Starting phenix.real_space_refine on Thu Mar 5 18:01:56 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7tco_25815/03_2026/7tco_25815.cif Found real_map, /net/cci-nas-00/data/ceres_data/7tco_25815/03_2026/7tco_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 { model { file = "/net/cci-nas-00/data/ceres_data/7tco_25815/03_2026/7tco_25815.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7tco_25815/03_2026/7tco_25815.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7tco_25815/03_2026/7tco_25815.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7tco_25815/03_2026/7tco_25815.map" } resolution = 4.19 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs 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): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/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: 5.51, per 1000 atoms: 0.23 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: 2.20 Conformation dependent library (CDL) restraints added in 1.2 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: 0.82 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: 3.82 Time building geometry restraints manager: 2.91 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: 0.02 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'E' selection = chain 'M' } ncs_group { reference = chain 'B' selection = chain 'F' selection = chain 'N' } ncs_group { reference = chain 'C' selection = chain 'G' selection = chain 'O' } ncs_group { reference = chain 'D' selection = chain 'H' selection = chain 'P' } ncs_group { reference = chain 'I' selection = chain 'Q' selection = chain 'V' } ncs_group { reference = chain 'J' selection = chain 'R' selection = chain 'W' } ncs_group { reference = chain 'K' selection = chain 'S' selection = chain 'X' } ncs_group { reference = chain 'L' selection = chain 'T' selection = chain 'Y' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.160 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.340 Check model and map are aligned: 0.050 Set scattering table: 0.070 Process input model: 21.390 Find NCS groups from input model: 0.540 Set up NCS constraints: 0.070 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:1.380 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.020 ------------------------------------------------------------------------------- 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 24528 Z= 0.270 Angle : 1.093 22.303 33384 Z= 0.544 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. 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 ARG 0.004 0.001 ARG A 298 TYR 0.030 0.002 TYR A 458 PHE 0.024 0.002 PHE M 376 TRP 0.016 0.002 TRP D 96 HIS 0.011 0.002 HIS G 35 Details of bonding type rmsd covalent geometry : bond 0.00542 (24462) covalent geometry : angle 1.05961 (33204) SS BOND : bond 0.00690 ( 18) SS BOND : angle 1.42133 ( 36) hydrogen bonds : bond 0.14815 ( 816) hydrogen bonds : angle 7.73231 ( 2286) link_ALPHA1-3 : bond 0.00163 ( 6) link_ALPHA1-3 : angle 4.46287 ( 18) link_ALPHA1-6 : bond 0.01928 ( 6) link_ALPHA1-6 : angle 3.99359 ( 18) link_BETA1-4 : bond 0.00818 ( 21) link_BETA1-4 : angle 3.65894 ( 63) link_NAG-ASN : bond 0.01153 ( 15) link_NAG-ASN : angle 4.85159 ( 45) *********************** 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 to be fit. rotamer outliers: 0 poor density : 88 time to evaluate : 0.990 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: 0.8843 (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: 0.1624 time to fit residues: 23.4272 Evaluate side-chains 65 residues out of total 2601 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 65 time to evaluate : 0.919 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 197 optimal weight: 30.0000 chunk 215 optimal weight: 3.9990 chunk 20 optimal weight: 6.9990 chunk 132 optimal weight: 6.9990 chunk 261 optimal weight: 5.9990 chunk 248 optimal weight: 0.0060 chunk 207 optimal weight: 20.0000 chunk 155 optimal weight: 5.9990 chunk 244 optimal weight: 0.7980 chunk 183 optimal weight: 9.9990 chunk 111 optimal weight: 6.9990 overall best weight: 3.3602 ------------------------------------------------------------------------------- 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 = 0.3045 r_free = 0.3045 target = 0.029638 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2811 r_free = 0.2811 target = 0.025059 restraints weight = 342825.100| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.2845 r_free = 0.2845 target = 0.025721 restraints weight = 187288.035| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.2868 r_free = 0.2868 target = 0.026164 restraints weight = 122760.136| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.2884 r_free = 0.2884 target = 0.026461 restraints weight = 90476.251| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 21)----------------| | r_work = 0.2893 r_free = 0.2893 target = 0.026653 restraints weight = 72718.293| |-----------------------------------------------------------------------------| r_work (final): 0.2884 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8276 moved from start: 0.1154 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 24528 Z= 0.162 Angle : 0.737 11.802 33384 Z= 0.354 Chirality : 0.047 0.372 3900 Planarity : 0.005 0.048 4155 Dihedral : 15.009 111.008 4368 Min Nonbonded Distance : 2.382 Molprobity Statistics. All-atom Clashscore : 4.97 Ramachandran Plot: Outliers : 0.10 % Allowed : 5.93 % Favored : 93.97 % Rotamer: Outliers : 0.00 % Allowed : 3.43 % Favored : 96.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.63 % Cis-general : 0.11 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.92 (0.16), residues: 2919 helix: 0.25 (0.27), residues: 384 sheet: -0.29 (0.17), residues: 912 loop : -0.98 (0.16), residues: 1623 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 588 TYR 0.017 0.001 TYR O 91 PHE 0.013 0.001 PHE B 519 TRP 0.010 0.001 TRP B 631 HIS 0.004 0.001 HIS M 374 Details of bonding type rmsd covalent geometry : bond 0.00336 (24462) covalent geometry : angle 0.70326 (33204) SS BOND : bond 0.00679 ( 18) SS BOND : angle 0.96358 ( 36) hydrogen bonds : bond 0.03800 ( 816) hydrogen bonds : angle 6.04297 ( 2286) link_ALPHA1-3 : bond 0.00890 ( 6) link_ALPHA1-3 : angle 4.54360 ( 18) link_ALPHA1-6 : bond 0.01841 ( 6) link_ALPHA1-6 : angle 2.85682 ( 18) link_BETA1-4 : bond 0.00523 ( 21) link_BETA1-4 : angle 2.79265 ( 63) link_NAG-ASN : bond 0.00663 ( 15) link_NAG-ASN : angle 3.85868 ( 45) *********************** 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 73 residues out of total 2601 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 73 time to evaluate : 0.792 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: 0.9015 (ppp) cc_final: 0.8353 (ppp) REVERT: C 89 MET cc_start: 0.8523 (tpt) cc_final: 0.8083 (tpp) REVERT: E 95 MET cc_start: 0.8918 (ppp) cc_final: 0.8507 (ppp) REVERT: E 473 MET cc_start: 0.7596 (tpp) cc_final: 0.7317 (tpp) REVERT: M 84 MET cc_start: 0.7777 (mpp) cc_final: 0.7500 (mpp) REVERT: M 95 MET cc_start: 0.8992 (ppp) cc_final: 0.8609 (ppp) REVERT: M 473 MET cc_start: 0.7532 (tpp) cc_final: 0.7307 (tpp) REVERT: O 89 MET cc_start: 0.8744 (tpp) cc_final: 0.8475 (tpp) outliers start: 0 outliers final: 0 residues processed: 73 average time/residue: 0.1603 time to fit residues: 19.2517 Evaluate side-chains 58 residues out of total 2601 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 58 time to evaluate : 0.895 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 174 optimal weight: 30.0000 chunk 110 optimal weight: 0.6980 chunk 235 optimal weight: 10.0000 chunk 241 optimal weight: 8.9990 chunk 249 optimal weight: 8.9990 chunk 99 optimal weight: 5.9990 chunk 162 optimal weight: 2.9990 chunk 49 optimal weight: 5.9990 chunk 33 optimal weight: 5.9990 chunk 284 optimal weight: 10.0000 chunk 56 optimal weight: 1.9990 overall best weight: 3.5388 ------------------------------------------------------------------------------- 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 = 0.3029 r_free = 0.3029 target = 0.029291 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2794 r_free = 0.2794 target = 0.024714 restraints weight = 344587.853| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 22)----------------| | r_work = 0.2828 r_free = 0.2828 target = 0.025363 restraints weight = 187928.814| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.2850 r_free = 0.2850 target = 0.025810 restraints weight = 123260.841| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.2865 r_free = 0.2865 target = 0.026098 restraints weight = 91083.265| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.2876 r_free = 0.2876 target = 0.026304 restraints weight = 73610.643| |-----------------------------------------------------------------------------| r_work (final): 0.2866 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8303 moved from start: 0.1590 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 24528 Z= 0.160 Angle : 0.700 11.953 33384 Z= 0.342 Chirality : 0.047 0.362 3900 Planarity : 0.004 0.048 4155 Dihedral : 12.894 110.329 4368 Min Nonbonded Distance : 2.341 Molprobity Statistics. All-atom Clashscore : 5.65 Ramachandran Plot: Outliers : 0.10 % Allowed : 6.89 % Favored : 93.01 % Rotamer: Outliers : 0.08 % Allowed : 2.20 % Favored : 97.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.63 % Cis-general : 0.11 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.76 (0.16), residues: 2919 helix: 0.77 (0.28), residues: 384 sheet: -0.33 (0.17), residues: 921 loop : -0.89 (0.16), residues: 1614 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG M 192 TYR 0.026 0.001 TYR E 458 PHE 0.012 0.001 PHE D 71 TRP 0.011 0.001 TRP D 96 HIS 0.003 0.001 HIS H 198 Details of bonding type rmsd covalent geometry : bond 0.00335 (24462) covalent geometry : angle 0.66920 (33204) SS BOND : bond 0.00585 ( 18) SS BOND : angle 0.92522 ( 36) hydrogen bonds : bond 0.03614 ( 816) hydrogen bonds : angle 5.79211 ( 2286) link_ALPHA1-3 : bond 0.00888 ( 6) link_ALPHA1-3 : angle 3.37912 ( 18) link_ALPHA1-6 : bond 0.02243 ( 6) link_ALPHA1-6 : angle 3.22965 ( 18) link_BETA1-4 : bond 0.00386 ( 21) link_BETA1-4 : angle 2.66377 ( 63) link_NAG-ASN : bond 0.00690 ( 15) link_NAG-ASN : angle 3.66172 ( 45) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5838 Ramachandran restraints generated. 2919 Oldfield, 0 Emsley, 2919 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5838 Ramachandran restraints generated. 2919 Oldfield, 0 Emsley, 2919 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 76 residues out of total 2601 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 74 time to evaluate : 1.095 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: 0.9068 (ppp) cc_final: 0.8476 (ppp) REVERT: A 104 MET cc_start: 0.9359 (ppp) cc_final: 0.9110 (ppp) REVERT: A 396 MET cc_start: 0.6410 (mmt) cc_final: 0.6009 (mmt) REVERT: C 89 MET cc_start: 0.8624 (tpt) cc_final: 0.8219 (tpp) REVERT: E 95 MET cc_start: 0.8960 (ppp) cc_final: 0.8743 (ppp) REVERT: E 104 MET cc_start: 0.9345 (ppp) cc_final: 0.9078 (ppp) REVERT: E 473 MET cc_start: 0.7667 (tpp) cc_final: 0.7314 (tpp) REVERT: G 75 MET cc_start: 0.8234 (mpp) cc_final: 0.7978 (mpp) REVERT: G 89 MET cc_start: 0.8928 (tpp) cc_final: 0.8719 (tpp) REVERT: M 84 MET cc_start: 0.7744 (mpp) cc_final: 0.7511 (mpp) REVERT: M 95 MET cc_start: 0.9018 (ppp) cc_final: 0.8596 (ppp) REVERT: M 104 MET cc_start: 0.9353 (ppp) cc_final: 0.9046 (ppp) REVERT: M 473 MET cc_start: 0.7774 (tpp) cc_final: 0.7497 (tpp) REVERT: O 75 MET cc_start: 0.8677 (mtm) cc_final: 0.8320 (mpp) REVERT: O 89 MET cc_start: 0.8846 (tpp) cc_final: 0.8615 (tpp) outliers start: 2 outliers final: 0 residues processed: 76 average time/residue: 0.1662 time to fit residues: 21.1021 Evaluate side-chains 57 residues out of total 2601 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 57 time to evaluate : 0.947 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 133 optimal weight: 20.0000 chunk 117 optimal weight: 9.9990 chunk 78 optimal weight: 0.9990 chunk 82 optimal weight: 8.9990 chunk 75 optimal weight: 0.0980 chunk 181 optimal weight: 1.9990 chunk 229 optimal weight: 7.9990 chunk 98 optimal weight: 4.9990 chunk 171 optimal weight: 30.0000 chunk 179 optimal weight: 10.0000 chunk 272 optimal weight: 20.0000 overall best weight: 3.2188 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3017 r_free = 0.3017 target = 0.029082 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2784 r_free = 0.2784 target = 0.024552 restraints weight = 342723.870| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.2818 r_free = 0.2818 target = 0.025197 restraints weight = 186984.138| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.2840 r_free = 0.2840 target = 0.025633 restraints weight = 122921.577| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.2856 r_free = 0.2856 target = 0.025926 restraints weight = 90810.387| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.2865 r_free = 0.2865 target = 0.026113 restraints weight = 73112.621| |-----------------------------------------------------------------------------| r_work (final): 0.2857 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8318 moved from start: 0.1990 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 24528 Z= 0.150 Angle : 0.673 10.129 33384 Z= 0.327 Chirality : 0.046 0.352 3900 Planarity : 0.004 0.046 4155 Dihedral : 11.732 103.913 4368 Min Nonbonded Distance : 2.377 Molprobity Statistics. All-atom Clashscore : 6.30 Ramachandran Plot: Outliers : 0.10 % Allowed : 6.71 % Favored : 93.18 % Rotamer: Outliers : 0.00 % Allowed : 2.24 % Favored : 97.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.63 % Cis-general : 0.11 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.67 (0.16), residues: 2919 helix: 1.07 (0.28), residues: 387 sheet: -0.31 (0.17), residues: 930 loop : -0.87 (0.16), residues: 1602 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 192 TYR 0.011 0.001 TYR E 458 PHE 0.011 0.001 PHE D 71 TRP 0.016 0.001 TRP D 96 HIS 0.004 0.001 HIS C 100D Details of bonding type rmsd covalent geometry : bond 0.00316 (24462) covalent geometry : angle 0.64108 (33204) SS BOND : bond 0.00518 ( 18) SS BOND : angle 0.97583 ( 36) hydrogen bonds : bond 0.03209 ( 816) hydrogen bonds : angle 5.51602 ( 2286) link_ALPHA1-3 : bond 0.00818 ( 6) link_ALPHA1-3 : angle 3.74625 ( 18) link_ALPHA1-6 : bond 0.02470 ( 6) link_ALPHA1-6 : angle 3.83111 ( 18) link_BETA1-4 : bond 0.00411 ( 21) link_BETA1-4 : angle 2.47020 ( 63) link_NAG-ASN : bond 0.00668 ( 15) link_NAG-ASN : angle 3.46863 ( 45) *********************** 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 75 residues out of total 2601 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 75 time to evaluate : 0.713 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 95 MET cc_start: 0.9090 (ppp) cc_final: 0.8424 (ppp) REVERT: A 104 MET cc_start: 0.9320 (ppp) cc_final: 0.9029 (ppp) REVERT: A 396 MET cc_start: 0.6320 (mmt) cc_final: 0.5863 (mmt) REVERT: B 530 MET cc_start: 0.6952 (mmm) cc_final: 0.6624 (mmm) REVERT: B 626 MET cc_start: 0.7541 (tpp) cc_final: 0.7288 (tpp) REVERT: C 89 MET cc_start: 0.8624 (tpt) cc_final: 0.8307 (tpp) REVERT: E 95 MET cc_start: 0.8985 (ppp) cc_final: 0.8728 (ppp) REVERT: E 104 MET cc_start: 0.9289 (ppp) cc_final: 0.9030 (ppp) REVERT: E 473 MET cc_start: 0.7798 (tpp) cc_final: 0.7437 (tpp) REVERT: F 535 MET cc_start: 0.9131 (mpp) cc_final: 0.8835 (mpp) REVERT: M 84 MET cc_start: 0.7753 (mpp) cc_final: 0.7252 (mpp) REVERT: M 95 MET cc_start: 0.9053 (ppp) cc_final: 0.8637 (ppp) REVERT: M 104 MET cc_start: 0.9320 (ppp) cc_final: 0.9087 (ppp) REVERT: M 396 MET cc_start: 0.6857 (mmt) cc_final: 0.6476 (mmt) REVERT: M 473 MET cc_start: 0.7890 (tpp) cc_final: 0.7568 (tpp) REVERT: O 89 MET cc_start: 0.8913 (tpp) cc_final: 0.8642 (tpp) outliers start: 0 outliers final: 0 residues processed: 75 average time/residue: 0.1563 time to fit residues: 19.4298 Evaluate side-chains 56 residues out of total 2601 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 56 time to evaluate : 0.614 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 101 optimal weight: 20.0000 chunk 205 optimal weight: 9.9990 chunk 190 optimal weight: 10.0000 chunk 13 optimal weight: 8.9990 chunk 213 optimal weight: 4.9990 chunk 186 optimal weight: 10.0000 chunk 55 optimal weight: 7.9990 chunk 177 optimal weight: 2.9990 chunk 277 optimal weight: 6.9990 chunk 18 optimal weight: 9.9990 chunk 133 optimal weight: 20.0000 overall best weight: 6.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 80 ASN A 321AGLN C 95 ASN M 321AGLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2958 r_free = 0.2958 target = 0.027952 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2729 r_free = 0.2729 target = 0.023615 restraints weight = 349205.426| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.2761 r_free = 0.2761 target = 0.024221 restraints weight = 191731.969| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.2783 r_free = 0.2783 target = 0.024628 restraints weight = 126620.664| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.2797 r_free = 0.2797 target = 0.024901 restraints weight = 94478.195| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.2807 r_free = 0.2807 target = 0.025089 restraints weight = 76823.973| |-----------------------------------------------------------------------------| r_work (final): 0.2799 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8413 moved from start: 0.2823 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.044 24528 Z= 0.263 Angle : 0.804 10.645 33384 Z= 0.393 Chirality : 0.048 0.360 3900 Planarity : 0.005 0.047 4155 Dihedral : 11.595 95.698 4368 Min Nonbonded Distance : 2.338 Molprobity Statistics. All-atom Clashscore : 10.39 Ramachandran Plot: Outliers : 0.03 % Allowed : 8.19 % Favored : 91.78 % Rotamer: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.63 % Cis-general : 0.11 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.92 (0.16), residues: 2919 helix: 0.84 (0.27), residues: 387 sheet: -0.47 (0.17), residues: 900 loop : -1.04 (0.16), residues: 1632 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 192 TYR 0.019 0.002 TYR A 217 PHE 0.019 0.002 PHE P 71 TRP 0.041 0.002 TRP H 96 HIS 0.006 0.002 HIS P 198 Details of bonding type rmsd covalent geometry : bond 0.00555 (24462) covalent geometry : angle 0.77453 (33204) SS BOND : bond 0.00600 ( 18) SS BOND : angle 1.07941 ( 36) hydrogen bonds : bond 0.03953 ( 816) hydrogen bonds : angle 5.86167 ( 2286) link_ALPHA1-3 : bond 0.00516 ( 6) link_ALPHA1-3 : angle 3.58990 ( 18) link_ALPHA1-6 : bond 0.02659 ( 6) link_ALPHA1-6 : angle 4.27858 ( 18) link_BETA1-4 : bond 0.00399 ( 21) link_BETA1-4 : angle 2.57256 ( 63) link_NAG-ASN : bond 0.00758 ( 15) link_NAG-ASN : angle 3.77923 ( 45) *********************** 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 67 residues out of total 2601 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 67 time to evaluate : 0.907 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 95 MET cc_start: 0.9214 (ppp) cc_final: 0.8542 (ppp) REVERT: A 396 MET cc_start: 0.6648 (mmt) cc_final: 0.6203 (mmt) REVERT: B 530 MET cc_start: 0.7261 (mmm) cc_final: 0.6724 (mmm) REVERT: C 89 MET cc_start: 0.8782 (tpt) cc_final: 0.8455 (tpp) REVERT: E 473 MET cc_start: 0.7757 (tpp) cc_final: 0.7441 (tpp) REVERT: G 89 MET cc_start: 0.9259 (tpp) cc_final: 0.9028 (tpp) REVERT: M 95 MET cc_start: 0.9166 (ppp) cc_final: 0.8654 (ppp) REVERT: M 473 MET cc_start: 0.8008 (tpp) cc_final: 0.7751 (tpp) REVERT: N 535 MET cc_start: 0.9112 (mpp) cc_final: 0.8700 (mpp) REVERT: O 89 MET cc_start: 0.9047 (tpp) cc_final: 0.8615 (tpp) outliers start: 0 outliers final: 0 residues processed: 67 average time/residue: 0.1609 time to fit residues: 18.0086 Evaluate side-chains 55 residues out of total 2601 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 55 time to evaluate : 0.933 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 207 optimal weight: 8.9990 chunk 230 optimal weight: 6.9990 chunk 29 optimal weight: 2.9990 chunk 263 optimal weight: 9.9990 chunk 231 optimal weight: 1.9990 chunk 102 optimal weight: 20.0000 chunk 168 optimal weight: 4.9990 chunk 243 optimal weight: 9.9990 chunk 246 optimal weight: 10.0000 chunk 265 optimal weight: 6.9990 chunk 17 optimal weight: 0.1980 overall best weight: 3.4388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 321AGLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2977 r_free = 0.2977 target = 0.028293 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2747 r_free = 0.2747 target = 0.023894 restraints weight = 347752.513| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.2779 r_free = 0.2779 target = 0.024512 restraints weight = 190819.980| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.2801 r_free = 0.2801 target = 0.024924 restraints weight = 126326.876| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.2815 r_free = 0.2815 target = 0.025201 restraints weight = 94294.109| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.2826 r_free = 0.2826 target = 0.025399 restraints weight = 76647.504| |-----------------------------------------------------------------------------| r_work (final): 0.2817 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8381 moved from start: 0.2917 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 24528 Z= 0.159 Angle : 0.696 11.425 33384 Z= 0.338 Chirality : 0.047 0.410 3900 Planarity : 0.004 0.046 4155 Dihedral : 10.819 84.017 4368 Min Nonbonded Distance : 2.361 Molprobity Statistics. All-atom Clashscore : 7.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.61 % Favored : 93.39 % Rotamer: Outliers : 0.00 % Allowed : 1.70 % Favored : 98.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.63 % Cis-general : 0.11 % Twisted Proline : 0.00 % Twisted General : 0.11 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.75 (0.16), residues: 2919 helix: 1.15 (0.28), residues: 387 sheet: -0.38 (0.17), residues: 942 loop : -0.96 (0.16), residues: 1590 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 192 TYR 0.021 0.001 TYR M 458 PHE 0.025 0.002 PHE N 519 TRP 0.022 0.002 TRP H 96 HIS 0.003 0.001 HIS O 100D Details of bonding type rmsd covalent geometry : bond 0.00332 (24462) covalent geometry : angle 0.66124 (33204) SS BOND : bond 0.00426 ( 18) SS BOND : angle 0.89410 ( 36) hydrogen bonds : bond 0.03371 ( 816) hydrogen bonds : angle 5.57793 ( 2286) link_ALPHA1-3 : bond 0.00766 ( 6) link_ALPHA1-3 : angle 3.58825 ( 18) link_ALPHA1-6 : bond 0.02287 ( 6) link_ALPHA1-6 : angle 4.57089 ( 18) link_BETA1-4 : bond 0.00426 ( 21) link_BETA1-4 : angle 2.37611 ( 63) link_NAG-ASN : bond 0.00685 ( 15) link_NAG-ASN : angle 3.85418 ( 45) *********************** 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 62 residues out of total 2601 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 62 time to evaluate : 0.910 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 95 MET cc_start: 0.9152 (ppp) cc_final: 0.8504 (ppp) REVERT: A 104 MET cc_start: 0.9354 (ppp) cc_final: 0.9128 (ppp) REVERT: B 530 MET cc_start: 0.7305 (mmm) cc_final: 0.6668 (mmm) REVERT: C 89 MET cc_start: 0.8817 (tpt) cc_final: 0.8561 (tpp) REVERT: E 104 MET cc_start: 0.9353 (ppp) cc_final: 0.9078 (ppp) REVERT: E 473 MET cc_start: 0.7718 (tpp) cc_final: 0.7356 (tpp) REVERT: G 89 MET cc_start: 0.9058 (tpp) cc_final: 0.8737 (tpp) REVERT: M 95 MET cc_start: 0.9125 (ppp) cc_final: 0.8636 (ppp) REVERT: M 104 MET cc_start: 0.9307 (ppp) cc_final: 0.9066 (ppp) REVERT: M 473 MET cc_start: 0.7964 (tpp) cc_final: 0.7681 (tpp) REVERT: N 535 MET cc_start: 0.9124 (mpp) cc_final: 0.8684 (mpp) REVERT: O 75 MET cc_start: 0.9266 (mmm) cc_final: 0.9046 (mpp) REVERT: O 89 MET cc_start: 0.9022 (tpp) cc_final: 0.8618 (tpp) outliers start: 0 outliers final: 0 residues processed: 62 average time/residue: 0.1687 time to fit residues: 17.0559 Evaluate side-chains 55 residues out of total 2601 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 55 time to evaluate : 0.870 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 230 optimal weight: 8.9990 chunk 223 optimal weight: 6.9990 chunk 125 optimal weight: 2.9990 chunk 177 optimal weight: 6.9990 chunk 254 optimal weight: 0.9980 chunk 203 optimal weight: 20.0000 chunk 152 optimal weight: 5.9990 chunk 33 optimal weight: 20.0000 chunk 263 optimal weight: 7.9990 chunk 186 optimal weight: 10.0000 chunk 91 optimal weight: 9.9990 overall best weight: 4.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 651 ASN N 651 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2951 r_free = 0.2951 target = 0.027804 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2722 r_free = 0.2722 target = 0.023478 restraints weight = 349858.881| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.2754 r_free = 0.2754 target = 0.024085 restraints weight = 191656.817| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.2776 r_free = 0.2776 target = 0.024496 restraints weight = 126808.603| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.2790 r_free = 0.2790 target = 0.024778 restraints weight = 94472.382| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.2800 r_free = 0.2800 target = 0.024961 restraints weight = 76482.389| |-----------------------------------------------------------------------------| r_work (final): 0.2792 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8418 moved from start: 0.3326 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 24528 Z= 0.202 Angle : 0.731 13.125 33384 Z= 0.354 Chirality : 0.048 0.432 3900 Planarity : 0.004 0.046 4155 Dihedral : 10.441 77.729 4368 Min Nonbonded Distance : 2.277 Molprobity Statistics. All-atom Clashscore : 8.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.22 % Favored : 91.78 % Rotamer: Outliers : 0.00 % Allowed : 1.54 % Favored : 98.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.63 % Cis-general : 0.11 % Twisted Proline : 0.00 % Twisted General : 0.11 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.87 (0.16), residues: 2919 helix: 1.06 (0.27), residues: 387 sheet: -0.51 (0.17), residues: 933 loop : -0.99 (0.16), residues: 1599 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 192 TYR 0.014 0.001 TYR M 458 PHE 0.015 0.002 PHE D 71 TRP 0.026 0.002 TRP H 96 HIS 0.003 0.001 HIS C 100D Details of bonding type rmsd covalent geometry : bond 0.00427 (24462) covalent geometry : angle 0.69722 (33204) SS BOND : bond 0.00620 ( 18) SS BOND : angle 0.92427 ( 36) hydrogen bonds : bond 0.03508 ( 816) hydrogen bonds : angle 5.63693 ( 2286) link_ALPHA1-3 : bond 0.00924 ( 6) link_ALPHA1-3 : angle 3.10618 ( 18) link_ALPHA1-6 : bond 0.01556 ( 6) link_ALPHA1-6 : angle 3.26946 ( 18) link_BETA1-4 : bond 0.00515 ( 21) link_BETA1-4 : angle 2.41950 ( 63) link_NAG-ASN : bond 0.00791 ( 15) link_NAG-ASN : angle 4.56922 ( 45) *********************** 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 66 residues out of total 2601 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 66 time to evaluate : 0.829 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 95 MET cc_start: 0.9182 (ppp) cc_final: 0.8605 (ppp) REVERT: A 104 MET cc_start: 0.9426 (ppp) cc_final: 0.9080 (ppp) REVERT: B 530 MET cc_start: 0.7524 (mmm) cc_final: 0.6790 (mmm) REVERT: B 626 MET cc_start: 0.6705 (tpt) cc_final: 0.6069 (tpp) REVERT: E 95 MET cc_start: 0.9011 (ppp) cc_final: 0.8570 (ppp) REVERT: E 104 MET cc_start: 0.9355 (ppp) cc_final: 0.9113 (ppp) REVERT: E 473 MET cc_start: 0.7766 (tpp) cc_final: 0.7422 (tpp) REVERT: F 530 MET cc_start: 0.7782 (mmm) cc_final: 0.7475 (mmm) REVERT: M 95 MET cc_start: 0.9136 (ppp) cc_final: 0.8616 (ppp) REVERT: M 104 MET cc_start: 0.9322 (ppp) cc_final: 0.9047 (ppp) REVERT: M 473 MET cc_start: 0.8001 (tpp) cc_final: 0.7699 (tpp) REVERT: N 535 MET cc_start: 0.9207 (mpp) cc_final: 0.8781 (mpp) REVERT: O 89 MET cc_start: 0.9070 (tpp) cc_final: 0.8641 (tpp) outliers start: 0 outliers final: 0 residues processed: 66 average time/residue: 0.1597 time to fit residues: 17.6136 Evaluate side-chains 58 residues out of total 2601 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 58 time to evaluate : 0.961 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 240 optimal weight: 1.9990 chunk 197 optimal weight: 5.9990 chunk 185 optimal weight: 8.9990 chunk 83 optimal weight: 5.9990 chunk 285 optimal weight: 9.9990 chunk 221 optimal weight: 7.9990 chunk 267 optimal weight: 3.9990 chunk 218 optimal weight: 7.9990 chunk 150 optimal weight: 6.9990 chunk 209 optimal weight: 8.9990 chunk 248 optimal weight: 6.9990 overall best weight: 4.9990 ------------------------------------------------------------------------------- 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 = 0.2942 r_free = 0.2942 target = 0.027596 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2714 r_free = 0.2714 target = 0.023292 restraints weight = 348396.114| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.2746 r_free = 0.2746 target = 0.023898 restraints weight = 191614.122| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.2767 r_free = 0.2767 target = 0.024298 restraints weight = 127012.964| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.2782 r_free = 0.2782 target = 0.024580 restraints weight = 94934.453| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.2792 r_free = 0.2792 target = 0.024766 restraints weight = 77130.963| |-----------------------------------------------------------------------------| r_work (final): 0.2784 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8428 moved from start: 0.3622 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 24528 Z= 0.197 Angle : 0.712 12.373 33384 Z= 0.349 Chirality : 0.047 0.414 3900 Planarity : 0.004 0.046 4155 Dihedral : 9.715 72.512 4368 Min Nonbonded Distance : 2.415 Molprobity Statistics. All-atom Clashscore : 9.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.16 % Favored : 92.84 % Rotamer: Outliers : 0.00 % Allowed : 0.96 % Favored : 99.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.63 % Cis-general : 0.11 % Twisted Proline : 0.00 % Twisted General : 0.11 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.86 (0.16), residues: 2919 helix: 1.12 (0.27), residues: 384 sheet: -0.46 (0.17), residues: 903 loop : -1.03 (0.16), residues: 1632 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 192 TYR 0.023 0.001 TYR C 91 PHE 0.014 0.002 PHE P 71 TRP 0.020 0.002 TRP H 96 HIS 0.003 0.001 HIS P 198 Details of bonding type rmsd covalent geometry : bond 0.00418 (24462) covalent geometry : angle 0.67856 (33204) SS BOND : bond 0.00609 ( 18) SS BOND : angle 1.08713 ( 36) hydrogen bonds : bond 0.03452 ( 816) hydrogen bonds : angle 5.62455 ( 2286) link_ALPHA1-3 : bond 0.00495 ( 6) link_ALPHA1-3 : angle 3.61818 ( 18) link_ALPHA1-6 : bond 0.01669 ( 6) link_ALPHA1-6 : angle 3.05114 ( 18) link_BETA1-4 : bond 0.00426 ( 21) link_BETA1-4 : angle 2.44507 ( 63) link_NAG-ASN : bond 0.00457 ( 15) link_NAG-ASN : angle 4.26574 ( 45) *********************** 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 to be fit. rotamer outliers: 0 poor density : 64 time to evaluate : 0.941 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 95 MET cc_start: 0.9188 (ppp) cc_final: 0.8589 (ppp) REVERT: A 104 MET cc_start: 0.9388 (ppp) cc_final: 0.9113 (ppp) REVERT: B 530 MET cc_start: 0.7644 (mmm) cc_final: 0.7027 (mmm) REVERT: B 626 MET cc_start: 0.6538 (tpt) cc_final: 0.5963 (tpp) REVERT: E 104 MET cc_start: 0.9383 (ppp) cc_final: 0.9126 (ppp) REVERT: E 473 MET cc_start: 0.7781 (tpp) cc_final: 0.7412 (tpp) REVERT: G 89 MET cc_start: 0.9302 (tpp) cc_final: 0.9096 (tpp) REVERT: M 95 MET cc_start: 0.9149 (ppp) cc_final: 0.8617 (ppp) REVERT: M 396 MET cc_start: 0.6899 (mmt) cc_final: 0.6670 (mmt) REVERT: M 473 MET cc_start: 0.8059 (tpp) cc_final: 0.7719 (tpp) REVERT: O 89 MET cc_start: 0.9058 (tpp) cc_final: 0.8857 (tpp) outliers start: 0 outliers final: 0 residues processed: 64 average time/residue: 0.1652 time to fit residues: 17.5052 Evaluate side-chains 57 residues out of total 2601 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 57 time to evaluate : 0.755 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 263 optimal weight: 6.9990 chunk 153 optimal weight: 7.9990 chunk 183 optimal weight: 8.9990 chunk 71 optimal weight: 4.9990 chunk 81 optimal weight: 0.8980 chunk 270 optimal weight: 30.0000 chunk 244 optimal weight: 9.9990 chunk 226 optimal weight: 3.9990 chunk 108 optimal weight: 20.0000 chunk 15 optimal weight: 7.9990 chunk 149 optimal weight: 10.0000 overall best weight: 4.9788 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2930 r_free = 0.2930 target = 0.027355 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2698 r_free = 0.2698 target = 0.023040 restraints weight = 350044.166| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.2731 r_free = 0.2731 target = 0.023651 restraints weight = 192561.972| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 20)----------------| | r_work = 0.2753 r_free = 0.2753 target = 0.024048 restraints weight = 127289.883| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.2768 r_free = 0.2768 target = 0.024327 restraints weight = 95231.324| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.2778 r_free = 0.2778 target = 0.024515 restraints weight = 77441.160| |-----------------------------------------------------------------------------| r_work (final): 0.2770 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8440 moved from start: 0.3825 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 24528 Z= 0.200 Angle : 0.708 12.200 33384 Z= 0.346 Chirality : 0.047 0.404 3900 Planarity : 0.004 0.046 4155 Dihedral : 9.499 71.986 4368 Min Nonbonded Distance : 2.410 Molprobity Statistics. All-atom Clashscore : 9.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.50 % Favored : 91.50 % Rotamer: Outliers : 0.00 % Allowed : 0.58 % Favored : 99.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.63 % Cis-general : 0.11 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.91 (0.16), residues: 2919 helix: 1.11 (0.27), residues: 384 sheet: -0.45 (0.17), residues: 900 loop : -1.11 (0.16), residues: 1635 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG M 192 TYR 0.026 0.001 TYR C 91 PHE 0.014 0.002 PHE A 361 TRP 0.018 0.002 TRP H 96 HIS 0.003 0.001 HIS C 35 Details of bonding type rmsd covalent geometry : bond 0.00425 (24462) covalent geometry : angle 0.67776 (33204) SS BOND : bond 0.00557 ( 18) SS BOND : angle 1.02174 ( 36) hydrogen bonds : bond 0.03425 ( 816) hydrogen bonds : angle 5.61065 ( 2286) link_ALPHA1-3 : bond 0.00476 ( 6) link_ALPHA1-3 : angle 2.89530 ( 18) link_ALPHA1-6 : bond 0.01847 ( 6) link_ALPHA1-6 : angle 2.98999 ( 18) link_BETA1-4 : bond 0.00365 ( 21) link_BETA1-4 : angle 2.44222 ( 63) link_NAG-ASN : bond 0.00583 ( 15) link_NAG-ASN : angle 4.14524 ( 45) *********************** 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 66 residues out of total 2601 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 66 time to evaluate : 0.919 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 95 MET cc_start: 0.9163 (ppp) cc_final: 0.8582 (ppp) REVERT: A 104 MET cc_start: 0.9434 (ppp) cc_final: 0.9107 (ppp) REVERT: A 396 MET cc_start: 0.6833 (mmt) cc_final: 0.6549 (mmt) REVERT: B 530 MET cc_start: 0.7828 (mmm) cc_final: 0.7182 (mmm) REVERT: B 626 MET cc_start: 0.6550 (tpt) cc_final: 0.6024 (tpp) REVERT: E 95 MET cc_start: 0.9038 (ppp) cc_final: 0.8623 (ppp) REVERT: E 473 MET cc_start: 0.7901 (tpp) cc_final: 0.7495 (tpp) REVERT: F 530 MET cc_start: 0.7747 (mmm) cc_final: 0.7485 (mmm) REVERT: G 89 MET cc_start: 0.9156 (tpp) cc_final: 0.8879 (tpp) REVERT: M 95 MET cc_start: 0.9147 (ppp) cc_final: 0.8623 (ppp) REVERT: M 473 MET cc_start: 0.8111 (tpp) cc_final: 0.7757 (tpp) REVERT: O 89 MET cc_start: 0.9054 (tpp) cc_final: 0.8838 (tpp) outliers start: 0 outliers final: 0 residues processed: 66 average time/residue: 0.1645 time to fit residues: 17.9038 Evaluate side-chains 55 residues out of total 2601 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 55 time to evaluate : 0.958 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 174 optimal weight: 9.9990 chunk 248 optimal weight: 3.9990 chunk 126 optimal weight: 8.9990 chunk 63 optimal weight: 4.9990 chunk 25 optimal weight: 20.0000 chunk 189 optimal weight: 0.7980 chunk 270 optimal weight: 20.0000 chunk 275 optimal weight: 10.0000 chunk 249 optimal weight: 5.9990 chunk 117 optimal weight: 10.0000 chunk 41 optimal weight: 9.9990 overall best weight: 4.9588 ------------------------------------------------------------------------------- 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 = 0.2926 r_free = 0.2926 target = 0.027266 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2696 r_free = 0.2696 target = 0.022975 restraints weight = 351942.502| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.2729 r_free = 0.2729 target = 0.023583 restraints weight = 192938.197| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 20)----------------| | r_work = 0.2751 r_free = 0.2751 target = 0.023987 restraints weight = 127429.243| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.2765 r_free = 0.2765 target = 0.024263 restraints weight = 95037.911| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.2775 r_free = 0.2775 target = 0.024436 restraints weight = 77272.561| |-----------------------------------------------------------------------------| r_work (final): 0.2767 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8444 moved from start: 0.4043 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 24528 Z= 0.200 Angle : 0.710 12.076 33384 Z= 0.348 Chirality : 0.047 0.426 3900 Planarity : 0.004 0.048 4155 Dihedral : 9.067 67.189 4368 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 9.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.78 % Favored : 92.22 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.98 (0.16), residues: 2919 helix: 1.09 (0.27), residues: 384 sheet: -0.54 (0.17), residues: 912 loop : -1.12 (0.16), residues: 1623 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG M 192 TYR 0.016 0.001 TYR C 91 PHE 0.014 0.002 PHE E 361 TRP 0.016 0.002 TRP H 96 HIS 0.003 0.001 HIS M 355 Details of bonding type rmsd covalent geometry : bond 0.00425 (24462) covalent geometry : angle 0.67917 (33204) SS BOND : bond 0.00547 ( 18) SS BOND : angle 1.06950 ( 36) hydrogen bonds : bond 0.03436 ( 816) hydrogen bonds : angle 5.63625 ( 2286) link_ALPHA1-3 : bond 0.00416 ( 6) link_ALPHA1-3 : angle 3.45891 ( 18) link_ALPHA1-6 : bond 0.01897 ( 6) link_ALPHA1-6 : angle 2.92866 ( 18) link_BETA1-4 : bond 0.00364 ( 21) link_BETA1-4 : angle 2.39544 ( 63) link_NAG-ASN : bond 0.00546 ( 15) link_NAG-ASN : angle 4.09154 ( 45) ********************** 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 63 residues out of total 2601 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 63 time to evaluate : 0.981 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: 0.9168 (ppp) cc_final: 0.8591 (ppp) REVERT: B 530 MET cc_start: 0.8006 (mmm) cc_final: 0.7363 (mmm) REVERT: B 626 MET cc_start: 0.6481 (tpt) cc_final: 0.6239 (tpp) REVERT: C 89 MET cc_start: 0.8911 (tpp) cc_final: 0.8554 (tpp) REVERT: E 95 MET cc_start: 0.9030 (ppp) cc_final: 0.8625 (ppp) REVERT: E 104 MET cc_start: 0.9336 (ppp) cc_final: 0.9099 (ppp) REVERT: E 473 MET cc_start: 0.7945 (tpp) cc_final: 0.7527 (tpp) REVERT: F 530 MET cc_start: 0.7812 (mmm) cc_final: 0.7543 (mmm) REVERT: G 89 MET cc_start: 0.9200 (tpp) cc_final: 0.8786 (tpp) REVERT: M 95 MET cc_start: 0.9144 (ppp) cc_final: 0.8596 (ppp) REVERT: M 396 MET cc_start: 0.6959 (mmt) cc_final: 0.6742 (mmt) REVERT: M 473 MET cc_start: 0.8132 (tpp) cc_final: 0.7763 (tpp) outliers start: 0 outliers final: 0 residues processed: 63 average time/residue: 0.1681 time to fit residues: 17.6427 Evaluate side-chains 54 residues out of total 2601 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 54 time to evaluate : 0.906 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 172 optimal weight: 0.9990 chunk 93 optimal weight: 20.0000 chunk 3 optimal weight: 20.0000 chunk 168 optimal weight: 0.6980 chunk 164 optimal weight: 9.9990 chunk 72 optimal weight: 20.0000 chunk 154 optimal weight: 2.9990 chunk 181 optimal weight: 1.9990 chunk 237 optimal weight: 0.3980 chunk 235 optimal weight: 1.9990 chunk 283 optimal weight: 9.9990 overall best weight: 1.2186 ------------------------------------------------------------------------------- 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 = 0.2963 r_free = 0.2963 target = 0.027913 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2733 r_free = 0.2733 target = 0.023519 restraints weight = 342257.903| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.2766 r_free = 0.2766 target = 0.024148 restraints weight = 185709.263| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.2788 r_free = 0.2788 target = 0.024566 restraints weight = 122269.566| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.2803 r_free = 0.2803 target = 0.024851 restraints weight = 90795.902| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.2813 r_free = 0.2813 target = 0.025043 restraints weight = 73470.353| |-----------------------------------------------------------------------------| r_work (final): 0.2805 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8380 moved from start: 0.4001 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 24528 Z= 0.108 Angle : 0.645 11.448 33384 Z= 0.312 Chirality : 0.047 0.421 3900 Planarity : 0.004 0.044 4155 Dihedral : 8.201 64.127 4368 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 6.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.10 % Favored : 93.90 % Rotamer: Outliers : 0.00 % Allowed : 0.31 % Favored : 99.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.63 % Cis-general : 0.11 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.59 (0.16), residues: 2919 helix: 1.23 (0.28), residues: 402 sheet: -0.19 (0.18), residues: 897 loop : -0.91 (0.16), residues: 1620 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG H 108 TYR 0.021 0.001 TYR O 91 PHE 0.010 0.001 PHE P 87 TRP 0.015 0.001 TRP D 148 HIS 0.003 0.001 HIS C 100D Details of bonding type rmsd covalent geometry : bond 0.00221 (24462) covalent geometry : angle 0.61348 (33204) SS BOND : bond 0.00342 ( 18) SS BOND : angle 0.89963 ( 36) hydrogen bonds : bond 0.02975 ( 816) hydrogen bonds : angle 5.17134 ( 2286) link_ALPHA1-3 : bond 0.00592 ( 6) link_ALPHA1-3 : angle 3.55389 ( 18) link_ALPHA1-6 : bond 0.02181 ( 6) link_ALPHA1-6 : angle 3.10037 ( 18) link_BETA1-4 : bond 0.00564 ( 21) link_BETA1-4 : angle 2.17485 ( 63) link_NAG-ASN : bond 0.00716 ( 15) link_NAG-ASN : angle 3.85613 ( 45) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2711.30 seconds wall clock time: 48 minutes 36.81 seconds (2916.81 seconds total)