Starting phenix.real_space_refine on Tue May 20 15:09:43 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8sar_40277/05_2025/8sar_40277_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8sar_40277/05_2025/8sar_40277.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.82 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8sar_40277/05_2025/8sar_40277.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8sar_40277/05_2025/8sar_40277.map" model { file = "/net/cci-nas-00/data/ceres_data/8sar_40277/05_2025/8sar_40277_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8sar_40277/05_2025/8sar_40277_neut.cif" } resolution = 3.82 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= 0.014 sd= 0.283 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 141 5.16 5 C 12452 2.51 5 N 3335 2.21 5 O 4035 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 52 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 19963 Number of models: 1 Model: "" Number of chains: 27 Chain: "A" Number of atoms: 3607 Number of conformers: 1 Conformer: "" Number of residues, atoms: 461, 3607 Classifications: {'peptide': 461} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 23, 'TRANS': 437} Chain breaks: 1 Chain: "B" Number of atoms: 983 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 983 Classifications: {'peptide': 124} Link IDs: {'PTRANS': 1, 'TRANS': 122} Chain: "C" Number of atoms: 996 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 996 Classifications: {'peptide': 126} Link IDs: {'PTRANS': 5, 'TRANS': 120} Chain: "D" Number of atoms: 805 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 805 Classifications: {'peptide': 110} Link IDs: {'PTRANS': 5, 'TRANS': 104} Chain: "F" Number of atoms: 3615 Number of conformers: 1 Conformer: "" Number of residues, atoms: 462, 3615 Classifications: {'peptide': 462} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 23, 'TRANS': 438} Chain: "G" Number of atoms: 983 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 983 Classifications: {'peptide': 124} Link IDs: {'PTRANS': 1, 'TRANS': 122} Chain: "H" Number of atoms: 996 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 996 Classifications: {'peptide': 126} Link IDs: {'PTRANS': 5, 'TRANS': 120} Chain: "I" Number of atoms: 805 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 805 Classifications: {'peptide': 110} Link IDs: {'PTRANS': 5, 'TRANS': 104} Chain: "K" Number of atoms: 3615 Number of conformers: 1 Conformer: "" Number of residues, atoms: 462, 3615 Classifications: {'peptide': 462} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 23, 'TRANS': 438} Chain: "L" Number of atoms: 983 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 983 Classifications: {'peptide': 124} Link IDs: {'PTRANS': 1, 'TRANS': 122} Chain: "M" Number of atoms: 996 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 996 Classifications: {'peptide': 126} Link IDs: {'PTRANS': 5, 'TRANS': 120} Chain: "N" Number of atoms: 805 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 805 Classifications: {'peptide': 110} Link IDs: {'PTRANS': 5, 'TRANS': 104} Chain: "J" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "O" Number of atoms: 127 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 127 Unusual residues: {'BMA': 1, 'MAN': 8, 'NAG': 2} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 33 Unresolved non-hydrogen chiralities: 11 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: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "S" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "T" Number of atoms: 116 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 116 Unusual residues: {'BMA': 1, 'MAN': 7, 'NAG': 2} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 10 Chain: "U" 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: "V" 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: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "Y" Number of atoms: 127 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 127 Unusual residues: {'BMA': 1, 'MAN': 8, 'NAG': 2} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 33 Unresolved non-hydrogen chiralities: 11 Chain: "Z" 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: "a" 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: "A" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "F" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "K" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 11.80, per 1000 atoms: 0.59 Number of scatterers: 19963 At special positions: 0 Unit cell: (157.768, 157.768, 137.514, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 141 16.00 O 4035 8.00 N 3335 7.00 C 12452 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=45, 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 126 " - pdb=" SG CYS A 196 " distance=2.03 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 157 " distance=2.03 Simple disulfide: pdb=" SG CYS A 201 " - pdb=" SG CYS A 433 " distance=2.04 Simple disulfide: pdb=" SG CYS A 218 " - pdb=" SG CYS A 247 " distance=2.03 Simple disulfide: pdb=" SG CYS A 228 " - pdb=" SG CYS A 239 " distance=2.03 Simple disulfide: pdb=" SG CYS A 296 " - pdb=" SG CYS A 331 " distance=2.05 Simple disulfide: pdb=" SG CYS A 378 " - pdb=" SG CYS A 445 " distance=2.04 Simple disulfide: pdb=" SG CYS A 385 " - pdb=" SG CYS A 418 " distance=2.03 Simple disulfide: pdb=" SG CYS A 501 " - pdb=" SG CYS B 605 " distance=2.03 Simple disulfide: pdb=" SG CYS B 598 " - pdb=" SG CYS B 604 " distance=2.03 Simple disulfide: pdb=" SG CYS C 22 " - pdb=" SG CYS C 96 " distance=2.03 Simple disulfide: pdb=" SG CYS D 22 " - pdb=" SG CYS D 90 " distance=2.03 Simple disulfide: pdb=" SG CYS D 91 " - pdb=" SG CYS D 101 " distance=2.03 Simple disulfide: pdb=" SG CYS F 54 " - pdb=" SG CYS F 74 " distance=2.03 Simple disulfide: pdb=" SG CYS F 119 " - pdb=" SG CYS F 205 " distance=2.03 Simple disulfide: pdb=" SG CYS F 126 " - pdb=" SG CYS F 196 " distance=2.02 Simple disulfide: pdb=" SG CYS F 131 " - pdb=" SG CYS F 157 " distance=2.03 Simple disulfide: pdb=" SG CYS F 201 " - pdb=" SG CYS F 433 " distance=2.04 Simple disulfide: pdb=" SG CYS F 218 " - pdb=" SG CYS F 247 " distance=2.03 Simple disulfide: pdb=" SG CYS F 228 " - pdb=" SG CYS F 239 " distance=2.03 Simple disulfide: pdb=" SG CYS F 296 " - pdb=" SG CYS F 331 " distance=2.05 Simple disulfide: pdb=" SG CYS F 378 " - pdb=" SG CYS F 445 " distance=2.04 Simple disulfide: pdb=" SG CYS F 385 " - pdb=" SG CYS F 418 " distance=2.03 Simple disulfide: pdb=" SG CYS F 501 " - pdb=" SG CYS G 605 " distance=2.03 Simple disulfide: pdb=" SG CYS G 598 " - pdb=" SG CYS G 604 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.03 Simple disulfide: pdb=" SG CYS I 22 " - pdb=" SG CYS I 90 " distance=2.03 Simple disulfide: pdb=" SG CYS I 91 " - pdb=" SG CYS I 101 " distance=2.03 Simple disulfide: pdb=" SG CYS K 54 " - pdb=" SG CYS K 74 " distance=2.03 Simple disulfide: pdb=" SG CYS K 119 " - pdb=" SG CYS K 205 " distance=2.03 Simple disulfide: pdb=" SG CYS K 126 " - pdb=" SG CYS K 196 " distance=2.03 Simple disulfide: pdb=" SG CYS K 131 " - pdb=" SG CYS K 157 " distance=2.03 Simple disulfide: pdb=" SG CYS K 201 " - pdb=" SG CYS K 433 " distance=2.04 Simple disulfide: pdb=" SG CYS K 218 " - pdb=" SG CYS K 247 " distance=2.03 Simple disulfide: pdb=" SG CYS K 228 " - pdb=" SG CYS K 239 " distance=2.03 Simple disulfide: pdb=" SG CYS K 296 " - pdb=" SG CYS K 331 " distance=2.05 Simple disulfide: pdb=" SG CYS K 378 " - pdb=" SG CYS K 445 " distance=2.03 Simple disulfide: pdb=" SG CYS K 385 " - pdb=" SG CYS K 418 " distance=2.03 Simple disulfide: pdb=" SG CYS K 501 " - pdb=" SG CYS L 605 " distance=2.03 Simple disulfide: pdb=" SG CYS L 598 " - pdb=" SG CYS L 604 " distance=2.03 Simple disulfide: pdb=" SG CYS M 22 " - pdb=" SG CYS M 96 " distance=2.03 Simple disulfide: pdb=" SG CYS N 22 " - pdb=" SG CYS N 90 " distance=2.03 Simple disulfide: pdb=" SG CYS N 91 " - pdb=" SG CYS N 101 " 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 J 4 " - " MAN J 5 " " MAN O 4 " - " MAN O 5 " " MAN O 5 " - " MAN O 6 " " MAN O 8 " - " MAN O 9 " " MAN O 10 " - " MAN O 11 " " MAN S 4 " - " MAN S 5 " " MAN T 4 " - " MAN T 5 " " MAN T 5 " - " MAN T 6 " " MAN T 8 " - " MAN T 9 " " MAN X 4 " - " MAN X 5 " " MAN Y 4 " - " MAN Y 5 " " MAN Y 5 " - " MAN Y 6 " " MAN Y 8 " - " MAN Y 9 " " MAN Y 10 " - " MAN Y 11 " ALPHA1-3 " BMA J 3 " - " MAN J 4 " " BMA O 3 " - " MAN O 4 " " MAN O 7 " - " MAN O 8 " " BMA S 3 " - " MAN S 4 " " BMA T 3 " - " MAN T 4 " " MAN T 7 " - " MAN T 10 " " BMA X 3 " - " MAN X 4 " " BMA Y 3 " - " MAN Y 4 " " MAN Y 7 " - " MAN Y 8 " ALPHA1-6 " BMA O 3 " - " MAN O 7 " " MAN O 7 " - " MAN O 10 " " BMA T 3 " - " MAN T 7 " " MAN T 7 " - " MAN T 8 " " BMA Y 3 " - " MAN Y 7 " " MAN Y 7 " - " MAN Y 10 " BETA1-4 " NAG J 1 " - " NAG J 2 " " NAG J 2 " - " BMA J 3 " " NAG O 1 " - " NAG O 2 " " NAG O 2 " - " BMA O 3 " " NAG P 1 " - " NAG P 2 " " NAG Q 1 " - " NAG Q 2 " " NAG Q 2 " - " BMA Q 3 " " NAG S 1 " - " NAG S 2 " " NAG S 2 " - " BMA S 3 " " NAG T 1 " - " NAG T 2 " " NAG T 2 " - " BMA T 3 " " NAG U 1 " - " NAG U 2 " " NAG V 1 " - " NAG V 2 " " NAG X 1 " - " NAG X 2 " " NAG X 2 " - " BMA X 3 " " NAG Y 1 " - " NAG Y 2 " " NAG Y 2 " - " BMA Y 3 " " NAG Z 1 " - " NAG Z 2 " " NAG a 1 " - " NAG a 2 " NAG-ASN " NAG A 601 " - " ASN A 138 " " NAG F 601 " - " ASN F 138 " " NAG J 1 " - " ASN A 301 " " NAG K 601 " - " ASN K 138 " " NAG O 1 " - " ASN A 332 " " NAG P 1 " - " ASN A 156 " " NAG Q 1 " - " ASN A 442 " " NAG S 1 " - " ASN F 301 " " NAG T 1 " - " ASN F 332 " " NAG U 1 " - " ASN F 156 " " NAG V 1 " - " ASN F 442 " " NAG X 1 " - " ASN K 301 " " NAG Y 1 " - " ASN K 332 " " NAG Z 1 " - " ASN K 156 " " NAG a 1 " - " ASN K 442 " Time building additional restraints: 5.29 Conformation dependent library (CDL) restraints added in 2.3 seconds 4878 Ramachandran restraints generated. 2439 Oldfield, 0 Emsley, 2439 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4540 Finding SS restraints... Secondary structure from input PDB file: 50 helices and 53 sheets defined 19.0% alpha, 32.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.69 Creating SS restraints... Processing helix chain 'A' and resid 58 through 63 Processing helix chain 'A' and resid 68 through 73 removed outlier: 3.573A pdb=" N HIS A 72 " --> pdb=" O VAL A 68 " (cutoff:3.500A) Processing helix chain 'A' and resid 98 through 115 removed outlier: 4.281A pdb=" N ASP A 102 " --> pdb=" O ASN A 98 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N GLU A 106 " --> pdb=" O ASP A 102 " (cutoff:3.500A) Processing helix chain 'A' and resid 123 through 127 removed outlier: 4.017A pdb=" N VAL A 127 " --> pdb=" O PRO A 124 " (cutoff:3.500A) Processing helix chain 'A' and resid 335 through 351 Processing helix chain 'A' and resid 368 through 373 removed outlier: 3.669A pdb=" N THR A 373 " --> pdb=" O MET A 369 " (cutoff:3.500A) Processing helix chain 'A' and resid 387 through 391 Processing helix chain 'A' and resid 475 through 480 removed outlier: 3.689A pdb=" N TRP A 479 " --> pdb=" O MET A 475 " (cutoff:3.500A) Processing helix chain 'B' and resid 537 through 542 Processing helix chain 'B' and resid 572 through 596 removed outlier: 3.571A pdb=" N LEU B 576 " --> pdb=" O GLY B 572 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N TRP B 596 " --> pdb=" O LEU B 592 " (cutoff:3.500A) Processing helix chain 'B' and resid 618 through 624 removed outlier: 3.588A pdb=" N ASP B 624 " --> pdb=" O SER B 620 " (cutoff:3.500A) Processing helix chain 'B' and resid 627 through 636 removed outlier: 3.831A pdb=" N GLU B 634 " --> pdb=" O GLN B 630 " (cutoff:3.500A) Processing helix chain 'B' and resid 638 through 663 removed outlier: 4.450A pdb=" N GLY B 644 " --> pdb=" O GLN B 640 " (cutoff:3.500A) removed outlier: 4.385A pdb=" N GLU B 647 " --> pdb=" O TYR B 643 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N GLN B 653 " --> pdb=" O SER B 649 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N GLU B 654 " --> pdb=" O GLN B 650 " (cutoff:3.500A) removed outlier: 4.868A pdb=" N LYS B 655 " --> pdb=" O ASN B 651 " (cutoff:3.500A) removed outlier: 6.398A pdb=" N ASN B 656 " --> pdb=" O GLN B 652 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N GLU B 657 " --> pdb=" O GLN B 653 " (cutoff:3.500A) Processing helix chain 'C' and resid 61 through 65 removed outlier: 3.646A pdb=" N GLN C 65 " --> pdb=" O ARG C 62 " (cutoff:3.500A) Processing helix chain 'C' and resid 87 through 91 Processing helix chain 'D' and resid 81 through 85 removed outlier: 3.505A pdb=" N ASP D 84 " --> pdb=" O ARG D 81 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N GLU D 85 " --> pdb=" O ALA D 82 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 81 through 85' Processing helix chain 'F' and resid 58 through 63 Processing helix chain 'F' and resid 68 through 73 removed outlier: 3.534A pdb=" N HIS F 72 " --> pdb=" O VAL F 68 " (cutoff:3.500A) Processing helix chain 'F' and resid 98 through 115 removed outlier: 4.222A pdb=" N ASP F 102 " --> pdb=" O ASN F 98 " (cutoff:3.500A) removed outlier: 4.252A pdb=" N GLU F 106 " --> pdb=" O ASP F 102 " (cutoff:3.500A) Processing helix chain 'F' and resid 123 through 127 removed outlier: 3.904A pdb=" N CYS F 126 " --> pdb=" O THR F 123 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N VAL F 127 " --> pdb=" O PRO F 124 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 123 through 127' Processing helix chain 'F' and resid 335 through 351 Processing helix chain 'F' and resid 368 through 373 removed outlier: 3.877A pdb=" N THR F 373 " --> pdb=" O MET F 369 " (cutoff:3.500A) Processing helix chain 'F' and resid 387 through 391 Processing helix chain 'F' and resid 475 through 480 Processing helix chain 'F' and resid 481 through 484 removed outlier: 5.132A pdb=" N TYR F 484 " --> pdb=" O SER F 481 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 481 through 484' Processing helix chain 'G' and resid 537 through 542 Processing helix chain 'G' and resid 572 through 596 removed outlier: 3.648A pdb=" N LEU G 576 " --> pdb=" O GLY G 572 " (cutoff:3.500A) removed outlier: 4.122A pdb=" N TRP G 596 " --> pdb=" O LEU G 592 " (cutoff:3.500A) Processing helix chain 'G' and resid 611 through 616 removed outlier: 4.319A pdb=" N SER G 615 " --> pdb=" O ASN G 611 " (cutoff:3.500A) Processing helix chain 'G' and resid 619 through 624 Processing helix chain 'G' and resid 627 through 636 removed outlier: 3.762A pdb=" N GLU G 634 " --> pdb=" O GLN G 630 " (cutoff:3.500A) Processing helix chain 'G' and resid 638 through 649 removed outlier: 4.024A pdb=" N GLY G 644 " --> pdb=" O GLN G 640 " (cutoff:3.500A) removed outlier: 4.238A pdb=" N GLU G 647 " --> pdb=" O TYR G 643 " (cutoff:3.500A) Processing helix chain 'G' and resid 653 through 663 Processing helix chain 'H' and resid 87 through 91 Processing helix chain 'K' and resid 58 through 63 Processing helix chain 'K' and resid 68 through 74 Processing helix chain 'K' and resid 98 through 115 removed outlier: 4.233A pdb=" N ASP K 102 " --> pdb=" O ASN K 98 " (cutoff:3.500A) removed outlier: 4.185A pdb=" N GLU K 106 " --> pdb=" O ASP K 102 " (cutoff:3.500A) Processing helix chain 'K' and resid 123 through 127 removed outlier: 4.033A pdb=" N VAL K 127 " --> pdb=" O PRO K 124 " (cutoff:3.500A) Processing helix chain 'K' and resid 335 through 350 Processing helix chain 'K' and resid 368 through 373 removed outlier: 3.826A pdb=" N THR K 373 " --> pdb=" O MET K 369 " (cutoff:3.500A) Processing helix chain 'K' and resid 387 through 391 Processing helix chain 'K' and resid 475 through 480 removed outlier: 3.614A pdb=" N TRP K 479 " --> pdb=" O MET K 475 " (cutoff:3.500A) Processing helix chain 'L' and resid 537 through 542 Processing helix chain 'L' and resid 572 through 596 removed outlier: 3.576A pdb=" N LEU L 576 " --> pdb=" O GLY L 572 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N TRP L 596 " --> pdb=" O LEU L 592 " (cutoff:3.500A) Processing helix chain 'L' and resid 611 through 615 Processing helix chain 'L' and resid 619 through 624 Processing helix chain 'L' and resid 627 through 636 removed outlier: 3.845A pdb=" N GLU L 634 " --> pdb=" O GLN L 630 " (cutoff:3.500A) Processing helix chain 'L' and resid 638 through 652 removed outlier: 4.110A pdb=" N GLY L 644 " --> pdb=" O GLN L 640 " (cutoff:3.500A) removed outlier: 4.311A pdb=" N GLU L 647 " --> pdb=" O TYR L 643 " (cutoff:3.500A) Processing helix chain 'L' and resid 654 through 663 removed outlier: 4.300A pdb=" N LEU L 660 " --> pdb=" O ASN L 656 " (cutoff:3.500A) Processing helix chain 'M' and resid 87 through 91 Processing helix chain 'N' and resid 81 through 85 removed outlier: 3.531A pdb=" N ASP N 84 " --> pdb=" O ARG N 81 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N GLU N 85 " --> pdb=" O ALA N 82 " (cutoff:3.500A) No H-bonds generated for 'chain 'N' and resid 81 through 85' Processing sheet with id=AA1, first strand: chain 'A' and resid 494 through 499 removed outlier: 5.142A pdb=" N VAL A 36 " --> pdb=" O THR B 606 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N CYS B 604 " --> pdb=" O VAL A 38 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 45 through 46 removed outlier: 3.517A 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 removed outlier: 3.628A pdb=" N PHE A 53 " --> pdb=" O CYS A 218 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 91 through 94 removed outlier: 3.533A pdb=" N GLU A 91 " --> pdb=" O CYS A 239 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 130 through 131 Processing sheet with id=AA6, first strand: chain 'A' and resid 181 through 183 Processing sheet with id=AA7, first strand: chain 'A' and resid 259 through 260 removed outlier: 3.742A pdb=" N GLY A 451 " --> pdb=" O LEU A 260 " (cutoff:3.500A) removed outlier: 7.508A pdb=" N GLY A 451 " --> pdb=" O THR A 290 " (cutoff:3.500A) removed outlier: 11.165A pdb=" N THR A 290 " --> pdb=" O GLY A 451 " (cutoff:3.500A) removed outlier: 12.140A pdb=" N LEU A 453 " --> pdb=" O LEU A 288 " (cutoff:3.500A) removed outlier: 11.989A pdb=" N LEU A 288 " --> pdb=" O LEU A 453 " (cutoff:3.500A) removed outlier: 11.004A pdb=" N THR A 455 " --> pdb=" O VAL A 286 " (cutoff:3.500A) removed outlier: 11.228A pdb=" N VAL A 286 " --> pdb=" O THR A 455 " (cutoff:3.500A) removed outlier: 7.518A pdb=" N GLU A 293 " --> pdb=" O SER A 334 " (cutoff:3.500A) removed outlier: 4.800A pdb=" N SER A 334 " --> pdb=" O GLU A 293 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N VAL A 295 " --> pdb=" O ASN A 332 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N ASN A 332 " --> pdb=" O VAL A 295 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N THR A 297 " --> pdb=" O HIS A 330 " (cutoff:3.500A) removed outlier: 4.206A pdb=" N HIS A 330 " --> pdb=" O THR A 297 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N LYS A 421 " --> pdb=" O PHE A 382 " (cutoff:3.500A) removed outlier: 4.499A pdb=" N PHE A 382 " --> pdb=" O LYS A 421 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 271 through 273 removed outlier: 11.228A pdb=" N VAL A 286 " --> pdb=" O THR A 455 " (cutoff:3.500A) removed outlier: 11.004A pdb=" N THR A 455 " --> pdb=" O VAL A 286 " (cutoff:3.500A) removed outlier: 11.989A pdb=" N LEU A 288 " --> pdb=" O LEU A 453 " (cutoff:3.500A) removed outlier: 12.140A pdb=" N LEU A 453 " --> pdb=" O LEU A 288 " (cutoff:3.500A) removed outlier: 11.165A pdb=" N THR A 290 " --> pdb=" O GLY A 451 " (cutoff:3.500A) removed outlier: 7.508A pdb=" N GLY A 451 " --> pdb=" O THR A 290 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 304 through 308 Processing sheet with id=AB1, first strand: chain 'A' and resid 359 through 360 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 10 through 12 removed outlier: 5.144A pdb=" N TYR C 33 " --> pdb=" O GLY C 99 " (cutoff:3.500A) removed outlier: 6.599A pdb=" N ILE C 34 " --> pdb=" O TRP C 50 " (cutoff:3.500A) removed outlier: 4.424A pdb=" N TRP C 50 " --> pdb=" O ILE C 34 " (cutoff:3.500A) removed outlier: 6.384A pdb=" N TRP C 36 " --> pdb=" O MET C 48 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 18 through 20 Processing sheet with id=AB5, first strand: chain 'D' and resid 9 through 12 removed outlier: 6.608A pdb=" N TRP D 37 " --> pdb=" O MET D 49 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 9 through 12 Processing sheet with id=AB7, first strand: chain 'D' and resid 18 through 23 Processing sheet with id=AB8, first strand: chain 'D' and resid 18 through 23 Processing sheet with id=AB9, first strand: chain 'F' and resid 494 through 499 removed outlier: 4.990A pdb=" N VAL F 36 " --> pdb=" O THR G 606 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N CYS G 604 " --> pdb=" O VAL F 38 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'F' and resid 45 through 47 removed outlier: 3.756A pdb=" N ILE F 225 " --> pdb=" O VAL F 245 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'F' and resid 75 through 76 removed outlier: 7.007A pdb=" N CYS F 54 " --> pdb=" O VAL F 75 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'F' and resid 91 through 94 Processing sheet with id=AC4, first strand: chain 'F' and resid 170 through 177 Processing sheet with id=AC5, first strand: chain 'F' and resid 202 through 203 removed outlier: 6.678A pdb=" N THR F 202 " --> pdb=" O TYR F 435 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'F' and resid 259 through 260 removed outlier: 3.759A pdb=" N GLY F 451 " --> pdb=" O LEU F 260 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N ILE F 443 " --> pdb=" O ARG F 298 " (cutoff:3.500A) removed outlier: 7.462A pdb=" N GLY F 451 " --> pdb=" O THR F 290 " (cutoff:3.500A) removed outlier: 11.092A pdb=" N THR F 290 " --> pdb=" O GLY F 451 " (cutoff:3.500A) removed outlier: 12.079A pdb=" N LEU F 453 " --> pdb=" O LEU F 288 " (cutoff:3.500A) removed outlier: 11.964A pdb=" N LEU F 288 " --> pdb=" O LEU F 453 " (cutoff:3.500A) removed outlier: 10.994A pdb=" N THR F 455 " --> pdb=" O VAL F 286 " (cutoff:3.500A) removed outlier: 11.188A pdb=" N VAL F 286 " --> pdb=" O THR F 455 " (cutoff:3.500A) removed outlier: 7.504A pdb=" N GLU F 293 " --> pdb=" O SER F 334 " (cutoff:3.500A) removed outlier: 4.764A pdb=" N SER F 334 " --> pdb=" O GLU F 293 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N VAL F 295 " --> pdb=" O ASN F 332 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N ASN F 332 " --> pdb=" O VAL F 295 " (cutoff:3.500A) removed outlier: 4.058A pdb=" N THR F 297 " --> pdb=" O HIS F 330 " (cutoff:3.500A) removed outlier: 4.198A pdb=" N HIS F 330 " --> pdb=" O THR F 297 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N LYS F 421 " --> pdb=" O PHE F 382 " (cutoff:3.500A) removed outlier: 4.432A pdb=" N PHE F 382 " --> pdb=" O LYS F 421 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'F' and resid 271 through 273 removed outlier: 11.188A pdb=" N VAL F 286 " --> pdb=" O THR F 455 " (cutoff:3.500A) removed outlier: 10.994A pdb=" N THR F 455 " --> pdb=" O VAL F 286 " (cutoff:3.500A) removed outlier: 11.964A pdb=" N LEU F 288 " --> pdb=" O LEU F 453 " (cutoff:3.500A) removed outlier: 12.079A pdb=" N LEU F 453 " --> pdb=" O LEU F 288 " (cutoff:3.500A) removed outlier: 11.092A pdb=" N THR F 290 " --> pdb=" O GLY F 451 " (cutoff:3.500A) removed outlier: 7.462A pdb=" N GLY F 451 " --> pdb=" O THR F 290 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N ILE F 443 " --> pdb=" O ARG F 298 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'F' and resid 304 through 308 Processing sheet with id=AC9, first strand: chain 'F' and resid 359 through 360 Processing sheet with id=AD1, first strand: chain 'H' and resid 3 through 6 Processing sheet with id=AD2, first strand: chain 'H' and resid 10 through 12 removed outlier: 5.140A pdb=" N TYR H 33 " --> pdb=" O GLY H 99 " (cutoff:3.500A) removed outlier: 6.752A pdb=" N ILE H 34 " --> pdb=" O TRP H 50 " (cutoff:3.500A) removed outlier: 4.494A pdb=" N TRP H 50 " --> pdb=" O ILE H 34 " (cutoff:3.500A) removed outlier: 6.378A pdb=" N TRP H 36 " --> pdb=" O MET H 48 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'H' and resid 10 through 12 removed outlier: 4.118A pdb=" N HIS H 116 " --> pdb=" O THR H 98 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'H' and resid 18 through 20 Processing sheet with id=AD5, first strand: chain 'I' and resid 9 through 12 removed outlier: 3.604A pdb=" N GLY I 12 " --> pdb=" O THR I 108 " (cutoff:3.500A) removed outlier: 6.660A pdb=" N TRP I 37 " --> pdb=" O MET I 49 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N MET I 49 " --> pdb=" O TRP I 37 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'I' and resid 9 through 12 removed outlier: 3.604A pdb=" N GLY I 12 " --> pdb=" O THR I 108 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'I' and resid 18 through 23 Processing sheet with id=AD8, first strand: chain 'I' and resid 18 through 23 Processing sheet with id=AD9, first strand: chain 'K' and resid 494 through 499 removed outlier: 5.166A pdb=" N VAL K 36 " --> pdb=" O THR L 606 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N CYS L 604 " --> pdb=" O VAL K 38 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'K' and resid 45 through 46 removed outlier: 3.525A pdb=" N ILE K 225 " --> pdb=" O VAL K 245 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'K' and resid 75 through 76 Processing sheet with id=AE3, first strand: chain 'K' and resid 91 through 94 removed outlier: 3.517A pdb=" N GLU K 91 " --> pdb=" O CYS K 239 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'K' and resid 170 through 177 Processing sheet with id=AE5, first strand: chain 'K' and resid 259 through 260 removed outlier: 3.744A pdb=" N GLY K 451 " --> pdb=" O LEU K 260 " (cutoff:3.500A) removed outlier: 7.515A pdb=" N GLY K 451 " --> pdb=" O THR K 290 " (cutoff:3.500A) removed outlier: 11.205A pdb=" N THR K 290 " --> pdb=" O GLY K 451 " (cutoff:3.500A) removed outlier: 12.030A pdb=" N LEU K 453 " --> pdb=" O LEU K 288 " (cutoff:3.500A) removed outlier: 11.892A pdb=" N LEU K 288 " --> pdb=" O LEU K 453 " (cutoff:3.500A) removed outlier: 10.969A pdb=" N THR K 455 " --> pdb=" O VAL K 286 " (cutoff:3.500A) removed outlier: 11.192A pdb=" N VAL K 286 " --> pdb=" O THR K 455 " (cutoff:3.500A) removed outlier: 7.531A pdb=" N GLU K 293 " --> pdb=" O SER K 334 " (cutoff:3.500A) removed outlier: 4.788A pdb=" N SER K 334 " --> pdb=" O GLU K 293 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N VAL K 295 " --> pdb=" O ASN K 332 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N ASN K 332 " --> pdb=" O VAL K 295 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N THR K 297 " --> pdb=" O HIS K 330 " (cutoff:3.500A) removed outlier: 4.212A pdb=" N HIS K 330 " --> pdb=" O THR K 297 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N LYS K 421 " --> pdb=" O PHE K 382 " (cutoff:3.500A) removed outlier: 4.459A pdb=" N PHE K 382 " --> pdb=" O LYS K 421 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'K' and resid 271 through 273 removed outlier: 11.192A pdb=" N VAL K 286 " --> pdb=" O THR K 455 " (cutoff:3.500A) removed outlier: 10.969A pdb=" N THR K 455 " --> pdb=" O VAL K 286 " (cutoff:3.500A) removed outlier: 11.892A pdb=" N LEU K 288 " --> pdb=" O LEU K 453 " (cutoff:3.500A) removed outlier: 12.030A pdb=" N LEU K 453 " --> pdb=" O LEU K 288 " (cutoff:3.500A) removed outlier: 11.205A pdb=" N THR K 290 " --> pdb=" O GLY K 451 " (cutoff:3.500A) removed outlier: 7.515A pdb=" N GLY K 451 " --> pdb=" O THR K 290 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'K' and resid 302 through 308 removed outlier: 5.938A pdb=" N THR K 303 " --> pdb=" O GLY K 321 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'K' and resid 359 through 360 Processing sheet with id=AE9, first strand: chain 'K' and resid 423 through 424 Processing sheet with id=AF1, first strand: chain 'M' and resid 3 through 6 Processing sheet with id=AF2, first strand: chain 'M' and resid 10 through 12 removed outlier: 5.140A pdb=" N TYR M 33 " --> pdb=" O GLY M 99 " (cutoff:3.500A) removed outlier: 6.744A pdb=" N ILE M 34 " --> pdb=" O TRP M 50 " (cutoff:3.500A) removed outlier: 4.517A pdb=" N TRP M 50 " --> pdb=" O ILE M 34 " (cutoff:3.500A) removed outlier: 6.531A pdb=" N TRP M 36 " --> pdb=" O MET M 48 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'M' and resid 10 through 12 removed outlier: 4.106A pdb=" N HIS M 116 " --> pdb=" O THR M 98 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'M' and resid 18 through 20 Processing sheet with id=AF5, first strand: chain 'N' and resid 9 through 12 removed outlier: 6.697A pdb=" N TRP N 37 " --> pdb=" O MET N 49 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N MET N 49 " --> pdb=" O TRP N 37 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'N' and resid 9 through 12 Processing sheet with id=AF7, first strand: chain 'N' and resid 18 through 23 Processing sheet with id=AF8, first strand: chain 'N' and resid 18 through 23 693 hydrogen bonds defined for protein. 1788 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: 7.17 Time building geometry restraints manager: 6.13 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.35: 6333 1.35 - 1.47: 5310 1.47 - 1.60: 8544 1.60 - 1.73: 4 1.73 - 1.86: 191 Bond restraints: 20382 Sorted by residual: bond pdb=" C1 MAN T 10 " pdb=" C2 MAN T 10 " ideal model delta sigma weight residual 1.526 1.611 -0.085 2.00e-02 2.50e+03 1.81e+01 bond pdb=" C1 MAN Y 8 " pdb=" C2 MAN Y 8 " ideal model delta sigma weight residual 1.526 1.611 -0.085 2.00e-02 2.50e+03 1.81e+01 bond pdb=" C1 MAN O 8 " pdb=" C2 MAN O 8 " ideal model delta sigma weight residual 1.526 1.607 -0.081 2.00e-02 2.50e+03 1.65e+01 bond pdb=" C2 MAN Y 8 " pdb=" O2 MAN Y 8 " ideal model delta sigma weight residual 1.407 1.480 -0.073 2.00e-02 2.50e+03 1.34e+01 bond pdb=" C2 MAN T 10 " pdb=" O2 MAN T 10 " ideal model delta sigma weight residual 1.407 1.480 -0.073 2.00e-02 2.50e+03 1.33e+01 ... (remaining 20377 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.85: 27310 3.85 - 7.70: 370 7.70 - 11.55: 35 11.55 - 15.40: 2 15.40 - 19.25: 1 Bond angle restraints: 27718 Sorted by residual: angle pdb=" C LEU F 122 " pdb=" N THR F 123 " pdb=" CA THR F 123 " ideal model delta sigma weight residual 121.80 141.05 -19.25 2.44e+00 1.68e-01 6.22e+01 angle pdb=" N ASN G 651 " pdb=" CA ASN G 651 " pdb=" C ASN G 651 " ideal model delta sigma weight residual 112.57 103.79 8.78 1.13e+00 7.83e-01 6.03e+01 angle pdb=" C LEU K 122 " pdb=" N THR K 123 " pdb=" CA THR K 123 " ideal model delta sigma weight residual 121.80 137.14 -15.34 2.44e+00 1.68e-01 3.95e+01 angle pdb=" C LEU A 122 " pdb=" N THR A 123 " pdb=" CA THR A 123 " ideal model delta sigma weight residual 121.80 137.03 -15.23 2.44e+00 1.68e-01 3.90e+01 angle pdb=" C MET B 535 " pdb=" N THR B 536 " pdb=" CA THR B 536 " ideal model delta sigma weight residual 122.08 130.65 -8.57 1.47e+00 4.63e-01 3.40e+01 ... (remaining 27713 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.89: 12104 22.89 - 45.78: 712 45.78 - 68.67: 95 68.67 - 91.56: 69 91.56 - 114.45: 28 Dihedral angle restraints: 13008 sinusoidal: 5911 harmonic: 7097 Sorted by residual: dihedral pdb=" CB CYS F 201 " pdb=" SG CYS F 201 " pdb=" SG CYS F 433 " pdb=" CB CYS F 433 " ideal model delta sinusoidal sigma weight residual -86.00 1.14 -87.14 1 1.00e+01 1.00e-02 9.12e+01 dihedral pdb=" CA GLY A 431 " pdb=" C GLY A 431 " pdb=" N ARG A 432 " pdb=" CA ARG A 432 " ideal model delta harmonic sigma weight residual -180.00 -144.10 -35.90 0 5.00e+00 4.00e-02 5.16e+01 dihedral pdb=" CA CYS A 433 " pdb=" C CYS A 433 " pdb=" N MET A 434 " pdb=" CA MET A 434 " ideal model delta harmonic sigma weight residual 180.00 147.13 32.87 0 5.00e+00 4.00e-02 4.32e+01 ... (remaining 13005 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.189: 3258 0.189 - 0.379: 37 0.379 - 0.568: 0 0.568 - 0.757: 0 0.757 - 0.946: 1 Chirality restraints: 3296 Sorted by residual: chirality pdb=" C1 NAG A 601 " pdb=" ND2 ASN A 138 " pdb=" C2 NAG A 601 " pdb=" O5 NAG A 601 " both_signs ideal model delta sigma weight residual False -2.40 -1.45 -0.95 2.00e-01 2.50e+01 2.24e+01 chirality pdb=" C4 NAG K 601 " pdb=" C3 NAG K 601 " pdb=" C5 NAG K 601 " pdb=" O4 NAG K 601 " both_signs ideal model delta sigma weight residual False -2.53 -2.21 -0.32 2.00e-01 2.50e+01 2.51e+00 chirality pdb=" CA THR F 123 " pdb=" N THR F 123 " pdb=" C THR F 123 " pdb=" CB THR F 123 " both_signs ideal model delta sigma weight residual False 2.53 2.22 0.31 2.00e-01 2.50e+01 2.38e+00 ... (remaining 3293 not shown) Planarity restraints: 3468 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LYS K 178 " -0.049 5.00e-02 4.00e+02 7.33e-02 8.59e+00 pdb=" N PRO K 179 " 0.127 5.00e-02 4.00e+02 pdb=" CA PRO K 179 " -0.037 5.00e-02 4.00e+02 pdb=" CD PRO K 179 " -0.041 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ILE K 424 " 0.015 2.00e-02 2.50e+03 2.93e-02 8.59e+00 pdb=" C ILE K 424 " -0.051 2.00e-02 2.50e+03 pdb=" O ILE K 424 " 0.019 2.00e-02 2.50e+03 pdb=" N ASN K 425 " 0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LYS F 178 " -0.048 5.00e-02 4.00e+02 7.15e-02 8.18e+00 pdb=" N PRO F 179 " 0.124 5.00e-02 4.00e+02 pdb=" CA PRO F 179 " -0.036 5.00e-02 4.00e+02 pdb=" CD PRO F 179 " -0.040 5.00e-02 4.00e+02 ... (remaining 3465 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 3842 2.78 - 3.31: 17582 3.31 - 3.84: 32335 3.84 - 4.37: 36117 4.37 - 4.90: 64001 Nonbonded interactions: 153877 Sorted by model distance: nonbonded pdb=" OH TYR I 48 " pdb=" O3 MAN T 5 " model vdw 2.247 3.040 nonbonded pdb=" OG1 THR H 87 " pdb=" OD1 ASP H 89 " model vdw 2.263 3.040 nonbonded pdb=" OH TYR N 48 " pdb=" O3 MAN Y 5 " model vdw 2.265 3.040 nonbonded pdb=" OH TYR D 48 " pdb=" O3 MAN O 5 " model vdw 2.268 3.040 nonbonded pdb=" OG1 THR M 87 " pdb=" OD1 ASP M 89 " model vdw 2.269 3.040 ... (remaining 153872 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = (chain 'F' and (resid 32 through 321 or resid 322 through 505 or resid 601)) selection = (chain 'K' and (resid 32 through 321 or resid 322 through 505 or resid 601)) } ncs_group { reference = chain 'B' selection = chain 'G' selection = chain 'L' } ncs_group { reference = chain 'C' selection = chain 'H' selection = chain 'M' } ncs_group { reference = chain 'D' selection = chain 'I' selection = chain 'N' } ncs_group { reference = chain 'J' selection = chain 'S' selection = chain 'X' } ncs_group { reference = (chain 'O' and (resid 2 or resid 5 through 11)) selection = (chain 'T' and (resid 1 or resid 4 through 10)) selection = (chain 'Y' and (resid 2 or resid 5 through 11)) } ncs_group { reference = chain 'P' selection = chain 'U' selection = chain 'V' selection = chain 'Z' selection = chain 'a' } 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: 1.750 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.960 Check model and map are aligned: 0.140 Set scattering table: 0.160 Process input model: 44.090 Find NCS groups from input model: 0.980 Set up NCS constraints: 0.120 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.730 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 50.960 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7155 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.085 20490 Z= 0.291 Angle : 1.149 20.246 27997 Z= 0.601 Chirality : 0.064 0.946 3296 Planarity : 0.007 0.082 3453 Dihedral : 16.340 114.450 8333 Min Nonbonded Distance : 2.247 Molprobity Statistics. All-atom Clashscore : 4.44 Ramachandran Plot: Outliers : 0.41 % Allowed : 7.42 % Favored : 92.17 % Rotamer: Outliers : 0.00 % Allowed : 0.65 % Favored : 99.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.30 % 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: -2.28 (0.15), residues: 2439 helix: -2.62 (0.20), residues: 400 sheet: -0.19 (0.20), residues: 665 loop : -1.89 (0.14), residues: 1374 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.003 TRP F 479 HIS 0.016 0.002 HIS K 249 PHE 0.016 0.002 PHE K 391 TYR 0.020 0.002 TYR K 399 ARG 0.017 0.001 ARG D 81 Details of bonding type rmsd link_NAG-ASN : bond 0.00713 ( 15) link_NAG-ASN : angle 5.23436 ( 45) link_ALPHA1-6 : bond 0.00274 ( 6) link_ALPHA1-6 : angle 2.17913 ( 18) link_BETA1-4 : bond 0.01239 ( 19) link_BETA1-4 : angle 3.02705 ( 57) link_ALPHA1-2 : bond 0.00794 ( 14) link_ALPHA1-2 : angle 2.99921 ( 42) link_ALPHA1-3 : bond 0.00669 ( 9) link_ALPHA1-3 : angle 2.23515 ( 27) hydrogen bonds : bond 0.15245 ( 628) hydrogen bonds : angle 7.44171 ( 1788) SS BOND : bond 0.00607 ( 45) SS BOND : angle 1.69274 ( 90) covalent geometry : bond 0.00589 (20382) covalent geometry : angle 1.11271 (27718) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4878 Ramachandran restraints generated. 2439 Oldfield, 0 Emsley, 2439 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4878 Ramachandran restraints generated. 2439 Oldfield, 0 Emsley, 2439 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 2138 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 126 time to evaluate : 2.103 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 104 MET cc_start: 0.8404 (ttt) cc_final: 0.8162 (ttt) REVERT: A 434 MET cc_start: 0.7578 (ttm) cc_final: 0.7369 (ttm) REVERT: B 571 TRP cc_start: 0.3757 (t60) cc_final: 0.3536 (t60) REVERT: D 84 ASP cc_start: 0.4123 (m-30) cc_final: 0.3884 (m-30) REVERT: F 434 MET cc_start: 0.7943 (ttm) cc_final: 0.7737 (ttm) REVERT: F 475 MET cc_start: 0.7929 (pmm) cc_final: 0.7618 (pmm) REVERT: G 603 ILE cc_start: 0.6787 (mm) cc_final: 0.6586 (mm) REVERT: G 626 MET cc_start: 0.5267 (mmm) cc_final: 0.4970 (tpt) REVERT: L 535 MET cc_start: 0.6318 (mtm) cc_final: 0.6096 (mpp) outliers start: 0 outliers final: 0 residues processed: 126 average time/residue: 0.2834 time to fit residues: 58.2486 Evaluate side-chains 104 residues out of total 2138 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 104 time to evaluate : 2.073 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: chunk 205 optimal weight: 8.9990 chunk 184 optimal weight: 3.9990 chunk 102 optimal weight: 2.9990 chunk 62 optimal weight: 6.9990 chunk 124 optimal weight: 0.8980 chunk 98 optimal weight: 1.9990 chunk 190 optimal weight: 10.0000 chunk 73 optimal weight: 10.0000 chunk 115 optimal weight: 3.9990 chunk 141 optimal weight: 9.9990 chunk 220 optimal weight: 10.0000 overall best weight: 2.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 249 HIS A 287 HIS B 540 GLN F 249 HIS F 461 ASN G 540 GLN K 249 HIS L 540 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3661 r_free = 0.3661 target = 0.075473 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.065114 restraints weight = 92097.761| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3454 r_free = 0.3454 target = 0.066561 restraints weight = 54954.019| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3478 r_free = 0.3478 target = 0.067533 restraints weight = 39177.612| |-----------------------------------------------------------------------------| r_work (final): 0.3475 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7207 moved from start: 0.1052 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 20490 Z= 0.143 Angle : 0.701 17.125 27997 Z= 0.348 Chirality : 0.047 0.712 3296 Planarity : 0.005 0.064 3453 Dihedral : 11.778 90.828 3907 Min Nonbonded Distance : 2.414 Molprobity Statistics. All-atom Clashscore : 6.04 Ramachandran Plot: Outliers : 0.37 % Allowed : 6.81 % Favored : 92.82 % Rotamer: Outliers : 0.51 % Allowed : 6.45 % Favored : 93.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.81 (0.16), residues: 2439 helix: -1.46 (0.24), residues: 393 sheet: -0.23 (0.20), residues: 685 loop : -1.66 (0.15), residues: 1361 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP B 628 HIS 0.011 0.001 HIS K 249 PHE 0.011 0.001 PHE C 32 TYR 0.017 0.001 TYR N 48 ARG 0.007 0.000 ARG A 432 Details of bonding type rmsd link_NAG-ASN : bond 0.00479 ( 15) link_NAG-ASN : angle 3.77607 ( 45) link_ALPHA1-6 : bond 0.00344 ( 6) link_ALPHA1-6 : angle 1.69617 ( 18) link_BETA1-4 : bond 0.00551 ( 19) link_BETA1-4 : angle 2.35678 ( 57) link_ALPHA1-2 : bond 0.00714 ( 14) link_ALPHA1-2 : angle 2.50077 ( 42) link_ALPHA1-3 : bond 0.00808 ( 9) link_ALPHA1-3 : angle 1.98482 ( 27) hydrogen bonds : bond 0.03569 ( 628) hydrogen bonds : angle 5.85268 ( 1788) SS BOND : bond 0.00466 ( 45) SS BOND : angle 1.81371 ( 90) covalent geometry : bond 0.00313 (20382) covalent geometry : angle 0.66067 (27718) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4878 Ramachandran restraints generated. 2439 Oldfield, 0 Emsley, 2439 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4878 Ramachandran restraints generated. 2439 Oldfield, 0 Emsley, 2439 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 2138 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 118 time to evaluate : 2.059 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 100 MET cc_start: 0.7049 (mtp) cc_final: 0.6849 (mtp) REVERT: B 530 MET cc_start: 0.5559 (mmt) cc_final: 0.5283 (mmt) REVERT: D 84 ASP cc_start: 0.4233 (m-30) cc_final: 0.3953 (m-30) outliers start: 11 outliers final: 2 residues processed: 124 average time/residue: 0.3126 time to fit residues: 63.4230 Evaluate side-chains 98 residues out of total 2138 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 96 time to evaluate : 2.180 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 461 ASN Chi-restraints excluded: chain L residue 530 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: chunk 87 optimal weight: 10.0000 chunk 57 optimal weight: 5.9990 chunk 201 optimal weight: 0.0970 chunk 156 optimal weight: 5.9990 chunk 157 optimal weight: 7.9990 chunk 19 optimal weight: 20.0000 chunk 193 optimal weight: 10.0000 chunk 158 optimal weight: 6.9990 chunk 146 optimal weight: 10.0000 chunk 12 optimal weight: 0.9980 chunk 170 optimal weight: 1.9990 overall best weight: 3.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 249 HIS F 249 HIS H 116 HIS K 249 HIS K 287 HIS M 116 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3646 r_free = 0.3646 target = 0.074838 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.064503 restraints weight = 92121.041| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.065930 restraints weight = 55573.502| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3462 r_free = 0.3462 target = 0.066864 restraints weight = 39840.324| |-----------------------------------------------------------------------------| r_work (final): 0.3459 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7238 moved from start: 0.1456 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 20490 Z= 0.144 Angle : 0.669 16.327 27997 Z= 0.332 Chirality : 0.046 0.623 3296 Planarity : 0.004 0.057 3453 Dihedral : 10.745 88.377 3907 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 6.19 Ramachandran Plot: Outliers : 0.29 % Allowed : 7.26 % Favored : 92.46 % Rotamer: Outliers : 1.31 % Allowed : 9.87 % Favored : 88.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.62 (0.16), residues: 2439 helix: -0.89 (0.26), residues: 393 sheet: -0.23 (0.20), residues: 674 loop : -1.60 (0.15), residues: 1372 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 571 HIS 0.012 0.001 HIS F 249 PHE 0.012 0.002 PHE C 32 TYR 0.021 0.001 TYR F 61 ARG 0.006 0.000 ARG B 617 Details of bonding type rmsd link_NAG-ASN : bond 0.00512 ( 15) link_NAG-ASN : angle 3.54648 ( 45) link_ALPHA1-6 : bond 0.00364 ( 6) link_ALPHA1-6 : angle 1.85521 ( 18) link_BETA1-4 : bond 0.00536 ( 19) link_BETA1-4 : angle 2.07517 ( 57) link_ALPHA1-2 : bond 0.00827 ( 14) link_ALPHA1-2 : angle 2.57433 ( 42) link_ALPHA1-3 : bond 0.00965 ( 9) link_ALPHA1-3 : angle 1.58330 ( 27) hydrogen bonds : bond 0.03406 ( 628) hydrogen bonds : angle 5.51329 ( 1788) SS BOND : bond 0.00560 ( 45) SS BOND : angle 1.44203 ( 90) covalent geometry : bond 0.00314 (20382) covalent geometry : angle 0.63367 (27718) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4878 Ramachandran restraints generated. 2439 Oldfield, 0 Emsley, 2439 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4878 Ramachandran restraints generated. 2439 Oldfield, 0 Emsley, 2439 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 2138 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 105 time to evaluate : 2.380 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 100 MET cc_start: 0.7048 (mtp) cc_final: 0.6820 (mtp) REVERT: D 10 VAL cc_start: 0.4852 (p) cc_final: 0.4393 (m) REVERT: D 84 ASP cc_start: 0.4304 (m-30) cc_final: 0.4007 (m-30) REVERT: G 520 LEU cc_start: 0.6174 (OUTLIER) cc_final: 0.5747 (tp) REVERT: N 10 VAL cc_start: 0.5549 (p) cc_final: 0.5194 (m) outliers start: 28 outliers final: 8 residues processed: 123 average time/residue: 0.3289 time to fit residues: 66.9728 Evaluate side-chains 105 residues out of total 2138 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 96 time to evaluate : 2.330 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 284 ILE Chi-restraints excluded: chain B residue 584 GLU Chi-restraints excluded: chain F residue 434 MET Chi-restraints excluded: chain G residue 520 LEU Chi-restraints excluded: chain K residue 68 VAL Chi-restraints excluded: chain K residue 284 ILE Chi-restraints excluded: chain L residue 530 MET Chi-restraints excluded: chain M residue 18 VAL Chi-restraints excluded: chain M residue 48 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: chunk 63 optimal weight: 9.9990 chunk 67 optimal weight: 7.9990 chunk 226 optimal weight: 5.9990 chunk 187 optimal weight: 3.9990 chunk 151 optimal weight: 20.0000 chunk 81 optimal weight: 10.0000 chunk 203 optimal weight: 10.0000 chunk 89 optimal weight: 7.9990 chunk 51 optimal weight: 7.9990 chunk 167 optimal weight: 8.9990 chunk 45 optimal weight: 6.9990 overall best weight: 6.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 249 HIS A 422 GLN ** C 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 113 ASN D 32 HIS F 249 HIS F 287 HIS F 422 GLN ** H 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 32 HIS K 249 HIS K 422 GLN ** M 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3593 r_free = 0.3593 target = 0.072588 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.062243 restraints weight = 94018.442| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3380 r_free = 0.3380 target = 0.063595 restraints weight = 57338.599| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.064506 restraints weight = 41611.773| |-----------------------------------------------------------------------------| r_work (final): 0.3401 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7352 moved from start: 0.2191 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.057 20490 Z= 0.250 Angle : 0.799 16.091 27997 Z= 0.397 Chirality : 0.051 0.689 3296 Planarity : 0.005 0.065 3453 Dihedral : 10.933 89.029 3907 Min Nonbonded Distance : 2.408 Molprobity Statistics. All-atom Clashscore : 8.69 Ramachandran Plot: Outliers : 0.29 % Allowed : 9.64 % Favored : 90.08 % Rotamer: Outliers : 2.48 % Allowed : 11.69 % Favored : 85.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.92 (0.16), residues: 2439 helix: -1.00 (0.26), residues: 393 sheet: -0.40 (0.20), residues: 662 loop : -1.86 (0.15), residues: 1384 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP B 571 HIS 0.011 0.002 HIS F 249 PHE 0.020 0.003 PHE B 522 TYR 0.017 0.002 TYR F 361 ARG 0.005 0.001 ARG F 432 Details of bonding type rmsd link_NAG-ASN : bond 0.00594 ( 15) link_NAG-ASN : angle 3.76981 ( 45) link_ALPHA1-6 : bond 0.00355 ( 6) link_ALPHA1-6 : angle 1.97417 ( 18) link_BETA1-4 : bond 0.00552 ( 19) link_BETA1-4 : angle 2.12371 ( 57) link_ALPHA1-2 : bond 0.00722 ( 14) link_ALPHA1-2 : angle 2.78323 ( 42) link_ALPHA1-3 : bond 0.00812 ( 9) link_ALPHA1-3 : angle 1.80792 ( 27) hydrogen bonds : bond 0.03915 ( 628) hydrogen bonds : angle 5.89987 ( 1788) SS BOND : bond 0.00444 ( 45) SS BOND : angle 1.72274 ( 90) covalent geometry : bond 0.00566 (20382) covalent geometry : angle 0.76527 (27718) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4878 Ramachandran restraints generated. 2439 Oldfield, 0 Emsley, 2439 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4878 Ramachandran restraints generated. 2439 Oldfield, 0 Emsley, 2439 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 2138 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 105 time to evaluate : 2.344 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 10 VAL cc_start: 0.5067 (p) cc_final: 0.4819 (m) REVERT: F 125 LEU cc_start: 0.9024 (OUTLIER) cc_final: 0.8668 (tt) REVERT: G 520 LEU cc_start: 0.6356 (OUTLIER) cc_final: 0.5895 (tp) REVERT: I 10 VAL cc_start: 0.5341 (p) cc_final: 0.4998 (m) REVERT: N 10 VAL cc_start: 0.5478 (p) cc_final: 0.5196 (m) outliers start: 53 outliers final: 26 residues processed: 145 average time/residue: 0.2686 time to fit residues: 65.7900 Evaluate side-chains 123 residues out of total 2138 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 95 time to evaluate : 2.166 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 VAL Chi-restraints excluded: chain A residue 75 VAL Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 136 VAL Chi-restraints excluded: chain A residue 249 HIS Chi-restraints excluded: chain A residue 284 ILE Chi-restraints excluded: chain B residue 584 GLU Chi-restraints excluded: chain B residue 661 LEU Chi-restraints excluded: chain F residue 68 VAL Chi-restraints excluded: chain F residue 112 TRP Chi-restraints excluded: chain F residue 125 LEU Chi-restraints excluded: chain F residue 136 VAL Chi-restraints excluded: chain F residue 202 THR Chi-restraints excluded: chain F residue 249 HIS Chi-restraints excluded: chain F residue 284 ILE Chi-restraints excluded: chain G residue 520 LEU Chi-restraints excluded: chain K residue 52 LEU Chi-restraints excluded: chain K residue 68 VAL Chi-restraints excluded: chain K residue 75 VAL Chi-restraints excluded: chain K residue 136 VAL Chi-restraints excluded: chain K residue 284 ILE Chi-restraints excluded: chain K residue 399 TYR Chi-restraints excluded: chain K residue 439 ILE Chi-restraints excluded: chain L residue 530 MET Chi-restraints excluded: chain L residue 627 THR Chi-restraints excluded: chain M residue 18 VAL Chi-restraints excluded: chain M residue 58 THR Chi-restraints excluded: chain N residue 108 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: chunk 144 optimal weight: 7.9990 chunk 92 optimal weight: 4.9990 chunk 105 optimal weight: 7.9990 chunk 196 optimal weight: 1.9990 chunk 129 optimal weight: 8.9990 chunk 117 optimal weight: 0.0010 chunk 47 optimal weight: 6.9990 chunk 227 optimal weight: 0.6980 chunk 200 optimal weight: 6.9990 chunk 62 optimal weight: 10.0000 chunk 18 optimal weight: 10.0000 overall best weight: 2.9392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 249 HIS H 119 GLN K 249 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3621 r_free = 0.3621 target = 0.073755 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.063320 restraints weight = 93013.269| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.064723 restraints weight = 55980.985| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.065669 restraints weight = 40301.665| |-----------------------------------------------------------------------------| r_work (final): 0.3431 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7299 moved from start: 0.2179 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.072 20490 Z= 0.143 Angle : 0.681 15.710 27997 Z= 0.337 Chirality : 0.046 0.580 3296 Planarity : 0.004 0.056 3453 Dihedral : 10.115 83.644 3907 Min Nonbonded Distance : 2.424 Molprobity Statistics. All-atom Clashscore : 7.14 Ramachandran Plot: Outliers : 0.29 % Allowed : 7.50 % Favored : 92.21 % Rotamer: Outliers : 2.57 % Allowed : 13.19 % Favored : 84.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.70 (0.16), residues: 2439 helix: -0.70 (0.26), residues: 393 sheet: -0.31 (0.20), residues: 705 loop : -1.74 (0.16), residues: 1341 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP B 571 HIS 0.020 0.002 HIS A 249 PHE 0.012 0.002 PHE F 376 TYR 0.016 0.001 TYR F 61 ARG 0.003 0.000 ARG H 38 Details of bonding type rmsd link_NAG-ASN : bond 0.00425 ( 15) link_NAG-ASN : angle 3.36780 ( 45) link_ALPHA1-6 : bond 0.00353 ( 6) link_ALPHA1-6 : angle 1.86284 ( 18) link_BETA1-4 : bond 0.00455 ( 19) link_BETA1-4 : angle 1.90545 ( 57) link_ALPHA1-2 : bond 0.00837 ( 14) link_ALPHA1-2 : angle 2.61349 ( 42) link_ALPHA1-3 : bond 0.00975 ( 9) link_ALPHA1-3 : angle 1.63329 ( 27) hydrogen bonds : bond 0.03268 ( 628) hydrogen bonds : angle 5.48497 ( 1788) SS BOND : bond 0.00450 ( 45) SS BOND : angle 1.87418 ( 90) covalent geometry : bond 0.00314 (20382) covalent geometry : angle 0.64505 (27718) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4878 Ramachandran restraints generated. 2439 Oldfield, 0 Emsley, 2439 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4878 Ramachandran restraints generated. 2439 Oldfield, 0 Emsley, 2439 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 2138 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 100 time to evaluate : 2.120 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 423 ILE cc_start: 0.8529 (mm) cc_final: 0.8325 (mm) REVERT: D 10 VAL cc_start: 0.5108 (p) cc_final: 0.4809 (m) REVERT: F 125 LEU cc_start: 0.8975 (OUTLIER) cc_final: 0.8515 (tt) REVERT: G 520 LEU cc_start: 0.6327 (OUTLIER) cc_final: 0.5908 (tp) REVERT: I 10 VAL cc_start: 0.5444 (p) cc_final: 0.5064 (m) REVERT: K 125 LEU cc_start: 0.8995 (OUTLIER) cc_final: 0.8728 (tt) REVERT: N 10 VAL cc_start: 0.5362 (p) cc_final: 0.5140 (m) outliers start: 55 outliers final: 25 residues processed: 149 average time/residue: 0.3310 time to fit residues: 84.3439 Evaluate side-chains 121 residues out of total 2138 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 93 time to evaluate : 2.346 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 202 THR Chi-restraints excluded: chain A residue 284 ILE Chi-restraints excluded: chain A residue 455 THR Chi-restraints excluded: chain A residue 489 VAL Chi-restraints excluded: chain B residue 584 GLU Chi-restraints excluded: chain C residue 4 LEU Chi-restraints excluded: chain D residue 108 THR Chi-restraints excluded: chain F residue 68 VAL Chi-restraints excluded: chain F residue 125 LEU Chi-restraints excluded: chain F residue 136 VAL Chi-restraints excluded: chain F residue 284 ILE Chi-restraints excluded: chain F residue 439 ILE Chi-restraints excluded: chain G residue 520 LEU Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain K residue 36 VAL Chi-restraints excluded: chain K residue 52 LEU Chi-restraints excluded: chain K residue 68 VAL Chi-restraints excluded: chain K residue 125 LEU Chi-restraints excluded: chain K residue 284 ILE Chi-restraints excluded: chain K residue 399 TYR Chi-restraints excluded: chain K residue 439 ILE Chi-restraints excluded: chain K residue 489 VAL Chi-restraints excluded: chain L residue 584 GLU Chi-restraints excluded: chain L residue 622 ILE Chi-restraints excluded: chain M residue 18 VAL Chi-restraints excluded: chain M residue 58 THR Chi-restraints excluded: chain M residue 69 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: chunk 2 optimal weight: 9.9990 chunk 84 optimal weight: 10.0000 chunk 143 optimal weight: 20.0000 chunk 94 optimal weight: 9.9990 chunk 55 optimal weight: 10.0000 chunk 121 optimal weight: 0.9980 chunk 132 optimal weight: 9.9990 chunk 46 optimal weight: 9.9990 chunk 231 optimal weight: 5.9990 chunk 161 optimal weight: 5.9990 chunk 176 optimal weight: 7.9990 overall best weight: 6.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 652 GLN K 105 HIS K 249 HIS K 258 GLN ** M 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3586 r_free = 0.3586 target = 0.072310 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3341 r_free = 0.3341 target = 0.062043 restraints weight = 94074.729| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3374 r_free = 0.3374 target = 0.063369 restraints weight = 57979.995| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.064250 restraints weight = 42272.218| |-----------------------------------------------------------------------------| r_work (final): 0.3394 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7367 moved from start: 0.2522 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.062 20490 Z= 0.237 Angle : 0.777 15.963 27997 Z= 0.383 Chirality : 0.050 0.647 3296 Planarity : 0.005 0.065 3453 Dihedral : 10.529 85.905 3907 Min Nonbonded Distance : 2.392 Molprobity Statistics. All-atom Clashscore : 8.77 Ramachandran Plot: Outliers : 0.29 % Allowed : 10.17 % Favored : 89.54 % Rotamer: Outliers : 3.27 % Allowed : 14.08 % Favored : 82.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.98 (0.16), residues: 2439 helix: -0.81 (0.26), residues: 393 sheet: -0.55 (0.20), residues: 664 loop : -1.90 (0.15), residues: 1382 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP B 628 HIS 0.011 0.002 HIS K 249 PHE 0.021 0.002 PHE B 522 TYR 0.014 0.002 TYR F 484 ARG 0.004 0.001 ARG L 585 Details of bonding type rmsd link_NAG-ASN : bond 0.00535 ( 15) link_NAG-ASN : angle 3.62472 ( 45) link_ALPHA1-6 : bond 0.00268 ( 6) link_ALPHA1-6 : angle 2.04829 ( 18) link_BETA1-4 : bond 0.00547 ( 19) link_BETA1-4 : angle 2.04133 ( 57) link_ALPHA1-2 : bond 0.00726 ( 14) link_ALPHA1-2 : angle 2.70639 ( 42) link_ALPHA1-3 : bond 0.00804 ( 9) link_ALPHA1-3 : angle 1.82710 ( 27) hydrogen bonds : bond 0.03747 ( 628) hydrogen bonds : angle 5.75106 ( 1788) SS BOND : bond 0.00506 ( 45) SS BOND : angle 2.21674 ( 90) covalent geometry : bond 0.00542 (20382) covalent geometry : angle 0.73978 (27718) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4878 Ramachandran restraints generated. 2439 Oldfield, 0 Emsley, 2439 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4878 Ramachandran restraints generated. 2439 Oldfield, 0 Emsley, 2439 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 2138 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 99 time to evaluate : 2.120 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 423 ILE cc_start: 0.8582 (mm) cc_final: 0.8381 (mm) REVERT: D 10 VAL cc_start: 0.4968 (p) cc_final: 0.4735 (m) REVERT: F 125 LEU cc_start: 0.9044 (OUTLIER) cc_final: 0.8486 (tt) REVERT: G 520 LEU cc_start: 0.6313 (OUTLIER) cc_final: 0.5908 (tp) REVERT: I 10 VAL cc_start: 0.5600 (p) cc_final: 0.5286 (m) REVERT: K 125 LEU cc_start: 0.9066 (OUTLIER) cc_final: 0.8703 (tt) outliers start: 70 outliers final: 45 residues processed: 158 average time/residue: 0.2897 time to fit residues: 75.6930 Evaluate side-chains 146 residues out of total 2138 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 98 time to evaluate : 2.371 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 68 VAL Chi-restraints excluded: chain A residue 75 VAL Chi-restraints excluded: chain A residue 109 ILE Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 136 VAL Chi-restraints excluded: chain A residue 161 THR Chi-restraints excluded: chain A residue 202 THR Chi-restraints excluded: chain A residue 284 ILE Chi-restraints excluded: chain A residue 455 THR Chi-restraints excluded: chain A residue 489 VAL Chi-restraints excluded: chain B residue 529 THR Chi-restraints excluded: chain B residue 584 GLU Chi-restraints excluded: chain D residue 108 THR Chi-restraints excluded: chain F residue 68 VAL Chi-restraints excluded: chain F residue 125 LEU Chi-restraints excluded: chain F residue 136 VAL Chi-restraints excluded: chain F residue 202 THR Chi-restraints excluded: chain F residue 284 ILE Chi-restraints excluded: chain F residue 439 ILE Chi-restraints excluded: chain F residue 455 THR Chi-restraints excluded: chain F residue 461 ASN Chi-restraints excluded: chain G residue 520 LEU Chi-restraints excluded: chain G residue 589 ASP Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain I residue 108 THR Chi-restraints excluded: chain K residue 36 VAL Chi-restraints excluded: chain K residue 42 VAL Chi-restraints excluded: chain K residue 52 LEU Chi-restraints excluded: chain K residue 68 VAL Chi-restraints excluded: chain K residue 75 VAL Chi-restraints excluded: chain K residue 120 VAL Chi-restraints excluded: chain K residue 123 THR Chi-restraints excluded: chain K residue 125 LEU Chi-restraints excluded: chain K residue 249 HIS Chi-restraints excluded: chain K residue 284 ILE Chi-restraints excluded: chain K residue 399 TYR Chi-restraints excluded: chain K residue 439 ILE Chi-restraints excluded: chain K residue 455 THR Chi-restraints excluded: chain K residue 489 VAL Chi-restraints excluded: chain L residue 530 MET Chi-restraints excluded: chain L residue 622 ILE Chi-restraints excluded: chain L residue 661 LEU Chi-restraints excluded: chain M residue 18 VAL Chi-restraints excluded: chain M residue 58 THR Chi-restraints excluded: chain M residue 69 THR Chi-restraints excluded: chain N residue 105 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: chunk 142 optimal weight: 9.9990 chunk 82 optimal weight: 8.9990 chunk 44 optimal weight: 5.9990 chunk 121 optimal weight: 5.9990 chunk 151 optimal weight: 20.0000 chunk 231 optimal weight: 0.0770 chunk 195 optimal weight: 3.9990 chunk 71 optimal weight: 0.0070 chunk 114 optimal weight: 6.9990 chunk 223 optimal weight: 9.9990 chunk 79 optimal weight: 6.9990 overall best weight: 3.2162 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 652 GLN ** F 258 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 249 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3608 r_free = 0.3608 target = 0.073192 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.062829 restraints weight = 92985.351| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.064192 restraints weight = 56813.026| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.065100 restraints weight = 41178.953| |-----------------------------------------------------------------------------| r_work (final): 0.3416 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7326 moved from start: 0.2516 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 20490 Z= 0.152 Angle : 0.705 17.658 27997 Z= 0.345 Chirality : 0.051 1.252 3296 Planarity : 0.004 0.058 3453 Dihedral : 10.017 82.325 3907 Min Nonbonded Distance : 2.403 Molprobity Statistics. All-atom Clashscore : 7.80 Ramachandran Plot: Outliers : 0.25 % Allowed : 8.28 % Favored : 91.47 % Rotamer: Outliers : 2.85 % Allowed : 14.55 % Favored : 82.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.84 (0.16), residues: 2439 helix: -0.74 (0.26), residues: 405 sheet: -0.46 (0.20), residues: 689 loop : -1.82 (0.16), residues: 1345 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP B 628 HIS 0.014 0.001 HIS K 249 PHE 0.012 0.002 PHE A 391 TYR 0.015 0.001 TYR F 61 ARG 0.003 0.000 ARG F 446 Details of bonding type rmsd link_NAG-ASN : bond 0.01174 ( 15) link_NAG-ASN : angle 4.03009 ( 45) link_ALPHA1-6 : bond 0.00349 ( 6) link_ALPHA1-6 : angle 1.87637 ( 18) link_BETA1-4 : bond 0.00457 ( 19) link_BETA1-4 : angle 1.94411 ( 57) link_ALPHA1-2 : bond 0.00813 ( 14) link_ALPHA1-2 : angle 2.61673 ( 42) link_ALPHA1-3 : bond 0.00905 ( 9) link_ALPHA1-3 : angle 1.70570 ( 27) hydrogen bonds : bond 0.03339 ( 628) hydrogen bonds : angle 5.58730 ( 1788) SS BOND : bond 0.00529 ( 45) SS BOND : angle 1.98777 ( 90) covalent geometry : bond 0.00335 (20382) covalent geometry : angle 0.66351 (27718) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4878 Ramachandran restraints generated. 2439 Oldfield, 0 Emsley, 2439 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4878 Ramachandran restraints generated. 2439 Oldfield, 0 Emsley, 2439 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 2138 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 102 time to evaluate : 2.267 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 10 VAL cc_start: 0.4915 (p) cc_final: 0.4592 (m) REVERT: F 125 LEU cc_start: 0.8984 (OUTLIER) cc_final: 0.8488 (tt) REVERT: G 520 LEU cc_start: 0.6404 (OUTLIER) cc_final: 0.5864 (tp) REVERT: I 10 VAL cc_start: 0.5460 (p) cc_final: 0.5159 (m) REVERT: K 125 LEU cc_start: 0.9030 (OUTLIER) cc_final: 0.8736 (tt) REVERT: K 340 ASP cc_start: 0.5971 (OUTLIER) cc_final: 0.5735 (t0) outliers start: 61 outliers final: 41 residues processed: 155 average time/residue: 0.2739 time to fit residues: 71.5392 Evaluate side-chains 140 residues out of total 2138 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 95 time to evaluate : 2.230 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 68 VAL Chi-restraints excluded: chain A residue 75 VAL Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 136 VAL Chi-restraints excluded: chain A residue 161 THR Chi-restraints excluded: chain A residue 202 THR Chi-restraints excluded: chain A residue 284 ILE Chi-restraints excluded: chain A residue 489 VAL Chi-restraints excluded: chain B residue 529 THR Chi-restraints excluded: chain B residue 584 GLU Chi-restraints excluded: chain D residue 41 TYR Chi-restraints excluded: chain D residue 108 THR Chi-restraints excluded: chain F residue 68 VAL Chi-restraints excluded: chain F residue 125 LEU Chi-restraints excluded: chain F residue 136 VAL Chi-restraints excluded: chain F residue 284 ILE Chi-restraints excluded: chain F residue 439 ILE Chi-restraints excluded: chain F residue 455 THR Chi-restraints excluded: chain F residue 461 ASN Chi-restraints excluded: chain G residue 520 LEU Chi-restraints excluded: chain G residue 589 ASP Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain I residue 108 THR Chi-restraints excluded: chain K residue 36 VAL Chi-restraints excluded: chain K residue 42 VAL Chi-restraints excluded: chain K residue 52 LEU Chi-restraints excluded: chain K residue 68 VAL Chi-restraints excluded: chain K residue 75 VAL Chi-restraints excluded: chain K residue 120 VAL Chi-restraints excluded: chain K residue 125 LEU Chi-restraints excluded: chain K residue 284 ILE Chi-restraints excluded: chain K residue 340 ASP Chi-restraints excluded: chain K residue 399 TYR Chi-restraints excluded: chain K residue 439 ILE Chi-restraints excluded: chain K residue 455 THR Chi-restraints excluded: chain K residue 489 VAL Chi-restraints excluded: chain L residue 584 GLU Chi-restraints excluded: chain L residue 622 ILE Chi-restraints excluded: chain M residue 18 VAL Chi-restraints excluded: chain M residue 58 THR Chi-restraints excluded: chain M residue 69 THR Chi-restraints excluded: chain N residue 41 TYR Chi-restraints excluded: chain N residue 105 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: chunk 171 optimal weight: 4.9990 chunk 27 optimal weight: 10.0000 chunk 155 optimal weight: 2.9990 chunk 165 optimal weight: 20.0000 chunk 25 optimal weight: 6.9990 chunk 10 optimal weight: 20.0000 chunk 90 optimal weight: 9.9990 chunk 197 optimal weight: 10.0000 chunk 173 optimal weight: 10.0000 chunk 178 optimal weight: 9.9990 chunk 95 optimal weight: 4.9990 overall best weight: 5.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** M 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 40 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 = 0.3584 r_free = 0.3584 target = 0.072284 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.061816 restraints weight = 93933.643| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3367 r_free = 0.3367 target = 0.063180 restraints weight = 56842.220| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.064096 restraints weight = 41014.449| |-----------------------------------------------------------------------------| r_work (final): 0.3387 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7376 moved from start: 0.2783 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.063 20490 Z= 0.230 Angle : 0.779 17.231 27997 Z= 0.381 Chirality : 0.054 1.321 3296 Planarity : 0.005 0.063 3453 Dihedral : 10.411 84.386 3907 Min Nonbonded Distance : 2.389 Molprobity Statistics. All-atom Clashscore : 8.85 Ramachandran Plot: Outliers : 0.25 % Allowed : 10.46 % Favored : 89.30 % Rotamer: Outliers : 2.95 % Allowed : 14.83 % Favored : 82.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.13 % 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: -2.06 (0.16), residues: 2439 helix: -0.81 (0.26), residues: 393 sheet: -0.62 (0.20), residues: 658 loop : -1.96 (0.15), residues: 1388 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP B 628 HIS 0.006 0.001 HIS H 116 PHE 0.020 0.002 PHE L 522 TYR 0.015 0.002 TYR A 484 ARG 0.004 0.001 ARG L 585 Details of bonding type rmsd link_NAG-ASN : bond 0.00711 ( 15) link_NAG-ASN : angle 3.99577 ( 45) link_ALPHA1-6 : bond 0.00241 ( 6) link_ALPHA1-6 : angle 2.07206 ( 18) link_BETA1-4 : bond 0.00551 ( 19) link_BETA1-4 : angle 2.10111 ( 57) link_ALPHA1-2 : bond 0.00741 ( 14) link_ALPHA1-2 : angle 2.65231 ( 42) link_ALPHA1-3 : bond 0.00826 ( 9) link_ALPHA1-3 : angle 1.91469 ( 27) hydrogen bonds : bond 0.03693 ( 628) hydrogen bonds : angle 5.78435 ( 1788) SS BOND : bond 0.00514 ( 45) SS BOND : angle 2.01974 ( 90) covalent geometry : bond 0.00524 (20382) covalent geometry : angle 0.74005 (27718) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4878 Ramachandran restraints generated. 2439 Oldfield, 0 Emsley, 2439 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4878 Ramachandran restraints generated. 2439 Oldfield, 0 Emsley, 2439 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 2138 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 97 time to evaluate : 2.106 Fit side-chains revert: symmetry clash REVERT: D 10 VAL cc_start: 0.4984 (p) cc_final: 0.4694 (m) REVERT: F 125 LEU cc_start: 0.9038 (OUTLIER) cc_final: 0.8469 (tt) REVERT: G 520 LEU cc_start: 0.6490 (OUTLIER) cc_final: 0.5945 (tp) REVERT: G 641 ILE cc_start: 0.8218 (OUTLIER) cc_final: 0.7767 (pt) REVERT: I 10 VAL cc_start: 0.5572 (p) cc_final: 0.5348 (m) REVERT: K 125 LEU cc_start: 0.9067 (OUTLIER) cc_final: 0.8791 (tt) REVERT: K 340 ASP cc_start: 0.6147 (OUTLIER) cc_final: 0.5892 (t0) outliers start: 63 outliers final: 48 residues processed: 149 average time/residue: 0.2543 time to fit residues: 63.9344 Evaluate side-chains 147 residues out of total 2138 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 94 time to evaluate : 2.184 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 68 VAL Chi-restraints excluded: chain A residue 75 VAL Chi-restraints excluded: chain A residue 109 ILE Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 136 VAL Chi-restraints excluded: chain A residue 161 THR Chi-restraints excluded: chain A residue 202 THR Chi-restraints excluded: chain A residue 284 ILE Chi-restraints excluded: chain A residue 455 THR Chi-restraints excluded: chain A residue 489 VAL Chi-restraints excluded: chain B residue 529 THR Chi-restraints excluded: chain B residue 584 GLU Chi-restraints excluded: chain C residue 58 THR Chi-restraints excluded: chain D residue 105 THR Chi-restraints excluded: chain D residue 108 THR Chi-restraints excluded: chain F residue 68 VAL Chi-restraints excluded: chain F residue 125 LEU Chi-restraints excluded: chain F residue 136 VAL Chi-restraints excluded: chain F residue 161 THR Chi-restraints excluded: chain F residue 284 ILE Chi-restraints excluded: chain F residue 439 ILE Chi-restraints excluded: chain F residue 455 THR Chi-restraints excluded: chain F residue 461 ASN Chi-restraints excluded: chain G residue 520 LEU Chi-restraints excluded: chain G residue 589 ASP Chi-restraints excluded: chain G residue 641 ILE Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain I residue 108 THR Chi-restraints excluded: chain K residue 36 VAL Chi-restraints excluded: chain K residue 42 VAL Chi-restraints excluded: chain K residue 52 LEU Chi-restraints excluded: chain K residue 68 VAL Chi-restraints excluded: chain K residue 75 VAL Chi-restraints excluded: chain K residue 120 VAL Chi-restraints excluded: chain K residue 125 LEU Chi-restraints excluded: chain K residue 284 ILE Chi-restraints excluded: chain K residue 340 ASP Chi-restraints excluded: chain K residue 399 TYR Chi-restraints excluded: chain K residue 439 ILE Chi-restraints excluded: chain K residue 455 THR Chi-restraints excluded: chain K residue 489 VAL Chi-restraints excluded: chain L residue 530 MET Chi-restraints excluded: chain L residue 584 GLU Chi-restraints excluded: chain L residue 622 ILE Chi-restraints excluded: chain L residue 661 LEU Chi-restraints excluded: chain M residue 18 VAL Chi-restraints excluded: chain M residue 58 THR Chi-restraints excluded: chain M residue 69 THR Chi-restraints excluded: chain N residue 41 TYR Chi-restraints excluded: chain N residue 105 THR Chi-restraints excluded: chain N residue 108 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: chunk 213 optimal weight: 6.9990 chunk 126 optimal weight: 8.9990 chunk 164 optimal weight: 7.9990 chunk 232 optimal weight: 1.9990 chunk 227 optimal weight: 20.0000 chunk 136 optimal weight: 5.9990 chunk 236 optimal weight: 7.9990 chunk 22 optimal weight: 10.0000 chunk 8 optimal weight: 7.9990 chunk 143 optimal weight: 20.0000 chunk 141 optimal weight: 20.0000 overall best weight: 6.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3581 r_free = 0.3581 target = 0.072181 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3332 r_free = 0.3332 target = 0.061774 restraints weight = 93836.628| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.063110 restraints weight = 57348.134| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.064007 restraints weight = 41703.007| |-----------------------------------------------------------------------------| r_work (final): 0.3385 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7383 moved from start: 0.2879 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.059 20490 Z= 0.233 Angle : 0.792 23.201 27997 Z= 0.385 Chirality : 0.050 0.337 3296 Planarity : 0.005 0.063 3453 Dihedral : 10.729 83.785 3907 Min Nonbonded Distance : 2.393 Molprobity Statistics. All-atom Clashscore : 8.92 Ramachandran Plot: Outliers : 0.29 % Allowed : 10.25 % Favored : 89.46 % Rotamer: Outliers : 2.90 % Allowed : 15.25 % Favored : 81.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: -2.24 (0.16), residues: 2439 helix: -1.08 (0.25), residues: 419 sheet: -0.66 (0.20), residues: 675 loop : -2.11 (0.15), residues: 1345 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP B 628 HIS 0.006 0.001 HIS H 116 PHE 0.017 0.002 PHE L 522 TYR 0.015 0.002 TYR A 484 ARG 0.004 0.001 ARG L 585 Details of bonding type rmsd link_NAG-ASN : bond 0.00466 ( 15) link_NAG-ASN : angle 4.78789 ( 45) link_ALPHA1-6 : bond 0.00256 ( 6) link_ALPHA1-6 : angle 2.10204 ( 18) link_BETA1-4 : bond 0.00546 ( 19) link_BETA1-4 : angle 2.11874 ( 57) link_ALPHA1-2 : bond 0.00801 ( 14) link_ALPHA1-2 : angle 2.61159 ( 42) link_ALPHA1-3 : bond 0.00846 ( 9) link_ALPHA1-3 : angle 1.96260 ( 27) hydrogen bonds : bond 0.03671 ( 628) hydrogen bonds : angle 5.83931 ( 1788) SS BOND : bond 0.00499 ( 45) SS BOND : angle 2.05618 ( 90) covalent geometry : bond 0.00532 (20382) covalent geometry : angle 0.74576 (27718) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4878 Ramachandran restraints generated. 2439 Oldfield, 0 Emsley, 2439 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4878 Ramachandran restraints generated. 2439 Oldfield, 0 Emsley, 2439 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 2138 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 95 time to evaluate : 2.108 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 10 VAL cc_start: 0.4965 (p) cc_final: 0.4697 (m) REVERT: F 125 LEU cc_start: 0.9038 (OUTLIER) cc_final: 0.8414 (tt) REVERT: G 520 LEU cc_start: 0.6521 (OUTLIER) cc_final: 0.5965 (tp) REVERT: G 641 ILE cc_start: 0.8186 (OUTLIER) cc_final: 0.7715 (pt) REVERT: I 84 ASP cc_start: 0.4925 (t0) cc_final: 0.4642 (t0) REVERT: K 125 LEU cc_start: 0.9072 (OUTLIER) cc_final: 0.8734 (tt) REVERT: K 340 ASP cc_start: 0.6158 (OUTLIER) cc_final: 0.5902 (t0) outliers start: 62 outliers final: 50 residues processed: 148 average time/residue: 0.2497 time to fit residues: 62.5972 Evaluate side-chains 148 residues out of total 2138 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 93 time to evaluate : 2.104 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 68 VAL Chi-restraints excluded: chain A residue 75 VAL Chi-restraints excluded: chain A residue 109 ILE Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 136 VAL Chi-restraints excluded: chain A residue 161 THR Chi-restraints excluded: chain A residue 202 THR Chi-restraints excluded: chain A residue 284 ILE Chi-restraints excluded: chain A residue 434 MET Chi-restraints excluded: chain A residue 455 THR Chi-restraints excluded: chain A residue 489 VAL Chi-restraints excluded: chain B residue 529 THR Chi-restraints excluded: chain B residue 584 GLU Chi-restraints excluded: chain D residue 105 THR Chi-restraints excluded: chain D residue 108 THR Chi-restraints excluded: chain F residue 68 VAL Chi-restraints excluded: chain F residue 125 LEU Chi-restraints excluded: chain F residue 136 VAL Chi-restraints excluded: chain F residue 161 THR Chi-restraints excluded: chain F residue 202 THR Chi-restraints excluded: chain F residue 244 THR Chi-restraints excluded: chain F residue 284 ILE Chi-restraints excluded: chain F residue 439 ILE Chi-restraints excluded: chain F residue 455 THR Chi-restraints excluded: chain F residue 461 ASN Chi-restraints excluded: chain G residue 520 LEU Chi-restraints excluded: chain G residue 589 ASP Chi-restraints excluded: chain G residue 641 ILE Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain I residue 25 THR Chi-restraints excluded: chain I residue 108 THR Chi-restraints excluded: chain K residue 36 VAL Chi-restraints excluded: chain K residue 42 VAL Chi-restraints excluded: chain K residue 52 LEU Chi-restraints excluded: chain K residue 68 VAL Chi-restraints excluded: chain K residue 75 VAL Chi-restraints excluded: chain K residue 120 VAL Chi-restraints excluded: chain K residue 123 THR Chi-restraints excluded: chain K residue 125 LEU Chi-restraints excluded: chain K residue 284 ILE Chi-restraints excluded: chain K residue 340 ASP Chi-restraints excluded: chain K residue 399 TYR Chi-restraints excluded: chain K residue 439 ILE Chi-restraints excluded: chain K residue 455 THR Chi-restraints excluded: chain K residue 489 VAL Chi-restraints excluded: chain L residue 530 MET Chi-restraints excluded: chain L residue 584 GLU Chi-restraints excluded: chain M residue 18 VAL Chi-restraints excluded: chain M residue 58 THR Chi-restraints excluded: chain M residue 69 THR Chi-restraints excluded: chain N residue 41 TYR Chi-restraints excluded: chain N residue 105 THR Chi-restraints excluded: chain N residue 108 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: chunk 27 optimal weight: 5.9990 chunk 126 optimal weight: 0.0980 chunk 210 optimal weight: 4.9990 chunk 88 optimal weight: 5.9990 chunk 52 optimal weight: 1.9990 chunk 40 optimal weight: 6.9990 chunk 225 optimal weight: 7.9990 chunk 109 optimal weight: 3.9990 chunk 4 optimal weight: 20.0000 chunk 145 optimal weight: 10.0000 chunk 134 optimal weight: 9.9990 overall best weight: 3.4188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3603 r_free = 0.3603 target = 0.073105 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.062644 restraints weight = 94013.712| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.064013 restraints weight = 57166.778| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.064932 restraints weight = 41327.952| |-----------------------------------------------------------------------------| r_work (final): 0.3409 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7344 moved from start: 0.2851 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 20490 Z= 0.157 Angle : 0.701 14.301 27997 Z= 0.342 Chirality : 0.047 0.269 3296 Planarity : 0.004 0.058 3453 Dihedral : 10.041 80.481 3907 Min Nonbonded Distance : 2.410 Molprobity Statistics. All-atom Clashscore : 8.16 Ramachandran Plot: Outliers : 0.25 % Allowed : 9.31 % Favored : 90.45 % Rotamer: Outliers : 2.62 % Allowed : 15.76 % Favored : 81.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -2.04 (0.16), residues: 2439 helix: -0.84 (0.26), residues: 417 sheet: -0.54 (0.20), residues: 679 loop : -2.01 (0.16), residues: 1343 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP B 631 HIS 0.004 0.001 HIS H 116 PHE 0.012 0.002 PHE H 32 TYR 0.013 0.001 TYR F 484 ARG 0.003 0.000 ARG G 542 Details of bonding type rmsd link_NAG-ASN : bond 0.00451 ( 15) link_NAG-ASN : angle 3.55869 ( 45) link_ALPHA1-6 : bond 0.00302 ( 6) link_ALPHA1-6 : angle 1.94295 ( 18) link_BETA1-4 : bond 0.00463 ( 19) link_BETA1-4 : angle 1.99739 ( 57) link_ALPHA1-2 : bond 0.00820 ( 14) link_ALPHA1-2 : angle 2.55457 ( 42) link_ALPHA1-3 : bond 0.00894 ( 9) link_ALPHA1-3 : angle 1.82020 ( 27) hydrogen bonds : bond 0.03278 ( 628) hydrogen bonds : angle 5.55748 ( 1788) SS BOND : bond 0.00464 ( 45) SS BOND : angle 1.84565 ( 90) covalent geometry : bond 0.00353 (20382) covalent geometry : angle 0.66440 (27718) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4878 Ramachandran restraints generated. 2439 Oldfield, 0 Emsley, 2439 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4878 Ramachandran restraints generated. 2439 Oldfield, 0 Emsley, 2439 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 2138 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 97 time to evaluate : 2.165 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 10 VAL cc_start: 0.4983 (p) cc_final: 0.4737 (m) REVERT: F 125 LEU cc_start: 0.8987 (OUTLIER) cc_final: 0.8399 (tt) REVERT: G 520 LEU cc_start: 0.6512 (OUTLIER) cc_final: 0.5914 (tp) REVERT: G 641 ILE cc_start: 0.8163 (OUTLIER) cc_final: 0.7715 (pt) REVERT: I 84 ASP cc_start: 0.4903 (t0) cc_final: 0.4581 (t0) REVERT: K 125 LEU cc_start: 0.9039 (OUTLIER) cc_final: 0.8766 (tt) REVERT: K 340 ASP cc_start: 0.6056 (OUTLIER) cc_final: 0.5761 (t0) REVERT: L 649 SER cc_start: 0.8065 (t) cc_final: 0.7193 (p) outliers start: 56 outliers final: 45 residues processed: 146 average time/residue: 0.2589 time to fit residues: 64.2379 Evaluate side-chains 146 residues out of total 2138 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 96 time to evaluate : 2.211 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 68 VAL Chi-restraints excluded: chain A residue 75 VAL Chi-restraints excluded: chain A residue 109 ILE Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 161 THR Chi-restraints excluded: chain A residue 202 THR Chi-restraints excluded: chain A residue 284 ILE Chi-restraints excluded: chain A residue 455 THR Chi-restraints excluded: chain A residue 489 VAL Chi-restraints excluded: chain B residue 529 THR Chi-restraints excluded: chain B residue 584 GLU Chi-restraints excluded: chain D residue 105 THR Chi-restraints excluded: chain D residue 108 THR Chi-restraints excluded: chain F residue 68 VAL Chi-restraints excluded: chain F residue 125 LEU Chi-restraints excluded: chain F residue 136 VAL Chi-restraints excluded: chain F residue 161 THR Chi-restraints excluded: chain F residue 202 THR Chi-restraints excluded: chain F residue 244 THR Chi-restraints excluded: chain F residue 284 ILE Chi-restraints excluded: chain F residue 439 ILE Chi-restraints excluded: chain F residue 455 THR Chi-restraints excluded: chain G residue 520 LEU Chi-restraints excluded: chain G residue 589 ASP Chi-restraints excluded: chain G residue 641 ILE Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain I residue 25 THR Chi-restraints excluded: chain I residue 108 THR Chi-restraints excluded: chain K residue 36 VAL Chi-restraints excluded: chain K residue 42 VAL Chi-restraints excluded: chain K residue 52 LEU Chi-restraints excluded: chain K residue 68 VAL Chi-restraints excluded: chain K residue 75 VAL Chi-restraints excluded: chain K residue 120 VAL Chi-restraints excluded: chain K residue 125 LEU Chi-restraints excluded: chain K residue 284 ILE Chi-restraints excluded: chain K residue 340 ASP Chi-restraints excluded: chain K residue 399 TYR Chi-restraints excluded: chain K residue 439 ILE Chi-restraints excluded: chain K residue 455 THR Chi-restraints excluded: chain K residue 489 VAL Chi-restraints excluded: chain L residue 584 GLU Chi-restraints excluded: chain M residue 18 VAL Chi-restraints excluded: chain M residue 58 THR Chi-restraints excluded: chain M residue 69 THR Chi-restraints excluded: chain N residue 41 TYR Chi-restraints excluded: chain N residue 105 THR Chi-restraints excluded: chain N residue 108 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: chunk 156 optimal weight: 0.7980 chunk 158 optimal weight: 30.0000 chunk 159 optimal weight: 10.0000 chunk 186 optimal weight: 9.9990 chunk 226 optimal weight: 0.0470 chunk 217 optimal weight: 3.9990 chunk 98 optimal weight: 10.0000 chunk 208 optimal weight: 8.9990 chunk 181 optimal weight: 10.0000 chunk 236 optimal weight: 9.9990 chunk 24 optimal weight: 4.9990 overall best weight: 3.7684 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3603 r_free = 0.3603 target = 0.073108 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.062673 restraints weight = 93665.201| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.064053 restraints weight = 56461.063| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.064979 restraints weight = 40675.357| |-----------------------------------------------------------------------------| r_work (final): 0.3410 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7341 moved from start: 0.2916 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 20490 Z= 0.164 Angle : 0.700 13.889 27997 Z= 0.342 Chirality : 0.047 0.270 3296 Planarity : 0.004 0.058 3453 Dihedral : 9.725 79.383 3907 Min Nonbonded Distance : 2.405 Molprobity Statistics. All-atom Clashscore : 8.31 Ramachandran Plot: Outliers : 0.21 % Allowed : 9.43 % Favored : 90.36 % Rotamer: Outliers : 2.25 % Allowed : 16.37 % Favored : 81.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.00 (0.16), residues: 2439 helix: -0.78 (0.26), residues: 417 sheet: -0.52 (0.20), residues: 679 loop : -1.99 (0.16), residues: 1343 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP B 631 HIS 0.004 0.001 HIS H 116 PHE 0.013 0.002 PHE F 376 TYR 0.015 0.001 TYR F 484 ARG 0.003 0.000 ARG G 542 Details of bonding type rmsd link_NAG-ASN : bond 0.00470 ( 15) link_NAG-ASN : angle 2.94171 ( 45) link_ALPHA1-6 : bond 0.00335 ( 6) link_ALPHA1-6 : angle 1.85887 ( 18) link_BETA1-4 : bond 0.00459 ( 19) link_BETA1-4 : angle 1.96218 ( 57) link_ALPHA1-2 : bond 0.00778 ( 14) link_ALPHA1-2 : angle 2.57076 ( 42) link_ALPHA1-3 : bond 0.00883 ( 9) link_ALPHA1-3 : angle 1.81297 ( 27) hydrogen bonds : bond 0.03290 ( 628) hydrogen bonds : angle 5.53864 ( 1788) SS BOND : bond 0.00461 ( 45) SS BOND : angle 1.88008 ( 90) covalent geometry : bond 0.00371 (20382) covalent geometry : angle 0.66807 (27718) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4890.37 seconds wall clock time: 87 minutes 58.77 seconds (5278.77 seconds total)