Starting phenix.real_space_refine on Fri Aug 9 23:08:00 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8srk_40734/08_2024/8srk_40734.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8srk_40734/08_2024/8srk_40734.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.14 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8srk_40734/08_2024/8srk_40734.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8srk_40734/08_2024/8srk_40734.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8srk_40734/08_2024/8srk_40734.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8srk_40734/08_2024/8srk_40734.cif" } resolution = 4.14 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= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians Ca 8 9.91 5 P 8 5.49 5 S 104 5.16 5 C 17420 2.51 5 N 4836 2.21 5 O 4952 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped None Time to flip residues: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/chem_data/mon_lib" Total number of atoms: 27328 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 6710 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1071, 6710 Classifications: {'peptide': 1071} Incomplete info: {'truncation_to_alanine': 524} Link IDs: {'PCIS': 2, 'PTRANS': 37, 'TRANS': 1031} Chain breaks: 2 Unresolved non-hydrogen bonds: 1910 Unresolved non-hydrogen angles: 2391 Unresolved non-hydrogen dihedrals: 1560 Unresolved non-hydrogen chiralities: 156 Planarities with less than four sites: {'GLN:plan1': 30, 'HIS:plan': 14, 'TYR:plan': 8, 'ASN:plan1': 26, 'TRP:plan': 1, 'ASP:plan': 52, 'PHE:plan': 36, 'GLU:plan': 51, 'ARG:plan': 37} Unresolved non-hydrogen planarities: 1094 Chain: "B" Number of atoms: 6710 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1071, 6710 Classifications: {'peptide': 1071} Incomplete info: {'truncation_to_alanine': 524} Link IDs: {'PCIS': 2, 'PTRANS': 37, 'TRANS': 1031} Chain breaks: 2 Unresolved non-hydrogen bonds: 1910 Unresolved non-hydrogen angles: 2391 Unresolved non-hydrogen dihedrals: 1560 Unresolved non-hydrogen chiralities: 156 Planarities with less than four sites: {'GLN:plan1': 30, 'HIS:plan': 14, 'TYR:plan': 8, 'ASN:plan1': 26, 'TRP:plan': 1, 'ASP:plan': 52, 'PHE:plan': 36, 'GLU:plan': 51, 'ARG:plan': 37} Unresolved non-hydrogen planarities: 1094 Chain: "C" Number of atoms: 6710 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1071, 6710 Classifications: {'peptide': 1071} Incomplete info: {'truncation_to_alanine': 524} Link IDs: {'PCIS': 2, 'PTRANS': 37, 'TRANS': 1031} Chain breaks: 2 Unresolved non-hydrogen bonds: 1910 Unresolved non-hydrogen angles: 2391 Unresolved non-hydrogen dihedrals: 1560 Unresolved non-hydrogen chiralities: 156 Planarities with less than four sites: {'GLN:plan1': 30, 'HIS:plan': 14, 'TYR:plan': 8, 'ASN:plan1': 26, 'TRP:plan': 1, 'ASP:plan': 52, 'PHE:plan': 36, 'GLU:plan': 51, 'ARG:plan': 37} Unresolved non-hydrogen planarities: 1094 Chain: "D" Number of atoms: 6710 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1071, 6710 Classifications: {'peptide': 1071} Incomplete info: {'truncation_to_alanine': 524} Link IDs: {'PCIS': 2, 'PTRANS': 37, 'TRANS': 1031} Chain breaks: 2 Unresolved non-hydrogen bonds: 1910 Unresolved non-hydrogen angles: 2391 Unresolved non-hydrogen dihedrals: 1560 Unresolved non-hydrogen chiralities: 156 Planarities with less than four sites: {'GLN:plan1': 30, 'HIS:plan': 14, 'TYR:plan': 8, 'ASN:plan1': 26, 'TRP:plan': 1, 'ASP:plan': 52, 'PHE:plan': 36, 'GLU:plan': 51, 'ARG:plan': 37} Unresolved non-hydrogen planarities: 1094 Chain: "A" Number of atoms: 122 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 122 Unusual residues: {' CA': 2, 'APR': 1, 'CLR': 3} Classifications: {'undetermined': 6} Link IDs: {None: 5} Chain: "B" Number of atoms: 122 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 122 Unusual residues: {' CA': 2, 'APR': 1, 'CLR': 3} Classifications: {'undetermined': 6} Link IDs: {None: 5} Chain: "C" Number of atoms: 122 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 122 Unusual residues: {' CA': 2, 'APR': 1, 'CLR': 3} Classifications: {'undetermined': 6} Link IDs: {None: 5} Chain: "D" Number of atoms: 122 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 122 Unusual residues: {' CA': 2, 'APR': 1, 'CLR': 3} Classifications: {'undetermined': 6} Link IDs: {None: 5} Time building chain proxies: 15.73, per 1000 atoms: 0.58 Number of scatterers: 27328 At special positions: 0 Unit cell: (149.64, 149.64, 153.12, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Ca 8 19.99 S 104 16.00 P 8 15.00 O 4952 8.00 N 4836 7.00 C 17420 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS A 997 " - pdb=" SG CYS A1006 " distance=2.03 Simple disulfide: pdb=" SG CYS B 997 " - pdb=" SG CYS B1006 " distance=2.03 Simple disulfide: pdb=" SG CYS C 997 " - pdb=" SG CYS C1006 " distance=2.03 Simple disulfide: pdb=" SG CYS D 997 " - pdb=" SG CYS D1006 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 10.89 Conformation dependent library (CDL) restraints added in 5.5 seconds 8520 Ramachandran restraints generated. 4260 Oldfield, 0 Emsley, 4260 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8136 Finding SS restraints... Secondary structure from input PDB file: 185 helices and 12 sheets defined 66.9% alpha, 4.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.95 Creating SS restraints... Processing helix chain 'A' and resid 72 through 76 Processing helix chain 'A' and resid 118 through 135 removed outlier: 3.536A pdb=" N ALA A 122 " --> pdb=" O ASP A 118 " (cutoff:3.500A) Processing helix chain 'A' and resid 157 through 175 Processing helix chain 'A' and resid 187 through 203 removed outlier: 3.537A pdb=" N LEU A 191 " --> pdb=" O GLY A 187 " (cutoff:3.500A) Processing helix chain 'A' and resid 221 through 227 Processing helix chain 'A' and resid 271 through 286 removed outlier: 3.683A pdb=" N PHE A 286 " --> pdb=" O ALA A 282 " (cutoff:3.500A) Processing helix chain 'A' and resid 298 through 312 removed outlier: 3.782A pdb=" N LEU A 302 " --> pdb=" O GLY A 298 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N GLY A 303 " --> pdb=" O PRO A 299 " (cutoff:3.500A) Processing helix chain 'A' and resid 322 through 335 Processing helix chain 'A' and resid 346 through 358 Processing helix chain 'A' and resid 362 through 377 Processing helix chain 'A' and resid 395 through 406 Processing helix chain 'A' and resid 410 through 419 removed outlier: 3.535A pdb=" N MET A 419 " --> pdb=" O LEU A 415 " (cutoff:3.500A) Processing helix chain 'A' and resid 424 through 437 Processing helix chain 'A' and resid 439 through 457 removed outlier: 4.194A pdb=" N ILE A 443 " --> pdb=" O GLN A 439 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N ALA A 444 " --> pdb=" O HIS A 440 " (cutoff:3.500A) removed outlier: 4.592A pdb=" N ASN A 448 " --> pdb=" O ALA A 444 " (cutoff:3.500A) removed outlier: 4.782A pdb=" N ASP A 449 " --> pdb=" O ALA A 445 " (cutoff:3.500A) Processing helix chain 'A' and resid 459 through 469 Processing helix chain 'A' and resid 472 through 476 removed outlier: 3.550A pdb=" N GLU A 475 " --> pdb=" O LYS A 472 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N LEU A 476 " --> pdb=" O ILE A 473 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 472 through 476' Processing helix chain 'A' and resid 487 through 492 Processing helix chain 'A' and resid 494 through 509 Processing helix chain 'A' and resid 513 through 521 removed outlier: 3.564A pdb=" N ARG A 517 " --> pdb=" O SER A 513 " (cutoff:3.500A) Processing helix chain 'A' and resid 556 through 569 removed outlier: 3.673A pdb=" N LEU A 567 " --> pdb=" O ILE A 563 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N SER A 569 " --> pdb=" O ALA A 565 " (cutoff:3.500A) Processing helix chain 'A' and resid 577 through 582 removed outlier: 3.942A pdb=" N ILE A 580 " --> pdb=" O ASP A 577 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N TYR A 581 " --> pdb=" O PHE A 578 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N ASP A 582 " --> pdb=" O THR A 579 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 577 through 582' Processing helix chain 'A' and resid 590 through 610 Processing helix chain 'A' and resid 612 through 623 Processing helix chain 'A' and resid 625 through 640 Processing helix chain 'A' and resid 651 through 680 removed outlier: 3.788A pdb=" N LEU A 668 " --> pdb=" O LYS A 664 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N ALA A 669 " --> pdb=" O PHE A 665 " (cutoff:3.500A) removed outlier: 4.116A pdb=" N VAL A 670 " --> pdb=" O GLU A 666 " (cutoff:3.500A) Processing helix chain 'A' and resid 680 through 689 removed outlier: 3.603A pdb=" N HIS A 689 " --> pdb=" O SER A 685 " (cutoff:3.500A) Processing helix chain 'A' and resid 699 through 708 Processing helix chain 'A' and resid 709 through 714 removed outlier: 3.718A pdb=" N LEU A 713 " --> pdb=" O SER A 709 " (cutoff:3.500A) Processing helix chain 'A' and resid 715 through 728 Processing helix chain 'A' and resid 735 through 745 removed outlier: 3.511A pdb=" N VAL A 739 " --> pdb=" O SER A 735 " (cutoff:3.500A) Processing helix chain 'A' and resid 788 through 799 Processing helix chain 'A' and resid 801 through 826 Processing helix chain 'A' and resid 833 through 856 removed outlier: 3.532A pdb=" N TRP A 837 " --> pdb=" O SER A 833 " (cutoff:3.500A) Processing helix chain 'A' and resid 859 through 866 removed outlier: 3.649A pdb=" N TYR A 863 " --> pdb=" O GLY A 859 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ILE A 864 " --> pdb=" O ILE A 860 " (cutoff:3.500A) Processing helix chain 'A' and resid 866 through 889 removed outlier: 3.530A pdb=" N ARG A 870 " --> pdb=" O ASP A 866 " (cutoff:3.500A) removed outlier: 4.495A pdb=" N ASP A 889 " --> pdb=" O THR A 885 " (cutoff:3.500A) Processing helix chain 'A' and resid 892 through 911 removed outlier: 4.156A pdb=" N PHE A 905 " --> pdb=" O GLY A 901 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N TRP A 911 " --> pdb=" O VAL A 907 " (cutoff:3.500A) Processing helix chain 'A' and resid 915 through 919 removed outlier: 3.587A pdb=" N ALA A 919 " --> pdb=" O ARG A 916 " (cutoff:3.500A) Processing helix chain 'A' and resid 923 through 961 removed outlier: 4.149A pdb=" N LYS A 927 " --> pdb=" O ASN A 923 " (cutoff:3.500A) removed outlier: 4.934A pdb=" N LYS A 936 " --> pdb=" O MET A 932 " (cutoff:3.500A) removed outlier: 4.647A pdb=" N ASP A 937 " --> pdb=" O GLU A 933 " (cutoff:3.500A) removed outlier: 4.990A pdb=" N ILE A 947 " --> pdb=" O PHE A 943 " (cutoff:3.500A) removed outlier: 4.535A pdb=" N PHE A 948 " --> pdb=" O LEU A 944 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N SER A 961 " --> pdb=" O GLN A 957 " (cutoff:3.500A) Processing helix chain 'A' and resid 967 through 980 removed outlier: 3.648A pdb=" N PHE A 971 " --> pdb=" O SER A 967 " (cutoff:3.500A) removed outlier: 5.466A pdb=" N ARG A 977 " --> pdb=" O GLY A 973 " (cutoff:3.500A) Proline residue: A 978 - end of helix Processing helix chain 'A' and resid 987 through 995 Processing helix chain 'A' and resid 1013 through 1028 removed outlier: 3.604A pdb=" N LEU A1023 " --> pdb=" O ALA A1019 " (cutoff:3.500A) Processing helix chain 'A' and resid 1028 through 1066 removed outlier: 3.732A pdb=" N ILE A1034 " --> pdb=" O VAL A1030 " (cutoff:3.500A) removed outlier: 6.759A pdb=" N GLU A1046 " --> pdb=" O MET A1042 " (cutoff:3.500A) removed outlier: 5.401A pdb=" N ALA A1047 " --> pdb=" O LYS A1043 " (cutoff:3.500A) Processing helix chain 'A' and resid 1070 through 1072 No H-bonds generated for 'chain 'A' and resid 1070 through 1072' Processing helix chain 'A' and resid 1073 through 1090 Processing helix chain 'A' and resid 1102 through 1129 removed outlier: 3.557A pdb=" N GLN A1129 " --> pdb=" O GLU A1125 " (cutoff:3.500A) Processing helix chain 'A' and resid 1131 through 1168 removed outlier: 3.911A pdb=" N ARG A1135 " --> pdb=" O MET A1131 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N ALA A1168 " --> pdb=" O LEU A1164 " (cutoff:3.500A) Processing helix chain 'B' and resid 72 through 76 Processing helix chain 'B' and resid 118 through 135 removed outlier: 3.536A pdb=" N ALA B 122 " --> pdb=" O ASP B 118 " (cutoff:3.500A) Processing helix chain 'B' and resid 157 through 175 Processing helix chain 'B' and resid 187 through 203 removed outlier: 3.537A pdb=" N LEU B 191 " --> pdb=" O GLY B 187 " (cutoff:3.500A) Processing helix chain 'B' and resid 221 through 227 Processing helix chain 'B' and resid 271 through 286 removed outlier: 3.683A pdb=" N PHE B 286 " --> pdb=" O ALA B 282 " (cutoff:3.500A) Processing helix chain 'B' and resid 298 through 312 removed outlier: 3.782A pdb=" N LEU B 302 " --> pdb=" O GLY B 298 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N GLY B 303 " --> pdb=" O PRO B 299 " (cutoff:3.500A) Processing helix chain 'B' and resid 322 through 335 Processing helix chain 'B' and resid 346 through 358 Processing helix chain 'B' and resid 362 through 377 Processing helix chain 'B' and resid 395 through 406 Processing helix chain 'B' and resid 410 through 419 removed outlier: 3.535A pdb=" N MET B 419 " --> pdb=" O LEU B 415 " (cutoff:3.500A) Processing helix chain 'B' and resid 424 through 437 Processing helix chain 'B' and resid 439 through 457 removed outlier: 4.195A pdb=" N ILE B 443 " --> pdb=" O GLN B 439 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N ALA B 444 " --> pdb=" O HIS B 440 " (cutoff:3.500A) removed outlier: 4.592A pdb=" N ASN B 448 " --> pdb=" O ALA B 444 " (cutoff:3.500A) removed outlier: 4.782A pdb=" N ASP B 449 " --> pdb=" O ALA B 445 " (cutoff:3.500A) Processing helix chain 'B' and resid 459 through 469 Processing helix chain 'B' and resid 472 through 476 removed outlier: 3.550A pdb=" N GLU B 475 " --> pdb=" O LYS B 472 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N LEU B 476 " --> pdb=" O ILE B 473 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 472 through 476' Processing helix chain 'B' and resid 487 through 492 Processing helix chain 'B' and resid 494 through 509 Processing helix chain 'B' and resid 513 through 521 removed outlier: 3.564A pdb=" N ARG B 517 " --> pdb=" O SER B 513 " (cutoff:3.500A) Processing helix chain 'B' and resid 556 through 569 removed outlier: 3.674A pdb=" N LEU B 567 " --> pdb=" O ILE B 563 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N SER B 569 " --> pdb=" O ALA B 565 " (cutoff:3.500A) Processing helix chain 'B' and resid 577 through 582 removed outlier: 3.942A pdb=" N ILE B 580 " --> pdb=" O ASP B 577 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N TYR B 581 " --> pdb=" O PHE B 578 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N ASP B 582 " --> pdb=" O THR B 579 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 577 through 582' Processing helix chain 'B' and resid 590 through 610 Processing helix chain 'B' and resid 612 through 623 Processing helix chain 'B' and resid 625 through 640 Processing helix chain 'B' and resid 651 through 680 removed outlier: 3.788A pdb=" N LEU B 668 " --> pdb=" O LYS B 664 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N ALA B 669 " --> pdb=" O PHE B 665 " (cutoff:3.500A) removed outlier: 4.117A pdb=" N VAL B 670 " --> pdb=" O GLU B 666 " (cutoff:3.500A) Processing helix chain 'B' and resid 680 through 689 removed outlier: 3.603A pdb=" N HIS B 689 " --> pdb=" O SER B 685 " (cutoff:3.500A) Processing helix chain 'B' and resid 699 through 708 Processing helix chain 'B' and resid 709 through 714 removed outlier: 3.718A pdb=" N LEU B 713 " --> pdb=" O SER B 709 " (cutoff:3.500A) Processing helix chain 'B' and resid 715 through 728 Processing helix chain 'B' and resid 735 through 745 removed outlier: 3.511A pdb=" N VAL B 739 " --> pdb=" O SER B 735 " (cutoff:3.500A) Processing helix chain 'B' and resid 788 through 799 Processing helix chain 'B' and resid 801 through 826 Processing helix chain 'B' and resid 833 through 856 removed outlier: 3.532A pdb=" N TRP B 837 " --> pdb=" O SER B 833 " (cutoff:3.500A) Processing helix chain 'B' and resid 859 through 866 removed outlier: 3.649A pdb=" N TYR B 863 " --> pdb=" O GLY B 859 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ILE B 864 " --> pdb=" O ILE B 860 " (cutoff:3.500A) Processing helix chain 'B' and resid 866 through 889 removed outlier: 3.530A pdb=" N ARG B 870 " --> pdb=" O ASP B 866 " (cutoff:3.500A) removed outlier: 4.494A pdb=" N ASP B 889 " --> pdb=" O THR B 885 " (cutoff:3.500A) Processing helix chain 'B' and resid 892 through 911 removed outlier: 4.156A pdb=" N PHE B 905 " --> pdb=" O GLY B 901 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N TRP B 911 " --> pdb=" O VAL B 907 " (cutoff:3.500A) Processing helix chain 'B' and resid 915 through 919 removed outlier: 3.587A pdb=" N ALA B 919 " --> pdb=" O ARG B 916 " (cutoff:3.500A) Processing helix chain 'B' and resid 923 through 961 removed outlier: 4.149A pdb=" N LYS B 927 " --> pdb=" O ASN B 923 " (cutoff:3.500A) removed outlier: 4.934A pdb=" N LYS B 936 " --> pdb=" O MET B 932 " (cutoff:3.500A) removed outlier: 4.647A pdb=" N ASP B 937 " --> pdb=" O GLU B 933 " (cutoff:3.500A) removed outlier: 4.990A pdb=" N ILE B 947 " --> pdb=" O PHE B 943 " (cutoff:3.500A) removed outlier: 4.535A pdb=" N PHE B 948 " --> pdb=" O LEU B 944 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N SER B 961 " --> pdb=" O GLN B 957 " (cutoff:3.500A) Processing helix chain 'B' and resid 967 through 980 removed outlier: 3.648A pdb=" N PHE B 971 " --> pdb=" O SER B 967 " (cutoff:3.500A) removed outlier: 5.466A pdb=" N ARG B 977 " --> pdb=" O GLY B 973 " (cutoff:3.500A) Proline residue: B 978 - end of helix Processing helix chain 'B' and resid 987 through 995 Processing helix chain 'B' and resid 1013 through 1028 removed outlier: 3.604A pdb=" N LEU B1023 " --> pdb=" O ALA B1019 " (cutoff:3.500A) Processing helix chain 'B' and resid 1028 through 1066 removed outlier: 3.733A pdb=" N ILE B1034 " --> pdb=" O VAL B1030 " (cutoff:3.500A) removed outlier: 6.759A pdb=" N GLU B1046 " --> pdb=" O MET B1042 " (cutoff:3.500A) removed outlier: 5.401A pdb=" N ALA B1047 " --> pdb=" O LYS B1043 " (cutoff:3.500A) Processing helix chain 'B' and resid 1070 through 1072 No H-bonds generated for 'chain 'B' and resid 1070 through 1072' Processing helix chain 'B' and resid 1073 through 1090 Processing helix chain 'B' and resid 1102 through 1129 removed outlier: 3.557A pdb=" N GLN B1129 " --> pdb=" O GLU B1125 " (cutoff:3.500A) Processing helix chain 'B' and resid 1131 through 1168 removed outlier: 3.911A pdb=" N ARG B1135 " --> pdb=" O MET B1131 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N ALA B1168 " --> pdb=" O LEU B1164 " (cutoff:3.500A) Processing helix chain 'C' and resid 72 through 76 Processing helix chain 'C' and resid 118 through 135 removed outlier: 3.536A pdb=" N ALA C 122 " --> pdb=" O ASP C 118 " (cutoff:3.500A) Processing helix chain 'C' and resid 157 through 175 Processing helix chain 'C' and resid 187 through 203 removed outlier: 3.537A pdb=" N LEU C 191 " --> pdb=" O GLY C 187 " (cutoff:3.500A) Processing helix chain 'C' and resid 221 through 227 Processing helix chain 'C' and resid 271 through 286 removed outlier: 3.683A pdb=" N PHE C 286 " --> pdb=" O ALA C 282 " (cutoff:3.500A) Processing helix chain 'C' and resid 298 through 312 removed outlier: 3.782A pdb=" N LEU C 302 " --> pdb=" O GLY C 298 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N GLY C 303 " --> pdb=" O PRO C 299 " (cutoff:3.500A) Processing helix chain 'C' and resid 322 through 335 Processing helix chain 'C' and resid 346 through 358 Processing helix chain 'C' and resid 362 through 377 Processing helix chain 'C' and resid 395 through 406 Processing helix chain 'C' and resid 410 through 419 removed outlier: 3.535A pdb=" N MET C 419 " --> pdb=" O LEU C 415 " (cutoff:3.500A) Processing helix chain 'C' and resid 424 through 437 Processing helix chain 'C' and resid 439 through 457 removed outlier: 4.194A pdb=" N ILE C 443 " --> pdb=" O GLN C 439 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N ALA C 444 " --> pdb=" O HIS C 440 " (cutoff:3.500A) removed outlier: 4.592A pdb=" N ASN C 448 " --> pdb=" O ALA C 444 " (cutoff:3.500A) removed outlier: 4.782A pdb=" N ASP C 449 " --> pdb=" O ALA C 445 " (cutoff:3.500A) Processing helix chain 'C' and resid 459 through 469 Processing helix chain 'C' and resid 472 through 476 removed outlier: 3.550A pdb=" N GLU C 475 " --> pdb=" O LYS C 472 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N LEU C 476 " --> pdb=" O ILE C 473 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 472 through 476' Processing helix chain 'C' and resid 487 through 492 Processing helix chain 'C' and resid 494 through 509 Processing helix chain 'C' and resid 513 through 521 removed outlier: 3.564A pdb=" N ARG C 517 " --> pdb=" O SER C 513 " (cutoff:3.500A) Processing helix chain 'C' and resid 556 through 569 removed outlier: 3.673A pdb=" N LEU C 567 " --> pdb=" O ILE C 563 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N SER C 569 " --> pdb=" O ALA C 565 " (cutoff:3.500A) Processing helix chain 'C' and resid 577 through 582 removed outlier: 3.941A pdb=" N ILE C 580 " --> pdb=" O ASP C 577 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N TYR C 581 " --> pdb=" O PHE C 578 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N ASP C 582 " --> pdb=" O THR C 579 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 577 through 582' Processing helix chain 'C' and resid 590 through 610 Processing helix chain 'C' and resid 612 through 623 Processing helix chain 'C' and resid 625 through 640 Processing helix chain 'C' and resid 651 through 680 removed outlier: 3.788A pdb=" N LEU C 668 " --> pdb=" O LYS C 664 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N ALA C 669 " --> pdb=" O PHE C 665 " (cutoff:3.500A) removed outlier: 4.117A pdb=" N VAL C 670 " --> pdb=" O GLU C 666 " (cutoff:3.500A) Processing helix chain 'C' and resid 680 through 689 removed outlier: 3.603A pdb=" N HIS C 689 " --> pdb=" O SER C 685 " (cutoff:3.500A) Processing helix chain 'C' and resid 699 through 708 Processing helix chain 'C' and resid 709 through 714 removed outlier: 3.718A pdb=" N LEU C 713 " --> pdb=" O SER C 709 " (cutoff:3.500A) Processing helix chain 'C' and resid 715 through 728 Processing helix chain 'C' and resid 735 through 745 removed outlier: 3.511A pdb=" N VAL C 739 " --> pdb=" O SER C 735 " (cutoff:3.500A) Processing helix chain 'C' and resid 788 through 799 Processing helix chain 'C' and resid 801 through 826 Processing helix chain 'C' and resid 833 through 856 removed outlier: 3.531A pdb=" N TRP C 837 " --> pdb=" O SER C 833 " (cutoff:3.500A) Processing helix chain 'C' and resid 859 through 866 removed outlier: 3.650A pdb=" N TYR C 863 " --> pdb=" O GLY C 859 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ILE C 864 " --> pdb=" O ILE C 860 " (cutoff:3.500A) Processing helix chain 'C' and resid 866 through 889 removed outlier: 3.530A pdb=" N ARG C 870 " --> pdb=" O ASP C 866 " (cutoff:3.500A) removed outlier: 4.495A pdb=" N ASP C 889 " --> pdb=" O THR C 885 " (cutoff:3.500A) Processing helix chain 'C' and resid 892 through 911 removed outlier: 4.156A pdb=" N PHE C 905 " --> pdb=" O GLY C 901 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N TRP C 911 " --> pdb=" O VAL C 907 " (cutoff:3.500A) Processing helix chain 'C' and resid 915 through 919 removed outlier: 3.587A pdb=" N ALA C 919 " --> pdb=" O ARG C 916 " (cutoff:3.500A) Processing helix chain 'C' and resid 923 through 961 removed outlier: 4.149A pdb=" N LYS C 927 " --> pdb=" O ASN C 923 " (cutoff:3.500A) removed outlier: 4.934A pdb=" N LYS C 936 " --> pdb=" O MET C 932 " (cutoff:3.500A) removed outlier: 4.647A pdb=" N ASP C 937 " --> pdb=" O GLU C 933 " (cutoff:3.500A) removed outlier: 4.990A pdb=" N ILE C 947 " --> pdb=" O PHE C 943 " (cutoff:3.500A) removed outlier: 4.536A pdb=" N PHE C 948 " --> pdb=" O LEU C 944 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N SER C 961 " --> pdb=" O GLN C 957 " (cutoff:3.500A) Processing helix chain 'C' and resid 967 through 980 removed outlier: 3.648A pdb=" N PHE C 971 " --> pdb=" O SER C 967 " (cutoff:3.500A) removed outlier: 5.466A pdb=" N ARG C 977 " --> pdb=" O GLY C 973 " (cutoff:3.500A) Proline residue: C 978 - end of helix Processing helix chain 'C' and resid 987 through 995 Processing helix chain 'C' and resid 1013 through 1028 removed outlier: 3.604A pdb=" N LEU C1023 " --> pdb=" O ALA C1019 " (cutoff:3.500A) Processing helix chain 'C' and resid 1028 through 1066 removed outlier: 3.733A pdb=" N ILE C1034 " --> pdb=" O VAL C1030 " (cutoff:3.500A) removed outlier: 6.760A pdb=" N GLU C1046 " --> pdb=" O MET C1042 " (cutoff:3.500A) removed outlier: 5.401A pdb=" N ALA C1047 " --> pdb=" O LYS C1043 " (cutoff:3.500A) Processing helix chain 'C' and resid 1070 through 1072 No H-bonds generated for 'chain 'C' and resid 1070 through 1072' Processing helix chain 'C' and resid 1073 through 1090 Processing helix chain 'C' and resid 1102 through 1129 removed outlier: 3.557A pdb=" N GLN C1129 " --> pdb=" O GLU C1125 " (cutoff:3.500A) Processing helix chain 'C' and resid 1131 through 1168 removed outlier: 3.911A pdb=" N ARG C1135 " --> pdb=" O MET C1131 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N ALA C1168 " --> pdb=" O LEU C1164 " (cutoff:3.500A) Processing helix chain 'D' and resid 72 through 76 Processing helix chain 'D' and resid 118 through 135 removed outlier: 3.536A pdb=" N ALA D 122 " --> pdb=" O ASP D 118 " (cutoff:3.500A) Processing helix chain 'D' and resid 157 through 175 Processing helix chain 'D' and resid 187 through 203 removed outlier: 3.537A pdb=" N LEU D 191 " --> pdb=" O GLY D 187 " (cutoff:3.500A) Processing helix chain 'D' and resid 221 through 227 Processing helix chain 'D' and resid 271 through 286 removed outlier: 3.683A pdb=" N PHE D 286 " --> pdb=" O ALA D 282 " (cutoff:3.500A) Processing helix chain 'D' and resid 298 through 312 removed outlier: 3.782A pdb=" N LEU D 302 " --> pdb=" O GLY D 298 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N GLY D 303 " --> pdb=" O PRO D 299 " (cutoff:3.500A) Processing helix chain 'D' and resid 322 through 335 Processing helix chain 'D' and resid 346 through 358 Processing helix chain 'D' and resid 362 through 377 Processing helix chain 'D' and resid 395 through 406 Processing helix chain 'D' and resid 410 through 419 removed outlier: 3.535A pdb=" N MET D 419 " --> pdb=" O LEU D 415 " (cutoff:3.500A) Processing helix chain 'D' and resid 424 through 437 Processing helix chain 'D' and resid 439 through 457 removed outlier: 4.194A pdb=" N ILE D 443 " --> pdb=" O GLN D 439 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N ALA D 444 " --> pdb=" O HIS D 440 " (cutoff:3.500A) removed outlier: 4.592A pdb=" N ASN D 448 " --> pdb=" O ALA D 444 " (cutoff:3.500A) removed outlier: 4.782A pdb=" N ASP D 449 " --> pdb=" O ALA D 445 " (cutoff:3.500A) Processing helix chain 'D' and resid 459 through 469 Processing helix chain 'D' and resid 472 through 476 removed outlier: 3.550A pdb=" N GLU D 475 " --> pdb=" O LYS D 472 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N LEU D 476 " --> pdb=" O ILE D 473 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 472 through 476' Processing helix chain 'D' and resid 487 through 492 Processing helix chain 'D' and resid 494 through 509 Processing helix chain 'D' and resid 513 through 521 removed outlier: 3.564A pdb=" N ARG D 517 " --> pdb=" O SER D 513 " (cutoff:3.500A) Processing helix chain 'D' and resid 556 through 569 removed outlier: 3.674A pdb=" N LEU D 567 " --> pdb=" O ILE D 563 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N SER D 569 " --> pdb=" O ALA D 565 " (cutoff:3.500A) Processing helix chain 'D' and resid 577 through 582 removed outlier: 3.941A pdb=" N ILE D 580 " --> pdb=" O ASP D 577 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N TYR D 581 " --> pdb=" O PHE D 578 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N ASP D 582 " --> pdb=" O THR D 579 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 577 through 582' Processing helix chain 'D' and resid 590 through 610 Processing helix chain 'D' and resid 612 through 623 Processing helix chain 'D' and resid 625 through 640 Processing helix chain 'D' and resid 651 through 680 removed outlier: 3.788A pdb=" N LEU D 668 " --> pdb=" O LYS D 664 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N ALA D 669 " --> pdb=" O PHE D 665 " (cutoff:3.500A) removed outlier: 4.116A pdb=" N VAL D 670 " --> pdb=" O GLU D 666 " (cutoff:3.500A) Processing helix chain 'D' and resid 680 through 689 removed outlier: 3.603A pdb=" N HIS D 689 " --> pdb=" O SER D 685 " (cutoff:3.500A) Processing helix chain 'D' and resid 692 through 696 removed outlier: 4.076A pdb=" N ASN D 696 " --> pdb=" O ASP D 693 " (cutoff:3.500A) Processing helix chain 'D' and resid 699 through 708 Processing helix chain 'D' and resid 709 through 714 removed outlier: 3.718A pdb=" N LEU D 713 " --> pdb=" O SER D 709 " (cutoff:3.500A) Processing helix chain 'D' and resid 715 through 728 Processing helix chain 'D' and resid 735 through 745 removed outlier: 3.511A pdb=" N VAL D 739 " --> pdb=" O SER D 735 " (cutoff:3.500A) Processing helix chain 'D' and resid 788 through 799 Processing helix chain 'D' and resid 801 through 826 Processing helix chain 'D' and resid 833 through 856 removed outlier: 3.532A pdb=" N TRP D 837 " --> pdb=" O SER D 833 " (cutoff:3.500A) Processing helix chain 'D' and resid 859 through 866 removed outlier: 3.650A pdb=" N TYR D 863 " --> pdb=" O GLY D 859 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ILE D 864 " --> pdb=" O ILE D 860 " (cutoff:3.500A) Processing helix chain 'D' and resid 866 through 889 removed outlier: 3.530A pdb=" N ARG D 870 " --> pdb=" O ASP D 866 " (cutoff:3.500A) removed outlier: 4.495A pdb=" N ASP D 889 " --> pdb=" O THR D 885 " (cutoff:3.500A) Processing helix chain 'D' and resid 892 through 911 removed outlier: 4.157A pdb=" N PHE D 905 " --> pdb=" O GLY D 901 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N TRP D 911 " --> pdb=" O VAL D 907 " (cutoff:3.500A) Processing helix chain 'D' and resid 915 through 919 removed outlier: 3.587A pdb=" N ALA D 919 " --> pdb=" O ARG D 916 " (cutoff:3.500A) Processing helix chain 'D' and resid 923 through 961 removed outlier: 4.149A pdb=" N LYS D 927 " --> pdb=" O ASN D 923 " (cutoff:3.500A) removed outlier: 4.934A pdb=" N LYS D 936 " --> pdb=" O MET D 932 " (cutoff:3.500A) removed outlier: 4.647A pdb=" N ASP D 937 " --> pdb=" O GLU D 933 " (cutoff:3.500A) removed outlier: 4.990A pdb=" N ILE D 947 " --> pdb=" O PHE D 943 " (cutoff:3.500A) removed outlier: 4.535A pdb=" N PHE D 948 " --> pdb=" O LEU D 944 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N SER D 961 " --> pdb=" O GLN D 957 " (cutoff:3.500A) Processing helix chain 'D' and resid 967 through 980 removed outlier: 3.649A pdb=" N PHE D 971 " --> pdb=" O SER D 967 " (cutoff:3.500A) removed outlier: 5.466A pdb=" N ARG D 977 " --> pdb=" O GLY D 973 " (cutoff:3.500A) Proline residue: D 978 - end of helix Processing helix chain 'D' and resid 987 through 995 Processing helix chain 'D' and resid 1013 through 1028 removed outlier: 3.603A pdb=" N LEU D1023 " --> pdb=" O ALA D1019 " (cutoff:3.500A) Processing helix chain 'D' and resid 1028 through 1066 removed outlier: 3.733A pdb=" N ILE D1034 " --> pdb=" O VAL D1030 " (cutoff:3.500A) removed outlier: 6.759A pdb=" N GLU D1046 " --> pdb=" O MET D1042 " (cutoff:3.500A) removed outlier: 5.401A pdb=" N ALA D1047 " --> pdb=" O LYS D1043 " (cutoff:3.500A) Processing helix chain 'D' and resid 1070 through 1072 No H-bonds generated for 'chain 'D' and resid 1070 through 1072' Processing helix chain 'D' and resid 1073 through 1090 Processing helix chain 'D' and resid 1102 through 1129 removed outlier: 3.557A pdb=" N GLN D1129 " --> pdb=" O GLU D1125 " (cutoff:3.500A) Processing helix chain 'D' and resid 1131 through 1168 removed outlier: 3.910A pdb=" N ARG D1135 " --> pdb=" O MET D1131 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N ALA D1168 " --> pdb=" O LEU D1164 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 56 through 60 Processing sheet with id=AA2, first strand: chain 'A' and resid 80 through 81 Processing sheet with id=AA3, first strand: chain 'A' and resid 232 through 236 removed outlier: 6.581A pdb=" N THR A 98 " --> pdb=" O ILE A 233 " (cutoff:3.500A) removed outlier: 8.011A pdb=" N LEU A 259 " --> pdb=" O PRO A 109 " (cutoff:3.500A) removed outlier: 6.691A pdb=" N LEU A 111 " --> pdb=" O LEU A 259 " (cutoff:3.500A) removed outlier: 7.508A pdb=" N ASP A 261 " --> pdb=" O LEU A 111 " (cutoff:3.500A) removed outlier: 6.716A pdb=" N LEU A 113 " --> pdb=" O ASP A 261 " (cutoff:3.500A) removed outlier: 5.955A pdb=" N ILE A 144 " --> pdb=" O VAL A 291 " (cutoff:3.500A) removed outlier: 6.861A pdb=" N ILE A 293 " --> pdb=" O ILE A 144 " (cutoff:3.500A) removed outlier: 6.005A pdb=" N SER A 146 " --> pdb=" O ILE A 293 " (cutoff:3.500A) removed outlier: 7.661A pdb=" N VAL A 316 " --> pdb=" O VAL A 290 " (cutoff:3.500A) removed outlier: 5.859A pdb=" N THR A 292 " --> pdb=" O VAL A 316 " (cutoff:3.500A) removed outlier: 7.203A pdb=" N VAL A 318 " --> pdb=" O THR A 292 " (cutoff:3.500A) removed outlier: 7.238A pdb=" N VAL A 294 " --> pdb=" O VAL A 318 " (cutoff:3.500A) removed outlier: 6.746A pdb=" N ILE A 315 " --> pdb=" O VAL A 384 " (cutoff:3.500A) removed outlier: 7.812A pdb=" N TYR A 386 " --> pdb=" O ILE A 315 " (cutoff:3.500A) removed outlier: 6.414A pdb=" N VAL A 317 " --> pdb=" O TYR A 386 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 56 through 60 Processing sheet with id=AA5, first strand: chain 'B' and resid 80 through 81 Processing sheet with id=AA6, first strand: chain 'B' and resid 232 through 236 removed outlier: 6.581A pdb=" N THR B 98 " --> pdb=" O ILE B 233 " (cutoff:3.500A) removed outlier: 8.011A pdb=" N LEU B 259 " --> pdb=" O PRO B 109 " (cutoff:3.500A) removed outlier: 6.690A pdb=" N LEU B 111 " --> pdb=" O LEU B 259 " (cutoff:3.500A) removed outlier: 7.507A pdb=" N ASP B 261 " --> pdb=" O LEU B 111 " (cutoff:3.500A) removed outlier: 6.716A pdb=" N LEU B 113 " --> pdb=" O ASP B 261 " (cutoff:3.500A) removed outlier: 5.955A pdb=" N ILE B 144 " --> pdb=" O VAL B 291 " (cutoff:3.500A) removed outlier: 6.861A pdb=" N ILE B 293 " --> pdb=" O ILE B 144 " (cutoff:3.500A) removed outlier: 6.005A pdb=" N SER B 146 " --> pdb=" O ILE B 293 " (cutoff:3.500A) removed outlier: 7.660A pdb=" N VAL B 316 " --> pdb=" O VAL B 290 " (cutoff:3.500A) removed outlier: 5.859A pdb=" N THR B 292 " --> pdb=" O VAL B 316 " (cutoff:3.500A) removed outlier: 7.203A pdb=" N VAL B 318 " --> pdb=" O THR B 292 " (cutoff:3.500A) removed outlier: 7.238A pdb=" N VAL B 294 " --> pdb=" O VAL B 318 " (cutoff:3.500A) removed outlier: 6.746A pdb=" N ILE B 315 " --> pdb=" O VAL B 384 " (cutoff:3.500A) removed outlier: 7.812A pdb=" N TYR B 386 " --> pdb=" O ILE B 315 " (cutoff:3.500A) removed outlier: 6.414A pdb=" N VAL B 317 " --> pdb=" O TYR B 386 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 56 through 60 Processing sheet with id=AA8, first strand: chain 'C' and resid 80 through 81 Processing sheet with id=AA9, first strand: chain 'C' and resid 232 through 236 removed outlier: 6.582A pdb=" N THR C 98 " --> pdb=" O ILE C 233 " (cutoff:3.500A) removed outlier: 8.011A pdb=" N LEU C 259 " --> pdb=" O PRO C 109 " (cutoff:3.500A) removed outlier: 6.691A pdb=" N LEU C 111 " --> pdb=" O LEU C 259 " (cutoff:3.500A) removed outlier: 7.508A pdb=" N ASP C 261 " --> pdb=" O LEU C 111 " (cutoff:3.500A) removed outlier: 6.716A pdb=" N LEU C 113 " --> pdb=" O ASP C 261 " (cutoff:3.500A) removed outlier: 5.955A pdb=" N ILE C 144 " --> pdb=" O VAL C 291 " (cutoff:3.500A) removed outlier: 6.861A pdb=" N ILE C 293 " --> pdb=" O ILE C 144 " (cutoff:3.500A) removed outlier: 6.004A pdb=" N SER C 146 " --> pdb=" O ILE C 293 " (cutoff:3.500A) removed outlier: 7.661A pdb=" N VAL C 316 " --> pdb=" O VAL C 290 " (cutoff:3.500A) removed outlier: 5.859A pdb=" N THR C 292 " --> pdb=" O VAL C 316 " (cutoff:3.500A) removed outlier: 7.202A pdb=" N VAL C 318 " --> pdb=" O THR C 292 " (cutoff:3.500A) removed outlier: 7.238A pdb=" N VAL C 294 " --> pdb=" O VAL C 318 " (cutoff:3.500A) removed outlier: 6.746A pdb=" N ILE C 315 " --> pdb=" O VAL C 384 " (cutoff:3.500A) removed outlier: 7.812A pdb=" N TYR C 386 " --> pdb=" O ILE C 315 " (cutoff:3.500A) removed outlier: 6.413A pdb=" N VAL C 317 " --> pdb=" O TYR C 386 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 56 through 60 Processing sheet with id=AB2, first strand: chain 'D' and resid 80 through 81 Processing sheet with id=AB3, first strand: chain 'D' and resid 232 through 236 removed outlier: 6.581A pdb=" N THR D 98 " --> pdb=" O ILE D 233 " (cutoff:3.500A) removed outlier: 8.010A pdb=" N LEU D 259 " --> pdb=" O PRO D 109 " (cutoff:3.500A) removed outlier: 6.691A pdb=" N LEU D 111 " --> pdb=" O LEU D 259 " (cutoff:3.500A) removed outlier: 7.508A pdb=" N ASP D 261 " --> pdb=" O LEU D 111 " (cutoff:3.500A) removed outlier: 6.716A pdb=" N LEU D 113 " --> pdb=" O ASP D 261 " (cutoff:3.500A) removed outlier: 5.955A pdb=" N ILE D 144 " --> pdb=" O VAL D 291 " (cutoff:3.500A) removed outlier: 6.862A pdb=" N ILE D 293 " --> pdb=" O ILE D 144 " (cutoff:3.500A) removed outlier: 6.005A pdb=" N SER D 146 " --> pdb=" O ILE D 293 " (cutoff:3.500A) removed outlier: 7.661A pdb=" N VAL D 316 " --> pdb=" O VAL D 290 " (cutoff:3.500A) removed outlier: 5.859A pdb=" N THR D 292 " --> pdb=" O VAL D 316 " (cutoff:3.500A) removed outlier: 7.203A pdb=" N VAL D 318 " --> pdb=" O THR D 292 " (cutoff:3.500A) removed outlier: 7.238A pdb=" N VAL D 294 " --> pdb=" O VAL D 318 " (cutoff:3.500A) removed outlier: 6.746A pdb=" N ILE D 315 " --> pdb=" O VAL D 384 " (cutoff:3.500A) removed outlier: 7.811A pdb=" N TYR D 386 " --> pdb=" O ILE D 315 " (cutoff:3.500A) removed outlier: 6.414A pdb=" N VAL D 317 " --> pdb=" O TYR D 386 " (cutoff:3.500A) 2033 hydrogen bonds defined for protein. 6036 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 10.85 Time building geometry restraints manager: 11.51 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 4587 1.32 - 1.44: 7210 1.44 - 1.57: 15903 1.57 - 1.69: 16 1.69 - 1.81: 188 Bond restraints: 27904 Sorted by residual: bond pdb=" CA SER A1025 " pdb=" CB SER A1025 " ideal model delta sigma weight residual 1.528 1.463 0.066 1.56e-02 4.11e+03 1.78e+01 bond pdb=" CA SER D1025 " pdb=" CB SER D1025 " ideal model delta sigma weight residual 1.528 1.463 0.066 1.56e-02 4.11e+03 1.78e+01 bond pdb=" CA SER B1025 " pdb=" CB SER B1025 " ideal model delta sigma weight residual 1.528 1.463 0.066 1.56e-02 4.11e+03 1.78e+01 bond pdb=" CA SER C1025 " pdb=" CB SER C1025 " ideal model delta sigma weight residual 1.528 1.463 0.066 1.56e-02 4.11e+03 1.78e+01 bond pdb=" C4 APR D6003 " pdb=" C5 APR D6003 " ideal model delta sigma weight residual 1.386 1.467 -0.081 2.00e-02 2.50e+03 1.65e+01 ... (remaining 27899 not shown) Histogram of bond angle deviations from ideal: 98.36 - 105.97: 825 105.97 - 113.58: 15216 113.58 - 121.19: 14051 121.19 - 128.80: 8305 128.80 - 136.41: 215 Bond angle restraints: 38612 Sorted by residual: angle pdb=" N TYR A 216 " pdb=" CA TYR A 216 " pdb=" C TYR A 216 " ideal model delta sigma weight residual 113.28 103.25 10.03 1.22e+00 6.72e-01 6.75e+01 angle pdb=" N TYR C 216 " pdb=" CA TYR C 216 " pdb=" C TYR C 216 " ideal model delta sigma weight residual 113.28 103.25 10.03 1.22e+00 6.72e-01 6.75e+01 angle pdb=" N TYR B 216 " pdb=" CA TYR B 216 " pdb=" C TYR B 216 " ideal model delta sigma weight residual 113.28 103.25 10.03 1.22e+00 6.72e-01 6.75e+01 angle pdb=" N TYR D 216 " pdb=" CA TYR D 216 " pdb=" C TYR D 216 " ideal model delta sigma weight residual 113.28 103.30 9.98 1.22e+00 6.72e-01 6.69e+01 angle pdb=" N GLN A1055 " pdb=" CA GLN A1055 " pdb=" C GLN A1055 " ideal model delta sigma weight residual 111.82 103.23 8.59 1.16e+00 7.43e-01 5.48e+01 ... (remaining 38607 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.50: 16163 23.50 - 47.01: 534 47.01 - 70.51: 151 70.51 - 94.02: 16 94.02 - 117.52: 12 Dihedral angle restraints: 16876 sinusoidal: 4372 harmonic: 12504 Sorted by residual: dihedral pdb=" CA THR B1001 " pdb=" C THR B1001 " pdb=" N PRO B1002 " pdb=" CA PRO B1002 " ideal model delta harmonic sigma weight residual -180.00 -150.47 -29.53 0 5.00e+00 4.00e-02 3.49e+01 dihedral pdb=" CA THR C1001 " pdb=" C THR C1001 " pdb=" N PRO C1002 " pdb=" CA PRO C1002 " ideal model delta harmonic sigma weight residual -180.00 -150.48 -29.52 0 5.00e+00 4.00e-02 3.49e+01 dihedral pdb=" CA THR A1001 " pdb=" C THR A1001 " pdb=" N PRO A1002 " pdb=" CA PRO A1002 " ideal model delta harmonic sigma weight residual 180.00 -150.48 -29.52 0 5.00e+00 4.00e-02 3.49e+01 ... (remaining 16873 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.088: 4131 0.088 - 0.175: 525 0.175 - 0.263: 96 0.263 - 0.351: 24 0.351 - 0.438: 8 Chirality restraints: 4784 Sorted by residual: chirality pdb=" CB VAL C 907 " pdb=" CA VAL C 907 " pdb=" CG1 VAL C 907 " pdb=" CG2 VAL C 907 " both_signs ideal model delta sigma weight residual False -2.63 -2.19 -0.44 2.00e-01 2.50e+01 4.81e+00 chirality pdb=" CB VAL D 907 " pdb=" CA VAL D 907 " pdb=" CG1 VAL D 907 " pdb=" CG2 VAL D 907 " both_signs ideal model delta sigma weight residual False -2.63 -2.19 -0.44 2.00e-01 2.50e+01 4.80e+00 chirality pdb=" CB VAL B 907 " pdb=" CA VAL B 907 " pdb=" CG1 VAL B 907 " pdb=" CG2 VAL B 907 " both_signs ideal model delta sigma weight residual False -2.63 -2.19 -0.44 2.00e-01 2.50e+01 4.76e+00 ... (remaining 4781 not shown) Planarity restraints: 5048 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA PHE D 905 " -0.015 2.00e-02 2.50e+03 3.09e-02 9.53e+00 pdb=" C PHE D 905 " 0.053 2.00e-02 2.50e+03 pdb=" O PHE D 905 " -0.020 2.00e-02 2.50e+03 pdb=" N LEU D 906 " -0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PHE B 905 " 0.015 2.00e-02 2.50e+03 3.09e-02 9.52e+00 pdb=" C PHE B 905 " -0.053 2.00e-02 2.50e+03 pdb=" O PHE B 905 " 0.020 2.00e-02 2.50e+03 pdb=" N LEU B 906 " 0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLY B1024 " 0.015 2.00e-02 2.50e+03 3.09e-02 9.52e+00 pdb=" C GLY B1024 " -0.053 2.00e-02 2.50e+03 pdb=" O GLY B1024 " 0.020 2.00e-02 2.50e+03 pdb=" N SER B1025 " 0.018 2.00e-02 2.50e+03 ... (remaining 5045 not shown) Histogram of nonbonded interaction distances: 2.36 - 2.87: 10146 2.87 - 3.38: 24596 3.38 - 3.89: 44803 3.89 - 4.39: 46134 4.39 - 4.90: 78703 Nonbonded interactions: 204382 Sorted by model distance: nonbonded pdb=" O ARG A1135 " pdb=" OG1 THR A1139 " model vdw 2.364 3.040 nonbonded pdb=" O ARG C1135 " pdb=" OG1 THR C1139 " model vdw 2.364 3.040 nonbonded pdb=" O ARG B1135 " pdb=" OG1 THR B1139 " model vdw 2.364 3.040 nonbonded pdb=" O ARG D1135 " pdb=" OG1 THR D1139 " model vdw 2.364 3.040 nonbonded pdb=" O LEU D 873 " pdb=" OG1 THR D 877 " model vdw 2.380 3.040 ... (remaining 204377 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' and (resid 52 through 1168 or resid 1706)) selection = (chain 'B' and (resid 52 through 1168 or resid 1706)) selection = (chain 'C' and (resid 52 through 1168 or resid 1706)) selection = (chain 'D' and (resid 52 through 1168 or resid 6006)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.560 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: 1.000 Check model and map are aligned: 0.210 Set scattering table: 0.250 Process input model: 72.260 Find NCS groups from input model: 1.670 Set up NCS constraints: 0.130 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.680 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 79.790 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8045 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 : 0.008 0.081 27904 Z= 0.545 Angle : 1.228 10.253 38612 Z= 0.759 Chirality : 0.065 0.438 4784 Planarity : 0.009 0.058 5048 Dihedral : 14.145 117.520 8728 Min Nonbonded Distance : 2.364 Molprobity Statistics. All-atom Clashscore : 4.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Rotamer: Outliers : 0.50 % Allowed : 2.18 % Favored : 97.32 % Cbeta Deviations : 0.10 % Peptide Plane: Cis-proline : 5.13 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -5.16 (0.09), residues: 4260 helix: -4.06 (0.05), residues: 2780 sheet: -0.55 (0.37), residues: 224 loop : -1.68 (0.15), residues: 1256 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.003 TRP B 842 HIS 0.010 0.001 HIS A 903 PHE 0.037 0.004 PHE C 941 TYR 0.028 0.003 TYR B 952 ARG 0.010 0.001 ARG C 614 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8520 Ramachandran restraints generated. 4260 Oldfield, 0 Emsley, 4260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8520 Ramachandran restraints generated. 4260 Oldfield, 0 Emsley, 4260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 336 residues out of total 3700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 328 time to evaluate : 2.955 Fit side-chains REVERT: A 456 MET cc_start: 0.9028 (tpp) cc_final: 0.8786 (tpp) REVERT: A 683 MET cc_start: 0.8864 (mmm) cc_final: 0.8419 (tpp) REVERT: A 874 ILE cc_start: 0.9534 (mm) cc_final: 0.9294 (tt) REVERT: A 1021 TYR cc_start: 0.9310 (t80) cc_final: 0.9088 (t80) REVERT: A 1150 MET cc_start: 0.9072 (tpp) cc_final: 0.8634 (tmm) REVERT: B 456 MET cc_start: 0.9025 (tpp) cc_final: 0.8794 (tpp) REVERT: B 683 MET cc_start: 0.8862 (mmm) cc_final: 0.8419 (tpp) REVERT: B 874 ILE cc_start: 0.9533 (mm) cc_final: 0.9292 (tt) REVERT: B 1021 TYR cc_start: 0.9325 (t80) cc_final: 0.9111 (t80) REVERT: B 1150 MET cc_start: 0.9072 (tpp) cc_final: 0.8119 (mmp) REVERT: C 456 MET cc_start: 0.9025 (tpp) cc_final: 0.8794 (tpp) REVERT: C 683 MET cc_start: 0.8858 (mmm) cc_final: 0.8423 (tpp) REVERT: C 874 ILE cc_start: 0.9534 (mm) cc_final: 0.9294 (tt) REVERT: C 1021 TYR cc_start: 0.9325 (t80) cc_final: 0.9111 (t80) REVERT: C 1150 MET cc_start: 0.9072 (tpp) cc_final: 0.8200 (mmm) REVERT: D 456 MET cc_start: 0.9025 (tpp) cc_final: 0.8794 (tpp) REVERT: D 683 MET cc_start: 0.8860 (mmm) cc_final: 0.8425 (tpp) REVERT: D 874 ILE cc_start: 0.9534 (mm) cc_final: 0.9293 (tt) REVERT: D 1021 TYR cc_start: 0.9324 (t80) cc_final: 0.9113 (t80) REVERT: D 1150 MET cc_start: 0.9072 (tpp) cc_final: 0.8853 (mmm) outliers start: 8 outliers final: 0 residues processed: 332 average time/residue: 0.3284 time to fit residues: 181.2137 Evaluate side-chains 252 residues out of total 3700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 252 time to evaluate : 2.672 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 428 random chunks: chunk 361 optimal weight: 5.9990 chunk 324 optimal weight: 50.0000 chunk 180 optimal weight: 10.0000 chunk 110 optimal weight: 50.0000 chunk 218 optimal weight: 50.0000 chunk 173 optimal weight: 10.0000 chunk 335 optimal weight: 7.9990 chunk 129 optimal weight: 20.0000 chunk 203 optimal weight: 4.9990 chunk 249 optimal weight: 8.9990 chunk 388 optimal weight: 3.9990 overall best weight: 6.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 592 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1078 HIS ** B 592 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1078 HIS ** C 592 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1078 HIS ** D 592 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1078 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8272 moved from start: 0.2304 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.079 27904 Z= 0.416 Angle : 0.731 8.401 38612 Z= 0.392 Chirality : 0.041 0.153 4784 Planarity : 0.005 0.038 5048 Dihedral : 9.165 84.847 5416 Min Nonbonded Distance : 2.159 Molprobity Statistics. All-atom Clashscore : 5.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.90 % Favored : 98.10 % Rotamer: Outliers : 0.25 % Allowed : 4.24 % Favored : 95.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.13 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.09 (0.11), residues: 4260 helix: -0.49 (0.08), residues: 2848 sheet: -0.46 (0.39), residues: 232 loop : -0.93 (0.17), residues: 1180 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP A 842 HIS 0.005 0.001 HIS B 715 PHE 0.020 0.003 PHE B 905 TYR 0.025 0.002 TYR D 917 ARG 0.007 0.001 ARG D1135 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8520 Ramachandran restraints generated. 4260 Oldfield, 0 Emsley, 4260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8520 Ramachandran restraints generated. 4260 Oldfield, 0 Emsley, 4260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 265 residues out of total 3700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 261 time to evaluate : 2.972 Fit side-chains REVERT: A 76 MET cc_start: 0.9023 (mmm) cc_final: 0.8541 (ppp) REVERT: A 602 MET cc_start: 0.9083 (mmm) cc_final: 0.8713 (mmm) REVERT: A 683 MET cc_start: 0.9155 (mmm) cc_final: 0.8721 (tpp) REVERT: A 687 MET cc_start: 0.9488 (tmm) cc_final: 0.9237 (tmm) REVERT: A 1036 MET cc_start: 0.9428 (mmt) cc_final: 0.8967 (mmt) REVERT: A 1058 GLU cc_start: 0.9134 (mt-10) cc_final: 0.8719 (mm-30) REVERT: A 1138 MET cc_start: 0.8875 (ppp) cc_final: 0.8568 (ppp) REVERT: A 1150 MET cc_start: 0.9139 (tpp) cc_final: 0.8671 (tmm) REVERT: B 76 MET cc_start: 0.9024 (mmm) cc_final: 0.8539 (ppp) REVERT: B 602 MET cc_start: 0.9084 (mmm) cc_final: 0.8717 (mmm) REVERT: B 683 MET cc_start: 0.9156 (mmm) cc_final: 0.8721 (tpp) REVERT: B 687 MET cc_start: 0.9488 (tmm) cc_final: 0.9238 (tmm) REVERT: B 1058 GLU cc_start: 0.9130 (mt-10) cc_final: 0.8713 (mm-30) REVERT: B 1138 MET cc_start: 0.8875 (ppp) cc_final: 0.8570 (ppp) REVERT: B 1150 MET cc_start: 0.9140 (tpp) cc_final: 0.8669 (tmm) REVERT: C 76 MET cc_start: 0.9027 (mmm) cc_final: 0.8540 (ppp) REVERT: C 602 MET cc_start: 0.9083 (mmm) cc_final: 0.8715 (mmm) REVERT: C 683 MET cc_start: 0.9158 (mmm) cc_final: 0.8725 (tpp) REVERT: C 687 MET cc_start: 0.9489 (tmm) cc_final: 0.9237 (tmm) REVERT: C 1058 GLU cc_start: 0.9130 (mt-10) cc_final: 0.8712 (mm-30) REVERT: C 1138 MET cc_start: 0.8875 (ppp) cc_final: 0.8567 (ppp) REVERT: C 1150 MET cc_start: 0.9141 (tpp) cc_final: 0.8671 (tmm) REVERT: D 76 MET cc_start: 0.9026 (mmm) cc_final: 0.8541 (ppp) REVERT: D 602 MET cc_start: 0.9080 (mmm) cc_final: 0.8714 (mmm) REVERT: D 683 MET cc_start: 0.9159 (mmm) cc_final: 0.8724 (tpp) REVERT: D 687 MET cc_start: 0.9488 (tmm) cc_final: 0.9236 (tmm) REVERT: D 1036 MET cc_start: 0.9469 (mmm) cc_final: 0.9179 (mmm) REVERT: D 1058 GLU cc_start: 0.9130 (mt-10) cc_final: 0.8712 (mm-30) REVERT: D 1138 MET cc_start: 0.8876 (ppp) cc_final: 0.8569 (ppp) REVERT: D 1150 MET cc_start: 0.9140 (tpp) cc_final: 0.8669 (tmm) outliers start: 4 outliers final: 0 residues processed: 265 average time/residue: 0.3419 time to fit residues: 157.8387 Evaluate side-chains 219 residues out of total 3700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 219 time to evaluate : 2.961 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 428 random chunks: chunk 216 optimal weight: 40.0000 chunk 120 optimal weight: 50.0000 chunk 323 optimal weight: 40.0000 chunk 264 optimal weight: 5.9990 chunk 107 optimal weight: 60.0000 chunk 389 optimal weight: 0.0010 chunk 420 optimal weight: 50.0000 chunk 346 optimal weight: 50.0000 chunk 386 optimal weight: 0.9980 chunk 132 optimal weight: 50.0000 chunk 312 optimal weight: 5.9990 overall best weight: 10.5994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 82 HIS ** A1038 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 82 HIS ** B1038 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 82 HIS ** C1038 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 82 HIS ** D1038 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8369 moved from start: 0.3404 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 0.109 27904 Z= 0.635 Angle : 0.868 10.067 38612 Z= 0.459 Chirality : 0.045 0.191 4784 Planarity : 0.005 0.047 5048 Dihedral : 7.948 88.760 5416 Min Nonbonded Distance : 2.173 Molprobity Statistics. All-atom Clashscore : 8.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 0.50 % Allowed : 7.36 % Favored : 92.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.13 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.44 (0.13), residues: 4260 helix: 0.83 (0.09), residues: 2856 sheet: -0.71 (0.39), residues: 208 loop : -0.63 (0.18), residues: 1196 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.003 TRP B 842 HIS 0.006 0.002 HIS C 682 PHE 0.031 0.003 PHE B 948 TYR 0.035 0.003 TYR D 917 ARG 0.006 0.001 ARG C1135 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8520 Ramachandran restraints generated. 4260 Oldfield, 0 Emsley, 4260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8520 Ramachandran restraints generated. 4260 Oldfield, 0 Emsley, 4260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 235 residues out of total 3700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 227 time to evaluate : 3.110 Fit side-chains REVERT: A 76 MET cc_start: 0.9081 (mmm) cc_final: 0.8818 (mmm) REVERT: A 676 CYS cc_start: 0.9325 (m) cc_final: 0.9072 (t) REVERT: A 683 MET cc_start: 0.9318 (mmm) cc_final: 0.8907 (tpp) REVERT: A 687 MET cc_start: 0.9610 (tmm) cc_final: 0.9323 (tmm) REVERT: A 933 GLU cc_start: 0.9315 (tm-30) cc_final: 0.9082 (tm-30) REVERT: A 1036 MET cc_start: 0.9473 (mmt) cc_final: 0.8854 (mmt) REVERT: A 1058 GLU cc_start: 0.9066 (mt-10) cc_final: 0.8727 (mm-30) REVERT: A 1138 MET cc_start: 0.8947 (ppp) cc_final: 0.8511 (ppp) REVERT: A 1150 MET cc_start: 0.8998 (tpp) cc_final: 0.8642 (tmm) REVERT: B 76 MET cc_start: 0.9069 (mmm) cc_final: 0.8818 (mmm) REVERT: B 676 CYS cc_start: 0.9328 (m) cc_final: 0.9068 (t) REVERT: B 683 MET cc_start: 0.9321 (mmm) cc_final: 0.8918 (tpp) REVERT: B 933 GLU cc_start: 0.9314 (tm-30) cc_final: 0.9092 (tm-30) REVERT: B 1036 MET cc_start: 0.9445 (mmt) cc_final: 0.8868 (mmt) REVERT: B 1058 GLU cc_start: 0.9062 (mt-10) cc_final: 0.8725 (mm-30) REVERT: B 1138 MET cc_start: 0.8947 (ppp) cc_final: 0.8510 (ppp) REVERT: B 1150 MET cc_start: 0.8994 (tpp) cc_final: 0.8641 (tmm) REVERT: C 76 MET cc_start: 0.9071 (mmm) cc_final: 0.8817 (mmm) REVERT: C 676 CYS cc_start: 0.9327 (m) cc_final: 0.9068 (t) REVERT: C 683 MET cc_start: 0.9321 (mmm) cc_final: 0.8916 (tpp) REVERT: C 933 GLU cc_start: 0.9309 (tm-30) cc_final: 0.9092 (tm-30) REVERT: C 1036 MET cc_start: 0.9441 (mmt) cc_final: 0.8869 (mmt) REVERT: C 1058 GLU cc_start: 0.9061 (mt-10) cc_final: 0.8725 (mm-30) REVERT: C 1138 MET cc_start: 0.8944 (ppp) cc_final: 0.8506 (ppp) REVERT: C 1150 MET cc_start: 0.8996 (tpp) cc_final: 0.8641 (tmm) REVERT: D 76 MET cc_start: 0.9072 (mmm) cc_final: 0.8817 (mmm) REVERT: D 676 CYS cc_start: 0.9326 (m) cc_final: 0.9071 (t) REVERT: D 683 MET cc_start: 0.9321 (mmm) cc_final: 0.8911 (tpp) REVERT: D 687 MET cc_start: 0.9607 (tmm) cc_final: 0.9324 (tmm) REVERT: D 933 GLU cc_start: 0.9313 (tm-30) cc_final: 0.9089 (tm-30) REVERT: D 1058 GLU cc_start: 0.9064 (mt-10) cc_final: 0.8723 (mm-30) REVERT: D 1138 MET cc_start: 0.8946 (ppp) cc_final: 0.8511 (ppp) REVERT: D 1150 MET cc_start: 0.8996 (tpp) cc_final: 0.8641 (tmm) outliers start: 8 outliers final: 4 residues processed: 235 average time/residue: 0.3092 time to fit residues: 126.5528 Evaluate side-chains 220 residues out of total 3700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 216 time to evaluate : 2.852 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 428 random chunks: chunk 384 optimal weight: 1.9990 chunk 292 optimal weight: 0.9990 chunk 202 optimal weight: 0.8980 chunk 43 optimal weight: 0.0570 chunk 185 optimal weight: 0.9990 chunk 261 optimal weight: 20.0000 chunk 390 optimal weight: 0.9980 chunk 413 optimal weight: 0.9980 chunk 204 optimal weight: 0.9980 chunk 370 optimal weight: 0.9990 chunk 111 optimal weight: 50.0000 overall best weight: 0.7898 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Sorry: Reduce crashed with command 'molprobity.reduce -quiet -trim -'. Dumping stdin to file 'reduce_failure.pdb'. Return code: -15 Dumping stderr: