded: chain A residue 957 GLN Chi-restraints excluded: chain B residue 200 TYR Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 582 LEU Chi-restraints excluded: chain B residue 630 THR Chi-restraints excluded: chain B residue 915 VAL Chi-restraints excluded: chain C residue 45 SER Chi-restraints excluded: chain C residue 48 LEU Chi-restraints excluded: chain C residue 638 THR Chi-restraints excluded: chain C residue 786 LYS Chi-restraints excluded: chain C residue 860 VAL Chi-restraints excluded: chain C residue 915 VAL Chi-restraints excluded: chain C residue 1092 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 366 random chunks: chunk 267 optimal weight: 0.0980 chunk 177 optimal weight: 0.0040 chunk 302 optimal weight: 0.6980 chunk 24 optimal weight: 20.0000 chunk 184 optimal weight: 0.9990 chunk 2 optimal weight: 0.4980 chunk 140 optimal weight: 1.9990 chunk 170 optimal weight: 0.0870 chunk 82 optimal weight: 0.7980 chunk 35 optimal weight: 30.0000 chunk 282 optimal weight: 5.9990 overall best weight: 0.2770 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 675 GLN ** B 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 935 GLN C1119 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4497 r_free = 0.4497 target = 0.173552 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3586 r_free = 0.3586 target = 0.103735 restraints weight = 58216.649| |-----------------------------------------------------------------------------| r_work (start): 0.3258 rms_B_bonded: 3.81 r_work: 0.3052 rms_B_bonded: 3.64 restraints_weight: 0.5000 r_work (final): 0.3052 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8078 moved from start: 0.1879 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.053 29143 Z= 0.106 Angle : 0.535 12.135 39701 Z= 0.282 Chirality : 0.044 0.202 4497 Planarity : 0.004 0.130 5147 Dihedral : 4.302 39.953 3943 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 5.44 Ramachandran Plot: Outliers : 0.22 % Allowed : 4.34 % Favored : 95.44 % Rotamer: Outliers : 1.23 % Allowed : 10.20 % Favored : 88.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.03 % Twisted Proline : 0.57 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.04 (0.14), residues: 3639 helix: 1.94 (0.20), residues: 715 sheet: 0.33 (0.17), residues: 858 loop : -0.91 (0.13), residues: 2066 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 104 HIS 0.005 0.001 HIS A 146 PHE 0.027 0.001 PHE A 168 TYR 0.019 0.001 TYR B 160 ARG 0.005 0.000 ARG A 237 Details of bonding type rmsd hydrogen bonds : bond 0.03678 ( 1166) hydrogen bonds : angle 5.25072 ( 3126) SS BOND : bond 0.00406 ( 38) SS BOND : angle 0.74701 ( 76) covalent geometry : bond 0.00231 (29105) covalent geometry : angle 0.53458 (39625) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7278 Ramachandran restraints generated. 3639 Oldfield, 0 Emsley, 3639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7278 Ramachandran restraints generated. 3639 Oldfield, 0 Emsley, 3639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 3171 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 137 time to evaluate : 2.884 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 52 GLN cc_start: 0.8958 (tm-30) cc_final: 0.8476 (tm-30) REVERT: A 200 TYR cc_start: 0.8519 (OUTLIER) cc_final: 0.8192 (t80) REVERT: A 239 GLN cc_start: 0.7366 (mm110) cc_final: 0.6329 (mp10) REVERT: A 855 PHE cc_start: 0.7563 (OUTLIER) cc_final: 0.7172 (m-80) REVERT: B 129 LYS cc_start: 0.8935 (mtmm) cc_final: 0.8717 (tttp) REVERT: B 133 PHE cc_start: 0.7742 (m-10) cc_final: 0.6743 (m-10) REVERT: B 675 GLN cc_start: 0.8094 (pp30) cc_final: 0.7817 (pp30) REVERT: B 762 GLN cc_start: 0.8857 (mt0) cc_final: 0.8538 (mt0) REVERT: C 55 PHE cc_start: 0.7935 (m-80) cc_final: 0.7692 (m-80) REVERT: C 118 LEU cc_start: 0.6931 (OUTLIER) cc_final: 0.6591 (pp) REVERT: C 189 LEU cc_start: 0.9179 (mt) cc_final: 0.8937 (mt) REVERT: C 273 ARG cc_start: 0.6404 (mmt90) cc_final: 0.6161 (mmt90) REVERT: C 568 ASP cc_start: 0.8531 (t0) cc_final: 0.8261 (t0) REVERT: C 634 ARG cc_start: 0.8161 (tpt170) cc_final: 0.7771 (tmt-80) REVERT: C 740 MET cc_start: 0.8849 (ttp) cc_final: 0.8619 (ttm) REVERT: C 786 LYS cc_start: 0.8810 (OUTLIER) cc_final: 0.8501 (pmtt) REVERT: D 82 MET cc_start: 0.0294 (mpp) cc_final: -0.0187 (pmm) REVERT: D 101 MET cc_start: 0.7253 (mpt) cc_final: 0.7048 (mmp) REVERT: F 101 MET cc_start: 0.3102 (mtt) cc_final: 0.0329 (ptp) outliers start: 39 outliers final: 16 residues processed: 164 average time/residue: 1.0648 time to fit residues: 218.0392 Evaluate side-chains 145 residues out of total 3171 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 125 time to evaluate : 3.216 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 200 TYR Chi-restraints excluded: chain A residue 547 THR Chi-restraints excluded: chain A residue 590 CYS Chi-restraints excluded: chain A residue 632 THR Chi-restraints excluded: chain A residue 855 PHE Chi-restraints excluded: chain A residue 957 GLN Chi-restraints excluded: chain B residue 179 LEU Chi-restraints excluded: chain B residue 200 TYR Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain C residue 48 LEU Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 533 LEU Chi-restraints excluded: chain C residue 582 LEU Chi-restraints excluded: chain C residue 632 THR Chi-restraints excluded: chain C residue 786 LYS Chi-restraints excluded: chain C residue 860 VAL Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain C residue 1092 GLU Chi-restraints excluded: chain D residue 102 THR Chi-restraints excluded: chain E residue 102 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 366 random chunks: chunk 136 optimal weight: 4.9990 chunk 274 optimal weight: 1.9990 chunk 361 optimal weight: 6.9990 chunk 237 optimal weight: 0.9990 chunk 33 optimal weight: 50.0000 chunk 182 optimal weight: 3.9990 chunk 28 optimal weight: 0.5980 chunk 25 optimal weight: 2.9990 chunk 60 optimal weight: 3.9990 chunk 114 optimal weight: 4.9990 chunk 74 optimal weight: 1.9990 overall best weight: 1.7188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 992 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 564 GLN C 239 GLN C 935 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4469 r_free = 0.4469 target = 0.171207 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.095483 restraints weight = 58256.397| |-----------------------------------------------------------------------------| r_work (start): 0.3178 rms_B_bonded: 3.25 r_work: 0.3031 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work (final): 0.3031 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8149 moved from start: 0.2107 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.061 29143 Z= 0.231 Angle : 0.577 12.163 39701 Z= 0.304 Chirality : 0.045 0.218 4497 Planarity : 0.004 0.137 5147 Dihedral : 4.391 42.009 3942 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 5.67 Ramachandran Plot: Outliers : 0.25 % Allowed : 4.70 % Favored : 95.05 % Rotamer: Outliers : 1.45 % Allowed : 10.83 % Favored : 87.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.03 % Twisted Proline : 0.57 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.10 (0.14), residues: 3639 helix: 1.79 (0.20), residues: 719 sheet: 0.40 (0.18), residues: 795 loop : -0.94 (0.13), residues: 2125 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 104 HIS 0.003 0.001 HIS A 49 PHE 0.021 0.001 PHE B 168 TYR 0.021 0.001 TYR A1067 ARG 0.005 0.000 ARG C 905 Details of bonding type rmsd hydrogen bonds : bond 0.04280 ( 1166) hydrogen bonds : angle 5.39918 ( 3126) SS BOND : bond 0.00375 ( 38) SS BOND : angle 0.99803 ( 76) covalent geometry : bond 0.00540 (29105) covalent geometry : angle 0.57590 (39625) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7278 Ramachandran restraints generated. 3639 Oldfield, 0 Emsley, 3639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7278 Ramachandran restraints generated. 3639 Oldfield, 0 Emsley, 3639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 3171 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 128 time to evaluate : 2.939 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 52 GLN cc_start: 0.8896 (tm-30) cc_final: 0.8464 (tm-30) REVERT: A 200 TYR cc_start: 0.8342 (OUTLIER) cc_final: 0.8084 (t80) REVERT: A 239 GLN cc_start: 0.7463 (mm110) cc_final: 0.6503 (mp10) REVERT: B 237 ARG cc_start: 0.8812 (mtp-110) cc_final: 0.8286 (ttp-110) REVERT: B 675 GLN cc_start: 0.8141 (pp30) cc_final: 0.7931 (pp30) REVERT: C 55 PHE cc_start: 0.7935 (m-80) cc_final: 0.7727 (m-80) REVERT: C 118 LEU cc_start: 0.6923 (OUTLIER) cc_final: 0.6565 (pp) REVERT: C 153 MET cc_start: 0.8186 (pp-130) cc_final: 0.7880 (pp-130) REVERT: C 189 LEU cc_start: 0.9114 (mt) cc_final: 0.8866 (mt) REVERT: C 273 ARG cc_start: 0.6593 (mmt90) cc_final: 0.6328 (mmt90) REVERT: C 634 ARG cc_start: 0.8203 (tpt170) cc_final: 0.7848 (tmt-80) REVERT: C 740 MET cc_start: 0.9030 (ttp) cc_final: 0.8785 (ttm) REVERT: C 786 LYS cc_start: 0.8837 (OUTLIER) cc_final: 0.8634 (pmtt) REVERT: D 82 MET cc_start: 0.0615 (mpp) cc_final: 0.0071 (pmm) REVERT: F 101 MET cc_start: 0.3214 (mtt) cc_final: 0.0102 (ptp) outliers start: 46 outliers final: 24 residues processed: 163 average time/residue: 1.0614 time to fit residues: 214.9877 Evaluate side-chains 148 residues out of total 3171 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 121 time to evaluate : 2.840 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 83 VAL Chi-restraints excluded: chain A residue 200 TYR Chi-restraints excluded: chain A residue 307 THR Chi-restraints excluded: chain A residue 547 THR Chi-restraints excluded: chain A residue 590 CYS Chi-restraints excluded: chain A residue 632 THR Chi-restraints excluded: chain A residue 957 GLN Chi-restraints excluded: chain B residue 179 LEU Chi-restraints excluded: chain B residue 200 TYR Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 362 VAL Chi-restraints excluded: chain B residue 582 LEU Chi-restraints excluded: chain B residue 630 THR Chi-restraints excluded: chain B residue 858 LEU Chi-restraints excluded: chain B residue 915 VAL Chi-restraints excluded: chain C residue 48 LEU Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 632 THR Chi-restraints excluded: chain C residue 638 THR Chi-restraints excluded: chain C residue 732 THR Chi-restraints excluded: chain C residue 786 LYS Chi-restraints excluded: chain C residue 860 VAL Chi-restraints excluded: chain C residue 907 ASN Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain C residue 1092 GLU Chi-restraints excluded: chain D residue 102 THR Chi-restraints excluded: chain E residue 102 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 366 random chunks: chunk 33 optimal weight: 40.0000 chunk 250 optimal weight: 0.8980 chunk 210 optimal weight: 1.9990 chunk 326 optimal weight: 0.6980 chunk 187 optimal weight: 0.7980 chunk 334 optimal weight: 0.9980 chunk 235 optimal weight: 0.0870 chunk 300 optimal weight: 4.9990 chunk 346 optimal weight: 0.8980 chunk 222 optimal weight: 6.9990 chunk 299 optimal weight: 1.9990 overall best weight: 0.6758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 675 GLN ** A 992 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 935 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4485 r_free = 0.4485 target = 0.172508 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3525 r_free = 0.3525 target = 0.101466 restraints weight = 57921.436| |-----------------------------------------------------------------------------| r_work (start): 0.3220 rms_B_bonded: 3.26 r_work: 0.3051 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work: 0.2902 rms_B_bonded: 4.94 restraints_weight: 0.2500 r_work (final): 0.2902 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8177 moved from start: 0.2149 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 29143 Z= 0.126 Angle : 0.541 12.605 39701 Z= 0.283 Chirality : 0.044 0.243 4497 Planarity : 0.004 0.136 5147 Dihedral : 4.278 40.269 3942 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 5.51 Ramachandran Plot: Outliers : 0.25 % Allowed : 4.45 % Favored : 95.30 % Rotamer: Outliers : 1.23 % Allowed : 11.46 % Favored : 87.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.03 % Twisted Proline : 0.57 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.07 (0.14), residues: 3639 helix: 1.80 (0.20), residues: 728 sheet: 0.47 (0.18), residues: 804 loop : -0.96 (0.13), residues: 2107 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP C 104 HIS 0.002 0.000 HIS B 146 PHE 0.031 0.001 PHE A 168 TYR 0.018 0.001 TYR B 265 ARG 0.003 0.000 ARG A 78 Details of bonding type rmsd hydrogen bonds : bond 0.03770 ( 1166) hydrogen bonds : angle 5.22194 ( 3126) SS BOND : bond 0.00202 ( 38) SS BOND : angle 1.38068 ( 76) covalent geometry : bond 0.00285 (29105) covalent geometry : angle 0.53786 (39625) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7278 Ramachandran restraints generated. 3639 Oldfield, 0 Emsley, 3639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7278 Ramachandran restraints generated. 3639 Oldfield, 0 Emsley, 3639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 3171 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 132 time to evaluate : 2.879 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 52 GLN cc_start: 0.8953 (tm-30) cc_final: 0.8501 (tm-30) REVERT: A 200 TYR cc_start: 0.8618 (OUTLIER) cc_final: 0.8317 (t80) REVERT: A 239 GLN cc_start: 0.7388 (mm110) cc_final: 0.6398 (mp10) REVERT: B 129 LYS cc_start: 0.8855 (mtmm) cc_final: 0.8568 (tttp) REVERT: B 675 GLN cc_start: 0.8191 (pp30) cc_final: 0.7970 (pp30) REVERT: B 762 GLN cc_start: 0.9051 (mt0) cc_final: 0.8725 (mt0) REVERT: C 55 PHE cc_start: 0.8124 (m-80) cc_final: 0.7845 (m-80) REVERT: C 118 LEU cc_start: 0.6655 (OUTLIER) cc_final: 0.6336 (pp) REVERT: C 153 MET cc_start: 0.8019 (pp-130) cc_final: 0.7755 (pp-130) REVERT: C 189 LEU cc_start: 0.9235 (OUTLIER) cc_final: 0.9024 (mt) REVERT: C 273 ARG cc_start: 0.6424 (mmt90) cc_final: 0.6218 (mmt90) REVERT: C 634 ARG cc_start: 0.8216 (tpt170) cc_final: 0.7829 (tmt-80) REVERT: C 786 LYS cc_start: 0.8994 (OUTLIER) cc_final: 0.8735 (pmtt) REVERT: D 82 MET cc_start: 0.0889 (mpp) cc_final: 0.0366 (pmm) REVERT: F 101 MET cc_start: 0.3298 (mtt) cc_final: 0.0103 (ptp) outliers start: 39 outliers final: 22 residues processed: 156 average time/residue: 1.0260 time to fit residues: 200.0453 Evaluate side-chains 152 residues out of total 3171 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 126 time to evaluate : 2.875 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 200 TYR Chi-restraints excluded: chain A residue 547 THR Chi-restraints excluded: chain A residue 590 CYS Chi-restraints excluded: chain A residue 632 THR Chi-restraints excluded: chain A residue 957 GLN Chi-restraints excluded: chain B residue 179 LEU Chi-restraints excluded: chain B residue 200 TYR Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 362 VAL Chi-restraints excluded: chain B residue 532 ASN Chi-restraints excluded: chain B residue 629 LEU Chi-restraints excluded: chain B residue 630 THR Chi-restraints excluded: chain B residue 858 LEU Chi-restraints excluded: chain B residue 915 VAL Chi-restraints excluded: chain C residue 48 LEU Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 171 VAL Chi-restraints excluded: chain C residue 189 LEU Chi-restraints excluded: chain C residue 226 LEU Chi-restraints excluded: chain C residue 533 LEU Chi-restraints excluded: chain C residue 632 THR Chi-restraints excluded: chain C residue 786 LYS Chi-restraints excluded: chain C residue 860 VAL Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain C residue 1092 GLU Chi-restraints excluded: chain D residue 102 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 366 random chunks: chunk 212 optimal weight: 0.8980 chunk 177 optimal weight: 4.9990 chunk 261 optimal weight: 30.0000 chunk 140 optimal weight: 0.6980 chunk 253 optimal weight: 50.0000 chunk 25 optimal weight: 2.9990 chunk 59 optimal weight: 0.8980 chunk 36 optimal weight: 40.0000 chunk 5 optimal weight: 1.9990 chunk 310 optimal weight: 2.9990 chunk 332 optimal weight: 7.9990 overall best weight: 1.4984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 331 ASN A 675 GLN ** A 992 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 580 GLN C 935 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4469 r_free = 0.4469 target = 0.171127 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3476 r_free = 0.3476 target = 0.096138 restraints weight = 58046.863| |-----------------------------------------------------------------------------| r_work (start): 0.3186 rms_B_bonded: 3.37 r_work: 0.3023 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work: 0.2887 rms_B_bonded: 4.61 restraints_weight: 0.2500 r_work (final): 0.2887 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8280 moved from start: 0.2312 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.070 29143 Z= 0.206 Angle : 0.576 12.603 39701 Z= 0.303 Chirality : 0.045 0.246 4497 Planarity : 0.004 0.138 5147 Dihedral : 4.370 40.298 3942 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 6.22 Ramachandran Plot: Outliers : 0.25 % Allowed : 4.86 % Favored : 94.89 % Rotamer: Outliers : 1.20 % Allowed : 11.81 % Favored : 86.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.03 % Twisted Proline : 0.57 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.14 (0.14), residues: 3639 helix: 1.69 (0.20), residues: 729 sheet: 0.38 (0.17), residues: 798 loop : -0.95 (0.13), residues: 2112 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 104 HIS 0.003 0.001 HIS A 49 PHE 0.023 0.001 PHE B 168 TYR 0.020 0.001 TYR A1067 ARG 0.004 0.000 ARG A 78 Details of bonding type rmsd hydrogen bonds : bond 0.04165 ( 1166) hydrogen bonds : angle 5.32693 ( 3126) SS BOND : bond 0.00263 ( 38) SS BOND : angle 1.73362 ( 76) covalent geometry : bond 0.00480 (29105) covalent geometry : angle 0.57113 (39625) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7278 Ramachandran restraints generated. 3639 Oldfield, 0 Emsley, 3639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7278 Ramachandran restraints generated. 3639 Oldfield, 0 Emsley, 3639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 3171 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 125 time to evaluate : 3.083 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 52 GLN cc_start: 0.9003 (tm-30) cc_final: 0.8587 (tm-30) REVERT: A 177 MET cc_start: 0.0435 (OUTLIER) cc_final: -0.0167 (pmm) REVERT: A 200 TYR cc_start: 0.8491 (OUTLIER) cc_final: 0.8182 (t80) REVERT: A 239 GLN cc_start: 0.7490 (mm110) cc_final: 0.6560 (mp10) REVERT: B 237 ARG cc_start: 0.8757 (mtp-110) cc_final: 0.7988 (ttp-110) REVERT: B 675 GLN cc_start: 0.8273 (pp30) cc_final: 0.8047 (pp30) REVERT: B 762 GLN cc_start: 0.8989 (mt0) cc_final: 0.8648 (mt0) REVERT: C 55 PHE cc_start: 0.8116 (m-80) cc_final: 0.7857 (m-80) REVERT: C 118 LEU cc_start: 0.6594 (OUTLIER) cc_final: 0.6228 (pp) REVERT: C 153 MET cc_start: 0.8031 (pp-130) cc_final: 0.7791 (pp-130) REVERT: C 634 ARG cc_start: 0.8138 (tpt170) cc_final: 0.7839 (tmt-80) REVERT: D 82 MET cc_start: 0.0916 (mpp) cc_final: 0.0386 (pmm) REVERT: E 101 MET cc_start: 0.2729 (ptm) cc_final: 0.1957 (mpp) REVERT: F 101 MET cc_start: 0.3773 (mtt) cc_final: 0.0527 (ptp) outliers start: 38 outliers final: 27 residues processed: 153 average time/residue: 1.0402 time to fit residues: 198.3325 Evaluate side-chains 155 residues out of total 3171 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 125 time to evaluate : 2.884 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 177 MET Chi-restraints excluded: chain A residue 200 TYR Chi-restraints excluded: chain A residue 547 THR Chi-restraints excluded: chain A residue 590 CYS Chi-restraints excluded: chain A residue 632 THR Chi-restraints excluded: chain A residue 915 VAL Chi-restraints excluded: chain A residue 957 GLN Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 179 LEU Chi-restraints excluded: chain B residue 200 TYR Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 362 VAL Chi-restraints excluded: chain B residue 582 LEU Chi-restraints excluded: chain B residue 630 THR Chi-restraints excluded: chain B residue 858 LEU Chi-restraints excluded: chain B residue 915 VAL Chi-restraints excluded: chain C residue 48 LEU Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 171 VAL Chi-restraints excluded: chain C residue 533 LEU Chi-restraints excluded: chain C residue 534 VAL Chi-restraints excluded: chain C residue 632 THR Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 860 VAL Chi-restraints excluded: chain C residue 915 VAL Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain C residue 1136 THR Chi-restraints excluded: chain D residue 102 THR Chi-restraints excluded: chain E residue 102 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 366 random chunks: chunk 283 optimal weight: 0.6980 chunk 350 optimal weight: 6.9990 chunk 72 optimal weight: 3.9990 chunk 99 optimal weight: 1.9990 chunk 58 optimal weight: 1.9990 chunk 15 optimal weight: 7.9990 chunk 119 optimal weight: 7.9990 chunk 196 optimal weight: 0.9990 chunk 191 optimal weight: 0.6980 chunk 176 optimal weight: 2.9990 chunk 52 optimal weight: 1.9990 overall best weight: 1.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 992 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 388 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4472 r_free = 0.4472 target = 0.171403 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3533 r_free = 0.3533 target = 0.100668 restraints weight = 57710.740| |-----------------------------------------------------------------------------| r_work (start): 0.3187 rms_B_bonded: 3.74 r_work: 0.2995 rms_B_bonded: 3.50 restraints_weight: 0.5000 r_work (final): 0.2995 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8113 moved from start: 0.2406 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 29143 Z= 0.181 Angle : 0.564 12.394 39701 Z= 0.297 Chirality : 0.045 0.238 4497 Planarity : 0.004 0.139 5147 Dihedral : 4.366 39.804 3942 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 6.28 Ramachandran Plot: Outliers : 0.25 % Allowed : 4.64 % Favored : 95.11 % Rotamer: Outliers : 1.29 % Allowed : 11.84 % Favored : 86.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.03 % Twisted Proline : 0.57 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.15 (0.14), residues: 3639 helix: 1.72 (0.20), residues: 722 sheet: 0.35 (0.18), residues: 804 loop : -0.95 (0.13), residues: 2113 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP C 104 HIS 0.003 0.001 HIS C1083 PHE 0.029 0.001 PHE A 168 TYR 0.019 0.001 TYR A1067 ARG 0.007 0.000 ARG D 71 Details of bonding type rmsd hydrogen bonds : bond 0.04042 ( 1166) hydrogen bonds : angle 5.27680 ( 3126) SS BOND : bond 0.00268 ( 38) SS BOND : angle 1.42830 ( 76) covalent geometry : bond 0.00418 (29105) covalent geometry : angle 0.56125 (39625) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7278 Ramachandran restraints generated. 3639 Oldfield, 0 Emsley, 3639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7278 Ramachandran restraints generated. 3639 Oldfield, 0 Emsley, 3639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 3171 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 128 time to evaluate : 2.856 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 52 GLN cc_start: 0.8936 (tm-30) cc_final: 0.8479 (tm-30) REVERT: A 177 MET cc_start: 0.0433 (OUTLIER) cc_final: -0.0167 (pmm) REVERT: A 200 TYR cc_start: 0.8500 (OUTLIER) cc_final: 0.8168 (t80) REVERT: A 239 GLN cc_start: 0.7353 (mm110) cc_final: 0.6424 (mp10) REVERT: B 133 PHE cc_start: 0.7732 (m-10) cc_final: 0.6826 (m-10) REVERT: B 762 GLN cc_start: 0.8908 (mt0) cc_final: 0.8554 (mt0) REVERT: C 55 PHE cc_start: 0.8109 (m-80) cc_final: 0.7841 (m-80) REVERT: C 118 LEU cc_start: 0.6354 (OUTLIER) cc_final: 0.6039 (pp) REVERT: C 153 MET cc_start: 0.8025 (pp-130) cc_final: 0.7796 (pp-130) REVERT: C 189 LEU cc_start: 0.9180 (tp) cc_final: 0.8938 (mt) REVERT: C 190 ARG cc_start: 0.7745 (ptm-80) cc_final: 0.7037 (ptp90) REVERT: C 634 ARG cc_start: 0.8006 (tpt170) cc_final: 0.7548 (tmt-80) REVERT: C 860 VAL cc_start: 0.7875 (OUTLIER) cc_final: 0.7650 (p) REVERT: D 82 MET cc_start: 0.0856 (mpp) cc_final: 0.0344 (pmm) REVERT: E 101 MET cc_start: 0.2284 (ptm) cc_final: 0.1577 (mpp) REVERT: F 101 MET cc_start: 0.2626 (mtt) cc_final: -0.0606 (ptp) outliers start: 41 outliers final: 28 residues processed: 159 average time/residue: 1.0880 time to fit residues: 215.0394 Evaluate side-chains 155 residues out of total 3171 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 123 time to evaluate : 3.229 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 177 MET Chi-restraints excluded: chain A residue 200 TYR Chi-restraints excluded: chain A residue 547 THR Chi-restraints excluded: chain A residue 590 CYS Chi-restraints excluded: chain A residue 632 THR Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 915 VAL Chi-restraints excluded: chain A residue 957 GLN Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 200 TYR Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 362 VAL Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 582 LEU Chi-restraints excluded: chain B residue 630 THR Chi-restraints excluded: chain B residue 858 LEU Chi-restraints excluded: chain B residue 915 VAL Chi-restraints excluded: chain C residue 48 LEU Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 171 VAL Chi-restraints excluded: chain C residue 533 LEU Chi-restraints excluded: chain C residue 534 VAL Chi-restraints excluded: chain C residue 632 THR Chi-restraints excluded: chain C residue 732 THR Chi-restraints excluded: chain C residue 786 LYS Chi-restraints excluded: chain C residue 860 VAL Chi-restraints excluded: chain C residue 911 VAL Chi-restraints excluded: chain C residue 915 VAL Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain D residue 102 THR Chi-restraints excluded: chain E residue 102 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 366 random chunks: chunk 86 optimal weight: 0.5980 chunk 179 optimal weight: 0.6980 chunk 21 optimal weight: 5.9990 chunk 60 optimal weight: 0.5980 chunk 318 optimal weight: 0.9980 chunk 154 optimal weight: 0.8980 chunk 97 optimal weight: 0.8980 chunk 99 optimal weight: 1.9990 chunk 91 optimal weight: 2.9990 chunk 78 optimal weight: 1.9990 chunk 209 optimal weight: 0.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 992 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 675 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4481 r_free = 0.4481 target = 0.172093 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3540 r_free = 0.3540 target = 0.101087 restraints weight = 57848.013| |-----------------------------------------------------------------------------| r_work (start): 0.3208 rms_B_bonded: 3.44 r_work: 0.3049 rms_B_bonded: 3.28 restraints_weight: 0.5000 r_work (final): 0.3049 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8069 moved from start: 0.2453 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 29143 Z= 0.132 Angle : 0.551 12.210 39701 Z= 0.288 Chirality : 0.044 0.237 4497 Planarity : 0.004 0.138 5147 Dihedral : 4.287 39.188 3942 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 6.49 Ramachandran Plot: Outliers : 0.22 % Allowed : 4.73 % Favored : 95.05 % Rotamer: Outliers : 1.23 % Allowed : 12.09 % Favored : 86.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.03 % Twisted Proline : 0.57 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.09 (0.14), residues: 3639 helix: 1.81 (0.20), residues: 722 sheet: 0.37 (0.17), residues: 816 loop : -0.93 (0.13), residues: 2101 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRP C 104 HIS 0.002 0.000 HIS C1083 PHE 0.026 0.001 PHE B 133 TYR 0.019 0.001 TYR B 265 ARG 0.014 0.000 ARG A 319 Details of bonding type rmsd hydrogen bonds : bond 0.03794 ( 1166) hydrogen bonds : angle 5.16861 ( 3126) SS BOND : bond 0.00207 ( 38) SS BOND : angle 1.21998 ( 76) covalent geometry : bond 0.00302 (29105) covalent geometry : angle 0.54865 (39625) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7278 Ramachandran restraints generated. 3639 Oldfield, 0 Emsley, 3639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7278 Ramachandran restraints generated. 3639 Oldfield, 0 Emsley, 3639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 3171 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 124 time to evaluate : 3.519 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 52 GLN cc_start: 0.8894 (tm-30) cc_final: 0.8403 (tm-30) REVERT: A 177 MET cc_start: 0.1081 (OUTLIER) cc_final: 0.0643 (pmm) REVERT: A 200 TYR cc_start: 0.8393 (OUTLIER) cc_final: 0.8073 (t80) REVERT: A 239 GLN cc_start: 0.7419 (mm110) cc_final: 0.6450 (mp10) REVERT: A 675 GLN cc_start: 0.7810 (tp-100) cc_final: 0.7207 (pp30) REVERT: B 762 GLN cc_start: 0.8903 (mt0) cc_final: 0.8561 (mt0) REVERT: B 964 LYS cc_start: 0.9170 (ttmm) cc_final: 0.8868 (ttpt) REVERT: C 55 PHE cc_start: 0.8106 (m-80) cc_final: 0.7836 (m-80) REVERT: C 118 LEU cc_start: 0.6378 (OUTLIER) cc_final: 0.6053 (pp) REVERT: C 153 MET cc_start: 0.8005 (pp-130) cc_final: 0.7783 (pp-130) REVERT: C 189 LEU cc_start: 0.9115 (tp) cc_final: 0.8872 (mt) REVERT: C 190 ARG cc_start: 0.7725 (ptm-80) cc_final: 0.7031 (ptp90) REVERT: C 860 VAL cc_start: 0.7813 (OUTLIER) cc_final: 0.7590 (p) REVERT: C 979 ASP cc_start: 0.8214 (m-30) cc_final: 0.7975 (t0) REVERT: D 82 MET cc_start: 0.0823 (mpp) cc_final: 0.0318 (pmm) REVERT: E 101 MET cc_start: 0.2194 (ptm) cc_final: 0.1467 (mpp) REVERT: F 101 MET cc_start: 0.2440 (mtt) cc_final: -0.1029 (ptp) outliers start: 39 outliers final: 31 residues processed: 155 average time/residue: 0.9324 time to fit residues: 184.0674 Evaluate side-chains 158 residues out of total 3171 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 123 time to evaluate : 2.773 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 177 MET Chi-restraints excluded: chain A residue 200 TYR Chi-restraints excluded: chain A residue 483 VAL Chi-restraints excluded: chain A residue 547 THR Chi-restraints excluded: chain A residue 590 CYS Chi-restraints excluded: chain A residue 632 THR Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 915 VAL Chi-restraints excluded: chain A residue 957 GLN Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain B residue 200 TYR Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 362 VAL Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 582 LEU Chi-restraints excluded: chain B residue 629 LEU Chi-restraints excluded: chain B residue 630 THR Chi-restraints excluded: chain B residue 858 LEU Chi-restraints excluded: chain B residue 915 VAL Chi-restraints excluded: chain C residue 48 LEU Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 171 VAL Chi-restraints excluded: chain C residue 362 VAL Chi-restraints excluded: chain C residue 533 LEU Chi-restraints excluded: chain C residue 534 VAL Chi-restraints excluded: chain C residue 632 THR Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 732 THR Chi-restraints excluded: chain C residue 786 LYS Chi-restraints excluded: chain C residue 860 VAL Chi-restraints excluded: chain C residue 915 VAL Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain D residue 102 THR Chi-restraints excluded: chain E residue 102 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 366 random chunks: chunk 69 optimal weight: 1.9990 chunk 326 optimal weight: 0.6980 chunk 321 optimal weight: 2.9990 chunk 100 optimal weight: 0.9980 chunk 312 optimal weight: 0.5980 chunk 92 optimal weight: 2.9990 chunk 207 optimal weight: 0.5980 chunk 96 optimal weight: 1.9990 chunk 352 optimal weight: 4.9990 chunk 347 optimal weight: 0.7980 chunk 184 optimal weight: 2.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 992 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 675 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 935 GLN C 969 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4483 r_free = 0.4483 target = 0.172271 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3540 r_free = 0.3540 target = 0.101391 restraints weight = 58075.607| |-----------------------------------------------------------------------------| r_work (start): 0.3216 rms_B_bonded: 3.49 r_work: 0.3048 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.3048 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8072 moved from start: 0.2511 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 29143 Z= 0.131 Angle : 0.543 12.031 39701 Z= 0.285 Chirality : 0.044 0.235 4497 Planarity : 0.004 0.142 5147 Dihedral : 4.230 44.892 3942 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 6.53 Ramachandran Plot: Outliers : 0.22 % Allowed : 4.51 % Favored : 95.27 % Rotamer: Outliers : 1.20 % Allowed : 12.06 % Favored : 86.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.03 % Twisted Proline : 0.57 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.05 (0.14), residues: 3639 helix: 1.81 (0.20), residues: 729 sheet: 0.36 (0.17), residues: 827 loop : -0.89 (0.13), residues: 2083 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP C 104 HIS 0.002 0.000 HIS C1083 PHE 0.030 0.001 PHE A 168 TYR 0.018 0.001 TYR B 265 ARG 0.014 0.000 ARG A 319 Details of bonding type rmsd hydrogen bonds : bond 0.03737 ( 1166) hydrogen bonds : angle 5.10399 ( 3126) SS BOND : bond 0.00198 ( 38) SS BOND : angle 1.12029 ( 76) covalent geometry : bond 0.00301 (29105) covalent geometry : angle 0.54177 (39625) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 36810.01 seconds wall clock time: 627 minutes 13.87 seconds (37633.87 seconds total)