Starting phenix.real_space_refine on Sun Aug 24 13:16:42 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8sar_40277/08_2025/8sar_40277_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8sar_40277/08_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 { model { file = "/net/cci-nas-00/data/ceres_data/8sar_40277/08_2025/8sar_40277_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8sar_40277/08_2025/8sar_40277_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8sar_40277/08_2025/8sar_40277.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8sar_40277/08_2025/8sar_40277.map" } resolution = 3.82 write_initial_geo_file = False refinement { macro_cycles = 10 } 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): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/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: 5.21, per 1000 atoms: 0.26 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: 2.20 Conformation dependent library (CDL) restraints added in 929.1 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 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: 0.91 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: 4.47 Time building geometry restraints manager: 2.84 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 601)) selection = (chain 'K' and (resid 32 through 321 or resid 322 through 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: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.870 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.030 Extract box with map and model: 0.430 Check model and map are aligned: 0.070 Set scattering table: 0.070 Process input model: 21.230 Find NCS groups from input model: 0.480 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.450 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.720 ------------------------------------------------------------------------------- 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 : 4.41 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. 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 ARG 0.017 0.001 ARG D 81 TYR 0.020 0.002 TYR K 399 PHE 0.016 0.002 PHE K 391 TRP 0.038 0.003 TRP F 479 HIS 0.016 0.002 HIS K 249 Details of bonding type rmsd covalent geometry : bond 0.00589 (20382) covalent geometry : angle 1.11271 (27718) SS BOND : bond 0.00607 ( 45) SS BOND : angle 1.69274 ( 90) hydrogen bonds : bond 0.15245 ( 628) hydrogen bonds : angle 7.44171 ( 1788) 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) 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_NAG-ASN : bond 0.00713 ( 15) link_NAG-ASN : angle 5.23436 ( 45) *********************** 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 : 0.817 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: 0.1380 time to fit residues: 28.6119 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 : 0.808 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: chunk 216 optimal weight: 9.9990 chunk 98 optimal weight: 1.9990 chunk 194 optimal weight: 0.1980 chunk 227 optimal weight: 10.0000 chunk 107 optimal weight: 7.9990 chunk 10 optimal weight: 8.9990 chunk 66 optimal weight: 0.7980 chunk 130 optimal weight: 6.9990 chunk 124 optimal weight: 9.9990 chunk 103 optimal weight: 0.9980 chunk 235 optimal weight: 9.9990 overall best weight: 2.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 249 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: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3671 r_free = 0.3671 target = 0.075901 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3430 r_free = 0.3430 target = 0.065571 restraints weight = 92113.206| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3466 r_free = 0.3466 target = 0.067035 restraints weight = 54754.377| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3490 r_free = 0.3490 target = 0.068013 restraints weight = 38826.867| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.068672 restraints weight = 30916.934| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3516 r_free = 0.3516 target = 0.069113 restraints weight = 26459.842| |-----------------------------------------------------------------------------| r_work (final): 0.3515 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7144 moved from start: 0.0934 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.066 20490 Z= 0.130 Angle : 0.691 17.384 27997 Z= 0.343 Chirality : 0.047 0.701 3296 Planarity : 0.005 0.064 3453 Dihedral : 11.979 91.485 3907 Min Nonbonded Distance : 2.404 Molprobity Statistics. All-atom Clashscore : 5.58 Ramachandran Plot: Outliers : 0.37 % Allowed : 6.77 % Favored : 92.87 % Rotamer: Outliers : 0.47 % Allowed : 5.85 % Favored : 93.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.81 (0.16), residues: 2439 helix: -1.49 (0.24), residues: 393 sheet: -0.22 (0.20), residues: 679 loop : -1.65 (0.15), residues: 1367 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 432 TYR 0.016 0.001 TYR N 48 PHE 0.010 0.001 PHE C 32 TRP 0.020 0.001 TRP B 628 HIS 0.012 0.001 HIS K 249 Details of bonding type rmsd covalent geometry : bond 0.00278 (20382) covalent geometry : angle 0.64909 (27718) SS BOND : bond 0.00368 ( 45) SS BOND : angle 1.82761 ( 90) hydrogen bonds : bond 0.03640 ( 628) hydrogen bonds : angle 5.91001 ( 1788) link_ALPHA1-2 : bond 0.00805 ( 14) link_ALPHA1-2 : angle 2.48939 ( 42) link_ALPHA1-3 : bond 0.00922 ( 9) link_ALPHA1-3 : angle 1.82839 ( 27) link_ALPHA1-6 : bond 0.00400 ( 6) link_ALPHA1-6 : angle 1.72176 ( 18) link_BETA1-4 : bond 0.00602 ( 19) link_BETA1-4 : angle 2.35546 ( 57) link_NAG-ASN : bond 0.00454 ( 15) link_NAG-ASN : angle 3.81260 ( 45) *********************** 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 128 residues out of total 2138 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 118 time to evaluate : 0.878 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 84 ASP cc_start: 0.4254 (m-30) cc_final: 0.3992 (m-30) outliers start: 10 outliers final: 2 residues processed: 123 average time/residue: 0.1369 time to fit residues: 27.7734 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 : 0.872 ------------------------------------------------------------------------------- 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 145 optimal weight: 8.9990 chunk 191 optimal weight: 7.9990 chunk 238 optimal weight: 20.0000 chunk 102 optimal weight: 2.9990 chunk 168 optimal weight: 10.0000 chunk 222 optimal weight: 10.0000 chunk 188 optimal weight: 0.5980 chunk 176 optimal weight: 6.9990 chunk 96 optimal weight: 9.9990 chunk 25 optimal weight: 6.9990 chunk 29 optimal weight: 6.9990 overall best weight: 4.9188 ------------------------------------------------------------------------------- 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 F 249 HIS F 287 HIS I 32 HIS K 249 HIS K 287 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3620 r_free = 0.3620 target = 0.073710 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.063402 restraints weight = 93427.267| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.064777 restraints weight = 56696.935| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.065696 restraints weight = 41035.942| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.066312 restraints weight = 33100.652| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.066717 restraints weight = 28607.158| |-----------------------------------------------------------------------------| r_work (final): 0.3456 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7257 moved from start: 0.1637 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.076 20490 Z= 0.204 Angle : 0.753 16.541 27997 Z= 0.375 Chirality : 0.049 0.661 3296 Planarity : 0.005 0.062 3453 Dihedral : 11.324 91.566 3907 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 7.34 Ramachandran Plot: Outliers : 0.29 % Allowed : 8.36 % Favored : 91.35 % Rotamer: Outliers : 1.40 % Allowed : 10.34 % Favored : 88.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.79 (0.16), residues: 2439 helix: -0.99 (0.26), residues: 393 sheet: -0.31 (0.20), residues: 690 loop : -1.75 (0.15), residues: 1356 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 617 TYR 0.023 0.002 TYR F 61 PHE 0.019 0.002 PHE K 53 TRP 0.019 0.002 TRP B 628 HIS 0.011 0.002 HIS A 249 Details of bonding type rmsd covalent geometry : bond 0.00456 (20382) covalent geometry : angle 0.71624 (27718) SS BOND : bond 0.00326 ( 45) SS BOND : angle 1.88054 ( 90) hydrogen bonds : bond 0.03759 ( 628) hydrogen bonds : angle 5.75250 ( 1788) link_ALPHA1-2 : bond 0.00825 ( 14) link_ALPHA1-2 : angle 2.65833 ( 42) link_ALPHA1-3 : bond 0.00961 ( 9) link_ALPHA1-3 : angle 1.72077 ( 27) link_ALPHA1-6 : bond 0.00354 ( 6) link_ALPHA1-6 : angle 1.93943 ( 18) link_BETA1-4 : bond 0.00630 ( 19) link_BETA1-4 : angle 2.17070 ( 57) link_NAG-ASN : bond 0.00596 ( 15) link_NAG-ASN : angle 3.76883 ( 45) *********************** 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 136 residues out of total 2138 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 106 time to evaluate : 0.711 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 10 VAL cc_start: 0.4960 (p) cc_final: 0.4564 (m) REVERT: G 520 LEU cc_start: 0.6057 (OUTLIER) cc_final: 0.5773 (tp) REVERT: N 10 VAL cc_start: 0.5472 (p) cc_final: 0.5097 (m) outliers start: 30 outliers final: 11 residues processed: 125 average time/residue: 0.1340 time to fit residues: 27.8216 Evaluate side-chains 108 residues out of total 2138 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 96 time to evaluate : 0.780 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 VAL Chi-restraints excluded: chain A residue 249 HIS Chi-restraints excluded: chain A residue 284 ILE Chi-restraints excluded: chain B residue 584 GLU Chi-restraints excluded: chain F residue 284 ILE Chi-restraints excluded: chain G residue 520 LEU Chi-restraints excluded: chain G residue 589 ASP 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 Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: chunk 231 optimal weight: 5.9990 chunk 24 optimal weight: 7.9990 chunk 56 optimal weight: 8.9990 chunk 213 optimal weight: 10.0000 chunk 214 optimal weight: 9.9990 chunk 205 optimal weight: 6.9990 chunk 62 optimal weight: 3.9990 chunk 211 optimal weight: 0.9990 chunk 78 optimal weight: 10.0000 chunk 57 optimal weight: 8.9990 chunk 207 optimal weight: 2.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 249 HIS H 116 HIS K 249 HIS K 422 GLN M 116 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3620 r_free = 0.3620 target = 0.073706 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3374 r_free = 0.3374 target = 0.063293 restraints weight = 93654.528| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.064682 restraints weight = 56609.027| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.065607 restraints weight = 40911.830| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.066227 restraints weight = 33033.210| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.066636 restraints weight = 28568.086| |-----------------------------------------------------------------------------| r_work (final): 0.3455 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7260 moved from start: 0.1899 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 20490 Z= 0.172 Angle : 0.701 16.021 27997 Z= 0.347 Chirality : 0.047 0.621 3296 Planarity : 0.004 0.059 3453 Dihedral : 10.488 87.005 3907 Min Nonbonded Distance : 2.381 Molprobity Statistics. All-atom Clashscore : 7.01 Ramachandran Plot: Outliers : 0.29 % Allowed : 8.24 % Favored : 91.47 % 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 : 0.09 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.71 (0.16), residues: 2439 helix: -0.76 (0.26), residues: 393 sheet: -0.29 (0.20), residues: 688 loop : -1.74 (0.15), residues: 1358 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG F 432 TYR 0.014 0.002 TYR F 61 PHE 0.012 0.002 PHE K 53 TRP 0.032 0.002 TRP B 571 HIS 0.030 0.002 HIS A 249 Details of bonding type rmsd covalent geometry : bond 0.00384 (20382) covalent geometry : angle 0.66570 (27718) SS BOND : bond 0.00358 ( 45) SS BOND : angle 1.65309 ( 90) hydrogen bonds : bond 0.03398 ( 628) hydrogen bonds : angle 5.56540 ( 1788) link_ALPHA1-2 : bond 0.00806 ( 14) link_ALPHA1-2 : angle 2.61245 ( 42) link_ALPHA1-3 : bond 0.00874 ( 9) link_ALPHA1-3 : angle 1.70958 ( 27) link_ALPHA1-6 : bond 0.00333 ( 6) link_ALPHA1-6 : angle 1.92779 ( 18) link_BETA1-4 : bond 0.00499 ( 19) link_BETA1-4 : angle 2.05204 ( 57) link_NAG-ASN : bond 0.00459 ( 15) link_NAG-ASN : angle 3.49401 ( 45) *********************** 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 148 residues out of total 2138 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 101 time to evaluate : 0.819 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 10 VAL cc_start: 0.4621 (p) cc_final: 0.4324 (m) REVERT: F 125 LEU cc_start: 0.8980 (OUTLIER) cc_final: 0.8737 (tt) REVERT: G 520 LEU cc_start: 0.6280 (OUTLIER) cc_final: 0.5839 (tp) REVERT: I 10 VAL cc_start: 0.5095 (p) cc_final: 0.4716 (m) REVERT: L 649 SER cc_start: 0.8393 (t) cc_final: 0.7679 (p) REVERT: N 10 VAL cc_start: 0.5450 (p) cc_final: 0.5117 (m) outliers start: 47 outliers final: 20 residues processed: 137 average time/residue: 0.1287 time to fit residues: 29.8602 Evaluate side-chains 117 residues out of total 2138 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 95 time to evaluate : 0.809 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 VAL 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 112 TRP Chi-restraints excluded: chain F residue 125 LEU Chi-restraints excluded: chain F residue 136 VAL Chi-restraints excluded: chain F residue 202 THR Chi-restraints excluded: chain F residue 249 HIS Chi-restraints excluded: chain F residue 284 ILE Chi-restraints excluded: chain F residue 434 MET Chi-restraints excluded: chain G residue 520 LEU Chi-restraints excluded: chain G residue 589 ASP 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 1 optimal weight: 0.4980 chunk 126 optimal weight: 1.9990 chunk 135 optimal weight: 2.9990 chunk 51 optimal weight: 6.9990 chunk 70 optimal weight: 1.9990 chunk 96 optimal weight: 6.9990 chunk 196 optimal weight: 2.9990 chunk 197 optimal weight: 6.9990 chunk 90 optimal weight: 1.9990 chunk 68 optimal weight: 9.9990 chunk 234 optimal weight: 6.9990 overall best weight: 1.8988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 249 HIS F 422 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 = 0.3639 r_free = 0.3639 target = 0.074475 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.064033 restraints weight = 92907.146| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3428 r_free = 0.3428 target = 0.065438 restraints weight = 55963.000| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.066361 restraints weight = 40387.720| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3467 r_free = 0.3467 target = 0.066990 restraints weight = 32706.418| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3477 r_free = 0.3477 target = 0.067412 restraints weight = 28240.348| |-----------------------------------------------------------------------------| r_work (final): 0.3475 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7223 moved from start: 0.1976 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.072 20490 Z= 0.119 Angle : 0.649 15.660 27997 Z= 0.319 Chirality : 0.046 0.570 3296 Planarity : 0.004 0.054 3453 Dihedral : 9.786 82.282 3907 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 6.50 Ramachandran Plot: Outliers : 0.29 % Allowed : 7.50 % Favored : 92.21 % Rotamer: Outliers : 2.06 % Allowed : 12.82 % Favored : 85.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.54 (0.16), residues: 2439 helix: -0.54 (0.27), residues: 393 sheet: -0.21 (0.20), residues: 693 loop : -1.63 (0.16), residues: 1353 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG H 38 TYR 0.016 0.001 TYR F 61 PHE 0.010 0.001 PHE F 376 TRP 0.026 0.001 TRP B 571 HIS 0.019 0.001 HIS F 249 Details of bonding type rmsd covalent geometry : bond 0.00257 (20382) covalent geometry : angle 0.61047 (27718) SS BOND : bond 0.00413 ( 45) SS BOND : angle 1.97775 ( 90) hydrogen bonds : bond 0.03034 ( 628) hydrogen bonds : angle 5.28803 ( 1788) link_ALPHA1-2 : bond 0.00802 ( 14) link_ALPHA1-2 : angle 2.59773 ( 42) link_ALPHA1-3 : bond 0.00992 ( 9) link_ALPHA1-3 : angle 1.54027 ( 27) link_ALPHA1-6 : bond 0.00411 ( 6) link_ALPHA1-6 : angle 1.77625 ( 18) link_BETA1-4 : bond 0.00443 ( 19) link_BETA1-4 : angle 1.88102 ( 57) link_NAG-ASN : bond 0.00407 ( 15) link_NAG-ASN : angle 3.30158 ( 45) *********************** 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 146 residues out of total 2138 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 102 time to evaluate : 0.815 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 10 VAL cc_start: 0.5096 (p) cc_final: 0.4774 (m) REVERT: F 125 LEU cc_start: 0.8917 (OUTLIER) cc_final: 0.8664 (tt) REVERT: G 520 LEU cc_start: 0.6261 (OUTLIER) cc_final: 0.5793 (tp) REVERT: I 10 VAL cc_start: 0.5200 (p) cc_final: 0.4845 (m) REVERT: L 649 SER cc_start: 0.8351 (t) cc_final: 0.7635 (p) REVERT: N 10 VAL cc_start: 0.5488 (p) cc_final: 0.5179 (m) outliers start: 44 outliers final: 15 residues processed: 141 average time/residue: 0.1282 time to fit residues: 30.6093 Evaluate side-chains 110 residues out of total 2138 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 93 time to evaluate : 0.793 ------------------------------------------------------------------------------- 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 C residue 4 LEU 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 G residue 520 LEU Chi-restraints excluded: chain G residue 589 ASP Chi-restraints excluded: chain K residue 36 VAL Chi-restraints excluded: chain K residue 68 VAL Chi-restraints excluded: chain L residue 530 MET Chi-restraints excluded: chain L residue 622 ILE Chi-restraints excluded: chain M residue 18 VAL Chi-restraints excluded: chain M residue 58 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: chunk 44 optimal weight: 9.9990 chunk 221 optimal weight: 9.9990 chunk 173 optimal weight: 10.0000 chunk 144 optimal weight: 8.9990 chunk 66 optimal weight: 8.9990 chunk 154 optimal weight: 20.0000 chunk 116 optimal weight: 20.0000 chunk 18 optimal weight: 1.9990 chunk 53 optimal weight: 20.0000 chunk 117 optimal weight: 0.3980 chunk 133 optimal weight: 8.9990 overall best weight: 5.8788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 422 GLN C 113 ASN D 32 HIS K 105 HIS K 249 HIS ** 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: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3593 r_free = 0.3593 target = 0.072547 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.062221 restraints weight = 93222.039| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 50)----------------| | r_work = 0.3380 r_free = 0.3380 target = 0.063563 restraints weight = 57109.964| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.064451 restraints weight = 41613.542| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.065021 restraints weight = 33787.653| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.065436 restraints weight = 29462.491| |-----------------------------------------------------------------------------| r_work (final): 0.3425 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7316 moved from start: 0.2405 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.067 20490 Z= 0.225 Angle : 0.763 15.811 27997 Z= 0.376 Chirality : 0.049 0.637 3296 Planarity : 0.005 0.064 3453 Dihedral : 10.318 85.133 3907 Min Nonbonded Distance : 2.407 Molprobity Statistics. All-atom Clashscore : 8.39 Ramachandran Plot: Outliers : 0.25 % Allowed : 9.96 % Favored : 89.79 % Rotamer: Outliers : 2.81 % Allowed : 13.61 % Favored : 83.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.17 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.86 (0.16), residues: 2439 helix: -0.71 (0.26), residues: 393 sheet: -0.42 (0.20), residues: 684 loop : -1.87 (0.15), residues: 1362 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG L 585 TYR 0.015 0.002 TYR A 361 PHE 0.021 0.002 PHE B 522 TRP 0.020 0.002 TRP B 628 HIS 0.012 0.002 HIS K 249 Details of bonding type rmsd covalent geometry : bond 0.00513 (20382) covalent geometry : angle 0.72569 (27718) SS BOND : bond 0.00639 ( 45) SS BOND : angle 2.20046 ( 90) hydrogen bonds : bond 0.03644 ( 628) hydrogen bonds : angle 5.64872 ( 1788) link_ALPHA1-2 : bond 0.00698 ( 14) link_ALPHA1-2 : angle 2.73516 ( 42) link_ALPHA1-3 : bond 0.00774 ( 9) link_ALPHA1-3 : angle 1.68733 ( 27) link_ALPHA1-6 : bond 0.00303 ( 6) link_ALPHA1-6 : angle 1.99200 ( 18) link_BETA1-4 : bond 0.00539 ( 19) link_BETA1-4 : angle 1.95371 ( 57) link_NAG-ASN : bond 0.00525 ( 15) link_NAG-ASN : angle 3.62182 ( 45) *********************** 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 160 residues out of total 2138 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 100 time to evaluate : 0.816 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 626 MET cc_start: 0.5485 (mmm) cc_final: 0.5236 (tpt) REVERT: D 10 VAL cc_start: 0.4974 (p) cc_final: 0.4723 (m) REVERT: F 125 LEU cc_start: 0.9045 (OUTLIER) cc_final: 0.8556 (tt) REVERT: F 426 MET cc_start: 0.7296 (ttp) cc_final: 0.7048 (ttt) REVERT: G 520 LEU cc_start: 0.6337 (OUTLIER) cc_final: 0.5900 (tp) REVERT: G 641 ILE cc_start: 0.8173 (OUTLIER) cc_final: 0.7742 (pt) REVERT: I 10 VAL cc_start: 0.5451 (p) cc_final: 0.5138 (m) REVERT: N 10 VAL cc_start: 0.5357 (p) cc_final: 0.5103 (m) outliers start: 60 outliers final: 38 residues processed: 150 average time/residue: 0.1244 time to fit residues: 31.8369 Evaluate side-chains 136 residues out of total 2138 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 95 time to evaluate : 0.776 ------------------------------------------------------------------------------- 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 125 LEU Chi-restraints excluded: chain A residue 161 THR Chi-restraints excluded: chain A residue 202 THR Chi-restraints excluded: chain A residue 284 ILE Chi-restraints excluded: chain A residue 455 THR Chi-restraints excluded: chain A residue 489 VAL Chi-restraints excluded: chain B residue 529 THR Chi-restraints excluded: chain B residue 584 GLU Chi-restraints excluded: chain B residue 627 THR 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 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 589 ASP Chi-restraints excluded: chain G residue 641 ILE Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain I residue 108 THR Chi-restraints excluded: chain K residue 36 VAL Chi-restraints excluded: chain K residue 42 VAL Chi-restraints excluded: chain K residue 68 VAL Chi-restraints excluded: chain K residue 75 VAL Chi-restraints excluded: chain K residue 202 THR Chi-restraints excluded: chain K residue 284 ILE Chi-restraints excluded: chain K residue 439 ILE Chi-restraints excluded: chain K residue 455 THR Chi-restraints excluded: chain K residue 489 VAL Chi-restraints excluded: chain L residue 530 MET Chi-restraints excluded: chain L residue 622 ILE Chi-restraints excluded: chain 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 108 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: chunk 201 optimal weight: 0.0670 chunk 168 optimal weight: 6.9990 chunk 59 optimal weight: 1.9990 chunk 227 optimal weight: 0.8980 chunk 29 optimal weight: 2.9990 chunk 202 optimal weight: 5.9990 chunk 156 optimal weight: 3.9990 chunk 128 optimal weight: 20.0000 chunk 216 optimal weight: 7.9990 chunk 64 optimal weight: 10.0000 chunk 35 optimal weight: 30.0000 overall best weight: 1.9924 ------------------------------------------------------------------------------- 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 = 0.3627 r_free = 0.3627 target = 0.073985 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3380 r_free = 0.3380 target = 0.063530 restraints weight = 93618.864| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.064912 restraints weight = 56958.538| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.065843 restraints weight = 41283.461| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.066455 restraints weight = 33353.501| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.066847 restraints weight = 28938.527| |-----------------------------------------------------------------------------| r_work (final): 0.3460 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7250 moved from start: 0.2376 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 20490 Z= 0.121 Angle : 0.652 15.387 27997 Z= 0.320 Chirality : 0.046 0.543 3296 Planarity : 0.004 0.055 3453 Dihedral : 9.482 78.813 3907 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 7.14 Ramachandran Plot: Outliers : 0.25 % Allowed : 7.30 % Favored : 92.46 % Rotamer: Outliers : 2.29 % Allowed : 14.55 % Favored : 83.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.64 (0.16), residues: 2439 helix: -0.56 (0.26), residues: 405 sheet: -0.28 (0.20), residues: 669 loop : -1.71 (0.16), residues: 1365 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG F 446 TYR 0.010 0.001 TYR A 484 PHE 0.012 0.001 PHE A 391 TRP 0.017 0.001 TRP B 571 HIS 0.013 0.001 HIS K 249 Details of bonding type rmsd covalent geometry : bond 0.00261 (20382) covalent geometry : angle 0.61436 (27718) SS BOND : bond 0.00502 ( 45) SS BOND : angle 1.98969 ( 90) hydrogen bonds : bond 0.03029 ( 628) hydrogen bonds : angle 5.32486 ( 1788) link_ALPHA1-2 : bond 0.00815 ( 14) link_ALPHA1-2 : angle 2.60699 ( 42) link_ALPHA1-3 : bond 0.00929 ( 9) link_ALPHA1-3 : angle 1.57776 ( 27) link_ALPHA1-6 : bond 0.00435 ( 6) link_ALPHA1-6 : angle 1.77179 ( 18) link_BETA1-4 : bond 0.00434 ( 19) link_BETA1-4 : angle 1.85159 ( 57) link_NAG-ASN : bond 0.00423 ( 15) link_NAG-ASN : angle 3.21526 ( 45) *********************** 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 152 residues out of total 2138 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 103 time to evaluate : 0.750 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 626 MET cc_start: 0.5678 (mmm) cc_final: 0.5463 (tpt) REVERT: D 10 VAL cc_start: 0.4676 (p) cc_final: 0.4459 (m) REVERT: F 125 LEU cc_start: 0.8924 (OUTLIER) cc_final: 0.8553 (tt) REVERT: G 520 LEU cc_start: 0.6411 (OUTLIER) cc_final: 0.5848 (tp) REVERT: G 641 ILE cc_start: 0.8187 (OUTLIER) cc_final: 0.7728 (pt) REVERT: I 10 VAL cc_start: 0.5360 (p) cc_final: 0.5046 (m) outliers start: 49 outliers final: 31 residues processed: 143 average time/residue: 0.1195 time to fit residues: 29.4116 Evaluate side-chains 131 residues out of total 2138 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 97 time to evaluate : 0.810 ------------------------------------------------------------------------------- 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 161 THR Chi-restraints excluded: chain A residue 202 THR Chi-restraints excluded: chain A residue 284 ILE Chi-restraints excluded: chain A residue 455 THR Chi-restraints excluded: chain A residue 489 VAL Chi-restraints excluded: chain B residue 584 GLU Chi-restraints excluded: chain D residue 41 TYR Chi-restraints excluded: chain D residue 108 THR Chi-restraints excluded: chain F residue 68 VAL Chi-restraints excluded: chain F residue 125 LEU Chi-restraints excluded: chain F residue 136 VAL Chi-restraints excluded: chain F residue 202 THR 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 G residue 589 ASP Chi-restraints excluded: chain G residue 641 ILE Chi-restraints excluded: chain K residue 36 VAL Chi-restraints excluded: chain K residue 68 VAL Chi-restraints excluded: chain K residue 202 THR Chi-restraints excluded: chain K residue 284 ILE Chi-restraints excluded: chain K residue 399 TYR Chi-restraints excluded: chain K residue 439 ILE Chi-restraints excluded: chain K residue 489 VAL Chi-restraints excluded: chain L residue 530 MET Chi-restraints excluded: chain L residue 584 GLU Chi-restraints excluded: chain M residue 18 VAL Chi-restraints excluded: chain M residue 58 THR Chi-restraints excluded: chain M residue 69 THR Chi-restraints excluded: chain N residue 105 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: chunk 32 optimal weight: 20.0000 chunk 168 optimal weight: 8.9990 chunk 53 optimal weight: 20.0000 chunk 145 optimal weight: 10.0000 chunk 44 optimal weight: 9.9990 chunk 75 optimal weight: 0.5980 chunk 171 optimal weight: 2.9990 chunk 62 optimal weight: 9.9990 chunk 69 optimal weight: 1.9990 chunk 37 optimal weight: 6.9990 chunk 42 optimal weight: 9.9990 overall best weight: 4.3188 ------------------------------------------------------------------------------- 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 = 0.3606 r_free = 0.3606 target = 0.073083 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.062656 restraints weight = 93732.861| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.064041 restraints weight = 56495.177| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.064958 restraints weight = 40729.513| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3430 r_free = 0.3430 target = 0.065555 restraints weight = 32938.931| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.065953 restraints weight = 28562.405| |-----------------------------------------------------------------------------| r_work (final): 0.3438 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7293 moved from start: 0.2568 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= 0.178 Angle : 0.711 16.729 27997 Z= 0.346 Chirality : 0.047 0.257 3296 Planarity : 0.004 0.060 3453 Dihedral : 9.641 79.108 3907 Min Nonbonded Distance : 2.406 Molprobity Statistics. All-atom Clashscore : 7.88 Ramachandran Plot: Outliers : 0.21 % Allowed : 9.55 % Favored : 90.24 % Rotamer: Outliers : 2.43 % Allowed : 14.50 % Favored : 83.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.77 (0.16), residues: 2439 helix: -0.64 (0.26), residues: 405 sheet: -0.37 (0.20), residues: 664 loop : -1.80 (0.15), residues: 1370 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG F 432 TYR 0.013 0.001 TYR A 484 PHE 0.015 0.002 PHE B 522 TRP 0.044 0.002 TRP G 571 HIS 0.011 0.001 HIS K 249 Details of bonding type rmsd covalent geometry : bond 0.00403 (20382) covalent geometry : angle 0.66708 (27718) SS BOND : bond 0.00490 ( 45) SS BOND : angle 2.04554 ( 90) hydrogen bonds : bond 0.03273 ( 628) hydrogen bonds : angle 5.42033 ( 1788) link_ALPHA1-2 : bond 0.00714 ( 14) link_ALPHA1-2 : angle 2.66793 ( 42) link_ALPHA1-3 : bond 0.00851 ( 9) link_ALPHA1-3 : angle 1.69605 ( 27) link_ALPHA1-6 : bond 0.00345 ( 6) link_ALPHA1-6 : angle 1.89527 ( 18) link_BETA1-4 : bond 0.00497 ( 19) link_BETA1-4 : angle 1.87726 ( 57) link_NAG-ASN : bond 0.00650 ( 15) link_NAG-ASN : angle 4.24260 ( 45) *********************** 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 152 residues out of total 2138 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 100 time to evaluate : 1.265 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 10 VAL cc_start: 0.4728 (p) cc_final: 0.4516 (m) REVERT: F 125 LEU cc_start: 0.8998 (OUTLIER) cc_final: 0.8521 (tt) REVERT: G 520 LEU cc_start: 0.6624 (OUTLIER) cc_final: 0.6028 (tp) REVERT: G 641 ILE cc_start: 0.8228 (OUTLIER) cc_final: 0.7768 (pt) REVERT: I 10 VAL cc_start: 0.5373 (p) cc_final: 0.5097 (m) outliers start: 52 outliers final: 37 residues processed: 144 average time/residue: 0.1283 time to fit residues: 31.1820 Evaluate side-chains 139 residues out of total 2138 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 99 time to evaluate : 0.807 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 68 VAL Chi-restraints excluded: chain A residue 75 VAL Chi-restraints excluded: chain A residue 109 ILE Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 161 THR Chi-restraints excluded: chain A residue 202 THR Chi-restraints excluded: chain A residue 284 ILE Chi-restraints excluded: chain A residue 455 THR Chi-restraints excluded: chain A residue 489 VAL Chi-restraints excluded: chain B residue 584 GLU Chi-restraints excluded: chain D residue 108 THR Chi-restraints excluded: chain F residue 68 VAL Chi-restraints excluded: chain F residue 125 LEU Chi-restraints excluded: chain F residue 136 VAL Chi-restraints excluded: chain F residue 202 THR Chi-restraints excluded: chain F residue 284 ILE Chi-restraints excluded: chain F residue 439 ILE Chi-restraints excluded: chain F residue 455 THR Chi-restraints excluded: chain G residue 520 LEU Chi-restraints excluded: chain G residue 589 ASP Chi-restraints excluded: chain G residue 641 ILE Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain 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 120 VAL Chi-restraints excluded: chain K residue 202 THR 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 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 106 optimal weight: 5.9990 chunk 138 optimal weight: 9.9990 chunk 71 optimal weight: 0.1980 chunk 54 optimal weight: 2.9990 chunk 17 optimal weight: 3.9990 chunk 40 optimal weight: 10.0000 chunk 115 optimal weight: 0.9980 chunk 197 optimal weight: 20.0000 chunk 33 optimal weight: 6.9990 chunk 9 optimal weight: 9.9990 chunk 210 optimal weight: 5.9990 overall best weight: 2.8386 ------------------------------------------------------------------------------- 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 = 0.3619 r_free = 0.3619 target = 0.073621 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.063232 restraints weight = 92652.194| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.064606 restraints weight = 56702.265| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3430 r_free = 0.3430 target = 0.065526 restraints weight = 41174.092| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3444 r_free = 0.3444 target = 0.066130 restraints weight = 33276.612| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3453 r_free = 0.3453 target = 0.066517 restraints weight = 28866.567| |-----------------------------------------------------------------------------| r_work (final): 0.3452 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7270 moved from start: 0.2593 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 20490 Z= 0.139 Angle : 0.671 15.730 27997 Z= 0.328 Chirality : 0.048 0.758 3296 Planarity : 0.004 0.057 3453 Dihedral : 9.254 76.270 3907 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 7.80 Ramachandran Plot: Outliers : 0.25 % Allowed : 8.28 % Favored : 91.47 % Rotamer: Outliers : 1.78 % Allowed : 15.34 % Favored : 82.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.67 (0.16), residues: 2439 helix: -0.53 (0.27), residues: 405 sheet: -0.33 (0.20), residues: 675 loop : -1.73 (0.16), residues: 1359 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG H 38 TYR 0.011 0.001 TYR A 484 PHE 0.011 0.002 PHE A 391 TRP 0.037 0.002 TRP G 571 HIS 0.006 0.001 HIS K 249 Details of bonding type rmsd covalent geometry : bond 0.00307 (20382) covalent geometry : angle 0.63449 (27718) SS BOND : bond 0.00462 ( 45) SS BOND : angle 1.92441 ( 90) hydrogen bonds : bond 0.03078 ( 628) hydrogen bonds : angle 5.30992 ( 1788) link_ALPHA1-2 : bond 0.00766 ( 14) link_ALPHA1-2 : angle 2.62386 ( 42) link_ALPHA1-3 : bond 0.00906 ( 9) link_ALPHA1-3 : angle 1.64134 ( 27) link_ALPHA1-6 : bond 0.00439 ( 6) link_ALPHA1-6 : angle 1.79301 ( 18) link_BETA1-4 : bond 0.00440 ( 19) link_BETA1-4 : angle 1.82532 ( 57) link_NAG-ASN : bond 0.00477 ( 15) link_NAG-ASN : angle 3.30104 ( 45) *********************** 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 137 residues out of total 2138 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 99 time to evaluate : 0.815 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 10 VAL cc_start: 0.4811 (p) cc_final: 0.4549 (m) REVERT: F 125 LEU cc_start: 0.8931 (OUTLIER) cc_final: 0.8441 (tt) REVERT: G 641 ILE cc_start: 0.8226 (OUTLIER) cc_final: 0.7753 (pt) REVERT: I 10 VAL cc_start: 0.5233 (p) cc_final: 0.4970 (m) outliers start: 38 outliers final: 34 residues processed: 133 average time/residue: 0.1279 time to fit residues: 28.9132 Evaluate side-chains 133 residues out of total 2138 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 97 time to evaluate : 0.842 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 68 VAL Chi-restraints excluded: chain A residue 75 VAL Chi-restraints excluded: chain A residue 109 ILE Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 161 THR Chi-restraints excluded: chain A residue 202 THR Chi-restraints excluded: chain A residue 284 ILE Chi-restraints excluded: chain A residue 455 THR Chi-restraints excluded: chain A residue 489 VAL Chi-restraints excluded: chain B residue 584 GLU Chi-restraints excluded: chain D residue 108 THR Chi-restraints excluded: chain F residue 68 VAL Chi-restraints excluded: chain F residue 125 LEU Chi-restraints excluded: chain F residue 136 VAL Chi-restraints excluded: chain F residue 202 THR Chi-restraints excluded: chain F residue 284 ILE Chi-restraints excluded: chain F residue 439 ILE Chi-restraints excluded: chain G residue 589 ASP 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 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 L residue 661 LEU Chi-restraints excluded: chain M residue 18 VAL Chi-restraints excluded: chain M residue 58 THR Chi-restraints excluded: chain M residue 69 THR Chi-restraints excluded: chain N residue 41 TYR Chi-restraints excluded: chain N residue 105 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: chunk 11 optimal weight: 1.9990 chunk 230 optimal weight: 9.9990 chunk 65 optimal weight: 10.0000 chunk 67 optimal weight: 20.0000 chunk 89 optimal weight: 3.9990 chunk 16 optimal weight: 6.9990 chunk 208 optimal weight: 10.0000 chunk 37 optimal weight: 0.9980 chunk 96 optimal weight: 10.0000 chunk 8 optimal weight: 0.0070 chunk 226 optimal weight: 0.8980 overall best weight: 1.5802 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3645 r_free = 0.3645 target = 0.074864 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.064348 restraints weight = 93227.805| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3436 r_free = 0.3436 target = 0.065768 restraints weight = 56180.834| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.066720 restraints weight = 40322.854| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.067338 restraints weight = 32455.218| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.3483 r_free = 0.3483 target = 0.067759 restraints weight = 28061.974| |-----------------------------------------------------------------------------| r_work (final): 0.3482 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7217 moved from start: 0.2654 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 20490 Z= 0.108 Angle : 0.624 15.838 27997 Z= 0.304 Chirality : 0.045 0.575 3296 Planarity : 0.004 0.052 3453 Dihedral : 8.325 68.257 3907 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 6.86 Ramachandran Plot: Outliers : 0.25 % Allowed : 7.54 % Favored : 92.21 % Rotamer: Outliers : 1.64 % Allowed : 15.43 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.49 (0.17), residues: 2439 helix: -0.37 (0.27), residues: 411 sheet: -0.19 (0.21), residues: 664 loop : -1.64 (0.16), residues: 1364 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG K 432 TYR 0.011 0.001 TYR F 484 PHE 0.012 0.001 PHE F 53 TRP 0.037 0.002 TRP G 571 HIS 0.008 0.001 HIS K 249 Details of bonding type rmsd covalent geometry : bond 0.00231 (20382) covalent geometry : angle 0.58906 (27718) SS BOND : bond 0.00416 ( 45) SS BOND : angle 1.73646 ( 90) hydrogen bonds : bond 0.02746 ( 628) hydrogen bonds : angle 5.06834 ( 1788) link_ALPHA1-2 : bond 0.00780 ( 14) link_ALPHA1-2 : angle 2.60683 ( 42) link_ALPHA1-3 : bond 0.00957 ( 9) link_ALPHA1-3 : angle 1.55381 ( 27) link_ALPHA1-6 : bond 0.00579 ( 6) link_ALPHA1-6 : angle 1.59194 ( 18) link_BETA1-4 : bond 0.00427 ( 19) link_BETA1-4 : angle 1.70454 ( 57) link_NAG-ASN : bond 0.00527 ( 15) link_NAG-ASN : angle 3.15626 ( 45) ********************** 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 144 residues out of total 2138 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 109 time to evaluate : 0.467 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 123 LEU cc_start: 0.5902 (tp) cc_final: 0.5658 (tt) REVERT: D 10 VAL cc_start: 0.4451 (p) cc_final: 0.4169 (m) REVERT: F 125 LEU cc_start: 0.8877 (OUTLIER) cc_final: 0.8452 (tt) REVERT: I 10 VAL cc_start: 0.5239 (p) cc_final: 0.4974 (m) REVERT: M 123 LEU cc_start: 0.6172 (tp) cc_final: 0.5793 (tt) outliers start: 35 outliers final: 30 residues processed: 141 average time/residue: 0.1139 time to fit residues: 26.6653 Evaluate side-chains 135 residues out of total 2138 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 104 time to evaluate : 0.615 ------------------------------------------------------------------------------- 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 202 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 D residue 108 THR Chi-restraints excluded: chain F residue 68 VAL Chi-restraints excluded: chain F residue 125 LEU Chi-restraints excluded: chain F residue 136 VAL Chi-restraints excluded: chain F residue 284 ILE Chi-restraints excluded: chain F residue 439 ILE Chi-restraints excluded: chain G residue 584 GLU 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 68 VAL Chi-restraints excluded: chain K residue 120 VAL Chi-restraints excluded: chain K residue 202 THR Chi-restraints excluded: chain K residue 284 ILE Chi-restraints excluded: chain K residue 455 THR Chi-restraints excluded: chain K residue 489 VAL Chi-restraints excluded: chain L residue 661 LEU Chi-restraints excluded: chain M residue 18 VAL Chi-restraints excluded: chain M residue 58 THR Chi-restraints excluded: chain M residue 69 THR Chi-restraints excluded: chain N residue 41 TYR Chi-restraints excluded: chain N residue 105 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: chunk 237 optimal weight: 0.0060 chunk 52 optimal weight: 5.9990 chunk 90 optimal weight: 10.0000 chunk 121 optimal weight: 9.9990 chunk 167 optimal weight: 3.9990 chunk 173 optimal weight: 6.9990 chunk 107 optimal weight: 3.9990 chunk 155 optimal weight: 2.9990 chunk 126 optimal weight: 0.0970 chunk 224 optimal weight: 0.8980 chunk 41 optimal weight: 6.9990 overall best weight: 1.5998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3644 r_free = 0.3644 target = 0.074842 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.064332 restraints weight = 92934.176| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.065755 restraints weight = 55763.931| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3458 r_free = 0.3458 target = 0.066709 restraints weight = 39915.441| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3472 r_free = 0.3472 target = 0.067329 restraints weight = 32071.416| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3482 r_free = 0.3482 target = 0.067754 restraints weight = 27714.522| |-----------------------------------------------------------------------------| r_work (final): 0.3481 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7217 moved from start: 0.2721 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.052 20490 Z= 0.109 Angle : 0.633 16.242 27997 Z= 0.306 Chirality : 0.045 0.255 3296 Planarity : 0.004 0.050 3453 Dihedral : 8.050 67.291 3907 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 7.11 Ramachandran Plot: Outliers : 0.25 % Allowed : 7.01 % Favored : 92.74 % Rotamer: Outliers : 1.73 % Allowed : 15.81 % Favored : 82.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.40 (0.17), residues: 2439 helix: -0.30 (0.27), residues: 411 sheet: -0.12 (0.21), residues: 660 loop : -1.57 (0.16), residues: 1368 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG K 432 TYR 0.021 0.001 TYR K 61 PHE 0.011 0.001 PHE A 53 TRP 0.033 0.001 TRP G 571 HIS 0.004 0.001 HIS K 249 Details of bonding type rmsd covalent geometry : bond 0.00235 (20382) covalent geometry : angle 0.59428 (27718) SS BOND : bond 0.00424 ( 45) SS BOND : angle 1.71951 ( 90) hydrogen bonds : bond 0.02736 ( 628) hydrogen bonds : angle 5.01711 ( 1788) link_ALPHA1-2 : bond 0.00740 ( 14) link_ALPHA1-2 : angle 2.61428 ( 42) link_ALPHA1-3 : bond 0.00932 ( 9) link_ALPHA1-3 : angle 1.51929 ( 27) link_ALPHA1-6 : bond 0.00642 ( 6) link_ALPHA1-6 : angle 1.52853 ( 18) link_BETA1-4 : bond 0.00411 ( 19) link_BETA1-4 : angle 1.65266 ( 57) link_NAG-ASN : bond 0.00585 ( 15) link_NAG-ASN : angle 3.68736 ( 45) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2840.49 seconds wall clock time: 50 minutes 35.40 seconds (3035.40 seconds total)