Starting phenix.real_space_refine on Tue May 20 12:15:15 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8sax_40283/05_2025/8sax_40283_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8sax_40283/05_2025/8sax_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/cci-nas-00/data/ceres_data/8sax_40283/05_2025/8sax_40283.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8sax_40283/05_2025/8sax_40283.map" model { file = "/net/cci-nas-00/data/ceres_data/8sax_40283/05_2025/8sax_40283_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8sax_40283/05_2025/8sax_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-5687/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: 11.03, per 1000 atoms: 0.56 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: 5.31 Conformation dependent library (CDL) restraints added in 2.4 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: 2.73 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: 6.88 Time building geometry restraints manager: 6.13 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: 0.06 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: 0.010 Normalize map: mean=0, sd=1: 0.120 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.710 Check model and map are aligned: 0.130 Set scattering table: 0.180 Process input model: 43.760 Find NCS groups from input model: 0.680 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: 0.000 Load rotamer database and sin/cos tables:2.770 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 48.510 ------------------------------------------------------------------------------- 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 20349 Z= 0.201 Angle : 0.774 25.146 27762 Z= 0.336 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 Details of bonding type rmsd link_NAG-ASN : bond 0.02161 ( 9) link_NAG-ASN : angle 11.48210 ( 27) link_ALPHA1-6 : bond 0.00575 ( 6) link_ALPHA1-6 : angle 1.33898 ( 18) link_BETA1-4 : bond 0.00649 ( 18) link_BETA1-4 : angle 2.61643 ( 54) link_ALPHA1-2 : bond 0.00490 ( 6) link_ALPHA1-2 : angle 1.99175 ( 18) link_ALPHA1-3 : bond 0.01824 ( 9) link_ALPHA1-3 : angle 5.58765 ( 27) hydrogen bonds : bond 0.16446 ( 638) hydrogen bonds : angle 6.40057 ( 1752) SS BOND : bond 0.00218 ( 30) SS BOND : angle 0.66779 ( 60) covalent geometry : bond 0.00413 (20271) covalent geometry : angle 0.65193 (27558) *********************** 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 to be fit. rotamer outliers: 45 poor density : 362 time to evaluate : 2.193 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: 0.3254 time to fit residues: 196.3650 Evaluate side-chains 194 residues out of total 2142 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 180 time to evaluate : 2.189 ------------------------------------------------------------------------------- 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: 7.9990 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3809 r_free = 0.3809 target = 0.088151 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.073742 restraints weight = 77356.604| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3535 r_free = 0.3535 target = 0.075619 restraints weight = 48649.795| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.075923 restraints weight = 35072.276| |-----------------------------------------------------------------------------| r_work (final): 0.3518 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7715 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 20349 Z= 0.165 Angle : 0.711 16.207 27762 Z= 0.341 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 Details of bonding type rmsd link_NAG-ASN : bond 0.00408 ( 9) link_NAG-ASN : angle 2.54764 ( 27) link_ALPHA1-6 : bond 0.00840 ( 6) link_ALPHA1-6 : angle 1.87908 ( 18) link_BETA1-4 : bond 0.00456 ( 18) link_BETA1-4 : angle 2.98898 ( 54) link_ALPHA1-2 : bond 0.00425 ( 6) link_ALPHA1-2 : angle 2.36200 ( 18) link_ALPHA1-3 : bond 0.02444 ( 9) link_ALPHA1-3 : angle 5.53046 ( 27) hydrogen bonds : bond 0.03965 ( 638) hydrogen bonds : angle 5.12715 ( 1752) SS BOND : bond 0.00234 ( 30) SS BOND : angle 0.90244 ( 60) covalent geometry : bond 0.00365 (20271) covalent geometry : angle 0.66947 (27558) *********************** 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 to be fit. rotamer outliers: 58 poor density : 195 time to evaluate : 2.291 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: A 369 MET cc_start: 0.8354 (ttt) cc_final: 0.8137 (ttt) REVERT: B 530 MET cc_start: 0.7189 (mmp) cc_final: 0.6825 (mmt) REVERT: B 534 SER cc_start: 0.8791 (t) cc_final: 0.8534 (p) REVERT: B 535 MET cc_start: 0.7869 (mtm) cc_final: 0.7610 (mpp) REVERT: B 574 LYS cc_start: 0.7588 (pttm) cc_final: 0.7378 (pttm) REVERT: B 631 TRP cc_start: 0.8639 (t-100) cc_final: 0.7546 (t-100) REVERT: C 81 MET cc_start: 0.8251 (tmm) cc_final: 0.7999 (tmm) REVERT: C 112 PRO cc_start: 0.9284 (Cg_endo) cc_final: 0.9078 (Cg_exo) REVERT: D 37 TRP cc_start: 0.6960 (m100) cc_final: 0.6727 (m100) REVERT: E 95 MET cc_start: 0.7990 (ttp) cc_final: 0.7704 (tmm) REVERT: E 287 HIS cc_start: 0.8549 (OUTLIER) cc_final: 0.7646 (m-70) REVERT: E 381 GLU cc_start: 0.8249 (mm-30) cc_final: 0.7740 (mm-30) REVERT: F 534 SER cc_start: 0.8895 (t) cc_final: 0.8519 (p) REVERT: F 543 ASN cc_start: 0.8274 (m110) cc_final: 0.8026 (m110) REVERT: F 659 ASP cc_start: 0.6535 (m-30) cc_final: 0.6152 (m-30) REVERT: G 114 PHE cc_start: 0.8461 (OUTLIER) cc_final: 0.8210 (p90) REVERT: H 49 MET cc_start: 0.7244 (mmm) cc_final: 0.7043 (mmm) REVERT: H 84 ASP cc_start: 0.5658 (m-30) cc_final: 0.5105 (m-30) REVERT: I 333 ILE cc_start: 0.7520 (mt) cc_final: 0.7261 (mm) REVERT: J 535 MET cc_start: 0.8418 (mtm) cc_final: 0.7919 (mpp) REVERT: J 659 ASP cc_start: 0.6818 (m-30) cc_final: 0.6314 (m-30) REVERT: K 81 MET cc_start: 0.9063 (tmm) cc_final: 0.8644 (tmm) REVERT: K 90 ASP cc_start: 0.7105 (t0) cc_final: 0.6581 (p0) REVERT: K 105 TYR cc_start: 0.8491 (m-80) cc_final: 0.8072 (m-80) REVERT: K 115 ASP cc_start: 0.8181 (p0) cc_final: 0.7111 (p0) REVERT: K 116 TYR cc_start: 0.7717 (m-80) cc_final: 0.7158 (m-80) REVERT: K 125 VAL cc_start: 0.6576 (OUTLIER) cc_final: 0.6212 (m) outliers start: 58 outliers final: 25 residues processed: 241 average time/residue: 0.2926 time to fit residues: 111.4552 Evaluate side-chains 181 residues out of total 2142 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 153 time to evaluate : 2.207 ------------------------------------------------------------------------------- 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 16 optimal weight: 4.9990 chunk 141 optimal weight: 0.9990 chunk 237 optimal weight: 1.9990 chunk 173 optimal weight: 9.9990 chunk 70 optimal weight: 8.9990 chunk 39 optimal weight: 7.9990 chunk 14 optimal weight: 0.0270 chunk 163 optimal weight: 9.9990 chunk 30 optimal weight: 10.0000 chunk 149 optimal weight: 6.9990 chunk 29 optimal weight: 5.9990 overall best weight: 2.8046 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 590 GLN G 39 GLN H 6 GLN ** H 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 287 HIS J 575 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3766 r_free = 0.3766 target = 0.088113 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3485 r_free = 0.3485 target = 0.072111 restraints weight = 79397.127| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3490 r_free = 0.3490 target = 0.073507 restraints weight = 45974.720| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3506 r_free = 0.3506 target = 0.074260 restraints weight = 32798.746| |-----------------------------------------------------------------------------| r_work (final): 0.3481 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7805 moved from start: 0.2736 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 20349 Z= 0.137 Angle : 0.660 16.496 27762 Z= 0.314 Chirality : 0.046 0.405 3243 Planarity : 0.004 0.046 3450 Dihedral : 10.448 96.151 3715 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 4.12 Ramachandran Plot: Outliers : 0.36 % Allowed : 3.60 % Favored : 96.04 % Rotamer: Outliers : 2.27 % Allowed : 11.00 % Favored : 86.73 % 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: -0.63 (0.17), residues: 2472 helix: 1.12 (0.29), residues: 384 sheet: 0.23 (0.19), residues: 681 loop : -1.22 (0.16), residues: 1407 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP G 50 HIS 0.023 0.001 HIS I 287 PHE 0.014 0.001 PHE K 114 TYR 0.017 0.001 TYR F 586 ARG 0.009 0.000 ARG G 87 Details of bonding type rmsd link_NAG-ASN : bond 0.00760 ( 9) link_NAG-ASN : angle 2.28908 ( 27) link_ALPHA1-6 : bond 0.00622 ( 6) link_ALPHA1-6 : angle 1.89766 ( 18) link_BETA1-4 : bond 0.00409 ( 18) link_BETA1-4 : angle 2.55678 ( 54) link_ALPHA1-2 : bond 0.00474 ( 6) link_ALPHA1-2 : angle 2.30839 ( 18) link_ALPHA1-3 : bond 0.02497 ( 9) link_ALPHA1-3 : angle 5.56115 ( 27) hydrogen bonds : bond 0.03559 ( 638) hydrogen bonds : angle 4.82584 ( 1752) SS BOND : bond 0.00286 ( 30) SS BOND : angle 0.71039 ( 60) covalent geometry : bond 0.00297 (20271) covalent geometry : angle 0.61934 (27558) *********************** REFINEMENT MACRO_CYCLE 3 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 215 residues out of total 2142 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 167 time to evaluate : 2.026 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 530 MET cc_start: 0.7380 (mmp) cc_final: 0.7079 (mmp) REVERT: B 534 SER cc_start: 0.8865 (t) cc_final: 0.8618 (p) REVERT: B 535 MET cc_start: 0.8056 (mtm) cc_final: 0.7700 (mpp) REVERT: B 631 TRP cc_start: 0.8452 (t-100) cc_final: 0.7721 (t-100) REVERT: C 81 MET cc_start: 0.8433 (tmm) cc_final: 0.8154 (tmm) REVERT: C 112 PRO cc_start: 0.9385 (Cg_endo) cc_final: 0.9179 (Cg_exo) REVERT: C 114 PHE cc_start: 0.8211 (OUTLIER) cc_final: 0.7967 (p90) REVERT: D 37 TRP cc_start: 0.7047 (m100) cc_final: 0.6824 (m100) REVERT: D 81 GLN cc_start: 0.7170 (mp10) cc_final: 0.6931 (pm20) REVERT: D 83 GLU cc_start: 0.8994 (mt-10) cc_final: 0.8611 (mt-10) REVERT: E 287 HIS cc_start: 0.8600 (OUTLIER) cc_final: 0.7764 (m-70) REVERT: E 381 GLU cc_start: 0.8260 (mm-30) cc_final: 0.8015 (mm-30) REVERT: E 426 MET cc_start: 0.6298 (mtm) cc_final: 0.5336 (mtm) REVERT: F 534 SER cc_start: 0.8917 (t) cc_final: 0.8553 (p) REVERT: F 543 ASN cc_start: 0.8375 (m110) cc_final: 0.8054 (m110) REVERT: F 659 ASP cc_start: 0.6846 (m-30) cc_final: 0.6470 (m-30) REVERT: H 49 MET cc_start: 0.7336 (mmm) cc_final: 0.7086 (mmm) REVERT: H 84 ASP cc_start: 0.5498 (m-30) cc_final: 0.5197 (m-30) REVERT: I 104 MET cc_start: 0.9088 (OUTLIER) cc_final: 0.8422 (tpt) REVERT: J 535 MET cc_start: 0.8550 (mtm) cc_final: 0.8019 (mpp) REVERT: J 543 ASN cc_start: 0.8704 (m110) cc_final: 0.8438 (m110) REVERT: J 659 ASP cc_start: 0.6822 (m-30) cc_final: 0.6295 (m-30) REVERT: K 81 MET cc_start: 0.8998 (tmm) cc_final: 0.8344 (tmm) REVERT: K 90 ASP cc_start: 0.6983 (t0) cc_final: 0.6422 (p0) REVERT: K 102 ILE cc_start: 0.8188 (mt) cc_final: 0.7928 (pt) REVERT: K 105 TYR cc_start: 0.8470 (m-80) cc_final: 0.8094 (m-80) REVERT: K 115 ASP cc_start: 0.8065 (p0) cc_final: 0.7145 (p0) REVERT: K 116 TYR cc_start: 0.7691 (m-80) cc_final: 0.7339 (m-80) REVERT: K 125 VAL cc_start: 0.6282 (OUTLIER) cc_final: 0.5834 (m) outliers start: 48 outliers final: 32 residues processed: 205 average time/residue: 0.2700 time to fit residues: 89.5828 Evaluate side-chains 183 residues out of total 2142 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 147 time to evaluate : 2.029 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 213 ILE 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 B residue 602 LEU Chi-restraints excluded: chain C residue 51 ILE Chi-restraints excluded: chain C residue 114 PHE Chi-restraints excluded: chain D residue 19 THR Chi-restraints excluded: chain D residue 28 ASP Chi-restraints excluded: chain D residue 72 THR Chi-restraints excluded: chain D residue 90 CYS Chi-restraints excluded: chain D residue 107 LEU Chi-restraints excluded: chain E residue 120 VAL 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 G residue 28 THR Chi-restraints excluded: chain H residue 19 THR Chi-restraints excluded: chain H residue 36 SER Chi-restraints excluded: chain H residue 48 LEU Chi-restraints excluded: chain H residue 72 THR Chi-restraints excluded: chain I residue 104 MET Chi-restraints excluded: chain I residue 120 VAL Chi-restraints excluded: chain I residue 202 THR Chi-restraints excluded: chain I residue 288 LEU Chi-restraints excluded: chain I residue 295 VAL Chi-restraints excluded: chain I residue 325 ASP Chi-restraints excluded: chain I residue 494 LEU Chi-restraints excluded: chain J residue 576 LEU Chi-restraints excluded: chain J residue 605 CYS Chi-restraints excluded: chain K residue 28 THR Chi-restraints excluded: chain K residue 51 ILE Chi-restraints excluded: chain K residue 125 VAL Chi-restraints excluded: chain L residue 19 THR Chi-restraints excluded: chain L residue 48 LEU Chi-restraints excluded: chain L residue 75 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 246 random chunks: chunk 156 optimal weight: 20.0000 chunk 172 optimal weight: 20.0000 chunk 54 optimal weight: 0.0040 chunk 101 optimal weight: 20.0000 chunk 134 optimal weight: 5.9990 chunk 90 optimal weight: 0.4980 chunk 141 optimal weight: 3.9990 chunk 147 optimal weight: 5.9990 chunk 181 optimal weight: 0.0970 chunk 163 optimal weight: 0.2980 chunk 8 optimal weight: 0.7980 overall best weight: 0.3390 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 71 ASN H 81 GLN I 279 ASN I 343 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3825 r_free = 0.3825 target = 0.088867 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3517 r_free = 0.3517 target = 0.073577 restraints weight = 77122.852| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3540 r_free = 0.3540 target = 0.076138 restraints weight = 48354.418| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3558 r_free = 0.3558 target = 0.076657 restraints weight = 33073.233| |-----------------------------------------------------------------------------| r_work (final): 0.3535 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7733 moved from start: 0.2912 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 20349 Z= 0.109 Angle : 0.624 16.776 27762 Z= 0.294 Chirality : 0.046 0.416 3243 Planarity : 0.003 0.040 3450 Dihedral : 9.249 95.050 3713 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 3.48 Ramachandran Plot: Outliers : 0.36 % Allowed : 3.44 % Favored : 96.20 % Rotamer: Outliers : 1.98 % Allowed : 11.33 % Favored : 86.69 % 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: -0.51 (0.17), residues: 2472 helix: 1.14 (0.29), residues: 381 sheet: 0.36 (0.20), residues: 687 loop : -1.15 (0.16), residues: 1404 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP E 96 HIS 0.003 0.000 HIS E 374 PHE 0.014 0.001 PHE I 53 TYR 0.021 0.001 TYR H 51 ARG 0.003 0.000 ARG I 166 Details of bonding type rmsd link_NAG-ASN : bond 0.00453 ( 9) link_NAG-ASN : angle 1.93161 ( 27) link_ALPHA1-6 : bond 0.00866 ( 6) link_ALPHA1-6 : angle 1.95069 ( 18) link_BETA1-4 : bond 0.00454 ( 18) link_BETA1-4 : angle 2.28990 ( 54) link_ALPHA1-2 : bond 0.00636 ( 6) link_ALPHA1-2 : angle 2.28013 ( 18) link_ALPHA1-3 : bond 0.02476 ( 9) link_ALPHA1-3 : angle 5.71791 ( 27) hydrogen bonds : bond 0.03074 ( 638) hydrogen bonds : angle 4.62365 ( 1752) SS BOND : bond 0.00270 ( 30) SS BOND : angle 0.58610 ( 60) covalent geometry : bond 0.00220 (20271) covalent geometry : angle 0.58312 (27558) *********************** REFINEMENT MACRO_CYCLE 4 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 206 residues out of total 2142 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 164 time to evaluate : 2.235 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 426 MET cc_start: 0.7067 (mtm) cc_final: 0.6469 (mtm) REVERT: B 534 SER cc_start: 0.8793 (t) cc_final: 0.8555 (p) REVERT: B 535 MET cc_start: 0.7988 (mtm) cc_final: 0.7611 (mpp) REVERT: B 631 TRP cc_start: 0.8545 (t-100) cc_final: 0.7959 (t-100) REVERT: C 81 MET cc_start: 0.8484 (tmm) cc_final: 0.8166 (tmm) REVERT: C 114 PHE cc_start: 0.8022 (OUTLIER) cc_final: 0.7605 (p90) REVERT: D 87 ASP cc_start: 0.8639 (m-30) cc_final: 0.8125 (m-30) REVERT: E 287 HIS cc_start: 0.8441 (OUTLIER) cc_final: 0.7589 (m-70) REVERT: E 381 GLU cc_start: 0.8150 (mm-30) cc_final: 0.7876 (mm-30) REVERT: F 534 SER cc_start: 0.8887 (t) cc_final: 0.8526 (p) REVERT: F 543 ASN cc_start: 0.8354 (m110) cc_final: 0.8016 (m110) REVERT: F 585 ARG cc_start: 0.6932 (mtp85) cc_final: 0.6624 (mtp85) REVERT: F 659 ASP cc_start: 0.6787 (m-30) cc_final: 0.6416 (m-30) REVERT: G 12 LYS cc_start: 0.8435 (mmmm) cc_final: 0.8169 (mmtp) REVERT: G 48 MET cc_start: 0.8182 (mtm) cc_final: 0.7884 (mtt) REVERT: G 114 PHE cc_start: 0.7990 (OUTLIER) cc_final: 0.7692 (p90) REVERT: G 125 VAL cc_start: 0.4337 (OUTLIER) cc_final: 0.4112 (m) REVERT: H 49 MET cc_start: 0.7265 (mmm) cc_final: 0.7031 (mmm) REVERT: H 51 TYR cc_start: 0.3730 (OUTLIER) cc_final: 0.2947 (m-80) REVERT: H 83 GLU cc_start: 0.9262 (mt-10) cc_final: 0.8256 (pp20) REVERT: J 535 MET cc_start: 0.8688 (mtm) cc_final: 0.8128 (mpp) REVERT: J 659 ASP cc_start: 0.6772 (m-30) cc_final: 0.6239 (m-30) REVERT: K 81 MET cc_start: 0.8839 (tmm) cc_final: 0.8411 (tmm) REVERT: K 90 ASP cc_start: 0.6927 (t0) cc_final: 0.6270 (p0) REVERT: K 102 ILE cc_start: 0.8073 (mt) cc_final: 0.7849 (pt) REVERT: K 105 TYR cc_start: 0.8535 (m-80) cc_final: 0.8178 (m-80) REVERT: K 115 ASP cc_start: 0.7973 (p0) cc_final: 0.7367 (p0) REVERT: K 116 TYR cc_start: 0.7757 (m-80) cc_final: 0.7380 (m-80) REVERT: K 125 VAL cc_start: 0.6279 (OUTLIER) cc_final: 0.5919 (m) outliers start: 42 outliers final: 25 residues processed: 197 average time/residue: 0.2788 time to fit residues: 89.2995 Evaluate side-chains 176 residues out of total 2142 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 145 time to evaluate : 2.190 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 83 GLU Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 138 THR Chi-restraints excluded: chain A residue 213 ILE Chi-restraints excluded: chain A residue 287 HIS Chi-restraints excluded: chain A residue 295 VAL Chi-restraints excluded: chain A residue 296 CYS Chi-restraints excluded: chain B residue 543 ASN Chi-restraints excluded: chain C residue 51 ILE Chi-restraints excluded: chain C residue 114 PHE Chi-restraints excluded: chain D residue 19 THR Chi-restraints excluded: chain D residue 90 CYS 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 G residue 28 THR Chi-restraints excluded: chain G residue 90 ASP Chi-restraints excluded: chain G residue 114 PHE Chi-restraints excluded: chain G residue 125 VAL Chi-restraints excluded: chain H residue 19 THR Chi-restraints excluded: chain H residue 48 LEU Chi-restraints excluded: chain H residue 51 TYR Chi-restraints excluded: chain H residue 107 LEU Chi-restraints excluded: chain I residue 295 VAL Chi-restraints excluded: chain K residue 28 THR Chi-restraints excluded: chain K residue 51 ILE Chi-restraints excluded: chain K residue 125 VAL Chi-restraints excluded: chain L residue 19 THR Chi-restraints excluded: chain L residue 48 LEU Chi-restraints excluded: chain L residue 72 THR Chi-restraints excluded: chain L residue 75 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 246 random chunks: chunk 70 optimal weight: 5.9990 chunk 33 optimal weight: 10.0000 chunk 145 optimal weight: 10.0000 chunk 122 optimal weight: 6.9990 chunk 208 optimal weight: 9.9990 chunk 118 optimal weight: 50.0000 chunk 204 optimal weight: 10.0000 chunk 63 optimal weight: 20.0000 chunk 182 optimal weight: 0.9980 chunk 231 optimal weight: 9.9990 chunk 100 optimal weight: 0.0070 overall best weight: 4.8004 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 279 ASN D 71 ASN D 81 GLN E 279 ASN I 374 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3735 r_free = 0.3735 target = 0.086487 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.068930 restraints weight = 80485.667| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.071096 restraints weight = 44735.533| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3479 r_free = 0.3479 target = 0.072526 restraints weight = 31735.750| |-----------------------------------------------------------------------------| r_work (final): 0.3459 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7914 moved from start: 0.3483 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 20349 Z= 0.175 Angle : 0.665 17.243 27762 Z= 0.318 Chirality : 0.046 0.350 3243 Planarity : 0.004 0.058 3450 Dihedral : 8.858 89.445 3713 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 4.58 Ramachandran Plot: Outliers : 0.36 % Allowed : 3.76 % Favored : 95.87 % Rotamer: Outliers : 2.64 % Allowed : 11.66 % Favored : 85.69 % 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: -0.60 (0.17), residues: 2472 helix: 1.13 (0.29), residues: 390 sheet: 0.35 (0.20), residues: 681 loop : -1.27 (0.16), residues: 1401 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP D 37 HIS 0.005 0.001 HIS K 35 PHE 0.022 0.002 PHE I 53 TYR 0.019 0.001 TYR J 586 ARG 0.003 0.000 ARG K 85 Details of bonding type rmsd link_NAG-ASN : bond 0.00254 ( 9) link_NAG-ASN : angle 1.96282 ( 27) link_ALPHA1-6 : bond 0.00785 ( 6) link_ALPHA1-6 : angle 1.67110 ( 18) link_BETA1-4 : bond 0.00456 ( 18) link_BETA1-4 : angle 2.20183 ( 54) link_ALPHA1-2 : bond 0.00339 ( 6) link_ALPHA1-2 : angle 2.21546 ( 18) link_ALPHA1-3 : bond 0.02463 ( 9) link_ALPHA1-3 : angle 5.80958 ( 27) hydrogen bonds : bond 0.03507 ( 638) hydrogen bonds : angle 4.64217 ( 1752) SS BOND : bond 0.00431 ( 30) SS BOND : angle 0.81946 ( 60) covalent geometry : bond 0.00389 (20271) covalent geometry : angle 0.62702 (27558) *********************** REFINEMENT MACRO_CYCLE 5 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 209 residues out of total 2142 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 153 time to evaluate : 2.333 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 530 MET cc_start: 0.7231 (mmp) cc_final: 0.6775 (mmt) REVERT: B 534 SER cc_start: 0.8916 (t) cc_final: 0.8575 (p) REVERT: B 535 MET cc_start: 0.8123 (mtm) cc_final: 0.7883 (mpp) REVERT: B 626 MET cc_start: 0.8179 (mmm) cc_final: 0.7865 (tpt) REVERT: D 87 ASP cc_start: 0.8699 (m-30) cc_final: 0.8311 (m-30) REVERT: E 104 MET cc_start: 0.9262 (OUTLIER) cc_final: 0.9041 (ttp) REVERT: E 287 HIS cc_start: 0.8571 (OUTLIER) cc_final: 0.7880 (m-70) REVERT: E 381 GLU cc_start: 0.8362 (mm-30) cc_final: 0.8153 (mm-30) REVERT: F 534 SER cc_start: 0.8920 (t) cc_final: 0.8586 (p) REVERT: F 543 ASN cc_start: 0.8360 (m110) cc_final: 0.8049 (m110) REVERT: F 659 ASP cc_start: 0.6908 (m-30) cc_final: 0.6523 (m-30) REVERT: H 49 MET cc_start: 0.7258 (mmm) cc_final: 0.6998 (mmm) REVERT: H 83 GLU cc_start: 0.9303 (mt-10) cc_final: 0.8340 (pp20) REVERT: I 104 MET cc_start: 0.9018 (OUTLIER) cc_final: 0.8385 (tpt) REVERT: J 535 MET cc_start: 0.8709 (mtm) cc_final: 0.8220 (mpp) REVERT: J 543 ASN cc_start: 0.8828 (m110) cc_final: 0.8593 (m110) REVERT: J 659 ASP cc_start: 0.7259 (m-30) cc_final: 0.6764 (m-30) REVERT: K 81 MET cc_start: 0.8827 (tmm) cc_final: 0.8504 (tmm) REVERT: K 90 ASP cc_start: 0.6768 (t0) cc_final: 0.6265 (p0) REVERT: K 105 TYR cc_start: 0.8614 (m-80) cc_final: 0.8348 (m-80) REVERT: K 115 ASP cc_start: 0.8182 (p0) cc_final: 0.7401 (p0) REVERT: K 116 TYR cc_start: 0.7684 (m-80) cc_final: 0.7333 (m-80) REVERT: K 125 VAL cc_start: 0.6370 (OUTLIER) cc_final: 0.6065 (m) outliers start: 56 outliers final: 41 residues processed: 199 average time/residue: 0.2803 time to fit residues: 89.9906 Evaluate side-chains 184 residues out of total 2142 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 139 time to evaluate : 2.055 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 83 GLU Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 213 ILE Chi-restraints excluded: chain A residue 287 HIS Chi-restraints excluded: chain A residue 295 VAL Chi-restraints excluded: chain B residue 574 LYS Chi-restraints excluded: chain B residue 602 LEU Chi-restraints excluded: chain C residue 51 ILE Chi-restraints excluded: chain C residue 114 PHE Chi-restraints excluded: chain D residue 19 THR Chi-restraints excluded: chain D residue 28 ASP Chi-restraints excluded: chain D residue 72 THR Chi-restraints excluded: chain D residue 90 CYS Chi-restraints excluded: chain E residue 85 VAL Chi-restraints excluded: chain E residue 90 THR Chi-restraints excluded: chain E residue 104 MET Chi-restraints excluded: chain E residue 120 VAL Chi-restraints excluded: chain E residue 127 VAL Chi-restraints excluded: chain E residue 149 VAL Chi-restraints excluded: chain E residue 244 THR Chi-restraints excluded: chain E residue 287 HIS Chi-restraints excluded: chain E residue 295 VAL Chi-restraints excluded: chain G residue 28 THR Chi-restraints excluded: chain H residue 19 THR Chi-restraints excluded: chain H residue 36 SER Chi-restraints excluded: chain H residue 48 LEU Chi-restraints excluded: chain H residue 51 TYR Chi-restraints excluded: chain H residue 107 LEU Chi-restraints excluded: chain I residue 90 THR Chi-restraints excluded: chain I residue 104 MET Chi-restraints excluded: chain I residue 120 VAL Chi-restraints excluded: chain I residue 149 VAL Chi-restraints excluded: chain I residue 202 THR Chi-restraints excluded: chain I residue 288 LEU 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 605 CYS Chi-restraints excluded: chain J residue 641 ILE Chi-restraints excluded: chain K residue 28 THR Chi-restraints excluded: chain K residue 51 ILE Chi-restraints excluded: chain K residue 125 VAL Chi-restraints excluded: chain L residue 19 THR Chi-restraints excluded: chain L residue 48 LEU Chi-restraints excluded: chain L residue 75 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 246 random chunks: chunk 206 optimal weight: 20.0000 chunk 233 optimal weight: 7.9990 chunk 19 optimal weight: 8.9990 chunk 13 optimal weight: 10.0000 chunk 118 optimal weight: 50.0000 chunk 18 optimal weight: 0.7980 chunk 155 optimal weight: 0.0370 chunk 69 optimal weight: 3.9990 chunk 92 optimal weight: 9.9990 chunk 100 optimal weight: 9.9990 chunk 48 optimal weight: 10.0000 overall best weight: 4.3664 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 591 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3554 r_free = 0.3554 target = 0.080229 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3237 r_free = 0.3237 target = 0.065474 restraints weight = 80336.546| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3240 r_free = 0.3240 target = 0.066140 restraints weight = 52447.286| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3253 r_free = 0.3253 target = 0.066762 restraints weight = 45691.121| |-----------------------------------------------------------------------------| r_work (final): 0.3251 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8005 moved from start: 0.4012 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 20349 Z= 0.163 Angle : 0.665 17.211 27762 Z= 0.317 Chirality : 0.045 0.367 3243 Planarity : 0.004 0.051 3450 Dihedral : 8.383 84.438 3713 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 4.79 Ramachandran Plot: Outliers : 0.36 % Allowed : 4.21 % Favored : 95.43 % Rotamer: Outliers : 3.12 % Allowed : 11.90 % Favored : 84.99 % 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: -0.64 (0.17), residues: 2472 helix: 1.03 (0.29), residues: 390 sheet: 0.40 (0.20), residues: 693 loop : -1.34 (0.16), residues: 1389 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP D 37 HIS 0.004 0.001 HIS E 105 PHE 0.021 0.002 PHE I 53 TYR 0.021 0.001 TYR C 116 ARG 0.004 0.000 ARG D 63 Details of bonding type rmsd link_NAG-ASN : bond 0.00261 ( 9) link_NAG-ASN : angle 2.04968 ( 27) link_ALPHA1-6 : bond 0.00885 ( 6) link_ALPHA1-6 : angle 1.82014 ( 18) link_BETA1-4 : bond 0.00355 ( 18) link_BETA1-4 : angle 2.03319 ( 54) link_ALPHA1-2 : bond 0.00328 ( 6) link_ALPHA1-2 : angle 2.09859 ( 18) link_ALPHA1-3 : bond 0.02478 ( 9) link_ALPHA1-3 : angle 5.85851 ( 27) hydrogen bonds : bond 0.03491 ( 638) hydrogen bonds : angle 4.63217 ( 1752) SS BOND : bond 0.00347 ( 30) SS BOND : angle 0.70040 ( 60) covalent geometry : bond 0.00359 (20271) covalent geometry : angle 0.62771 (27558) *********************** REFINEMENT MACRO_CYCLE 6 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 216 residues out of total 2142 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 150 time to evaluate : 2.076 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 434 MET cc_start: 0.8816 (ptm) cc_final: 0.8576 (ptp) REVERT: B 534 SER cc_start: 0.8922 (t) cc_final: 0.8684 (p) REVERT: B 591 GLN cc_start: 0.8485 (OUTLIER) cc_final: 0.8016 (mm-40) REVERT: B 631 TRP cc_start: 0.8788 (t-100) cc_final: 0.7654 (t-100) REVERT: E 112 TRP cc_start: 0.8465 (t-100) cc_final: 0.7973 (t-100) REVERT: E 287 HIS cc_start: 0.8719 (OUTLIER) cc_final: 0.8036 (m-70) REVERT: F 534 SER cc_start: 0.8850 (t) cc_final: 0.8627 (p) REVERT: F 543 ASN cc_start: 0.8270 (m110) cc_final: 0.8063 (m110) REVERT: F 659 ASP cc_start: 0.7074 (m-30) cc_final: 0.6701 (m-30) REVERT: H 81 GLN cc_start: 0.8154 (pm20) cc_final: 0.7890 (pm20) REVERT: H 83 GLU cc_start: 0.9369 (mt-10) cc_final: 0.8381 (pp20) REVERT: I 104 MET cc_start: 0.8834 (OUTLIER) cc_final: 0.8203 (tpt) REVERT: J 530 MET cc_start: 0.6485 (mmp) cc_final: 0.6221 (mmp) REVERT: J 586 TYR cc_start: 0.6893 (t80) cc_final: 0.6686 (t80) REVERT: J 659 ASP cc_start: 0.7286 (m-30) cc_final: 0.6738 (m-30) REVERT: K 81 MET cc_start: 0.8695 (tmm) cc_final: 0.8305 (tmm) REVERT: K 82 GLU cc_start: 0.7875 (mm-30) cc_final: 0.7605 (mm-30) REVERT: K 90 ASP cc_start: 0.6654 (t0) cc_final: 0.6174 (p0) REVERT: K 115 ASP cc_start: 0.8193 (p0) cc_final: 0.7391 (p0) REVERT: K 116 TYR cc_start: 0.7651 (m-80) cc_final: 0.7291 (m-80) REVERT: K 125 VAL cc_start: 0.6407 (OUTLIER) cc_final: 0.6191 (m) REVERT: L 81 GLN cc_start: 0.8075 (mp10) cc_final: 0.7785 (mp10) outliers start: 66 outliers final: 46 residues processed: 205 average time/residue: 0.2641 time to fit residues: 88.9540 Evaluate side-chains 190 residues out of total 2142 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 140 time to evaluate : 2.139 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 83 GLU Chi-restraints excluded: chain A residue 90 THR Chi-restraints excluded: chain A residue 100 MET Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 138 THR Chi-restraints excluded: chain A residue 149 VAL Chi-restraints excluded: chain A residue 213 ILE Chi-restraints excluded: chain A residue 287 HIS Chi-restraints excluded: chain A residue 295 VAL Chi-restraints excluded: chain A residue 296 CYS Chi-restraints excluded: chain B residue 574 LYS Chi-restraints excluded: chain B residue 576 LEU Chi-restraints excluded: chain B residue 591 GLN Chi-restraints excluded: chain B residue 602 LEU Chi-restraints excluded: chain C residue 51 ILE Chi-restraints excluded: chain D residue 19 THR Chi-restraints excluded: chain D residue 28 ASP Chi-restraints excluded: chain D residue 72 THR Chi-restraints excluded: chain E residue 85 VAL Chi-restraints excluded: chain E residue 90 THR Chi-restraints excluded: chain E residue 111 LEU Chi-restraints excluded: chain E residue 127 VAL Chi-restraints excluded: chain E residue 140 THR Chi-restraints excluded: chain E residue 149 VAL Chi-restraints excluded: chain E residue 287 HIS Chi-restraints excluded: chain E residue 295 VAL Chi-restraints excluded: chain G residue 28 THR Chi-restraints excluded: chain G residue 51 ILE Chi-restraints excluded: chain G residue 90 ASP Chi-restraints excluded: chain H residue 19 THR Chi-restraints excluded: chain H residue 36 SER Chi-restraints excluded: chain H residue 48 LEU Chi-restraints excluded: chain H residue 51 TYR Chi-restraints excluded: chain H residue 107 LEU Chi-restraints excluded: chain I residue 90 THR Chi-restraints excluded: chain I residue 104 MET Chi-restraints excluded: chain I residue 120 VAL Chi-restraints excluded: chain I residue 149 VAL Chi-restraints excluded: chain I residue 295 VAL Chi-restraints excluded: chain I residue 325 ASP Chi-restraints excluded: chain J residue 605 CYS Chi-restraints excluded: chain J residue 641 ILE Chi-restraints excluded: chain K residue 28 THR Chi-restraints excluded: chain K residue 51 ILE Chi-restraints excluded: chain K residue 68 VAL Chi-restraints excluded: chain K residue 125 VAL Chi-restraints excluded: chain L residue 19 THR Chi-restraints excluded: chain L residue 48 LEU Chi-restraints excluded: chain L residue 72 THR Chi-restraints excluded: chain L residue 75 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 246 random chunks: chunk 56 optimal weight: 7.9990 chunk 111 optimal weight: 10.0000 chunk 235 optimal weight: 40.0000 chunk 117 optimal weight: 9.9990 chunk 243 optimal weight: 20.0000 chunk 7 optimal weight: 0.9990 chunk 64 optimal weight: 2.9990 chunk 43 optimal weight: 0.6980 chunk 85 optimal weight: 40.0000 chunk 11 optimal weight: 5.9990 chunk 50 optimal weight: 5.9990 overall best weight: 3.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3554 r_free = 0.3554 target = 0.080225 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3240 r_free = 0.3240 target = 0.065585 restraints weight = 79780.012| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3244 r_free = 0.3244 target = 0.066307 restraints weight = 52218.285| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3258 r_free = 0.3258 target = 0.066935 restraints weight = 45032.537| |-----------------------------------------------------------------------------| r_work (final): 0.3259 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8008 moved from start: 0.4258 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 20349 Z= 0.139 Angle : 0.658 17.059 27762 Z= 0.312 Chirality : 0.045 0.366 3243 Planarity : 0.004 0.049 3450 Dihedral : 8.146 82.584 3713 Min Nonbonded Distance : 2.400 Molprobity Statistics. All-atom Clashscore : 5.25 Ramachandran Plot: Outliers : 0.36 % Allowed : 4.33 % Favored : 95.31 % Rotamer: Outliers : 3.07 % Allowed : 12.28 % Favored : 84.66 % 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: -0.60 (0.17), residues: 2472 helix: 1.13 (0.29), residues: 390 sheet: 0.45 (0.20), residues: 693 loop : -1.35 (0.16), residues: 1389 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP E 427 HIS 0.003 0.001 HIS K 35 PHE 0.014 0.001 PHE C 114 TYR 0.016 0.001 TYR C 116 ARG 0.002 0.000 ARG G 87 Details of bonding type rmsd link_NAG-ASN : bond 0.00282 ( 9) link_NAG-ASN : angle 1.95528 ( 27) link_ALPHA1-6 : bond 0.00893 ( 6) link_ALPHA1-6 : angle 1.75585 ( 18) link_BETA1-4 : bond 0.00361 ( 18) link_BETA1-4 : angle 1.98779 ( 54) link_ALPHA1-2 : bond 0.00354 ( 6) link_ALPHA1-2 : angle 2.04266 ( 18) link_ALPHA1-3 : bond 0.02511 ( 9) link_ALPHA1-3 : angle 5.88181 ( 27) hydrogen bonds : bond 0.03304 ( 638) hydrogen bonds : angle 4.58092 ( 1752) SS BOND : bond 0.00318 ( 30) SS BOND : angle 0.53655 ( 60) covalent geometry : bond 0.00305 (20271) covalent geometry : angle 0.62034 (27558) *********************** REFINEMENT MACRO_CYCLE 7 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 206 residues out of total 2142 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 141 time to evaluate : 2.236 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 530 MET cc_start: 0.7079 (mmp) cc_final: 0.6248 (mmt) REVERT: B 534 SER cc_start: 0.8918 (t) cc_final: 0.8684 (p) REVERT: B 626 MET cc_start: 0.8210 (tpt) cc_final: 0.7887 (tpt) REVERT: D 87 ASP cc_start: 0.8550 (m-30) cc_final: 0.8297 (m-30) REVERT: E 112 TRP cc_start: 0.8550 (t-100) cc_final: 0.7844 (t-100) REVERT: E 287 HIS cc_start: 0.8687 (OUTLIER) cc_final: 0.8018 (m-70) REVERT: E 426 MET cc_start: 0.6872 (ptp) cc_final: 0.5127 (ptp) REVERT: F 534 SER cc_start: 0.8837 (t) cc_final: 0.8573 (p) REVERT: F 543 ASN cc_start: 0.8285 (m110) cc_final: 0.8080 (m110) REVERT: F 659 ASP cc_start: 0.7117 (m-30) cc_final: 0.6707 (m-30) REVERT: H 83 GLU cc_start: 0.9348 (mt-10) cc_final: 0.8401 (pp20) REVERT: I 104 MET cc_start: 0.8820 (OUTLIER) cc_final: 0.8262 (tpt) REVERT: J 659 ASP cc_start: 0.7308 (m-30) cc_final: 0.6758 (m-30) REVERT: K 81 MET cc_start: 0.8697 (tmm) cc_final: 0.8375 (tmm) REVERT: K 82 GLU cc_start: 0.7874 (mm-30) cc_final: 0.7582 (mm-30) REVERT: K 90 ASP cc_start: 0.6652 (t0) cc_final: 0.6172 (p0) REVERT: K 116 TYR cc_start: 0.7662 (m-80) cc_final: 0.7340 (m-80) outliers start: 65 outliers final: 54 residues processed: 193 average time/residue: 0.2759 time to fit residues: 88.5296 Evaluate side-chains 189 residues out of total 2142 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 133 time to evaluate : 2.286 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 83 GLU Chi-restraints excluded: chain A residue 90 THR Chi-restraints excluded: chain A residue 104 MET Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 149 VAL Chi-restraints excluded: chain A residue 213 ILE Chi-restraints excluded: chain A residue 287 HIS Chi-restraints excluded: chain A residue 295 VAL Chi-restraints excluded: chain A residue 296 CYS Chi-restraints excluded: chain B residue 574 LYS Chi-restraints excluded: chain B residue 602 LEU Chi-restraints excluded: chain C residue 51 ILE Chi-restraints excluded: chain D residue 19 THR Chi-restraints excluded: chain D residue 48 LEU Chi-restraints excluded: chain D residue 72 THR Chi-restraints excluded: chain E residue 85 VAL Chi-restraints excluded: chain E residue 90 THR Chi-restraints excluded: chain E residue 111 LEU Chi-restraints excluded: chain E residue 120 VAL Chi-restraints excluded: chain E residue 127 VAL Chi-restraints excluded: chain E residue 140 THR Chi-restraints excluded: chain E residue 149 VAL Chi-restraints excluded: chain E residue 244 THR Chi-restraints excluded: chain E residue 287 HIS Chi-restraints excluded: chain E residue 295 VAL Chi-restraints excluded: chain F residue 529 THR Chi-restraints excluded: chain F residue 573 ILE Chi-restraints excluded: chain F residue 605 CYS Chi-restraints excluded: chain G residue 28 THR Chi-restraints excluded: chain G residue 51 ILE Chi-restraints excluded: chain G residue 90 ASP Chi-restraints excluded: chain H residue 19 THR Chi-restraints excluded: chain H residue 22 CYS Chi-restraints excluded: chain H residue 35 VAL Chi-restraints excluded: chain H residue 36 SER Chi-restraints excluded: chain H residue 48 LEU Chi-restraints excluded: chain H residue 51 TYR Chi-restraints excluded: chain H residue 107 LEU Chi-restraints excluded: chain I residue 104 MET Chi-restraints excluded: chain I residue 149 VAL Chi-restraints excluded: chain I residue 202 THR Chi-restraints excluded: chain I residue 240 SER Chi-restraints excluded: chain I residue 295 VAL Chi-restraints excluded: chain I residue 325 ASP Chi-restraints excluded: chain I residue 374 HIS Chi-restraints excluded: chain I residue 494 LEU Chi-restraints excluded: chain J residue 518 VAL Chi-restraints excluded: chain J residue 576 LEU Chi-restraints excluded: chain J residue 605 CYS Chi-restraints excluded: chain K residue 28 THR Chi-restraints excluded: chain K residue 51 ILE Chi-restraints excluded: chain K residue 68 VAL Chi-restraints excluded: chain L residue 19 THR Chi-restraints excluded: chain L residue 48 LEU Chi-restraints excluded: chain L residue 72 THR Chi-restraints excluded: chain L residue 75 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 246 random chunks: chunk 135 optimal weight: 2.9990 chunk 138 optimal weight: 0.4980 chunk 219 optimal weight: 2.9990 chunk 11 optimal weight: 1.9990 chunk 48 optimal weight: 1.9990 chunk 28 optimal weight: 7.9990 chunk 67 optimal weight: 4.9990 chunk 65 optimal weight: 5.9990 chunk 199 optimal weight: 0.1980 chunk 205 optimal weight: 10.0000 chunk 66 optimal weight: 7.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 343 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3579 r_free = 0.3579 target = 0.081412 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3266 r_free = 0.3266 target = 0.066678 restraints weight = 80245.966| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3271 r_free = 0.3271 target = 0.067490 restraints weight = 52989.546| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3284 r_free = 0.3284 target = 0.068094 restraints weight = 44562.613| |-----------------------------------------------------------------------------| r_work (final): 0.3262 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7974 moved from start: 0.4375 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 20349 Z= 0.111 Angle : 0.635 17.271 27762 Z= 0.300 Chirality : 0.045 0.385 3243 Planarity : 0.003 0.046 3450 Dihedral : 7.813 81.897 3712 Min Nonbonded Distance : 2.375 Molprobity Statistics. All-atom Clashscore : 4.74 Ramachandran Plot: Outliers : 0.36 % Allowed : 3.84 % Favored : 95.79 % Rotamer: Outliers : 2.55 % Allowed : 12.65 % Favored : 84.80 % 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: -0.56 (0.17), residues: 2472 helix: 1.20 (0.29), residues: 390 sheet: 0.45 (0.20), residues: 687 loop : -1.31 (0.16), residues: 1395 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP E 427 HIS 0.003 0.000 HIS A 374 PHE 0.012 0.001 PHE C 114 TYR 0.015 0.001 TYR A 435 ARG 0.002 0.000 ARG I 166 Details of bonding type rmsd link_NAG-ASN : bond 0.00378 ( 9) link_NAG-ASN : angle 1.85646 ( 27) link_ALPHA1-6 : bond 0.01017 ( 6) link_ALPHA1-6 : angle 1.76414 ( 18) link_BETA1-4 : bond 0.00358 ( 18) link_BETA1-4 : angle 1.89781 ( 54) link_ALPHA1-2 : bond 0.00485 ( 6) link_ALPHA1-2 : angle 1.97641 ( 18) link_ALPHA1-3 : bond 0.02533 ( 9) link_ALPHA1-3 : angle 5.91673 ( 27) hydrogen bonds : bond 0.02974 ( 638) hydrogen bonds : angle 4.47962 ( 1752) SS BOND : bond 0.00229 ( 30) SS BOND : angle 0.48405 ( 60) covalent geometry : bond 0.00233 (20271) covalent geometry : angle 0.59750 (27558) *********************** REFINEMENT MACRO_CYCLE 8 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 199 residues out of total 2142 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 145 time to evaluate : 2.100 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 95 MET cc_start: 0.7495 (ttp) cc_final: 0.7279 (ttp) REVERT: B 534 SER cc_start: 0.8843 (t) cc_final: 0.8606 (p) REVERT: B 631 TRP cc_start: 0.8867 (t-100) cc_final: 0.7616 (t-100) REVERT: D 87 ASP cc_start: 0.8640 (m-30) cc_final: 0.8355 (m-30) REVERT: E 112 TRP cc_start: 0.8544 (t-100) cc_final: 0.7809 (t-100) REVERT: E 287 HIS cc_start: 0.8557 (OUTLIER) cc_final: 0.7981 (m-70) REVERT: E 426 MET cc_start: 0.7047 (ptp) cc_final: 0.5231 (ptp) REVERT: F 534 SER cc_start: 0.8807 (t) cc_final: 0.8511 (p) REVERT: F 543 ASN cc_start: 0.8413 (m110) cc_final: 0.8157 (m110) REVERT: F 659 ASP cc_start: 0.7107 (m-30) cc_final: 0.6698 (m-30) REVERT: H 81 GLN cc_start: 0.7869 (pm20) cc_final: 0.7499 (pm20) REVERT: H 83 GLU cc_start: 0.9325 (mt-10) cc_final: 0.8467 (pp20) REVERT: I 104 MET cc_start: 0.8896 (OUTLIER) cc_final: 0.8379 (tpt) REVERT: J 530 MET cc_start: 0.6499 (mmp) cc_final: 0.6245 (mmp) REVERT: J 657 GLU cc_start: 0.8705 (tm-30) cc_final: 0.8447 (mm-30) REVERT: J 659 ASP cc_start: 0.7296 (m-30) cc_final: 0.6746 (m-30) REVERT: K 81 MET cc_start: 0.8715 (tmm) cc_final: 0.8339 (tmm) REVERT: K 90 ASP cc_start: 0.6686 (t0) cc_final: 0.6114 (p0) REVERT: K 115 ASP cc_start: 0.8098 (p0) cc_final: 0.7315 (p0) REVERT: K 116 TYR cc_start: 0.7688 (m-80) cc_final: 0.7297 (m-80) REVERT: L 81 GLN cc_start: 0.8294 (pm20) cc_final: 0.8012 (mp10) REVERT: L 84 ASP cc_start: 0.7375 (m-30) cc_final: 0.6842 (m-30) outliers start: 54 outliers final: 37 residues processed: 190 average time/residue: 0.2632 time to fit residues: 82.3729 Evaluate side-chains 175 residues out of total 2142 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 136 time to evaluate : 2.022 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 140 THR Chi-restraints excluded: chain A residue 149 VAL Chi-restraints excluded: chain A residue 287 HIS Chi-restraints excluded: chain A residue 295 VAL Chi-restraints excluded: chain A residue 296 CYS Chi-restraints excluded: chain B residue 602 LEU Chi-restraints excluded: chain C residue 51 ILE Chi-restraints excluded: chain D residue 19 THR Chi-restraints excluded: chain D residue 48 LEU Chi-restraints excluded: chain D residue 72 THR Chi-restraints excluded: chain E residue 90 THR Chi-restraints excluded: chain E residue 120 VAL Chi-restraints excluded: chain E residue 127 VAL Chi-restraints excluded: chain E residue 244 THR Chi-restraints excluded: chain E residue 287 HIS Chi-restraints excluded: chain F residue 529 THR Chi-restraints excluded: chain F residue 605 CYS Chi-restraints excluded: chain G residue 28 THR Chi-restraints excluded: chain G residue 51 ILE Chi-restraints excluded: chain H residue 19 THR Chi-restraints excluded: chain H residue 22 CYS Chi-restraints excluded: chain H residue 36 SER Chi-restraints excluded: chain H residue 48 LEU Chi-restraints excluded: chain H residue 51 TYR Chi-restraints excluded: chain H residue 107 LEU Chi-restraints excluded: chain I residue 104 MET Chi-restraints excluded: chain I residue 120 VAL Chi-restraints excluded: chain I residue 149 VAL Chi-restraints excluded: chain I residue 295 VAL Chi-restraints excluded: chain J residue 605 CYS Chi-restraints excluded: chain K residue 28 THR Chi-restraints excluded: chain K residue 51 ILE Chi-restraints excluded: chain K residue 68 VAL Chi-restraints excluded: chain K residue 114 PHE Chi-restraints excluded: chain L residue 19 THR Chi-restraints excluded: chain L residue 48 LEU Chi-restraints excluded: chain L residue 72 THR Chi-restraints excluded: chain L residue 75 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 246 random chunks: chunk 46 optimal weight: 0.0470 chunk 154 optimal weight: 30.0000 chunk 228 optimal weight: 7.9990 chunk 6 optimal weight: 20.0000 chunk 151 optimal weight: 4.9990 chunk 22 optimal weight: 20.0000 chunk 35 optimal weight: 10.0000 chunk 183 optimal weight: 10.0000 chunk 226 optimal weight: 7.9990 chunk 225 optimal weight: 0.9980 chunk 179 optimal weight: 10.0000 overall best weight: 4.4084 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 6 GLN E 374 HIS E 478 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3520 r_free = 0.3520 target = 0.078641 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3199 r_free = 0.3199 target = 0.063864 restraints weight = 79519.123| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3202 r_free = 0.3202 target = 0.064482 restraints weight = 53229.790| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3217 r_free = 0.3217 target = 0.065166 restraints weight = 46189.689| |-----------------------------------------------------------------------------| r_work (final): 0.3215 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8055 moved from start: 0.4748 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 20349 Z= 0.166 Angle : 0.680 17.347 27762 Z= 0.325 Chirality : 0.045 0.343 3243 Planarity : 0.004 0.049 3450 Dihedral : 7.897 77.926 3711 Min Nonbonded Distance : 2.399 Molprobity Statistics. All-atom Clashscore : 5.58 Ramachandran Plot: Outliers : 0.36 % Allowed : 4.57 % Favored : 95.06 % Rotamer: Outliers : 2.46 % Allowed : 13.08 % Favored : 84.47 % 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: -0.65 (0.17), residues: 2472 helix: 1.10 (0.29), residues: 390 sheet: 0.36 (0.19), residues: 720 loop : -1.38 (0.17), residues: 1362 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP D 37 HIS 0.003 0.001 HIS E 105 PHE 0.013 0.002 PHE K 114 TYR 0.016 0.001 TYR H 51 ARG 0.002 0.000 ARG I 192 Details of bonding type rmsd link_NAG-ASN : bond 0.00230 ( 9) link_NAG-ASN : angle 1.93936 ( 27) link_ALPHA1-6 : bond 0.00878 ( 6) link_ALPHA1-6 : angle 1.59151 ( 18) link_BETA1-4 : bond 0.00372 ( 18) link_BETA1-4 : angle 1.91620 ( 54) link_ALPHA1-2 : bond 0.00233 ( 6) link_ALPHA1-2 : angle 2.01422 ( 18) link_ALPHA1-3 : bond 0.02472 ( 9) link_ALPHA1-3 : angle 5.94723 ( 27) hydrogen bonds : bond 0.03457 ( 638) hydrogen bonds : angle 4.58042 ( 1752) SS BOND : bond 0.00373 ( 30) SS BOND : angle 0.58096 ( 60) covalent geometry : bond 0.00369 (20271) covalent geometry : angle 0.64432 (27558) *********************** REFINEMENT MACRO_CYCLE 9 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 189 residues out of total 2142 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 137 time to evaluate : 2.269 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 95 MET cc_start: 0.7539 (ttp) cc_final: 0.7338 (ttp) REVERT: B 534 SER cc_start: 0.8749 (t) cc_final: 0.8516 (p) REVERT: E 287 HIS cc_start: 0.8640 (OUTLIER) cc_final: 0.8044 (m-70) REVERT: F 659 ASP cc_start: 0.7225 (m-30) cc_final: 0.6823 (m-30) REVERT: I 104 MET cc_start: 0.8893 (OUTLIER) cc_final: 0.8359 (tpt) REVERT: J 530 MET cc_start: 0.6524 (mmp) cc_final: 0.6299 (mmp) REVERT: J 657 GLU cc_start: 0.8722 (tm-30) cc_final: 0.8484 (mm-30) REVERT: J 659 ASP cc_start: 0.7350 (m-30) cc_final: 0.6825 (m-30) REVERT: K 81 MET cc_start: 0.8570 (tmm) cc_final: 0.8295 (tmm) REVERT: K 115 ASP cc_start: 0.8209 (p0) cc_final: 0.7234 (p0) REVERT: K 116 TYR cc_start: 0.7686 (m-80) cc_final: 0.7274 (m-80) REVERT: L 84 ASP cc_start: 0.7377 (m-30) cc_final: 0.6869 (m-30) outliers start: 52 outliers final: 40 residues processed: 183 average time/residue: 0.2655 time to fit residues: 79.6311 Evaluate side-chains 169 residues out of total 2142 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 127 time to evaluate : 2.119 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 THR Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 149 VAL Chi-restraints excluded: chain A residue 213 ILE Chi-restraints excluded: chain A residue 287 HIS Chi-restraints excluded: chain A residue 295 VAL Chi-restraints excluded: chain A residue 296 CYS Chi-restraints excluded: chain B residue 602 LEU Chi-restraints excluded: chain C residue 51 ILE Chi-restraints excluded: chain D residue 19 THR Chi-restraints excluded: chain D residue 72 THR Chi-restraints excluded: chain E residue 85 VAL Chi-restraints excluded: chain E residue 90 THR Chi-restraints excluded: chain E residue 111 LEU Chi-restraints excluded: chain E residue 120 VAL Chi-restraints excluded: chain E residue 127 VAL Chi-restraints excluded: chain E residue 140 THR Chi-restraints excluded: chain E residue 149 VAL Chi-restraints excluded: chain E residue 244 THR Chi-restraints excluded: chain E residue 287 HIS Chi-restraints excluded: chain E residue 308 ARG Chi-restraints excluded: chain F residue 605 CYS Chi-restraints excluded: chain G residue 28 THR Chi-restraints excluded: chain G residue 51 ILE Chi-restraints excluded: chain H residue 19 THR Chi-restraints excluded: chain H residue 22 CYS Chi-restraints excluded: chain H residue 36 SER Chi-restraints excluded: chain H residue 48 LEU Chi-restraints excluded: chain H residue 107 LEU Chi-restraints excluded: chain I residue 104 MET Chi-restraints excluded: chain I residue 120 VAL Chi-restraints excluded: chain I residue 149 VAL Chi-restraints excluded: chain I residue 240 SER Chi-restraints excluded: chain I residue 295 VAL Chi-restraints excluded: chain J residue 605 CYS Chi-restraints excluded: chain K residue 28 THR Chi-restraints excluded: chain K residue 51 ILE Chi-restraints excluded: chain K residue 68 VAL Chi-restraints excluded: chain L residue 19 THR Chi-restraints excluded: chain L residue 48 LEU Chi-restraints excluded: chain L residue 72 THR Chi-restraints excluded: chain L residue 75 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 246 random chunks: chunk 205 optimal weight: 20.0000 chunk 35 optimal weight: 8.9990 chunk 208 optimal weight: 9.9990 chunk 178 optimal weight: 5.9990 chunk 216 optimal weight: 2.9990 chunk 113 optimal weight: 20.0000 chunk 65 optimal weight: 9.9990 chunk 243 optimal weight: 9.9990 chunk 184 optimal weight: 7.9990 chunk 244 optimal weight: 10.0000 chunk 105 optimal weight: 30.0000 overall best weight: 7.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 287 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3645 r_free = 0.3645 target = 0.082457 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3276 r_free = 0.3276 target = 0.064098 restraints weight = 80175.142| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3325 r_free = 0.3325 target = 0.066234 restraints weight = 44807.364| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.067637 restraints weight = 32044.818| |-----------------------------------------------------------------------------| r_work (final): 0.3331 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8090 moved from start: 0.5229 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 20349 Z= 0.233 Angle : 0.757 17.645 27762 Z= 0.362 Chirality : 0.047 0.330 3243 Planarity : 0.004 0.051 3450 Dihedral : 8.182 73.526 3711 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 6.81 Ramachandran Plot: Outliers : 0.36 % Allowed : 5.02 % Favored : 94.62 % Rotamer: Outliers : 2.64 % Allowed : 13.22 % Favored : 84.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: -0.94 (0.17), residues: 2472 helix: 0.78 (0.27), residues: 393 sheet: 0.13 (0.19), residues: 741 loop : -1.55 (0.17), residues: 1338 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP D 37 HIS 0.006 0.001 HIS K 35 PHE 0.020 0.002 PHE G 114 TYR 0.014 0.002 TYR C 116 ARG 0.004 0.001 ARG D 63 Details of bonding type rmsd link_NAG-ASN : bond 0.00275 ( 9) link_NAG-ASN : angle 2.25576 ( 27) link_ALPHA1-6 : bond 0.00780 ( 6) link_ALPHA1-6 : angle 1.75343 ( 18) link_BETA1-4 : bond 0.00444 ( 18) link_BETA1-4 : angle 1.93829 ( 54) link_ALPHA1-2 : bond 0.00220 ( 6) link_ALPHA1-2 : angle 2.03350 ( 18) link_ALPHA1-3 : bond 0.02521 ( 9) link_ALPHA1-3 : angle 6.02949 ( 27) hydrogen bonds : bond 0.03910 ( 638) hydrogen bonds : angle 4.79880 ( 1752) SS BOND : bond 0.00411 ( 30) SS BOND : angle 0.67110 ( 60) covalent geometry : bond 0.00528 (20271) covalent geometry : angle 0.72342 (27558) ********************** REFINEMENT MACRO_CYCLE 10 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 186 residues out of total 2142 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 130 time to evaluate : 2.093 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 534 SER cc_start: 0.8844 (t) cc_final: 0.8552 (p) REVERT: D 49 MET cc_start: 0.6716 (mmp) cc_final: 0.6225 (mmp) REVERT: D 87 ASP cc_start: 0.8865 (m-30) cc_final: 0.8516 (m-30) REVERT: E 287 HIS cc_start: 0.8326 (OUTLIER) cc_final: 0.7478 (m90) REVERT: F 659 ASP cc_start: 0.7162 (m-30) cc_final: 0.6841 (m-30) REVERT: I 95 MET cc_start: 0.7550 (ttp) cc_final: 0.7328 (ptt) REVERT: I 104 MET cc_start: 0.9174 (OUTLIER) cc_final: 0.8592 (tpt) REVERT: J 530 MET cc_start: 0.6948 (mmp) cc_final: 0.6619 (mmp) REVERT: J 657 GLU cc_start: 0.8861 (tm-30) cc_final: 0.8521 (mm-30) REVERT: J 659 ASP cc_start: 0.7508 (m-30) cc_final: 0.6943 (m-30) REVERT: K 81 MET cc_start: 0.8729 (tmm) cc_final: 0.8055 (tmm) REVERT: K 116 TYR cc_start: 0.7890 (m-80) cc_final: 0.7433 (m-80) REVERT: L 84 ASP cc_start: 0.7361 (m-30) cc_final: 0.6881 (m-30) outliers start: 56 outliers final: 48 residues processed: 183 average time/residue: 0.2704 time to fit residues: 81.6886 Evaluate side-chains 173 residues out of total 2142 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 123 time to evaluate : 2.262 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 83 GLU Chi-restraints excluded: chain A residue 89 VAL Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 149 VAL Chi-restraints excluded: chain A residue 213 ILE Chi-restraints excluded: chain A residue 287 HIS Chi-restraints excluded: chain A residue 295 VAL Chi-restraints excluded: chain A residue 296 CYS Chi-restraints excluded: chain B residue 574 LYS Chi-restraints excluded: chain B residue 602 LEU Chi-restraints excluded: chain C residue 51 ILE Chi-restraints excluded: chain C residue 68 VAL Chi-restraints excluded: chain C residue 114 PHE Chi-restraints excluded: chain D residue 19 THR Chi-restraints excluded: chain D residue 72 THR Chi-restraints excluded: chain E residue 85 VAL Chi-restraints excluded: chain E residue 90 THR Chi-restraints excluded: chain E residue 111 LEU Chi-restraints excluded: chain E residue 120 VAL Chi-restraints excluded: chain E residue 140 THR Chi-restraints excluded: chain E residue 149 VAL Chi-restraints excluded: chain E residue 244 THR Chi-restraints excluded: chain E residue 287 HIS Chi-restraints excluded: chain E residue 308 ARG Chi-restraints excluded: chain F residue 605 CYS Chi-restraints excluded: chain F residue 647 GLU Chi-restraints excluded: chain G residue 28 THR Chi-restraints excluded: chain G residue 51 ILE Chi-restraints excluded: chain H residue 19 THR Chi-restraints excluded: chain H residue 36 SER Chi-restraints excluded: chain H residue 48 LEU Chi-restraints excluded: chain H residue 107 LEU Chi-restraints excluded: chain I residue 104 MET Chi-restraints excluded: chain I residue 120 VAL Chi-restraints excluded: chain I residue 149 VAL Chi-restraints excluded: chain I residue 202 THR Chi-restraints excluded: chain I residue 240 SER Chi-restraints excluded: chain I residue 288 LEU Chi-restraints excluded: chain I residue 295 VAL Chi-restraints excluded: chain I residue 374 HIS Chi-restraints excluded: chain I residue 494 LEU Chi-restraints excluded: chain J residue 576 LEU Chi-restraints excluded: chain J residue 605 CYS Chi-restraints excluded: chain K residue 28 THR Chi-restraints excluded: chain K residue 51 ILE Chi-restraints excluded: chain K residue 68 VAL Chi-restraints excluded: chain K residue 114 PHE Chi-restraints excluded: chain L residue 19 THR Chi-restraints excluded: chain L residue 48 LEU Chi-restraints excluded: chain L residue 72 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 246 random chunks: chunk 172 optimal weight: 0.9980 chunk 38 optimal weight: 9.9990 chunk 210 optimal weight: 0.2980 chunk 174 optimal weight: 7.9990 chunk 105 optimal weight: 20.0000 chunk 41 optimal weight: 2.9990 chunk 53 optimal weight: 4.9990 chunk 48 optimal weight: 20.0000 chunk 244 optimal weight: 7.9990 chunk 217 optimal weight: 2.9990 chunk 165 optimal weight: 0.7980 overall best weight: 1.6184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 1 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 374 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3698 r_free = 0.3698 target = 0.084923 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3339 r_free = 0.3339 target = 0.066718 restraints weight = 79674.292| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.068980 restraints weight = 43534.741| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.070462 restraints weight = 30634.922| |-----------------------------------------------------------------------------| r_work (final): 0.3402 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7998 moved from start: 0.5228 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 20349 Z= 0.118 Angle : 0.678 17.574 27762 Z= 0.320 Chirality : 0.046 0.401 3243 Planarity : 0.004 0.045 3450 Dihedral : 7.768 75.897 3711 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 5.38 Ramachandran Plot: Outliers : 0.36 % Allowed : 4.13 % Favored : 95.51 % Rotamer: Outliers : 1.98 % Allowed : 14.16 % Favored : 83.85 % 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: -0.71 (0.17), residues: 2472 helix: 1.05 (0.29), residues: 390 sheet: 0.27 (0.18), residues: 750 loop : -1.42 (0.17), residues: 1332 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP D 37 HIS 0.008 0.001 HIS E 374 PHE 0.016 0.001 PHE I 53 TYR 0.015 0.001 TYR K 33 ARG 0.002 0.000 ARG G 87 Details of bonding type rmsd link_NAG-ASN : bond 0.00414 ( 9) link_NAG-ASN : angle 1.95818 ( 27) link_ALPHA1-6 : bond 0.01003 ( 6) link_ALPHA1-6 : angle 1.83974 ( 18) link_BETA1-4 : bond 0.00352 ( 18) link_BETA1-4 : angle 1.83752 ( 54) link_ALPHA1-2 : bond 0.00489 ( 6) link_ALPHA1-2 : angle 1.91292 ( 18) link_ALPHA1-3 : bond 0.02619 ( 9) link_ALPHA1-3 : angle 6.02822 ( 27) hydrogen bonds : bond 0.03204 ( 638) hydrogen bonds : angle 4.56788 ( 1752) SS BOND : bond 0.00272 ( 30) SS BOND : angle 0.51353 ( 60) covalent geometry : bond 0.00252 (20271) covalent geometry : angle 0.64169 (27558) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4976.31 seconds wall clock time: 89 minutes 17.37 seconds (5357.37 seconds total)