Starting phenix.real_space_refine on Sat Aug 10 08:40:43 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8cyc_27074/08_2024/8cyc_27074.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8cyc_27074/08_2024/8cyc_27074.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8cyc_27074/08_2024/8cyc_27074.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8cyc_27074/08_2024/8cyc_27074.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8cyc_27074/08_2024/8cyc_27074.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8cyc_27074/08_2024/8cyc_27074.cif" } resolution = 2.9 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= 0.019 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 123 5.16 5 C 18247 2.51 5 N 4831 2.21 5 O 5496 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 298": "OE1" <-> "OE2" Residue "A GLU 1017": "OE1" <-> "OE2" Residue "A GLU 1031": "OE1" <-> "OE2" Residue "B PHE 541": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 660": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 745": "OD1" <-> "OD2" Residue "C GLU 298": "OE1" <-> "OE2" Residue "F PHE 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/chem_data/mon_lib" Total number of atoms: 28697 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 8560 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1097, 8560 Classifications: {'peptide': 1097} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 55, 'TRANS': 1041} 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: 8594 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1102, 8594 Classifications: {'peptide': 1102} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 55, 'TRANS': 1046} 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: 8564 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1097, 8564 Classifications: {'peptide': 1097} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 55, 'TRANS': 1041} 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: 993 Number of conformers: 1 Conformer: "" Number of residues, atoms: 127, 993 Classifications: {'peptide': 127} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 123} Chain: "E" Number of atoms: 993 Number of conformers: 1 Conformer: "" Number of residues, atoms: 127, 993 Classifications: {'peptide': 127} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 123} Chain: "F" Number of atoms: 993 Number of conformers: 1 Conformer: "" Number of residues, atoms: 127, 993 Classifications: {'peptide': 127} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 123} Time building chain proxies: 16.30, per 1000 atoms: 0.57 Number of scatterers: 28697 At special positions: 0 Unit cell: (159.43, 165.85, 194.74, 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 123 16.00 O 5496 8.00 N 4831 7.00 C 18247 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=43, symmetry=0 Simple disulfide: pdb=" SG CYS A 15 " - pdb=" SG CYS A 136 " distance=2.03 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.03 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=2.03 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 15 " - pdb=" SG CYS B 136 " distance=2.03 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " 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 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 15 " - pdb=" SG CYS C 136 " distance=2.03 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 166 " 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 96 " distance=2.03 Simple disulfide: pdb=" SG CYS E 22 " - pdb=" SG CYS E 96 " distance=2.03 Simple disulfide: pdb=" SG CYS F 22 " - pdb=" SG CYS F 96 " 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: 10.37 Conformation dependent library (CDL) restraints added in 5.1 seconds 7306 Ramachandran restraints generated. 3653 Oldfield, 0 Emsley, 3653 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6842 Finding SS restraints... Secondary structure from input PDB file: 77 helices and 57 sheets defined 23.3% alpha, 26.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.35 Creating SS restraints... Processing helix chain 'A' and resid 294 through 303 Processing helix chain 'A' and resid 338 through 343 Processing helix chain 'A' and resid 349 through 353 removed outlier: 3.870A pdb=" N TRP A 353 " --> pdb=" O VAL A 350 " (cutoff:3.500A) Processing helix chain 'A' and resid 365 through 370 Processing helix chain 'A' and resid 405 through 410 removed outlier: 4.083A pdb=" N ARG A 408 " --> pdb=" O ASP A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 422 Processing helix chain 'A' and resid 629 through 638 removed outlier: 5.767A pdb=" N VAL A 635 " --> pdb=" O PRO A 631 " (cutoff:3.500A) removed outlier: 4.361A pdb=" N TYR A 636 " --> pdb=" O THR A 632 " (cutoff:3.500A) Processing helix chain 'A' and resid 737 through 743 Processing helix chain 'A' and resid 746 through 755 removed outlier: 3.536A 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 removed outlier: 4.126A pdb=" N VAL A 826 " --> pdb=" O LEU A 822 " (cutoff:3.500A) Processing helix chain 'A' and resid 866 through 885 Processing helix chain 'A' and resid 897 through 909 Processing helix chain 'A' and resid 914 through 920 Processing helix chain 'A' and resid 920 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 1032 removed outlier: 4.840A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) Processing helix chain 'A' and resid 1141 through 1147 Processing helix chain 'B' and resid 294 through 304 Processing helix chain 'B' and resid 337 through 343 removed outlier: 3.766A pdb=" N VAL B 341 " --> pdb=" O PRO B 337 " (cutoff:3.500A) Processing helix chain 'B' and resid 349 through 353 removed outlier: 3.706A pdb=" N TRP B 353 " --> pdb=" O VAL B 350 " (cutoff:3.500A) Processing helix chain 'B' and resid 364 through 371 removed outlier: 4.571A pdb=" N LEU B 368 " --> pdb=" O ASP B 364 " (cutoff:3.500A) Processing helix chain 'B' and resid 383 through 389 removed outlier: 4.120A pdb=" N ASP B 389 " --> pdb=" O THR B 385 " (cutoff:3.500A) Processing helix chain 'B' and resid 406 through 410 Processing helix chain 'B' and resid 439 through 443 removed outlier: 3.570A pdb=" N ASP B 442 " --> pdb=" O ASN B 439 " (cutoff:3.500A) Processing helix chain 'B' and resid 502 through 506 removed outlier: 3.875A pdb=" N GLN B 506 " --> pdb=" O VAL B 503 " (cutoff:3.500A) Processing helix chain 'B' and resid 616 through 623 removed outlier: 3.791A pdb=" N VAL B 620 " --> pdb=" O CYS B 617 " (cutoff:3.500A) Proline residue: B 621 - end of helix Processing helix chain 'B' and resid 633 through 638 removed outlier: 3.609A pdb=" N THR B 638 " --> pdb=" O ARG B 634 " (cutoff:3.500A) Processing helix chain 'B' and resid 737 through 743 Processing helix chain 'B' and resid 746 through 755 removed outlier: 3.567A 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 removed outlier: 3.680A pdb=" N LYS B 825 " --> pdb=" O LEU B 821 " (cutoff:3.500A) Processing helix chain 'B' and resid 866 through 884 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 919 removed outlier: 3.708A pdb=" N TYR B 917 " --> pdb=" O GLN B 913 " (cutoff:3.500A) Processing helix chain 'B' and resid 919 through 941 Processing helix chain 'B' and resid 942 through 944 No H-bonds generated for 'chain 'B' and resid 942 through 944' 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 1032 removed outlier: 4.722A 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 removed outlier: 3.678A pdb=" N GLU C 298 " --> pdb=" O ASP C 294 " (cutoff:3.500A) Processing helix chain 'C' and resid 337 through 343 removed outlier: 4.065A pdb=" N VAL C 341 " --> pdb=" O PRO C 337 " (cutoff:3.500A) Processing helix chain 'C' and resid 349 through 353 Processing helix chain 'C' and resid 365 through 370 Processing helix chain 'C' and resid 383 through 387 removed outlier: 3.944A pdb=" N LEU C 387 " --> pdb=" O PRO C 384 " (cutoff:3.500A) Processing helix chain 'C' and resid 406 through 411 Processing helix chain 'C' and resid 416 through 422 removed outlier: 3.654A pdb=" N ASN C 422 " --> pdb=" O ILE C 418 " (cutoff:3.500A) Processing helix chain 'C' and resid 438 through 443 removed outlier: 3.507A pdb=" N SER C 443 " --> pdb=" O ASN C 439 " (cutoff:3.500A) Processing helix chain 'C' and resid 629 through 634 Processing helix chain 'C' and resid 635 through 637 No H-bonds generated for 'chain 'C' and resid 635 through 637' Processing helix chain 'C' and resid 737 through 743 Processing helix chain 'C' and resid 746 through 755 removed outlier: 3.622A 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 817 through 826 Processing helix chain 'C' and resid 866 through 885 Processing helix chain 'C' and resid 886 through 890 removed outlier: 3.665A pdb=" N GLY C 889 " --> pdb=" O TRP C 886 " (cutoff:3.500A) Processing helix chain 'C' and resid 897 through 909 removed outlier: 3.542A pdb=" N ILE C 909 " --> pdb=" O ARG C 905 " (cutoff:3.500A) Processing helix chain 'C' and resid 913 through 919 removed outlier: 3.817A pdb=" N TYR C 917 " --> pdb=" O GLN C 913 " (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 1033 removed outlier: 4.174A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) Processing helix chain 'C' and resid 1116 through 1118 No H-bonds generated for 'chain 'C' and resid 1116 through 1118' Processing helix chain 'C' and resid 1140 through 1147 removed outlier: 4.061A pdb=" N GLU C1144 " --> pdb=" O PRO C1140 " (cutoff:3.500A) Processing helix chain 'D' and resid 26 through 32 removed outlier: 3.524A pdb=" N SER D 30 " --> pdb=" O ARG D 27 " (cutoff:3.500A) Processing helix chain 'D' and resid 87 through 91 Processing helix chain 'D' and resid 104 through 110 removed outlier: 3.619A pdb=" N TYR D 108 " --> pdb=" O SER D 104 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N TYR D 109 " --> pdb=" O ARG D 105 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N ASN D 110 " --> pdb=" O SER D 106 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 104 through 110' Processing helix chain 'E' and resid 87 through 91 Processing helix chain 'E' and resid 104 through 109 removed outlier: 3.645A pdb=" N TYR E 109 " --> pdb=" O ARG E 105 " (cutoff:3.500A) Processing helix chain 'F' and resid 87 through 91 Processing helix chain 'F' and resid 104 through 114 removed outlier: 4.034A pdb=" N TYR F 109 " --> pdb=" O SER F 106 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N ASN F 110 " --> pdb=" O LYS F 107 " (cutoff:3.500A) removed outlier: 5.684A pdb=" N LEU F 111 " --> pdb=" O TYR F 108 " (cutoff:3.500A) removed outlier: 6.566A pdb=" N ASP F 112 " --> pdb=" O TYR F 109 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N GLU F 113 " --> pdb=" O ASN F 110 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N TYR F 114 " --> pdb=" O LEU F 111 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 27 through 30 removed outlier: 4.047A pdb=" N ALA A 27 " --> pdb=" O TRP A 64 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 27 through 30 removed outlier: 4.047A pdb=" N ALA A 27 " --> pdb=" O TRP A 64 " (cutoff:3.500A) removed outlier: 8.120A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 6.522A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 4.220A pdb=" N ALA A 264 " --> pdb=" O THR A 95 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 36 through 37 removed outlier: 6.601A pdb=" N VAL A 36 " --> pdb=" O LEU A 223 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'A' and resid 47 through 55 removed outlier: 3.906A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 118 through 121 Processing sheet with id=AA6, first strand: chain 'A' and resid 141 through 143 removed outlier: 6.334A pdb=" N LEU A 141 " --> pdb=" O LEU A 244 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'A' and resid 311 through 318 removed outlier: 3.508A pdb=" N THR A 599 " --> pdb=" O GLY A 311 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N TYR A 313 " --> pdb=" O VAL A 597 " (cutoff:3.500A) removed outlier: 7.342A pdb=" N VAL A 595 " --> pdb=" O THR A 315 " (cutoff:3.500A) removed outlier: 5.087A pdb=" N ASN A 317 " --> pdb=" O GLY A 593 " (cutoff:3.500A) removed outlier: 7.207A pdb=" N GLY A 593 " --> pdb=" O ASN A 317 " (cutoff:3.500A) removed outlier: 4.071A pdb=" N GLY A 594 " --> pdb=" O GLN A 613 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 354 through 358 removed outlier: 3.740A pdb=" N ASN A 394 " --> pdb=" O GLU A 516 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 361 through 362 removed outlier: 7.223A pdb=" N CYS A 361 " --> pdb=" O CYS A 525 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AB2, first strand: chain 'A' and resid 473 through 474 removed outlier: 4.137A pdb=" N TYR A 473 " --> pdb=" O TYR A 489 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N TYR A 489 " --> pdb=" O TYR A 473 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'A' and resid 538 through 543 removed outlier: 5.658A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) removed outlier: 6.478A pdb=" N GLY A 566 " --> pdb=" O ASP A 574 " (cutoff:3.500A) removed outlier: 6.766A pdb=" N PHE A 565 " --> pdb=" O PHE C 43 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 654 through 655 removed outlier: 5.508A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 8.199A pdb=" N THR A 696 " --> pdb=" O GLU A 654 " (cutoff:3.500A) removed outlier: 6.651A pdb=" N ILE A 670 " --> pdb=" O ILE A 666 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 711 through 728 removed outlier: 3.960A pdb=" N ILE A 714 " --> pdb=" O LYS A1073 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N LYS A1073 " --> pdb=" O ILE A 714 " (cutoff:3.500A) removed outlier: 6.486A pdb=" N GLN A1071 " --> pdb=" O THR A 716 " (cutoff:3.500A) removed outlier: 6.406A pdb=" N PHE A 718 " --> pdb=" O PRO A1069 " (cutoff:3.500A) removed outlier: 7.076A pdb=" N ILE A 720 " --> pdb=" O TYR A1067 " (cutoff:3.500A) removed outlier: 7.056A pdb=" N TYR A1067 " --> pdb=" O ILE A 720 " (cutoff:3.500A) removed outlier: 6.841A pdb=" N VAL A 722 " --> pdb=" O VAL A1065 " (cutoff:3.500A) removed outlier: 6.769A pdb=" N VAL A1065 " --> pdb=" O VAL A 722 " (cutoff:3.500A) removed outlier: 6.939A pdb=" N THR A 724 " --> pdb=" O LEU A1063 " (cutoff:3.500A) removed outlier: 6.904A pdb=" N LEU A1063 " --> pdb=" O THR A 724 " (cutoff:3.500A) removed outlier: 6.940A pdb=" N ILE A 726 " --> pdb=" O VAL A1061 " (cutoff:3.500A) removed outlier: 6.948A pdb=" N VAL A1061 " --> pdb=" O ILE A 726 " (cutoff:3.500A) removed outlier: 6.388A pdb=" N GLY A1059 " --> pdb=" O PRO A 728 " (cutoff:3.500A) removed outlier: 6.822A pdb=" N GLY A1059 " --> pdb=" O SER A1055 " (cutoff:3.500A) removed outlier: 5.128A pdb=" N SER A1055 " --> pdb=" O GLY A1059 " (cutoff:3.500A) removed outlier: 6.729A pdb=" N VAL A1061 " --> pdb=" O PRO A1053 " (cutoff:3.500A) removed outlier: 6.472A pdb=" N LEU A1063 " --> pdb=" O SER A1051 " (cutoff:3.500A) removed outlier: 4.575A pdb=" N SER A1051 " --> pdb=" O LEU A1063 " (cutoff:3.500A) removed outlier: 6.944A pdb=" N VAL A1065 " --> pdb=" O LEU A1049 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 734 through 736 Processing sheet with id=AB7, first strand: chain 'A' and resid 787 through 789 Processing sheet with id=AB8, first strand: chain 'A' and resid 1120 through 1125 removed outlier: 4.260A pdb=" N ALA A1087 " --> pdb=" O SER A1123 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'A' and resid 1094 through 1097 Processing sheet with id=AC1, first strand: chain 'B' and resid 27 through 30 removed outlier: 3.893A pdb=" N ALA B 27 " --> pdb=" O TRP B 64 " (cutoff:3.500A) removed outlier: 7.976A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 6.137A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N ALA B 264 " --> pdb=" O THR B 95 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N VAL B 227 " --> pdb=" O ILE B 203 " (cutoff:3.500A) removed outlier: 6.062A pdb=" N SER B 205 " --> pdb=" O PRO B 225 " (cutoff:3.500A) removed outlier: 8.967A pdb=" N HIS B 207 " --> pdb=" O LEU B 223 " (cutoff:3.500A) removed outlier: 8.804A pdb=" N LEU B 223 " --> pdb=" O HIS B 207 " (cutoff:3.500A) removed outlier: 7.439A pdb=" N VAL B 36 " --> pdb=" O LEU B 223 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 27 through 30 removed outlier: 3.893A pdb=" N ALA B 27 " --> pdb=" O TRP B 64 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 47 through 55 removed outlier: 3.947A 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: 6.125A pdb=" N ALA B 243 " --> pdb=" O ILE B 101 " (cutoff:3.500A) removed outlier: 5.650A pdb=" N ILE B 101 " --> pdb=" O ALA B 243 " (cutoff:3.500A) removed outlier: 6.412A pdb=" N ARG B 102 " --> pdb=" O ASN B 121 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N PHE B 168 " --> pdb=" O VAL B 130 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 151 through 153 removed outlier: 3.789A pdb=" N SER B 151 " --> pdb=" O HIS B 146 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N HIS B 146 " --> pdb=" O SER B 151 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N ARG B 246 " --> pdb=" O VAL B 143 " (cutoff:3.500A) removed outlier: 6.027A pdb=" N TYR B 145 " --> pdb=" O ARG B 246 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 311 through 318 removed outlier: 6.938A pdb=" N VAL B 595 " --> pdb=" O THR B 315 " (cutoff:3.500A) removed outlier: 5.267A pdb=" N ASN B 317 " --> pdb=" O GLY B 593 " (cutoff:3.500A) removed outlier: 7.292A pdb=" N GLY B 593 " --> pdb=" O ASN B 317 " (cutoff:3.500A) removed outlier: 5.057A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 325 through 326 Processing sheet with id=AC8, first strand: chain 'B' and resid 354 through 357 removed outlier: 3.831A pdb=" N ILE B 434 " --> pdb=" O VAL B 511 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AD1, first strand: chain 'B' and resid 473 through 474 removed outlier: 4.023A pdb=" N TYR B 473 " --> pdb=" O TYR B 489 " (cutoff:3.500A) removed outlier: 4.353A pdb=" N TYR B 489 " --> pdb=" O TYR B 473 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD1 Processing sheet with id=AD2, first strand: chain 'B' and resid 654 through 655 removed outlier: 5.759A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 8.538A pdb=" N THR B 696 " --> pdb=" O GLU B 654 " (cutoff:3.500A) removed outlier: 6.447A pdb=" N ILE B 670 " --> pdb=" O ILE B 666 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 711 through 728 removed outlier: 6.471A pdb=" N GLN B1071 " --> pdb=" O THR B 716 " (cutoff:3.500A) removed outlier: 6.460A pdb=" N PHE B 718 " --> pdb=" O PRO B1069 " (cutoff:3.500A) removed outlier: 7.087A pdb=" N ILE B 720 " --> pdb=" O TYR B1067 " (cutoff:3.500A) removed outlier: 7.052A pdb=" N TYR B1067 " --> pdb=" O ILE B 720 " (cutoff:3.500A) removed outlier: 6.816A pdb=" N VAL B 722 " --> pdb=" O VAL B1065 " (cutoff:3.500A) removed outlier: 6.786A pdb=" N VAL B1065 " --> pdb=" O VAL B 722 " (cutoff:3.500A) removed outlier: 6.880A pdb=" N THR B 724 " --> pdb=" O LEU B1063 " (cutoff:3.500A) removed outlier: 6.940A pdb=" N LEU B1063 " --> pdb=" O THR B 724 " (cutoff:3.500A) removed outlier: 6.939A pdb=" N ILE B 726 " --> pdb=" O VAL B1061 " (cutoff:3.500A) removed outlier: 6.956A pdb=" N VAL B1061 " --> pdb=" O ILE B 726 " (cutoff:3.500A) removed outlier: 6.212A pdb=" N GLY B1059 " --> pdb=" O PRO B 728 " (cutoff:3.500A) removed outlier: 5.886A pdb=" N TYR B1067 " --> pdb=" O HIS B1048 " (cutoff:3.500A) removed outlier: 5.823A pdb=" N HIS B1048 " --> pdb=" O TYR B1067 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 787 through 789 Processing sheet with id=AD5, first strand: chain 'B' and resid 1120 through 1122 Processing sheet with id=AD6, first strand: chain 'B' and resid 1094 through 1097 removed outlier: 4.514A pdb=" N GLN B1106 " --> pdb=" O GLU B1111 " (cutoff:3.500A) removed outlier: 5.296A pdb=" N GLU B1111 " --> pdb=" O GLN B1106 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 27 through 30 removed outlier: 3.887A pdb=" N ALA C 27 " --> pdb=" O TRP C 64 " (cutoff:3.500A) removed outlier: 8.288A pdb=" N ASN C 61 " --> pdb=" O TYR C 269 " (cutoff:3.500A) removed outlier: 6.034A pdb=" N TYR C 269 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 4.095A pdb=" N ALA C 264 " --> pdb=" O THR C 95 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N THR C 95 " --> pdb=" O ALA C 264 " (cutoff:3.500A) removed outlier: 4.092A pdb=" N LYS C 187 " --> pdb=" O ILE C 210 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N ILE C 197 " --> pdb=" O TYR C 200 " (cutoff:3.500A) removed outlier: 5.524A pdb=" N PHE C 201 " --> pdb=" O ASP C 228 " (cutoff:3.500A) removed outlier: 4.112A pdb=" N ASP C 228 " --> pdb=" O PHE C 201 " (cutoff:3.500A) removed outlier: 7.160A pdb=" N ILE C 203 " --> pdb=" O LEU C 226 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 47 through 55 removed outlier: 7.711A pdb=" N THR C 274 " --> pdb=" O ASP C 290 " (cutoff:3.500A) removed outlier: 5.259A pdb=" N ASP C 290 " --> pdb=" O THR C 274 " (cutoff:3.500A) removed outlier: 6.751A pdb=" N LEU C 276 " --> pdb=" O ALA C 288 " (cutoff:3.500A) removed outlier: 4.420A pdb=" N ALA C 288 " --> pdb=" O LEU C 276 " (cutoff:3.500A) removed outlier: 6.793A pdb=" N LYS C 278 " --> pdb=" O THR C 286 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 164 through 171 removed outlier: 6.343A pdb=" N CYS C 166 " --> pdb=" O GLU C 132 " (cutoff:3.500A) removed outlier: 7.505A pdb=" N GLU C 132 " --> pdb=" O CYS C 166 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 151 through 157 removed outlier: 3.584A pdb=" N SER C 151 " --> pdb=" O HIS C 146 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N HIS C 146 " --> pdb=" O SER C 151 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N SER C 155 " --> pdb=" O GLY C 142 " (cutoff:3.500A) removed outlier: 7.052A pdb=" N GLY C 142 " --> pdb=" O SER C 155 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N LEU C 244 " --> pdb=" O LEU C 141 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N VAL C 143 " --> pdb=" O LEU C 244 " (cutoff:3.500A) removed outlier: 5.029A pdb=" N ARG C 246 " --> pdb=" O VAL C 143 " (cutoff:3.500A) removed outlier: 7.549A pdb=" N TYR C 145 " --> pdb=" O ARG C 246 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 311 through 317 removed outlier: 3.607A pdb=" N THR C 599 " --> pdb=" O GLY C 311 " (cutoff:3.500A) removed outlier: 6.987A pdb=" N VAL C 595 " --> pdb=" O THR C 315 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N GLY C 594 " --> pdb=" O GLN C 613 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 326 through 328 removed outlier: 5.949A pdb=" N ASP C 574 " --> pdb=" O ILE C 587 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 354 through 358 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 452 through 454 Processing sheet with id=AE7, first strand: chain 'C' and resid 654 through 655 removed outlier: 5.701A pdb=" N GLU C 654 " --> pdb=" O ALA C 694 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'C' and resid 711 through 728 removed outlier: 4.003A pdb=" N LYS C1073 " --> pdb=" O ILE C 714 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N GLN C1071 " --> pdb=" O THR C 716 " (cutoff:3.500A) removed outlier: 6.393A pdb=" N PHE C 718 " --> pdb=" O PRO C1069 " (cutoff:3.500A) removed outlier: 7.102A pdb=" N ILE C 720 " --> pdb=" O TYR C1067 " (cutoff:3.500A) removed outlier: 7.100A pdb=" N TYR C1067 " --> pdb=" O ILE C 720 " (cutoff:3.500A) removed outlier: 6.912A pdb=" N VAL C 722 " --> pdb=" O VAL C1065 " (cutoff:3.500A) removed outlier: 6.927A pdb=" N VAL C1065 " --> pdb=" O VAL C 722 " (cutoff:3.500A) removed outlier: 6.998A pdb=" N THR C 724 " --> pdb=" O LEU C1063 " (cutoff:3.500A) removed outlier: 6.954A pdb=" N LEU C1063 " --> pdb=" O THR C 724 " (cutoff:3.500A) removed outlier: 6.853A pdb=" N ILE C 726 " --> pdb=" O VAL C1061 " (cutoff:3.500A) removed outlier: 6.924A pdb=" N VAL C1061 " --> pdb=" O ILE C 726 " (cutoff:3.500A) removed outlier: 6.008A pdb=" N GLY C1059 " --> pdb=" O PRO C 728 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N MET C1050 " --> pdb=" O VAL C1065 " (cutoff:3.500A) removed outlier: 6.385A pdb=" N TYR C1067 " --> pdb=" O HIS C1048 " (cutoff:3.500A) removed outlier: 6.498A pdb=" N HIS C1048 " --> pdb=" O TYR C1067 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'C' and resid 733 through 736 removed outlier: 4.363A pdb=" N LYS C 733 " --> pdb=" O LEU C 861 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'C' and resid 807 through 808 removed outlier: 4.469A pdb=" N ARG C 815 " --> pdb=" O ASP C 808 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'C' and resid 1120 through 1125 removed outlier: 4.000A pdb=" N ALA C1087 " --> pdb=" O SER C1123 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'C' and resid 1094 through 1097 Processing sheet with id=AF4, first strand: chain 'D' and resid 3 through 7 removed outlier: 4.089A pdb=" N GLN D 3 " --> pdb=" O SER D 25 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'D' and resid 10 through 13 removed outlier: 6.069A pdb=" N GLY D 10 " --> pdb=" O THR D 124 " (cutoff:3.500A) removed outlier: 7.624A pdb=" N SER D 126 " --> pdb=" O GLY D 10 " (cutoff:3.500A) removed outlier: 6.349A pdb=" N VAL D 12 " --> pdb=" O SER D 126 " (cutoff:3.500A) removed outlier: 6.057A pdb=" N ARG D 38 " --> pdb=" O PHE D 47 " (cutoff:3.500A) removed outlier: 5.406A pdb=" N PHE D 47 " --> pdb=" O ARG D 38 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'D' and resid 10 through 13 removed outlier: 6.069A pdb=" N GLY D 10 " --> pdb=" O THR D 124 " (cutoff:3.500A) removed outlier: 7.624A pdb=" N SER D 126 " --> pdb=" O GLY D 10 " (cutoff:3.500A) removed outlier: 6.349A pdb=" N VAL D 12 " --> pdb=" O SER D 126 " (cutoff:3.500A) removed outlier: 4.556A pdb=" N VAL D 98 " --> pdb=" O ASP D 116 " (cutoff:3.500A) removed outlier: 4.625A pdb=" N ASP D 116 " --> pdb=" O VAL D 98 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'E' and resid 3 through 7 removed outlier: 3.692A pdb=" N GLN E 3 " --> pdb=" O SER E 25 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N CYS E 22 " --> pdb=" O VAL E 79 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N VAL E 79 " --> pdb=" O CYS E 22 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N THR E 69 " --> pdb=" O GLN E 82 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'E' and resid 11 through 13 removed outlier: 6.772A pdb=" N VAL E 12 " --> pdb=" O SER E 126 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF8 Processing sheet with id=AF9, first strand: chain 'E' and resid 58 through 60 removed outlier: 5.902A pdb=" N PHE E 47 " --> pdb=" O ARG E 38 " (cutoff:3.500A) removed outlier: 6.401A pdb=" N ARG E 38 " --> pdb=" O PHE E 47 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ALA E 49 " --> pdb=" O TRP E 36 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'F' and resid 3 through 7 Processing sheet with id=AG2, first strand: chain 'F' and resid 10 through 13 removed outlier: 6.172A pdb=" N ARG F 38 " --> pdb=" O PHE F 47 " (cutoff:3.500A) removed outlier: 5.918A pdb=" N PHE F 47 " --> pdb=" O ARG F 38 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'F' and resid 10 through 13 removed outlier: 4.112A pdb=" N VAL F 98 " --> pdb=" O ASP F 116 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N ASP F 116 " --> pdb=" O VAL F 98 " (cutoff:3.500A) 1111 hydrogen bonds defined for protein. 2997 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: 12.46 Time building geometry restraints manager: 11.46 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 9348 1.34 - 1.46: 7064 1.46 - 1.58: 12807 1.58 - 1.70: 0 1.70 - 1.82: 156 Bond restraints: 29375 Sorted by residual: bond pdb=" N VAL B 826 " pdb=" CA VAL B 826 " ideal model delta sigma weight residual 1.459 1.497 -0.038 1.25e-02 6.40e+03 9.21e+00 bond pdb=" CA SER C 50 " pdb=" CB SER C 50 " ideal model delta sigma weight residual 1.527 1.492 0.034 1.27e-02 6.20e+03 7.34e+00 bond pdb=" N LEU B 822 " pdb=" CA LEU B 822 " ideal model delta sigma weight residual 1.457 1.489 -0.032 1.24e-02 6.50e+03 6.56e+00 bond pdb=" N ASP B 830 " pdb=" CA ASP B 830 " ideal model delta sigma weight residual 1.457 1.488 -0.031 1.29e-02 6.01e+03 5.62e+00 bond pdb=" N THR B 827 " pdb=" CA THR B 827 " ideal model delta sigma weight residual 1.454 1.484 -0.030 1.32e-02 5.74e+03 5.19e+00 ... (remaining 29370 not shown) Histogram of bond angle deviations from ideal: 99.76 - 106.61: 796 106.61 - 113.45: 15653 113.45 - 120.30: 10077 120.30 - 127.15: 13183 127.15 - 134.00: 275 Bond angle restraints: 39984 Sorted by residual: angle pdb=" C PHE B 32 " pdb=" CA PHE B 32 " pdb=" CB PHE B 32 " ideal model delta sigma weight residual 117.23 110.50 6.73 1.36e+00 5.41e-01 2.45e+01 angle pdb=" N VAL C 83 " pdb=" CA VAL C 83 " pdb=" C VAL C 83 " ideal model delta sigma weight residual 111.77 107.75 4.02 1.04e+00 9.25e-01 1.49e+01 angle pdb=" N ILE C 410 " pdb=" CA ILE C 410 " pdb=" C ILE C 410 " ideal model delta sigma weight residual 112.29 108.80 3.49 9.40e-01 1.13e+00 1.38e+01 angle pdb=" CA THR B 827 " pdb=" C THR B 827 " pdb=" O THR B 827 " ideal model delta sigma weight residual 121.87 117.90 3.97 1.10e+00 8.26e-01 1.30e+01 angle pdb=" N PHE B 823 " pdb=" CA PHE B 823 " pdb=" C PHE B 823 " ideal model delta sigma weight residual 111.33 107.00 4.33 1.21e+00 6.83e-01 1.28e+01 ... (remaining 39979 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.94: 15809 17.94 - 35.88: 1336 35.88 - 53.82: 228 53.82 - 71.76: 57 71.76 - 89.70: 26 Dihedral angle restraints: 17456 sinusoidal: 6778 harmonic: 10678 Sorted by residual: dihedral pdb=" CB CYS A 662 " pdb=" SG CYS A 662 " pdb=" SG CYS A 671 " pdb=" CB CYS A 671 " ideal model delta sinusoidal sigma weight residual 93.00 4.26 88.74 1 1.00e+01 1.00e-02 9.39e+01 dihedral pdb=" CB CYS B1082 " pdb=" SG CYS B1082 " pdb=" SG CYS B1126 " pdb=" CB CYS B1126 " ideal model delta sinusoidal sigma weight residual -86.00 -10.11 -75.89 1 1.00e+01 1.00e-02 7.26e+01 dihedral pdb=" CB CYS A1082 " pdb=" SG CYS A1082 " pdb=" SG CYS A1126 " pdb=" CB CYS A1126 " ideal model delta sinusoidal sigma weight residual -86.00 -16.81 -69.19 1 1.00e+01 1.00e-02 6.19e+01 ... (remaining 17453 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.043: 3377 0.043 - 0.087: 746 0.087 - 0.130: 336 0.130 - 0.173: 13 0.173 - 0.217: 6 Chirality restraints: 4478 Sorted by residual: chirality pdb=" CB ILE A 105 " pdb=" CA ILE A 105 " pdb=" CG1 ILE A 105 " pdb=" CG2 ILE A 105 " both_signs ideal model delta sigma weight residual False 2.64 2.86 -0.22 2.00e-01 2.50e+01 1.17e+00 chirality pdb=" CA ILE A 119 " pdb=" N ILE A 119 " pdb=" C ILE A 119 " pdb=" CB ILE A 119 " both_signs ideal model delta sigma weight residual False 2.43 2.64 -0.20 2.00e-01 2.50e+01 1.03e+00 chirality pdb=" CA ASN B 824 " pdb=" N ASN B 824 " pdb=" C ASN B 824 " pdb=" CB ASN B 824 " both_signs ideal model delta sigma weight residual False 2.51 2.70 -0.19 2.00e-01 2.50e+01 9.22e-01 ... (remaining 4475 not shown) Planarity restraints: 5210 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP A 104 " -0.019 2.00e-02 2.50e+03 1.83e-02 8.34e+00 pdb=" CG TRP A 104 " 0.048 2.00e-02 2.50e+03 pdb=" CD1 TRP A 104 " -0.023 2.00e-02 2.50e+03 pdb=" CD2 TRP A 104 " 0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP A 104 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP A 104 " -0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP A 104 " 0.001 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 104 " 0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 104 " -0.009 2.00e-02 2.50e+03 pdb=" CH2 TRP A 104 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR C 421 " -0.017 2.00e-02 2.50e+03 1.91e-02 7.31e+00 pdb=" CG TYR C 421 " 0.047 2.00e-02 2.50e+03 pdb=" CD1 TYR C 421 " -0.010 2.00e-02 2.50e+03 pdb=" CD2 TYR C 421 " -0.016 2.00e-02 2.50e+03 pdb=" CE1 TYR C 421 " -0.007 2.00e-02 2.50e+03 pdb=" CE2 TYR C 421 " -0.001 2.00e-02 2.50e+03 pdb=" CZ TYR C 421 " 0.005 2.00e-02 2.50e+03 pdb=" OH TYR C 421 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C CYS A 336 " -0.043 5.00e-02 4.00e+02 6.60e-02 6.97e+00 pdb=" N PRO A 337 " 0.114 5.00e-02 4.00e+02 pdb=" CA PRO A 337 " -0.035 5.00e-02 4.00e+02 pdb=" CD PRO A 337 " -0.036 5.00e-02 4.00e+02 ... (remaining 5207 not shown) Histogram of nonbonded interaction distances: 2.19 - 2.73: 1369 2.73 - 3.27: 28063 3.27 - 3.81: 47436 3.81 - 4.36: 54668 4.36 - 4.90: 95587 Nonbonded interactions: 227123 Sorted by model distance: nonbonded pdb=" OE2 GLU B 773 " pdb=" NE2 GLN B 774 " model vdw 2.186 3.120 nonbonded pdb=" OG SER C 721 " pdb=" OG1 THR C1066 " model vdw 2.208 3.040 nonbonded pdb=" OH TYR C 380 " pdb=" O SER F 30 " model vdw 2.212 3.040 nonbonded pdb=" NZ LYS B 733 " pdb=" O PRO B 862 " model vdw 2.220 3.120 nonbonded pdb=" OE1 GLN A 134 " pdb=" OG SER A 161 " model vdw 2.238 3.040 ... (remaining 227118 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 13 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 827 or resid 854 through 1147)) \ selection = (chain 'C' and (resid 13 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: 2.940 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: 0.030 Extract box with map and model: 1.200 Check model and map are aligned: 0.220 Set scattering table: 0.280 Process input model: 76.740 Find NCS groups from input model: 1.160 Set up NCS constraints: 0.120 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:10.590 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 93.290 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7009 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 0.067 29375 Z= 0.140 Angle : 0.530 7.565 39984 Z= 0.294 Chirality : 0.043 0.217 4478 Planarity : 0.004 0.066 5210 Dihedral : 13.709 89.703 10485 Min Nonbonded Distance : 2.186 Molprobity Statistics. All-atom Clashscore : 8.20 Ramachandran Plot: Outliers : 0.30 % Allowed : 5.42 % Favored : 94.28 % Rotamer: Outliers : 0.16 % Allowed : 0.31 % Favored : 99.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.06 (0.14), residues: 3653 helix: 1.65 (0.20), residues: 724 sheet: 0.61 (0.18), residues: 816 loop : -0.95 (0.13), residues: 2113 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.048 0.001 TRP A 104 HIS 0.003 0.000 HIS A1048 PHE 0.017 0.001 PHE C1121 TYR 0.047 0.001 TYR C 421 ARG 0.002 0.000 ARG C 357 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7306 Ramachandran restraints generated. 3653 Oldfield, 0 Emsley, 3653 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7306 Ramachandran restraints generated. 3653 Oldfield, 0 Emsley, 3653 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 336 residues out of total 3179 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 331 time to evaluate : 3.075 Fit side-chains REVERT: B 146 HIS cc_start: 0.7101 (m90) cc_final: 0.6545 (m90) REVERT: B 153 MET cc_start: 0.6648 (mpp) cc_final: 0.6300 (mpt) REVERT: C 113 LYS cc_start: 0.9052 (tptp) cc_final: 0.8814 (tptp) REVERT: C 198 ASP cc_start: 0.7640 (t0) cc_final: 0.7393 (t0) REVERT: C 1138 TYR cc_start: 0.6768 (t80) cc_final: 0.6470 (t80) REVERT: D 83 MET cc_start: -0.0579 (mmt) cc_final: -0.1271 (mpt) outliers start: 5 outliers final: 4 residues processed: 334 average time/residue: 0.9880 time to fit residues: 408.7179 Evaluate side-chains 215 residues out of total 3179 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 211 time to evaluate : 3.009 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 827 THR Chi-restraints excluded: chain B residue 828 LEU Chi-restraints excluded: chain B residue 979 ASP Chi-restraints excluded: chain C residue 50 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 364 random chunks: chunk 307 optimal weight: 1.9990 chunk 275 optimal weight: 3.9990 chunk 153 optimal weight: 20.0000 chunk 94 optimal weight: 2.9990 chunk 186 optimal weight: 3.9990 chunk 147 optimal weight: 20.0000 chunk 285 optimal weight: 4.9990 chunk 110 optimal weight: 4.9990 chunk 173 optimal weight: 0.2980 chunk 212 optimal weight: 3.9990 chunk 330 optimal weight: 40.0000 overall best weight: 2.6588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 394 ASN ** A 437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 658 ASN A 804 GLN ** A 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 137 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 913 GLN B 935 GLN B 954 GLN C 146 HIS ** C 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 856 ASN ** C 907 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 992 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1010 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1011 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1058 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7420 moved from start: 0.2297 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.081 29375 Z= 0.478 Angle : 0.731 11.848 39984 Z= 0.382 Chirality : 0.050 0.205 4478 Planarity : 0.005 0.066 5210 Dihedral : 4.982 123.440 3983 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 11.95 Ramachandran Plot: Outliers : 0.22 % Allowed : 6.68 % Favored : 93.10 % Rotamer: Outliers : 2.08 % Allowed : 9.45 % Favored : 88.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.64 (0.13), residues: 3653 helix: 0.45 (0.19), residues: 725 sheet: 0.29 (0.17), residues: 838 loop : -1.05 (0.13), residues: 2090 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.003 TRP A 104 HIS 0.014 0.002 HIS C1064 PHE 0.034 0.003 PHE B 898 TYR 0.025 0.002 TYR C 279 ARG 0.009 0.001 ARG B 765 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7306 Ramachandran restraints generated. 3653 Oldfield, 0 Emsley, 3653 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7306 Ramachandran restraints generated. 3653 Oldfield, 0 Emsley, 3653 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 276 residues out of total 3179 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 210 time to evaluate : 3.167 Fit side-chains revert: symmetry clash REVERT: A 52 GLN cc_start: 0.8012 (tp40) cc_final: 0.7667 (tp-100) REVERT: A 918 GLU cc_start: 0.7732 (OUTLIER) cc_final: 0.7440 (pm20) REVERT: A 1081 ILE cc_start: 0.5348 (OUTLIER) cc_final: 0.4752 (mp) REVERT: B 94 SER cc_start: 0.7973 (OUTLIER) cc_final: 0.7669 (t) REVERT: B 146 HIS cc_start: 0.7215 (m90) cc_final: 0.6786 (m90) REVERT: B 817 PHE cc_start: 0.7164 (OUTLIER) cc_final: 0.6374 (m-80) REVERT: B 824 ASN cc_start: 0.8489 (OUTLIER) cc_final: 0.8287 (t0) REVERT: C 54 LEU cc_start: 0.8766 (OUTLIER) cc_final: 0.8525 (mp) REVERT: C 113 LYS cc_start: 0.9116 (tptp) cc_final: 0.8902 (tptp) REVERT: C 129 LYS cc_start: 0.7488 (tptt) cc_final: 0.7195 (tptt) REVERT: C 238 PHE cc_start: 0.8869 (OUTLIER) cc_final: 0.8261 (p90) REVERT: C 354 ASN cc_start: 0.7410 (t0) cc_final: 0.6968 (p0) REVERT: C 515 PHE cc_start: 0.8009 (m-10) cc_final: 0.7780 (m-10) REVERT: C 614 ASP cc_start: 0.7170 (t70) cc_final: 0.6927 (t0) REVERT: C 661 GLU cc_start: 0.8141 (OUTLIER) cc_final: 0.7841 (tt0) REVERT: C 957 GLN cc_start: 0.8054 (tp40) cc_final: 0.7653 (tp-100) REVERT: C 1138 TYR cc_start: 0.7045 (t80) cc_final: 0.6666 (t80) REVERT: D 83 MET cc_start: -0.0110 (mmt) cc_final: -0.1441 (mpt) outliers start: 66 outliers final: 29 residues processed: 256 average time/residue: 0.9814 time to fit residues: 312.2286 Evaluate side-chains 208 residues out of total 3179 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 171 time to evaluate : 3.036 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 84 LEU Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain A residue 629 LEU Chi-restraints excluded: chain A residue 656 VAL Chi-restraints excluded: chain A residue 912 THR Chi-restraints excluded: chain A residue 918 GLU Chi-restraints excluded: chain A residue 923 ILE Chi-restraints excluded: chain A residue 929 SER Chi-restraints excluded: chain A residue 980 ILE Chi-restraints excluded: chain A residue 1081 ILE Chi-restraints excluded: chain A residue 1117 THR Chi-restraints excluded: chain B residue 84 LEU Chi-restraints excluded: chain B residue 94 SER Chi-restraints excluded: chain B residue 175 PHE Chi-restraints excluded: chain B residue 549 THR Chi-restraints excluded: chain B residue 754 LEU Chi-restraints excluded: chain B residue 773 GLU Chi-restraints excluded: chain B residue 787 GLN Chi-restraints excluded: chain B residue 817 PHE Chi-restraints excluded: chain B residue 824 ASN Chi-restraints excluded: chain B residue 827 THR Chi-restraints excluded: chain B residue 864 LEU Chi-restraints excluded: chain B residue 922 LEU Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain B residue 1120 THR Chi-restraints excluded: chain B residue 1136 THR Chi-restraints excluded: chain C residue 54 LEU Chi-restraints excluded: chain C residue 238 PHE Chi-restraints excluded: chain C residue 528 LYS Chi-restraints excluded: chain C residue 592 PHE Chi-restraints excluded: chain C residue 661 GLU Chi-restraints excluded: chain C residue 720 ILE Chi-restraints excluded: chain C residue 740 MET Chi-restraints excluded: chain C residue 990 GLU Chi-restraints excluded: chain C residue 1027 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 364 random chunks: chunk 183 optimal weight: 0.6980 chunk 102 optimal weight: 2.9990 chunk 275 optimal weight: 0.7980 chunk 225 optimal weight: 8.9990 chunk 91 optimal weight: 0.8980 chunk 331 optimal weight: 8.9990 chunk 357 optimal weight: 8.9990 chunk 294 optimal weight: 0.6980 chunk 328 optimal weight: 20.0000 chunk 112 optimal weight: 0.9980 chunk 265 optimal weight: 5.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 762 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1005 GLN ** B 137 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 188 ASN B 625 HIS B 913 GLN ** B 957 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 856 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7333 moved from start: 0.2250 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 29375 Z= 0.189 Angle : 0.558 9.663 39984 Z= 0.285 Chirality : 0.044 0.175 4478 Planarity : 0.004 0.055 5210 Dihedral : 4.004 32.216 3978 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 9.11 Ramachandran Plot: Outliers : 0.22 % Allowed : 5.37 % Favored : 94.42 % Rotamer: Outliers : 1.86 % Allowed : 12.88 % Favored : 85.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.41 (0.14), residues: 3653 helix: 1.07 (0.19), residues: 717 sheet: 0.29 (0.17), residues: 855 loop : -1.02 (0.13), residues: 2081 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP E 36 HIS 0.009 0.001 HIS B 625 PHE 0.027 0.001 PHE B 592 TYR 0.020 0.001 TYR A1067 ARG 0.006 0.000 ARG A 765 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7306 Ramachandran restraints generated. 3653 Oldfield, 0 Emsley, 3653 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7306 Ramachandran restraints generated. 3653 Oldfield, 0 Emsley, 3653 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 264 residues out of total 3179 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 205 time to evaluate : 2.885 Fit side-chains REVERT: A 52 GLN cc_start: 0.7997 (tp40) cc_final: 0.7683 (tp-100) REVERT: A 81 ASN cc_start: 0.8074 (m-40) cc_final: 0.7640 (p0) REVERT: A 153 MET cc_start: 0.6264 (OUTLIER) cc_final: 0.6003 (pp-130) REVERT: A 1081 ILE cc_start: 0.5347 (OUTLIER) cc_final: 0.4833 (mp) REVERT: B 94 SER cc_start: 0.8237 (OUTLIER) cc_final: 0.7929 (t) REVERT: B 146 HIS cc_start: 0.7163 (m90) cc_final: 0.6658 (m90) REVERT: B 153 MET cc_start: 0.7326 (mpt) cc_final: 0.6951 (mpt) REVERT: B 269 TYR cc_start: 0.7584 (m-80) cc_final: 0.7360 (m-80) REVERT: B 731 MET cc_start: 0.6074 (ppp) cc_final: 0.5748 (ppp) REVERT: B 886 TRP cc_start: 0.6602 (p90) cc_final: 0.6362 (p90) REVERT: C 113 LYS cc_start: 0.9070 (tptp) cc_final: 0.8866 (tptp) REVERT: C 129 LYS cc_start: 0.7499 (tptt) cc_final: 0.7216 (tptt) REVERT: C 354 ASN cc_start: 0.7416 (t0) cc_final: 0.6949 (p0) REVERT: C 614 ASP cc_start: 0.7114 (t70) cc_final: 0.6853 (t0) REVERT: C 661 GLU cc_start: 0.8018 (OUTLIER) cc_final: 0.7711 (tt0) REVERT: C 916 LEU cc_start: 0.8016 (OUTLIER) cc_final: 0.7812 (tm) REVERT: C 1038 LYS cc_start: 0.6467 (OUTLIER) cc_final: 0.6020 (tmtt) REVERT: C 1138 TYR cc_start: 0.7069 (t80) cc_final: 0.6613 (t80) REVERT: D 83 MET cc_start: -0.0155 (mmt) cc_final: -0.1472 (mpt) outliers start: 59 outliers final: 25 residues processed: 247 average time/residue: 0.8736 time to fit residues: 275.0967 Evaluate side-chains 212 residues out of total 3179 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 181 time to evaluate : 3.001 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 84 LEU Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 153 MET Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain A residue 622 VAL Chi-restraints excluded: chain A residue 629 LEU Chi-restraints excluded: chain A residue 826 VAL Chi-restraints excluded: chain A residue 918 GLU Chi-restraints excluded: chain A residue 980 ILE Chi-restraints excluded: chain A residue 1081 ILE Chi-restraints excluded: chain A residue 1114 ILE Chi-restraints excluded: chain B residue 94 SER Chi-restraints excluded: chain B residue 175 PHE Chi-restraints excluded: chain B residue 299 THR Chi-restraints excluded: chain B residue 549 THR Chi-restraints excluded: chain B residue 620 VAL Chi-restraints excluded: chain B residue 754 LEU Chi-restraints excluded: chain B residue 775 ASP Chi-restraints excluded: chain B residue 864 LEU Chi-restraints excluded: chain B residue 1136 THR Chi-restraints excluded: chain C residue 146 HIS Chi-restraints excluded: chain C residue 592 PHE Chi-restraints excluded: chain C residue 661 GLU Chi-restraints excluded: chain C residue 720 ILE Chi-restraints excluded: chain C residue 724 THR Chi-restraints excluded: chain C residue 736 VAL Chi-restraints excluded: chain C residue 916 LEU Chi-restraints excluded: chain C residue 940 SER Chi-restraints excluded: chain C residue 1038 LYS Chi-restraints excluded: chain C residue 1063 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/iotbx/cli_parser.py", line 946, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/programs/real_space_refine.py", line 200, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 766, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1479, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1381, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1262, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 62.1208 > 50: distance: 21 - 115: 11.137 distance: 87 - 92: 9.445 distance: 92 - 93: 15.814 distance: 93 - 94: 22.533 distance: 93 - 96: 22.374 distance: 94 - 95: 25.855 distance: 94 - 100: 19.887 distance: 96 - 97: 8.531 distance: 96 - 98: 15.289 distance: 97 - 99: 20.178 distance: 101 - 102: 8.474 distance: 102 - 103: 5.677 distance: 102 - 104: 43.319 distance: 104 - 105: 7.286 distance: 105 - 106: 28.900 distance: 105 - 108: 16.908 distance: 106 - 107: 27.422 distance: 106 - 112: 13.850 distance: 108 - 109: 12.656 distance: 108 - 110: 12.615 distance: 109 - 111: 15.696 distance: 113 - 116: 11.836 distance: 114 - 115: 16.125 distance: 114 - 119: 8.419 distance: 116 - 117: 30.095 distance: 116 - 118: 17.897 distance: 119 - 120: 7.792 distance: 120 - 121: 8.206 distance: 120 - 123: 8.943 distance: 121 - 127: 17.289 distance: 123 - 124: 6.289 distance: 124 - 125: 8.202 distance: 124 - 126: 5.247 distance: 127 - 128: 10.565 distance: 128 - 129: 9.380 distance: 128 - 131: 5.970 distance: 129 - 130: 5.109 distance: 129 - 135: 3.445 distance: 131 - 132: 8.331 distance: 132 - 133: 15.539 distance: 132 - 134: 19.740 distance: 135 - 136: 4.771 distance: 136 - 137: 8.915 distance: 136 - 139: 5.153 distance: 137 - 138: 8.338 distance: 137 - 142: 7.203 distance: 139 - 140: 13.472 distance: 139 - 141: 14.722 distance: 142 - 143: 5.375 distance: 143 - 144: 8.291 distance: 143 - 146: 5.422 distance: 144 - 145: 11.952 distance: 144 - 149: 5.746 distance: 146 - 147: 13.042 distance: 146 - 148: 15.117 distance: 150 - 151: 4.934 distance: 150 - 153: 3.400 distance: 151 - 152: 9.154 distance: 151 - 161: 10.328 distance: 153 - 154: 4.536 distance: 154 - 155: 12.856 distance: 154 - 156: 7.075 distance: 155 - 157: 13.167 distance: 156 - 158: 7.706 distance: 158 - 159: 7.022 distance: 159 - 160: 7.621 distance: 161 - 162: 6.071 distance: 162 - 163: 6.477 distance: 162 - 165: 7.353 distance: 163 - 164: 5.896 distance: 163 - 169: 6.128 distance: 165 - 166: 14.551 distance: 166 - 167: 11.016