Starting phenix.real_space_refine on Tue Jun 17 15:42:40 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8sar_40277/06_2025/8sar_40277_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8sar_40277/06_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_40277/06_2025/8sar_40277.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8sar_40277/06_2025/8sar_40277.map" model { file = "/net/cci-nas-00/data/ceres_data/8sar_40277/06_2025/8sar_40277_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8sar_40277/06_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): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/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: 14.33, per 1000 atoms: 0.72 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: 6.40 Conformation dependent library (CDL) restraints added in 2.7 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: 3.38 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: 8.86 Time building geometry restraints manager: 7.51 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: 2.020 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: 0.820 Check model and map are aligned: 0.140 Set scattering table: 0.180 Process input model: 55.470 Find NCS groups from input model: 1.190 Set up NCS constraints: 0.160 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: 0.020 Load rotamer database and sin/cos tables:3.380 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 63.400 ------------------------------------------------------------------------------- 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 : 2.183 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: 0.2870 time to fit residues: 59.0161 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 : 2.306 ------------------------------------------------------------------------------- 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 = 36)----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.065111 restraints weight = 92097.780| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3454 r_free = 0.3454 target = 0.066557 restraints weight = 54959.038| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3477 r_free = 0.3477 target = 0.067525 restraints weight = 39225.755| |-----------------------------------------------------------------------------| 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 1.69616 ( 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 : 2.515 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 100 MET cc_start: 0.7051 (mtp) cc_final: 0.6851 (mtp) REVERT: B 530 MET cc_start: 0.5559 (mmt) cc_final: 0.5283 (mmt) REVERT: D 84 ASP cc_start: 0.4232 (m-30) cc_final: 0.3952 (m-30) outliers start: 11 outliers final: 2 residues processed: 124 average time/residue: 0.3131 time to fit residues: 64.4017 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 : 2.541 ------------------------------------------------------------------------------- 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: 2.9990 chunk 201 optimal weight: 0.0060 chunk 156 optimal weight: 5.9990 chunk 157 optimal weight: 6.9990 chunk 19 optimal weight: 20.0000 chunk 193 optimal weight: 10.0000 chunk 158 optimal weight: 20.0000 chunk 146 optimal weight: 10.0000 chunk 12 optimal weight: 2.9990 chunk 170 optimal weight: 6.9990 overall best weight: 3.8004 ------------------------------------------------------------------------------- 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 F 287 HIS H 116 HIS K 249 HIS K 287 HIS M 116 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3636 r_free = 0.3636 target = 0.074414 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.064059 restraints weight = 92450.148| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.065451 restraints weight = 55956.101| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3450 r_free = 0.3450 target = 0.066381 restraints weight = 40322.985| |-----------------------------------------------------------------------------| r_work (final): 0.3447 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7261 moved from start: 0.1494 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 20490 Z= 0.165 Angle : 0.693 16.493 27997 Z= 0.344 Chirality : 0.047 0.640 3296 Planarity : 0.004 0.059 3453 Dihedral : 10.987 89.653 3907 Min Nonbonded Distance : 2.413 Molprobity Statistics. All-atom Clashscore : 6.73 Ramachandran Plot: Outliers : 0.29 % Allowed : 7.71 % Favored : 92.00 % Rotamer: Outliers : 1.26 % Allowed : 9.78 % Favored : 88.96 % 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: -1.68 (0.16), residues: 2439 helix: -0.95 (0.26), residues: 393 sheet: -0.28 (0.20), residues: 690 loop : -1.65 (0.15), residues: 1356 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP B 628 HIS 0.012 0.002 HIS F 249 PHE 0.014 0.002 PHE K 53 TYR 0.019 0.002 TYR F 61 ARG 0.004 0.000 ARG F 432 Details of bonding type rmsd link_NAG-ASN : bond 0.00529 ( 15) link_NAG-ASN : angle 3.62901 ( 45) link_ALPHA1-6 : bond 0.00345 ( 6) link_ALPHA1-6 : angle 1.90109 ( 18) link_BETA1-4 : bond 0.00551 ( 19) link_BETA1-4 : angle 2.11941 ( 57) link_ALPHA1-2 : bond 0.00790 ( 14) link_ALPHA1-2 : angle 2.57739 ( 42) link_ALPHA1-3 : bond 0.00898 ( 9) link_ALPHA1-3 : angle 1.63793 ( 27) hydrogen bonds : bond 0.03526 ( 628) hydrogen bonds : angle 5.61235 ( 1788) SS BOND : bond 0.00672 ( 45) SS BOND : angle 1.54473 ( 90) covalent geometry : bond 0.00365 (20382) covalent geometry : angle 0.65718 (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: 27 poor density : 106 time to evaluate : 2.447 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 100 MET cc_start: 0.7001 (mtp) cc_final: 0.6765 (mtp) REVERT: D 10 VAL cc_start: 0.5130 (p) cc_final: 0.4754 (m) REVERT: D 84 ASP cc_start: 0.4348 (m-30) cc_final: 0.4045 (m-30) REVERT: G 520 LEU cc_start: 0.6200 (OUTLIER) cc_final: 0.5777 (tp) REVERT: N 10 VAL cc_start: 0.5560 (p) cc_final: 0.5207 (m) outliers start: 27 outliers final: 10 residues processed: 124 average time/residue: 0.2880 time to fit residues: 60.2209 Evaluate side-chains 108 residues out of total 2138 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 97 time to evaluate : 2.404 ------------------------------------------------------------------------------- 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 284 ILE 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 K residue 439 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: 6.9990 chunk 67 optimal weight: 6.9990 chunk 226 optimal weight: 0.9990 chunk 187 optimal weight: 0.9980 chunk 151 optimal weight: 20.0000 chunk 81 optimal weight: 10.0000 chunk 203 optimal weight: 20.0000 chunk 89 optimal weight: 5.9990 chunk 51 optimal weight: 7.9990 chunk 167 optimal weight: 10.0000 chunk 45 optimal weight: 5.9990 overall best weight: 4.1988 ------------------------------------------------------------------------------- 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** D 32 HIS ** D 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 249 HIS F 422 GLN 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: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3619 r_free = 0.3619 target = 0.073691 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.063269 restraints weight = 93352.385| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.064662 restraints weight = 56549.599| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3430 r_free = 0.3430 target = 0.065587 restraints weight = 40829.568| |-----------------------------------------------------------------------------| r_work (final): 0.3428 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7299 moved from start: 0.1987 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 20490 Z= 0.173 Angle : 0.699 15.816 27997 Z= 0.346 Chirality : 0.048 0.623 3296 Planarity : 0.004 0.059 3453 Dihedral : 10.168 84.633 3907 Min Nonbonded Distance : 2.419 Molprobity Statistics. All-atom Clashscore : 7.06 Ramachandran Plot: Outliers : 0.29 % Allowed : 8.45 % Favored : 91.27 % Rotamer: Outliers : 2.20 % Allowed : 11.79 % Favored : 86.01 % 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: -1.65 (0.16), residues: 2439 helix: -0.74 (0.26), residues: 393 sheet: -0.27 (0.20), residues: 698 loop : -1.68 (0.15), residues: 1348 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP B 571 HIS 0.012 0.002 HIS F 249 PHE 0.014 0.002 PHE K 53 TYR 0.016 0.002 TYR F 61 ARG 0.004 0.000 ARG F 432 Details of bonding type rmsd link_NAG-ASN : bond 0.00480 ( 15) link_NAG-ASN : angle 3.49557 ( 45) link_ALPHA1-6 : bond 0.00336 ( 6) link_ALPHA1-6 : angle 1.88109 ( 18) link_BETA1-4 : bond 0.00486 ( 19) link_BETA1-4 : angle 1.95474 ( 57) link_ALPHA1-2 : bond 0.00775 ( 14) link_ALPHA1-2 : angle 2.64363 ( 42) link_ALPHA1-3 : bond 0.00865 ( 9) link_ALPHA1-3 : angle 1.64170 ( 27) hydrogen bonds : bond 0.03416 ( 628) hydrogen bonds : angle 5.52036 ( 1788) SS BOND : bond 0.00418 ( 45) SS BOND : angle 1.49952 ( 90) covalent geometry : bond 0.00387 (20382) covalent geometry : angle 0.66571 (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 151 residues out of total 2138 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 104 time to evaluate : 2.159 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 100 MET cc_start: 0.6821 (mtp) cc_final: 0.6610 (mtp) REVERT: D 10 VAL cc_start: 0.4731 (p) cc_final: 0.4364 (m) REVERT: F 125 LEU cc_start: 0.8986 (OUTLIER) cc_final: 0.8559 (tt) REVERT: G 520 LEU cc_start: 0.6275 (OUTLIER) cc_final: 0.5839 (tp) REVERT: I 10 VAL cc_start: 0.5280 (p) cc_final: 0.4866 (m) REVERT: N 10 VAL cc_start: 0.5501 (p) cc_final: 0.5189 (m) outliers start: 47 outliers final: 20 residues processed: 139 average time/residue: 0.2795 time to fit residues: 65.5829 Evaluate side-chains 116 residues out of total 2138 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 94 time to evaluate : 2.451 ------------------------------------------------------------------------------- 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 249 HIS Chi-restraints excluded: chain A residue 284 ILE Chi-restraints excluded: chain B residue 584 GLU 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 434 MET 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 284 ILE Chi-restraints excluded: chain K residue 439 ILE Chi-restraints excluded: chain K residue 489 VAL Chi-restraints excluded: chain L residue 530 MET 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: 9.9990 chunk 92 optimal weight: 10.0000 chunk 105 optimal weight: 3.9990 chunk 196 optimal weight: 0.9990 chunk 129 optimal weight: 6.9990 chunk 117 optimal weight: 0.4980 chunk 47 optimal weight: 8.9990 chunk 227 optimal weight: 4.9990 chunk 200 optimal weight: 1.9990 chunk 62 optimal weight: 9.9990 chunk 18 optimal weight: 3.9990 overall best weight: 2.2988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 249 HIS K 249 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3636 r_free = 0.3636 target = 0.074372 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.063913 restraints weight = 93363.696| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3425 r_free = 0.3425 target = 0.065321 restraints weight = 56391.199| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.066249 restraints weight = 40728.910| |-----------------------------------------------------------------------------| r_work (final): 0.3445 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7270 moved from start: 0.2046 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 20490 Z= 0.125 Angle : 0.648 15.541 27997 Z= 0.319 Chirality : 0.046 0.569 3296 Planarity : 0.004 0.055 3453 Dihedral : 9.662 80.642 3907 Min Nonbonded Distance : 2.424 Molprobity Statistics. All-atom Clashscore : 6.93 Ramachandran Plot: Outliers : 0.29 % Allowed : 7.05 % Favored : 92.66 % Rotamer: Outliers : 2.15 % Allowed : 13.14 % Favored : 84.71 % 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: -1.53 (0.16), residues: 2439 helix: -0.54 (0.27), residues: 393 sheet: -0.22 (0.20), residues: 701 loop : -1.62 (0.16), residues: 1345 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP B 571 HIS 0.022 0.001 HIS A 249 PHE 0.010 0.001 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 0.00428 ( 15) link_NAG-ASN : angle 3.29582 ( 45) link_ALPHA1-6 : bond 0.00408 ( 6) link_ALPHA1-6 : angle 1.78204 ( 18) link_BETA1-4 : bond 0.00446 ( 19) link_BETA1-4 : angle 1.80525 ( 57) link_ALPHA1-2 : bond 0.00798 ( 14) link_ALPHA1-2 : angle 2.61171 ( 42) link_ALPHA1-3 : bond 0.00959 ( 9) link_ALPHA1-3 : angle 1.52824 ( 27) hydrogen bonds : bond 0.03074 ( 628) hydrogen bonds : angle 5.30109 ( 1788) SS BOND : bond 0.00377 ( 45) SS BOND : angle 1.83298 ( 90) covalent geometry : bond 0.00273 (20382) covalent geometry : angle 0.61175 (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 149 residues out of total 2138 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 103 time to evaluate : 2.424 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 10 VAL cc_start: 0.4543 (p) cc_final: 0.4208 (m) REVERT: F 125 LEU cc_start: 0.8918 (OUTLIER) cc_final: 0.8566 (tt) REVERT: F 426 MET cc_start: 0.7176 (ttp) cc_final: 0.6917 (ttt) REVERT: G 520 LEU cc_start: 0.6264 (OUTLIER) cc_final: 0.5800 (tp) REVERT: I 10 VAL cc_start: 0.5410 (p) cc_final: 0.5027 (m) REVERT: K 125 LEU cc_start: 0.8942 (OUTLIER) cc_final: 0.8737 (tt) REVERT: N 10 VAL cc_start: 0.5447 (p) cc_final: 0.5154 (m) outliers start: 46 outliers final: 17 residues processed: 143 average time/residue: 0.2673 time to fit residues: 64.6877 Evaluate side-chains 116 residues out of total 2138 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 96 time to evaluate : 2.368 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 161 THR Chi-restraints excluded: chain A residue 284 ILE 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 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 K residue 36 VAL 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 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: 5.9990 chunk 84 optimal weight: 7.9990 chunk 143 optimal weight: 9.9990 chunk 94 optimal weight: 0.9990 chunk 55 optimal weight: 9.9990 chunk 121 optimal weight: 3.9990 chunk 132 optimal weight: 0.1980 chunk 46 optimal weight: 10.0000 chunk 231 optimal weight: 6.9990 chunk 161 optimal weight: 20.0000 chunk 176 optimal weight: 0.0040 overall best weight: 2.2398 ------------------------------------------------------------------------------- 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 = 0.3638 r_free = 0.3638 target = 0.074494 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.064052 restraints weight = 93022.029| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.065470 restraints weight = 55554.695| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.066433 restraints weight = 39763.506| |-----------------------------------------------------------------------------| r_work (final): 0.3450 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7261 moved from start: 0.2181 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 20490 Z= 0.122 Angle : 0.636 15.738 27997 Z= 0.312 Chirality : 0.045 0.560 3296 Planarity : 0.004 0.053 3453 Dihedral : 9.215 76.634 3907 Min Nonbonded Distance : 2.367 Molprobity Statistics. All-atom Clashscore : 6.83 Ramachandran Plot: Outliers : 0.25 % Allowed : 7.71 % Favored : 92.05 % Rotamer: Outliers : 2.06 % Allowed : 14.17 % Favored : 83.77 % 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: -1.44 (0.17), residues: 2439 helix: -0.36 (0.27), residues: 393 sheet: -0.21 (0.20), residues: 689 loop : -1.56 (0.16), residues: 1357 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP L 631 HIS 0.013 0.001 HIS K 249 PHE 0.012 0.001 PHE F 53 TYR 0.013 0.001 TYR F 61 ARG 0.002 0.000 ARG H 38 Details of bonding type rmsd link_NAG-ASN : bond 0.00436 ( 15) link_NAG-ASN : angle 3.24053 ( 45) link_ALPHA1-6 : bond 0.00451 ( 6) link_ALPHA1-6 : angle 1.72534 ( 18) link_BETA1-4 : bond 0.00450 ( 19) link_BETA1-4 : angle 1.73418 ( 57) link_ALPHA1-2 : bond 0.00779 ( 14) link_ALPHA1-2 : angle 2.62093 ( 42) link_ALPHA1-3 : bond 0.00911 ( 9) link_ALPHA1-3 : angle 1.50363 ( 27) hydrogen bonds : bond 0.02964 ( 628) hydrogen bonds : angle 5.18707 ( 1788) SS BOND : bond 0.00516 ( 45) SS BOND : angle 1.82918 ( 90) covalent geometry : bond 0.00267 (20382) covalent geometry : angle 0.59944 (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 148 residues out of total 2138 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 104 time to evaluate : 2.707 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 10 VAL cc_start: 0.4326 (p) cc_final: 0.4050 (m) REVERT: F 125 LEU cc_start: 0.8923 (OUTLIER) cc_final: 0.8633 (tt) REVERT: G 520 LEU cc_start: 0.6524 (OUTLIER) cc_final: 0.5935 (tp) REVERT: I 10 VAL cc_start: 0.5388 (p) cc_final: 0.5041 (m) REVERT: N 10 VAL cc_start: 0.5454 (p) cc_final: 0.5169 (m) outliers start: 44 outliers final: 25 residues processed: 142 average time/residue: 0.3293 time to fit residues: 79.2907 Evaluate side-chains 125 residues out of total 2138 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 98 time to evaluate : 3.500 ------------------------------------------------------------------------------- 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 125 LEU Chi-restraints excluded: chain A residue 161 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 D residue 108 THR Chi-restraints excluded: chain F residue 68 VAL Chi-restraints excluded: chain F residue 75 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 42 VAL Chi-restraints excluded: chain K residue 52 LEU Chi-restraints excluded: chain K residue 68 VAL Chi-restraints excluded: chain K residue 284 ILE Chi-restraints excluded: chain K residue 394 THR Chi-restraints excluded: chain K residue 399 TYR Chi-restraints excluded: chain K residue 489 VAL Chi-restraints excluded: chain M residue 18 VAL Chi-restraints excluded: chain M residue 69 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: 0.9990 chunk 44 optimal weight: 8.9990 chunk 121 optimal weight: 3.9990 chunk 151 optimal weight: 20.0000 chunk 231 optimal weight: 0.2980 chunk 195 optimal weight: 5.9990 chunk 71 optimal weight: 2.9990 chunk 114 optimal weight: 5.9990 chunk 223 optimal weight: 2.9990 chunk 79 optimal weight: 0.0170 overall best weight: 1.4624 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 249 HIS K 249 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3653 r_free = 0.3653 target = 0.075087 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.064662 restraints weight = 92056.951| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3446 r_free = 0.3446 target = 0.066105 restraints weight = 54994.456| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3469 r_free = 0.3469 target = 0.067061 restraints weight = 39305.460| |-----------------------------------------------------------------------------| r_work (final): 0.3467 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7233 moved from start: 0.2292 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.047 20490 Z= 0.105 Angle : 0.615 15.032 27997 Z= 0.301 Chirality : 0.045 0.533 3296 Planarity : 0.004 0.051 3453 Dihedral : 8.628 70.502 3907 Min Nonbonded Distance : 2.403 Molprobity Statistics. All-atom Clashscore : 6.70 Ramachandran Plot: Outliers : 0.25 % Allowed : 6.97 % Favored : 92.78 % Rotamer: Outliers : 1.78 % Allowed : 14.87 % Favored : 83.35 % 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: -1.39 (0.17), residues: 2439 helix: -0.33 (0.27), residues: 405 sheet: -0.18 (0.20), residues: 681 loop : -1.52 (0.16), residues: 1353 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.048 0.001 TRP G 571 HIS 0.014 0.001 HIS K 249 PHE 0.011 0.001 PHE F 53 TYR 0.011 0.001 TYR F 61 ARG 0.005 0.000 ARG K 446 Details of bonding type rmsd link_NAG-ASN : bond 0.00431 ( 15) link_NAG-ASN : angle 3.11543 ( 45) link_ALPHA1-6 : bond 0.00573 ( 6) link_ALPHA1-6 : angle 1.60185 ( 18) link_BETA1-4 : bond 0.00435 ( 19) link_BETA1-4 : angle 1.65099 ( 57) link_ALPHA1-2 : bond 0.00770 ( 14) link_ALPHA1-2 : angle 2.60804 ( 42) link_ALPHA1-3 : bond 0.00959 ( 9) link_ALPHA1-3 : angle 1.47739 ( 27) hydrogen bonds : bond 0.02812 ( 628) hydrogen bonds : angle 5.08206 ( 1788) SS BOND : bond 0.00487 ( 45) SS BOND : angle 1.75279 ( 90) covalent geometry : bond 0.00224 (20382) covalent geometry : angle 0.57980 (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 153 residues out of total 2138 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 115 time to evaluate : 2.745 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 626 MET cc_start: 0.5945 (mmm) cc_final: 0.5649 (tpt) REVERT: D 10 VAL cc_start: 0.4286 (p) cc_final: 0.4026 (m) REVERT: F 125 LEU cc_start: 0.8866 (OUTLIER) cc_final: 0.8614 (tt) REVERT: G 520 LEU cc_start: 0.6568 (OUTLIER) cc_final: 0.5928 (tp) REVERT: G 641 ILE cc_start: 0.8359 (OUTLIER) cc_final: 0.7963 (pt) REVERT: I 10 VAL cc_start: 0.5333 (p) cc_final: 0.5006 (m) REVERT: N 10 VAL cc_start: 0.5394 (p) cc_final: 0.5143 (m) outliers start: 38 outliers final: 20 residues processed: 148 average time/residue: 0.3899 time to fit residues: 96.8117 Evaluate side-chains 124 residues out of total 2138 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 101 time to evaluate : 4.382 ------------------------------------------------------------------------------- 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 284 ILE Chi-restraints excluded: chain A residue 489 VAL Chi-restraints excluded: chain B residue 584 GLU Chi-restraints excluded: chain B residue 627 THR Chi-restraints excluded: chain D residue 41 TYR Chi-restraints excluded: chain F residue 68 VAL Chi-restraints excluded: chain F residue 125 LEU Chi-restraints excluded: chain F residue 202 THR Chi-restraints excluded: chain F residue 439 ILE Chi-restraints excluded: chain G residue 520 LEU Chi-restraints excluded: chain G residue 641 ILE Chi-restraints excluded: chain I residue 108 THR 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 399 TYR Chi-restraints excluded: chain K residue 455 THR Chi-restraints excluded: chain K residue 489 VAL 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: chunk 171 optimal weight: 0.0980 chunk 27 optimal weight: 9.9990 chunk 155 optimal weight: 20.0000 chunk 165 optimal weight: 8.9990 chunk 25 optimal weight: 0.7980 chunk 10 optimal weight: 30.0000 chunk 90 optimal weight: 9.9990 chunk 197 optimal weight: 20.0000 chunk 173 optimal weight: 6.9990 chunk 178 optimal weight: 5.9990 chunk 95 optimal weight: 7.9990 overall best weight: 4.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 249 HIS H 113 ASN K 105 HIS K 249 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3620 r_free = 0.3620 target = 0.073666 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.063251 restraints weight = 93548.980| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.064645 restraints weight = 56078.811| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.065583 restraints weight = 40381.244| |-----------------------------------------------------------------------------| r_work (final): 0.3429 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7303 moved from start: 0.2500 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 20490 Z= 0.173 Angle : 0.692 14.656 27997 Z= 0.336 Chirality : 0.047 0.249 3296 Planarity : 0.004 0.057 3453 Dihedral : 8.954 70.237 3907 Min Nonbonded Distance : 2.404 Molprobity Statistics. All-atom Clashscore : 7.57 Ramachandran Plot: Outliers : 0.21 % Allowed : 8.77 % Favored : 91.02 % Rotamer: Outliers : 2.10 % Allowed : 14.97 % Favored : 82.93 % 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: -1.53 (0.17), residues: 2439 helix: -0.41 (0.27), residues: 405 sheet: -0.23 (0.20), residues: 701 loop : -1.68 (0.16), residues: 1333 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP G 571 HIS 0.012 0.001 HIS K 249 PHE 0.014 0.002 PHE B 522 TYR 0.012 0.001 TYR A 484 ARG 0.004 0.000 ARG F 432 Details of bonding type rmsd link_NAG-ASN : bond 0.00993 ( 15) link_NAG-ASN : angle 3.90273 ( 45) link_ALPHA1-6 : bond 0.00480 ( 6) link_ALPHA1-6 : angle 1.79499 ( 18) link_BETA1-4 : bond 0.00466 ( 19) link_BETA1-4 : angle 1.72878 ( 57) link_ALPHA1-2 : bond 0.00688 ( 14) link_ALPHA1-2 : angle 2.70672 ( 42) link_ALPHA1-3 : bond 0.00792 ( 9) link_ALPHA1-3 : angle 1.61084 ( 27) hydrogen bonds : bond 0.03202 ( 628) hydrogen bonds : angle 5.28428 ( 1788) SS BOND : bond 0.00456 ( 45) SS BOND : angle 1.90103 ( 90) covalent geometry : bond 0.00390 (20382) covalent geometry : angle 0.65198 (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 149 residues out of total 2138 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 104 time to evaluate : 2.587 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 626 MET cc_start: 0.5882 (mmm) cc_final: 0.5484 (tpt) REVERT: D 10 VAL cc_start: 0.4333 (p) cc_final: 0.4080 (m) REVERT: F 125 LEU cc_start: 0.8969 (OUTLIER) cc_final: 0.8550 (tt) REVERT: G 641 ILE cc_start: 0.8383 (OUTLIER) cc_final: 0.7973 (pt) REVERT: I 10 VAL cc_start: 0.5386 (p) cc_final: 0.5082 (m) REVERT: N 10 VAL cc_start: 0.5418 (p) cc_final: 0.5211 (m) outliers start: 45 outliers final: 31 residues processed: 144 average time/residue: 0.3846 time to fit residues: 91.4782 Evaluate side-chains 135 residues out of total 2138 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 102 time to evaluate : 2.779 ------------------------------------------------------------------------------- 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 120 VAL Chi-restraints excluded: chain A residue 125 LEU 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 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 202 THR Chi-restraints excluded: chain F residue 249 HIS 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 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 68 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 K residue 455 THR Chi-restraints excluded: chain K residue 489 VAL 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: chunk 213 optimal weight: 2.9990 chunk 126 optimal weight: 10.0000 chunk 164 optimal weight: 5.9990 chunk 232 optimal weight: 0.9980 chunk 227 optimal weight: 20.0000 chunk 136 optimal weight: 3.9990 chunk 236 optimal weight: 9.9990 chunk 22 optimal weight: 8.9990 chunk 8 optimal weight: 6.9990 chunk 143 optimal weight: 20.0000 chunk 141 optimal weight: 8.9990 overall best weight: 4.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 249 HIS K 249 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3618 r_free = 0.3618 target = 0.073602 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.063151 restraints weight = 93134.292| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.064558 restraints weight = 56066.315| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3428 r_free = 0.3428 target = 0.065479 restraints weight = 40427.530| |-----------------------------------------------------------------------------| r_work (final): 0.3426 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7310 moved from start: 0.2587 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 20490 Z= 0.170 Angle : 0.687 17.415 27997 Z= 0.334 Chirality : 0.047 0.283 3296 Planarity : 0.004 0.059 3453 Dihedral : 8.886 70.500 3907 Min Nonbonded Distance : 2.410 Molprobity Statistics. All-atom Clashscore : 7.67 Ramachandran Plot: Outliers : 0.21 % Allowed : 8.28 % Favored : 91.51 % Rotamer: Outliers : 1.96 % Allowed : 15.11 % Favored : 82.93 % 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: -1.59 (0.16), residues: 2439 helix: -0.44 (0.27), residues: 405 sheet: -0.25 (0.20), residues: 682 loop : -1.72 (0.16), residues: 1352 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP G 571 HIS 0.018 0.001 HIS F 249 PHE 0.012 0.002 PHE C 32 TYR 0.012 0.001 TYR A 484 ARG 0.003 0.000 ARG F 432 Details of bonding type rmsd link_NAG-ASN : bond 0.00725 ( 15) link_NAG-ASN : angle 3.98369 ( 45) link_ALPHA1-6 : bond 0.00491 ( 6) link_ALPHA1-6 : angle 1.82745 ( 18) link_BETA1-4 : bond 0.00465 ( 19) link_BETA1-4 : angle 1.76153 ( 57) link_ALPHA1-2 : bond 0.00753 ( 14) link_ALPHA1-2 : angle 2.67352 ( 42) link_ALPHA1-3 : bond 0.00864 ( 9) link_ALPHA1-3 : angle 1.66486 ( 27) hydrogen bonds : bond 0.03183 ( 628) hydrogen bonds : angle 5.30287 ( 1788) SS BOND : bond 0.00445 ( 45) SS BOND : angle 1.87449 ( 90) covalent geometry : bond 0.00383 (20382) covalent geometry : angle 0.64599 (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 144 residues out of total 2138 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 102 time to evaluate : 2.385 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 626 MET cc_start: 0.5928 (mmm) cc_final: 0.5507 (tpt) REVERT: F 125 LEU cc_start: 0.8962 (OUTLIER) cc_final: 0.8495 (tt) REVERT: G 641 ILE cc_start: 0.8409 (OUTLIER) cc_final: 0.7988 (pt) REVERT: I 10 VAL cc_start: 0.5301 (p) cc_final: 0.5009 (m) outliers start: 42 outliers final: 33 residues processed: 141 average time/residue: 0.3653 time to fit residues: 88.4049 Evaluate side-chains 134 residues out of total 2138 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 99 time to evaluate : 2.266 ------------------------------------------------------------------------------- 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 109 ILE Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 125 LEU 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 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 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 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 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: chunk 27 optimal weight: 4.9990 chunk 126 optimal weight: 7.9990 chunk 210 optimal weight: 3.9990 chunk 88 optimal weight: 10.0000 chunk 52 optimal weight: 8.9990 chunk 40 optimal weight: 9.9990 chunk 225 optimal weight: 4.9990 chunk 109 optimal weight: 4.9990 chunk 4 optimal weight: 0.9980 chunk 145 optimal weight: 10.0000 chunk 134 optimal weight: 5.9990 overall best weight: 3.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 249 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3617 r_free = 0.3617 target = 0.073557 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.063102 restraints weight = 93883.398| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.064503 restraints weight = 56590.117| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.065452 restraints weight = 40729.321| |-----------------------------------------------------------------------------| r_work (final): 0.3425 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7313 moved from start: 0.2717 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 20490 Z= 0.167 Angle : 0.686 17.867 27997 Z= 0.334 Chirality : 0.047 0.349 3296 Planarity : 0.004 0.059 3453 Dihedral : 8.753 71.330 3907 Min Nonbonded Distance : 2.406 Molprobity Statistics. All-atom Clashscore : 7.77 Ramachandran Plot: Outliers : 0.21 % Allowed : 8.86 % Favored : 90.94 % Rotamer: Outliers : 2.01 % Allowed : 15.15 % Favored : 82.83 % 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: -1.65 (0.16), residues: 2439 helix: -0.45 (0.27), residues: 405 sheet: -0.34 (0.20), residues: 686 loop : -1.75 (0.16), residues: 1348 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP G 571 HIS 0.012 0.001 HIS K 249 PHE 0.012 0.002 PHE H 32 TYR 0.012 0.001 TYR A 484 ARG 0.003 0.000 ARG G 542 Details of bonding type rmsd link_NAG-ASN : bond 0.00650 ( 15) link_NAG-ASN : angle 3.87890 ( 45) link_ALPHA1-6 : bond 0.00525 ( 6) link_ALPHA1-6 : angle 1.76622 ( 18) link_BETA1-4 : bond 0.00446 ( 19) link_BETA1-4 : angle 1.80653 ( 57) link_ALPHA1-2 : bond 0.00751 ( 14) link_ALPHA1-2 : angle 2.64983 ( 42) link_ALPHA1-3 : bond 0.00850 ( 9) link_ALPHA1-3 : angle 1.69308 ( 27) hydrogen bonds : bond 0.03174 ( 628) hydrogen bonds : angle 5.32680 ( 1788) SS BOND : bond 0.00465 ( 45) SS BOND : angle 1.87056 ( 90) covalent geometry : bond 0.00375 (20382) covalent geometry : angle 0.64611 (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 142 residues out of total 2138 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 99 time to evaluate : 4.339 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 626 MET cc_start: 0.5969 (mmm) cc_final: 0.5474 (tpt) REVERT: F 125 LEU cc_start: 0.8984 (OUTLIER) cc_final: 0.8430 (tt) REVERT: G 520 LEU cc_start: 0.6454 (OUTLIER) cc_final: 0.5846 (tp) REVERT: G 641 ILE cc_start: 0.8354 (OUTLIER) cc_final: 0.7932 (pt) REVERT: I 10 VAL cc_start: 0.5333 (p) cc_final: 0.5055 (m) outliers start: 43 outliers final: 34 residues processed: 139 average time/residue: 0.4298 time to fit residues: 104.5760 Evaluate side-chains 135 residues out of total 2138 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 98 time to evaluate : 2.368 ------------------------------------------------------------------------------- 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 109 ILE Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 125 LEU 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 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 G residue 520 LEU 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 120 VAL 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: chunk 156 optimal weight: 0.0870 chunk 158 optimal weight: 6.9990 chunk 159 optimal weight: 9.9990 chunk 186 optimal weight: 0.8980 chunk 226 optimal weight: 6.9990 chunk 217 optimal weight: 10.0000 chunk 98 optimal weight: 6.9990 chunk 208 optimal weight: 0.4980 chunk 181 optimal weight: 7.9990 chunk 236 optimal weight: 2.9990 chunk 24 optimal weight: 2.9990 overall best weight: 1.4962 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 249 HIS K 258 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3642 r_free = 0.3642 target = 0.074650 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3397 r_free = 0.3397 target = 0.064201 restraints weight = 92693.598| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.065640 restraints weight = 55388.735| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3456 r_free = 0.3456 target = 0.066596 restraints weight = 39645.486| |-----------------------------------------------------------------------------| r_work (final): 0.3454 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7259 moved from start: 0.2715 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 20490 Z= 0.110 Angle : 0.640 18.051 27997 Z= 0.310 Chirality : 0.045 0.334 3296 Planarity : 0.004 0.053 3453 Dihedral : 8.181 68.313 3907 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 7.09 Ramachandran Plot: Outliers : 0.21 % Allowed : 6.85 % Favored : 92.95 % Rotamer: Outliers : 1.50 % Allowed : 15.81 % Favored : 82.69 % 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: -1.47 (0.17), residues: 2439 helix: -0.29 (0.27), residues: 405 sheet: -0.21 (0.21), residues: 671 loop : -1.62 (0.16), residues: 1363 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP G 571 HIS 0.007 0.001 HIS K 249 PHE 0.013 0.001 PHE A 376 TYR 0.009 0.001 TYR K 61 ARG 0.003 0.000 ARG C 38 Details of bonding type rmsd link_NAG-ASN : bond 0.00601 ( 15) link_NAG-ASN : angle 3.73563 ( 45) link_ALPHA1-6 : bond 0.00697 ( 6) link_ALPHA1-6 : angle 1.48083 ( 18) link_BETA1-4 : bond 0.00409 ( 19) link_BETA1-4 : angle 1.70669 ( 57) link_ALPHA1-2 : bond 0.00810 ( 14) link_ALPHA1-2 : angle 2.62273 ( 42) link_ALPHA1-3 : bond 0.00962 ( 9) link_ALPHA1-3 : angle 1.53746 ( 27) hydrogen bonds : bond 0.02863 ( 628) hydrogen bonds : angle 5.15032 ( 1788) SS BOND : bond 0.00464 ( 45) SS BOND : angle 1.76537 ( 90) covalent geometry : bond 0.00235 (20382) covalent geometry : angle 0.60116 (27718) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7290.88 seconds wall clock time: 135 minutes 24.53 seconds (8124.53 seconds total)