Starting phenix.real_space_refine on Tue Oct 15 06:51:00 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sb4_40290/10_2024/8sb4_40290_neut.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sb4_40290/10_2024/8sb4_40290.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sb4_40290/10_2024/8sb4_40290.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sb4_40290/10_2024/8sb4_40290.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sb4_40290/10_2024/8sb4_40290_neut.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sb4_40290/10_2024/8sb4_40290_neut.cif" } resolution = 3.6 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 sd= 0.024 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 135 5.16 5 C 12525 2.51 5 N 3345 2.21 5 O 4036 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 36 residue(s): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5477/modules/chem_data/mon_lib" Total number of atoms: 20041 Number of models: 1 Model: "" Number of chains: 24 Chain: "A" Number of atoms: 3615 Number of conformers: 1 Conformer: "" Number of residues, atoms: 462, 3615 Classifications: {'peptide': 462} Modifications used: {'COO': 1} Link IDs: {'CIS': 2, 'PCIS': 1, 'PTRANS': 22, 'TRANS': 436} Chain: "B" Number of atoms: 1034 Number of conformers: 1 Conformer: "" Number of residues, atoms: 132, 1034 Classifications: {'peptide': 132} Link IDs: {'PTRANS': 1, 'TRANS': 130} Chain: "C" Number of atoms: 986 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 986 Classifications: {'peptide': 126} Link IDs: {'PTRANS': 6, 'TRANS': 119} Chain: "D" Number of atoms: 816 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 816 Classifications: {'peptide': 110} Link IDs: {'CIS': 1, 'PTRANS': 5, 'TRANS': 103} Chain: "F" Number of atoms: 3615 Number of conformers: 1 Conformer: "" Number of residues, atoms: 462, 3615 Classifications: {'peptide': 462} Modifications used: {'COO': 1} Link IDs: {'CIS': 2, 'PCIS': 1, 'PTRANS': 22, 'TRANS': 436} Chain: "G" Number of atoms: 1034 Number of conformers: 1 Conformer: "" Number of residues, atoms: 132, 1034 Classifications: {'peptide': 132} Link IDs: {'PTRANS': 1, 'TRANS': 130} Chain: "H" Number of atoms: 986 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 986 Classifications: {'peptide': 126} Link IDs: {'PTRANS': 6, 'TRANS': 119} Chain: "I" Number of atoms: 816 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 816 Classifications: {'peptide': 110} Link IDs: {'CIS': 1, 'PTRANS': 5, 'TRANS': 103} Chain: "K" Number of atoms: 3615 Number of conformers: 1 Conformer: "" Number of residues, atoms: 462, 3615 Classifications: {'peptide': 462} Modifications used: {'COO': 1} Link IDs: {'CIS': 2, 'PCIS': 1, 'PTRANS': 22, 'TRANS': 436} Chain: "L" Number of atoms: 1034 Number of conformers: 1 Conformer: "" Number of residues, atoms: 132, 1034 Classifications: {'peptide': 132} Link IDs: {'PTRANS': 1, 'TRANS': 130} Chain: "M" Number of atoms: 986 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 986 Classifications: {'peptide': 126} Link IDs: {'PTRANS': 6, 'TRANS': 119} Chain: "N" Number of atoms: 816 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 816 Classifications: {'peptide': 110} Link IDs: {'CIS': 1, 'PTRANS': 5, 'TRANS': 103} Chain: "E" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "J" Number of atoms: 105 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 105 Unusual residues: {'BMA': 1, 'MAN': 6, 'NAG': 2} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 9 Chain: "O" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "P" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Q" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "R" Number of atoms: 94 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 94 Unusual residues: {'BMA': 1, 'MAN': 5, 'NAG': 2} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 8 Chain: "S" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "T" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "U" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "V" Number of atoms: 105 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 105 Unusual residues: {'BMA': 1, 'MAN': 6, 'NAG': 2} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 9 Chain: "W" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "X" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Time building chain proxies: 11.80, per 1000 atoms: 0.59 Number of scatterers: 20041 At special positions: 0 Unit cell: (158.834, 159.9, 137.514, 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 135 16.00 O 4036 8.00 N 3345 7.00 C 12525 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=42, symmetry=0 Simple disulfide: pdb=" SG CYS A 54 " - pdb=" SG CYS A 74 " distance=2.04 Simple disulfide: pdb=" SG CYS A 119 " - pdb=" SG CYS A 205 " distance=2.03 Simple disulfide: pdb=" SG CYS A 126 " - pdb=" SG CYS A 196 " distance=2.03 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 157 " distance=2.03 Simple disulfide: pdb=" SG CYS A 201 " - pdb=" SG CYS A 433 " distance=2.03 Simple disulfide: pdb=" SG CYS A 218 " - pdb=" SG CYS A 247 " distance=2.03 Simple disulfide: pdb=" SG CYS A 228 " - pdb=" SG CYS A 239 " distance=2.03 Simple disulfide: pdb=" SG CYS A 296 " - pdb=" SG CYS A 331 " distance=2.03 Simple disulfide: pdb=" SG CYS A 378 " - pdb=" SG CYS A 445 " distance=2.02 Simple disulfide: pdb=" SG CYS A 385 " - pdb=" SG CYS A 418 " distance=2.03 Simple disulfide: pdb=" SG CYS A 501 " - pdb=" SG CYS B 605 " distance=2.03 Simple disulfide: pdb=" SG CYS B 598 " - pdb=" SG CYS B 604 " distance=2.03 Simple disulfide: pdb=" SG CYS C 22 " - pdb=" SG CYS C 96 " distance=2.03 Simple disulfide: pdb=" SG CYS D 22 " - pdb=" SG CYS D 90 " distance=2.03 Simple disulfide: pdb=" SG CYS F 54 " - pdb=" SG CYS F 74 " distance=2.03 Simple disulfide: pdb=" SG CYS F 119 " - pdb=" SG CYS F 205 " distance=2.03 Simple disulfide: pdb=" SG CYS F 126 " - pdb=" SG CYS F 196 " distance=2.03 Simple disulfide: pdb=" SG CYS F 131 " - pdb=" SG CYS F 157 " distance=2.03 Simple disulfide: pdb=" SG CYS F 201 " - pdb=" SG CYS F 433 " distance=2.03 Simple disulfide: pdb=" SG CYS F 218 " - pdb=" SG CYS F 247 " distance=2.05 Simple disulfide: pdb=" SG CYS F 228 " - pdb=" SG CYS F 239 " distance=2.03 Simple disulfide: pdb=" SG CYS F 296 " - pdb=" SG CYS F 331 " distance=2.03 Simple disulfide: pdb=" SG CYS F 378 " - pdb=" SG CYS F 445 " distance=2.02 Simple disulfide: pdb=" SG CYS F 385 " - pdb=" SG CYS F 418 " distance=2.03 Simple disulfide: pdb=" SG CYS F 501 " - pdb=" SG CYS G 605 " distance=2.03 Simple disulfide: pdb=" SG CYS G 598 " - pdb=" SG CYS G 604 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.03 Simple disulfide: pdb=" SG CYS I 22 " - pdb=" SG CYS I 90 " distance=2.03 Simple disulfide: pdb=" SG CYS K 54 " - pdb=" SG CYS K 74 " distance=2.04 Simple disulfide: pdb=" SG CYS K 119 " - pdb=" SG CYS K 205 " distance=2.03 Simple disulfide: pdb=" SG CYS K 126 " - pdb=" SG CYS K 196 " distance=2.03 Simple disulfide: pdb=" SG CYS K 131 " - pdb=" SG CYS K 157 " distance=2.03 Simple disulfide: pdb=" SG CYS K 201 " - pdb=" SG CYS K 433 " distance=2.03 Simple disulfide: pdb=" SG CYS K 218 " - pdb=" SG CYS K 247 " distance=2.03 Simple disulfide: pdb=" SG CYS K 228 " - pdb=" SG CYS K 239 " distance=2.03 Simple disulfide: pdb=" SG CYS K 296 " - pdb=" SG CYS K 331 " distance=2.03 Simple disulfide: pdb=" SG CYS K 378 " - pdb=" SG CYS K 445 " distance=2.02 Simple disulfide: pdb=" SG CYS K 385 " - pdb=" SG CYS K 418 " distance=2.03 Simple disulfide: pdb=" SG CYS K 501 " - pdb=" SG CYS L 605 " distance=2.03 Simple disulfide: pdb=" SG CYS L 598 " - pdb=" SG CYS L 604 " distance=2.02 Simple disulfide: pdb=" SG CYS M 22 " - pdb=" SG CYS M 96 " distance=2.03 Simple disulfide: pdb=" SG CYS N 22 " - pdb=" SG CYS N 90 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied ALPHA1-2 " MAN E 4 " - " MAN E 5 " " MAN J 4 " - " MAN J 5 " " MAN J 5 " - " MAN J 6 " " MAN J 8 " - " MAN J 9 " " MAN Q 4 " - " MAN Q 5 " " MAN R 4 " - " MAN R 5 " " MAN R 5 " - " MAN R 6 " " MAN U 4 " - " MAN U 5 " " MAN V 4 " - " MAN V 5 " " MAN V 5 " - " MAN V 6 " " MAN V 8 " - " MAN V 9 " ALPHA1-3 " BMA E 3 " - " MAN E 4 " " BMA J 3 " - " MAN J 4 " " BMA Q 3 " - " MAN Q 4 " " BMA R 3 " - " MAN R 4 " " BMA U 3 " - " MAN U 4 " " BMA V 3 " - " MAN V 4 " ALPHA1-6 " BMA J 3 " - " MAN J 7 " " MAN J 7 " - " MAN J 8 " " BMA R 3 " - " MAN R 7 " " MAN R 7 " - " MAN R 8 " " BMA V 3 " - " MAN V 7 " " MAN V 7 " - " MAN V 8 " BETA1-4 " NAG E 1 " - " NAG E 2 " " NAG E 2 " - " BMA E 3 " " NAG J 1 " - " NAG J 2 " " NAG J 2 " - " BMA J 3 " " NAG O 1 " - " NAG O 2 " " NAG O 2 " - " BMA O 3 " " NAG P 1 " - " NAG P 2 " " NAG Q 1 " - " NAG Q 2 " " NAG Q 2 " - " BMA Q 3 " " NAG R 1 " - " NAG R 2 " " NAG R 2 " - " BMA R 3 " " NAG S 1 " - " NAG S 2 " " NAG S 2 " - " BMA S 3 " " NAG T 1 " - " NAG T 2 " " NAG U 1 " - " NAG U 2 " " NAG U 2 " - " BMA U 3 " " NAG V 1 " - " NAG V 2 " " NAG V 2 " - " BMA V 3 " " NAG W 1 " - " NAG W 2 " " NAG W 2 " - " BMA W 3 " " NAG X 1 " - " NAG X 2 " NAG-ASN " NAG E 1 " - " ASN A 301 " " NAG J 1 " - " ASN A 332 " " NAG O 1 " - " ASN A 156 " " NAG P 1 " - " ASN A 442 " " NAG Q 1 " - " ASN F 301 " " NAG R 1 " - " ASN F 332 " " NAG S 1 " - " ASN F 156 " " NAG T 1 " - " ASN F 442 " " NAG U 1 " - " ASN K 301 " " NAG V 1 " - " ASN K 332 " " NAG W 1 " - " ASN K 156 " " NAG X 1 " - " ASN K 442 " Time building additional restraints: 5.78 Conformation dependent library (CDL) restraints added in 2.7 seconds 4932 Ramachandran restraints generated. 2466 Oldfield, 0 Emsley, 2466 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4578 Finding SS restraints... Secondary structure from input PDB file: 51 helices and 35 sheets defined 19.4% alpha, 22.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.91 Creating SS restraints... Processing helix chain 'A' and resid 69 through 74 removed outlier: 3.882A pdb=" N CYS A 74 " --> pdb=" O ALA A 70 " (cutoff:3.500A) Processing helix chain 'A' and resid 98 through 116 removed outlier: 4.157A pdb=" N ASP A 102 " --> pdb=" O ASN A 98 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N GLU A 106 " --> pdb=" O ASP A 102 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N SER A 115 " --> pdb=" O LEU A 111 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N LEU A 116 " --> pdb=" O TRP A 112 " (cutoff:3.500A) Processing helix chain 'A' and resid 177 through 179 No H-bonds generated for 'chain 'A' and resid 177 through 179' Processing helix chain 'A' and resid 334 through 351 removed outlier: 3.962A pdb=" N ASP A 340 " --> pdb=" O GLU A 336 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N GLN A 343 " --> pdb=" O ASN A 339 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N GLU A 348 " --> pdb=" O LYS A 344 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N LYS A 351 " --> pdb=" O ILE A 347 " (cutoff:3.500A) Processing helix chain 'A' and resid 368 through 373 Processing helix chain 'A' and resid 475 through 481 Processing helix chain 'B' and resid 529 through 535 Processing helix chain 'B' and resid 537 through 542 Processing helix chain 'B' and resid 573 through 596 removed outlier: 3.562A pdb=" N VAL B 583 " --> pdb=" O ARG B 579 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N TRP B 596 " --> pdb=" O LEU B 592 " (cutoff:3.500A) Processing helix chain 'B' and resid 611 through 615 removed outlier: 3.626A pdb=" N TRP B 614 " --> pdb=" O ASN B 611 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N SER B 615 " --> pdb=" O SER B 612 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 611 through 615' Processing helix chain 'B' and resid 618 through 624 Processing helix chain 'B' and resid 627 through 636 removed outlier: 4.653A pdb=" N LYS B 633 " --> pdb=" O LEU B 629 " (cutoff:3.500A) removed outlier: 4.509A pdb=" N GLU B 634 " --> pdb=" O GLN B 630 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N ILE B 635 " --> pdb=" O TRP B 631 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N SER B 636 " --> pdb=" O ASP B 632 " (cutoff:3.500A) Processing helix chain 'B' and resid 638 through 664 removed outlier: 4.164A pdb=" N GLY B 644 " --> pdb=" O GLN B 640 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N ASN B 651 " --> pdb=" O GLU B 647 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N LYS B 655 " --> pdb=" O ASN B 651 " (cutoff:3.500A) removed outlier: 4.820A pdb=" N ASN B 656 " --> pdb=" O GLN B 652 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N GLU B 657 " --> pdb=" O GLN B 653 " (cutoff:3.500A) removed outlier: 4.232A pdb=" N ALA B 662 " --> pdb=" O GLN B 658 " (cutoff:3.500A) Processing helix chain 'C' and resid 28 through 30 No H-bonds generated for 'chain 'C' and resid 28 through 30' Processing helix chain 'C' and resid 87 through 91 Processing helix chain 'D' and resid 81 through 85 removed outlier: 3.753A pdb=" N GLU D 85 " --> pdb=" O ALA D 82 " (cutoff:3.500A) Processing helix chain 'F' and resid 58 through 61 removed outlier: 4.488A pdb=" N TYR F 61 " --> pdb=" O ALA F 58 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 58 through 61' Processing helix chain 'F' and resid 68 through 72 Processing helix chain 'F' and resid 98 through 116 removed outlier: 4.110A pdb=" N ASP F 102 " --> pdb=" O ASN F 98 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N GLU F 106 " --> pdb=" O ASP F 102 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N SER F 115 " --> pdb=" O LEU F 111 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N LEU F 116 " --> pdb=" O TRP F 112 " (cutoff:3.500A) Processing helix chain 'F' and resid 177 through 179 No H-bonds generated for 'chain 'F' and resid 177 through 179' Processing helix chain 'F' and resid 334 through 351 removed outlier: 3.973A pdb=" N ASP F 340 " --> pdb=" O GLU F 336 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N GLN F 343 " --> pdb=" O ASN F 339 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N GLU F 348 " --> pdb=" O LYS F 344 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N LYS F 351 " --> pdb=" O ILE F 347 " (cutoff:3.500A) Processing helix chain 'F' and resid 368 through 373 Processing helix chain 'F' and resid 475 through 481 removed outlier: 3.544A pdb=" N SER F 481 " --> pdb=" O ASP F 477 " (cutoff:3.500A) Processing helix chain 'G' and resid 529 through 535 Processing helix chain 'G' and resid 537 through 542 Processing helix chain 'G' and resid 573 through 596 removed outlier: 3.545A pdb=" N ALA G 582 " --> pdb=" O ALA G 578 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N VAL G 583 " --> pdb=" O ARG G 579 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N TRP G 596 " --> pdb=" O LEU G 592 " (cutoff:3.500A) Processing helix chain 'G' and resid 611 through 615 removed outlier: 3.581A pdb=" N TRP G 614 " --> pdb=" O ASN G 611 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N SER G 615 " --> pdb=" O SER G 612 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 611 through 615' Processing helix chain 'G' and resid 618 through 624 removed outlier: 3.658A pdb=" N ILE G 622 " --> pdb=" O ASN G 618 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ASP G 624 " --> pdb=" O SER G 620 " (cutoff:3.500A) Processing helix chain 'G' and resid 627 through 636 removed outlier: 4.756A pdb=" N LYS G 633 " --> pdb=" O LEU G 629 " (cutoff:3.500A) removed outlier: 4.559A pdb=" N GLU G 634 " --> pdb=" O GLN G 630 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N ILE G 635 " --> pdb=" O TRP G 631 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N SER G 636 " --> pdb=" O ASP G 632 " (cutoff:3.500A) Processing helix chain 'G' and resid 638 through 664 removed outlier: 4.413A pdb=" N GLY G 644 " --> pdb=" O GLN G 640 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N ASN G 651 " --> pdb=" O GLU G 647 " (cutoff:3.500A) removed outlier: 4.141A pdb=" N ASN G 656 " --> pdb=" O GLN G 652 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N GLU G 657 " --> pdb=" O GLN G 653 " (cutoff:3.500A) removed outlier: 4.230A pdb=" N ALA G 662 " --> pdb=" O GLN G 658 " (cutoff:3.500A) Processing helix chain 'H' and resid 28 through 30 No H-bonds generated for 'chain 'H' and resid 28 through 30' Processing helix chain 'H' and resid 87 through 91 Processing helix chain 'I' and resid 81 through 85 removed outlier: 3.728A pdb=" N GLU I 85 " --> pdb=" O ALA I 82 " (cutoff:3.500A) Processing helix chain 'K' and resid 58 through 61 removed outlier: 4.413A pdb=" N TYR K 61 " --> pdb=" O ALA K 58 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 58 through 61' Processing helix chain 'K' and resid 69 through 74 removed outlier: 3.813A pdb=" N CYS K 74 " --> pdb=" O ALA K 70 " (cutoff:3.500A) Processing helix chain 'K' and resid 98 through 116 removed outlier: 4.190A pdb=" N ASP K 102 " --> pdb=" O ASN K 98 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N GLU K 106 " --> pdb=" O ASP K 102 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N LEU K 116 " --> pdb=" O TRP K 112 " (cutoff:3.500A) Processing helix chain 'K' and resid 177 through 179 No H-bonds generated for 'chain 'K' and resid 177 through 179' Processing helix chain 'K' and resid 335 through 351 removed outlier: 3.973A pdb=" N ASP K 340 " --> pdb=" O GLU K 336 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N GLN K 343 " --> pdb=" O ASN K 339 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N GLU K 348 " --> pdb=" O LYS K 344 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N LYS K 351 " --> pdb=" O ILE K 347 " (cutoff:3.500A) Processing helix chain 'K' and resid 368 through 373 Processing helix chain 'K' and resid 475 through 481 Processing helix chain 'K' and resid 482 through 484 No H-bonds generated for 'chain 'K' and resid 482 through 484' Processing helix chain 'L' and resid 529 through 535 Processing helix chain 'L' and resid 537 through 542 Processing helix chain 'L' and resid 573 through 596 removed outlier: 3.536A pdb=" N ALA L 582 " --> pdb=" O ALA L 578 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N VAL L 583 " --> pdb=" O ARG L 579 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N TRP L 596 " --> pdb=" O LEU L 592 " (cutoff:3.500A) Processing helix chain 'L' and resid 611 through 615 removed outlier: 3.803A pdb=" N TRP L 614 " --> pdb=" O ASN L 611 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N SER L 615 " --> pdb=" O SER L 612 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 611 through 615' Processing helix chain 'L' and resid 618 through 624 removed outlier: 3.560A pdb=" N ASP L 624 " --> pdb=" O SER L 620 " (cutoff:3.500A) Processing helix chain 'L' and resid 627 through 636 removed outlier: 4.722A pdb=" N LYS L 633 " --> pdb=" O LEU L 629 " (cutoff:3.500A) removed outlier: 4.485A pdb=" N GLU L 634 " --> pdb=" O GLN L 630 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N ILE L 635 " --> pdb=" O TRP L 631 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N SER L 636 " --> pdb=" O ASP L 632 " (cutoff:3.500A) Processing helix chain 'L' and resid 638 through 664 removed outlier: 4.099A pdb=" N GLY L 644 " --> pdb=" O GLN L 640 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N ASN L 651 " --> pdb=" O GLU L 647 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N ASN L 656 " --> pdb=" O GLN L 652 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N GLU L 657 " --> pdb=" O GLN L 653 " (cutoff:3.500A) removed outlier: 4.118A pdb=" N ALA L 662 " --> pdb=" O GLN L 658 " (cutoff:3.500A) Processing helix chain 'M' and resid 28 through 30 No H-bonds generated for 'chain 'M' and resid 28 through 30' Processing helix chain 'M' and resid 87 through 91 Processing helix chain 'N' and resid 81 through 85 removed outlier: 3.794A pdb=" N GLU N 85 " --> pdb=" O ALA N 82 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 494 through 499 removed outlier: 5.452A pdb=" N VAL A 36 " --> pdb=" O THR B 606 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N THR B 606 " --> pdb=" O VAL A 36 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 45 through 47 removed outlier: 4.263A pdb=" N ILE A 225 " --> pdb=" O VAL A 245 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 75 through 76 Processing sheet with id=AA4, first strand: chain 'A' and resid 91 through 94 Processing sheet with id=AA5, first strand: chain 'A' and resid 166 through 176 removed outlier: 6.181A pdb=" N LYS A 168 " --> pdb=" O THR A 163 " (cutoff:3.500A) removed outlier: 4.437A pdb=" N THR A 163 " --> pdb=" O LYS A 168 " (cutoff:3.500A) removed outlier: 4.492A pdb=" N ASN A 156 " --> pdb=" O SER A 132 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 202 through 203 removed outlier: 6.622A pdb=" N THR A 202 " --> pdb=" O TYR A 435 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 271 through 273 removed outlier: 6.550A pdb=" N ASN A 301 " --> pdb=" O ILE A 322 " (cutoff:3.500A) removed outlier: 4.720A pdb=" N ILE A 322 " --> pdb=" O ASN A 301 " (cutoff:3.500A) removed outlier: 6.888A pdb=" N THR A 303 " --> pdb=" O GLY A 321 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 316 through 323 current: chain 'A' and resid 381 through 386 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 381 through 386 current: chain 'A' and resid 467 through 470 Processing sheet with id=AA8, first strand: chain 'C' and resid 3 through 6 removed outlier: 3.551A pdb=" N THR C 78 " --> pdb=" O ASP C 73 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 32 through 39 removed outlier: 6.599A pdb=" N ILE C 34 " --> pdb=" O TRP C 50 " (cutoff:3.500A) removed outlier: 4.458A pdb=" N TRP C 50 " --> pdb=" O ILE C 34 " (cutoff:3.500A) removed outlier: 6.662A pdb=" N TRP C 36 " --> pdb=" O MET C 48 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ASN C 59 " --> pdb=" O TRP C 50 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 58 through 59 current: chain 'C' and resid 116 through 117 Processing sheet with id=AB1, first strand: chain 'D' and resid 20 through 23 Processing sheet with id=AB2, first strand: chain 'D' and resid 47 through 50 removed outlier: 6.391A pdb=" N TRP D 37 " --> pdb=" O ILE D 49 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'F' and resid 494 through 499 removed outlier: 5.440A pdb=" N VAL F 36 " --> pdb=" O THR G 606 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N THR G 606 " --> pdb=" O VAL F 36 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'F' and resid 45 through 47 removed outlier: 4.374A pdb=" N ILE F 225 " --> pdb=" O VAL F 245 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'F' and resid 75 through 76 Processing sheet with id=AB6, first strand: chain 'F' and resid 91 through 94 Processing sheet with id=AB7, first strand: chain 'F' and resid 166 through 176 removed outlier: 6.165A pdb=" N LYS F 168 " --> pdb=" O THR F 163 " (cutoff:3.500A) removed outlier: 4.367A pdb=" N THR F 163 " --> pdb=" O LYS F 168 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'F' and resid 202 through 203 removed outlier: 6.602A pdb=" N THR F 202 " --> pdb=" O TYR F 435 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'F' and resid 259 through 260 WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 259 through 260 current: chain 'F' and resid 284 through 308 removed outlier: 6.457A pdb=" N ASN F 301 " --> pdb=" O ILE F 322 " (cutoff:3.500A) removed outlier: 4.593A pdb=" N ILE F 322 " --> pdb=" O ASN F 301 " (cutoff:3.500A) removed outlier: 6.770A pdb=" N THR F 303 " --> pdb=" O GLY F 321 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 316 through 323 current: chain 'F' and resid 381 through 386 WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 381 through 386 current: chain 'F' and resid 467 through 470 Processing sheet with id=AC1, first strand: chain 'H' and resid 3 through 6 removed outlier: 3.623A pdb=" N THR H 78 " --> pdb=" O ASP H 73 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'H' and resid 58 through 59 removed outlier: 6.660A pdb=" N TRP H 36 " --> pdb=" O MET H 48 " (cutoff:3.500A) removed outlier: 4.441A pdb=" N TRP H 50 " --> pdb=" O ILE H 34 " (cutoff:3.500A) removed outlier: 6.594A pdb=" N ILE H 34 " --> pdb=" O TRP H 50 " (cutoff:3.500A) removed outlier: 4.708A pdb=" N TYR H 33 " --> pdb=" O GLY H 99 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'I' and resid 9 through 12 removed outlier: 3.592A pdb=" N THR I 108 " --> pdb=" O VAL I 10 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'I' and resid 20 through 22 Processing sheet with id=AC5, first strand: chain 'I' and resid 47 through 50 removed outlier: 6.506A pdb=" N TRP I 37 " --> pdb=" O ILE I 49 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'K' and resid 494 through 499 removed outlier: 5.481A pdb=" N VAL K 36 " --> pdb=" O THR L 606 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N THR L 606 " --> pdb=" O VAL K 36 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'K' and resid 45 through 47 removed outlier: 4.204A pdb=" N ILE K 225 " --> pdb=" O VAL K 245 " (cutoff:3.500A) removed outlier: 4.611A pdb=" N VAL K 242 " --> pdb=" O LEU K 86 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'K' and resid 75 through 76 Processing sheet with id=AC9, first strand: chain 'K' and resid 91 through 94 Processing sheet with id=AD1, first strand: chain 'K' and resid 166 through 176 removed outlier: 6.128A pdb=" N LYS K 168 " --> pdb=" O THR K 163 " (cutoff:3.500A) removed outlier: 4.496A pdb=" N THR K 163 " --> pdb=" O LYS K 168 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N LYS K 170 " --> pdb=" O THR K 161 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'K' and resid 202 through 203 removed outlier: 6.562A pdb=" N THR K 202 " --> pdb=" O TYR K 435 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'K' and resid 271 through 273 removed outlier: 6.556A pdb=" N ASN K 301 " --> pdb=" O ILE K 322 " (cutoff:3.500A) removed outlier: 4.641A pdb=" N ILE K 322 " --> pdb=" O ASN K 301 " (cutoff:3.500A) removed outlier: 6.835A pdb=" N THR K 303 " --> pdb=" O GLY K 321 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'K' and resid 316 through 323 current: chain 'K' and resid 381 through 386 WARNING: can't find start of bonding for strands! previous: chain 'K' and resid 381 through 386 current: chain 'K' and resid 467 through 470 Processing sheet with id=AD4, first strand: chain 'M' and resid 3 through 6 removed outlier: 3.594A pdb=" N THR M 78 " --> pdb=" O ASP M 73 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'M' and resid 58 through 59 removed outlier: 6.682A pdb=" N TRP M 36 " --> pdb=" O MET M 48 " (cutoff:3.500A) removed outlier: 4.447A pdb=" N TRP M 50 " --> pdb=" O ILE M 34 " (cutoff:3.500A) removed outlier: 6.609A pdb=" N ILE M 34 " --> pdb=" O TRP M 50 " (cutoff:3.500A) removed outlier: 4.692A pdb=" N TYR M 33 " --> pdb=" O GLY M 99 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'N' and resid 9 through 12 Processing sheet with id=AD7, first strand: chain 'N' and resid 20 through 23 Processing sheet with id=AD8, first strand: chain 'N' and resid 47 through 50 removed outlier: 6.432A pdb=" N TRP N 37 " --> pdb=" O ILE N 49 " (cutoff:3.500A) 534 hydrogen bonds defined for protein. 1419 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: 6.41 Time building geometry restraints manager: 6.30 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.35: 6356 1.35 - 1.49: 5447 1.49 - 1.62: 8481 1.62 - 1.76: 0 1.76 - 1.89: 183 Bond restraints: 20467 Sorted by residual: bond pdb=" N VAL N 60 " pdb=" CA VAL N 60 " ideal model delta sigma weight residual 1.460 1.493 -0.034 1.10e-02 8.26e+03 9.37e+00 bond pdb=" C2 MAN R 5 " pdb=" O2 MAN R 5 " ideal model delta sigma weight residual 1.407 1.467 -0.060 2.00e-02 2.50e+03 9.06e+00 bond pdb=" C HIS N 41 " pdb=" N PRO N 42 " ideal model delta sigma weight residual 1.332 1.365 -0.033 1.12e-02 7.97e+03 8.62e+00 bond pdb=" C1 MAN J 8 " pdb=" C2 MAN J 8 " ideal model delta sigma weight residual 1.526 1.585 -0.059 2.00e-02 2.50e+03 8.57e+00 bond pdb=" N VAL D 60 " pdb=" CA VAL D 60 " ideal model delta sigma weight residual 1.459 1.494 -0.035 1.19e-02 7.06e+03 8.50e+00 ... (remaining 20462 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.28: 26941 2.28 - 4.56: 744 4.56 - 6.84: 128 6.84 - 9.12: 21 9.12 - 11.40: 6 Bond angle restraints: 27840 Sorted by residual: angle pdb=" C ASN F 67 " pdb=" N VAL F 68 " pdb=" CA VAL F 68 " ideal model delta sigma weight residual 121.70 133.10 -11.40 1.80e+00 3.09e-01 4.01e+01 angle pdb=" C ASN K 67 " pdb=" N VAL K 68 " pdb=" CA VAL K 68 " ideal model delta sigma weight residual 121.70 132.65 -10.95 1.80e+00 3.09e-01 3.70e+01 angle pdb=" C ASN A 67 " pdb=" N VAL A 68 " pdb=" CA VAL A 68 " ideal model delta sigma weight residual 121.70 132.16 -10.46 1.80e+00 3.09e-01 3.38e+01 angle pdb=" C ASN A 403 " pdb=" N SER A 404 " pdb=" CA SER A 404 " ideal model delta sigma weight residual 121.70 131.95 -10.25 1.80e+00 3.09e-01 3.24e+01 angle pdb=" C ASN K 403 " pdb=" N SER K 404 " pdb=" CA SER K 404 " ideal model delta sigma weight residual 121.70 131.90 -10.20 1.80e+00 3.09e-01 3.21e+01 ... (remaining 27835 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.59: 11970 21.59 - 43.18: 781 43.18 - 64.77: 78 64.77 - 86.36: 83 86.36 - 107.94: 38 Dihedral angle restraints: 12950 sinusoidal: 5786 harmonic: 7164 Sorted by residual: dihedral pdb=" CB CYS B 598 " pdb=" SG CYS B 598 " pdb=" SG CYS B 604 " pdb=" CB CYS B 604 " ideal model delta sinusoidal sigma weight residual -86.00 -173.13 87.13 1 1.00e+01 1.00e-02 9.12e+01 dihedral pdb=" CB CYS L 598 " pdb=" SG CYS L 598 " pdb=" SG CYS L 604 " pdb=" CB CYS L 604 " ideal model delta sinusoidal sigma weight residual -86.00 -159.15 73.15 1 1.00e+01 1.00e-02 6.82e+01 dihedral pdb=" CA GLY A 431 " pdb=" C GLY A 431 " pdb=" N ARG A 432 " pdb=" CA ARG A 432 " ideal model delta harmonic sigma weight residual -180.00 -148.67 -31.33 0 5.00e+00 4.00e-02 3.93e+01 ... (remaining 12947 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.062: 2690 0.062 - 0.123: 466 0.123 - 0.184: 115 0.184 - 0.246: 8 0.246 - 0.307: 10 Chirality restraints: 3289 Sorted by residual: chirality pdb=" C5 BMA U 3 " pdb=" C4 BMA U 3 " pdb=" C6 BMA U 3 " pdb=" O5 BMA U 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.58 0.31 2.00e-01 2.50e+01 2.36e+00 chirality pdb=" C5 BMA Q 3 " pdb=" C4 BMA Q 3 " pdb=" C6 BMA Q 3 " pdb=" O5 BMA Q 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.58 0.31 2.00e-01 2.50e+01 2.36e+00 chirality pdb=" C5 BMA E 3 " pdb=" C4 BMA E 3 " pdb=" C6 BMA E 3 " pdb=" O5 BMA E 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.58 0.31 2.00e-01 2.50e+01 2.35e+00 ... (remaining 3286 not shown) Planarity restraints: 3492 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL K 75 " -0.062 5.00e-02 4.00e+02 8.92e-02 1.27e+01 pdb=" N PRO K 76 " 0.154 5.00e-02 4.00e+02 pdb=" CA PRO K 76 " -0.042 5.00e-02 4.00e+02 pdb=" CD PRO K 76 " -0.050 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TRP F 112 " -0.018 2.00e-02 2.50e+03 2.00e-02 1.00e+01 pdb=" CG TRP F 112 " 0.052 2.00e-02 2.50e+03 pdb=" CD1 TRP F 112 " -0.026 2.00e-02 2.50e+03 pdb=" CD2 TRP F 112 " 0.007 2.00e-02 2.50e+03 pdb=" NE1 TRP F 112 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP F 112 " -0.002 2.00e-02 2.50e+03 pdb=" CE3 TRP F 112 " -0.014 2.00e-02 2.50e+03 pdb=" CZ2 TRP F 112 " -0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP F 112 " -0.000 2.00e-02 2.50e+03 pdb=" CH2 TRP F 112 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG B 585 " -0.236 9.50e-02 1.11e+02 1.06e-01 7.40e+00 pdb=" NE ARG B 585 " 0.018 2.00e-02 2.50e+03 pdb=" CZ ARG B 585 " -0.010 2.00e-02 2.50e+03 pdb=" NH1 ARG B 585 " 0.006 2.00e-02 2.50e+03 pdb=" NH2 ARG B 585 " -0.004 2.00e-02 2.50e+03 ... (remaining 3489 not shown) Histogram of nonbonded interaction distances: 2.07 - 2.64: 234 2.64 - 3.20: 18054 3.20 - 3.77: 28572 3.77 - 4.33: 41555 4.33 - 4.90: 68057 Nonbonded interactions: 156472 Sorted by model distance: nonbonded pdb=" OG1 THR D 5 " pdb=" OG1 THR D 23 " model vdw 2.071 3.040 nonbonded pdb=" OG1 THR N 5 " pdb=" OG1 THR N 23 " model vdw 2.073 3.040 nonbonded pdb=" OG1 THR I 5 " pdb=" OG1 THR I 23 " model vdw 2.090 3.040 nonbonded pdb=" O THR M 30 " pdb=" OG SER M 54 " model vdw 2.098 3.040 nonbonded pdb=" OG1 THR F 163 " pdb=" OE1 GLU F 164 " model vdw 2.117 3.040 ... (remaining 156467 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 'F' selection = chain 'K' } ncs_group { reference = chain 'B' selection = chain 'G' selection = chain 'L' } ncs_group { reference = chain 'C' selection = chain 'H' selection = chain 'M' } ncs_group { reference = chain 'D' selection = chain 'I' selection = chain 'N' } ncs_group { reference = chain 'E' selection = chain 'Q' selection = chain 'U' } ncs_group { reference = (chain 'J' and (resid 2 or resid 5 through 9)) selection = (chain 'R' and (resid 1 or resid 4 through 8)) selection = (chain 'V' and (resid 2 or resid 5 through 9)) } ncs_group { reference = chain 'O' selection = chain 'S' selection = chain 'W' } ncs_group { reference = chain 'P' selection = chain 'T' selection = chain 'X' } 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: 0.360 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: 0.010 Extract box with map and model: 0.870 Check model and map are aligned: 0.160 Set scattering table: 0.200 Process input model: 44.650 Find NCS groups from input model: 0.690 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:2.730 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 49.810 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7316 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.084 20467 Z= 0.364 Angle : 0.933 11.405 27840 Z= 0.490 Chirality : 0.054 0.307 3289 Planarity : 0.006 0.106 3480 Dihedral : 16.323 107.944 8246 Min Nonbonded Distance : 2.071 Molprobity Statistics. All-atom Clashscore : 2.69 Ramachandran Plot: Outliers : 0.32 % Allowed : 4.83 % Favored : 94.85 % Rotamer: Outliers : 0.00 % Allowed : 0.32 % Favored : 99.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.38 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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: -1.55 (0.16), residues: 2466 helix: -1.74 (0.24), residues: 354 sheet: -0.26 (0.19), residues: 660 loop : -1.20 (0.15), residues: 1452 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.052 0.002 TRP F 112 HIS 0.008 0.002 HIS I 41 PHE 0.017 0.002 PHE K 391 TYR 0.020 0.002 TYR D 51 ARG 0.016 0.001 ARG A 252 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4932 Ramachandran restraints generated. 2466 Oldfield, 0 Emsley, 2466 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4932 Ramachandran restraints generated. 2466 Oldfield, 0 Emsley, 2466 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 637 residues out of total 2154 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 637 time to evaluate : 2.363 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 107 ASP cc_start: 0.6775 (m-30) cc_final: 0.6556 (m-30) REVERT: A 121 LYS cc_start: 0.7017 (ptpt) cc_final: 0.6689 (ttmm) REVERT: B 535 MET cc_start: 0.8113 (mtt) cc_final: 0.7418 (mtt) REVERT: B 632 ASP cc_start: 0.7977 (t70) cc_final: 0.7567 (t0) REVERT: B 661 LEU cc_start: 0.8854 (tp) cc_final: 0.8465 (mt) REVERT: C 7 SER cc_start: 0.7703 (p) cc_final: 0.7294 (p) REVERT: C 21 SER cc_start: 0.7955 (p) cc_final: 0.7623 (t) REVERT: C 43 GLN cc_start: 0.7377 (tp40) cc_final: 0.6783 (mp10) REVERT: C 84 ASN cc_start: 0.8031 (t0) cc_final: 0.7798 (t0) REVERT: D 92 SER cc_start: 0.8913 (p) cc_final: 0.8694 (p) REVERT: F 54 CYS cc_start: 0.5359 (p) cc_final: 0.5133 (p) REVERT: F 103 GLN cc_start: 0.7654 (mt0) cc_final: 0.7146 (tm-30) REVERT: F 442 ASN cc_start: 0.8083 (p0) cc_final: 0.7867 (p0) REVERT: G 604 CYS cc_start: 0.6761 (t) cc_final: 0.6492 (t) REVERT: G 632 ASP cc_start: 0.7831 (t70) cc_final: 0.7434 (t0) REVERT: G 660 LEU cc_start: 0.7691 (mt) cc_final: 0.7289 (tt) REVERT: G 661 LEU cc_start: 0.8850 (tp) cc_final: 0.8439 (mt) REVERT: H 13 LYS cc_start: 0.7485 (mmpt) cc_final: 0.7262 (mmtt) REVERT: H 43 GLN cc_start: 0.7495 (tp40) cc_final: 0.6727 (mp10) REVERT: H 84 ASN cc_start: 0.8452 (t0) cc_final: 0.8185 (t0) REVERT: I 25 THR cc_start: 0.8086 (t) cc_final: 0.7589 (m) REVERT: I 36 SER cc_start: 0.8859 (m) cc_final: 0.8656 (t) REVERT: I 38 TYR cc_start: 0.8087 (m-80) cc_final: 0.7114 (m-80) REVERT: I 93 TYR cc_start: 0.8918 (t80) cc_final: 0.8391 (t80) REVERT: K 162 THR cc_start: 0.8345 (m) cc_final: 0.8053 (p) REVERT: L 608 VAL cc_start: 0.8485 (t) cc_final: 0.7955 (t) REVERT: L 634 GLU cc_start: 0.8143 (mt-10) cc_final: 0.7844 (mt-10) REVERT: M 122 LEU cc_start: 0.7846 (mt) cc_final: 0.7435 (mp) outliers start: 0 outliers final: 0 residues processed: 637 average time/residue: 0.3451 time to fit residues: 327.0876 Evaluate side-chains 420 residues out of total 2154 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 420 time to evaluate : 2.300 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 246 random chunks: chunk 207 optimal weight: 7.9990 chunk 186 optimal weight: 10.0000 chunk 103 optimal weight: 1.9990 chunk 63 optimal weight: 10.0000 chunk 125 optimal weight: 1.9990 chunk 99 optimal weight: 9.9990 chunk 192 optimal weight: 8.9990 chunk 74 optimal weight: 3.9990 chunk 117 optimal weight: 10.0000 chunk 143 optimal weight: 8.9990 chunk 223 optimal weight: 9.9990 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 287 HIS B 590 GLN ** B 630 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 658 GLN C 6 GLN C 43 GLN F 287 HIS F 352 HIS G 575 GLN G 630 GLN H 43 GLN H 113 ASN K 287 HIS K 352 HIS L 590 GLN L 630 GLN M 6 GLN M 39 GLN M 43 GLN N 41 HIS Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7631 moved from start: 0.3223 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.061 20467 Z= 0.416 Angle : 0.808 9.884 27840 Z= 0.416 Chirality : 0.052 0.340 3289 Planarity : 0.006 0.062 3480 Dihedral : 11.561 75.704 3794 Min Nonbonded Distance : 2.366 Molprobity Statistics. All-atom Clashscore : 6.04 Ramachandran Plot: Outliers : 0.45 % Allowed : 4.46 % Favored : 95.09 % Rotamer: Outliers : 2.69 % Allowed : 11.70 % Favored : 85.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.38 % 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: -1.48 (0.16), residues: 2466 helix: -1.60 (0.24), residues: 375 sheet: -0.25 (0.19), residues: 690 loop : -1.17 (0.15), residues: 1401 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP K 35 HIS 0.007 0.002 HIS K 330 PHE 0.024 0.003 PHE F 376 TYR 0.028 0.002 TYR D 93 ARG 0.008 0.001 ARG I 63 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4932 Ramachandran restraints generated. 2466 Oldfield, 0 Emsley, 2466 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4932 Ramachandran restraints generated. 2466 Oldfield, 0 Emsley, 2466 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 494 residues out of total 2154 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 436 time to evaluate : 2.248 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 121 LYS cc_start: 0.7423 (ptpt) cc_final: 0.7115 (ttmm) REVERT: A 207 LYS cc_start: 0.7309 (tmtt) cc_final: 0.6731 (tmtt) REVERT: A 210 PHE cc_start: 0.8533 (m-80) cc_final: 0.8331 (m-80) REVERT: A 211 GLU cc_start: 0.8123 (tt0) cc_final: 0.7812 (pt0) REVERT: B 632 ASP cc_start: 0.8225 (t0) cc_final: 0.7700 (t0) REVERT: B 661 LEU cc_start: 0.8724 (tp) cc_final: 0.8412 (mt) REVERT: C 7 SER cc_start: 0.8017 (p) cc_final: 0.7681 (p) REVERT: C 21 SER cc_start: 0.8155 (p) cc_final: 0.7862 (t) REVERT: C 38 ARG cc_start: 0.8178 (OUTLIER) cc_final: 0.7639 (ttp80) REVERT: C 43 GLN cc_start: 0.7181 (tp-100) cc_final: 0.6636 (mp10) REVERT: C 81 MET cc_start: 0.8114 (tmm) cc_final: 0.7391 (tmm) REVERT: D 23 THR cc_start: 0.7481 (p) cc_final: 0.7139 (t) REVERT: D 52 GLU cc_start: 0.7896 (tt0) cc_final: 0.7683 (mt-10) REVERT: D 63 ARG cc_start: 0.6969 (OUTLIER) cc_final: 0.6178 (ptm-80) REVERT: F 54 CYS cc_start: 0.5492 (p) cc_final: 0.5223 (p) REVERT: F 57 ASP cc_start: 0.7632 (t0) cc_final: 0.7090 (p0) REVERT: F 103 GLN cc_start: 0.7715 (mt0) cc_final: 0.7210 (tm-30) REVERT: F 164 GLU cc_start: 0.7445 (pm20) cc_final: 0.7078 (pm20) REVERT: G 632 ASP cc_start: 0.8100 (t70) cc_final: 0.7672 (t0) REVERT: G 659 ASP cc_start: 0.8237 (m-30) cc_final: 0.7854 (t70) REVERT: G 661 LEU cc_start: 0.8904 (tp) cc_final: 0.8394 (mt) REVERT: H 43 GLN cc_start: 0.7541 (tp-100) cc_final: 0.7229 (mp10) REVERT: H 84 ASN cc_start: 0.8322 (t0) cc_final: 0.8106 (t0) REVERT: I 20 ILE cc_start: 0.6969 (mt) cc_final: 0.6753 (mt) REVERT: I 36 SER cc_start: 0.9034 (m) cc_final: 0.8643 (t) REVERT: I 38 TYR cc_start: 0.8228 (m-80) cc_final: 0.7652 (m-80) REVERT: K 103 GLN cc_start: 0.7749 (mt0) cc_final: 0.7487 (tm-30) REVERT: K 116 LEU cc_start: 0.8481 (OUTLIER) cc_final: 0.8119 (mp) REVERT: K 162 THR cc_start: 0.8409 (m) cc_final: 0.8201 (p) REVERT: K 207 LYS cc_start: 0.8028 (mtpp) cc_final: 0.7667 (tttp) REVERT: K 475 MET cc_start: 0.6748 (mmt) cc_final: 0.6531 (mmm) REVERT: L 584 GLU cc_start: 0.8243 (mm-30) cc_final: 0.7725 (mt-10) REVERT: N 23 THR cc_start: 0.7567 (p) cc_final: 0.7192 (t) outliers start: 58 outliers final: 33 residues processed: 464 average time/residue: 0.3098 time to fit residues: 218.6877 Evaluate side-chains 405 residues out of total 2154 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 369 time to evaluate : 2.263 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 110 SER Chi-restraints excluded: chain A residue 128 THR Chi-restraints excluded: chain A residue 283 ILE Chi-restraints excluded: chain A residue 364 SER Chi-restraints excluded: chain A residue 414 ILE Chi-restraints excluded: chain A residue 499 THR Chi-restraints excluded: chain B residue 530 MET Chi-restraints excluded: chain B residue 602 LEU Chi-restraints excluded: chain C residue 38 ARG Chi-restraints excluded: chain C residue 70 MET Chi-restraints excluded: chain C residue 123 VAL Chi-restraints excluded: chain D residue 45 VAL Chi-restraints excluded: chain D residue 53 VAL Chi-restraints excluded: chain D residue 63 ARG Chi-restraints excluded: chain F residue 102 ASP Chi-restraints excluded: chain F residue 110 SER Chi-restraints excluded: chain F residue 171 LYS Chi-restraints excluded: chain F residue 283 ILE Chi-restraints excluded: chain F residue 364 SER Chi-restraints excluded: chain F residue 414 ILE Chi-restraints excluded: chain F residue 481 SER Chi-restraints excluded: chain G residue 592 LEU Chi-restraints excluded: chain H residue 108 THR Chi-restraints excluded: chain H residue 123 VAL Chi-restraints excluded: chain I residue 5 THR Chi-restraints excluded: chain I residue 29 VAL Chi-restraints excluded: chain I residue 45 VAL Chi-restraints excluded: chain K residue 116 LEU Chi-restraints excluded: chain K residue 181 ILE Chi-restraints excluded: chain K residue 364 SER Chi-restraints excluded: chain K residue 414 ILE Chi-restraints excluded: chain K residue 499 THR Chi-restraints excluded: chain L residue 606 THR Chi-restraints excluded: chain L residue 661 LEU Chi-restraints excluded: chain N residue 39 GLN Chi-restraints excluded: chain N residue 45 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 246 random chunks: chunk 124 optimal weight: 3.9990 chunk 69 optimal weight: 0.6980 chunk 185 optimal weight: 0.6980 chunk 152 optimal weight: 0.8980 chunk 61 optimal weight: 10.0000 chunk 223 optimal weight: 0.6980 chunk 241 optimal weight: 50.0000 chunk 199 optimal weight: 9.9990 chunk 221 optimal weight: 5.9990 chunk 76 optimal weight: 9.9990 chunk 179 optimal weight: 5.9990 overall best weight: 1.3982 ------------------------------------------------------------------------------- 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: