Starting phenix.real_space_refine on Sun Jul 5 00:01:40 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7tco_25815/07_2026/7tco_25815.cif Found real_map, /net/cci-nas-00/data/ceres_data/7tco_25815/07_2026/7tco_25815.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.19 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7tco_25815/07_2026/7tco_25815.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7tco_25815/07_2026/7tco_25815.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7tco_25815/07_2026/7tco_25815.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7tco_25815/07_2026/7tco_25815.map" restraint_files = "/net/cci-nas-00/data/ceres_data/7tco_25815/07_2026/7tco_25815.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7tco_25815/07_2026/7tco_25815.cif" } resolution = 4.19 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.009 sd= 0.145 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 141 5.16 5 C 15030 2.51 5 N 4068 2.21 5 O 4734 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 15 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 23973 Number of models: 1 Model: "" Number of chains: 27 Chain: "A" Number of atoms: 3465 Number of conformers: 1 Conformer: "" Number of residues, atoms: 440, 3465 Classifications: {'peptide': 440} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 20, 'TRANS': 418} Chain breaks: 4 Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'TRP:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "B" Number of atoms: 969 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 969 Classifications: {'peptide': 122} Link IDs: {'CIS': 1, 'PTRANS': 1, 'TRANS': 119} Chain breaks: 1 Chain: "C" Number of atoms: 1677 Number of conformers: 1 Conformer: "" Number of residues, atoms: 220, 1677 Classifications: {'peptide': 220} Link IDs: {'PCIS': 2, 'PTRANS': 11, 'TRANS': 206} Chain breaks: 1 Chain: "D" Number of atoms: 1635 Number of conformers: 1 Conformer: "" Number of residues, atoms: 211, 1635 Classifications: {'peptide': 211} Link IDs: {'PCIS': 2, 'PTRANS': 7, 'TRANS': 201} Chain: "E" Number of atoms: 3465 Number of conformers: 1 Conformer: "" Number of residues, atoms: 440, 3465 Classifications: {'peptide': 440} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 20, 'TRANS': 418} Chain breaks: 4 Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'TRP:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "F" Number of atoms: 969 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 969 Classifications: {'peptide': 122} Link IDs: {'CIS': 1, 'PTRANS': 1, 'TRANS': 119} Chain breaks: 1 Chain: "G" Number of atoms: 1677 Number of conformers: 1 Conformer: "" Number of residues, atoms: 220, 1677 Classifications: {'peptide': 220} Link IDs: {'PCIS': 2, 'PTRANS': 11, 'TRANS': 206} Chain breaks: 1 Chain: "H" Number of atoms: 1635 Number of conformers: 1 Conformer: "" Number of residues, atoms: 211, 1635 Classifications: {'peptide': 211} Link IDs: {'PCIS': 2, 'PTRANS': 7, 'TRANS': 201} Chain: "M" Number of atoms: 3465 Number of conformers: 1 Conformer: "" Number of residues, atoms: 440, 3465 Classifications: {'peptide': 440} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 20, 'TRANS': 418} Chain breaks: 4 Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'TRP:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "N" Number of atoms: 969 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 969 Classifications: {'peptide': 122} Link IDs: {'CIS': 1, 'PTRANS': 1, 'TRANS': 119} Chain breaks: 1 Chain: "O" Number of atoms: 1677 Number of conformers: 1 Conformer: "" Number of residues, atoms: 220, 1677 Classifications: {'peptide': 220} Link IDs: {'PCIS': 2, 'PTRANS': 11, 'TRANS': 206} Chain breaks: 1 Chain: "P" Number of atoms: 1635 Number of conformers: 1 Conformer: "" Number of residues, atoms: 211, 1635 Classifications: {'peptide': 211} Link IDs: {'PCIS': 2, 'PTRANS': 7, 'TRANS': 201} Chain: "I" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen 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 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 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 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 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 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 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 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 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 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 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 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 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 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 chiralities: 4 Time building chain proxies: 5.84, per 1000 atoms: 0.24 Number of scatterers: 23973 At special positions: 0 Unit cell: (172.8, 185.76, 117.72, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 141 16.00 O 4734 8.00 N 4068 7.00 C 15030 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=18, symmetry=0 Simple disulfide: pdb=" SG CYS A 126 " - pdb=" SG CYS A 196 " distance=2.02 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 157 " distance=2.03 Simple disulfide: pdb=" SG CYS A 228 " - pdb=" SG CYS A 239 " distance=2.03 Simple disulfide: pdb=" SG CYS A 378 " - pdb=" SG CYS A 445 " distance=2.03 Simple disulfide: pdb=" SG CYS B 598 " - pdb=" SG CYS B 604 " distance=2.02 Simple disulfide: pdb=" SG CYS D 23 " - pdb=" SG CYS D 88 " distance=2.04 Simple disulfide: pdb=" SG CYS E 126 " - pdb=" SG CYS E 196 " distance=2.02 Simple disulfide: pdb=" SG CYS E 131 " - pdb=" SG CYS E 157 " distance=2.03 Simple disulfide: pdb=" SG CYS E 228 " - pdb=" SG CYS E 239 " distance=2.03 Simple disulfide: pdb=" SG CYS E 378 " - pdb=" SG CYS E 445 " distance=2.03 Simple disulfide: pdb=" SG CYS F 598 " - pdb=" SG CYS F 604 " distance=2.02 Simple disulfide: pdb=" SG CYS H 23 " - pdb=" SG CYS H 88 " distance=2.04 Simple disulfide: pdb=" SG CYS M 126 " - pdb=" SG CYS M 196 " distance=2.03 Simple disulfide: pdb=" SG CYS M 131 " - pdb=" SG CYS M 157 " distance=2.03 Simple disulfide: pdb=" SG CYS M 228 " - pdb=" SG CYS M 239 " distance=2.03 Simple disulfide: pdb=" SG CYS M 378 " - pdb=" SG CYS M 445 " distance=2.03 Simple disulfide: pdb=" SG CYS N 598 " - pdb=" SG CYS N 604 " distance=2.02 Simple disulfide: pdb=" SG CYS P 23 " - pdb=" SG CYS P 88 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied ALPHA1-3 " BMA K 3 " - " MAN K 6 " " BMA L 3 " - " MAN L 4 " " BMA S 3 " - " MAN S 6 " " BMA T 3 " - " MAN T 4 " " BMA X 3 " - " MAN X 6 " " BMA Y 3 " - " MAN Y 4 " ALPHA1-6 " BMA K 3 " - " MAN K 4 " " MAN K 4 " - " MAN K 5 " " BMA S 3 " - " MAN S 4 " " MAN S 4 " - " MAN S 5 " " BMA X 3 " - " MAN X 4 " " MAN X 4 " - " MAN X 5 " BETA1-4 " NAG I 1 " - " NAG I 2 " " NAG I 2 " - " BMA I 3 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG K 2 " - " BMA K 3 " " NAG L 1 " - " NAG L 2 " " NAG L 2 " - " BMA L 3 " " NAG Q 1 " - " NAG Q 2 " " NAG Q 2 " - " BMA Q 3 " " NAG R 1 " - " NAG R 2 " " NAG S 1 " - " NAG S 2 " " NAG S 2 " - " BMA S 3 " " NAG T 1 " - " NAG T 2 " " NAG T 2 " - " BMA T 3 " " NAG V 1 " - " NAG V 2 " " NAG V 2 " - " BMA V 3 " " NAG W 1 " - " NAG W 2 " " NAG X 1 " - " NAG X 2 " " NAG X 2 " - " BMA X 3 " " NAG Y 1 " - " NAG Y 2 " " NAG Y 2 " - " BMA Y 3 " NAG-ASN " NAG A 602 " - " ASN A 392 " " NAG A 604 " - " ASN A 230 " " NAG E 602 " - " ASN E 392 " " NAG E 604 " - " ASN E 230 " " NAG J 1 " - " ASN A 339 " " NAG K 1 " - " ASN A 197 " " NAG L 1 " - " ASN A 262 " " NAG M 602 " - " ASN M 392 " " NAG M 604 " - " ASN M 230 " " NAG R 1 " - " ASN E 339 " " NAG S 1 " - " ASN E 197 " " NAG T 1 " - " ASN E 262 " " NAG W 1 " - " ASN M 339 " " NAG X 1 " - " ASN M 197 " " NAG Y 1 " - " ASN M 262 " Time building additional restraints: 2.26 Conformation dependent library (CDL) restraints added in 1.3 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: 1.02 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: 5.51 Time building geometry restraints manager: 3.04 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 - 17.24: 13000 17.24 - 34.48: 990 34.48 - 51.72: 179 51.72 - 68.96: 24 68.96 - 86.20: 42 Dihedral angle restraints: 14235 sinusoidal: 5604 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 14232 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: 0.04 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: 3.230 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.310 Check model and map are aligned: 0.070 Set scattering table: 0.070 Process input model: 24.490 Find NCS groups from input model: 0.560 Set up NCS constraints: 0.070 Set refine NCS operators: 0.010 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.770 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.600 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8207 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 : 13.379 86.198 8625 Min Nonbonded Distance : 2.228 Molprobity Statistics. All-atom Clashscore : 2.57 Ramachandran Plot: Outliers : 0.10 % Allowed : 6.41 % Favored : 93.49 % Rotamer: Outliers : 0.00 % Allowed : 0.27 % Favored : 99.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.63 % Cis-general : 0.11 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.29 (0.15), residues: 2919 helix: -0.64 (0.26), residues: 363 sheet: -0.30 (0.16), residues: 927 loop : -1.22 (0.15), residues: 1629 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 298 TYR 0.030 0.002 TYR A 458 PHE 0.024 0.002 PHE M 376 TRP 0.016 0.002 TRP D 96 HIS 0.011 0.002 HIS G 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00542 / 0.27 (24462) covalent geometry : angle 1.05961 / 0.54 (33204) SS BOND : bond 0.00690 / 0.41 ( 18) SS BOND : angle 1.42133 / 0.82 ( 36) hydrogen bonds : bond 0.14815 / 9.55 ( 816) hydrogen bonds : angle 7.73231 / 5.34 ( 2286) link_ALPHA1-3 : bond 0.00163 / 0.09 ( 6) link_ALPHA1-3 : angle 4.46287 / 3.44 ( 18) link_ALPHA1-6 : bond 0.01928 / 1.01 ( 6) link_ALPHA1-6 : angle 3.99359 / 2.77 ( 18) link_BETA1-4 : bond 0.00818 / 0.49 ( 21) link_BETA1-4 : angle 3.65894 / 2.68 ( 63) link_NAG-ASN : bond 0.01153 / 0.64 ( 15) link_NAG-ASN : angle 4.85159 / 3.28 ( 45) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5838 Ramachandran restraints generated. 2919 Oldfield, 0 Emsley, 2919 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5838 Ramachandran restraints generated. 2919 Oldfield, 0 Emsley, 2919 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 2601 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 88 time to evaluate : 0.943 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 95 MET cc_start: 0.8936 (ppp) cc_final: 0.8587 (ppp) REVERT: C 89 MET cc_start: 0.9183 (tpt) cc_final: 0.8843 (tpp) REVERT: E 95 MET cc_start: 0.8927 (ppp) cc_final: 0.8587 (ppp) REVERT: F 626 MET cc_start: 0.7442 (tpt) cc_final: 0.7092 (tpp) REVERT: G 80 MET cc_start: 0.7467 (mtt) cc_final: 0.7241 (ttm) REVERT: M 95 MET cc_start: 0.8929 (ppp) cc_final: 0.8594 (ppp) outliers start: 0 outliers final: 0 residues processed: 88 average time/residue: 0.1769 time to fit residues: 25.2934 Evaluate side-chains 65 residues out of total 2601 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 65 time to evaluate : 0.912 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 197 optimal weight: 30.0000 chunk 215 optimal weight: 3.9990 chunk 20 optimal weight: 6.9990 chunk 132 optimal weight: 6.9990 chunk 261 optimal weight: 5.9990 chunk 248 optimal weight: 0.0060 chunk 207 optimal weight: 20.0000 chunk 155 optimal weight: 5.9990 chunk 244 optimal weight: 0.7980 chunk 183 optimal weight: 9.9990 chunk 111 optimal weight: 6.9990 overall best weight: 3.3602 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3044 r_free = 0.3044 target = 0.029639 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2812 r_free = 0.2812 target = 0.025064 restraints weight = 342820.640| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.2845 r_free = 0.2845 target = 0.025722 restraints weight = 186594.784| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.2868 r_free = 0.2868 target = 0.026165 restraints weight = 122300.454| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.2883 r_free = 0.2883 target = 0.026459 restraints weight = 90391.187| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.2894 r_free = 0.2894 target = 0.026661 restraints weight = 72653.307| |-----------------------------------------------------------------------------| r_work (final): 0.2885 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8234 moved from start: 0.1140 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 24528 Z= 0.158 Angle : 0.694 11.961 33384 Z= 0.344 Chirality : 0.046 0.361 3900 Planarity : 0.005 0.048 4155 Dihedral : 5.569 20.033 3213 Min Nonbonded Distance : 2.393 Molprobity Statistics. All-atom Clashscore : 5.00 Ramachandran Plot: Outliers : 0.10 % Allowed : 6.03 % Favored : 93.87 % Rotamer: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.63 % Cis-general : 0.11 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.92 (0.15), residues: 2919 helix: 0.24 (0.27), residues: 384 sheet: -0.29 (0.17), residues: 912 loop : -0.99 (0.16), residues: 1623 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG O 210 TYR 0.017 0.001 TYR O 91 PHE 0.013 0.001 PHE D 71 TRP 0.010 0.001 TRP B 631 HIS 0.004 0.001 HIS M 374 Details of bonding type rmsd/Z covalent geometry : bond 0.00331 / 0.16 (24462) covalent geometry : angle 0.66378 / 0.34 (33204) SS BOND : bond 0.00555 / 0.31 ( 18) SS BOND : angle 0.96766 / 0.54 ( 36) hydrogen bonds : bond 0.03736 / 2.50 ( 816) hydrogen bonds : angle 6.03748 / 4.15 ( 2286) link_ALPHA1-3 : bond 0.00285 / 0.13 ( 6) link_ALPHA1-3 : angle 3.59900 / 2.74 ( 18) link_ALPHA1-6 : bond 0.00509 / 0.24 ( 6) link_ALPHA1-6 : angle 3.03291 / 1.96 ( 18) link_BETA1-4 : bond 0.00583 / 0.39 ( 21) link_BETA1-4 : angle 2.44869 / 1.89 ( 63) link_NAG-ASN : bond 0.00630 / 0.37 ( 15) link_NAG-ASN : angle 3.77233 / 2.60 ( 45) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5838 Ramachandran restraints generated. 2919 Oldfield, 0 Emsley, 2919 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5838 Ramachandran restraints generated. 2919 Oldfield, 0 Emsley, 2919 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 73 residues out of total 2601 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 73 time to evaluate : 1.051 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: 0.9019 (ppp) cc_final: 0.8354 (ppp) REVERT: C 89 MET cc_start: 0.8494 (tpt) cc_final: 0.8046 (tpp) REVERT: E 95 MET cc_start: 0.8919 (ppp) cc_final: 0.8491 (ppp) REVERT: G 75 MET cc_start: 0.8436 (mpp) cc_final: 0.8218 (mpp) REVERT: M 84 MET cc_start: 0.7808 (mpp) cc_final: 0.7543 (mpp) REVERT: M 95 MET cc_start: 0.8993 (ppp) cc_final: 0.8602 (ppp) REVERT: M 473 MET cc_start: 0.7534 (tpp) cc_final: 0.7308 (tpp) outliers start: 0 outliers final: 0 residues processed: 73 average time/residue: 0.1778 time to fit residues: 21.4499 Evaluate side-chains 58 residues out of total 2601 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 58 time to evaluate : 1.109 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 174 optimal weight: 30.0000 chunk 110 optimal weight: 2.9990 chunk 235 optimal weight: 6.9990 chunk 241 optimal weight: 20.0000 chunk 249 optimal weight: 8.9990 chunk 99 optimal weight: 5.9990 chunk 162 optimal weight: 1.9990 chunk 49 optimal weight: 4.9990 chunk 33 optimal weight: 3.9990 chunk 284 optimal weight: 10.0000 chunk 56 optimal weight: 1.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3035 r_free = 0.3035 target = 0.029410 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2801 r_free = 0.2801 target = 0.024825 restraints weight = 343136.683| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 23)----------------| | r_work = 0.2834 r_free = 0.2834 target = 0.025474 restraints weight = 187250.301| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.2857 r_free = 0.2857 target = 0.025921 restraints weight = 122973.477| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.2873 r_free = 0.2873 target = 0.026221 restraints weight = 90766.985| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.2882 r_free = 0.2882 target = 0.026413 restraints weight = 73019.153| |-----------------------------------------------------------------------------| r_work (final): 0.2873 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8255 moved from start: 0.1536 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 24528 Z= 0.148 Angle : 0.664 11.441 33384 Z= 0.331 Chirality : 0.046 0.361 3900 Planarity : 0.004 0.048 4155 Dihedral : 5.294 20.094 3213 Min Nonbonded Distance : 2.369 Molprobity Statistics. All-atom Clashscore : 5.14 Ramachandran Plot: Outliers : 0.10 % Allowed : 6.68 % Favored : 93.22 % Rotamer: Outliers : 0.08 % Allowed : 2.35 % Favored : 97.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.63 % Cis-general : 0.11 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.75 (0.16), residues: 2919 helix: 0.78 (0.28), residues: 384 sheet: -0.34 (0.17), residues: 927 loop : -0.88 (0.16), residues: 1608 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG F 588 TYR 0.021 0.001 TYR E 458 PHE 0.011 0.001 PHE D 71 TRP 0.016 0.001 TRP D 94 HIS 0.003 0.001 HIS C 100D Details of bonding type rmsd/Z covalent geometry : bond 0.00308 / 0.15 (24462) covalent geometry : angle 0.63674 / 0.32 (33204) SS BOND : bond 0.00307 / 0.19 ( 18) SS BOND : angle 0.93270 / 0.54 ( 36) hydrogen bonds : bond 0.03558 / 2.41 ( 816) hydrogen bonds : angle 5.75245 / 3.94 ( 2286) link_ALPHA1-3 : bond 0.00389 / 0.20 ( 6) link_ALPHA1-3 : angle 3.09119 / 2.35 ( 18) link_ALPHA1-6 : bond 0.01021 / 0.46 ( 6) link_ALPHA1-6 : angle 2.93495 / 1.88 ( 18) link_BETA1-4 : bond 0.00413 / 0.26 ( 21) link_BETA1-4 : angle 2.23539 / 1.70 ( 63) link_NAG-ASN : bond 0.00691 / 0.40 ( 15) link_NAG-ASN : angle 3.61710 / 2.47 ( 45) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5838 Ramachandran restraints generated. 2919 Oldfield, 0 Emsley, 2919 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5838 Ramachandran restraints generated. 2919 Oldfield, 0 Emsley, 2919 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 76 residues out of total 2601 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 74 time to evaluate : 1.077 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: 0.9062 (ppp) cc_final: 0.8462 (ppp) REVERT: A 104 MET cc_start: 0.9320 (ppp) cc_final: 0.9026 (ppp) REVERT: A 396 MET cc_start: 0.6357 (mmt) cc_final: 0.5958 (mmt) REVERT: C 89 MET cc_start: 0.8621 (tpt) cc_final: 0.8196 (tpp) REVERT: E 95 MET cc_start: 0.8956 (ppp) cc_final: 0.8729 (ppp) REVERT: E 104 MET cc_start: 0.9348 (ppp) cc_final: 0.9073 (ppp) REVERT: G 89 MET cc_start: 0.8859 (tpp) cc_final: 0.8643 (tpp) REVERT: M 84 MET cc_start: 0.7748 (mpp) cc_final: 0.7518 (mpp) REVERT: M 95 MET cc_start: 0.9006 (ppp) cc_final: 0.8583 (ppp) REVERT: M 104 MET cc_start: 0.9360 (ppp) cc_final: 0.9056 (ppp) REVERT: M 473 MET cc_start: 0.7778 (tpp) cc_final: 0.7499 (tpp) REVERT: O 75 MET cc_start: 0.8679 (mtm) cc_final: 0.8327 (mpp) REVERT: O 89 MET cc_start: 0.8809 (tpp) cc_final: 0.8598 (tpp) outliers start: 2 outliers final: 0 residues processed: 76 average time/residue: 0.1791 time to fit residues: 22.5158 Evaluate side-chains 57 residues out of total 2601 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 57 time to evaluate : 0.977 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 133 optimal weight: 20.0000 chunk 117 optimal weight: 20.0000 chunk 78 optimal weight: 0.9990 chunk 82 optimal weight: 6.9990 chunk 75 optimal weight: 30.0000 chunk 181 optimal weight: 0.9980 chunk 229 optimal weight: 7.9990 chunk 98 optimal weight: 8.9990 chunk 171 optimal weight: 9.9990 chunk 179 optimal weight: 0.1980 chunk 272 optimal weight: 20.0000 overall best weight: 3.4386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.3012 r_free = 0.3012 target = 0.028980 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2781 r_free = 0.2781 target = 0.024494 restraints weight = 343777.491| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.2814 r_free = 0.2814 target = 0.025136 restraints weight = 188457.487| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.2837 r_free = 0.2837 target = 0.025571 restraints weight = 123883.778| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.2852 r_free = 0.2852 target = 0.025859 restraints weight = 91535.219| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.2861 r_free = 0.2861 target = 0.026047 restraints weight = 73689.882| |-----------------------------------------------------------------------------| r_work (final): 0.2853 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8287 moved from start: 0.2066 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 24528 Z= 0.154 Angle : 0.657 11.185 33384 Z= 0.326 Chirality : 0.046 0.350 3900 Planarity : 0.004 0.046 4155 Dihedral : 5.128 21.208 3213 Min Nonbonded Distance : 2.385 Molprobity Statistics. All-atom Clashscore : 6.13 Ramachandran Plot: Outliers : 0.10 % Allowed : 6.89 % Favored : 93.01 % Rotamer: Outliers : 0.00 % Allowed : 2.24 % Favored : 97.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.63 % Cis-general : 0.11 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.63 (0.16), residues: 2919 helix: 1.11 (0.28), residues: 387 sheet: -0.19 (0.17), residues: 912 loop : -0.91 (0.16), residues: 1620 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 83 TYR 0.010 0.001 TYR D 186 PHE 0.012 0.001 PHE D 71 TRP 0.016 0.001 TRP P 96 HIS 0.004 0.001 HIS C 100D Details of bonding type rmsd/Z covalent geometry : bond 0.00325 / 0.15 (24462) covalent geometry : angle 0.63211 / 0.32 (33204) SS BOND : bond 0.00926 / 0.48 ( 18) SS BOND : angle 0.85436 / 0.49 ( 36) hydrogen bonds : bond 0.03185 / 2.15 ( 816) hydrogen bonds : angle 5.48259 / 3.76 ( 2286) link_ALPHA1-3 : bond 0.00279 / 0.14 ( 6) link_ALPHA1-3 : angle 3.01690 / 2.29 ( 18) link_ALPHA1-6 : bond 0.01025 / 0.46 ( 6) link_ALPHA1-6 : angle 2.72040 / 1.70 ( 18) link_BETA1-4 : bond 0.00315 / 0.19 ( 21) link_BETA1-4 : angle 2.08743 / 1.58 ( 63) link_NAG-ASN : bond 0.00622 / 0.36 ( 15) link_NAG-ASN : angle 3.41889 / 2.34 ( 45) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5838 Ramachandran restraints generated. 2919 Oldfield, 0 Emsley, 2919 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5838 Ramachandran restraints generated. 2919 Oldfield, 0 Emsley, 2919 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 74 residues out of total 2601 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 74 time to evaluate : 0.985 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 95 MET cc_start: 0.9102 (ppp) cc_final: 0.8425 (ppp) REVERT: A 104 MET cc_start: 0.9309 (ppp) cc_final: 0.9047 (ppp) REVERT: A 396 MET cc_start: 0.6327 (mmt) cc_final: 0.5862 (mmt) REVERT: B 530 MET cc_start: 0.6966 (mmm) cc_final: 0.6632 (mmm) REVERT: C 89 MET cc_start: 0.8655 (tpt) cc_final: 0.8383 (tpp) REVERT: E 104 MET cc_start: 0.9295 (ppp) cc_final: 0.9034 (ppp) REVERT: F 535 MET cc_start: 0.9195 (mpp) cc_final: 0.8903 (mpp) REVERT: M 84 MET cc_start: 0.7727 (mpp) cc_final: 0.7221 (mpp) REVERT: M 95 MET cc_start: 0.9042 (ppp) cc_final: 0.8629 (ppp) REVERT: M 104 MET cc_start: 0.9314 (ppp) cc_final: 0.9071 (ppp) REVERT: M 473 MET cc_start: 0.7918 (tpp) cc_final: 0.7587 (tpp) REVERT: O 89 MET cc_start: 0.8908 (tpp) cc_final: 0.8488 (tpp) outliers start: 0 outliers final: 0 residues processed: 74 average time/residue: 0.1666 time to fit residues: 20.4802 Evaluate side-chains 56 residues out of total 2601 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 56 time to evaluate : 0.766 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 101 optimal weight: 8.9990 chunk 205 optimal weight: 7.9990 chunk 190 optimal weight: 7.9990 chunk 13 optimal weight: 20.0000 chunk 213 optimal weight: 5.9990 chunk 186 optimal weight: 0.9980 chunk 55 optimal weight: 10.0000 chunk 177 optimal weight: 6.9990 chunk 277 optimal weight: 9.9990 chunk 18 optimal weight: 10.0000 chunk 133 optimal weight: 0.2980 overall best weight: 4.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... M 321AGLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2991 r_free = 0.2991 target = 0.028587 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2762 r_free = 0.2762 target = 0.024163 restraints weight = 343892.347| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.2795 r_free = 0.2795 target = 0.024787 restraints weight = 188312.036| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.2817 r_free = 0.2817 target = 0.025208 restraints weight = 124098.004| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 18)----------------| | r_work = 0.2831 r_free = 0.2831 target = 0.025487 restraints weight = 92225.924| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.2841 r_free = 0.2841 target = 0.025678 restraints weight = 74957.687| |-----------------------------------------------------------------------------| r_work (final): 0.2832 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8321 moved from start: 0.2442 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 24528 Z= 0.184 Angle : 0.672 14.735 33384 Z= 0.333 Chirality : 0.046 0.349 3900 Planarity : 0.004 0.045 4155 Dihedral : 5.337 44.214 3213 Min Nonbonded Distance : 2.364 Molprobity Statistics. All-atom Clashscore : 7.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.54 % Favored : 92.46 % Rotamer: Outliers : 0.00 % Allowed : 2.31 % Favored : 97.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.63 % Cis-general : 0.11 % Twisted Proline : 0.00 % Twisted General : 0.11 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.63 (0.16), residues: 2919 helix: 1.15 (0.28), residues: 387 sheet: -0.23 (0.18), residues: 876 loop : -0.88 (0.16), residues: 1656 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 192 TYR 0.012 0.001 TYR M 458 PHE 0.014 0.002 PHE H 71 TRP 0.029 0.001 TRP H 96 HIS 0.004 0.001 HIS C 100D Details of bonding type rmsd/Z covalent geometry : bond 0.00391 / 0.18 (24462) covalent geometry : angle 0.64837 / 0.33 (33204) SS BOND : bond 0.00465 / 0.29 ( 18) SS BOND : angle 0.88828 / 0.52 ( 36) hydrogen bonds : bond 0.03396 / 2.30 ( 816) hydrogen bonds : angle 5.54176 / 3.80 ( 2286) link_ALPHA1-3 : bond 0.00352 / 0.20 ( 6) link_ALPHA1-3 : angle 2.95652 / 2.21 ( 18) link_ALPHA1-6 : bond 0.01126 / 0.51 ( 6) link_ALPHA1-6 : angle 2.69996 / 1.70 ( 18) link_BETA1-4 : bond 0.00300 / 0.18 ( 21) link_BETA1-4 : angle 2.02219 / 1.52 ( 63) link_NAG-ASN : bond 0.00634 / 0.37 ( 15) link_NAG-ASN : angle 3.44133 / 2.35 ( 45) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5838 Ramachandran restraints generated. 2919 Oldfield, 0 Emsley, 2919 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5838 Ramachandran restraints generated. 2919 Oldfield, 0 Emsley, 2919 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 64 residues out of total 2601 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 64 time to evaluate : 0.718 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 95 MET cc_start: 0.9126 (ppp) cc_final: 0.8427 (ppp) REVERT: A 396 MET cc_start: 0.6399 (mmt) cc_final: 0.5946 (mmt) REVERT: B 530 MET cc_start: 0.7277 (mmm) cc_final: 0.6768 (mmm) REVERT: C 89 MET cc_start: 0.8706 (tpt) cc_final: 0.8423 (tpp) REVERT: E 95 MET cc_start: 0.9026 (ppp) cc_final: 0.8561 (ppp) REVERT: G 89 MET cc_start: 0.9155 (tpp) cc_final: 0.8895 (tpp) REVERT: M 95 MET cc_start: 0.9083 (ppp) cc_final: 0.8660 (ppp) REVERT: M 473 MET cc_start: 0.8004 (tpp) cc_final: 0.7690 (tpp) REVERT: O 89 MET cc_start: 0.8984 (tpp) cc_final: 0.8567 (tpp) outliers start: 0 outliers final: 0 residues processed: 64 average time/residue: 0.1764 time to fit residues: 18.7298 Evaluate side-chains 56 residues out of total 2601 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 56 time to evaluate : 0.920 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 207 optimal weight: 10.0000 chunk 230 optimal weight: 10.0000 chunk 29 optimal weight: 0.9990 chunk 263 optimal weight: 9.9990 chunk 231 optimal weight: 1.9990 chunk 102 optimal weight: 30.0000 chunk 168 optimal weight: 5.9990 chunk 243 optimal weight: 1.9990 chunk 246 optimal weight: 10.0000 chunk 265 optimal weight: 5.9990 chunk 17 optimal weight: 6.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 321AGLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2989 r_free = 0.2989 target = 0.028540 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2760 r_free = 0.2760 target = 0.024126 restraints weight = 346953.475| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.2793 r_free = 0.2793 target = 0.024754 restraints weight = 189435.625| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.2814 r_free = 0.2814 target = 0.025170 restraints weight = 124779.044| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.2829 r_free = 0.2829 target = 0.025457 restraints weight = 92972.182| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.2839 r_free = 0.2839 target = 0.025643 restraints weight = 75144.573| |-----------------------------------------------------------------------------| r_work (final): 0.2830 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8320 moved from start: 0.2739 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 24528 Z= 0.150 Angle : 0.648 12.512 33384 Z= 0.321 Chirality : 0.045 0.343 3900 Planarity : 0.004 0.045 4155 Dihedral : 5.167 34.223 3213 Min Nonbonded Distance : 2.399 Molprobity Statistics. All-atom Clashscore : 6.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.78 % Favored : 93.22 % Rotamer: Outliers : 0.00 % Allowed : 1.31 % Favored : 98.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.63 % Cis-general : 0.11 % Twisted Proline : 0.00 % Twisted General : 0.11 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.56 (0.16), residues: 2919 helix: 1.35 (0.28), residues: 387 sheet: -0.25 (0.18), residues: 897 loop : -0.84 (0.16), residues: 1635 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG M 456 TYR 0.024 0.001 TYR M 458 PHE 0.028 0.002 PHE N 519 TRP 0.025 0.001 TRP H 94 HIS 0.005 0.001 HIS D 198 Details of bonding type rmsd/Z covalent geometry : bond 0.00315 / 0.15 (24462) covalent geometry : angle 0.62570 / 0.32 (33204) SS BOND : bond 0.00397 / 0.25 ( 18) SS BOND : angle 0.85742 / 0.48 ( 36) hydrogen bonds : bond 0.03201 / 2.17 ( 816) hydrogen bonds : angle 5.37620 / 3.69 ( 2286) link_ALPHA1-3 : bond 0.00298 / 0.16 ( 6) link_ALPHA1-3 : angle 2.88705 / 2.18 ( 18) link_ALPHA1-6 : bond 0.00892 / 0.40 ( 6) link_ALPHA1-6 : angle 2.51743 / 1.58 ( 18) link_BETA1-4 : bond 0.00311 / 0.19 ( 21) link_BETA1-4 : angle 1.89969 / 1.42 ( 63) link_NAG-ASN : bond 0.00621 / 0.36 ( 15) link_NAG-ASN : angle 3.30307 / 2.24 ( 45) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5838 Ramachandran restraints generated. 2919 Oldfield, 0 Emsley, 2919 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5838 Ramachandran restraints generated. 2919 Oldfield, 0 Emsley, 2919 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 62 residues out of total 2601 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 62 time to evaluate : 0.963 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 95 MET cc_start: 0.9106 (ppp) cc_final: 0.8427 (ppp) REVERT: A 104 MET cc_start: 0.9365 (ppp) cc_final: 0.9126 (ppp) REVERT: A 396 MET cc_start: 0.6377 (mmt) cc_final: 0.5906 (mmt) REVERT: B 530 MET cc_start: 0.7338 (mmm) cc_final: 0.6867 (mmm) REVERT: C 89 MET cc_start: 0.8767 (tpt) cc_final: 0.8519 (tpp) REVERT: E 104 MET cc_start: 0.9385 (ppp) cc_final: 0.9124 (ppp) REVERT: F 530 MET cc_start: 0.7481 (mmm) cc_final: 0.7131 (mmm) REVERT: G 89 MET cc_start: 0.9053 (tpp) cc_final: 0.8710 (tpp) REVERT: M 95 MET cc_start: 0.9029 (ppp) cc_final: 0.8571 (ppp) REVERT: M 104 MET cc_start: 0.9342 (ppp) cc_final: 0.9101 (ppp) REVERT: M 473 MET cc_start: 0.7932 (tpp) cc_final: 0.7638 (tpp) REVERT: O 75 MET cc_start: 0.9204 (mmm) cc_final: 0.8992 (mpp) REVERT: O 89 MET cc_start: 0.9017 (tpp) cc_final: 0.8595 (tpp) outliers start: 0 outliers final: 0 residues processed: 62 average time/residue: 0.1756 time to fit residues: 17.7371 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 : 1.003 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 230 optimal weight: 8.9990 chunk 223 optimal weight: 10.0000 chunk 125 optimal weight: 9.9990 chunk 177 optimal weight: 6.9990 chunk 254 optimal weight: 10.0000 chunk 203 optimal weight: 20.0000 chunk 152 optimal weight: 2.9990 chunk 33 optimal weight: 6.9990 chunk 263 optimal weight: 8.9990 chunk 186 optimal weight: 10.0000 chunk 91 optimal weight: 5.9990 overall best weight: 6.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 95 ASN E 80 ASN E 321AGLN F 651 ASN N 651 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2934 r_free = 0.2934 target = 0.027531 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2709 r_free = 0.2709 target = 0.023269 restraints weight = 352716.927| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.2740 r_free = 0.2740 target = 0.023874 restraints weight = 195126.713| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.2761 r_free = 0.2761 target = 0.024270 restraints weight = 128865.424| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.2776 r_free = 0.2776 target = 0.024545 restraints weight = 96087.346| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.2786 r_free = 0.2786 target = 0.024738 restraints weight = 78054.261| |-----------------------------------------------------------------------------| r_work (final): 0.2778 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8410 moved from start: 0.3432 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.045 24528 Z= 0.262 Angle : 0.789 12.088 33384 Z= 0.389 Chirality : 0.048 0.346 3900 Planarity : 0.005 0.045 4155 Dihedral : 5.745 34.389 3213 Min Nonbonded Distance : 2.381 Molprobity Statistics. All-atom Clashscore : 11.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.36 % Favored : 91.64 % Rotamer: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.63 % Cis-general : 0.11 % Twisted Proline : 0.00 % Twisted General : 0.11 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.93 (0.16), residues: 2919 helix: 0.90 (0.27), residues: 387 sheet: -0.52 (0.17), residues: 909 loop : -1.02 (0.16), residues: 1623 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG E 192 TYR 0.020 0.002 TYR A 217 PHE 0.019 0.002 PHE D 71 TRP 0.018 0.002 TRP H 96 HIS 0.008 0.002 HIS C 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00554 / 0.26 (24462) covalent geometry : angle 0.76648 / 0.38 (33204) SS BOND : bond 0.00558 / 0.35 ( 18) SS BOND : angle 1.03663 / 0.65 ( 36) hydrogen bonds : bond 0.03822 / 2.56 ( 816) hydrogen bonds : angle 5.87927 / 4.02 ( 2286) link_ALPHA1-3 : bond 0.00350 / 0.18 ( 6) link_ALPHA1-3 : angle 2.84107 / 2.07 ( 18) link_ALPHA1-6 : bond 0.01108 / 0.50 ( 6) link_ALPHA1-6 : angle 2.63224 / 1.63 ( 18) link_BETA1-4 : bond 0.00329 / 0.19 ( 21) link_BETA1-4 : angle 1.90590 / 1.41 ( 63) link_NAG-ASN : bond 0.01771 / 0.83 ( 15) link_NAG-ASN : angle 4.07611 / 2.74 ( 45) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5838 Ramachandran restraints generated. 2919 Oldfield, 0 Emsley, 2919 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5838 Ramachandran restraints generated. 2919 Oldfield, 0 Emsley, 2919 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 63 residues out of total 2601 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 63 time to evaluate : 1.014 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 95 MET cc_start: 0.9225 (ppp) cc_final: 0.8574 (ppp) REVERT: A 104 MET cc_start: 0.9418 (ppp) cc_final: 0.9118 (ppp) REVERT: B 530 MET cc_start: 0.7517 (mmm) cc_final: 0.6989 (mmm) REVERT: C 89 MET cc_start: 0.8848 (tpt) cc_final: 0.8567 (tpp) REVERT: E 95 MET cc_start: 0.9099 (ppp) cc_final: 0.8698 (ppp) REVERT: E 104 MET cc_start: 0.9367 (ppp) cc_final: 0.9118 (ppp) REVERT: M 84 MET cc_start: 0.8069 (mpp) cc_final: 0.7289 (mpp) REVERT: M 95 MET cc_start: 0.9186 (ppp) cc_final: 0.8648 (ppp) REVERT: M 434 MET cc_start: 0.8762 (ptp) cc_final: 0.8528 (ptp) REVERT: M 473 MET cc_start: 0.8052 (tpp) cc_final: 0.7780 (tpp) REVERT: O 89 MET cc_start: 0.9055 (tpp) cc_final: 0.8617 (tpp) outliers start: 0 outliers final: 0 residues processed: 63 average time/residue: 0.1749 time to fit residues: 18.2739 Evaluate side-chains 58 residues out of total 2601 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 58 time to evaluate : 0.994 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 240 optimal weight: 6.9990 chunk 197 optimal weight: 8.9990 chunk 185 optimal weight: 9.9990 chunk 83 optimal weight: 8.9990 chunk 285 optimal weight: 8.9990 chunk 221 optimal weight: 5.9990 chunk 267 optimal weight: 0.9990 chunk 218 optimal weight: 0.8980 chunk 150 optimal weight: 5.9990 chunk 209 optimal weight: 8.9990 chunk 248 optimal weight: 8.9990 overall best weight: 4.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2951 r_free = 0.2951 target = 0.027798 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2724 r_free = 0.2724 target = 0.023478 restraints weight = 347899.772| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.2756 r_free = 0.2756 target = 0.024085 restraints weight = 190819.562| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.2778 r_free = 0.2778 target = 0.024492 restraints weight = 126240.912| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.2792 r_free = 0.2792 target = 0.024773 restraints weight = 94424.608| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.2802 r_free = 0.2802 target = 0.024959 restraints weight = 76619.654| |-----------------------------------------------------------------------------| r_work (final): 0.2794 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8383 moved from start: 0.3504 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 24528 Z= 0.172 Angle : 0.688 13.039 33384 Z= 0.338 Chirality : 0.046 0.417 3900 Planarity : 0.004 0.045 4155 Dihedral : 5.413 31.836 3213 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 8.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.19 % Favored : 92.81 % Rotamer: Outliers : 0.00 % Allowed : 0.69 % Favored : 99.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.63 % Cis-general : 0.11 % Twisted Proline : 0.00 % Twisted General : 0.11 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.77 (0.16), residues: 2919 helix: 1.13 (0.27), residues: 384 sheet: -0.34 (0.17), residues: 891 loop : -1.00 (0.16), residues: 1644 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG M 192 TYR 0.015 0.001 TYR M 458 PHE 0.016 0.002 PHE H 118 TRP 0.014 0.001 TRP H 148 HIS 0.003 0.001 HIS D 38 Details of bonding type rmsd/Z covalent geometry : bond 0.00364 / 0.17 (24462) covalent geometry : angle 0.65663 / 0.33 (33204) SS BOND : bond 0.00602 / 0.41 ( 18) SS BOND : angle 0.99589 / 0.58 ( 36) hydrogen bonds : bond 0.03356 / 2.26 ( 816) hydrogen bonds : angle 5.59557 / 3.83 ( 2286) link_ALPHA1-3 : bond 0.00251 / 0.13 ( 6) link_ALPHA1-3 : angle 2.87425 / 2.16 ( 18) link_ALPHA1-6 : bond 0.01214 / 0.54 ( 6) link_ALPHA1-6 : angle 2.58457 / 1.63 ( 18) link_BETA1-4 : bond 0.00263 / 0.15 ( 21) link_BETA1-4 : angle 1.94433 / 1.48 ( 63) link_NAG-ASN : bond 0.00447 / 0.28 ( 15) link_NAG-ASN : angle 4.61960 / 3.04 ( 45) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5838 Ramachandran restraints generated. 2919 Oldfield, 0 Emsley, 2919 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5838 Ramachandran restraints generated. 2919 Oldfield, 0 Emsley, 2919 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 65 residues out of total 2601 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 65 time to evaluate : 0.994 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: 0.9173 (ppp) cc_final: 0.8541 (ppp) REVERT: A 104 MET cc_start: 0.9388 (ppp) cc_final: 0.9104 (ppp) REVERT: B 530 MET cc_start: 0.7560 (mmm) cc_final: 0.6937 (mmm) REVERT: D 118 PHE cc_start: 0.7955 (m-80) cc_final: 0.7711 (m-80) REVERT: E 95 MET cc_start: 0.9016 (ppp) cc_final: 0.8551 (ppp) REVERT: E 104 MET cc_start: 0.9383 (ppp) cc_final: 0.9117 (ppp) REVERT: F 530 MET cc_start: 0.7693 (mmm) cc_final: 0.7413 (mmm) REVERT: M 95 MET cc_start: 0.9130 (ppp) cc_final: 0.8604 (ppp) REVERT: M 473 MET cc_start: 0.8077 (tpp) cc_final: 0.7699 (tpp) REVERT: O 89 MET cc_start: 0.9014 (tpp) cc_final: 0.8592 (tpp) outliers start: 0 outliers final: 0 residues processed: 65 average time/residue: 0.1665 time to fit residues: 18.0236 Evaluate side-chains 56 residues out of total 2601 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 56 time to evaluate : 0.946 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 263 optimal weight: 20.0000 chunk 153 optimal weight: 5.9990 chunk 183 optimal weight: 20.0000 chunk 71 optimal weight: 6.9990 chunk 81 optimal weight: 2.9990 chunk 270 optimal weight: 30.0000 chunk 244 optimal weight: 8.9990 chunk 226 optimal weight: 1.9990 chunk 108 optimal weight: 20.0000 chunk 15 optimal weight: 5.9990 chunk 149 optimal weight: 1.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.027734 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2722 r_free = 0.2722 target = 0.023395 restraints weight = 349370.334| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.2755 r_free = 0.2755 target = 0.024019 restraints weight = 191598.701| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.2777 r_free = 0.2777 target = 0.024429 restraints weight = 126049.261| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.2791 r_free = 0.2791 target = 0.024707 restraints weight = 93745.146| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.2801 r_free = 0.2801 target = 0.024899 restraints weight = 76164.950| |-----------------------------------------------------------------------------| r_work (final): 0.2793 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8384 moved from start: 0.3697 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 24528 Z= 0.162 Angle : 0.671 11.972 33384 Z= 0.328 Chirality : 0.046 0.401 3900 Planarity : 0.004 0.045 4155 Dihedral : 5.262 29.887 3213 Min Nonbonded Distance : 2.395 Molprobity Statistics. All-atom Clashscore : 8.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.91 % Favored : 92.09 % Rotamer: Outliers : 0.00 % Allowed : 0.58 % Favored : 99.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.63 % Cis-general : 0.11 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.76 (0.16), residues: 2919 helix: 1.24 (0.28), residues: 384 sheet: -0.36 (0.17), residues: 900 loop : -1.00 (0.16), residues: 1635 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG M 192 TYR 0.016 0.001 TYR G 91 PHE 0.013 0.001 PHE D 118 TRP 0.015 0.001 TRP D 148 HIS 0.003 0.001 HIS C 100D Details of bonding type rmsd/Z covalent geometry : bond 0.00345 / 0.16 (24462) covalent geometry : angle 0.64329 / 0.32 (33204) SS BOND : bond 0.00448 / 0.29 ( 18) SS BOND : angle 0.97818 / 0.58 ( 36) hydrogen bonds : bond 0.03229 / 2.18 ( 816) hydrogen bonds : angle 5.44950 / 3.72 ( 2286) link_ALPHA1-3 : bond 0.00289 / 0.15 ( 6) link_ALPHA1-3 : angle 2.89245 / 2.18 ( 18) link_ALPHA1-6 : bond 0.01034 / 0.46 ( 6) link_ALPHA1-6 : angle 2.42683 / 1.54 ( 18) link_BETA1-4 : bond 0.00286 / 0.16 ( 21) link_BETA1-4 : angle 1.94521 / 1.49 ( 63) link_NAG-ASN : bond 0.00476 / 0.25 ( 15) link_NAG-ASN : angle 4.16822 / 2.75 ( 45) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5838 Ramachandran restraints generated. 2919 Oldfield, 0 Emsley, 2919 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5838 Ramachandran restraints generated. 2919 Oldfield, 0 Emsley, 2919 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 66 residues out of total 2601 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 66 time to evaluate : 0.807 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 95 MET cc_start: 0.9132 (ppp) cc_final: 0.8563 (ppp) REVERT: B 530 MET cc_start: 0.7637 (mmm) cc_final: 0.6964 (mmm) REVERT: D 118 PHE cc_start: 0.7933 (m-80) cc_final: 0.7646 (m-80) REVERT: E 104 MET cc_start: 0.9365 (ppp) cc_final: 0.9098 (ppp) REVERT: E 396 MET cc_start: 0.6700 (mmt) cc_final: 0.6495 (mmt) REVERT: F 530 MET cc_start: 0.7824 (mmm) cc_final: 0.7551 (mmm) REVERT: M 84 MET cc_start: 0.7955 (mpp) cc_final: 0.7304 (mpp) REVERT: M 95 MET cc_start: 0.9106 (ppp) cc_final: 0.8589 (ppp) REVERT: M 396 MET cc_start: 0.7030 (mmt) cc_final: 0.6743 (mmt) REVERT: M 473 MET cc_start: 0.8099 (tpp) cc_final: 0.7716 (tpp) REVERT: O 89 MET cc_start: 0.9056 (tpp) cc_final: 0.8642 (tpp) outliers start: 0 outliers final: 0 residues processed: 66 average time/residue: 0.1746 time to fit residues: 19.2916 Evaluate side-chains 57 residues out of total 2601 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 57 time to evaluate : 0.949 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 174 optimal weight: 30.0000 chunk 248 optimal weight: 7.9990 chunk 126 optimal weight: 20.0000 chunk 63 optimal weight: 5.9990 chunk 25 optimal weight: 20.0000 chunk 189 optimal weight: 20.0000 chunk 270 optimal weight: 30.0000 chunk 275 optimal weight: 20.0000 chunk 249 optimal weight: 0.5980 chunk 117 optimal weight: 9.9990 chunk 41 optimal weight: 1.9990 overall best weight: 5.3188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... O 95 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2926 r_free = 0.2926 target = 0.027291 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2697 r_free = 0.2697 target = 0.022997 restraints weight = 351471.906| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.2730 r_free = 0.2730 target = 0.023603 restraints weight = 192396.286| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.2751 r_free = 0.2751 target = 0.024010 restraints weight = 127258.787| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.2766 r_free = 0.2766 target = 0.024286 restraints weight = 95056.389| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.2776 r_free = 0.2776 target = 0.024469 restraints weight = 77049.698| |-----------------------------------------------------------------------------| r_work (final): 0.2768 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8411 moved from start: 0.3942 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= 0.209 Angle : 0.713 12.048 33384 Z= 0.349 Chirality : 0.047 0.397 3900 Planarity : 0.004 0.045 4155 Dihedral : 5.418 28.692 3213 Min Nonbonded Distance : 2.320 Molprobity Statistics. All-atom Clashscore : 9.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.08 % Favored : 91.92 % Rotamer: Outliers : 0.00 % Allowed : 0.27 % Favored : 99.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.63 % Cis-general : 0.11 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.92 (0.16), residues: 2919 helix: 0.97 (0.27), residues: 402 sheet: -0.60 (0.17), residues: 915 loop : -1.00 (0.16), residues: 1602 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG M 192 TYR 0.024 0.002 TYR N 643 PHE 0.020 0.002 PHE D 118 TRP 0.016 0.002 TRP D 148 HIS 0.003 0.001 HIS A 355 Details of bonding type rmsd/Z covalent geometry : bond 0.00447 / 0.21 (24462) covalent geometry : angle 0.68635 / 0.34 (33204) SS BOND : bond 0.00542 / 0.35 ( 18) SS BOND : angle 1.01295 / 0.57 ( 36) hydrogen bonds : bond 0.03441 / 2.31 ( 816) hydrogen bonds : angle 5.60238 / 3.82 ( 2286) link_ALPHA1-3 : bond 0.00202 / 0.11 ( 6) link_ALPHA1-3 : angle 2.83138 / 2.11 ( 18) link_ALPHA1-6 : bond 0.01019 / 0.45 ( 6) link_ALPHA1-6 : angle 2.49316 / 1.57 ( 18) link_BETA1-4 : bond 0.00252 / 0.14 ( 21) link_BETA1-4 : angle 2.00302 / 1.54 ( 63) link_NAG-ASN : bond 0.00538 / 0.31 ( 15) link_NAG-ASN : angle 4.16490 / 2.75 ( 45) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5838 Ramachandran restraints generated. 2919 Oldfield, 0 Emsley, 2919 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5838 Ramachandran restraints generated. 2919 Oldfield, 0 Emsley, 2919 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 65 residues out of total 2601 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 65 time to evaluate : 0.993 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: 0.9160 (ppp) cc_final: 0.8566 (ppp) REVERT: A 396 MET cc_start: 0.6773 (mmt) cc_final: 0.6473 (mmt) REVERT: B 530 MET cc_start: 0.7843 (mmm) cc_final: 0.7048 (mmm) REVERT: D 118 PHE cc_start: 0.8075 (m-80) cc_final: 0.7751 (m-80) REVERT: E 95 MET cc_start: 0.9039 (ppp) cc_final: 0.8639 (ppp) REVERT: E 396 MET cc_start: 0.6849 (mmt) cc_final: 0.6543 (mmt) REVERT: F 530 MET cc_start: 0.7873 (mmm) cc_final: 0.7584 (mmm) REVERT: M 84 MET cc_start: 0.7918 (mpp) cc_final: 0.7303 (mpp) REVERT: M 95 MET cc_start: 0.9145 (ppp) cc_final: 0.8603 (ppp) REVERT: M 473 MET cc_start: 0.8123 (tpp) cc_final: 0.7754 (tpp) REVERT: O 75 MET cc_start: 0.9364 (mmm) cc_final: 0.9016 (mpp) REVERT: O 89 MET cc_start: 0.9063 (tpp) cc_final: 0.8827 (tpp) outliers start: 0 outliers final: 0 residues processed: 65 average time/residue: 0.1793 time to fit residues: 19.3104 Evaluate side-chains 54 residues out of total 2601 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 54 time to evaluate : 0.979 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 172 optimal weight: 0.9990 chunk 93 optimal weight: 10.0000 chunk 3 optimal weight: 20.0000 chunk 168 optimal weight: 0.1980 chunk 164 optimal weight: 3.9990 chunk 72 optimal weight: 7.9990 chunk 154 optimal weight: 5.9990 chunk 181 optimal weight: 0.8980 chunk 237 optimal weight: 2.9990 chunk 235 optimal weight: 0.0060 chunk 283 optimal weight: 3.9990 overall best weight: 1.0200 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2966 r_free = 0.2966 target = 0.027965 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2735 r_free = 0.2735 target = 0.023550 restraints weight = 342297.422| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.2768 r_free = 0.2768 target = 0.024179 restraints weight = 186395.773| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.2791 r_free = 0.2791 target = 0.024604 restraints weight = 122469.657| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.2805 r_free = 0.2805 target = 0.024883 restraints weight = 90777.090| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.2815 r_free = 0.2815 target = 0.025075 restraints weight = 73517.837| |-----------------------------------------------------------------------------| r_work (final): 0.2807 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8345 moved from start: 0.3899 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 24528 Z= 0.104 Angle : 0.637 11.062 33384 Z= 0.310 Chirality : 0.046 0.409 3900 Planarity : 0.004 0.045 4155 Dihedral : 4.906 26.440 3213 Min Nonbonded Distance : 2.419 Molprobity Statistics. All-atom Clashscore : 6.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.17 % Favored : 93.83 % Rotamer: Outliers : 0.00 % Allowed : 0.23 % Favored : 99.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.63 % Cis-general : 0.11 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.54 (0.16), residues: 2919 helix: 1.22 (0.28), residues: 402 sheet: -0.13 (0.18), residues: 897 loop : -0.89 (0.16), residues: 1620 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG H 108 TYR 0.015 0.001 TYR G 91 PHE 0.010 0.001 PHE P 87 TRP 0.031 0.001 TRP N 614 HIS 0.002 0.001 HIS C 100D Details of bonding type rmsd/Z covalent geometry : bond 0.00215 / 0.10 (24462) covalent geometry : angle 0.61046 / 0.30 (33204) SS BOND : bond 0.00343 / 0.22 ( 18) SS BOND : angle 0.88911 / 0.52 ( 36) hydrogen bonds : bond 0.02960 / 1.99 ( 816) hydrogen bonds : angle 5.13438 / 3.52 ( 2286) link_ALPHA1-3 : bond 0.00443 / 0.23 ( 6) link_ALPHA1-3 : angle 2.99651 / 2.30 ( 18) link_ALPHA1-6 : bond 0.01081 / 0.51 ( 6) link_ALPHA1-6 : angle 2.24988 / 1.44 ( 18) link_BETA1-4 : bond 0.00481 / 0.30 ( 21) link_BETA1-4 : angle 1.86641 / 1.44 ( 63) link_NAG-ASN : bond 0.00643 / 0.36 ( 15) link_NAG-ASN : angle 3.83555 / 2.53 ( 45) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2969.44 seconds wall clock time: 53 minutes 14.83 seconds (3194.83 seconds total)