Starting phenix.real_space_refine on Tue Nov 19 20:51:09 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sar_40277/11_2024/8sar_40277_neut.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sar_40277/11_2024/8sar_40277.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.82 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sar_40277/11_2024/8sar_40277.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sar_40277/11_2024/8sar_40277.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sar_40277/11_2024/8sar_40277_neut.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sar_40277/11_2024/8sar_40277_neut.cif" } resolution = 3.82 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.014 sd= 0.283 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 141 5.16 5 C 12452 2.51 5 N 3335 2.21 5 O 4035 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 52 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/chem_data/mon_lib" Total number of atoms: 19963 Number of models: 1 Model: "" Number of chains: 27 Chain: "A" Number of atoms: 3607 Number of conformers: 1 Conformer: "" Number of residues, atoms: 461, 3607 Classifications: {'peptide': 461} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 23, 'TRANS': 437} Chain breaks: 1 Chain: "B" Number of atoms: 983 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 983 Classifications: {'peptide': 124} Link IDs: {'PTRANS': 1, 'TRANS': 122} Chain: "C" Number of atoms: 996 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 996 Classifications: {'peptide': 126} Link IDs: {'PTRANS': 5, 'TRANS': 120} Chain: "D" Number of atoms: 805 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 805 Classifications: {'peptide': 110} Link IDs: {'PTRANS': 5, 'TRANS': 104} Chain: "F" Number of atoms: 3615 Number of conformers: 1 Conformer: "" Number of residues, atoms: 462, 3615 Classifications: {'peptide': 462} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 23, 'TRANS': 438} Chain: "G" Number of atoms: 983 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 983 Classifications: {'peptide': 124} Link IDs: {'PTRANS': 1, 'TRANS': 122} Chain: "H" Number of atoms: 996 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 996 Classifications: {'peptide': 126} Link IDs: {'PTRANS': 5, 'TRANS': 120} Chain: "I" Number of atoms: 805 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 805 Classifications: {'peptide': 110} Link IDs: {'PTRANS': 5, 'TRANS': 104} Chain: "K" Number of atoms: 3615 Number of conformers: 1 Conformer: "" Number of residues, atoms: 462, 3615 Classifications: {'peptide': 462} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 23, 'TRANS': 438} Chain: "L" Number of atoms: 983 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 983 Classifications: {'peptide': 124} Link IDs: {'PTRANS': 1, 'TRANS': 122} Chain: "M" Number of atoms: 996 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 996 Classifications: {'peptide': 126} Link IDs: {'PTRANS': 5, 'TRANS': 120} Chain: "N" Number of atoms: 805 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 805 Classifications: {'peptide': 110} Link IDs: {'PTRANS': 5, 'TRANS': 104} Chain: "J" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "O" Number of atoms: 127 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 127 Unusual residues: {'BMA': 1, 'MAN': 8, 'NAG': 2} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 33 Unresolved non-hydrogen chiralities: 11 Chain: "P" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Q" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "S" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "T" Number of atoms: 116 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 116 Unusual residues: {'BMA': 1, 'MAN': 7, 'NAG': 2} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 10 Chain: "U" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "V" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "X" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "Y" Number of atoms: 127 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 127 Unusual residues: {'BMA': 1, 'MAN': 8, 'NAG': 2} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 33 Unresolved non-hydrogen chiralities: 11 Chain: "Z" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "a" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "F" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "K" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 13.12, per 1000 atoms: 0.66 Number of scatterers: 19963 At special positions: 0 Unit cell: (157.768, 157.768, 137.514, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 141 16.00 O 4035 8.00 N 3335 7.00 C 12452 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=45, symmetry=0 Simple disulfide: pdb=" SG CYS A 54 " - pdb=" SG CYS A 74 " distance=2.03 Simple disulfide: pdb=" SG CYS A 119 " - pdb=" SG CYS A 205 " distance=2.03 Simple disulfide: pdb=" SG CYS A 126 " - pdb=" SG CYS A 196 " distance=2.03 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 157 " distance=2.03 Simple disulfide: pdb=" SG CYS A 201 " - pdb=" SG CYS A 433 " distance=2.04 Simple disulfide: pdb=" SG CYS A 218 " - pdb=" SG CYS A 247 " distance=2.03 Simple disulfide: pdb=" SG CYS A 228 " - pdb=" SG CYS A 239 " distance=2.03 Simple disulfide: pdb=" SG CYS A 296 " - pdb=" SG CYS A 331 " distance=2.05 Simple disulfide: pdb=" SG CYS A 378 " - pdb=" SG CYS A 445 " distance=2.04 Simple disulfide: pdb=" SG CYS A 385 " - pdb=" SG CYS A 418 " distance=2.03 Simple disulfide: pdb=" SG CYS A 501 " - pdb=" SG CYS B 605 " distance=2.03 Simple disulfide: pdb=" SG CYS B 598 " - pdb=" SG CYS B 604 " distance=2.03 Simple disulfide: pdb=" SG CYS C 22 " - pdb=" SG CYS C 96 " distance=2.03 Simple disulfide: pdb=" SG CYS D 22 " - pdb=" SG CYS D 90 " distance=2.03 Simple disulfide: pdb=" SG CYS D 91 " - pdb=" SG CYS D 101 " distance=2.03 Simple disulfide: pdb=" SG CYS F 54 " - pdb=" SG CYS F 74 " distance=2.03 Simple disulfide: pdb=" SG CYS F 119 " - pdb=" SG CYS F 205 " distance=2.03 Simple disulfide: pdb=" SG CYS F 126 " - pdb=" SG CYS F 196 " distance=2.02 Simple disulfide: pdb=" SG CYS F 131 " - pdb=" SG CYS F 157 " distance=2.03 Simple disulfide: pdb=" SG CYS F 201 " - pdb=" SG CYS F 433 " distance=2.04 Simple disulfide: pdb=" SG CYS F 218 " - pdb=" SG CYS F 247 " distance=2.03 Simple disulfide: pdb=" SG CYS F 228 " - pdb=" SG CYS F 239 " distance=2.03 Simple disulfide: pdb=" SG CYS F 296 " - pdb=" SG CYS F 331 " distance=2.05 Simple disulfide: pdb=" SG CYS F 378 " - pdb=" SG CYS F 445 " distance=2.04 Simple disulfide: pdb=" SG CYS F 385 " - pdb=" SG CYS F 418 " distance=2.03 Simple disulfide: pdb=" SG CYS F 501 " - pdb=" SG CYS G 605 " distance=2.03 Simple disulfide: pdb=" SG CYS G 598 " - pdb=" SG CYS G 604 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.03 Simple disulfide: pdb=" SG CYS I 22 " - pdb=" SG CYS I 90 " distance=2.03 Simple disulfide: pdb=" SG CYS I 91 " - pdb=" SG CYS I 101 " distance=2.03 Simple disulfide: pdb=" SG CYS K 54 " - pdb=" SG CYS K 74 " distance=2.03 Simple disulfide: pdb=" SG CYS K 119 " - pdb=" SG CYS K 205 " distance=2.03 Simple disulfide: pdb=" SG CYS K 126 " - pdb=" SG CYS K 196 " distance=2.03 Simple disulfide: pdb=" SG CYS K 131 " - pdb=" SG CYS K 157 " distance=2.03 Simple disulfide: pdb=" SG CYS K 201 " - pdb=" SG CYS K 433 " distance=2.04 Simple disulfide: pdb=" SG CYS K 218 " - pdb=" SG CYS K 247 " distance=2.03 Simple disulfide: pdb=" SG CYS K 228 " - pdb=" SG CYS K 239 " distance=2.03 Simple disulfide: pdb=" SG CYS K 296 " - pdb=" SG CYS K 331 " distance=2.05 Simple disulfide: pdb=" SG CYS K 378 " - pdb=" SG CYS K 445 " distance=2.03 Simple disulfide: pdb=" SG CYS K 385 " - pdb=" SG CYS K 418 " distance=2.03 Simple disulfide: pdb=" SG CYS K 501 " - pdb=" SG CYS L 605 " distance=2.03 Simple disulfide: pdb=" SG CYS L 598 " - pdb=" SG CYS L 604 " distance=2.03 Simple disulfide: pdb=" SG CYS M 22 " - pdb=" SG CYS M 96 " distance=2.03 Simple disulfide: pdb=" SG CYS N 22 " - pdb=" SG CYS N 90 " distance=2.03 Simple disulfide: pdb=" SG CYS N 91 " - pdb=" SG CYS N 101 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied ALPHA1-2 " MAN J 4 " - " MAN J 5 " " MAN O 4 " - " MAN O 5 " " MAN O 5 " - " MAN O 6 " " MAN O 8 " - " MAN O 9 " " MAN O 10 " - " MAN O 11 " " MAN S 4 " - " MAN S 5 " " MAN T 4 " - " MAN T 5 " " MAN T 5 " - " MAN T 6 " " MAN T 8 " - " MAN T 9 " " MAN X 4 " - " MAN X 5 " " MAN Y 4 " - " MAN Y 5 " " MAN Y 5 " - " MAN Y 6 " " MAN Y 8 " - " MAN Y 9 " " MAN Y 10 " - " MAN Y 11 " ALPHA1-3 " BMA J 3 " - " MAN J 4 " " BMA O 3 " - " MAN O 4 " " MAN O 7 " - " MAN O 8 " " BMA S 3 " - " MAN S 4 " " BMA T 3 " - " MAN T 4 " " MAN T 7 " - " MAN T 10 " " BMA X 3 " - " MAN X 4 " " BMA Y 3 " - " MAN Y 4 " " MAN Y 7 " - " MAN Y 8 " ALPHA1-6 " BMA O 3 " - " MAN O 7 " " MAN O 7 " - " MAN O 10 " " BMA T 3 " - " MAN T 7 " " MAN T 7 " - " MAN T 8 " " BMA Y 3 " - " MAN Y 7 " " MAN Y 7 " - " MAN Y 10 " BETA1-4 " NAG J 1 " - " NAG J 2 " " NAG J 2 " - " BMA J 3 " " NAG O 1 " - " NAG O 2 " " NAG O 2 " - " BMA O 3 " " NAG P 1 " - " NAG P 2 " " NAG Q 1 " - " NAG Q 2 " " NAG Q 2 " - " BMA Q 3 " " NAG S 1 " - " NAG S 2 " " NAG S 2 " - " BMA S 3 " " NAG T 1 " - " NAG T 2 " " NAG T 2 " - " BMA T 3 " " NAG U 1 " - " NAG U 2 " " NAG V 1 " - " NAG V 2 " " NAG X 1 " - " NAG X 2 " " NAG X 2 " - " BMA X 3 " " NAG Y 1 " - " NAG Y 2 " " NAG Y 2 " - " BMA Y 3 " " NAG Z 1 " - " NAG Z 2 " " NAG a 1 " - " NAG a 2 " NAG-ASN " NAG A 601 " - " ASN A 138 " " NAG F 601 " - " ASN F 138 " " NAG J 1 " - " ASN A 301 " " NAG K 601 " - " ASN K 138 " " NAG O 1 " - " ASN A 332 " " NAG P 1 " - " ASN A 156 " " NAG Q 1 " - " ASN A 442 " " NAG S 1 " - " ASN F 301 " " NAG T 1 " - " ASN F 332 " " NAG U 1 " - " ASN F 156 " " NAG V 1 " - " ASN F 442 " " NAG X 1 " - " ASN K 301 " " NAG Y 1 " - " ASN K 332 " " NAG Z 1 " - " ASN K 156 " " NAG a 1 " - " ASN K 442 " Time building additional restraints: 5.72 Conformation dependent library (CDL) restraints added in 2.5 seconds 4878 Ramachandran restraints generated. 2439 Oldfield, 0 Emsley, 2439 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4540 Finding SS restraints... Secondary structure from input PDB file: 50 helices and 53 sheets defined 19.0% alpha, 32.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.19 Creating SS restraints... Processing helix chain 'A' and resid 58 through 63 Processing helix chain 'A' and resid 68 through 73 removed outlier: 3.573A pdb=" N HIS A 72 " --> pdb=" O VAL A 68 " (cutoff:3.500A) Processing helix chain 'A' and resid 98 through 115 removed outlier: 4.281A pdb=" N ASP A 102 " --> pdb=" O ASN A 98 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N GLU A 106 " --> pdb=" O ASP A 102 " (cutoff:3.500A) Processing helix chain 'A' and resid 123 through 127 removed outlier: 4.017A pdb=" N VAL A 127 " --> pdb=" O PRO A 124 " (cutoff:3.500A) Processing helix chain 'A' and resid 335 through 351 Processing helix chain 'A' and resid 368 through 373 removed outlier: 3.669A pdb=" N THR A 373 " --> pdb=" O MET A 369 " (cutoff:3.500A) Processing helix chain 'A' and resid 387 through 391 Processing helix chain 'A' and resid 475 through 480 removed outlier: 3.689A pdb=" N TRP A 479 " --> pdb=" O MET A 475 " (cutoff:3.500A) Processing helix chain 'B' and resid 537 through 542 Processing helix chain 'B' and resid 572 through 596 removed outlier: 3.571A pdb=" N LEU B 576 " --> pdb=" O GLY B 572 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N TRP B 596 " --> pdb=" O LEU B 592 " (cutoff:3.500A) Processing helix chain 'B' and resid 618 through 624 removed outlier: 3.588A pdb=" N ASP B 624 " --> pdb=" O SER B 620 " (cutoff:3.500A) Processing helix chain 'B' and resid 627 through 636 removed outlier: 3.831A pdb=" N GLU B 634 " --> pdb=" O GLN B 630 " (cutoff:3.500A) Processing helix chain 'B' and resid 638 through 663 removed outlier: 4.450A pdb=" N GLY B 644 " --> pdb=" O GLN B 640 " (cutoff:3.500A) removed outlier: 4.385A pdb=" N GLU B 647 " --> pdb=" O TYR B 643 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N GLN B 653 " --> pdb=" O SER B 649 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N GLU B 654 " --> pdb=" O GLN B 650 " (cutoff:3.500A) removed outlier: 4.868A pdb=" N LYS B 655 " --> pdb=" O ASN B 651 " (cutoff:3.500A) removed outlier: 6.398A pdb=" N ASN B 656 " --> pdb=" O GLN B 652 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N GLU B 657 " --> pdb=" O GLN B 653 " (cutoff:3.500A) Processing helix chain 'C' and resid 61 through 65 removed outlier: 3.646A pdb=" N GLN C 65 " --> pdb=" O ARG C 62 " (cutoff:3.500A) Processing helix chain 'C' and resid 87 through 91 Processing helix chain 'D' and resid 81 through 85 removed outlier: 3.505A pdb=" N ASP D 84 " --> pdb=" O ARG D 81 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N GLU D 85 " --> pdb=" O ALA D 82 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 81 through 85' Processing helix chain 'F' and resid 58 through 63 Processing helix chain 'F' and resid 68 through 73 removed outlier: 3.534A pdb=" N HIS F 72 " --> pdb=" O VAL F 68 " (cutoff:3.500A) Processing helix chain 'F' and resid 98 through 115 removed outlier: 4.222A pdb=" N ASP F 102 " --> pdb=" O ASN F 98 " (cutoff:3.500A) removed outlier: 4.252A pdb=" N GLU F 106 " --> pdb=" O ASP F 102 " (cutoff:3.500A) Processing helix chain 'F' and resid 123 through 127 removed outlier: 3.904A pdb=" N CYS F 126 " --> pdb=" O THR F 123 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N VAL F 127 " --> pdb=" O PRO F 124 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 123 through 127' Processing helix chain 'F' and resid 335 through 351 Processing helix chain 'F' and resid 368 through 373 removed outlier: 3.877A pdb=" N THR F 373 " --> pdb=" O MET F 369 " (cutoff:3.500A) Processing helix chain 'F' and resid 387 through 391 Processing helix chain 'F' and resid 475 through 480 Processing helix chain 'F' and resid 481 through 484 removed outlier: 5.132A pdb=" N TYR F 484 " --> pdb=" O SER F 481 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 481 through 484' Processing helix chain 'G' and resid 537 through 542 Processing helix chain 'G' and resid 572 through 596 removed outlier: 3.648A pdb=" N LEU G 576 " --> pdb=" O GLY G 572 " (cutoff:3.500A) removed outlier: 4.122A pdb=" N TRP G 596 " --> pdb=" O LEU G 592 " (cutoff:3.500A) Processing helix chain 'G' and resid 611 through 616 removed outlier: 4.319A pdb=" N SER G 615 " --> pdb=" O ASN G 611 " (cutoff:3.500A) Processing helix chain 'G' and resid 619 through 624 Processing helix chain 'G' and resid 627 through 636 removed outlier: 3.762A pdb=" N GLU G 634 " --> pdb=" O GLN G 630 " (cutoff:3.500A) Processing helix chain 'G' and resid 638 through 649 removed outlier: 4.024A pdb=" N GLY G 644 " --> pdb=" O GLN G 640 " (cutoff:3.500A) removed outlier: 4.238A pdb=" N GLU G 647 " --> pdb=" O TYR G 643 " (cutoff:3.500A) Processing helix chain 'G' and resid 653 through 663 Processing helix chain 'H' and resid 87 through 91 Processing helix chain 'K' and resid 58 through 63 Processing helix chain 'K' and resid 68 through 74 Processing helix chain 'K' and resid 98 through 115 removed outlier: 4.233A pdb=" N ASP K 102 " --> pdb=" O ASN K 98 " (cutoff:3.500A) removed outlier: 4.185A pdb=" N GLU K 106 " --> pdb=" O ASP K 102 " (cutoff:3.500A) Processing helix chain 'K' and resid 123 through 127 removed outlier: 4.033A pdb=" N VAL K 127 " --> pdb=" O PRO K 124 " (cutoff:3.500A) Processing helix chain 'K' and resid 335 through 350 Processing helix chain 'K' and resid 368 through 373 removed outlier: 3.826A pdb=" N THR K 373 " --> pdb=" O MET K 369 " (cutoff:3.500A) Processing helix chain 'K' and resid 387 through 391 Processing helix chain 'K' and resid 475 through 480 removed outlier: 3.614A pdb=" N TRP K 479 " --> pdb=" O MET K 475 " (cutoff:3.500A) Processing helix chain 'L' and resid 537 through 542 Processing helix chain 'L' and resid 572 through 596 removed outlier: 3.576A pdb=" N LEU L 576 " --> pdb=" O GLY L 572 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N TRP L 596 " --> pdb=" O LEU L 592 " (cutoff:3.500A) Processing helix chain 'L' and resid 611 through 615 Processing helix chain 'L' and resid 619 through 624 Processing helix chain 'L' and resid 627 through 636 removed outlier: 3.845A pdb=" N GLU L 634 " --> pdb=" O GLN L 630 " (cutoff:3.500A) Processing helix chain 'L' and resid 638 through 652 removed outlier: 4.110A pdb=" N GLY L 644 " --> pdb=" O GLN L 640 " (cutoff:3.500A) removed outlier: 4.311A pdb=" N GLU L 647 " --> pdb=" O TYR L 643 " (cutoff:3.500A) Processing helix chain 'L' and resid 654 through 663 removed outlier: 4.300A pdb=" N LEU L 660 " --> pdb=" O ASN L 656 " (cutoff:3.500A) Processing helix chain 'M' and resid 87 through 91 Processing helix chain 'N' and resid 81 through 85 removed outlier: 3.531A pdb=" N ASP N 84 " --> pdb=" O ARG N 81 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N GLU N 85 " --> pdb=" O ALA N 82 " (cutoff:3.500A) No H-bonds generated for 'chain 'N' and resid 81 through 85' Processing sheet with id=AA1, first strand: chain 'A' and resid 494 through 499 removed outlier: 5.142A pdb=" N VAL A 36 " --> pdb=" O THR B 606 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N CYS B 604 " --> pdb=" O VAL A 38 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 45 through 46 removed outlier: 3.517A pdb=" N ILE A 225 " --> pdb=" O VAL A 245 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 75 through 76 removed outlier: 3.628A pdb=" N PHE A 53 " --> pdb=" O CYS A 218 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 91 through 94 removed outlier: 3.533A pdb=" N GLU A 91 " --> pdb=" O CYS A 239 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 130 through 131 Processing sheet with id=AA6, first strand: chain 'A' and resid 181 through 183 Processing sheet with id=AA7, first strand: chain 'A' and resid 259 through 260 removed outlier: 3.742A pdb=" N GLY A 451 " --> pdb=" O LEU A 260 " (cutoff:3.500A) removed outlier: 7.508A pdb=" N GLY A 451 " --> pdb=" O THR A 290 " (cutoff:3.500A) removed outlier: 11.165A pdb=" N THR A 290 " --> pdb=" O GLY A 451 " (cutoff:3.500A) removed outlier: 12.140A pdb=" N LEU A 453 " --> pdb=" O LEU A 288 " (cutoff:3.500A) removed outlier: 11.989A pdb=" N LEU A 288 " --> pdb=" O LEU A 453 " (cutoff:3.500A) removed outlier: 11.004A pdb=" N THR A 455 " --> pdb=" O VAL A 286 " (cutoff:3.500A) removed outlier: 11.228A pdb=" N VAL A 286 " --> pdb=" O THR A 455 " (cutoff:3.500A) removed outlier: 7.518A pdb=" N GLU A 293 " --> pdb=" O SER A 334 " (cutoff:3.500A) removed outlier: 4.800A pdb=" N SER A 334 " --> pdb=" O GLU A 293 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N VAL A 295 " --> pdb=" O ASN A 332 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N ASN A 332 " --> pdb=" O VAL A 295 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N THR A 297 " --> pdb=" O HIS A 330 " (cutoff:3.500A) removed outlier: 4.206A pdb=" N HIS A 330 " --> pdb=" O THR A 297 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N LYS A 421 " --> pdb=" O PHE A 382 " (cutoff:3.500A) removed outlier: 4.499A pdb=" N PHE A 382 " --> pdb=" O LYS A 421 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 271 through 273 removed outlier: 11.228A pdb=" N VAL A 286 " --> pdb=" O THR A 455 " (cutoff:3.500A) removed outlier: 11.004A pdb=" N THR A 455 " --> pdb=" O VAL A 286 " (cutoff:3.500A) removed outlier: 11.989A pdb=" N LEU A 288 " --> pdb=" O LEU A 453 " (cutoff:3.500A) removed outlier: 12.140A pdb=" N LEU A 453 " --> pdb=" O LEU A 288 " (cutoff:3.500A) removed outlier: 11.165A pdb=" N THR A 290 " --> pdb=" O GLY A 451 " (cutoff:3.500A) removed outlier: 7.508A pdb=" N GLY A 451 " --> pdb=" O THR A 290 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 304 through 308 Processing sheet with id=AB1, first strand: chain 'A' and resid 359 through 360 Processing sheet with id=AB2, first strand: chain 'C' and resid 3 through 6 Processing sheet with id=AB3, first strand: chain 'C' and resid 10 through 12 removed outlier: 5.144A pdb=" N TYR C 33 " --> pdb=" O GLY C 99 " (cutoff:3.500A) removed outlier: 6.599A pdb=" N ILE C 34 " --> pdb=" O TRP C 50 " (cutoff:3.500A) removed outlier: 4.424A pdb=" N TRP C 50 " --> pdb=" O ILE C 34 " (cutoff:3.500A) removed outlier: 6.384A pdb=" N TRP C 36 " --> pdb=" O MET C 48 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 18 through 20 Processing sheet with id=AB5, first strand: chain 'D' and resid 9 through 12 removed outlier: 6.608A pdb=" N TRP D 37 " --> pdb=" O MET D 49 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 9 through 12 Processing sheet with id=AB7, first strand: chain 'D' and resid 18 through 23 Processing sheet with id=AB8, first strand: chain 'D' and resid 18 through 23 Processing sheet with id=AB9, first strand: chain 'F' and resid 494 through 499 removed outlier: 4.990A pdb=" N VAL F 36 " --> pdb=" O THR G 606 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N CYS G 604 " --> pdb=" O VAL F 38 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'F' and resid 45 through 47 removed outlier: 3.756A pdb=" N ILE F 225 " --> pdb=" O VAL F 245 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'F' and resid 75 through 76 removed outlier: 7.007A pdb=" N CYS F 54 " --> pdb=" O VAL F 75 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'F' and resid 91 through 94 Processing sheet with id=AC4, first strand: chain 'F' and resid 170 through 177 Processing sheet with id=AC5, first strand: chain 'F' and resid 202 through 203 removed outlier: 6.678A pdb=" N THR F 202 " --> pdb=" O TYR F 435 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'F' and resid 259 through 260 removed outlier: 3.759A pdb=" N GLY F 451 " --> pdb=" O LEU F 260 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N ILE F 443 " --> pdb=" O ARG F 298 " (cutoff:3.500A) removed outlier: 7.462A pdb=" N GLY F 451 " --> pdb=" O THR F 290 " (cutoff:3.500A) removed outlier: 11.092A pdb=" N THR F 290 " --> pdb=" O GLY F 451 " (cutoff:3.500A) removed outlier: 12.079A pdb=" N LEU F 453 " --> pdb=" O LEU F 288 " (cutoff:3.500A) removed outlier: 11.964A pdb=" N LEU F 288 " --> pdb=" O LEU F 453 " (cutoff:3.500A) removed outlier: 10.994A pdb=" N THR F 455 " --> pdb=" O VAL F 286 " (cutoff:3.500A) removed outlier: 11.188A pdb=" N VAL F 286 " --> pdb=" O THR F 455 " (cutoff:3.500A) removed outlier: 7.504A pdb=" N GLU F 293 " --> pdb=" O SER F 334 " (cutoff:3.500A) removed outlier: 4.764A pdb=" N SER F 334 " --> pdb=" O GLU F 293 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N VAL F 295 " --> pdb=" O ASN F 332 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N ASN F 332 " --> pdb=" O VAL F 295 " (cutoff:3.500A) removed outlier: 4.058A pdb=" N THR F 297 " --> pdb=" O HIS F 330 " (cutoff:3.500A) removed outlier: 4.198A pdb=" N HIS F 330 " --> pdb=" O THR F 297 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N LYS F 421 " --> pdb=" O PHE F 382 " (cutoff:3.500A) removed outlier: 4.432A pdb=" N PHE F 382 " --> pdb=" O LYS F 421 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'F' and resid 271 through 273 removed outlier: 11.188A pdb=" N VAL F 286 " --> pdb=" O THR F 455 " (cutoff:3.500A) removed outlier: 10.994A pdb=" N THR F 455 " --> pdb=" O VAL F 286 " (cutoff:3.500A) removed outlier: 11.964A pdb=" N LEU F 288 " --> pdb=" O LEU F 453 " (cutoff:3.500A) removed outlier: 12.079A pdb=" N LEU F 453 " --> pdb=" O LEU F 288 " (cutoff:3.500A) removed outlier: 11.092A pdb=" N THR F 290 " --> pdb=" O GLY F 451 " (cutoff:3.500A) removed outlier: 7.462A pdb=" N GLY F 451 " --> pdb=" O THR F 290 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N ILE F 443 " --> pdb=" O ARG F 298 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'F' and resid 304 through 308 Processing sheet with id=AC9, first strand: chain 'F' and resid 359 through 360 Processing sheet with id=AD1, first strand: chain 'H' and resid 3 through 6 Processing sheet with id=AD2, first strand: chain 'H' and resid 10 through 12 removed outlier: 5.140A pdb=" N TYR H 33 " --> pdb=" O GLY H 99 " (cutoff:3.500A) removed outlier: 6.752A pdb=" N ILE H 34 " --> pdb=" O TRP H 50 " (cutoff:3.500A) removed outlier: 4.494A pdb=" N TRP H 50 " --> pdb=" O ILE H 34 " (cutoff:3.500A) removed outlier: 6.378A pdb=" N TRP H 36 " --> pdb=" O MET H 48 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'H' and resid 10 through 12 removed outlier: 4.118A pdb=" N HIS H 116 " --> pdb=" O THR H 98 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'H' and resid 18 through 20 Processing sheet with id=AD5, first strand: chain 'I' and resid 9 through 12 removed outlier: 3.604A pdb=" N GLY I 12 " --> pdb=" O THR I 108 " (cutoff:3.500A) removed outlier: 6.660A pdb=" N TRP I 37 " --> pdb=" O MET I 49 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N MET I 49 " --> pdb=" O TRP I 37 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'I' and resid 9 through 12 removed outlier: 3.604A pdb=" N GLY I 12 " --> pdb=" O THR I 108 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'I' and resid 18 through 23 Processing sheet with id=AD8, first strand: chain 'I' and resid 18 through 23 Processing sheet with id=AD9, first strand: chain 'K' and resid 494 through 499 removed outlier: 5.166A pdb=" N VAL K 36 " --> pdb=" O THR L 606 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N CYS L 604 " --> pdb=" O VAL K 38 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'K' and resid 45 through 46 removed outlier: 3.525A pdb=" N ILE K 225 " --> pdb=" O VAL K 245 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'K' and resid 75 through 76 Processing sheet with id=AE3, first strand: chain 'K' and resid 91 through 94 removed outlier: 3.517A pdb=" N GLU K 91 " --> pdb=" O CYS K 239 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'K' and resid 170 through 177 Processing sheet with id=AE5, first strand: chain 'K' and resid 259 through 260 removed outlier: 3.744A pdb=" N GLY K 451 " --> pdb=" O LEU K 260 " (cutoff:3.500A) removed outlier: 7.515A pdb=" N GLY K 451 " --> pdb=" O THR K 290 " (cutoff:3.500A) removed outlier: 11.205A pdb=" N THR K 290 " --> pdb=" O GLY K 451 " (cutoff:3.500A) removed outlier: 12.030A pdb=" N LEU K 453 " --> pdb=" O LEU K 288 " (cutoff:3.500A) removed outlier: 11.892A pdb=" N LEU K 288 " --> pdb=" O LEU K 453 " (cutoff:3.500A) removed outlier: 10.969A pdb=" N THR K 455 " --> pdb=" O VAL K 286 " (cutoff:3.500A) removed outlier: 11.192A pdb=" N VAL K 286 " --> pdb=" O THR K 455 " (cutoff:3.500A) removed outlier: 7.531A pdb=" N GLU K 293 " --> pdb=" O SER K 334 " (cutoff:3.500A) removed outlier: 4.788A pdb=" N SER K 334 " --> pdb=" O GLU K 293 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N VAL K 295 " --> pdb=" O ASN K 332 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N ASN K 332 " --> pdb=" O VAL K 295 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N THR K 297 " --> pdb=" O HIS K 330 " (cutoff:3.500A) removed outlier: 4.212A pdb=" N HIS K 330 " --> pdb=" O THR K 297 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N LYS K 421 " --> pdb=" O PHE K 382 " (cutoff:3.500A) removed outlier: 4.459A pdb=" N PHE K 382 " --> pdb=" O LYS K 421 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'K' and resid 271 through 273 removed outlier: 11.192A pdb=" N VAL K 286 " --> pdb=" O THR K 455 " (cutoff:3.500A) removed outlier: 10.969A pdb=" N THR K 455 " --> pdb=" O VAL K 286 " (cutoff:3.500A) removed outlier: 11.892A pdb=" N LEU K 288 " --> pdb=" O LEU K 453 " (cutoff:3.500A) removed outlier: 12.030A pdb=" N LEU K 453 " --> pdb=" O LEU K 288 " (cutoff:3.500A) removed outlier: 11.205A pdb=" N THR K 290 " --> pdb=" O GLY K 451 " (cutoff:3.500A) removed outlier: 7.515A pdb=" N GLY K 451 " --> pdb=" O THR K 290 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'K' and resid 302 through 308 removed outlier: 5.938A pdb=" N THR K 303 " --> pdb=" O GLY K 321 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'K' and resid 359 through 360 Processing sheet with id=AE9, first strand: chain 'K' and resid 423 through 424 Processing sheet with id=AF1, first strand: chain 'M' and resid 3 through 6 Processing sheet with id=AF2, first strand: chain 'M' and resid 10 through 12 removed outlier: 5.140A pdb=" N TYR M 33 " --> pdb=" O GLY M 99 " (cutoff:3.500A) removed outlier: 6.744A pdb=" N ILE M 34 " --> pdb=" O TRP M 50 " (cutoff:3.500A) removed outlier: 4.517A pdb=" N TRP M 50 " --> pdb=" O ILE M 34 " (cutoff:3.500A) removed outlier: 6.531A pdb=" N TRP M 36 " --> pdb=" O MET M 48 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'M' and resid 10 through 12 removed outlier: 4.106A pdb=" N HIS M 116 " --> pdb=" O THR M 98 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'M' and resid 18 through 20 Processing sheet with id=AF5, first strand: chain 'N' and resid 9 through 12 removed outlier: 6.697A pdb=" N TRP N 37 " --> pdb=" O MET N 49 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N MET N 49 " --> pdb=" O TRP N 37 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'N' and resid 9 through 12 Processing sheet with id=AF7, first strand: chain 'N' and resid 18 through 23 Processing sheet with id=AF8, first strand: chain 'N' and resid 18 through 23 693 hydrogen bonds defined for protein. 1788 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 7.43 Time building geometry restraints manager: 6.50 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.35: 6333 1.35 - 1.47: 5310 1.47 - 1.60: 8544 1.60 - 1.73: 4 1.73 - 1.86: 191 Bond restraints: 20382 Sorted by residual: bond pdb=" C1 MAN T 10 " pdb=" C2 MAN T 10 " ideal model delta sigma weight residual 1.526 1.611 -0.085 2.00e-02 2.50e+03 1.81e+01 bond pdb=" C1 MAN Y 8 " pdb=" C2 MAN Y 8 " ideal model delta sigma weight residual 1.526 1.611 -0.085 2.00e-02 2.50e+03 1.81e+01 bond pdb=" C1 MAN O 8 " pdb=" C2 MAN O 8 " ideal model delta sigma weight residual 1.526 1.607 -0.081 2.00e-02 2.50e+03 1.65e+01 bond pdb=" C2 MAN Y 8 " pdb=" O2 MAN Y 8 " ideal model delta sigma weight residual 1.407 1.480 -0.073 2.00e-02 2.50e+03 1.34e+01 bond pdb=" C2 MAN T 10 " pdb=" O2 MAN T 10 " ideal model delta sigma weight residual 1.407 1.480 -0.073 2.00e-02 2.50e+03 1.33e+01 ... (remaining 20377 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.85: 27310 3.85 - 7.70: 370 7.70 - 11.55: 35 11.55 - 15.40: 2 15.40 - 19.25: 1 Bond angle restraints: 27718 Sorted by residual: angle pdb=" C LEU F 122 " pdb=" N THR F 123 " pdb=" CA THR F 123 " ideal model delta sigma weight residual 121.80 141.05 -19.25 2.44e+00 1.68e-01 6.22e+01 angle pdb=" N ASN G 651 " pdb=" CA ASN G 651 " pdb=" C ASN G 651 " ideal model delta sigma weight residual 112.57 103.79 8.78 1.13e+00 7.83e-01 6.03e+01 angle pdb=" C LEU K 122 " pdb=" N THR K 123 " pdb=" CA THR K 123 " ideal model delta sigma weight residual 121.80 137.14 -15.34 2.44e+00 1.68e-01 3.95e+01 angle pdb=" C LEU A 122 " pdb=" N THR A 123 " pdb=" CA THR A 123 " ideal model delta sigma weight residual 121.80 137.03 -15.23 2.44e+00 1.68e-01 3.90e+01 angle pdb=" C MET B 535 " pdb=" N THR B 536 " pdb=" CA THR B 536 " ideal model delta sigma weight residual 122.08 130.65 -8.57 1.47e+00 4.63e-01 3.40e+01 ... (remaining 27713 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.89: 12104 22.89 - 45.78: 712 45.78 - 68.67: 95 68.67 - 91.56: 69 91.56 - 114.45: 28 Dihedral angle restraints: 13008 sinusoidal: 5911 harmonic: 7097 Sorted by residual: dihedral pdb=" CB CYS F 201 " pdb=" SG CYS F 201 " pdb=" SG CYS F 433 " pdb=" CB CYS F 433 " ideal model delta sinusoidal sigma weight residual -86.00 1.14 -87.14 1 1.00e+01 1.00e-02 9.12e+01 dihedral pdb=" CA GLY A 431 " pdb=" C GLY A 431 " pdb=" N ARG A 432 " pdb=" CA ARG A 432 " ideal model delta harmonic sigma weight residual -180.00 -144.10 -35.90 0 5.00e+00 4.00e-02 5.16e+01 dihedral pdb=" CA CYS A 433 " pdb=" C CYS A 433 " pdb=" N MET A 434 " pdb=" CA MET A 434 " ideal model delta harmonic sigma weight residual 180.00 147.13 32.87 0 5.00e+00 4.00e-02 4.32e+01 ... (remaining 13005 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.189: 3258 0.189 - 0.379: 37 0.379 - 0.568: 0 0.568 - 0.757: 0 0.757 - 0.946: 1 Chirality restraints: 3296 Sorted by residual: chirality pdb=" C1 NAG A 601 " pdb=" ND2 ASN A 138 " pdb=" C2 NAG A 601 " pdb=" O5 NAG A 601 " both_signs ideal model delta sigma weight residual False -2.40 -1.45 -0.95 2.00e-01 2.50e+01 2.24e+01 chirality pdb=" C4 NAG K 601 " pdb=" C3 NAG K 601 " pdb=" C5 NAG K 601 " pdb=" O4 NAG K 601 " both_signs ideal model delta sigma weight residual False -2.53 -2.21 -0.32 2.00e-01 2.50e+01 2.51e+00 chirality pdb=" CA THR F 123 " pdb=" N THR F 123 " pdb=" C THR F 123 " pdb=" CB THR F 123 " both_signs ideal model delta sigma weight residual False 2.53 2.22 0.31 2.00e-01 2.50e+01 2.38e+00 ... (remaining 3293 not shown) Planarity restraints: 3468 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LYS K 178 " -0.049 5.00e-02 4.00e+02 7.33e-02 8.59e+00 pdb=" N PRO K 179 " 0.127 5.00e-02 4.00e+02 pdb=" CA PRO K 179 " -0.037 5.00e-02 4.00e+02 pdb=" CD PRO K 179 " -0.041 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ILE K 424 " 0.015 2.00e-02 2.50e+03 2.93e-02 8.59e+00 pdb=" C ILE K 424 " -0.051 2.00e-02 2.50e+03 pdb=" O ILE K 424 " 0.019 2.00e-02 2.50e+03 pdb=" N ASN K 425 " 0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LYS F 178 " -0.048 5.00e-02 4.00e+02 7.15e-02 8.18e+00 pdb=" N PRO F 179 " 0.124 5.00e-02 4.00e+02 pdb=" CA PRO F 179 " -0.036 5.00e-02 4.00e+02 pdb=" CD PRO F 179 " -0.040 5.00e-02 4.00e+02 ... (remaining 3465 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 3842 2.78 - 3.31: 17582 3.31 - 3.84: 32335 3.84 - 4.37: 36117 4.37 - 4.90: 64001 Nonbonded interactions: 153877 Sorted by model distance: nonbonded pdb=" OH TYR I 48 " pdb=" O3 MAN T 5 " model vdw 2.247 3.040 nonbonded pdb=" OG1 THR H 87 " pdb=" OD1 ASP H 89 " model vdw 2.263 3.040 nonbonded pdb=" OH TYR N 48 " pdb=" O3 MAN Y 5 " model vdw 2.265 3.040 nonbonded pdb=" OH TYR D 48 " pdb=" O3 MAN O 5 " model vdw 2.268 3.040 nonbonded pdb=" OG1 THR M 87 " pdb=" OD1 ASP M 89 " model vdw 2.269 3.040 ... (remaining 153872 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = (chain 'F' and (resid 32 through 321 or resid 322 through 505 or resid 601)) selection = (chain 'K' and (resid 32 through 321 or resid 322 through 505 or resid 601)) } ncs_group { reference = chain 'B' selection = chain 'G' selection = chain 'L' } ncs_group { reference = chain 'C' selection = chain 'H' selection = chain 'M' } ncs_group { reference = chain 'D' selection = chain 'I' selection = chain 'N' } ncs_group { reference = chain 'J' selection = chain 'S' selection = chain 'X' } ncs_group { reference = (chain 'O' and (resid 2 or resid 5 through 11)) selection = (chain 'T' and (resid 1 or resid 4 through 10)) selection = (chain 'Y' and (resid 2 or resid 5 through 11)) } ncs_group { reference = chain 'P' selection = chain 'U' selection = chain 'V' selection = chain 'Z' selection = chain 'a' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.990 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.000 Check model and map are aligned: 0.190 Set scattering table: 0.100 Process input model: 48.040 Find NCS groups from input model: 0.940 Set up NCS constraints: 0.130 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:3.030 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 56.420 ------------------------------------------------------------------------------- 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 20382 Z= 0.391 Angle : 1.113 19.245 27718 Z= 0.595 Chirality : 0.064 0.946 3296 Planarity : 0.007 0.082 3453 Dihedral : 16.340 114.450 8333 Min Nonbonded Distance : 2.247 Molprobity Statistics. All-atom Clashscore : 4.44 Ramachandran Plot: Outliers : 0.41 % Allowed : 7.42 % Favored : 92.17 % Rotamer: Outliers : 0.00 % Allowed : 0.65 % Favored : 99.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.30 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.28 (0.15), residues: 2439 helix: -2.62 (0.20), residues: 400 sheet: -0.19 (0.20), residues: 665 loop : -1.89 (0.14), residues: 1374 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.003 TRP F 479 HIS 0.016 0.002 HIS K 249 PHE 0.016 0.002 PHE K 391 TYR 0.020 0.002 TYR K 399 ARG 0.017 0.001 ARG D 81 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4878 Ramachandran restraints generated. 2439 Oldfield, 0 Emsley, 2439 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4878 Ramachandran restraints generated. 2439 Oldfield, 0 Emsley, 2439 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 2138 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 126 time to evaluate : 2.133 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: 0.3056 time to fit residues: 63.2630 Evaluate side-chains 104 residues out of total 2138 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 104 time to evaluate : 2.281 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: chunk 205 optimal weight: 8.9990 chunk 184 optimal weight: 3.9990 chunk 102 optimal weight: 2.9990 chunk 62 optimal weight: 6.9990 chunk 124 optimal weight: 0.8980 chunk 98 optimal weight: 1.9990 chunk 190 optimal weight: 10.0000 chunk 73 optimal weight: 10.0000 chunk 115 optimal weight: 4.9990 chunk 141 optimal weight: 9.9990 chunk 220 optimal weight: 10.0000 overall best weight: 2.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 249 HIS A 287 HIS B 540 GLN F 249 HIS F 461 ASN G 540 GLN K 249 HIS L 540 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7206 moved from start: 0.1022 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 20382 Z= 0.212 Angle : 0.665 15.235 27718 Z= 0.341 Chirality : 0.047 0.706 3296 Planarity : 0.005 0.062 3453 Dihedral : 11.934 91.773 3907 Min Nonbonded Distance : 2.415 Molprobity Statistics. All-atom Clashscore : 5.89 Ramachandran Plot: Outliers : 0.37 % Allowed : 6.93 % Favored : 92.70 % Rotamer: Outliers : 0.56 % Allowed : 6.27 % Favored : 93.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.80 (0.16), residues: 2439 helix: -1.49 (0.24), residues: 393 sheet: -0.15 (0.20), residues: 671 loop : -1.67 (0.15), residues: 1375 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP B 628 HIS 0.011 0.001 HIS K 249 PHE 0.011 0.001 PHE C 32 TYR 0.017 0.001 TYR N 48 ARG 0.005 0.000 ARG A 432 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4878 Ramachandran restraints generated. 2439 Oldfield, 0 Emsley, 2439 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4878 Ramachandran restraints generated. 2439 Oldfield, 0 Emsley, 2439 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 2138 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 117 time to evaluate : 2.311 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 530 MET cc_start: 0.5575 (mmt) cc_final: 0.5303 (mmt) REVERT: D 84 ASP cc_start: 0.4226 (m-30) cc_final: 0.3956 (m-30) outliers start: 12 outliers final: 2 residues processed: 123 average time/residue: 0.3070 time to fit residues: 61.6147 Evaluate side-chains 98 residues out of total 2138 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 96 time to evaluate : 2.357 ------------------------------------------------------------------------------- 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 122 optimal weight: 5.9990 chunk 68 optimal weight: 9.9990 chunk 183 optimal weight: 6.9990 chunk 150 optimal weight: 0.0030 chunk 60 optimal weight: 3.9990 chunk 221 optimal weight: 9.9990 chunk 238 optimal weight: 30.0000 chunk 196 optimal weight: 10.0000 chunk 219 optimal weight: 0.0040 chunk 75 optimal weight: 4.9990 chunk 177 optimal weight: 6.9990 overall best weight: 3.0008 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 249 HIS F 249 HIS H 116 HIS K 249 HIS K 287 HIS M 116 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7232 moved from start: 0.1448 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 20382 Z= 0.207 Angle : 0.633 13.918 27718 Z= 0.324 Chirality : 0.046 0.624 3296 Planarity : 0.004 0.057 3453 Dihedral : 10.823 88.628 3907 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 6.09 Ramachandran Plot: Outliers : 0.29 % Allowed : 7.30 % Favored : 92.41 % Rotamer: Outliers : 1.26 % Allowed : 9.73 % Favored : 89.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.63 (0.16), residues: 2439 helix: -0.90 (0.26), residues: 393 sheet: -0.23 (0.20), residues: 685 loop : -1.61 (0.15), residues: 1361 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 628 HIS 0.012 0.001 HIS F 249 PHE 0.012 0.001 PHE C 32 TYR 0.022 0.001 TYR F 61 ARG 0.003 0.000 ARG H 38 *********************** 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 134 residues out of total 2138 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 107 time to evaluate : 2.121 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 10 VAL cc_start: 0.4809 (p) cc_final: 0.4353 (m) REVERT: D 84 ASP cc_start: 0.4283 (m-30) cc_final: 0.4000 (m-30) REVERT: G 520 LEU cc_start: 0.6170 (OUTLIER) cc_final: 0.5738 (tp) REVERT: N 10 VAL cc_start: 0.5552 (p) cc_final: 0.5195 (m) outliers start: 27 outliers final: 8 residues processed: 125 average time/residue: 0.2942 time to fit residues: 60.6867 Evaluate side-chains 105 residues out of total 2138 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 96 time to evaluate : 2.230 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 284 ILE Chi-restraints excluded: chain B residue 584 GLU Chi-restraints excluded: chain F residue 434 MET Chi-restraints excluded: chain G residue 520 LEU Chi-restraints excluded: chain K residue 68 VAL Chi-restraints excluded: chain K residue 284 ILE Chi-restraints excluded: chain L residue 530 MET Chi-restraints excluded: chain M residue 18 VAL Chi-restraints excluded: chain M residue 48 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: chunk 218 optimal weight: 7.9990 chunk 166 optimal weight: 0.9980 chunk 114 optimal weight: 7.9990 chunk 24 optimal weight: 5.9990 chunk 105 optimal weight: 10.0000 chunk 148 optimal weight: 7.9990 chunk 221 optimal weight: 5.9990 chunk 234 optimal weight: 7.9990 chunk 115 optimal weight: 4.9990 chunk 210 optimal weight: 0.0270 chunk 63 optimal weight: 10.0000 overall best weight: 3.6044 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 249 HIS D 32 HIS F 249 HIS F 287 HIS I 32 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: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7267 moved from start: 0.1867 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 20382 Z= 0.227 Angle : 0.641 15.243 27718 Z= 0.325 Chirality : 0.047 0.613 3296 Planarity : 0.004 0.058 3453 Dihedral : 9.930 83.467 3907 Min Nonbonded Distance : 2.417 Molprobity Statistics. All-atom Clashscore : 6.96 Ramachandran Plot: Outliers : 0.29 % Allowed : 8.20 % Favored : 91.51 % Rotamer: Outliers : 1.92 % Allowed : 11.69 % Favored : 86.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.55 (0.16), residues: 2439 helix: -0.63 (0.26), residues: 393 sheet: -0.22 (0.20), residues: 678 loop : -1.61 (0.15), residues: 1368 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP B 571 HIS 0.013 0.002 HIS F 249 PHE 0.012 0.002 PHE K 53 TYR 0.015 0.001 TYR F 61 ARG 0.003 0.000 ARG F 432 *********************** 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 144 residues out of total 2138 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 103 time to evaluate : 2.084 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 125 LEU cc_start: 0.8969 (OUTLIER) cc_final: 0.8721 (tt) REVERT: G 520 LEU cc_start: 0.6254 (OUTLIER) cc_final: 0.5797 (tp) REVERT: I 10 VAL cc_start: 0.5018 (p) cc_final: 0.4666 (m) REVERT: L 649 SER cc_start: 0.8399 (t) cc_final: 0.7666 (p) REVERT: N 10 VAL cc_start: 0.5485 (p) cc_final: 0.5172 (m) outliers start: 41 outliers final: 16 residues processed: 133 average time/residue: 0.2856 time to fit residues: 63.7624 Evaluate side-chains 111 residues out of total 2138 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 93 time to evaluate : 2.511 ------------------------------------------------------------------------------- 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 284 ILE Chi-restraints excluded: chain B residue 584 GLU Chi-restraints excluded: chain F residue 68 VAL Chi-restraints excluded: chain F residue 125 LEU Chi-restraints excluded: chain F residue 136 VAL Chi-restraints excluded: chain F residue 284 ILE Chi-restraints excluded: chain F residue 434 MET Chi-restraints excluded: chain G residue 520 LEU Chi-restraints excluded: chain K residue 52 LEU Chi-restraints excluded: chain K residue 68 VAL Chi-restraints excluded: chain K residue 284 ILE Chi-restraints excluded: chain K residue 439 ILE Chi-restraints excluded: chain K residue 489 VAL Chi-restraints excluded: chain L residue 530 MET Chi-restraints excluded: chain M residue 18 VAL Chi-restraints excluded: chain M residue 58 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: chunk 195 optimal weight: 7.9990 chunk 133 optimal weight: 1.9990 chunk 3 optimal weight: 0.1980 chunk 174 optimal weight: 4.9990 chunk 96 optimal weight: 10.0000 chunk 200 optimal weight: 7.9990 chunk 162 optimal weight: 10.0000 chunk 0 optimal weight: 10.0000 chunk 119 optimal weight: 0.0970 chunk 210 optimal weight: 20.0000 chunk 59 optimal weight: 0.4980 overall best weight: 1.5582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 249 HIS F 249 HIS K 249 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7221 moved from start: 0.1960 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 20382 Z= 0.154 Angle : 0.583 14.016 27718 Z= 0.295 Chirality : 0.045 0.554 3296 Planarity : 0.004 0.052 3453 Dihedral : 9.112 76.905 3907 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 6.22 Ramachandran Plot: Outliers : 0.25 % Allowed : 6.85 % Favored : 92.91 % Rotamer: Outliers : 2.06 % Allowed : 12.86 % Favored : 85.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.39 (0.17), residues: 2439 helix: -0.34 (0.27), residues: 393 sheet: -0.17 (0.20), residues: 691 loop : -1.53 (0.16), residues: 1355 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP B 571 HIS 0.013 0.001 HIS K 249 PHE 0.009 0.001 PHE F 53 TYR 0.017 0.001 TYR F 61 ARG 0.003 0.000 ARG C 38 *********************** 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 151 residues out of total 2138 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 107 time to evaluate : 2.365 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 10 VAL cc_start: 0.4438 (p) cc_final: 0.4068 (m) REVERT: D 51 TYR cc_start: 0.7669 (p90) cc_final: 0.6918 (p90) REVERT: F 125 LEU cc_start: 0.8868 (OUTLIER) cc_final: 0.8648 (tt) REVERT: G 520 LEU cc_start: 0.6343 (OUTLIER) cc_final: 0.5747 (tp) REVERT: G 595 ILE cc_start: 0.9067 (OUTLIER) cc_final: 0.8863 (mm) REVERT: I 10 VAL cc_start: 0.5336 (p) cc_final: 0.4935 (m) REVERT: L 649 SER cc_start: 0.8331 (t) cc_final: 0.7631 (p) REVERT: N 10 VAL cc_start: 0.5378 (p) cc_final: 0.5086 (m) outliers start: 44 outliers final: 12 residues processed: 145 average time/residue: 0.2799 time to fit residues: 68.3191 Evaluate side-chains 110 residues out of total 2138 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 95 time to evaluate : 2.463 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 249 HIS 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 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 G residue 520 LEU Chi-restraints excluded: chain G residue 595 ILE Chi-restraints excluded: chain K residue 36 VAL Chi-restraints excluded: chain K residue 68 VAL 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 79 optimal weight: 4.9990 chunk 211 optimal weight: 9.9990 chunk 46 optimal weight: 10.0000 chunk 137 optimal weight: 6.9990 chunk 57 optimal weight: 9.9990 chunk 235 optimal weight: 20.0000 chunk 195 optimal weight: 10.0000 chunk 108 optimal weight: 9.9990 chunk 19 optimal weight: 20.0000 chunk 77 optimal weight: 40.0000 chunk 123 optimal weight: 10.0000 overall best weight: 8.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 422 GLN ** C 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 113 ASN F 249 HIS F 422 GLN ** H 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 113 ASN K 105 HIS K 249 HIS K 422 GLN ** M 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7370 moved from start: 0.2532 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.079 20382 Z= 0.457 Angle : 0.829 13.467 27718 Z= 0.420 Chirality : 0.053 0.686 3296 Planarity : 0.005 0.070 3453 Dihedral : 10.625 84.265 3907 Min Nonbonded Distance : 2.390 Molprobity Statistics. All-atom Clashscore : 9.69 Ramachandran Plot: Outliers : 0.25 % Allowed : 10.50 % Favored : 89.26 % Rotamer: Outliers : 2.67 % Allowed : 13.56 % Favored : 83.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.13 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.03 (0.16), residues: 2439 helix: -0.86 (0.26), residues: 392 sheet: -0.53 (0.20), residues: 671 loop : -1.97 (0.15), residues: 1376 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.003 TRP C 36 HIS 0.032 0.003 HIS A 249 PHE 0.027 0.003 PHE B 522 TYR 0.017 0.002 TYR I 48 ARG 0.006 0.001 ARG L 585 *********************** 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 158 residues out of total 2138 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 101 time to evaluate : 2.324 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 626 MET cc_start: 0.5628 (mmm) cc_final: 0.5384 (tpt) REVERT: C 81 MET cc_start: 0.6143 (tpp) cc_final: 0.5925 (tpp) REVERT: F 125 LEU cc_start: 0.9070 (OUTLIER) cc_final: 0.8460 (tt) REVERT: F 426 MET cc_start: 0.7351 (ttp) cc_final: 0.7123 (ttt) REVERT: G 520 LEU cc_start: 0.6380 (OUTLIER) cc_final: 0.5951 (tp) REVERT: I 10 VAL cc_start: 0.5493 (p) cc_final: 0.5192 (m) REVERT: N 10 VAL cc_start: 0.5443 (p) cc_final: 0.5181 (m) outliers start: 57 outliers final: 33 residues processed: 148 average time/residue: 0.2854 time to fit residues: 70.6204 Evaluate side-chains 127 residues out of total 2138 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 92 time to evaluate : 2.106 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 68 VAL Chi-restraints excluded: chain A residue 75 VAL Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 161 THR Chi-restraints excluded: chain A residue 284 ILE Chi-restraints excluded: chain A residue 455 THR Chi-restraints excluded: chain A residue 489 VAL Chi-restraints excluded: chain B residue 584 GLU Chi-restraints excluded: chain D residue 108 THR Chi-restraints excluded: chain F residue 68 VAL Chi-restraints excluded: chain F residue 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 439 ILE Chi-restraints excluded: chain G residue 520 LEU Chi-restraints excluded: chain G residue 589 ASP Chi-restraints excluded: chain I residue 108 THR Chi-restraints excluded: chain K residue 36 VAL Chi-restraints excluded: chain K residue 42 VAL Chi-restraints excluded: chain K residue 52 LEU Chi-restraints excluded: chain K residue 68 VAL Chi-restraints excluded: chain K residue 75 VAL Chi-restraints excluded: chain K residue 136 VAL Chi-restraints excluded: chain K residue 284 ILE Chi-restraints excluded: chain K residue 399 TYR Chi-restraints excluded: chain K residue 439 ILE Chi-restraints excluded: chain L residue 530 MET Chi-restraints excluded: chain M residue 18 VAL 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 226 optimal weight: 5.9990 chunk 26 optimal weight: 8.9990 chunk 133 optimal weight: 0.9980 chunk 171 optimal weight: 0.8980 chunk 197 optimal weight: 10.0000 chunk 131 optimal weight: 0.9990 chunk 234 optimal weight: 6.9990 chunk 146 optimal weight: 3.9990 chunk 142 optimal weight: 5.9990 chunk 108 optimal weight: 10.0000 chunk 144 optimal weight: 5.9990 overall best weight: 2.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 249 HIS F 249 HIS H 119 GLN K 249 HIS K 258 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7297 moved from start: 0.2449 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 20382 Z= 0.202 Angle : 0.650 13.413 27718 Z= 0.328 Chirality : 0.050 1.009 3296 Planarity : 0.004 0.056 3453 Dihedral : 9.698 78.564 3907 Min Nonbonded Distance : 2.424 Molprobity Statistics. All-atom Clashscore : 7.62 Ramachandran Plot: Outliers : 0.25 % Allowed : 7.59 % Favored : 92.17 % Rotamer: Outliers : 2.29 % Allowed : 14.87 % Favored : 82.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.76 (0.16), residues: 2439 helix: -0.69 (0.26), residues: 405 sheet: -0.25 (0.20), residues: 669 loop : -1.84 (0.15), residues: 1365 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP B 628 HIS 0.022 0.001 HIS F 249 PHE 0.014 0.002 PHE A 391 TYR 0.013 0.001 TYR F 61 ARG 0.003 0.000 ARG H 38 *********************** 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 151 residues out of total 2138 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 102 time to evaluate : 2.370 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 626 MET cc_start: 0.5901 (mmm) cc_final: 0.5563 (tpt) REVERT: D 10 VAL cc_start: 0.4683 (p) cc_final: 0.4470 (m) REVERT: F 125 LEU cc_start: 0.8965 (OUTLIER) cc_final: 0.8469 (tt) REVERT: G 520 LEU cc_start: 0.6423 (OUTLIER) cc_final: 0.5867 (tp) REVERT: I 10 VAL cc_start: 0.5377 (p) cc_final: 0.5077 (m) outliers start: 49 outliers final: 35 residues processed: 144 average time/residue: 0.2731 time to fit residues: 66.3324 Evaluate side-chains 131 residues out of total 2138 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 94 time to evaluate : 2.232 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 68 VAL Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 136 VAL Chi-restraints excluded: chain A residue 161 THR Chi-restraints excluded: chain A residue 202 THR Chi-restraints excluded: chain A residue 284 ILE Chi-restraints excluded: chain A residue 489 VAL Chi-restraints excluded: chain B residue 584 GLU Chi-restraints excluded: chain B residue 627 THR Chi-restraints excluded: chain D residue 41 TYR Chi-restraints excluded: chain F residue 68 VAL Chi-restraints excluded: chain F residue 125 LEU Chi-restraints excluded: chain F residue 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 H residue 5 VAL Chi-restraints excluded: chain K residue 36 VAL Chi-restraints excluded: chain K residue 52 LEU Chi-restraints excluded: chain K residue 68 VAL Chi-restraints excluded: chain K residue 120 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 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 Chi-restraints excluded: chain N residue 108 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: chunk 93 optimal weight: 10.0000 chunk 139 optimal weight: 8.9990 chunk 70 optimal weight: 8.9990 chunk 46 optimal weight: 0.0040 chunk 45 optimal weight: 6.9990 chunk 148 optimal weight: 20.0000 chunk 159 optimal weight: 0.0470 chunk 115 optimal weight: 0.7980 chunk 21 optimal weight: 0.7980 chunk 184 optimal weight: 0.3980 chunk 213 optimal weight: 6.9990 overall best weight: 0.4090 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 113 ASN K 249 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7221 moved from start: 0.2467 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 20382 Z= 0.143 Angle : 0.588 16.419 27718 Z= 0.297 Chirality : 0.046 0.705 3296 Planarity : 0.004 0.049 3453 Dihedral : 8.608 70.284 3907 Min Nonbonded Distance : 2.388 Molprobity Statistics. All-atom Clashscore : 6.65 Ramachandran Plot: Outliers : 0.25 % Allowed : 7.01 % Favored : 92.74 % Rotamer: Outliers : 1.54 % Allowed : 15.53 % Favored : 82.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.39 (0.17), residues: 2439 helix: -0.18 (0.27), residues: 387 sheet: -0.07 (0.20), residues: 684 loop : -1.64 (0.16), residues: 1368 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP F 112 HIS 0.014 0.001 HIS K 249 PHE 0.012 0.001 PHE F 53 TYR 0.012 0.001 TYR K 217 ARG 0.003 0.000 ARG D 81 *********************** 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 141 residues out of total 2138 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 108 time to evaluate : 2.329 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 123 LEU cc_start: 0.5875 (tp) cc_final: 0.5655 (tt) REVERT: D 10 VAL cc_start: 0.4408 (p) cc_final: 0.4112 (m) REVERT: F 125 LEU cc_start: 0.8810 (OUTLIER) cc_final: 0.8482 (tt) REVERT: I 10 VAL cc_start: 0.5265 (p) cc_final: 0.4968 (m) REVERT: K 107 ASP cc_start: 0.6594 (m-30) cc_final: 0.6312 (m-30) REVERT: L 649 SER cc_start: 0.8066 (t) cc_final: 0.7113 (p) REVERT: M 123 LEU cc_start: 0.5993 (tp) cc_final: 0.5591 (tt) outliers start: 33 outliers final: 18 residues processed: 137 average time/residue: 0.2805 time to fit residues: 64.6450 Evaluate side-chains 122 residues out of total 2138 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 103 time to evaluate : 2.124 ------------------------------------------------------------------------------- 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 136 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 F residue 68 VAL Chi-restraints excluded: chain F residue 125 LEU Chi-restraints excluded: chain F residue 439 ILE Chi-restraints excluded: chain F residue 455 THR Chi-restraints excluded: chain K residue 36 VAL Chi-restraints excluded: chain K residue 68 VAL Chi-restraints excluded: chain K residue 284 ILE Chi-restraints excluded: chain K residue 489 VAL Chi-restraints excluded: chain L residue 584 GLU Chi-restraints excluded: chain M residue 18 VAL Chi-restraints excluded: chain M residue 58 THR Chi-restraints excluded: chain M residue 69 THR Chi-restraints excluded: chain N residue 105 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: chunk 224 optimal weight: 0.0020 chunk 204 optimal weight: 9.9990 chunk 218 optimal weight: 8.9990 chunk 131 optimal weight: 8.9990 chunk 95 optimal weight: 7.9990 chunk 171 optimal weight: 0.0870 chunk 66 optimal weight: 10.0000 chunk 197 optimal weight: 7.9990 chunk 206 optimal weight: 7.9990 chunk 217 optimal weight: 5.9990 chunk 143 optimal weight: 20.0000 overall best weight: 4.4172 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7302 moved from start: 0.2638 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 20382 Z= 0.265 Angle : 0.664 15.549 27718 Z= 0.332 Chirality : 0.049 0.824 3296 Planarity : 0.004 0.057 3453 Dihedral : 9.002 71.220 3907 Min Nonbonded Distance : 2.375 Molprobity Statistics. All-atom Clashscore : 7.80 Ramachandran Plot: Outliers : 0.25 % Allowed : 8.69 % Favored : 91.06 % Rotamer: Outliers : 1.68 % Allowed : 15.81 % Favored : 82.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.62 (0.16), residues: 2439 helix: -0.47 (0.27), residues: 405 sheet: -0.30 (0.20), residues: 674 loop : -1.71 (0.16), residues: 1360 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.049 0.002 TRP G 571 HIS 0.012 0.001 HIS K 249 PHE 0.015 0.002 PHE L 522 TYR 0.013 0.001 TYR F 484 ARG 0.003 0.000 ARG F 432 *********************** 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 135 residues out of total 2138 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 99 time to evaluate : 2.162 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 10 VAL cc_start: 0.4345 (p) cc_final: 0.4112 (m) REVERT: F 125 LEU cc_start: 0.8952 (OUTLIER) cc_final: 0.8479 (tt) REVERT: I 10 VAL cc_start: 0.5222 (p) cc_final: 0.4936 (m) outliers start: 36 outliers final: 29 residues processed: 130 average time/residue: 0.2702 time to fit residues: 59.4460 Evaluate side-chains 128 residues out of total 2138 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 98 time to evaluate : 2.269 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 68 VAL Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 136 VAL Chi-restraints excluded: chain A residue 284 ILE Chi-restraints excluded: chain A residue 489 VAL Chi-restraints excluded: chain B residue 584 GLU Chi-restraints excluded: chain B residue 627 THR Chi-restraints excluded: chain F residue 42 VAL 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 439 ILE Chi-restraints excluded: chain F residue 455 THR Chi-restraints excluded: chain K residue 36 VAL Chi-restraints excluded: chain K residue 52 LEU Chi-restraints excluded: chain K residue 68 VAL Chi-restraints excluded: chain K residue 120 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 584 GLU Chi-restraints excluded: chain M residue 18 VAL Chi-restraints excluded: chain M residue 58 THR Chi-restraints excluded: chain M residue 69 THR Chi-restraints excluded: chain N residue 41 TYR Chi-restraints excluded: chain N residue 105 THR Chi-restraints excluded: chain N residue 108 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: chunk 230 optimal weight: 10.0000 chunk 140 optimal weight: 6.9990 chunk 109 optimal weight: 9.9990 chunk 160 optimal weight: 10.0000 chunk 242 optimal weight: 7.9990 chunk 222 optimal weight: 5.9990 chunk 192 optimal weight: 10.0000 chunk 20 optimal weight: 8.9990 chunk 148 optimal weight: 9.9990 chunk 118 optimal weight: 1.9990 chunk 153 optimal weight: 5.9990 overall best weight: 5.7990 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7346 moved from start: 0.2898 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.059 20382 Z= 0.332 Angle : 0.725 15.084 27718 Z= 0.363 Chirality : 0.051 0.812 3296 Planarity : 0.005 0.062 3453 Dihedral : 9.614 75.180 3907 Min Nonbonded Distance : 2.391 Molprobity Statistics. All-atom Clashscore : 8.85 Ramachandran Plot: Outliers : 0.25 % Allowed : 10.13 % Favored : 89.63 % Rotamer: Outliers : 1.68 % Allowed : 15.58 % Favored : 82.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.96 (0.16), residues: 2439 helix: -0.74 (0.26), residues: 405 sheet: -0.53 (0.20), residues: 664 loop : -1.92 (0.15), residues: 1370 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.002 TRP G 571 HIS 0.011 0.001 HIS K 249 PHE 0.016 0.002 PHE L 522 TYR 0.014 0.002 TYR A 484 ARG 0.004 0.001 ARG F 432 ********************** 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 134 residues out of total 2138 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 98 time to evaluate : 2.167 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 10 VAL cc_start: 0.4788 (p) cc_final: 0.4557 (m) REVERT: F 125 LEU cc_start: 0.9020 (OUTLIER) cc_final: 0.8401 (tt) REVERT: I 10 VAL cc_start: 0.5250 (p) cc_final: 0.5025 (m) REVERT: K 340 ASP cc_start: 0.6100 (OUTLIER) cc_final: 0.5872 (t0) outliers start: 36 outliers final: 33 residues processed: 129 average time/residue: 0.2708 time to fit residues: 58.8814 Evaluate side-chains 131 residues out of total 2138 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 96 time to evaluate : 2.086 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 68 VAL Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 136 VAL Chi-restraints excluded: chain A residue 202 THR Chi-restraints excluded: chain A residue 284 ILE Chi-restraints excluded: chain A residue 489 VAL Chi-restraints excluded: chain B residue 529 THR Chi-restraints excluded: chain B residue 584 GLU Chi-restraints excluded: chain B residue 627 THR Chi-restraints excluded: chain F residue 42 VAL Chi-restraints excluded: chain F residue 68 VAL Chi-restraints excluded: chain F residue 125 LEU Chi-restraints excluded: chain F residue 439 ILE Chi-restraints excluded: chain F residue 455 THR Chi-restraints excluded: chain G residue 589 ASP Chi-restraints excluded: chain K residue 36 VAL Chi-restraints excluded: chain K residue 42 VAL Chi-restraints excluded: chain K residue 52 LEU Chi-restraints excluded: chain K residue 68 VAL Chi-restraints excluded: chain K residue 120 VAL Chi-restraints excluded: chain K residue 249 HIS Chi-restraints excluded: chain K residue 284 ILE Chi-restraints excluded: chain K residue 340 ASP Chi-restraints excluded: chain K residue 399 TYR Chi-restraints excluded: chain K residue 439 ILE Chi-restraints excluded: chain K residue 455 THR Chi-restraints excluded: chain K residue 489 VAL Chi-restraints excluded: chain L residue 584 GLU Chi-restraints excluded: chain M residue 18 VAL Chi-restraints excluded: chain M residue 58 THR Chi-restraints excluded: chain M residue 69 THR Chi-restraints excluded: chain N residue 41 TYR Chi-restraints excluded: chain N residue 105 THR Chi-restraints excluded: chain N residue 108 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: chunk 205 optimal weight: 0.5980 chunk 59 optimal weight: 9.9990 chunk 177 optimal weight: 8.9990 chunk 28 optimal weight: 10.0000 chunk 53 optimal weight: 20.0000 chunk 193 optimal weight: 0.9990 chunk 80 optimal weight: 8.9990 chunk 198 optimal weight: 0.0170 chunk 24 optimal weight: 3.9990 chunk 35 optimal weight: 0.6980 chunk 169 optimal weight: 2.9990 overall best weight: 1.0622 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 249 HIS K 249 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3640 r_free = 0.3640 target = 0.074676 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.064129 restraints weight = 92552.456| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.065535 restraints weight = 56138.968| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.066470 restraints weight = 40519.066| |-----------------------------------------------------------------------------| r_work (final): 0.3449 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7271 moved from start: 0.2810 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.048 20382 Z= 0.156 Angle : 0.619 14.655 27718 Z= 0.310 Chirality : 0.047 0.695 3296 Planarity : 0.004 0.053 3453 Dihedral : 8.615 70.113 3907 Min Nonbonded Distance : 2.397 Molprobity Statistics. All-atom Clashscore : 7.39 Ramachandran Plot: Outliers : 0.25 % Allowed : 6.89 % Favored : 92.87 % Rotamer: Outliers : 1.54 % Allowed : 15.86 % Favored : 82.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.61 (0.17), residues: 2439 helix: -0.43 (0.27), residues: 405 sheet: -0.25 (0.20), residues: 672 loop : -1.74 (0.16), residues: 1362 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.002 TRP G 571 HIS 0.017 0.001 HIS K 249 PHE 0.011 0.001 PHE F 53 TYR 0.012 0.001 TYR K 61 ARG 0.003 0.000 ARG H 38 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2889.41 seconds wall clock time: 55 minutes 26.26 seconds (3326.26 seconds total)