Starting phenix.real_space_refine on Tue Jun 17 12:25:46 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8sax_40283/06_2025/8sax_40283_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8sax_40283/06_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_40283/06_2025/8sax_40283.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8sax_40283/06_2025/8sax_40283.map" model { file = "/net/cci-nas-00/data/ceres_data/8sax_40283/06_2025/8sax_40283_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8sax_40283/06_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): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/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: 12.23, per 1000 atoms: 0.62 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: 5.39 Conformation dependent library (CDL) restraints added in 2.5 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: 2.87 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: 7.42 Time building geometry restraints manager: 6.33 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: 0.000 Normalize map: mean=0, sd=1: 0.160 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 0.760 Check model and map are aligned: 0.140 Set scattering table: 0.170 Process input model: 47.700 Find NCS groups from input model: 0.720 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:2.960 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 52.770 ------------------------------------------------------------------------------- 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 : 2.132 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: 0.3362 time to fit residues: 202.0469 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 : 2.186 ------------------------------------------------------------------------------- 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 = 0.3781 r_free = 0.3781 target = 0.088932 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.073049 restraints weight = 79806.864| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3510 r_free = 0.3510 target = 0.074475 restraints weight = 47128.659| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.075217 restraints weight = 33413.325| |-----------------------------------------------------------------------------| r_work (final): 0.3509 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7734 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 0.90243 ( 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 : 2.377 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: 0.8349 (ttt) cc_final: 0.8126 (ttt) REVERT: B 530 MET cc_start: 0.7194 (mmp) cc_final: 0.6831 (mmt) REVERT: B 534 SER cc_start: 0.8800 (t) cc_final: 0.8537 (p) REVERT: B 535 MET cc_start: 0.7897 (mtm) cc_final: 0.7615 (mpp) REVERT: B 574 LYS cc_start: 0.7641 (pttm) cc_final: 0.7438 (pttm) REVERT: B 631 TRP cc_start: 0.8640 (t-100) cc_final: 0.7546 (t-100) REVERT: C 81 MET cc_start: 0.8212 (tmm) cc_final: 0.7977 (tmm) REVERT: D 37 TRP cc_start: 0.6937 (m100) cc_final: 0.6705 (m100) REVERT: E 95 MET cc_start: 0.7986 (ttp) cc_final: 0.7710 (tmm) REVERT: E 287 HIS cc_start: 0.8565 (OUTLIER) cc_final: 0.7660 (m-70) REVERT: E 381 GLU cc_start: 0.8238 (mm-30) cc_final: 0.7756 (mm-30) REVERT: F 534 SER cc_start: 0.8892 (t) cc_final: 0.8509 (p) REVERT: F 543 ASN cc_start: 0.8260 (m110) cc_final: 0.8012 (m110) REVERT: F 659 ASP cc_start: 0.6541 (m-30) cc_final: 0.6154 (m-30) REVERT: G 114 PHE cc_start: 0.8507 (OUTLIER) cc_final: 0.8263 (p90) REVERT: H 49 MET cc_start: 0.7239 (mmm) cc_final: 0.7037 (mmm) REVERT: H 84 ASP cc_start: 0.5651 (m-30) cc_final: 0.5089 (m-30) REVERT: I 333 ILE cc_start: 0.7518 (mt) cc_final: 0.7263 (mm) REVERT: J 535 MET cc_start: 0.8444 (mtm) cc_final: 0.7926 (mpp) REVERT: J 659 ASP cc_start: 0.6810 (m-30) cc_final: 0.6308 (m-30) REVERT: K 81 MET cc_start: 0.9041 (tmm) cc_final: 0.8623 (tmm) REVERT: K 90 ASP cc_start: 0.7084 (t0) cc_final: 0.6572 (p0) REVERT: K 105 TYR cc_start: 0.8432 (m-80) cc_final: 0.8036 (m-80) REVERT: K 115 ASP cc_start: 0.8073 (p0) cc_final: 0.7089 (p0) REVERT: K 116 TYR cc_start: 0.7672 (m-80) cc_final: 0.7273 (m-80) REVERT: K 125 VAL cc_start: 0.6576 (OUTLIER) cc_final: 0.6203 (m) outliers start: 58 outliers final: 25 residues processed: 241 average time/residue: 0.3000 time to fit residues: 113.9319 Evaluate side-chains 180 residues out of total 2142 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 152 time to evaluate : 2.156 ------------------------------------------------------------------------------- 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: 4.9990 chunk 237 optimal weight: 9.9990 chunk 173 optimal weight: 0.9990 chunk 70 optimal weight: 2.9990 chunk 39 optimal weight: 6.9990 chunk 14 optimal weight: 0.2980 chunk 163 optimal weight: 6.9990 chunk 30 optimal weight: 4.9990 chunk 149 optimal weight: 6.9990 chunk 29 optimal weight: 5.9990 overall best weight: 2.8588 ------------------------------------------------------------------------------- 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** J 575 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3766 r_free = 0.3766 target = 0.088110 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3485 r_free = 0.3485 target = 0.072103 restraints weight = 79395.113| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3490 r_free = 0.3490 target = 0.073473 restraints weight = 46043.462| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3506 r_free = 0.3506 target = 0.074221 restraints weight = 32897.498| |-----------------------------------------------------------------------------| r_work (final): 0.3480 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7804 moved from start: 0.2710 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 20349 Z= 0.141 Angle : 0.663 16.590 27762 Z= 0.316 Chirality : 0.046 0.411 3243 Planarity : 0.004 0.053 3450 Dihedral : 10.532 96.929 3715 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 4.15 Ramachandran Plot: Outliers : 0.36 % Allowed : 3.60 % Favored : 96.04 % Rotamer: Outliers : 2.17 % Allowed : 11.28 % Favored : 86.54 % 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: 1.13 (0.29), residues: 384 sheet: 0.25 (0.20), residues: 657 loop : -1.23 (0.16), residues: 1431 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP G 50 HIS 0.019 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 0.00776 ( 9) link_NAG-ASN : angle 2.33185 ( 27) link_ALPHA1-6 : bond 0.00694 ( 6) link_ALPHA1-6 : angle 1.92999 ( 18) link_BETA1-4 : bond 0.00457 ( 18) link_BETA1-4 : angle 2.61261 ( 54) link_ALPHA1-2 : bond 0.00458 ( 6) link_ALPHA1-2 : angle 2.32260 ( 18) link_ALPHA1-3 : bond 0.02504 ( 9) link_ALPHA1-3 : angle 5.56225 ( 27) hydrogen bonds : bond 0.03575 ( 638) hydrogen bonds : angle 4.84025 ( 1752) SS BOND : bond 0.00259 ( 30) SS BOND : angle 0.70412 ( 60) covalent geometry : bond 0.00304 (20271) covalent geometry : angle 0.62162 (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 212 residues out of total 2142 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 166 time to evaluate : 2.462 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 530 MET cc_start: 0.7372 (mmp) cc_final: 0.7083 (mmp) REVERT: B 534 SER cc_start: 0.8863 (t) cc_final: 0.8616 (p) REVERT: B 535 MET cc_start: 0.8052 (mtm) cc_final: 0.7698 (mpp) REVERT: B 631 TRP cc_start: 0.8452 (t-100) cc_final: 0.7722 (t-100) REVERT: C 81 MET cc_start: 0.8438 (tmm) cc_final: 0.8150 (tmm) REVERT: C 114 PHE cc_start: 0.8199 (OUTLIER) cc_final: 0.7952 (p90) REVERT: D 37 TRP cc_start: 0.7042 (m100) cc_final: 0.6826 (m100) REVERT: D 81 GLN cc_start: 0.7122 (mp10) cc_final: 0.6871 (pm20) REVERT: D 83 GLU cc_start: 0.8999 (mt-10) cc_final: 0.8604 (mt-10) REVERT: E 287 HIS cc_start: 0.8599 (OUTLIER) cc_final: 0.7763 (m-70) REVERT: E 381 GLU cc_start: 0.8255 (mm-30) cc_final: 0.8013 (mm-30) REVERT: E 426 MET cc_start: 0.6296 (mtm) cc_final: 0.5405 (mtm) REVERT: E 434 MET cc_start: 0.6839 (ttp) cc_final: 0.6627 (mtp) REVERT: F 534 SER cc_start: 0.8914 (t) cc_final: 0.8551 (p) REVERT: F 543 ASN cc_start: 0.8372 (m110) cc_final: 0.8053 (m110) REVERT: F 659 ASP cc_start: 0.6845 (m-30) cc_final: 0.6470 (m-30) REVERT: H 49 MET cc_start: 0.7334 (mmm) cc_final: 0.7089 (mmm) REVERT: H 84 ASP cc_start: 0.5479 (m-30) cc_final: 0.5175 (m-30) REVERT: I 104 MET cc_start: 0.9092 (OUTLIER) cc_final: 0.8413 (tpt) REVERT: J 535 MET cc_start: 0.8547 (mtm) cc_final: 0.7998 (mpp) REVERT: J 543 ASN cc_start: 0.8703 (m110) cc_final: 0.8437 (m110) REVERT: J 659 ASP cc_start: 0.6824 (m-30) cc_final: 0.6296 (m-30) REVERT: K 81 MET cc_start: 0.9000 (tmm) cc_final: 0.8444 (tmm) REVERT: K 90 ASP cc_start: 0.6985 (t0) cc_final: 0.6427 (p0) REVERT: K 102 ILE cc_start: 0.8180 (mt) cc_final: 0.7952 (pt) REVERT: K 105 TYR cc_start: 0.8470 (m-80) cc_final: 0.8092 (m-80) REVERT: K 115 ASP cc_start: 0.8063 (p0) cc_final: 0.7145 (p0) REVERT: K 116 TYR cc_start: 0.7686 (m-80) cc_final: 0.7336 (m-80) REVERT: K 125 VAL cc_start: 0.6285 (OUTLIER) cc_final: 0.5843 (m) outliers start: 46 outliers final: 31 residues processed: 203 average time/residue: 0.2962 time to fit residues: 97.7819 Evaluate side-chains 181 residues out of total 2142 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 146 time to evaluate : 2.251 ------------------------------------------------------------------------------- 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 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: 9.9990 chunk 172 optimal weight: 10.0000 chunk 54 optimal weight: 5.9990 chunk 101 optimal weight: 20.0000 chunk 134 optimal weight: 1.9990 chunk 90 optimal weight: 10.0000 chunk 141 optimal weight: 7.9990 chunk 147 optimal weight: 9.9990 chunk 181 optimal weight: 0.9990 chunk 163 optimal weight: 20.0000 chunk 8 optimal weight: 0.9980 overall best weight: 3.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 279 ASN ** B 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 71 ASN E 279 ASN ** H 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 279 ASN I 343 GLN I 374 HIS J 577 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3736 r_free = 0.3736 target = 0.086634 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3455 r_free = 0.3455 target = 0.070683 restraints weight = 79960.262| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3464 r_free = 0.3464 target = 0.072322 restraints weight = 44323.826| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.072725 restraints weight = 32655.062| |-----------------------------------------------------------------------------| r_work (final): 0.3458 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7915 moved from start: 0.3518 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 20349 Z= 0.155 Angle : 0.659 16.689 27762 Z= 0.317 Chirality : 0.046 0.379 3243 Planarity : 0.004 0.050 3450 Dihedral : 9.079 88.968 3713 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 4.51 Ramachandran Plot: Outliers : 0.36 % Allowed : 4.17 % Favored : 95.47 % Rotamer: Outliers : 2.55 % Allowed : 11.24 % Favored : 86.21 % 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: 1.01 (0.29), residues: 390 sheet: 0.24 (0.19), residues: 705 loop : -1.25 (0.16), residues: 1377 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP E 96 HIS 0.006 0.001 HIS I 287 PHE 0.020 0.002 PHE I 53 TYR 0.022 0.001 TYR H 51 ARG 0.003 0.000 ARG G 87 Details of bonding type rmsd link_NAG-ASN : bond 0.00465 ( 9) link_NAG-ASN : angle 2.02333 ( 27) link_ALPHA1-6 : bond 0.00758 ( 6) link_ALPHA1-6 : angle 1.76246 ( 18) link_BETA1-4 : bond 0.00436 ( 18) link_BETA1-4 : angle 2.19976 ( 54) link_ALPHA1-2 : bond 0.00385 ( 6) link_ALPHA1-2 : angle 2.21895 ( 18) link_ALPHA1-3 : bond 0.02484 ( 9) link_ALPHA1-3 : angle 5.66509 ( 27) hydrogen bonds : bond 0.03540 ( 638) hydrogen bonds : angle 4.70804 ( 1752) SS BOND : bond 0.00341 ( 30) SS BOND : angle 0.72207 ( 60) covalent geometry : bond 0.00337 (20271) covalent geometry : angle 0.62169 (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 211 residues out of total 2142 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 157 time to evaluate : 2.750 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 534 SER cc_start: 0.8929 (t) cc_final: 0.8613 (p) REVERT: B 535 MET cc_start: 0.8141 (mtm) cc_final: 0.7908 (mpp) REVERT: D 87 ASP cc_start: 0.8706 (m-30) cc_final: 0.8278 (m-30) REVERT: D 107 LEU cc_start: 0.8258 (OUTLIER) cc_final: 0.8038 (tt) REVERT: E 287 HIS cc_start: 0.8595 (OUTLIER) cc_final: 0.7883 (m-70) REVERT: E 381 GLU cc_start: 0.8385 (mm-30) cc_final: 0.8142 (mm-30) REVERT: E 426 MET cc_start: 0.6506 (mtm) cc_final: 0.4893 (mtm) REVERT: F 534 SER cc_start: 0.8929 (t) cc_final: 0.8590 (p) REVERT: F 543 ASN cc_start: 0.8343 (m110) cc_final: 0.8049 (m110) REVERT: F 585 ARG cc_start: 0.7343 (mtp85) cc_final: 0.7091 (mtp85) REVERT: F 659 ASP cc_start: 0.6980 (m-30) cc_final: 0.6591 (m-30) REVERT: G 12 LYS cc_start: 0.8354 (mmmm) cc_final: 0.8118 (mmtp) REVERT: H 84 ASP cc_start: 0.4836 (m-30) cc_final: 0.4550 (m-30) REVERT: I 104 MET cc_start: 0.9039 (OUTLIER) cc_final: 0.8400 (tpt) REVERT: J 535 MET cc_start: 0.8671 (mtm) cc_final: 0.8280 (mpp) REVERT: J 543 ASN cc_start: 0.8794 (m110) cc_final: 0.8580 (m110) REVERT: J 659 ASP cc_start: 0.7304 (m-30) cc_final: 0.6795 (m-30) REVERT: K 81 MET cc_start: 0.8852 (tmm) cc_final: 0.8261 (tmm) REVERT: K 90 ASP cc_start: 0.7049 (t0) cc_final: 0.6422 (p0) REVERT: K 105 TYR cc_start: 0.8586 (m-80) cc_final: 0.8285 (m-80) REVERT: K 115 ASP cc_start: 0.8102 (p0) cc_final: 0.7241 (p0) REVERT: K 116 TYR cc_start: 0.7706 (m-80) cc_final: 0.7307 (m-80) REVERT: K 125 VAL cc_start: 0.6363 (OUTLIER) cc_final: 0.6070 (m) outliers start: 54 outliers final: 38 residues processed: 200 average time/residue: 0.3338 time to fit residues: 108.5213 Evaluate side-chains 183 residues out of total 2142 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 141 time to evaluate : 3.226 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 D residue 107 LEU Chi-restraints excluded: chain E residue 95 MET 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 48 LEU Chi-restraints excluded: chain H residue 51 TYR 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 202 THR 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 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 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: 7.9990 chunk 33 optimal weight: 5.9990 chunk 145 optimal weight: 10.0000 chunk 122 optimal weight: 2.9990 chunk 208 optimal weight: 10.0000 chunk 118 optimal weight: 50.0000 chunk 204 optimal weight: 5.9990 chunk 63 optimal weight: 7.9990 chunk 182 optimal weight: 5.9990 chunk 231 optimal weight: 20.0000 chunk 100 optimal weight: 10.0000 overall best weight: 5.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 374 HIS ** D 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 374 HIS H 81 GLN J 577 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3522 r_free = 0.3522 target = 0.078553 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3201 r_free = 0.3201 target = 0.063879 restraints weight = 80788.284| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3208 r_free = 0.3208 target = 0.064676 restraints weight = 52839.434| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3221 r_free = 0.3221 target = 0.065265 restraints weight = 44582.292| |-----------------------------------------------------------------------------| r_work (final): 0.3204 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8063 moved from start: 0.4330 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= 0.205 Angle : 0.718 17.080 27762 Z= 0.344 Chirality : 0.046 0.347 3243 Planarity : 0.004 0.054 3450 Dihedral : 8.681 80.636 3713 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 5.66 Ramachandran Plot: Outliers : 0.36 % Allowed : 4.41 % Favored : 95.23 % Rotamer: Outliers : 3.64 % Allowed : 11.52 % Favored : 84.84 % 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: -0.77 (0.17), residues: 2472 helix: 1.02 (0.28), residues: 387 sheet: 0.24 (0.19), residues: 729 loop : -1.44 (0.16), residues: 1356 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP K 47 HIS 0.008 0.001 HIS K 35 PHE 0.016 0.002 PHE E 93 TYR 0.018 0.002 TYR E 435 ARG 0.003 0.000 ARG J 617 Details of bonding type rmsd link_NAG-ASN : bond 0.00280 ( 9) link_NAG-ASN : angle 2.27405 ( 27) link_ALPHA1-6 : bond 0.00797 ( 6) link_ALPHA1-6 : angle 1.73130 ( 18) link_BETA1-4 : bond 0.00462 ( 18) link_BETA1-4 : angle 2.15484 ( 54) link_ALPHA1-2 : bond 0.00238 ( 6) link_ALPHA1-2 : angle 2.19688 ( 18) link_ALPHA1-3 : bond 0.02504 ( 9) link_ALPHA1-3 : angle 5.87265 ( 27) hydrogen bonds : bond 0.03872 ( 638) hydrogen bonds : angle 4.75457 ( 1752) SS BOND : bond 0.00413 ( 30) SS BOND : angle 0.76905 ( 60) covalent geometry : bond 0.00456 (20271) covalent geometry : angle 0.68212 (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 227 residues out of total 2142 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 150 time to evaluate : 3.031 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 530 MET cc_start: 0.7404 (mmp) cc_final: 0.6619 (mmp) REVERT: B 534 SER cc_start: 0.8972 (t) cc_final: 0.8685 (p) REVERT: D 107 LEU cc_start: 0.8580 (OUTLIER) cc_final: 0.8268 (tt) REVERT: E 34 LEU cc_start: 0.8079 (OUTLIER) cc_final: 0.7753 (mp) REVERT: E 287 HIS cc_start: 0.8761 (OUTLIER) cc_final: 0.8122 (m-70) REVERT: F 534 SER cc_start: 0.9068 (t) cc_final: 0.8813 (p) REVERT: F 543 ASN cc_start: 0.8373 (m110) cc_final: 0.8136 (m110) REVERT: F 659 ASP cc_start: 0.7178 (m-30) cc_final: 0.6797 (m-30) REVERT: H 49 MET cc_start: 0.7058 (mmm) cc_final: 0.6764 (mmm) REVERT: I 104 MET cc_start: 0.8944 (OUTLIER) cc_final: 0.8370 (tpt) REVERT: J 659 ASP cc_start: 0.7491 (m-30) cc_final: 0.6953 (m-30) REVERT: K 81 MET cc_start: 0.8681 (tmm) cc_final: 0.8137 (tmm) REVERT: K 115 ASP cc_start: 0.8283 (p0) cc_final: 0.7387 (p0) REVERT: K 116 TYR cc_start: 0.7708 (m-80) cc_final: 0.7318 (m-80) REVERT: K 125 VAL cc_start: 0.6456 (OUTLIER) cc_final: 0.6240 (m) outliers start: 77 outliers final: 50 residues processed: 216 average time/residue: 0.2949 time to fit residues: 103.2027 Evaluate side-chains 192 residues out of total 2142 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 137 time to evaluate : 2.931 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 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 D residue 19 THR Chi-restraints excluded: chain D residue 28 ASP Chi-restraints excluded: chain D residue 107 LEU Chi-restraints excluded: chain E residue 34 LEU 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 E residue 374 HIS Chi-restraints excluded: chain F residue 641 ILE 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 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 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 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 Chi-restraints excluded: chain L residue 107 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 246 random chunks: chunk 206 optimal weight: 7.9990 chunk 233 optimal weight: 4.9990 chunk 19 optimal weight: 8.9990 chunk 13 optimal weight: 9.9990 chunk 118 optimal weight: 2.9990 chunk 18 optimal weight: 1.9990 chunk 155 optimal weight: 7.9990 chunk 69 optimal weight: 5.9990 chunk 92 optimal weight: 20.0000 chunk 100 optimal weight: 8.9990 chunk 48 optimal weight: 10.0000 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 6 GLN D 71 ASN E 287 HIS E 374 HIS G 119 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3524 r_free = 0.3524 target = 0.078658 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3204 r_free = 0.3204 target = 0.064098 restraints weight = 80487.523| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3215 r_free = 0.3215 target = 0.065050 restraints weight = 51305.702| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3225 r_free = 0.3225 target = 0.065500 restraints weight = 44379.173| |-----------------------------------------------------------------------------| r_work (final): 0.3207 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8065 moved from start: 0.4599 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 20349 Z= 0.173 Angle : 0.688 17.180 27762 Z= 0.327 Chirality : 0.046 0.360 3243 Planarity : 0.004 0.051 3450 Dihedral : 8.452 79.909 3713 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 5.94 Ramachandran Plot: Outliers : 0.36 % Allowed : 4.37 % Favored : 95.27 % Rotamer: Outliers : 3.45 % Allowed : 12.04 % Favored : 84.51 % 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: -0.80 (0.17), residues: 2472 helix: 1.03 (0.29), residues: 387 sheet: 0.17 (0.19), residues: 741 loop : -1.46 (0.17), residues: 1344 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP K 47 HIS 0.004 0.001 HIS E 105 PHE 0.018 0.002 PHE C 114 TYR 0.018 0.001 TYR H 51 ARG 0.002 0.000 ARG G 87 Details of bonding type rmsd link_NAG-ASN : bond 0.00256 ( 9) link_NAG-ASN : angle 2.15931 ( 27) link_ALPHA1-6 : bond 0.00809 ( 6) link_ALPHA1-6 : angle 1.85651 ( 18) link_BETA1-4 : bond 0.00378 ( 18) link_BETA1-4 : angle 2.06453 ( 54) link_ALPHA1-2 : bond 0.00302 ( 6) link_ALPHA1-2 : angle 2.10616 ( 18) link_ALPHA1-3 : bond 0.02555 ( 9) link_ALPHA1-3 : angle 5.92132 ( 27) hydrogen bonds : bond 0.03651 ( 638) hydrogen bonds : angle 4.73454 ( 1752) SS BOND : bond 0.00333 ( 30) SS BOND : angle 0.56588 ( 60) covalent geometry : bond 0.00385 (20271) covalent geometry : angle 0.65057 (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 215 residues out of total 2142 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 142 time to evaluate : 2.475 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 95 MET cc_start: 0.7559 (ttp) cc_final: 0.7317 (ttp) REVERT: B 530 MET cc_start: 0.7364 (mmp) cc_final: 0.7083 (mmp) REVERT: D 87 ASP cc_start: 0.8527 (m-30) cc_final: 0.8269 (m-30) REVERT: D 107 LEU cc_start: 0.8615 (OUTLIER) cc_final: 0.8351 (tt) REVERT: E 287 HIS cc_start: 0.8497 (OUTLIER) cc_final: 0.7558 (m90) REVERT: E 475 MET cc_start: 0.8028 (mmm) cc_final: 0.7788 (mmm) REVERT: F 534 SER cc_start: 0.8933 (t) cc_final: 0.8678 (p) REVERT: F 543 ASN cc_start: 0.8383 (m110) cc_final: 0.8127 (m110) REVERT: F 659 ASP cc_start: 0.7253 (m-30) cc_final: 0.6864 (m-30) REVERT: G 12 LYS cc_start: 0.8737 (mmmm) cc_final: 0.8427 (mmtp) REVERT: I 104 MET cc_start: 0.8931 (OUTLIER) cc_final: 0.8381 (tpt) REVERT: J 659 ASP cc_start: 0.7513 (m-30) cc_final: 0.6968 (m-30) REVERT: K 81 MET cc_start: 0.8610 (tmm) cc_final: 0.8334 (tmm) REVERT: K 115 ASP cc_start: 0.8197 (p0) cc_final: 0.7273 (p0) REVERT: K 116 TYR cc_start: 0.7642 (m-80) cc_final: 0.7254 (m-80) outliers start: 73 outliers final: 55 residues processed: 202 average time/residue: 0.3493 time to fit residues: 116.7350 Evaluate side-chains 196 residues out of total 2142 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 138 time to evaluate : 3.087 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 83 GLU Chi-restraints excluded: chain A residue 85 VAL Chi-restraints excluded: chain A residue 89 VAL Chi-restraints excluded: chain A residue 90 THR Chi-restraints excluded: chain A residue 100 MET Chi-restraints excluded: chain A residue 104 MET Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 140 THR 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 28 ASP Chi-restraints excluded: chain D residue 72 THR Chi-restraints excluded: chain D residue 107 LEU 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 E residue 374 HIS Chi-restraints excluded: chain F residue 576 LEU 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 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 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 534 SER Chi-restraints excluded: chain J residue 543 ASN 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 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 246 random chunks: chunk 56 optimal weight: 4.9990 chunk 111 optimal weight: 10.0000 chunk 235 optimal weight: 2.9990 chunk 117 optimal weight: 0.9990 chunk 243 optimal weight: 20.0000 chunk 7 optimal weight: 9.9990 chunk 64 optimal weight: 5.9990 chunk 43 optimal weight: 10.0000 chunk 85 optimal weight: 40.0000 chunk 11 optimal weight: 10.0000 chunk 50 optimal weight: 6.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 39 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3520 r_free = 0.3520 target = 0.078530 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3193 r_free = 0.3193 target = 0.063613 restraints weight = 79932.297| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3199 r_free = 0.3199 target = 0.064438 restraints weight = 51491.027| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3213 r_free = 0.3213 target = 0.065038 restraints weight = 43298.421| |-----------------------------------------------------------------------------| r_work (final): 0.3194 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8084 moved from start: 0.4836 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 20349 Z= 0.162 Angle : 0.682 17.130 27762 Z= 0.324 Chirality : 0.045 0.354 3243 Planarity : 0.004 0.051 3450 Dihedral : 8.267 77.620 3712 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 6.20 Ramachandran Plot: Outliers : 0.36 % Allowed : 4.53 % Favored : 95.11 % Rotamer: Outliers : 3.40 % Allowed : 12.94 % Favored : 83.66 % 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: -0.78 (0.17), residues: 2472 helix: 1.04 (0.29), residues: 387 sheet: 0.26 (0.19), residues: 729 loop : -1.49 (0.16), residues: 1356 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP K 47 HIS 0.018 0.001 HIS E 374 PHE 0.016 0.002 PHE C 114 TYR 0.016 0.001 TYR D 51 ARG 0.002 0.000 ARG G 87 Details of bonding type rmsd link_NAG-ASN : bond 0.00266 ( 9) link_NAG-ASN : angle 2.09433 ( 27) link_ALPHA1-6 : bond 0.00856 ( 6) link_ALPHA1-6 : angle 1.81893 ( 18) link_BETA1-4 : bond 0.00369 ( 18) link_BETA1-4 : angle 2.01620 ( 54) link_ALPHA1-2 : bond 0.00295 ( 6) link_ALPHA1-2 : angle 2.08522 ( 18) link_ALPHA1-3 : bond 0.02444 ( 9) link_ALPHA1-3 : angle 5.91406 ( 27) hydrogen bonds : bond 0.03561 ( 638) hydrogen bonds : angle 4.69561 ( 1752) SS BOND : bond 0.00324 ( 30) SS BOND : angle 0.56582 ( 60) covalent geometry : bond 0.00362 (20271) covalent geometry : angle 0.64533 (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 210 residues out of total 2142 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 138 time to evaluate : 2.420 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 95 MET cc_start: 0.7607 (ttp) cc_final: 0.7370 (ttp) REVERT: D 87 ASP cc_start: 0.8587 (m-30) cc_final: 0.8383 (m-30) REVERT: D 107 LEU cc_start: 0.8617 (OUTLIER) cc_final: 0.8212 (tt) REVERT: E 287 HIS cc_start: 0.8487 (OUTLIER) cc_final: 0.7586 (m90) REVERT: E 475 MET cc_start: 0.8156 (mmm) cc_final: 0.7745 (mmm) REVERT: F 534 SER cc_start: 0.8936 (t) cc_final: 0.8673 (p) REVERT: F 543 ASN cc_start: 0.8456 (m110) cc_final: 0.8161 (m110) REVERT: F 659 ASP cc_start: 0.7322 (m-30) cc_final: 0.6909 (m-30) REVERT: G 12 LYS cc_start: 0.8693 (mmmm) cc_final: 0.8364 (mmtp) REVERT: I 104 MET cc_start: 0.9002 (OUTLIER) cc_final: 0.8457 (tpt) REVERT: J 657 GLU cc_start: 0.8755 (tm-30) cc_final: 0.8495 (mm-30) REVERT: J 659 ASP cc_start: 0.7466 (m-30) cc_final: 0.6910 (m-30) REVERT: K 34 MET cc_start: 0.8745 (mmt) cc_final: 0.8529 (mmt) REVERT: K 81 MET cc_start: 0.8616 (tmm) cc_final: 0.8362 (tmm) REVERT: K 115 ASP cc_start: 0.8231 (p0) cc_final: 0.7290 (p0) REVERT: K 116 TYR cc_start: 0.7720 (m-80) cc_final: 0.7272 (m-80) REVERT: L 81 GLN cc_start: 0.7587 (mp10) cc_final: 0.7296 (mp10) outliers start: 72 outliers final: 56 residues processed: 196 average time/residue: 0.3295 time to fit residues: 105.8831 Evaluate side-chains 193 residues out of total 2142 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 134 time to evaluate : 2.144 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 VAL Chi-restraints excluded: chain A residue 89 VAL 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 140 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 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 51 TYR Chi-restraints excluded: chain D residue 72 THR Chi-restraints excluded: chain D residue 107 LEU Chi-restraints excluded: chain E residue 85 VAL 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 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 E residue 308 ARG Chi-restraints excluded: chain F residue 576 LEU Chi-restraints excluded: chain F residue 605 CYS Chi-restraints excluded: chain F residue 624 ASP 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 35 VAL 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 213 ILE 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 J residue 576 LEU Chi-restraints excluded: chain J residue 595 ILE 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 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: 5.9990 chunk 138 optimal weight: 0.0060 chunk 219 optimal weight: 9.9990 chunk 11 optimal weight: 6.9990 chunk 48 optimal weight: 0.9980 chunk 28 optimal weight: 7.9990 chunk 67 optimal weight: 2.9990 chunk 65 optimal weight: 20.0000 chunk 199 optimal weight: 10.0000 chunk 205 optimal weight: 20.0000 chunk 66 optimal weight: 8.9990 overall best weight: 3.4002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 374 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3679 r_free = 0.3679 target = 0.084031 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3318 r_free = 0.3318 target = 0.065758 restraints weight = 80008.884| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.067975 restraints weight = 43794.036| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.069421 restraints weight = 31015.562| |-----------------------------------------------------------------------------| r_work (final): 0.3344 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8051 moved from start: 0.5029 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 20349 Z= 0.142 Angle : 0.674 17.375 27762 Z= 0.320 Chirality : 0.046 0.373 3243 Planarity : 0.004 0.048 3450 Dihedral : 8.044 77.063 3712 Min Nonbonded Distance : 2.357 Molprobity Statistics. All-atom Clashscore : 5.84 Ramachandran Plot: Outliers : 0.36 % Allowed : 4.65 % Favored : 94.98 % Rotamer: Outliers : 2.93 % Allowed : 13.22 % 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: -0.78 (0.17), residues: 2472 helix: 1.07 (0.29), residues: 387 sheet: 0.19 (0.19), residues: 744 loop : -1.46 (0.17), residues: 1341 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP K 47 HIS 0.015 0.001 HIS E 374 PHE 0.014 0.001 PHE C 114 TYR 0.019 0.001 TYR K 33 ARG 0.002 0.000 ARG F 585 Details of bonding type rmsd link_NAG-ASN : bond 0.00287 ( 9) link_NAG-ASN : angle 2.00682 ( 27) link_ALPHA1-6 : bond 0.00904 ( 6) link_ALPHA1-6 : angle 1.80813 ( 18) link_BETA1-4 : bond 0.00350 ( 18) link_BETA1-4 : angle 1.92986 ( 54) link_ALPHA1-2 : bond 0.00326 ( 6) link_ALPHA1-2 : angle 2.02723 ( 18) link_ALPHA1-3 : bond 0.02562 ( 9) link_ALPHA1-3 : angle 5.98475 ( 27) hydrogen bonds : bond 0.03359 ( 638) hydrogen bonds : angle 4.64202 ( 1752) SS BOND : bond 0.00284 ( 30) SS BOND : angle 0.52588 ( 60) covalent geometry : bond 0.00313 (20271) covalent geometry : angle 0.63711 (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 202 residues out of total 2142 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 140 time to evaluate : 2.280 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 530 MET cc_start: 0.7685 (mmp) cc_final: 0.7413 (mmm) REVERT: B 574 LYS cc_start: 0.7699 (OUTLIER) cc_final: 0.7416 (pttt) REVERT: D 107 LEU cc_start: 0.8538 (OUTLIER) cc_final: 0.8295 (tt) REVERT: E 287 HIS cc_start: 0.8395 (OUTLIER) cc_final: 0.7547 (m90) REVERT: E 475 MET cc_start: 0.8305 (mmm) cc_final: 0.7927 (mmm) REVERT: F 534 SER cc_start: 0.8963 (t) cc_final: 0.8546 (p) REVERT: F 543 ASN cc_start: 0.8566 (m110) cc_final: 0.8225 (m110) REVERT: F 659 ASP cc_start: 0.7323 (m-30) cc_final: 0.6985 (m-30) REVERT: H 83 GLU cc_start: 0.9367 (mt-10) cc_final: 0.8686 (pp20) REVERT: J 602 LEU cc_start: 0.7830 (OUTLIER) cc_final: 0.7609 (mt) REVERT: J 657 GLU cc_start: 0.8834 (tm-30) cc_final: 0.8574 (mm-30) REVERT: J 659 ASP cc_start: 0.7458 (m-30) cc_final: 0.6879 (m-30) REVERT: K 34 MET cc_start: 0.8490 (mmt) cc_final: 0.8276 (mmt) REVERT: K 81 MET cc_start: 0.8730 (tmm) cc_final: 0.8436 (tmm) REVERT: K 116 TYR cc_start: 0.7824 (m-80) cc_final: 0.7457 (m-80) REVERT: L 81 GLN cc_start: 0.7325 (mp10) cc_final: 0.7055 (mp10) outliers start: 62 outliers final: 44 residues processed: 194 average time/residue: 0.2864 time to fit residues: 90.5988 Evaluate side-chains 179 residues out of total 2142 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 131 time to evaluate : 2.340 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 VAL 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 D residue 19 THR Chi-restraints excluded: chain D residue 72 THR Chi-restraints excluded: chain D residue 107 LEU Chi-restraints excluded: chain E residue 85 VAL 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 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 E residue 374 HIS Chi-restraints excluded: chain F residue 576 LEU 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 35 VAL Chi-restraints excluded: chain H residue 36 SER Chi-restraints excluded: chain H residue 48 LEU 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 213 ILE Chi-restraints excluded: chain I residue 295 VAL Chi-restraints excluded: chain I residue 494 LEU Chi-restraints excluded: chain J residue 576 LEU Chi-restraints excluded: chain J residue 595 ILE Chi-restraints excluded: chain J residue 602 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 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: 0.0370 chunk 154 optimal weight: 40.0000 chunk 228 optimal weight: 7.9990 chunk 6 optimal weight: 20.0000 chunk 151 optimal weight: 0.9980 chunk 22 optimal weight: 20.0000 chunk 35 optimal weight: 20.0000 chunk 183 optimal weight: 20.0000 chunk 226 optimal weight: 9.9990 chunk 225 optimal weight: 9.9990 chunk 179 optimal weight: 0.0370 overall best weight: 3.8140 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 374 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3672 r_free = 0.3672 target = 0.083693 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3308 r_free = 0.3308 target = 0.065348 restraints weight = 79305.595| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3359 r_free = 0.3359 target = 0.067588 restraints weight = 43688.505| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.069032 restraints weight = 30957.963| |-----------------------------------------------------------------------------| r_work (final): 0.3364 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8048 moved from start: 0.5164 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 20349 Z= 0.152 Angle : 0.684 17.426 27762 Z= 0.325 Chirality : 0.045 0.364 3243 Planarity : 0.004 0.048 3450 Dihedral : 7.994 75.830 3711 Min Nonbonded Distance : 2.352 Molprobity Statistics. All-atom Clashscore : 6.15 Ramachandran Plot: Outliers : 0.36 % Allowed : 4.53 % Favored : 95.11 % Rotamer: Outliers : 2.83 % Allowed : 14.07 % Favored : 83.10 % 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: -0.78 (0.17), residues: 2472 helix: 1.08 (0.29), residues: 387 sheet: 0.19 (0.19), residues: 744 loop : -1.47 (0.17), residues: 1341 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP K 47 HIS 0.023 0.001 HIS E 374 PHE 0.013 0.001 PHE I 53 TYR 0.013 0.001 TYR D 51 ARG 0.002 0.000 ARG F 585 Details of bonding type rmsd link_NAG-ASN : bond 0.00276 ( 9) link_NAG-ASN : angle 1.99938 ( 27) link_ALPHA1-6 : bond 0.00894 ( 6) link_ALPHA1-6 : angle 1.74770 ( 18) link_BETA1-4 : bond 0.00357 ( 18) link_BETA1-4 : angle 1.89961 ( 54) link_ALPHA1-2 : bond 0.00278 ( 6) link_ALPHA1-2 : angle 2.00960 ( 18) link_ALPHA1-3 : bond 0.02544 ( 9) link_ALPHA1-3 : angle 5.99120 ( 27) hydrogen bonds : bond 0.03426 ( 638) hydrogen bonds : angle 4.64025 ( 1752) SS BOND : bond 0.00296 ( 30) SS BOND : angle 0.54590 ( 60) covalent geometry : bond 0.00337 (20271) covalent geometry : angle 0.64838 (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 192 residues out of total 2142 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 132 time to evaluate : 2.840 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 574 LYS cc_start: 0.7730 (OUTLIER) cc_final: 0.7469 (pttt) REVERT: D 87 ASP cc_start: 0.8910 (m-30) cc_final: 0.8601 (m-30) REVERT: D 107 LEU cc_start: 0.8504 (OUTLIER) cc_final: 0.8273 (tt) REVERT: E 287 HIS cc_start: 0.8357 (OUTLIER) cc_final: 0.7504 (m90) REVERT: E 475 MET cc_start: 0.8388 (mmm) cc_final: 0.7923 (mmm) REVERT: F 534 SER cc_start: 0.8951 (t) cc_final: 0.8514 (p) REVERT: F 543 ASN cc_start: 0.8609 (m110) cc_final: 0.8251 (m110) REVERT: F 659 ASP cc_start: 0.7123 (m-30) cc_final: 0.6805 (m-30) REVERT: H 83 GLU cc_start: 0.9348 (mt-10) cc_final: 0.8632 (pp20) REVERT: I 104 MET cc_start: 0.9155 (OUTLIER) cc_final: 0.8640 (tpt) REVERT: J 602 LEU cc_start: 0.7847 (OUTLIER) cc_final: 0.7630 (mt) REVERT: J 657 GLU cc_start: 0.8851 (tm-30) cc_final: 0.8580 (mm-30) REVERT: J 659 ASP cc_start: 0.7485 (m-30) cc_final: 0.6902 (m-30) REVERT: K 81 MET cc_start: 0.8763 (tmm) cc_final: 0.8428 (tmm) REVERT: K 115 ASP cc_start: 0.8271 (p0) cc_final: 0.7311 (p0) REVERT: K 116 TYR cc_start: 0.7900 (m-80) cc_final: 0.7473 (m-80) REVERT: L 81 GLN cc_start: 0.7297 (mp10) cc_final: 0.7044 (mp10) outliers start: 60 outliers final: 50 residues processed: 188 average time/residue: 0.3506 time to fit residues: 106.4568 Evaluate side-chains 184 residues out of total 2142 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 129 time to evaluate : 2.888 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 VAL 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 D residue 19 THR Chi-restraints excluded: chain D residue 51 TYR Chi-restraints excluded: chain D residue 72 THR Chi-restraints excluded: chain D residue 107 LEU 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 E residue 374 HIS Chi-restraints excluded: chain F residue 576 LEU 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 35 VAL 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 149 VAL Chi-restraints excluded: chain I residue 202 THR Chi-restraints excluded: chain I residue 213 ILE Chi-restraints excluded: chain I residue 240 SER Chi-restraints excluded: chain I residue 295 VAL Chi-restraints excluded: chain I residue 494 LEU Chi-restraints excluded: chain J residue 576 LEU Chi-restraints excluded: chain J residue 595 ILE Chi-restraints excluded: chain J residue 602 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 246 random chunks: chunk 205 optimal weight: 10.0000 chunk 35 optimal weight: 0.9990 chunk 208 optimal weight: 1.9990 chunk 178 optimal weight: 5.9990 chunk 216 optimal weight: 2.9990 chunk 113 optimal weight: 20.0000 chunk 65 optimal weight: 20.0000 chunk 243 optimal weight: 10.0000 chunk 184 optimal weight: 9.9990 chunk 244 optimal weight: 8.9990 chunk 105 optimal weight: 5.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3674 r_free = 0.3674 target = 0.083769 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.065446 restraints weight = 79795.340| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3360 r_free = 0.3360 target = 0.067682 restraints weight = 43946.078| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.069137 restraints weight = 31129.040| |-----------------------------------------------------------------------------| r_work (final): 0.3366 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8035 moved from start: 0.5272 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 20349 Z= 0.147 Angle : 0.686 17.442 27762 Z= 0.325 Chirality : 0.046 0.369 3243 Planarity : 0.004 0.047 3450 Dihedral : 7.935 75.145 3711 Min Nonbonded Distance : 2.390 Molprobity Statistics. All-atom Clashscore : 6.25 Ramachandran Plot: Outliers : 0.36 % Allowed : 4.69 % Favored : 94.94 % Rotamer: Outliers : 2.83 % Allowed : 14.26 % Favored : 82.91 % 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: -0.79 (0.17), residues: 2472 helix: 1.12 (0.29), residues: 384 sheet: 0.19 (0.19), residues: 744 loop : -1.48 (0.17), residues: 1344 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP K 47 HIS 0.021 0.001 HIS E 374 PHE 0.014 0.001 PHE I 53 TYR 0.013 0.001 TYR D 51 ARG 0.002 0.000 ARG I 192 Details of bonding type rmsd link_NAG-ASN : bond 0.00282 ( 9) link_NAG-ASN : angle 1.99166 ( 27) link_ALPHA1-6 : bond 0.00902 ( 6) link_ALPHA1-6 : angle 1.74245 ( 18) link_BETA1-4 : bond 0.00351 ( 18) link_BETA1-4 : angle 1.86311 ( 54) link_ALPHA1-2 : bond 0.00283 ( 6) link_ALPHA1-2 : angle 1.97572 ( 18) link_ALPHA1-3 : bond 0.02553 ( 9) link_ALPHA1-3 : angle 6.00059 ( 27) hydrogen bonds : bond 0.03411 ( 638) hydrogen bonds : angle 4.64589 ( 1752) SS BOND : bond 0.00293 ( 30) SS BOND : angle 0.54351 ( 60) covalent geometry : bond 0.00325 (20271) covalent geometry : angle 0.65003 (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 192 residues out of total 2142 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 132 time to evaluate : 3.641 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 574 LYS cc_start: 0.7734 (OUTLIER) cc_final: 0.7502 (pttt) REVERT: B 626 MET cc_start: 0.5729 (tpt) cc_final: 0.5501 (tpt) REVERT: D 1 GLN cc_start: 0.3182 (pp30) cc_final: 0.2805 (pp30) REVERT: D 87 ASP cc_start: 0.8940 (m-30) cc_final: 0.8624 (m-30) REVERT: D 107 LEU cc_start: 0.8482 (OUTLIER) cc_final: 0.8263 (tt) REVERT: E 287 HIS cc_start: 0.8315 (OUTLIER) cc_final: 0.7464 (m90) REVERT: E 475 MET cc_start: 0.8447 (mmm) cc_final: 0.7959 (mmm) REVERT: F 530 MET cc_start: 0.6654 (mmp) cc_final: 0.5698 (mmp) REVERT: F 534 SER cc_start: 0.8927 (t) cc_final: 0.8427 (p) REVERT: F 543 ASN cc_start: 0.8637 (m110) cc_final: 0.8261 (m110) REVERT: F 626 MET cc_start: 0.7485 (tpt) cc_final: 0.6798 (tpt) REVERT: F 659 ASP cc_start: 0.7138 (m-30) cc_final: 0.6843 (m-30) REVERT: I 104 MET cc_start: 0.9177 (OUTLIER) cc_final: 0.8659 (tpt) REVERT: J 602 LEU cc_start: 0.7851 (OUTLIER) cc_final: 0.7632 (mt) REVERT: J 655 LYS cc_start: 0.8822 (OUTLIER) cc_final: 0.8484 (tppp) REVERT: J 657 GLU cc_start: 0.8855 (tm-30) cc_final: 0.8593 (mm-30) REVERT: J 659 ASP cc_start: 0.7489 (m-30) cc_final: 0.6910 (m-30) REVERT: K 81 MET cc_start: 0.8775 (tmm) cc_final: 0.8418 (tmm) REVERT: K 115 ASP cc_start: 0.8296 (p0) cc_final: 0.7311 (p0) REVERT: K 116 TYR cc_start: 0.7950 (m-80) cc_final: 0.7488 (m-80) REVERT: L 81 GLN cc_start: 0.7256 (mp10) cc_final: 0.7009 (mp10) outliers start: 60 outliers final: 50 residues processed: 188 average time/residue: 0.3167 time to fit residues: 98.1205 Evaluate side-chains 188 residues out of total 2142 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 132 time to evaluate : 2.383 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 VAL 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 30 THR Chi-restraints excluded: chain C residue 51 ILE Chi-restraints excluded: chain C residue 68 VAL Chi-restraints excluded: chain D residue 19 THR Chi-restraints excluded: chain D residue 51 TYR Chi-restraints excluded: chain D residue 72 THR Chi-restraints excluded: chain D residue 107 LEU 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 576 LEU 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 35 VAL 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 149 VAL Chi-restraints excluded: chain I residue 202 THR Chi-restraints excluded: chain I residue 213 ILE Chi-restraints excluded: chain I residue 240 SER Chi-restraints excluded: chain I residue 295 VAL Chi-restraints excluded: chain I residue 494 LEU Chi-restraints excluded: chain J residue 576 LEU Chi-restraints excluded: chain J residue 595 ILE Chi-restraints excluded: chain J residue 602 LEU Chi-restraints excluded: chain J residue 605 CYS Chi-restraints excluded: chain J residue 655 LYS 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 172 optimal weight: 0.8980 chunk 38 optimal weight: 7.9990 chunk 210 optimal weight: 0.3980 chunk 174 optimal weight: 10.0000 chunk 105 optimal weight: 10.0000 chunk 41 optimal weight: 20.0000 chunk 53 optimal weight: 10.0000 chunk 48 optimal weight: 20.0000 chunk 244 optimal weight: 6.9990 chunk 217 optimal weight: 10.0000 chunk 165 optimal weight: 3.9990 overall best weight: 4.0586 ------------------------------------------------------------------------------- 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 = 0.3666 r_free = 0.3666 target = 0.083462 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3299 r_free = 0.3299 target = 0.065056 restraints weight = 79971.356| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.067256 restraints weight = 43925.729| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.3382 r_free = 0.3382 target = 0.068706 restraints weight = 31191.409| |-----------------------------------------------------------------------------| r_work (final): 0.3354 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8066 moved from start: 0.5481 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 20349 Z= 0.157 Angle : 0.693 17.517 27762 Z= 0.328 Chirality : 0.046 0.364 3243 Planarity : 0.004 0.048 3450 Dihedral : 7.914 73.874 3711 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 6.56 Ramachandran Plot: Outliers : 0.36 % Allowed : 4.73 % Favored : 94.90 % Rotamer: Outliers : 2.79 % Allowed : 14.40 % Favored : 82.81 % 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: -0.82 (0.17), residues: 2472 helix: 1.10 (0.29), residues: 384 sheet: 0.15 (0.19), residues: 744 loop : -1.49 (0.17), residues: 1344 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 427 HIS 0.005 0.001 HIS E 374 PHE 0.015 0.001 PHE I 53 TYR 0.014 0.001 TYR D 51 ARG 0.002 0.000 ARG I 192 Details of bonding type rmsd link_NAG-ASN : bond 0.00258 ( 9) link_NAG-ASN : angle 2.01553 ( 27) link_ALPHA1-6 : bond 0.00883 ( 6) link_ALPHA1-6 : angle 1.71098 ( 18) link_BETA1-4 : bond 0.00354 ( 18) link_BETA1-4 : angle 1.81599 ( 54) link_ALPHA1-2 : bond 0.00248 ( 6) link_ALPHA1-2 : angle 1.96067 ( 18) link_ALPHA1-3 : bond 0.02549 ( 9) link_ALPHA1-3 : angle 6.01685 ( 27) hydrogen bonds : bond 0.03469 ( 638) hydrogen bonds : angle 4.64247 ( 1752) SS BOND : bond 0.00314 ( 30) SS BOND : angle 0.55477 ( 60) covalent geometry : bond 0.00349 (20271) covalent geometry : angle 0.65763 (27558) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6060.12 seconds wall clock time: 110 minutes 55.44 seconds (6655.44 seconds total)