Starting phenix.real_space_refine on Tue May 20 12:47:41 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8sau_40280/05_2025/8sau_40280_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8sau_40280/05_2025/8sau_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/cci-nas-00/data/ceres_data/8sau_40280/05_2025/8sau_40280.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8sau_40280/05_2025/8sau_40280.map" model { file = "/net/cci-nas-00/data/ceres_data/8sau_40280/05_2025/8sau_40280_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8sau_40280/05_2025/8sau_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-5687/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: 12.01, per 1000 atoms: 0.60 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: 5.34 Conformation dependent library (CDL) restraints added in 2.3 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: 2.17 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: 6.58 Time building geometry restraints manager: 6.19 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: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.490 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: 0.710 Check model and map are aligned: 0.130 Set scattering table: 0.170 Process input model: 44.200 Find NCS groups from input model: 0.630 Set up NCS constraints: 0.130 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.020 Load rotamer database and sin/cos tables:2.830 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 52.340 ------------------------------------------------------------------------------- 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 20418 Z= 0.291 Angle : 1.051 14.655 27897 Z= 0.532 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 Details of bonding type rmsd link_NAG-ASN : bond 0.00392 ( 12) link_NAG-ASN : angle 2.85546 ( 36) link_ALPHA1-6 : bond 0.01122 ( 6) link_ALPHA1-6 : angle 3.52162 ( 18) link_BETA1-4 : bond 0.01031 ( 22) link_BETA1-4 : angle 4.75993 ( 66) link_ALPHA1-2 : bond 0.01499 ( 10) link_ALPHA1-2 : angle 4.18809 ( 30) link_ALPHA1-3 : bond 0.01235 ( 7) link_ALPHA1-3 : angle 3.19003 ( 21) hydrogen bonds : bond 0.22267 ( 515) hydrogen bonds : angle 8.59366 ( 1356) SS BOND : bond 0.00802 ( 45) SS BOND : angle 2.96705 ( 90) covalent geometry : bond 0.00630 (20316) covalent geometry : angle 0.99326 (27636) *********************** 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 : 2.120 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: 0.3258 time to fit residues: 277.8920 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 : 2.289 ------------------------------------------------------------------------------- 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: 1.9990 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: 1.2784 ------------------------------------------------------------------------------- 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 41 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 62 HIS F 241 ASN F 287 HIS G 590 GLN H 113 ASN H 116 HIS K 287 HIS L 543 ASN M 119 GLN N 62 HIS Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4450 r_free = 0.4450 target = 0.205026 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.4042 r_free = 0.4042 target = 0.166889 restraints weight = 26146.954| |-----------------------------------------------------------------------------| r_work (start): 0.4088 rms_B_bonded: 2.87 r_work: 0.3898 rms_B_bonded: 3.81 restraints_weight: 0.5000 r_work (final): 0.3898 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7566 moved from start: 0.3045 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.066 20418 Z= 0.231 Angle : 0.837 16.580 27897 Z= 0.423 Chirality : 0.053 0.331 3261 Planarity : 0.005 0.077 3453 Dihedral : 12.982 97.096 3777 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 5.22 Ramachandran Plot: Outliers : 0.25 % Allowed : 5.81 % Favored : 93.94 % Rotamer: Outliers : 2.11 % Allowed : 10.42 % Favored : 87.46 % 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: -2.05 (0.16), residues: 2442 helix: -0.81 (0.25), residues: 429 sheet: -1.22 (0.19), residues: 669 loop : -1.60 (0.16), residues: 1344 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP B 631 HIS 0.008 0.002 HIS N 62 PHE 0.027 0.002 PHE C 64 TYR 0.022 0.002 TYR D 48 ARG 0.005 0.001 ARG K 273 Details of bonding type rmsd link_NAG-ASN : bond 0.00832 ( 12) link_NAG-ASN : angle 2.08175 ( 36) link_ALPHA1-6 : bond 0.00383 ( 6) link_ALPHA1-6 : angle 1.97390 ( 18) link_BETA1-4 : bond 0.00852 ( 22) link_BETA1-4 : angle 2.62155 ( 66) link_ALPHA1-2 : bond 0.00573 ( 10) link_ALPHA1-2 : angle 2.37005 ( 30) link_ALPHA1-3 : bond 0.01233 ( 7) link_ALPHA1-3 : angle 2.06373 ( 21) hydrogen bonds : bond 0.05435 ( 515) hydrogen bonds : angle 6.30660 ( 1356) SS BOND : bond 0.01038 ( 45) SS BOND : angle 2.39738 ( 90) covalent geometry : bond 0.00542 (20316) covalent geometry : angle 0.80927 (27636) *********************** 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 410 residues out of total 2130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 365 time to evaluate : 2.251 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 92 ASN cc_start: 0.7577 (p0) cc_final: 0.7362 (p0) REVERT: B 542 ARG cc_start: 0.8127 (mtp180) cc_final: 0.7680 (mtp180) REVERT: B 648 GLU cc_start: 0.7091 (tm-30) cc_final: 0.6881 (pt0) REVERT: B 655 LYS cc_start: 0.7392 (pttm) cc_final: 0.6813 (mmtm) REVERT: C 116 HIS cc_start: 0.5078 (m90) cc_final: 0.4752 (m-70) REVERT: D 80 LEU cc_start: 0.5804 (mp) cc_final: 0.4940 (tt) REVERT: F 117 LYS cc_start: 0.8085 (mmmt) cc_final: 0.7593 (mttt) REVERT: F 475 MET cc_start: 0.6238 (mmm) cc_final: 0.5964 (mmt) REVERT: G 625 ASN cc_start: 0.7911 (p0) cc_final: 0.7403 (t0) REVERT: G 655 LYS cc_start: 0.7951 (ttpt) cc_final: 0.7328 (mmtm) REVERT: K 95 MET cc_start: 0.8569 (ttp) cc_final: 0.8172 (ttp) REVERT: K 113 ASP cc_start: 0.8185 (t0) cc_final: 0.7926 (m-30) REVERT: K 114 GLN cc_start: 0.7650 (tt0) cc_final: 0.7017 (tt0) REVERT: K 502 LYS cc_start: 0.8214 (ttmm) cc_final: 0.8003 (ttmm) REVERT: L 542 ARG cc_start: 0.8230 (mtp180) cc_final: 0.7865 (mtm180) REVERT: L 585 ARG cc_start: 0.8119 (mtm-85) cc_final: 0.7899 (mtm-85) REVERT: L 648 GLU cc_start: 0.7852 (tp30) cc_final: 0.6879 (pt0) REVERT: M 48 MET cc_start: 0.8170 (mtp) cc_final: 0.7790 (mtm) REVERT: N 87 ASP cc_start: 0.7398 (m-30) cc_final: 0.7074 (m-30) outliers start: 45 outliers final: 28 residues processed: 392 average time/residue: 0.3385 time to fit residues: 197.8867 Evaluate side-chains 329 residues out of total 2130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 301 time to evaluate : 2.263 ------------------------------------------------------------------------------- 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 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 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 I residue 21 SER Chi-restraints excluded: chain I residue 85 GLU 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 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 25 THR 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 175 optimal weight: 0.9980 chunk 194 optimal weight: 3.9990 chunk 14 optimal weight: 0.0170 chunk 173 optimal weight: 0.8980 chunk 103 optimal weight: 0.0670 chunk 201 optimal weight: 0.3980 chunk 70 optimal weight: 3.9990 chunk 114 optimal weight: 0.5980 chunk 38 optimal weight: 1.9990 chunk 100 optimal weight: 1.9990 chunk 224 optimal weight: 1.9990 overall best weight: 0.3956 ------------------------------------------------------------------------------- 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 F 343 GLN K 105 HIS K 241 ASN K 362 ASN L 577 GLN M 119 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4462 r_free = 0.4462 target = 0.206471 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4075 r_free = 0.4075 target = 0.170619 restraints weight = 26023.733| |-----------------------------------------------------------------------------| r_work (start): 0.4126 rms_B_bonded: 2.78 r_work: 0.3942 rms_B_bonded: 3.61 restraints_weight: 0.5000 r_work (final): 0.3942 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7499 moved from start: 0.3552 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 20418 Z= 0.133 Angle : 0.695 17.735 27897 Z= 0.346 Chirality : 0.047 0.232 3261 Planarity : 0.004 0.051 3453 Dihedral : 10.960 89.114 3777 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 5.15 Ramachandran Plot: Outliers : 0.25 % Allowed : 5.49 % Favored : 94.27 % Rotamer: Outliers : 3.47 % Allowed : 11.97 % Favored : 84.55 % 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: -1.71 (0.16), residues: 2442 helix: -0.37 (0.26), residues: 411 sheet: -1.02 (0.20), residues: 588 loop : -1.43 (0.15), residues: 1443 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP K 112 HIS 0.004 0.001 HIS N 41 PHE 0.016 0.001 PHE C 64 TYR 0.020 0.001 TYR D 48 ARG 0.006 0.001 ARG A 308 Details of bonding type rmsd link_NAG-ASN : bond 0.00404 ( 12) link_NAG-ASN : angle 1.74446 ( 36) link_ALPHA1-6 : bond 0.00690 ( 6) link_ALPHA1-6 : angle 2.16238 ( 18) link_BETA1-4 : bond 0.00771 ( 22) link_BETA1-4 : angle 2.28261 ( 66) link_ALPHA1-2 : bond 0.00644 ( 10) link_ALPHA1-2 : angle 2.36935 ( 30) link_ALPHA1-3 : bond 0.01338 ( 7) link_ALPHA1-3 : angle 1.00380 ( 21) hydrogen bonds : bond 0.04540 ( 515) hydrogen bonds : angle 5.83724 ( 1356) SS BOND : bond 0.00499 ( 45) SS BOND : angle 2.21422 ( 90) covalent geometry : bond 0.00299 (20316) covalent geometry : angle 0.66717 (27636) *********************** 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 392 residues out of total 2130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 318 time to evaluate : 2.087 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 57 ASP cc_start: 0.6672 (OUTLIER) cc_final: 0.6167 (t70) REVERT: A 92 ASN cc_start: 0.7528 (p0) cc_final: 0.7295 (p0) REVERT: A 340 ASP cc_start: 0.8008 (t0) cc_final: 0.7479 (m-30) REVERT: B 542 ARG cc_start: 0.8052 (mtp180) cc_final: 0.7663 (mtp180) REVERT: B 648 GLU cc_start: 0.6961 (tm-30) cc_final: 0.6744 (pt0) REVERT: B 655 LYS cc_start: 0.7485 (pttm) cc_final: 0.6907 (mmtm) REVERT: C 116 HIS cc_start: 0.4724 (m90) cc_final: 0.4392 (m-70) REVERT: D 80 LEU cc_start: 0.5813 (mp) cc_final: 0.5104 (tt) REVERT: F 95 MET cc_start: 0.8821 (ttp) cc_final: 0.8508 (ttp) REVERT: F 117 LYS cc_start: 0.8099 (mmmt) cc_final: 0.7573 (mttt) REVERT: F 434 MET cc_start: 0.8163 (OUTLIER) cc_final: 0.7951 (ttp) REVERT: K 113 ASP cc_start: 0.8073 (t0) cc_final: 0.7844 (m-30) REVERT: K 114 GLN cc_start: 0.7425 (tt0) cc_final: 0.6815 (tt0) REVERT: K 284 ILE cc_start: 0.8736 (OUTLIER) cc_final: 0.8278 (mt) REVERT: K 362 ASN cc_start: 0.7628 (OUTLIER) cc_final: 0.7416 (t0) REVERT: K 502 LYS cc_start: 0.8292 (ttmm) cc_final: 0.8071 (ttmm) REVERT: L 542 ARG cc_start: 0.8146 (mtp180) cc_final: 0.7671 (mtm-85) REVERT: L 648 GLU cc_start: 0.7757 (tp30) cc_final: 0.6894 (pt0) REVERT: N 87 ASP cc_start: 0.7289 (m-30) cc_final: 0.6955 (m-30) outliers start: 74 outliers final: 39 residues processed: 363 average time/residue: 0.3148 time to fit residues: 173.1232 Evaluate side-chains 341 residues out of total 2130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 298 time to evaluate : 2.299 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 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 45 LEU 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 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 434 MET Chi-restraints excluded: chain F residue 499 THR 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 35 VAL Chi-restraints excluded: chain K residue 57 ASP Chi-restraints excluded: chain K residue 125 LEU 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 362 ASN Chi-restraints excluded: chain K residue 455 THR Chi-restraints excluded: chain L residue 528 SER Chi-restraints excluded: chain M residue 5 VAL Chi-restraints excluded: chain M residue 20 VAL 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 28 ASP 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 117 optimal weight: 4.9990 chunk 2 optimal weight: 1.9990 chunk 130 optimal weight: 0.3980 chunk 113 optimal weight: 6.9990 chunk 70 optimal weight: 4.9990 chunk 212 optimal weight: 0.5980 chunk 110 optimal weight: 1.9990 chunk 222 optimal weight: 4.9990 chunk 217 optimal weight: 0.0980 chunk 123 optimal weight: 0.9980 chunk 63 optimal weight: 0.8980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 653 GLN G 543 ASN H 119 GLN K 246 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4452 r_free = 0.4452 target = 0.205116 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4091 r_free = 0.4091 target = 0.170750 restraints weight = 26436.477| |-----------------------------------------------------------------------------| r_work (start): 0.4117 rms_B_bonded: 2.83 r_work: 0.3960 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work (final): 0.3960 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7514 moved from start: 0.3997 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 20418 Z= 0.137 Angle : 0.671 18.885 27897 Z= 0.333 Chirality : 0.046 0.229 3261 Planarity : 0.004 0.044 3453 Dihedral : 10.093 87.630 3777 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 5.51 Ramachandran Plot: Outliers : 0.20 % Allowed : 5.12 % Favored : 94.68 % Rotamer: Outliers : 3.15 % Allowed : 14.23 % Favored : 82.63 % 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: -1.48 (0.16), residues: 2442 helix: -0.17 (0.26), residues: 411 sheet: -0.79 (0.19), residues: 648 loop : -1.32 (0.16), residues: 1383 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP K 45 HIS 0.005 0.001 HIS C 35 PHE 0.018 0.001 PHE C 64 TYR 0.019 0.001 TYR D 48 ARG 0.005 0.000 ARG A 308 Details of bonding type rmsd link_NAG-ASN : bond 0.00440 ( 12) link_NAG-ASN : angle 1.68699 ( 36) link_ALPHA1-6 : bond 0.00600 ( 6) link_ALPHA1-6 : angle 2.02932 ( 18) link_BETA1-4 : bond 0.00820 ( 22) link_BETA1-4 : angle 2.07815 ( 66) link_ALPHA1-2 : bond 0.00619 ( 10) link_ALPHA1-2 : angle 2.13569 ( 30) link_ALPHA1-3 : bond 0.01140 ( 7) link_ALPHA1-3 : angle 1.35837 ( 21) hydrogen bonds : bond 0.04213 ( 515) hydrogen bonds : angle 5.63905 ( 1356) SS BOND : bond 0.00451 ( 45) SS BOND : angle 2.14374 ( 90) covalent geometry : bond 0.00319 (20316) covalent geometry : angle 0.64586 (27636) *********************** 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 360 residues out of total 2130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 293 time to evaluate : 2.109 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 57 ASP cc_start: 0.6671 (t70) cc_final: 0.6375 (p0) REVERT: A 340 ASP cc_start: 0.7924 (t0) cc_final: 0.7398 (m-30) REVERT: A 476 ARG cc_start: 0.8092 (mpp80) cc_final: 0.7777 (mpt-90) REVERT: B 542 ARG cc_start: 0.8125 (mtp180) cc_final: 0.7742 (mtp180) REVERT: B 655 LYS cc_start: 0.7400 (pttm) cc_final: 0.6926 (mmtm) REVERT: D 87 ASP cc_start: 0.7331 (m-30) cc_final: 0.6885 (m-30) REVERT: F 95 MET cc_start: 0.8776 (ttp) cc_final: 0.8519 (ttp) REVERT: F 117 LYS cc_start: 0.8001 (mmmt) cc_final: 0.7543 (mttt) REVERT: F 424 ILE cc_start: 0.8768 (mm) cc_final: 0.8498 (mm) REVERT: K 284 ILE cc_start: 0.8798 (OUTLIER) cc_final: 0.8285 (mt) REVERT: L 542 ARG cc_start: 0.8053 (mtp180) cc_final: 0.7656 (mtm-85) REVERT: L 626 MET cc_start: 0.7276 (ttm) cc_final: 0.7011 (ttm) REVERT: L 648 GLU cc_start: 0.7793 (tp30) cc_final: 0.6854 (pt0) outliers start: 67 outliers final: 44 residues processed: 330 average time/residue: 0.3253 time to fit residues: 162.6741 Evaluate side-chains 315 residues out of total 2130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 270 time to evaluate : 2.000 ------------------------------------------------------------------------------- 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 271 VAL Chi-restraints excluded: chain A residue 394 THR Chi-restraints excluded: chain A residue 433 CYS Chi-restraints excluded: chain A residue 499 THR Chi-restraints excluded: chain B residue 647 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 45 LEU Chi-restraints excluded: chain D residue 21 SER Chi-restraints excluded: chain D residue 22 CYS Chi-restraints excluded: chain D residue 90 CYS Chi-restraints excluded: chain D residue 99 VAL Chi-restraints excluded: chain F residue 180 ASP Chi-restraints excluded: chain F residue 213 ILE 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 499 THR Chi-restraints excluded: chain G residue 543 ASN 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 116 HIS Chi-restraints excluded: chain I residue 21 SER Chi-restraints excluded: chain I residue 25 THR Chi-restraints excluded: chain I residue 35 VAL Chi-restraints excluded: chain I residue 99 VAL 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 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 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 25 THR 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 28 optimal weight: 1.9990 chunk 41 optimal weight: 5.9990 chunk 33 optimal weight: 2.9990 chunk 157 optimal weight: 9.9990 chunk 58 optimal weight: 5.9990 chunk 132 optimal weight: 1.9990 chunk 175 optimal weight: 2.9990 chunk 107 optimal weight: 1.9990 chunk 148 optimal weight: 1.9990 chunk 93 optimal weight: 3.9990 chunk 40 optimal weight: 0.5980 overall best weight: 1.7188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 246 GLN D 41 HIS I 40 GLN L 575 GLN L 653 GLN M 52 ASN N 41 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4368 r_free = 0.4368 target = 0.196340 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4017 r_free = 0.4017 target = 0.161105 restraints weight = 26416.753| |-----------------------------------------------------------------------------| r_work (start): 0.3965 rms_B_bonded: 3.04 r_work: 0.3763 rms_B_bonded: 3.44 restraints_weight: 0.5000 r_work (final): 0.3763 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7714 moved from start: 0.4728 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.081 20418 Z= 0.260 Angle : 0.792 20.817 27897 Z= 0.395 Chirality : 0.051 0.260 3261 Planarity : 0.005 0.048 3453 Dihedral : 10.725 96.162 3777 Min Nonbonded Distance : 2.317 Molprobity Statistics. All-atom Clashscore : 7.12 Ramachandran Plot: Outliers : 0.16 % Allowed : 5.98 % Favored : 93.86 % Rotamer: Outliers : 4.27 % Allowed : 15.40 % 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: -1.58 (0.16), residues: 2442 helix: -0.07 (0.26), residues: 390 sheet: -0.82 (0.19), residues: 639 loop : -1.46 (0.16), residues: 1413 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP K 45 HIS 0.011 0.002 HIS D 62 PHE 0.027 0.002 PHE C 64 TYR 0.021 0.002 TYR I 48 ARG 0.009 0.001 ARG L 579 Details of bonding type rmsd link_NAG-ASN : bond 0.00527 ( 12) link_NAG-ASN : angle 2.28280 ( 36) link_ALPHA1-6 : bond 0.00528 ( 6) link_ALPHA1-6 : angle 1.92902 ( 18) link_BETA1-4 : bond 0.00878 ( 22) link_BETA1-4 : angle 2.21953 ( 66) link_ALPHA1-2 : bond 0.00505 ( 10) link_ALPHA1-2 : angle 2.10388 ( 30) link_ALPHA1-3 : bond 0.01097 ( 7) link_ALPHA1-3 : angle 1.60240 ( 21) hydrogen bonds : bond 0.05446 ( 515) hydrogen bonds : angle 5.87687 ( 1356) SS BOND : bond 0.00661 ( 45) SS BOND : angle 2.50631 ( 90) covalent geometry : bond 0.00631 (20316) covalent geometry : angle 0.76533 (27636) *********************** 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 385 residues out of total 2130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 294 time to evaluate : 2.123 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 476 ARG cc_start: 0.8110 (mpp80) cc_final: 0.7800 (mpt-90) REVERT: B 542 ARG cc_start: 0.8201 (mtp180) cc_final: 0.7902 (mtp180) REVERT: B 655 LYS cc_start: 0.7648 (pttm) cc_final: 0.7119 (mmtm) REVERT: C 81 MET cc_start: 0.7217 (tmm) cc_final: 0.7014 (ttp) REVERT: D 87 ASP cc_start: 0.7482 (m-30) cc_final: 0.7077 (m-30) REVERT: F 95 MET cc_start: 0.8843 (ttp) cc_final: 0.8576 (ttp) REVERT: F 117 LYS cc_start: 0.8121 (mmmt) cc_final: 0.7627 (mttt) REVERT: F 164 GLU cc_start: 0.6302 (OUTLIER) cc_final: 0.6073 (pm20) REVERT: F 336 GLU cc_start: 0.7542 (pm20) cc_final: 0.7323 (pm20) REVERT: F 434 MET cc_start: 0.8519 (ttm) cc_final: 0.8313 (ttm) REVERT: G 625 ASN cc_start: 0.7473 (p0) cc_final: 0.7048 (t0) REVERT: G 655 LYS cc_start: 0.7797 (tmmt) cc_final: 0.7065 (mmtm) REVERT: I 87 ASP cc_start: 0.7229 (m-30) cc_final: 0.6836 (m-30) REVERT: K 164 GLU cc_start: 0.6538 (OUTLIER) cc_final: 0.6050 (pm20) REVERT: K 477 ASP cc_start: 0.8202 (m-30) cc_final: 0.7789 (m-30) REVERT: L 542 ARG cc_start: 0.8235 (mtp180) cc_final: 0.7937 (mtm180) REVERT: L 610 TRP cc_start: 0.7965 (t-100) cc_final: 0.7760 (t-100) REVERT: L 648 GLU cc_start: 0.7992 (tp30) cc_final: 0.6889 (pt0) outliers start: 91 outliers final: 55 residues processed: 346 average time/residue: 0.3192 time to fit residues: 166.8205 Evaluate side-chains 323 residues out of total 2130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 266 time to evaluate : 1.910 ------------------------------------------------------------------------------- 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 499 THR Chi-restraints excluded: chain B residue 595 ILE 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 29 VAL 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 154 MET 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 433 CYS 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 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 35 VAL Chi-restraints excluded: chain I residue 99 VAL 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 295 VAL Chi-restraints excluded: chain K residue 347 ILE Chi-restraints excluded: chain K residue 369 MET 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 528 SER 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 23 THR 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 109 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: chunk 99 optimal weight: 2.9990 chunk 36 optimal weight: 2.9990 chunk 195 optimal weight: 0.0870 chunk 225 optimal weight: 1.9990 chunk 102 optimal weight: 0.9990 chunk 8 optimal weight: 1.9990 chunk 33 optimal weight: 0.9980 chunk 223 optimal weight: 0.6980 chunk 180 optimal weight: 0.6980 chunk 167 optimal weight: 0.0980 chunk 202 optimal weight: 0.5980 overall best weight: 0.4358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 543 ASN C 119 GLN G 625 ASN N 39 GLN N 54 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4405 r_free = 0.4405 target = 0.200286 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4019 r_free = 0.4019 target = 0.164552 restraints weight = 26395.048| |-----------------------------------------------------------------------------| r_work (start): 0.4011 rms_B_bonded: 3.17 r_work: 0.3833 rms_B_bonded: 3.43 restraints_weight: 0.5000 r_work (final): 0.3833 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7603 moved from start: 0.4918 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.081 20418 Z= 0.121 Angle : 0.654 19.250 27897 Z= 0.324 Chirality : 0.045 0.260 3261 Planarity : 0.004 0.045 3453 Dihedral : 9.648 86.672 3777 Min Nonbonded Distance : 2.317 Molprobity Statistics. All-atom Clashscore : 5.87 Ramachandran Plot: Outliers : 0.16 % Allowed : 5.04 % Favored : 94.80 % Rotamer: Outliers : 3.33 % Allowed : 17.46 % Favored : 79.20 % 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: -1.27 (0.16), residues: 2442 helix: 0.40 (0.27), residues: 381 sheet: -0.57 (0.20), residues: 630 loop : -1.33 (0.16), residues: 1431 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP F 112 HIS 0.004 0.001 HIS F 287 PHE 0.019 0.001 PHE C 64 TYR 0.019 0.001 TYR D 48 ARG 0.006 0.001 ARG F 500 Details of bonding type rmsd link_NAG-ASN : bond 0.00355 ( 12) link_NAG-ASN : angle 1.49678 ( 36) link_ALPHA1-6 : bond 0.00666 ( 6) link_ALPHA1-6 : angle 1.93560 ( 18) link_BETA1-4 : bond 0.00720 ( 22) link_BETA1-4 : angle 1.84802 ( 66) link_ALPHA1-2 : bond 0.00543 ( 10) link_ALPHA1-2 : angle 2.04224 ( 30) link_ALPHA1-3 : bond 0.01202 ( 7) link_ALPHA1-3 : angle 1.22294 ( 21) hydrogen bonds : bond 0.04138 ( 515) hydrogen bonds : angle 5.53921 ( 1356) SS BOND : bond 0.00309 ( 45) SS BOND : angle 2.05676 ( 90) covalent geometry : bond 0.00274 (20316) covalent geometry : angle 0.63120 (27636) *********************** 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 339 residues out of total 2130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 268 time to evaluate : 1.999 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 57 ASP cc_start: 0.6540 (t70) cc_final: 0.6140 (t70) REVERT: A 284 ILE cc_start: 0.8794 (OUTLIER) cc_final: 0.8228 (mt) REVERT: A 476 ARG cc_start: 0.8038 (mpp80) cc_final: 0.7784 (mpt-90) REVERT: B 542 ARG cc_start: 0.8143 (mtp180) cc_final: 0.7858 (mtp180) REVERT: B 625 ASN cc_start: 0.7809 (p0) cc_final: 0.7344 (t0) REVERT: B 655 LYS cc_start: 0.7476 (pttm) cc_final: 0.7030 (mmtm) REVERT: C 81 MET cc_start: 0.7175 (tmm) cc_final: 0.6773 (ttp) REVERT: D 87 ASP cc_start: 0.7381 (m-30) cc_final: 0.6982 (m-30) REVERT: F 95 MET cc_start: 0.8871 (ttp) cc_final: 0.8632 (ttp) REVERT: F 117 LYS cc_start: 0.8108 (mmmt) cc_final: 0.7540 (mttt) REVERT: G 625 ASN cc_start: 0.7317 (p0) cc_final: 0.7009 (t0) REVERT: G 655 LYS cc_start: 0.7692 (tmmt) cc_final: 0.7048 (mmtm) REVERT: I 28 ASP cc_start: 0.7216 (OUTLIER) cc_final: 0.6935 (t70) REVERT: I 87 ASP cc_start: 0.7162 (m-30) cc_final: 0.6787 (m-30) REVERT: K 164 GLU cc_start: 0.6548 (OUTLIER) cc_final: 0.6039 (pm20) REVERT: K 359 ILE cc_start: 0.5844 (OUTLIER) cc_final: 0.5245 (mm) REVERT: L 542 ARG cc_start: 0.8160 (mtp180) cc_final: 0.7805 (mtm180) REVERT: L 588 ARG cc_start: 0.8307 (ttm110) cc_final: 0.8043 (ttm-80) REVERT: L 610 TRP cc_start: 0.8016 (t-100) cc_final: 0.7781 (t-100) REVERT: L 626 MET cc_start: 0.7412 (ttm) cc_final: 0.7168 (ttm) REVERT: L 629 LEU cc_start: 0.8349 (OUTLIER) cc_final: 0.7938 (mt) REVERT: L 648 GLU cc_start: 0.7811 (tp30) cc_final: 0.6784 (pt0) REVERT: L 655 LYS cc_start: 0.7883 (tmmt) cc_final: 0.7141 (mmtm) outliers start: 71 outliers final: 42 residues processed: 318 average time/residue: 0.3346 time to fit residues: 158.4966 Evaluate side-chains 301 residues out of total 2130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 254 time to evaluate : 2.271 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 TRP Chi-restraints excluded: chain A residue 109 ILE 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 499 THR Chi-restraints excluded: chain B residue 605 CYS Chi-restraints excluded: chain C residue 5 VAL Chi-restraints excluded: chain C residue 30 THR Chi-restraints excluded: chain C residue 45 LEU Chi-restraints excluded: chain D residue 25 THR Chi-restraints excluded: chain D residue 47 LYS Chi-restraints excluded: chain D residue 90 CYS Chi-restraints excluded: chain D residue 99 VAL Chi-restraints excluded: chain F residue 125 LEU 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 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 H residue 30 THR 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 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 359 ILE Chi-restraints excluded: chain K residue 445 CYS Chi-restraints excluded: chain K residue 455 THR Chi-restraints excluded: chain L residue 629 LEU 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 39 GLN Chi-restraints excluded: chain N residue 91 CYS Chi-restraints excluded: chain N residue 99 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: chunk 101 optimal weight: 0.4980 chunk 48 optimal weight: 0.7980 chunk 118 optimal weight: 0.9990 chunk 226 optimal weight: 2.9990 chunk 182 optimal weight: 0.9990 chunk 215 optimal weight: 2.9990 chunk 90 optimal weight: 1.9990 chunk 83 optimal weight: 0.3980 chunk 59 optimal weight: 5.9990 chunk 187 optimal weight: 2.9990 chunk 209 optimal weight: 0.0470 overall best weight: 0.5480 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 543 ASN C 119 GLN G 543 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4400 r_free = 0.4400 target = 0.199684 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4043 r_free = 0.4043 target = 0.164386 restraints weight = 26297.666| |-----------------------------------------------------------------------------| r_work (start): 0.4070 rms_B_bonded: 2.93 r_work: 0.3909 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work (final): 0.3909 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7582 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 : 0.003 0.085 20418 Z= 0.129 Angle : 0.649 22.521 27897 Z= 0.318 Chirality : 0.045 0.281 3261 Planarity : 0.004 0.043 3453 Dihedral : 9.240 85.122 3777 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 6.07 Ramachandran Plot: Outliers : 0.16 % Allowed : 5.32 % Favored : 94.51 % Rotamer: Outliers : 3.24 % Allowed : 17.79 % Favored : 78.97 % 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 (0.16), residues: 2442 helix: 0.08 (0.26), residues: 417 sheet: -0.44 (0.20), residues: 621 loop : -1.28 (0.16), residues: 1404 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP F 45 HIS 0.004 0.001 HIS M 35 PHE 0.021 0.001 PHE C 64 TYR 0.015 0.001 TYR D 48 ARG 0.006 0.000 ARG K 166 Details of bonding type rmsd link_NAG-ASN : bond 0.00326 ( 12) link_NAG-ASN : angle 1.53670 ( 36) link_ALPHA1-6 : bond 0.00637 ( 6) link_ALPHA1-6 : angle 1.90508 ( 18) link_BETA1-4 : bond 0.00721 ( 22) link_BETA1-4 : angle 1.78370 ( 66) link_ALPHA1-2 : bond 0.00481 ( 10) link_ALPHA1-2 : angle 1.95748 ( 30) link_ALPHA1-3 : bond 0.01193 ( 7) link_ALPHA1-3 : angle 1.28129 ( 21) hydrogen bonds : bond 0.04026 ( 515) hydrogen bonds : angle 5.40563 ( 1356) SS BOND : bond 0.00457 ( 45) SS BOND : angle 1.94831 ( 90) covalent geometry : bond 0.00303 (20316) covalent geometry : angle 0.62779 (27636) *********************** 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 328 residues out of total 2130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 259 time to evaluate : 2.092 Fit side-chains revert: symmetry clash REVERT: A 284 ILE cc_start: 0.8722 (OUTLIER) cc_final: 0.8220 (mt) REVERT: A 424 ILE cc_start: 0.8750 (mm) cc_final: 0.8474 (mm) REVERT: A 476 ARG cc_start: 0.8083 (mpp80) cc_final: 0.7842 (mpt-90) REVERT: A 500 ARG cc_start: 0.7552 (mmm-85) cc_final: 0.7289 (mtp85) REVERT: B 542 ARG cc_start: 0.8112 (mtp180) cc_final: 0.7713 (mtp180) REVERT: B 625 ASN cc_start: 0.7762 (p0) cc_final: 0.7459 (t0) REVERT: B 629 LEU cc_start: 0.7839 (tp) cc_final: 0.7370 (mt) REVERT: B 655 LYS cc_start: 0.7542 (pttm) cc_final: 0.7140 (mmtm) REVERT: D 87 ASP cc_start: 0.7317 (m-30) cc_final: 0.6950 (m-30) REVERT: F 88 ASN cc_start: 0.8072 (t0) cc_final: 0.7689 (m-40) REVERT: F 95 MET cc_start: 0.8887 (ttp) cc_final: 0.8642 (ttp) REVERT: F 117 LYS cc_start: 0.8089 (mmmt) cc_final: 0.7526 (mttt) REVERT: F 424 ILE cc_start: 0.8659 (mm) cc_final: 0.8456 (mm) REVERT: G 655 LYS cc_start: 0.7731 (tmmt) cc_final: 0.7134 (mmtm) REVERT: I 87 ASP cc_start: 0.7125 (m-30) cc_final: 0.6749 (m-30) REVERT: K 83 GLU cc_start: 0.7476 (tt0) cc_final: 0.7191 (tt0) REVERT: K 164 GLU cc_start: 0.6531 (OUTLIER) cc_final: 0.6031 (pm20) REVERT: K 359 ILE cc_start: 0.5868 (OUTLIER) cc_final: 0.5503 (mt) REVERT: L 588 ARG cc_start: 0.8294 (ttm110) cc_final: 0.8050 (ttm-80) REVERT: L 626 MET cc_start: 0.7445 (ttm) cc_final: 0.7152 (ttm) REVERT: L 629 LEU cc_start: 0.8337 (OUTLIER) cc_final: 0.8035 (mt) REVERT: L 632 ASP cc_start: 0.7457 (t0) cc_final: 0.7141 (t0) REVERT: L 648 GLU cc_start: 0.7801 (tp30) cc_final: 0.6830 (pt0) REVERT: L 655 LYS cc_start: 0.7777 (tmmt) cc_final: 0.7103 (mmtm) outliers start: 69 outliers final: 43 residues processed: 302 average time/residue: 0.3269 time to fit residues: 147.4710 Evaluate side-chains 298 residues out of total 2130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 251 time to evaluate : 1.932 ------------------------------------------------------------------------------- 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 181 ILE 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 595 ILE 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 25 THR Chi-restraints excluded: chain D residue 47 LYS Chi-restraints excluded: chain D residue 90 CYS Chi-restraints excluded: chain D residue 99 VAL Chi-restraints excluded: chain F residue 125 LEU Chi-restraints excluded: chain F residue 180 ASP Chi-restraints excluded: chain F residue 271 VAL Chi-restraints excluded: chain F residue 284 ILE Chi-restraints excluded: chain F residue 455 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 72 THR Chi-restraints excluded: chain I residue 99 VAL 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 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 359 ILE Chi-restraints excluded: chain K residue 445 CYS Chi-restraints excluded: chain K residue 455 THR Chi-restraints excluded: chain L residue 629 LEU 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 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 170 optimal weight: 0.3980 chunk 110 optimal weight: 1.9990 chunk 39 optimal weight: 0.6980 chunk 108 optimal weight: 0.1980 chunk 207 optimal weight: 3.9990 chunk 174 optimal weight: 3.9990 chunk 206 optimal weight: 0.7980 chunk 36 optimal weight: 0.0470 chunk 179 optimal weight: 0.7980 chunk 138 optimal weight: 0.9990 chunk 29 optimal weight: 2.9990 overall best weight: 0.4278 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 543 ASN ** L 653 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4406 r_free = 0.4406 target = 0.200369 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4050 r_free = 0.4050 target = 0.164868 restraints weight = 26466.041| |-----------------------------------------------------------------------------| r_work (start): 0.4081 rms_B_bonded: 3.03 r_work: 0.3921 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work (final): 0.3921 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7572 moved from start: 0.5213 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.089 20418 Z= 0.119 Angle : 0.634 21.486 27897 Z= 0.310 Chirality : 0.045 0.275 3261 Planarity : 0.004 0.043 3453 Dihedral : 8.746 81.379 3777 Min Nonbonded Distance : 2.297 Molprobity Statistics. All-atom Clashscore : 6.04 Ramachandran Plot: Outliers : 0.16 % Allowed : 4.87 % Favored : 94.96 % Rotamer: Outliers : 2.82 % Allowed : 18.45 % Favored : 78.73 % 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: -1.14 (0.17), residues: 2442 helix: 0.36 (0.27), residues: 399 sheet: -0.49 (0.20), residues: 657 loop : -1.23 (0.16), residues: 1386 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP F 45 HIS 0.003 0.001 HIS M 116 PHE 0.019 0.001 PHE C 64 TYR 0.015 0.001 TYR D 48 ARG 0.006 0.000 ARG G 542 Details of bonding type rmsd link_NAG-ASN : bond 0.00307 ( 12) link_NAG-ASN : angle 1.44941 ( 36) link_ALPHA1-6 : bond 0.00705 ( 6) link_ALPHA1-6 : angle 1.88669 ( 18) link_BETA1-4 : bond 0.00688 ( 22) link_BETA1-4 : angle 1.68195 ( 66) link_ALPHA1-2 : bond 0.00473 ( 10) link_ALPHA1-2 : angle 1.90766 ( 30) link_ALPHA1-3 : bond 0.01192 ( 7) link_ALPHA1-3 : angle 1.23109 ( 21) hydrogen bonds : bond 0.03834 ( 515) hydrogen bonds : angle 5.31650 ( 1356) SS BOND : bond 0.00420 ( 45) SS BOND : angle 1.92955 ( 90) covalent geometry : bond 0.00278 (20316) covalent geometry : angle 0.61377 (27636) *********************** 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 328 residues out of total 2130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 268 time to evaluate : 2.153 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 284 ILE cc_start: 0.8707 (OUTLIER) cc_final: 0.8194 (mt) REVERT: A 424 ILE cc_start: 0.8740 (mm) cc_final: 0.8480 (mm) REVERT: A 476 ARG cc_start: 0.8032 (mpp80) cc_final: 0.7813 (mpt-90) REVERT: B 542 ARG cc_start: 0.8066 (mtp180) cc_final: 0.7700 (mtp180) REVERT: B 625 ASN cc_start: 0.7710 (p0) cc_final: 0.7400 (t0) REVERT: B 654 GLU cc_start: 0.7577 (OUTLIER) cc_final: 0.7259 (tt0) REVERT: B 655 LYS cc_start: 0.7471 (pttm) cc_final: 0.7101 (mmtm) REVERT: D 87 ASP cc_start: 0.7303 (m-30) cc_final: 0.6908 (m-30) REVERT: F 88 ASN cc_start: 0.8007 (t0) cc_final: 0.7762 (m-40) REVERT: F 95 MET cc_start: 0.8886 (ttp) cc_final: 0.8624 (ttp) REVERT: F 117 LYS cc_start: 0.8113 (mmmt) cc_final: 0.7514 (mttt) REVERT: G 655 LYS cc_start: 0.7791 (tmmt) cc_final: 0.7271 (tppt) REVERT: H 51 MET cc_start: 0.7329 (tpt) cc_final: 0.7086 (ttp) REVERT: I 87 ASP cc_start: 0.7104 (m-30) cc_final: 0.6722 (m-30) REVERT: K 95 MET cc_start: 0.8896 (ttp) cc_final: 0.8664 (ttp) REVERT: K 164 GLU cc_start: 0.6578 (OUTLIER) cc_final: 0.6066 (pm20) REVERT: K 284 ILE cc_start: 0.8773 (OUTLIER) cc_final: 0.8236 (mt) REVERT: K 359 ILE cc_start: 0.5842 (OUTLIER) cc_final: 0.5346 (mm) REVERT: L 530 MET cc_start: 0.8590 (mtp) cc_final: 0.8302 (mtp) REVERT: L 542 ARG cc_start: 0.8234 (mtp180) cc_final: 0.7746 (mtm-85) REVERT: L 588 ARG cc_start: 0.8254 (ttm110) cc_final: 0.8009 (ttm-80) REVERT: L 626 MET cc_start: 0.7424 (ttm) cc_final: 0.7021 (ttm) REVERT: L 629 LEU cc_start: 0.8214 (OUTLIER) cc_final: 0.7936 (mt) REVERT: L 632 ASP cc_start: 0.7449 (t0) cc_final: 0.7112 (t0) REVERT: L 648 GLU cc_start: 0.7697 (tp30) cc_final: 0.6778 (pt0) REVERT: L 655 LYS cc_start: 0.7794 (tmmt) cc_final: 0.7137 (mmtm) outliers start: 60 outliers final: 43 residues processed: 303 average time/residue: 0.3471 time to fit residues: 156.2443 Evaluate side-chains 304 residues out of total 2130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 255 time to evaluate : 1.902 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 TRP 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 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 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 47 LYS Chi-restraints excluded: chain D residue 90 CYS Chi-restraints excluded: chain F residue 125 LEU Chi-restraints excluded: chain F residue 180 ASP Chi-restraints excluded: chain F residue 271 VAL Chi-restraints excluded: chain F residue 284 ILE Chi-restraints excluded: chain F residue 455 THR 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 72 THR Chi-restraints excluded: chain I residue 90 CYS Chi-restraints excluded: chain I residue 99 VAL Chi-restraints excluded: chain K residue 45 TRP 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 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 445 CYS Chi-restraints excluded: chain K residue 455 THR Chi-restraints excluded: chain K residue 494 LEU Chi-restraints excluded: chain L residue 629 LEU Chi-restraints excluded: chain M residue 5 VAL Chi-restraints excluded: chain M residue 30 THR Chi-restraints excluded: chain N residue 28 ASP 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: chunk 9 optimal weight: 1.9990 chunk 179 optimal weight: 0.6980 chunk 56 optimal weight: 1.9990 chunk 176 optimal weight: 0.0050 chunk 215 optimal weight: 3.9990 chunk 216 optimal weight: 2.9990 chunk 183 optimal weight: 0.0270 chunk 127 optimal weight: 3.9990 chunk 132 optimal weight: 0.9980 chunk 0 optimal weight: 3.9990 chunk 180 optimal weight: 2.9990 overall best weight: 0.7454 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 543 ASN ** L 653 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4402 r_free = 0.4402 target = 0.199634 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4071 r_free = 0.4071 target = 0.166121 restraints weight = 26305.893| |-----------------------------------------------------------------------------| r_work (start): 0.4066 rms_B_bonded: 2.91 r_work: 0.3840 rms_B_bonded: 3.49 restraints_weight: 0.5000 r_work (final): 0.3840 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7631 moved from start: 0.5385 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.085 20418 Z= 0.143 Angle : 0.660 22.017 27897 Z= 0.323 Chirality : 0.046 0.266 3261 Planarity : 0.004 0.042 3453 Dihedral : 8.671 80.976 3777 Min Nonbonded Distance : 2.357 Molprobity Statistics. All-atom Clashscore : 6.12 Ramachandran Plot: Outliers : 0.16 % Allowed : 5.12 % Favored : 94.72 % Rotamer: Outliers : 3.33 % Allowed : 18.12 % Favored : 78.54 % 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: -1.18 (0.16), residues: 2442 helix: 0.21 (0.26), residues: 417 sheet: -0.36 (0.20), residues: 615 loop : -1.30 (0.16), residues: 1410 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP F 45 HIS 0.005 0.001 HIS C 35 PHE 0.022 0.001 PHE C 64 TYR 0.015 0.001 TYR D 48 ARG 0.006 0.001 ARG K 166 Details of bonding type rmsd link_NAG-ASN : bond 0.00306 ( 12) link_NAG-ASN : angle 1.65079 ( 36) link_ALPHA1-6 : bond 0.00665 ( 6) link_ALPHA1-6 : angle 1.82573 ( 18) link_BETA1-4 : bond 0.00702 ( 22) link_BETA1-4 : angle 1.74356 ( 66) link_ALPHA1-2 : bond 0.00455 ( 10) link_ALPHA1-2 : angle 1.80840 ( 30) link_ALPHA1-3 : bond 0.01201 ( 7) link_ALPHA1-3 : angle 1.20795 ( 21) hydrogen bonds : bond 0.04043 ( 515) hydrogen bonds : angle 5.32770 ( 1356) SS BOND : bond 0.00457 ( 45) SS BOND : angle 2.28881 ( 90) covalent geometry : bond 0.00340 (20316) covalent geometry : angle 0.63679 (27636) *********************** 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 344 residues out of total 2130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 273 time to evaluate : 2.167 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 57 ASP cc_start: 0.6545 (t70) cc_final: 0.6242 (t70) REVERT: A 424 ILE cc_start: 0.8759 (mm) cc_final: 0.8525 (mm) REVERT: A 476 ARG cc_start: 0.8066 (mpp80) cc_final: 0.7854 (mpt-90) REVERT: B 542 ARG cc_start: 0.8149 (mtp180) cc_final: 0.7797 (mtp180) REVERT: B 625 ASN cc_start: 0.7824 (p0) cc_final: 0.7528 (t0) REVERT: B 654 GLU cc_start: 0.7582 (OUTLIER) cc_final: 0.7247 (tt0) REVERT: B 655 LYS cc_start: 0.7410 (pttm) cc_final: 0.7089 (mmtm) REVERT: D 31 LYS cc_start: 0.6985 (ttmt) cc_final: 0.6665 (tttt) REVERT: D 87 ASP cc_start: 0.7318 (m-30) cc_final: 0.6896 (m-30) REVERT: F 88 ASN cc_start: 0.8011 (t0) cc_final: 0.7767 (m-40) REVERT: F 95 MET cc_start: 0.8924 (ttp) cc_final: 0.8705 (ttp) REVERT: F 117 LYS cc_start: 0.8231 (mmmt) cc_final: 0.7630 (mttt) REVERT: F 164 GLU cc_start: 0.6373 (OUTLIER) cc_final: 0.6079 (pm20) REVERT: F 476 ARG cc_start: 0.7858 (mpp80) cc_final: 0.7524 (mtt-85) REVERT: G 655 LYS cc_start: 0.7868 (tmmt) cc_final: 0.7326 (tppt) REVERT: H 51 MET cc_start: 0.7372 (tpt) cc_final: 0.7074 (ttp) REVERT: I 87 ASP cc_start: 0.7100 (m-30) cc_final: 0.6704 (m-30) REVERT: K 95 MET cc_start: 0.8870 (ttp) cc_final: 0.8627 (ttp) REVERT: K 164 GLU cc_start: 0.6610 (OUTLIER) cc_final: 0.6093 (pm20) REVERT: K 284 ILE cc_start: 0.8798 (OUTLIER) cc_final: 0.8234 (mt) REVERT: K 359 ILE cc_start: 0.5678 (OUTLIER) cc_final: 0.5278 (mt) REVERT: K 476 ARG cc_start: 0.7516 (mtt-85) cc_final: 0.7307 (mtt-85) REVERT: L 530 MET cc_start: 0.8607 (mtp) cc_final: 0.8310 (mtp) REVERT: L 542 ARG cc_start: 0.8302 (mtp180) cc_final: 0.7867 (mtm-85) REVERT: L 588 ARG cc_start: 0.8312 (ttm110) cc_final: 0.8097 (ttm-80) REVERT: L 626 MET cc_start: 0.7559 (ttm) cc_final: 0.7116 (ttm) REVERT: L 629 LEU cc_start: 0.8293 (OUTLIER) cc_final: 0.8021 (mt) REVERT: L 632 ASP cc_start: 0.7553 (t0) cc_final: 0.7191 (t0) REVERT: L 648 GLU cc_start: 0.7758 (tp30) cc_final: 0.6769 (pt0) REVERT: L 655 LYS cc_start: 0.7822 (tmmt) cc_final: 0.7218 (mmtm) outliers start: 71 outliers final: 54 residues processed: 320 average time/residue: 0.3427 time to fit residues: 164.2254 Evaluate side-chains 322 residues out of total 2130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 262 time to evaluate : 2.100 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 TRP 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 181 ILE 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 654 GLU Chi-restraints excluded: chain C residue 5 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 47 LYS 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 45 TRP 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 284 ILE Chi-restraints excluded: chain F residue 445 CYS Chi-restraints excluded: chain F residue 455 THR 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 72 THR Chi-restraints excluded: chain I residue 90 CYS Chi-restraints excluded: chain I residue 99 VAL Chi-restraints excluded: chain K residue 45 TRP 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 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 445 CYS Chi-restraints excluded: chain K residue 455 THR Chi-restraints excluded: chain K residue 494 LEU 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: chunk 81 optimal weight: 2.9990 chunk 39 optimal weight: 0.3980 chunk 163 optimal weight: 0.8980 chunk 201 optimal weight: 0.5980 chunk 61 optimal weight: 0.6980 chunk 177 optimal weight: 0.6980 chunk 137 optimal weight: 0.9980 chunk 35 optimal weight: 4.9990 chunk 115 optimal weight: 1.9990 chunk 136 optimal weight: 0.8980 chunk 45 optimal weight: 2.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 54 ASN L 630 GLN L 653 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4404 r_free = 0.4404 target = 0.199972 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4080 r_free = 0.4080 target = 0.167123 restraints weight = 26444.121| |-----------------------------------------------------------------------------| r_work (start): 0.4074 rms_B_bonded: 2.78 r_work: 0.3838 rms_B_bonded: 3.52 restraints_weight: 0.5000 r_work (final): 0.3838 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7624 moved from start: 0.5526 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.086 20418 Z= 0.135 Angle : 0.648 21.847 27897 Z= 0.319 Chirality : 0.045 0.270 3261 Planarity : 0.004 0.044 3453 Dihedral : 8.441 78.299 3777 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 6.22 Ramachandran Plot: Outliers : 0.16 % Allowed : 5.04 % Favored : 94.80 % Rotamer: Outliers : 2.91 % Allowed : 19.20 % Favored : 77.89 % 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: -1.14 (0.17), residues: 2442 helix: 0.45 (0.27), residues: 399 sheet: -0.47 (0.20), residues: 651 loop : -1.28 (0.16), residues: 1392 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP F 45 HIS 0.004 0.001 HIS C 35 PHE 0.019 0.001 PHE C 64 TYR 0.015 0.001 TYR F 395 ARG 0.008 0.001 ARG K 166 Details of bonding type rmsd link_NAG-ASN : bond 0.00290 ( 12) link_NAG-ASN : angle 1.51293 ( 36) link_ALPHA1-6 : bond 0.00677 ( 6) link_ALPHA1-6 : angle 1.78762 ( 18) link_BETA1-4 : bond 0.00679 ( 22) link_BETA1-4 : angle 1.69203 ( 66) link_ALPHA1-2 : bond 0.00439 ( 10) link_ALPHA1-2 : angle 1.77487 ( 30) link_ALPHA1-3 : bond 0.01171 ( 7) link_ALPHA1-3 : angle 1.19000 ( 21) hydrogen bonds : bond 0.03898 ( 515) hydrogen bonds : angle 5.28399 ( 1356) SS BOND : bond 0.00422 ( 45) SS BOND : angle 2.18364 ( 90) covalent geometry : bond 0.00322 (20316) covalent geometry : angle 0.62639 (27636) ********************** 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 325 residues out of total 2130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 263 time to evaluate : 2.099 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 57 ASP cc_start: 0.6534 (t70) cc_final: 0.6215 (t70) REVERT: A 284 ILE cc_start: 0.8671 (OUTLIER) cc_final: 0.8153 (mt) REVERT: A 424 ILE cc_start: 0.8803 (mm) cc_final: 0.8557 (mm) REVERT: B 542 ARG cc_start: 0.8181 (mtp180) cc_final: 0.7918 (mtp180) REVERT: B 625 ASN cc_start: 0.7750 (p0) cc_final: 0.7510 (t0) REVERT: B 654 GLU cc_start: 0.7600 (OUTLIER) cc_final: 0.7295 (tt0) REVERT: B 655 LYS cc_start: 0.7539 (pttm) cc_final: 0.7282 (tppt) REVERT: B 656 ASN cc_start: 0.7570 (m-40) cc_final: 0.7244 (m-40) REVERT: D 31 LYS cc_start: 0.6983 (ttmt) cc_final: 0.6712 (tttt) REVERT: D 87 ASP cc_start: 0.7282 (m-30) cc_final: 0.6888 (m-30) REVERT: F 88 ASN cc_start: 0.8112 (t0) cc_final: 0.7800 (m-40) REVERT: F 95 MET cc_start: 0.8917 (ttp) cc_final: 0.8710 (ttp) REVERT: F 117 LYS cc_start: 0.8202 (mmmt) cc_final: 0.7668 (mttt) REVERT: F 164 GLU cc_start: 0.6386 (OUTLIER) cc_final: 0.6116 (pm20) REVERT: F 476 ARG cc_start: 0.7894 (mpp80) cc_final: 0.7488 (mtt-85) REVERT: G 655 LYS cc_start: 0.7902 (tmmt) cc_final: 0.7379 (tppt) REVERT: H 51 MET cc_start: 0.7412 (tpt) cc_final: 0.7123 (ttp) REVERT: I 87 ASP cc_start: 0.7137 (m-30) cc_final: 0.6734 (m-30) REVERT: K 164 GLU cc_start: 0.6569 (OUTLIER) cc_final: 0.6065 (pm20) REVERT: K 284 ILE cc_start: 0.8784 (OUTLIER) cc_final: 0.8226 (mt) REVERT: K 359 ILE cc_start: 0.5831 (OUTLIER) cc_final: 0.5456 (mt) REVERT: L 530 MET cc_start: 0.8624 (mtp) cc_final: 0.8368 (mtp) REVERT: L 542 ARG cc_start: 0.8207 (mtp180) cc_final: 0.7800 (mtm-85) REVERT: L 588 ARG cc_start: 0.8320 (ttm110) cc_final: 0.8066 (ttm-80) REVERT: L 625 ASN cc_start: 0.8040 (p0) cc_final: 0.7228 (t0) REVERT: L 626 MET cc_start: 0.7535 (ttm) cc_final: 0.7088 (ttm) REVERT: L 629 LEU cc_start: 0.8264 (OUTLIER) cc_final: 0.8009 (mt) REVERT: L 632 ASP cc_start: 0.7584 (t0) cc_final: 0.7176 (t0) REVERT: L 648 GLU cc_start: 0.7731 (tp30) cc_final: 0.6746 (pt0) REVERT: L 655 LYS cc_start: 0.7867 (tmmt) cc_final: 0.7327 (tppt) outliers start: 62 outliers final: 53 residues processed: 304 average time/residue: 0.3333 time to fit residues: 151.9390 Evaluate side-chains 315 residues out of total 2130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 255 time to evaluate : 2.298 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 TRP 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 433 CYS 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 654 GLU Chi-restraints excluded: chain C residue 5 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 47 LYS Chi-restraints excluded: chain D residue 54 ASN Chi-restraints excluded: chain D residue 90 CYS Chi-restraints excluded: chain D residue 109 VAL Chi-restraints excluded: chain F residue 45 TRP 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 284 ILE Chi-restraints excluded: chain F residue 445 CYS Chi-restraints excluded: chain F residue 455 THR 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 72 THR Chi-restraints excluded: chain I residue 90 CYS Chi-restraints excluded: chain I residue 99 VAL Chi-restraints excluded: chain K residue 45 TRP 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 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 445 CYS Chi-restraints excluded: chain K residue 455 THR Chi-restraints excluded: chain K residue 494 LEU 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: chunk 134 optimal weight: 0.9980 chunk 55 optimal weight: 0.0270 chunk 230 optimal weight: 0.3980 chunk 78 optimal weight: 5.9990 chunk 5 optimal weight: 3.9990 chunk 159 optimal weight: 6.9990 chunk 223 optimal weight: 0.9990 chunk 209 optimal weight: 3.9990 chunk 169 optimal weight: 0.9980 chunk 23 optimal weight: 3.9990 chunk 72 optimal weight: 3.9990 overall best weight: 0.6840 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 54 ASN G 543 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4401 r_free = 0.4401 target = 0.199659 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4072 r_free = 0.4072 target = 0.166520 restraints weight = 26540.694| |-----------------------------------------------------------------------------| r_work (start): 0.4078 rms_B_bonded: 2.65 r_work: 0.3897 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work (final): 0.3897 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7602 moved from start: 0.5579 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.081 20418 Z= 0.137 Angle : 0.652 21.937 27897 Z= 0.321 Chirality : 0.046 0.265 3261 Planarity : 0.004 0.043 3453 Dihedral : 8.348 77.399 3777 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 6.38 Ramachandran Plot: Outliers : 0.16 % Allowed : 5.08 % Favored : 94.76 % Rotamer: Outliers : 3.15 % Allowed : 19.34 % Favored : 77.51 % 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: -1.12 (0.17), residues: 2442 helix: 0.48 (0.27), residues: 399 sheet: -0.34 (0.21), residues: 615 loop : -1.32 (0.16), residues: 1428 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP F 45 HIS 0.004 0.001 HIS C 35 PHE 0.021 0.001 PHE C 64 TYR 0.014 0.001 TYR I 48 ARG 0.007 0.001 ARG K 166 Details of bonding type rmsd link_NAG-ASN : bond 0.00286 ( 12) link_NAG-ASN : angle 1.53238 ( 36) link_ALPHA1-6 : bond 0.00658 ( 6) link_ALPHA1-6 : angle 1.76389 ( 18) link_BETA1-4 : bond 0.00679 ( 22) link_BETA1-4 : angle 1.67734 ( 66) link_ALPHA1-2 : bond 0.00427 ( 10) link_ALPHA1-2 : angle 1.74712 ( 30) link_ALPHA1-3 : bond 0.01154 ( 7) link_ALPHA1-3 : angle 1.20298 ( 21) hydrogen bonds : bond 0.03918 ( 515) hydrogen bonds : angle 5.27972 ( 1356) SS BOND : bond 0.00408 ( 45) SS BOND : angle 2.11994 ( 90) covalent geometry : bond 0.00328 (20316) covalent geometry : angle 0.63117 (27636) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9461.18 seconds wall clock time: 165 minutes 55.58 seconds (9955.58 seconds total)