Starting phenix.real_space_refine (version: 1.21rc1) on Mon May 8 18:35:13 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sas_40278/05_2023/8sas_40278_neut.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sas_40278/05_2023/8sas_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sas_40278/05_2023/8sas_40278.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sas_40278/05_2023/8sas_40278.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sas_40278/05_2023/8sas_40278_neut.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sas_40278/05_2023/8sas_40278_neut.pdb" } resolution = 4.0 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- 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 Residue "A PHE 159": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 191": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 435": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 159": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 217": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 522": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K TYR 191": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K TYR 217": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K TYR 361": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K TYR 484": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4953/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 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 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 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 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 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 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 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 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 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 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 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 chiralities: 4 Time building chain proxies: 9.91, per 1000 atoms: 0.49 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 - 3.50 Amino acid : False - 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: 9.61 Conformation dependent library (CDL) restraints added in 2.9 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: 1.37 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: 6.37 Time building geometry restraints manager: 10.17 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: 98.33 - 105.86: 467 105.86 - 113.40: 11464 113.40 - 120.93: 8814 120.93 - 128.46: 6840 128.46 - 136.00: 264 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 - 17.73: 10634 17.73 - 35.45: 912 35.45 - 53.18: 150 53.18 - 70.91: 27 70.91 - 88.64: 25 Dihedral angle restraints: 11748 sinusoidal: 4638 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 11745 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 2.440 nonbonded pdb=" OG SER I 299 " pdb=" O THR I 302 " model vdw 2.042 2.440 nonbonded pdb=" OG1 THR F 163 " pdb=" OE1 GLU F 164 " model vdw 2.047 2.440 nonbonded pdb=" O VAL F 36 " pdb=" OG1 THR G 606 " model vdw 2.060 2.440 nonbonded pdb=" OG1 THR F 161 " pdb=" O LYS F 170 " model vdw 2.077 2.440 ... (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 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: 2.670 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: 0.030 Extract box with map and model: 12.740 Check model and map are aligned: 0.260 Set scattering table: 0.160 Process input model: 52.260 Find NCS groups from input model: 1.140 Set up NCS constraints: 0.200 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:3.010 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 72.470 ------------------------------------------------------------------------------- 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 20463 Z= 0.522 Angle : 1.182 15.665 27849 Z= 0.631 Chirality : 0.061 0.305 3327 Planarity : 0.008 0.151 3456 Dihedral : 13.803 88.636 7065 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 % 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 *********************** 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 fitting. rotamer outliers: 0 poor density : 748 time to evaluate : 2.340 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 outliers start: 0 outliers final: 0 residues processed: 748 average time/residue: 0.3342 time to fit residues: 369.5033 Evaluate side-chains 361 residues out of total 2142 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 361 time to evaluate : 2.173 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.9356 ------------------------------------------------------------------------------- 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: 0.7980 chunk 184 optimal weight: 0.8980 chunk 102 optimal weight: 1.9990 chunk 62 optimal weight: 1.9990 chunk 124 optimal weight: 0.8980 chunk 98 optimal weight: 0.0570 chunk 190 optimal weight: 1.9990 chunk 73 optimal weight: 1.9990 chunk 115 optimal weight: 0.8980 chunk 141 optimal weight: 0.7980 chunk 220 optimal weight: 0.1980 overall best weight: 0.5498 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 280 ASN B 577 GLN D 271 HIS F 287 HIS F 300 ASN F 330 HIS F 417 GLN G 577 GLN G 630 GLN ** H 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 116 HIS I 292 HIS ** K 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 651 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7394 moved from start: 0.3618 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.063 20463 Z= 0.239 Angle : 0.806 11.920 27849 Z= 0.409 Chirality : 0.049 0.286 3327 Planarity : 0.006 0.091 3456 Dihedral : 6.664 33.745 2652 Min Nonbonded Distance : 2.096 Molprobity Statistics. All-atom Clashscore : 9.23 Ramachandran Plot: Outliers : 0.33 % Allowed : 6.41 % Favored : 93.26 % Rotamer Outliers : 3.97 % 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: -2.61 (0.16), residues: 2448 helix: -1.19 (0.29), residues: 303 sheet: -1.38 (0.19), residues: 645 loop : -2.08 (0.15), residues: 1500 *********************** 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 500 residues out of total 2142 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 85 poor density : 415 time to evaluate : 2.417 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 outliers start: 85 outliers final: 48 residues processed: 462 average time/residue: 0.3145 time to fit residues: 223.5147 Evaluate side-chains 374 residues out of total 2142 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 326 time to evaluate : 2.311 Switching outliers to nearest non-outliers outliers start: 48 outliers final: 0 residues processed: 48 average time/residue: 0.1952 time to fit residues: 20.4721 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: chunk 122 optimal weight: 4.9990 chunk 68 optimal weight: 3.9990 chunk 183 optimal weight: 2.9990 chunk 150 optimal weight: 0.8980 chunk 60 optimal weight: 3.9990 chunk 221 optimal weight: 0.2980 chunk 238 optimal weight: 0.0670 chunk 196 optimal weight: 0.9990 chunk 219 optimal weight: 6.9990 chunk 75 optimal weight: 0.0060 chunk 177 optimal weight: 0.9990 overall best weight: 0.4536 ------------------------------------------------------------------------------- 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** D 246 GLN F 246 GLN F 302 ASN F 362 ASN F 417 GLN ** H 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7457 moved from start: 0.4275 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.065 20463 Z= 0.190 Angle : 0.710 11.485 27849 Z= 0.357 Chirality : 0.046 0.215 3327 Planarity : 0.005 0.069 3456 Dihedral : 6.095 34.349 2652 Min Nonbonded Distance : 2.131 Molprobity Statistics. All-atom Clashscore : 9.38 Ramachandran Plot: Outliers : 0.33 % Allowed : 6.17 % Favored : 93.50 % Rotamer Outliers : 2.52 % 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: -0.83 (0.29), residues: 311 sheet: -1.20 (0.19), residues: 691 loop : -2.05 (0.15), residues: 1446 *********************** 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 421 residues out of total 2142 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 367 time to evaluate : 2.429 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 54 outliers final: 24 residues processed: 396 average time/residue: 0.2979 time to fit residues: 186.3041 Evaluate side-chains 318 residues out of total 2142 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 294 time to evaluate : 2.163 Switching outliers to nearest non-outliers outliers start: 24 outliers final: 0 residues processed: 24 average time/residue: 0.1899 time to fit residues: 11.7510 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: chunk 218 optimal weight: 3.9990 chunk 166 optimal weight: 7.9990 chunk 114 optimal weight: 4.9990 chunk 24 optimal weight: 0.0770 chunk 105 optimal weight: 4.9990 chunk 148 optimal weight: 2.9990 chunk 221 optimal weight: 5.9990 chunk 234 optimal weight: 8.9990 chunk 115 optimal weight: 1.9990 chunk 210 optimal weight: 3.9990 chunk 63 optimal weight: 2.9990 overall best weight: 2.4146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 279 ASN A 289 HIS A 300 ASN ** B 577 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 63 ASN ** F 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 105 HIS ** F 417 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 591 GLN ** K 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 374 HIS ** L 575 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 6 GLN ** M 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7796 moved from start: 0.5628 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.007 0.085 20463 Z= 0.478 Angle : 0.896 12.423 27849 Z= 0.452 Chirality : 0.052 0.236 3327 Planarity : 0.006 0.083 3456 Dihedral : 6.546 34.188 2652 Min Nonbonded Distance : 1.930 Molprobity Statistics. All-atom Clashscore : 14.59 Ramachandran Plot: Outliers : 0.33 % Allowed : 8.62 % Favored : 91.05 % Rotamer Outliers : 4.44 % 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 (0.15), residues: 2448 helix: -1.16 (0.27), residues: 333 sheet: -1.31 (0.19), residues: 665 loop : -2.23 (0.14), residues: 1450 *********************** 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 437 residues out of total 2142 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 95 poor density : 342 time to evaluate : 2.245 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 outliers start: 95 outliers final: 64 residues processed: 405 average time/residue: 0.2939 time to fit residues: 187.2981 Evaluate side-chains 351 residues out of total 2142 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 287 time to evaluate : 2.322 Switching outliers to nearest non-outliers outliers start: 64 outliers final: 0 residues processed: 64 average time/residue: 0.2054 time to fit residues: 27.2835 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: chunk 195 optimal weight: 0.7980 chunk 133 optimal weight: 0.7980 chunk 3 optimal weight: 0.0030 chunk 174 optimal weight: 1.9990 chunk 96 optimal weight: 0.8980 chunk 200 optimal weight: 0.9990 chunk 162 optimal weight: 3.9990 chunk 0 optimal weight: 3.9990 chunk 119 optimal weight: 0.9990 chunk 210 optimal weight: 0.2980 chunk 59 optimal weight: 5.9990 overall best weight: 0.5590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 417 GLN ** G 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 246 GLN K 422 GLN ** L 575 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7696 moved from start: 0.5829 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.058 20463 Z= 0.193 Angle : 0.717 12.015 27849 Z= 0.358 Chirality : 0.046 0.212 3327 Planarity : 0.005 0.059 3456 Dihedral : 5.949 34.966 2652 Min Nonbonded Distance : 2.078 Molprobity Statistics. All-atom Clashscore : 11.08 Ramachandran Plot: Outliers : 0.33 % Allowed : 6.05 % Favored : 93.63 % Rotamer Outliers : 1.91 % 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: -2.47 (0.16), residues: 2448 helix: -0.75 (0.29), residues: 331 sheet: -1.11 (0.18), residues: 669 loop : -2.19 (0.15), residues: 1448 *********************** 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 381 residues out of total 2142 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 340 time to evaluate : 2.365 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 outliers start: 41 outliers final: 16 residues processed: 367 average time/residue: 0.2986 time to fit residues: 173.9354 Evaluate side-chains 309 residues out of total 2142 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 293 time to evaluate : 2.495 Switching outliers to nearest non-outliers outliers start: 16 outliers final: 0 residues processed: 16 average time/residue: 0.2287 time to fit residues: 9.3044 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: chunk 79 optimal weight: 0.7980 chunk 211 optimal weight: 1.9990 chunk 46 optimal weight: 3.9990 chunk 137 optimal weight: 0.8980 chunk 57 optimal weight: 0.8980 chunk 235 optimal weight: 0.8980 chunk 195 optimal weight: 1.9990 chunk 108 optimal weight: 0.0970 chunk 19 optimal weight: 4.9990 chunk 77 optimal weight: 10.0000 chunk 123 optimal weight: 0.0980 overall best weight: 0.5578 ------------------------------------------------------------------------------- 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** ** C 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 246 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 271 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 575 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 59 ASN ** M 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7701 moved from start: 0.6075 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.057 20463 Z= 0.193 Angle : 0.702 10.933 27849 Z= 0.348 Chirality : 0.045 0.223 3327 Planarity : 0.005 0.076 3456 Dihedral : 5.711 31.974 2652 Min Nonbonded Distance : 2.077 Molprobity Statistics. All-atom Clashscore : 11.51 Ramachandran Plot: Outliers : 0.29 % Allowed : 7.07 % Favored : 92.65 % Rotamer Outliers : 2.29 % 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: -0.43 (0.30), residues: 325 sheet: -1.04 (0.18), residues: 672 loop : -2.10 (0.15), residues: 1451 *********************** 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 374 residues out of total 2142 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 325 time to evaluate : 2.435 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 outliers start: 49 outliers final: 32 residues processed: 355 average time/residue: 0.2902 time to fit residues: 163.7603 Evaluate side-chains 323 residues out of total 2142 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 291 time to evaluate : 2.268 Switching outliers to nearest non-outliers outliers start: 32 outliers final: 0 residues processed: 32 average time/residue: 0.1965 time to fit residues: 14.5060 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: chunk 226 optimal weight: 5.9990 chunk 26 optimal weight: 0.8980 chunk 133 optimal weight: 0.8980 chunk 171 optimal weight: 2.9990 chunk 197 optimal weight: 5.9990 chunk 131 optimal weight: 0.0470 chunk 234 optimal weight: 5.9990 chunk 146 optimal weight: 0.7980 chunk 142 optimal weight: 1.9990 chunk 108 optimal weight: 0.9990 chunk 144 optimal weight: 0.5980 overall best weight: 0.6478 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 280 ASN ** B 577 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 246 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 271 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 311 GLN ** K 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 262 ASN ** L 575 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 59 ASN ** M 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7704 moved from start: 0.6297 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.084 20463 Z= 0.207 Angle : 0.696 10.877 27849 Z= 0.345 Chirality : 0.045 0.204 3327 Planarity : 0.004 0.069 3456 Dihedral : 5.584 31.942 2652 Min Nonbonded Distance : 2.054 Molprobity Statistics. All-atom Clashscore : 11.33 Ramachandran Plot: Outliers : 0.29 % Allowed : 6.45 % Favored : 93.26 % Rotamer Outliers : 1.17 % 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: -0.37 (0.29), residues: 336 sheet: -0.91 (0.19), residues: 642 loop : -2.05 (0.15), residues: 1470 *********************** 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 335 residues out of total 2142 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 310 time to evaluate : 2.223 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 25 outliers final: 14 residues processed: 329 average time/residue: 0.2847 time to fit residues: 150.5405 Evaluate side-chains 301 residues out of total 2142 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 287 time to evaluate : 2.284 Switching outliers to nearest non-outliers outliers start: 14 outliers final: 0 residues processed: 14 average time/residue: 0.1724 time to fit residues: 7.7137 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: chunk 93 optimal weight: 2.9990 chunk 139 optimal weight: 3.9990 chunk 70 optimal weight: 7.9990 chunk 46 optimal weight: 4.9990 chunk 45 optimal weight: 2.9990 chunk 148 optimal weight: 3.9990 chunk 159 optimal weight: 7.9990 chunk 115 optimal weight: 1.9990 chunk 21 optimal weight: 2.9990 chunk 184 optimal weight: 3.9990 chunk 213 optimal weight: 2.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 389 ASN ** C 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 63 ASN ** D 271 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 279 ASN ** H 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 63 ASN ** K 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 575 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 246 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7891 moved from start: 0.6932 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.008 0.135 20463 Z= 0.541 Angle : 0.905 13.885 27849 Z= 0.453 Chirality : 0.051 0.243 3327 Planarity : 0.006 0.076 3456 Dihedral : 6.280 33.247 2652 Min Nonbonded Distance : 2.035 Molprobity Statistics. All-atom Clashscore : 16.80 Ramachandran Plot: Outliers : 0.29 % Allowed : 8.99 % Favored : 90.73 % Rotamer Outliers : 2.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.38 % Twisted Proline : 0.00 % Twisted General : 0.17 % 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 (0.16), residues: 2448 helix: -0.75 (0.29), residues: 339 sheet: -0.98 (0.19), residues: 675 loop : -2.21 (0.15), residues: 1434 *********************** 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 353 residues out of total 2142 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 297 time to evaluate : 2.310 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 56 outliers final: 42 residues processed: 328 average time/residue: 0.2965 time to fit residues: 156.8168 Evaluate side-chains 317 residues out of total 2142 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 275 time to evaluate : 2.348 Switching outliers to nearest non-outliers outliers start: 42 outliers final: 0 residues processed: 42 average time/residue: 0.1941 time to fit residues: 18.2455 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: chunk 224 optimal weight: 0.3980 chunk 204 optimal weight: 2.9990 chunk 218 optimal weight: 1.9990 chunk 131 optimal weight: 0.8980 chunk 95 optimal weight: 0.7980 chunk 171 optimal weight: 0.5980 chunk 66 optimal weight: 6.9990 chunk 197 optimal weight: 4.9990 chunk 206 optimal weight: 0.6980 chunk 217 optimal weight: 2.9990 chunk 143 optimal weight: 0.7980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 577 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 271 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 279 ASN ** H 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 287 HIS ** L 575 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: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7789 moved from start: 0.6978 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.057 20463 Z= 0.219 Angle : 0.771 18.526 27849 Z= 0.383 Chirality : 0.047 0.491 3327 Planarity : 0.005 0.068 3456 Dihedral : 5.860 34.986 2652 Min Nonbonded Distance : 2.121 Molprobity Statistics. All-atom Clashscore : 13.09 Ramachandran Plot: Outliers : 0.29 % Allowed : 6.58 % Favored : 93.14 % Rotamer Outliers : 0.47 % 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: -0.58 (0.29), residues: 342 sheet: -0.87 (0.19), residues: 636 loop : -2.12 (0.15), residues: 1470 *********************** 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 323 residues out of total 2142 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 313 time to evaluate : 2.511 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 outliers start: 10 outliers final: 5 residues processed: 319 average time/residue: 0.2950 time to fit residues: 151.3734 Evaluate side-chains 293 residues out of total 2142 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 288 time to evaluate : 2.263 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.1895 time to fit residues: 4.9158 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: chunk 230 optimal weight: 2.9990 chunk 140 optimal weight: 0.0170 chunk 109 optimal weight: 2.9990 chunk 160 optimal weight: 2.9990 chunk 242 optimal weight: 0.9980 chunk 222 optimal weight: 0.9980 chunk 192 optimal weight: 4.9990 chunk 20 optimal weight: 1.9990 chunk 148 optimal weight: 4.9990 chunk 118 optimal weight: 1.9990 chunk 153 optimal weight: 2.9990 overall best weight: 1.2022 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 577 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 271 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 279 ASN ** H 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 575 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: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7821 moved from start: 0.7175 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.067 20463 Z= 0.277 Angle : 0.770 14.721 27849 Z= 0.382 Chirality : 0.047 0.334 3327 Planarity : 0.005 0.073 3456 Dihedral : 5.823 34.042 2652 Min Nonbonded Distance : 2.120 Molprobity Statistics. All-atom Clashscore : 14.28 Ramachandran Plot: Outliers : 0.29 % Allowed : 8.42 % Favored : 91.30 % Rotamer Outliers : 0.61 % 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: -2.23 (0.16), residues: 2448 helix: -0.60 (0.29), residues: 342 sheet: -0.80 (0.19), residues: 669 loop : -2.12 (0.15), residues: 1437 ********************** 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 311 residues out of total 2142 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 298 time to evaluate : 2.330 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 outliers start: 13 outliers final: 9 residues processed: 304 average time/residue: 0.2907 time to fit residues: 142.1247 Evaluate side-chains 292 residues out of total 2142 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 283 time to evaluate : 2.333 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 0 residues processed: 9 average time/residue: 0.2253 time to fit residues: 6.5309 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: chunk 205 optimal weight: 2.9990 chunk 59 optimal weight: 20.0000 chunk 177 optimal weight: 2.9990 chunk 28 optimal weight: 1.9990 chunk 53 optimal weight: 0.9990 chunk 193 optimal weight: 10.0000 chunk 80 optimal weight: 0.9980 chunk 198 optimal weight: 7.9990 chunk 24 optimal weight: 2.9990 chunk 35 optimal weight: 0.8980 chunk 169 optimal weight: 2.9990 overall best weight: 1.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 577 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 62 GLN ** D 271 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 651 ASN ** H 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 575 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 651 ASN ** 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 = 0.3893 r_free = 0.3893 target = 0.136986 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3489 r_free = 0.3489 target = 0.107998 restraints weight = 44093.650| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3474 r_free = 0.3474 target = 0.108109 restraints weight = 33792.830| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3493 r_free = 0.3493 target = 0.109542 restraints weight = 29749.230| |-----------------------------------------------------------------------------| r_work (final): 0.3499 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7899 moved from start: 0.7423 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.078 20463 Z= 0.327 Angle : 0.790 14.108 27849 Z= 0.393 Chirality : 0.048 0.297 3327 Planarity : 0.005 0.066 3456 Dihedral : 5.894 33.617 2652 Min Nonbonded Distance : 2.036 Molprobity Statistics. All-atom Clashscore : 14.56 Ramachandran Plot: Outliers : 0.29 % Allowed : 8.33 % Favored : 91.38 % Rotamer Outliers : 0.75 % 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: -2.21 (0.16), residues: 2448 helix: -0.44 (0.29), residues: 327 sheet: -0.79 (0.19), residues: 669 loop : -2.14 (0.15), residues: 1452 =============================================================================== Job complete usr+sys time: 4215.78 seconds wall clock time: 77 minutes 49.34 seconds (4669.34 seconds total)