Starting phenix.real_space_refine on Tue May 20 17:01:30 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8sas_40278/05_2025/8sas_40278_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8sas_40278/05_2025/8sas_40278.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8sas_40278/05_2025/8sas_40278.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8sas_40278/05_2025/8sas_40278.map" model { file = "/net/cci-nas-00/data/ceres_data/8sas_40278/05_2025/8sas_40278_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8sas_40278/05_2025/8sas_40278_neut.cif" } resolution = 4.0 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.354 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 132 5.16 5 C 12531 2.51 5 N 3318 2.21 5 O 4047 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 10 residue(s): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 20028 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: 997 Number of conformers: 1 Conformer: "" Number of residues, atoms: 127, 997 Classifications: {'peptide': 127} Link IDs: {'PTRANS': 5, 'TRANS': 121} Chain: "D" Number of atoms: 815 Number of conformers: 1 Conformer: "" Number of residues, atoms: 111, 815 Classifications: {'peptide': 111} Link IDs: {'CIS': 1, 'PTRANS': 6, 'TRANS': 103} 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: 997 Number of conformers: 1 Conformer: "" Number of residues, atoms: 127, 997 Classifications: {'peptide': 127} Link IDs: {'PTRANS': 5, 'TRANS': 121} Chain: "I" Number of atoms: 815 Number of conformers: 1 Conformer: "" Number of residues, atoms: 111, 815 Classifications: {'peptide': 111} Link IDs: {'CIS': 1, 'PTRANS': 6, 'TRANS': 103} 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: 997 Number of conformers: 1 Conformer: "" Number of residues, atoms: 127, 997 Classifications: {'peptide': 127} Link IDs: {'PTRANS': 5, 'TRANS': 121} Chain: "N" Number of atoms: 815 Number of conformers: 1 Conformer: "" Number of residues, atoms: 111, 815 Classifications: {'peptide': 111} Link IDs: {'CIS': 1, 'PTRANS': 6, 'TRANS': 103} Chain: "E" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "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: 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: "Q" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 72 Unusual residues: {'BMA': 1, 'MAN': 3, 'NAG': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 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: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 72 Unusual residues: {'BMA': 1, 'MAN': 3, 'NAG': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 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: 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: "X" 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 Time building chain proxies: 12.28, per 1000 atoms: 0.61 Number of scatterers: 20028 At special positions: 0 Unit cell: (160.966, 162.032, 143.91, 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 132 16.00 O 4047 8.00 N 3318 7.00 C 12531 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=2.04 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=2.04 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=2.04 Simple disulfide: pdb=" SG CYS A 228 " - pdb=" SG CYS A 239 " distance=2.03 Simple disulfide: pdb=" SG CYS A 296 " - pdb=" SG CYS A 331 " distance=2.03 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=2.02 Simple disulfide: pdb=" SG CYS A 501 " - pdb=" SG CYS B 605 " distance=2.03 Simple disulfide: pdb=" SG CYS B 598 " - pdb=" SG CYS B 604 " distance=2.03 Simple disulfide: pdb=" SG CYS C 22 " - pdb=" SG CYS C 96 " distance=2.03 Simple disulfide: pdb=" SG CYS D 252 " - pdb=" SG CYS D 320 " distance=2.04 Simple disulfide: pdb=" SG CYS D 321 " - pdb=" SG CYS D 331 " distance=2.03 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=2.02 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=2.04 Simple disulfide: pdb=" SG CYS F 201 " - pdb=" SG CYS F 433 " distance=2.01 Simple disulfide: pdb=" SG CYS F 218 " - pdb=" SG CYS F 247 " distance=2.03 Simple disulfide: pdb=" SG CYS F 228 " - pdb=" SG CYS F 239 " distance=2.03 Simple disulfide: pdb=" SG CYS F 296 " - pdb=" SG CYS F 331 " distance=2.02 Simple disulfide: pdb=" SG CYS F 378 " - pdb=" SG CYS F 445 " distance=2.05 Simple disulfide: pdb=" SG CYS F 385 " - pdb=" SG CYS F 418 " distance=2.03 Simple disulfide: pdb=" SG CYS F 501 " - pdb=" SG CYS G 605 " distance=2.03 Simple disulfide: pdb=" SG CYS G 598 " - pdb=" SG CYS G 604 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.03 Simple disulfide: pdb=" SG CYS I 252 " - pdb=" SG CYS I 320 " distance=2.03 Simple disulfide: pdb=" SG CYS I 321 " - pdb=" SG CYS I 331 " distance=2.03 Simple disulfide: pdb=" SG CYS K 54 " - pdb=" SG CYS K 74 " distance=2.03 Simple disulfide: pdb=" SG CYS K 119 " - pdb=" SG CYS K 205 " distance=2.04 Simple disulfide: pdb=" SG CYS K 126 " - pdb=" SG CYS K 196 " distance=2.04 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=2.02 Simple disulfide: pdb=" SG CYS K 218 " - pdb=" SG CYS K 247 " distance=2.02 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=2.04 Simple disulfide: pdb=" SG CYS N 252 " - pdb=" SG CYS N 320 " distance=2.04 Simple disulfide: pdb=" SG CYS N 321 " - pdb=" SG CYS N 331 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied ALPHA1-2 " MAN J 4 " - " MAN J 5 " " MAN J 5 " - " MAN J 6 " " MAN J 8 " - " MAN J 9 " " MAN Q 4 " - " MAN Q 5 " " 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 U 4 " - " MAN U 5 " " MAN V 4 " - " MAN V 5 " " MAN V 5 " - " MAN V 6 " 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 " " MAN V 7 " - " MAN V 8 " " BMA X 3 " - " MAN X 4 " ALPHA1-6 " BMA E 3 " - " MAN E 5 " " BMA J 3 " - " MAN J 7 " " MAN J 7 " - " MAN J 8 " " BMA Q 3 " - " MAN Q 6 " " BMA R 3 " - " MAN R 7 " " MAN R 7 " - " MAN R 10 " " BMA U 3 " - " MAN U 6 " " BMA V 3 " - " MAN V 7 " " MAN V 7 " - " MAN V 9 " " BMA W 3 " - " MAN W 4 " 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 P 2 " - " BMA P 3 " " 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 X 2 " - " BMA X 3 " NAG-ASN " NAG E 1 " - " ASN A 301 " " NAG J 1 " - " ASN A 332 " " NAG O 1 " - " ASN A 156 " " NAG P 1 " - " ASN A 442 " " NAG Q 1 " - " ASN F 301 " " NAG R 1 " - " ASN F 332 " " NAG S 1 " - " ASN F 156 " " NAG T 1 " - " ASN F 442 " " NAG U 1 " - " ASN K 301 " " NAG V 1 " - " ASN K 332 " " NAG W 1 " - " ASN K 156 " " NAG X 1 " - " ASN K 442 " Time building additional restraints: 5.61 Conformation dependent library (CDL) restraints added in 2.6 seconds 4896 Ramachandran restraints generated. 2448 Oldfield, 0 Emsley, 2448 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4548 Finding SS restraints... Secondary structure from input PDB file: 53 helices and 46 sheets defined 17.8% alpha, 24.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.45 Creating SS restraints... Processing helix chain 'A' and resid 57 through 61 removed outlier: 3.852A pdb=" N ALA A 60 " --> pdb=" O ASP A 57 " (cutoff:3.500A) Processing helix chain 'A' and resid 69 through 74 Processing helix chain 'A' and resid 99 through 116 removed outlier: 3.658A pdb=" N GLN A 114 " --> pdb=" O SER A 110 " (cutoff:3.500A) removed outlier: 4.168A pdb=" N LEU A 116 " --> pdb=" O TRP A 112 " (cutoff:3.500A) Processing helix chain 'A' and resid 335 through 353 removed outlier: 3.670A pdb=" N GLU A 348 " --> pdb=" O LYS A 344 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N LYS A 351 " --> pdb=" O ILE A 347 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N HIS A 352 " --> pdb=" O GLU A 348 " (cutoff:3.500A) Processing helix chain 'A' and resid 475 through 480 removed outlier: 3.568A pdb=" N ARG A 480 " --> pdb=" O ARG A 476 " (cutoff:3.500A) Processing helix chain 'B' and resid 530 through 534 removed outlier: 3.583A pdb=" N SER B 534 " --> pdb=" O GLY B 531 " (cutoff:3.500A) Processing helix chain 'B' and resid 537 through 542 Processing helix chain 'B' and resid 571 through 577 removed outlier: 3.667A pdb=" N GLN B 575 " --> pdb=" O TRP B 571 " (cutoff:3.500A) Processing helix chain 'B' and resid 580 through 596 removed outlier: 3.867A pdb=" N LEU B 587 " --> pdb=" O VAL B 583 " (cutoff:3.500A) removed outlier: 4.765A pdb=" N ARG B 588 " --> pdb=" O GLU B 584 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N TRP B 596 " --> pdb=" O LEU B 592 " (cutoff:3.500A) Processing helix chain 'B' and resid 611 through 615 Processing helix chain 'B' and resid 618 through 625 Processing helix chain 'B' and resid 627 through 636 Processing helix chain 'B' and resid 638 through 649 Processing helix chain 'B' and resid 650 through 654 Processing helix chain 'B' and resid 659 through 664 Processing helix chain 'C' and resid 87 through 91 removed outlier: 3.524A pdb=" N THR C 91 " --> pdb=" O SER C 88 " (cutoff:3.500A) Processing helix chain 'D' and resid 311 through 315 Processing helix chain 'F' and resid 99 through 115 removed outlier: 3.694A pdb=" N GLN F 114 " --> pdb=" O SER F 110 " (cutoff:3.500A) 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: 4.310A pdb=" N ILE F 347 " --> pdb=" O GLN F 343 " (cutoff:3.500A) removed outlier: 4.412A pdb=" N GLU F 348 " --> pdb=" O LYS F 344 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N LEU F 349 " --> pdb=" O VAL F 345 " (cutoff:3.500A) Processing helix chain 'F' and resid 387 through 391 Processing helix chain 'F' and resid 475 through 484 removed outlier: 3.654A pdb=" N ARG F 480 " --> pdb=" O ARG F 476 " (cutoff:3.500A) removed outlier: 5.939A pdb=" N SER F 481 " --> pdb=" O ASP F 477 " (cutoff:3.500A) removed outlier: 4.796A pdb=" N GLU F 482 " --> pdb=" O ASN F 478 " (cutoff:3.500A) Processing helix chain 'G' and resid 529 through 534 Processing helix chain 'G' and resid 537 through 542 removed outlier: 3.797A pdb=" N ALA G 541 " --> pdb=" O LEU G 537 " (cutoff:3.500A) Processing helix chain 'G' and resid 571 through 580 removed outlier: 5.232A pdb=" N ALA G 578 " --> pdb=" O LYS G 574 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N ARG G 579 " --> pdb=" O GLN G 575 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N VAL G 580 " --> pdb=" O LEU G 576 " (cutoff:3.500A) Processing helix chain 'G' and resid 580 through 585 removed outlier: 3.550A pdb=" N GLU G 584 " --> pdb=" O VAL G 580 " (cutoff:3.500A) Processing helix chain 'G' and resid 585 through 596 Processing helix chain 'G' and resid 618 through 625 removed outlier: 3.701A pdb=" N ILE G 622 " --> pdb=" O ASN G 618 " (cutoff:3.500A) Processing helix chain 'G' and resid 627 through 636 removed outlier: 3.543A pdb=" N TRP G 631 " --> pdb=" O THR G 627 " (cutoff:3.500A) Processing helix chain 'G' and resid 638 through 649 Processing helix chain 'G' and resid 649 through 654 Processing helix chain 'G' and resid 656 through 663 removed outlier: 4.538A pdb=" N LEU G 663 " --> pdb=" O ASP G 659 " (cutoff:3.500A) Processing helix chain 'H' and resid 28 through 30 No H-bonds generated for 'chain 'H' and resid 28 through 30' Processing helix chain 'H' and resid 88 through 92 removed outlier: 3.689A pdb=" N THR H 91 " --> pdb=" O SER H 88 " (cutoff:3.500A) Processing helix chain 'I' and resid 258 through 262 removed outlier: 3.777A pdb=" N LYS I 261 " --> pdb=" O ASP I 258 " (cutoff:3.500A) removed outlier: 4.326A pdb=" N PHE I 262 " --> pdb=" O VAL I 259 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 258 through 262' Processing helix chain 'I' and resid 311 through 315 removed outlier: 3.540A pdb=" N GLU I 315 " --> pdb=" O VAL I 312 " (cutoff:3.500A) Processing helix chain 'K' and resid 69 through 74 removed outlier: 3.776A pdb=" N CYS K 74 " --> pdb=" O ALA K 70 " (cutoff:3.500A) Processing helix chain 'K' and resid 98 through 116 removed outlier: 4.508A pdb=" N ASP K 102 " --> pdb=" O ASN K 98 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N GLU K 106 " --> pdb=" O ASP K 102 " (cutoff:3.500A) 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 334 through 350 Processing helix chain 'K' and resid 474 through 484 removed outlier: 4.455A pdb=" N GLU K 482 " --> pdb=" O ASN K 478 " (cutoff:3.500A) removed outlier: 4.137A pdb=" N TYR K 484 " --> pdb=" O ARG K 480 " (cutoff:3.500A) Processing helix chain 'L' and resid 520 through 524 removed outlier: 4.145A pdb=" N LEU L 523 " --> pdb=" O LEU L 520 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N GLY L 524 " --> pdb=" O GLY L 521 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 520 through 524' Processing helix chain 'L' and resid 571 through 580 removed outlier: 4.446A pdb=" N GLN L 577 " --> pdb=" O ILE L 573 " (cutoff:3.500A) removed outlier: 7.190A pdb=" N ALA L 578 " --> pdb=" O LYS L 574 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N ARG L 579 " --> pdb=" O GLN L 575 " (cutoff:3.500A) Processing helix chain 'L' and resid 580 through 585 Processing helix chain 'L' and resid 585 through 596 removed outlier: 3.896A pdb=" N TRP L 596 " --> pdb=" O LEU L 592 " (cutoff:3.500A) Processing helix chain 'L' and resid 618 through 624 Processing helix chain 'L' and resid 627 through 636 Processing helix chain 'L' and resid 638 through 650 Processing helix chain 'L' and resid 651 through 656 removed outlier: 3.767A pdb=" N ASN L 656 " --> pdb=" O GLN L 652 " (cutoff:3.500A) Processing helix chain 'L' and resid 659 through 663 removed outlier: 3.810A pdb=" N ALA L 662 " --> pdb=" O ASP L 659 " (cutoff:3.500A) Processing helix chain 'M' and resid 28 through 30 No H-bonds generated for 'chain 'M' and resid 28 through 30' Processing helix chain 'N' and resid 258 through 262 Processing helix chain 'N' and resid 311 through 315 Processing sheet with id=AA1, first strand: chain 'A' and resid 495 through 496 removed outlier: 3.791A pdb=" N GLY A 495 " --> pdb=" O TYR A 39 " (cutoff:3.500A) removed outlier: 5.331A pdb=" N VAL B 608 " --> pdb=" O VAL A 36 " (cutoff:3.500A) removed outlier: 9.761A pdb=" N VAL A 38 " --> pdb=" O THR B 606 " (cutoff:3.500A) removed outlier: 8.177A pdb=" N THR B 606 " --> pdb=" O VAL A 38 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 45 through 47 Processing sheet with id=AA3, first strand: chain 'A' and resid 91 through 92 removed outlier: 3.502A pdb=" N GLU A 91 " --> pdb=" O CYS A 239 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 170 through 173 removed outlier: 4.572A pdb=" N ASN A 156 " --> pdb=" O SER A 132 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 272 through 273 removed outlier: 4.250A pdb=" N ARG A 273 " --> pdb=" O ILE A 285 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ILE A 285 " --> pdb=" O ARG A 273 " (cutoff:3.500A) removed outlier: 6.407A pdb=" N GLU A 293 " --> pdb=" O SER A 334 " (cutoff:3.500A) removed outlier: 4.267A pdb=" N SER A 334 " --> pdb=" O GLU A 293 " (cutoff:3.500A) removed outlier: 4.584A pdb=" N PHE A 382 " --> pdb=" O LYS A 421 " (cutoff:3.500A) removed outlier: 4.200A pdb=" N PHE A 383 " --> pdb=" O PHE A 376 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N PHE A 376 " --> pdb=" O PHE A 383 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 272 through 273 removed outlier: 4.250A pdb=" N ARG A 273 " --> pdb=" O ILE A 285 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ILE A 285 " --> pdb=" O ARG A 273 " (cutoff:3.500A) removed outlier: 7.758A pdb=" N THR A 450 " --> pdb=" O LEU A 288 " (cutoff:3.500A) removed outlier: 10.720A pdb=" N THR A 290 " --> pdb=" O ASN A 448 " (cutoff:3.500A) removed outlier: 9.712A pdb=" N ASN A 448 " --> pdb=" O THR A 290 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 304 through 308 removed outlier: 3.549A pdb=" N ALA A 319 " --> pdb=" O LYS A 305 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N VAL A 307 " --> pdb=" O PHE A 317 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N PHE A 317 " --> pdb=" O VAL A 307 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 359 through 360 removed outlier: 4.102A pdb=" N ILE A 359 " --> pdb=" O TYR A 395 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N TYR A 395 " --> pdb=" O ILE A 359 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'A' and resid 423 through 425 Processing sheet with id=AB1, first strand: chain 'C' and resid 10 through 12 removed outlier: 3.610A pdb=" N THR C 124 " --> pdb=" O GLU C 10 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N LYS C 12 " --> pdb=" O THR C 124 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N VAL C 93 " --> pdb=" O LEU C 39 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N VAL C 37 " --> pdb=" O TYR C 95 " (cutoff:3.500A) removed outlier: 4.505A pdb=" N TYR C 33 " --> pdb=" O GLY C 99 " (cutoff:3.500A) removed outlier: 6.521A pdb=" N ILE C 34 " --> pdb=" O TRP C 50 " (cutoff:3.500A) removed outlier: 4.359A pdb=" N TRP C 50 " --> pdb=" O ILE C 34 " (cutoff:3.500A) removed outlier: 6.864A pdb=" N TRP C 36 " --> pdb=" O LEU C 48 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N ASN C 59 " --> pdb=" O TRP C 50 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 20 through 22 removed outlier: 3.734A pdb=" N ALA C 79 " --> pdb=" O CYS C 22 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 247 through 253 removed outlier: 3.675A pdb=" N ALA D 303 " --> pdb=" O CYS D 252 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 277 through 281 removed outlier: 6.215A pdb=" N TYR D 278 " --> pdb=" O GLN D 269 " (cutoff:3.500A) removed outlier: 7.606A pdb=" N GLN D 269 " --> pdb=" O TYR D 278 " (cutoff:3.500A) removed outlier: 4.065A pdb=" N ILE D 280 " --> pdb=" O TRP D 267 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 277 through 281 removed outlier: 6.215A pdb=" N TYR D 278 " --> pdb=" O GLN D 269 " (cutoff:3.500A) removed outlier: 7.606A pdb=" N GLN D 269 " --> pdb=" O TYR D 278 " (cutoff:3.500A) removed outlier: 4.065A pdb=" N ILE D 280 " --> pdb=" O TRP D 267 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'F' and resid 35 through 40 removed outlier: 3.710A pdb=" N THR F 499 " --> pdb=" O TRP F 35 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'F' and resid 45 through 47 removed outlier: 3.568A pdb=" N LYS F 487 " --> pdb=" O LEU F 226 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N ILE F 225 " --> pdb=" O VAL F 245 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N VAL F 245 " --> pdb=" O ILE F 225 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'F' and resid 75 through 76 removed outlier: 7.055A pdb=" N CYS F 54 " --> pdb=" O VAL F 75 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'F' and resid 169 through 176 removed outlier: 3.585A pdb=" N ALA F 174 " --> pdb=" O CYS F 157 " (cutoff:3.500A) removed outlier: 4.157A pdb=" N CYS F 157 " --> pdb=" O ALA F 174 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N TYR F 191 " --> pdb=" O LEU F 129 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'F' and resid 259 through 260 removed outlier: 6.614A pdb=" N LEU F 260 " --> pdb=" O THR F 450 " (cutoff:3.500A) removed outlier: 4.169A pdb=" N VAL F 292 " --> pdb=" O ILE F 449 " (cutoff:3.500A) removed outlier: 7.559A pdb=" N GLY F 451 " --> pdb=" O THR F 290 " (cutoff:3.500A) removed outlier: 11.279A pdb=" N THR F 290 " --> pdb=" O GLY F 451 " (cutoff:3.500A) removed outlier: 12.407A pdb=" N LEU F 453 " --> pdb=" O LEU F 288 " (cutoff:3.500A) removed outlier: 12.321A pdb=" N LEU F 288 " --> pdb=" O LEU F 453 " (cutoff:3.500A) removed outlier: 11.092A pdb=" N THR F 455 " --> pdb=" O VAL F 286 " (cutoff:3.500A) removed outlier: 11.485A pdb=" N VAL F 286 " --> pdb=" O THR F 455 " (cutoff:3.500A) removed outlier: 11.768A pdb=" N ASP F 457 " --> pdb=" O ILE F 284 " (cutoff:3.500A) removed outlier: 12.582A pdb=" N ILE F 284 " --> pdb=" O ASP F 457 " (cutoff:3.500A) removed outlier: 6.247A pdb=" N GLU F 293 " --> pdb=" O SER F 334 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N SER F 334 " --> pdb=" O GLU F 293 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N PHE F 382 " --> pdb=" O LYS F 421 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N GLU F 381 " --> pdb=" O CYS F 378 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N CYS F 378 " --> pdb=" O GLU F 381 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'F' and resid 271 through 273 removed outlier: 12.582A pdb=" N ILE F 284 " --> pdb=" O ASP F 457 " (cutoff:3.500A) removed outlier: 11.768A pdb=" N ASP F 457 " --> pdb=" O ILE F 284 " (cutoff:3.500A) removed outlier: 11.485A pdb=" N VAL F 286 " --> pdb=" O THR F 455 " (cutoff:3.500A) removed outlier: 11.092A pdb=" N THR F 455 " --> pdb=" O VAL F 286 " (cutoff:3.500A) removed outlier: 12.321A pdb=" N LEU F 288 " --> pdb=" O LEU F 453 " (cutoff:3.500A) removed outlier: 12.407A pdb=" N LEU F 453 " --> pdb=" O LEU F 288 " (cutoff:3.500A) removed outlier: 11.279A pdb=" N THR F 290 " --> pdb=" O GLY F 451 " (cutoff:3.500A) removed outlier: 7.559A pdb=" N GLY F 451 " --> pdb=" O THR F 290 " (cutoff:3.500A) removed outlier: 4.169A pdb=" N VAL F 292 " --> pdb=" O ILE F 449 " (cutoff:3.500A) removed outlier: 4.106A pdb=" N THR F 467 " --> pdb=" O ASP F 457 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'F' and resid 304 through 308 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 3 through 6 removed outlier: 4.040A pdb=" N VAL H 5 " --> pdb=" O ALA H 23 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N ALA H 23 " --> pdb=" O VAL H 5 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'H' and resid 10 through 12 removed outlier: 6.391A pdb=" N GLU H 10 " --> pdb=" O THR H 124 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC6 Processing sheet with id=AC7, first strand: chain 'H' and resid 59 through 60 removed outlier: 4.060A pdb=" N ASN H 59 " --> pdb=" O TRP H 50 " (cutoff:3.500A) removed outlier: 5.720A pdb=" N TRP H 47 " --> pdb=" O ARG H 38 " (cutoff:3.500A) removed outlier: 6.942A pdb=" N ARG H 38 " --> pdb=" O TRP H 47 " (cutoff:3.500A) removed outlier: 4.325A pdb=" N GLY H 49 " --> pdb=" O TRP H 36 " (cutoff:3.500A) removed outlier: 4.744A pdb=" N TYR H 33 " --> pdb=" O GLY H 99 " (cutoff:3.500A) removed outlier: 4.459A pdb=" N HIS H 116 " --> pdb=" O THR H 98 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'I' and resid 248 through 253 removed outlier: 3.597A pdb=" N ILE I 248 " --> pdb=" O ILE I 307 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N SER I 299 " --> pdb=" O THR I 302 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N SER I 304 " --> pdb=" O SER I 297 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'I' and resid 277 through 280 removed outlier: 3.708A pdb=" N LEU I 279 " --> pdb=" O TRP I 267 " (cutoff:3.500A) removed outlier: 6.150A pdb=" N TRP I 267 " --> pdb=" O LEU I 279 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'I' and resid 277 through 280 removed outlier: 3.708A pdb=" N LEU I 279 " --> pdb=" O TRP I 267 " (cutoff:3.500A) removed outlier: 6.150A pdb=" N TRP I 267 " --> pdb=" O LEU I 279 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'K' and resid 495 through 499 removed outlier: 3.976A 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 47 Processing sheet with id=AD4, first strand: chain 'K' and resid 55 through 56 removed outlier: 4.101A pdb=" N SER K 56 " --> pdb=" O VAL K 75 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD4 Processing sheet with id=AD5, first strand: chain 'K' and resid 91 through 94 removed outlier: 4.195A pdb=" N GLU K 91 " --> pdb=" O CYS K 239 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N GLY K 237 " --> pdb=" O PHE K 93 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'K' and resid 129 through 130 removed outlier: 3.546A pdb=" N TYR K 191 " --> pdb=" O LEU K 129 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'K' and resid 155 through 161 removed outlier: 4.080A pdb=" N CYS K 157 " --> pdb=" O ALA K 174 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N ALA K 174 " --> pdb=" O CYS K 157 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N LYS K 170 " --> pdb=" O THR K 161 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'K' and resid 259 through 260 removed outlier: 3.770A pdb=" N GLY K 451 " --> pdb=" O LEU K 260 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ARG K 273 " --> pdb=" O ILE K 285 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'K' and resid 259 through 260 removed outlier: 3.770A pdb=" N GLY K 451 " --> pdb=" O LEU K 260 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'K' and resid 330 through 333 removed outlier: 3.692A pdb=" N HIS K 330 " --> pdb=" O THR K 297 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'K' and resid 304 through 309 removed outlier: 4.014A pdb=" N GLN K 315 " --> pdb=" O ILE K 309 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'K' and resid 359 through 360 removed outlier: 3.747A pdb=" N ILE K 359 " --> pdb=" O TYR K 395 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N TYR K 395 " --> pdb=" O ILE K 359 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE3 Processing sheet with id=AE4, first strand: chain 'K' and resid 374 through 375 removed outlier: 3.516A pdb=" N PHE K 382 " --> pdb=" O LYS K 421 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'K' and resid 423 through 424 Processing sheet with id=AE6, first strand: chain 'M' and resid 10 through 12 removed outlier: 3.684A pdb=" N THR M 124 " --> pdb=" O GLU M 10 " (cutoff:3.500A) removed outlier: 4.157A pdb=" N VAL M 93 " --> pdb=" O LEU M 39 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N VAL M 37 " --> pdb=" O TYR M 95 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N HIS M 35 " --> pdb=" O VAL M 97 " (cutoff:3.500A) removed outlier: 4.450A pdb=" N TYR M 33 " --> pdb=" O GLY M 99 " (cutoff:3.500A) removed outlier: 4.050A pdb=" N GLY M 49 " --> pdb=" O TRP M 36 " (cutoff:3.500A) removed outlier: 6.406A pdb=" N ARG M 38 " --> pdb=" O TRP M 47 " (cutoff:3.500A) removed outlier: 4.849A pdb=" N TRP M 47 " --> pdb=" O ARG M 38 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'M' and resid 20 through 22 removed outlier: 3.967A pdb=" N VAL M 20 " --> pdb=" O MET M 81 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N THR M 78 " --> pdb=" O ASP M 73 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N THR M 71 " --> pdb=" O TYR M 80 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'N' and resid 239 through 240 Processing sheet with id=AE9, first strand: chain 'N' and resid 249 through 253 removed outlier: 3.637A pdb=" N THR N 302 " --> pdb=" O SER N 299 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N SER N 304 " --> pdb=" O SER N 297 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'N' and resid 274 through 281 removed outlier: 5.314A pdb=" N ALA N 275 " --> pdb=" O HIS N 271 " (cutoff:3.500A) removed outlier: 5.399A pdb=" N HIS N 271 " --> pdb=" O ALA N 275 " (cutoff:3.500A) removed outlier: 6.453A pdb=" N TRP N 267 " --> pdb=" O LEU N 279 " (cutoff:3.500A) removed outlier: 4.243A pdb=" N TYR N 281 " --> pdb=" O VAL N 265 " (cutoff:3.500A) removed outlier: 6.424A pdb=" N VAL N 265 " --> pdb=" O TYR N 281 " (cutoff:3.500A) 503 hydrogen bonds defined for protein. 1305 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 7.13 Time building geometry restraints manager: 6.50 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.35: 6264 1.35 - 1.48: 5496 1.48 - 1.61: 8526 1.61 - 1.74: 3 1.74 - 1.88: 174 Bond restraints: 20463 Sorted by residual: bond pdb=" CA GLN K 258 " pdb=" C GLN K 258 " ideal model delta sigma weight residual 1.527 1.455 0.072 1.21e-02 6.83e+03 3.54e+01 bond pdb=" C1 MAN R 11 " pdb=" C2 MAN R 11 " ideal model delta sigma weight residual 1.526 1.631 -0.105 2.00e-02 2.50e+03 2.77e+01 bond pdb=" C1 MAN R 7 " pdb=" C2 MAN R 7 " ideal model delta sigma weight residual 1.526 1.615 -0.089 2.00e-02 2.50e+03 1.98e+01 bond pdb=" C1 MAN J 8 " pdb=" C2 MAN J 8 " ideal model delta sigma weight residual 1.526 1.614 -0.088 2.00e-02 2.50e+03 1.93e+01 bond pdb=" CA GLU K 370 " pdb=" C GLU K 370 " ideal model delta sigma weight residual 1.525 1.581 -0.056 1.35e-02 5.49e+03 1.74e+01 ... (remaining 20458 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.13: 27043 3.13 - 6.27: 739 6.27 - 9.40: 58 9.40 - 12.53: 7 12.53 - 15.67: 2 Bond angle restraints: 27849 Sorted by residual: angle pdb=" C ASN K 67 " pdb=" N VAL K 68 " pdb=" CA VAL K 68 " ideal model delta sigma weight residual 121.70 136.00 -14.30 1.80e+00 3.09e-01 6.31e+01 angle pdb=" C ASN F 67 " pdb=" N VAL F 68 " pdb=" CA VAL F 68 " ideal model delta sigma weight residual 121.70 133.76 -12.06 1.80e+00 3.09e-01 4.49e+01 angle pdb=" C SER D 326 " pdb=" N ALA D 327 " pdb=" CA ALA D 327 " ideal model delta sigma weight residual 121.70 132.16 -10.46 1.80e+00 3.09e-01 3.38e+01 angle pdb=" C ASN A 67 " pdb=" N VAL A 68 " pdb=" CA VAL A 68 " ideal model delta sigma weight residual 121.70 131.90 -10.20 1.80e+00 3.09e-01 3.21e+01 angle pdb=" C SER N 326 " pdb=" N ALA N 327 " pdb=" CA ALA N 327 " ideal model delta sigma weight residual 121.70 131.82 -10.12 1.80e+00 3.09e-01 3.16e+01 ... (remaining 27844 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.58: 12136 22.58 - 45.15: 683 45.15 - 67.73: 88 67.73 - 90.31: 95 90.31 - 112.88: 48 Dihedral angle restraints: 13050 sinusoidal: 5940 harmonic: 7110 Sorted by residual: dihedral pdb=" CA CYS K 247 " pdb=" C CYS K 247 " pdb=" N THR K 248 " pdb=" CA THR K 248 " ideal model delta harmonic sigma weight residual -180.00 -128.62 -51.38 0 5.00e+00 4.00e-02 1.06e+02 dihedral pdb=" CB CYS K 228 " pdb=" SG CYS K 228 " pdb=" SG CYS K 239 " pdb=" CB CYS K 239 " ideal model delta sinusoidal sigma weight residual -86.00 0.39 -86.39 1 1.00e+01 1.00e-02 9.00e+01 dihedral pdb=" CB CYS K 501 " pdb=" SG CYS K 501 " pdb=" SG CYS L 605 " pdb=" CB CYS L 605 " ideal model delta sinusoidal sigma weight residual -86.00 0.30 -86.30 1 1.00e+01 1.00e-02 8.98e+01 ... (remaining 13047 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.061: 2517 0.061 - 0.122: 628 0.122 - 0.183: 139 0.183 - 0.244: 28 0.244 - 0.305: 15 Chirality restraints: 3327 Sorted by residual: chirality pdb=" C1 MAN R 11 " pdb=" O2 MAN R 10 " pdb=" C2 MAN R 11 " pdb=" O5 MAN R 11 " both_signs ideal model delta sigma weight residual False 2.40 2.36 0.04 2.00e-02 2.50e+03 3.77e+00 chirality pdb=" CA PRO D 272 " pdb=" N PRO D 272 " pdb=" C PRO D 272 " pdb=" CB PRO D 272 " both_signs ideal model delta sigma weight residual False 2.72 2.41 0.31 2.00e-01 2.50e+01 2.33e+00 chirality pdb=" C5 BMA T 3 " pdb=" C4 BMA T 3 " pdb=" C6 BMA T 3 " pdb=" O5 BMA T 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.58 0.30 2.00e-01 2.50e+01 2.28e+00 ... (remaining 3324 not shown) Planarity restraints: 3468 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C HIS D 271 " -0.098 5.00e-02 4.00e+02 1.51e-01 3.65e+01 pdb=" N PRO D 272 " 0.261 5.00e-02 4.00e+02 pdb=" CA PRO D 272 " -0.089 5.00e-02 4.00e+02 pdb=" CD PRO D 272 " -0.074 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TRP M 36 " -0.003 2.00e-02 2.50e+03 2.22e-02 1.23e+01 pdb=" CG TRP M 36 " -0.002 2.00e-02 2.50e+03 pdb=" CD1 TRP M 36 " -0.000 2.00e-02 2.50e+03 pdb=" CD2 TRP M 36 " 0.015 2.00e-02 2.50e+03 pdb=" NE1 TRP M 36 " -0.021 2.00e-02 2.50e+03 pdb=" CE2 TRP M 36 " -0.010 2.00e-02 2.50e+03 pdb=" CE3 TRP M 36 " 0.031 2.00e-02 2.50e+03 pdb=" CZ2 TRP M 36 " 0.040 2.00e-02 2.50e+03 pdb=" CZ3 TRP M 36 " -0.038 2.00e-02 2.50e+03 pdb=" CH2 TRP M 36 " -0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP K 338 " 0.024 2.00e-02 2.50e+03 2.14e-02 1.15e+01 pdb=" CG TRP K 338 " -0.058 2.00e-02 2.50e+03 pdb=" CD1 TRP K 338 " 0.025 2.00e-02 2.50e+03 pdb=" CD2 TRP K 338 " -0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP K 338 " -0.002 2.00e-02 2.50e+03 pdb=" CE2 TRP K 338 " 0.002 2.00e-02 2.50e+03 pdb=" CE3 TRP K 338 " 0.004 2.00e-02 2.50e+03 pdb=" CZ2 TRP K 338 " 0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP K 338 " 0.002 2.00e-02 2.50e+03 pdb=" CH2 TRP K 338 " 0.003 2.00e-02 2.50e+03 ... (remaining 3465 not shown) Histogram of nonbonded interaction distances: 2.00 - 2.58: 216 2.58 - 3.16: 16854 3.16 - 3.74: 28691 3.74 - 4.32: 39941 4.32 - 4.90: 65398 Nonbonded interactions: 151100 Sorted by model distance: nonbonded pdb=" OG1 THR A 163 " pdb=" OE1 GLU A 164 " model vdw 2.002 3.040 nonbonded pdb=" OG SER I 299 " pdb=" O THR I 302 " model vdw 2.042 3.040 nonbonded pdb=" OG1 THR F 163 " pdb=" OE1 GLU F 164 " model vdw 2.047 3.040 nonbonded pdb=" O VAL F 36 " pdb=" OG1 THR G 606 " model vdw 2.060 3.040 nonbonded pdb=" OG1 THR F 161 " pdb=" O LYS F 170 " model vdw 2.077 3.040 ... (remaining 151095 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 'J' selection = chain 'V' } ncs_group { reference = chain 'O' selection = chain 'P' selection = chain 'S' selection = chain 'T' } ncs_group { reference = chain 'Q' selection = chain 'U' } ncs_group { reference = chain 'W' 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.270 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.810 Check model and map are aligned: 0.140 Set scattering table: 0.200 Process input model: 46.300 Find NCS groups from input model: 0.760 Set up NCS constraints: 0.130 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.870 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 53.510 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7002 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 : 0.008 0.105 20574 Z= 0.396 Angle : 1.236 15.665 28137 Z= 0.642 Chirality : 0.061 0.305 3327 Planarity : 0.008 0.151 3456 Dihedral : 17.265 112.884 8367 Min Nonbonded Distance : 2.002 Molprobity Statistics. All-atom Clashscore : 4.09 Ramachandran Plot: Outliers : 0.45 % Allowed : 8.66 % Favored : 90.89 % Rotamer: Outliers : 0.00 % Allowed : 0.28 % Favored : 99.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.38 % Twisted Proline : 0.95 % Twisted General : 0.21 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.16 (0.15), residues: 2448 helix: -2.10 (0.26), residues: 298 sheet: -1.75 (0.20), residues: 590 loop : -2.34 (0.14), residues: 1560 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.058 0.003 TRP K 338 HIS 0.028 0.004 HIS N 270 PHE 0.029 0.004 PHE F 468 TYR 0.034 0.003 TYR A 486 ARG 0.057 0.002 ARG L 542 Details of bonding type rmsd link_NAG-ASN : bond 0.01137 ( 12) link_NAG-ASN : angle 2.95607 ( 36) link_ALPHA1-6 : bond 0.01302 ( 10) link_ALPHA1-6 : angle 3.66093 ( 30) link_BETA1-4 : bond 0.01202 ( 24) link_BETA1-4 : angle 4.89971 ( 72) link_ALPHA1-2 : bond 0.01555 ( 11) link_ALPHA1-2 : angle 4.79578 ( 33) link_ALPHA1-3 : bond 0.01021 ( 9) link_ALPHA1-3 : angle 4.02625 ( 27) hydrogen bonds : bond 0.27455 ( 486) hydrogen bonds : angle 10.44079 ( 1305) SS BOND : bond 0.00663 ( 45) SS BOND : angle 2.15913 ( 90) covalent geometry : bond 0.00819 (20463) covalent geometry : angle 1.18206 (27849) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4896 Ramachandran restraints generated. 2448 Oldfield, 0 Emsley, 2448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4896 Ramachandran restraints generated. 2448 Oldfield, 0 Emsley, 2448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 748 residues out of total 2142 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 748 time to evaluate : 2.141 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 114 GLN cc_start: 0.7733 (tt0) cc_final: 0.7447 (tt0) REVERT: A 154 MET cc_start: 0.8638 (pmm) cc_final: 0.8139 (pmm) REVERT: B 530 MET cc_start: 0.8283 (mmm) cc_final: 0.7958 (mpp) REVERT: C 101 TRP cc_start: 0.7573 (t60) cc_final: 0.7113 (t60) REVERT: D 282 GLU cc_start: 0.7676 (mt-10) cc_final: 0.7288 (mt-10) REVERT: D 301 ASN cc_start: 0.8315 (m-40) cc_final: 0.7992 (t0) REVERT: D 326 SER cc_start: 0.7837 (m) cc_final: 0.6917 (p) REVERT: F 104 MET cc_start: 0.8814 (ttt) cc_final: 0.8517 (ttt) REVERT: F 161 THR cc_start: 0.6053 (p) cc_final: 0.5741 (p) REVERT: F 268 LYS cc_start: 0.8109 (ptmt) cc_final: 0.7851 (mttm) REVERT: F 318 TYR cc_start: 0.8362 (m-80) cc_final: 0.7829 (m-10) REVERT: F 427 TRP cc_start: 0.7686 (m-90) cc_final: 0.7459 (m-90) REVERT: G 610 TRP cc_start: 0.6804 (t-100) cc_final: 0.6081 (t-100) REVERT: H 84 ARG cc_start: 0.7175 (mpp80) cc_final: 0.6712 (mtm110) REVERT: I 305 LEU cc_start: 0.5430 (mp) cc_final: 0.4661 (tt) REVERT: I 326 SER cc_start: 0.7351 (m) cc_final: 0.6950 (p) REVERT: K 42 VAL cc_start: 0.9196 (t) cc_final: 0.8925 (p) REVERT: K 84 LEU cc_start: 0.7241 (tp) cc_final: 0.7010 (tt) REVERT: K 96 TRP cc_start: 0.7900 (m-90) cc_final: 0.7103 (m-90) REVERT: L 603 ILE cc_start: 0.9049 (mm) cc_final: 0.8832 (tt) REVERT: L 645 LEU cc_start: 0.8330 (mt) cc_final: 0.8019 (tp) REVERT: L 647 GLU cc_start: 0.6995 (pp20) cc_final: 0.6778 (pp20) REVERT: M 3 GLN cc_start: 0.7409 (tm-30) cc_final: 0.7004 (tm-30) REVERT: M 38 ARG cc_start: 0.7475 (ttp-170) cc_final: 0.7058 (ttp80) REVERT: M 103 SER cc_start: 0.8523 (t) cc_final: 0.8222 (p) REVERT: N 259 VAL cc_start: 0.8093 (t) cc_final: 0.7117 (p) REVERT: N 267 TRP cc_start: 0.7822 (m100) cc_final: 0.7586 (m100) REVERT: N 279 LEU cc_start: 0.8761 (pp) cc_final: 0.8504 (pp) REVERT: N 301 ASN cc_start: 0.7542 (m-40) cc_final: 0.6853 (t0) REVERT: N 336 LYS cc_start: 0.8700 (tptt) cc_final: 0.8429 (tppt) outliers start: 0 outliers final: 0 residues processed: 748 average time/residue: 0.3273 time to fit residues: 362.0775 Evaluate side-chains 371 residues out of total 2142 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 371 time to evaluate : 2.026 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: chunk 205 optimal weight: 0.9990 chunk 184 optimal weight: 1.9990 chunk 102 optimal weight: 0.7980 chunk 62 optimal weight: 0.7980 chunk 124 optimal weight: 0.9980 chunk 98 optimal weight: 0.0070 chunk 190 optimal weight: 3.9990 chunk 73 optimal weight: 1.9990 chunk 115 optimal weight: 0.7980 chunk 141 optimal weight: 0.9990 chunk 220 optimal weight: 6.9990 overall best weight: 0.6798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 577 GLN B 653 GLN D 271 HIS ** F 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 287 HIS F 300 ASN F 330 HIS G 577 GLN G 630 GLN ** H 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 116 HIS L 651 ASN L 653 GLN ** M 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4057 r_free = 0.4057 target = 0.150932 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3662 r_free = 0.3662 target = 0.120491 restraints weight = 43920.717| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3673 r_free = 0.3673 target = 0.122592 restraints weight = 30277.022| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3684 r_free = 0.3684 target = 0.123329 restraints weight = 23833.423| |-----------------------------------------------------------------------------| r_work (final): 0.3684 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7462 moved from start: 0.3542 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 20574 Z= 0.176 Angle : 0.850 12.949 28137 Z= 0.422 Chirality : 0.050 0.267 3327 Planarity : 0.006 0.097 3456 Dihedral : 13.044 84.161 3954 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 7.07 Ramachandran Plot: Outliers : 0.33 % Allowed : 6.05 % Favored : 93.63 % Rotamer: Outliers : 3.03 % Allowed : 13.63 % Favored : 83.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.38 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.68 (0.16), residues: 2448 helix: -1.30 (0.28), residues: 312 sheet: -1.40 (0.19), residues: 657 loop : -2.14 (0.15), residues: 1479 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP K 479 HIS 0.008 0.002 HIS F 249 PHE 0.033 0.002 PHE C 114 TYR 0.019 0.002 TYR K 217 ARG 0.005 0.001 ARG H 38 Details of bonding type rmsd link_NAG-ASN : bond 0.00562 ( 12) link_NAG-ASN : angle 1.82656 ( 36) link_ALPHA1-6 : bond 0.01520 ( 10) link_ALPHA1-6 : angle 2.40158 ( 30) link_BETA1-4 : bond 0.00955 ( 24) link_BETA1-4 : angle 3.16274 ( 72) link_ALPHA1-2 : bond 0.01332 ( 11) link_ALPHA1-2 : angle 2.82907 ( 33) link_ALPHA1-3 : bond 0.01051 ( 9) link_ALPHA1-3 : angle 1.95671 ( 27) hydrogen bonds : bond 0.05085 ( 486) hydrogen bonds : angle 6.98405 ( 1305) SS BOND : bond 0.00621 ( 45) SS BOND : angle 1.68202 ( 90) covalent geometry : bond 0.00383 (20463) covalent geometry : angle 0.81956 (27849) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4896 Ramachandran restraints generated. 2448 Oldfield, 0 Emsley, 2448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4896 Ramachandran restraints generated. 2448 Oldfield, 0 Emsley, 2448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 489 residues out of total 2142 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 424 time to evaluate : 2.043 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 57 ASP cc_start: 0.6511 (t0) cc_final: 0.6096 (p0) REVERT: A 83 GLU cc_start: 0.7678 (tm-30) cc_final: 0.7395 (tm-30) REVERT: A 128 THR cc_start: 0.8804 (p) cc_final: 0.8591 (t) REVERT: A 180 ASP cc_start: 0.7968 (p0) cc_final: 0.7730 (p0) REVERT: A 184 LEU cc_start: 0.8486 (tt) cc_final: 0.6791 (tp) REVERT: B 530 MET cc_start: 0.8898 (mmm) cc_final: 0.8235 (mpp) REVERT: B 656 ASN cc_start: 0.8063 (t0) cc_final: 0.7806 (t0) REVERT: C 101 TRP cc_start: 0.8058 (t60) cc_final: 0.7397 (t60) REVERT: D 282 GLU cc_start: 0.7718 (mt-10) cc_final: 0.7409 (mt-10) REVERT: D 301 ASN cc_start: 0.8566 (m-40) cc_final: 0.8164 (m-40) REVERT: F 104 MET cc_start: 0.9045 (ttt) cc_final: 0.8654 (ttm) REVERT: F 268 LYS cc_start: 0.8344 (ptmt) cc_final: 0.7893 (mttm) REVERT: F 318 TYR cc_start: 0.7906 (m-80) cc_final: 0.7633 (m-10) REVERT: F 387 THR cc_start: 0.8090 (p) cc_final: 0.7549 (t) REVERT: F 426 MET cc_start: 0.7823 (OUTLIER) cc_final: 0.7564 (ptp) REVERT: G 630 GLN cc_start: 0.8858 (OUTLIER) cc_final: 0.8323 (mp10) REVERT: H 39 LEU cc_start: 0.8327 (mt) cc_final: 0.8083 (mt) REVERT: H 84 ARG cc_start: 0.7329 (mpp80) cc_final: 0.7039 (mtm180) REVERT: I 305 LEU cc_start: 0.5607 (mp) cc_final: 0.4648 (tt) REVERT: K 96 TRP cc_start: 0.7917 (m-90) cc_final: 0.7189 (m-90) REVERT: L 646 LEU cc_start: 0.9269 (OUTLIER) cc_final: 0.9062 (mm) REVERT: M 10 GLU cc_start: 0.6925 (pm20) cc_final: 0.6724 (pm20) REVERT: M 103 SER cc_start: 0.8753 (t) cc_final: 0.8545 (p) REVERT: N 301 ASN cc_start: 0.7459 (m-40) cc_final: 0.7037 (t0) outliers start: 65 outliers final: 36 residues processed: 459 average time/residue: 0.3049 time to fit residues: 217.3657 Evaluate side-chains 370 residues out of total 2142 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 331 time to evaluate : 2.096 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 VAL Chi-restraints excluded: chain A residue 90 THR Chi-restraints excluded: chain A residue 202 THR Chi-restraints excluded: chain A residue 245 VAL Chi-restraints excluded: chain A residue 297 THR Chi-restraints excluded: chain A residue 450 THR Chi-restraints excluded: chain B residue 592 LEU Chi-restraints excluded: chain B residue 641 ILE Chi-restraints excluded: chain D residue 248 ILE Chi-restraints excluded: chain D residue 306 THR Chi-restraints excluded: chain D residue 307 ILE Chi-restraints excluded: chain F residue 84 LEU Chi-restraints excluded: chain F residue 182 VAL Chi-restraints excluded: chain F residue 201 CYS Chi-restraints excluded: chain F residue 288 LEU Chi-restraints excluded: chain F residue 377 ASN Chi-restraints excluded: chain F residue 426 MET Chi-restraints excluded: chain G residue 529 THR Chi-restraints excluded: chain G residue 580 VAL Chi-restraints excluded: chain G residue 615 SER Chi-restraints excluded: chain G residue 623 TRP Chi-restraints excluded: chain G residue 624 ASP Chi-restraints excluded: chain G residue 630 GLN Chi-restraints excluded: chain H residue 18 VAL Chi-restraints excluded: chain H residue 28 THR Chi-restraints excluded: chain H residue 74 THR Chi-restraints excluded: chain I residue 253 THR Chi-restraints excluded: chain K residue 46 LYS Chi-restraints excluded: chain K residue 72 HIS Chi-restraints excluded: chain K residue 128 THR Chi-restraints excluded: chain K residue 182 VAL Chi-restraints excluded: chain K residue 215 ILE Chi-restraints excluded: chain K residue 249 HIS Chi-restraints excluded: chain K residue 445 CYS Chi-restraints excluded: chain L residue 580 VAL Chi-restraints excluded: chain L residue 608 VAL Chi-restraints excluded: chain L residue 646 LEU Chi-restraints excluded: chain M residue 115 ASP Chi-restraints excluded: chain N residue 265 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: chunk 213 optimal weight: 0.9990 chunk 207 optimal weight: 2.9990 chunk 122 optimal weight: 5.9990 chunk 168 optimal weight: 3.9990 chunk 46 optimal weight: 0.0170 chunk 2 optimal weight: 3.9990 chunk 48 optimal weight: 0.9980 chunk 101 optimal weight: 4.9990 chunk 153 optimal weight: 0.9990 chunk 64 optimal weight: 5.9990 chunk 37 optimal weight: 0.9980 overall best weight: 0.8022 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 63 ASN D 246 GLN F 187 ASN F 362 ASN ** G 575 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 591 GLN ** G 630 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 62 GLN ** L 575 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 63 ASN ** M 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3995 r_free = 0.3995 target = 0.145966 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3573 r_free = 0.3573 target = 0.114384 restraints weight = 42913.881| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3589 r_free = 0.3589 target = 0.116591 restraints weight = 28542.070| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3603 r_free = 0.3603 target = 0.117625 restraints weight = 21675.541| |-----------------------------------------------------------------------------| r_work (final): 0.3603 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7585 moved from start: 0.4393 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 20574 Z= 0.173 Angle : 0.796 14.090 28137 Z= 0.390 Chirality : 0.049 0.224 3327 Planarity : 0.005 0.078 3456 Dihedral : 9.792 59.869 3954 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 8.34 Ramachandran Plot: Outliers : 0.33 % Allowed : 6.33 % Favored : 93.34 % Rotamer: Outliers : 3.83 % Allowed : 16.25 % Favored : 79.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.38 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.42 (0.16), residues: 2448 helix: -0.81 (0.29), residues: 314 sheet: -1.18 (0.19), residues: 639 loop : -2.06 (0.15), residues: 1495 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.002 TRP D 267 HIS 0.005 0.001 HIS K 216 PHE 0.026 0.002 PHE C 114 TYR 0.026 0.002 TYR N 278 ARG 0.006 0.001 ARG B 542 Details of bonding type rmsd link_NAG-ASN : bond 0.00460 ( 12) link_NAG-ASN : angle 1.86442 ( 36) link_ALPHA1-6 : bond 0.01824 ( 10) link_ALPHA1-6 : angle 3.01928 ( 30) link_BETA1-4 : bond 0.00753 ( 24) link_BETA1-4 : angle 2.70862 ( 72) link_ALPHA1-2 : bond 0.01574 ( 11) link_ALPHA1-2 : angle 2.91863 ( 33) link_ALPHA1-3 : bond 0.01113 ( 9) link_ALPHA1-3 : angle 1.39634 ( 27) hydrogen bonds : bond 0.04429 ( 486) hydrogen bonds : angle 6.25574 ( 1305) SS BOND : bond 0.00426 ( 45) SS BOND : angle 1.76778 ( 90) covalent geometry : bond 0.00367 (20463) covalent geometry : angle 0.76445 (27849) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4896 Ramachandran restraints generated. 2448 Oldfield, 0 Emsley, 2448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4896 Ramachandran restraints generated. 2448 Oldfield, 0 Emsley, 2448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 466 residues out of total 2142 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 384 time to evaluate : 2.111 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 49 LYS cc_start: 0.8847 (mtmt) cc_final: 0.8596 (mtpt) REVERT: A 57 ASP cc_start: 0.6861 (t0) cc_final: 0.6229 (p0) REVERT: A 83 GLU cc_start: 0.7787 (tm-30) cc_final: 0.7493 (tm-30) REVERT: B 530 MET cc_start: 0.8885 (mmm) cc_final: 0.8174 (mpp) REVERT: B 542 ARG cc_start: 0.7410 (ttp80) cc_final: 0.7144 (ttt-90) REVERT: B 656 ASN cc_start: 0.8234 (t0) cc_final: 0.7993 (t0) REVERT: C 60 GLN cc_start: 0.8118 (pm20) cc_final: 0.7355 (mm-40) REVERT: C 101 TRP cc_start: 0.8272 (t60) cc_final: 0.7547 (t60) REVERT: C 122 LEU cc_start: 0.8969 (OUTLIER) cc_final: 0.8766 (pp) REVERT: D 282 GLU cc_start: 0.7827 (mt-10) cc_final: 0.7369 (mt-10) REVERT: D 314 ASP cc_start: 0.7628 (m-30) cc_final: 0.7258 (m-30) REVERT: F 104 MET cc_start: 0.9047 (ttt) cc_final: 0.8453 (ttt) REVERT: F 268 LYS cc_start: 0.8381 (ptmt) cc_final: 0.7900 (mttm) REVERT: G 530 MET cc_start: 0.8392 (mpp) cc_final: 0.8171 (mpp) REVERT: H 84 ARG cc_start: 0.7446 (mpp80) cc_final: 0.7076 (mtm110) REVERT: I 259 VAL cc_start: 0.8545 (t) cc_final: 0.8116 (p) REVERT: I 284 LYS cc_start: 0.8431 (OUTLIER) cc_final: 0.7948 (mmtp) REVERT: K 288 LEU cc_start: 0.6750 (mm) cc_final: 0.6029 (mm) REVERT: L 529 THR cc_start: 0.8500 (p) cc_final: 0.8080 (t) REVERT: L 630 GLN cc_start: 0.8461 (OUTLIER) cc_final: 0.7537 (mp10) REVERT: L 633 LYS cc_start: 0.9137 (OUTLIER) cc_final: 0.8875 (pptt) REVERT: M 38 ARG cc_start: 0.7296 (ttm110) cc_final: 0.6704 (mtp85) REVERT: M 59 ASN cc_start: 0.8566 (t0) cc_final: 0.8006 (t0) REVERT: M 103 SER cc_start: 0.8961 (t) cc_final: 0.8755 (p) REVERT: N 301 ASN cc_start: 0.7771 (m-40) cc_final: 0.7314 (t0) outliers start: 82 outliers final: 48 residues processed: 427 average time/residue: 0.3046 time to fit residues: 205.5518 Evaluate side-chains 369 residues out of total 2142 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 317 time to evaluate : 2.118 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 VAL Chi-restraints excluded: chain A residue 95 MET Chi-restraints excluded: chain A residue 245 VAL Chi-restraints excluded: chain A residue 297 THR Chi-restraints excluded: chain A residue 372 THR Chi-restraints excluded: chain A residue 388 SER Chi-restraints excluded: chain B residue 537 LEU Chi-restraints excluded: chain B residue 592 LEU Chi-restraints excluded: chain B residue 641 ILE Chi-restraints excluded: chain C residue 28 THR Chi-restraints excluded: chain C residue 63 ASN Chi-restraints excluded: chain C residue 76 ILE Chi-restraints excluded: chain C residue 97 VAL Chi-restraints excluded: chain C residue 122 LEU Chi-restraints excluded: chain D residue 247 SER Chi-restraints excluded: chain D residue 248 ILE Chi-restraints excluded: chain D residue 306 THR Chi-restraints excluded: chain F residue 75 VAL Chi-restraints excluded: chain F residue 182 VAL Chi-restraints excluded: chain F residue 297 THR Chi-restraints excluded: chain F residue 446 ARG Chi-restraints excluded: chain F residue 450 THR Chi-restraints excluded: chain G residue 529 THR Chi-restraints excluded: chain G residue 581 LEU Chi-restraints excluded: chain G residue 615 SER Chi-restraints excluded: chain G residue 623 TRP Chi-restraints excluded: chain G residue 624 ASP Chi-restraints excluded: chain H residue 18 VAL Chi-restraints excluded: chain H residue 74 THR Chi-restraints excluded: chain H residue 97 VAL Chi-restraints excluded: chain I residue 284 LYS Chi-restraints excluded: chain I residue 326 SER Chi-restraints excluded: chain I residue 340 LEU Chi-restraints excluded: chain K residue 46 LYS Chi-restraints excluded: chain K residue 72 HIS Chi-restraints excluded: chain K residue 182 VAL Chi-restraints excluded: chain K residue 202 THR Chi-restraints excluded: chain K residue 215 ILE Chi-restraints excluded: chain K residue 249 HIS Chi-restraints excluded: chain K residue 289 HIS Chi-restraints excluded: chain K residue 434 MET Chi-restraints excluded: chain K residue 445 CYS Chi-restraints excluded: chain L residue 580 VAL Chi-restraints excluded: chain L residue 592 LEU Chi-restraints excluded: chain L residue 615 SER Chi-restraints excluded: chain L residue 630 GLN Chi-restraints excluded: chain L residue 633 LYS Chi-restraints excluded: chain M residue 13 ASN Chi-restraints excluded: chain M residue 97 VAL Chi-restraints excluded: chain M residue 115 ASP Chi-restraints excluded: chain N residue 265 VAL Chi-restraints excluded: chain N residue 314 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: chunk 199 optimal weight: 4.9990 chunk 114 optimal weight: 3.9990 chunk 23 optimal weight: 5.9990 chunk 158 optimal weight: 5.9990 chunk 73 optimal weight: 3.9990 chunk 205 optimal weight: 2.9990 chunk 179 optimal weight: 3.9990 chunk 3 optimal weight: 2.9990 chunk 156 optimal weight: 4.9990 chunk 214 optimal weight: 3.9990 chunk 70 optimal weight: 6.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 114 GLN A 280 ASN A 289 HIS A 300 ASN ** A 362 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 63 ASN C 116 HIS D 246 GLN ** F 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 105 HIS F 203 GLN ** I 236 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 651 ASN M 3 GLN ** M 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 246 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3792 r_free = 0.3792 target = 0.130579 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.098059 restraints weight = 43951.645| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.099347 restraints weight = 30124.631| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.100235 restraints weight = 24597.603| |-----------------------------------------------------------------------------| r_work (final): 0.3331 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7993 moved from start: 0.6167 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 0.108 20574 Z= 0.430 Angle : 1.094 16.943 28137 Z= 0.542 Chirality : 0.057 0.225 3327 Planarity : 0.007 0.102 3456 Dihedral : 9.391 59.046 3954 Min Nonbonded Distance : 2.388 Molprobity Statistics. All-atom Clashscore : 14.97 Ramachandran Plot: Outliers : 0.45 % Allowed : 8.46 % Favored : 91.09 % Rotamer: Outliers : 6.30 % Allowed : 18.77 % Favored : 74.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.38 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.78 (0.15), residues: 2448 helix: -1.26 (0.28), residues: 313 sheet: -1.31 (0.18), residues: 690 loop : -2.34 (0.14), residues: 1445 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.043 0.004 TRP M 47 HIS 0.015 0.003 HIS A 330 PHE 0.051 0.004 PHE C 114 TYR 0.032 0.003 TYR C 33 ARG 0.011 0.001 ARG A 59 Details of bonding type rmsd link_NAG-ASN : bond 0.00804 ( 12) link_NAG-ASN : angle 3.22119 ( 36) link_ALPHA1-6 : bond 0.01970 ( 10) link_ALPHA1-6 : angle 3.24315 ( 30) link_BETA1-4 : bond 0.00827 ( 24) link_BETA1-4 : angle 3.01676 ( 72) link_ALPHA1-2 : bond 0.01285 ( 11) link_ALPHA1-2 : angle 2.83421 ( 33) link_ALPHA1-3 : bond 0.00873 ( 9) link_ALPHA1-3 : angle 2.25371 ( 27) hydrogen bonds : bond 0.05816 ( 486) hydrogen bonds : angle 6.67837 ( 1305) SS BOND : bond 0.00842 ( 45) SS BOND : angle 2.47378 ( 90) covalent geometry : bond 0.00989 (20463) covalent geometry : angle 1.06110 (27849) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4896 Ramachandran restraints generated. 2448 Oldfield, 0 Emsley, 2448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4896 Ramachandran restraints generated. 2448 Oldfield, 0 Emsley, 2448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 475 residues out of total 2142 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 135 poor density : 340 time to evaluate : 2.134 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 117 LYS cc_start: 0.8749 (mmmt) cc_final: 0.8473 (mmtp) REVERT: A 280 ASN cc_start: 0.8677 (m-40) cc_final: 0.8160 (t0) REVERT: A 317 PHE cc_start: 0.9013 (OUTLIER) cc_final: 0.8019 (p90) REVERT: A 439 ILE cc_start: 0.9616 (tp) cc_final: 0.9305 (mm) REVERT: B 530 MET cc_start: 0.9186 (mmm) cc_final: 0.8774 (mpp) REVERT: B 632 ASP cc_start: 0.8504 (t0) cc_final: 0.8130 (t0) REVERT: B 634 GLU cc_start: 0.7593 (mt-10) cc_final: 0.7225 (mt-10) REVERT: D 280 ILE cc_start: 0.7877 (mm) cc_final: 0.7617 (mm) REVERT: D 314 ASP cc_start: 0.7702 (m-30) cc_final: 0.7315 (m-30) REVERT: F 268 LYS cc_start: 0.8497 (ptmt) cc_final: 0.8078 (mttm) REVERT: G 542 ARG cc_start: 0.8391 (tmt170) cc_final: 0.8189 (tmt170) REVERT: G 593 LEU cc_start: 0.9292 (OUTLIER) cc_final: 0.9080 (mp) REVERT: G 634 GLU cc_start: 0.7903 (mt-10) cc_final: 0.7582 (mt-10) REVERT: H 6 GLN cc_start: 0.6547 (pt0) cc_final: 0.5896 (pt0) REVERT: I 285 LYS cc_start: 0.6764 (OUTLIER) cc_final: 0.6415 (mtmm) REVERT: K 369 MET cc_start: 0.7472 (tpp) cc_final: 0.7092 (ttt) REVERT: K 427 TRP cc_start: 0.8372 (m-10) cc_final: 0.8104 (m-10) REVERT: M 38 ARG cc_start: 0.7957 (ttm170) cc_final: 0.7757 (mtp-110) REVERT: M 104 ASP cc_start: 0.8510 (t0) cc_final: 0.8281 (t70) REVERT: N 301 ASN cc_start: 0.8279 (m-40) cc_final: 0.7916 (t0) outliers start: 135 outliers final: 95 residues processed: 433 average time/residue: 0.2788 time to fit residues: 189.3230 Evaluate side-chains 380 residues out of total 2142 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 282 time to evaluate : 2.091 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 VAL Chi-restraints excluded: chain A residue 85 VAL Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 128 THR Chi-restraints excluded: chain A residue 198 THR Chi-restraints excluded: chain A residue 202 THR Chi-restraints excluded: chain A residue 215 ILE Chi-restraints excluded: chain A residue 245 VAL Chi-restraints excluded: chain A residue 288 LEU Chi-restraints excluded: chain A residue 297 THR Chi-restraints excluded: chain A residue 317 PHE Chi-restraints excluded: chain A residue 345 VAL Chi-restraints excluded: chain A residue 373 THR Chi-restraints excluded: chain A residue 388 SER Chi-restraints excluded: chain A residue 426 MET Chi-restraints excluded: chain A residue 446 ARG Chi-restraints excluded: chain A residue 450 THR Chi-restraints excluded: chain B residue 529 THR Chi-restraints excluded: chain B residue 537 LEU Chi-restraints excluded: chain B residue 545 LEU Chi-restraints excluded: chain B residue 641 ILE Chi-restraints excluded: chain C residue 28 THR Chi-restraints excluded: chain C residue 63 ASN Chi-restraints excluded: chain C residue 97 VAL Chi-restraints excluded: chain D residue 247 SER Chi-restraints excluded: chain D residue 248 ILE Chi-restraints excluded: chain D residue 250 ILE Chi-restraints excluded: chain D residue 255 THR Chi-restraints excluded: chain D residue 259 VAL Chi-restraints excluded: chain D residue 306 THR Chi-restraints excluded: chain D residue 340 LEU Chi-restraints excluded: chain F residue 111 LEU Chi-restraints excluded: chain F residue 120 VAL Chi-restraints excluded: chain F residue 182 VAL Chi-restraints excluded: chain F residue 202 THR Chi-restraints excluded: chain F residue 215 ILE Chi-restraints excluded: chain F residue 217 TYR Chi-restraints excluded: chain F residue 271 VAL Chi-restraints excluded: chain F residue 345 VAL Chi-restraints excluded: chain F residue 377 ASN Chi-restraints excluded: chain F residue 378 CYS Chi-restraints excluded: chain F residue 387 THR Chi-restraints excluded: chain F residue 446 ARG Chi-restraints excluded: chain F residue 450 THR Chi-restraints excluded: chain G residue 529 THR Chi-restraints excluded: chain G residue 583 VAL Chi-restraints excluded: chain G residue 593 LEU Chi-restraints excluded: chain G residue 595 ILE Chi-restraints excluded: chain G residue 606 THR Chi-restraints excluded: chain G residue 608 VAL Chi-restraints excluded: chain G residue 615 SER Chi-restraints excluded: chain G residue 624 ASP Chi-restraints excluded: chain G residue 626 MET Chi-restraints excluded: chain H residue 18 VAL Chi-restraints excluded: chain H residue 73 ASP Chi-restraints excluded: chain H residue 74 THR Chi-restraints excluded: chain H residue 97 VAL Chi-restraints excluded: chain H residue 98 THR Chi-restraints excluded: chain I residue 248 ILE Chi-restraints excluded: chain I residue 285 LYS Chi-restraints excluded: chain I residue 295 SER Chi-restraints excluded: chain I residue 340 LEU Chi-restraints excluded: chain K residue 34 LEU Chi-restraints excluded: chain K residue 42 VAL Chi-restraints excluded: chain K residue 85 VAL Chi-restraints excluded: chain K residue 95 MET Chi-restraints excluded: chain K residue 113 ASP Chi-restraints excluded: chain K residue 120 VAL Chi-restraints excluded: chain K residue 182 VAL Chi-restraints excluded: chain K residue 202 THR Chi-restraints excluded: chain K residue 213 ILE Chi-restraints excluded: chain K residue 215 ILE Chi-restraints excluded: chain K residue 217 TYR Chi-restraints excluded: chain K residue 218 CYS Chi-restraints excluded: chain K residue 245 VAL Chi-restraints excluded: chain K residue 249 HIS Chi-restraints excluded: chain K residue 271 VAL Chi-restraints excluded: chain K residue 292 VAL Chi-restraints excluded: chain K residue 374 HIS Chi-restraints excluded: chain K residue 434 MET Chi-restraints excluded: chain K residue 445 CYS Chi-restraints excluded: chain K residue 501 CYS Chi-restraints excluded: chain L residue 539 VAL Chi-restraints excluded: chain L residue 580 VAL Chi-restraints excluded: chain L residue 581 LEU Chi-restraints excluded: chain L residue 592 LEU Chi-restraints excluded: chain L residue 608 VAL Chi-restraints excluded: chain L residue 615 SER Chi-restraints excluded: chain M residue 3 GLN Chi-restraints excluded: chain M residue 13 ASN Chi-restraints excluded: chain M residue 39 LEU Chi-restraints excluded: chain M residue 72 ARG Chi-restraints excluded: chain M residue 97 VAL Chi-restraints excluded: chain M residue 115 ASP Chi-restraints excluded: chain N residue 259 VAL Chi-restraints excluded: chain N residue 265 VAL Chi-restraints excluded: chain N residue 314 ASP Chi-restraints excluded: chain N residue 339 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: chunk 242 optimal weight: 3.9990 chunk 192 optimal weight: 0.7980 chunk 43 optimal weight: 0.6980 chunk 140 optimal weight: 0.9980 chunk 4 optimal weight: 0.1980 chunk 132 optimal weight: 0.9980 chunk 29 optimal weight: 0.6980 chunk 31 optimal weight: 1.9990 chunk 156 optimal weight: 2.9990 chunk 102 optimal weight: 0.9980 chunk 208 optimal weight: 0.0770 overall best weight: 0.4938 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 63 ASN D 246 GLN ** F 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 6 GLN H 62 GLN H 63 ASN H 119 GLN ** I 236 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 311 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 246 GLN ** L 575 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 3 GLN ** M 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 269 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3868 r_free = 0.3868 target = 0.136303 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3450 r_free = 0.3450 target = 0.106087 restraints weight = 43086.550| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.107501 restraints weight = 35074.399| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3471 r_free = 0.3471 target = 0.108480 restraints weight = 24895.627| |-----------------------------------------------------------------------------| r_work (final): 0.3471 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7770 moved from start: 0.6225 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.077 20574 Z= 0.147 Angle : 0.800 13.656 28137 Z= 0.394 Chirality : 0.048 0.280 3327 Planarity : 0.005 0.082 3456 Dihedral : 8.426 59.032 3954 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 9.96 Ramachandran Plot: Outliers : 0.33 % Allowed : 6.00 % Favored : 93.67 % Rotamer: Outliers : 4.48 % Allowed : 21.76 % Favored : 73.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.38 % Twisted Proline : 0.00 % Twisted General : 0.13 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.41 (0.15), residues: 2448 helix: -0.45 (0.30), residues: 303 sheet: -0.97 (0.19), residues: 657 loop : -2.24 (0.14), residues: 1488 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.047 0.002 TRP M 47 HIS 0.007 0.001 HIS F 249 PHE 0.017 0.002 PHE D 323 TYR 0.026 0.002 TYR B 643 ARG 0.009 0.001 ARG B 542 Details of bonding type rmsd link_NAG-ASN : bond 0.00495 ( 12) link_NAG-ASN : angle 2.02965 ( 36) link_ALPHA1-6 : bond 0.01426 ( 10) link_ALPHA1-6 : angle 2.90585 ( 30) link_BETA1-4 : bond 0.00590 ( 24) link_BETA1-4 : angle 2.27832 ( 72) link_ALPHA1-2 : bond 0.01329 ( 11) link_ALPHA1-2 : angle 2.68214 ( 33) link_ALPHA1-3 : bond 0.00904 ( 9) link_ALPHA1-3 : angle 1.43319 ( 27) hydrogen bonds : bond 0.03995 ( 486) hydrogen bonds : angle 5.87455 ( 1305) SS BOND : bond 0.00428 ( 45) SS BOND : angle 2.20480 ( 90) covalent geometry : bond 0.00327 (20463) covalent geometry : angle 0.77007 (27849) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4896 Ramachandran restraints generated. 2448 Oldfield, 0 Emsley, 2448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4896 Ramachandran restraints generated. 2448 Oldfield, 0 Emsley, 2448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 457 residues out of total 2142 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 361 time to evaluate : 2.112 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 49 LYS cc_start: 0.8806 (mtmt) cc_final: 0.8601 (mtpt) REVERT: A 84 LEU cc_start: 0.7952 (tp) cc_final: 0.7651 (tt) REVERT: A 280 ASN cc_start: 0.8575 (m-40) cc_final: 0.8032 (t0) REVERT: A 439 ILE cc_start: 0.9597 (tp) cc_final: 0.9248 (mm) REVERT: A 490 LYS cc_start: 0.8521 (OUTLIER) cc_final: 0.8307 (ttmm) REVERT: B 529 THR cc_start: 0.8995 (p) cc_final: 0.8777 (t) REVERT: B 530 MET cc_start: 0.9009 (mmm) cc_final: 0.8381 (mpp) REVERT: B 581 LEU cc_start: 0.8157 (tp) cc_final: 0.7849 (tp) REVERT: B 632 ASP cc_start: 0.8576 (t0) cc_final: 0.8129 (t0) REVERT: B 639 THR cc_start: 0.8575 (p) cc_final: 0.8366 (t) REVERT: C 10 GLU cc_start: 0.8312 (tp30) cc_final: 0.7789 (tm-30) REVERT: C 60 GLN cc_start: 0.8179 (pm20) cc_final: 0.7650 (mm-40) REVERT: D 314 ASP cc_start: 0.7710 (m-30) cc_final: 0.7351 (m-30) REVERT: F 268 LYS cc_start: 0.8535 (ptmt) cc_final: 0.8033 (mttm) REVERT: F 423 ILE cc_start: 0.8995 (OUTLIER) cc_final: 0.8753 (mp) REVERT: F 434 MET cc_start: 0.8172 (ttm) cc_final: 0.7863 (ttm) REVERT: G 542 ARG cc_start: 0.8109 (tmt170) cc_final: 0.7829 (tmt170) REVERT: H 6 GLN cc_start: 0.6630 (pt0) cc_final: 0.5769 (pt0) REVERT: H 47 TRP cc_start: 0.8395 (t60) cc_final: 0.8194 (t60) REVERT: H 73 ASP cc_start: 0.7355 (OUTLIER) cc_final: 0.6607 (p0) REVERT: H 97 VAL cc_start: 0.8442 (OUTLIER) cc_final: 0.8172 (m) REVERT: I 234 LEU cc_start: 0.7663 (mt) cc_final: 0.7199 (mp) REVERT: K 104 MET cc_start: 0.8598 (ttt) cc_final: 0.8278 (ttt) REVERT: K 268 LYS cc_start: 0.8719 (pttt) cc_final: 0.8423 (mmtt) REVERT: K 280 ASN cc_start: 0.7839 (m-40) cc_final: 0.7557 (t0) REVERT: K 369 MET cc_start: 0.7315 (tpp) cc_final: 0.6792 (ttt) REVERT: K 377 ASN cc_start: 0.9128 (t0) cc_final: 0.8915 (t0) REVERT: K 423 ILE cc_start: 0.8980 (mt) cc_final: 0.8670 (mt) REVERT: K 479 TRP cc_start: 0.8465 (m-10) cc_final: 0.8093 (m-90) REVERT: L 529 THR cc_start: 0.8936 (p) cc_final: 0.8681 (t) REVERT: L 623 TRP cc_start: 0.8472 (OUTLIER) cc_final: 0.7869 (m-90) REVERT: M 10 GLU cc_start: 0.7231 (pm20) cc_final: 0.6773 (pp20) REVERT: M 90 ASP cc_start: 0.7935 (p0) cc_final: 0.7684 (p0) REVERT: M 104 ASP cc_start: 0.8457 (t0) cc_final: 0.8227 (t70) outliers start: 96 outliers final: 64 residues processed: 423 average time/residue: 0.2808 time to fit residues: 187.0387 Evaluate side-chains 370 residues out of total 2142 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 301 time to evaluate : 2.106 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 VAL Chi-restraints excluded: chain A residue 85 VAL Chi-restraints excluded: chain A residue 102 ASP Chi-restraints excluded: chain A residue 128 THR Chi-restraints excluded: chain A residue 215 ILE Chi-restraints excluded: chain A residue 265 LEU Chi-restraints excluded: chain A residue 293 GLU Chi-restraints excluded: chain A residue 297 THR Chi-restraints excluded: chain A residue 446 ARG Chi-restraints excluded: chain A residue 490 LYS Chi-restraints excluded: chain B residue 537 LEU Chi-restraints excluded: chain B residue 641 ILE Chi-restraints excluded: chain C residue 28 THR Chi-restraints excluded: chain C residue 70 MET Chi-restraints excluded: chain C residue 76 ILE Chi-restraints excluded: chain C residue 97 VAL Chi-restraints excluded: chain D residue 248 ILE Chi-restraints excluded: chain D residue 259 VAL Chi-restraints excluded: chain D residue 306 THR Chi-restraints excluded: chain D residue 340 LEU Chi-restraints excluded: chain F residue 46 LYS Chi-restraints excluded: chain F residue 75 VAL Chi-restraints excluded: chain F residue 111 LEU Chi-restraints excluded: chain F residue 182 VAL Chi-restraints excluded: chain F residue 215 ILE Chi-restraints excluded: chain F residue 217 TYR Chi-restraints excluded: chain F residue 292 VAL Chi-restraints excluded: chain F residue 297 THR Chi-restraints excluded: chain F residue 307 VAL Chi-restraints excluded: chain F residue 377 ASN Chi-restraints excluded: chain F residue 378 CYS Chi-restraints excluded: chain F residue 423 ILE Chi-restraints excluded: chain F residue 433 CYS Chi-restraints excluded: chain F residue 446 ARG Chi-restraints excluded: chain F residue 450 THR Chi-restraints excluded: chain G residue 595 ILE Chi-restraints excluded: chain G residue 624 ASP Chi-restraints excluded: chain H residue 18 VAL Chi-restraints excluded: chain H residue 63 ASN Chi-restraints excluded: chain H residue 73 ASP Chi-restraints excluded: chain H residue 74 THR Chi-restraints excluded: chain H residue 97 VAL Chi-restraints excluded: chain H residue 124 THR Chi-restraints excluded: chain I residue 248 ILE Chi-restraints excluded: chain I residue 253 THR Chi-restraints excluded: chain I residue 295 SER Chi-restraints excluded: chain I residue 340 LEU Chi-restraints excluded: chain K residue 46 LYS Chi-restraints excluded: chain K residue 68 VAL Chi-restraints excluded: chain K residue 72 HIS Chi-restraints excluded: chain K residue 182 VAL Chi-restraints excluded: chain K residue 202 THR Chi-restraints excluded: chain K residue 215 ILE Chi-restraints excluded: chain K residue 218 CYS Chi-restraints excluded: chain K residue 249 HIS Chi-restraints excluded: chain K residue 445 CYS Chi-restraints excluded: chain K residue 455 THR Chi-restraints excluded: chain K residue 481 SER Chi-restraints excluded: chain L residue 580 VAL Chi-restraints excluded: chain L residue 581 LEU Chi-restraints excluded: chain L residue 608 VAL Chi-restraints excluded: chain L residue 623 TRP Chi-restraints excluded: chain L residue 624 ASP Chi-restraints excluded: chain L residue 632 ASP Chi-restraints excluded: chain M residue 72 ARG Chi-restraints excluded: chain M residue 97 VAL Chi-restraints excluded: chain M residue 115 ASP Chi-restraints excluded: chain N residue 314 ASP Chi-restraints excluded: chain N residue 339 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: chunk 161 optimal weight: 8.9990 chunk 231 optimal weight: 0.0010 chunk 135 optimal weight: 3.9990 chunk 182 optimal weight: 3.9990 chunk 211 optimal weight: 1.9990 chunk 62 optimal weight: 1.9990 chunk 58 optimal weight: 0.1980 chunk 39 optimal weight: 1.9990 chunk 107 optimal weight: 1.9990 chunk 197 optimal weight: 4.9990 chunk 192 optimal weight: 0.6980 overall best weight: 0.9790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 62 GLN ** F 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 63 ASN ** H 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 236 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 311 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 287 HIS ** M 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 119 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 = 0.3853 r_free = 0.3853 target = 0.135182 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3382 r_free = 0.3382 target = 0.102530 restraints weight = 43051.404| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.104898 restraints weight = 29208.447| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.105433 restraints weight = 21848.942| |-----------------------------------------------------------------------------| r_work (final): 0.3413 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7858 moved from start: 0.6457 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 20574 Z= 0.163 Angle : 0.777 12.682 28137 Z= 0.382 Chirality : 0.047 0.225 3327 Planarity : 0.005 0.071 3456 Dihedral : 7.915 59.988 3954 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 9.91 Ramachandran Plot: Outliers : 0.33 % Allowed : 7.11 % Favored : 92.57 % Rotamer: Outliers : 4.53 % Allowed : 22.36 % Favored : 73.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.38 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.30 (0.16), residues: 2448 helix: -0.27 (0.30), residues: 309 sheet: -0.93 (0.19), residues: 672 loop : -2.19 (0.15), residues: 1467 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.054 0.002 TRP M 47 HIS 0.005 0.001 HIS A 330 PHE 0.015 0.002 PHE C 114 TYR 0.018 0.001 TYR N 278 ARG 0.005 0.000 ARG M 38 Details of bonding type rmsd link_NAG-ASN : bond 0.00506 ( 12) link_NAG-ASN : angle 1.93587 ( 36) link_ALPHA1-6 : bond 0.01162 ( 10) link_ALPHA1-6 : angle 2.48725 ( 30) link_BETA1-4 : bond 0.00631 ( 24) link_BETA1-4 : angle 2.25773 ( 72) link_ALPHA1-2 : bond 0.01288 ( 11) link_ALPHA1-2 : angle 2.56474 ( 33) link_ALPHA1-3 : bond 0.00888 ( 9) link_ALPHA1-3 : angle 1.48212 ( 27) hydrogen bonds : bond 0.03836 ( 486) hydrogen bonds : angle 5.63674 ( 1305) SS BOND : bond 0.00527 ( 45) SS BOND : angle 2.18777 ( 90) covalent geometry : bond 0.00372 (20463) covalent geometry : angle 0.74782 (27849) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4896 Ramachandran restraints generated. 2448 Oldfield, 0 Emsley, 2448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4896 Ramachandran restraints generated. 2448 Oldfield, 0 Emsley, 2448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 430 residues out of total 2142 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 97 poor density : 333 time to evaluate : 2.032 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 84 LEU cc_start: 0.8003 (tp) cc_final: 0.7724 (tt) REVERT: A 280 ASN cc_start: 0.8639 (m-40) cc_final: 0.8077 (t0) REVERT: A 288 LEU cc_start: 0.8971 (OUTLIER) cc_final: 0.8760 (mm) REVERT: A 439 ILE cc_start: 0.9596 (tp) cc_final: 0.9305 (mm) REVERT: A 490 LYS cc_start: 0.8564 (OUTLIER) cc_final: 0.8330 (ttmm) REVERT: B 529 THR cc_start: 0.8955 (p) cc_final: 0.8752 (t) REVERT: B 530 MET cc_start: 0.9018 (mmm) cc_final: 0.8388 (mpp) REVERT: B 581 LEU cc_start: 0.7944 (tp) cc_final: 0.7532 (tp) REVERT: B 630 GLN cc_start: 0.8087 (OUTLIER) cc_final: 0.7831 (pm20) REVERT: B 632 ASP cc_start: 0.8628 (t0) cc_final: 0.8146 (t0) REVERT: B 634 GLU cc_start: 0.7395 (mt-10) cc_final: 0.7067 (mt-10) REVERT: C 10 GLU cc_start: 0.8296 (tp30) cc_final: 0.7791 (tm-30) REVERT: C 51 MET cc_start: 0.8244 (tpp) cc_final: 0.8020 (ttt) REVERT: C 60 GLN cc_start: 0.8196 (pm20) cc_final: 0.7635 (mm-40) REVERT: D 272 PRO cc_start: 0.7702 (OUTLIER) cc_final: 0.7241 (Cg_endo) REVERT: D 314 ASP cc_start: 0.7596 (m-30) cc_final: 0.7392 (m-30) REVERT: F 268 LYS cc_start: 0.8473 (ptmt) cc_final: 0.7998 (mttm) REVERT: F 423 ILE cc_start: 0.9125 (OUTLIER) cc_final: 0.8881 (mp) REVERT: G 633 LYS cc_start: 0.8915 (pptt) cc_final: 0.7869 (pptt) REVERT: H 73 ASP cc_start: 0.7312 (OUTLIER) cc_final: 0.6592 (p0) REVERT: I 234 LEU cc_start: 0.7676 (mt) cc_final: 0.7252 (mp) REVERT: I 285 LYS cc_start: 0.6694 (OUTLIER) cc_final: 0.6460 (mtmm) REVERT: K 49 LYS cc_start: 0.8547 (tttt) cc_final: 0.8047 (mtpt) REVERT: K 104 MET cc_start: 0.8583 (ttt) cc_final: 0.8293 (ttt) REVERT: K 268 LYS cc_start: 0.8609 (pttt) cc_final: 0.8327 (mmtt) REVERT: K 369 MET cc_start: 0.7469 (tpp) cc_final: 0.6943 (ttt) REVERT: K 423 ILE cc_start: 0.9214 (mt) cc_final: 0.8835 (mt) REVERT: K 479 TRP cc_start: 0.8537 (m-10) cc_final: 0.8246 (m-90) REVERT: L 529 THR cc_start: 0.8925 (OUTLIER) cc_final: 0.8663 (t) REVERT: L 623 TRP cc_start: 0.8534 (OUTLIER) cc_final: 0.7905 (m-90) REVERT: L 633 LYS cc_start: 0.9281 (pptt) cc_final: 0.8982 (pptt) REVERT: M 10 GLU cc_start: 0.7407 (pm20) cc_final: 0.7055 (pp20) REVERT: M 51 MET cc_start: 0.7792 (tpp) cc_final: 0.7464 (ttt) REVERT: M 59 ASN cc_start: 0.8705 (t0) cc_final: 0.8082 (t0) REVERT: M 81 MET cc_start: 0.8448 (ttt) cc_final: 0.8197 (ttm) outliers start: 97 outliers final: 71 residues processed: 401 average time/residue: 0.2725 time to fit residues: 174.8344 Evaluate side-chains 388 residues out of total 2142 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 308 time to evaluate : 2.374 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 VAL Chi-restraints excluded: chain A residue 85 VAL Chi-restraints excluded: chain A residue 102 ASP Chi-restraints excluded: chain A residue 128 THR Chi-restraints excluded: chain A residue 184 LEU Chi-restraints excluded: chain A residue 198 THR Chi-restraints excluded: chain A residue 202 THR Chi-restraints excluded: chain A residue 215 ILE Chi-restraints excluded: chain A residue 245 VAL Chi-restraints excluded: chain A residue 265 LEU Chi-restraints excluded: chain A residue 271 VAL Chi-restraints excluded: chain A residue 288 LEU Chi-restraints excluded: chain A residue 293 GLU Chi-restraints excluded: chain A residue 297 THR Chi-restraints excluded: chain A residue 426 MET Chi-restraints excluded: chain A residue 446 ARG Chi-restraints excluded: chain A residue 490 LYS Chi-restraints excluded: chain B residue 537 LEU Chi-restraints excluded: chain B residue 630 GLN Chi-restraints excluded: chain B residue 641 ILE Chi-restraints excluded: chain C residue 28 THR Chi-restraints excluded: chain C residue 70 MET Chi-restraints excluded: chain C residue 76 ILE Chi-restraints excluded: chain C residue 97 VAL Chi-restraints excluded: chain D residue 248 ILE Chi-restraints excluded: chain D residue 259 VAL Chi-restraints excluded: chain D residue 272 PRO Chi-restraints excluded: chain D residue 306 THR Chi-restraints excluded: chain D residue 340 LEU Chi-restraints excluded: chain F residue 75 VAL Chi-restraints excluded: chain F residue 161 THR Chi-restraints excluded: chain F residue 182 VAL Chi-restraints excluded: chain F residue 215 ILE Chi-restraints excluded: chain F residue 217 TYR Chi-restraints excluded: chain F residue 292 VAL Chi-restraints excluded: chain F residue 297 THR Chi-restraints excluded: chain F residue 377 ASN Chi-restraints excluded: chain F residue 378 CYS Chi-restraints excluded: chain F residue 423 ILE Chi-restraints excluded: chain F residue 450 THR Chi-restraints excluded: chain G residue 595 ILE Chi-restraints excluded: chain G residue 606 THR Chi-restraints excluded: chain G residue 615 SER Chi-restraints excluded: chain G residue 624 ASP Chi-restraints excluded: chain G residue 647 GLU Chi-restraints excluded: chain H residue 18 VAL Chi-restraints excluded: chain H residue 63 ASN Chi-restraints excluded: chain H residue 73 ASP Chi-restraints excluded: chain H residue 74 THR Chi-restraints excluded: chain H residue 97 VAL Chi-restraints excluded: chain H residue 124 THR Chi-restraints excluded: chain I residue 248 ILE Chi-restraints excluded: chain I residue 285 LYS Chi-restraints excluded: chain I residue 288 SER Chi-restraints excluded: chain I residue 295 SER Chi-restraints excluded: chain I residue 340 LEU Chi-restraints excluded: chain K residue 68 VAL Chi-restraints excluded: chain K residue 72 HIS Chi-restraints excluded: chain K residue 85 VAL Chi-restraints excluded: chain K residue 182 VAL Chi-restraints excluded: chain K residue 188 THR Chi-restraints excluded: chain K residue 202 THR Chi-restraints excluded: chain K residue 215 ILE Chi-restraints excluded: chain K residue 218 CYS Chi-restraints excluded: chain K residue 249 HIS Chi-restraints excluded: chain K residue 292 VAL Chi-restraints excluded: chain K residue 445 CYS Chi-restraints excluded: chain K residue 501 CYS Chi-restraints excluded: chain L residue 529 THR Chi-restraints excluded: chain L residue 580 VAL Chi-restraints excluded: chain L residue 581 LEU Chi-restraints excluded: chain L residue 608 VAL Chi-restraints excluded: chain L residue 615 SER Chi-restraints excluded: chain L residue 623 TRP Chi-restraints excluded: chain M residue 6 GLN Chi-restraints excluded: chain M residue 97 VAL Chi-restraints excluded: chain M residue 103 SER Chi-restraints excluded: chain N residue 240 VAL Chi-restraints excluded: chain N residue 314 ASP Chi-restraints excluded: chain N residue 339 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: chunk 141 optimal weight: 0.0970 chunk 97 optimal weight: 0.2980 chunk 8 optimal weight: 2.9990 chunk 240 optimal weight: 8.9990 chunk 194 optimal weight: 6.9990 chunk 54 optimal weight: 3.9990 chunk 23 optimal weight: 0.7980 chunk 7 optimal weight: 2.9990 chunk 217 optimal weight: 2.9990 chunk 81 optimal weight: 3.9990 chunk 15 optimal weight: 0.6980 overall best weight: 0.9780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 339 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 63 ASN ** H 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 236 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 311 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 287 HIS M 3 GLN ** M 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 119 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 = 0.3924 r_free = 0.3924 target = 0.139375 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3522 r_free = 0.3522 target = 0.110036 restraints weight = 43538.643| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3517 r_free = 0.3517 target = 0.110477 restraints weight = 34705.331| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3532 r_free = 0.3532 target = 0.111778 restraints weight = 28286.724| |-----------------------------------------------------------------------------| r_work (final): 0.3536 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7836 moved from start: 0.6649 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.072 20574 Z= 0.160 Angle : 0.769 13.149 28137 Z= 0.377 Chirality : 0.047 0.225 3327 Planarity : 0.005 0.067 3456 Dihedral : 7.660 59.287 3954 Min Nonbonded Distance : 2.421 Molprobity Statistics. All-atom Clashscore : 9.45 Ramachandran Plot: Outliers : 0.33 % Allowed : 6.78 % Favored : 92.89 % Rotamer: Outliers : 4.53 % Allowed : 22.41 % Favored : 73.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.38 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.28 (0.16), residues: 2448 helix: -0.30 (0.30), residues: 321 sheet: -0.88 (0.18), residues: 687 loop : -2.21 (0.15), residues: 1440 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.002 TRP M 47 HIS 0.004 0.001 HIS A 330 PHE 0.029 0.002 PHE M 64 TYR 0.018 0.001 TYR B 643 ARG 0.004 0.000 ARG B 542 Details of bonding type rmsd link_NAG-ASN : bond 0.00478 ( 12) link_NAG-ASN : angle 1.87337 ( 36) link_ALPHA1-6 : bond 0.01088 ( 10) link_ALPHA1-6 : angle 2.51395 ( 30) link_BETA1-4 : bond 0.00623 ( 24) link_BETA1-4 : angle 2.18439 ( 72) link_ALPHA1-2 : bond 0.01252 ( 11) link_ALPHA1-2 : angle 2.50037 ( 33) link_ALPHA1-3 : bond 0.00866 ( 9) link_ALPHA1-3 : angle 1.48214 ( 27) hydrogen bonds : bond 0.03695 ( 486) hydrogen bonds : angle 5.51404 ( 1305) SS BOND : bond 0.00474 ( 45) SS BOND : angle 2.19197 ( 90) covalent geometry : bond 0.00368 (20463) covalent geometry : angle 0.74065 (27849) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4896 Ramachandran restraints generated. 2448 Oldfield, 0 Emsley, 2448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4896 Ramachandran restraints generated. 2448 Oldfield, 0 Emsley, 2448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 419 residues out of total 2142 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 97 poor density : 322 time to evaluate : 2.035 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 84 LEU cc_start: 0.8042 (tp) cc_final: 0.7760 (tt) REVERT: A 104 MET cc_start: 0.8697 (ttm) cc_final: 0.8174 (tpp) REVERT: A 217 TYR cc_start: 0.8652 (m-10) cc_final: 0.8078 (m-10) REVERT: A 280 ASN cc_start: 0.8572 (m-40) cc_final: 0.8117 (t0) REVERT: A 288 LEU cc_start: 0.8959 (OUTLIER) cc_final: 0.8738 (mm) REVERT: A 439 ILE cc_start: 0.9578 (tp) cc_final: 0.9309 (mm) REVERT: B 530 MET cc_start: 0.8958 (mmm) cc_final: 0.8348 (mmm) REVERT: B 581 LEU cc_start: 0.8032 (tp) cc_final: 0.7612 (tp) REVERT: B 630 GLN cc_start: 0.8036 (OUTLIER) cc_final: 0.7697 (pm20) REVERT: B 632 ASP cc_start: 0.8459 (t0) cc_final: 0.8026 (t0) REVERT: B 634 GLU cc_start: 0.7256 (mt-10) cc_final: 0.6978 (mt-10) REVERT: B 656 ASN cc_start: 0.7821 (t0) cc_final: 0.7620 (t0) REVERT: C 60 GLN cc_start: 0.8021 (pm20) cc_final: 0.7523 (mm-40) REVERT: D 272 PRO cc_start: 0.7589 (OUTLIER) cc_final: 0.7140 (Cg_endo) REVERT: D 311 GLN cc_start: 0.8745 (pm20) cc_final: 0.8484 (pm20) REVERT: D 314 ASP cc_start: 0.7784 (m-30) cc_final: 0.7450 (m-30) REVERT: F 268 LYS cc_start: 0.8398 (ptmt) cc_final: 0.7987 (mttm) REVERT: F 423 ILE cc_start: 0.8817 (OUTLIER) cc_final: 0.8538 (mp) REVERT: H 43 GLN cc_start: 0.7387 (pp30) cc_final: 0.7053 (pm20) REVERT: H 51 MET cc_start: 0.7828 (tpp) cc_final: 0.7546 (ttt) REVERT: I 234 LEU cc_start: 0.7876 (mt) cc_final: 0.7441 (mp) REVERT: I 285 LYS cc_start: 0.6852 (OUTLIER) cc_final: 0.6649 (mtmm) REVERT: K 49 LYS cc_start: 0.8482 (tttt) cc_final: 0.8050 (mtpt) REVERT: K 104 MET cc_start: 0.8574 (ttt) cc_final: 0.8287 (ttt) REVERT: K 268 LYS cc_start: 0.8586 (pttt) cc_final: 0.8343 (mmtt) REVERT: K 369 MET cc_start: 0.7477 (tpp) cc_final: 0.6907 (ttt) REVERT: K 423 ILE cc_start: 0.9248 (mt) cc_final: 0.8829 (mt) REVERT: K 479 TRP cc_start: 0.8507 (m-10) cc_final: 0.8302 (m-90) REVERT: L 623 TRP cc_start: 0.8502 (OUTLIER) cc_final: 0.7935 (m-90) REVERT: L 633 LYS cc_start: 0.9233 (pptt) cc_final: 0.9001 (pptt) REVERT: M 59 ASN cc_start: 0.8707 (t0) cc_final: 0.8114 (t0) outliers start: 97 outliers final: 77 residues processed: 386 average time/residue: 0.2794 time to fit residues: 171.7067 Evaluate side-chains 382 residues out of total 2142 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 299 time to evaluate : 2.088 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 VAL Chi-restraints excluded: chain A residue 85 VAL Chi-restraints excluded: chain A residue 102 ASP Chi-restraints excluded: chain A residue 128 THR Chi-restraints excluded: chain A residue 184 LEU Chi-restraints excluded: chain A residue 198 THR Chi-restraints excluded: chain A residue 203 GLN Chi-restraints excluded: chain A residue 215 ILE Chi-restraints excluded: chain A residue 245 VAL Chi-restraints excluded: chain A residue 265 LEU Chi-restraints excluded: chain A residue 271 VAL Chi-restraints excluded: chain A residue 288 LEU Chi-restraints excluded: chain A residue 297 THR Chi-restraints excluded: chain A residue 426 MET Chi-restraints excluded: chain A residue 446 ARG Chi-restraints excluded: chain B residue 537 LEU Chi-restraints excluded: chain B residue 592 LEU Chi-restraints excluded: chain B residue 630 GLN Chi-restraints excluded: chain B residue 641 ILE Chi-restraints excluded: chain C residue 28 THR Chi-restraints excluded: chain C residue 31 ASP Chi-restraints excluded: chain C residue 70 MET Chi-restraints excluded: chain C residue 76 ILE Chi-restraints excluded: chain C residue 97 VAL Chi-restraints excluded: chain D residue 248 ILE Chi-restraints excluded: chain D residue 259 VAL Chi-restraints excluded: chain D residue 272 PRO Chi-restraints excluded: chain D residue 306 THR Chi-restraints excluded: chain F residue 75 VAL Chi-restraints excluded: chain F residue 111 LEU Chi-restraints excluded: chain F residue 182 VAL Chi-restraints excluded: chain F residue 202 THR Chi-restraints excluded: chain F residue 215 ILE Chi-restraints excluded: chain F residue 217 TYR Chi-restraints excluded: chain F residue 289 HIS Chi-restraints excluded: chain F residue 292 VAL Chi-restraints excluded: chain F residue 297 THR Chi-restraints excluded: chain F residue 377 ASN Chi-restraints excluded: chain F residue 378 CYS Chi-restraints excluded: chain F residue 423 ILE Chi-restraints excluded: chain F residue 446 ARG Chi-restraints excluded: chain F residue 450 THR Chi-restraints excluded: chain G residue 583 VAL Chi-restraints excluded: chain G residue 595 ILE Chi-restraints excluded: chain G residue 606 THR Chi-restraints excluded: chain G residue 615 SER Chi-restraints excluded: chain G residue 624 ASP Chi-restraints excluded: chain G residue 647 GLU Chi-restraints excluded: chain H residue 18 VAL Chi-restraints excluded: chain H residue 63 ASN Chi-restraints excluded: chain H residue 74 THR Chi-restraints excluded: chain H residue 97 VAL Chi-restraints excluded: chain I residue 253 THR Chi-restraints excluded: chain I residue 259 VAL Chi-restraints excluded: chain I residue 285 LYS Chi-restraints excluded: chain I residue 288 SER Chi-restraints excluded: chain I residue 295 SER Chi-restraints excluded: chain I residue 340 LEU Chi-restraints excluded: chain K residue 68 VAL Chi-restraints excluded: chain K residue 85 VAL Chi-restraints excluded: chain K residue 182 VAL Chi-restraints excluded: chain K residue 188 THR Chi-restraints excluded: chain K residue 202 THR Chi-restraints excluded: chain K residue 215 ILE Chi-restraints excluded: chain K residue 218 CYS Chi-restraints excluded: chain K residue 292 VAL Chi-restraints excluded: chain K residue 414 ILE Chi-restraints excluded: chain K residue 445 CYS Chi-restraints excluded: chain K residue 501 CYS Chi-restraints excluded: chain L residue 580 VAL Chi-restraints excluded: chain L residue 581 LEU Chi-restraints excluded: chain L residue 608 VAL Chi-restraints excluded: chain L residue 615 SER Chi-restraints excluded: chain L residue 616 ASN Chi-restraints excluded: chain L residue 623 TRP Chi-restraints excluded: chain M residue 3 GLN Chi-restraints excluded: chain M residue 6 GLN Chi-restraints excluded: chain M residue 39 LEU Chi-restraints excluded: chain M residue 72 ARG Chi-restraints excluded: chain M residue 97 VAL Chi-restraints excluded: chain M residue 103 SER Chi-restraints excluded: chain N residue 240 VAL Chi-restraints excluded: chain N residue 339 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: chunk 13 optimal weight: 1.9990 chunk 167 optimal weight: 1.9990 chunk 47 optimal weight: 4.9990 chunk 162 optimal weight: 4.9990 chunk 149 optimal weight: 0.9980 chunk 16 optimal weight: 3.9990 chunk 200 optimal weight: 0.4980 chunk 98 optimal weight: 1.9990 chunk 175 optimal weight: 1.9990 chunk 170 optimal weight: 0.3980 chunk 196 optimal weight: 0.7980 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 339 ASN C 116 HIS ** F 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 63 ASN ** H 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 236 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 311 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 287 HIS ** M 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3924 r_free = 0.3924 target = 0.139296 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3520 r_free = 0.3520 target = 0.109897 restraints weight = 43717.040| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3511 r_free = 0.3511 target = 0.110354 restraints weight = 34212.349| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3526 r_free = 0.3526 target = 0.111559 restraints weight = 29082.689| |-----------------------------------------------------------------------------| r_work (final): 0.3531 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7841 moved from start: 0.6817 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 20574 Z= 0.157 Angle : 0.766 13.776 28137 Z= 0.376 Chirality : 0.047 0.226 3327 Planarity : 0.005 0.064 3456 Dihedral : 7.512 58.827 3954 Min Nonbonded Distance : 2.369 Molprobity Statistics. All-atom Clashscore : 9.56 Ramachandran Plot: Outliers : 0.33 % Allowed : 7.43 % Favored : 92.24 % Rotamer: Outliers : 4.25 % Allowed : 23.02 % Favored : 72.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.38 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.27 (0.16), residues: 2448 helix: -0.37 (0.29), residues: 357 sheet: -0.76 (0.18), residues: 681 loop : -2.29 (0.15), residues: 1410 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP M 47 HIS 0.007 0.001 HIS C 116 PHE 0.031 0.002 PHE M 64 TYR 0.027 0.001 TYR B 643 ARG 0.004 0.000 ARG B 542 Details of bonding type rmsd link_NAG-ASN : bond 0.00489 ( 12) link_NAG-ASN : angle 1.82102 ( 36) link_ALPHA1-6 : bond 0.00747 ( 10) link_ALPHA1-6 : angle 1.85613 ( 30) link_BETA1-4 : bond 0.00611 ( 24) link_BETA1-4 : angle 2.14626 ( 72) link_ALPHA1-2 : bond 0.01271 ( 11) link_ALPHA1-2 : angle 2.44730 ( 33) link_ALPHA1-3 : bond 0.00845 ( 9) link_ALPHA1-3 : angle 1.45957 ( 27) hydrogen bonds : bond 0.03685 ( 486) hydrogen bonds : angle 5.43329 ( 1305) SS BOND : bond 0.00446 ( 45) SS BOND : angle 1.98606 ( 90) covalent geometry : bond 0.00361 (20463) covalent geometry : angle 0.74216 (27849) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4896 Ramachandran restraints generated. 2448 Oldfield, 0 Emsley, 2448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4896 Ramachandran restraints generated. 2448 Oldfield, 0 Emsley, 2448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 405 residues out of total 2142 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 314 time to evaluate : 2.495 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 84 LEU cc_start: 0.8067 (tp) cc_final: 0.7811 (tt) REVERT: A 104 MET cc_start: 0.8712 (ttm) cc_final: 0.8107 (tpp) REVERT: A 217 TYR cc_start: 0.8631 (m-10) cc_final: 0.7999 (m-10) REVERT: A 280 ASN cc_start: 0.8614 (m-40) cc_final: 0.8267 (t0) REVERT: A 317 PHE cc_start: 0.8788 (OUTLIER) cc_final: 0.7671 (p90) REVERT: A 439 ILE cc_start: 0.9583 (tp) cc_final: 0.9359 (mm) REVERT: B 530 MET cc_start: 0.8769 (mmm) cc_final: 0.8310 (mmm) REVERT: B 632 ASP cc_start: 0.8470 (t0) cc_final: 0.8062 (t0) REVERT: C 60 GLN cc_start: 0.8034 (pm20) cc_final: 0.7519 (mm-40) REVERT: D 272 PRO cc_start: 0.7570 (OUTLIER) cc_final: 0.7120 (Cg_endo) REVERT: F 84 LEU cc_start: 0.8099 (tp) cc_final: 0.7740 (mt) REVERT: F 268 LYS cc_start: 0.8418 (ptmt) cc_final: 0.8011 (mttm) REVERT: F 423 ILE cc_start: 0.8801 (OUTLIER) cc_final: 0.8555 (mp) REVERT: H 51 MET cc_start: 0.7805 (tpp) cc_final: 0.7502 (ttt) REVERT: H 97 VAL cc_start: 0.8458 (OUTLIER) cc_final: 0.8214 (m) REVERT: I 234 LEU cc_start: 0.7912 (mt) cc_final: 0.7463 (mp) REVERT: I 248 ILE cc_start: 0.6256 (OUTLIER) cc_final: 0.5919 (mt) REVERT: K 49 LYS cc_start: 0.8470 (tttt) cc_final: 0.7988 (mtpt) REVERT: K 104 MET cc_start: 0.8595 (ttt) cc_final: 0.8287 (ttt) REVERT: K 268 LYS cc_start: 0.8626 (pttt) cc_final: 0.8392 (mmtt) REVERT: K 280 ASN cc_start: 0.7995 (m-40) cc_final: 0.7781 (t0) REVERT: K 369 MET cc_start: 0.7534 (tpp) cc_final: 0.6952 (ttt) REVERT: K 423 ILE cc_start: 0.9265 (mt) cc_final: 0.8836 (mt) REVERT: L 633 LYS cc_start: 0.9229 (pptt) cc_final: 0.8985 (pptt) REVERT: M 13 ASN cc_start: 0.8068 (p0) cc_final: 0.7332 (m110) REVERT: M 59 ASN cc_start: 0.8627 (t0) cc_final: 0.8096 (t0) outliers start: 91 outliers final: 75 residues processed: 378 average time/residue: 0.2864 time to fit residues: 173.7023 Evaluate side-chains 378 residues out of total 2142 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 298 time to evaluate : 2.322 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 VAL Chi-restraints excluded: chain A residue 85 VAL Chi-restraints excluded: chain A residue 102 ASP Chi-restraints excluded: chain A residue 128 THR Chi-restraints excluded: chain A residue 184 LEU Chi-restraints excluded: chain A residue 198 THR Chi-restraints excluded: chain A residue 202 THR Chi-restraints excluded: chain A residue 203 GLN Chi-restraints excluded: chain A residue 215 ILE Chi-restraints excluded: chain A residue 245 VAL Chi-restraints excluded: chain A residue 265 LEU Chi-restraints excluded: chain A residue 271 VAL Chi-restraints excluded: chain A residue 297 THR Chi-restraints excluded: chain A residue 317 PHE Chi-restraints excluded: chain A residue 446 ARG Chi-restraints excluded: chain B residue 537 LEU Chi-restraints excluded: chain B residue 592 LEU Chi-restraints excluded: chain B residue 641 ILE Chi-restraints excluded: chain C residue 31 ASP Chi-restraints excluded: chain C residue 70 MET Chi-restraints excluded: chain C residue 76 ILE Chi-restraints excluded: chain C residue 97 VAL Chi-restraints excluded: chain D residue 248 ILE Chi-restraints excluded: chain D residue 259 VAL Chi-restraints excluded: chain D residue 272 PRO Chi-restraints excluded: chain D residue 306 THR Chi-restraints excluded: chain F residue 75 VAL Chi-restraints excluded: chain F residue 120 VAL Chi-restraints excluded: chain F residue 182 VAL Chi-restraints excluded: chain F residue 202 THR Chi-restraints excluded: chain F residue 215 ILE Chi-restraints excluded: chain F residue 289 HIS Chi-restraints excluded: chain F residue 292 VAL Chi-restraints excluded: chain F residue 297 THR Chi-restraints excluded: chain F residue 377 ASN Chi-restraints excluded: chain F residue 378 CYS Chi-restraints excluded: chain F residue 423 ILE Chi-restraints excluded: chain F residue 446 ARG Chi-restraints excluded: chain F residue 450 THR Chi-restraints excluded: chain G residue 583 VAL Chi-restraints excluded: chain G residue 595 ILE Chi-restraints excluded: chain G residue 606 THR Chi-restraints excluded: chain G residue 615 SER Chi-restraints excluded: chain G residue 624 ASP Chi-restraints excluded: chain G residue 647 GLU Chi-restraints excluded: chain H residue 18 VAL Chi-restraints excluded: chain H residue 63 ASN Chi-restraints excluded: chain H residue 74 THR Chi-restraints excluded: chain H residue 97 VAL Chi-restraints excluded: chain H residue 124 THR Chi-restraints excluded: chain I residue 248 ILE Chi-restraints excluded: chain I residue 253 THR Chi-restraints excluded: chain I residue 288 SER Chi-restraints excluded: chain I residue 295 SER Chi-restraints excluded: chain I residue 340 LEU Chi-restraints excluded: chain K residue 68 VAL Chi-restraints excluded: chain K residue 72 HIS Chi-restraints excluded: chain K residue 85 VAL Chi-restraints excluded: chain K residue 182 VAL Chi-restraints excluded: chain K residue 188 THR Chi-restraints excluded: chain K residue 202 THR Chi-restraints excluded: chain K residue 213 ILE Chi-restraints excluded: chain K residue 215 ILE Chi-restraints excluded: chain K residue 218 CYS Chi-restraints excluded: chain K residue 271 VAL Chi-restraints excluded: chain K residue 292 VAL Chi-restraints excluded: chain K residue 414 ILE Chi-restraints excluded: chain K residue 445 CYS Chi-restraints excluded: chain K residue 501 CYS Chi-restraints excluded: chain L residue 580 VAL Chi-restraints excluded: chain L residue 581 LEU Chi-restraints excluded: chain L residue 608 VAL Chi-restraints excluded: chain L residue 615 SER Chi-restraints excluded: chain L residue 616 ASN Chi-restraints excluded: chain M residue 39 LEU Chi-restraints excluded: chain M residue 72 ARG Chi-restraints excluded: chain M residue 97 VAL Chi-restraints excluded: chain N residue 240 VAL Chi-restraints excluded: chain N residue 257 TYR Chi-restraints excluded: chain N residue 339 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: chunk 230 optimal weight: 3.9990 chunk 229 optimal weight: 0.9990 chunk 192 optimal weight: 2.9990 chunk 45 optimal weight: 2.9990 chunk 57 optimal weight: 0.9990 chunk 162 optimal weight: 4.9990 chunk 238 optimal weight: 10.0000 chunk 43 optimal weight: 0.0570 chunk 222 optimal weight: 0.6980 chunk 25 optimal weight: 1.9990 chunk 159 optimal weight: 0.9990 overall best weight: 0.7504 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 63 ASN ** H 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 236 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 246 GLN ** I 311 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 3 GLN ** M 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 119 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 = 0.3931 r_free = 0.3931 target = 0.139787 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3531 r_free = 0.3531 target = 0.110673 restraints weight = 43418.721| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3526 r_free = 0.3526 target = 0.111343 restraints weight = 34247.968| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3540 r_free = 0.3540 target = 0.112467 restraints weight = 28459.563| |-----------------------------------------------------------------------------| r_work (final): 0.3545 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7822 moved from start: 0.6924 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 20574 Z= 0.145 Angle : 0.756 13.291 28137 Z= 0.372 Chirality : 0.046 0.198 3327 Planarity : 0.005 0.059 3456 Dihedral : 7.268 57.241 3954 Min Nonbonded Distance : 2.323 Molprobity Statistics. All-atom Clashscore : 9.00 Ramachandran Plot: Outliers : 0.29 % Allowed : 7.11 % Favored : 92.61 % Rotamer: Outliers : 4.06 % Allowed : 23.62 % Favored : 72.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.38 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.19 (0.16), residues: 2448 helix: -0.35 (0.29), residues: 357 sheet: -0.65 (0.19), residues: 660 loop : -2.24 (0.15), residues: 1431 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.043 0.002 TRP K 479 HIS 0.004 0.001 HIS A 374 PHE 0.027 0.001 PHE M 64 TYR 0.025 0.001 TYR M 94 ARG 0.004 0.000 ARG B 542 Details of bonding type rmsd link_NAG-ASN : bond 0.00468 ( 12) link_NAG-ASN : angle 1.71945 ( 36) link_ALPHA1-6 : bond 0.00659 ( 10) link_ALPHA1-6 : angle 1.69970 ( 30) link_BETA1-4 : bond 0.00606 ( 24) link_BETA1-4 : angle 2.08640 ( 72) link_ALPHA1-2 : bond 0.01309 ( 11) link_ALPHA1-2 : angle 2.42420 ( 33) link_ALPHA1-3 : bond 0.00860 ( 9) link_ALPHA1-3 : angle 1.42458 ( 27) hydrogen bonds : bond 0.03659 ( 486) hydrogen bonds : angle 5.40246 ( 1305) SS BOND : bond 0.00456 ( 45) SS BOND : angle 1.85023 ( 90) covalent geometry : bond 0.00333 (20463) covalent geometry : angle 0.73445 (27849) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4896 Ramachandran restraints generated. 2448 Oldfield, 0 Emsley, 2448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4896 Ramachandran restraints generated. 2448 Oldfield, 0 Emsley, 2448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 399 residues out of total 2142 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 312 time to evaluate : 2.381 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 84 LEU cc_start: 0.8118 (tp) cc_final: 0.7903 (tt) REVERT: A 104 MET cc_start: 0.8732 (ttm) cc_final: 0.7998 (tpp) REVERT: A 217 TYR cc_start: 0.8575 (m-10) cc_final: 0.7892 (m-10) REVERT: A 280 ASN cc_start: 0.8614 (m-40) cc_final: 0.8327 (t0) REVERT: A 317 PHE cc_start: 0.8775 (OUTLIER) cc_final: 0.7660 (p90) REVERT: A 439 ILE cc_start: 0.9597 (tp) cc_final: 0.9333 (mm) REVERT: B 530 MET cc_start: 0.8732 (mmm) cc_final: 0.8301 (mmm) REVERT: B 632 ASP cc_start: 0.8273 (t0) cc_final: 0.7906 (t0) REVERT: F 84 LEU cc_start: 0.8119 (tp) cc_final: 0.7805 (mt) REVERT: F 195 ASN cc_start: 0.8224 (t0) cc_final: 0.8017 (t0) REVERT: F 268 LYS cc_start: 0.8401 (ptmt) cc_final: 0.8040 (mttm) REVERT: F 423 ILE cc_start: 0.8830 (OUTLIER) cc_final: 0.8487 (mt) REVERT: H 51 MET cc_start: 0.7761 (tpp) cc_final: 0.7521 (ttt) REVERT: H 97 VAL cc_start: 0.8474 (OUTLIER) cc_final: 0.8247 (m) REVERT: I 234 LEU cc_start: 0.7911 (mt) cc_final: 0.7454 (mp) REVERT: K 49 LYS cc_start: 0.8391 (tttt) cc_final: 0.7944 (mtmt) REVERT: K 104 MET cc_start: 0.8567 (ttt) cc_final: 0.8267 (ttt) REVERT: K 268 LYS cc_start: 0.8604 (pttt) cc_final: 0.8400 (mmtt) REVERT: K 280 ASN cc_start: 0.7998 (m-40) cc_final: 0.7786 (t0) REVERT: K 369 MET cc_start: 0.7557 (tpp) cc_final: 0.6965 (ttt) REVERT: K 423 ILE cc_start: 0.9207 (mt) cc_final: 0.8766 (mt) REVERT: K 427 TRP cc_start: 0.8341 (m-10) cc_final: 0.8101 (m-10) REVERT: L 633 LYS cc_start: 0.9234 (pptt) cc_final: 0.8982 (pptt) REVERT: M 13 ASN cc_start: 0.8088 (p0) cc_final: 0.7468 (m110) REVERT: M 59 ASN cc_start: 0.8566 (t0) cc_final: 0.8091 (t0) outliers start: 87 outliers final: 75 residues processed: 375 average time/residue: 0.2783 time to fit residues: 167.9290 Evaluate side-chains 374 residues out of total 2142 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 296 time to evaluate : 2.386 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 VAL Chi-restraints excluded: chain A residue 85 VAL Chi-restraints excluded: chain A residue 102 ASP Chi-restraints excluded: chain A residue 128 THR Chi-restraints excluded: chain A residue 184 LEU Chi-restraints excluded: chain A residue 202 THR Chi-restraints excluded: chain A residue 203 GLN Chi-restraints excluded: chain A residue 215 ILE Chi-restraints excluded: chain A residue 245 VAL Chi-restraints excluded: chain A residue 265 LEU Chi-restraints excluded: chain A residue 297 THR Chi-restraints excluded: chain A residue 317 PHE Chi-restraints excluded: chain A residue 446 ARG Chi-restraints excluded: chain B residue 537 LEU Chi-restraints excluded: chain B residue 592 LEU Chi-restraints excluded: chain B residue 641 ILE Chi-restraints excluded: chain C residue 31 ASP Chi-restraints excluded: chain C residue 70 MET Chi-restraints excluded: chain C residue 76 ILE Chi-restraints excluded: chain C residue 97 VAL Chi-restraints excluded: chain D residue 248 ILE Chi-restraints excluded: chain D residue 259 VAL Chi-restraints excluded: chain D residue 306 THR Chi-restraints excluded: chain F residue 75 VAL Chi-restraints excluded: chain F residue 120 VAL Chi-restraints excluded: chain F residue 182 VAL Chi-restraints excluded: chain F residue 202 THR Chi-restraints excluded: chain F residue 215 ILE Chi-restraints excluded: chain F residue 271 VAL Chi-restraints excluded: chain F residue 289 HIS Chi-restraints excluded: chain F residue 292 VAL Chi-restraints excluded: chain F residue 297 THR Chi-restraints excluded: chain F residue 377 ASN Chi-restraints excluded: chain F residue 378 CYS Chi-restraints excluded: chain F residue 423 ILE Chi-restraints excluded: chain F residue 446 ARG Chi-restraints excluded: chain F residue 450 THR Chi-restraints excluded: chain G residue 583 VAL Chi-restraints excluded: chain G residue 595 ILE Chi-restraints excluded: chain G residue 606 THR Chi-restraints excluded: chain G residue 615 SER Chi-restraints excluded: chain G residue 624 ASP Chi-restraints excluded: chain G residue 647 GLU Chi-restraints excluded: chain H residue 18 VAL Chi-restraints excluded: chain H residue 63 ASN Chi-restraints excluded: chain H residue 74 THR Chi-restraints excluded: chain H residue 97 VAL Chi-restraints excluded: chain H residue 124 THR Chi-restraints excluded: chain I residue 253 THR Chi-restraints excluded: chain I residue 288 SER Chi-restraints excluded: chain I residue 295 SER Chi-restraints excluded: chain K residue 68 VAL Chi-restraints excluded: chain K residue 72 HIS Chi-restraints excluded: chain K residue 85 VAL Chi-restraints excluded: chain K residue 182 VAL Chi-restraints excluded: chain K residue 188 THR Chi-restraints excluded: chain K residue 202 THR Chi-restraints excluded: chain K residue 213 ILE Chi-restraints excluded: chain K residue 215 ILE Chi-restraints excluded: chain K residue 218 CYS Chi-restraints excluded: chain K residue 271 VAL Chi-restraints excluded: chain K residue 292 VAL Chi-restraints excluded: chain K residue 445 CYS Chi-restraints excluded: chain K residue 481 SER Chi-restraints excluded: chain K residue 501 CYS Chi-restraints excluded: chain L residue 580 VAL Chi-restraints excluded: chain L residue 581 LEU Chi-restraints excluded: chain L residue 608 VAL Chi-restraints excluded: chain L residue 615 SER Chi-restraints excluded: chain L residue 616 ASN Chi-restraints excluded: chain M residue 3 GLN Chi-restraints excluded: chain M residue 39 LEU Chi-restraints excluded: chain M residue 72 ARG Chi-restraints excluded: chain M residue 97 VAL Chi-restraints excluded: chain M residue 103 SER Chi-restraints excluded: chain N residue 240 VAL Chi-restraints excluded: chain N residue 257 TYR Chi-restraints excluded: chain N residue 339 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: chunk 229 optimal weight: 1.9990 chunk 74 optimal weight: 3.9990 chunk 161 optimal weight: 7.9990 chunk 163 optimal weight: 0.0970 chunk 108 optimal weight: 2.9990 chunk 49 optimal weight: 0.9980 chunk 16 optimal weight: 3.9990 chunk 217 optimal weight: 0.9990 chunk 31 optimal weight: 0.0170 chunk 164 optimal weight: 0.8980 chunk 8 optimal weight: 0.2980 overall best weight: 0.4616 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 577 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 287 HIS H 63 ASN ** H 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 236 GLN ** I 311 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 119 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 = 0.3942 r_free = 0.3942 target = 0.140731 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3543 r_free = 0.3543 target = 0.111405 restraints weight = 43600.681| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3543 r_free = 0.3543 target = 0.112546 restraints weight = 35267.947| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3555 r_free = 0.3555 target = 0.113471 restraints weight = 27059.191| |-----------------------------------------------------------------------------| r_work (final): 0.3561 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7802 moved from start: 0.7012 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 20574 Z= 0.134 Angle : 0.763 14.412 28137 Z= 0.375 Chirality : 0.046 0.195 3327 Planarity : 0.005 0.060 3456 Dihedral : 7.030 56.889 3954 Min Nonbonded Distance : 2.300 Molprobity Statistics. All-atom Clashscore : 8.67 Ramachandran Plot: Outliers : 0.25 % Allowed : 7.07 % Favored : 92.69 % Rotamer: Outliers : 3.50 % Allowed : 24.18 % Favored : 72.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.38 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.12 (0.16), residues: 2448 helix: -0.12 (0.30), residues: 339 sheet: -0.71 (0.18), residues: 702 loop : -2.20 (0.15), residues: 1407 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.046 0.002 TRP I 267 HIS 0.005 0.001 HIS A 374 PHE 0.026 0.001 PHE M 64 TYR 0.019 0.001 TYR B 643 ARG 0.005 0.000 ARG M 38 Details of bonding type rmsd link_NAG-ASN : bond 0.00461 ( 12) link_NAG-ASN : angle 1.62034 ( 36) link_ALPHA1-6 : bond 0.00609 ( 10) link_ALPHA1-6 : angle 1.64177 ( 30) link_BETA1-4 : bond 0.00605 ( 24) link_BETA1-4 : angle 2.01913 ( 72) link_ALPHA1-2 : bond 0.01316 ( 11) link_ALPHA1-2 : angle 2.40375 ( 33) link_ALPHA1-3 : bond 0.00884 ( 9) link_ALPHA1-3 : angle 1.36505 ( 27) hydrogen bonds : bond 0.03540 ( 486) hydrogen bonds : angle 5.33059 ( 1305) SS BOND : bond 0.00436 ( 45) SS BOND : angle 1.73037 ( 90) covalent geometry : bond 0.00302 (20463) covalent geometry : angle 0.74405 (27849) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4896 Ramachandran restraints generated. 2448 Oldfield, 0 Emsley, 2448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4896 Ramachandran restraints generated. 2448 Oldfield, 0 Emsley, 2448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 385 residues out of total 2142 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 310 time to evaluate : 2.131 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 104 MET cc_start: 0.8699 (ttm) cc_final: 0.8258 (tpp) REVERT: A 280 ASN cc_start: 0.8593 (m-40) cc_final: 0.8327 (t0) REVERT: B 530 MET cc_start: 0.8612 (mmm) cc_final: 0.8247 (mmm) REVERT: B 632 ASP cc_start: 0.8318 (t0) cc_final: 0.7919 (t0) REVERT: B 634 GLU cc_start: 0.7278 (mt-10) cc_final: 0.7073 (pt0) REVERT: C 31 ASP cc_start: 0.7347 (OUTLIER) cc_final: 0.7121 (t0) REVERT: D 301 ASN cc_start: 0.8656 (t0) cc_final: 0.8281 (t0) REVERT: F 84 LEU cc_start: 0.8106 (tp) cc_final: 0.7801 (mt) REVERT: F 104 MET cc_start: 0.8807 (ttt) cc_final: 0.8484 (tpp) REVERT: F 178 LYS cc_start: 0.8829 (OUTLIER) cc_final: 0.8502 (mttt) REVERT: F 195 ASN cc_start: 0.8219 (t0) cc_final: 0.8002 (t0) REVERT: F 268 LYS cc_start: 0.8371 (ptmt) cc_final: 0.8027 (mttm) REVERT: F 423 ILE cc_start: 0.8871 (OUTLIER) cc_final: 0.8614 (mt) REVERT: H 47 TRP cc_start: 0.8232 (t60) cc_final: 0.7875 (t60) REVERT: H 51 MET cc_start: 0.7755 (tpp) cc_final: 0.7529 (ttt) REVERT: H 97 VAL cc_start: 0.8454 (OUTLIER) cc_final: 0.8254 (m) REVERT: I 234 LEU cc_start: 0.7879 (mt) cc_final: 0.7426 (mp) REVERT: K 49 LYS cc_start: 0.8307 (tttt) cc_final: 0.7854 (mtmt) REVERT: K 104 MET cc_start: 0.8532 (ttt) cc_final: 0.8215 (ttt) REVERT: K 280 ASN cc_start: 0.8019 (m-40) cc_final: 0.7808 (t0) REVERT: K 369 MET cc_start: 0.7592 (tpp) cc_final: 0.6933 (ttt) REVERT: K 390 LEU cc_start: 0.7149 (OUTLIER) cc_final: 0.6933 (mt) REVERT: K 423 ILE cc_start: 0.9188 (mt) cc_final: 0.8770 (mt) REVERT: L 633 LYS cc_start: 0.9248 (pptt) cc_final: 0.8983 (pptt) REVERT: M 13 ASN cc_start: 0.8099 (p0) cc_final: 0.7496 (m-40) REVERT: M 51 MET cc_start: 0.7551 (tpp) cc_final: 0.7290 (ttt) REVERT: M 59 ASN cc_start: 0.8524 (t0) cc_final: 0.8042 (t0) outliers start: 75 outliers final: 64 residues processed: 363 average time/residue: 0.2601 time to fit residues: 153.6367 Evaluate side-chains 366 residues out of total 2142 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 297 time to evaluate : 2.218 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 VAL Chi-restraints excluded: chain A residue 85 VAL Chi-restraints excluded: chain A residue 102 ASP Chi-restraints excluded: chain A residue 128 THR Chi-restraints excluded: chain A residue 184 LEU Chi-restraints excluded: chain A residue 202 THR Chi-restraints excluded: chain A residue 203 GLN Chi-restraints excluded: chain A residue 215 ILE Chi-restraints excluded: chain A residue 245 VAL Chi-restraints excluded: chain A residue 265 LEU Chi-restraints excluded: chain A residue 288 LEU Chi-restraints excluded: chain A residue 297 THR Chi-restraints excluded: chain A residue 446 ARG Chi-restraints excluded: chain B residue 592 LEU Chi-restraints excluded: chain B residue 641 ILE Chi-restraints excluded: chain C residue 31 ASP Chi-restraints excluded: chain C residue 69 THR Chi-restraints excluded: chain C residue 76 ILE Chi-restraints excluded: chain C residue 97 VAL Chi-restraints excluded: chain D residue 248 ILE Chi-restraints excluded: chain D residue 259 VAL Chi-restraints excluded: chain D residue 306 THR Chi-restraints excluded: chain F residue 75 VAL Chi-restraints excluded: chain F residue 120 VAL Chi-restraints excluded: chain F residue 178 LYS Chi-restraints excluded: chain F residue 182 VAL Chi-restraints excluded: chain F residue 202 THR Chi-restraints excluded: chain F residue 215 ILE Chi-restraints excluded: chain F residue 271 VAL Chi-restraints excluded: chain F residue 289 HIS Chi-restraints excluded: chain F residue 292 VAL Chi-restraints excluded: chain F residue 297 THR Chi-restraints excluded: chain F residue 377 ASN Chi-restraints excluded: chain F residue 378 CYS Chi-restraints excluded: chain F residue 423 ILE Chi-restraints excluded: chain F residue 450 THR Chi-restraints excluded: chain G residue 583 VAL Chi-restraints excluded: chain G residue 595 ILE Chi-restraints excluded: chain G residue 624 ASP Chi-restraints excluded: chain H residue 18 VAL Chi-restraints excluded: chain H residue 63 ASN Chi-restraints excluded: chain H residue 74 THR Chi-restraints excluded: chain H residue 97 VAL Chi-restraints excluded: chain H residue 124 THR Chi-restraints excluded: chain I residue 253 THR Chi-restraints excluded: chain I residue 288 SER Chi-restraints excluded: chain I residue 295 SER Chi-restraints excluded: chain K residue 68 VAL Chi-restraints excluded: chain K residue 72 HIS Chi-restraints excluded: chain K residue 85 VAL Chi-restraints excluded: chain K residue 182 VAL Chi-restraints excluded: chain K residue 202 THR Chi-restraints excluded: chain K residue 215 ILE Chi-restraints excluded: chain K residue 218 CYS Chi-restraints excluded: chain K residue 292 VAL Chi-restraints excluded: chain K residue 390 LEU Chi-restraints excluded: chain K residue 445 CYS Chi-restraints excluded: chain K residue 481 SER Chi-restraints excluded: chain K residue 501 CYS Chi-restraints excluded: chain L residue 580 VAL Chi-restraints excluded: chain L residue 581 LEU Chi-restraints excluded: chain L residue 608 VAL Chi-restraints excluded: chain L residue 615 SER Chi-restraints excluded: chain L residue 616 ASN Chi-restraints excluded: chain M residue 39 LEU Chi-restraints excluded: chain M residue 97 VAL Chi-restraints excluded: chain N residue 240 VAL Chi-restraints excluded: chain N residue 257 TYR Chi-restraints excluded: chain N residue 339 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: chunk 38 optimal weight: 0.3980 chunk 28 optimal weight: 2.9990 chunk 79 optimal weight: 0.7980 chunk 191 optimal weight: 1.9990 chunk 121 optimal weight: 3.9990 chunk 126 optimal weight: 1.9990 chunk 153 optimal weight: 0.9990 chunk 118 optimal weight: 3.9990 chunk 149 optimal weight: 0.9990 chunk 69 optimal weight: 0.9990 chunk 154 optimal weight: 0.6980 overall best weight: 0.7784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 577 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 607 ASN ** D 271 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 63 ASN ** H 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 311 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3934 r_free = 0.3934 target = 0.140076 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3536 r_free = 0.3536 target = 0.110943 restraints weight = 43916.421| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3526 r_free = 0.3526 target = 0.111371 restraints weight = 34679.173| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.112655 restraints weight = 29376.945| |-----------------------------------------------------------------------------| r_work (final): 0.3548 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7822 moved from start: 0.7124 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 20574 Z= 0.145 Angle : 0.750 12.695 28137 Z= 0.370 Chirality : 0.046 0.200 3327 Planarity : 0.005 0.060 3456 Dihedral : 6.888 57.356 3954 Min Nonbonded Distance : 2.285 Molprobity Statistics. All-atom Clashscore : 9.20 Ramachandran Plot: Outliers : 0.25 % Allowed : 6.78 % Favored : 92.97 % Rotamer: Outliers : 3.83 % Allowed : 24.23 % Favored : 71.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.38 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.12 (0.16), residues: 2448 helix: -0.22 (0.29), residues: 357 sheet: -0.68 (0.18), residues: 708 loop : -2.21 (0.15), residues: 1383 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.043 0.002 TRP I 267 HIS 0.004 0.001 HIS A 374 PHE 0.025 0.001 PHE M 64 TYR 0.018 0.001 TYR B 643 ARG 0.003 0.000 ARG B 542 Details of bonding type rmsd link_NAG-ASN : bond 0.00449 ( 12) link_NAG-ASN : angle 1.68463 ( 36) link_ALPHA1-6 : bond 0.00610 ( 10) link_ALPHA1-6 : angle 1.59552 ( 30) link_BETA1-4 : bond 0.00596 ( 24) link_BETA1-4 : angle 2.00702 ( 72) link_ALPHA1-2 : bond 0.01322 ( 11) link_ALPHA1-2 : angle 2.38605 ( 33) link_ALPHA1-3 : bond 0.00832 ( 9) link_ALPHA1-3 : angle 1.39845 ( 27) hydrogen bonds : bond 0.03620 ( 486) hydrogen bonds : angle 5.36708 ( 1305) SS BOND : bond 0.00439 ( 45) SS BOND : angle 1.70750 ( 90) covalent geometry : bond 0.00333 (20463) covalent geometry : angle 0.73012 (27849) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6303.79 seconds wall clock time: 111 minutes 54.11 seconds (6714.11 seconds total)