Starting phenix.real_space_refine on Mon Mar 18 04:30:40 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sax_40283/03_2024/8sax_40283_neut.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sax_40283/03_2024/8sax_40283.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/8sax_40283/03_2024/8sax_40283.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sax_40283/03_2024/8sax_40283.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sax_40283/03_2024/8sax_40283_neut.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sax_40283/03_2024/8sax_40283_neut.pdb" } 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= 0.058 sd= 0.370 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 135 5.16 5 C 12405 2.51 5 N 3330 2.21 5 O 3990 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 176": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 223": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 382": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 27": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 89": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 176": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 223": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 382": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 27": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 89": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 176": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 223": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 382": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K TYR 27": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 89": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 19860 Number of models: 1 Model: "" Number of chains: 24 Chain: "A" Number of atoms: 3582 Number of conformers: 1 Conformer: "" Number of residues, atoms: 462, 3582 Classifications: {'peptide': 462} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PCIS': 1, 'PTRANS': 22, 'TRANS': 438} Unresolved non-hydrogen bonds: 33 Unresolved non-hydrogen angles: 43 Unresolved non-hydrogen dihedrals: 28 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'TYR:plan': 1, 'GLU:plan': 2, 'ASN:plan1': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 23 Chain: "B" Number of atoms: 1034 Number of conformers: 1 Conformer: "" Number of residues, atoms: 132, 1034 Classifications: {'peptide': 132} Link IDs: {'PTRANS': 1, 'TRANS': 130} Chain: "C" Number of atoms: 993 Number of conformers: 1 Conformer: "" Number of residues, atoms: 127, 993 Classifications: {'peptide': 127} Link IDs: {'PTRANS': 4, 'TRANS': 122} Chain: "D" Number of atoms: 800 Number of conformers: 1 Conformer: "" Number of residues, atoms: 111, 800 Classifications: {'peptide': 111} Link IDs: {'PTRANS': 5, 'TRANS': 105} Chain: "E" Number of atoms: 3582 Number of conformers: 1 Conformer: "" Number of residues, atoms: 462, 3582 Classifications: {'peptide': 462} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PCIS': 1, 'PTRANS': 22, 'TRANS': 438} Unresolved non-hydrogen bonds: 33 Unresolved non-hydrogen angles: 43 Unresolved non-hydrogen dihedrals: 28 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'TYR:plan': 1, 'GLU:plan': 2, 'ASN:plan1': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 23 Chain: "F" Number of atoms: 1034 Number of conformers: 1 Conformer: "" Number of residues, atoms: 132, 1034 Classifications: {'peptide': 132} Link IDs: {'PTRANS': 1, 'TRANS': 130} Chain: "G" Number of atoms: 993 Number of conformers: 1 Conformer: "" Number of residues, atoms: 127, 993 Classifications: {'peptide': 127} Link IDs: {'PTRANS': 4, 'TRANS': 122} Chain: "H" Number of atoms: 800 Number of conformers: 1 Conformer: "" Number of residues, atoms: 111, 800 Classifications: {'peptide': 111} Link IDs: {'PTRANS': 5, 'TRANS': 105} Chain: "I" Number of atoms: 3582 Number of conformers: 1 Conformer: "" Number of residues, atoms: 462, 3582 Classifications: {'peptide': 462} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PCIS': 1, 'PTRANS': 22, 'TRANS': 438} Unresolved non-hydrogen bonds: 33 Unresolved non-hydrogen angles: 43 Unresolved non-hydrogen dihedrals: 28 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'TYR:plan': 1, 'GLU:plan': 2, 'ASN:plan1': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 23 Chain: "J" Number of atoms: 1034 Number of conformers: 1 Conformer: "" Number of residues, atoms: 132, 1034 Classifications: {'peptide': 132} Link IDs: {'PTRANS': 1, 'TRANS': 130} Chain: "K" Number of atoms: 993 Number of conformers: 1 Conformer: "" Number of residues, atoms: 127, 993 Classifications: {'peptide': 127} Link IDs: {'PTRANS': 4, 'TRANS': 122} Chain: "L" Number of atoms: 800 Number of conformers: 1 Conformer: "" Number of residues, atoms: 111, 800 Classifications: {'peptide': 111} Link IDs: {'PTRANS': 5, 'TRANS': 105} Chain: "M" 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: "N" 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: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "P" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Q" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "R" Number of atoms: 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: "S" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "T" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "U" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "V" Number of atoms: 105 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 105 Unusual residues: {'BMA': 1, 'MAN': 6, 'NAG': 2} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 9 Chain: "W" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "X" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Time building chain proxies: 10.89, per 1000 atoms: 0.55 Number of scatterers: 19860 At special positions: 0 Unit cell: (165.24, 166.86, 142.56, 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 135 16.00 O 3990 8.00 N 3330 7.00 C 12405 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=30, symmetry=0 Simple disulfide: pdb=" SG CYS A 54 " - pdb=" SG CYS A 74 " distance=2.03 Simple disulfide: pdb=" SG CYS A 119 " - pdb=" SG CYS A 205 " distance=2.03 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 157 " distance=2.03 Simple disulfide: pdb=" SG CYS A 201 " - pdb=" SG CYS A 433 " distance=2.03 Simple disulfide: pdb=" SG CYS A 218 " - pdb=" SG CYS A 247 " distance=2.03 Simple disulfide: pdb=" SG CYS A 228 " - pdb=" SG CYS A 239 " distance=2.03 Simple disulfide: pdb=" SG CYS A 378 " - pdb=" SG CYS A 445 " 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 22 " - pdb=" SG CYS D 90 " distance=2.03 Simple disulfide: pdb=" SG CYS E 54 " - pdb=" SG CYS E 74 " distance=2.03 Simple disulfide: pdb=" SG CYS E 119 " - pdb=" SG CYS E 205 " distance=2.03 Simple disulfide: pdb=" SG CYS E 131 " - pdb=" SG CYS E 157 " distance=2.03 Simple disulfide: pdb=" SG CYS E 201 " - pdb=" SG CYS E 433 " distance=2.03 Simple disulfide: pdb=" SG CYS E 218 " - pdb=" SG CYS E 247 " distance=2.03 Simple disulfide: pdb=" SG CYS E 228 " - pdb=" SG CYS E 239 " distance=2.03 Simple disulfide: pdb=" SG CYS E 378 " - pdb=" SG CYS E 445 " distance=2.03 Simple disulfide: pdb=" SG CYS F 598 " - pdb=" SG CYS F 604 " distance=2.03 Simple disulfide: pdb=" SG CYS G 22 " - pdb=" SG CYS G 96 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 90 " distance=2.04 Simple disulfide: pdb=" SG CYS I 54 " - pdb=" SG CYS I 74 " distance=2.04 Simple disulfide: pdb=" SG CYS I 119 " - pdb=" SG CYS I 205 " distance=2.03 Simple disulfide: pdb=" SG CYS I 131 " - pdb=" SG CYS I 157 " distance=2.03 Simple disulfide: pdb=" SG CYS I 201 " - pdb=" SG CYS I 433 " distance=2.03 Simple disulfide: pdb=" SG CYS I 218 " - pdb=" SG CYS I 247 " distance=2.03 Simple disulfide: pdb=" SG CYS I 228 " - pdb=" SG CYS I 239 " distance=2.03 Simple disulfide: pdb=" SG CYS I 378 " - pdb=" SG CYS I 445 " distance=2.03 Simple disulfide: pdb=" SG CYS J 598 " - pdb=" SG CYS J 604 " distance=2.03 Simple disulfide: pdb=" SG CYS K 22 " - pdb=" SG CYS K 96 " distance=2.03 Simple disulfide: pdb=" SG CYS L 22 " - pdb=" SG CYS L 90 " 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 N 4 " - " MAN N 5 " " MAN N 5 " - " MAN N 6 " " MAN R 4 " - " MAN R 5 " " MAN R 5 " - " MAN R 6 " " MAN V 4 " - " MAN V 5 " " MAN V 5 " - " MAN V 6 " ALPHA1-3 " BMA M 3 " - " MAN M 4 " " BMA N 3 " - " MAN N 4 " " MAN N 7 " - " MAN N 8 " " 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 " ALPHA1-6 " BMA N 3 " - " MAN N 7 " " MAN N 7 " - " MAN N 9 " " BMA R 3 " - " MAN R 7 " " MAN R 7 " - " MAN R 9 " " BMA V 3 " - " MAN V 7 " " MAN V 7 " - " MAN V 9 " BETA1-4 " NAG M 1 " - " NAG M 2 " " NAG M 2 " - " BMA M 3 " " NAG N 1 " - " NAG N 2 " " NAG N 2 " - " BMA N 3 " " NAG O 1 " - " NAG O 2 " " NAG P 1 " - " NAG P 2 " " NAG Q 1 " - " NAG Q 2 " " NAG Q 2 " - " BMA Q 3 " " NAG R 1 " - " NAG R 2 " " NAG R 2 " - " BMA R 3 " " NAG S 1 " - " NAG S 2 " " NAG T 1 " - " NAG T 2 " " 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 X 1 " - " NAG X 2 " NAG-ASN " NAG M 1 " - " ASN A 301 " " NAG O 1 " - " ASN A 156 " " NAG P 1 " - " ASN A 442 " " NAG Q 1 " - " ASN E 301 " " NAG S 1 " - " ASN E 156 " " NAG T 1 " - " ASN E 442 " " NAG U 1 " - " ASN I 301 " " NAG W 1 " - " ASN I 156 " " NAG X 1 " - " ASN I 442 " Time building additional restraints: 8.36 Conformation dependent library (CDL) restraints added in 3.7 seconds 4944 Ramachandran restraints generated. 2472 Oldfield, 0 Emsley, 2472 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4572 Finding SS restraints... Secondary structure from input PDB file: 48 helices and 45 sheets defined 18.6% alpha, 29.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.55 Creating SS restraints... Processing helix chain 'A' and resid 58 through 63 removed outlier: 4.032A pdb=" N LYS A 63 " --> pdb=" O ARG A 59 " (cutoff:3.500A) Processing helix chain 'A' and resid 69 through 74 Processing helix chain 'A' and resid 99 through 116 removed outlier: 3.712A pdb=" N LEU A 116 " --> pdb=" O TRP A 112 " (cutoff:3.500A) Processing helix chain 'A' and resid 335 through 351 removed outlier: 4.052A pdb=" N LYS A 351 " --> pdb=" O ILE A 347 " (cutoff:3.500A) Processing helix chain 'A' and resid 368 through 373 Processing helix chain 'A' and resid 474 through 481 removed outlier: 4.205A pdb=" N ASN A 478 " --> pdb=" O ASP A 474 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N SER A 481 " --> pdb=" O ASP A 477 " (cutoff:3.500A) Processing helix chain 'B' and resid 529 through 535 removed outlier: 4.245A pdb=" N MET B 535 " --> pdb=" O GLY B 531 " (cutoff:3.500A) Processing helix chain 'B' and resid 537 through 543 removed outlier: 3.604A pdb=" N ALA B 541 " --> pdb=" O LEU B 537 " (cutoff:3.500A) Processing helix chain 'B' and resid 571 through 579 removed outlier: 3.670A pdb=" N GLN B 575 " --> pdb=" O TRP B 571 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N LEU B 576 " --> pdb=" O GLY B 572 " (cutoff:3.500A) Processing helix chain 'B' and resid 581 through 596 removed outlier: 4.623A pdb=" N ARG B 585 " --> pdb=" O LEU B 581 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N LEU B 587 " --> pdb=" O VAL B 583 " (cutoff:3.500A) Processing helix chain 'B' and resid 618 through 624 removed outlier: 3.697A pdb=" N ILE B 622 " --> pdb=" O ASN B 618 " (cutoff:3.500A) Processing helix chain 'B' and resid 627 through 635 Processing helix chain 'B' and resid 639 through 664 removed outlier: 3.537A pdb=" N GLU B 648 " --> pdb=" O GLY B 644 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N GLN B 650 " --> pdb=" O LEU B 646 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N ASN B 651 " --> pdb=" O GLU B 647 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N ASP B 664 " --> pdb=" O LEU B 660 " (cutoff:3.500A) Processing helix chain 'C' and resid 28 through 30 No H-bonds generated for 'chain 'C' and resid 28 through 30' Processing helix chain 'C' and resid 87 through 91 removed outlier: 4.020A pdb=" N THR C 91 " --> pdb=" O SER C 88 " (cutoff:3.500A) Processing helix chain 'D' and resid 81 through 85 removed outlier: 3.670A pdb=" N GLU D 85 " --> pdb=" O ALA D 82 " (cutoff:3.500A) Processing helix chain 'E' and resid 58 through 63 removed outlier: 4.032A pdb=" N LYS E 63 " --> pdb=" O ARG E 59 " (cutoff:3.500A) Processing helix chain 'E' and resid 69 through 74 Processing helix chain 'E' and resid 99 through 116 removed outlier: 3.712A pdb=" N LEU E 116 " --> pdb=" O TRP E 112 " (cutoff:3.500A) Processing helix chain 'E' and resid 335 through 351 removed outlier: 4.052A pdb=" N LYS E 351 " --> pdb=" O ILE E 347 " (cutoff:3.500A) Processing helix chain 'E' and resid 368 through 373 Processing helix chain 'E' and resid 474 through 481 removed outlier: 4.205A pdb=" N ASN E 478 " --> pdb=" O ASP E 474 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N SER E 481 " --> pdb=" O ASP E 477 " (cutoff:3.500A) Processing helix chain 'F' and resid 529 through 535 removed outlier: 4.246A pdb=" N MET F 535 " --> pdb=" O GLY F 531 " (cutoff:3.500A) Processing helix chain 'F' and resid 537 through 543 removed outlier: 3.604A pdb=" N ALA F 541 " --> pdb=" O LEU F 537 " (cutoff:3.500A) Processing helix chain 'F' and resid 571 through 579 removed outlier: 3.670A pdb=" N GLN F 575 " --> pdb=" O TRP F 571 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N LEU F 576 " --> pdb=" O GLY F 572 " (cutoff:3.500A) Processing helix chain 'F' and resid 581 through 596 removed outlier: 4.624A pdb=" N ARG F 585 " --> pdb=" O LEU F 581 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N LEU F 587 " --> pdb=" O VAL F 583 " (cutoff:3.500A) Processing helix chain 'F' and resid 618 through 624 removed outlier: 3.697A pdb=" N ILE F 622 " --> pdb=" O ASN F 618 " (cutoff:3.500A) Processing helix chain 'F' and resid 627 through 635 Processing helix chain 'F' and resid 639 through 664 removed outlier: 3.537A pdb=" N GLU F 648 " --> pdb=" O GLY F 644 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N GLN F 650 " --> pdb=" O LEU F 646 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N ASN F 651 " --> pdb=" O GLU F 647 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N ASP F 664 " --> pdb=" O LEU F 660 " (cutoff:3.500A) Processing helix chain 'G' and resid 28 through 30 No H-bonds generated for 'chain 'G' and resid 28 through 30' Processing helix chain 'G' and resid 87 through 91 removed outlier: 4.020A pdb=" N THR G 91 " --> pdb=" O SER G 88 " (cutoff:3.500A) Processing helix chain 'H' and resid 81 through 85 removed outlier: 3.670A pdb=" N GLU H 85 " --> pdb=" O ALA H 82 " (cutoff:3.500A) Processing helix chain 'I' and resid 58 through 63 removed outlier: 4.033A pdb=" N LYS I 63 " --> pdb=" O ARG I 59 " (cutoff:3.500A) Processing helix chain 'I' and resid 69 through 74 Processing helix chain 'I' and resid 99 through 116 removed outlier: 3.712A pdb=" N LEU I 116 " --> pdb=" O TRP I 112 " (cutoff:3.500A) Processing helix chain 'I' and resid 335 through 351 removed outlier: 4.052A pdb=" N LYS I 351 " --> pdb=" O ILE I 347 " (cutoff:3.500A) Processing helix chain 'I' and resid 368 through 373 Processing helix chain 'I' and resid 474 through 481 removed outlier: 4.204A pdb=" N ASN I 478 " --> pdb=" O ASP I 474 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N SER I 481 " --> pdb=" O ASP I 477 " (cutoff:3.500A) Processing helix chain 'J' and resid 529 through 535 removed outlier: 4.246A pdb=" N MET J 535 " --> pdb=" O GLY J 531 " (cutoff:3.500A) Processing helix chain 'J' and resid 537 through 543 removed outlier: 3.604A pdb=" N ALA J 541 " --> pdb=" O LEU J 537 " (cutoff:3.500A) Processing helix chain 'J' and resid 571 through 579 removed outlier: 3.669A pdb=" N GLN J 575 " --> pdb=" O TRP J 571 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N LEU J 576 " --> pdb=" O GLY J 572 " (cutoff:3.500A) Processing helix chain 'J' and resid 581 through 596 removed outlier: 4.623A pdb=" N ARG J 585 " --> pdb=" O LEU J 581 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N LEU J 587 " --> pdb=" O VAL J 583 " (cutoff:3.500A) Processing helix chain 'J' and resid 618 through 624 removed outlier: 3.697A pdb=" N ILE J 622 " --> pdb=" O ASN J 618 " (cutoff:3.500A) Processing helix chain 'J' and resid 627 through 635 Processing helix chain 'J' and resid 639 through 664 removed outlier: 3.536A pdb=" N GLU J 648 " --> pdb=" O GLY J 644 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N GLN J 650 " --> pdb=" O LEU J 646 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N ASN J 651 " --> pdb=" O GLU J 647 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N ASP J 664 " --> pdb=" O LEU J 660 " (cutoff:3.500A) Processing helix chain 'K' and resid 28 through 30 No H-bonds generated for 'chain 'K' and resid 28 through 30' Processing helix chain 'K' and resid 87 through 91 removed outlier: 4.020A pdb=" N THR K 91 " --> pdb=" O SER K 88 " (cutoff:3.500A) Processing helix chain 'L' and resid 81 through 85 removed outlier: 3.670A pdb=" N GLU L 85 " --> pdb=" O ALA L 82 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 494 through 499 removed outlier: 4.843A pdb=" N VAL A 36 " --> pdb=" O THR B 606 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 45 through 47 removed outlier: 3.902A pdb=" N ILE A 225 " --> pdb=" O VAL A 245 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 75 through 76 Processing sheet with id=AA4, first strand: chain 'A' and resid 91 through 94 removed outlier: 4.366A pdb=" N GLU A 91 " --> pdb=" O CYS A 239 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N CYS A 239 " --> pdb=" O GLU A 91 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 169 through 177 Processing sheet with id=AA6, first strand: chain 'A' and resid 259 through 260 removed outlier: 4.232A pdb=" N GLY A 451 " --> pdb=" O LEU A 260 " (cutoff:3.500A) removed outlier: 9.687A pdb=" N ASN A 448 " --> pdb=" O THR A 290 " (cutoff:3.500A) removed outlier: 11.027A pdb=" N THR A 290 " --> pdb=" O ASN A 448 " (cutoff:3.500A) removed outlier: 6.947A pdb=" N THR A 450 " --> pdb=" O LEU A 288 " (cutoff:3.500A) removed outlier: 7.327A pdb=" N GLU A 293 " --> pdb=" O SER A 334 " (cutoff:3.500A) removed outlier: 4.330A pdb=" N SER A 334 " --> pdb=" O GLU A 293 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N LYS A 421 " --> pdb=" O PHE A 382 " (cutoff:3.500A) removed outlier: 4.383A pdb=" N PHE A 382 " --> pdb=" O LYS A 421 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 272 through 273 removed outlier: 6.947A pdb=" N THR A 450 " --> pdb=" O LEU A 288 " (cutoff:3.500A) removed outlier: 11.027A pdb=" N THR A 290 " --> pdb=" O ASN A 448 " (cutoff:3.500A) removed outlier: 9.687A pdb=" N ASN A 448 " --> pdb=" O THR A 290 " (cutoff:3.500A) removed outlier: 6.719A pdb=" N LYS A 360 " --> pdb=" O PHE A 468 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N GLY A 393 " --> pdb=" O TYR A 361 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 302 through 304 removed outlier: 6.302A pdb=" N THR A 303 " --> pdb=" O GLY A 321 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 307 through 308 Processing sheet with id=AB1, first strand: chain 'A' and resid 423 through 425 Processing sheet with id=AB2, first strand: chain 'C' and resid 3 through 6 Processing sheet with id=AB3, first strand: chain 'C' and resid 9 through 11 removed outlier: 3.657A pdb=" N THR C 124 " --> pdb=" O GLU C 10 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N GLY C 99 " --> pdb=" O TYR C 33 " (cutoff:3.500A) removed outlier: 5.428A pdb=" N TYR C 33 " --> pdb=" O GLY C 99 " (cutoff:3.500A) removed outlier: 6.651A pdb=" N MET C 34 " --> pdb=" O TRP C 50 " (cutoff:3.500A) removed outlier: 4.565A pdb=" N TRP C 50 " --> pdb=" O MET C 34 " (cutoff:3.500A) removed outlier: 7.052A pdb=" N TRP C 36 " --> pdb=" O MET C 48 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 9 through 12 Processing sheet with id=AB5, first strand: chain 'D' and resid 9 through 12 Processing sheet with id=AB6, first strand: chain 'D' and resid 18 through 23 Processing sheet with id=AB7, first strand: chain 'E' and resid 494 through 499 removed outlier: 4.891A pdb=" N VAL E 36 " --> pdb=" O THR F 606 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'E' and resid 45 through 47 removed outlier: 3.903A pdb=" N ILE E 225 " --> pdb=" O VAL E 245 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'E' and resid 75 through 76 Processing sheet with id=AC1, first strand: chain 'E' and resid 91 through 94 removed outlier: 4.366A pdb=" N GLU E 91 " --> pdb=" O CYS E 239 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N CYS E 239 " --> pdb=" O GLU E 91 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'E' and resid 169 through 177 Processing sheet with id=AC3, first strand: chain 'E' and resid 259 through 260 removed outlier: 4.232A pdb=" N GLY E 451 " --> pdb=" O LEU E 260 " (cutoff:3.500A) removed outlier: 9.687A pdb=" N ASN E 448 " --> pdb=" O THR E 290 " (cutoff:3.500A) removed outlier: 11.026A pdb=" N THR E 290 " --> pdb=" O ASN E 448 " (cutoff:3.500A) removed outlier: 6.946A pdb=" N THR E 450 " --> pdb=" O LEU E 288 " (cutoff:3.500A) removed outlier: 7.327A pdb=" N GLU E 293 " --> pdb=" O SER E 334 " (cutoff:3.500A) removed outlier: 4.331A pdb=" N SER E 334 " --> pdb=" O GLU E 293 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N LYS E 421 " --> pdb=" O PHE E 382 " (cutoff:3.500A) removed outlier: 4.383A pdb=" N PHE E 382 " --> pdb=" O LYS E 421 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'E' and resid 272 through 273 removed outlier: 6.946A pdb=" N THR E 450 " --> pdb=" O LEU E 288 " (cutoff:3.500A) removed outlier: 11.026A pdb=" N THR E 290 " --> pdb=" O ASN E 448 " (cutoff:3.500A) removed outlier: 9.687A pdb=" N ASN E 448 " --> pdb=" O THR E 290 " (cutoff:3.500A) removed outlier: 6.719A pdb=" N LYS E 360 " --> pdb=" O PHE E 468 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N GLY E 393 " --> pdb=" O TYR E 361 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'E' and resid 302 through 304 removed outlier: 6.302A pdb=" N THR E 303 " --> pdb=" O GLY E 321 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'E' and resid 307 through 308 Processing sheet with id=AC7, first strand: chain 'E' and resid 423 through 425 Processing sheet with id=AC8, first strand: chain 'G' and resid 3 through 6 Processing sheet with id=AC9, first strand: chain 'G' and resid 9 through 11 removed outlier: 3.658A pdb=" N THR G 124 " --> pdb=" O GLU G 10 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N GLY G 99 " --> pdb=" O TYR G 33 " (cutoff:3.500A) removed outlier: 5.429A pdb=" N TYR G 33 " --> pdb=" O GLY G 99 " (cutoff:3.500A) removed outlier: 6.651A pdb=" N MET G 34 " --> pdb=" O TRP G 50 " (cutoff:3.500A) removed outlier: 4.566A pdb=" N TRP G 50 " --> pdb=" O MET G 34 " (cutoff:3.500A) removed outlier: 7.053A pdb=" N TRP G 36 " --> pdb=" O MET G 48 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'H' and resid 9 through 12 Processing sheet with id=AD2, first strand: chain 'H' and resid 9 through 12 Processing sheet with id=AD3, first strand: chain 'H' and resid 18 through 23 Processing sheet with id=AD4, first strand: chain 'I' and resid 494 through 499 removed outlier: 4.940A pdb=" N VAL I 36 " --> pdb=" O THR J 606 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'I' and resid 45 through 47 removed outlier: 3.903A pdb=" N ILE I 225 " --> pdb=" O VAL I 245 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'I' and resid 75 through 76 Processing sheet with id=AD7, first strand: chain 'I' and resid 91 through 94 removed outlier: 4.366A pdb=" N GLU I 91 " --> pdb=" O CYS I 239 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N CYS I 239 " --> pdb=" O GLU I 91 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'I' and resid 169 through 177 Processing sheet with id=AD9, first strand: chain 'I' and resid 259 through 260 removed outlier: 4.232A pdb=" N GLY I 451 " --> pdb=" O LEU I 260 " (cutoff:3.500A) removed outlier: 9.687A pdb=" N ASN I 448 " --> pdb=" O THR I 290 " (cutoff:3.500A) removed outlier: 11.027A pdb=" N THR I 290 " --> pdb=" O ASN I 448 " (cutoff:3.500A) removed outlier: 6.947A pdb=" N THR I 450 " --> pdb=" O LEU I 288 " (cutoff:3.500A) removed outlier: 7.328A pdb=" N GLU I 293 " --> pdb=" O SER I 334 " (cutoff:3.500A) removed outlier: 4.330A pdb=" N SER I 334 " --> pdb=" O GLU I 293 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N LYS I 421 " --> pdb=" O PHE I 382 " (cutoff:3.500A) removed outlier: 4.383A pdb=" N PHE I 382 " --> pdb=" O LYS I 421 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'I' and resid 272 through 273 removed outlier: 6.947A pdb=" N THR I 450 " --> pdb=" O LEU I 288 " (cutoff:3.500A) removed outlier: 11.027A pdb=" N THR I 290 " --> pdb=" O ASN I 448 " (cutoff:3.500A) removed outlier: 9.687A pdb=" N ASN I 448 " --> pdb=" O THR I 290 " (cutoff:3.500A) removed outlier: 6.719A pdb=" N LYS I 360 " --> pdb=" O PHE I 468 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N GLY I 393 " --> pdb=" O TYR I 361 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'I' and resid 302 through 304 removed outlier: 6.302A pdb=" N THR I 303 " --> pdb=" O GLY I 321 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'I' and resid 307 through 308 Processing sheet with id=AE4, first strand: chain 'I' and resid 423 through 425 Processing sheet with id=AE5, first strand: chain 'K' and resid 3 through 6 Processing sheet with id=AE6, first strand: chain 'K' and resid 9 through 11 removed outlier: 3.500A pdb=" N GLU K 10 " --> pdb=" O LEU K 122 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N THR K 124 " --> pdb=" O GLU K 10 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N GLY K 99 " --> pdb=" O TYR K 33 " (cutoff:3.500A) removed outlier: 5.428A pdb=" N TYR K 33 " --> pdb=" O GLY K 99 " (cutoff:3.500A) removed outlier: 6.651A pdb=" N MET K 34 " --> pdb=" O TRP K 50 " (cutoff:3.500A) removed outlier: 4.565A pdb=" N TRP K 50 " --> pdb=" O MET K 34 " (cutoff:3.500A) removed outlier: 7.053A pdb=" N TRP K 36 " --> pdb=" O MET K 48 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'L' and resid 9 through 12 Processing sheet with id=AE8, first strand: chain 'L' and resid 9 through 12 Processing sheet with id=AE9, first strand: chain 'L' and resid 18 through 23 668 hydrogen bonds defined for protein. 1752 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: 6.81 Time building geometry restraints manager: 8.98 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 6318 1.34 - 1.46: 4887 1.46 - 1.58: 8883 1.58 - 1.70: 0 1.70 - 1.81: 183 Bond restraints: 20271 Sorted by residual: bond pdb=" C3 MAN N 7 " pdb=" O3 MAN N 7 " ideal model delta sigma weight residual 1.408 1.484 -0.076 2.00e-02 2.50e+03 1.44e+01 bond pdb=" C3 MAN V 7 " pdb=" O3 MAN V 7 " ideal model delta sigma weight residual 1.408 1.484 -0.076 2.00e-02 2.50e+03 1.44e+01 bond pdb=" C3 MAN R 7 " pdb=" O3 MAN R 7 " ideal model delta sigma weight residual 1.408 1.484 -0.076 2.00e-02 2.50e+03 1.44e+01 bond pdb=" C1 MAN V 8 " pdb=" C2 MAN V 8 " ideal model delta sigma weight residual 1.526 1.574 -0.048 2.00e-02 2.50e+03 5.82e+00 bond pdb=" C1 MAN R 8 " pdb=" C2 MAN R 8 " ideal model delta sigma weight residual 1.526 1.573 -0.047 2.00e-02 2.50e+03 5.64e+00 ... (remaining 20266 not shown) Histogram of bond angle deviations from ideal: 100.65 - 107.32: 728 107.32 - 113.99: 11611 113.99 - 120.66: 7380 120.66 - 127.33: 7581 127.33 - 134.00: 258 Bond angle restraints: 27558 Sorted by residual: angle pdb=" C LEU I 122 " pdb=" N THR I 123 " pdb=" CA THR I 123 " ideal model delta sigma weight residual 121.80 131.62 -9.82 2.44e+00 1.68e-01 1.62e+01 angle pdb=" C LEU A 122 " pdb=" N THR A 123 " pdb=" CA THR A 123 " ideal model delta sigma weight residual 121.80 131.58 -9.78 2.44e+00 1.68e-01 1.61e+01 angle pdb=" C LEU E 122 " pdb=" N THR E 123 " pdb=" CA THR E 123 " ideal model delta sigma weight residual 121.80 131.54 -9.74 2.44e+00 1.68e-01 1.59e+01 angle pdb=" C2 MAN V 7 " pdb=" C3 MAN V 7 " pdb=" O3 MAN V 7 " ideal model delta sigma weight residual 107.58 118.20 -10.62 3.00e+00 1.11e-01 1.25e+01 angle pdb=" C2 MAN N 7 " pdb=" C3 MAN N 7 " pdb=" O3 MAN N 7 " ideal model delta sigma weight residual 107.58 118.20 -10.62 3.00e+00 1.11e-01 1.25e+01 ... (remaining 27553 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.55: 12349 24.55 - 49.11: 272 49.11 - 73.66: 39 73.66 - 98.22: 48 98.22 - 122.77: 24 Dihedral angle restraints: 12732 sinusoidal: 5571 harmonic: 7161 Sorted by residual: dihedral pdb=" CA VAL B 580 " pdb=" C VAL B 580 " pdb=" N LEU B 581 " pdb=" CA LEU B 581 " ideal model delta harmonic sigma weight residual 180.00 158.27 21.73 0 5.00e+00 4.00e-02 1.89e+01 dihedral pdb=" CA VAL F 580 " pdb=" C VAL F 580 " pdb=" N LEU F 581 " pdb=" CA LEU F 581 " ideal model delta harmonic sigma weight residual 180.00 158.30 21.70 0 5.00e+00 4.00e-02 1.88e+01 dihedral pdb=" CA VAL J 580 " pdb=" C VAL J 580 " pdb=" N LEU J 581 " pdb=" CA LEU J 581 " ideal model delta harmonic sigma weight residual 180.00 158.31 21.69 0 5.00e+00 4.00e-02 1.88e+01 ... (remaining 12729 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.209: 3231 0.209 - 0.417: 9 0.417 - 0.626: 0 0.626 - 0.834: 0 0.834 - 1.043: 3 Chirality restraints: 3243 Sorted by residual: chirality pdb=" C1 NAG P 1 " pdb=" ND2 ASN A 442 " pdb=" C2 NAG P 1 " pdb=" O5 NAG P 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.36 -1.04 2.00e-01 2.50e+01 2.72e+01 chirality pdb=" C1 NAG T 1 " pdb=" ND2 ASN E 442 " pdb=" C2 NAG T 1 " pdb=" O5 NAG T 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.36 -1.04 2.00e-01 2.50e+01 2.72e+01 chirality pdb=" C1 NAG X 1 " pdb=" ND2 ASN I 442 " pdb=" C2 NAG X 1 " pdb=" O5 NAG X 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.36 -1.04 2.00e-01 2.50e+01 2.71e+01 ... (remaining 3240 not shown) Planarity restraints: 3459 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ARG E 298 " 0.024 5.00e-02 4.00e+02 3.58e-02 2.05e+00 pdb=" N PRO E 299 " -0.062 5.00e-02 4.00e+02 pdb=" CA PRO E 299 " 0.018 5.00e-02 4.00e+02 pdb=" CD PRO E 299 " 0.020 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ARG A 298 " 0.024 5.00e-02 4.00e+02 3.57e-02 2.03e+00 pdb=" N PRO A 299 " -0.062 5.00e-02 4.00e+02 pdb=" CA PRO A 299 " 0.018 5.00e-02 4.00e+02 pdb=" CD PRO A 299 " 0.020 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ARG I 298 " 0.024 5.00e-02 4.00e+02 3.56e-02 2.03e+00 pdb=" N PRO I 299 " -0.062 5.00e-02 4.00e+02 pdb=" CA PRO I 299 " 0.018 5.00e-02 4.00e+02 pdb=" CD PRO I 299 " 0.020 5.00e-02 4.00e+02 ... (remaining 3456 not shown) Histogram of nonbonded interaction distances: 2.03 - 2.61: 185 2.61 - 3.18: 17039 3.18 - 3.75: 27253 3.75 - 4.33: 36691 4.33 - 4.90: 62884 Nonbonded interactions: 144052 Sorted by model distance: nonbonded pdb=" O4 BMA R 3 " pdb=" O6 MAN R 5 " model vdw 2.035 2.440 nonbonded pdb=" O4 BMA N 3 " pdb=" O6 MAN N 5 " model vdw 2.035 2.440 nonbonded pdb=" O4 BMA V 3 " pdb=" O6 MAN V 5 " model vdw 2.035 2.440 nonbonded pdb=" O3 NAG X 1 " pdb=" O5 NAG X 2 " model vdw 2.159 2.440 nonbonded pdb=" O3 NAG P 1 " pdb=" O5 NAG P 2 " model vdw 2.159 2.440 ... (remaining 144047 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 'E' selection = chain 'I' } ncs_group { reference = chain 'B' selection = chain 'F' selection = chain 'J' } ncs_group { reference = chain 'C' selection = chain 'G' selection = chain 'K' } ncs_group { reference = chain 'D' selection = chain 'H' selection = chain 'L' } ncs_group { reference = chain 'M' selection = chain 'Q' selection = chain 'U' } ncs_group { reference = chain 'N' selection = chain 'R' selection = chain 'V' } ncs_group { reference = chain 'O' selection = chain 'P' selection = chain 'S' selection = chain 'T' selection = 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: 0.090 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.020 Extract box with map and model: 1.770 Check model and map are aligned: 0.320 Set scattering table: 0.180 Process input model: 54.520 Find NCS groups from input model: 1.210 Set up NCS constraints: 0.230 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.920 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 61.280 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7329 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 : 0.004 0.076 20271 Z= 0.274 Angle : 0.652 10.621 27558 Z= 0.307 Chirality : 0.056 1.043 3243 Planarity : 0.003 0.036 3450 Dihedral : 13.454 122.772 8070 Min Nonbonded Distance : 2.035 Molprobity Statistics. All-atom Clashscore : 2.64 Ramachandran Plot: Outliers : 0.36 % Allowed : 2.67 % Favored : 96.97 % Rotamer: Outliers : 2.12 % Allowed : 4.67 % Favored : 93.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.49 (0.17), residues: 2472 helix: 1.48 (0.30), residues: 366 sheet: 0.22 (0.19), residues: 657 loop : -1.09 (0.16), residues: 1449 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP F 571 HIS 0.002 0.000 HIS A 249 PHE 0.007 0.001 PHE G 114 TYR 0.008 0.001 TYR H 93 ARG 0.002 0.000 ARG A 456 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4944 Ramachandran restraints generated. 2472 Oldfield, 0 Emsley, 2472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4944 Ramachandran restraints generated. 2472 Oldfield, 0 Emsley, 2472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 407 residues out of total 2142 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 362 time to evaluate : 2.311 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: symmetry clash revert: symmetry clash REVERT: A 333 ILE cc_start: 0.6888 (mt) cc_final: 0.6621 (mm) REVERT: A 390 LEU cc_start: 0.9063 (OUTLIER) cc_final: 0.8856 (tp) REVERT: B 534 SER cc_start: 0.8886 (t) cc_final: 0.8549 (p) REVERT: B 535 MET cc_start: 0.7988 (mtm) cc_final: 0.7537 (mpp) REVERT: B 586 TYR cc_start: 0.6544 (t80) cc_final: 0.6114 (t80) REVERT: B 630 GLN cc_start: 0.8677 (pt0) cc_final: 0.8327 (pt0) REVERT: B 631 TRP cc_start: 0.8364 (t-100) cc_final: 0.7675 (t-100) REVERT: C 81 MET cc_start: 0.8346 (tmm) cc_final: 0.8104 (tmm) REVERT: C 112 PRO cc_start: 0.9239 (Cg_endo) cc_final: 0.8957 (Cg_exo) REVERT: C 114 PHE cc_start: 0.7354 (OUTLIER) cc_final: 0.7014 (p90) REVERT: C 115 ASP cc_start: 0.6042 (t70) cc_final: 0.5794 (t0) REVERT: D 37 TRP cc_start: 0.7382 (m100) cc_final: 0.6773 (m100) REVERT: E 95 MET cc_start: 0.7955 (ttp) cc_final: 0.7554 (tmm) REVERT: E 101 VAL cc_start: 0.9350 (m) cc_final: 0.9082 (p) REVERT: E 287 HIS cc_start: 0.8212 (OUTLIER) cc_final: 0.7369 (m-70) REVERT: F 534 SER cc_start: 0.8827 (t) cc_final: 0.8436 (p) REVERT: F 543 ASN cc_start: 0.8439 (m110) cc_final: 0.8227 (m110) REVERT: F 616 ASN cc_start: 0.8266 (t0) cc_final: 0.7973 (t0) REVERT: F 659 ASP cc_start: 0.6317 (m-30) cc_final: 0.5975 (m-30) REVERT: G 114 PHE cc_start: 0.7387 (OUTLIER) cc_final: 0.6757 (p90) REVERT: H 48 LEU cc_start: 0.6121 (OUTLIER) cc_final: 0.5236 (pt) REVERT: H 84 ASP cc_start: 0.6655 (m-30) cc_final: 0.5508 (m-30) REVERT: I 95 MET cc_start: 0.7816 (ttp) cc_final: 0.7098 (tmm) REVERT: I 333 ILE cc_start: 0.7035 (mt) cc_final: 0.6753 (mm) REVERT: I 369 MET cc_start: 0.8113 (ttm) cc_final: 0.7897 (ttt) REVERT: I 381 GLU cc_start: 0.8290 (mm-30) cc_final: 0.7951 (mm-30) REVERT: J 535 MET cc_start: 0.8604 (mtm) cc_final: 0.7995 (mpp) REVERT: J 543 ASN cc_start: 0.8548 (m110) cc_final: 0.8177 (m110) REVERT: J 659 ASP cc_start: 0.6711 (m-30) cc_final: 0.6228 (m-30) REVERT: K 12 LYS cc_start: 0.7648 (mmtt) cc_final: 0.7375 (mmmm) REVERT: K 81 MET cc_start: 0.9086 (tmm) cc_final: 0.8577 (tmm) REVERT: K 90 ASP cc_start: 0.7001 (t0) cc_final: 0.6529 (p0) REVERT: K 105 TYR cc_start: 0.8509 (m-80) cc_final: 0.8099 (m-80) REVERT: K 116 TYR cc_start: 0.7295 (m-80) cc_final: 0.6823 (m-80) REVERT: K 125 VAL cc_start: 0.5847 (OUTLIER) cc_final: 0.5138 (m) outliers start: 45 outliers final: 8 residues processed: 402 average time/residue: 0.3271 time to fit residues: 196.5907 Evaluate side-chains 194 residues out of total 2142 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 180 time to evaluate : 2.512 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 LEU Chi-restraints excluded: chain A residue 287 HIS Chi-restraints excluded: chain A residue 295 VAL Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain C residue 114 PHE Chi-restraints excluded: chain E residue 287 HIS Chi-restraints excluded: chain E residue 295 VAL Chi-restraints excluded: chain G residue 114 PHE Chi-restraints excluded: chain H residue 29 VAL Chi-restraints excluded: chain H residue 48 LEU Chi-restraints excluded: chain I residue 295 VAL Chi-restraints excluded: chain K residue 51 ILE Chi-restraints excluded: chain K residue 125 VAL Chi-restraints excluded: chain L residue 48 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 246 random chunks: chunk 207 optimal weight: 10.0000 chunk 186 optimal weight: 0.9990 chunk 103 optimal weight: 5.9990 chunk 63 optimal weight: 20.0000 chunk 125 optimal weight: 1.9990 chunk 99 optimal weight: 7.9990 chunk 192 optimal weight: 20.0000 chunk 74 optimal weight: 20.0000 chunk 117 optimal weight: 20.0000 chunk 143 optimal weight: 6.9990 chunk 223 optimal weight: 20.0000 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 611 ASN F 575 GLN F 611 ASN J 575 GLN J 611 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7608 moved from start: 0.2407 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 20271 Z= 0.287 Angle : 0.700 11.428 27558 Z= 0.347 Chirality : 0.047 0.411 3243 Planarity : 0.004 0.064 3450 Dihedral : 11.739 101.314 3722 Min Nonbonded Distance : 2.156 Molprobity Statistics. All-atom Clashscore : 5.81 Ramachandran Plot: Outliers : 0.36 % Allowed : 4.13 % Favored : 95.51 % Rotamer: Outliers : 3.31 % Allowed : 9.58 % Favored : 87.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.76 (0.17), residues: 2472 helix: 1.11 (0.29), residues: 369 sheet: 0.15 (0.20), residues: 624 loop : -1.26 (0.16), residues: 1479 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP G 50 HIS 0.005 0.001 HIS G 35 PHE 0.024 0.002 PHE C 29 TYR 0.015 0.002 TYR I 217 ARG 0.006 0.001 ARG I 166 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4944 Ramachandran restraints generated. 2472 Oldfield, 0 Emsley, 2472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4944 Ramachandran restraints generated. 2472 Oldfield, 0 Emsley, 2472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 255 residues out of total 2142 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 185 time to evaluate : 2.505 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: A 83 GLU cc_start: 0.8845 (OUTLIER) cc_final: 0.8575 (pp20) REVERT: B 530 MET cc_start: 0.7242 (mmp) cc_final: 0.6851 (mmp) REVERT: B 534 SER cc_start: 0.8852 (t) cc_final: 0.8599 (p) REVERT: B 535 MET cc_start: 0.8243 (mtm) cc_final: 0.7790 (mpp) REVERT: B 574 LYS cc_start: 0.7650 (pttm) cc_final: 0.7430 (pttm) REVERT: B 631 TRP cc_start: 0.8562 (t-100) cc_final: 0.7623 (t-100) REVERT: C 81 MET cc_start: 0.8446 (tmm) cc_final: 0.8102 (tmm) REVERT: C 112 PRO cc_start: 0.9439 (Cg_endo) cc_final: 0.9199 (Cg_exo) REVERT: C 114 PHE cc_start: 0.8258 (OUTLIER) cc_final: 0.7777 (p90) REVERT: C 115 ASP cc_start: 0.6972 (t70) cc_final: 0.6311 (t70) REVERT: D 37 TRP cc_start: 0.7141 (m100) cc_final: 0.6778 (m100) REVERT: D 48 LEU cc_start: 0.7231 (OUTLIER) cc_final: 0.6995 (pt) REVERT: E 95 MET cc_start: 0.8040 (ttp) cc_final: 0.7734 (tmm) REVERT: E 287 HIS cc_start: 0.8236 (OUTLIER) cc_final: 0.7368 (m-70) REVERT: E 381 GLU cc_start: 0.8135 (mm-30) cc_final: 0.7640 (mm-30) REVERT: F 534 SER cc_start: 0.8973 (t) cc_final: 0.8554 (p) REVERT: F 543 ASN cc_start: 0.8398 (m110) cc_final: 0.8081 (m110) REVERT: F 659 ASP cc_start: 0.6535 (m-30) cc_final: 0.6152 (m-30) REVERT: G 114 PHE cc_start: 0.8389 (OUTLIER) cc_final: 0.8148 (p90) REVERT: H 49 MET cc_start: 0.7305 (mmm) cc_final: 0.6849 (mmm) REVERT: H 84 ASP cc_start: 0.5926 (m-30) cc_final: 0.5397 (m-30) REVERT: I 123 THR cc_start: 0.8636 (OUTLIER) cc_final: 0.8425 (t) REVERT: I 381 GLU cc_start: 0.8275 (mm-30) cc_final: 0.7959 (mm-30) REVERT: J 535 MET cc_start: 0.8708 (mtm) cc_final: 0.8070 (mpp) REVERT: J 659 ASP cc_start: 0.6985 (m-30) cc_final: 0.6482 (m-30) REVERT: K 12 LYS cc_start: 0.7863 (mmtt) cc_final: 0.7643 (mmmt) REVERT: K 81 MET cc_start: 0.9105 (tmm) cc_final: 0.8612 (tmm) REVERT: K 90 ASP cc_start: 0.7200 (t0) cc_final: 0.6666 (p0) REVERT: K 105 TYR cc_start: 0.8812 (m-80) cc_final: 0.8340 (m-80) REVERT: K 115 ASP cc_start: 0.8504 (p0) cc_final: 0.7553 (p0) REVERT: K 116 TYR cc_start: 0.7836 (m-80) cc_final: 0.7344 (m-80) REVERT: K 125 VAL cc_start: 0.6538 (OUTLIER) cc_final: 0.6171 (m) REVERT: L 84 ASP cc_start: 0.7194 (m-30) cc_final: 0.6934 (m-30) outliers start: 70 outliers final: 32 residues processed: 239 average time/residue: 0.3005 time to fit residues: 113.3817 Evaluate side-chains 188 residues out of total 2142 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 149 time to evaluate : 2.910 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 83 GLU Chi-restraints excluded: chain A residue 104 MET Chi-restraints excluded: chain A residue 287 HIS Chi-restraints excluded: chain A residue 295 VAL Chi-restraints excluded: chain B residue 543 ASN Chi-restraints excluded: chain C residue 51 ILE Chi-restraints excluded: chain C residue 114 PHE Chi-restraints excluded: chain D residue 28 ASP Chi-restraints excluded: chain D residue 48 LEU Chi-restraints excluded: chain D residue 87 ASP Chi-restraints excluded: chain D residue 90 CYS Chi-restraints excluded: chain D residue 107 LEU Chi-restraints excluded: chain E residue 123 THR Chi-restraints excluded: chain E residue 127 VAL Chi-restraints excluded: chain E residue 287 HIS Chi-restraints excluded: chain E residue 295 VAL Chi-restraints excluded: chain F residue 641 ILE Chi-restraints excluded: chain G residue 5 VAL Chi-restraints excluded: chain G residue 28 THR Chi-restraints excluded: chain G residue 114 PHE Chi-restraints excluded: chain H residue 28 ASP Chi-restraints excluded: chain H residue 48 LEU Chi-restraints excluded: chain I residue 123 THR Chi-restraints excluded: chain I residue 202 THR Chi-restraints excluded: chain I residue 240 SER Chi-restraints excluded: chain I residue 287 HIS Chi-restraints excluded: chain I residue 295 VAL Chi-restraints excluded: chain I residue 325 ASP Chi-restraints excluded: chain I residue 494 LEU Chi-restraints excluded: chain J residue 529 THR Chi-restraints excluded: chain J residue 576 LEU Chi-restraints excluded: chain J residue 641 ILE Chi-restraints excluded: chain K residue 28 THR Chi-restraints excluded: chain K residue 45 LEU Chi-restraints excluded: chain K residue 51 ILE Chi-restraints excluded: chain K residue 125 VAL Chi-restraints excluded: chain L residue 48 LEU Chi-restraints excluded: chain L residue 75 LEU Chi-restraints excluded: chain L residue 87 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 246 random chunks: chunk 124 optimal weight: 8.9990 chunk 69 optimal weight: 1.9990 chunk 185 optimal weight: 7.9990 chunk 152 optimal weight: 0.0770 chunk 61 optimal weight: 7.9990 chunk 223 optimal weight: 1.9990 chunk 241 optimal weight: 30.0000 chunk 199 optimal weight: 6.9990 chunk 221 optimal weight: 10.0000 chunk 76 optimal weight: 3.9990 chunk 179 optimal weight: 9.9990 overall best weight: 3.0146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 279 ASN F 590 GLN H 6 GLN H 81 GLN I 279 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7644 moved from start: 0.2907 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 20271 Z= 0.197 Angle : 0.610 11.611 27558 Z= 0.302 Chirality : 0.045 0.414 3243 Planarity : 0.004 0.045 3450 Dihedral : 10.492 90.824 3717 Min Nonbonded Distance : 2.145 Molprobity Statistics. All-atom Clashscore : 5.58 Ramachandran Plot: Outliers : 0.36 % Allowed : 3.24 % Favored : 96.40 % Rotamer: Outliers : 2.50 % Allowed : 11.47 % Favored : 86.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.68 (0.17), residues: 2472 helix: 1.15 (0.29), residues: 384 sheet: 0.26 (0.20), residues: 657 loop : -1.29 (0.16), residues: 1431 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP E 427 HIS 0.003 0.001 HIS K 35 PHE 0.014 0.001 PHE K 114 TYR 0.020 0.001 TYR F 586 ARG 0.007 0.000 ARG E 59 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4944 Ramachandran restraints generated. 2472 Oldfield, 0 Emsley, 2472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4944 Ramachandran restraints generated. 2472 Oldfield, 0 Emsley, 2472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 212 residues out of total 2142 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 159 time to evaluate : 2.233 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 530 MET cc_start: 0.7437 (mmp) cc_final: 0.7042 (mmp) REVERT: B 534 SER cc_start: 0.8916 (t) cc_final: 0.8667 (p) REVERT: B 535 MET cc_start: 0.8342 (mtm) cc_final: 0.7839 (mpp) REVERT: B 631 TRP cc_start: 0.8470 (t-100) cc_final: 0.7705 (t-100) REVERT: C 81 MET cc_start: 0.8587 (tmm) cc_final: 0.8266 (tmm) REVERT: C 112 PRO cc_start: 0.9467 (Cg_endo) cc_final: 0.9220 (Cg_exo) REVERT: C 114 PHE cc_start: 0.8112 (OUTLIER) cc_final: 0.7587 (p90) REVERT: E 95 MET cc_start: 0.7862 (ttp) cc_final: 0.7570 (tmm) REVERT: E 104 MET cc_start: 0.9043 (tpp) cc_final: 0.8791 (ttp) REVERT: E 287 HIS cc_start: 0.8225 (OUTLIER) cc_final: 0.7495 (m-70) REVERT: E 381 GLU cc_start: 0.8277 (mm-30) cc_final: 0.7847 (mm-30) REVERT: F 534 SER cc_start: 0.8990 (t) cc_final: 0.8582 (p) REVERT: F 543 ASN cc_start: 0.8416 (m110) cc_final: 0.8078 (m110) REVERT: F 659 ASP cc_start: 0.6596 (m-30) cc_final: 0.6208 (m-30) REVERT: G 114 PHE cc_start: 0.8280 (OUTLIER) cc_final: 0.8016 (p90) REVERT: H 49 MET cc_start: 0.7253 (mmm) cc_final: 0.6898 (mmm) REVERT: I 381 GLU cc_start: 0.8268 (mm-30) cc_final: 0.7922 (mm-30) REVERT: J 535 MET cc_start: 0.8845 (mtm) cc_final: 0.8256 (mpp) REVERT: J 659 ASP cc_start: 0.6853 (m-30) cc_final: 0.6347 (m-30) REVERT: K 12 LYS cc_start: 0.7790 (mmtt) cc_final: 0.7513 (mmmm) REVERT: K 81 MET cc_start: 0.9064 (tmm) cc_final: 0.8454 (tmm) REVERT: K 90 ASP cc_start: 0.7024 (t0) cc_final: 0.6462 (p0) REVERT: K 115 ASP cc_start: 0.8482 (p0) cc_final: 0.7452 (p0) REVERT: K 116 TYR cc_start: 0.7859 (m-80) cc_final: 0.7335 (m-80) REVERT: K 125 VAL cc_start: 0.6488 (OUTLIER) cc_final: 0.6030 (m) outliers start: 53 outliers final: 33 residues processed: 202 average time/residue: 0.2934 time to fit residues: 94.0446 Evaluate side-chains 183 residues out of total 2142 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 146 time to evaluate : 2.305 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 213 ILE Chi-restraints excluded: chain A residue 287 HIS Chi-restraints excluded: chain A residue 295 VAL Chi-restraints excluded: chain B residue 543 ASN Chi-restraints excluded: chain B residue 602 LEU Chi-restraints excluded: chain C residue 51 ILE Chi-restraints excluded: chain C residue 114 PHE Chi-restraints excluded: chain D residue 28 ASP Chi-restraints excluded: chain D residue 33 ASN Chi-restraints excluded: chain D residue 72 THR Chi-restraints excluded: chain D residue 87 ASP Chi-restraints excluded: chain D residue 90 CYS Chi-restraints excluded: chain D residue 107 LEU Chi-restraints excluded: chain E residue 120 VAL Chi-restraints excluded: chain E residue 127 VAL Chi-restraints excluded: chain E residue 240 SER Chi-restraints excluded: chain E residue 287 HIS Chi-restraints excluded: chain E residue 295 VAL Chi-restraints excluded: chain F residue 605 CYS Chi-restraints excluded: chain G residue 28 THR Chi-restraints excluded: chain G residue 90 ASP Chi-restraints excluded: chain G residue 114 PHE Chi-restraints excluded: chain H residue 48 LEU Chi-restraints excluded: chain H residue 72 THR Chi-restraints excluded: chain I residue 120 VAL Chi-restraints excluded: chain I residue 202 THR Chi-restraints excluded: chain I residue 240 SER Chi-restraints excluded: chain I residue 287 HIS Chi-restraints excluded: chain I residue 295 VAL Chi-restraints excluded: chain I residue 325 ASP Chi-restraints excluded: chain J residue 576 LEU Chi-restraints excluded: chain K residue 28 THR Chi-restraints excluded: chain K residue 51 ILE Chi-restraints excluded: chain K residue 125 VAL Chi-restraints excluded: chain L residue 48 LEU Chi-restraints excluded: chain L residue 75 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 246 random chunks: chunk 221 optimal weight: 20.0000 chunk 168 optimal weight: 40.0000 chunk 116 optimal weight: 9.9990 chunk 24 optimal weight: 20.0000 chunk 106 optimal weight: 6.9990 chunk 150 optimal weight: 20.0000 chunk 224 optimal weight: 30.0000 chunk 237 optimal weight: 0.0270 chunk 117 optimal weight: 20.0000 chunk 212 optimal weight: 20.0000 chunk 64 optimal weight: 6.9990 overall best weight: 8.8048 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 279 ASN A 374 HIS B 611 ASN E 287 HIS E 374 HIS F 575 GLN I 343 GLN I 374 HIS ** J 575 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 577 GLN J 611 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7849 moved from start: 0.4310 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.054 20271 Z= 0.418 Angle : 0.756 12.619 27558 Z= 0.381 Chirality : 0.048 0.346 3243 Planarity : 0.005 0.058 3450 Dihedral : 9.979 76.305 3717 Min Nonbonded Distance : 2.050 Molprobity Statistics. All-atom Clashscore : 9.09 Ramachandran Plot: Outliers : 0.36 % Allowed : 5.66 % Favored : 93.97 % Rotamer: Outliers : 3.68 % Allowed : 11.43 % Favored : 84.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.09 (0.17), residues: 2472 helix: 0.68 (0.28), residues: 387 sheet: 0.05 (0.18), residues: 738 loop : -1.65 (0.16), residues: 1347 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP D 37 HIS 0.012 0.002 HIS K 35 PHE 0.029 0.003 PHE G 114 TYR 0.022 0.002 TYR G 33 ARG 0.015 0.001 ARG G 87 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4944 Ramachandran restraints generated. 2472 Oldfield, 0 Emsley, 2472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4944 Ramachandran restraints generated. 2472 Oldfield, 0 Emsley, 2472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 223 residues out of total 2142 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 78 poor density : 145 time to evaluate : 2.171 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 535 MET cc_start: 0.8615 (mtm) cc_final: 0.8082 (mpp) REVERT: B 659 ASP cc_start: 0.6808 (OUTLIER) cc_final: 0.6568 (p0) REVERT: C 115 ASP cc_start: 0.8841 (p0) cc_final: 0.8627 (p0) REVERT: D 107 LEU cc_start: 0.8285 (OUTLIER) cc_final: 0.8003 (tt) REVERT: E 95 MET cc_start: 0.7812 (ttp) cc_final: 0.7508 (tmm) REVERT: E 287 HIS cc_start: 0.8204 (OUTLIER) cc_final: 0.7151 (m90) REVERT: E 381 GLU cc_start: 0.8541 (mm-30) cc_final: 0.8036 (mm-30) REVERT: E 475 MET cc_start: 0.8640 (mmm) cc_final: 0.8421 (mmm) REVERT: F 534 SER cc_start: 0.9161 (t) cc_final: 0.8729 (p) REVERT: F 543 ASN cc_start: 0.8506 (m110) cc_final: 0.8137 (m110) REVERT: F 585 ARG cc_start: 0.7864 (mtp85) cc_final: 0.7590 (mtp-110) REVERT: F 659 ASP cc_start: 0.7173 (m-30) cc_final: 0.6805 (m-30) REVERT: G 12 LYS cc_start: 0.8484 (mmmm) cc_final: 0.8105 (mmtp) REVERT: I 104 MET cc_start: 0.9224 (OUTLIER) cc_final: 0.8700 (tpt) REVERT: I 381 GLU cc_start: 0.8466 (mm-30) cc_final: 0.7982 (mm-30) REVERT: J 530 MET cc_start: 0.6621 (mmp) cc_final: 0.6313 (mmp) REVERT: J 534 SER cc_start: 0.8698 (t) cc_final: 0.8354 (p) REVERT: J 535 MET cc_start: 0.8952 (mtm) cc_final: 0.8318 (mpp) REVERT: J 543 ASN cc_start: 0.8907 (m110) cc_final: 0.8626 (m110) REVERT: J 659 ASP cc_start: 0.7546 (m-30) cc_final: 0.7002 (m-30) REVERT: K 12 LYS cc_start: 0.7924 (mmtt) cc_final: 0.7611 (mmmm) REVERT: K 81 MET cc_start: 0.8909 (tmm) cc_final: 0.8365 (tmm) REVERT: K 90 ASP cc_start: 0.7153 (t0) cc_final: 0.6739 (p0) REVERT: K 116 TYR cc_start: 0.7977 (m-80) cc_final: 0.7439 (m-80) outliers start: 78 outliers final: 54 residues processed: 210 average time/residue: 0.2770 time to fit residues: 94.0581 Evaluate side-chains 189 residues out of total 2142 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 131 time to evaluate : 2.306 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 138 THR Chi-restraints excluded: chain A residue 149 VAL Chi-restraints excluded: chain A residue 202 THR Chi-restraints excluded: chain A residue 213 ILE Chi-restraints excluded: chain A residue 244 THR Chi-restraints excluded: chain A residue 262 ASN Chi-restraints excluded: chain A residue 287 HIS Chi-restraints excluded: chain A residue 295 VAL Chi-restraints excluded: chain B residue 543 ASN Chi-restraints excluded: chain B residue 574 LYS Chi-restraints excluded: chain B residue 602 LEU Chi-restraints excluded: chain B residue 659 ASP Chi-restraints excluded: chain C residue 30 THR Chi-restraints excluded: chain C residue 51 ILE Chi-restraints excluded: chain C residue 107 ASP Chi-restraints excluded: chain D residue 28 ASP Chi-restraints excluded: chain D residue 33 ASN Chi-restraints excluded: chain D residue 72 THR Chi-restraints excluded: chain D residue 87 ASP Chi-restraints excluded: chain D residue 107 LEU Chi-restraints excluded: chain E residue 34 LEU Chi-restraints excluded: chain E residue 85 VAL Chi-restraints excluded: chain E residue 90 THR Chi-restraints excluded: chain E residue 111 LEU Chi-restraints excluded: chain E residue 120 VAL Chi-restraints excluded: chain E residue 140 THR Chi-restraints excluded: chain E residue 149 VAL Chi-restraints excluded: chain E residue 244 THR Chi-restraints excluded: chain E residue 262 ASN Chi-restraints excluded: chain E residue 287 HIS Chi-restraints excluded: chain E residue 295 VAL Chi-restraints excluded: chain F residue 605 CYS Chi-restraints excluded: chain F residue 641 ILE Chi-restraints excluded: chain G residue 28 THR Chi-restraints excluded: chain G residue 107 ASP Chi-restraints excluded: chain H residue 19 THR Chi-restraints excluded: chain H residue 48 LEU Chi-restraints excluded: chain H residue 51 TYR Chi-restraints excluded: chain I residue 104 MET Chi-restraints excluded: chain I residue 120 VAL Chi-restraints excluded: chain I residue 149 VAL Chi-restraints excluded: chain I residue 202 THR Chi-restraints excluded: chain I residue 287 HIS Chi-restraints excluded: chain I residue 288 LEU Chi-restraints excluded: chain I residue 295 VAL Chi-restraints excluded: chain I residue 325 ASP Chi-restraints excluded: chain I residue 374 HIS Chi-restraints excluded: chain I residue 494 LEU Chi-restraints excluded: chain J residue 576 LEU Chi-restraints excluded: chain J residue 641 ILE Chi-restraints excluded: chain K residue 28 THR Chi-restraints excluded: chain K residue 51 ILE Chi-restraints excluded: chain L residue 33 ASN Chi-restraints excluded: chain L residue 48 LEU Chi-restraints excluded: chain L residue 72 THR Chi-restraints excluded: chain L residue 75 LEU Chi-restraints excluded: chain L residue 87 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 246 random chunks: chunk 198 optimal weight: 9.9990 chunk 134 optimal weight: 8.9990 chunk 3 optimal weight: 40.0000 chunk 177 optimal weight: 5.9990 chunk 98 optimal weight: 20.0000 chunk 202 optimal weight: 5.9990 chunk 164 optimal weight: 9.9990 chunk 0 optimal weight: 10.0000 chunk 121 optimal weight: 7.9990 chunk 213 optimal weight: 6.9990 chunk 60 optimal weight: 7.9990 overall best weight: 6.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 374 HIS E 374 HIS F 575 GLN ** I 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 575 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7867 moved from start: 0.4725 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 20271 Z= 0.336 Angle : 0.685 12.456 27558 Z= 0.341 Chirality : 0.046 0.373 3243 Planarity : 0.004 0.054 3450 Dihedral : 9.422 74.372 3712 Min Nonbonded Distance : 2.075 Molprobity Statistics. All-atom Clashscore : 8.81 Ramachandran Plot: Outliers : 0.36 % Allowed : 4.77 % Favored : 94.86 % Rotamer: Outliers : 4.11 % Allowed : 11.99 % Favored : 83.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.16 (0.17), residues: 2472 helix: 0.74 (0.28), residues: 387 sheet: -0.00 (0.18), residues: 744 loop : -1.75 (0.16), residues: 1341 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP B 631 HIS 0.028 0.002 HIS I 374 PHE 0.020 0.002 PHE G 114 TYR 0.015 0.002 TYR E 384 ARG 0.003 0.000 ARG I 298 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4944 Ramachandran restraints generated. 2472 Oldfield, 0 Emsley, 2472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4944 Ramachandran restraints generated. 2472 Oldfield, 0 Emsley, 2472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 219 residues out of total 2142 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 87 poor density : 132 time to evaluate : 2.457 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 535 MET cc_start: 0.8713 (mtm) cc_final: 0.8206 (mpp) REVERT: B 659 ASP cc_start: 0.6792 (OUTLIER) cc_final: 0.6579 (p0) REVERT: C 115 ASP cc_start: 0.8892 (p0) cc_final: 0.8423 (p0) REVERT: D 107 LEU cc_start: 0.8481 (OUTLIER) cc_final: 0.8084 (tt) REVERT: E 95 MET cc_start: 0.7816 (ttp) cc_final: 0.7561 (tmm) REVERT: E 287 HIS cc_start: 0.8250 (OUTLIER) cc_final: 0.7285 (m90) REVERT: E 475 MET cc_start: 0.8660 (mmm) cc_final: 0.8378 (mmm) REVERT: F 534 SER cc_start: 0.9115 (t) cc_final: 0.8700 (p) REVERT: F 543 ASN cc_start: 0.8625 (m110) cc_final: 0.8227 (m110) REVERT: F 585 ARG cc_start: 0.7960 (mtp85) cc_final: 0.7729 (mtp-110) REVERT: F 659 ASP cc_start: 0.7298 (m-30) cc_final: 0.6911 (m-30) REVERT: I 95 MET cc_start: 0.8067 (ttp) cc_final: 0.6794 (tmm) REVERT: I 104 MET cc_start: 0.9234 (OUTLIER) cc_final: 0.8658 (tpt) REVERT: J 530 MET cc_start: 0.6432 (mmp) cc_final: 0.6229 (mmp) REVERT: J 534 SER cc_start: 0.8727 (t) cc_final: 0.8404 (p) REVERT: J 535 MET cc_start: 0.8974 (mtm) cc_final: 0.8338 (mpp) REVERT: J 543 ASN cc_start: 0.8934 (m110) cc_final: 0.8629 (m110) REVERT: J 659 ASP cc_start: 0.7594 (m-30) cc_final: 0.7057 (m-30) REVERT: K 12 LYS cc_start: 0.7947 (mmtt) cc_final: 0.7736 (mmmt) REVERT: K 34 MET cc_start: 0.8756 (mmt) cc_final: 0.8499 (mmt) REVERT: K 81 MET cc_start: 0.8824 (tmm) cc_final: 0.8404 (tmm) REVERT: K 116 TYR cc_start: 0.7977 (m-80) cc_final: 0.7392 (m-80) outliers start: 87 outliers final: 59 residues processed: 204 average time/residue: 0.2693 time to fit residues: 90.3539 Evaluate side-chains 190 residues out of total 2142 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 127 time to evaluate : 2.354 ------------------------------------------------------------------------------- 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 120 VAL Chi-restraints excluded: chain A residue 140 THR Chi-restraints excluded: chain A residue 213 ILE Chi-restraints excluded: chain A residue 287 HIS Chi-restraints excluded: chain A residue 295 VAL Chi-restraints excluded: chain A residue 374 HIS Chi-restraints excluded: chain B residue 534 SER Chi-restraints excluded: chain B residue 543 ASN Chi-restraints excluded: chain B residue 574 LYS Chi-restraints excluded: chain B residue 602 LEU Chi-restraints excluded: chain B residue 659 ASP Chi-restraints excluded: chain C residue 30 THR Chi-restraints excluded: chain C residue 51 ILE Chi-restraints excluded: chain D residue 28 ASP Chi-restraints excluded: chain D residue 33 ASN Chi-restraints excluded: chain D residue 72 THR Chi-restraints excluded: chain D residue 87 ASP Chi-restraints excluded: chain D residue 107 LEU Chi-restraints excluded: chain E residue 34 LEU Chi-restraints excluded: chain E residue 90 THR Chi-restraints excluded: chain E residue 111 LEU Chi-restraints excluded: chain E residue 120 VAL Chi-restraints excluded: chain E residue 127 VAL Chi-restraints excluded: chain E residue 140 THR Chi-restraints excluded: chain E residue 149 VAL Chi-restraints excluded: chain E residue 244 THR Chi-restraints excluded: chain E residue 262 ASN Chi-restraints excluded: chain E residue 287 HIS Chi-restraints excluded: chain E residue 295 VAL Chi-restraints excluded: chain E residue 374 HIS Chi-restraints excluded: chain F residue 587 LEU Chi-restraints excluded: chain F residue 605 CYS Chi-restraints excluded: chain F residue 641 ILE Chi-restraints excluded: chain G residue 28 THR Chi-restraints excluded: chain G residue 51 ILE Chi-restraints excluded: chain G residue 90 ASP Chi-restraints excluded: chain H residue 35 VAL Chi-restraints excluded: chain H residue 48 LEU Chi-restraints excluded: chain H residue 51 TYR Chi-restraints excluded: chain I residue 104 MET Chi-restraints excluded: chain I residue 120 VAL Chi-restraints excluded: chain I residue 149 VAL Chi-restraints excluded: chain I residue 202 THR Chi-restraints excluded: chain I residue 240 SER Chi-restraints excluded: chain I residue 271 VAL Chi-restraints excluded: chain I residue 287 HIS Chi-restraints excluded: chain I residue 295 VAL Chi-restraints excluded: chain I residue 325 ASP Chi-restraints excluded: chain I residue 494 LEU Chi-restraints excluded: chain J residue 576 LEU Chi-restraints excluded: chain J residue 587 LEU Chi-restraints excluded: chain J residue 595 ILE Chi-restraints excluded: chain J residue 641 ILE Chi-restraints excluded: chain K residue 28 THR Chi-restraints excluded: chain K residue 51 ILE Chi-restraints excluded: chain K residue 68 VAL Chi-restraints excluded: chain L residue 33 ASN Chi-restraints excluded: chain L residue 48 LEU Chi-restraints excluded: chain L residue 72 THR Chi-restraints excluded: chain L residue 75 LEU Chi-restraints excluded: chain L residue 87 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 246 random chunks: chunk 80 optimal weight: 6.9990 chunk 214 optimal weight: 7.9990 chunk 47 optimal weight: 7.9990 chunk 139 optimal weight: 10.0000 chunk 58 optimal weight: 9.9990 chunk 238 optimal weight: 9.9990 chunk 197 optimal weight: 3.9990 chunk 110 optimal weight: 9.9990 chunk 19 optimal weight: 8.9990 chunk 78 optimal weight: 40.0000 chunk 124 optimal weight: 8.9990 overall best weight: 7.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 6 GLN ** F 575 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 374 HIS ** J 575 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7893 moved from start: 0.5067 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 20271 Z= 0.346 Angle : 0.696 12.479 27558 Z= 0.345 Chirality : 0.047 0.364 3243 Planarity : 0.004 0.054 3450 Dihedral : 9.257 72.352 3712 Min Nonbonded Distance : 2.085 Molprobity Statistics. All-atom Clashscore : 9.42 Ramachandran Plot: Outliers : 0.36 % Allowed : 6.03 % Favored : 93.61 % Rotamer: Outliers : 4.34 % Allowed : 11.80 % Favored : 83.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.28 (0.16), residues: 2472 helix: 0.74 (0.28), residues: 387 sheet: -0.10 (0.18), residues: 750 loop : -1.84 (0.16), residues: 1335 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP F 631 HIS 0.027 0.002 HIS A 374 PHE 0.018 0.002 PHE G 114 TYR 0.017 0.002 TYR D 51 ARG 0.004 0.000 ARG J 617 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4944 Ramachandran restraints generated. 2472 Oldfield, 0 Emsley, 2472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4944 Ramachandran restraints generated. 2472 Oldfield, 0 Emsley, 2472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 222 residues out of total 2142 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 92 poor density : 130 time to evaluate : 2.314 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 535 MET cc_start: 0.8775 (mtm) cc_final: 0.8347 (mpp) REVERT: C 115 ASP cc_start: 0.9030 (p0) cc_final: 0.8544 (p0) REVERT: D 107 LEU cc_start: 0.8474 (OUTLIER) cc_final: 0.8075 (tt) REVERT: E 104 MET cc_start: 0.9166 (OUTLIER) cc_final: 0.8783 (ttp) REVERT: E 287 HIS cc_start: 0.8284 (OUTLIER) cc_final: 0.7291 (m90) REVERT: E 475 MET cc_start: 0.8691 (mmm) cc_final: 0.8254 (mmm) REVERT: F 543 ASN cc_start: 0.8593 (m110) cc_final: 0.8231 (m110) REVERT: F 585 ARG cc_start: 0.8010 (mtp85) cc_final: 0.7785 (mtp-110) REVERT: F 659 ASP cc_start: 0.7045 (m-30) cc_final: 0.6742 (m-30) REVERT: I 95 MET cc_start: 0.8032 (ttp) cc_final: 0.6779 (tmm) REVERT: I 104 MET cc_start: 0.9307 (OUTLIER) cc_final: 0.8811 (tpt) REVERT: J 530 MET cc_start: 0.6322 (mmp) cc_final: 0.6122 (mmp) REVERT: J 534 SER cc_start: 0.8912 (t) cc_final: 0.8554 (p) REVERT: J 535 MET cc_start: 0.8884 (mtm) cc_final: 0.8312 (mpp) REVERT: J 543 ASN cc_start: 0.8911 (m110) cc_final: 0.8607 (m110) REVERT: J 659 ASP cc_start: 0.7646 (m-30) cc_final: 0.7117 (m-30) REVERT: K 12 LYS cc_start: 0.7979 (mmtt) cc_final: 0.7763 (mmmt) REVERT: K 81 MET cc_start: 0.8779 (tmm) cc_final: 0.8340 (tmm) REVERT: K 116 TYR cc_start: 0.7974 (m-80) cc_final: 0.7373 (m-80) outliers start: 92 outliers final: 68 residues processed: 205 average time/residue: 0.2672 time to fit residues: 88.8525 Evaluate side-chains 197 residues out of total 2142 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 125 time to evaluate : 2.340 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 VAL Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 140 THR Chi-restraints excluded: chain A residue 149 VAL Chi-restraints excluded: chain A residue 202 THR Chi-restraints excluded: chain A residue 244 THR Chi-restraints excluded: chain A residue 262 ASN Chi-restraints excluded: chain A residue 287 HIS Chi-restraints excluded: chain A residue 295 VAL Chi-restraints excluded: chain A residue 373 THR Chi-restraints excluded: chain B residue 534 SER Chi-restraints excluded: chain B residue 543 ASN Chi-restraints excluded: chain B residue 574 LYS Chi-restraints excluded: chain B residue 602 LEU Chi-restraints excluded: chain C residue 30 THR Chi-restraints excluded: chain C residue 51 ILE Chi-restraints excluded: chain C residue 114 PHE Chi-restraints excluded: chain D residue 19 THR Chi-restraints excluded: chain D residue 28 ASP Chi-restraints excluded: chain D residue 33 ASN Chi-restraints excluded: chain D residue 51 TYR Chi-restraints excluded: chain D residue 72 THR Chi-restraints excluded: chain D residue 87 ASP Chi-restraints excluded: chain D residue 107 LEU Chi-restraints excluded: chain E residue 34 LEU Chi-restraints excluded: chain E residue 85 VAL Chi-restraints excluded: chain E residue 90 THR Chi-restraints excluded: chain E residue 104 MET Chi-restraints excluded: chain E residue 111 LEU Chi-restraints excluded: chain E residue 120 VAL Chi-restraints excluded: chain E residue 127 VAL Chi-restraints excluded: chain E residue 140 THR Chi-restraints excluded: chain E residue 149 VAL Chi-restraints excluded: chain E residue 240 SER Chi-restraints excluded: chain E residue 244 THR Chi-restraints excluded: chain E residue 287 HIS Chi-restraints excluded: chain E residue 295 VAL Chi-restraints excluded: chain F residue 587 LEU Chi-restraints excluded: chain F residue 602 LEU Chi-restraints excluded: chain F residue 605 CYS Chi-restraints excluded: chain F residue 641 ILE Chi-restraints excluded: chain G residue 28 THR Chi-restraints excluded: chain G residue 51 ILE Chi-restraints excluded: chain H residue 35 VAL Chi-restraints excluded: chain H residue 48 LEU Chi-restraints excluded: chain H residue 51 TYR Chi-restraints excluded: chain H residue 107 LEU Chi-restraints excluded: chain I residue 104 MET Chi-restraints excluded: chain I residue 120 VAL Chi-restraints excluded: chain I residue 149 VAL Chi-restraints excluded: chain I residue 202 THR Chi-restraints excluded: chain I residue 213 ILE Chi-restraints excluded: chain I residue 240 SER Chi-restraints excluded: chain I residue 262 ASN Chi-restraints excluded: chain I residue 271 VAL Chi-restraints excluded: chain I residue 287 HIS Chi-restraints excluded: chain I residue 288 LEU Chi-restraints excluded: chain I residue 295 VAL Chi-restraints excluded: chain I residue 325 ASP Chi-restraints excluded: chain I residue 374 HIS Chi-restraints excluded: chain I residue 494 LEU Chi-restraints excluded: chain J residue 576 LEU Chi-restraints excluded: chain J residue 595 ILE Chi-restraints excluded: chain J residue 641 ILE Chi-restraints excluded: chain K residue 28 THR Chi-restraints excluded: chain K residue 51 ILE Chi-restraints excluded: chain K residue 68 VAL Chi-restraints excluded: chain L residue 33 ASN Chi-restraints excluded: chain L residue 48 LEU Chi-restraints excluded: chain L residue 72 THR Chi-restraints excluded: chain L residue 75 LEU Chi-restraints excluded: chain L residue 87 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 246 random chunks: chunk 229 optimal weight: 9.9990 chunk 26 optimal weight: 5.9990 chunk 135 optimal weight: 4.9990 chunk 173 optimal weight: 7.9990 chunk 134 optimal weight: 3.9990 chunk 200 optimal weight: 50.0000 chunk 132 optimal weight: 9.9990 chunk 237 optimal weight: 8.9990 chunk 148 optimal weight: 20.0000 chunk 144 optimal weight: 7.9990 chunk 109 optimal weight: 0.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 374 HIS ** D 1 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 575 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 575 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 607 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7877 moved from start: 0.5209 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 20271 Z= 0.253 Angle : 0.666 13.637 27558 Z= 0.329 Chirality : 0.046 0.378 3243 Planarity : 0.004 0.050 3450 Dihedral : 8.971 72.017 3712 Min Nonbonded Distance : 2.104 Molprobity Statistics. All-atom Clashscore : 8.68 Ramachandran Plot: Outliers : 0.36 % Allowed : 5.54 % Favored : 94.09 % Rotamer: Outliers : 3.73 % Allowed : 12.84 % Favored : 83.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.17 (0.17), residues: 2472 helix: 0.84 (0.28), residues: 387 sheet: -0.06 (0.18), residues: 735 loop : -1.75 (0.16), residues: 1350 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP J 571 HIS 0.015 0.001 HIS I 374 PHE 0.016 0.002 PHE G 114 TYR 0.014 0.001 TYR D 51 ARG 0.002 0.000 ARG J 617 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4944 Ramachandran restraints generated. 2472 Oldfield, 0 Emsley, 2472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4944 Ramachandran restraints generated. 2472 Oldfield, 0 Emsley, 2472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 213 residues out of total 2142 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 79 poor density : 134 time to evaluate : 2.322 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 535 MET cc_start: 0.8776 (mtm) cc_final: 0.8349 (mpp) REVERT: B 626 MET cc_start: 0.8695 (tpt) cc_final: 0.8436 (tpt) REVERT: C 115 ASP cc_start: 0.9022 (p0) cc_final: 0.8509 (p0) REVERT: D 107 LEU cc_start: 0.8504 (OUTLIER) cc_final: 0.8183 (tt) REVERT: E 95 MET cc_start: 0.7275 (tmm) cc_final: 0.6925 (tmm) REVERT: E 104 MET cc_start: 0.9182 (OUTLIER) cc_final: 0.8770 (ttp) REVERT: E 287 HIS cc_start: 0.8245 (OUTLIER) cc_final: 0.7285 (m90) REVERT: E 475 MET cc_start: 0.8584 (mmm) cc_final: 0.8013 (mmm) REVERT: F 534 SER cc_start: 0.9151 (t) cc_final: 0.8740 (p) REVERT: F 543 ASN cc_start: 0.8619 (m110) cc_final: 0.8227 (m110) REVERT: F 585 ARG cc_start: 0.7982 (mtp85) cc_final: 0.7766 (mtp-110) REVERT: F 659 ASP cc_start: 0.7090 (m-30) cc_final: 0.6794 (m-30) REVERT: I 95 MET cc_start: 0.8268 (ttp) cc_final: 0.7118 (tmm) REVERT: I 104 MET cc_start: 0.9282 (OUTLIER) cc_final: 0.8805 (tpt) REVERT: J 534 SER cc_start: 0.8971 (t) cc_final: 0.8634 (p) REVERT: J 535 MET cc_start: 0.8888 (mtm) cc_final: 0.8314 (mpp) REVERT: J 543 ASN cc_start: 0.8886 (m110) cc_final: 0.8563 (m110) REVERT: J 655 LYS cc_start: 0.8859 (OUTLIER) cc_final: 0.8467 (tppp) REVERT: J 659 ASP cc_start: 0.7634 (m-30) cc_final: 0.7094 (m-30) REVERT: K 12 LYS cc_start: 0.7997 (mmtt) cc_final: 0.7767 (mmmt) REVERT: K 81 MET cc_start: 0.8732 (tmm) cc_final: 0.8288 (tmm) REVERT: K 116 TYR cc_start: 0.7983 (m-80) cc_final: 0.7359 (m-80) outliers start: 79 outliers final: 64 residues processed: 197 average time/residue: 0.2812 time to fit residues: 89.7215 Evaluate side-chains 196 residues out of total 2142 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 127 time to evaluate : 2.283 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 VAL Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 202 THR Chi-restraints excluded: chain A residue 213 ILE Chi-restraints excluded: chain A residue 244 THR Chi-restraints excluded: chain A residue 262 ASN Chi-restraints excluded: chain A residue 287 HIS Chi-restraints excluded: chain A residue 295 VAL Chi-restraints excluded: chain A residue 374 HIS Chi-restraints excluded: chain B residue 543 ASN Chi-restraints excluded: chain B residue 574 LYS Chi-restraints excluded: chain B residue 602 LEU Chi-restraints excluded: chain C residue 30 THR Chi-restraints excluded: chain C residue 51 ILE Chi-restraints excluded: chain C residue 114 PHE Chi-restraints excluded: chain D residue 19 THR Chi-restraints excluded: chain D residue 28 ASP Chi-restraints excluded: chain D residue 33 ASN Chi-restraints excluded: chain D residue 51 TYR Chi-restraints excluded: chain D residue 72 THR Chi-restraints excluded: chain D residue 87 ASP Chi-restraints excluded: chain D residue 107 LEU Chi-restraints excluded: chain E residue 85 VAL Chi-restraints excluded: chain E residue 90 THR Chi-restraints excluded: chain E residue 104 MET Chi-restraints excluded: chain E residue 120 VAL Chi-restraints excluded: chain E residue 127 VAL Chi-restraints excluded: chain E residue 140 THR Chi-restraints excluded: chain E residue 149 VAL Chi-restraints excluded: chain E residue 240 SER Chi-restraints excluded: chain E residue 244 THR Chi-restraints excluded: chain E residue 262 ASN Chi-restraints excluded: chain E residue 287 HIS Chi-restraints excluded: chain E residue 295 VAL Chi-restraints excluded: chain E residue 333 ILE Chi-restraints excluded: chain F residue 587 LEU Chi-restraints excluded: chain F residue 602 LEU Chi-restraints excluded: chain F residue 605 CYS Chi-restraints excluded: chain F residue 641 ILE Chi-restraints excluded: chain G residue 28 THR Chi-restraints excluded: chain G residue 51 ILE Chi-restraints excluded: chain G residue 90 ASP Chi-restraints excluded: chain H residue 35 VAL Chi-restraints excluded: chain H residue 48 LEU Chi-restraints excluded: chain H residue 51 TYR Chi-restraints excluded: chain H residue 107 LEU Chi-restraints excluded: chain I residue 104 MET Chi-restraints excluded: chain I residue 120 VAL Chi-restraints excluded: chain I residue 149 VAL Chi-restraints excluded: chain I residue 202 THR Chi-restraints excluded: chain I residue 213 ILE Chi-restraints excluded: chain I residue 240 SER Chi-restraints excluded: chain I residue 287 HIS Chi-restraints excluded: chain I residue 295 VAL Chi-restraints excluded: chain I residue 302 ASN Chi-restraints excluded: chain I residue 325 ASP Chi-restraints excluded: chain I residue 494 LEU Chi-restraints excluded: chain J residue 576 LEU Chi-restraints excluded: chain J residue 595 ILE Chi-restraints excluded: chain J residue 641 ILE Chi-restraints excluded: chain J residue 655 LYS Chi-restraints excluded: chain K residue 28 THR Chi-restraints excluded: chain K residue 51 ILE Chi-restraints excluded: chain K residue 68 VAL Chi-restraints excluded: chain L residue 33 ASN Chi-restraints excluded: chain L residue 48 LEU Chi-restraints excluded: chain L residue 72 THR Chi-restraints excluded: chain L residue 75 LEU Chi-restraints excluded: chain L residue 87 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 246 random chunks: chunk 146 optimal weight: 6.9990 chunk 94 optimal weight: 5.9990 chunk 141 optimal weight: 7.9990 chunk 71 optimal weight: 30.0000 chunk 46 optimal weight: 0.0770 chunk 45 optimal weight: 8.9990 chunk 150 optimal weight: 2.9990 chunk 161 optimal weight: 7.9990 chunk 117 optimal weight: 6.9990 chunk 22 optimal weight: 0.0470 chunk 186 optimal weight: 5.9990 overall best weight: 3.0242 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 374 HIS ** D 1 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 575 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 575 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7857 moved from start: 0.5276 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 20271 Z= 0.193 Angle : 0.637 13.302 27558 Z= 0.311 Chirality : 0.045 0.387 3243 Planarity : 0.004 0.048 3450 Dihedral : 8.655 72.895 3712 Min Nonbonded Distance : 2.133 Molprobity Statistics. All-atom Clashscore : 7.99 Ramachandran Plot: Outliers : 0.36 % Allowed : 5.10 % Favored : 94.54 % Rotamer: Outliers : 3.49 % Allowed : 13.46 % Favored : 83.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.09 (0.17), residues: 2472 helix: 0.87 (0.28), residues: 387 sheet: -0.01 (0.18), residues: 741 loop : -1.68 (0.16), residues: 1344 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP J 571 HIS 0.010 0.001 HIS A 374 PHE 0.015 0.001 PHE K 114 TYR 0.013 0.001 TYR D 51 ARG 0.002 0.000 ARG F 617 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4944 Ramachandran restraints generated. 2472 Oldfield, 0 Emsley, 2472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4944 Ramachandran restraints generated. 2472 Oldfield, 0 Emsley, 2472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 205 residues out of total 2142 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 74 poor density : 131 time to evaluate : 2.365 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 426 MET cc_start: 0.6711 (mtm) cc_final: 0.6492 (mtm) REVERT: B 535 MET cc_start: 0.8778 (mtm) cc_final: 0.8240 (mpp) REVERT: C 115 ASP cc_start: 0.9007 (p0) cc_final: 0.8462 (p0) REVERT: D 107 LEU cc_start: 0.8467 (OUTLIER) cc_final: 0.8080 (tt) REVERT: E 95 MET cc_start: 0.7245 (tmm) cc_final: 0.6899 (tmm) REVERT: E 104 MET cc_start: 0.9206 (OUTLIER) cc_final: 0.8842 (ttp) REVERT: E 287 HIS cc_start: 0.8193 (OUTLIER) cc_final: 0.7227 (m90) REVERT: E 475 MET cc_start: 0.8600 (OUTLIER) cc_final: 0.8044 (mmm) REVERT: F 534 SER cc_start: 0.9010 (t) cc_final: 0.8620 (p) REVERT: F 543 ASN cc_start: 0.8628 (m110) cc_final: 0.8230 (m110) REVERT: F 585 ARG cc_start: 0.8022 (mtp85) cc_final: 0.7776 (mtp-110) REVERT: F 659 ASP cc_start: 0.7086 (m-30) cc_final: 0.6776 (m-30) REVERT: I 95 MET cc_start: 0.8133 (ttp) cc_final: 0.7082 (tmm) REVERT: J 530 MET cc_start: 0.6722 (mmp) cc_final: 0.6398 (mmp) REVERT: J 534 SER cc_start: 0.8970 (t) cc_final: 0.8660 (p) REVERT: J 535 MET cc_start: 0.8880 (mtm) cc_final: 0.8316 (mpp) REVERT: J 543 ASN cc_start: 0.8896 (m110) cc_final: 0.8568 (m110) REVERT: J 655 LYS cc_start: 0.8799 (OUTLIER) cc_final: 0.8456 (tppp) REVERT: J 657 GLU cc_start: 0.8937 (tm-30) cc_final: 0.8565 (mm-30) REVERT: J 659 ASP cc_start: 0.7604 (m-30) cc_final: 0.7060 (m-30) REVERT: K 12 LYS cc_start: 0.8002 (mmtt) cc_final: 0.7768 (mmmt) REVERT: K 34 MET cc_start: 0.8785 (mmt) cc_final: 0.8545 (mmt) REVERT: K 81 MET cc_start: 0.8698 (tmm) cc_final: 0.8244 (tmm) REVERT: K 115 ASP cc_start: 0.8410 (p0) cc_final: 0.7594 (p0) REVERT: K 116 TYR cc_start: 0.8002 (m-80) cc_final: 0.7356 (m-80) outliers start: 74 outliers final: 57 residues processed: 190 average time/residue: 0.2813 time to fit residues: 86.1855 Evaluate side-chains 189 residues out of total 2142 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 127 time to evaluate : 2.291 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 VAL Chi-restraints excluded: chain A residue 89 VAL Chi-restraints excluded: chain A residue 149 VAL Chi-restraints excluded: chain A residue 202 THR Chi-restraints excluded: chain A residue 213 ILE Chi-restraints excluded: chain A residue 244 THR Chi-restraints excluded: chain A residue 262 ASN Chi-restraints excluded: chain A residue 287 HIS Chi-restraints excluded: chain A residue 295 VAL Chi-restraints excluded: chain A residue 296 CYS Chi-restraints excluded: chain A residue 374 HIS Chi-restraints excluded: chain B residue 543 ASN Chi-restraints excluded: chain B residue 574 LYS Chi-restraints excluded: chain B residue 602 LEU Chi-restraints excluded: chain C residue 30 THR Chi-restraints excluded: chain C residue 51 ILE Chi-restraints excluded: chain C residue 114 PHE Chi-restraints excluded: chain D residue 28 ASP Chi-restraints excluded: chain D residue 33 ASN Chi-restraints excluded: chain D residue 51 TYR Chi-restraints excluded: chain D residue 72 THR Chi-restraints excluded: chain D residue 87 ASP Chi-restraints excluded: chain D residue 107 LEU Chi-restraints excluded: chain E residue 85 VAL Chi-restraints excluded: chain E residue 104 MET Chi-restraints excluded: chain E residue 120 VAL Chi-restraints excluded: chain E residue 127 VAL Chi-restraints excluded: chain E residue 140 THR Chi-restraints excluded: chain E residue 149 VAL Chi-restraints excluded: chain E residue 244 THR Chi-restraints excluded: chain E residue 262 ASN Chi-restraints excluded: chain E residue 287 HIS Chi-restraints excluded: chain E residue 333 ILE Chi-restraints excluded: chain E residue 475 MET Chi-restraints excluded: chain F residue 587 LEU Chi-restraints excluded: chain F residue 602 LEU Chi-restraints excluded: chain F residue 605 CYS Chi-restraints excluded: chain G residue 28 THR Chi-restraints excluded: chain G residue 51 ILE Chi-restraints excluded: chain H residue 48 LEU Chi-restraints excluded: chain H residue 107 LEU Chi-restraints excluded: chain I residue 120 VAL Chi-restraints excluded: chain I residue 149 VAL Chi-restraints excluded: chain I residue 202 THR Chi-restraints excluded: chain I residue 213 ILE Chi-restraints excluded: chain I residue 240 SER Chi-restraints excluded: chain I residue 287 HIS Chi-restraints excluded: chain I residue 295 VAL Chi-restraints excluded: chain I residue 302 ASN Chi-restraints excluded: chain I residue 325 ASP Chi-restraints excluded: chain I residue 494 LEU Chi-restraints excluded: chain J residue 576 LEU Chi-restraints excluded: chain J residue 595 ILE Chi-restraints excluded: chain J residue 647 GLU Chi-restraints excluded: chain J residue 655 LYS Chi-restraints excluded: chain K residue 28 THR Chi-restraints excluded: chain K residue 51 ILE Chi-restraints excluded: chain K residue 68 VAL Chi-restraints excluded: chain L residue 48 LEU Chi-restraints excluded: chain L residue 72 THR Chi-restraints excluded: chain L residue 75 LEU Chi-restraints excluded: chain L residue 87 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 246 random chunks: chunk 215 optimal weight: 5.9990 chunk 227 optimal weight: 20.0000 chunk 207 optimal weight: 8.9990 chunk 220 optimal weight: 20.0000 chunk 132 optimal weight: 8.9990 chunk 96 optimal weight: 0.5980 chunk 173 optimal weight: 0.0050 chunk 67 optimal weight: 20.0000 chunk 199 optimal weight: 6.9990 chunk 208 optimal weight: 9.9990 chunk 145 optimal weight: 1.9990 overall best weight: 3.1200 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 1 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 575 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 575 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7855 moved from start: 0.5358 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 20271 Z= 0.200 Angle : 0.645 13.077 27558 Z= 0.315 Chirality : 0.045 0.379 3243 Planarity : 0.004 0.047 3450 Dihedral : 8.459 72.890 3711 Min Nonbonded Distance : 2.143 Molprobity Statistics. All-atom Clashscore : 8.14 Ramachandran Plot: Outliers : 0.36 % Allowed : 4.94 % Favored : 94.70 % Rotamer: Outliers : 3.07 % Allowed : 14.26 % Favored : 82.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.05 (0.17), residues: 2472 helix: 0.92 (0.28), residues: 387 sheet: -0.02 (0.19), residues: 747 loop : -1.64 (0.17), residues: 1338 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP C 47 HIS 0.014 0.001 HIS A 374 PHE 0.015 0.001 PHE K 114 TYR 0.015 0.001 TYR H 51 ARG 0.003 0.000 ARG L 63 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4944 Ramachandran restraints generated. 2472 Oldfield, 0 Emsley, 2472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4944 Ramachandran restraints generated. 2472 Oldfield, 0 Emsley, 2472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 2142 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 130 time to evaluate : 3.230 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 104 MET cc_start: 0.9000 (ttp) cc_final: 0.8287 (tmm) REVERT: B 535 MET cc_start: 0.8755 (mtm) cc_final: 0.8166 (mpp) REVERT: C 115 ASP cc_start: 0.9071 (p0) cc_final: 0.8549 (p0) REVERT: D 1 GLN cc_start: 0.3262 (pp30) cc_final: 0.2965 (pp30) REVERT: E 95 MET cc_start: 0.7241 (tmm) cc_final: 0.6891 (tmm) REVERT: E 104 MET cc_start: 0.9223 (OUTLIER) cc_final: 0.8851 (ttp) REVERT: E 287 HIS cc_start: 0.8154 (OUTLIER) cc_final: 0.7263 (m90) REVERT: E 475 MET cc_start: 0.8623 (mmm) cc_final: 0.8029 (mmm) REVERT: F 534 SER cc_start: 0.9008 (t) cc_final: 0.8611 (p) REVERT: F 543 ASN cc_start: 0.8675 (m110) cc_final: 0.8288 (m110) REVERT: F 585 ARG cc_start: 0.8020 (mtp85) cc_final: 0.7777 (mtp-110) REVERT: F 659 ASP cc_start: 0.7087 (m-30) cc_final: 0.6784 (m-30) REVERT: I 95 MET cc_start: 0.8061 (ttp) cc_final: 0.7058 (tmm) REVERT: J 530 MET cc_start: 0.6688 (mmp) cc_final: 0.6357 (mmp) REVERT: J 534 SER cc_start: 0.9055 (t) cc_final: 0.8833 (p) REVERT: J 535 MET cc_start: 0.8768 (mtm) cc_final: 0.8209 (mpp) REVERT: J 543 ASN cc_start: 0.8901 (m110) cc_final: 0.8568 (m110) REVERT: J 655 LYS cc_start: 0.8791 (OUTLIER) cc_final: 0.8449 (tppp) REVERT: J 657 GLU cc_start: 0.8923 (tm-30) cc_final: 0.8576 (mm-30) REVERT: J 659 ASP cc_start: 0.7481 (m-30) cc_final: 0.6944 (m-30) REVERT: K 12 LYS cc_start: 0.8008 (mmtt) cc_final: 0.7768 (mmmt) REVERT: K 34 MET cc_start: 0.8792 (mmt) cc_final: 0.8550 (mmt) REVERT: K 81 MET cc_start: 0.8664 (tmm) cc_final: 0.8211 (tmm) REVERT: K 115 ASP cc_start: 0.8431 (p0) cc_final: 0.7577 (p0) REVERT: K 116 TYR cc_start: 0.7955 (m-80) cc_final: 0.7331 (m-80) outliers start: 65 outliers final: 53 residues processed: 186 average time/residue: 0.2967 time to fit residues: 89.5070 Evaluate side-chains 184 residues out of total 2142 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 128 time to evaluate : 1.887 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 VAL Chi-restraints excluded: chain A residue 89 VAL Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 140 THR Chi-restraints excluded: chain A residue 149 VAL Chi-restraints excluded: chain A residue 202 THR Chi-restraints excluded: chain A residue 213 ILE Chi-restraints excluded: chain A residue 244 THR Chi-restraints excluded: chain A residue 262 ASN Chi-restraints excluded: chain A residue 287 HIS Chi-restraints excluded: chain A residue 295 VAL Chi-restraints excluded: chain A residue 296 CYS Chi-restraints excluded: chain B residue 602 LEU Chi-restraints excluded: chain C residue 30 THR Chi-restraints excluded: chain C residue 51 ILE Chi-restraints excluded: chain D residue 33 ASN Chi-restraints excluded: chain D residue 72 THR Chi-restraints excluded: chain D residue 87 ASP Chi-restraints excluded: chain E residue 85 VAL Chi-restraints excluded: chain E residue 90 THR Chi-restraints excluded: chain E residue 104 MET Chi-restraints excluded: chain E residue 120 VAL Chi-restraints excluded: chain E residue 127 VAL Chi-restraints excluded: chain E residue 140 THR Chi-restraints excluded: chain E residue 149 VAL Chi-restraints excluded: chain E residue 244 THR Chi-restraints excluded: chain E residue 262 ASN Chi-restraints excluded: chain E residue 287 HIS Chi-restraints excluded: chain E residue 333 ILE Chi-restraints excluded: chain F residue 587 LEU Chi-restraints excluded: chain F residue 602 LEU Chi-restraints excluded: chain F residue 605 CYS Chi-restraints excluded: chain G residue 28 THR Chi-restraints excluded: chain G residue 51 ILE Chi-restraints excluded: chain H residue 48 LEU Chi-restraints excluded: chain H residue 107 LEU Chi-restraints excluded: chain I residue 120 VAL Chi-restraints excluded: chain I residue 149 VAL Chi-restraints excluded: chain I residue 202 THR Chi-restraints excluded: chain I residue 213 ILE Chi-restraints excluded: chain I residue 240 SER Chi-restraints excluded: chain I residue 287 HIS Chi-restraints excluded: chain I residue 295 VAL Chi-restraints excluded: chain I residue 302 ASN Chi-restraints excluded: chain I residue 325 ASP Chi-restraints excluded: chain I residue 494 LEU Chi-restraints excluded: chain J residue 576 LEU Chi-restraints excluded: chain J residue 647 GLU Chi-restraints excluded: chain J residue 655 LYS Chi-restraints excluded: chain K residue 28 THR Chi-restraints excluded: chain K residue 51 ILE Chi-restraints excluded: chain K residue 68 VAL Chi-restraints excluded: chain L residue 48 LEU Chi-restraints excluded: chain L residue 72 THR Chi-restraints excluded: chain L residue 75 LEU Chi-restraints excluded: chain L residue 87 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 246 random chunks: chunk 233 optimal weight: 6.9990 chunk 142 optimal weight: 10.0000 chunk 110 optimal weight: 6.9990 chunk 162 optimal weight: 6.9990 chunk 245 optimal weight: 10.0000 chunk 225 optimal weight: 5.9990 chunk 195 optimal weight: 7.9990 chunk 20 optimal weight: 20.0000 chunk 150 optimal weight: 5.9990 chunk 119 optimal weight: 10.0000 chunk 155 optimal weight: 7.9990 overall best weight: 6.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 374 HIS ** D 1 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 575 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 575 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7909 moved from start: 0.5686 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 20271 Z= 0.326 Angle : 0.706 13.278 27558 Z= 0.348 Chirality : 0.046 0.342 3243 Planarity : 0.004 0.060 3450 Dihedral : 8.700 69.939 3711 Min Nonbonded Distance : 2.107 Molprobity Statistics. All-atom Clashscore : 10.09 Ramachandran Plot: Outliers : 0.36 % Allowed : 6.03 % Favored : 93.61 % Rotamer: Outliers : 3.02 % Allowed : 14.68 % Favored : 82.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.27 (0.17), residues: 2472 helix: 0.76 (0.28), residues: 387 sheet: -0.10 (0.18), residues: 738 loop : -1.83 (0.16), residues: 1347 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 427 HIS 0.005 0.001 HIS G 35 PHE 0.020 0.002 PHE G 114 TYR 0.013 0.002 TYR H 51 ARG 0.006 0.001 ARG I 500 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4944 Ramachandran restraints generated. 2472 Oldfield, 0 Emsley, 2472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4944 Ramachandran restraints generated. 2472 Oldfield, 0 Emsley, 2472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 2142 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 131 time to evaluate : 2.320 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 104 MET cc_start: 0.9083 (ttp) cc_final: 0.8348 (tmm) REVERT: B 535 MET cc_start: 0.8828 (mtm) cc_final: 0.8128 (mpp) REVERT: C 115 ASP cc_start: 0.9070 (p0) cc_final: 0.8540 (p0) REVERT: D 1 GLN cc_start: 0.3586 (pp30) cc_final: 0.3351 (pp30) REVERT: E 95 MET cc_start: 0.7498 (tmm) cc_final: 0.7133 (tmm) REVERT: E 104 MET cc_start: 0.9239 (OUTLIER) cc_final: 0.8812 (ttp) REVERT: E 287 HIS cc_start: 0.8230 (OUTLIER) cc_final: 0.7269 (m90) REVERT: E 381 GLU cc_start: 0.8681 (mm-30) cc_final: 0.8333 (mp0) REVERT: E 475 MET cc_start: 0.8694 (mmm) cc_final: 0.8067 (mmm) REVERT: F 534 SER cc_start: 0.8954 (t) cc_final: 0.8532 (p) REVERT: F 543 ASN cc_start: 0.8686 (m110) cc_final: 0.8317 (m110) REVERT: F 585 ARG cc_start: 0.8251 (mtp85) cc_final: 0.8006 (mtp-110) REVERT: F 659 ASP cc_start: 0.7192 (m-30) cc_final: 0.6902 (m-30) REVERT: I 95 MET cc_start: 0.8232 (ttp) cc_final: 0.7094 (tmm) REVERT: J 535 MET cc_start: 0.8837 (mtm) cc_final: 0.8326 (mpp) REVERT: J 543 ASN cc_start: 0.8923 (m110) cc_final: 0.8589 (m110) REVERT: J 655 LYS cc_start: 0.8888 (OUTLIER) cc_final: 0.8429 (tppp) REVERT: J 657 GLU cc_start: 0.8952 (tm-30) cc_final: 0.8606 (mm-30) REVERT: J 659 ASP cc_start: 0.7842 (m-30) cc_final: 0.7248 (m-30) REVERT: K 12 LYS cc_start: 0.8051 (mmtt) cc_final: 0.7785 (mmmt) REVERT: K 81 MET cc_start: 0.8676 (tmm) cc_final: 0.8270 (tmm) REVERT: K 116 TYR cc_start: 0.8012 (m-80) cc_final: 0.7365 (m-80) outliers start: 64 outliers final: 58 residues processed: 188 average time/residue: 0.2641 time to fit residues: 80.6806 Evaluate side-chains 185 residues out of total 2142 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 124 time to evaluate : 2.459 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 VAL Chi-restraints excluded: chain A residue 89 VAL Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 140 THR Chi-restraints excluded: chain A residue 149 VAL Chi-restraints excluded: chain A residue 202 THR Chi-restraints excluded: chain A residue 244 THR Chi-restraints excluded: chain A residue 262 ASN Chi-restraints excluded: chain A residue 287 HIS Chi-restraints excluded: chain A residue 295 VAL Chi-restraints excluded: chain A residue 296 CYS Chi-restraints excluded: chain A residue 374 HIS Chi-restraints excluded: chain B residue 602 LEU Chi-restraints excluded: chain C residue 30 THR Chi-restraints excluded: chain C residue 51 ILE Chi-restraints excluded: chain C residue 68 VAL Chi-restraints excluded: chain D residue 51 TYR Chi-restraints excluded: chain D residue 72 THR Chi-restraints excluded: chain D residue 87 ASP Chi-restraints excluded: chain E residue 85 VAL Chi-restraints excluded: chain E residue 90 THR Chi-restraints excluded: chain E residue 104 MET Chi-restraints excluded: chain E residue 120 VAL Chi-restraints excluded: chain E residue 127 VAL Chi-restraints excluded: chain E residue 140 THR Chi-restraints excluded: chain E residue 149 VAL Chi-restraints excluded: chain E residue 244 THR Chi-restraints excluded: chain E residue 262 ASN Chi-restraints excluded: chain E residue 287 HIS Chi-restraints excluded: chain E residue 333 ILE Chi-restraints excluded: chain F residue 587 LEU Chi-restraints excluded: chain F residue 602 LEU Chi-restraints excluded: chain F residue 605 CYS Chi-restraints excluded: chain G residue 28 THR Chi-restraints excluded: chain G residue 51 ILE Chi-restraints excluded: chain H residue 48 LEU Chi-restraints excluded: chain H residue 51 TYR Chi-restraints excluded: chain H residue 107 LEU Chi-restraints excluded: chain I residue 120 VAL Chi-restraints excluded: chain I residue 149 VAL Chi-restraints excluded: chain I residue 202 THR Chi-restraints excluded: chain I residue 213 ILE Chi-restraints excluded: chain I residue 240 SER Chi-restraints excluded: chain I residue 262 ASN Chi-restraints excluded: chain I residue 271 VAL Chi-restraints excluded: chain I residue 287 HIS Chi-restraints excluded: chain I residue 295 VAL Chi-restraints excluded: chain I residue 325 ASP Chi-restraints excluded: chain I residue 494 LEU Chi-restraints excluded: chain J residue 576 LEU Chi-restraints excluded: chain J residue 595 ILE Chi-restraints excluded: chain J residue 647 GLU Chi-restraints excluded: chain J residue 655 LYS Chi-restraints excluded: chain K residue 28 THR Chi-restraints excluded: chain K residue 51 ILE Chi-restraints excluded: chain K residue 68 VAL Chi-restraints excluded: chain L residue 33 ASN Chi-restraints excluded: chain L residue 48 LEU Chi-restraints excluded: chain L residue 72 THR Chi-restraints excluded: chain L residue 75 LEU Chi-restraints excluded: chain L residue 87 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 246 random chunks: chunk 207 optimal weight: 5.9990 chunk 59 optimal weight: 20.0000 chunk 179 optimal weight: 10.0000 chunk 28 optimal weight: 7.9990 chunk 54 optimal weight: 0.2980 chunk 195 optimal weight: 7.9990 chunk 81 optimal weight: 7.9990 chunk 200 optimal weight: 0.7980 chunk 24 optimal weight: 9.9990 chunk 36 optimal weight: 3.9990 chunk 171 optimal weight: 3.9990 overall best weight: 3.0186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 374 HIS ** D 1 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 575 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 575 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3664 r_free = 0.3664 target = 0.083228 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.064947 restraints weight = 80057.823| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 55)----------------| | r_work = 0.3347 r_free = 0.3347 target = 0.067144 restraints weight = 44905.358| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.068556 restraints weight = 31976.450| |-----------------------------------------------------------------------------| r_work (final): 0.3338 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8103 moved from start: 0.5696 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 20271 Z= 0.195 Angle : 0.654 12.742 27558 Z= 0.319 Chirality : 0.046 0.390 3243 Planarity : 0.004 0.056 3450 Dihedral : 8.414 71.881 3711 Min Nonbonded Distance : 2.124 Molprobity Statistics. All-atom Clashscore : 8.83 Ramachandran Plot: Outliers : 0.36 % Allowed : 4.94 % Favored : 94.70 % Rotamer: Outliers : 2.97 % Allowed : 14.78 % Favored : 82.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.10 (0.17), residues: 2472 helix: 0.84 (0.28), residues: 387 sheet: -0.03 (0.18), residues: 744 loop : -1.67 (0.17), residues: 1341 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A 427 HIS 0.021 0.001 HIS A 374 PHE 0.016 0.001 PHE A 376 TYR 0.015 0.001 TYR H 51 ARG 0.009 0.000 ARG I 500 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3167.77 seconds wall clock time: 59 minutes 14.81 seconds (3554.81 seconds total)