Starting phenix.real_space_refine on Tue Oct 15 06:53:19 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sax_40283/10_2024/8sax_40283_neut.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sax_40283/10_2024/8sax_40283.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sax_40283/10_2024/8sax_40283.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sax_40283/10_2024/8sax_40283.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sax_40283/10_2024/8sax_40283_neut.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sax_40283/10_2024/8sax_40283_neut.cif" } resolution = 4.0 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= 0.058 sd= 0.370 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 12405 2.51 5 N 3330 2.21 5 O 3990 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 15 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5477/modules/chem_data/mon_lib" Total number of atoms: 19860 Number of models: 1 Model: "" Number of chains: 24 Chain: "A" Number of atoms: 3582 Number of conformers: 1 Conformer: "" Number of residues, atoms: 462, 3582 Classifications: {'peptide': 462} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PCIS': 1, 'PTRANS': 22, 'TRANS': 438} Unresolved non-hydrogen bonds: 33 Unresolved non-hydrogen angles: 43 Unresolved non-hydrogen dihedrals: 28 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'TYR:plan': 1, 'GLU:plan': 2, 'ASN:plan1': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 23 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: 993 Number of conformers: 1 Conformer: "" Number of residues, atoms: 127, 993 Classifications: {'peptide': 127} Link IDs: {'PTRANS': 4, 'TRANS': 122} Chain: "D" Number of atoms: 800 Number of conformers: 1 Conformer: "" Number of residues, atoms: 111, 800 Classifications: {'peptide': 111} Link IDs: {'PTRANS': 5, 'TRANS': 105} Chain: "E" Number of atoms: 3582 Number of conformers: 1 Conformer: "" Number of residues, atoms: 462, 3582 Classifications: {'peptide': 462} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PCIS': 1, 'PTRANS': 22, 'TRANS': 438} Unresolved non-hydrogen bonds: 33 Unresolved non-hydrogen angles: 43 Unresolved non-hydrogen dihedrals: 28 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'TYR:plan': 1, 'GLU:plan': 2, 'ASN:plan1': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 23 Chain: "F" 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: "G" Number of atoms: 993 Number of conformers: 1 Conformer: "" Number of residues, atoms: 127, 993 Classifications: {'peptide': 127} Link IDs: {'PTRANS': 4, 'TRANS': 122} Chain: "H" Number of atoms: 800 Number of conformers: 1 Conformer: "" Number of residues, atoms: 111, 800 Classifications: {'peptide': 111} Link IDs: {'PTRANS': 5, 'TRANS': 105} Chain: "I" Number of atoms: 3582 Number of conformers: 1 Conformer: "" Number of residues, atoms: 462, 3582 Classifications: {'peptide': 462} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PCIS': 1, 'PTRANS': 22, 'TRANS': 438} Unresolved non-hydrogen bonds: 33 Unresolved non-hydrogen angles: 43 Unresolved non-hydrogen dihedrals: 28 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'TYR:plan': 1, 'GLU:plan': 2, 'ASN:plan1': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 23 Chain: "J" 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: "K" Number of atoms: 993 Number of conformers: 1 Conformer: "" Number of residues, atoms: 127, 993 Classifications: {'peptide': 127} Link IDs: {'PTRANS': 4, 'TRANS': 122} Chain: "L" Number of atoms: 800 Number of conformers: 1 Conformer: "" Number of residues, atoms: 111, 800 Classifications: {'peptide': 111} Link IDs: {'PTRANS': 5, 'TRANS': 105} Chain: "M" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "N" 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: 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: "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: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "R" 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: "S" 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: "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: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 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: 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: "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: 11.72, per 1000 atoms: 0.59 Number of scatterers: 19860 At special positions: 0 Unit cell: (165.24, 166.86, 142.56, 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 3990 8.00 N 3330 7.00 C 12405 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=30, symmetry=0 Simple disulfide: pdb=" SG CYS A 54 " - pdb=" SG CYS A 74 " distance=2.03 Simple disulfide: pdb=" SG CYS A 119 " - pdb=" SG CYS A 205 " 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 378 " - pdb=" SG CYS A 445 " 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 E 54 " - pdb=" SG CYS E 74 " distance=2.03 Simple disulfide: pdb=" SG CYS E 119 " - pdb=" SG CYS E 205 " distance=2.03 Simple disulfide: pdb=" SG CYS E 131 " - pdb=" SG CYS E 157 " distance=2.03 Simple disulfide: pdb=" SG CYS E 201 " - pdb=" SG CYS E 433 " distance=2.03 Simple disulfide: pdb=" SG CYS E 218 " - pdb=" SG CYS E 247 " distance=2.03 Simple disulfide: pdb=" SG CYS E 228 " - pdb=" SG CYS E 239 " distance=2.03 Simple disulfide: pdb=" SG CYS E 378 " - pdb=" SG CYS E 445 " distance=2.03 Simple disulfide: pdb=" SG CYS F 598 " - pdb=" SG CYS F 604 " distance=2.03 Simple disulfide: pdb=" SG CYS G 22 " - pdb=" SG CYS G 96 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 90 " distance=2.04 Simple disulfide: pdb=" SG CYS I 54 " - pdb=" SG CYS I 74 " distance=2.04 Simple disulfide: pdb=" SG CYS I 119 " - pdb=" SG CYS I 205 " distance=2.03 Simple disulfide: pdb=" SG CYS I 131 " - pdb=" SG CYS I 157 " distance=2.03 Simple disulfide: pdb=" SG CYS I 201 " - pdb=" SG CYS I 433 " distance=2.03 Simple disulfide: pdb=" SG CYS I 218 " - pdb=" SG CYS I 247 " distance=2.03 Simple disulfide: pdb=" SG CYS I 228 " - pdb=" SG CYS I 239 " distance=2.03 Simple disulfide: pdb=" SG CYS I 378 " - pdb=" SG CYS I 445 " distance=2.03 Simple disulfide: pdb=" SG CYS J 598 " - pdb=" SG CYS J 604 " distance=2.03 Simple disulfide: pdb=" SG CYS K 22 " - pdb=" SG CYS K 96 " distance=2.03 Simple disulfide: pdb=" SG CYS L 22 " - pdb=" SG CYS L 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 N 4 " - " MAN N 5 " " MAN N 5 " - " MAN N 6 " " MAN R 4 " - " MAN R 5 " " MAN R 5 " - " MAN R 6 " " MAN V 4 " - " MAN V 5 " " MAN V 5 " - " MAN V 6 " ALPHA1-3 " BMA M 3 " - " MAN M 4 " " BMA N 3 " - " MAN N 4 " " MAN N 7 " - " MAN N 8 " " BMA Q 3 " - " MAN Q 4 " " BMA R 3 " - " MAN R 4 " " MAN R 7 " - " MAN R 8 " " BMA U 3 " - " MAN U 4 " " BMA V 3 " - " MAN V 4 " " MAN V 7 " - " MAN V 8 " ALPHA1-6 " BMA N 3 " - " MAN N 7 " " MAN N 7 " - " MAN N 9 " " BMA R 3 " - " MAN R 7 " " MAN R 7 " - " MAN R 9 " " BMA V 3 " - " MAN V 7 " " MAN V 7 " - " MAN V 9 " BETA1-4 " NAG M 1 " - " NAG M 2 " " NAG M 2 " - " BMA M 3 " " NAG N 1 " - " NAG N 2 " " NAG N 2 " - " BMA N 3 " " NAG O 1 " - " NAG O 2 " " 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 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 X 1 " - " NAG X 2 " NAG-ASN " NAG M 1 " - " ASN A 301 " " NAG O 1 " - " ASN A 156 " " NAG P 1 " - " ASN A 442 " " NAG Q 1 " - " ASN E 301 " " NAG S 1 " - " ASN E 156 " " NAG T 1 " - " ASN E 442 " " NAG U 1 " - " ASN I 301 " " NAG W 1 " - " ASN I 156 " " NAG X 1 " - " ASN I 442 " Time building additional restraints: 5.66 Conformation dependent library (CDL) restraints added in 2.6 seconds 4944 Ramachandran restraints generated. 2472 Oldfield, 0 Emsley, 2472 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4572 Finding SS restraints... Secondary structure from input PDB file: 48 helices and 45 sheets defined 18.6% alpha, 29.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.01 Creating SS restraints... Processing helix chain 'A' and resid 58 through 63 removed outlier: 4.032A pdb=" N LYS A 63 " --> pdb=" O ARG A 59 " (cutoff:3.500A) Processing helix chain 'A' and resid 69 through 74 Processing helix chain 'A' and resid 99 through 116 removed outlier: 3.712A pdb=" N LEU A 116 " --> pdb=" O TRP A 112 " (cutoff:3.500A) Processing helix chain 'A' and resid 335 through 351 removed outlier: 4.052A 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 474 through 481 removed outlier: 4.205A pdb=" N ASN A 478 " --> pdb=" O ASP A 474 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N SER A 481 " --> pdb=" O ASP A 477 " (cutoff:3.500A) Processing helix chain 'B' and resid 529 through 535 removed outlier: 4.245A pdb=" N MET B 535 " --> pdb=" O GLY B 531 " (cutoff:3.500A) Processing helix chain 'B' and resid 537 through 543 removed outlier: 3.604A pdb=" N ALA B 541 " --> pdb=" O LEU B 537 " (cutoff:3.500A) Processing helix chain 'B' and resid 571 through 579 removed outlier: 3.670A pdb=" N GLN B 575 " --> pdb=" O TRP B 571 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N LEU B 576 " --> pdb=" O GLY B 572 " (cutoff:3.500A) Processing helix chain 'B' and resid 581 through 596 removed outlier: 4.623A pdb=" N ARG B 585 " --> pdb=" O LEU B 581 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N LEU B 587 " --> pdb=" O VAL B 583 " (cutoff:3.500A) Processing helix chain 'B' and resid 618 through 624 removed outlier: 3.697A pdb=" N ILE B 622 " --> pdb=" O ASN B 618 " (cutoff:3.500A) Processing helix chain 'B' and resid 627 through 635 Processing helix chain 'B' and resid 639 through 664 removed outlier: 3.537A pdb=" N GLU B 648 " --> pdb=" O GLY B 644 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N GLN B 650 " --> pdb=" O LEU B 646 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N ASN B 651 " --> pdb=" O GLU B 647 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N ASP B 664 " --> pdb=" O LEU B 660 " (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 removed outlier: 4.020A pdb=" N THR C 91 " --> pdb=" O SER C 88 " (cutoff:3.500A) Processing helix chain 'D' and resid 81 through 85 removed outlier: 3.670A pdb=" N GLU D 85 " --> pdb=" O ALA D 82 " (cutoff:3.500A) Processing helix chain 'E' and resid 58 through 63 removed outlier: 4.032A pdb=" N LYS E 63 " --> pdb=" O ARG E 59 " (cutoff:3.500A) Processing helix chain 'E' and resid 69 through 74 Processing helix chain 'E' and resid 99 through 116 removed outlier: 3.712A pdb=" N LEU E 116 " --> pdb=" O TRP E 112 " (cutoff:3.500A) Processing helix chain 'E' and resid 335 through 351 removed outlier: 4.052A pdb=" N LYS E 351 " --> pdb=" O ILE E 347 " (cutoff:3.500A) Processing helix chain 'E' and resid 368 through 373 Processing helix chain 'E' and resid 474 through 481 removed outlier: 4.205A pdb=" N ASN E 478 " --> pdb=" O ASP E 474 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N SER E 481 " --> pdb=" O ASP E 477 " (cutoff:3.500A) Processing helix chain 'F' and resid 529 through 535 removed outlier: 4.246A pdb=" N MET F 535 " --> pdb=" O GLY F 531 " (cutoff:3.500A) Processing helix chain 'F' and resid 537 through 543 removed outlier: 3.604A pdb=" N ALA F 541 " --> pdb=" O LEU F 537 " (cutoff:3.500A) Processing helix chain 'F' and resid 571 through 579 removed outlier: 3.670A pdb=" N GLN F 575 " --> pdb=" O TRP F 571 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N LEU F 576 " --> pdb=" O GLY F 572 " (cutoff:3.500A) Processing helix chain 'F' and resid 581 through 596 removed outlier: 4.624A pdb=" N ARG F 585 " --> pdb=" O LEU F 581 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N LEU F 587 " --> pdb=" O VAL F 583 " (cutoff:3.500A) Processing helix chain 'F' and resid 618 through 624 removed outlier: 3.697A pdb=" N ILE F 622 " --> pdb=" O ASN F 618 " (cutoff:3.500A) Processing helix chain 'F' and resid 627 through 635 Processing helix chain 'F' and resid 639 through 664 removed outlier: 3.537A pdb=" N GLU F 648 " --> pdb=" O GLY F 644 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N GLN F 650 " --> pdb=" O LEU F 646 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N ASN F 651 " --> pdb=" O GLU F 647 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N ASP F 664 " --> pdb=" O LEU F 660 " (cutoff:3.500A) Processing helix chain 'G' and resid 28 through 30 No H-bonds generated for 'chain 'G' and resid 28 through 30' Processing helix chain 'G' and resid 87 through 91 removed outlier: 4.020A pdb=" N THR G 91 " --> pdb=" O SER G 88 " (cutoff:3.500A) Processing helix chain 'H' and resid 81 through 85 removed outlier: 3.670A pdb=" N GLU H 85 " --> pdb=" O ALA H 82 " (cutoff:3.500A) Processing helix chain 'I' and resid 58 through 63 removed outlier: 4.033A pdb=" N LYS I 63 " --> pdb=" O ARG I 59 " (cutoff:3.500A) Processing helix chain 'I' and resid 69 through 74 Processing helix chain 'I' and resid 99 through 116 removed outlier: 3.712A pdb=" N LEU I 116 " --> pdb=" O TRP I 112 " (cutoff:3.500A) Processing helix chain 'I' and resid 335 through 351 removed outlier: 4.052A pdb=" N LYS I 351 " --> pdb=" O ILE I 347 " (cutoff:3.500A) Processing helix chain 'I' and resid 368 through 373 Processing helix chain 'I' and resid 474 through 481 removed outlier: 4.204A pdb=" N ASN I 478 " --> pdb=" O ASP I 474 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N SER I 481 " --> pdb=" O ASP I 477 " (cutoff:3.500A) Processing helix chain 'J' and resid 529 through 535 removed outlier: 4.246A pdb=" N MET J 535 " --> pdb=" O GLY J 531 " (cutoff:3.500A) Processing helix chain 'J' and resid 537 through 543 removed outlier: 3.604A pdb=" N ALA J 541 " --> pdb=" O LEU J 537 " (cutoff:3.500A) Processing helix chain 'J' and resid 571 through 579 removed outlier: 3.669A pdb=" N GLN J 575 " --> pdb=" O TRP J 571 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N LEU J 576 " --> pdb=" O GLY J 572 " (cutoff:3.500A) Processing helix chain 'J' and resid 581 through 596 removed outlier: 4.623A pdb=" N ARG J 585 " --> pdb=" O LEU J 581 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N LEU J 587 " --> pdb=" O VAL J 583 " (cutoff:3.500A) Processing helix chain 'J' and resid 618 through 624 removed outlier: 3.697A pdb=" N ILE J 622 " --> pdb=" O ASN J 618 " (cutoff:3.500A) Processing helix chain 'J' and resid 627 through 635 Processing helix chain 'J' and resid 639 through 664 removed outlier: 3.536A pdb=" N GLU J 648 " --> pdb=" O GLY J 644 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N GLN J 650 " --> pdb=" O LEU J 646 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N ASN J 651 " --> pdb=" O GLU J 647 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N ASP J 664 " --> pdb=" O LEU J 660 " (cutoff:3.500A) Processing helix chain 'K' and resid 28 through 30 No H-bonds generated for 'chain 'K' and resid 28 through 30' Processing helix chain 'K' and resid 87 through 91 removed outlier: 4.020A pdb=" N THR K 91 " --> pdb=" O SER K 88 " (cutoff:3.500A) Processing helix chain 'L' and resid 81 through 85 removed outlier: 3.670A pdb=" N GLU L 85 " --> pdb=" O ALA L 82 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 494 through 499 removed outlier: 4.843A pdb=" N VAL A 36 " --> pdb=" O THR B 606 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 45 through 47 removed outlier: 3.902A 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 removed outlier: 4.366A pdb=" N GLU A 91 " --> pdb=" O CYS A 239 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N CYS A 239 " --> pdb=" O GLU A 91 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 169 through 177 Processing sheet with id=AA6, first strand: chain 'A' and resid 259 through 260 removed outlier: 4.232A pdb=" N GLY A 451 " --> pdb=" O LEU A 260 " (cutoff:3.500A) removed outlier: 9.687A pdb=" N ASN A 448 " --> pdb=" O THR A 290 " (cutoff:3.500A) removed outlier: 11.027A pdb=" N THR A 290 " --> pdb=" O ASN A 448 " (cutoff:3.500A) removed outlier: 6.947A pdb=" N THR A 450 " --> pdb=" O LEU A 288 " (cutoff:3.500A) removed outlier: 7.327A pdb=" N GLU A 293 " --> pdb=" O SER A 334 " (cutoff:3.500A) removed outlier: 4.330A pdb=" N SER A 334 " --> pdb=" O GLU A 293 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N LYS A 421 " --> pdb=" O PHE A 382 " (cutoff:3.500A) removed outlier: 4.383A pdb=" N PHE A 382 " --> pdb=" O LYS A 421 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 272 through 273 removed outlier: 6.947A pdb=" N THR A 450 " --> pdb=" O LEU A 288 " (cutoff:3.500A) removed outlier: 11.027A pdb=" N THR A 290 " --> pdb=" O ASN A 448 " (cutoff:3.500A) removed outlier: 9.687A pdb=" N ASN A 448 " --> pdb=" O THR A 290 " (cutoff:3.500A) removed outlier: 6.719A pdb=" N LYS A 360 " --> pdb=" O PHE A 468 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N GLY A 393 " --> pdb=" O TYR A 361 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 302 through 304 removed outlier: 6.302A pdb=" N THR A 303 " --> pdb=" O GLY A 321 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 307 through 308 Processing sheet with id=AB1, first strand: chain 'A' and resid 423 through 425 Processing sheet with id=AB2, first strand: chain 'C' and resid 3 through 6 Processing sheet with id=AB3, first strand: chain 'C' and resid 9 through 11 removed outlier: 3.657A pdb=" N THR C 124 " --> pdb=" O GLU C 10 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N GLY C 99 " --> pdb=" O TYR C 33 " (cutoff:3.500A) removed outlier: 5.428A pdb=" N TYR C 33 " --> pdb=" O GLY C 99 " (cutoff:3.500A) removed outlier: 6.651A pdb=" N MET C 34 " --> pdb=" O TRP C 50 " (cutoff:3.500A) removed outlier: 4.565A pdb=" N TRP C 50 " --> pdb=" O MET C 34 " (cutoff:3.500A) removed outlier: 7.052A pdb=" N TRP C 36 " --> pdb=" O MET C 48 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 9 through 12 Processing sheet with id=AB5, first strand: chain 'D' and resid 9 through 12 Processing sheet with id=AB6, first strand: chain 'D' and resid 18 through 23 Processing sheet with id=AB7, first strand: chain 'E' and resid 494 through 499 removed outlier: 4.891A pdb=" N VAL E 36 " --> pdb=" O THR F 606 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'E' and resid 45 through 47 removed outlier: 3.903A pdb=" N ILE E 225 " --> pdb=" O VAL E 245 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'E' and resid 75 through 76 Processing sheet with id=AC1, first strand: chain 'E' and resid 91 through 94 removed outlier: 4.366A pdb=" N GLU E 91 " --> pdb=" O CYS E 239 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N CYS E 239 " --> pdb=" O GLU E 91 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'E' and resid 169 through 177 Processing sheet with id=AC3, first strand: chain 'E' and resid 259 through 260 removed outlier: 4.232A pdb=" N GLY E 451 " --> pdb=" O LEU E 260 " (cutoff:3.500A) removed outlier: 9.687A pdb=" N ASN E 448 " --> pdb=" O THR E 290 " (cutoff:3.500A) removed outlier: 11.026A pdb=" N THR E 290 " --> pdb=" O ASN E 448 " (cutoff:3.500A) removed outlier: 6.946A pdb=" N THR E 450 " --> pdb=" O LEU E 288 " (cutoff:3.500A) removed outlier: 7.327A pdb=" N GLU E 293 " --> pdb=" O SER E 334 " (cutoff:3.500A) removed outlier: 4.331A pdb=" N SER E 334 " --> pdb=" O GLU E 293 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N LYS E 421 " --> pdb=" O PHE E 382 " (cutoff:3.500A) removed outlier: 4.383A pdb=" N PHE E 382 " --> pdb=" O LYS E 421 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'E' and resid 272 through 273 removed outlier: 6.946A pdb=" N THR E 450 " --> pdb=" O LEU E 288 " (cutoff:3.500A) removed outlier: 11.026A pdb=" N THR E 290 " --> pdb=" O ASN E 448 " (cutoff:3.500A) removed outlier: 9.687A pdb=" N ASN E 448 " --> pdb=" O THR E 290 " (cutoff:3.500A) removed outlier: 6.719A pdb=" N LYS E 360 " --> pdb=" O PHE E 468 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N GLY E 393 " --> pdb=" O TYR E 361 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'E' and resid 302 through 304 removed outlier: 6.302A pdb=" N THR E 303 " --> pdb=" O GLY E 321 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'E' and resid 307 through 308 Processing sheet with id=AC7, first strand: chain 'E' and resid 423 through 425 Processing sheet with id=AC8, first strand: chain 'G' and resid 3 through 6 Processing sheet with id=AC9, first strand: chain 'G' and resid 9 through 11 removed outlier: 3.658A pdb=" N THR G 124 " --> pdb=" O GLU G 10 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N GLY G 99 " --> pdb=" O TYR G 33 " (cutoff:3.500A) removed outlier: 5.429A pdb=" N TYR G 33 " --> pdb=" O GLY G 99 " (cutoff:3.500A) removed outlier: 6.651A pdb=" N MET G 34 " --> pdb=" O TRP G 50 " (cutoff:3.500A) removed outlier: 4.566A pdb=" N TRP G 50 " --> pdb=" O MET G 34 " (cutoff:3.500A) removed outlier: 7.053A pdb=" N TRP G 36 " --> pdb=" O MET G 48 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'H' and resid 9 through 12 Processing sheet with id=AD2, first strand: chain 'H' and resid 9 through 12 Processing sheet with id=AD3, first strand: chain 'H' and resid 18 through 23 Processing sheet with id=AD4, first strand: chain 'I' and resid 494 through 499 removed outlier: 4.940A pdb=" N VAL I 36 " --> pdb=" O THR J 606 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'I' and resid 45 through 47 removed outlier: 3.903A pdb=" N ILE I 225 " --> pdb=" O VAL I 245 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'I' and resid 75 through 76 Processing sheet with id=AD7, first strand: chain 'I' and resid 91 through 94 removed outlier: 4.366A pdb=" N GLU I 91 " --> pdb=" O CYS I 239 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N CYS I 239 " --> pdb=" O GLU I 91 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'I' and resid 169 through 177 Processing sheet with id=AD9, first strand: chain 'I' and resid 259 through 260 removed outlier: 4.232A pdb=" N GLY I 451 " --> pdb=" O LEU I 260 " (cutoff:3.500A) removed outlier: 9.687A pdb=" N ASN I 448 " --> pdb=" O THR I 290 " (cutoff:3.500A) removed outlier: 11.027A pdb=" N THR I 290 " --> pdb=" O ASN I 448 " (cutoff:3.500A) removed outlier: 6.947A pdb=" N THR I 450 " --> pdb=" O LEU I 288 " (cutoff:3.500A) removed outlier: 7.328A pdb=" N GLU I 293 " --> pdb=" O SER I 334 " (cutoff:3.500A) removed outlier: 4.330A pdb=" N SER I 334 " --> pdb=" O GLU I 293 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N LYS I 421 " --> pdb=" O PHE I 382 " (cutoff:3.500A) removed outlier: 4.383A pdb=" N PHE I 382 " --> pdb=" O LYS I 421 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'I' and resid 272 through 273 removed outlier: 6.947A pdb=" N THR I 450 " --> pdb=" O LEU I 288 " (cutoff:3.500A) removed outlier: 11.027A pdb=" N THR I 290 " --> pdb=" O ASN I 448 " (cutoff:3.500A) removed outlier: 9.687A pdb=" N ASN I 448 " --> pdb=" O THR I 290 " (cutoff:3.500A) removed outlier: 6.719A pdb=" N LYS I 360 " --> pdb=" O PHE I 468 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N GLY I 393 " --> pdb=" O TYR I 361 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'I' and resid 302 through 304 removed outlier: 6.302A pdb=" N THR I 303 " --> pdb=" O GLY I 321 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'I' and resid 307 through 308 Processing sheet with id=AE4, first strand: chain 'I' and resid 423 through 425 Processing sheet with id=AE5, first strand: chain 'K' and resid 3 through 6 Processing sheet with id=AE6, first strand: chain 'K' and resid 9 through 11 removed outlier: 3.500A pdb=" N GLU K 10 " --> pdb=" O LEU K 122 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N THR K 124 " --> pdb=" O GLU K 10 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N GLY K 99 " --> pdb=" O TYR K 33 " (cutoff:3.500A) removed outlier: 5.428A pdb=" N TYR K 33 " --> pdb=" O GLY K 99 " (cutoff:3.500A) removed outlier: 6.651A pdb=" N MET K 34 " --> pdb=" O TRP K 50 " (cutoff:3.500A) removed outlier: 4.565A pdb=" N TRP K 50 " --> pdb=" O MET K 34 " (cutoff:3.500A) removed outlier: 7.053A pdb=" N TRP K 36 " --> pdb=" O MET K 48 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'L' and resid 9 through 12 Processing sheet with id=AE8, first strand: chain 'L' and resid 9 through 12 Processing sheet with id=AE9, first strand: chain 'L' and resid 18 through 23 668 hydrogen bonds defined for protein. 1752 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: 8.24 Time building geometry restraints manager: 6.42 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 6318 1.34 - 1.46: 4887 1.46 - 1.58: 8883 1.58 - 1.70: 0 1.70 - 1.81: 183 Bond restraints: 20271 Sorted by residual: bond pdb=" C3 MAN N 7 " pdb=" O3 MAN N 7 " ideal model delta sigma weight residual 1.408 1.484 -0.076 2.00e-02 2.50e+03 1.44e+01 bond pdb=" C3 MAN V 7 " pdb=" O3 MAN V 7 " ideal model delta sigma weight residual 1.408 1.484 -0.076 2.00e-02 2.50e+03 1.44e+01 bond pdb=" C3 MAN R 7 " pdb=" O3 MAN R 7 " ideal model delta sigma weight residual 1.408 1.484 -0.076 2.00e-02 2.50e+03 1.44e+01 bond pdb=" C1 MAN V 8 " pdb=" C2 MAN V 8 " ideal model delta sigma weight residual 1.526 1.574 -0.048 2.00e-02 2.50e+03 5.82e+00 bond pdb=" C1 MAN R 8 " pdb=" C2 MAN R 8 " ideal model delta sigma weight residual 1.526 1.573 -0.047 2.00e-02 2.50e+03 5.64e+00 ... (remaining 20266 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.12: 27140 2.12 - 4.25: 304 4.25 - 6.37: 99 6.37 - 8.50: 9 8.50 - 10.62: 6 Bond angle restraints: 27558 Sorted by residual: angle pdb=" C LEU I 122 " pdb=" N THR I 123 " pdb=" CA THR I 123 " ideal model delta sigma weight residual 121.80 131.62 -9.82 2.44e+00 1.68e-01 1.62e+01 angle pdb=" C LEU A 122 " pdb=" N THR A 123 " pdb=" CA THR A 123 " ideal model delta sigma weight residual 121.80 131.58 -9.78 2.44e+00 1.68e-01 1.61e+01 angle pdb=" C LEU E 122 " pdb=" N THR E 123 " pdb=" CA THR E 123 " ideal model delta sigma weight residual 121.80 131.54 -9.74 2.44e+00 1.68e-01 1.59e+01 angle pdb=" C2 MAN V 7 " pdb=" C3 MAN V 7 " pdb=" O3 MAN V 7 " ideal model delta sigma weight residual 107.58 118.20 -10.62 3.00e+00 1.11e-01 1.25e+01 angle pdb=" C2 MAN N 7 " pdb=" C3 MAN N 7 " pdb=" O3 MAN N 7 " ideal model delta sigma weight residual 107.58 118.20 -10.62 3.00e+00 1.11e-01 1.25e+01 ... (remaining 27553 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.55: 12349 24.55 - 49.11: 272 49.11 - 73.66: 39 73.66 - 98.22: 48 98.22 - 122.77: 24 Dihedral angle restraints: 12732 sinusoidal: 5571 harmonic: 7161 Sorted by residual: dihedral pdb=" CA VAL B 580 " pdb=" C VAL B 580 " pdb=" N LEU B 581 " pdb=" CA LEU B 581 " ideal model delta harmonic sigma weight residual 180.00 158.27 21.73 0 5.00e+00 4.00e-02 1.89e+01 dihedral pdb=" CA VAL F 580 " pdb=" C VAL F 580 " pdb=" N LEU F 581 " pdb=" CA LEU F 581 " ideal model delta harmonic sigma weight residual 180.00 158.30 21.70 0 5.00e+00 4.00e-02 1.88e+01 dihedral pdb=" CA VAL J 580 " pdb=" C VAL J 580 " pdb=" N LEU J 581 " pdb=" CA LEU J 581 " ideal model delta harmonic sigma weight residual 180.00 158.31 21.69 0 5.00e+00 4.00e-02 1.88e+01 ... (remaining 12729 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.209: 3231 0.209 - 0.417: 9 0.417 - 0.626: 0 0.626 - 0.834: 0 0.834 - 1.043: 3 Chirality restraints: 3243 Sorted by residual: chirality pdb=" C1 NAG P 1 " pdb=" ND2 ASN A 442 " pdb=" C2 NAG P 1 " pdb=" O5 NAG P 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.36 -1.04 2.00e-01 2.50e+01 2.72e+01 chirality pdb=" C1 NAG T 1 " pdb=" ND2 ASN E 442 " pdb=" C2 NAG T 1 " pdb=" O5 NAG T 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.36 -1.04 2.00e-01 2.50e+01 2.72e+01 chirality pdb=" C1 NAG X 1 " pdb=" ND2 ASN I 442 " pdb=" C2 NAG X 1 " pdb=" O5 NAG X 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.36 -1.04 2.00e-01 2.50e+01 2.71e+01 ... (remaining 3240 not shown) Planarity restraints: 3459 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ARG E 298 " 0.024 5.00e-02 4.00e+02 3.58e-02 2.05e+00 pdb=" N PRO E 299 " -0.062 5.00e-02 4.00e+02 pdb=" CA PRO E 299 " 0.018 5.00e-02 4.00e+02 pdb=" CD PRO E 299 " 0.020 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ARG A 298 " 0.024 5.00e-02 4.00e+02 3.57e-02 2.03e+00 pdb=" N PRO A 299 " -0.062 5.00e-02 4.00e+02 pdb=" CA PRO A 299 " 0.018 5.00e-02 4.00e+02 pdb=" CD PRO A 299 " 0.020 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ARG I 298 " 0.024 5.00e-02 4.00e+02 3.56e-02 2.03e+00 pdb=" N PRO I 299 " -0.062 5.00e-02 4.00e+02 pdb=" CA PRO I 299 " 0.018 5.00e-02 4.00e+02 pdb=" CD PRO I 299 " 0.020 5.00e-02 4.00e+02 ... (remaining 3456 not shown) Histogram of nonbonded interaction distances: 2.03 - 2.61: 185 2.61 - 3.18: 17039 3.18 - 3.75: 27253 3.75 - 4.33: 36691 4.33 - 4.90: 62884 Nonbonded interactions: 144052 Sorted by model distance: nonbonded pdb=" O4 BMA R 3 " pdb=" O6 MAN R 5 " model vdw 2.035 3.040 nonbonded pdb=" O4 BMA N 3 " pdb=" O6 MAN N 5 " model vdw 2.035 3.040 nonbonded pdb=" O4 BMA V 3 " pdb=" O6 MAN V 5 " model vdw 2.035 3.040 nonbonded pdb=" O3 NAG X 1 " pdb=" O5 NAG X 2 " model vdw 2.159 3.040 nonbonded pdb=" O3 NAG P 1 " pdb=" O5 NAG P 2 " model vdw 2.159 3.040 ... (remaining 144047 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 'E' selection = chain 'I' } ncs_group { reference = chain 'B' selection = chain 'F' selection = chain 'J' } ncs_group { reference = chain 'C' selection = chain 'G' selection = chain 'K' } ncs_group { reference = chain 'D' selection = chain 'H' selection = chain 'L' } ncs_group { reference = chain 'M' selection = chain 'Q' selection = chain 'U' } ncs_group { reference = chain 'N' selection = chain 'R' selection = chain 'V' } ncs_group { reference = chain 'O' selection = chain 'P' selection = chain 'S' selection = chain 'T' selection = chain 'W' 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: 0.190 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: 0.730 Check model and map are aligned: 0.130 Set scattering table: 0.140 Process input model: 47.210 Find NCS groups from input model: 0.680 Set up NCS constraints: 0.150 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: 0.000 Load rotamer database and sin/cos tables:2.820 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 52.060 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7329 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 : 0.004 0.076 20271 Z= 0.274 Angle : 0.652 10.621 27558 Z= 0.307 Chirality : 0.056 1.043 3243 Planarity : 0.003 0.036 3450 Dihedral : 13.454 122.772 8070 Min Nonbonded Distance : 2.035 Molprobity Statistics. All-atom Clashscore : 2.64 Ramachandran Plot: Outliers : 0.36 % Allowed : 2.67 % Favored : 96.97 % Rotamer: Outliers : 2.12 % Allowed : 4.67 % Favored : 93.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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: -0.49 (0.17), residues: 2472 helix: 1.48 (0.30), residues: 366 sheet: 0.22 (0.19), residues: 657 loop : -1.09 (0.16), residues: 1449 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP F 571 HIS 0.002 0.000 HIS A 249 PHE 0.007 0.001 PHE G 114 TYR 0.008 0.001 TYR H 93 ARG 0.002 0.000 ARG A 456 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4944 Ramachandran restraints generated. 2472 Oldfield, 0 Emsley, 2472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4944 Ramachandran restraints generated. 2472 Oldfield, 0 Emsley, 2472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 407 residues out of total 2142 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 362 time to evaluate : 2.442 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 333 ILE cc_start: 0.6888 (mt) cc_final: 0.6621 (mm) REVERT: A 390 LEU cc_start: 0.9063 (OUTLIER) cc_final: 0.8856 (tp) REVERT: B 534 SER cc_start: 0.8886 (t) cc_final: 0.8549 (p) REVERT: B 535 MET cc_start: 0.7988 (mtm) cc_final: 0.7537 (mpp) REVERT: B 586 TYR cc_start: 0.6544 (t80) cc_final: 0.6114 (t80) REVERT: B 630 GLN cc_start: 0.8677 (pt0) cc_final: 0.8327 (pt0) REVERT: B 631 TRP cc_start: 0.8364 (t-100) cc_final: 0.7675 (t-100) REVERT: C 81 MET cc_start: 0.8346 (tmm) cc_final: 0.8104 (tmm) REVERT: C 112 PRO cc_start: 0.9239 (Cg_endo) cc_final: 0.8957 (Cg_exo) REVERT: C 114 PHE cc_start: 0.7354 (OUTLIER) cc_final: 0.7014 (p90) REVERT: C 115 ASP cc_start: 0.6042 (t70) cc_final: 0.5794 (t0) REVERT: D 37 TRP cc_start: 0.7382 (m100) cc_final: 0.6773 (m100) REVERT: E 95 MET cc_start: 0.7955 (ttp) cc_final: 0.7554 (tmm) REVERT: E 101 VAL cc_start: 0.9350 (m) cc_final: 0.9082 (p) REVERT: E 287 HIS cc_start: 0.8212 (OUTLIER) cc_final: 0.7369 (m-70) REVERT: F 534 SER cc_start: 0.8827 (t) cc_final: 0.8436 (p) REVERT: F 543 ASN cc_start: 0.8439 (m110) cc_final: 0.8227 (m110) REVERT: F 616 ASN cc_start: 0.8266 (t0) cc_final: 0.7973 (t0) REVERT: F 659 ASP cc_start: 0.6317 (m-30) cc_final: 0.5975 (m-30) REVERT: G 114 PHE cc_start: 0.7387 (OUTLIER) cc_final: 0.6757 (p90) REVERT: H 48 LEU cc_start: 0.6121 (OUTLIER) cc_final: 0.5236 (pt) REVERT: H 84 ASP cc_start: 0.6655 (m-30) cc_final: 0.5508 (m-30) REVERT: I 95 MET cc_start: 0.7816 (ttp) cc_final: 0.7098 (tmm) REVERT: I 333 ILE cc_start: 0.7035 (mt) cc_final: 0.6753 (mm) REVERT: I 369 MET cc_start: 0.8113 (ttm) cc_final: 0.7897 (ttt) REVERT: I 381 GLU cc_start: 0.8290 (mm-30) cc_final: 0.7951 (mm-30) REVERT: J 535 MET cc_start: 0.8604 (mtm) cc_final: 0.7995 (mpp) REVERT: J 543 ASN cc_start: 0.8548 (m110) cc_final: 0.8177 (m110) REVERT: J 659 ASP cc_start: 0.6711 (m-30) cc_final: 0.6228 (m-30) REVERT: K 12 LYS cc_start: 0.7648 (mmtt) cc_final: 0.7375 (mmmm) REVERT: K 81 MET cc_start: 0.9086 (tmm) cc_final: 0.8577 (tmm) REVERT: K 90 ASP cc_start: 0.7001 (t0) cc_final: 0.6529 (p0) REVERT: K 105 TYR cc_start: 0.8509 (m-80) cc_final: 0.8099 (m-80) REVERT: K 116 TYR cc_start: 0.7295 (m-80) cc_final: 0.6823 (m-80) REVERT: K 125 VAL cc_start: 0.5847 (OUTLIER) cc_final: 0.5138 (m) outliers start: 45 outliers final: 8 residues processed: 402 average time/residue: 0.3412 time to fit residues: 205.3921 Evaluate side-chains 194 residues out of total 2142 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 180 time to evaluate : 2.341 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 LEU Chi-restraints excluded: chain A residue 287 HIS Chi-restraints excluded: chain A residue 295 VAL Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain C residue 114 PHE Chi-restraints excluded: chain E residue 287 HIS Chi-restraints excluded: chain E residue 295 VAL Chi-restraints excluded: chain G residue 114 PHE Chi-restraints excluded: chain H residue 29 VAL Chi-restraints excluded: chain H residue 48 LEU Chi-restraints excluded: chain I residue 295 VAL Chi-restraints excluded: chain K residue 51 ILE Chi-restraints excluded: chain K residue 125 VAL Chi-restraints excluded: chain L residue 48 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 246 random chunks: chunk 207 optimal weight: 0.4980 chunk 186 optimal weight: 10.0000 chunk 103 optimal weight: 0.9980 chunk 63 optimal weight: 20.0000 chunk 125 optimal weight: 3.9990 chunk 99 optimal weight: 7.9990 chunk 192 optimal weight: 5.9990 chunk 74 optimal weight: 20.0000 chunk 117 optimal weight: 10.0000 chunk 143 optimal weight: 6.9990 chunk 223 optimal weight: 20.0000 overall best weight: 3.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 575 GLN I 287 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7551 moved from start: 0.2150 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 20271 Z= 0.241 Angle : 0.669 11.475 27558 Z= 0.331 Chirality : 0.048 0.448 3243 Planarity : 0.004 0.064 3450 Dihedral : 11.734 102.867 3722 Min Nonbonded Distance : 2.355 Molprobity Statistics. All-atom Clashscore : 4.66 Ramachandran Plot: Outliers : 0.36 % Allowed : 3.72 % Favored : 95.91 % Rotamer: Outliers : 2.74 % Allowed : 9.25 % Favored : 88.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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: -0.61 (0.17), residues: 2472 helix: 1.27 (0.29), residues: 366 sheet: 0.26 (0.20), residues: 654 loop : -1.20 (0.16), residues: 1452 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP G 50 HIS 0.005 0.001 HIS G 35 PHE 0.022 0.002 PHE C 29 TYR 0.014 0.001 TYR I 217 ARG 0.007 0.001 ARG I 166 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4944 Ramachandran restraints generated. 2472 Oldfield, 0 Emsley, 2472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4944 Ramachandran restraints generated. 2472 Oldfield, 0 Emsley, 2472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 253 residues out of total 2142 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 195 time to evaluate : 2.485 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 530 MET cc_start: 0.7221 (mmp) cc_final: 0.6904 (mmt) REVERT: B 534 SER cc_start: 0.8810 (t) cc_final: 0.8558 (p) REVERT: B 535 MET cc_start: 0.8047 (mtm) cc_final: 0.7650 (mpp) REVERT: B 574 LYS cc_start: 0.7540 (pttm) cc_final: 0.7319 (pttm) REVERT: B 631 TRP cc_start: 0.8630 (t-100) cc_final: 0.7474 (t-100) REVERT: C 81 MET cc_start: 0.8408 (tmm) cc_final: 0.8086 (tmm) REVERT: C 112 PRO cc_start: 0.9339 (Cg_endo) cc_final: 0.9103 (Cg_exo) REVERT: D 37 TRP cc_start: 0.6978 (m100) cc_final: 0.6650 (m100) REVERT: E 95 MET cc_start: 0.8042 (ttp) cc_final: 0.7653 (tmm) REVERT: E 287 HIS cc_start: 0.8212 (OUTLIER) cc_final: 0.7298 (m-70) REVERT: E 381 GLU cc_start: 0.8197 (mm-30) cc_final: 0.7507 (mm-30) REVERT: F 534 SER cc_start: 0.8932 (t) cc_final: 0.8519 (p) REVERT: F 543 ASN cc_start: 0.8344 (m110) cc_final: 0.8056 (m110) REVERT: F 659 ASP cc_start: 0.6453 (m-30) cc_final: 0.6064 (m-30) REVERT: G 114 PHE cc_start: 0.8159 (OUTLIER) cc_final: 0.7890 (p90) REVERT: H 49 MET cc_start: 0.7224 (mmm) cc_final: 0.6992 (mmm) REVERT: H 84 ASP cc_start: 0.5855 (m-30) cc_final: 0.5273 (m-30) REVERT: I 333 ILE cc_start: 0.7339 (mt) cc_final: 0.7063 (mm) REVERT: I 381 GLU cc_start: 0.8380 (mm-30) cc_final: 0.8029 (mm-30) REVERT: J 535 MET cc_start: 0.8628 (mtm) cc_final: 0.8012 (mpp) REVERT: J 659 ASP cc_start: 0.6809 (m-30) cc_final: 0.6292 (m-30) REVERT: K 12 LYS cc_start: 0.7809 (mmtt) cc_final: 0.7607 (mmmt) REVERT: K 81 MET cc_start: 0.9097 (tmm) cc_final: 0.8642 (tmm) REVERT: K 90 ASP cc_start: 0.7148 (t0) cc_final: 0.6630 (p0) REVERT: K 105 TYR cc_start: 0.8763 (m-80) cc_final: 0.8270 (m-80) REVERT: K 115 ASP cc_start: 0.8269 (p0) cc_final: 0.7145 (p0) REVERT: K 116 TYR cc_start: 0.7784 (m-80) cc_final: 0.7178 (m-80) REVERT: K 125 VAL cc_start: 0.6536 (OUTLIER) cc_final: 0.6156 (m) outliers start: 58 outliers final: 25 residues processed: 241 average time/residue: 0.3113 time to fit residues: 117.7831 Evaluate side-chains 183 residues out of total 2142 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 155 time to evaluate : 2.273 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 287 HIS Chi-restraints excluded: chain A residue 295 VAL Chi-restraints excluded: chain B residue 543 ASN Chi-restraints excluded: chain C residue 51 ILE Chi-restraints excluded: chain D residue 19 THR Chi-restraints excluded: chain D residue 90 CYS Chi-restraints excluded: chain D residue 107 LEU Chi-restraints excluded: chain E residue 123 THR Chi-restraints excluded: chain E residue 127 VAL Chi-restraints excluded: chain E residue 287 HIS Chi-restraints excluded: chain E residue 295 VAL Chi-restraints excluded: chain F residue 641 ILE Chi-restraints excluded: chain G residue 28 THR Chi-restraints excluded: chain G residue 90 ASP Chi-restraints excluded: chain G residue 114 PHE Chi-restraints excluded: chain H residue 19 THR Chi-restraints excluded: chain H residue 48 LEU Chi-restraints excluded: chain I residue 202 THR Chi-restraints excluded: chain I residue 287 HIS Chi-restraints excluded: chain I residue 295 VAL Chi-restraints excluded: chain I residue 325 ASP Chi-restraints excluded: chain J residue 576 LEU Chi-restraints excluded: chain J residue 641 ILE Chi-restraints excluded: chain K residue 28 THR Chi-restraints excluded: chain K residue 45 LEU Chi-restraints excluded: chain K residue 51 ILE Chi-restraints excluded: chain K residue 125 VAL Chi-restraints excluded: chain L residue 48 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 246 random chunks: chunk 124 optimal weight: 10.0000 chunk 69 optimal weight: 9.9990 chunk 185 optimal weight: 8.9990 chunk 152 optimal weight: 0.9990 chunk 61 optimal weight: 9.9990 chunk 223 optimal weight: 4.9990 chunk 241 optimal weight: 6.9990 chunk 199 optimal weight: 9.9990 chunk 221 optimal weight: 9.9990 chunk 76 optimal weight: 10.0000 chunk 179 optimal weight: 10.0000 overall best weight: 6.3990 ------------------------------------------------------------------------------- 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: