Starting phenix.real_space_refine on Tue Mar 19 11:28:42 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tco_25815/03_2024/7tco_25815.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tco_25815/03_2024/7tco_25815.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.19 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tco_25815/03_2024/7tco_25815.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tco_25815/03_2024/7tco_25815.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tco_25815/03_2024/7tco_25815.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tco_25815/03_2024/7tco_25815.pdb" } resolution = 4.19 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= 0.009 sd= 0.145 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 141 5.16 5 C 15030 2.51 5 N 4068 2.21 5 O 4734 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ASP 167": "OD1" <-> "OD2" Residue "C TYR 79": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 87": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 209": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 167": "OD1" <-> "OD2" Residue "G TYR 79": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 87": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 209": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M ASP 167": "OD1" <-> "OD2" Residue "O TYR 79": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O TYR 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P PHE 87": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P PHE 209": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 23973 Number of models: 1 Model: "" Number of chains: 27 Chain: "A" Number of atoms: 3465 Number of conformers: 1 Conformer: "" Number of residues, atoms: 440, 3465 Classifications: {'peptide': 440} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 20, 'TRANS': 418} Chain breaks: 4 Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'TRP:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "B" Number of atoms: 969 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 969 Classifications: {'peptide': 122} Link IDs: {'CIS': 1, 'PTRANS': 1, 'TRANS': 119} Chain breaks: 1 Chain: "C" Number of atoms: 1677 Number of conformers: 1 Conformer: "" Number of residues, atoms: 220, 1677 Classifications: {'peptide': 220} Link IDs: {'PCIS': 2, 'PTRANS': 11, 'TRANS': 206} Chain breaks: 1 Chain: "D" Number of atoms: 1635 Number of conformers: 1 Conformer: "" Number of residues, atoms: 211, 1635 Classifications: {'peptide': 211} Link IDs: {'PCIS': 2, 'PTRANS': 7, 'TRANS': 201} Chain: "E" Number of atoms: 3465 Number of conformers: 1 Conformer: "" Number of residues, atoms: 440, 3465 Classifications: {'peptide': 440} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 20, 'TRANS': 418} Chain breaks: 4 Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'TRP:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "F" Number of atoms: 969 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 969 Classifications: {'peptide': 122} Link IDs: {'CIS': 1, 'PTRANS': 1, 'TRANS': 119} Chain breaks: 1 Chain: "G" Number of atoms: 1677 Number of conformers: 1 Conformer: "" Number of residues, atoms: 220, 1677 Classifications: {'peptide': 220} Link IDs: {'PCIS': 2, 'PTRANS': 11, 'TRANS': 206} Chain breaks: 1 Chain: "H" Number of atoms: 1635 Number of conformers: 1 Conformer: "" Number of residues, atoms: 211, 1635 Classifications: {'peptide': 211} Link IDs: {'PCIS': 2, 'PTRANS': 7, 'TRANS': 201} Chain: "M" Number of atoms: 3465 Number of conformers: 1 Conformer: "" Number of residues, atoms: 440, 3465 Classifications: {'peptide': 440} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 20, 'TRANS': 418} Chain breaks: 4 Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'TRP:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "N" Number of atoms: 969 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 969 Classifications: {'peptide': 122} Link IDs: {'CIS': 1, 'PTRANS': 1, 'TRANS': 119} Chain breaks: 1 Chain: "O" Number of atoms: 1677 Number of conformers: 1 Conformer: "" Number of residues, atoms: 220, 1677 Classifications: {'peptide': 220} Link IDs: {'PCIS': 2, 'PTRANS': 11, 'TRANS': 206} Chain breaks: 1 Chain: "P" Number of atoms: 1635 Number of conformers: 1 Conformer: "" Number of residues, atoms: 211, 1635 Classifications: {'peptide': 211} Link IDs: {'PCIS': 2, 'PTRANS': 7, 'TRANS': 201} Chain: "I" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "J" 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: "K" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 72 Unusual residues: {'BMA': 1, 'MAN': 3, 'NAG': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "L" 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: "Q" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "R" 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: "S" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 72 Unusual residues: {'BMA': 1, 'MAN': 3, 'NAG': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "T" 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: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "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: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 72 Unusual residues: {'BMA': 1, 'MAN': 3, 'NAG': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "Y" 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: "A" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'NAG': 4} 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: "E" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'NAG': 4} 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: "M" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'NAG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Time building chain proxies: 12.83, per 1000 atoms: 0.54 Number of scatterers: 23973 At special positions: 0 Unit cell: (172.8, 185.76, 117.72, 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 141 16.00 O 4734 8.00 N 4068 7.00 C 15030 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=18, symmetry=0 Simple disulfide: pdb=" SG CYS A 126 " - pdb=" SG CYS A 196 " distance=2.02 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 157 " 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=2.02 Simple disulfide: pdb=" SG CYS D 23 " - pdb=" SG CYS D 88 " distance=2.04 Simple disulfide: pdb=" SG CYS E 126 " - pdb=" SG CYS E 196 " distance=2.02 Simple disulfide: pdb=" SG CYS E 131 " - pdb=" SG CYS E 157 " 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=2.02 Simple disulfide: pdb=" SG CYS H 23 " - pdb=" SG CYS H 88 " distance=2.04 Simple disulfide: pdb=" SG CYS M 126 " - pdb=" SG CYS M 196 " distance=2.03 Simple disulfide: pdb=" SG CYS M 131 " - pdb=" SG CYS M 157 " distance=2.03 Simple disulfide: pdb=" SG CYS M 228 " - pdb=" SG CYS M 239 " distance=2.03 Simple disulfide: pdb=" SG CYS M 378 " - pdb=" SG CYS M 445 " distance=2.03 Simple disulfide: pdb=" SG CYS N 598 " - pdb=" SG CYS N 604 " distance=2.02 Simple disulfide: pdb=" SG CYS P 23 " - pdb=" SG CYS P 88 " distance=2.04 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 ALPHA1-3 " BMA K 3 " - " MAN K 6 " " BMA L 3 " - " MAN L 4 " " BMA S 3 " - " MAN S 6 " " BMA T 3 " - " MAN T 4 " " BMA X 3 " - " MAN X 6 " " BMA Y 3 " - " MAN Y 4 " ALPHA1-6 " BMA K 3 " - " MAN K 4 " " MAN K 4 " - " MAN K 5 " " BMA S 3 " - " MAN S 4 " " MAN S 4 " - " MAN S 5 " " BMA X 3 " - " MAN X 4 " " MAN X 4 " - " MAN X 5 " BETA1-4 " NAG I 1 " - " NAG I 2 " " NAG I 2 " - " BMA I 3 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG K 2 " - " BMA K 3 " " NAG L 1 " - " NAG L 2 " " NAG L 2 " - " BMA L 3 " " NAG Q 1 " - " NAG Q 2 " " NAG Q 2 " - " BMA Q 3 " " NAG R 1 " - " NAG R 2 " " NAG S 1 " - " NAG S 2 " " NAG S 2 " - " BMA S 3 " " NAG T 1 " - " NAG T 2 " " NAG T 2 " - " BMA T 3 " " NAG V 1 " - " NAG V 2 " " NAG V 2 " - " BMA V 3 " " NAG W 1 " - " NAG W 2 " " NAG X 1 " - " NAG X 2 " " NAG X 2 " - " BMA X 3 " " NAG Y 1 " - " NAG Y 2 " " NAG Y 2 " - " BMA Y 3 " NAG-ASN " NAG A 602 " - " ASN A 392 " " NAG A 604 " - " ASN A 230 " " NAG E 602 " - " ASN E 392 " " NAG E 604 " - " ASN E 230 " " NAG J 1 " - " ASN A 339 " " NAG K 1 " - " ASN A 197 " " NAG L 1 " - " ASN A 262 " " NAG M 602 " - " ASN M 392 " " NAG M 604 " - " ASN M 230 " " NAG R 1 " - " ASN E 339 " " NAG S 1 " - " ASN E 197 " " NAG T 1 " - " ASN E 262 " " NAG W 1 " - " ASN M 339 " " NAG X 1 " - " ASN M 197 " " NAG Y 1 " - " ASN M 262 " Time building additional restraints: 9.68 Conformation dependent library (CDL) restraints added in 3.7 seconds 5838 Ramachandran restraints generated. 2919 Oldfield, 0 Emsley, 2919 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5556 Finding SS restraints... Secondary structure from input PDB file: 54 helices and 63 sheets defined 17.0% alpha, 37.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.25 Creating SS restraints... Processing helix chain 'A' and resid 99 through 117 Processing helix chain 'A' and resid 122 through 127 removed outlier: 4.041A pdb=" N VAL A 127 " --> pdb=" O PRO A 124 " (cutoff:3.500A) Processing helix chain 'A' and resid 205 through 209 removed outlier: 3.511A pdb=" N VAL A 208 " --> pdb=" O CYS A 205 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N SER A 209 " --> pdb=" O PRO A 206 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 205 through 209' Processing helix chain 'A' and resid 335 through 350 Processing helix chain 'A' and resid 368 through 373 Processing helix chain 'A' and resid 473 through 479 removed outlier: 3.672A pdb=" N TRP A 477 " --> pdb=" O MET A 473 " (cutoff:3.500A) Processing helix chain 'B' and resid 529 through 535 removed outlier: 3.976A pdb=" N MET B 535 " --> pdb=" O GLY B 531 " (cutoff:3.500A) Processing helix chain 'B' and resid 536 through 543 removed outlier: 4.092A pdb=" N GLN B 540 " --> pdb=" O THR B 536 " (cutoff:3.500A) removed outlier: 4.156A pdb=" N ASN B 543 " --> pdb=" O VAL B 539 " (cutoff:3.500A) Processing helix chain 'B' and resid 576 through 597 removed outlier: 3.773A pdb=" N VAL B 580 " --> pdb=" O LEU B 576 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N TYR B 586 " --> pdb=" O ALA B 582 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N LEU B 587 " --> pdb=" O VAL B 583 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N LEU B 592 " --> pdb=" O ARG B 588 " (cutoff:3.500A) Processing helix chain 'B' and resid 611 through 615 Processing helix chain 'B' and resid 621 through 625 Processing helix chain 'B' and resid 628 through 636 Processing helix chain 'B' and resid 638 through 663 removed outlier: 3.944A pdb=" N TYR B 643 " --> pdb=" O THR B 639 " (cutoff:3.500A) removed outlier: 4.911A pdb=" N GLY B 644 " --> pdb=" O GLN B 640 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N LEU B 645 " --> pdb=" O ILE B 641 " (cutoff:3.500A) Processing helix chain 'C' and resid 61 through 64 removed outlier: 4.143A pdb=" N ARG C 64 " --> pdb=" O GLY C 61 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 61 through 64' Processing helix chain 'C' and resid 83 through 87 removed outlier: 3.724A pdb=" N THR C 87 " --> pdb=" O TYR C 84 " (cutoff:3.500A) Processing helix chain 'C' and resid 187 through 190 Processing helix chain 'D' and resid 121 through 128 Processing helix chain 'D' and resid 182 through 188 removed outlier: 3.741A pdb=" N LYS D 188 " --> pdb=" O ALA D 184 " (cutoff:3.500A) Processing helix chain 'E' and resid 99 through 117 Processing helix chain 'E' and resid 122 through 127 removed outlier: 4.042A pdb=" N VAL E 127 " --> pdb=" O PRO E 124 " (cutoff:3.500A) Processing helix chain 'E' and resid 205 through 209 removed outlier: 3.759A pdb=" N SER E 209 " --> pdb=" O PRO E 206 " (cutoff:3.500A) Processing helix chain 'E' and resid 335 through 350 Processing helix chain 'E' and resid 368 through 373 Processing helix chain 'E' and resid 473 through 479 removed outlier: 3.653A pdb=" N TRP E 477 " --> pdb=" O MET E 473 " (cutoff:3.500A) Processing helix chain 'F' and resid 529 through 535 removed outlier: 3.981A pdb=" N MET F 535 " --> pdb=" O GLY F 531 " (cutoff:3.500A) Processing helix chain 'F' and resid 536 through 543 removed outlier: 4.094A pdb=" N GLN F 540 " --> pdb=" O THR F 536 " (cutoff:3.500A) removed outlier: 4.157A pdb=" N ASN F 543 " --> pdb=" O VAL F 539 " (cutoff:3.500A) Processing helix chain 'F' and resid 576 through 597 removed outlier: 3.775A pdb=" N VAL F 580 " --> pdb=" O LEU F 576 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N TYR F 586 " --> pdb=" O ALA F 582 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N LEU F 587 " --> pdb=" O VAL F 583 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N LEU F 592 " --> pdb=" O ARG F 588 " (cutoff:3.500A) Processing helix chain 'F' and resid 611 through 615 Processing helix chain 'F' and resid 621 through 625 Processing helix chain 'F' and resid 628 through 636 Processing helix chain 'F' and resid 638 through 663 removed outlier: 3.935A pdb=" N TYR F 643 " --> pdb=" O THR F 639 " (cutoff:3.500A) removed outlier: 4.910A pdb=" N GLY F 644 " --> pdb=" O GLN F 640 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N LEU F 645 " --> pdb=" O ILE F 641 " (cutoff:3.500A) Processing helix chain 'G' and resid 61 through 64 removed outlier: 4.148A pdb=" N ARG G 64 " --> pdb=" O GLY G 61 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 61 through 64' Processing helix chain 'G' and resid 83 through 87 removed outlier: 3.741A pdb=" N THR G 87 " --> pdb=" O TYR G 84 " (cutoff:3.500A) Processing helix chain 'G' and resid 187 through 190 Processing helix chain 'H' and resid 121 through 128 Processing helix chain 'H' and resid 182 through 188 removed outlier: 3.832A pdb=" N LYS H 188 " --> pdb=" O ALA H 184 " (cutoff:3.500A) Processing helix chain 'M' and resid 99 through 117 Processing helix chain 'M' and resid 122 through 127 removed outlier: 3.530A pdb=" N LEU M 125 " --> pdb=" O LEU M 122 " (cutoff:3.500A) removed outlier: 4.089A pdb=" N VAL M 127 " --> pdb=" O PRO M 124 " (cutoff:3.500A) Processing helix chain 'M' and resid 205 through 209 removed outlier: 3.507A pdb=" N VAL M 208 " --> pdb=" O CYS M 205 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N SER M 209 " --> pdb=" O PRO M 206 " (cutoff:3.500A) No H-bonds generated for 'chain 'M' and resid 205 through 209' Processing helix chain 'M' and resid 335 through 350 Processing helix chain 'M' and resid 368 through 373 Processing helix chain 'M' and resid 473 through 479 removed outlier: 3.672A pdb=" N TRP M 477 " --> pdb=" O MET M 473 " (cutoff:3.500A) Processing helix chain 'N' and resid 529 through 535 removed outlier: 3.520A pdb=" N ALA N 533 " --> pdb=" O THR N 529 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N MET N 535 " --> pdb=" O GLY N 531 " (cutoff:3.500A) Processing helix chain 'N' and resid 536 through 543 removed outlier: 4.093A pdb=" N GLN N 540 " --> pdb=" O THR N 536 " (cutoff:3.500A) removed outlier: 4.152A pdb=" N ASN N 543 " --> pdb=" O VAL N 539 " (cutoff:3.500A) Processing helix chain 'N' and resid 576 through 597 removed outlier: 3.781A pdb=" N VAL N 580 " --> pdb=" O LEU N 576 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N TYR N 586 " --> pdb=" O ALA N 582 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N LEU N 592 " --> pdb=" O ARG N 588 " (cutoff:3.500A) Processing helix chain 'N' and resid 611 through 615 Processing helix chain 'N' and resid 621 through 625 Processing helix chain 'N' and resid 628 through 636 Processing helix chain 'N' and resid 638 through 663 removed outlier: 3.939A pdb=" N TYR N 643 " --> pdb=" O THR N 639 " (cutoff:3.500A) removed outlier: 4.910A pdb=" N GLY N 644 " --> pdb=" O GLN N 640 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N LEU N 645 " --> pdb=" O ILE N 641 " (cutoff:3.500A) Processing helix chain 'O' and resid 61 through 64 removed outlier: 4.143A pdb=" N ARG O 64 " --> pdb=" O GLY O 61 " (cutoff:3.500A) No H-bonds generated for 'chain 'O' and resid 61 through 64' Processing helix chain 'O' and resid 83 through 87 removed outlier: 3.741A pdb=" N THR O 87 " --> pdb=" O TYR O 84 " (cutoff:3.500A) Processing helix chain 'O' and resid 187 through 190 Processing helix chain 'P' and resid 121 through 128 Processing helix chain 'P' and resid 182 through 188 removed outlier: 3.729A pdb=" N LYS P 188 " --> pdb=" O ALA P 184 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 494 through 497 removed outlier: 5.631A pdb=" N VAL B 608 " --> pdb=" O VAL A 36 " (cutoff:3.500A) removed outlier: 8.216A pdb=" N VAL A 38 " --> pdb=" O THR B 606 " (cutoff:3.500A) removed outlier: 7.754A pdb=" N THR B 606 " --> pdb=" O VAL A 38 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 45 through 47 removed outlier: 4.190A pdb=" N ILE A 225 " --> pdb=" O VAL A 245 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 53 through 54 Processing sheet with id=AA4, first strand: chain 'A' and resid 91 through 94 Processing sheet with id=AA5, first strand: chain 'A' and resid 129 through 130 Processing sheet with id=AA6, first strand: chain 'A' and resid 158 through 161 Processing sheet with id=AA7, first strand: chain 'A' and resid 201 through 203 removed outlier: 6.426A pdb=" N THR A 202 " --> pdb=" O TYR A 435 " (cutoff:3.500A) removed outlier: 7.197A pdb=" N ARG A 432 " --> pdb=" O MET A 426 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 259 through 261 removed outlier: 6.777A pdb=" N LEU A 260 " --> pdb=" O THR A 450 " (cutoff:3.500A) removed outlier: 10.163A pdb=" N THR A 444 " --> pdb=" O ILE A 294 " (cutoff:3.500A) removed outlier: 11.411A pdb=" N ILE A 294 " --> pdb=" O THR A 444 " (cutoff:3.500A) removed outlier: 9.886A pdb=" N ILE A 446 " --> pdb=" O VAL A 292 " (cutoff:3.500A) removed outlier: 10.864A pdb=" N VAL A 292 " --> pdb=" O ILE A 446 " (cutoff:3.500A) removed outlier: 9.502A pdb=" N ASN A 448 " --> pdb=" O GLU A 290 " (cutoff:3.500A) removed outlier: 10.009A pdb=" N GLU A 290 " --> pdb=" O ASN A 448 " (cutoff:3.500A) removed outlier: 6.995A pdb=" N THR A 450 " --> pdb=" O LEU A 288 " (cutoff:3.500A) removed outlier: 6.996A pdb=" N LYS A 293 " --> pdb=" O ASN A 334 " (cutoff:3.500A) removed outlier: 4.362A pdb=" N ASN A 334 " --> pdb=" O LYS A 293 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 271 through 273 removed outlier: 6.995A pdb=" N THR A 450 " --> pdb=" O LEU A 288 " (cutoff:3.500A) removed outlier: 10.009A pdb=" N GLU A 290 " --> pdb=" O ASN A 448 " (cutoff:3.500A) removed outlier: 9.502A pdb=" N ASN A 448 " --> pdb=" O GLU A 290 " (cutoff:3.500A) removed outlier: 10.864A pdb=" N VAL A 292 " --> pdb=" O ILE A 446 " (cutoff:3.500A) removed outlier: 9.886A pdb=" N ILE A 446 " --> pdb=" O VAL A 292 " (cutoff:3.500A) removed outlier: 11.411A pdb=" N ILE A 294 " --> pdb=" O THR A 444 " (cutoff:3.500A) removed outlier: 10.163A pdb=" N THR A 444 " --> pdb=" O ILE A 294 " (cutoff:3.500A) removed outlier: 5.755A pdb=" N ASN A 357 " --> pdb=" O GLU A 464 " (cutoff:3.500A) removed outlier: 7.268A pdb=" N PHE A 466 " --> pdb=" O ASN A 357 " (cutoff:3.500A) removed outlier: 6.026A pdb=" N THR A 359 " --> pdb=" O PHE A 466 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 301 through 308 removed outlier: 6.931A pdb=" N ASN A 301 " --> pdb=" O VAL A 322 " (cutoff:3.500A) removed outlier: 4.654A pdb=" N VAL A 322 " --> pdb=" O ASN A 301 " (cutoff:3.500A) removed outlier: 6.466A pdb=" N THR A 303 " --> pdb=" O GLY A 321 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 4 through 7 Processing sheet with id=AB3, first strand: chain 'C' and resid 10 through 12 removed outlier: 6.399A pdb=" N GLY C 10 " --> pdb=" O ILE C 110 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N TYR C 33 " --> pdb=" O ASN C 95 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N GLY C 49 " --> pdb=" O TRP C 36 " (cutoff:3.500A) removed outlier: 6.832A pdb=" N ARG C 38 " --> pdb=" O LEU C 47 " (cutoff:3.500A) removed outlier: 5.597A pdb=" N LEU C 47 " --> pdb=" O ARG C 38 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 10 through 12 removed outlier: 6.399A pdb=" N GLY C 10 " --> pdb=" O ILE C 110 " (cutoff:3.500A) removed outlier: 7.164A pdb=" N CYS C 92 " --> pdb=" O HIS C 102 " (cutoff:3.500A) removed outlier: 7.209A pdb=" N HIS C 102 " --> pdb=" O CYS C 92 " (cutoff:3.500A) removed outlier: 7.426A pdb=" N ARG C 94 " --> pdb=" O TYR C 100E" (cutoff:3.500A) removed outlier: 4.890A pdb=" N TYR C 100E" --> pdb=" O ARG C 94 " (cutoff:3.500A) removed outlier: 4.908A pdb=" N VAL C 96 " --> pdb=" O LEU C 100C" (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 120 through 124 removed outlier: 3.773A pdb=" N GLY C 139 " --> pdb=" O LEU C 124 " (cutoff:3.500A) removed outlier: 6.012A pdb=" N TYR C 176 " --> pdb=" O ASP C 144 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 120 through 124 removed outlier: 3.773A pdb=" N GLY C 139 " --> pdb=" O LEU C 124 " (cutoff:3.500A) removed outlier: 6.012A pdb=" N TYR C 176 " --> pdb=" O ASP C 144 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 151 through 154 Processing sheet with id=AB8, first strand: chain 'D' and resid 5 through 7 Processing sheet with id=AB9, first strand: chain 'D' and resid 10 through 13 removed outlier: 6.479A pdb=" N LEU D 11 " --> pdb=" O ASP D 105 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N VAL D 85 " --> pdb=" O HIS D 38 " (cutoff:3.500A) removed outlier: 6.829A pdb=" N VAL D 33 " --> pdb=" O TYR D 49 " (cutoff:3.500A) removed outlier: 4.843A pdb=" N TYR D 49 " --> pdb=" O VAL D 33 " (cutoff:3.500A) removed outlier: 6.552A pdb=" N TRP D 35 " --> pdb=" O LEU D 47 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'D' and resid 10 through 13 removed outlier: 6.479A pdb=" N LEU D 11 " --> pdb=" O ASP D 105 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N GLN D 90 " --> pdb=" O THR D 97 " (cutoff:3.500A) removed outlier: 4.136A pdb=" N THR D 97 " --> pdb=" O GLN D 90 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'D' and resid 114 through 118 removed outlier: 5.711A pdb=" N TYR D 173 " --> pdb=" O ASN D 138 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'D' and resid 153 through 155 removed outlier: 4.428A pdb=" N TRP D 148 " --> pdb=" O GLN D 155 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'E' and resid 494 through 497 removed outlier: 5.631A pdb=" N VAL F 608 " --> pdb=" O VAL E 36 " (cutoff:3.500A) removed outlier: 8.214A pdb=" N VAL E 38 " --> pdb=" O THR F 606 " (cutoff:3.500A) removed outlier: 7.757A pdb=" N THR F 606 " --> pdb=" O VAL E 38 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'E' and resid 45 through 47 removed outlier: 4.166A pdb=" N ILE E 225 " --> pdb=" O VAL E 245 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'E' and resid 53 through 54 Processing sheet with id=AC7, first strand: chain 'E' and resid 91 through 94 Processing sheet with id=AC8, first strand: chain 'E' and resid 129 through 130 Processing sheet with id=AC9, first strand: chain 'E' and resid 158 through 161 Processing sheet with id=AD1, first strand: chain 'E' and resid 201 through 203 removed outlier: 6.392A pdb=" N THR E 202 " --> pdb=" O TYR E 435 " (cutoff:3.500A) removed outlier: 7.164A pdb=" N ARG E 432 " --> pdb=" O MET E 426 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'E' and resid 259 through 261 removed outlier: 6.770A pdb=" N LEU E 260 " --> pdb=" O THR E 450 " (cutoff:3.500A) removed outlier: 10.161A pdb=" N THR E 444 " --> pdb=" O ILE E 294 " (cutoff:3.500A) removed outlier: 11.410A pdb=" N ILE E 294 " --> pdb=" O THR E 444 " (cutoff:3.500A) removed outlier: 9.887A pdb=" N ILE E 446 " --> pdb=" O VAL E 292 " (cutoff:3.500A) removed outlier: 10.866A pdb=" N VAL E 292 " --> pdb=" O ILE E 446 " (cutoff:3.500A) removed outlier: 9.506A pdb=" N ASN E 448 " --> pdb=" O GLU E 290 " (cutoff:3.500A) removed outlier: 10.005A pdb=" N GLU E 290 " --> pdb=" O ASN E 448 " (cutoff:3.500A) removed outlier: 6.992A pdb=" N THR E 450 " --> pdb=" O LEU E 288 " (cutoff:3.500A) removed outlier: 6.999A pdb=" N LYS E 293 " --> pdb=" O ASN E 334 " (cutoff:3.500A) removed outlier: 4.365A pdb=" N ASN E 334 " --> pdb=" O LYS E 293 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'E' and resid 271 through 273 removed outlier: 6.992A pdb=" N THR E 450 " --> pdb=" O LEU E 288 " (cutoff:3.500A) removed outlier: 10.005A pdb=" N GLU E 290 " --> pdb=" O ASN E 448 " (cutoff:3.500A) removed outlier: 9.506A pdb=" N ASN E 448 " --> pdb=" O GLU E 290 " (cutoff:3.500A) removed outlier: 10.866A pdb=" N VAL E 292 " --> pdb=" O ILE E 446 " (cutoff:3.500A) removed outlier: 9.887A pdb=" N ILE E 446 " --> pdb=" O VAL E 292 " (cutoff:3.500A) removed outlier: 11.410A pdb=" N ILE E 294 " --> pdb=" O THR E 444 " (cutoff:3.500A) removed outlier: 10.161A pdb=" N THR E 444 " --> pdb=" O ILE E 294 " (cutoff:3.500A) removed outlier: 5.745A pdb=" N ASN E 357 " --> pdb=" O GLU E 464 " (cutoff:3.500A) removed outlier: 7.258A pdb=" N PHE E 466 " --> pdb=" O ASN E 357 " (cutoff:3.500A) removed outlier: 6.034A pdb=" N THR E 359 " --> pdb=" O PHE E 466 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'E' and resid 301 through 308 removed outlier: 6.934A pdb=" N ASN E 301 " --> pdb=" O VAL E 322 " (cutoff:3.500A) removed outlier: 4.656A pdb=" N VAL E 322 " --> pdb=" O ASN E 301 " (cutoff:3.500A) removed outlier: 6.470A pdb=" N THR E 303 " --> pdb=" O GLY E 321 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'G' and resid 4 through 7 Processing sheet with id=AD6, first strand: chain 'G' and resid 10 through 12 removed outlier: 6.421A pdb=" N GLY G 10 " --> pdb=" O ILE G 110 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N TYR G 33 " --> pdb=" O ASN G 95 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N GLY G 49 " --> pdb=" O TRP G 36 " (cutoff:3.500A) removed outlier: 6.820A pdb=" N ARG G 38 " --> pdb=" O LEU G 47 " (cutoff:3.500A) removed outlier: 5.600A pdb=" N LEU G 47 " --> pdb=" O ARG G 38 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'G' and resid 10 through 12 removed outlier: 6.421A pdb=" N GLY G 10 " --> pdb=" O ILE G 110 " (cutoff:3.500A) removed outlier: 7.152A pdb=" N CYS G 92 " --> pdb=" O HIS G 102 " (cutoff:3.500A) removed outlier: 7.199A pdb=" N HIS G 102 " --> pdb=" O CYS G 92 " (cutoff:3.500A) removed outlier: 7.417A pdb=" N ARG G 94 " --> pdb=" O TYR G 100E" (cutoff:3.500A) removed outlier: 4.888A pdb=" N TYR G 100E" --> pdb=" O ARG G 94 " (cutoff:3.500A) removed outlier: 4.911A pdb=" N VAL G 96 " --> pdb=" O LEU G 100C" (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'G' and resid 120 through 124 removed outlier: 3.771A pdb=" N GLY G 139 " --> pdb=" O LEU G 124 " (cutoff:3.500A) removed outlier: 6.008A pdb=" N TYR G 176 " --> pdb=" O ASP G 144 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'G' and resid 120 through 124 removed outlier: 3.771A pdb=" N GLY G 139 " --> pdb=" O LEU G 124 " (cutoff:3.500A) removed outlier: 6.008A pdb=" N TYR G 176 " --> pdb=" O ASP G 144 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'G' and resid 151 through 154 Processing sheet with id=AE2, first strand: chain 'H' and resid 5 through 7 Processing sheet with id=AE3, first strand: chain 'H' and resid 10 through 13 removed outlier: 6.425A pdb=" N LEU H 11 " --> pdb=" O ASP H 105 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N VAL H 85 " --> pdb=" O HIS H 38 " (cutoff:3.500A) removed outlier: 6.827A pdb=" N VAL H 33 " --> pdb=" O TYR H 49 " (cutoff:3.500A) removed outlier: 4.839A pdb=" N TYR H 49 " --> pdb=" O VAL H 33 " (cutoff:3.500A) removed outlier: 6.551A pdb=" N TRP H 35 " --> pdb=" O LEU H 47 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'H' and resid 10 through 13 removed outlier: 6.425A pdb=" N LEU H 11 " --> pdb=" O ASP H 105 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N GLN H 90 " --> pdb=" O THR H 97 " (cutoff:3.500A) removed outlier: 4.139A pdb=" N THR H 97 " --> pdb=" O GLN H 90 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'H' and resid 114 through 118 removed outlier: 5.712A pdb=" N TYR H 173 " --> pdb=" O ASN H 138 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'H' and resid 153 through 155 removed outlier: 4.425A pdb=" N TRP H 148 " --> pdb=" O GLN H 155 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'M' and resid 494 through 497 removed outlier: 5.632A pdb=" N VAL N 608 " --> pdb=" O VAL M 36 " (cutoff:3.500A) removed outlier: 8.219A pdb=" N VAL M 38 " --> pdb=" O THR N 606 " (cutoff:3.500A) removed outlier: 7.757A pdb=" N THR N 606 " --> pdb=" O VAL M 38 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'M' and resid 45 through 47 removed outlier: 4.200A pdb=" N ILE M 225 " --> pdb=" O VAL M 245 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'M' and resid 53 through 54 Processing sheet with id=AF1, first strand: chain 'M' and resid 91 through 94 Processing sheet with id=AF2, first strand: chain 'M' and resid 129 through 130 Processing sheet with id=AF3, first strand: chain 'M' and resid 158 through 161 Processing sheet with id=AF4, first strand: chain 'M' and resid 201 through 203 removed outlier: 6.434A pdb=" N THR M 202 " --> pdb=" O TYR M 435 " (cutoff:3.500A) removed outlier: 7.199A pdb=" N ARG M 432 " --> pdb=" O MET M 426 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'M' and resid 259 through 261 removed outlier: 6.774A pdb=" N LEU M 260 " --> pdb=" O THR M 450 " (cutoff:3.500A) removed outlier: 10.158A pdb=" N THR M 444 " --> pdb=" O ILE M 294 " (cutoff:3.500A) removed outlier: 11.408A pdb=" N ILE M 294 " --> pdb=" O THR M 444 " (cutoff:3.500A) removed outlier: 9.877A pdb=" N ILE M 446 " --> pdb=" O VAL M 292 " (cutoff:3.500A) removed outlier: 10.854A pdb=" N VAL M 292 " --> pdb=" O ILE M 446 " (cutoff:3.500A) removed outlier: 9.509A pdb=" N ASN M 448 " --> pdb=" O GLU M 290 " (cutoff:3.500A) removed outlier: 10.012A pdb=" N GLU M 290 " --> pdb=" O ASN M 448 " (cutoff:3.500A) removed outlier: 6.991A pdb=" N THR M 450 " --> pdb=" O LEU M 288 " (cutoff:3.500A) removed outlier: 7.005A pdb=" N LYS M 293 " --> pdb=" O ASN M 334 " (cutoff:3.500A) removed outlier: 4.367A pdb=" N ASN M 334 " --> pdb=" O LYS M 293 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'M' and resid 271 through 273 removed outlier: 6.991A pdb=" N THR M 450 " --> pdb=" O LEU M 288 " (cutoff:3.500A) removed outlier: 10.012A pdb=" N GLU M 290 " --> pdb=" O ASN M 448 " (cutoff:3.500A) removed outlier: 9.509A pdb=" N ASN M 448 " --> pdb=" O GLU M 290 " (cutoff:3.500A) removed outlier: 10.854A pdb=" N VAL M 292 " --> pdb=" O ILE M 446 " (cutoff:3.500A) removed outlier: 9.877A pdb=" N ILE M 446 " --> pdb=" O VAL M 292 " (cutoff:3.500A) removed outlier: 11.408A pdb=" N ILE M 294 " --> pdb=" O THR M 444 " (cutoff:3.500A) removed outlier: 10.158A pdb=" N THR M 444 " --> pdb=" O ILE M 294 " (cutoff:3.500A) removed outlier: 5.725A pdb=" N ASN M 357 " --> pdb=" O GLU M 464 " (cutoff:3.500A) removed outlier: 7.224A pdb=" N PHE M 466 " --> pdb=" O ASN M 357 " (cutoff:3.500A) removed outlier: 6.026A pdb=" N THR M 359 " --> pdb=" O PHE M 466 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'M' and resid 301 through 308 removed outlier: 6.933A pdb=" N ASN M 301 " --> pdb=" O VAL M 322 " (cutoff:3.500A) removed outlier: 4.653A pdb=" N VAL M 322 " --> pdb=" O ASN M 301 " (cutoff:3.500A) removed outlier: 6.468A pdb=" N THR M 303 " --> pdb=" O GLY M 321 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'O' and resid 4 through 7 Processing sheet with id=AF9, first strand: chain 'O' and resid 10 through 12 removed outlier: 6.419A pdb=" N GLY O 10 " --> pdb=" O ILE O 110 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N TYR O 33 " --> pdb=" O ASN O 95 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N GLY O 49 " --> pdb=" O TRP O 36 " (cutoff:3.500A) removed outlier: 6.841A pdb=" N ARG O 38 " --> pdb=" O LEU O 47 " (cutoff:3.500A) removed outlier: 5.590A pdb=" N LEU O 47 " --> pdb=" O ARG O 38 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'O' and resid 10 through 12 removed outlier: 6.419A pdb=" N GLY O 10 " --> pdb=" O ILE O 110 " (cutoff:3.500A) removed outlier: 7.141A pdb=" N CYS O 92 " --> pdb=" O HIS O 102 " (cutoff:3.500A) removed outlier: 7.182A pdb=" N HIS O 102 " --> pdb=" O CYS O 92 " (cutoff:3.500A) removed outlier: 7.412A pdb=" N ARG O 94 " --> pdb=" O TYR O 100E" (cutoff:3.500A) removed outlier: 4.881A pdb=" N TYR O 100E" --> pdb=" O ARG O 94 " (cutoff:3.500A) removed outlier: 4.905A pdb=" N VAL O 96 " --> pdb=" O LEU O 100C" (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'O' and resid 120 through 124 removed outlier: 3.774A pdb=" N GLY O 139 " --> pdb=" O LEU O 124 " (cutoff:3.500A) removed outlier: 6.014A pdb=" N TYR O 176 " --> pdb=" O ASP O 144 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'O' and resid 120 through 124 removed outlier: 3.774A pdb=" N GLY O 139 " --> pdb=" O LEU O 124 " (cutoff:3.500A) removed outlier: 6.014A pdb=" N TYR O 176 " --> pdb=" O ASP O 144 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'O' and resid 151 through 154 Processing sheet with id=AG5, first strand: chain 'P' and resid 5 through 7 Processing sheet with id=AG6, first strand: chain 'P' and resid 10 through 13 removed outlier: 6.426A pdb=" N LEU P 11 " --> pdb=" O ASP P 105 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N VAL P 85 " --> pdb=" O HIS P 38 " (cutoff:3.500A) removed outlier: 6.825A pdb=" N VAL P 33 " --> pdb=" O TYR P 49 " (cutoff:3.500A) removed outlier: 4.839A pdb=" N TYR P 49 " --> pdb=" O VAL P 33 " (cutoff:3.500A) removed outlier: 6.554A pdb=" N TRP P 35 " --> pdb=" O LEU P 47 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'P' and resid 10 through 13 removed outlier: 6.426A pdb=" N LEU P 11 " --> pdb=" O ASP P 105 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N GLN P 90 " --> pdb=" O THR P 97 " (cutoff:3.500A) removed outlier: 4.127A pdb=" N THR P 97 " --> pdb=" O GLN P 90 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'P' and resid 114 through 118 removed outlier: 5.714A pdb=" N TYR P 173 " --> pdb=" O ASN P 138 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'P' and resid 153 through 155 removed outlier: 4.426A pdb=" N TRP P 148 " --> pdb=" O GLN P 155 " (cutoff:3.500A) 891 hydrogen bonds defined for protein. 2286 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: 9.41 Time building geometry restraints manager: 10.63 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 7575 1.34 - 1.47: 6020 1.47 - 1.59: 10675 1.59 - 1.71: 3 1.71 - 1.84: 189 Bond restraints: 24462 Sorted by residual: bond pdb=" C1 MAN K 4 " pdb=" O5 MAN K 4 " ideal model delta sigma weight residual 1.399 1.500 -0.101 2.00e-02 2.50e+03 2.54e+01 bond pdb=" C1 MAN S 4 " pdb=" O5 MAN S 4 " ideal model delta sigma weight residual 1.399 1.499 -0.100 2.00e-02 2.50e+03 2.49e+01 bond pdb=" C1 MAN X 4 " pdb=" O5 MAN X 4 " ideal model delta sigma weight residual 1.399 1.493 -0.094 2.00e-02 2.50e+03 2.19e+01 bond pdb=" C5 MAN X 4 " pdb=" O5 MAN X 4 " ideal model delta sigma weight residual 1.418 1.506 -0.088 2.00e-02 2.50e+03 1.95e+01 bond pdb=" C5 MAN S 4 " pdb=" O5 MAN S 4 " ideal model delta sigma weight residual 1.418 1.499 -0.081 2.00e-02 2.50e+03 1.66e+01 ... (remaining 24457 not shown) Histogram of bond angle deviations from ideal: 96.29 - 105.83: 521 105.83 - 115.38: 15568 115.38 - 124.92: 16556 124.92 - 134.46: 556 134.46 - 144.00: 3 Bond angle restraints: 33204 Sorted by residual: angle pdb=" C MET F 626 " pdb=" N THR F 627 " pdb=" CA THR F 627 " ideal model delta sigma weight residual 121.70 144.00 -22.30 1.80e+00 3.09e-01 1.54e+02 angle pdb=" C MET B 626 " pdb=" N THR B 627 " pdb=" CA THR B 627 " ideal model delta sigma weight residual 121.70 143.68 -21.98 1.80e+00 3.09e-01 1.49e+02 angle pdb=" C MET N 626 " pdb=" N THR N 627 " pdb=" CA THR N 627 " ideal model delta sigma weight residual 121.70 143.35 -21.65 1.80e+00 3.09e-01 1.45e+02 angle pdb=" C ASN B 625 " pdb=" N MET B 626 " pdb=" CA MET B 626 " ideal model delta sigma weight residual 121.54 132.08 -10.54 1.91e+00 2.74e-01 3.05e+01 angle pdb=" C ASN F 625 " pdb=" N MET F 626 " pdb=" CA MET F 626 " ideal model delta sigma weight residual 121.54 131.96 -10.42 1.91e+00 2.74e-01 2.98e+01 ... (remaining 33199 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.98: 14538 24.98 - 49.97: 598 49.97 - 74.95: 89 74.95 - 99.93: 108 99.93 - 124.92: 57 Dihedral angle restraints: 15390 sinusoidal: 6759 harmonic: 8631 Sorted by residual: dihedral pdb=" CB CYS F 598 " pdb=" SG CYS F 598 " pdb=" SG CYS F 604 " pdb=" CB CYS F 604 " ideal model delta sinusoidal sigma weight residual -86.00 -140.26 54.26 1 1.00e+01 1.00e-02 3.99e+01 dihedral pdb=" CB CYS B 598 " pdb=" SG CYS B 598 " pdb=" SG CYS B 604 " pdb=" CB CYS B 604 " ideal model delta sinusoidal sigma weight residual -86.00 -140.16 54.16 1 1.00e+01 1.00e-02 3.98e+01 dihedral pdb=" CB CYS N 598 " pdb=" SG CYS N 598 " pdb=" SG CYS N 604 " pdb=" CB CYS N 604 " ideal model delta sinusoidal sigma weight residual -86.00 -139.93 53.93 1 1.00e+01 1.00e-02 3.95e+01 ... (remaining 15387 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.077: 3275 0.077 - 0.154: 538 0.154 - 0.232: 52 0.232 - 0.309: 19 0.309 - 0.386: 16 Chirality restraints: 3900 Sorted by residual: chirality pdb=" C2 NAG E 603 " pdb=" C1 NAG E 603 " pdb=" C3 NAG E 603 " pdb=" N2 NAG E 603 " both_signs ideal model delta sigma weight residual False -2.49 -2.11 -0.39 2.00e-01 2.50e+01 3.72e+00 chirality pdb=" C2 NAG M 603 " pdb=" C1 NAG M 603 " pdb=" C3 NAG M 603 " pdb=" N2 NAG M 603 " both_signs ideal model delta sigma weight residual False -2.49 -2.11 -0.38 2.00e-01 2.50e+01 3.65e+00 chirality pdb=" C2 NAG A 603 " pdb=" C1 NAG A 603 " pdb=" C3 NAG A 603 " pdb=" N2 NAG A 603 " both_signs ideal model delta sigma weight residual False -2.49 -2.11 -0.38 2.00e-01 2.50e+01 3.59e+00 ... (remaining 3897 not shown) Planarity restraints: 4170 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL O 184 " -0.040 5.00e-02 4.00e+02 6.06e-02 5.87e+00 pdb=" N PRO O 185 " 0.105 5.00e-02 4.00e+02 pdb=" CA PRO O 185 " -0.031 5.00e-02 4.00e+02 pdb=" CD PRO O 185 " -0.034 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL G 184 " -0.040 5.00e-02 4.00e+02 6.02e-02 5.81e+00 pdb=" N PRO G 185 " 0.104 5.00e-02 4.00e+02 pdb=" CA PRO G 185 " -0.031 5.00e-02 4.00e+02 pdb=" CD PRO G 185 " -0.033 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL C 184 " -0.040 5.00e-02 4.00e+02 6.01e-02 5.78e+00 pdb=" N PRO C 185 " 0.104 5.00e-02 4.00e+02 pdb=" CA PRO C 185 " -0.031 5.00e-02 4.00e+02 pdb=" CD PRO C 185 " -0.033 5.00e-02 4.00e+02 ... (remaining 4167 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.76: 3173 2.76 - 3.30: 22184 3.30 - 3.83: 39172 3.83 - 4.37: 44368 4.37 - 4.90: 77139 Nonbonded interactions: 186036 Sorted by model distance: nonbonded pdb=" O SER F 528 " pdb=" OG1 THR F 627 " model vdw 2.228 2.440 nonbonded pdb=" O SER B 528 " pdb=" OG1 THR B 627 " model vdw 2.235 2.440 nonbonded pdb=" O SER N 528 " pdb=" OG1 THR N 627 " model vdw 2.245 2.440 nonbonded pdb=" OD1 ASN A 262 " pdb=" OG SER A 447 " model vdw 2.289 2.440 nonbonded pdb=" OG1 THR E 37 " pdb=" O CYS F 604 " model vdw 2.289 2.440 ... (remaining 186031 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 'M' } ncs_group { reference = chain 'B' selection = chain 'F' selection = chain 'N' } ncs_group { reference = chain 'C' selection = chain 'G' selection = chain 'O' } ncs_group { reference = chain 'D' selection = chain 'H' selection = chain 'P' } ncs_group { reference = chain 'I' selection = chain 'Q' selection = chain 'V' } ncs_group { reference = chain 'J' selection = chain 'R' selection = chain 'W' } ncs_group { reference = chain 'K' selection = chain 'S' selection = chain 'X' } ncs_group { reference = chain 'L' selection = chain 'T' selection = chain 'Y' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.160 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 8.020 Check model and map are aligned: 0.380 Set scattering table: 0.220 Process input model: 62.410 Find NCS groups from input model: 1.730 Set up NCS constraints: 0.300 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.670 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 77.920 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8255 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 : 0.005 0.101 24462 Z= 0.349 Angle : 1.060 22.303 33204 Z= 0.537 Chirality : 0.062 0.386 3900 Planarity : 0.007 0.061 4155 Dihedral : 18.064 124.916 9780 Min Nonbonded Distance : 2.228 Molprobity Statistics. All-atom Clashscore : 2.57 Ramachandran Plot: Outliers : 0.10 % Allowed : 6.41 % Favored : 93.49 % Rotamer: Outliers : 0.00 % Allowed : 0.27 % Favored : 99.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.63 % Cis-general : 0.11 % 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: -1.29 (0.15), residues: 2919 helix: -0.64 (0.26), residues: 363 sheet: -0.30 (0.16), residues: 927 loop : -1.22 (0.15), residues: 1629 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP D 96 HIS 0.011 0.002 HIS G 35 PHE 0.024 0.002 PHE M 376 TYR 0.030 0.002 TYR A 458 ARG 0.004 0.001 ARG A 298 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5838 Ramachandran restraints generated. 2919 Oldfield, 0 Emsley, 2919 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5838 Ramachandran restraints generated. 2919 Oldfield, 0 Emsley, 2919 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 2601 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 88 time to evaluate : 2.791 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 95 MET cc_start: 0.8936 (ppp) cc_final: 0.8587 (ppp) REVERT: C 89 MET cc_start: 0.9183 (tpt) cc_final: 0.8842 (tpp) REVERT: E 95 MET cc_start: 0.8927 (ppp) cc_final: 0.8587 (ppp) REVERT: F 626 MET cc_start: 0.7442 (tpt) cc_final: 0.7092 (tpp) REVERT: G 80 MET cc_start: 0.7467 (mtt) cc_final: 0.7241 (ttm) REVERT: M 95 MET cc_start: 0.8929 (ppp) cc_final: 0.8594 (ppp) outliers start: 0 outliers final: 0 residues processed: 88 average time/residue: 0.3642 time to fit residues: 52.4338 Evaluate side-chains 65 residues out of total 2601 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 65 time to evaluate : 2.810 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 250 optimal weight: 8.9990 chunk 225 optimal weight: 10.0000 chunk 124 optimal weight: 10.0000 chunk 76 optimal weight: 9.9990 chunk 151 optimal weight: 0.6980 chunk 120 optimal weight: 10.0000 chunk 232 optimal weight: 9.9990 chunk 90 optimal weight: 1.9990 chunk 141 optimal weight: 10.0000 chunk 173 optimal weight: 10.0000 chunk 269 optimal weight: 0.7980 overall best weight: 4.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 80 ASN ** F 651 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 651 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8335 moved from start: 0.1352 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 24462 Z= 0.264 Angle : 0.727 12.372 33204 Z= 0.359 Chirality : 0.047 0.380 3900 Planarity : 0.005 0.049 4155 Dihedral : 14.628 112.195 4368 Min Nonbonded Distance : 1.995 Molprobity Statistics. All-atom Clashscore : 9.11 Ramachandran Plot: Outliers : 0.10 % Allowed : 7.09 % Favored : 92.81 % Rotamer: Outliers : 0.00 % Allowed : 3.47 % Favored : 96.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.63 % Cis-general : 0.11 % 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: -0.94 (0.16), residues: 2919 helix: 0.46 (0.27), residues: 387 sheet: -0.39 (0.17), residues: 909 loop : -1.01 (0.16), residues: 1623 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP N 631 HIS 0.004 0.001 HIS M 105 PHE 0.017 0.002 PHE A 361 TYR 0.017 0.001 TYR O 91 ARG 0.003 0.000 ARG B 588 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5838 Ramachandran restraints generated. 2919 Oldfield, 0 Emsley, 2919 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5838 Ramachandran restraints generated. 2919 Oldfield, 0 Emsley, 2919 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 69 residues out of total 2601 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 69 time to evaluate : 2.766 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 95 MET cc_start: 0.9059 (ppp) cc_final: 0.8382 (ppp) REVERT: C 89 MET cc_start: 0.9114 (tpt) cc_final: 0.8788 (tpp) REVERT: E 95 MET cc_start: 0.8957 (ppp) cc_final: 0.8560 (ppp) REVERT: E 473 MET cc_start: 0.7839 (tpp) cc_final: 0.7550 (tpp) REVERT: M 95 MET cc_start: 0.9030 (ppp) cc_final: 0.8667 (ppp) REVERT: M 473 MET cc_start: 0.7593 (tpp) cc_final: 0.7381 (tpp) outliers start: 0 outliers final: 0 residues processed: 69 average time/residue: 0.3589 time to fit residues: 42.0048 Evaluate side-chains 55 residues out of total 2601 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 55 time to evaluate : 2.701 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 149 optimal weight: 8.9990 chunk 83 optimal weight: 10.0000 chunk 224 optimal weight: 20.0000 chunk 183 optimal weight: 9.9990 chunk 74 optimal weight: 10.0000 chunk 270 optimal weight: 30.0000 chunk 291 optimal weight: 0.7980 chunk 240 optimal weight: 5.9990 chunk 267 optimal weight: 10.0000 chunk 92 optimal weight: 9.9990 chunk 216 optimal weight: 6.9990 overall best weight: 6.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 651 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 80 ASN ** F 651 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 80 ASN ** N 651 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8415 moved from start: 0.2250 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.059 24462 Z= 0.358 Angle : 0.778 12.348 33204 Z= 0.390 Chirality : 0.048 0.365 3900 Planarity : 0.005 0.050 4155 Dihedral : 13.206 114.424 4368 Min Nonbonded Distance : 2.107 Molprobity Statistics. All-atom Clashscore : 12.54 Ramachandran Plot: Outliers : 0.10 % Allowed : 8.43 % Favored : 91.47 % Rotamer: Outliers : 0.12 % Allowed : 4.32 % Favored : 95.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.63 % Cis-general : 0.11 % 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: -1.03 (0.16), residues: 2919 helix: 0.52 (0.27), residues: 387 sheet: -0.61 (0.17), residues: 906 loop : -0.99 (0.16), residues: 1626 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP M 427 HIS 0.006 0.001 HIS E 374 PHE 0.018 0.002 PHE B 519 TYR 0.027 0.002 TYR E 458 ARG 0.004 0.001 ARG F 588 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5838 Ramachandran restraints generated. 2919 Oldfield, 0 Emsley, 2919 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5838 Ramachandran restraints generated. 2919 Oldfield, 0 Emsley, 2919 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 76 residues out of total 2601 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 73 time to evaluate : 2.803 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 95 MET cc_start: 0.9196 (ppp) cc_final: 0.8390 (ppp) REVERT: A 104 MET cc_start: 0.9419 (ppp) cc_final: 0.9191 (ppp) REVERT: A 396 MET cc_start: 0.6832 (mmt) cc_final: 0.6398 (mmt) REVERT: B 530 MET cc_start: 0.7018 (mmm) cc_final: 0.6750 (mmm) REVERT: C 89 MET cc_start: 0.9265 (tpt) cc_final: 0.8986 (tpp) REVERT: E 104 MET cc_start: 0.9381 (ppp) cc_final: 0.9153 (ppp) REVERT: E 473 MET cc_start: 0.7838 (tpp) cc_final: 0.7531 (tpp) REVERT: G 89 MET cc_start: 0.9355 (tpp) cc_final: 0.9148 (tpp) REVERT: M 84 MET cc_start: 0.7679 (mpp) cc_final: 0.6987 (mpp) REVERT: M 95 MET cc_start: 0.9192 (ppp) cc_final: 0.8777 (ppp) REVERT: M 104 MET cc_start: 0.9410 (ppp) cc_final: 0.9159 (ppp) REVERT: M 473 MET cc_start: 0.7981 (tpp) cc_final: 0.7721 (tpp) REVERT: N 535 MET cc_start: 0.9141 (mpp) cc_final: 0.8761 (mpp) REVERT: O 89 MET cc_start: 0.9427 (tpp) cc_final: 0.9092 (tpp) outliers start: 3 outliers final: 0 residues processed: 76 average time/residue: 0.3607 time to fit residues: 46.8019 Evaluate side-chains 54 residues out of total 2601 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 54 time to evaluate : 2.740 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 266 optimal weight: 0.0970 chunk 203 optimal weight: 20.0000 chunk 140 optimal weight: 0.6980 chunk 29 optimal weight: 6.9990 chunk 128 optimal weight: 7.9990 chunk 181 optimal weight: 8.9990 chunk 271 optimal weight: 4.9990 chunk 287 optimal weight: 20.0000 chunk 141 optimal weight: 5.9990 chunk 256 optimal weight: 9.9990 chunk 77 optimal weight: 7.9990 overall best weight: 3.7584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 651 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 651 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 651 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8391 moved from start: 0.2452 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 24462 Z= 0.229 Angle : 0.657 9.578 33204 Z= 0.330 Chirality : 0.046 0.350 3900 Planarity : 0.004 0.048 4155 Dihedral : 12.382 108.466 4368 Min Nonbonded Distance : 1.973 Molprobity Statistics. All-atom Clashscore : 10.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.23 % Favored : 92.77 % Rotamer: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.63 % Cis-general : 0.11 % Twisted Proline : 0.00 % Twisted General : 0.11 % 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: -0.97 (0.16), residues: 2919 helix: 0.80 (0.27), residues: 387 sheet: -0.56 (0.17), residues: 909 loop : -1.03 (0.16), residues: 1623 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP H 96 HIS 0.004 0.001 HIS C 100D PHE 0.016 0.002 PHE E 53 TYR 0.015 0.001 TYR E 458 ARG 0.002 0.000 ARG H 18 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5838 Ramachandran restraints generated. 2919 Oldfield, 0 Emsley, 2919 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5838 Ramachandran restraints generated. 2919 Oldfield, 0 Emsley, 2919 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 68 residues out of total 2601 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 68 time to evaluate : 2.735 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 95 MET cc_start: 0.9251 (ppp) cc_final: 0.8470 (ppp) REVERT: A 104 MET cc_start: 0.9344 (ppp) cc_final: 0.9128 (ppp) REVERT: A 396 MET cc_start: 0.6646 (mmt) cc_final: 0.6143 (mmt) REVERT: B 530 MET cc_start: 0.7146 (mmm) cc_final: 0.6729 (mmm) REVERT: B 535 MET cc_start: 0.9199 (mpp) cc_final: 0.8918 (mpp) REVERT: B 626 MET cc_start: 0.7541 (tpp) cc_final: 0.7215 (tpp) REVERT: C 89 MET cc_start: 0.9287 (tpt) cc_final: 0.9047 (tpp) REVERT: E 95 MET cc_start: 0.9071 (ppp) cc_final: 0.8663 (ppp) REVERT: E 104 MET cc_start: 0.9313 (ppp) cc_final: 0.9092 (ppp) REVERT: E 473 MET cc_start: 0.7866 (tpp) cc_final: 0.7520 (tpp) REVERT: M 95 MET cc_start: 0.9228 (ppp) cc_final: 0.8767 (ppp) REVERT: M 104 MET cc_start: 0.9319 (ppp) cc_final: 0.9097 (ppp) REVERT: M 473 MET cc_start: 0.7988 (tpp) cc_final: 0.7687 (tpp) REVERT: N 535 MET cc_start: 0.9162 (mpp) cc_final: 0.8853 (mpp) REVERT: O 89 MET cc_start: 0.9397 (tpp) cc_final: 0.9047 (tpp) outliers start: 0 outliers final: 0 residues processed: 68 average time/residue: 0.3821 time to fit residues: 43.1997 Evaluate side-chains 57 residues out of total 2601 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 57 time to evaluate : 2.700 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 239 optimal weight: 7.9990 chunk 162 optimal weight: 9.9990 chunk 4 optimal weight: 9.9990 chunk 213 optimal weight: 0.6980 chunk 118 optimal weight: 6.9990 chunk 244 optimal weight: 20.0000 chunk 198 optimal weight: 9.9990 chunk 0 optimal weight: 10.0000 chunk 146 optimal weight: 0.9990 chunk 257 optimal weight: 9.9990 chunk 72 optimal weight: 30.0000 overall best weight: 5.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 651 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 651 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 651 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8429 moved from start: 0.2999 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 24462 Z= 0.303 Angle : 0.705 9.579 33204 Z= 0.354 Chirality : 0.047 0.351 3900 Planarity : 0.004 0.047 4155 Dihedral : 11.905 102.323 4368 Min Nonbonded Distance : 2.025 Molprobity Statistics. All-atom Clashscore : 13.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.91 % Favored : 91.09 % Rotamer: Outliers : 0.00 % Allowed : 3.70 % Favored : 96.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.63 % Cis-general : 0.11 % Twisted Proline : 0.00 % Twisted General : 0.11 % 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: -1.02 (0.16), residues: 2919 helix: 0.77 (0.27), residues: 405 sheet: -0.64 (0.17), residues: 912 loop : -1.05 (0.16), residues: 1602 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP C 36 HIS 0.005 0.001 HIS C 35 PHE 0.026 0.002 PHE F 519 TYR 0.015 0.002 TYR M 458 ARG 0.003 0.000 ARG G 83 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5838 Ramachandran restraints generated. 2919 Oldfield, 0 Emsley, 2919 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5838 Ramachandran restraints generated. 2919 Oldfield, 0 Emsley, 2919 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 64 residues out of total 2601 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 64 time to evaluate : 2.721 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 95 MET cc_start: 0.9271 (ppp) cc_final: 0.8542 (ppp) REVERT: B 530 MET cc_start: 0.7563 (mmm) cc_final: 0.7067 (mmm) REVERT: B 535 MET cc_start: 0.9209 (mpp) cc_final: 0.8868 (mpp) REVERT: E 473 MET cc_start: 0.7919 (tpp) cc_final: 0.7574 (tpp) REVERT: G 89 MET cc_start: 0.9580 (tpp) cc_final: 0.9369 (tpp) REVERT: M 95 MET cc_start: 0.9270 (ppp) cc_final: 0.8734 (ppp) REVERT: M 473 MET cc_start: 0.8081 (tpp) cc_final: 0.7797 (tpp) REVERT: N 535 MET cc_start: 0.9233 (mpp) cc_final: 0.9015 (mpp) REVERT: O 89 MET cc_start: 0.9473 (tpp) cc_final: 0.9087 (tpp) outliers start: 0 outliers final: 0 residues processed: 64 average time/residue: 0.3929 time to fit residues: 41.7839 Evaluate side-chains 57 residues out of total 2601 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 57 time to evaluate : 2.825 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 96 optimal weight: 10.0000 chunk 258 optimal weight: 8.9990 chunk 56 optimal weight: 3.9990 chunk 168 optimal weight: 9.9990 chunk 70 optimal weight: 9.9990 chunk 287 optimal weight: 2.9990 chunk 238 optimal weight: 10.0000 chunk 133 optimal weight: 6.9990 chunk 23 optimal weight: 10.0000 chunk 95 optimal weight: 7.9990 chunk 150 optimal weight: 1.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 651 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 651 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 651 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8430 moved from start: 0.3233 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 24462 Z= 0.266 Angle : 0.677 10.988 33204 Z= 0.339 Chirality : 0.047 0.421 3900 Planarity : 0.004 0.047 4155 Dihedral : 11.526 93.713 4368 Min Nonbonded Distance : 2.055 Molprobity Statistics. All-atom Clashscore : 13.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.43 % Favored : 92.57 % Rotamer: Outliers : 0.00 % Allowed : 1.35 % Favored : 98.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.63 % Cis-general : 0.11 % Twisted Proline : 0.00 % Twisted General : 0.11 % 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: -0.92 (0.16), residues: 2919 helix: 0.81 (0.27), residues: 405 sheet: -0.48 (0.17), residues: 873 loop : -1.03 (0.16), residues: 1641 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.002 TRP P 94 HIS 0.007 0.001 HIS H 198 PHE 0.013 0.002 PHE D 71 TYR 0.022 0.001 TYR C 91 ARG 0.004 0.000 ARG M 456 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5838 Ramachandran restraints generated. 2919 Oldfield, 0 Emsley, 2919 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5838 Ramachandran restraints generated. 2919 Oldfield, 0 Emsley, 2919 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 66 residues out of total 2601 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 66 time to evaluate : 2.295 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 84 MET cc_start: 0.7983 (mpp) cc_final: 0.7736 (mpp) REVERT: A 95 MET cc_start: 0.9250 (ppp) cc_final: 0.8544 (ppp) REVERT: A 104 MET cc_start: 0.9441 (ppp) cc_final: 0.9170 (ppp) REVERT: B 530 MET cc_start: 0.7667 (mmm) cc_final: 0.6939 (mmm) REVERT: B 535 MET cc_start: 0.9251 (mpp) cc_final: 0.8866 (mpp) REVERT: E 95 MET cc_start: 0.9059 (ppp) cc_final: 0.8657 (ppp) REVERT: E 104 MET cc_start: 0.9447 (ppp) cc_final: 0.9211 (ppp) REVERT: E 473 MET cc_start: 0.7938 (tpp) cc_final: 0.7557 (tpp) REVERT: M 95 MET cc_start: 0.9219 (ppp) cc_final: 0.8667 (ppp) REVERT: M 104 MET cc_start: 0.9442 (ppp) cc_final: 0.9233 (ppp) REVERT: M 396 MET cc_start: 0.6771 (mmt) cc_final: 0.6327 (mmt) REVERT: M 473 MET cc_start: 0.8109 (tpp) cc_final: 0.7738 (tpp) REVERT: N 535 MET cc_start: 0.9290 (mpp) cc_final: 0.8946 (mpp) REVERT: O 89 MET cc_start: 0.9492 (tpp) cc_final: 0.9089 (tpp) outliers start: 0 outliers final: 0 residues processed: 66 average time/residue: 0.3971 time to fit residues: 43.0479 Evaluate side-chains 56 residues out of total 2601 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 56 time to evaluate : 2.583 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 277 optimal weight: 1.9990 chunk 32 optimal weight: 6.9990 chunk 163 optimal weight: 6.9990 chunk 209 optimal weight: 20.0000 chunk 162 optimal weight: 3.9990 chunk 241 optimal weight: 20.0000 chunk 160 optimal weight: 0.3980 chunk 286 optimal weight: 20.0000 chunk 179 optimal weight: 9.9990 chunk 174 optimal weight: 8.9990 chunk 132 optimal weight: 20.0000 overall best weight: 4.0788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 651 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 651 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 651 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8429 moved from start: 0.3435 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 24462 Z= 0.239 Angle : 0.659 13.612 33204 Z= 0.328 Chirality : 0.046 0.392 3900 Planarity : 0.004 0.046 4155 Dihedral : 10.952 83.156 4368 Min Nonbonded Distance : 2.017 Molprobity Statistics. All-atom Clashscore : 12.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.70 % Favored : 91.30 % Rotamer: Outliers : 0.00 % Allowed : 1.27 % Favored : 98.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.63 % Cis-general : 0.11 % Twisted Proline : 0.00 % Twisted General : 0.11 % 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: -0.88 (0.16), residues: 2919 helix: 0.91 (0.27), residues: 405 sheet: -0.42 (0.17), residues: 873 loop : -1.05 (0.16), residues: 1641 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 610 HIS 0.004 0.001 HIS C 35 PHE 0.012 0.001 PHE N 519 TYR 0.020 0.001 TYR M 458 ARG 0.003 0.000 ARG G 83 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5838 Ramachandran restraints generated. 2919 Oldfield, 0 Emsley, 2919 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5838 Ramachandran restraints generated. 2919 Oldfield, 0 Emsley, 2919 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 63 residues out of total 2601 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 63 time to evaluate : 2.883 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 95 MET cc_start: 0.9225 (ppp) cc_final: 0.8459 (ppp) REVERT: A 104 MET cc_start: 0.9438 (ppp) cc_final: 0.9178 (ppp) REVERT: B 530 MET cc_start: 0.7765 (mmm) cc_final: 0.7026 (mmm) REVERT: B 535 MET cc_start: 0.9242 (mpp) cc_final: 0.8846 (mpp) REVERT: B 626 MET cc_start: 0.7306 (tpp) cc_final: 0.6683 (tpp) REVERT: E 95 MET cc_start: 0.9036 (ppp) cc_final: 0.8636 (ppp) REVERT: E 104 MET cc_start: 0.9424 (ppp) cc_final: 0.9197 (ppp) REVERT: E 396 MET cc_start: 0.6840 (mmt) cc_final: 0.6405 (mmt) REVERT: E 473 MET cc_start: 0.8052 (tpp) cc_final: 0.7633 (tpp) REVERT: M 95 MET cc_start: 0.9189 (ppp) cc_final: 0.8622 (ppp) REVERT: M 396 MET cc_start: 0.6794 (mmt) cc_final: 0.6377 (mmt) REVERT: M 473 MET cc_start: 0.8166 (tpp) cc_final: 0.7769 (tpp) REVERT: N 535 MET cc_start: 0.9305 (mpp) cc_final: 0.8943 (mpp) REVERT: O 89 MET cc_start: 0.9474 (tpp) cc_final: 0.9047 (tpp) outliers start: 0 outliers final: 0 residues processed: 63 average time/residue: 0.3824 time to fit residues: 40.0950 Evaluate side-chains 55 residues out of total 2601 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 55 time to evaluate : 2.749 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 177 optimal weight: 10.0000 chunk 114 optimal weight: 4.9990 chunk 170 optimal weight: 5.9990 chunk 86 optimal weight: 3.9990 chunk 56 optimal weight: 5.9990 chunk 55 optimal weight: 9.9990 chunk 181 optimal weight: 7.9990 chunk 195 optimal weight: 5.9990 chunk 141 optimal weight: 1.9990 chunk 26 optimal weight: 2.9990 chunk 225 optimal weight: 4.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 651 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 651 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 651 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8429 moved from start: 0.3662 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 24462 Z= 0.229 Angle : 0.644 12.985 33204 Z= 0.323 Chirality : 0.046 0.405 3900 Planarity : 0.004 0.045 4155 Dihedral : 9.886 75.939 4368 Min Nonbonded Distance : 2.031 Molprobity Statistics. All-atom Clashscore : 12.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.43 % Favored : 92.57 % Rotamer: Outliers : 0.00 % Allowed : 0.96 % Favored : 99.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.63 % Cis-general : 0.11 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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: -0.84 (0.16), residues: 2919 helix: 0.95 (0.27), residues: 405 sheet: -0.36 (0.18), residues: 873 loop : -1.05 (0.16), residues: 1641 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP B 610 HIS 0.003 0.001 HIS M 249 PHE 0.018 0.001 PHE N 519 TYR 0.017 0.001 TYR M 458 ARG 0.002 0.000 ARG G 83 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5838 Ramachandran restraints generated. 2919 Oldfield, 0 Emsley, 2919 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5838 Ramachandran restraints generated. 2919 Oldfield, 0 Emsley, 2919 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 63 residues out of total 2601 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 63 time to evaluate : 2.749 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 84 MET cc_start: 0.8218 (mpp) cc_final: 0.8015 (mpp) REVERT: A 95 MET cc_start: 0.9186 (ppp) cc_final: 0.8426 (ppp) REVERT: A 104 MET cc_start: 0.9436 (ppp) cc_final: 0.9157 (ppp) REVERT: B 530 MET cc_start: 0.8019 (mmm) cc_final: 0.7584 (mmm) REVERT: B 535 MET cc_start: 0.9266 (mpp) cc_final: 0.8843 (mpp) REVERT: B 626 MET cc_start: 0.7330 (tpp) cc_final: 0.6849 (tpp) REVERT: E 104 MET cc_start: 0.9438 (ppp) cc_final: 0.9194 (ppp) REVERT: E 473 MET cc_start: 0.8081 (tpp) cc_final: 0.7634 (tpp) REVERT: G 89 MET cc_start: 0.9590 (tpp) cc_final: 0.9330 (tpp) REVERT: M 95 MET cc_start: 0.9152 (ppp) cc_final: 0.8572 (ppp) REVERT: M 396 MET cc_start: 0.6802 (mmt) cc_final: 0.6459 (mmt) REVERT: M 473 MET cc_start: 0.8208 (tpp) cc_final: 0.7787 (tpp) REVERT: N 535 MET cc_start: 0.9333 (mpp) cc_final: 0.8968 (mpp) REVERT: O 75 MET cc_start: 0.9394 (mmm) cc_final: 0.9064 (mpp) outliers start: 0 outliers final: 0 residues processed: 63 average time/residue: 0.3779 time to fit residues: 40.2833 Evaluate side-chains 55 residues out of total 2601 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 55 time to evaluate : 2.744 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 260 optimal weight: 1.9990 chunk 274 optimal weight: 5.9990 chunk 250 optimal weight: 9.9990 chunk 266 optimal weight: 8.9990 chunk 160 optimal weight: 3.9990 chunk 116 optimal weight: 0.6980 chunk 209 optimal weight: 6.9990 chunk 81 optimal weight: 6.9990 chunk 241 optimal weight: 0.9990 chunk 252 optimal weight: 9.9990 chunk 265 optimal weight: 5.9990 overall best weight: 2.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 651 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 651 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 651 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8416 moved from start: 0.3745 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 24462 Z= 0.184 Angle : 0.615 13.244 33204 Z= 0.307 Chirality : 0.046 0.389 3900 Planarity : 0.004 0.046 4155 Dihedral : 9.381 77.836 4368 Min Nonbonded Distance : 2.046 Molprobity Statistics. All-atom Clashscore : 11.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.88 % Favored : 92.12 % Rotamer: Outliers : 0.00 % Allowed : 0.66 % Favored : 99.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.63 % Cis-general : 0.11 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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: -0.69 (0.16), residues: 2919 helix: 0.92 (0.27), residues: 423 sheet: -0.30 (0.18), residues: 870 loop : -0.90 (0.16), residues: 1626 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 610 HIS 0.003 0.001 HIS C 100D PHE 0.022 0.001 PHE F 519 TYR 0.019 0.001 TYR O 91 ARG 0.002 0.000 ARG P 211 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5838 Ramachandran restraints generated. 2919 Oldfield, 0 Emsley, 2919 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5838 Ramachandran restraints generated. 2919 Oldfield, 0 Emsley, 2919 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 64 residues out of total 2601 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 64 time to evaluate : 2.733 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 95 MET cc_start: 0.9167 (ppp) cc_final: 0.8433 (ppp) REVERT: B 530 MET cc_start: 0.8068 (mmm) cc_final: 0.7603 (mmm) REVERT: B 535 MET cc_start: 0.9247 (mpp) cc_final: 0.8809 (mpp) REVERT: B 626 MET cc_start: 0.7226 (tpp) cc_final: 0.6782 (tpp) REVERT: E 95 MET cc_start: 0.8949 (ppp) cc_final: 0.8556 (ppp) REVERT: E 104 MET cc_start: 0.9423 (ppp) cc_final: 0.9164 (ppp) REVERT: E 396 MET cc_start: 0.6780 (mmt) cc_final: 0.6572 (mmt) REVERT: E 473 MET cc_start: 0.8118 (tpp) cc_final: 0.7651 (tpp) REVERT: G 89 MET cc_start: 0.9533 (tpp) cc_final: 0.9225 (tpp) REVERT: M 95 MET cc_start: 0.9113 (ppp) cc_final: 0.8554 (ppp) REVERT: M 396 MET cc_start: 0.6811 (mmt) cc_final: 0.6434 (mmt) REVERT: M 473 MET cc_start: 0.8207 (tpp) cc_final: 0.7772 (tpp) REVERT: N 535 MET cc_start: 0.9342 (mpp) cc_final: 0.8955 (mpp) REVERT: O 89 MET cc_start: 0.9537 (tpp) cc_final: 0.9313 (tpp) outliers start: 0 outliers final: 0 residues processed: 64 average time/residue: 0.3899 time to fit residues: 41.5043 Evaluate side-chains 55 residues out of total 2601 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 55 time to evaluate : 2.692 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 175 optimal weight: 5.9990 chunk 282 optimal weight: 10.0000 chunk 172 optimal weight: 2.9990 chunk 133 optimal weight: 9.9990 chunk 196 optimal weight: 30.0000 chunk 295 optimal weight: 20.0000 chunk 272 optimal weight: 0.8980 chunk 235 optimal weight: 20.0000 chunk 24 optimal weight: 0.3980 chunk 181 optimal weight: 0.9980 chunk 144 optimal weight: 8.9990 overall best weight: 2.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 651 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 651 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 651 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8404 moved from start: 0.3842 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 24462 Z= 0.169 Angle : 0.599 9.575 33204 Z= 0.300 Chirality : 0.046 0.395 3900 Planarity : 0.004 0.044 4155 Dihedral : 8.823 74.920 4368 Min Nonbonded Distance : 2.063 Molprobity Statistics. All-atom Clashscore : 11.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.95 % Favored : 93.05 % Rotamer: Outliers : 0.00 % Allowed : 0.12 % Favored : 99.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.63 % Cis-general : 0.11 % 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: -0.59 (0.16), residues: 2919 helix: 1.05 (0.27), residues: 423 sheet: -0.22 (0.18), residues: 855 loop : -0.85 (0.16), residues: 1641 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP H 94 HIS 0.003 0.001 HIS C 100D PHE 0.016 0.001 PHE F 519 TYR 0.031 0.001 TYR E 458 ARG 0.003 0.000 ARG E 456 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5838 Ramachandran restraints generated. 2919 Oldfield, 0 Emsley, 2919 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5838 Ramachandran restraints generated. 2919 Oldfield, 0 Emsley, 2919 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 68 residues out of total 2601 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 68 time to evaluate : 2.715 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 95 MET cc_start: 0.9138 (ppp) cc_final: 0.8403 (ppp) REVERT: A 396 MET cc_start: 0.6807 (mmt) cc_final: 0.6489 (mmt) REVERT: B 530 MET cc_start: 0.8051 (mmm) cc_final: 0.7558 (mmm) REVERT: B 535 MET cc_start: 0.9252 (mpp) cc_final: 0.8800 (mpp) REVERT: B 626 MET cc_start: 0.7259 (tpp) cc_final: 0.6831 (tpp) REVERT: E 95 MET cc_start: 0.8880 (ppp) cc_final: 0.8496 (ppp) REVERT: E 104 MET cc_start: 0.9423 (ppp) cc_final: 0.9161 (ppp) REVERT: E 396 MET cc_start: 0.6661 (mmt) cc_final: 0.6447 (mmt) REVERT: E 473 MET cc_start: 0.8123 (tpp) cc_final: 0.7652 (tpp) REVERT: G 89 MET cc_start: 0.9583 (tpp) cc_final: 0.9289 (tpp) REVERT: M 95 MET cc_start: 0.9083 (ppp) cc_final: 0.8526 (ppp) REVERT: M 396 MET cc_start: 0.6834 (mmt) cc_final: 0.6571 (mmt) REVERT: M 473 MET cc_start: 0.8200 (tpp) cc_final: 0.7754 (tpp) REVERT: N 535 MET cc_start: 0.9348 (mpp) cc_final: 0.8934 (mpp) REVERT: O 89 MET cc_start: 0.9499 (tpp) cc_final: 0.9246 (tpp) outliers start: 0 outliers final: 0 residues processed: 68 average time/residue: 0.3807 time to fit residues: 43.2128 Evaluate side-chains 53 residues out of total 2601 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 53 time to evaluate : 2.702 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 187 optimal weight: 9.9990 chunk 250 optimal weight: 10.0000 chunk 72 optimal weight: 30.0000 chunk 217 optimal weight: 10.0000 chunk 34 optimal weight: 10.0000 chunk 65 optimal weight: 7.9990 chunk 235 optimal weight: 0.0270 chunk 98 optimal weight: 1.9990 chunk 242 optimal weight: 0.8980 chunk 29 optimal weight: 1.9990 chunk 43 optimal weight: 20.0000 overall best weight: 2.5844 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 651 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 651 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 651 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2977 r_free = 0.2977 target = 0.028230 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2754 r_free = 0.2754 target = 0.023909 restraints weight = 345844.062| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.2786 r_free = 0.2786 target = 0.024531 restraints weight = 188380.041| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.2807 r_free = 0.2807 target = 0.024938 restraints weight = 124080.766| |-----------------------------------------------------------------------------| r_work (final): 0.2796 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8406 moved from start: 0.3954 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 24462 Z= 0.177 Angle : 0.594 9.577 33204 Z= 0.297 Chirality : 0.046 0.387 3900 Planarity : 0.004 0.045 4155 Dihedral : 8.535 73.219 4368 Min Nonbonded Distance : 2.058 Molprobity Statistics. All-atom Clashscore : 11.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.95 % Favored : 92.05 % Rotamer: Outliers : 0.00 % Allowed : 0.23 % Favored : 99.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.63 % Cis-general : 0.11 % 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: -0.54 (0.16), residues: 2919 helix: 1.13 (0.28), residues: 423 sheet: -0.17 (0.18), residues: 855 loop : -0.84 (0.16), residues: 1641 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP D 94 HIS 0.003 0.001 HIS C 100D PHE 0.013 0.001 PHE F 519 TYR 0.030 0.001 TYR A 458 ARG 0.002 0.000 ARG A 456 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2976.27 seconds wall clock time: 57 minutes 7.50 seconds (3427.50 seconds total)