Starting phenix.real_space_refine on Sat Jun 21 02:02:04 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7tco_25815/06_2025/7tco_25815.cif Found real_map, /net/cci-nas-00/data/ceres_data/7tco_25815/06_2025/7tco_25815.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.19 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7tco_25815/06_2025/7tco_25815.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7tco_25815/06_2025/7tco_25815.map" model { file = "/net/cci-nas-00/data/ceres_data/7tco_25815/06_2025/7tco_25815.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7tco_25815/06_2025/7tco_25815.cif" } resolution = 4.19 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.009 sd= 0.145 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 141 5.16 5 C 15030 2.51 5 N 4068 2.21 5 O 4734 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 15 residue(s): 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 23973 Number of models: 1 Model: "" Number of chains: 27 Chain: "A" Number of atoms: 3465 Number of conformers: 1 Conformer: "" Number of residues, atoms: 440, 3465 Classifications: {'peptide': 440} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 20, 'TRANS': 418} Chain breaks: 4 Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'TRP:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "B" Number of atoms: 969 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 969 Classifications: {'peptide': 122} Link IDs: {'CIS': 1, 'PTRANS': 1, 'TRANS': 119} Chain breaks: 1 Chain: "C" Number of atoms: 1677 Number of conformers: 1 Conformer: "" Number of residues, atoms: 220, 1677 Classifications: {'peptide': 220} Link IDs: {'PCIS': 2, 'PTRANS': 11, 'TRANS': 206} Chain breaks: 1 Chain: "D" Number of atoms: 1635 Number of conformers: 1 Conformer: "" Number of residues, atoms: 211, 1635 Classifications: {'peptide': 211} Link IDs: {'PCIS': 2, 'PTRANS': 7, 'TRANS': 201} Chain: "E" Number of atoms: 3465 Number of conformers: 1 Conformer: "" Number of residues, atoms: 440, 3465 Classifications: {'peptide': 440} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 20, 'TRANS': 418} Chain breaks: 4 Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'TRP:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "F" Number of atoms: 969 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 969 Classifications: {'peptide': 122} Link IDs: {'CIS': 1, 'PTRANS': 1, 'TRANS': 119} Chain breaks: 1 Chain: "G" Number of atoms: 1677 Number of conformers: 1 Conformer: "" Number of residues, atoms: 220, 1677 Classifications: {'peptide': 220} Link IDs: {'PCIS': 2, 'PTRANS': 11, 'TRANS': 206} Chain breaks: 1 Chain: "H" Number of atoms: 1635 Number of conformers: 1 Conformer: "" Number of residues, atoms: 211, 1635 Classifications: {'peptide': 211} Link IDs: {'PCIS': 2, 'PTRANS': 7, 'TRANS': 201} Chain: "M" Number of atoms: 3465 Number of conformers: 1 Conformer: "" Number of residues, atoms: 440, 3465 Classifications: {'peptide': 440} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 20, 'TRANS': 418} Chain breaks: 4 Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'TRP:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "N" Number of atoms: 969 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 969 Classifications: {'peptide': 122} Link IDs: {'CIS': 1, 'PTRANS': 1, 'TRANS': 119} Chain breaks: 1 Chain: "O" Number of atoms: 1677 Number of conformers: 1 Conformer: "" Number of residues, atoms: 220, 1677 Classifications: {'peptide': 220} Link IDs: {'PCIS': 2, 'PTRANS': 11, 'TRANS': 206} Chain breaks: 1 Chain: "P" Number of atoms: 1635 Number of conformers: 1 Conformer: "" Number of residues, atoms: 211, 1635 Classifications: {'peptide': 211} Link IDs: {'PCIS': 2, 'PTRANS': 7, 'TRANS': 201} Chain: "I" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "K" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 72 Unusual residues: {'BMA': 1, 'MAN': 3, 'NAG': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "L" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "Q" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "R" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "S" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 72 Unusual residues: {'BMA': 1, 'MAN': 3, 'NAG': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "T" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "V" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "W" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "X" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 72 Unusual residues: {'BMA': 1, 'MAN': 3, 'NAG': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "Y" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "A" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'NAG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "E" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'NAG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "M" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'NAG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Time building chain proxies: 14.67, per 1000 atoms: 0.61 Number of scatterers: 23973 At special positions: 0 Unit cell: (172.8, 185.76, 117.72, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 141 16.00 O 4734 8.00 N 4068 7.00 C 15030 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=18, symmetry=0 Simple disulfide: pdb=" SG CYS A 126 " - pdb=" SG CYS A 196 " distance=2.02 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 157 " distance=2.03 Simple disulfide: pdb=" SG CYS A 228 " - pdb=" SG CYS A 239 " distance=2.03 Simple disulfide: pdb=" SG CYS A 378 " - pdb=" SG CYS A 445 " distance=2.03 Simple disulfide: pdb=" SG CYS B 598 " - pdb=" SG CYS B 604 " distance=2.02 Simple disulfide: pdb=" SG CYS D 23 " - pdb=" SG CYS D 88 " distance=2.04 Simple disulfide: pdb=" SG CYS E 126 " - pdb=" SG CYS E 196 " distance=2.02 Simple disulfide: pdb=" SG CYS E 131 " - pdb=" SG CYS E 157 " distance=2.03 Simple disulfide: pdb=" SG CYS E 228 " - pdb=" SG CYS E 239 " distance=2.03 Simple disulfide: pdb=" SG CYS E 378 " - pdb=" SG CYS E 445 " distance=2.03 Simple disulfide: pdb=" SG CYS F 598 " - pdb=" SG CYS F 604 " distance=2.02 Simple disulfide: pdb=" SG CYS H 23 " - pdb=" SG CYS H 88 " distance=2.04 Simple disulfide: pdb=" SG CYS M 126 " - pdb=" SG CYS M 196 " distance=2.03 Simple disulfide: pdb=" SG CYS M 131 " - pdb=" SG CYS M 157 " distance=2.03 Simple disulfide: pdb=" SG CYS M 228 " - pdb=" SG CYS M 239 " distance=2.03 Simple disulfide: pdb=" SG CYS M 378 " - pdb=" SG CYS M 445 " distance=2.03 Simple disulfide: pdb=" SG CYS N 598 " - pdb=" SG CYS N 604 " distance=2.02 Simple disulfide: pdb=" SG CYS P 23 " - pdb=" SG CYS P 88 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied ALPHA1-3 " BMA K 3 " - " MAN K 6 " " BMA L 3 " - " MAN L 4 " " BMA S 3 " - " MAN S 6 " " BMA T 3 " - " MAN T 4 " " BMA X 3 " - " MAN X 6 " " BMA Y 3 " - " MAN Y 4 " ALPHA1-6 " BMA K 3 " - " MAN K 4 " " MAN K 4 " - " MAN K 5 " " BMA S 3 " - " MAN S 4 " " MAN S 4 " - " MAN S 5 " " BMA X 3 " - " MAN X 4 " " MAN X 4 " - " MAN X 5 " BETA1-4 " NAG I 1 " - " NAG I 2 " " NAG I 2 " - " BMA I 3 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG K 2 " - " BMA K 3 " " NAG L 1 " - " NAG L 2 " " NAG L 2 " - " BMA L 3 " " NAG Q 1 " - " NAG Q 2 " " NAG Q 2 " - " BMA Q 3 " " NAG R 1 " - " NAG R 2 " " NAG S 1 " - " NAG S 2 " " NAG S 2 " - " BMA S 3 " " NAG T 1 " - " NAG T 2 " " NAG T 2 " - " BMA T 3 " " NAG V 1 " - " NAG V 2 " " NAG V 2 " - " BMA V 3 " " NAG W 1 " - " NAG W 2 " " NAG X 1 " - " NAG X 2 " " NAG X 2 " - " BMA X 3 " " NAG Y 1 " - " NAG Y 2 " " NAG Y 2 " - " BMA Y 3 " NAG-ASN " NAG A 602 " - " ASN A 392 " " NAG A 604 " - " ASN A 230 " " NAG E 602 " - " ASN E 392 " " NAG E 604 " - " ASN E 230 " " NAG J 1 " - " ASN A 339 " " NAG K 1 " - " ASN A 197 " " NAG L 1 " - " ASN A 262 " " NAG M 602 " - " ASN M 392 " " NAG M 604 " - " ASN M 230 " " NAG R 1 " - " ASN E 339 " " NAG S 1 " - " ASN E 197 " " NAG T 1 " - " ASN E 262 " " NAG W 1 " - " ASN M 339 " " NAG X 1 " - " ASN M 197 " " NAG Y 1 " - " ASN M 262 " Time building additional restraints: 6.68 Conformation dependent library (CDL) restraints added in 3.0 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: 4.24 Creating SS restraints... Processing helix chain 'A' and resid 99 through 117 Processing helix chain 'A' and resid 122 through 127 removed outlier: 4.041A pdb=" N VAL A 127 " --> pdb=" O PRO A 124 " (cutoff:3.500A) Processing helix chain 'A' and resid 205 through 209 removed outlier: 3.511A pdb=" N VAL A 208 " --> pdb=" O CYS A 205 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N SER A 209 " --> pdb=" O PRO A 206 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 205 through 209' Processing helix chain 'A' and resid 335 through 350 Processing helix chain 'A' and resid 368 through 373 Processing helix chain 'A' and resid 473 through 479 removed outlier: 3.672A pdb=" N TRP A 477 " --> pdb=" O MET A 473 " (cutoff:3.500A) Processing helix chain 'B' and resid 529 through 535 removed outlier: 3.976A pdb=" N MET B 535 " --> pdb=" O GLY B 531 " (cutoff:3.500A) Processing helix chain 'B' and resid 536 through 543 removed outlier: 4.092A pdb=" N GLN B 540 " --> pdb=" O THR B 536 " (cutoff:3.500A) removed outlier: 4.156A pdb=" N ASN B 543 " --> pdb=" O VAL B 539 " (cutoff:3.500A) Processing helix chain 'B' and resid 576 through 597 removed outlier: 3.773A pdb=" N VAL B 580 " --> pdb=" O LEU B 576 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N TYR B 586 " --> pdb=" O ALA B 582 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N LEU B 587 " --> pdb=" O VAL B 583 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N LEU B 592 " --> pdb=" O ARG B 588 " (cutoff:3.500A) Processing helix chain 'B' and resid 611 through 615 Processing helix chain 'B' and resid 621 through 625 Processing helix chain 'B' and resid 628 through 636 Processing helix chain 'B' and resid 638 through 663 removed outlier: 3.944A pdb=" N TYR B 643 " --> pdb=" O THR B 639 " (cutoff:3.500A) removed outlier: 4.911A pdb=" N GLY B 644 " --> pdb=" O GLN B 640 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N LEU B 645 " --> pdb=" O ILE B 641 " (cutoff:3.500A) Processing helix chain 'C' and resid 61 through 64 removed outlier: 4.143A pdb=" N ARG C 64 " --> pdb=" O GLY C 61 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 61 through 64' Processing helix chain 'C' and resid 83 through 87 removed outlier: 3.724A pdb=" N THR C 87 " --> pdb=" O TYR C 84 " (cutoff:3.500A) Processing helix chain 'C' and resid 187 through 190 Processing helix chain 'D' and resid 121 through 128 Processing helix chain 'D' and resid 182 through 188 removed outlier: 3.741A pdb=" N LYS D 188 " --> pdb=" O ALA D 184 " (cutoff:3.500A) Processing helix chain 'E' and resid 99 through 117 Processing helix chain 'E' and resid 122 through 127 removed outlier: 4.042A pdb=" N VAL E 127 " --> pdb=" O PRO E 124 " (cutoff:3.500A) Processing helix chain 'E' and resid 205 through 209 removed outlier: 3.759A pdb=" N SER E 209 " --> pdb=" O PRO E 206 " (cutoff:3.500A) Processing helix chain 'E' and resid 335 through 350 Processing helix chain 'E' and resid 368 through 373 Processing helix chain 'E' and resid 473 through 479 removed outlier: 3.653A pdb=" N TRP E 477 " --> pdb=" O MET E 473 " (cutoff:3.500A) Processing helix chain 'F' and resid 529 through 535 removed outlier: 3.981A pdb=" N MET F 535 " --> pdb=" O GLY F 531 " (cutoff:3.500A) Processing helix chain 'F' and resid 536 through 543 removed outlier: 4.094A pdb=" N GLN F 540 " --> pdb=" O THR F 536 " (cutoff:3.500A) removed outlier: 4.157A pdb=" N ASN F 543 " --> pdb=" O VAL F 539 " (cutoff:3.500A) Processing helix chain 'F' and resid 576 through 597 removed outlier: 3.775A pdb=" N VAL F 580 " --> pdb=" O LEU F 576 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N TYR F 586 " --> pdb=" O ALA F 582 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N LEU F 587 " --> pdb=" O VAL F 583 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N LEU F 592 " --> pdb=" O ARG F 588 " (cutoff:3.500A) Processing helix chain 'F' and resid 611 through 615 Processing helix chain 'F' and resid 621 through 625 Processing helix chain 'F' and resid 628 through 636 Processing helix chain 'F' and resid 638 through 663 removed outlier: 3.935A pdb=" N TYR F 643 " --> pdb=" O THR F 639 " (cutoff:3.500A) removed outlier: 4.910A pdb=" N GLY F 644 " --> pdb=" O GLN F 640 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N LEU F 645 " --> pdb=" O ILE F 641 " (cutoff:3.500A) Processing helix chain 'G' and resid 61 through 64 removed outlier: 4.148A pdb=" N ARG G 64 " --> pdb=" O GLY G 61 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 61 through 64' Processing helix chain 'G' and resid 83 through 87 removed outlier: 3.741A pdb=" N THR G 87 " --> pdb=" O TYR G 84 " (cutoff:3.500A) Processing helix chain 'G' and resid 187 through 190 Processing helix chain 'H' and resid 121 through 128 Processing helix chain 'H' and resid 182 through 188 removed outlier: 3.832A pdb=" N LYS H 188 " --> pdb=" O ALA H 184 " (cutoff:3.500A) Processing helix chain 'M' and resid 99 through 117 Processing helix chain 'M' and resid 122 through 127 removed outlier: 3.530A pdb=" N LEU M 125 " --> pdb=" O LEU M 122 " (cutoff:3.500A) removed outlier: 4.089A pdb=" N VAL M 127 " --> pdb=" O PRO M 124 " (cutoff:3.500A) Processing helix chain 'M' and resid 205 through 209 removed outlier: 3.507A pdb=" N VAL M 208 " --> pdb=" O CYS M 205 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N SER M 209 " --> pdb=" O PRO M 206 " (cutoff:3.500A) No H-bonds generated for 'chain 'M' and resid 205 through 209' Processing helix chain 'M' and resid 335 through 350 Processing helix chain 'M' and resid 368 through 373 Processing helix chain 'M' and resid 473 through 479 removed outlier: 3.672A pdb=" N TRP M 477 " --> pdb=" O MET M 473 " (cutoff:3.500A) Processing helix chain 'N' and resid 529 through 535 removed outlier: 3.520A pdb=" N ALA N 533 " --> pdb=" O THR N 529 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N MET N 535 " --> pdb=" O GLY N 531 " (cutoff:3.500A) Processing helix chain 'N' and resid 536 through 543 removed outlier: 4.093A pdb=" N GLN N 540 " --> pdb=" O THR N 536 " (cutoff:3.500A) removed outlier: 4.152A pdb=" N ASN N 543 " --> pdb=" O VAL N 539 " (cutoff:3.500A) Processing helix chain 'N' and resid 576 through 597 removed outlier: 3.781A pdb=" N VAL N 580 " --> pdb=" O LEU N 576 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N TYR N 586 " --> pdb=" O ALA N 582 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N LEU N 592 " --> pdb=" O ARG N 588 " (cutoff:3.500A) Processing helix chain 'N' and resid 611 through 615 Processing helix chain 'N' and resid 621 through 625 Processing helix chain 'N' and resid 628 through 636 Processing helix chain 'N' and resid 638 through 663 removed outlier: 3.939A pdb=" N TYR N 643 " --> pdb=" O THR N 639 " (cutoff:3.500A) removed outlier: 4.910A pdb=" N GLY N 644 " --> pdb=" O GLN N 640 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N LEU N 645 " --> pdb=" O ILE N 641 " (cutoff:3.500A) Processing helix chain 'O' and resid 61 through 64 removed outlier: 4.143A pdb=" N ARG O 64 " --> pdb=" O GLY O 61 " (cutoff:3.500A) No H-bonds generated for 'chain 'O' and resid 61 through 64' Processing helix chain 'O' and resid 83 through 87 removed outlier: 3.741A pdb=" N THR O 87 " --> pdb=" O TYR O 84 " (cutoff:3.500A) Processing helix chain 'O' and resid 187 through 190 Processing helix chain 'P' and resid 121 through 128 Processing helix chain 'P' and resid 182 through 188 removed outlier: 3.729A pdb=" N LYS P 188 " --> pdb=" O ALA P 184 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 494 through 497 removed outlier: 5.631A pdb=" N VAL B 608 " --> pdb=" O VAL A 36 " (cutoff:3.500A) removed outlier: 8.216A pdb=" N VAL A 38 " --> pdb=" O THR B 606 " (cutoff:3.500A) removed outlier: 7.754A pdb=" N THR B 606 " --> pdb=" O VAL A 38 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 45 through 47 removed outlier: 4.190A pdb=" N ILE A 225 " --> pdb=" O VAL A 245 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 53 through 54 Processing sheet with id=AA4, first strand: chain 'A' and resid 91 through 94 Processing sheet with id=AA5, first strand: chain 'A' and resid 129 through 130 Processing sheet with id=AA6, first strand: chain 'A' and resid 158 through 161 Processing sheet with id=AA7, first strand: chain 'A' and resid 201 through 203 removed outlier: 6.426A pdb=" N THR A 202 " --> pdb=" O TYR A 435 " (cutoff:3.500A) removed outlier: 7.197A pdb=" N ARG A 432 " --> pdb=" O MET A 426 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 259 through 261 removed outlier: 6.777A pdb=" N LEU A 260 " --> pdb=" O THR A 450 " (cutoff:3.500A) removed outlier: 10.163A pdb=" N THR A 444 " --> pdb=" O ILE A 294 " (cutoff:3.500A) removed outlier: 11.411A pdb=" N ILE A 294 " --> pdb=" O THR A 444 " (cutoff:3.500A) removed outlier: 9.886A pdb=" N ILE A 446 " --> pdb=" O VAL A 292 " (cutoff:3.500A) removed outlier: 10.864A pdb=" N VAL A 292 " --> pdb=" O ILE A 446 " (cutoff:3.500A) removed outlier: 9.502A pdb=" N ASN A 448 " --> pdb=" O GLU A 290 " (cutoff:3.500A) removed outlier: 10.009A pdb=" N GLU A 290 " --> pdb=" O ASN A 448 " (cutoff:3.500A) removed outlier: 6.995A pdb=" N THR A 450 " --> pdb=" O LEU A 288 " (cutoff:3.500A) removed outlier: 6.996A pdb=" N LYS A 293 " --> pdb=" O ASN A 334 " (cutoff:3.500A) removed outlier: 4.362A pdb=" N ASN A 334 " --> pdb=" O LYS A 293 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 271 through 273 removed outlier: 6.995A pdb=" N THR A 450 " --> pdb=" O LEU A 288 " (cutoff:3.500A) removed outlier: 10.009A pdb=" N GLU A 290 " --> pdb=" O ASN A 448 " (cutoff:3.500A) removed outlier: 9.502A pdb=" N ASN A 448 " --> pdb=" O GLU A 290 " (cutoff:3.500A) removed outlier: 10.864A pdb=" N VAL A 292 " --> pdb=" O ILE A 446 " (cutoff:3.500A) removed outlier: 9.886A pdb=" N ILE A 446 " --> pdb=" O VAL A 292 " (cutoff:3.500A) removed outlier: 11.411A pdb=" N ILE A 294 " --> pdb=" O THR A 444 " (cutoff:3.500A) removed outlier: 10.163A pdb=" N THR A 444 " --> pdb=" O ILE A 294 " (cutoff:3.500A) removed outlier: 5.755A pdb=" N ASN A 357 " --> pdb=" O GLU A 464 " (cutoff:3.500A) removed outlier: 7.268A pdb=" N PHE A 466 " --> pdb=" O ASN A 357 " (cutoff:3.500A) removed outlier: 6.026A pdb=" N THR A 359 " --> pdb=" O PHE A 466 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 301 through 308 removed outlier: 6.931A pdb=" N ASN A 301 " --> pdb=" O VAL A 322 " (cutoff:3.500A) removed outlier: 4.654A pdb=" N VAL A 322 " --> pdb=" O ASN A 301 " (cutoff:3.500A) removed outlier: 6.466A pdb=" N THR A 303 " --> pdb=" O GLY A 321 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 4 through 7 Processing sheet with id=AB3, first strand: chain 'C' and resid 10 through 12 removed outlier: 6.399A pdb=" N GLY C 10 " --> pdb=" O ILE C 110 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N TYR C 33 " --> pdb=" O ASN C 95 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N GLY C 49 " --> pdb=" O TRP C 36 " (cutoff:3.500A) removed outlier: 6.832A pdb=" N ARG C 38 " --> pdb=" O LEU C 47 " (cutoff:3.500A) removed outlier: 5.597A pdb=" N LEU C 47 " --> pdb=" O ARG C 38 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 10 through 12 removed outlier: 6.399A pdb=" N GLY C 10 " --> pdb=" O ILE C 110 " (cutoff:3.500A) removed outlier: 7.164A pdb=" N CYS C 92 " --> pdb=" O HIS C 102 " (cutoff:3.500A) removed outlier: 7.209A pdb=" N HIS C 102 " --> pdb=" O CYS C 92 " (cutoff:3.500A) removed outlier: 7.426A pdb=" N ARG C 94 " --> pdb=" O TYR C 100E" (cutoff:3.500A) removed outlier: 4.890A pdb=" N TYR C 100E" --> pdb=" O ARG C 94 " (cutoff:3.500A) removed outlier: 4.908A pdb=" N VAL C 96 " --> pdb=" O LEU C 100C" (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 120 through 124 removed outlier: 3.773A pdb=" N GLY C 139 " --> pdb=" O LEU C 124 " (cutoff:3.500A) removed outlier: 6.012A pdb=" N TYR C 176 " --> pdb=" O ASP C 144 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 120 through 124 removed outlier: 3.773A pdb=" N GLY C 139 " --> pdb=" O LEU C 124 " (cutoff:3.500A) removed outlier: 6.012A pdb=" N TYR C 176 " --> pdb=" O ASP C 144 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 151 through 154 Processing sheet with id=AB8, first strand: chain 'D' and resid 5 through 7 Processing sheet with id=AB9, first strand: chain 'D' and resid 10 through 13 removed outlier: 6.479A pdb=" N LEU D 11 " --> pdb=" O ASP D 105 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N VAL D 85 " --> pdb=" O HIS D 38 " (cutoff:3.500A) removed outlier: 6.829A pdb=" N VAL D 33 " --> pdb=" O TYR D 49 " (cutoff:3.500A) removed outlier: 4.843A pdb=" N TYR D 49 " --> pdb=" O VAL D 33 " (cutoff:3.500A) removed outlier: 6.552A pdb=" N TRP D 35 " --> pdb=" O LEU D 47 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'D' and resid 10 through 13 removed outlier: 6.479A pdb=" N LEU D 11 " --> pdb=" O ASP D 105 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N GLN D 90 " --> pdb=" O THR D 97 " (cutoff:3.500A) removed outlier: 4.136A pdb=" N THR D 97 " --> pdb=" O GLN D 90 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'D' and resid 114 through 118 removed outlier: 5.711A pdb=" N TYR D 173 " --> pdb=" O ASN D 138 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'D' and resid 153 through 155 removed outlier: 4.428A pdb=" N TRP D 148 " --> pdb=" O GLN D 155 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'E' and resid 494 through 497 removed outlier: 5.631A pdb=" N VAL F 608 " --> pdb=" O VAL E 36 " (cutoff:3.500A) removed outlier: 8.214A pdb=" N VAL E 38 " --> pdb=" O THR F 606 " (cutoff:3.500A) removed outlier: 7.757A pdb=" N THR F 606 " --> pdb=" O VAL E 38 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'E' and resid 45 through 47 removed outlier: 4.166A pdb=" N ILE E 225 " --> pdb=" O VAL E 245 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'E' and resid 53 through 54 Processing sheet with id=AC7, first strand: chain 'E' and resid 91 through 94 Processing sheet with id=AC8, first strand: chain 'E' and resid 129 through 130 Processing sheet with id=AC9, first strand: chain 'E' and resid 158 through 161 Processing sheet with id=AD1, first strand: chain 'E' and resid 201 through 203 removed outlier: 6.392A pdb=" N THR E 202 " --> pdb=" O TYR E 435 " (cutoff:3.500A) removed outlier: 7.164A pdb=" N ARG E 432 " --> pdb=" O MET E 426 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'E' and resid 259 through 261 removed outlier: 6.770A pdb=" N LEU E 260 " --> pdb=" O THR E 450 " (cutoff:3.500A) removed outlier: 10.161A pdb=" N THR E 444 " --> pdb=" O ILE E 294 " (cutoff:3.500A) removed outlier: 11.410A pdb=" N ILE E 294 " --> pdb=" O THR E 444 " (cutoff:3.500A) removed outlier: 9.887A pdb=" N ILE E 446 " --> pdb=" O VAL E 292 " (cutoff:3.500A) removed outlier: 10.866A pdb=" N VAL E 292 " --> pdb=" O ILE E 446 " (cutoff:3.500A) removed outlier: 9.506A pdb=" N ASN E 448 " --> pdb=" O GLU E 290 " (cutoff:3.500A) removed outlier: 10.005A pdb=" N GLU E 290 " --> pdb=" O ASN E 448 " (cutoff:3.500A) removed outlier: 6.992A pdb=" N THR E 450 " --> pdb=" O LEU E 288 " (cutoff:3.500A) removed outlier: 6.999A pdb=" N LYS E 293 " --> pdb=" O ASN E 334 " (cutoff:3.500A) removed outlier: 4.365A pdb=" N ASN E 334 " --> pdb=" O LYS E 293 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'E' and resid 271 through 273 removed outlier: 6.992A pdb=" N THR E 450 " --> pdb=" O LEU E 288 " (cutoff:3.500A) removed outlier: 10.005A pdb=" N GLU E 290 " --> pdb=" O ASN E 448 " (cutoff:3.500A) removed outlier: 9.506A pdb=" N ASN E 448 " --> pdb=" O GLU E 290 " (cutoff:3.500A) removed outlier: 10.866A pdb=" N VAL E 292 " --> pdb=" O ILE E 446 " (cutoff:3.500A) removed outlier: 9.887A pdb=" N ILE E 446 " --> pdb=" O VAL E 292 " (cutoff:3.500A) removed outlier: 11.410A pdb=" N ILE E 294 " --> pdb=" O THR E 444 " (cutoff:3.500A) removed outlier: 10.161A pdb=" N THR E 444 " --> pdb=" O ILE E 294 " (cutoff:3.500A) removed outlier: 5.745A pdb=" N ASN E 357 " --> pdb=" O GLU E 464 " (cutoff:3.500A) removed outlier: 7.258A pdb=" N PHE E 466 " --> pdb=" O ASN E 357 " (cutoff:3.500A) removed outlier: 6.034A pdb=" N THR E 359 " --> pdb=" O PHE E 466 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'E' and resid 301 through 308 removed outlier: 6.934A pdb=" N ASN E 301 " --> pdb=" O VAL E 322 " (cutoff:3.500A) removed outlier: 4.656A pdb=" N VAL E 322 " --> pdb=" O ASN E 301 " (cutoff:3.500A) removed outlier: 6.470A pdb=" N THR E 303 " --> pdb=" O GLY E 321 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'G' and resid 4 through 7 Processing sheet with id=AD6, first strand: chain 'G' and resid 10 through 12 removed outlier: 6.421A pdb=" N GLY G 10 " --> pdb=" O ILE G 110 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N TYR G 33 " --> pdb=" O ASN G 95 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N GLY G 49 " --> pdb=" O TRP G 36 " (cutoff:3.500A) removed outlier: 6.820A pdb=" N ARG G 38 " --> pdb=" O LEU G 47 " (cutoff:3.500A) removed outlier: 5.600A pdb=" N LEU G 47 " --> pdb=" O ARG G 38 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'G' and resid 10 through 12 removed outlier: 6.421A pdb=" N GLY G 10 " --> pdb=" O ILE G 110 " (cutoff:3.500A) removed outlier: 7.152A pdb=" N CYS G 92 " --> pdb=" O HIS G 102 " (cutoff:3.500A) removed outlier: 7.199A pdb=" N HIS G 102 " --> pdb=" O CYS G 92 " (cutoff:3.500A) removed outlier: 7.417A pdb=" N ARG G 94 " --> pdb=" O TYR G 100E" (cutoff:3.500A) removed outlier: 4.888A pdb=" N TYR G 100E" --> pdb=" O ARG G 94 " (cutoff:3.500A) removed outlier: 4.911A pdb=" N VAL G 96 " --> pdb=" O LEU G 100C" (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'G' and resid 120 through 124 removed outlier: 3.771A pdb=" N GLY G 139 " --> pdb=" O LEU G 124 " (cutoff:3.500A) removed outlier: 6.008A pdb=" N TYR G 176 " --> pdb=" O ASP G 144 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'G' and resid 120 through 124 removed outlier: 3.771A pdb=" N GLY G 139 " --> pdb=" O LEU G 124 " (cutoff:3.500A) removed outlier: 6.008A pdb=" N TYR G 176 " --> pdb=" O ASP G 144 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'G' and resid 151 through 154 Processing sheet with id=AE2, first strand: chain 'H' and resid 5 through 7 Processing sheet with id=AE3, first strand: chain 'H' and resid 10 through 13 removed outlier: 6.425A pdb=" N LEU H 11 " --> pdb=" O ASP H 105 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N VAL H 85 " --> pdb=" O HIS H 38 " (cutoff:3.500A) removed outlier: 6.827A pdb=" N VAL H 33 " --> pdb=" O TYR H 49 " (cutoff:3.500A) removed outlier: 4.839A pdb=" N TYR H 49 " --> pdb=" O VAL H 33 " (cutoff:3.500A) removed outlier: 6.551A pdb=" N TRP H 35 " --> pdb=" O LEU H 47 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'H' and resid 10 through 13 removed outlier: 6.425A pdb=" N LEU H 11 " --> pdb=" O ASP H 105 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N GLN H 90 " --> pdb=" O THR H 97 " (cutoff:3.500A) removed outlier: 4.139A pdb=" N THR H 97 " --> pdb=" O GLN H 90 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'H' and resid 114 through 118 removed outlier: 5.712A pdb=" N TYR H 173 " --> pdb=" O ASN H 138 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'H' and resid 153 through 155 removed outlier: 4.425A pdb=" N TRP H 148 " --> pdb=" O GLN H 155 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'M' and resid 494 through 497 removed outlier: 5.632A pdb=" N VAL N 608 " --> pdb=" O VAL M 36 " (cutoff:3.500A) removed outlier: 8.219A pdb=" N VAL M 38 " --> pdb=" O THR N 606 " (cutoff:3.500A) removed outlier: 7.757A pdb=" N THR N 606 " --> pdb=" O VAL M 38 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'M' and resid 45 through 47 removed outlier: 4.200A pdb=" N ILE M 225 " --> pdb=" O VAL M 245 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'M' and resid 53 through 54 Processing sheet with id=AF1, first strand: chain 'M' and resid 91 through 94 Processing sheet with id=AF2, first strand: chain 'M' and resid 129 through 130 Processing sheet with id=AF3, first strand: chain 'M' and resid 158 through 161 Processing sheet with id=AF4, first strand: chain 'M' and resid 201 through 203 removed outlier: 6.434A pdb=" N THR M 202 " --> pdb=" O TYR M 435 " (cutoff:3.500A) removed outlier: 7.199A pdb=" N ARG M 432 " --> pdb=" O MET M 426 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'M' and resid 259 through 261 removed outlier: 6.774A pdb=" N LEU M 260 " --> pdb=" O THR M 450 " (cutoff:3.500A) removed outlier: 10.158A pdb=" N THR M 444 " --> pdb=" O ILE M 294 " (cutoff:3.500A) removed outlier: 11.408A pdb=" N ILE M 294 " --> pdb=" O THR M 444 " (cutoff:3.500A) removed outlier: 9.877A pdb=" N ILE M 446 " --> pdb=" O VAL M 292 " (cutoff:3.500A) removed outlier: 10.854A pdb=" N VAL M 292 " --> pdb=" O ILE M 446 " (cutoff:3.500A) removed outlier: 9.509A pdb=" N ASN M 448 " --> pdb=" O GLU M 290 " (cutoff:3.500A) removed outlier: 10.012A pdb=" N GLU M 290 " --> pdb=" O ASN M 448 " (cutoff:3.500A) removed outlier: 6.991A pdb=" N THR M 450 " --> pdb=" O LEU M 288 " (cutoff:3.500A) removed outlier: 7.005A pdb=" N LYS M 293 " --> pdb=" O ASN M 334 " (cutoff:3.500A) removed outlier: 4.367A pdb=" N ASN M 334 " --> pdb=" O LYS M 293 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'M' and resid 271 through 273 removed outlier: 6.991A pdb=" N THR M 450 " --> pdb=" O LEU M 288 " (cutoff:3.500A) removed outlier: 10.012A pdb=" N GLU M 290 " --> pdb=" O ASN M 448 " (cutoff:3.500A) removed outlier: 9.509A pdb=" N ASN M 448 " --> pdb=" O GLU M 290 " (cutoff:3.500A) removed outlier: 10.854A pdb=" N VAL M 292 " --> pdb=" O ILE M 446 " (cutoff:3.500A) removed outlier: 9.877A pdb=" N ILE M 446 " --> pdb=" O VAL M 292 " (cutoff:3.500A) removed outlier: 11.408A pdb=" N ILE M 294 " --> pdb=" O THR M 444 " (cutoff:3.500A) removed outlier: 10.158A pdb=" N THR M 444 " --> pdb=" O ILE M 294 " (cutoff:3.500A) removed outlier: 5.725A pdb=" N ASN M 357 " --> pdb=" O GLU M 464 " (cutoff:3.500A) removed outlier: 7.224A pdb=" N PHE M 466 " --> pdb=" O ASN M 357 " (cutoff:3.500A) removed outlier: 6.026A pdb=" N THR M 359 " --> pdb=" O PHE M 466 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'M' and resid 301 through 308 removed outlier: 6.933A pdb=" N ASN M 301 " --> pdb=" O VAL M 322 " (cutoff:3.500A) removed outlier: 4.653A pdb=" N VAL M 322 " --> pdb=" O ASN M 301 " (cutoff:3.500A) removed outlier: 6.468A pdb=" N THR M 303 " --> pdb=" O GLY M 321 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'O' and resid 4 through 7 Processing sheet with id=AF9, first strand: chain 'O' and resid 10 through 12 removed outlier: 6.419A pdb=" N GLY O 10 " --> pdb=" O ILE O 110 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N TYR O 33 " --> pdb=" O ASN O 95 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N GLY O 49 " --> pdb=" O TRP O 36 " (cutoff:3.500A) removed outlier: 6.841A pdb=" N ARG O 38 " --> pdb=" O LEU O 47 " (cutoff:3.500A) removed outlier: 5.590A pdb=" N LEU O 47 " --> pdb=" O ARG O 38 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'O' and resid 10 through 12 removed outlier: 6.419A pdb=" N GLY O 10 " --> pdb=" O ILE O 110 " (cutoff:3.500A) removed outlier: 7.141A pdb=" N CYS O 92 " --> pdb=" O HIS O 102 " (cutoff:3.500A) removed outlier: 7.182A pdb=" N HIS O 102 " --> pdb=" O CYS O 92 " (cutoff:3.500A) removed outlier: 7.412A pdb=" N ARG O 94 " --> pdb=" O TYR O 100E" (cutoff:3.500A) removed outlier: 4.881A pdb=" N TYR O 100E" --> pdb=" O ARG O 94 " (cutoff:3.500A) removed outlier: 4.905A pdb=" N VAL O 96 " --> pdb=" O LEU O 100C" (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'O' and resid 120 through 124 removed outlier: 3.774A pdb=" N GLY O 139 " --> pdb=" O LEU O 124 " (cutoff:3.500A) removed outlier: 6.014A pdb=" N TYR O 176 " --> pdb=" O ASP O 144 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'O' and resid 120 through 124 removed outlier: 3.774A pdb=" N GLY O 139 " --> pdb=" O LEU O 124 " (cutoff:3.500A) removed outlier: 6.014A pdb=" N TYR O 176 " --> pdb=" O ASP O 144 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'O' and resid 151 through 154 Processing sheet with id=AG5, first strand: chain 'P' and resid 5 through 7 Processing sheet with id=AG6, first strand: chain 'P' and resid 10 through 13 removed outlier: 6.426A pdb=" N LEU P 11 " --> pdb=" O ASP P 105 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N VAL P 85 " --> pdb=" O HIS P 38 " (cutoff:3.500A) removed outlier: 6.825A pdb=" N VAL P 33 " --> pdb=" O TYR P 49 " (cutoff:3.500A) removed outlier: 4.839A pdb=" N TYR P 49 " --> pdb=" O VAL P 33 " (cutoff:3.500A) removed outlier: 6.554A pdb=" N TRP P 35 " --> pdb=" O LEU P 47 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'P' and resid 10 through 13 removed outlier: 6.426A pdb=" N LEU P 11 " --> pdb=" O ASP P 105 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N GLN P 90 " --> pdb=" O THR P 97 " (cutoff:3.500A) removed outlier: 4.127A pdb=" N THR P 97 " --> pdb=" O GLN P 90 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'P' and resid 114 through 118 removed outlier: 5.714A pdb=" N TYR P 173 " --> pdb=" O ASN P 138 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'P' and resid 153 through 155 removed outlier: 4.426A pdb=" N TRP P 148 " --> pdb=" O GLN P 155 " (cutoff:3.500A) 891 hydrogen bonds defined for protein. 2286 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 9.54 Time building geometry restraints manager: 7.67 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: 0.12 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: 2.330 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: 1.090 Check model and map are aligned: 0.200 Set scattering table: 0.240 Process input model: 56.590 Find NCS groups from input model: 1.130 Set up NCS constraints: 0.170 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.920 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 64.690 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.29 (0.15), residues: 2919 helix: -0.64 (0.26), residues: 363 sheet: -0.30 (0.16), residues: 927 loop : -1.22 (0.15), residues: 1629 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP D 96 HIS 0.011 0.002 HIS G 35 PHE 0.024 0.002 PHE M 376 TYR 0.030 0.002 TYR A 458 ARG 0.004 0.001 ARG A 298 Details of bonding type rmsd link_NAG-ASN : bond 0.01153 ( 15) link_NAG-ASN : angle 4.85159 ( 45) 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_ALPHA1-3 : bond 0.00163 ( 6) link_ALPHA1-3 : angle 4.46287 ( 18) hydrogen bonds : bond 0.14815 ( 816) hydrogen bonds : angle 7.73231 ( 2286) SS BOND : bond 0.00690 ( 18) SS BOND : angle 1.42133 ( 36) covalent geometry : bond 0.00542 (24462) covalent geometry : angle 1.05961 (33204) *********************** 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 : 2.913 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 95 MET cc_start: 0.8936 (ppp) cc_final: 0.8587 (ppp) REVERT: C 89 MET cc_start: 0.9183 (tpt) cc_final: 0.8842 (tpp) REVERT: E 95 MET cc_start: 0.8927 (ppp) cc_final: 0.8587 (ppp) REVERT: F 626 MET cc_start: 0.7442 (tpt) cc_final: 0.7092 (tpp) REVERT: G 80 MET cc_start: 0.7467 (mtt) cc_final: 0.7241 (ttm) REVERT: M 95 MET cc_start: 0.8929 (ppp) cc_final: 0.8594 (ppp) outliers start: 0 outliers final: 0 residues processed: 88 average time/residue: 0.3829 time to fit residues: 55.4089 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 : 2.615 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 250 optimal weight: 10.0000 chunk 225 optimal weight: 20.0000 chunk 124 optimal weight: 20.0000 chunk 76 optimal weight: 9.9990 chunk 151 optimal weight: 0.7980 chunk 120 optimal weight: 10.0000 chunk 232 optimal weight: 9.9990 chunk 90 optimal weight: 6.9990 chunk 141 optimal weight: 10.0000 chunk 173 optimal weight: 9.9990 chunk 269 optimal weight: 0.9980 overall best weight: 5.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 80 ASN E 80 ASN M 80 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3001 r_free = 0.3001 target = 0.028834 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2770 r_free = 0.2770 target = 0.024360 restraints weight = 348598.231| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.2803 r_free = 0.2803 target = 0.024985 restraints weight = 191189.138| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.2825 r_free = 0.2825 target = 0.025416 restraints weight = 126208.042| |-----------------------------------------------------------------------------| r_work (final): 0.2814 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8373 moved from start: 0.1639 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 24528 Z= 0.247 Angle : 0.826 12.280 33384 Z= 0.397 Chirality : 0.048 0.373 3900 Planarity : 0.005 0.050 4155 Dihedral : 14.666 110.286 4368 Min Nonbonded Distance : 2.322 Molprobity Statistics. All-atom Clashscore : 8.66 Ramachandran Plot: Outliers : 0.10 % Allowed : 6.89 % Favored : 93.01 % Rotamer: Outliers : 0.00 % Allowed : 4.59 % Favored : 95.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.63 % Cis-general : 0.11 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.02 (0.16), residues: 2919 helix: 0.31 (0.27), residues: 387 sheet: -0.47 (0.17), residues: 906 loop : -1.02 (0.16), residues: 1626 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP N 631 HIS 0.007 0.002 HIS A 374 PHE 0.029 0.002 PHE B 519 TYR 0.018 0.002 TYR O 91 ARG 0.005 0.001 ARG H 108 Details of bonding type rmsd link_NAG-ASN : bond 0.00711 ( 15) link_NAG-ASN : angle 3.91273 ( 45) link_ALPHA1-6 : bond 0.01616 ( 6) link_ALPHA1-6 : angle 3.11627 ( 18) link_BETA1-4 : bond 0.00470 ( 21) link_BETA1-4 : angle 2.96064 ( 63) link_ALPHA1-3 : bond 0.00491 ( 6) link_ALPHA1-3 : angle 4.74894 ( 18) hydrogen bonds : bond 0.03935 ( 816) hydrogen bonds : angle 6.15282 ( 2286) SS BOND : bond 0.00625 ( 18) SS BOND : angle 1.08831 ( 36) covalent geometry : bond 0.00524 (24462) covalent geometry : angle 0.79381 (33204) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5838 Ramachandran restraints generated. 2919 Oldfield, 0 Emsley, 2919 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5838 Ramachandran restraints generated. 2919 Oldfield, 0 Emsley, 2919 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 69 residues out of total 2601 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 69 time to evaluate : 2.970 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 95 MET cc_start: 0.9133 (ppp) cc_final: 0.8468 (ppp) REVERT: B 626 MET cc_start: 0.7418 (tpt) cc_final: 0.7110 (tpt) REVERT: C 89 MET cc_start: 0.8559 (tpt) cc_final: 0.8130 (tpp) REVERT: E 473 MET cc_start: 0.7818 (tpp) cc_final: 0.7571 (tpp) REVERT: G 75 MET cc_start: 0.8647 (mpp) cc_final: 0.8426 (mpp) REVERT: M 84 MET cc_start: 0.7700 (mpp) cc_final: 0.7440 (mpp) REVERT: M 95 MET cc_start: 0.9142 (ppp) cc_final: 0.8718 (ppp) REVERT: O 89 MET cc_start: 0.8794 (tpp) cc_final: 0.8460 (tpp) outliers start: 0 outliers final: 0 residues processed: 69 average time/residue: 0.3700 time to fit residues: 43.3553 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 : 2.917 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 138 optimal weight: 5.9990 chunk 139 optimal weight: 6.9990 chunk 15 optimal weight: 6.9990 chunk 45 optimal weight: 10.0000 chunk 294 optimal weight: 10.0000 chunk 32 optimal weight: 9.9990 chunk 222 optimal weight: 0.9980 chunk 176 optimal weight: 6.9990 chunk 68 optimal weight: 9.9990 chunk 150 optimal weight: 9.9990 chunk 245 optimal weight: 10.0000 overall best weight: 5.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 164 HIS O 164 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2982 r_free = 0.2982 target = 0.028355 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2748 r_free = 0.2748 target = 0.023907 restraints weight = 346268.113| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.2781 r_free = 0.2781 target = 0.024529 restraints weight = 190618.155| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.2804 r_free = 0.2804 target = 0.024956 restraints weight = 125946.450| |-----------------------------------------------------------------------------| r_work (final): 0.2793 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8406 moved from start: 0.2109 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 24528 Z= 0.224 Angle : 0.757 12.592 33384 Z= 0.374 Chirality : 0.048 0.363 3900 Planarity : 0.005 0.050 4155 Dihedral : 13.069 111.402 4368 Min Nonbonded Distance : 2.335 Molprobity Statistics. All-atom Clashscore : 7.40 Ramachandran Plot: Outliers : 0.10 % Allowed : 7.95 % Favored : 91.95 % Rotamer: Outliers : 0.00 % Allowed : 2.97 % Favored : 97.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.63 % Cis-general : 0.11 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.99 (0.16), residues: 2919 helix: 0.59 (0.27), residues: 387 sheet: -0.53 (0.17), residues: 939 loop : -1.01 (0.16), residues: 1593 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP P 94 HIS 0.004 0.001 HIS E 374 PHE 0.014 0.002 PHE D 71 TYR 0.023 0.002 TYR E 458 ARG 0.004 0.000 ARG M 192 Details of bonding type rmsd link_NAG-ASN : bond 0.00696 ( 15) link_NAG-ASN : angle 3.74845 ( 45) link_ALPHA1-6 : bond 0.02422 ( 6) link_ALPHA1-6 : angle 3.16332 ( 18) link_BETA1-4 : bond 0.00429 ( 21) link_BETA1-4 : angle 2.62523 ( 63) link_ALPHA1-3 : bond 0.00679 ( 6) link_ALPHA1-3 : angle 3.40439 ( 18) hydrogen bonds : bond 0.03938 ( 816) hydrogen bonds : angle 6.04159 ( 2286) SS BOND : bond 0.00721 ( 18) SS BOND : angle 1.15605 ( 36) covalent geometry : bond 0.00468 (24462) covalent geometry : angle 0.72866 (33204) *********************** 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 74 residues out of total 2601 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 74 time to evaluate : 2.914 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 95 MET cc_start: 0.9180 (ppp) cc_final: 0.8429 (ppp) REVERT: A 104 MET cc_start: 0.9412 (ppp) cc_final: 0.9173 (ppp) REVERT: A 396 MET cc_start: 0.6561 (mmt) cc_final: 0.6096 (mmt) REVERT: C 89 MET cc_start: 0.8724 (tpt) cc_final: 0.8380 (tpp) REVERT: E 95 MET cc_start: 0.9084 (ppp) cc_final: 0.8645 (ppp) REVERT: E 104 MET cc_start: 0.9384 (ppp) cc_final: 0.9123 (ppp) REVERT: E 473 MET cc_start: 0.7756 (tpp) cc_final: 0.7432 (tpp) REVERT: M 84 MET cc_start: 0.7710 (mpp) cc_final: 0.7128 (mpp) REVERT: M 95 MET cc_start: 0.9150 (ppp) cc_final: 0.8703 (ppp) REVERT: M 104 MET cc_start: 0.9438 (ppp) cc_final: 0.9199 (ppp) REVERT: M 473 MET cc_start: 0.7740 (tpp) cc_final: 0.7501 (tpp) REVERT: N 530 MET cc_start: 0.7954 (mmp) cc_final: 0.7736 (mmm) REVERT: N 535 MET cc_start: 0.9105 (mpp) cc_final: 0.8766 (mpp) REVERT: O 75 MET cc_start: 0.8852 (mtm) cc_final: 0.8481 (mpp) REVERT: O 89 MET cc_start: 0.8969 (tpp) cc_final: 0.8496 (tpp) outliers start: 0 outliers final: 0 residues processed: 74 average time/residue: 0.3693 time to fit residues: 46.4099 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 : 2.867 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 223 optimal weight: 8.9990 chunk 30 optimal weight: 5.9990 chunk 40 optimal weight: 5.9990 chunk 182 optimal weight: 10.0000 chunk 228 optimal weight: 10.0000 chunk 165 optimal weight: 8.9990 chunk 259 optimal weight: 3.9990 chunk 56 optimal weight: 0.2980 chunk 251 optimal weight: 8.9990 chunk 240 optimal weight: 3.9990 chunk 294 optimal weight: 8.9990 overall best weight: 4.0588 ------------------------------------------------------------------------------- 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 = 0.2984 r_free = 0.2984 target = 0.028456 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2752 r_free = 0.2752 target = 0.023998 restraints weight = 347241.647| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.2784 r_free = 0.2784 target = 0.024622 restraints weight = 190360.079| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.2807 r_free = 0.2807 target = 0.025042 restraints weight = 125564.496| |-----------------------------------------------------------------------------| r_work (final): 0.2795 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8399 moved from start: 0.2450 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= 0.175 Angle : 0.704 10.183 33384 Z= 0.344 Chirality : 0.047 0.353 3900 Planarity : 0.004 0.048 4155 Dihedral : 12.190 105.371 4368 Min Nonbonded Distance : 2.372 Molprobity Statistics. All-atom Clashscore : 7.55 Ramachandran Plot: Outliers : 0.03 % Allowed : 6.82 % Favored : 93.15 % Rotamer: Outliers : 0.04 % Allowed : 2.93 % Favored : 97.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.63 % Cis-general : 0.11 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.93 (0.16), residues: 2919 helix: 0.84 (0.27), residues: 387 sheet: -0.40 (0.17), residues: 924 loop : -1.09 (0.16), residues: 1608 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP P 96 HIS 0.004 0.001 HIS C 100D PHE 0.017 0.002 PHE M 53 TYR 0.015 0.001 TYR G 91 ARG 0.003 0.000 ARG A 192 Details of bonding type rmsd link_NAG-ASN : bond 0.00656 ( 15) link_NAG-ASN : angle 3.58309 ( 45) link_ALPHA1-6 : bond 0.02455 ( 6) link_ALPHA1-6 : angle 3.58648 ( 18) link_BETA1-4 : bond 0.00384 ( 21) link_BETA1-4 : angle 2.52331 ( 63) link_ALPHA1-3 : bond 0.00717 ( 6) link_ALPHA1-3 : angle 3.79813 ( 18) hydrogen bonds : bond 0.03473 ( 816) hydrogen bonds : angle 5.78743 ( 2286) SS BOND : bond 0.00450 ( 18) SS BOND : angle 0.86705 ( 36) covalent geometry : bond 0.00369 (24462) covalent geometry : angle 0.67308 (33204) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5838 Ramachandran restraints generated. 2919 Oldfield, 0 Emsley, 2919 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5838 Ramachandran restraints generated. 2919 Oldfield, 0 Emsley, 2919 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 68 residues out of total 2601 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 67 time to evaluate : 2.908 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 95 MET cc_start: 0.9156 (ppp) cc_final: 0.8414 (ppp) REVERT: A 104 MET cc_start: 0.9339 (ppp) cc_final: 0.9114 (ppp) REVERT: A 396 MET cc_start: 0.6643 (mmt) cc_final: 0.6188 (mmt) REVERT: B 530 MET cc_start: 0.6864 (mmm) cc_final: 0.6555 (mmm) REVERT: C 89 MET cc_start: 0.8705 (tpt) cc_final: 0.8422 (tpp) REVERT: E 104 MET cc_start: 0.9298 (ppp) cc_final: 0.9049 (ppp) REVERT: E 473 MET cc_start: 0.7752 (tpp) cc_final: 0.7432 (tpp) REVERT: M 95 MET cc_start: 0.9134 (ppp) cc_final: 0.8708 (ppp) REVERT: M 104 MET cc_start: 0.9345 (ppp) cc_final: 0.9143 (ppp) REVERT: M 473 MET cc_start: 0.7822 (tpp) cc_final: 0.7543 (tpp) REVERT: O 89 MET cc_start: 0.8988 (tpp) cc_final: 0.8599 (tpp) outliers start: 1 outliers final: 0 residues processed: 68 average time/residue: 0.3824 time to fit residues: 42.7779 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 : 2.667 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 103 optimal weight: 8.9990 chunk 102 optimal weight: 4.9990 chunk 82 optimal weight: 10.0000 chunk 262 optimal weight: 6.9990 chunk 141 optimal weight: 20.0000 chunk 41 optimal weight: 3.9990 chunk 40 optimal weight: 9.9990 chunk 51 optimal weight: 8.9990 chunk 223 optimal weight: 7.9990 chunk 272 optimal weight: 10.0000 chunk 218 optimal weight: 9.9990 overall best weight: 6.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 321AGLN C 95 ASN E 321AGLN M 321AGLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2942 r_free = 0.2942 target = 0.027660 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2712 r_free = 0.2712 target = 0.023344 restraints weight = 352079.115| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.2744 r_free = 0.2744 target = 0.023948 restraints weight = 194734.492| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.2766 r_free = 0.2766 target = 0.024354 restraints weight = 128677.925| |-----------------------------------------------------------------------------| r_work (final): 0.2755 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8466 moved from start: 0.3168 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.068 24528 Z= 0.262 Angle : 0.795 13.108 33384 Z= 0.390 Chirality : 0.048 0.362 3900 Planarity : 0.005 0.048 4155 Dihedral : 12.025 98.287 4368 Min Nonbonded Distance : 2.349 Molprobity Statistics. All-atom Clashscore : 11.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.77 % Favored : 91.23 % Rotamer: Outliers : 0.00 % Allowed : 3.55 % Favored : 96.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.63 % Cis-general : 0.11 % Twisted Proline : 0.00 % Twisted General : 0.11 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.10 (0.16), residues: 2919 helix: 0.50 (0.26), residues: 405 sheet: -0.52 (0.17), residues: 885 loop : -1.16 (0.16), residues: 1629 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP H 94 HIS 0.005 0.001 HIS M 417 PHE 0.020 0.002 PHE N 519 TYR 0.020 0.002 TYR E 458 ARG 0.007 0.001 ARG E 192 Details of bonding type rmsd link_NAG-ASN : bond 0.00820 ( 15) link_NAG-ASN : angle 4.02792 ( 45) link_ALPHA1-6 : bond 0.02401 ( 6) link_ALPHA1-6 : angle 3.83530 ( 18) link_BETA1-4 : bond 0.00377 ( 21) link_BETA1-4 : angle 2.50657 ( 63) link_ALPHA1-3 : bond 0.00499 ( 6) link_ALPHA1-3 : angle 3.58646 ( 18) hydrogen bonds : bond 0.04003 ( 816) hydrogen bonds : angle 6.00326 ( 2286) SS BOND : bond 0.00562 ( 18) SS BOND : angle 1.01301 ( 36) covalent geometry : bond 0.00555 (24462) covalent geometry : angle 0.76484 (33204) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5838 Ramachandran restraints generated. 2919 Oldfield, 0 Emsley, 2919 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5838 Ramachandran restraints generated. 2919 Oldfield, 0 Emsley, 2919 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 64 residues out of total 2601 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 64 time to evaluate : 2.653 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: 0.9238 (ppp) cc_final: 0.8564 (ppp) REVERT: B 530 MET cc_start: 0.7288 (mmm) cc_final: 0.6770 (mmm) REVERT: C 89 MET cc_start: 0.8814 (tpt) cc_final: 0.8596 (tpp) REVERT: E 95 MET cc_start: 0.9113 (ppp) cc_final: 0.8688 (ppp) REVERT: E 473 MET cc_start: 0.7807 (tpp) cc_final: 0.7503 (tpp) REVERT: F 626 MET cc_start: 0.6837 (tpt) cc_final: 0.6632 (tpp) REVERT: M 95 MET cc_start: 0.9201 (ppp) cc_final: 0.8683 (ppp) REVERT: M 473 MET cc_start: 0.8033 (tpp) cc_final: 0.7794 (tpp) REVERT: N 535 MET cc_start: 0.9108 (mmm) cc_final: 0.8906 (mmm) REVERT: O 89 MET cc_start: 0.9080 (tpp) cc_final: 0.8657 (tpp) outliers start: 0 outliers final: 0 residues processed: 64 average time/residue: 0.3716 time to fit residues: 39.7291 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 : 2.843 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 174 optimal weight: 0.0050 chunk 230 optimal weight: 3.9990 chunk 134 optimal weight: 7.9990 chunk 111 optimal weight: 0.9990 chunk 157 optimal weight: 3.9990 chunk 151 optimal weight: 6.9990 chunk 221 optimal weight: 3.9990 chunk 145 optimal weight: 6.9990 chunk 130 optimal weight: 0.0980 chunk 25 optimal weight: 9.9990 chunk 59 optimal weight: 3.9990 overall best weight: 1.8200 ------------------------------------------------------------------------------- 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 = 0.2978 r_free = 0.2978 target = 0.028259 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2746 r_free = 0.2746 target = 0.023828 restraints weight = 342416.634| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.2779 r_free = 0.2779 target = 0.024455 restraints weight = 186815.323| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.2801 r_free = 0.2801 target = 0.024874 restraints weight = 123537.212| |-----------------------------------------------------------------------------| r_work (final): 0.2789 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8405 moved from start: 0.3153 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= 0.127 Angle : 0.684 11.453 33384 Z= 0.330 Chirality : 0.047 0.411 3900 Planarity : 0.004 0.046 4155 Dihedral : 10.873 87.050 4368 Min Nonbonded Distance : 2.389 Molprobity Statistics. All-atom Clashscore : 6.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.68 % Favored : 93.32 % Rotamer: Outliers : 0.00 % Allowed : 1.04 % Favored : 98.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.63 % Cis-general : 0.11 % Twisted Proline : 0.00 % Twisted General : 0.11 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.73 (0.16), residues: 2919 helix: 1.16 (0.28), residues: 387 sheet: -0.26 (0.17), residues: 882 loop : -1.01 (0.16), residues: 1650 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP P 94 HIS 0.003 0.001 HIS C 100D PHE 0.014 0.001 PHE P 87 TYR 0.018 0.001 TYR M 458 ARG 0.003 0.000 ARG M 456 Details of bonding type rmsd link_NAG-ASN : bond 0.00909 ( 15) link_NAG-ASN : angle 4.22667 ( 45) link_ALPHA1-6 : bond 0.02768 ( 6) link_ALPHA1-6 : angle 4.44299 ( 18) link_BETA1-4 : bond 0.00545 ( 21) link_BETA1-4 : angle 2.33463 ( 63) link_ALPHA1-3 : bond 0.00906 ( 6) link_ALPHA1-3 : angle 3.61489 ( 18) hydrogen bonds : bond 0.03203 ( 816) hydrogen bonds : angle 5.46754 ( 2286) SS BOND : bond 0.00346 ( 18) SS BOND : angle 0.89714 ( 36) covalent geometry : bond 0.00256 (24462) covalent geometry : angle 0.64591 (33204) *********************** 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 68 residues out of total 2601 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 68 time to evaluate : 3.055 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 84 MET cc_start: 0.7982 (mpp) cc_final: 0.7733 (mpp) REVERT: A 95 MET cc_start: 0.9130 (ppp) cc_final: 0.8490 (ppp) REVERT: A 104 MET cc_start: 0.9373 (ppp) cc_final: 0.9139 (ppp) REVERT: B 530 MET cc_start: 0.7351 (mmm) cc_final: 0.6677 (mmm) REVERT: E 95 MET cc_start: 0.9003 (ppp) cc_final: 0.8542 (ppp) REVERT: E 104 MET cc_start: 0.9404 (ppp) cc_final: 0.9134 (ppp) REVERT: E 396 MET cc_start: 0.6804 (mmt) cc_final: 0.6408 (mmt) REVERT: E 473 MET cc_start: 0.7790 (tpp) cc_final: 0.7394 (tpp) REVERT: M 84 MET cc_start: 0.7967 (mpp) cc_final: 0.7700 (mpp) REVERT: M 95 MET cc_start: 0.9067 (ppp) cc_final: 0.8577 (ppp) REVERT: M 104 MET cc_start: 0.9397 (ppp) cc_final: 0.9176 (ppp) REVERT: M 473 MET cc_start: 0.7968 (tpp) cc_final: 0.7606 (tpp) REVERT: N 535 MET cc_start: 0.9089 (mmm) cc_final: 0.8876 (mmm) REVERT: O 89 MET cc_start: 0.8979 (tpp) cc_final: 0.8627 (tpt) outliers start: 0 outliers final: 0 residues processed: 68 average time/residue: 0.4019 time to fit residues: 45.8710 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 : 2.843 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 201 optimal weight: 9.9990 chunk 180 optimal weight: 6.9990 chunk 260 optimal weight: 8.9990 chunk 245 optimal weight: 6.9990 chunk 239 optimal weight: 3.9990 chunk 146 optimal weight: 8.9990 chunk 167 optimal weight: 20.0000 chunk 77 optimal weight: 7.9990 chunk 74 optimal weight: 10.0000 chunk 37 optimal weight: 0.0040 chunk 295 optimal weight: 30.0000 overall best weight: 5.2000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 95 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2951 r_free = 0.2951 target = 0.027773 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2721 r_free = 0.2721 target = 0.023436 restraints weight = 349799.300| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.2753 r_free = 0.2753 target = 0.024048 restraints weight = 191371.878| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.2775 r_free = 0.2775 target = 0.024453 restraints weight = 126700.315| |-----------------------------------------------------------------------------| r_work (final): 0.2763 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8452 moved from start: 0.3466 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= 0.207 Angle : 0.728 11.388 33384 Z= 0.353 Chirality : 0.047 0.378 3900 Planarity : 0.004 0.046 4155 Dihedral : 10.625 80.300 4368 Min Nonbonded Distance : 2.340 Molprobity Statistics. All-atom Clashscore : 9.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.50 % Favored : 91.50 % Rotamer: Outliers : 0.00 % Allowed : 1.19 % Favored : 98.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.63 % Cis-general : 0.11 % Twisted Proline : 0.00 % Twisted General : 0.11 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.96 (0.16), residues: 2919 helix: 0.96 (0.27), residues: 387 sheet: -0.51 (0.17), residues: 933 loop : -1.09 (0.16), residues: 1599 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP P 148 HIS 0.004 0.001 HIS G 100D PHE 0.015 0.002 PHE D 71 TYR 0.018 0.001 TYR C 91 ARG 0.005 0.000 ARG M 192 Details of bonding type rmsd link_NAG-ASN : bond 0.00587 ( 15) link_NAG-ASN : angle 4.04538 ( 45) link_ALPHA1-6 : bond 0.02328 ( 6) link_ALPHA1-6 : angle 4.63078 ( 18) link_BETA1-4 : bond 0.00340 ( 21) link_BETA1-4 : angle 2.42884 ( 63) link_ALPHA1-3 : bond 0.00681 ( 6) link_ALPHA1-3 : angle 3.51025 ( 18) hydrogen bonds : bond 0.03521 ( 816) hydrogen bonds : angle 5.64499 ( 2286) SS BOND : bond 0.00386 ( 18) SS BOND : angle 0.96539 ( 36) covalent geometry : bond 0.00440 (24462) covalent geometry : angle 0.69346 (33204) *********************** 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 : 3.051 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: 0.9200 (ppp) cc_final: 0.8574 (ppp) REVERT: A 104 MET cc_start: 0.9437 (ppp) cc_final: 0.9119 (ppp) REVERT: B 530 MET cc_start: 0.7434 (mmm) cc_final: 0.6689 (mmm) REVERT: E 104 MET cc_start: 0.9387 (ppp) cc_final: 0.9150 (ppp) REVERT: E 473 MET cc_start: 0.7859 (tpp) cc_final: 0.7527 (tpp) REVERT: F 530 MET cc_start: 0.7778 (mmm) cc_final: 0.7467 (mmm) REVERT: M 95 MET cc_start: 0.9164 (ppp) cc_final: 0.8632 (ppp) REVERT: M 473 MET cc_start: 0.8085 (tpp) cc_final: 0.7725 (tpp) REVERT: N 530 MET cc_start: 0.7927 (mmp) cc_final: 0.7482 (mmt) REVERT: N 535 MET cc_start: 0.9128 (mmm) cc_final: 0.8886 (mmm) REVERT: O 89 MET cc_start: 0.9084 (tpp) cc_final: 0.8862 (tpp) outliers start: 0 outliers final: 0 residues processed: 66 average time/residue: 0.3850 time to fit residues: 42.7670 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 : 2.810 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 134 optimal weight: 9.9990 chunk 283 optimal weight: 8.9990 chunk 236 optimal weight: 6.9990 chunk 220 optimal weight: 4.9990 chunk 27 optimal weight: 20.0000 chunk 158 optimal weight: 5.9990 chunk 280 optimal weight: 1.9990 chunk 71 optimal weight: 7.9990 chunk 239 optimal weight: 3.9990 chunk 184 optimal weight: 8.9990 chunk 129 optimal weight: 5.9990 overall best weight: 4.5990 ------------------------------------------------------------------------------- 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 = 0.2947 r_free = 0.2947 target = 0.027681 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2716 r_free = 0.2716 target = 0.023330 restraints weight = 346809.722| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2748 r_free = 0.2748 target = 0.023941 restraints weight = 191021.581| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.2771 r_free = 0.2771 target = 0.024361 restraints weight = 126131.678| |-----------------------------------------------------------------------------| r_work (final): 0.2760 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8452 moved from start: 0.3672 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 24528 Z= 0.187 Angle : 0.706 11.776 33384 Z= 0.343 Chirality : 0.047 0.401 3900 Planarity : 0.004 0.046 4155 Dihedral : 9.982 74.230 4368 Min Nonbonded Distance : 2.322 Molprobity Statistics. All-atom Clashscore : 8.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.50 % Favored : 92.50 % Rotamer: Outliers : 0.00 % Allowed : 1.27 % Favored : 98.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.63 % Cis-general : 0.11 % Twisted Proline : 0.00 % Twisted General : 0.11 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.97 (0.16), residues: 2919 helix: 1.00 (0.27), residues: 387 sheet: -0.51 (0.17), residues: 933 loop : -1.12 (0.16), residues: 1599 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP F 614 HIS 0.003 0.001 HIS C 100D PHE 0.012 0.002 PHE D 71 TYR 0.017 0.001 TYR M 458 ARG 0.003 0.000 ARG A 192 Details of bonding type rmsd link_NAG-ASN : bond 0.00543 ( 15) link_NAG-ASN : angle 3.98565 ( 45) link_ALPHA1-6 : bond 0.01734 ( 6) link_ALPHA1-6 : angle 4.16934 ( 18) link_BETA1-4 : bond 0.00395 ( 21) link_BETA1-4 : angle 2.32140 ( 63) link_ALPHA1-3 : bond 0.01031 ( 6) link_ALPHA1-3 : angle 3.11973 ( 18) hydrogen bonds : bond 0.03444 ( 816) hydrogen bonds : angle 5.57995 ( 2286) SS BOND : bond 0.00566 ( 18) SS BOND : angle 1.08812 ( 36) covalent geometry : bond 0.00397 (24462) covalent geometry : angle 0.67303 (33204) *********************** 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 65 residues out of total 2601 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 65 time to evaluate : 2.876 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: A 84 MET cc_start: 0.8104 (mpp) cc_final: 0.7889 (mpp) REVERT: A 95 MET cc_start: 0.9193 (ppp) cc_final: 0.8558 (ppp) REVERT: A 104 MET cc_start: 0.9397 (ppp) cc_final: 0.9121 (ppp) REVERT: A 396 MET cc_start: 0.6842 (mmt) cc_final: 0.6567 (mmt) REVERT: B 530 MET cc_start: 0.7599 (mmm) cc_final: 0.6816 (mmm) REVERT: E 95 MET cc_start: 0.9041 (ppp) cc_final: 0.8588 (ppp) REVERT: E 104 MET cc_start: 0.9402 (ppp) cc_final: 0.9148 (ppp) REVERT: E 473 MET cc_start: 0.7887 (tpp) cc_final: 0.7484 (tpp) REVERT: F 530 MET cc_start: 0.7787 (mmm) cc_final: 0.7446 (mmm) REVERT: M 95 MET cc_start: 0.9160 (ppp) cc_final: 0.8624 (ppp) REVERT: M 396 MET cc_start: 0.6939 (mmt) cc_final: 0.6677 (mmt) REVERT: M 473 MET cc_start: 0.8157 (tpp) cc_final: 0.7764 (tpp) REVERT: N 530 MET cc_start: 0.7860 (mmp) cc_final: 0.7499 (mmt) REVERT: N 535 MET cc_start: 0.9163 (mmm) cc_final: 0.8896 (mmm) REVERT: O 75 MET cc_start: 0.9343 (mmm) cc_final: 0.9054 (mpp) outliers start: 0 outliers final: 0 residues processed: 65 average time/residue: 0.3762 time to fit residues: 41.1399 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 : 2.823 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 228 optimal weight: 1.9990 chunk 206 optimal weight: 3.9990 chunk 155 optimal weight: 8.9990 chunk 243 optimal weight: 4.9990 chunk 168 optimal weight: 4.9990 chunk 166 optimal weight: 0.9980 chunk 187 optimal weight: 5.9990 chunk 25 optimal weight: 20.0000 chunk 110 optimal weight: 9.9990 chunk 82 optimal weight: 2.9990 chunk 195 optimal weight: 4.9990 overall best weight: 2.9988 ------------------------------------------------------------------------------- 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 = 0.2957 r_free = 0.2957 target = 0.027847 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2727 r_free = 0.2727 target = 0.023477 restraints weight = 347406.666| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.2760 r_free = 0.2760 target = 0.024099 restraints weight = 189499.256| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.2782 r_free = 0.2782 target = 0.024518 restraints weight = 124845.941| |-----------------------------------------------------------------------------| r_work (final): 0.2771 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8435 moved from start: 0.3749 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 24528 Z= 0.143 Angle : 0.667 11.546 33384 Z= 0.324 Chirality : 0.047 0.403 3900 Planarity : 0.004 0.045 4155 Dihedral : 9.410 70.126 4368 Min Nonbonded Distance : 2.371 Molprobity Statistics. All-atom Clashscore : 8.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.71 % Favored : 92.29 % Rotamer: Outliers : 0.00 % Allowed : 0.39 % Favored : 99.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.63 % Cis-general : 0.11 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.76 (0.16), residues: 2919 helix: 1.22 (0.27), residues: 384 sheet: -0.33 (0.17), residues: 900 loop : -1.01 (0.16), residues: 1635 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP F 614 HIS 0.003 0.001 HIS O 100D PHE 0.025 0.001 PHE N 519 TYR 0.020 0.001 TYR O 91 ARG 0.002 0.000 ARG A 192 Details of bonding type rmsd link_NAG-ASN : bond 0.00623 ( 15) link_NAG-ASN : angle 3.87945 ( 45) link_ALPHA1-6 : bond 0.01595 ( 6) link_ALPHA1-6 : angle 3.42271 ( 18) link_BETA1-4 : bond 0.00460 ( 21) link_BETA1-4 : angle 2.36986 ( 63) link_ALPHA1-3 : bond 0.00631 ( 6) link_ALPHA1-3 : angle 3.48304 ( 18) hydrogen bonds : bond 0.03264 ( 816) hydrogen bonds : angle 5.42379 ( 2286) SS BOND : bond 0.00458 ( 18) SS BOND : angle 1.07764 ( 36) covalent geometry : bond 0.00305 (24462) covalent geometry : angle 0.63397 (33204) *********************** 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 : 2.858 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: 0.9141 (ppp) cc_final: 0.8541 (ppp) REVERT: A 104 MET cc_start: 0.9441 (ppp) cc_final: 0.9084 (ppp) REVERT: A 396 MET cc_start: 0.6800 (mmt) cc_final: 0.6512 (mmt) REVERT: B 530 MET cc_start: 0.7582 (mmm) cc_final: 0.6917 (mmm) REVERT: E 95 MET cc_start: 0.8966 (ppp) cc_final: 0.8526 (ppp) REVERT: E 104 MET cc_start: 0.9391 (ppp) cc_final: 0.9123 (ppp) REVERT: E 473 MET cc_start: 0.7892 (tpp) cc_final: 0.7469 (tpp) REVERT: G 89 MET cc_start: 0.9235 (tpp) cc_final: 0.8862 (tpp) REVERT: M 95 MET cc_start: 0.9125 (ppp) cc_final: 0.8615 (ppp) REVERT: M 473 MET cc_start: 0.8161 (tpp) cc_final: 0.7744 (tpp) REVERT: N 530 MET cc_start: 0.7778 (mmp) cc_final: 0.7485 (mmt) REVERT: N 535 MET cc_start: 0.9215 (mmm) cc_final: 0.8951 (mmm) REVERT: O 75 MET cc_start: 0.9322 (mmm) cc_final: 0.9022 (mpp) REVERT: O 89 MET cc_start: 0.9199 (tpp) cc_final: 0.8895 (tpp) outliers start: 0 outliers final: 0 residues processed: 66 average time/residue: 0.3747 time to fit residues: 41.6224 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 : 2.799 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 122 optimal weight: 5.9990 chunk 83 optimal weight: 0.0570 chunk 80 optimal weight: 0.8980 chunk 19 optimal weight: 9.9990 chunk 27 optimal weight: 9.9990 chunk 276 optimal weight: 20.0000 chunk 22 optimal weight: 0.0770 chunk 256 optimal weight: 10.0000 chunk 63 optimal weight: 5.9990 chunk 79 optimal weight: 1.9990 chunk 193 optimal weight: 0.9990 overall best weight: 0.8060 ------------------------------------------------------------------------------- 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 = 0.2989 r_free = 0.2989 target = 0.028405 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2760 r_free = 0.2760 target = 0.023990 restraints weight = 343918.042| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.2793 r_free = 0.2793 target = 0.024631 restraints weight = 186815.760| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.2816 r_free = 0.2816 target = 0.025054 restraints weight = 122651.410| |-----------------------------------------------------------------------------| r_work (final): 0.2803 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8384 moved from start: 0.3784 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 24528 Z= 0.107 Angle : 0.641 10.822 33384 Z= 0.310 Chirality : 0.047 0.417 3900 Planarity : 0.004 0.045 4155 Dihedral : 8.605 67.322 4368 Min Nonbonded Distance : 2.391 Molprobity Statistics. All-atom Clashscore : 6.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.69 % Favored : 94.31 % Rotamer: Outliers : 0.00 % Allowed : 0.04 % Favored : 99.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.63 % Cis-general : 0.11 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.49 (0.16), residues: 2919 helix: 1.25 (0.28), residues: 402 sheet: -0.09 (0.18), residues: 882 loop : -0.85 (0.16), residues: 1635 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRP H 94 HIS 0.005 0.001 HIS O 100D PHE 0.017 0.001 PHE N 519 TYR 0.031 0.001 TYR E 458 ARG 0.006 0.000 ARG E 456 Details of bonding type rmsd link_NAG-ASN : bond 0.00730 ( 15) link_NAG-ASN : angle 3.70659 ( 45) link_ALPHA1-6 : bond 0.02046 ( 6) link_ALPHA1-6 : angle 3.10228 ( 18) link_BETA1-4 : bond 0.00543 ( 21) link_BETA1-4 : angle 2.23519 ( 63) link_ALPHA1-3 : bond 0.00706 ( 6) link_ALPHA1-3 : angle 3.29476 ( 18) hydrogen bonds : bond 0.02969 ( 816) hydrogen bonds : angle 5.08691 ( 2286) SS BOND : bond 0.00337 ( 18) SS BOND : angle 0.96306 ( 36) covalent geometry : bond 0.00216 (24462) covalent geometry : angle 0.61075 (33204) ********************** 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 69 residues out of total 2601 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 69 time to evaluate : 2.683 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 95 MET cc_start: 0.9050 (ppp) cc_final: 0.8456 (ppp) REVERT: A 104 MET cc_start: 0.9356 (ppp) cc_final: 0.9005 (ppp) REVERT: B 530 MET cc_start: 0.7719 (mmm) cc_final: 0.6933 (mmm) REVERT: C 89 MET cc_start: 0.8981 (tpp) cc_final: 0.8757 (tpp) REVERT: E 104 MET cc_start: 0.9390 (ppp) cc_final: 0.9113 (ppp) REVERT: E 473 MET cc_start: 0.7891 (tpp) cc_final: 0.7410 (tpp) REVERT: F 530 MET cc_start: 0.7664 (mmm) cc_final: 0.7423 (mmm) REVERT: G 89 MET cc_start: 0.9276 (tpp) cc_final: 0.8910 (tpp) REVERT: M 95 MET cc_start: 0.8942 (ppp) cc_final: 0.8429 (ppp) REVERT: M 473 MET cc_start: 0.8118 (tpp) cc_final: 0.7683 (tpp) REVERT: N 535 MET cc_start: 0.9111 (mmm) cc_final: 0.8840 (mmm) REVERT: O 75 MET cc_start: 0.9315 (mmm) cc_final: 0.8979 (mpp) REVERT: O 89 MET cc_start: 0.9152 (tpp) cc_final: 0.8845 (tpp) outliers start: 0 outliers final: 0 residues processed: 69 average time/residue: 0.3646 time to fit residues: 41.9067 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 : 2.659 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 84 optimal weight: 20.0000 chunk 6 optimal weight: 10.0000 chunk 272 optimal weight: 20.0000 chunk 154 optimal weight: 0.8980 chunk 185 optimal weight: 10.0000 chunk 166 optimal weight: 6.9990 chunk 267 optimal weight: 0.9990 chunk 110 optimal weight: 10.0000 chunk 52 optimal weight: 9.9990 chunk 103 optimal weight: 7.9990 chunk 285 optimal weight: 3.9990 overall best weight: 4.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2951 r_free = 0.2951 target = 0.027681 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2719 r_free = 0.2719 target = 0.023317 restraints weight = 347263.457| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.2752 r_free = 0.2752 target = 0.023932 restraints weight = 189738.469| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.2773 r_free = 0.2773 target = 0.024343 restraints weight = 125406.553| |-----------------------------------------------------------------------------| r_work (final): 0.2762 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8439 moved from start: 0.3970 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 24528 Z= 0.175 Angle : 0.670 10.996 33384 Z= 0.326 Chirality : 0.046 0.389 3900 Planarity : 0.004 0.045 4155 Dihedral : 8.606 65.152 4368 Min Nonbonded Distance : 2.386 Molprobity Statistics. All-atom Clashscore : 8.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.74 % Favored : 92.26 % Rotamer: Outliers : 0.00 % Allowed : 0.23 % Favored : 99.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.63 % Cis-general : 0.11 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.58 (0.16), residues: 2919 helix: 1.39 (0.28), residues: 384 sheet: -0.20 (0.18), residues: 906 loop : -0.91 (0.16), residues: 1629 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP F 614 HIS 0.004 0.001 HIS O 100D PHE 0.015 0.002 PHE N 519 TYR 0.019 0.001 TYR C 91 ARG 0.003 0.000 ARG A 192 Details of bonding type rmsd link_NAG-ASN : bond 0.00540 ( 15) link_NAG-ASN : angle 3.71151 ( 45) link_ALPHA1-6 : bond 0.01919 ( 6) link_ALPHA1-6 : angle 3.07831 ( 18) link_BETA1-4 : bond 0.00352 ( 21) link_BETA1-4 : angle 2.27017 ( 63) link_ALPHA1-3 : bond 0.00453 ( 6) link_ALPHA1-3 : angle 3.32765 ( 18) hydrogen bonds : bond 0.03205 ( 816) hydrogen bonds : angle 5.25061 ( 2286) SS BOND : bond 0.00447 ( 18) SS BOND : angle 0.91760 ( 36) covalent geometry : bond 0.00371 (24462) covalent geometry : angle 0.64131 (33204) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5531.95 seconds wall clock time: 98 minutes 48.29 seconds (5928.29 seconds total)