Starting phenix.real_space_refine on Tue Nov 19 19:53:50 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sau_40280/11_2024/8sau_40280_neut.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sau_40280/11_2024/8sau_40280.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sau_40280/11_2024/8sau_40280.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sau_40280/11_2024/8sau_40280.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sau_40280/11_2024/8sau_40280_neut.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sau_40280/11_2024/8sau_40280_neut.cif" } resolution = 3.3 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= 0.000 sd= 0.011 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 138 5.16 5 C 12429 2.51 5 N 3321 2.21 5 O 3996 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 35 residue(s): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/chem_data/mon_lib" Total number of atoms: 19884 Number of models: 1 Model: "" Number of chains: 24 Chain: "A" Number of atoms: 3615 Number of conformers: 1 Conformer: "" Number of residues, atoms: 462, 3615 Classifications: {'peptide': 462} Modifications used: {'COO': 1} Link IDs: {'CIS': 2, 'PCIS': 1, 'PTRANS': 22, 'TRANS': 436} 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: 992 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 992 Classifications: {'peptide': 126} Link IDs: {'CIS': 1, 'PTRANS': 5, 'TRANS': 119} 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: {'CIS': 2, 'PCIS': 1, 'PTRANS': 22, 'TRANS': 436} 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: 992 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 992 Classifications: {'peptide': 126} Link IDs: {'CIS': 1, 'PTRANS': 5, 'TRANS': 119} 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: {'CIS': 2, 'PCIS': 1, 'PTRANS': 22, 'TRANS': 436} 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: 992 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 992 Classifications: {'peptide': 126} Link IDs: {'CIS': 1, 'PTRANS': 5, 'TRANS': 119} 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: "E" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "J" Number of atoms: 105 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 105 Unusual residues: {'BMA': 1, 'MAN': 6, 'NAG': 2} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 9 Chain: "O" Number of atoms: 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: "P" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Q" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "R" Number of atoms: 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: "S" 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: "T" 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: "U" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "V" Number of atoms: 105 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 105 Unusual residues: {'BMA': 1, 'MAN': 6, 'NAG': 2} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 9 Chain: "W" Number of atoms: 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: "X" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Time building chain proxies: 12.35, per 1000 atoms: 0.62 Number of scatterers: 19884 At special positions: 0 Unit cell: (157.768, 158.834, 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 138 16.00 O 3996 8.00 N 3321 7.00 C 12429 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=2.02 Simple disulfide: pdb=" SG CYS A 218 " - pdb=" SG CYS A 247 " distance=2.06 Simple disulfide: pdb=" SG CYS A 228 " - pdb=" SG CYS A 239 " distance=2.04 Simple disulfide: pdb=" SG CYS A 296 " - pdb=" SG CYS A 331 " distance=2.03 Simple disulfide: pdb=" SG CYS A 378 " - pdb=" SG CYS A 445 " distance=2.03 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=2.02 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=2.04 Simple disulfide: pdb=" SG CYS F 54 " - pdb=" SG CYS F 74 " distance=2.04 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=2.03 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=2.02 Simple disulfide: pdb=" SG CYS F 218 " - pdb=" SG CYS F 247 " distance=2.05 Simple disulfide: pdb=" SG CYS F 228 " - pdb=" SG CYS F 239 " distance=2.04 Simple disulfide: pdb=" SG CYS F 296 " - pdb=" SG CYS F 331 " distance=2.03 Simple disulfide: pdb=" SG CYS F 378 " - pdb=" SG CYS F 445 " distance=2.03 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=2.04 Simple disulfide: pdb=" SG CYS G 598 " - pdb=" SG CYS G 604 " distance=2.04 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.02 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=2.04 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=2.03 Simple disulfide: pdb=" SG CYS K 218 " - pdb=" SG CYS K 247 " distance=2.05 Simple disulfide: pdb=" SG CYS K 228 " - pdb=" SG CYS K 239 " distance=2.04 Simple disulfide: pdb=" SG CYS K 296 " - pdb=" SG CYS K 331 " distance=2.03 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=2.04 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=2.02 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=2.04 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 J 5 " - " MAN J 6 " " MAN J 8 " - " MAN J 9 " " MAN R 4 " - " MAN R 5 " " MAN R 5 " - " MAN R 6 " " MAN R 8 " - " MAN R 9 " " MAN R 10 " - " MAN R 11 " " MAN V 4 " - " MAN V 5 " " MAN V 5 " - " MAN V 6 " " MAN V 8 " - " MAN V 9 " ALPHA1-3 " BMA E 3 " - " MAN E 4 " " BMA J 3 " - " MAN J 4 " " BMA Q 3 " - " MAN Q 4 " " BMA R 3 " - " MAN R 4 " " MAN R 7 " - " MAN R 8 " " BMA U 3 " - " MAN U 4 " " BMA V 3 " - " MAN V 4 " ALPHA1-6 " BMA J 3 " - " MAN J 7 " " MAN J 7 " - " MAN J 8 " " BMA R 3 " - " MAN R 7 " " MAN R 7 " - " MAN R 10 " " BMA V 3 " - " MAN V 7 " " MAN V 7 " - " MAN V 8 " BETA1-4 " NAG E 1 " - " NAG E 2 " " NAG E 2 " - " BMA E 3 " " 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 R 1 " - " NAG R 2 " " NAG R 2 " - " BMA R 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 U 2 " - " BMA U 3 " " NAG V 1 " - " NAG V 2 " " NAG V 2 " - " BMA V 3 " " NAG W 1 " - " NAG W 2 " " NAG W 2 " - " BMA W 3 " " NAG X 1 " - " NAG X 2 " NAG-ASN " NAG E 1 " - " ASN A 301 " " NAG J 1 " - " ASN A 332 " " NAG O 1 " - " ASN A 156 " " NAG P 1 " - " ASN A 442 " " NAG Q 1 " - " ASN F 301 " " NAG R 1 " - " ASN F 332 " " NAG S 1 " - " ASN F 156 " " NAG T 1 " - " ASN F 442 " " NAG U 1 " - " ASN K 301 " " NAG V 1 " - " ASN K 332 " " NAG W 1 " - " ASN K 156 " " NAG X 1 " - " ASN K 442 " Time building additional restraints: 6.29 Conformation dependent library (CDL) restraints added in 2.7 seconds 4884 Ramachandran restraints generated. 2442 Oldfield, 0 Emsley, 2442 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4542 Finding SS restraints... Secondary structure from input PDB file: 55 helices and 41 sheets defined 20.3% alpha, 21.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.59 Creating SS restraints... Processing helix chain 'A' and resid 57 through 61 Processing helix chain 'A' and resid 68 through 73 removed outlier: 3.535A pdb=" N ALA A 73 " --> pdb=" O TRP A 69 " (cutoff:3.500A) Processing helix chain 'A' and resid 99 through 116 Processing helix chain 'A' and resid 122 through 126 Processing helix chain 'A' and resid 177 through 179 No H-bonds generated for 'chain 'A' and resid 177 through 179' Processing helix chain 'A' and resid 335 through 350 removed outlier: 3.575A pdb=" N GLU A 348 " --> pdb=" O LYS A 344 " (cutoff:3.500A) Processing helix chain 'A' and resid 368 through 373 removed outlier: 3.670A pdb=" N THR A 373 " --> pdb=" O MET A 369 " (cutoff:3.500A) Processing helix chain 'A' and resid 474 through 481 removed outlier: 3.696A pdb=" N ASN A 478 " --> pdb=" O ASP A 474 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N SER A 481 " --> pdb=" O ASP A 477 " (cutoff:3.500A) Processing helix chain 'A' and resid 482 through 484 No H-bonds generated for 'chain 'A' and resid 482 through 484' Processing helix chain 'B' and resid 529 through 534 Processing helix chain 'B' and resid 537 through 542 Processing helix chain 'B' and resid 571 through 596 removed outlier: 4.015A pdb=" N GLN B 575 " --> pdb=" O TRP B 571 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N LEU B 576 " --> pdb=" O GLY B 572 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N ALA B 578 " --> pdb=" O LYS B 574 " (cutoff:3.500A) Processing helix chain 'B' and resid 611 through 615 Processing helix chain 'B' and resid 618 through 624 Processing helix chain 'B' and resid 627 through 636 removed outlier: 4.055A pdb=" N LYS B 633 " --> pdb=" O LEU B 629 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N GLU B 634 " --> pdb=" O GLN B 630 " (cutoff:3.500A) Processing helix chain 'B' and resid 638 through 664 removed outlier: 4.365A pdb=" N GLY B 644 " --> pdb=" O GLN B 640 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N LEU B 645 " --> pdb=" O ILE B 641 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N GLN B 650 " --> pdb=" O LEU B 646 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N ASN B 656 " --> pdb=" O GLN B 652 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N LEU B 661 " --> pdb=" O GLU B 657 " (cutoff:3.500A) Processing helix chain 'C' and resid 62 through 65 Processing helix chain 'C' and resid 87 through 91 Processing helix chain 'F' and resid 57 through 61 removed outlier: 3.630A pdb=" N ALA F 60 " --> pdb=" O ASP F 57 " (cutoff:3.500A) Processing helix chain 'F' and resid 68 through 73 Processing helix chain 'F' and resid 99 through 116 Processing helix chain 'F' and resid 122 through 126 Processing helix chain 'F' and resid 177 through 179 No H-bonds generated for 'chain 'F' and resid 177 through 179' Processing helix chain 'F' and resid 335 through 350 removed outlier: 3.607A pdb=" N GLU F 348 " --> pdb=" O LYS F 344 " (cutoff:3.500A) Processing helix chain 'F' and resid 368 through 373 removed outlier: 3.665A pdb=" N THR F 373 " --> pdb=" O MET F 369 " (cutoff:3.500A) Processing helix chain 'F' and resid 474 through 481 removed outlier: 3.654A pdb=" N SER F 481 " --> pdb=" O ASP F 477 " (cutoff:3.500A) Processing helix chain 'G' and resid 529 through 534 Processing helix chain 'G' and resid 537 through 542 Processing helix chain 'G' and resid 543 through 545 No H-bonds generated for 'chain 'G' and resid 543 through 545' Processing helix chain 'G' and resid 572 through 596 removed outlier: 3.674A pdb=" N LEU G 576 " --> pdb=" O GLY G 572 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N ALA G 578 " --> pdb=" O LYS G 574 " (cutoff:3.500A) Processing helix chain 'G' and resid 611 through 615 Processing helix chain 'G' and resid 618 through 624 Processing helix chain 'G' and resid 627 through 636 removed outlier: 4.128A pdb=" N LYS G 633 " --> pdb=" O LEU G 629 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N GLU G 634 " --> pdb=" O GLN G 630 " (cutoff:3.500A) Processing helix chain 'G' and resid 638 through 664 removed outlier: 4.346A pdb=" N GLY G 644 " --> pdb=" O GLN G 640 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N LEU G 645 " --> pdb=" O ILE G 641 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N GLN G 650 " --> pdb=" O LEU G 646 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N ASN G 656 " --> pdb=" O GLN G 652 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N LEU G 661 " --> pdb=" O GLU G 657 " (cutoff:3.500A) Processing helix chain 'H' and resid 62 through 65 Processing helix chain 'H' and resid 87 through 91 Processing helix chain 'K' and resid 57 through 61 removed outlier: 3.568A pdb=" N ALA K 60 " --> pdb=" O ASP K 57 " (cutoff:3.500A) Processing helix chain 'K' and resid 68 through 73 removed outlier: 3.511A pdb=" N ALA K 73 " --> pdb=" O TRP K 69 " (cutoff:3.500A) Processing helix chain 'K' and resid 99 through 116 Processing helix chain 'K' and resid 122 through 126 Processing helix chain 'K' and resid 177 through 179 No H-bonds generated for 'chain 'K' and resid 177 through 179' Processing helix chain 'K' and resid 335 through 350 removed outlier: 3.556A pdb=" N GLU K 348 " --> pdb=" O LYS K 344 " (cutoff:3.500A) Processing helix chain 'K' and resid 368 through 373 removed outlier: 3.609A pdb=" N THR K 373 " --> pdb=" O MET K 369 " (cutoff:3.500A) Processing helix chain 'K' and resid 474 through 481 removed outlier: 3.614A pdb=" N ASN K 478 " --> pdb=" O ASP K 474 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N SER K 481 " --> pdb=" O ASP K 477 " (cutoff:3.500A) Processing helix chain 'K' and resid 482 through 484 No H-bonds generated for 'chain 'K' and resid 482 through 484' Processing helix chain 'L' and resid 529 through 534 Processing helix chain 'L' and resid 537 through 542 Processing helix chain 'L' and resid 543 through 545 No H-bonds generated for 'chain 'L' and resid 543 through 545' Processing helix chain 'L' and resid 571 through 596 removed outlier: 3.864A pdb=" N GLN L 575 " --> pdb=" O TRP L 571 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N LEU L 576 " --> pdb=" O GLY L 572 " (cutoff:3.500A) Processing helix chain 'L' and resid 611 through 615 Processing helix chain 'L' and resid 618 through 624 Processing helix chain 'L' and resid 627 through 636 removed outlier: 4.013A pdb=" N LYS L 633 " --> pdb=" O LEU L 629 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N GLU L 634 " --> pdb=" O GLN L 630 " (cutoff:3.500A) Processing helix chain 'L' and resid 638 through 664 removed outlier: 4.477A pdb=" N GLY L 644 " --> pdb=" O GLN L 640 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N LEU L 645 " --> pdb=" O ILE L 641 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N GLN L 650 " --> pdb=" O LEU L 646 " (cutoff:3.500A) removed outlier: 4.051A pdb=" N ASN L 656 " --> pdb=" O GLN L 652 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N LEU L 661 " --> pdb=" O GLU L 657 " (cutoff:3.500A) Processing helix chain 'M' and resid 62 through 65 Processing helix chain 'M' and resid 87 through 91 Processing sheet with id=AA1, first strand: chain 'A' and resid 494 through 499 removed outlier: 3.729A pdb=" N THR A 499 " --> pdb=" O TRP A 35 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N TRP A 35 " --> pdb=" O THR A 499 " (cutoff:3.500A) removed outlier: 5.022A pdb=" N VAL A 36 " --> pdb=" O THR B 606 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 45 through 47 removed outlier: 4.017A pdb=" N ILE A 225 " --> pdb=" O VAL A 245 " (cutoff:3.500A) removed outlier: 4.772A pdb=" N VAL A 242 " --> pdb=" O LEU A 86 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 75 through 76 Processing sheet with id=AA4, first strand: chain 'A' and resid 91 through 94 removed outlier: 3.738A pdb=" N GLU A 91 " --> pdb=" O CYS A 239 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 169 through 176 removed outlier: 3.653A pdb=" N GLU A 172 " --> pdb=" O PHE A 159 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 259 through 260 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 259 through 260 current: chain 'A' and resid 284 through 302 removed outlier: 7.716A pdb=" N GLU A 293 " --> pdb=" O SER A 334 " (cutoff:3.500A) removed outlier: 4.838A pdb=" N SER A 334 " --> pdb=" O GLU A 293 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N VAL A 295 " --> pdb=" O ASN A 332 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 330 through 334 current: chain 'A' and resid 382 through 385 removed outlier: 4.518A pdb=" N PHE A 382 " --> pdb=" O LYS A 421 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 413 through 421 current: chain 'A' and resid 468 through 470 Processing sheet with id=AA7, first strand: chain 'A' and resid 304 through 308 Processing sheet with id=AA8, first strand: chain 'A' and resid 423 through 425 Processing sheet with id=AA9, first strand: chain 'C' and resid 2 through 3 Processing sheet with id=AB1, first strand: chain 'C' and resid 18 through 22 removed outlier: 3.510A pdb=" N LEU C 83 " --> pdb=" O VAL C 18 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N GLU C 82 " --> pdb=" O THR C 69 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N THR C 69 " --> pdb=" O GLU C 82 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 32 through 39 removed outlier: 6.634A pdb=" N ILE C 34 " --> pdb=" O TRP C 50 " (cutoff:3.500A) removed outlier: 4.728A pdb=" N TRP C 50 " --> pdb=" O ILE C 34 " (cutoff:3.500A) removed outlier: 6.807A pdb=" N TRP C 36 " --> pdb=" O MET C 48 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 58 through 60 current: chain 'C' and resid 116 through 117 Processing sheet with id=AB3, first strand: chain 'D' and resid 10 through 12 removed outlier: 3.906A pdb=" N GLY D 12 " --> pdb=" O THR D 108 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 19 through 23 Processing sheet with id=AB5, first strand: chain 'D' and resid 46 through 50 removed outlier: 5.948A pdb=" N TYR D 48 " --> pdb=" O GLN D 39 " (cutoff:3.500A) removed outlier: 7.182A pdb=" N GLN D 39 " --> pdb=" O TYR D 48 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N PHE D 38 " --> pdb=" O TYR D 89 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'F' and resid 494 through 499 removed outlier: 3.551A pdb=" N THR F 499 " --> pdb=" O TRP F 35 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N TRP F 35 " --> pdb=" O THR F 499 " (cutoff:3.500A) removed outlier: 5.152A pdb=" N VAL F 36 " --> pdb=" O THR G 606 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'F' and resid 45 through 46 removed outlier: 3.624A pdb=" N LYS F 46 " --> pdb=" O LYS F 490 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N ILE F 225 " --> pdb=" O VAL F 245 " (cutoff:3.500A) removed outlier: 4.792A pdb=" N VAL F 242 " --> pdb=" O LEU F 86 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'F' and resid 75 through 76 Processing sheet with id=AB9, first strand: chain 'F' and resid 91 through 94 removed outlier: 3.692A pdb=" N GLU F 91 " --> pdb=" O CYS F 239 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'F' and resid 173 through 176 Processing sheet with id=AC2, first strand: chain 'F' and resid 161 through 162 Processing sheet with id=AC3, first strand: chain 'F' and resid 259 through 261 WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 259 through 261 current: chain 'F' and resid 284 through 308 removed outlier: 6.623A pdb=" N ASN F 301 " --> pdb=" O ILE F 322 " (cutoff:3.500A) removed outlier: 5.109A pdb=" N ILE F 322 " --> pdb=" O ASN F 301 " (cutoff:3.500A) removed outlier: 4.354A pdb=" N THR F 303 " --> pdb=" O GLY F 321 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 316 through 323 current: chain 'F' and resid 382 through 385 removed outlier: 4.539A pdb=" N PHE F 382 " --> pdb=" O LYS F 421 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 413 through 421 current: chain 'F' and resid 468 through 470 Processing sheet with id=AC4, first strand: chain 'F' and resid 423 through 425 Processing sheet with id=AC5, first strand: chain 'H' and resid 2 through 3 Processing sheet with id=AC6, first strand: chain 'H' and resid 18 through 22 removed outlier: 4.023A pdb=" N GLU H 82 " --> pdb=" O THR H 69 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N THR H 69 " --> pdb=" O GLU H 82 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'H' and resid 32 through 39 removed outlier: 6.618A pdb=" N ILE H 34 " --> pdb=" O TRP H 50 " (cutoff:3.500A) removed outlier: 4.754A pdb=" N TRP H 50 " --> pdb=" O ILE H 34 " (cutoff:3.500A) removed outlier: 6.720A pdb=" N TRP H 36 " --> pdb=" O MET H 48 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'H' and resid 58 through 60 current: chain 'H' and resid 116 through 117 Processing sheet with id=AC8, first strand: chain 'I' and resid 10 through 12 removed outlier: 3.661A pdb=" N GLY I 12 " --> pdb=" O THR I 108 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'I' and resid 19 through 23 Processing sheet with id=AD1, first strand: chain 'I' and resid 46 through 50 removed outlier: 6.026A pdb=" N TYR I 48 " --> pdb=" O GLN I 39 " (cutoff:3.500A) removed outlier: 7.134A pdb=" N GLN I 39 " --> pdb=" O TYR I 48 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N PHE I 38 " --> pdb=" O TYR I 89 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'K' and resid 494 through 499 removed outlier: 3.875A pdb=" N THR K 499 " --> pdb=" O TRP K 35 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N TRP K 35 " --> pdb=" O THR K 499 " (cutoff:3.500A) removed outlier: 5.316A pdb=" N VAL K 36 " --> pdb=" O THR L 606 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'K' and resid 45 through 46 removed outlier: 3.641A pdb=" N LYS K 46 " --> pdb=" O LYS K 490 " (cutoff:3.500A) removed outlier: 4.099A pdb=" N ILE K 225 " --> pdb=" O VAL K 245 " (cutoff:3.500A) removed outlier: 4.833A pdb=" N VAL K 242 " --> pdb=" O LEU K 86 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'K' and resid 75 through 76 Processing sheet with id=AD5, first strand: chain 'K' and resid 91 through 94 removed outlier: 3.834A pdb=" N GLU K 91 " --> pdb=" O CYS K 239 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'K' and resid 169 through 176 removed outlier: 4.562A pdb=" N ASN K 156 " --> pdb=" O SER K 132 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'K' and resid 259 through 260 WARNING: can't find start of bonding for strands! previous: chain 'K' and resid 259 through 260 current: chain 'K' and resid 284 through 302 removed outlier: 7.712A pdb=" N GLU K 293 " --> pdb=" O SER K 334 " (cutoff:3.500A) removed outlier: 4.912A pdb=" N SER K 334 " --> pdb=" O GLU K 293 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N VAL K 295 " --> pdb=" O ASN K 332 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'K' and resid 330 through 334 current: chain 'K' and resid 382 through 385 removed outlier: 4.482A pdb=" N PHE K 382 " --> pdb=" O LYS K 421 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'K' and resid 413 through 421 current: chain 'K' and resid 467 through 470 Processing sheet with id=AD8, first strand: chain 'K' and resid 304 through 308 Processing sheet with id=AD9, first strand: chain 'K' and resid 423 through 425 Processing sheet with id=AE1, first strand: chain 'M' and resid 18 through 22 removed outlier: 3.946A pdb=" N GLU M 82 " --> pdb=" O THR M 69 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N THR M 69 " --> pdb=" O GLU M 82 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'M' and resid 32 through 39 removed outlier: 6.661A pdb=" N ILE M 34 " --> pdb=" O TRP M 50 " (cutoff:3.500A) removed outlier: 4.783A pdb=" N TRP M 50 " --> pdb=" O ILE M 34 " (cutoff:3.500A) removed outlier: 6.818A pdb=" N TRP M 36 " --> pdb=" O MET M 48 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'M' and resid 58 through 60 current: chain 'M' and resid 116 through 117 Processing sheet with id=AE3, first strand: chain 'N' and resid 10 through 12 removed outlier: 3.773A pdb=" N GLY N 12 " --> pdb=" O THR N 108 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'N' and resid 19 through 23 Processing sheet with id=AE5, first strand: chain 'N' and resid 48 through 50 removed outlier: 3.633A pdb=" N ILE N 50 " --> pdb=" O TRP N 37 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N PHE N 38 " --> pdb=" O TYR N 89 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N TYR N 89 " --> pdb=" O PHE N 38 " (cutoff:3.500A) 515 hydrogen bonds defined for protein. 1356 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: 6.56 Time building geometry restraints manager: 6.73 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: 6339 1.35 - 1.48: 5389 1.48 - 1.61: 8402 1.61 - 1.74: 3 1.74 - 1.86: 183 Bond restraints: 20316 Sorted by residual: bond pdb=" CA GLN I 39 " pdb=" CB GLN I 39 " ideal model delta sigma weight residual 1.526 1.600 -0.074 1.70e-02 3.46e+03 1.91e+01 bond pdb=" CB CYS K 433 " pdb=" SG CYS K 433 " ideal model delta sigma weight residual 1.808 1.706 0.102 3.30e-02 9.18e+02 9.64e+00 bond pdb=" CB CYS F 433 " pdb=" SG CYS F 433 " ideal model delta sigma weight residual 1.808 1.715 0.093 3.30e-02 9.18e+02 7.96e+00 bond pdb=" C5 MAN V 7 " pdb=" O5 MAN V 7 " ideal model delta sigma weight residual 1.418 1.471 -0.053 2.00e-02 2.50e+03 7.02e+00 bond pdb=" C5 MAN R 7 " pdb=" O5 MAN R 7 " ideal model delta sigma weight residual 1.418 1.470 -0.052 2.00e-02 2.50e+03 6.77e+00 ... (remaining 20311 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.44: 26759 2.44 - 4.89: 738 4.89 - 7.33: 115 7.33 - 9.78: 18 9.78 - 12.22: 6 Bond angle restraints: 27636 Sorted by residual: angle pdb=" C ASN A 67 " pdb=" N VAL A 68 " pdb=" CA VAL A 68 " ideal model delta sigma weight residual 121.70 133.92 -12.22 1.80e+00 3.09e-01 4.61e+01 angle pdb=" C ASN F 67 " pdb=" N VAL F 68 " pdb=" CA VAL F 68 " ideal model delta sigma weight residual 121.70 133.63 -11.93 1.80e+00 3.09e-01 4.39e+01 angle pdb=" C ASN K 67 " pdb=" N VAL K 68 " pdb=" CA VAL K 68 " ideal model delta sigma weight residual 121.70 133.53 -11.83 1.80e+00 3.09e-01 4.32e+01 angle pdb=" C SER M 25 " pdb=" N GLY M 26 " pdb=" CA GLY M 26 " ideal model delta sigma weight residual 121.70 131.44 -9.74 1.80e+00 3.09e-01 2.93e+01 angle pdb=" C SER C 25 " pdb=" N GLY C 26 " pdb=" CA GLY C 26 " ideal model delta sigma weight residual 121.70 131.35 -9.65 1.80e+00 3.09e-01 2.88e+01 ... (remaining 27631 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.14: 11866 22.14 - 44.27: 782 44.27 - 66.41: 87 66.41 - 88.55: 80 88.55 - 110.68: 43 Dihedral angle restraints: 12858 sinusoidal: 5763 harmonic: 7095 Sorted by residual: dihedral pdb=" CA VAL G 570 " pdb=" C VAL G 570 " pdb=" N TRP G 571 " pdb=" CA TRP G 571 " ideal model delta harmonic sigma weight residual 180.00 143.21 36.79 0 5.00e+00 4.00e-02 5.41e+01 dihedral pdb=" CA GLY K 431 " pdb=" C GLY K 431 " pdb=" N ARG K 432 " pdb=" CA ARG K 432 " ideal model delta harmonic sigma weight residual -180.00 -146.01 -33.99 0 5.00e+00 4.00e-02 4.62e+01 dihedral pdb=" CA GLY F 431 " pdb=" C GLY F 431 " pdb=" N ARG F 432 " pdb=" CA ARG F 432 " ideal model delta harmonic sigma weight residual 180.00 -146.65 -33.35 0 5.00e+00 4.00e-02 4.45e+01 ... (remaining 12855 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.067: 2715 0.067 - 0.133: 474 0.133 - 0.200: 60 0.200 - 0.267: 5 0.267 - 0.333: 7 Chirality restraints: 3261 Sorted by residual: chirality pdb=" C1 BMA T 3 " pdb=" O4 NAG T 2 " pdb=" C2 BMA T 3 " pdb=" O5 BMA T 3 " both_signs ideal model delta sigma weight residual False -2.40 -2.45 0.05 2.00e-02 2.50e+03 7.04e+00 chirality pdb=" C5 BMA O 3 " pdb=" C4 BMA O 3 " pdb=" C6 BMA O 3 " pdb=" O5 BMA O 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.61 0.33 2.00e-01 2.50e+01 2.77e+00 chirality pdb=" C1 NAG S 2 " pdb=" O4 NAG S 1 " pdb=" C2 NAG S 2 " pdb=" O5 NAG S 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.37 -0.03 2.00e-02 2.50e+03 2.74e+00 ... (remaining 3258 not shown) Planarity restraints: 3465 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ARG A 252 " -0.073 5.00e-02 4.00e+02 1.11e-01 1.97e+01 pdb=" N PRO A 253 " 0.192 5.00e-02 4.00e+02 pdb=" CA PRO A 253 " -0.060 5.00e-02 4.00e+02 pdb=" CD PRO A 253 " -0.060 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ARG K 252 " -0.068 5.00e-02 4.00e+02 1.04e-01 1.72e+01 pdb=" N PRO K 253 " 0.180 5.00e-02 4.00e+02 pdb=" CA PRO K 253 " -0.055 5.00e-02 4.00e+02 pdb=" CD PRO K 253 " -0.056 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TRP F 112 " -0.022 2.00e-02 2.50e+03 2.15e-02 1.16e+01 pdb=" CG TRP F 112 " 0.058 2.00e-02 2.50e+03 pdb=" CD1 TRP F 112 " -0.026 2.00e-02 2.50e+03 pdb=" CD2 TRP F 112 " -0.005 2.00e-02 2.50e+03 pdb=" NE1 TRP F 112 " 0.002 2.00e-02 2.50e+03 pdb=" CE2 TRP F 112 " 0.005 2.00e-02 2.50e+03 pdb=" CE3 TRP F 112 " -0.006 2.00e-02 2.50e+03 pdb=" CZ2 TRP F 112 " -0.006 2.00e-02 2.50e+03 pdb=" CZ3 TRP F 112 " -0.001 2.00e-02 2.50e+03 pdb=" CH2 TRP F 112 " 0.000 2.00e-02 2.50e+03 ... (remaining 3462 not shown) Histogram of nonbonded interaction distances: 2.06 - 2.63: 243 2.63 - 3.20: 18003 3.20 - 3.77: 28629 3.77 - 4.33: 41696 4.33 - 4.90: 67547 Nonbonded interactions: 156118 Sorted by model distance: nonbonded pdb=" O LEU K 84 " pdb=" OG SER K 243 " model vdw 2.063 3.040 nonbonded pdb=" OE2 GLU K 83 " pdb=" OG SER K 243 " model vdw 2.065 3.040 nonbonded pdb=" O LYS A 360 " pdb=" OG1 THR A 467 " model vdw 2.068 3.040 nonbonded pdb=" O LYS F 360 " pdb=" OG1 THR F 467 " model vdw 2.070 3.040 nonbonded pdb=" OE2 GLU A 83 " pdb=" OG SER A 243 " model vdw 2.088 3.040 ... (remaining 156113 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' selection = chain 'K' } 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 'E' selection = chain 'Q' selection = chain 'U' } ncs_group { reference = chain 'J' selection = chain 'V' } ncs_group { reference = chain 'O' selection = chain 'S' selection = chain 'T' selection = chain 'W' } ncs_group { reference = chain 'P' selection = chain 'X' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic 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: 3.540 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.810 Check model and map are aligned: 0.130 Set scattering table: 0.190 Process input model: 45.990 Find NCS groups from input model: 0.680 Set up NCS constraints: 0.140 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.920 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 54.430 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7127 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 0.102 20316 Z= 0.404 Angle : 0.993 12.219 27636 Z= 0.518 Chirality : 0.054 0.333 3261 Planarity : 0.006 0.111 3453 Dihedral : 16.966 110.682 8181 Min Nonbonded Distance : 2.063 Molprobity Statistics. All-atom Clashscore : 3.23 Ramachandran Plot: Outliers : 0.33 % Allowed : 7.17 % Favored : 92.51 % Rotamer: Outliers : 0.05 % Allowed : 0.09 % Favored : 99.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.38 % Twisted Proline : 0.00 % Twisted General : 0.34 % 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: -2.22 (0.16), residues: 2442 helix: -1.57 (0.23), residues: 444 sheet: -1.18 (0.19), residues: 642 loop : -1.56 (0.16), residues: 1356 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.058 0.003 TRP F 112 HIS 0.012 0.002 HIS A 105 PHE 0.031 0.002 PHE M 114 TYR 0.029 0.003 TYR D 48 ARG 0.016 0.001 ARG K 166 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4884 Ramachandran restraints generated. 2442 Oldfield, 0 Emsley, 2442 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4884 Ramachandran restraints generated. 2442 Oldfield, 0 Emsley, 2442 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 561 residues out of total 2130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 560 time to evaluate : 2.138 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 340 ASP cc_start: 0.7683 (t0) cc_final: 0.7284 (m-30) REVERT: B 617 ARG cc_start: 0.7543 (mtp180) cc_final: 0.6909 (ttm-80) REVERT: B 629 LEU cc_start: 0.7521 (tp) cc_final: 0.6896 (pp) REVERT: F 104 MET cc_start: 0.8541 (ttt) cc_final: 0.8298 (ttt) REVERT: F 114 GLN cc_start: 0.7660 (tt0) cc_final: 0.7304 (mp10) REVERT: F 344 LYS cc_start: 0.7914 (mttt) cc_final: 0.7617 (mttm) REVERT: F 426 MET cc_start: 0.5396 (mtm) cc_final: 0.5120 (mtp) REVERT: G 625 ASN cc_start: 0.7444 (p0) cc_final: 0.7184 (t0) REVERT: G 629 LEU cc_start: 0.7456 (tp) cc_final: 0.7242 (tp) REVERT: G 659 ASP cc_start: 0.7992 (m-30) cc_final: 0.7583 (m-30) REVERT: I 35 VAL cc_start: 0.8092 (t) cc_final: 0.7861 (p) REVERT: K 113 ASP cc_start: 0.8019 (t0) cc_final: 0.7755 (m-30) REVERT: K 114 GLN cc_start: 0.7500 (tt0) cc_final: 0.7058 (tt0) REVERT: K 340 ASP cc_start: 0.7988 (t0) cc_final: 0.7668 (m-30) REVERT: K 371 ILE cc_start: 0.7369 (mt) cc_final: 0.6879 (mt) REVERT: N 80 LEU cc_start: 0.6086 (mp) cc_final: 0.5854 (tt) outliers start: 1 outliers final: 0 residues processed: 561 average time/residue: 0.3228 time to fit residues: 275.2782 Evaluate side-chains 350 residues out of total 2130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 350 time to evaluate : 2.241 ------------------------------------------------------------------------------- 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: 2.9990 chunk 184 optimal weight: 3.9990 chunk 102 optimal weight: 0.6980 chunk 62 optimal weight: 0.7980 chunk 124 optimal weight: 0.8980 chunk 98 optimal weight: 2.9990 chunk 190 optimal weight: 0.9990 chunk 73 optimal weight: 2.9990 chunk 115 optimal weight: 1.9990 chunk 141 optimal weight: 1.9990 chunk 220 optimal weight: 2.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 241 ASN A 287 HIS B 653 GLN C 52 ASN C 60 ASN D 62 HIS F 241 ASN F 287 HIS G 590 GLN H 113 ASN H 116 HIS I 62 HIS K 287 HIS L 543 ASN M 113 ASN M 119 GLN ** N 62 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7451 moved from start: 0.2926 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.097 20316 Z= 0.326 Angle : 0.785 16.255 27636 Z= 0.403 Chirality : 0.052 0.355 3261 Planarity : 0.005 0.077 3453 Dihedral : 12.829 95.625 3777 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 5.20 Ramachandran Plot: Outliers : 0.25 % Allowed : 5.69 % Favored : 94.06 % Rotamer: Outliers : 2.02 % Allowed : 10.23 % Favored : 87.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.38 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.00 (0.16), residues: 2442 helix: -0.74 (0.25), residues: 429 sheet: -1.21 (0.19), residues: 669 loop : -1.57 (0.16), residues: 1344 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP B 631 HIS 0.007 0.002 HIS N 62 PHE 0.024 0.002 PHE C 64 TYR 0.021 0.002 TYR D 48 ARG 0.005 0.001 ARG N 63 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4884 Ramachandran restraints generated. 2442 Oldfield, 0 Emsley, 2442 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4884 Ramachandran restraints generated. 2442 Oldfield, 0 Emsley, 2442 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 397 residues out of total 2130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 354 time to evaluate : 2.171 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 92 ASN cc_start: 0.7282 (p0) cc_final: 0.7030 (p0) REVERT: B 655 LYS cc_start: 0.7327 (pttm) cc_final: 0.7057 (mmtm) REVERT: D 80 LEU cc_start: 0.6158 (mp) cc_final: 0.5602 (tt) REVERT: F 114 GLN cc_start: 0.7717 (tt0) cc_final: 0.6969 (mm-40) REVERT: G 625 ASN cc_start: 0.7539 (p0) cc_final: 0.7316 (t0) REVERT: G 655 LYS cc_start: 0.7794 (ttpt) cc_final: 0.7520 (mmtm) REVERT: K 114 GLN cc_start: 0.7579 (tt0) cc_final: 0.7012 (tt0) REVERT: L 647 GLU cc_start: 0.6983 (tt0) cc_final: 0.6761 (tt0) REVERT: L 648 GLU cc_start: 0.7602 (tp30) cc_final: 0.6917 (pt0) REVERT: M 48 MET cc_start: 0.8096 (mtp) cc_final: 0.7693 (mtm) outliers start: 43 outliers final: 26 residues processed: 380 average time/residue: 0.3428 time to fit residues: 196.1864 Evaluate side-chains 315 residues out of total 2130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 289 time to evaluate : 2.272 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 ASP Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 217 TYR Chi-restraints excluded: chain A residue 271 VAL Chi-restraints excluded: chain A residue 394 THR Chi-restraints excluded: chain C residue 5 VAL Chi-restraints excluded: chain D residue 21 SER Chi-restraints excluded: chain D residue 22 CYS Chi-restraints excluded: chain F residue 271 VAL Chi-restraints excluded: chain F residue 283 ILE Chi-restraints excluded: chain F residue 433 CYS Chi-restraints excluded: chain F residue 499 THR Chi-restraints excluded: chain G residue 622 ILE Chi-restraints excluded: chain G residue 654 GLU Chi-restraints excluded: chain H residue 30 THR Chi-restraints excluded: chain I residue 21 SER Chi-restraints excluded: chain I residue 72 THR Chi-restraints excluded: chain K residue 125 LEU Chi-restraints excluded: chain K residue 271 VAL Chi-restraints excluded: chain K residue 295 VAL Chi-restraints excluded: chain K residue 347 ILE Chi-restraints excluded: chain M residue 5 VAL Chi-restraints excluded: chain M residue 119 GLN Chi-restraints excluded: chain N residue 21 SER Chi-restraints excluded: chain N residue 35 VAL Chi-restraints excluded: chain N residue 91 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: chunk 122 optimal weight: 3.9990 chunk 68 optimal weight: 0.6980 chunk 183 optimal weight: 0.9980 chunk 150 optimal weight: 1.9990 chunk 60 optimal weight: 2.9990 chunk 221 optimal weight: 10.0000 chunk 238 optimal weight: 6.9990 chunk 196 optimal weight: 1.9990 chunk 219 optimal weight: 5.9990 chunk 75 optimal weight: 0.9980 chunk 177 optimal weight: 0.2980 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 195 ASN B 653 GLN C 116 HIS D 41 HIS F 343 GLN K 105 HIS K 241 ASN K 362 ASN L 577 GLN L 653 GLN M 52 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7529 moved from start: 0.3796 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.071 20316 Z= 0.280 Angle : 0.707 17.570 27636 Z= 0.361 Chirality : 0.049 0.254 3261 Planarity : 0.005 0.052 3453 Dihedral : 11.019 92.684 3777 Min Nonbonded Distance : 2.409 Molprobity Statistics. All-atom Clashscore : 6.02 Ramachandran Plot: Outliers : 0.25 % Allowed : 5.65 % Favored : 94.10 % Rotamer: Outliers : 4.08 % Allowed : 12.49 % Favored : 83.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.38 % 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: -1.73 (0.16), residues: 2442 helix: -0.45 (0.26), residues: 411 sheet: -1.01 (0.19), residues: 660 loop : -1.42 (0.16), residues: 1371 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP K 69 HIS 0.005 0.001 HIS H 35 PHE 0.017 0.002 PHE C 64 TYR 0.022 0.002 TYR D 48 ARG 0.010 0.001 ARG K 446 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4884 Ramachandran restraints generated. 2442 Oldfield, 0 Emsley, 2442 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4884 Ramachandran restraints generated. 2442 Oldfield, 0 Emsley, 2442 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 403 residues out of total 2130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 316 time to evaluate : 2.263 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 95 MET cc_start: 0.8896 (ttp) cc_final: 0.8600 (ttp) REVERT: A 340 ASP cc_start: 0.7932 (t0) cc_final: 0.7578 (m-30) REVERT: A 476 ARG cc_start: 0.7944 (mpp80) cc_final: 0.7599 (mpt-90) REVERT: B 655 LYS cc_start: 0.7393 (pttm) cc_final: 0.7080 (mmtm) REVERT: C 48 MET cc_start: 0.7902 (mtp) cc_final: 0.7487 (mtm) REVERT: D 87 ASP cc_start: 0.7067 (m-30) cc_final: 0.6755 (m-30) REVERT: F 95 MET cc_start: 0.8937 (ttp) cc_final: 0.8669 (ttp) REVERT: F 117 LYS cc_start: 0.7912 (mmmt) cc_final: 0.7687 (mttt) REVERT: F 434 MET cc_start: 0.8433 (OUTLIER) cc_final: 0.8180 (ttp) REVERT: G 570 VAL cc_start: 0.2231 (OUTLIER) cc_final: 0.1948 (m) REVERT: G 655 LYS cc_start: 0.7731 (ttpt) cc_final: 0.7499 (mmtm) REVERT: I 106 LYS cc_start: 0.6694 (OUTLIER) cc_final: 0.6487 (tmtt) REVERT: K 284 ILE cc_start: 0.8907 (OUTLIER) cc_final: 0.8449 (mt) REVERT: L 648 GLU cc_start: 0.7769 (tp30) cc_final: 0.6996 (pt0) REVERT: N 87 ASP cc_start: 0.7192 (m-30) cc_final: 0.6728 (t0) outliers start: 87 outliers final: 49 residues processed: 372 average time/residue: 0.3409 time to fit residues: 191.5138 Evaluate side-chains 340 residues out of total 2130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 287 time to evaluate : 2.061 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 180 ASP Chi-restraints excluded: chain A residue 213 ILE Chi-restraints excluded: chain A residue 217 TYR Chi-restraints excluded: chain A residue 271 VAL Chi-restraints excluded: chain A residue 394 THR Chi-restraints excluded: chain A residue 499 THR Chi-restraints excluded: chain C residue 5 VAL Chi-restraints excluded: chain C residue 30 THR Chi-restraints excluded: chain C residue 116 HIS Chi-restraints excluded: chain D residue 21 SER Chi-restraints excluded: chain D residue 22 CYS Chi-restraints excluded: chain D residue 29 VAL Chi-restraints excluded: chain D residue 99 VAL Chi-restraints excluded: chain D residue 109 VAL Chi-restraints excluded: chain F residue 180 ASP Chi-restraints excluded: chain F residue 181 ILE Chi-restraints excluded: chain F residue 255 VAL Chi-restraints excluded: chain F residue 271 VAL Chi-restraints excluded: chain F residue 283 ILE Chi-restraints excluded: chain F residue 430 VAL Chi-restraints excluded: chain F residue 434 MET Chi-restraints excluded: chain F residue 499 THR Chi-restraints excluded: chain G residue 570 VAL Chi-restraints excluded: chain G residue 622 ILE Chi-restraints excluded: chain G residue 635 ILE Chi-restraints excluded: chain G residue 654 GLU Chi-restraints excluded: chain H residue 30 THR Chi-restraints excluded: chain I residue 21 SER Chi-restraints excluded: chain I residue 25 THR Chi-restraints excluded: chain I residue 28 ASP Chi-restraints excluded: chain I residue 35 VAL Chi-restraints excluded: chain I residue 85 GLU Chi-restraints excluded: chain I residue 99 VAL Chi-restraints excluded: chain I residue 106 LYS Chi-restraints excluded: chain K residue 125 LEU Chi-restraints excluded: chain K residue 180 ASP Chi-restraints excluded: chain K residue 271 VAL Chi-restraints excluded: chain K residue 284 ILE Chi-restraints excluded: chain K residue 295 VAL Chi-restraints excluded: chain K residue 347 ILE Chi-restraints excluded: chain K residue 369 MET Chi-restraints excluded: chain K residue 455 THR Chi-restraints excluded: chain L residue 528 SER Chi-restraints excluded: chain L residue 535 MET Chi-restraints excluded: chain L residue 653 GLN Chi-restraints excluded: chain M residue 5 VAL Chi-restraints excluded: chain M residue 30 THR Chi-restraints excluded: chain M residue 55 THR Chi-restraints excluded: chain N residue 21 SER Chi-restraints excluded: chain N residue 35 VAL Chi-restraints excluded: chain N residue 91 CYS Chi-restraints excluded: chain N residue 99 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: chunk 218 optimal weight: 3.9990 chunk 166 optimal weight: 1.9990 chunk 114 optimal weight: 0.9980 chunk 24 optimal weight: 1.9990 chunk 105 optimal weight: 2.9990 chunk 148 optimal weight: 2.9990 chunk 221 optimal weight: 6.9990 chunk 234 optimal weight: 4.9990 chunk 115 optimal weight: 0.9990 chunk 210 optimal weight: 2.9990 chunk 63 optimal weight: 2.9990 overall best weight: 1.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 246 GLN F 105 HIS G 543 ASN H 119 GLN K 246 GLN N 41 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7661 moved from start: 0.4607 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.076 20316 Z= 0.427 Angle : 0.774 20.697 27636 Z= 0.393 Chirality : 0.051 0.272 3261 Planarity : 0.005 0.048 3453 Dihedral : 11.045 96.947 3777 Min Nonbonded Distance : 2.400 Molprobity Statistics. All-atom Clashscore : 7.17 Ramachandran Plot: Outliers : 0.20 % Allowed : 5.86 % Favored : 93.94 % Rotamer: Outliers : 4.55 % Allowed : 15.12 % Favored : 80.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.38 % 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: -1.78 (0.16), residues: 2442 helix: -0.32 (0.26), residues: 390 sheet: -1.11 (0.19), residues: 696 loop : -1.46 (0.16), residues: 1356 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.002 TRP K 112 HIS 0.036 0.002 HIS C 116 PHE 0.025 0.002 PHE C 64 TYR 0.021 0.002 TYR D 48 ARG 0.007 0.001 ARG A 308 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4884 Ramachandran restraints generated. 2442 Oldfield, 0 Emsley, 2442 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4884 Ramachandran restraints generated. 2442 Oldfield, 0 Emsley, 2442 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 383 residues out of total 2130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 97 poor density : 286 time to evaluate : 2.196 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 95 MET cc_start: 0.8922 (ttp) cc_final: 0.8583 (ttp) REVERT: A 476 ARG cc_start: 0.7913 (mpp80) cc_final: 0.7618 (mpt-90) REVERT: D 87 ASP cc_start: 0.7120 (m-30) cc_final: 0.6888 (m-30) REVERT: F 95 MET cc_start: 0.8947 (ttp) cc_final: 0.8733 (ttp) REVERT: F 117 LYS cc_start: 0.7923 (mmmt) cc_final: 0.7663 (mttt) REVERT: G 655 LYS cc_start: 0.7685 (ttpt) cc_final: 0.7458 (mmtm) REVERT: I 87 ASP cc_start: 0.7079 (m-30) cc_final: 0.6765 (m-30) REVERT: I 106 LYS cc_start: 0.6930 (OUTLIER) cc_final: 0.6686 (tmtt) REVERT: K 164 GLU cc_start: 0.6533 (OUTLIER) cc_final: 0.6039 (pm20) REVERT: K 477 ASP cc_start: 0.7906 (m-30) cc_final: 0.7494 (m-30) REVERT: L 648 GLU cc_start: 0.7728 (tp30) cc_final: 0.6992 (pt0) REVERT: L 655 LYS cc_start: 0.7989 (tmmt) cc_final: 0.7360 (mmtm) outliers start: 97 outliers final: 57 residues processed: 345 average time/residue: 0.3528 time to fit residues: 183.9037 Evaluate side-chains 321 residues out of total 2130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 262 time to evaluate : 2.217 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 109 ILE Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 180 ASP Chi-restraints excluded: chain A residue 271 VAL Chi-restraints excluded: chain A residue 394 THR Chi-restraints excluded: chain A residue 430 VAL Chi-restraints excluded: chain A residue 499 THR Chi-restraints excluded: chain B residue 592 LEU Chi-restraints excluded: chain B residue 595 ILE Chi-restraints excluded: chain B residue 629 LEU Chi-restraints excluded: chain C residue 5 VAL Chi-restraints excluded: chain C residue 20 VAL Chi-restraints excluded: chain C residue 30 THR Chi-restraints excluded: chain C residue 102 ILE Chi-restraints excluded: chain D residue 21 SER Chi-restraints excluded: chain D residue 90 CYS Chi-restraints excluded: chain D residue 99 VAL Chi-restraints excluded: chain D residue 109 VAL Chi-restraints excluded: chain F residue 120 VAL Chi-restraints excluded: chain F residue 125 LEU Chi-restraints excluded: chain F residue 180 ASP Chi-restraints excluded: chain F residue 182 VAL Chi-restraints excluded: chain F residue 255 VAL Chi-restraints excluded: chain F residue 271 VAL Chi-restraints excluded: chain F residue 283 ILE Chi-restraints excluded: chain F residue 284 ILE Chi-restraints excluded: chain F residue 414 ILE Chi-restraints excluded: chain F residue 499 THR Chi-restraints excluded: chain G residue 528 SER Chi-restraints excluded: chain G residue 622 ILE Chi-restraints excluded: chain G residue 654 GLU Chi-restraints excluded: chain H residue 30 THR Chi-restraints excluded: chain H residue 74 THR Chi-restraints excluded: chain I residue 21 SER Chi-restraints excluded: chain I residue 28 ASP Chi-restraints excluded: chain I residue 35 VAL Chi-restraints excluded: chain I residue 72 THR Chi-restraints excluded: chain I residue 99 VAL Chi-restraints excluded: chain I residue 106 LYS Chi-restraints excluded: chain K residue 109 ILE Chi-restraints excluded: chain K residue 120 VAL Chi-restraints excluded: chain K residue 125 LEU Chi-restraints excluded: chain K residue 164 GLU Chi-restraints excluded: chain K residue 180 ASP Chi-restraints excluded: chain K residue 271 VAL Chi-restraints excluded: chain K residue 295 VAL Chi-restraints excluded: chain K residue 326 ILE Chi-restraints excluded: chain K residue 347 ILE Chi-restraints excluded: chain K residue 430 VAL Chi-restraints excluded: chain K residue 455 THR Chi-restraints excluded: chain K residue 478 ASN Chi-restraints excluded: chain L residue 629 LEU Chi-restraints excluded: chain M residue 30 THR Chi-restraints excluded: chain M residue 55 THR Chi-restraints excluded: chain M residue 69 THR Chi-restraints excluded: chain N residue 21 SER Chi-restraints excluded: chain N residue 35 VAL Chi-restraints excluded: chain N residue 91 CYS Chi-restraints excluded: chain N residue 99 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: chunk 195 optimal weight: 1.9990 chunk 133 optimal weight: 0.4980 chunk 3 optimal weight: 0.6980 chunk 174 optimal weight: 2.9990 chunk 96 optimal weight: 0.9990 chunk 200 optimal weight: 0.2980 chunk 162 optimal weight: 0.9990 chunk 0 optimal weight: 2.9990 chunk 119 optimal weight: 0.0870 chunk 210 optimal weight: 0.0060 chunk 59 optimal weight: 5.9990 overall best weight: 0.3174 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 577 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 119 GLN G 543 ASN N 54 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7541 moved from start: 0.4794 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 20316 Z= 0.171 Angle : 0.631 18.560 27636 Z= 0.320 Chirality : 0.045 0.234 3261 Planarity : 0.004 0.046 3453 Dihedral : 9.662 85.795 3777 Min Nonbonded Distance : 2.405 Molprobity Statistics. All-atom Clashscore : 5.66 Ramachandran Plot: Outliers : 0.20 % Allowed : 5.36 % Favored : 94.43 % Rotamer: Outliers : 3.15 % Allowed : 17.51 % Favored : 79.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.38 % 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: -1.36 (0.16), residues: 2442 helix: 0.06 (0.26), residues: 399 sheet: -0.53 (0.20), residues: 621 loop : -1.38 (0.16), residues: 1422 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.001 TRP K 112 HIS 0.004 0.001 HIS C 116 PHE 0.018 0.001 PHE C 64 TYR 0.017 0.001 TYR A 61 ARG 0.005 0.001 ARG A 308 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4884 Ramachandran restraints generated. 2442 Oldfield, 0 Emsley, 2442 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4884 Ramachandran restraints generated. 2442 Oldfield, 0 Emsley, 2442 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 344 residues out of total 2130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 277 time to evaluate : 1.930 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 95 MET cc_start: 0.8897 (ttp) cc_final: 0.8657 (ttp) REVERT: A 284 ILE cc_start: 0.8978 (OUTLIER) cc_final: 0.8460 (mt) REVERT: A 476 ARG cc_start: 0.7843 (mpp80) cc_final: 0.7599 (mpt-90) REVERT: B 625 ASN cc_start: 0.7569 (p0) cc_final: 0.7259 (t0) REVERT: D 87 ASP cc_start: 0.6979 (m-30) cc_final: 0.6760 (m-30) REVERT: F 95 MET cc_start: 0.8917 (ttp) cc_final: 0.8704 (ttp) REVERT: F 117 LYS cc_start: 0.7849 (mmmt) cc_final: 0.7600 (mttt) REVERT: F 164 GLU cc_start: 0.6259 (OUTLIER) cc_final: 0.6033 (pm20) REVERT: I 87 ASP cc_start: 0.6861 (m-30) cc_final: 0.6576 (m-30) REVERT: I 106 LYS cc_start: 0.6753 (OUTLIER) cc_final: 0.6507 (tmtt) REVERT: K 164 GLU cc_start: 0.6429 (OUTLIER) cc_final: 0.5979 (pm20) REVERT: L 610 TRP cc_start: 0.7820 (t-100) cc_final: 0.7611 (t-100) REVERT: L 626 MET cc_start: 0.7345 (ttm) cc_final: 0.7021 (ttm) REVERT: L 648 GLU cc_start: 0.7602 (tp30) cc_final: 0.6993 (pt0) REVERT: L 655 LYS cc_start: 0.7789 (tmmt) cc_final: 0.7373 (mmtm) outliers start: 67 outliers final: 39 residues processed: 315 average time/residue: 0.3511 time to fit residues: 164.6210 Evaluate side-chains 303 residues out of total 2130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 260 time to evaluate : 2.235 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 TRP Chi-restraints excluded: chain A residue 271 VAL Chi-restraints excluded: chain A residue 284 ILE Chi-restraints excluded: chain A residue 499 THR Chi-restraints excluded: chain B residue 605 CYS Chi-restraints excluded: chain C residue 5 VAL Chi-restraints excluded: chain C residue 119 GLN Chi-restraints excluded: chain D residue 25 THR Chi-restraints excluded: chain D residue 90 CYS Chi-restraints excluded: chain F residue 125 LEU Chi-restraints excluded: chain F residue 164 GLU Chi-restraints excluded: chain F residue 180 ASP Chi-restraints excluded: chain F residue 271 VAL Chi-restraints excluded: chain F residue 433 CYS Chi-restraints excluded: chain F residue 455 THR Chi-restraints excluded: chain F residue 499 THR Chi-restraints excluded: chain G residue 622 ILE Chi-restraints excluded: chain G residue 626 MET Chi-restraints excluded: chain H residue 20 VAL Chi-restraints excluded: chain H residue 30 THR Chi-restraints excluded: chain I residue 25 THR Chi-restraints excluded: chain I residue 28 ASP Chi-restraints excluded: chain I residue 35 VAL Chi-restraints excluded: chain I residue 106 LYS Chi-restraints excluded: chain K residue 45 TRP Chi-restraints excluded: chain K residue 57 ASP Chi-restraints excluded: chain K residue 109 ILE Chi-restraints excluded: chain K residue 125 LEU Chi-restraints excluded: chain K residue 164 GLU Chi-restraints excluded: chain K residue 180 ASP Chi-restraints excluded: chain K residue 271 VAL Chi-restraints excluded: chain K residue 295 VAL Chi-restraints excluded: chain K residue 347 ILE Chi-restraints excluded: chain K residue 369 MET Chi-restraints excluded: chain K residue 445 CYS Chi-restraints excluded: chain L residue 528 SER Chi-restraints excluded: chain M residue 30 THR Chi-restraints excluded: chain M residue 45 LEU Chi-restraints excluded: chain N residue 21 SER Chi-restraints excluded: chain N residue 25 THR Chi-restraints excluded: chain N residue 35 VAL Chi-restraints excluded: chain N residue 54 ASN Chi-restraints excluded: chain N residue 91 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: chunk 79 optimal weight: 0.7980 chunk 211 optimal weight: 1.9990 chunk 46 optimal weight: 3.9990 chunk 137 optimal weight: 0.5980 chunk 57 optimal weight: 6.9990 chunk 235 optimal weight: 1.9990 chunk 195 optimal weight: 2.9990 chunk 108 optimal weight: 1.9990 chunk 19 optimal weight: 5.9990 chunk 77 optimal weight: 10.0000 chunk 123 optimal weight: 0.9990 overall best weight: 1.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 543 ASN ** B 577 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 653 GLN C 116 HIS G 543 ASN ** L 653 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7635 moved from start: 0.5064 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.082 20316 Z= 0.322 Angle : 0.688 19.474 27636 Z= 0.347 Chirality : 0.048 0.262 3261 Planarity : 0.004 0.045 3453 Dihedral : 9.882 90.893 3777 Min Nonbonded Distance : 2.357 Molprobity Statistics. All-atom Clashscore : 6.48 Ramachandran Plot: Outliers : 0.16 % Allowed : 5.45 % Favored : 94.39 % Rotamer: Outliers : 4.51 % Allowed : 16.85 % Favored : 78.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.38 % 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: -1.43 (0.16), residues: 2442 helix: 0.09 (0.26), residues: 399 sheet: -0.64 (0.20), residues: 654 loop : -1.43 (0.16), residues: 1389 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP K 112 HIS 0.007 0.001 HIS C 35 PHE 0.021 0.002 PHE C 64 TYR 0.017 0.002 TYR I 48 ARG 0.005 0.001 ARG K 166 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4884 Ramachandran restraints generated. 2442 Oldfield, 0 Emsley, 2442 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4884 Ramachandran restraints generated. 2442 Oldfield, 0 Emsley, 2442 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 362 residues out of total 2130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 266 time to evaluate : 2.111 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 500 ARG cc_start: 0.6981 (mmm-85) cc_final: 0.6772 (mtp85) REVERT: B 625 ASN cc_start: 0.7664 (p0) cc_final: 0.7427 (t0) REVERT: D 87 ASP cc_start: 0.7007 (m-30) cc_final: 0.6786 (m-30) REVERT: F 95 MET cc_start: 0.8927 (ttp) cc_final: 0.8711 (ttp) REVERT: F 117 LYS cc_start: 0.7924 (mmmt) cc_final: 0.7644 (mttt) REVERT: F 164 GLU cc_start: 0.6609 (OUTLIER) cc_final: 0.6334 (pm20) REVERT: I 87 ASP cc_start: 0.6910 (m-30) cc_final: 0.6597 (m-30) REVERT: I 106 LYS cc_start: 0.6899 (OUTLIER) cc_final: 0.6616 (tmtt) REVERT: K 164 GLU cc_start: 0.6507 (OUTLIER) cc_final: 0.6015 (pm20) REVERT: K 284 ILE cc_start: 0.8983 (OUTLIER) cc_final: 0.8500 (mt) REVERT: K 359 ILE cc_start: 0.6242 (OUTLIER) cc_final: 0.5931 (mt) REVERT: K 477 ASP cc_start: 0.7788 (m-30) cc_final: 0.7390 (m-30) REVERT: L 588 ARG cc_start: 0.8321 (ttm110) cc_final: 0.8086 (ttm-80) REVERT: L 610 TRP cc_start: 0.7798 (t-100) cc_final: 0.7570 (t-100) REVERT: L 648 GLU cc_start: 0.7673 (tp30) cc_final: 0.6905 (pt0) REVERT: L 655 LYS cc_start: 0.7798 (tmmt) cc_final: 0.7308 (mmtm) outliers start: 96 outliers final: 59 residues processed: 325 average time/residue: 0.3352 time to fit residues: 164.9851 Evaluate side-chains 319 residues out of total 2130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 255 time to evaluate : 2.180 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 ASN Chi-restraints excluded: chain A residue 109 ILE Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 180 ASP Chi-restraints excluded: chain A residue 271 VAL Chi-restraints excluded: chain A residue 284 ILE Chi-restraints excluded: chain A residue 445 CYS Chi-restraints excluded: chain A residue 499 THR Chi-restraints excluded: chain B residue 543 ASN Chi-restraints excluded: chain B residue 595 ILE Chi-restraints excluded: chain B residue 605 CYS Chi-restraints excluded: chain C residue 5 VAL Chi-restraints excluded: chain C residue 20 VAL Chi-restraints excluded: chain C residue 30 THR Chi-restraints excluded: chain C residue 55 THR Chi-restraints excluded: chain C residue 69 THR Chi-restraints excluded: chain D residue 25 THR Chi-restraints excluded: chain D residue 90 CYS Chi-restraints excluded: chain D residue 99 VAL Chi-restraints excluded: chain F residue 120 VAL Chi-restraints excluded: chain F residue 125 LEU Chi-restraints excluded: chain F residue 164 GLU Chi-restraints excluded: chain F residue 180 ASP Chi-restraints excluded: chain F residue 271 VAL Chi-restraints excluded: chain F residue 283 ILE Chi-restraints excluded: chain F residue 284 ILE Chi-restraints excluded: chain F residue 445 CYS Chi-restraints excluded: chain F residue 455 THR Chi-restraints excluded: chain F residue 499 THR Chi-restraints excluded: chain G residue 543 ASN Chi-restraints excluded: chain G residue 622 ILE Chi-restraints excluded: chain H residue 30 THR Chi-restraints excluded: chain I residue 21 SER Chi-restraints excluded: chain I residue 28 ASP Chi-restraints excluded: chain I residue 35 VAL Chi-restraints excluded: chain I residue 53 VAL Chi-restraints excluded: chain I residue 106 LYS Chi-restraints excluded: chain K residue 45 TRP Chi-restraints excluded: chain K residue 57 ASP Chi-restraints excluded: chain K residue 109 ILE Chi-restraints excluded: chain K residue 120 VAL Chi-restraints excluded: chain K residue 125 LEU Chi-restraints excluded: chain K residue 164 GLU Chi-restraints excluded: chain K residue 180 ASP Chi-restraints excluded: chain K residue 271 VAL Chi-restraints excluded: chain K residue 284 ILE Chi-restraints excluded: chain K residue 295 VAL Chi-restraints excluded: chain K residue 359 ILE Chi-restraints excluded: chain K residue 362 ASN Chi-restraints excluded: chain K residue 445 CYS Chi-restraints excluded: chain K residue 455 THR Chi-restraints excluded: chain K residue 478 ASN Chi-restraints excluded: chain L residue 528 SER Chi-restraints excluded: chain L residue 605 CYS Chi-restraints excluded: chain M residue 5 VAL Chi-restraints excluded: chain M residue 30 THR Chi-restraints excluded: chain M residue 45 LEU Chi-restraints excluded: chain M residue 55 THR Chi-restraints excluded: chain N residue 21 SER Chi-restraints excluded: chain N residue 35 VAL Chi-restraints excluded: chain N residue 91 CYS Chi-restraints excluded: chain N residue 99 VAL Chi-restraints excluded: chain N residue 105 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: chunk 226 optimal weight: 0.8980 chunk 26 optimal weight: 3.9990 chunk 133 optimal weight: 2.9990 chunk 171 optimal weight: 0.6980 chunk 197 optimal weight: 5.9990 chunk 131 optimal weight: 0.5980 chunk 234 optimal weight: 4.9990 chunk 146 optimal weight: 2.9990 chunk 142 optimal weight: 0.8980 chunk 108 optimal weight: 0.7980 chunk 144 optimal weight: 0.5980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 577 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 54 ASN ** L 653 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7601 moved from start: 0.5190 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.087 20316 Z= 0.224 Angle : 0.637 23.025 27636 Z= 0.319 Chirality : 0.046 0.285 3261 Planarity : 0.004 0.044 3453 Dihedral : 9.421 87.109 3777 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 6.25 Ramachandran Plot: Outliers : 0.16 % Allowed : 5.24 % Favored : 94.59 % Rotamer: Outliers : 3.62 % Allowed : 18.36 % Favored : 78.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.38 % 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: -1.26 (0.17), residues: 2442 helix: 0.29 (0.26), residues: 399 sheet: -0.55 (0.20), residues: 624 loop : -1.31 (0.16), residues: 1419 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.001 TRP K 112 HIS 0.005 0.001 HIS C 35 PHE 0.022 0.001 PHE C 64 TYR 0.016 0.001 TYR I 48 ARG 0.005 0.001 ARG M 38 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4884 Ramachandran restraints generated. 2442 Oldfield, 0 Emsley, 2442 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4884 Ramachandran restraints generated. 2442 Oldfield, 0 Emsley, 2442 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 333 residues out of total 2130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 256 time to evaluate : 2.167 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 629 LEU cc_start: 0.8206 (tp) cc_final: 0.7967 (mt) REVERT: D 87 ASP cc_start: 0.6960 (m-30) cc_final: 0.6748 (m-30) REVERT: F 117 LYS cc_start: 0.7919 (mmmt) cc_final: 0.7642 (mttt) REVERT: F 164 GLU cc_start: 0.6498 (OUTLIER) cc_final: 0.6142 (pm20) REVERT: I 87 ASP cc_start: 0.6849 (m-30) cc_final: 0.6532 (m-30) REVERT: I 106 LYS cc_start: 0.6865 (OUTLIER) cc_final: 0.6567 (tmtt) REVERT: K 164 GLU cc_start: 0.6487 (OUTLIER) cc_final: 0.5998 (pm20) REVERT: K 284 ILE cc_start: 0.8958 (OUTLIER) cc_final: 0.8508 (mt) REVERT: K 359 ILE cc_start: 0.6019 (OUTLIER) cc_final: 0.5699 (mm) REVERT: L 588 ARG cc_start: 0.8286 (ttm110) cc_final: 0.8077 (ttm-80) REVERT: L 626 MET cc_start: 0.7516 (ttm) cc_final: 0.7193 (ttm) REVERT: L 629 LEU cc_start: 0.8211 (OUTLIER) cc_final: 0.7920 (mt) REVERT: L 648 GLU cc_start: 0.7600 (tp30) cc_final: 0.6923 (pt0) REVERT: L 655 LYS cc_start: 0.7813 (tmmt) cc_final: 0.7373 (mmtm) outliers start: 77 outliers final: 57 residues processed: 310 average time/residue: 0.3559 time to fit residues: 164.8341 Evaluate side-chains 313 residues out of total 2130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 250 time to evaluate : 2.175 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 ASN Chi-restraints excluded: chain A residue 109 ILE Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 180 ASP Chi-restraints excluded: chain A residue 271 VAL Chi-restraints excluded: chain A residue 284 ILE Chi-restraints excluded: chain A residue 445 CYS Chi-restraints excluded: chain A residue 499 THR Chi-restraints excluded: chain B residue 605 CYS Chi-restraints excluded: chain B residue 654 GLU Chi-restraints excluded: chain C residue 5 VAL Chi-restraints excluded: chain C residue 30 THR Chi-restraints excluded: chain C residue 102 ILE Chi-restraints excluded: chain D residue 21 SER Chi-restraints excluded: chain D residue 25 THR Chi-restraints excluded: chain D residue 54 ASN Chi-restraints excluded: chain D residue 90 CYS Chi-restraints excluded: chain D residue 99 VAL Chi-restraints excluded: chain D residue 109 VAL Chi-restraints excluded: chain F residue 125 LEU Chi-restraints excluded: chain F residue 164 GLU Chi-restraints excluded: chain F residue 180 ASP Chi-restraints excluded: chain F residue 182 VAL Chi-restraints excluded: chain F residue 271 VAL Chi-restraints excluded: chain F residue 283 ILE Chi-restraints excluded: chain F residue 433 CYS Chi-restraints excluded: chain F residue 445 CYS Chi-restraints excluded: chain F residue 455 THR Chi-restraints excluded: chain F residue 499 THR Chi-restraints excluded: chain G residue 595 ILE Chi-restraints excluded: chain G residue 622 ILE Chi-restraints excluded: chain H residue 30 THR Chi-restraints excluded: chain I residue 21 SER Chi-restraints excluded: chain I residue 28 ASP Chi-restraints excluded: chain I residue 35 VAL Chi-restraints excluded: chain I residue 53 VAL Chi-restraints excluded: chain I residue 99 VAL Chi-restraints excluded: chain I residue 106 LYS Chi-restraints excluded: chain K residue 45 TRP Chi-restraints excluded: chain K residue 57 ASP Chi-restraints excluded: chain K residue 109 ILE Chi-restraints excluded: chain K residue 125 LEU Chi-restraints excluded: chain K residue 164 GLU Chi-restraints excluded: chain K residue 180 ASP Chi-restraints excluded: chain K residue 271 VAL Chi-restraints excluded: chain K residue 284 ILE Chi-restraints excluded: chain K residue 295 VAL Chi-restraints excluded: chain K residue 347 ILE Chi-restraints excluded: chain K residue 359 ILE Chi-restraints excluded: chain K residue 362 ASN Chi-restraints excluded: chain K residue 445 CYS Chi-restraints excluded: chain K residue 455 THR Chi-restraints excluded: chain L residue 605 CYS Chi-restraints excluded: chain L residue 629 LEU Chi-restraints excluded: chain L residue 653 GLN Chi-restraints excluded: chain M residue 5 VAL Chi-restraints excluded: chain M residue 30 THR Chi-restraints excluded: chain M residue 45 LEU Chi-restraints excluded: chain N residue 21 SER Chi-restraints excluded: chain N residue 35 VAL Chi-restraints excluded: chain N residue 91 CYS Chi-restraints excluded: chain N residue 99 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: chunk 93 optimal weight: 1.9990 chunk 139 optimal weight: 8.9990 chunk 70 optimal weight: 4.9990 chunk 46 optimal weight: 2.9990 chunk 45 optimal weight: 0.8980 chunk 148 optimal weight: 0.8980 chunk 159 optimal weight: 6.9990 chunk 115 optimal weight: 1.9990 chunk 21 optimal weight: 2.9990 chunk 184 optimal weight: 0.8980 chunk 213 optimal weight: 0.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 577 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 54 ASN G 543 ASN ** L 653 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7637 moved from start: 0.5387 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.090 20316 Z= 0.293 Angle : 0.668 23.285 27636 Z= 0.334 Chirality : 0.047 0.296 3261 Planarity : 0.004 0.043 3453 Dihedral : 9.479 88.889 3777 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 6.48 Ramachandran Plot: Outliers : 0.16 % Allowed : 5.53 % Favored : 94.31 % Rotamer: Outliers : 4.08 % Allowed : 18.12 % Favored : 77.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.38 % 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: -1.32 (0.17), residues: 2442 helix: 0.26 (0.26), residues: 399 sheet: -0.72 (0.20), residues: 660 loop : -1.30 (0.16), residues: 1383 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.002 TRP K 112 HIS 0.007 0.001 HIS C 35 PHE 0.024 0.002 PHE C 64 TYR 0.018 0.001 TYR F 395 ARG 0.007 0.001 ARG K 166 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4884 Ramachandran restraints generated. 2442 Oldfield, 0 Emsley, 2442 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4884 Ramachandran restraints generated. 2442 Oldfield, 0 Emsley, 2442 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 357 residues out of total 2130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 270 time to evaluate : 2.157 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 394 THR cc_start: 0.7091 (t) cc_final: 0.6478 (m) REVERT: B 629 LEU cc_start: 0.8237 (OUTLIER) cc_final: 0.7954 (mt) REVERT: C 119 GLN cc_start: 0.7077 (pm20) cc_final: 0.6729 (pm20) REVERT: D 87 ASP cc_start: 0.6975 (m-30) cc_final: 0.6753 (m-30) REVERT: F 117 LYS cc_start: 0.7950 (mmmt) cc_final: 0.7651 (mttt) REVERT: F 164 GLU cc_start: 0.6697 (OUTLIER) cc_final: 0.6281 (pm20) REVERT: I 87 ASP cc_start: 0.6862 (m-30) cc_final: 0.6539 (m-30) REVERT: I 106 LYS cc_start: 0.6893 (OUTLIER) cc_final: 0.6536 (tmtt) REVERT: K 95 MET cc_start: 0.8956 (ttp) cc_final: 0.8662 (ttp) REVERT: K 164 GLU cc_start: 0.6462 (OUTLIER) cc_final: 0.5978 (pm20) REVERT: K 284 ILE cc_start: 0.8985 (OUTLIER) cc_final: 0.8510 (mt) REVERT: K 359 ILE cc_start: 0.5942 (OUTLIER) cc_final: 0.5634 (mt) REVERT: L 588 ARG cc_start: 0.8388 (ttm110) cc_final: 0.8156 (ttm-80) REVERT: L 629 LEU cc_start: 0.8282 (OUTLIER) cc_final: 0.7981 (mt) REVERT: L 648 GLU cc_start: 0.7639 (tp30) cc_final: 0.6843 (pt0) REVERT: L 655 LYS cc_start: 0.7794 (tmmt) cc_final: 0.7446 (mmtm) outliers start: 87 outliers final: 62 residues processed: 328 average time/residue: 0.3560 time to fit residues: 174.5529 Evaluate side-chains 322 residues out of total 2130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 253 time to evaluate : 2.228 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 ASN Chi-restraints excluded: chain A residue 109 ILE Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 180 ASP Chi-restraints excluded: chain A residue 271 VAL Chi-restraints excluded: chain A residue 284 ILE Chi-restraints excluded: chain A residue 445 CYS Chi-restraints excluded: chain A residue 499 THR Chi-restraints excluded: chain B residue 595 ILE Chi-restraints excluded: chain B residue 605 CYS Chi-restraints excluded: chain B residue 629 LEU Chi-restraints excluded: chain B residue 654 GLU Chi-restraints excluded: chain C residue 5 VAL Chi-restraints excluded: chain C residue 20 VAL Chi-restraints excluded: chain C residue 30 THR Chi-restraints excluded: chain C residue 102 ILE Chi-restraints excluded: chain D residue 21 SER Chi-restraints excluded: chain D residue 25 THR Chi-restraints excluded: chain D residue 38 PHE Chi-restraints excluded: chain D residue 90 CYS Chi-restraints excluded: chain D residue 99 VAL Chi-restraints excluded: chain D residue 109 VAL Chi-restraints excluded: chain F residue 120 VAL Chi-restraints excluded: chain F residue 125 LEU Chi-restraints excluded: chain F residue 164 GLU Chi-restraints excluded: chain F residue 180 ASP Chi-restraints excluded: chain F residue 182 VAL Chi-restraints excluded: chain F residue 229 ASN Chi-restraints excluded: chain F residue 271 VAL Chi-restraints excluded: chain F residue 283 ILE Chi-restraints excluded: chain F residue 284 ILE Chi-restraints excluded: chain F residue 445 CYS Chi-restraints excluded: chain F residue 455 THR Chi-restraints excluded: chain G residue 595 ILE Chi-restraints excluded: chain G residue 622 ILE Chi-restraints excluded: chain H residue 30 THR Chi-restraints excluded: chain I residue 21 SER Chi-restraints excluded: chain I residue 35 VAL Chi-restraints excluded: chain I residue 99 VAL Chi-restraints excluded: chain I residue 106 LYS Chi-restraints excluded: chain K residue 45 TRP Chi-restraints excluded: chain K residue 109 ILE Chi-restraints excluded: chain K residue 120 VAL Chi-restraints excluded: chain K residue 125 LEU Chi-restraints excluded: chain K residue 164 GLU Chi-restraints excluded: chain K residue 180 ASP Chi-restraints excluded: chain K residue 271 VAL Chi-restraints excluded: chain K residue 284 ILE Chi-restraints excluded: chain K residue 295 VAL Chi-restraints excluded: chain K residue 359 ILE Chi-restraints excluded: chain K residue 362 ASN Chi-restraints excluded: chain K residue 445 CYS Chi-restraints excluded: chain K residue 452 LEU Chi-restraints excluded: chain K residue 455 THR Chi-restraints excluded: chain K residue 478 ASN Chi-restraints excluded: chain L residue 528 SER Chi-restraints excluded: chain L residue 605 CYS Chi-restraints excluded: chain L residue 629 LEU Chi-restraints excluded: chain L residue 653 GLN Chi-restraints excluded: chain M residue 5 VAL Chi-restraints excluded: chain M residue 30 THR Chi-restraints excluded: chain M residue 45 LEU Chi-restraints excluded: chain M residue 55 THR Chi-restraints excluded: chain N residue 21 SER Chi-restraints excluded: chain N residue 35 VAL Chi-restraints excluded: chain N residue 91 CYS Chi-restraints excluded: chain N residue 99 VAL 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: 0.8980 chunk 204 optimal weight: 1.9990 chunk 218 optimal weight: 0.6980 chunk 131 optimal weight: 0.7980 chunk 95 optimal weight: 1.9990 chunk 171 optimal weight: 0.8980 chunk 66 optimal weight: 7.9990 chunk 197 optimal weight: 3.9990 chunk 206 optimal weight: 0.6980 chunk 217 optimal weight: 2.9990 chunk 143 optimal weight: 0.4980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 577 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 543 ASN L 575 GLN L 577 GLN ** L 653 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7605 moved from start: 0.5508 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.092 20316 Z= 0.224 Angle : 0.642 22.421 27636 Z= 0.322 Chirality : 0.046 0.279 3261 Planarity : 0.004 0.043 3453 Dihedral : 9.047 85.371 3777 Min Nonbonded Distance : 2.402 Molprobity Statistics. All-atom Clashscore : 6.43 Ramachandran Plot: Outliers : 0.16 % Allowed : 5.04 % Favored : 94.80 % Rotamer: Outliers : 3.80 % Allowed : 18.83 % Favored : 77.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.38 % 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: -1.23 (0.17), residues: 2442 helix: 0.45 (0.26), residues: 399 sheet: -0.68 (0.20), residues: 660 loop : -1.26 (0.16), residues: 1383 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.042 0.001 TRP K 112 HIS 0.006 0.001 HIS F 105 PHE 0.021 0.001 PHE C 64 TYR 0.015 0.001 TYR D 48 ARG 0.006 0.001 ARG K 166 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4884 Ramachandran restraints generated. 2442 Oldfield, 0 Emsley, 2442 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4884 Ramachandran restraints generated. 2442 Oldfield, 0 Emsley, 2442 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 343 residues out of total 2130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 262 time to evaluate : 2.297 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 269 GLU cc_start: 0.7152 (pm20) cc_final: 0.6894 (pm20) REVERT: A 394 THR cc_start: 0.7016 (t) cc_final: 0.6622 (m) REVERT: B 629 LEU cc_start: 0.8200 (OUTLIER) cc_final: 0.7923 (mt) REVERT: C 119 GLN cc_start: 0.7065 (pm20) cc_final: 0.6775 (pm20) REVERT: D 31 LYS cc_start: 0.7444 (ttmt) cc_final: 0.7169 (tttt) REVERT: F 117 LYS cc_start: 0.7952 (mmmt) cc_final: 0.7641 (mttt) REVERT: F 164 GLU cc_start: 0.6682 (OUTLIER) cc_final: 0.6264 (pm20) REVERT: I 87 ASP cc_start: 0.6797 (m-30) cc_final: 0.6485 (m-30) REVERT: I 106 LYS cc_start: 0.6878 (OUTLIER) cc_final: 0.6547 (tmtt) REVERT: K 95 MET cc_start: 0.8922 (ttp) cc_final: 0.8649 (ttp) REVERT: K 164 GLU cc_start: 0.6398 (OUTLIER) cc_final: 0.5934 (pm20) REVERT: K 284 ILE cc_start: 0.8973 (OUTLIER) cc_final: 0.8521 (mt) REVERT: K 359 ILE cc_start: 0.5884 (OUTLIER) cc_final: 0.5544 (mm) REVERT: L 588 ARG cc_start: 0.8305 (ttm110) cc_final: 0.8088 (ttm-80) REVERT: L 629 LEU cc_start: 0.8277 (OUTLIER) cc_final: 0.8030 (mt) REVERT: L 648 GLU cc_start: 0.7567 (tp30) cc_final: 0.6855 (pt0) REVERT: L 655 LYS cc_start: 0.7809 (tmmt) cc_final: 0.7493 (mmtm) outliers start: 81 outliers final: 62 residues processed: 319 average time/residue: 0.3439 time to fit residues: 165.8176 Evaluate side-chains 321 residues out of total 2130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 252 time to evaluate : 2.115 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 ASN Chi-restraints excluded: chain A residue 109 ILE Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 180 ASP Chi-restraints excluded: chain A residue 271 VAL Chi-restraints excluded: chain A residue 284 ILE Chi-restraints excluded: chain A residue 445 CYS Chi-restraints excluded: chain A residue 499 THR Chi-restraints excluded: chain B residue 595 ILE Chi-restraints excluded: chain B residue 605 CYS Chi-restraints excluded: chain B residue 629 LEU Chi-restraints excluded: chain B residue 654 GLU Chi-restraints excluded: chain C residue 5 VAL Chi-restraints excluded: chain C residue 20 VAL Chi-restraints excluded: chain C residue 30 THR Chi-restraints excluded: chain C residue 102 ILE Chi-restraints excluded: chain D residue 21 SER Chi-restraints excluded: chain D residue 25 THR Chi-restraints excluded: chain D residue 28 ASP Chi-restraints excluded: chain D residue 90 CYS Chi-restraints excluded: chain D residue 99 VAL Chi-restraints excluded: chain D residue 109 VAL Chi-restraints excluded: chain F residue 120 VAL Chi-restraints excluded: chain F residue 125 LEU Chi-restraints excluded: chain F residue 164 GLU Chi-restraints excluded: chain F residue 180 ASP Chi-restraints excluded: chain F residue 182 VAL Chi-restraints excluded: chain F residue 271 VAL Chi-restraints excluded: chain F residue 283 ILE Chi-restraints excluded: chain F residue 284 ILE Chi-restraints excluded: chain F residue 445 CYS Chi-restraints excluded: chain F residue 455 THR Chi-restraints excluded: chain G residue 543 ASN Chi-restraints excluded: chain G residue 581 LEU Chi-restraints excluded: chain G residue 595 ILE Chi-restraints excluded: chain G residue 622 ILE Chi-restraints excluded: chain H residue 30 THR Chi-restraints excluded: chain I residue 21 SER Chi-restraints excluded: chain I residue 35 VAL Chi-restraints excluded: chain I residue 72 THR Chi-restraints excluded: chain I residue 99 VAL Chi-restraints excluded: chain I residue 106 LYS Chi-restraints excluded: chain K residue 57 ASP Chi-restraints excluded: chain K residue 120 VAL Chi-restraints excluded: chain K residue 125 LEU Chi-restraints excluded: chain K residue 161 THR Chi-restraints excluded: chain K residue 164 GLU Chi-restraints excluded: chain K residue 180 ASP Chi-restraints excluded: chain K residue 271 VAL Chi-restraints excluded: chain K residue 284 ILE Chi-restraints excluded: chain K residue 295 VAL Chi-restraints excluded: chain K residue 359 ILE Chi-restraints excluded: chain K residue 362 ASN Chi-restraints excluded: chain K residue 445 CYS Chi-restraints excluded: chain K residue 452 LEU Chi-restraints excluded: chain K residue 455 THR Chi-restraints excluded: chain L residue 528 SER Chi-restraints excluded: chain L residue 605 CYS Chi-restraints excluded: chain L residue 629 LEU Chi-restraints excluded: chain L residue 653 GLN Chi-restraints excluded: chain M residue 5 VAL Chi-restraints excluded: chain M residue 30 THR Chi-restraints excluded: chain M residue 45 LEU Chi-restraints excluded: chain N residue 21 SER Chi-restraints excluded: chain N residue 35 VAL Chi-restraints excluded: chain N residue 90 CYS Chi-restraints excluded: chain N residue 91 CYS Chi-restraints excluded: chain N residue 99 VAL Chi-restraints excluded: chain N residue 105 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: chunk 230 optimal weight: 0.4980 chunk 140 optimal weight: 5.9990 chunk 109 optimal weight: 1.9990 chunk 160 optimal weight: 1.9990 chunk 242 optimal weight: 1.9990 chunk 222 optimal weight: 4.9990 chunk 192 optimal weight: 2.9990 chunk 20 optimal weight: 2.9990 chunk 148 optimal weight: 1.9990 chunk 118 optimal weight: 0.9980 chunk 153 optimal weight: 0.5980 overall best weight: 1.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 577 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 543 ASN ** L 653 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7648 moved from start: 0.5646 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.089 20316 Z= 0.316 Angle : 0.703 23.195 27636 Z= 0.351 Chirality : 0.048 0.301 3261 Planarity : 0.004 0.043 3453 Dihedral : 9.278 87.655 3777 Min Nonbonded Distance : 2.366 Molprobity Statistics. All-atom Clashscore : 6.58 Ramachandran Plot: Outliers : 0.16 % Allowed : 5.57 % Favored : 94.27 % Rotamer: Outliers : 3.76 % Allowed : 19.20 % Favored : 77.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.38 % 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: 2442 helix: 0.06 (0.26), residues: 417 sheet: -0.70 (0.20), residues: 651 loop : -1.35 (0.16), residues: 1374 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.002 TRP K 112 HIS 0.008 0.001 HIS F 105 PHE 0.023 0.002 PHE C 64 TYR 0.017 0.001 TYR I 48 ARG 0.006 0.001 ARG G 542 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4884 Ramachandran restraints generated. 2442 Oldfield, 0 Emsley, 2442 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4884 Ramachandran restraints generated. 2442 Oldfield, 0 Emsley, 2442 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 341 residues out of total 2130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 261 time to evaluate : 2.303 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 269 GLU cc_start: 0.7111 (pm20) cc_final: 0.6896 (pm20) REVERT: A 394 THR cc_start: 0.7229 (t) cc_final: 0.6937 (m) REVERT: B 629 LEU cc_start: 0.8231 (OUTLIER) cc_final: 0.7959 (mt) REVERT: C 119 GLN cc_start: 0.7172 (pm20) cc_final: 0.6969 (pm20) REVERT: D 31 LYS cc_start: 0.7467 (ttmt) cc_final: 0.7201 (tttt) REVERT: D 87 ASP cc_start: 0.7063 (m-30) cc_final: 0.6785 (m-30) REVERT: F 117 LYS cc_start: 0.7960 (mmmt) cc_final: 0.7687 (mttt) REVERT: F 164 GLU cc_start: 0.6711 (OUTLIER) cc_final: 0.6287 (pm20) REVERT: I 87 ASP cc_start: 0.6832 (m-30) cc_final: 0.6496 (m-30) REVERT: I 106 LYS cc_start: 0.7002 (OUTLIER) cc_final: 0.6625 (tmtt) REVERT: K 95 MET cc_start: 0.8928 (ttp) cc_final: 0.8643 (ttp) REVERT: K 164 GLU cc_start: 0.6420 (OUTLIER) cc_final: 0.5946 (pm20) REVERT: K 284 ILE cc_start: 0.9008 (OUTLIER) cc_final: 0.8531 (mt) REVERT: K 359 ILE cc_start: 0.5955 (OUTLIER) cc_final: 0.5672 (mt) REVERT: K 477 ASP cc_start: 0.7715 (m-30) cc_final: 0.7342 (m-30) REVERT: L 588 ARG cc_start: 0.8391 (ttm110) cc_final: 0.8157 (ttm-80) REVERT: L 648 GLU cc_start: 0.7628 (tp30) cc_final: 0.6861 (pt0) REVERT: L 655 LYS cc_start: 0.7879 (tmmt) cc_final: 0.7559 (mmtm) REVERT: M 90 ASP cc_start: 0.5856 (t70) cc_final: 0.5600 (t0) outliers start: 80 outliers final: 63 residues processed: 317 average time/residue: 0.3394 time to fit residues: 163.7931 Evaluate side-chains 323 residues out of total 2130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 254 time to evaluate : 2.057 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 TRP Chi-restraints excluded: chain A residue 92 ASN Chi-restraints excluded: chain A residue 109 ILE Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 180 ASP Chi-restraints excluded: chain A residue 271 VAL Chi-restraints excluded: chain A residue 284 ILE Chi-restraints excluded: chain A residue 445 CYS Chi-restraints excluded: chain A residue 499 THR Chi-restraints excluded: chain B residue 595 ILE Chi-restraints excluded: chain B residue 605 CYS Chi-restraints excluded: chain B residue 629 LEU Chi-restraints excluded: chain B residue 654 GLU Chi-restraints excluded: chain C residue 5 VAL Chi-restraints excluded: chain C residue 20 VAL Chi-restraints excluded: chain C residue 30 THR Chi-restraints excluded: chain C residue 69 THR Chi-restraints excluded: chain C residue 102 ILE Chi-restraints excluded: chain D residue 21 SER Chi-restraints excluded: chain D residue 25 THR Chi-restraints excluded: chain D residue 28 ASP Chi-restraints excluded: chain D residue 90 CYS Chi-restraints excluded: chain D residue 99 VAL Chi-restraints excluded: chain D residue 109 VAL Chi-restraints excluded: chain F residue 120 VAL Chi-restraints excluded: chain F residue 125 LEU Chi-restraints excluded: chain F residue 164 GLU Chi-restraints excluded: chain F residue 180 ASP Chi-restraints excluded: chain F residue 182 VAL Chi-restraints excluded: chain F residue 229 ASN Chi-restraints excluded: chain F residue 271 VAL Chi-restraints excluded: chain F residue 283 ILE Chi-restraints excluded: chain F residue 284 ILE Chi-restraints excluded: chain F residue 445 CYS Chi-restraints excluded: chain F residue 455 THR Chi-restraints excluded: chain G residue 581 LEU Chi-restraints excluded: chain G residue 595 ILE Chi-restraints excluded: chain H residue 30 THR Chi-restraints excluded: chain I residue 21 SER Chi-restraints excluded: chain I residue 35 VAL Chi-restraints excluded: chain I residue 72 THR Chi-restraints excluded: chain I residue 99 VAL Chi-restraints excluded: chain I residue 106 LYS Chi-restraints excluded: chain K residue 45 TRP Chi-restraints excluded: chain K residue 120 VAL Chi-restraints excluded: chain K residue 125 LEU Chi-restraints excluded: chain K residue 161 THR Chi-restraints excluded: chain K residue 164 GLU Chi-restraints excluded: chain K residue 180 ASP Chi-restraints excluded: chain K residue 271 VAL Chi-restraints excluded: chain K residue 284 ILE Chi-restraints excluded: chain K residue 295 VAL Chi-restraints excluded: chain K residue 359 ILE Chi-restraints excluded: chain K residue 362 ASN Chi-restraints excluded: chain K residue 445 CYS Chi-restraints excluded: chain K residue 452 LEU Chi-restraints excluded: chain K residue 455 THR Chi-restraints excluded: chain K residue 478 ASN Chi-restraints excluded: chain L residue 528 SER Chi-restraints excluded: chain L residue 605 CYS Chi-restraints excluded: chain M residue 5 VAL Chi-restraints excluded: chain M residue 30 THR Chi-restraints excluded: chain N residue 21 SER Chi-restraints excluded: chain N residue 35 VAL Chi-restraints excluded: chain N residue 90 CYS Chi-restraints excluded: chain N residue 91 CYS Chi-restraints excluded: chain N residue 99 VAL Chi-restraints excluded: chain N residue 105 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: chunk 205 optimal weight: 1.9990 chunk 59 optimal weight: 0.1980 chunk 177 optimal weight: 0.7980 chunk 28 optimal weight: 0.9990 chunk 53 optimal weight: 4.9990 chunk 193 optimal weight: 0.9980 chunk 80 optimal weight: 5.9990 chunk 198 optimal weight: 5.9990 chunk 24 optimal weight: 0.7980 chunk 35 optimal weight: 0.0470 chunk 169 optimal weight: 0.5980 overall best weight: 0.4878 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 577 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 203 GLN G 543 ASN ** L 653 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4403 r_free = 0.4403 target = 0.199850 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4070 r_free = 0.4070 target = 0.166025 restraints weight = 26271.213| |-----------------------------------------------------------------------------| r_work (start): 0.4058 rms_B_bonded: 2.84 r_work: 0.3839 rms_B_bonded: 3.53 restraints_weight: 0.5000 r_work (final): 0.3839 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7635 moved from start: 0.5759 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.087 20316 Z= 0.195 Angle : 0.642 21.986 27636 Z= 0.320 Chirality : 0.045 0.263 3261 Planarity : 0.004 0.043 3453 Dihedral : 8.584 80.886 3777 Min Nonbonded Distance : 2.361 Molprobity Statistics. All-atom Clashscore : 6.35 Ramachandran Plot: Outliers : 0.16 % Allowed : 4.67 % Favored : 95.17 % Rotamer: Outliers : 2.86 % Allowed : 20.38 % Favored : 76.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.38 % 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: -1.22 (0.17), residues: 2442 helix: 0.48 (0.27), residues: 399 sheet: -0.59 (0.20), residues: 651 loop : -1.31 (0.16), residues: 1392 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.001 TRP K 112 HIS 0.007 0.001 HIS F 105 PHE 0.015 0.001 PHE C 64 TYR 0.015 0.001 TYR D 48 ARG 0.008 0.001 ARG B 585 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4612.80 seconds wall clock time: 85 minutes 10.24 seconds (5110.24 seconds total)