Starting phenix.real_space_refine on Sun Oct 12 02:00:26 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8sau_40280/10_2025/8sau_40280_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8sau_40280/10_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 { model { file = "/net/cci-nas-00/data/ceres_data/8sau_40280/10_2025/8sau_40280_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8sau_40280/10_2025/8sau_40280_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8sau_40280/10_2025/8sau_40280.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8sau_40280/10_2025/8sau_40280.map" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 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): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5842/lib/python3.9/site-packages/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: 4.88, per 1000 atoms: 0.25 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: 2.08 Conformation dependent library (CDL) restraints added in 891.8 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 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: 0.77 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: 3.79 Time building geometry restraints manager: 2.64 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.35: 6339 1.35 - 1.48: 5389 1.48 - 1.61: 8402 1.61 - 1.74: 3 1.74 - 1.86: 183 Bond restraints: 20316 Sorted by residual: bond pdb=" CA GLN I 39 " pdb=" CB GLN I 39 " ideal model delta sigma weight residual 1.526 1.600 -0.074 1.70e-02 3.46e+03 1.91e+01 bond pdb=" CB CYS K 433 " pdb=" SG CYS K 433 " ideal model delta sigma weight residual 1.808 1.706 0.102 3.30e-02 9.18e+02 9.64e+00 bond pdb=" CB CYS F 433 " pdb=" SG CYS F 433 " ideal model delta sigma weight residual 1.808 1.715 0.093 3.30e-02 9.18e+02 7.96e+00 bond pdb=" C5 MAN V 7 " pdb=" O5 MAN V 7 " ideal model delta sigma weight residual 1.418 1.471 -0.053 2.00e-02 2.50e+03 7.02e+00 bond pdb=" C5 MAN R 7 " pdb=" O5 MAN R 7 " ideal model delta sigma weight residual 1.418 1.470 -0.052 2.00e-02 2.50e+03 6.77e+00 ... (remaining 20311 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.44: 26759 2.44 - 4.89: 738 4.89 - 7.33: 115 7.33 - 9.78: 18 9.78 - 12.22: 6 Bond angle restraints: 27636 Sorted by residual: angle pdb=" C ASN A 67 " pdb=" N VAL A 68 " pdb=" CA VAL A 68 " ideal model delta sigma weight residual 121.70 133.92 -12.22 1.80e+00 3.09e-01 4.61e+01 angle pdb=" C ASN F 67 " pdb=" N VAL F 68 " pdb=" CA VAL F 68 " ideal model delta sigma weight residual 121.70 133.63 -11.93 1.80e+00 3.09e-01 4.39e+01 angle pdb=" C ASN K 67 " pdb=" N VAL K 68 " pdb=" CA VAL K 68 " ideal model delta sigma weight residual 121.70 133.53 -11.83 1.80e+00 3.09e-01 4.32e+01 angle pdb=" C SER M 25 " pdb=" N GLY M 26 " pdb=" CA GLY M 26 " ideal model delta sigma weight residual 121.70 131.44 -9.74 1.80e+00 3.09e-01 2.93e+01 angle pdb=" C SER C 25 " pdb=" N GLY C 26 " pdb=" CA GLY C 26 " ideal model delta sigma weight residual 121.70 131.35 -9.65 1.80e+00 3.09e-01 2.88e+01 ... (remaining 27631 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.14: 11866 22.14 - 44.27: 782 44.27 - 66.41: 87 66.41 - 88.55: 80 88.55 - 110.68: 43 Dihedral angle restraints: 12858 sinusoidal: 5763 harmonic: 7095 Sorted by residual: dihedral pdb=" CA VAL G 570 " pdb=" C VAL G 570 " pdb=" N TRP G 571 " pdb=" CA TRP G 571 " ideal model delta harmonic sigma weight residual 180.00 143.21 36.79 0 5.00e+00 4.00e-02 5.41e+01 dihedral pdb=" CA GLY K 431 " pdb=" C GLY K 431 " pdb=" N ARG K 432 " pdb=" CA ARG K 432 " ideal model delta harmonic sigma weight residual -180.00 -146.01 -33.99 0 5.00e+00 4.00e-02 4.62e+01 dihedral pdb=" CA GLY F 431 " pdb=" C GLY F 431 " pdb=" N ARG F 432 " pdb=" CA ARG F 432 " ideal model delta harmonic sigma weight residual 180.00 -146.65 -33.35 0 5.00e+00 4.00e-02 4.45e+01 ... (remaining 12855 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.067: 2715 0.067 - 0.133: 474 0.133 - 0.200: 60 0.200 - 0.267: 5 0.267 - 0.333: 7 Chirality restraints: 3261 Sorted by residual: chirality pdb=" C1 BMA T 3 " pdb=" O4 NAG T 2 " pdb=" C2 BMA T 3 " pdb=" O5 BMA T 3 " both_signs ideal model delta sigma weight residual False -2.40 -2.45 0.05 2.00e-02 2.50e+03 7.04e+00 chirality pdb=" C5 BMA O 3 " pdb=" C4 BMA O 3 " pdb=" C6 BMA O 3 " pdb=" O5 BMA O 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.61 0.33 2.00e-01 2.50e+01 2.77e+00 chirality pdb=" C1 NAG S 2 " pdb=" O4 NAG S 1 " pdb=" C2 NAG S 2 " pdb=" O5 NAG S 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.37 -0.03 2.00e-02 2.50e+03 2.74e+00 ... (remaining 3258 not shown) Planarity restraints: 3465 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ARG A 252 " -0.073 5.00e-02 4.00e+02 1.11e-01 1.97e+01 pdb=" N PRO A 253 " 0.192 5.00e-02 4.00e+02 pdb=" CA PRO A 253 " -0.060 5.00e-02 4.00e+02 pdb=" CD PRO A 253 " -0.060 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ARG K 252 " -0.068 5.00e-02 4.00e+02 1.04e-01 1.72e+01 pdb=" N PRO K 253 " 0.180 5.00e-02 4.00e+02 pdb=" CA PRO K 253 " -0.055 5.00e-02 4.00e+02 pdb=" CD PRO K 253 " -0.056 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TRP F 112 " -0.022 2.00e-02 2.50e+03 2.15e-02 1.16e+01 pdb=" CG TRP F 112 " 0.058 2.00e-02 2.50e+03 pdb=" CD1 TRP F 112 " -0.026 2.00e-02 2.50e+03 pdb=" CD2 TRP F 112 " -0.005 2.00e-02 2.50e+03 pdb=" NE1 TRP F 112 " 0.002 2.00e-02 2.50e+03 pdb=" CE2 TRP F 112 " 0.005 2.00e-02 2.50e+03 pdb=" CE3 TRP F 112 " -0.006 2.00e-02 2.50e+03 pdb=" CZ2 TRP F 112 " -0.006 2.00e-02 2.50e+03 pdb=" CZ3 TRP F 112 " -0.001 2.00e-02 2.50e+03 pdb=" CH2 TRP F 112 " 0.000 2.00e-02 2.50e+03 ... (remaining 3462 not shown) Histogram of nonbonded interaction distances: 2.06 - 2.63: 243 2.63 - 3.20: 18003 3.20 - 3.77: 28629 3.77 - 4.33: 41696 4.33 - 4.90: 67547 Nonbonded interactions: 156118 Sorted by model distance: nonbonded pdb=" O LEU K 84 " pdb=" OG SER K 243 " model vdw 2.063 3.040 nonbonded pdb=" OE2 GLU K 83 " pdb=" OG SER K 243 " model vdw 2.065 3.040 nonbonded pdb=" O LYS A 360 " pdb=" OG1 THR A 467 " model vdw 2.068 3.040 nonbonded pdb=" O LYS F 360 " pdb=" OG1 THR F 467 " model vdw 2.070 3.040 nonbonded pdb=" OE2 GLU A 83 " pdb=" OG SER A 243 " model vdw 2.088 3.040 ... (remaining 156113 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'F' selection = chain 'K' } ncs_group { reference = chain 'B' selection = chain 'G' selection = chain 'L' } ncs_group { reference = chain 'C' selection = chain 'H' selection = chain 'M' } ncs_group { reference = chain 'D' selection = chain 'I' selection = chain 'N' } ncs_group { reference = chain 'E' selection = chain 'Q' selection = chain 'U' } ncs_group { reference = chain 'J' selection = chain 'V' } ncs_group { reference = chain 'O' selection = chain 'S' selection = chain 'T' selection = chain 'W' } ncs_group { reference = chain 'P' selection = chain 'X' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.710 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: 0.010 Extract box with map and model: 0.290 Check model and map are aligned: 0.060 Set scattering table: 0.050 Process input model: 19.200 Find NCS groups from input model: 0.270 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.460 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.120 ------------------------------------------------------------------------------- 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 : 3.12 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.22 (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 ARG 0.016 0.001 ARG K 166 TYR 0.029 0.003 TYR D 48 PHE 0.031 0.002 PHE M 114 TRP 0.058 0.003 TRP F 112 HIS 0.012 0.002 HIS A 105 Details of bonding type rmsd covalent geometry : bond 0.00630 (20316) covalent geometry : angle 0.99326 (27636) SS BOND : bond 0.00802 ( 45) SS BOND : angle 2.96705 ( 90) hydrogen bonds : bond 0.22267 ( 515) hydrogen bonds : angle 8.59366 ( 1356) 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) 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_NAG-ASN : bond 0.00392 ( 12) link_NAG-ASN : angle 2.85546 ( 36) *********************** 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 : 0.757 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: 0.7285 (m-30) REVERT: B 617 ARG cc_start: 0.7543 (mtp180) cc_final: 0.6912 (ttm-80) REVERT: B 629 LEU cc_start: 0.7521 (tp) cc_final: 0.6897 (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: 0.7120 (mm-40) 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: 0.5119 (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: 0.7576 (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: 0.7758 (m-30) REVERT: K 114 GLN cc_start: 0.7500 (tt0) cc_final: 0.7055 (tt0) REVERT: K 340 ASP cc_start: 0.7988 (t0) cc_final: 0.7667 (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: 0.1453 time to fit residues: 124.0446 Evaluate side-chains 348 residues out of total 2130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 348 time to evaluate : 0.743 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: chunk 216 optimal weight: 1.9990 chunk 98 optimal weight: 3.9990 chunk 194 optimal weight: 4.9990 chunk 227 optimal weight: 0.8980 chunk 107 optimal weight: 0.9990 chunk 10 optimal weight: 4.9990 chunk 66 optimal weight: 6.9990 chunk 130 optimal weight: 0.1980 chunk 124 optimal weight: 3.9990 chunk 103 optimal weight: 1.9990 chunk 235 optimal weight: 0.6980 overall best weight: 0.9584 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** C 60 ASN ** D 41 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 62 HIS 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: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4482 r_free = 0.4482 target = 0.208342 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.4099 r_free = 0.4099 target = 0.171724 restraints weight = 26278.790| |-----------------------------------------------------------------------------| r_work (start): 0.4128 rms_B_bonded: 2.82 r_work: 0.3945 rms_B_bonded: 3.74 restraints_weight: 0.5000 r_work (final): 0.3945 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7505 moved from start: 0.2914 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.071 20418 Z= 0.195 Angle : 0.803 16.651 27897 Z= 0.405 Chirality : 0.051 0.295 3261 Planarity : 0.005 0.075 3453 Dihedral : 12.673 94.164 3777 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 5.38 Ramachandran Plot: Outliers : 0.25 % Allowed : 5.53 % Favored : 94.23 % Rotamer: Outliers : 2.02 % Allowed : 10.38 % Favored : 87.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.38 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.04 (0.16), residues: 2442 helix: -0.74 (0.25), residues: 429 sheet: -1.23 (0.18), residues: 675 loop : -1.60 (0.16), residues: 1338 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG M 38 TYR 0.021 0.002 TYR D 48 PHE 0.026 0.002 PHE C 64 TRP 0.017 0.002 TRP B 631 HIS 0.009 0.002 HIS N 62 Details of bonding type rmsd covalent geometry : bond 0.00452 (20316) covalent geometry : angle 0.77474 (27636) SS BOND : bond 0.00634 ( 45) SS BOND : angle 2.38963 ( 90) hydrogen bonds : bond 0.05107 ( 515) hydrogen bonds : angle 6.26501 ( 1356) link_ALPHA1-2 : bond 0.00681 ( 10) link_ALPHA1-2 : angle 2.28894 ( 30) link_ALPHA1-3 : bond 0.01248 ( 7) link_ALPHA1-3 : angle 2.03778 ( 21) link_ALPHA1-6 : bond 0.00436 ( 6) link_ALPHA1-6 : angle 1.98914 ( 18) link_BETA1-4 : bond 0.00877 ( 22) link_BETA1-4 : angle 2.54990 ( 66) link_NAG-ASN : bond 0.00691 ( 12) link_NAG-ASN : angle 1.91480 ( 36) *********************** 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 406 residues out of total 2130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 363 time to evaluate : 0.806 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 92 ASN cc_start: 0.7543 (p0) cc_final: 0.7166 (p0) REVERT: B 655 LYS cc_start: 0.7376 (pttm) cc_final: 0.6844 (mmtm) REVERT: C 51 MET cc_start: 0.7437 (tpt) cc_final: 0.7101 (ttt) REVERT: D 80 LEU cc_start: 0.5758 (mp) cc_final: 0.5008 (tt) REVERT: F 502 LYS cc_start: 0.8434 (mtpp) cc_final: 0.8206 (mtpp) REVERT: G 625 ASN cc_start: 0.7822 (p0) cc_final: 0.7359 (t0) REVERT: G 655 LYS cc_start: 0.7661 (OUTLIER) cc_final: 0.7268 (mmtm) REVERT: K 113 ASP cc_start: 0.8141 (t0) cc_final: 0.7908 (m-30) REVERT: K 114 GLN cc_start: 0.7637 (tt0) cc_final: 0.7018 (tt0) REVERT: L 542 ARG cc_start: 0.8153 (mtp180) cc_final: 0.7817 (mtm180) REVERT: L 648 GLU cc_start: 0.7798 (tp30) cc_final: 0.6873 (pt0) REVERT: M 48 MET cc_start: 0.8096 (mtp) cc_final: 0.7754 (mtm) REVERT: N 87 ASP cc_start: 0.7501 (m-30) cc_final: 0.7182 (m-30) outliers start: 43 outliers final: 26 residues processed: 388 average time/residue: 0.1628 time to fit residues: 94.4137 Evaluate side-chains 327 residues out of total 2130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 300 time to evaluate : 0.748 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 ASP 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 G residue 622 ILE Chi-restraints excluded: chain G residue 654 GLU Chi-restraints excluded: chain G residue 655 LYS 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 72 THR Chi-restraints excluded: chain I residue 85 GLU Chi-restraints excluded: chain K residue 123 THR Chi-restraints excluded: chain K residue 125 LEU Chi-restraints excluded: chain K residue 271 VAL Chi-restraints excluded: chain K residue 295 VAL Chi-restraints excluded: chain K residue 347 ILE Chi-restraints excluded: chain M residue 5 VAL Chi-restraints excluded: chain M residue 119 GLN Chi-restraints excluded: chain N residue 21 SER Chi-restraints excluded: chain N residue 35 VAL Chi-restraints excluded: chain N residue 91 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: chunk 37 optimal weight: 2.9990 chunk 71 optimal weight: 0.9990 chunk 127 optimal weight: 2.9990 chunk 125 optimal weight: 0.9990 chunk 218 optimal weight: 0.6980 chunk 113 optimal weight: 5.9990 chunk 96 optimal weight: 2.9990 chunk 206 optimal weight: 0.6980 chunk 91 optimal weight: 6.9990 chunk 145 optimal weight: 3.9990 chunk 87 optimal weight: 0.0870 overall best weight: 0.6962 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 195 ASN B 653 GLN ** C 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 116 HIS F 241 ASN F 343 GLN K 241 ASN K 362 ASN L 543 ASN L 577 GLN M 119 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4416 r_free = 0.4416 target = 0.201990 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.4010 r_free = 0.4010 target = 0.163911 restraints weight = 26382.511| |-----------------------------------------------------------------------------| r_work (start): 0.4053 rms_B_bonded: 2.87 r_work: 0.3873 rms_B_bonded: 3.74 restraints_weight: 0.5000 r_work (final): 0.3873 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7541 moved from start: 0.3564 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.071 20418 Z= 0.153 Angle : 0.709 17.824 27897 Z= 0.353 Chirality : 0.047 0.236 3261 Planarity : 0.004 0.052 3453 Dihedral : 10.944 90.538 3777 Min Nonbonded Distance : 2.392 Molprobity Statistics. All-atom Clashscore : 5.79 Ramachandran Plot: Outliers : 0.25 % Allowed : 5.36 % Favored : 94.39 % Rotamer: Outliers : 4.13 % Allowed : 11.64 % Favored : 84.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.38 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.71 (0.16), residues: 2442 helix: -0.42 (0.26), residues: 411 sheet: -1.02 (0.20), residues: 588 loop : -1.41 (0.15), residues: 1443 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG K 446 TYR 0.020 0.001 TYR I 48 PHE 0.026 0.001 PHE C 64 TRP 0.019 0.001 TRP K 112 HIS 0.005 0.001 HIS H 116 Details of bonding type rmsd covalent geometry : bond 0.00359 (20316) covalent geometry : angle 0.68123 (27636) SS BOND : bond 0.00490 ( 45) SS BOND : angle 2.23248 ( 90) hydrogen bonds : bond 0.04720 ( 515) hydrogen bonds : angle 5.83628 ( 1356) link_ALPHA1-2 : bond 0.00682 ( 10) link_ALPHA1-2 : angle 2.37198 ( 30) link_ALPHA1-3 : bond 0.01324 ( 7) link_ALPHA1-3 : angle 1.11126 ( 21) link_ALPHA1-6 : bond 0.00693 ( 6) link_ALPHA1-6 : angle 2.15545 ( 18) link_BETA1-4 : bond 0.00775 ( 22) link_BETA1-4 : angle 2.30467 ( 66) link_NAG-ASN : bond 0.00494 ( 12) link_NAG-ASN : angle 1.89708 ( 36) *********************** 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 406 residues out of total 2130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 318 time to evaluate : 0.900 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 57 ASP cc_start: 0.6601 (OUTLIER) cc_final: 0.6069 (t70) REVERT: A 92 ASN cc_start: 0.7629 (p0) cc_final: 0.7356 (p0) REVERT: A 95 MET cc_start: 0.8756 (ttp) cc_final: 0.8417 (ttp) REVERT: A 282 LYS cc_start: 0.7144 (mttp) cc_final: 0.6145 (mttp) REVERT: A 340 ASP cc_start: 0.8067 (t0) cc_final: 0.7520 (m-30) REVERT: B 655 LYS cc_start: 0.7516 (pttm) cc_final: 0.6914 (mmtm) REVERT: C 38 ARG cc_start: 0.7572 (ttp-170) cc_final: 0.7340 (ttp80) REVERT: C 48 MET cc_start: 0.8001 (mtp) cc_final: 0.7570 (mtm) REVERT: D 80 LEU cc_start: 0.5895 (mp) cc_final: 0.5073 (tt) REVERT: F 95 MET cc_start: 0.8840 (ttp) cc_final: 0.8539 (ttp) REVERT: G 570 VAL cc_start: 0.2268 (OUTLIER) cc_final: 0.1806 (m) REVERT: G 655 LYS cc_start: 0.7692 (OUTLIER) cc_final: 0.7349 (mmtm) REVERT: I 106 LYS cc_start: 0.6506 (OUTLIER) cc_final: 0.6248 (tmtt) REVERT: K 113 ASP cc_start: 0.8130 (t0) cc_final: 0.7888 (m-30) REVERT: K 114 GLN cc_start: 0.7455 (tt0) cc_final: 0.6837 (tt0) REVERT: K 284 ILE cc_start: 0.8766 (OUTLIER) cc_final: 0.8284 (mt) REVERT: K 362 ASN cc_start: 0.7622 (OUTLIER) cc_final: 0.7405 (t0) REVERT: L 648 GLU cc_start: 0.7877 (tp30) cc_final: 0.6904 (pt0) REVERT: N 87 ASP cc_start: 0.7382 (m-30) cc_final: 0.7058 (m-30) outliers start: 88 outliers final: 45 residues processed: 372 average time/residue: 0.1527 time to fit residues: 86.5846 Evaluate side-chains 345 residues out of total 2130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 294 time to evaluate : 0.701 ------------------------------------------------------------------------------- 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 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 B residue 629 LEU Chi-restraints excluded: chain C residue 5 VAL Chi-restraints excluded: chain C residue 30 THR Chi-restraints excluded: chain C residue 116 HIS Chi-restraints excluded: chain D residue 21 SER Chi-restraints excluded: chain D residue 22 CYS Chi-restraints excluded: chain D residue 29 VAL Chi-restraints excluded: chain D residue 99 VAL Chi-restraints excluded: chain F residue 180 ASP Chi-restraints excluded: chain F residue 181 ILE Chi-restraints excluded: chain F residue 271 VAL Chi-restraints excluded: chain F residue 283 ILE Chi-restraints excluded: chain F residue 499 THR Chi-restraints excluded: chain G residue 528 SER Chi-restraints excluded: chain G residue 570 VAL Chi-restraints excluded: chain G residue 622 ILE Chi-restraints excluded: chain G residue 654 GLU Chi-restraints excluded: chain G residue 655 LYS Chi-restraints excluded: chain H residue 30 THR Chi-restraints excluded: chain I residue 21 SER Chi-restraints excluded: chain I residue 25 THR Chi-restraints excluded: chain I residue 28 ASP Chi-restraints excluded: chain I residue 35 VAL Chi-restraints excluded: chain I residue 106 LYS Chi-restraints excluded: chain K residue 57 ASP Chi-restraints excluded: chain K residue 125 LEU Chi-restraints excluded: chain K residue 180 ASP Chi-restraints excluded: chain K residue 271 VAL Chi-restraints excluded: chain K residue 284 ILE Chi-restraints excluded: chain K residue 295 VAL Chi-restraints excluded: chain K residue 347 ILE Chi-restraints excluded: chain K residue 362 ASN Chi-restraints excluded: chain K residue 455 THR Chi-restraints excluded: chain L residue 528 SER Chi-restraints excluded: chain L residue 535 MET Chi-restraints excluded: chain M residue 5 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 143 optimal weight: 0.8980 chunk 215 optimal weight: 4.9990 chunk 156 optimal weight: 0.8980 chunk 198 optimal weight: 7.9990 chunk 53 optimal weight: 0.0970 chunk 112 optimal weight: 0.9990 chunk 98 optimal weight: 8.9990 chunk 205 optimal weight: 0.4980 chunk 230 optimal weight: 0.8980 chunk 203 optimal weight: 4.9990 chunk 217 optimal weight: 0.8980 overall best weight: 0.6578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 52 ASN G 543 ASN H 119 GLN K 246 GLN L 543 ASN M 52 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4449 r_free = 0.4449 target = 0.204635 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4097 r_free = 0.4097 target = 0.169693 restraints weight = 26447.103| |-----------------------------------------------------------------------------| r_work (start): 0.4111 rms_B_bonded: 3.03 r_work: 0.3955 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work (final): 0.3955 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7519 moved from start: 0.4009 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= 0.143 Angle : 0.677 19.045 27897 Z= 0.336 Chirality : 0.046 0.230 3261 Planarity : 0.004 0.045 3453 Dihedral : 10.151 88.306 3777 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 5.46 Ramachandran Plot: Outliers : 0.20 % Allowed : 5.08 % Favored : 94.72 % Rotamer: Outliers : 3.47 % Allowed : 14.55 % Favored : 81.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.38 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.54 (0.16), residues: 2442 helix: -0.25 (0.26), residues: 411 sheet: -0.83 (0.19), residues: 648 loop : -1.35 (0.16), residues: 1383 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 308 TYR 0.019 0.001 TYR D 48 PHE 0.019 0.001 PHE C 64 TRP 0.021 0.001 TRP K 69 HIS 0.015 0.001 HIS C 116 Details of bonding type rmsd covalent geometry : bond 0.00334 (20316) covalent geometry : angle 0.65221 (27636) SS BOND : bond 0.00419 ( 45) SS BOND : angle 2.13681 ( 90) hydrogen bonds : bond 0.04268 ( 515) hydrogen bonds : angle 5.65958 ( 1356) link_ALPHA1-2 : bond 0.00575 ( 10) link_ALPHA1-2 : angle 2.10870 ( 30) link_ALPHA1-3 : bond 0.01170 ( 7) link_ALPHA1-3 : angle 1.33127 ( 21) link_ALPHA1-6 : bond 0.00593 ( 6) link_ALPHA1-6 : angle 2.02835 ( 18) link_BETA1-4 : bond 0.00768 ( 22) link_BETA1-4 : angle 2.08007 ( 66) link_NAG-ASN : bond 0.00439 ( 12) link_NAG-ASN : angle 1.71153 ( 36) *********************** 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 353 residues out of total 2130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 279 time to evaluate : 0.802 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 57 ASP cc_start: 0.6673 (t70) cc_final: 0.6360 (p0) REVERT: A 340 ASP cc_start: 0.7907 (t0) cc_final: 0.7363 (m-30) REVERT: B 655 LYS cc_start: 0.7418 (pttm) cc_final: 0.6928 (mmtm) REVERT: C 38 ARG cc_start: 0.7699 (ttp-170) cc_final: 0.7484 (ttp80) REVERT: D 87 ASP cc_start: 0.7311 (m-30) cc_final: 0.6807 (m-30) REVERT: F 91 GLU cc_start: 0.5913 (mm-30) cc_final: 0.5630 (tt0) REVERT: F 95 MET cc_start: 0.8782 (ttp) cc_final: 0.8528 (ttp) REVERT: G 570 VAL cc_start: 0.2230 (OUTLIER) cc_final: 0.1781 (m) REVERT: G 655 LYS cc_start: 0.7580 (OUTLIER) cc_final: 0.7289 (mmtm) REVERT: I 106 LYS cc_start: 0.6626 (OUTLIER) cc_final: 0.6327 (tmtt) REVERT: L 626 MET cc_start: 0.7297 (ttm) cc_final: 0.7046 (ttm) REVERT: L 648 GLU cc_start: 0.7804 (tp30) cc_final: 0.6918 (pt0) REVERT: M 48 MET cc_start: 0.8051 (mtm) cc_final: 0.7781 (mtp) outliers start: 74 outliers final: 43 residues processed: 320 average time/residue: 0.1492 time to fit residues: 73.8721 Evaluate side-chains 305 residues out of total 2130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 259 time to evaluate : 0.701 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 180 ASP Chi-restraints excluded: chain A residue 213 ILE Chi-restraints excluded: chain A residue 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 C residue 5 VAL Chi-restraints excluded: chain C residue 102 ILE 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 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 570 VAL Chi-restraints excluded: chain G residue 622 ILE Chi-restraints excluded: chain G residue 654 GLU Chi-restraints excluded: chain G residue 655 LYS Chi-restraints excluded: chain H residue 30 THR Chi-restraints excluded: chain I residue 21 SER Chi-restraints excluded: chain I residue 25 THR Chi-restraints excluded: chain I residue 28 ASP Chi-restraints excluded: chain I residue 35 VAL Chi-restraints excluded: chain I residue 99 VAL Chi-restraints excluded: chain I residue 106 LYS Chi-restraints excluded: chain K residue 57 ASP Chi-restraints excluded: chain K residue 120 VAL Chi-restraints excluded: chain K residue 125 LEU Chi-restraints excluded: chain K residue 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 L residue 629 LEU Chi-restraints excluded: chain L residue 653 GLN Chi-restraints excluded: chain M residue 5 VAL Chi-restraints excluded: chain M residue 30 THR Chi-restraints excluded: chain M residue 55 THR Chi-restraints excluded: chain N residue 21 SER Chi-restraints excluded: chain N residue 35 VAL Chi-restraints excluded: chain N residue 91 CYS Chi-restraints excluded: chain N residue 99 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: chunk 98 optimal weight: 1.9990 chunk 139 optimal weight: 7.9990 chunk 80 optimal weight: 0.6980 chunk 93 optimal weight: 4.9990 chunk 69 optimal weight: 1.9990 chunk 147 optimal weight: 0.8980 chunk 152 optimal weight: 2.9990 chunk 239 optimal weight: 9.9990 chunk 188 optimal weight: 2.9990 chunk 170 optimal weight: 0.9990 chunk 213 optimal weight: 1.9990 overall best weight: 1.3186 ------------------------------------------------------------------------------- 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 H 116 HIS L 543 ASN L 653 GLN N 41 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4392 r_free = 0.4392 target = 0.198788 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4065 r_free = 0.4065 target = 0.165356 restraints weight = 26348.013| |-----------------------------------------------------------------------------| r_work (start): 0.4064 rms_B_bonded: 2.74 r_work: 0.3858 rms_B_bonded: 3.40 restraints_weight: 0.5000 r_work (final): 0.3858 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7664 moved from start: 0.4573 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.074 20418 Z= 0.211 Angle : 0.732 20.401 27897 Z= 0.364 Chirality : 0.048 0.250 3261 Planarity : 0.005 0.048 3453 Dihedral : 10.348 92.756 3777 Min Nonbonded Distance : 2.289 Molprobity Statistics. All-atom Clashscore : 6.35 Ramachandran Plot: Outliers : 0.16 % Allowed : 5.61 % Favored : 94.23 % Rotamer: Outliers : 4.08 % Allowed : 15.31 % Favored : 80.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.38 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.47 (0.16), residues: 2442 helix: 0.08 (0.27), residues: 390 sheet: -0.70 (0.20), residues: 627 loop : -1.42 (0.16), residues: 1425 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG K 456 TYR 0.019 0.002 TYR I 48 PHE 0.021 0.002 PHE C 64 TRP 0.017 0.002 TRP F 112 HIS 0.010 0.002 HIS C 35 Details of bonding type rmsd covalent geometry : bond 0.00510 (20316) covalent geometry : angle 0.70512 (27636) SS BOND : bond 0.00536 ( 45) SS BOND : angle 2.41183 ( 90) hydrogen bonds : bond 0.04906 ( 515) hydrogen bonds : angle 5.72261 ( 1356) link_ALPHA1-2 : bond 0.00506 ( 10) link_ALPHA1-2 : angle 2.06130 ( 30) link_ALPHA1-3 : bond 0.01162 ( 7) link_ALPHA1-3 : angle 1.38923 ( 21) link_ALPHA1-6 : bond 0.00535 ( 6) link_ALPHA1-6 : angle 1.95085 ( 18) link_BETA1-4 : bond 0.00819 ( 22) link_BETA1-4 : angle 2.10007 ( 66) link_NAG-ASN : bond 0.00467 ( 12) link_NAG-ASN : angle 2.05460 ( 36) *********************** 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 369 residues out of total 2130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 282 time to evaluate : 0.565 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 57 ASP cc_start: 0.6705 (OUTLIER) cc_final: 0.6333 (p0) REVERT: A 95 MET cc_start: 0.8915 (ttp) cc_final: 0.8622 (ttp) REVERT: B 655 LYS cc_start: 0.7608 (pttm) cc_final: 0.7109 (mmtm) REVERT: C 48 MET cc_start: 0.8117 (mtp) cc_final: 0.7859 (mtm) REVERT: D 87 ASP cc_start: 0.7462 (m-30) cc_final: 0.7038 (m-30) REVERT: F 57 ASP cc_start: 0.6518 (t70) cc_final: 0.6287 (t70) REVERT: F 91 GLU cc_start: 0.6076 (mm-30) cc_final: 0.5823 (tt0) REVERT: F 95 MET cc_start: 0.8849 (ttp) cc_final: 0.8596 (ttp) REVERT: G 570 VAL cc_start: 0.2676 (OUTLIER) cc_final: 0.2219 (m) REVERT: G 625 ASN cc_start: 0.7361 (p0) cc_final: 0.6939 (t0) REVERT: G 655 LYS cc_start: 0.7627 (OUTLIER) cc_final: 0.7333 (mmtm) REVERT: I 87 ASP cc_start: 0.7203 (m-30) cc_final: 0.6804 (m-30) REVERT: I 106 LYS cc_start: 0.6667 (OUTLIER) cc_final: 0.6295 (tmtt) REVERT: K 164 GLU cc_start: 0.6585 (OUTLIER) cc_final: 0.6084 (pm20) REVERT: K 477 ASP cc_start: 0.8076 (m-30) cc_final: 0.7682 (m-30) REVERT: L 648 GLU cc_start: 0.7917 (tp30) cc_final: 0.6925 (pt0) outliers start: 87 outliers final: 54 residues processed: 335 average time/residue: 0.1580 time to fit residues: 80.6148 Evaluate side-chains 317 residues out of total 2130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 258 time to evaluate : 0.756 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 TRP Chi-restraints excluded: chain A residue 57 ASP Chi-restraints excluded: chain A residue 109 ILE Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 180 ASP Chi-restraints excluded: chain A residue 271 VAL Chi-restraints excluded: chain A residue 394 THR Chi-restraints excluded: chain A residue 430 VAL Chi-restraints excluded: chain A residue 499 THR Chi-restraints excluded: chain B residue 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 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 430 VAL Chi-restraints excluded: chain F residue 433 CYS Chi-restraints excluded: chain F residue 499 THR Chi-restraints excluded: chain G residue 570 VAL Chi-restraints excluded: chain G residue 622 ILE Chi-restraints excluded: chain G residue 654 GLU Chi-restraints excluded: chain G residue 655 LYS Chi-restraints excluded: chain H residue 20 VAL Chi-restraints excluded: chain H residue 30 THR Chi-restraints excluded: chain I residue 21 SER Chi-restraints excluded: chain I residue 35 VAL Chi-restraints excluded: chain I residue 99 VAL Chi-restraints excluded: chain I residue 106 LYS Chi-restraints excluded: chain K residue 57 ASP Chi-restraints excluded: chain K residue 109 ILE Chi-restraints excluded: chain K residue 120 VAL Chi-restraints excluded: chain K residue 125 LEU Chi-restraints excluded: chain K residue 164 GLU Chi-restraints excluded: chain K residue 180 ASP Chi-restraints excluded: chain K residue 271 VAL Chi-restraints excluded: chain K residue 295 VAL 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 629 LEU Chi-restraints excluded: chain L residue 653 GLN Chi-restraints excluded: chain M residue 5 VAL Chi-restraints excluded: chain M residue 30 THR Chi-restraints excluded: chain M residue 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 Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: chunk 139 optimal weight: 7.9990 chunk 220 optimal weight: 6.9990 chunk 101 optimal weight: 0.7980 chunk 194 optimal weight: 1.9990 chunk 56 optimal weight: 0.8980 chunk 100 optimal weight: 0.8980 chunk 187 optimal weight: 1.9990 chunk 195 optimal weight: 0.7980 chunk 147 optimal weight: 2.9990 chunk 234 optimal weight: 3.9990 chunk 121 optimal weight: 0.5980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 543 ASN G 543 ASN L 543 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 = 0.4408 r_free = 0.4408 target = 0.200379 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4074 r_free = 0.4074 target = 0.166555 restraints weight = 26393.617| |-----------------------------------------------------------------------------| r_work (start): 0.4073 rms_B_bonded: 2.78 r_work: 0.3905 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work (final): 0.3905 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7602 moved from start: 0.4843 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.083 20418 Z= 0.150 Angle : 0.670 19.686 27897 Z= 0.332 Chirality : 0.046 0.272 3261 Planarity : 0.004 0.046 3453 Dihedral : 9.792 88.503 3777 Min Nonbonded Distance : 2.380 Molprobity Statistics. All-atom Clashscore : 5.92 Ramachandran Plot: Outliers : 0.16 % Allowed : 5.20 % Favored : 94.64 % Rotamer: Outliers : 4.08 % Allowed : 16.15 % Favored : 79.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.38 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.31 (0.16), residues: 2442 helix: 0.37 (0.27), residues: 381 sheet: -0.56 (0.20), residues: 624 loop : -1.38 (0.16), residues: 1437 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG F 500 TYR 0.017 0.001 TYR D 48 PHE 0.022 0.001 PHE C 64 TRP 0.019 0.001 TRP K 45 HIS 0.005 0.001 HIS C 35 Details of bonding type rmsd covalent geometry : bond 0.00356 (20316) covalent geometry : angle 0.64526 (27636) SS BOND : bond 0.00526 ( 45) SS BOND : angle 2.25426 ( 90) hydrogen bonds : bond 0.04346 ( 515) hydrogen bonds : angle 5.52228 ( 1356) link_ALPHA1-2 : bond 0.00495 ( 10) link_ALPHA1-2 : angle 1.98823 ( 30) link_ALPHA1-3 : bond 0.01204 ( 7) link_ALPHA1-3 : angle 1.31818 ( 21) link_ALPHA1-6 : bond 0.00583 ( 6) link_ALPHA1-6 : angle 1.94698 ( 18) link_BETA1-4 : bond 0.00725 ( 22) link_BETA1-4 : angle 1.90784 ( 66) link_NAG-ASN : bond 0.00335 ( 12) link_NAG-ASN : angle 1.66432 ( 36) *********************** 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 345 residues out of total 2130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 258 time to evaluate : 0.706 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 57 ASP cc_start: 0.6652 (OUTLIER) cc_final: 0.6255 (t70) REVERT: A 95 MET cc_start: 0.8935 (ttp) cc_final: 0.8668 (ttp) REVERT: B 625 ASN cc_start: 0.7815 (p0) cc_final: 0.7338 (t0) REVERT: B 655 LYS cc_start: 0.7520 (pttm) cc_final: 0.7111 (mmtm) REVERT: C 48 MET cc_start: 0.8021 (mtp) cc_final: 0.7661 (mtm) REVERT: D 87 ASP cc_start: 0.7352 (m-30) cc_final: 0.6961 (m-30) REVERT: F 91 GLU cc_start: 0.6162 (mm-30) cc_final: 0.5880 (tt0) REVERT: F 95 MET cc_start: 0.8856 (ttp) cc_final: 0.8614 (ttp) REVERT: F 164 GLU cc_start: 0.6311 (OUTLIER) cc_final: 0.6092 (pm20) REVERT: G 570 VAL cc_start: 0.2552 (OUTLIER) cc_final: 0.2138 (m) REVERT: G 625 ASN cc_start: 0.7367 (p0) cc_final: 0.6997 (t0) REVERT: G 655 LYS cc_start: 0.7629 (OUTLIER) cc_final: 0.7374 (mmtm) REVERT: I 28 ASP cc_start: 0.7405 (OUTLIER) cc_final: 0.7169 (t70) REVERT: I 87 ASP cc_start: 0.7187 (m-30) cc_final: 0.6806 (m-30) REVERT: I 106 LYS cc_start: 0.6668 (OUTLIER) cc_final: 0.6255 (tmtt) REVERT: K 164 GLU cc_start: 0.6535 (OUTLIER) cc_final: 0.6044 (pm20) REVERT: K 359 ILE cc_start: 0.5935 (OUTLIER) cc_final: 0.5560 (mt) REVERT: L 588 ARG cc_start: 0.8262 (ttm110) cc_final: 0.7989 (ttm-80) REVERT: L 632 ASP cc_start: 0.7435 (t0) cc_final: 0.7162 (t0) REVERT: L 648 GLU cc_start: 0.7819 (tp30) cc_final: 0.6944 (pt0) REVERT: L 655 LYS cc_start: 0.7923 (tmmt) cc_final: 0.7220 (mmtm) outliers start: 87 outliers final: 52 residues processed: 319 average time/residue: 0.1511 time to fit residues: 73.8716 Evaluate side-chains 311 residues out of total 2130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 251 time to evaluate : 0.760 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 ASP 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 629 LEU Chi-restraints excluded: chain C residue 5 VAL Chi-restraints excluded: chain C residue 30 THR Chi-restraints excluded: chain C residue 102 ILE Chi-restraints excluded: chain D residue 21 SER Chi-restraints excluded: chain D residue 25 THR Chi-restraints excluded: chain D residue 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 120 VAL Chi-restraints excluded: chain F residue 125 LEU Chi-restraints excluded: chain F residue 164 GLU Chi-restraints excluded: chain F residue 180 ASP Chi-restraints excluded: chain F residue 271 VAL Chi-restraints excluded: chain F residue 283 ILE Chi-restraints excluded: chain F residue 455 THR Chi-restraints excluded: chain F residue 499 THR Chi-restraints excluded: chain G residue 528 SER Chi-restraints excluded: chain G residue 570 VAL Chi-restraints excluded: chain G residue 622 ILE Chi-restraints excluded: chain G residue 655 LYS Chi-restraints excluded: chain H residue 20 VAL Chi-restraints excluded: chain H residue 30 THR Chi-restraints excluded: chain H residue 69 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 99 VAL Chi-restraints excluded: chain I residue 106 LYS Chi-restraints excluded: chain K residue 45 TRP Chi-restraints excluded: chain K residue 109 ILE Chi-restraints excluded: chain K residue 120 VAL Chi-restraints excluded: chain K residue 125 LEU Chi-restraints excluded: chain K residue 164 GLU Chi-restraints excluded: chain K residue 180 ASP Chi-restraints excluded: chain K residue 271 VAL Chi-restraints excluded: chain K residue 295 VAL Chi-restraints excluded: chain K residue 347 ILE Chi-restraints excluded: chain K residue 359 ILE Chi-restraints excluded: chain K residue 426 MET Chi-restraints excluded: chain K residue 445 CYS Chi-restraints excluded: chain K residue 455 THR Chi-restraints excluded: chain K residue 478 ASN Chi-restraints excluded: chain 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 28 ASP 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 109 optimal weight: 0.0970 chunk 203 optimal weight: 0.9980 chunk 50 optimal weight: 0.8980 chunk 25 optimal weight: 0.9990 chunk 143 optimal weight: 0.2980 chunk 93 optimal weight: 3.9990 chunk 28 optimal weight: 0.0670 chunk 111 optimal weight: 0.8980 chunk 19 optimal weight: 5.9990 chunk 97 optimal weight: 0.7980 chunk 26 optimal weight: 3.9990 overall best weight: 0.4316 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 543 ASN G 543 ASN G 625 ASN L 543 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4425 r_free = 0.4425 target = 0.202088 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.4086 r_free = 0.4086 target = 0.167591 restraints weight = 26365.339| |-----------------------------------------------------------------------------| r_work (start): 0.4086 rms_B_bonded: 2.85 r_work: 0.3929 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work (final): 0.3929 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7565 moved from start: 0.5001 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= 0.121 Angle : 0.639 18.690 27897 Z= 0.317 Chirality : 0.045 0.276 3261 Planarity : 0.004 0.045 3453 Dihedral : 9.186 84.127 3777 Min Nonbonded Distance : 2.316 Molprobity Statistics. All-atom Clashscore : 5.66 Ramachandran Plot: Outliers : 0.16 % Allowed : 5.20 % Favored : 94.64 % Rotamer: Outliers : 3.62 % Allowed : 17.18 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.19 (0.16), residues: 2442 helix: 0.33 (0.27), residues: 399 sheet: -0.39 (0.20), residues: 615 loop : -1.33 (0.16), residues: 1428 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG K 166 TYR 0.015 0.001 TYR D 48 PHE 0.020 0.001 PHE C 64 TRP 0.019 0.001 TRP F 112 HIS 0.003 0.001 HIS M 116 Details of bonding type rmsd covalent geometry : bond 0.00278 (20316) covalent geometry : angle 0.61747 (27636) SS BOND : bond 0.00578 ( 45) SS BOND : angle 2.04750 ( 90) hydrogen bonds : bond 0.03909 ( 515) hydrogen bonds : angle 5.35637 ( 1356) link_ALPHA1-2 : bond 0.00499 ( 10) link_ALPHA1-2 : angle 1.96046 ( 30) link_ALPHA1-3 : bond 0.01218 ( 7) link_ALPHA1-3 : angle 1.23904 ( 21) link_ALPHA1-6 : bond 0.00660 ( 6) link_ALPHA1-6 : angle 1.90810 ( 18) link_BETA1-4 : bond 0.00711 ( 22) link_BETA1-4 : angle 1.75064 ( 66) link_NAG-ASN : bond 0.00328 ( 12) link_NAG-ASN : angle 1.45993 ( 36) *********************** 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 341 residues out of total 2130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 264 time to evaluate : 0.787 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 57 ASP cc_start: 0.6616 (OUTLIER) cc_final: 0.6221 (t70) REVERT: A 95 MET cc_start: 0.8907 (ttp) cc_final: 0.8693 (ttp) REVERT: A 284 ILE cc_start: 0.8781 (OUTLIER) cc_final: 0.8205 (mt) REVERT: A 500 ARG cc_start: 0.7467 (mmm-85) cc_final: 0.7219 (mtp85) REVERT: B 625 ASN cc_start: 0.7776 (p0) cc_final: 0.7457 (t0) REVERT: B 629 LEU cc_start: 0.7894 (tp) cc_final: 0.7548 (mt) REVERT: B 655 LYS cc_start: 0.7551 (pttm) cc_final: 0.7141 (mmtm) REVERT: C 48 MET cc_start: 0.7920 (mtp) cc_final: 0.7583 (mtm) REVERT: D 87 ASP cc_start: 0.7281 (m-30) cc_final: 0.6897 (m-30) REVERT: F 88 ASN cc_start: 0.8013 (t0) cc_final: 0.7661 (m-40) REVERT: F 91 GLU cc_start: 0.6066 (mm-30) cc_final: 0.5793 (tt0) REVERT: F 95 MET cc_start: 0.8837 (ttp) cc_final: 0.8612 (ttp) REVERT: F 164 GLU cc_start: 0.6268 (OUTLIER) cc_final: 0.6042 (pm20) REVERT: F 269 GLU cc_start: 0.7607 (pm20) cc_final: 0.7358 (pm20) REVERT: F 424 ILE cc_start: 0.8714 (mm) cc_final: 0.8452 (mm) REVERT: G 625 ASN cc_start: 0.7378 (p0) cc_final: 0.7067 (t0) REVERT: I 28 ASP cc_start: 0.7380 (OUTLIER) cc_final: 0.7129 (t70) REVERT: I 106 LYS cc_start: 0.6600 (OUTLIER) cc_final: 0.6218 (tmtt) REVERT: K 83 GLU cc_start: 0.7426 (tt0) cc_final: 0.7129 (tt0) REVERT: K 95 MET cc_start: 0.8901 (ttp) cc_final: 0.8682 (ttp) REVERT: K 164 GLU cc_start: 0.6515 (OUTLIER) cc_final: 0.6014 (pm20) REVERT: K 359 ILE cc_start: 0.5850 (OUTLIER) cc_final: 0.5495 (mt) REVERT: L 588 ARG cc_start: 0.8261 (ttm110) cc_final: 0.8010 (ttm-80) REVERT: L 626 MET cc_start: 0.7393 (ttm) cc_final: 0.7103 (ttm) REVERT: L 629 LEU cc_start: 0.8335 (OUTLIER) cc_final: 0.8006 (mt) REVERT: L 632 ASP cc_start: 0.7341 (t0) cc_final: 0.7004 (t0) REVERT: L 648 GLU cc_start: 0.7771 (tp30) cc_final: 0.6808 (pt0) REVERT: L 655 LYS cc_start: 0.7731 (tmmt) cc_final: 0.7100 (mmtm) outliers start: 77 outliers final: 44 residues processed: 310 average time/residue: 0.1551 time to fit residues: 73.5009 Evaluate side-chains 303 residues out of total 2130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 251 time to evaluate : 0.813 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 TRP Chi-restraints excluded: chain A residue 57 ASP 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 595 ILE 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 D residue 25 THR Chi-restraints excluded: chain D residue 28 ASP 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 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 210 PHE 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 F residue 499 THR Chi-restraints excluded: chain G residue 528 SER Chi-restraints excluded: chain G residue 570 VAL 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 99 VAL Chi-restraints excluded: chain I residue 106 LYS Chi-restraints excluded: chain K residue 45 TRP Chi-restraints excluded: chain K residue 57 ASP Chi-restraints excluded: chain K residue 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 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 28 ASP Chi-restraints excluded: chain N residue 35 VAL Chi-restraints excluded: chain N residue 91 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: chunk 223 optimal weight: 2.9990 chunk 182 optimal weight: 0.6980 chunk 47 optimal weight: 1.9990 chunk 214 optimal weight: 0.5980 chunk 238 optimal weight: 6.9990 chunk 58 optimal weight: 4.9990 chunk 35 optimal weight: 5.9990 chunk 78 optimal weight: 6.9990 chunk 71 optimal weight: 0.1980 chunk 184 optimal weight: 0.7980 chunk 52 optimal weight: 0.6980 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 543 ASN G 543 ASN L 543 ASN ** N 41 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4414 r_free = 0.4414 target = 0.200844 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4082 r_free = 0.4082 target = 0.167118 restraints weight = 26314.738| |-----------------------------------------------------------------------------| r_work (start): 0.4072 rms_B_bonded: 2.77 r_work: 0.3857 rms_B_bonded: 3.44 restraints_weight: 0.5000 r_work (final): 0.3857 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7602 moved from start: 0.5221 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.087 20418 Z= 0.130 Angle : 0.639 23.298 27897 Z= 0.313 Chirality : 0.045 0.278 3261 Planarity : 0.004 0.044 3453 Dihedral : 8.708 81.609 3777 Min Nonbonded Distance : 2.415 Molprobity Statistics. All-atom Clashscore : 5.84 Ramachandran Plot: Outliers : 0.16 % Allowed : 5.08 % Favored : 94.76 % Rotamer: Outliers : 3.19 % Allowed : 17.56 % Favored : 79.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.38 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.15 (0.16), residues: 2442 helix: 0.36 (0.27), residues: 399 sheet: -0.34 (0.20), residues: 615 loop : -1.31 (0.16), residues: 1428 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG K 500 TYR 0.015 0.001 TYR I 48 PHE 0.020 0.001 PHE C 64 TRP 0.020 0.001 TRP F 45 HIS 0.004 0.001 HIS C 35 Details of bonding type rmsd covalent geometry : bond 0.00309 (20316) covalent geometry : angle 0.61870 (27636) SS BOND : bond 0.00327 ( 45) SS BOND : angle 1.95063 ( 90) hydrogen bonds : bond 0.03926 ( 515) hydrogen bonds : angle 5.27853 ( 1356) link_ALPHA1-2 : bond 0.00457 ( 10) link_ALPHA1-2 : angle 1.85796 ( 30) link_ALPHA1-3 : bond 0.01164 ( 7) link_ALPHA1-3 : angle 1.26618 ( 21) link_ALPHA1-6 : bond 0.00660 ( 6) link_ALPHA1-6 : angle 1.84787 ( 18) link_BETA1-4 : bond 0.00699 ( 22) link_BETA1-4 : angle 1.69566 ( 66) link_NAG-ASN : bond 0.00312 ( 12) link_NAG-ASN : angle 1.55638 ( 36) *********************** 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 330 residues out of total 2130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 262 time to evaluate : 0.767 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 57 ASP cc_start: 0.6579 (t70) cc_final: 0.6154 (t70) REVERT: A 284 ILE cc_start: 0.8721 (OUTLIER) cc_final: 0.8202 (mt) REVERT: A 424 ILE cc_start: 0.8770 (mm) cc_final: 0.8527 (mm) REVERT: B 542 ARG cc_start: 0.8381 (mtp180) cc_final: 0.8111 (mmm160) REVERT: B 625 ASN cc_start: 0.7800 (p0) cc_final: 0.7492 (t0) REVERT: B 654 GLU cc_start: 0.7553 (OUTLIER) cc_final: 0.7227 (tt0) REVERT: B 655 LYS cc_start: 0.7468 (pttm) cc_final: 0.7106 (mmtm) REVERT: C 48 MET cc_start: 0.7984 (mtp) cc_final: 0.7653 (mtm) REVERT: D 31 LYS cc_start: 0.7006 (ttmt) cc_final: 0.6625 (tttt) REVERT: D 87 ASP cc_start: 0.7302 (m-30) cc_final: 0.6902 (m-30) REVERT: F 88 ASN cc_start: 0.8015 (t0) cc_final: 0.7750 (m-40) REVERT: F 91 GLU cc_start: 0.6152 (mm-30) cc_final: 0.5768 (tt0) REVERT: F 95 MET cc_start: 0.8876 (ttp) cc_final: 0.8622 (ttp) REVERT: F 164 GLU cc_start: 0.6342 (OUTLIER) cc_final: 0.6101 (pm20) REVERT: F 424 ILE cc_start: 0.8743 (mm) cc_final: 0.8475 (mm) REVERT: G 585 ARG cc_start: 0.7909 (mtm-85) cc_final: 0.7694 (mtm-85) REVERT: G 625 ASN cc_start: 0.7289 (p0) cc_final: 0.7081 (t0) REVERT: H 51 MET cc_start: 0.7528 (tpt) cc_final: 0.7144 (ttp) REVERT: I 28 ASP cc_start: 0.7282 (OUTLIER) cc_final: 0.6998 (t70) REVERT: I 87 ASP cc_start: 0.7095 (m-30) cc_final: 0.6710 (m-30) REVERT: I 106 LYS cc_start: 0.6589 (OUTLIER) cc_final: 0.6149 (tmtt) REVERT: K 164 GLU cc_start: 0.6594 (OUTLIER) cc_final: 0.6087 (pm20) REVERT: K 359 ILE cc_start: 0.5815 (OUTLIER) cc_final: 0.5523 (mt) REVERT: L 588 ARG cc_start: 0.8248 (ttm110) cc_final: 0.8018 (ttm-80) REVERT: L 626 MET cc_start: 0.7466 (ttm) cc_final: 0.7179 (ttm) REVERT: L 629 LEU cc_start: 0.8269 (OUTLIER) cc_final: 0.7963 (mt) REVERT: L 632 ASP cc_start: 0.7403 (t0) cc_final: 0.7051 (t0) REVERT: L 648 GLU cc_start: 0.7763 (tp30) cc_final: 0.6774 (pt0) REVERT: L 655 LYS cc_start: 0.7736 (tmmt) cc_final: 0.7063 (mmtm) outliers start: 68 outliers final: 49 residues processed: 306 average time/residue: 0.1616 time to fit residues: 74.8283 Evaluate side-chains 312 residues out of total 2130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 255 time to evaluate : 0.718 ------------------------------------------------------------------------------- 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 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 28 ASP Chi-restraints excluded: chain D residue 90 CYS Chi-restraints excluded: chain D residue 99 VAL Chi-restraints excluded: chain F residue 120 VAL Chi-restraints excluded: chain F residue 125 LEU Chi-restraints excluded: chain F residue 164 GLU Chi-restraints excluded: chain F residue 180 ASP Chi-restraints excluded: chain F residue 210 PHE 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 F residue 477 ASP Chi-restraints excluded: chain F residue 499 THR Chi-restraints excluded: chain G residue 543 ASN Chi-restraints excluded: chain G residue 570 VAL 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 99 VAL Chi-restraints excluded: chain I residue 106 LYS Chi-restraints excluded: chain K residue 45 TRP Chi-restraints excluded: chain K residue 57 ASP Chi-restraints excluded: chain K residue 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 426 MET 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 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 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 49 optimal weight: 0.7980 chunk 12 optimal weight: 4.9990 chunk 159 optimal weight: 6.9990 chunk 177 optimal weight: 0.9990 chunk 37 optimal weight: 0.9980 chunk 167 optimal weight: 0.9990 chunk 222 optimal weight: 0.9990 chunk 56 optimal weight: 1.9990 chunk 235 optimal weight: 0.9990 chunk 36 optimal weight: 10.0000 chunk 186 optimal weight: 3.9990 overall best weight: 0.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 543 ASN L 543 ASN L 630 GLN ** L 653 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4381 r_free = 0.4381 target = 0.197879 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4033 r_free = 0.4033 target = 0.163248 restraints weight = 26252.205| |-----------------------------------------------------------------------------| r_work (start): 0.4055 rms_B_bonded: 2.77 r_work: 0.3886 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work (final): 0.3886 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7616 moved from start: 0.5365 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.088 20418 Z= 0.165 Angle : 0.676 22.343 27897 Z= 0.333 Chirality : 0.047 0.281 3261 Planarity : 0.004 0.045 3453 Dihedral : 8.835 82.670 3777 Min Nonbonded Distance : 2.263 Molprobity Statistics. All-atom Clashscore : 6.25 Ramachandran Plot: Outliers : 0.16 % Allowed : 4.95 % Favored : 94.88 % Rotamer: Outliers : 3.15 % Allowed : 18.17 % Favored : 78.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.38 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.22 (0.17), residues: 2442 helix: 0.36 (0.27), residues: 399 sheet: -0.52 (0.20), residues: 651 loop : -1.30 (0.16), residues: 1392 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG K 166 TYR 0.015 0.001 TYR D 48 PHE 0.022 0.001 PHE C 64 TRP 0.023 0.001 TRP F 45 HIS 0.006 0.001 HIS C 35 Details of bonding type rmsd covalent geometry : bond 0.00401 (20316) covalent geometry : angle 0.65180 (27636) SS BOND : bond 0.00420 ( 45) SS BOND : angle 2.34028 ( 90) hydrogen bonds : bond 0.04201 ( 515) hydrogen bonds : angle 5.35566 ( 1356) link_ALPHA1-2 : bond 0.00436 ( 10) link_ALPHA1-2 : angle 1.76603 ( 30) link_ALPHA1-3 : bond 0.01168 ( 7) link_ALPHA1-3 : angle 1.25222 ( 21) link_ALPHA1-6 : bond 0.00600 ( 6) link_ALPHA1-6 : angle 1.82522 ( 18) link_BETA1-4 : bond 0.00700 ( 22) link_BETA1-4 : angle 1.79825 ( 66) link_NAG-ASN : bond 0.00307 ( 12) link_NAG-ASN : angle 1.69110 ( 36) *********************** 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 329 residues out of total 2130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 262 time to evaluate : 0.770 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 57 ASP cc_start: 0.6620 (t70) cc_final: 0.6212 (t70) REVERT: B 542 ARG cc_start: 0.8420 (mtp180) cc_final: 0.8120 (mmm160) REVERT: B 625 ASN cc_start: 0.7879 (p0) cc_final: 0.7527 (t0) REVERT: B 654 GLU cc_start: 0.7612 (OUTLIER) cc_final: 0.7319 (tt0) REVERT: B 655 LYS cc_start: 0.7426 (pttm) cc_final: 0.7141 (mmtm) REVERT: C 48 MET cc_start: 0.8007 (mtp) cc_final: 0.7658 (mtm) REVERT: D 31 LYS cc_start: 0.7033 (ttmt) cc_final: 0.6781 (tttt) REVERT: D 87 ASP cc_start: 0.7283 (m-30) cc_final: 0.6891 (m-30) REVERT: F 88 ASN cc_start: 0.8015 (t0) cc_final: 0.7740 (m-40) REVERT: F 95 MET cc_start: 0.8882 (ttp) cc_final: 0.8627 (ttp) REVERT: F 164 GLU cc_start: 0.6506 (OUTLIER) cc_final: 0.6158 (pm20) REVERT: G 585 ARG cc_start: 0.7870 (mtm-85) cc_final: 0.7625 (mtm-85) REVERT: I 28 ASP cc_start: 0.7418 (OUTLIER) cc_final: 0.7137 (t70) REVERT: I 87 ASP cc_start: 0.7117 (m-30) cc_final: 0.6716 (m-30) REVERT: I 106 LYS cc_start: 0.6667 (OUTLIER) cc_final: 0.6180 (tmtt) REVERT: K 49 LYS cc_start: 0.8396 (mmtm) cc_final: 0.8162 (tppt) REVERT: K 164 GLU cc_start: 0.6634 (OUTLIER) cc_final: 0.6106 (pm20) REVERT: K 359 ILE cc_start: 0.5784 (OUTLIER) cc_final: 0.5402 (mt) REVERT: L 542 ARG cc_start: 0.8166 (mtp180) cc_final: 0.7779 (mtm-85) REVERT: L 588 ARG cc_start: 0.8242 (ttm110) cc_final: 0.8018 (ttm-80) REVERT: L 629 LEU cc_start: 0.8350 (OUTLIER) cc_final: 0.8061 (mt) REVERT: L 632 ASP cc_start: 0.7386 (t0) cc_final: 0.7011 (t0) REVERT: L 648 GLU cc_start: 0.7751 (tp30) cc_final: 0.6799 (pt0) REVERT: L 655 LYS cc_start: 0.7869 (tmmt) cc_final: 0.7234 (mmtm) outliers start: 67 outliers final: 55 residues processed: 304 average time/residue: 0.1628 time to fit residues: 74.2625 Evaluate side-chains 311 residues out of total 2130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 249 time to evaluate : 0.648 ------------------------------------------------------------------------------- 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 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 20 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 90 CYS Chi-restraints excluded: chain D residue 99 VAL Chi-restraints excluded: chain F residue 120 VAL Chi-restraints excluded: chain F residue 125 LEU Chi-restraints excluded: chain F residue 164 GLU Chi-restraints excluded: chain F residue 180 ASP Chi-restraints excluded: chain F residue 210 PHE Chi-restraints excluded: chain F residue 271 VAL Chi-restraints excluded: chain F residue 283 ILE Chi-restraints excluded: chain F residue 284 ILE Chi-restraints excluded: chain F residue 445 CYS Chi-restraints excluded: chain F residue 455 THR Chi-restraints excluded: chain F residue 477 ASP Chi-restraints excluded: chain F residue 499 THR Chi-restraints excluded: chain G residue 528 SER Chi-restraints excluded: chain G residue 543 ASN Chi-restraints excluded: chain G residue 570 VAL 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 99 VAL Chi-restraints excluded: chain I residue 106 LYS Chi-restraints excluded: chain K residue 45 TRP Chi-restraints excluded: chain K residue 57 ASP Chi-restraints excluded: chain K residue 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 543 ASN 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 90 CYS 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 83 optimal weight: 1.9990 chunk 196 optimal weight: 1.9990 chunk 212 optimal weight: 1.9990 chunk 155 optimal weight: 4.9990 chunk 107 optimal weight: 0.5980 chunk 31 optimal weight: 0.2980 chunk 77 optimal weight: 5.9990 chunk 185 optimal weight: 3.9990 chunk 21 optimal weight: 0.5980 chunk 168 optimal weight: 1.9990 chunk 96 optimal weight: 0.4980 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 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 = 0.4399 r_free = 0.4399 target = 0.199496 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4071 r_free = 0.4071 target = 0.166361 restraints weight = 26406.730| |-----------------------------------------------------------------------------| r_work (start): 0.4064 rms_B_bonded: 2.61 r_work: 0.3833 rms_B_bonded: 3.47 restraints_weight: 0.5000 r_work (final): 0.3833 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7641 moved from start: 0.5472 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.089 20418 Z= 0.148 Angle : 0.665 22.680 27897 Z= 0.326 Chirality : 0.046 0.281 3261 Planarity : 0.004 0.044 3453 Dihedral : 8.687 81.442 3777 Min Nonbonded Distance : 2.281 Molprobity Statistics. All-atom Clashscore : 6.15 Ramachandran Plot: Outliers : 0.16 % Allowed : 4.91 % Favored : 94.92 % Rotamer: Outliers : 3.15 % Allowed : 18.64 % Favored : 78.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.38 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.18 (0.17), residues: 2442 helix: 0.40 (0.27), residues: 399 sheet: -0.51 (0.20), residues: 651 loop : -1.28 (0.16), residues: 1392 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG K 166 TYR 0.016 0.001 TYR F 395 PHE 0.021 0.001 PHE C 64 TRP 0.021 0.001 TRP F 45 HIS 0.005 0.001 HIS C 35 Details of bonding type rmsd covalent geometry : bond 0.00357 (20316) covalent geometry : angle 0.64258 (27636) SS BOND : bond 0.00416 ( 45) SS BOND : angle 2.24793 ( 90) hydrogen bonds : bond 0.04083 ( 515) hydrogen bonds : angle 5.32936 ( 1356) link_ALPHA1-2 : bond 0.00440 ( 10) link_ALPHA1-2 : angle 1.76723 ( 30) link_ALPHA1-3 : bond 0.01087 ( 7) link_ALPHA1-3 : angle 1.22506 ( 21) link_ALPHA1-6 : bond 0.00632 ( 6) link_ALPHA1-6 : angle 1.78825 ( 18) link_BETA1-4 : bond 0.00693 ( 22) link_BETA1-4 : angle 1.74667 ( 66) link_NAG-ASN : bond 0.00290 ( 12) link_NAG-ASN : angle 1.58747 ( 36) ********************** 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 328 residues out of total 2130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 261 time to evaluate : 0.803 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 57 ASP cc_start: 0.6583 (t70) cc_final: 0.6154 (t70) REVERT: A 284 ILE cc_start: 0.8772 (OUTLIER) cc_final: 0.8244 (mt) REVERT: B 625 ASN cc_start: 0.7823 (p0) cc_final: 0.7532 (t0) REVERT: B 654 GLU cc_start: 0.7606 (OUTLIER) cc_final: 0.7317 (tt0) REVERT: B 656 ASN cc_start: 0.7586 (m-40) cc_final: 0.7280 (m-40) REVERT: D 31 LYS cc_start: 0.7098 (ttmt) cc_final: 0.6855 (tttt) REVERT: D 87 ASP cc_start: 0.7290 (m-30) cc_final: 0.6895 (m-30) REVERT: F 88 ASN cc_start: 0.8028 (t0) cc_final: 0.7741 (m-40) REVERT: F 95 MET cc_start: 0.8880 (ttp) cc_final: 0.8614 (ttp) REVERT: F 164 GLU cc_start: 0.6516 (OUTLIER) cc_final: 0.6164 (pm20) REVERT: G 542 ARG cc_start: 0.8444 (mtp180) cc_final: 0.8064 (mtp180) REVERT: G 585 ARG cc_start: 0.7904 (mtm-85) cc_final: 0.7665 (mtm-85) REVERT: I 28 ASP cc_start: 0.7350 (OUTLIER) cc_final: 0.7052 (t70) REVERT: I 87 ASP cc_start: 0.7165 (m-30) cc_final: 0.6753 (m-30) REVERT: I 106 LYS cc_start: 0.6592 (OUTLIER) cc_final: 0.6080 (tmtt) REVERT: K 49 LYS cc_start: 0.8431 (mmtm) cc_final: 0.8219 (tppt) REVERT: K 164 GLU cc_start: 0.6625 (OUTLIER) cc_final: 0.6102 (pm20) REVERT: K 359 ILE cc_start: 0.5665 (OUTLIER) cc_final: 0.5367 (mt) REVERT: L 530 MET cc_start: 0.8630 (mtp) cc_final: 0.8355 (mtp) REVERT: L 542 ARG cc_start: 0.8117 (mtp180) cc_final: 0.7666 (mtm-85) REVERT: L 588 ARG cc_start: 0.8257 (ttm110) cc_final: 0.8033 (ttm-80) REVERT: L 626 MET cc_start: 0.7539 (ttm) cc_final: 0.7142 (ttm) REVERT: L 629 LEU cc_start: 0.8259 (OUTLIER) cc_final: 0.7980 (mt) REVERT: L 632 ASP cc_start: 0.7505 (t0) cc_final: 0.7120 (t0) REVERT: L 648 GLU cc_start: 0.7749 (tp30) cc_final: 0.6797 (pt0) REVERT: L 655 LYS cc_start: 0.7921 (tmmt) cc_final: 0.7349 (tppt) REVERT: N 48 TYR cc_start: 0.7952 (t80) cc_final: 0.7654 (t80) outliers start: 67 outliers final: 53 residues processed: 304 average time/residue: 0.1628 time to fit residues: 73.7218 Evaluate side-chains 317 residues out of total 2130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 256 time to evaluate : 0.728 ------------------------------------------------------------------------------- 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 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 20 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 90 CYS Chi-restraints excluded: chain D residue 99 VAL Chi-restraints excluded: chain F residue 120 VAL Chi-restraints excluded: chain F residue 125 LEU Chi-restraints excluded: chain F residue 164 GLU Chi-restraints excluded: chain F residue 180 ASP Chi-restraints excluded: chain F residue 210 PHE 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 455 THR Chi-restraints excluded: chain F residue 477 ASP Chi-restraints excluded: chain F residue 499 THR Chi-restraints excluded: chain G residue 528 SER Chi-restraints excluded: chain G residue 570 VAL Chi-restraints excluded: chain G residue 622 ILE Chi-restraints excluded: chain H residue 30 THR Chi-restraints excluded: chain H residue 48 MET 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 99 VAL Chi-restraints excluded: chain I residue 106 LYS Chi-restraints excluded: chain K residue 45 TRP Chi-restraints excluded: chain K residue 57 ASP Chi-restraints excluded: chain K residue 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 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 90 CYS 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 123 optimal weight: 1.9990 chunk 133 optimal weight: 0.7980 chunk 187 optimal weight: 1.9990 chunk 87 optimal weight: 3.9990 chunk 60 optimal weight: 2.9990 chunk 113 optimal weight: 3.9990 chunk 156 optimal weight: 0.6980 chunk 165 optimal weight: 2.9990 chunk 162 optimal weight: 0.6980 chunk 78 optimal weight: 6.9990 chunk 176 optimal weight: 0.9990 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 543 ASN L 543 ASN ** L 653 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 41 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4380 r_free = 0.4380 target = 0.197272 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4052 r_free = 0.4052 target = 0.164290 restraints weight = 26439.962| |-----------------------------------------------------------------------------| r_work (start): 0.4050 rms_B_bonded: 2.71 r_work: 0.3861 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work (final): 0.3861 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7656 moved from start: 0.5678 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.084 20418 Z= 0.175 Angle : 0.693 23.289 27897 Z= 0.340 Chirality : 0.047 0.274 3261 Planarity : 0.004 0.045 3453 Dihedral : 8.775 82.831 3777 Min Nonbonded Distance : 2.394 Molprobity Statistics. All-atom Clashscore : 6.40 Ramachandran Plot: Outliers : 0.16 % Allowed : 5.24 % Favored : 94.59 % Rotamer: Outliers : 3.24 % Allowed : 18.40 % Favored : 78.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.38 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.20 (0.17), residues: 2442 helix: 0.67 (0.27), residues: 381 sheet: -0.65 (0.20), residues: 663 loop : -1.31 (0.16), residues: 1398 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 585 TYR 0.015 0.001 TYR D 48 PHE 0.014 0.002 PHE F 317 TRP 0.025 0.002 TRP F 45 HIS 0.007 0.001 HIS C 35 Details of bonding type rmsd covalent geometry : bond 0.00424 (20316) covalent geometry : angle 0.66994 (27636) SS BOND : bond 0.00429 ( 45) SS BOND : angle 2.35456 ( 90) hydrogen bonds : bond 0.04363 ( 515) hydrogen bonds : angle 5.44390 ( 1356) link_ALPHA1-2 : bond 0.00401 ( 10) link_ALPHA1-2 : angle 1.68436 ( 30) link_ALPHA1-3 : bond 0.01041 ( 7) link_ALPHA1-3 : angle 1.22756 ( 21) link_ALPHA1-6 : bond 0.00577 ( 6) link_ALPHA1-6 : angle 1.70807 ( 18) link_BETA1-4 : bond 0.00688 ( 22) link_BETA1-4 : angle 1.79682 ( 66) link_NAG-ASN : bond 0.00301 ( 12) link_NAG-ASN : angle 1.75435 ( 36) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4838.99 seconds wall clock time: 83 minutes 49.42 seconds (5029.42 seconds total)