Starting phenix.real_space_refine on Mon Sep 30 04:16:40 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tco_25815/09_2024/7tco_25815.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tco_25815/09_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_25815/09_2024/7tco_25815.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tco_25815/09_2024/7tco_25815.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tco_25815/09_2024/7tco_25815.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tco_25815/09_2024/7tco_25815.cif" } 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. Time to flip 15 residue(s): 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/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: 14.33, per 1000 atoms: 0.60 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 - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied ALPHA1-3 " 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: 6.76 Conformation dependent library (CDL) restraints added in 3.2 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: 3.97 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: 9.82 Time building geometry restraints manager: 7.77 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: 0.00 - 4.46: 32907 4.46 - 8.92: 262 8.92 - 13.38: 31 13.38 - 17.84: 1 17.84 - 22.30: 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 3.040 nonbonded pdb=" O SER B 528 " pdb=" OG1 THR B 627 " model vdw 2.235 3.040 nonbonded pdb=" O SER N 528 " pdb=" OG1 THR N 627 " model vdw 2.245 3.040 nonbonded pdb=" OD1 ASN A 262 " pdb=" OG SER A 447 " model vdw 2.289 3.040 nonbonded pdb=" OG1 THR E 37 " pdb=" O CYS F 604 " model vdw 2.289 3.040 ... (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 Time spend for trying shortcut: 0.00 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: 2.680 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.940 Check model and map are aligned: 0.180 Set scattering table: 0.210 Process input model: 56.400 Find NCS groups from input model: 0.890 Set up NCS constraints: 0.170 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:2.740 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 64.220 ------------------------------------------------------------------------------- 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 : 3.029 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: 0.3760 time to fit residues: 54.0256 Evaluate side-chains 65 residues out of total 2601 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 65 time to evaluate : 2.823 ------------------------------------------------------------------------------- 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: 10.0000 chunk 225 optimal weight: 20.0000 chunk 124 optimal weight: 20.0000 chunk 76 optimal weight: 9.9990 chunk 151 optimal weight: 0.7980 chunk 120 optimal weight: 10.0000 chunk 232 optimal weight: 9.9990 chunk 90 optimal weight: 6.9990 chunk 141 optimal weight: 10.0000 chunk 173 optimal weight: 9.9990 chunk 269 optimal weight: 0.9980 overall best weight: 5.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 80 ASN E 80 ASN M 80 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8373 moved from start: 0.1639 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 24462 Z= 0.341 Angle : 0.794 12.280 33204 Z= 0.390 Chirality : 0.048 0.373 3900 Planarity : 0.005 0.050 4155 Dihedral : 14.666 110.286 4368 Min Nonbonded Distance : 2.322 Molprobity Statistics. All-atom Clashscore : 8.66 Ramachandran Plot: Outliers : 0.10 % Allowed : 6.89 % Favored : 93.01 % Rotamer: Outliers : 0.00 % Allowed : 4.59 % Favored : 95.41 % 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: -1.02 (0.16), residues: 2919 helix: 0.31 (0.27), residues: 387 sheet: -0.47 (0.17), residues: 906 loop : -1.02 (0.16), residues: 1626 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP N 631 HIS 0.007 0.002 HIS A 374 PHE 0.029 0.002 PHE B 519 TYR 0.018 0.002 TYR O 91 ARG 0.005 0.001 ARG H 108 *********************** 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 : 3.176 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 95 MET cc_start: 0.9142 (ppp) cc_final: 0.8474 (ppp) REVERT: B 626 MET cc_start: 0.7449 (tpt) cc_final: 0.7133 (tpt) REVERT: C 89 MET cc_start: 0.9123 (tpt) cc_final: 0.8799 (tpp) REVERT: E 473 MET cc_start: 0.7898 (tpp) cc_final: 0.7641 (tpp) REVERT: G 75 MET cc_start: 0.8650 (mpp) cc_final: 0.8417 (mpp) REVERT: M 84 MET cc_start: 0.7688 (mpp) cc_final: 0.7427 (mpp) REVERT: M 95 MET cc_start: 0.9148 (ppp) cc_final: 0.8731 (ppp) REVERT: O 89 MET cc_start: 0.9308 (tpp) cc_final: 0.8998 (tpp) outliers start: 0 outliers final: 0 residues processed: 69 average time/residue: 0.3730 time to fit residues: 43.4245 Evaluate side-chains 55 residues out of total 2601 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 55 time to evaluate : 2.914 ------------------------------------------------------------------------------- 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: 7.9990 chunk 83 optimal weight: 4.9990 chunk 224 optimal weight: 10.0000 chunk 183 optimal weight: 20.0000 chunk 74 optimal weight: 5.9990 chunk 270 optimal weight: 10.0000 chunk 291 optimal weight: 8.9990 chunk 240 optimal weight: 5.9990 chunk 267 optimal weight: 10.0000 chunk 92 optimal weight: 9.9990 chunk 216 optimal weight: 8.9990 overall best weight: 6.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 164 HIS G 164 HIS O 164 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8435 moved from start: 0.2414 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.070 24462 Z= 0.360 Angle : 0.791 12.239 33204 Z= 0.398 Chirality : 0.049 0.364 3900 Planarity : 0.005 0.051 4155 Dihedral : 13.135 112.569 4368 Min Nonbonded Distance : 2.324 Molprobity Statistics. All-atom Clashscore : 8.94 Ramachandran Plot: Outliers : 0.10 % Allowed : 8.15 % Favored : 91.74 % Rotamer: Outliers : 0.00 % Allowed : 4.08 % Favored : 95.92 % 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: -1.08 (0.16), residues: 2919 helix: 0.39 (0.27), residues: 387 sheet: -0.59 (0.17), residues: 933 loop : -1.03 (0.16), residues: 1599 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP E 427 HIS 0.005 0.001 HIS E 374 PHE 0.016 0.002 PHE D 71 TYR 0.024 0.002 TYR A 458 ARG 0.005 0.001 ARG M 192 *********************** 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 73 residues out of total 2601 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 73 time to evaluate : 2.850 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 95 MET cc_start: 0.9228 (ppp) cc_final: 0.8443 (ppp) REVERT: A 104 MET cc_start: 0.9479 (ppp) cc_final: 0.9247 (ppp) REVERT: A 396 MET cc_start: 0.6700 (mmt) cc_final: 0.6218 (mmt) REVERT: C 89 MET cc_start: 0.9302 (tpt) cc_final: 0.9047 (tpp) REVERT: E 95 MET cc_start: 0.9160 (ppp) cc_final: 0.8725 (ppp) REVERT: E 104 MET cc_start: 0.9437 (ppp) cc_final: 0.9175 (ppp) REVERT: E 473 MET cc_start: 0.7801 (tpp) cc_final: 0.7492 (tpp) REVERT: M 95 MET cc_start: 0.9231 (ppp) cc_final: 0.8783 (ppp) REVERT: M 104 MET cc_start: 0.9492 (ppp) cc_final: 0.9252 (ppp) REVERT: M 473 MET cc_start: 0.7923 (tpp) cc_final: 0.7689 (tpp) REVERT: O 75 MET cc_start: 0.8952 (mtm) cc_final: 0.8523 (mpp) REVERT: O 89 MET cc_start: 0.9469 (tpp) cc_final: 0.8906 (tpp) outliers start: 0 outliers final: 0 residues processed: 73 average time/residue: 0.3547 time to fit residues: 43.7995 Evaluate side-chains 54 residues out of total 2601 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 54 time to evaluate : 2.995 ------------------------------------------------------------------------------- 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: 10.0000 chunk 203 optimal weight: 5.9990 chunk 140 optimal weight: 5.9990 chunk 29 optimal weight: 1.9990 chunk 128 optimal weight: 0.9990 chunk 181 optimal weight: 5.9990 chunk 271 optimal weight: 9.9990 chunk 287 optimal weight: 2.9990 chunk 141 optimal weight: 0.1980 chunk 256 optimal weight: 9.9990 chunk 77 optimal weight: 8.9990 overall best weight: 2.4388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8389 moved from start: 0.2517 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 24462 Z= 0.186 Angle : 0.652 9.650 33204 Z= 0.327 Chirality : 0.047 0.346 3900 Planarity : 0.004 0.048 4155 Dihedral : 12.126 105.610 4368 Min Nonbonded Distance : 2.378 Molprobity Statistics. All-atom Clashscore : 6.89 Ramachandran Plot: Outliers : 0.03 % Allowed : 6.41 % Favored : 93.56 % Rotamer: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % 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: -0.88 (0.16), residues: 2919 helix: 0.85 (0.27), residues: 387 sheet: -0.46 (0.17), residues: 939 loop : -1.00 (0.16), residues: 1593 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP H 96 HIS 0.004 0.001 HIS C 100D PHE 0.016 0.001 PHE E 53 TYR 0.015 0.001 TYR G 91 ARG 0.002 0.000 ARG D 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 70 residues out of total 2601 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 70 time to evaluate : 2.866 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 95 MET cc_start: 0.9148 (ppp) cc_final: 0.8419 (ppp) REVERT: A 104 MET cc_start: 0.9381 (ppp) cc_final: 0.9146 (ppp) REVERT: C 89 MET cc_start: 0.9312 (tpt) cc_final: 0.9104 (tpp) REVERT: E 95 MET cc_start: 0.9077 (ppp) cc_final: 0.8625 (ppp) REVERT: E 104 MET cc_start: 0.9334 (ppp) cc_final: 0.9065 (ppp) REVERT: E 473 MET cc_start: 0.7843 (tpp) cc_final: 0.7488 (tpp) REVERT: M 84 MET cc_start: 0.7737 (mpp) cc_final: 0.7017 (mpp) REVERT: M 95 MET cc_start: 0.9115 (ppp) cc_final: 0.8690 (ppp) REVERT: M 104 MET cc_start: 0.9363 (ppp) cc_final: 0.9134 (ppp) REVERT: M 473 MET cc_start: 0.7920 (tpp) cc_final: 0.7614 (tpp) REVERT: O 89 MET cc_start: 0.9459 (tpp) cc_final: 0.9088 (tpp) outliers start: 0 outliers final: 0 residues processed: 70 average time/residue: 0.3829 time to fit residues: 44.6777 Evaluate side-chains 55 residues out of total 2601 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 55 time to evaluate : 3.091 ------------------------------------------------------------------------------- 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: 4.9990 chunk 162 optimal weight: 6.9990 chunk 4 optimal weight: 9.9990 chunk 213 optimal weight: 10.0000 chunk 118 optimal weight: 20.0000 chunk 244 optimal weight: 9.9990 chunk 198 optimal weight: 10.0000 chunk 0 optimal weight: 10.0000 chunk 146 optimal weight: 0.9980 chunk 257 optimal weight: 10.0000 chunk 72 optimal weight: 30.0000 overall best weight: 6.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 321AGLN C 95 ASN E 321AGLN M 321AGLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8458 moved from start: 0.3174 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= 0.357 Angle : 0.756 9.600 33204 Z= 0.379 Chirality : 0.048 0.353 3900 Planarity : 0.005 0.047 4155 Dihedral : 12.001 98.947 4368 Min Nonbonded Distance : 2.347 Molprobity Statistics. All-atom Clashscore : 10.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.80 % Favored : 91.20 % Rotamer: Outliers : 0.00 % Allowed : 3.39 % Favored : 96.61 % 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: -1.12 (0.16), residues: 2919 helix: 0.70 (0.27), residues: 387 sheet: -0.63 (0.17), residues: 915 loop : -1.14 (0.16), residues: 1617 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP H 94 HIS 0.005 0.001 HIS M 417 PHE 0.018 0.002 PHE D 71 TYR 0.016 0.002 TYR A 217 ARG 0.007 0.001 ARG E 192 *********************** 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 65 residues out of total 2601 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 65 time to evaluate : 2.947 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: 0.9229 (ppp) cc_final: 0.8547 (ppp) REVERT: B 530 MET cc_start: 0.6968 (mmm) cc_final: 0.6711 (mmm) REVERT: B 535 MET cc_start: 0.9164 (mpp) cc_final: 0.8678 (mpp) REVERT: B 626 MET cc_start: 0.7679 (tpp) cc_final: 0.7344 (tpp) REVERT: E 95 MET cc_start: 0.9188 (ppp) cc_final: 0.8872 (ppp) REVERT: E 473 MET cc_start: 0.7900 (tpp) cc_final: 0.7566 (tpp) REVERT: M 95 MET cc_start: 0.9193 (ppp) cc_final: 0.8680 (ppp) REVERT: M 473 MET cc_start: 0.8074 (tpp) cc_final: 0.7823 (tpp) REVERT: N 530 MET cc_start: 0.7817 (mmp) cc_final: 0.7267 (mmt) REVERT: O 89 MET cc_start: 0.9522 (tpp) cc_final: 0.9109 (tpp) outliers start: 0 outliers final: 0 residues processed: 65 average time/residue: 0.3876 time to fit residues: 41.7459 Evaluate side-chains 57 residues out of total 2601 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 57 time to evaluate : 2.968 ------------------------------------------------------------------------------- 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: 5.9990 chunk 258 optimal weight: 3.9990 chunk 56 optimal weight: 2.9990 chunk 168 optimal weight: 5.9990 chunk 70 optimal weight: 8.9990 chunk 287 optimal weight: 0.5980 chunk 238 optimal weight: 10.0000 chunk 133 optimal weight: 20.0000 chunk 23 optimal weight: 2.9990 chunk 95 optimal weight: 20.0000 chunk 150 optimal weight: 5.9990 overall best weight: 3.3188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 95 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8427 moved from start: 0.3249 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 24462 Z= 0.210 Angle : 0.659 9.618 33204 Z= 0.329 Chirality : 0.047 0.404 3900 Planarity : 0.004 0.046 4155 Dihedral : 11.192 89.606 4368 Min Nonbonded Distance : 2.384 Molprobity Statistics. All-atom Clashscore : 8.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.99 % Favored : 93.01 % Rotamer: Outliers : 0.00 % Allowed : 1.39 % Favored : 98.61 % 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: 1.02 (0.28), residues: 387 sheet: -0.36 (0.17), residues: 882 loop : -1.09 (0.16), residues: 1650 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.001 TRP P 94 HIS 0.003 0.001 HIS O 100D PHE 0.013 0.001 PHE F 519 TYR 0.028 0.001 TYR M 458 ARG 0.003 0.000 ARG A 192 *********************** 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 : 2.926 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 84 MET cc_start: 0.7996 (mpp) cc_final: 0.7743 (mpp) REVERT: A 95 MET cc_start: 0.9176 (ppp) cc_final: 0.8500 (ppp) REVERT: A 104 MET cc_start: 0.9408 (ppp) cc_final: 0.9190 (ppp) REVERT: B 530 MET cc_start: 0.7010 (mmm) cc_final: 0.6595 (mmm) REVERT: E 95 MET cc_start: 0.9119 (ppp) cc_final: 0.8762 (ppp) REVERT: E 104 MET cc_start: 0.9427 (ppp) cc_final: 0.9174 (ppp) REVERT: E 473 MET cc_start: 0.7899 (tpp) cc_final: 0.7504 (tpp) REVERT: M 95 MET cc_start: 0.9146 (ppp) cc_final: 0.8607 (ppp) REVERT: M 104 MET cc_start: 0.9463 (ppp) cc_final: 0.9151 (ppp) REVERT: M 473 MET cc_start: 0.8058 (tpp) cc_final: 0.7685 (tpp) outliers start: 0 outliers final: 0 residues processed: 66 average time/residue: 0.3934 time to fit residues: 43.1606 Evaluate side-chains 55 residues out of total 2601 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 55 time to evaluate : 2.950 ------------------------------------------------------------------------------- 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: 0.0570 chunk 32 optimal weight: 10.0000 chunk 163 optimal weight: 4.9990 chunk 209 optimal weight: 8.9990 chunk 162 optimal weight: 7.9990 chunk 241 optimal weight: 20.0000 chunk 160 optimal weight: 7.9990 chunk 286 optimal weight: 20.0000 chunk 179 optimal weight: 8.9990 chunk 174 optimal weight: 30.0000 chunk 132 optimal weight: 10.0000 overall best weight: 6.0106 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8467 moved from start: 0.3626 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 24462 Z= 0.337 Angle : 0.732 10.547 33204 Z= 0.365 Chirality : 0.048 0.388 3900 Planarity : 0.004 0.046 4155 Dihedral : 11.070 81.626 4368 Min Nonbonded Distance : 2.342 Molprobity Statistics. All-atom Clashscore : 10.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.08 % Favored : 90.92 % Rotamer: Outliers : 0.00 % Allowed : 1.62 % Favored : 98.38 % 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: -1.14 (0.16), residues: 2919 helix: 0.68 (0.26), residues: 405 sheet: -0.65 (0.17), residues: 906 loop : -1.18 (0.16), residues: 1608 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP D 148 HIS 0.007 0.001 HIS C 35 PHE 0.016 0.002 PHE D 71 TYR 0.021 0.002 TYR O 91 ARG 0.005 0.000 ARG M 192 *********************** 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 65 residues out of total 2601 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 65 time to evaluate : 2.856 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: 0.9233 (ppp) cc_final: 0.8615 (ppp) REVERT: A 104 MET cc_start: 0.9474 (ppp) cc_final: 0.9168 (ppp) REVERT: B 530 MET cc_start: 0.7310 (mmm) cc_final: 0.6864 (mmm) REVERT: B 626 MET cc_start: 0.7655 (tpp) cc_final: 0.7101 (tpp) REVERT: E 104 MET cc_start: 0.9423 (ppp) cc_final: 0.9192 (ppp) REVERT: E 473 MET cc_start: 0.7976 (tpp) cc_final: 0.7622 (tpp) REVERT: M 84 MET cc_start: 0.7763 (mpp) cc_final: 0.7483 (mpp) REVERT: M 95 MET cc_start: 0.9193 (ppp) cc_final: 0.8665 (ppp) REVERT: M 473 MET cc_start: 0.8223 (tpp) cc_final: 0.7863 (tpp) outliers start: 0 outliers final: 0 residues processed: 65 average time/residue: 0.3921 time to fit residues: 42.1919 Evaluate side-chains 57 residues out of total 2601 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 57 time to evaluate : 2.816 ------------------------------------------------------------------------------- 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: 6.9990 chunk 114 optimal weight: 10.0000 chunk 170 optimal weight: 3.9990 chunk 86 optimal weight: 7.9990 chunk 56 optimal weight: 0.7980 chunk 55 optimal weight: 8.9990 chunk 181 optimal weight: 4.9990 chunk 195 optimal weight: 10.0000 chunk 141 optimal weight: 6.9990 chunk 26 optimal weight: 8.9990 chunk 225 optimal weight: 9.9990 overall best weight: 4.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: O 95 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8459 moved from start: 0.3790 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 24462 Z= 0.267 Angle : 0.686 10.368 33204 Z= 0.343 Chirality : 0.047 0.403 3900 Planarity : 0.004 0.046 4155 Dihedral : 10.443 75.979 4368 Min Nonbonded Distance : 2.319 Molprobity Statistics. All-atom Clashscore : 9.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.61 % Favored : 92.39 % Rotamer: Outliers : 0.00 % Allowed : 0.92 % Favored : 99.08 % 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: -1.07 (0.16), residues: 2919 helix: 0.87 (0.27), residues: 387 sheet: -0.47 (0.17), residues: 900 loop : -1.24 (0.15), residues: 1632 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP F 614 HIS 0.005 0.001 HIS M 417 PHE 0.012 0.002 PHE D 71 TYR 0.019 0.001 TYR O 91 ARG 0.003 0.000 ARG G 210 *********************** 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 64 residues out of total 2601 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 64 time to evaluate : 2.927 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 84 MET cc_start: 0.8191 (mpp) cc_final: 0.7951 (mpp) REVERT: A 95 MET cc_start: 0.9214 (ppp) cc_final: 0.8573 (ppp) REVERT: A 104 MET cc_start: 0.9446 (ppp) cc_final: 0.9177 (ppp) REVERT: B 530 MET cc_start: 0.7378 (mmm) cc_final: 0.6891 (mmm) REVERT: B 626 MET cc_start: 0.7475 (tpp) cc_final: 0.7027 (tpp) REVERT: E 104 MET cc_start: 0.9429 (ppp) cc_final: 0.9181 (ppp) REVERT: E 473 MET cc_start: 0.8059 (tpp) cc_final: 0.7635 (tpp) REVERT: F 530 MET cc_start: 0.7670 (mmm) cc_final: 0.7400 (mmm) REVERT: M 95 MET cc_start: 0.9179 (ppp) cc_final: 0.8648 (ppp) REVERT: M 396 MET cc_start: 0.6933 (mmt) cc_final: 0.6631 (mmt) REVERT: M 473 MET cc_start: 0.8230 (tpp) cc_final: 0.7845 (tpp) outliers start: 0 outliers final: 0 residues processed: 64 average time/residue: 0.3916 time to fit residues: 41.2785 Evaluate side-chains 55 residues out of total 2601 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 55 time to evaluate : 3.061 ------------------------------------------------------------------------------- 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: 0.9980 chunk 274 optimal weight: 6.9990 chunk 250 optimal weight: 2.9990 chunk 266 optimal weight: 6.9990 chunk 160 optimal weight: 7.9990 chunk 116 optimal weight: 5.9990 chunk 209 optimal weight: 6.9990 chunk 81 optimal weight: 4.9990 chunk 241 optimal weight: 5.9990 chunk 252 optimal weight: 10.0000 chunk 265 optimal weight: 0.8980 overall best weight: 3.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8444 moved from start: 0.3863 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 24462 Z= 0.203 Angle : 0.643 9.615 33204 Z= 0.320 Chirality : 0.047 0.401 3900 Planarity : 0.004 0.046 4155 Dihedral : 9.553 72.277 4368 Min Nonbonded Distance : 2.406 Molprobity Statistics. All-atom Clashscore : 8.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.61 % Favored : 92.39 % Rotamer: Outliers : 0.00 % Allowed : 0.35 % Favored : 99.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.63 % Cis-general : 0.11 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.91 (0.16), residues: 2919 helix: 0.93 (0.27), residues: 402 sheet: -0.44 (0.17), residues: 927 loop : -1.08 (0.16), residues: 1590 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP F 614 HIS 0.003 0.001 HIS O 100D PHE 0.010 0.001 PHE D 71 TYR 0.021 0.001 TYR O 91 ARG 0.002 0.000 ARG D 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 65 residues out of total 2601 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 65 time to evaluate : 2.726 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 95 MET cc_start: 0.9192 (ppp) cc_final: 0.8616 (ppp) REVERT: A 104 MET cc_start: 0.9431 (ppp) cc_final: 0.9176 (ppp) REVERT: B 530 MET cc_start: 0.7468 (mmm) cc_final: 0.6928 (mmm) REVERT: B 626 MET cc_start: 0.7397 (tpp) cc_final: 0.6793 (tpp) REVERT: E 95 MET cc_start: 0.9010 (ppp) cc_final: 0.8613 (ppp) REVERT: E 104 MET cc_start: 0.9425 (ppp) cc_final: 0.9164 (ppp) REVERT: E 473 MET cc_start: 0.8060 (tpp) cc_final: 0.7621 (tpp) REVERT: F 530 MET cc_start: 0.7743 (mmm) cc_final: 0.7479 (mmm) REVERT: G 89 MET cc_start: 0.9531 (tpp) cc_final: 0.9244 (tpp) REVERT: M 84 MET cc_start: 0.7974 (mpp) cc_final: 0.7762 (mpp) REVERT: M 95 MET cc_start: 0.9143 (ppp) cc_final: 0.8602 (ppp) REVERT: M 473 MET cc_start: 0.8244 (tpp) cc_final: 0.7846 (tpp) REVERT: O 75 MET cc_start: 0.9374 (mmm) cc_final: 0.9013 (mpp) outliers start: 0 outliers final: 0 residues processed: 65 average time/residue: 0.3822 time to fit residues: 41.2714 Evaluate side-chains 54 residues out of total 2601 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 54 time to evaluate : 2.862 ------------------------------------------------------------------------------- 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: 0.5980 chunk 282 optimal weight: 20.0000 chunk 172 optimal weight: 0.1980 chunk 133 optimal weight: 20.0000 chunk 196 optimal weight: 20.0000 chunk 295 optimal weight: 8.9990 chunk 272 optimal weight: 20.0000 chunk 235 optimal weight: 0.0010 chunk 24 optimal weight: 8.9990 chunk 181 optimal weight: 3.9990 chunk 144 optimal weight: 0.3980 overall best weight: 1.0388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8396 moved from start: 0.3900 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 24462 Z= 0.142 Angle : 0.612 9.580 33204 Z= 0.304 Chirality : 0.047 0.416 3900 Planarity : 0.004 0.044 4155 Dihedral : 8.577 68.532 4368 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 6.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.52 % Favored : 94.48 % Rotamer: Outliers : 0.00 % Allowed : 0.04 % Favored : 99.96 % 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: -0.55 (0.16), residues: 2919 helix: 1.25 (0.28), residues: 402 sheet: -0.12 (0.18), residues: 897 loop : -0.91 (0.16), residues: 1620 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.001 TRP H 94 HIS 0.004 0.001 HIS O 100D PHE 0.026 0.001 PHE F 519 TYR 0.023 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 67 residues out of total 2601 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 67 time to evaluate : 2.852 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 95 MET cc_start: 0.9114 (ppp) cc_final: 0.8489 (ppp) REVERT: A 104 MET cc_start: 0.9446 (ppp) cc_final: 0.9135 (ppp) REVERT: B 530 MET cc_start: 0.7506 (mmm) cc_final: 0.6945 (mmm) REVERT: B 626 MET cc_start: 0.7302 (tpp) cc_final: 0.6966 (tpp) REVERT: E 95 MET cc_start: 0.8888 (ppp) cc_final: 0.8387 (ppp) REVERT: E 104 MET cc_start: 0.9411 (ppp) cc_final: 0.9141 (ppp) REVERT: E 473 MET cc_start: 0.8037 (tpp) cc_final: 0.7557 (tpp) REVERT: F 530 MET cc_start: 0.7790 (mmm) cc_final: 0.7537 (mmm) REVERT: G 89 MET cc_start: 0.9559 (tpp) cc_final: 0.9283 (tpp) REVERT: M 84 MET cc_start: 0.7955 (mpp) cc_final: 0.7745 (mpp) REVERT: M 95 MET cc_start: 0.8948 (ppp) cc_final: 0.8404 (ppp) REVERT: M 473 MET cc_start: 0.8215 (tpp) cc_final: 0.7774 (tpp) REVERT: O 75 MET cc_start: 0.9353 (mmm) cc_final: 0.8967 (mpp) outliers start: 0 outliers final: 0 residues processed: 67 average time/residue: 0.3887 time to fit residues: 43.1611 Evaluate side-chains 55 residues out of total 2601 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 55 time to evaluate : 2.695 ------------------------------------------------------------------------------- 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: 20.0000 chunk 250 optimal weight: 9.9990 chunk 72 optimal weight: 20.0000 chunk 217 optimal weight: 6.9990 chunk 34 optimal weight: 3.9990 chunk 65 optimal weight: 20.0000 chunk 235 optimal weight: 0.7980 chunk 98 optimal weight: 8.9990 chunk 242 optimal weight: 3.9990 chunk 29 optimal weight: 1.9990 chunk 43 optimal weight: 6.9990 overall best weight: 3.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2951 r_free = 0.2951 target = 0.027673 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2719 r_free = 0.2719 target = 0.023305 restraints weight = 346792.861| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.2751 r_free = 0.2751 target = 0.023918 restraints weight = 190242.397| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.2773 r_free = 0.2773 target = 0.024329 restraints weight = 125790.937| |-----------------------------------------------------------------------------| r_work (final): 0.2762 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8437 moved from start: 0.4046 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= 0.216 Angle : 0.624 9.612 33204 Z= 0.312 Chirality : 0.046 0.393 3900 Planarity : 0.004 0.044 4155 Dihedral : 8.381 65.191 4368 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 7.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.37 % Favored : 92.63 % Rotamer: Outliers : 0.00 % Allowed : 0.50 % Favored : 99.50 % 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: -0.57 (0.16), residues: 2919 helix: 1.23 (0.28), residues: 402 sheet: -0.14 (0.18), residues: 894 loop : -0.92 (0.16), residues: 1623 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP F 614 HIS 0.004 0.001 HIS O 100D PHE 0.016 0.001 PHE F 519 TYR 0.019 0.001 TYR O 91 ARG 0.003 0.000 ARG M 192 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3029.35 seconds wall clock time: 57 minutes 33.81 seconds (3453.81 seconds total)