Starting phenix.real_space_refine on Sat Sep 12 11:07:44 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7ki6_22885/09_2026/7ki6_22885.cif Found real_map, /net/cci-nas-00/data/ceres_data/7ki6_22885/09_2026/7ki6_22885.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7ki6_22885/09_2026/7ki6_22885.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7ki6_22885/09_2026/7ki6_22885.map" restraint_files = "/net/cci-nas-00/data/ceres_data/7ki6_22885/09_2026/7ki6_22885.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7ki6_22885/09_2026/7ki6_22885.cif" model { file = "/net/cci-nas-00/data/ceres_data/7ki6_22885/09_2026/7ki6_22885.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7ki6_22885/09_2026/7ki6_22885.cif" } resolution = 2.8 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= 0.004 sd= 0.114 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 78 5.16 5 C 9807 2.51 5 N 2478 2.21 5 O 3090 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 84 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 15453 Number of models: 1 Model: "" Number of chains: 18 Chain: "A" Number of atoms: 3324 Number of conformers: 1 Conformer: "" Number of residues, atoms: 437, 3324 Classifications: {'peptide': 437} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 14, 'TRANS': 422} Chain breaks: 1 Unresolved non-hydrogen bonds: 26 Unresolved non-hydrogen angles: 33 Unresolved non-hydrogen dihedrals: 21 Planarities with less than four sites: {'HIS:plan': 1, 'ASP:plan': 1, 'ARG:plan': 1, 'GLU:plan': 2, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 24 Chain: "L" Number of atoms: 816 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 816 Classifications: {'peptide': 108} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 2, 'PTRANS': 2, 'TRANS': 103} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "H" Number of atoms: 927 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 927 Classifications: {'peptide': 117} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 4, 'TRANS': 112} Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 17 Unresolved non-hydrogen dihedrals: 13 Planarities with less than four sites: {'ASN:plan1': 1, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 7 Chain: "B" Number of atoms: 3324 Number of conformers: 1 Conformer: "" Number of residues, atoms: 437, 3324 Classifications: {'peptide': 437} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 14, 'TRANS': 422} Chain breaks: 1 Unresolved non-hydrogen bonds: 26 Unresolved non-hydrogen angles: 33 Unresolved non-hydrogen dihedrals: 21 Planarities with less than four sites: {'HIS:plan': 1, 'ASP:plan': 1, 'ARG:plan': 1, 'GLU:plan': 2, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 24 Chain: "C" Number of atoms: 816 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 816 Classifications: {'peptide': 108} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 2, 'PTRANS': 2, 'TRANS': 103} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "D" Number of atoms: 927 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 927 Classifications: {'peptide': 117} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 4, 'TRANS': 112} Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 17 Unresolved non-hydrogen dihedrals: 13 Planarities with less than four sites: {'ASN:plan1': 1, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 7 Chain: "E" Number of atoms: 3324 Number of conformers: 1 Conformer: "" Number of residues, atoms: 437, 3324 Classifications: {'peptide': 437} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 14, 'TRANS': 422} Chain breaks: 1 Unresolved non-hydrogen bonds: 26 Unresolved non-hydrogen angles: 33 Unresolved non-hydrogen dihedrals: 21 Planarities with less than four sites: {'HIS:plan': 1, 'ASP:plan': 1, 'ARG:plan': 1, 'GLU:plan': 2, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 24 Chain: "F" Number of atoms: 816 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 816 Classifications: {'peptide': 108} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 2, 'PTRANS': 2, 'TRANS': 103} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "G" Number of atoms: 927 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 927 Classifications: {'peptide': 117} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 4, 'TRANS': 112} Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 17 Unresolved non-hydrogen dihedrals: 13 Planarities with less than four sites: {'ASN:plan1': 1, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 7 Chain: "I" 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: "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: 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: "M" 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: "N" 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: "O" 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: "A" 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: "B" 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: "E" 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 Time building chain proxies: 3.06, per 1000 atoms: 0.20 Number of scatterers: 15453 At special positions: 0 Unit cell: (128.1, 130.2, 105, 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 78 16.00 O 3090 8.00 N 2478 7.00 C 9807 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=21, symmetry=0 Simple disulfide: pdb=" SG CYS A 71 " - pdb=" SG CYS A 192 " distance=2.04 Simple disulfide: pdb=" SG CYS A 331 " - pdb=" SG CYS A 340 " distance=2.03 Simple disulfide: pdb=" SG CYS A 355 " - pdb=" SG CYS A 363 " distance=2.01 Simple disulfide: pdb=" SG CYS A 387 " - pdb=" SG CYS A 392 " distance=2.09 Simple disulfide: pdb=" SG CYS A 394 " - pdb=" SG CYS A 417 " distance=2.04 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 87 " distance=2.02 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.03 Simple disulfide: pdb=" SG CYS B 71 " - pdb=" SG CYS B 192 " distance=2.04 Simple disulfide: pdb=" SG CYS B 331 " - pdb=" SG CYS B 340 " distance=2.03 Simple disulfide: pdb=" SG CYS B 355 " - pdb=" SG CYS B 363 " distance=2.01 Simple disulfide: pdb=" SG CYS B 387 " - pdb=" SG CYS B 392 " distance=2.09 Simple disulfide: pdb=" SG CYS B 394 " - pdb=" SG CYS B 417 " distance=2.04 Simple disulfide: pdb=" SG CYS C 23 " - pdb=" SG CYS C 87 " distance=2.02 Simple disulfide: pdb=" SG CYS D 22 " - pdb=" SG CYS D 96 " distance=2.03 Simple disulfide: pdb=" SG CYS E 71 " - pdb=" SG CYS E 192 " distance=2.04 Simple disulfide: pdb=" SG CYS E 331 " - pdb=" SG CYS E 340 " distance=2.03 Simple disulfide: pdb=" SG CYS E 355 " - pdb=" SG CYS E 363 " distance=2.01 Simple disulfide: pdb=" SG CYS E 387 " - pdb=" SG CYS E 392 " distance=2.09 Simple disulfide: pdb=" SG CYS E 394 " - pdb=" SG CYS E 417 " distance=2.04 Simple disulfide: pdb=" SG CYS F 23 " - pdb=" SG CYS F 87 " distance=2.02 Simple disulfide: pdb=" SG CYS G 22 " - pdb=" SG CYS G 96 " distance=2.03 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 BETA1-4 " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG O 1 " - " NAG O 2 " NAG-ASN " NAG A 601 " - " ASN A 99 " " NAG A 602 " - " ASN A 67 " " NAG B 601 " - " ASN B 99 " " NAG B 602 " - " ASN B 67 " " NAG E 601 " - " ASN E 99 " " NAG E 602 " - " ASN E 67 " " NAG I 1 " - " ASN A 414 " " NAG J 1 " - " ASN A 464 " " NAG K 1 " - " ASN B 414 " " NAG M 1 " - " ASN B 464 " " NAG N 1 " - " ASN E 414 " " NAG O 1 " - " ASN E 464 " Time building additional restraints: 0.99 Conformation dependent library (CDL) restraints added in 586.4 milliseconds 3924 Ramachandran restraints generated. 1962 Oldfield, 0 Emsley, 1962 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3726 Finding SS restraints... Secondary structure from input PDB file: 66 helices and 33 sheets defined 29.9% alpha, 41.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.31 Creating SS restraints... Processing helix chain 'A' and resid 29 through 35 Processing helix chain 'A' and resid 65 through 72 removed outlier: 6.151A pdb=" N LYS A 70 " --> pdb=" O ASN A 67 " (cutoff:3.500A) Processing helix chain 'A' and resid 74 through 99 Proline residue: A 89 - end of helix removed outlier: 3.785A pdb=" N TYR A 97 " --> pdb=" O ALA A 93 " (cutoff:3.500A) Processing helix chain 'A' and resid 117 through 121 Processing helix chain 'A' and resid 125 through 145 removed outlier: 3.885A pdb=" N LYS A 139 " --> pdb=" O TYR A 135 " (cutoff:3.500A) removed outlier: 4.289A pdb=" N ASN A 140 " --> pdb=" O GLU A 136 " (cutoff:3.500A) removed outlier: 4.365A pdb=" N ASN A 143 " --> pdb=" O LYS A 139 " (cutoff:3.500A) Processing helix chain 'A' and resid 147 through 153 Processing helix chain 'A' and resid 175 through 183 Processing helix chain 'A' and resid 184 through 187 Processing helix chain 'A' and resid 191 through 215 removed outlier: 4.300A pdb=" N PHE A 212 " --> pdb=" O SER A 208 " (cutoff:3.500A) removed outlier: 4.515A pdb=" N VAL A 213 " --> pdb=" O ASP A 209 " (cutoff:3.500A) Processing helix chain 'A' and resid 228 through 232 Processing helix chain 'A' and resid 233 through 236 Processing helix chain 'A' and resid 238 through 246 Processing helix chain 'A' and resid 252 through 259 Processing helix chain 'A' and resid 328 through 331 Processing helix chain 'A' and resid 349 through 357 Processing helix chain 'A' and resid 359 through 363 Processing helix chain 'A' and resid 437 through 441 Processing helix chain 'A' and resid 452 through 471 removed outlier: 3.520A pdb=" N SER A 457 " --> pdb=" O LYS A 453 " (cutoff:3.500A) Processing helix chain 'L' and resid 78 through 82 Processing helix chain 'H' and resid 62 through 65 Processing helix chain 'H' and resid 74 through 76 No H-bonds generated for 'chain 'H' and resid 74 through 76' Processing helix chain 'H' and resid 87 through 91 Processing helix chain 'B' and resid 29 through 35 Processing helix chain 'B' and resid 65 through 72 removed outlier: 6.151A pdb=" N LYS B 70 " --> pdb=" O ASN B 67 " (cutoff:3.500A) Processing helix chain 'B' and resid 74 through 99 Proline residue: B 89 - end of helix removed outlier: 3.785A pdb=" N TYR B 97 " --> pdb=" O ALA B 93 " (cutoff:3.500A) Processing helix chain 'B' and resid 117 through 121 Processing helix chain 'B' and resid 125 through 145 removed outlier: 3.885A pdb=" N LYS B 139 " --> pdb=" O TYR B 135 " (cutoff:3.500A) removed outlier: 4.289A pdb=" N ASN B 140 " --> pdb=" O GLU B 136 " (cutoff:3.500A) removed outlier: 4.365A pdb=" N ASN B 143 " --> pdb=" O LYS B 139 " (cutoff:3.500A) Processing helix chain 'B' and resid 147 through 153 Processing helix chain 'B' and resid 175 through 183 Processing helix chain 'B' and resid 184 through 187 Processing helix chain 'B' and resid 191 through 215 removed outlier: 4.301A pdb=" N PHE B 212 " --> pdb=" O SER B 208 " (cutoff:3.500A) removed outlier: 4.514A pdb=" N VAL B 213 " --> pdb=" O ASP B 209 " (cutoff:3.500A) Processing helix chain 'B' and resid 228 through 232 Processing helix chain 'B' and resid 233 through 236 Processing helix chain 'B' and resid 238 through 246 Processing helix chain 'B' and resid 252 through 259 Processing helix chain 'B' and resid 328 through 331 Processing helix chain 'B' and resid 349 through 357 Processing helix chain 'B' and resid 359 through 363 Processing helix chain 'B' and resid 437 through 441 Processing helix chain 'B' and resid 452 through 471 removed outlier: 3.519A pdb=" N SER B 457 " --> pdb=" O LYS B 453 " (cutoff:3.500A) Processing helix chain 'C' and resid 78 through 82 Processing helix chain 'D' and resid 62 through 65 Processing helix chain 'D' and resid 74 through 76 No H-bonds generated for 'chain 'D' and resid 74 through 76' Processing helix chain 'D' and resid 87 through 91 Processing helix chain 'E' and resid 29 through 35 Processing helix chain 'E' and resid 65 through 72 removed outlier: 6.151A pdb=" N LYS E 70 " --> pdb=" O ASN E 67 " (cutoff:3.500A) Processing helix chain 'E' and resid 74 through 99 Proline residue: E 89 - end of helix removed outlier: 3.786A pdb=" N TYR E 97 " --> pdb=" O ALA E 93 " (cutoff:3.500A) Processing helix chain 'E' and resid 117 through 121 Processing helix chain 'E' and resid 125 through 145 removed outlier: 3.885A pdb=" N LYS E 139 " --> pdb=" O TYR E 135 " (cutoff:3.500A) removed outlier: 4.289A pdb=" N ASN E 140 " --> pdb=" O GLU E 136 " (cutoff:3.500A) removed outlier: 4.365A pdb=" N ASN E 143 " --> pdb=" O LYS E 139 " (cutoff:3.500A) Processing helix chain 'E' and resid 147 through 153 Processing helix chain 'E' and resid 175 through 183 Processing helix chain 'E' and resid 184 through 187 Processing helix chain 'E' and resid 191 through 215 removed outlier: 4.300A pdb=" N PHE E 212 " --> pdb=" O SER E 208 " (cutoff:3.500A) removed outlier: 4.514A pdb=" N VAL E 213 " --> pdb=" O ASP E 209 " (cutoff:3.500A) Processing helix chain 'E' and resid 228 through 232 Processing helix chain 'E' and resid 233 through 236 Processing helix chain 'E' and resid 238 through 246 Processing helix chain 'E' and resid 252 through 259 Processing helix chain 'E' and resid 328 through 331 Processing helix chain 'E' and resid 349 through 357 Processing helix chain 'E' and resid 359 through 363 Processing helix chain 'E' and resid 437 through 441 Processing helix chain 'E' and resid 452 through 471 removed outlier: 3.519A pdb=" N SER E 457 " --> pdb=" O LYS E 453 " (cutoff:3.500A) Processing helix chain 'F' and resid 78 through 82 Processing helix chain 'G' and resid 62 through 65 Processing helix chain 'G' and resid 74 through 76 No H-bonds generated for 'chain 'G' and resid 74 through 76' Processing helix chain 'G' and resid 87 through 91 Processing sheet with id=AA1, first strand: chain 'A' and resid 158 through 164 removed outlier: 6.540A pdb=" N LYS A 167 " --> pdb=" O GLU A 163 " (cutoff:3.500A) removed outlier: 10.574A pdb=" N THR A 168 " --> pdb=" O THR A 54 " (cutoff:3.500A) removed outlier: 6.607A pdb=" N ASP A 56 " --> pdb=" O THR A 168 " (cutoff:3.500A) removed outlier: 4.788A pdb=" N TYR A 170 " --> pdb=" O ASP A 56 " (cutoff:3.500A) removed outlier: 5.995A pdb=" N VAL A 39 " --> pdb=" O LEU A 296 " (cutoff:3.500A) removed outlier: 4.746A pdb=" N LEU A 296 " --> pdb=" O VAL A 39 " (cutoff:3.500A) removed outlier: 6.615A pdb=" N GLY A 41 " --> pdb=" O GLN A 294 " (cutoff:3.500A) removed outlier: 7.484A pdb=" N GLN A 294 " --> pdb=" O GLY A 41 " (cutoff:3.500A) removed outlier: 8.806A pdb=" N THR A 43 " --> pdb=" O TYR A 292 " (cutoff:3.500A) removed outlier: 8.399A pdb=" N TYR A 292 " --> pdb=" O THR A 43 " (cutoff:3.500A) removed outlier: 10.152A pdb=" N LYS A 45 " --> pdb=" O GLN A 290 " (cutoff:3.500A) removed outlier: 10.195A pdb=" N GLN A 290 " --> pdb=" O LYS A 45 " (cutoff:3.500A) removed outlier: 6.352A pdb=" N LYS A 47 " --> pdb=" O ILE A 288 " (cutoff:3.500A) removed outlier: 6.639A pdb=" N ILE A 288 " --> pdb=" O LYS A 47 " (cutoff:3.500A) removed outlier: 5.664A pdb=" N LYS A 49 " --> pdb=" O THR A 286 " (cutoff:3.500A) removed outlier: 6.139A pdb=" N THR A 286 " --> pdb=" O LYS A 49 " (cutoff:3.500A) removed outlier: 5.117A pdb=" N ASN A 51 " --> pdb=" O ILE A 284 " (cutoff:3.500A) removed outlier: 4.172A pdb=" N ILE A 284 " --> pdb=" O ASN A 51 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 275 through 298 current: chain 'A' and resid 332 through 333 Processing sheet with id=AA2, first strand: chain 'A' and resid 226 through 227 removed outlier: 4.119A pdb=" N MET A 226 " --> pdb=" O GLY A 264 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N ALA A 263 " --> pdb=" O TYR A 281 " (cutoff:3.500A) removed outlier: 6.540A pdb=" N ILE A 277 " --> pdb=" O VAL A 267 " (cutoff:3.500A) removed outlier: 4.779A pdb=" N VAL A 269 " --> pdb=" O TYR A 275 " (cutoff:3.500A) removed outlier: 6.850A pdb=" N TYR A 275 " --> pdb=" O VAL A 269 " (cutoff:3.500A) removed outlier: 4.172A pdb=" N ILE A 284 " --> pdb=" O ASN A 51 " (cutoff:3.500A) removed outlier: 5.117A pdb=" N ASN A 51 " --> pdb=" O ILE A 284 " (cutoff:3.500A) removed outlier: 6.139A pdb=" N THR A 286 " --> pdb=" O LYS A 49 " (cutoff:3.500A) removed outlier: 5.664A pdb=" N LYS A 49 " --> pdb=" O THR A 286 " (cutoff:3.500A) removed outlier: 6.639A pdb=" N ILE A 288 " --> pdb=" O LYS A 47 " (cutoff:3.500A) removed outlier: 6.352A pdb=" N LYS A 47 " --> pdb=" O ILE A 288 " (cutoff:3.500A) removed outlier: 10.195A pdb=" N GLN A 290 " --> pdb=" O LYS A 45 " (cutoff:3.500A) removed outlier: 10.152A pdb=" N LYS A 45 " --> pdb=" O GLN A 290 " (cutoff:3.500A) removed outlier: 8.399A pdb=" N TYR A 292 " --> pdb=" O THR A 43 " (cutoff:3.500A) removed outlier: 8.806A pdb=" N THR A 43 " --> pdb=" O TYR A 292 " (cutoff:3.500A) removed outlier: 7.484A pdb=" N GLN A 294 " --> pdb=" O GLY A 41 " (cutoff:3.500A) removed outlier: 6.615A pdb=" N GLY A 41 " --> pdb=" O GLN A 294 " (cutoff:3.500A) removed outlier: 4.746A pdb=" N LEU A 296 " --> pdb=" O VAL A 39 " (cutoff:3.500A) removed outlier: 5.995A pdb=" N VAL A 39 " --> pdb=" O LEU A 296 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 38 through 60 current: chain 'A' and resid 322 through 326 Processing sheet with id=AA3, first strand: chain 'A' and resid 101 through 102 removed outlier: 6.575A pdb=" N MET A 115 " --> pdb=" O SER B 428 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 122 through 124 Processing sheet with id=AA5, first strand: chain 'A' and resid 301 through 302 Processing sheet with id=AA6, first strand: chain 'A' and resid 410 through 412 Processing sheet with id=AA7, first strand: chain 'A' and resid 392 through 394 Processing sheet with id=AA8, first strand: chain 'L' and resid 4 through 5 removed outlier: 5.484A pdb=" N THR L 68 " --> pdb=" O ALA L 25 " (cutoff:3.500A) removed outlier: 9.622A pdb=" N SER L 27 " --> pdb=" O SER L 66 " (cutoff:3.500A) removed outlier: 9.954A pdb=" N SER L 66 " --> pdb=" O SER L 27 " (cutoff:3.500A) removed outlier: 11.339A pdb=" N VAL L 29 " --> pdb=" O SER L 64 " (cutoff:3.500A) removed outlier: 11.802A pdb=" N SER L 64 " --> pdb=" O VAL L 29 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'L' and resid 10 through 13 removed outlier: 6.698A pdb=" N MET L 11 " --> pdb=" O GLU L 104 " (cutoff:3.500A) removed outlier: 6.502A pdb=" N TRP L 34 " --> pdb=" O LEU L 46 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'L' and resid 10 through 13 removed outlier: 6.698A pdb=" N MET L 11 " --> pdb=" O GLU L 104 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'H' and resid 3 through 7 Processing sheet with id=AB3, first strand: chain 'H' and resid 58 through 60 removed outlier: 6.544A pdb=" N TRP H 37 " --> pdb=" O MET H 49 " (cutoff:3.500A) removed outlier: 4.348A pdb=" N TYR H 51 " --> pdb=" O TRP H 35 " (cutoff:3.500A) removed outlier: 6.222A pdb=" N TRP H 35 " --> pdb=" O TYR H 51 " (cutoff:3.500A) removed outlier: 4.109A pdb=" N TYR H 108 " --> pdb=" O ARG H 98 " (cutoff:3.500A) removed outlier: 7.532A pdb=" N GLY H 100 " --> pdb=" O MET H 106 " (cutoff:3.500A) removed outlier: 6.224A pdb=" N MET H 106 " --> pdb=" O GLY H 100 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'H' and resid 58 through 60 removed outlier: 6.544A pdb=" N TRP H 37 " --> pdb=" O MET H 49 " (cutoff:3.500A) removed outlier: 4.348A pdb=" N TYR H 51 " --> pdb=" O TRP H 35 " (cutoff:3.500A) removed outlier: 6.222A pdb=" N TRP H 35 " --> pdb=" O TYR H 51 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 158 through 164 removed outlier: 6.539A pdb=" N LYS B 167 " --> pdb=" O GLU B 163 " (cutoff:3.500A) removed outlier: 10.574A pdb=" N THR B 168 " --> pdb=" O THR B 54 " (cutoff:3.500A) removed outlier: 6.607A pdb=" N ASP B 56 " --> pdb=" O THR B 168 " (cutoff:3.500A) removed outlier: 4.788A pdb=" N TYR B 170 " --> pdb=" O ASP B 56 " (cutoff:3.500A) removed outlier: 5.995A pdb=" N VAL B 39 " --> pdb=" O LEU B 296 " (cutoff:3.500A) removed outlier: 4.746A pdb=" N LEU B 296 " --> pdb=" O VAL B 39 " (cutoff:3.500A) removed outlier: 6.616A pdb=" N GLY B 41 " --> pdb=" O GLN B 294 " (cutoff:3.500A) removed outlier: 7.484A pdb=" N GLN B 294 " --> pdb=" O GLY B 41 " (cutoff:3.500A) removed outlier: 8.806A pdb=" N THR B 43 " --> pdb=" O TYR B 292 " (cutoff:3.500A) removed outlier: 8.399A pdb=" N TYR B 292 " --> pdb=" O THR B 43 " (cutoff:3.500A) removed outlier: 10.151A pdb=" N LYS B 45 " --> pdb=" O GLN B 290 " (cutoff:3.500A) removed outlier: 10.195A pdb=" N GLN B 290 " --> pdb=" O LYS B 45 " (cutoff:3.500A) removed outlier: 6.352A pdb=" N LYS B 47 " --> pdb=" O ILE B 288 " (cutoff:3.500A) removed outlier: 6.639A pdb=" N ILE B 288 " --> pdb=" O LYS B 47 " (cutoff:3.500A) removed outlier: 5.664A pdb=" N LYS B 49 " --> pdb=" O THR B 286 " (cutoff:3.500A) removed outlier: 6.139A pdb=" N THR B 286 " --> pdb=" O LYS B 49 " (cutoff:3.500A) removed outlier: 5.117A pdb=" N ASN B 51 " --> pdb=" O ILE B 284 " (cutoff:3.500A) removed outlier: 4.171A pdb=" N ILE B 284 " --> pdb=" O ASN B 51 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 275 through 298 current: chain 'B' and resid 332 through 333 Processing sheet with id=AB6, first strand: chain 'B' and resid 226 through 227 removed outlier: 4.119A pdb=" N MET B 226 " --> pdb=" O GLY B 264 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N ALA B 263 " --> pdb=" O TYR B 281 " (cutoff:3.500A) removed outlier: 6.540A pdb=" N ILE B 277 " --> pdb=" O VAL B 267 " (cutoff:3.500A) removed outlier: 4.779A pdb=" N VAL B 269 " --> pdb=" O TYR B 275 " (cutoff:3.500A) removed outlier: 6.850A pdb=" N TYR B 275 " --> pdb=" O VAL B 269 " (cutoff:3.500A) removed outlier: 4.171A pdb=" N ILE B 284 " --> pdb=" O ASN B 51 " (cutoff:3.500A) removed outlier: 5.117A pdb=" N ASN B 51 " --> pdb=" O ILE B 284 " (cutoff:3.500A) removed outlier: 6.139A pdb=" N THR B 286 " --> pdb=" O LYS B 49 " (cutoff:3.500A) removed outlier: 5.664A pdb=" N LYS B 49 " --> pdb=" O THR B 286 " (cutoff:3.500A) removed outlier: 6.639A pdb=" N ILE B 288 " --> pdb=" O LYS B 47 " (cutoff:3.500A) removed outlier: 6.352A pdb=" N LYS B 47 " --> pdb=" O ILE B 288 " (cutoff:3.500A) removed outlier: 10.195A pdb=" N GLN B 290 " --> pdb=" O LYS B 45 " (cutoff:3.500A) removed outlier: 10.151A pdb=" N LYS B 45 " --> pdb=" O GLN B 290 " (cutoff:3.500A) removed outlier: 8.399A pdb=" N TYR B 292 " --> pdb=" O THR B 43 " (cutoff:3.500A) removed outlier: 8.806A pdb=" N THR B 43 " --> pdb=" O TYR B 292 " (cutoff:3.500A) removed outlier: 7.484A pdb=" N GLN B 294 " --> pdb=" O GLY B 41 " (cutoff:3.500A) removed outlier: 6.616A pdb=" N GLY B 41 " --> pdb=" O GLN B 294 " (cutoff:3.500A) removed outlier: 4.746A pdb=" N LEU B 296 " --> pdb=" O VAL B 39 " (cutoff:3.500A) removed outlier: 5.995A pdb=" N VAL B 39 " --> pdb=" O LEU B 296 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 38 through 60 current: chain 'B' and resid 322 through 326 Processing sheet with id=AB7, first strand: chain 'B' and resid 101 through 102 removed outlier: 6.574A pdb=" N MET B 115 " --> pdb=" O SER E 428 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 122 through 124 Processing sheet with id=AB9, first strand: chain 'B' and resid 301 through 302 Processing sheet with id=AC1, first strand: chain 'C' and resid 4 through 5 removed outlier: 5.484A pdb=" N THR C 68 " --> pdb=" O ALA C 25 " (cutoff:3.500A) removed outlier: 9.622A pdb=" N SER C 27 " --> pdb=" O SER C 66 " (cutoff:3.500A) removed outlier: 9.954A pdb=" N SER C 66 " --> pdb=" O SER C 27 " (cutoff:3.500A) removed outlier: 11.338A pdb=" N VAL C 29 " --> pdb=" O SER C 64 " (cutoff:3.500A) removed outlier: 11.802A pdb=" N SER C 64 " --> pdb=" O VAL C 29 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 10 through 13 removed outlier: 6.698A pdb=" N MET C 11 " --> pdb=" O GLU C 104 " (cutoff:3.500A) removed outlier: 6.502A pdb=" N TRP C 34 " --> pdb=" O LEU C 46 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 10 through 13 removed outlier: 6.698A pdb=" N MET C 11 " --> pdb=" O GLU C 104 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'D' and resid 3 through 7 Processing sheet with id=AC5, first strand: chain 'D' and resid 58 through 60 removed outlier: 6.544A pdb=" N TRP D 37 " --> pdb=" O MET D 49 " (cutoff:3.500A) removed outlier: 4.348A pdb=" N TYR D 51 " --> pdb=" O TRP D 35 " (cutoff:3.500A) removed outlier: 6.222A pdb=" N TRP D 35 " --> pdb=" O TYR D 51 " (cutoff:3.500A) removed outlier: 4.109A pdb=" N TYR D 108 " --> pdb=" O ARG D 98 " (cutoff:3.500A) removed outlier: 7.532A pdb=" N GLY D 100 " --> pdb=" O MET D 106 " (cutoff:3.500A) removed outlier: 6.223A pdb=" N MET D 106 " --> pdb=" O GLY D 100 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'D' and resid 58 through 60 removed outlier: 6.544A pdb=" N TRP D 37 " --> pdb=" O MET D 49 " (cutoff:3.500A) removed outlier: 4.348A pdb=" N TYR D 51 " --> pdb=" O TRP D 35 " (cutoff:3.500A) removed outlier: 6.222A pdb=" N TRP D 35 " --> pdb=" O TYR D 51 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'E' and resid 158 through 164 removed outlier: 6.539A pdb=" N LYS E 167 " --> pdb=" O GLU E 163 " (cutoff:3.500A) removed outlier: 10.574A pdb=" N THR E 168 " --> pdb=" O THR E 54 " (cutoff:3.500A) removed outlier: 6.606A pdb=" N ASP E 56 " --> pdb=" O THR E 168 " (cutoff:3.500A) removed outlier: 4.788A pdb=" N TYR E 170 " --> pdb=" O ASP E 56 " (cutoff:3.500A) removed outlier: 5.995A pdb=" N VAL E 39 " --> pdb=" O LEU E 296 " (cutoff:3.500A) removed outlier: 4.746A pdb=" N LEU E 296 " --> pdb=" O VAL E 39 " (cutoff:3.500A) removed outlier: 6.616A pdb=" N GLY E 41 " --> pdb=" O GLN E 294 " (cutoff:3.500A) removed outlier: 7.484A pdb=" N GLN E 294 " --> pdb=" O GLY E 41 " (cutoff:3.500A) removed outlier: 8.805A pdb=" N THR E 43 " --> pdb=" O TYR E 292 " (cutoff:3.500A) removed outlier: 8.399A pdb=" N TYR E 292 " --> pdb=" O THR E 43 " (cutoff:3.500A) removed outlier: 10.152A pdb=" N LYS E 45 " --> pdb=" O GLN E 290 " (cutoff:3.500A) removed outlier: 10.195A pdb=" N GLN E 290 " --> pdb=" O LYS E 45 " (cutoff:3.500A) removed outlier: 6.353A pdb=" N LYS E 47 " --> pdb=" O ILE E 288 " (cutoff:3.500A) removed outlier: 6.639A pdb=" N ILE E 288 " --> pdb=" O LYS E 47 " (cutoff:3.500A) removed outlier: 5.665A pdb=" N LYS E 49 " --> pdb=" O THR E 286 " (cutoff:3.500A) removed outlier: 6.138A pdb=" N THR E 286 " --> pdb=" O LYS E 49 " (cutoff:3.500A) removed outlier: 5.117A pdb=" N ASN E 51 " --> pdb=" O ILE E 284 " (cutoff:3.500A) removed outlier: 4.171A pdb=" N ILE E 284 " --> pdb=" O ASN E 51 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 275 through 298 current: chain 'E' and resid 332 through 333 Processing sheet with id=AC8, first strand: chain 'E' and resid 226 through 227 removed outlier: 4.119A pdb=" N MET E 226 " --> pdb=" O GLY E 264 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N ALA E 263 " --> pdb=" O TYR E 281 " (cutoff:3.500A) removed outlier: 6.540A pdb=" N ILE E 277 " --> pdb=" O VAL E 267 " (cutoff:3.500A) removed outlier: 4.779A pdb=" N VAL E 269 " --> pdb=" O TYR E 275 " (cutoff:3.500A) removed outlier: 6.850A pdb=" N TYR E 275 " --> pdb=" O VAL E 269 " (cutoff:3.500A) removed outlier: 4.171A pdb=" N ILE E 284 " --> pdb=" O ASN E 51 " (cutoff:3.500A) removed outlier: 5.117A pdb=" N ASN E 51 " --> pdb=" O ILE E 284 " (cutoff:3.500A) removed outlier: 6.138A pdb=" N THR E 286 " --> pdb=" O LYS E 49 " (cutoff:3.500A) removed outlier: 5.665A pdb=" N LYS E 49 " --> pdb=" O THR E 286 " (cutoff:3.500A) removed outlier: 6.639A pdb=" N ILE E 288 " --> pdb=" O LYS E 47 " (cutoff:3.500A) removed outlier: 6.353A pdb=" N LYS E 47 " --> pdb=" O ILE E 288 " (cutoff:3.500A) removed outlier: 10.195A pdb=" N GLN E 290 " --> pdb=" O LYS E 45 " (cutoff:3.500A) removed outlier: 10.152A pdb=" N LYS E 45 " --> pdb=" O GLN E 290 " (cutoff:3.500A) removed outlier: 8.399A pdb=" N TYR E 292 " --> pdb=" O THR E 43 " (cutoff:3.500A) removed outlier: 8.805A pdb=" N THR E 43 " --> pdb=" O TYR E 292 " (cutoff:3.500A) removed outlier: 7.484A pdb=" N GLN E 294 " --> pdb=" O GLY E 41 " (cutoff:3.500A) removed outlier: 6.616A pdb=" N GLY E 41 " --> pdb=" O GLN E 294 " (cutoff:3.500A) removed outlier: 4.746A pdb=" N LEU E 296 " --> pdb=" O VAL E 39 " (cutoff:3.500A) removed outlier: 5.995A pdb=" N VAL E 39 " --> pdb=" O LEU E 296 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 38 through 60 current: chain 'E' and resid 322 through 326 Processing sheet with id=AC9, first strand: chain 'E' and resid 301 through 302 Processing sheet with id=AD1, first strand: chain 'F' and resid 4 through 5 removed outlier: 5.485A pdb=" N THR F 68 " --> pdb=" O ALA F 25 " (cutoff:3.500A) removed outlier: 9.622A pdb=" N SER F 27 " --> pdb=" O SER F 66 " (cutoff:3.500A) removed outlier: 9.954A pdb=" N SER F 66 " --> pdb=" O SER F 27 " (cutoff:3.500A) removed outlier: 11.339A pdb=" N VAL F 29 " --> pdb=" O SER F 64 " (cutoff:3.500A) removed outlier: 11.802A pdb=" N SER F 64 " --> pdb=" O VAL F 29 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'F' and resid 10 through 13 removed outlier: 6.698A pdb=" N MET F 11 " --> pdb=" O GLU F 104 " (cutoff:3.500A) removed outlier: 6.502A pdb=" N TRP F 34 " --> pdb=" O LEU F 46 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'F' and resid 10 through 13 removed outlier: 6.698A pdb=" N MET F 11 " --> pdb=" O GLU F 104 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'G' and resid 3 through 7 Processing sheet with id=AD5, first strand: chain 'G' and resid 58 through 60 removed outlier: 6.544A pdb=" N TRP G 37 " --> pdb=" O MET G 49 " (cutoff:3.500A) removed outlier: 4.349A pdb=" N TYR G 51 " --> pdb=" O TRP G 35 " (cutoff:3.500A) removed outlier: 6.222A pdb=" N TRP G 35 " --> pdb=" O TYR G 51 " (cutoff:3.500A) removed outlier: 4.108A pdb=" N TYR G 108 " --> pdb=" O ARG G 98 " (cutoff:3.500A) removed outlier: 7.532A pdb=" N GLY G 100 " --> pdb=" O MET G 106 " (cutoff:3.500A) removed outlier: 6.224A pdb=" N MET G 106 " --> pdb=" O GLY G 100 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'G' and resid 58 through 60 removed outlier: 6.544A pdb=" N TRP G 37 " --> pdb=" O MET G 49 " (cutoff:3.500A) removed outlier: 4.349A pdb=" N TYR G 51 " --> pdb=" O TRP G 35 " (cutoff:3.500A) removed outlier: 6.222A pdb=" N TRP G 35 " --> pdb=" O TYR G 51 " (cutoff:3.500A) 713 hydrogen bonds defined for protein. 1815 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: 2.89 Time building geometry restraints manager: 1.33 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 3958 1.33 - 1.46: 4350 1.46 - 1.59: 7307 1.59 - 1.72: 9 1.72 - 1.85: 111 Bond restraints: 15735 Sorted by residual: bond pdb=" CG MET B 411 " pdb=" SD MET B 411 " ideal model delta sigma weight residual 1.803 1.717 0.086 2.50e-02 1.60e+03 1.19e+01 bond pdb=" CG MET A 411 " pdb=" SD MET A 411 " ideal model delta sigma weight residual 1.803 1.717 0.086 2.50e-02 1.60e+03 1.18e+01 bond pdb=" NE ARG E 365 " pdb=" CZ ARG E 365 " ideal model delta sigma weight residual 1.326 1.364 -0.038 1.10e-02 8.26e+03 1.17e+01 bond pdb=" CG MET E 411 " pdb=" SD MET E 411 " ideal model delta sigma weight residual 1.803 1.718 0.085 2.50e-02 1.60e+03 1.16e+01 bond pdb=" NE ARG A 365 " pdb=" CZ ARG A 365 " ideal model delta sigma weight residual 1.326 1.363 -0.037 1.10e-02 8.26e+03 1.16e+01 ... (remaining 15730 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.79: 18048 1.79 - 3.59: 2776 3.59 - 5.38: 491 5.38 - 7.17: 93 7.17 - 8.97: 6 Bond angle restraints: 21414 Sorted by residual: angle pdb=" C GLY E 215 " pdb=" N PRO E 216 " pdb=" CA PRO E 216 " ideal model delta sigma weight residual 119.56 128.53 -8.97 1.02e+00 9.61e-01 7.73e+01 angle pdb=" C GLY A 215 " pdb=" N PRO A 216 " pdb=" CA PRO A 216 " ideal model delta sigma weight residual 119.56 128.51 -8.95 1.02e+00 9.61e-01 7.70e+01 angle pdb=" C GLY B 215 " pdb=" N PRO B 216 " pdb=" CA PRO B 216 " ideal model delta sigma weight residual 119.56 128.51 -8.95 1.02e+00 9.61e-01 7.70e+01 angle pdb=" N VAL E 75 " pdb=" CA VAL E 75 " pdb=" C VAL E 75 " ideal model delta sigma weight residual 110.42 117.46 -7.04 9.60e-01 1.09e+00 5.37e+01 angle pdb=" N VAL A 75 " pdb=" CA VAL A 75 " pdb=" C VAL A 75 " ideal model delta sigma weight residual 110.42 117.44 -7.02 9.60e-01 1.09e+00 5.35e+01 ... (remaining 21409 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.36: 8927 17.36 - 34.72: 265 34.72 - 52.08: 69 52.08 - 69.45: 39 69.45 - 86.81: 15 Dihedral angle restraints: 9315 sinusoidal: 3501 harmonic: 5814 Sorted by residual: dihedral pdb=" CB CYS E 71 " pdb=" SG CYS E 71 " pdb=" SG CYS E 192 " pdb=" CB CYS E 192 " ideal model delta sinusoidal sigma weight residual -86.00 -118.97 32.97 1 1.00e+01 1.00e-02 1.55e+01 dihedral pdb=" CB CYS A 71 " pdb=" SG CYS A 71 " pdb=" SG CYS A 192 " pdb=" CB CYS A 192 " ideal model delta sinusoidal sigma weight residual -86.00 -118.94 32.94 1 1.00e+01 1.00e-02 1.54e+01 dihedral pdb=" CB CYS B 71 " pdb=" SG CYS B 71 " pdb=" SG CYS B 192 " pdb=" CB CYS B 192 " ideal model delta sinusoidal sigma weight residual -86.00 -118.93 32.93 1 1.00e+01 1.00e-02 1.54e+01 ... (remaining 9312 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.084: 1784 0.084 - 0.168: 625 0.168 - 0.253: 137 0.253 - 0.337: 35 0.337 - 0.421: 14 Chirality restraints: 2595 Sorted by residual: chirality pdb=" C1 NAG M 2 " pdb=" O4 NAG M 1 " pdb=" C2 NAG M 2 " pdb=" O5 NAG M 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.61 0.21 2.00e-02 2.50e+03 1.13e+02 chirality pdb=" C1 NAG J 2 " pdb=" O4 NAG J 1 " pdb=" C2 NAG J 2 " pdb=" O5 NAG J 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.61 0.21 2.00e-02 2.50e+03 1.10e+02 chirality pdb=" C1 NAG O 2 " pdb=" O4 NAG O 1 " pdb=" C2 NAG O 2 " pdb=" O5 NAG O 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.61 0.21 2.00e-02 2.50e+03 1.10e+02 ... (remaining 2592 not shown) Planarity restraints: 2664 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN E 67 " 0.045 2.00e-02 2.50e+03 4.55e-02 2.59e+01 pdb=" CG ASN E 67 " -0.022 2.00e-02 2.50e+03 pdb=" OD1 ASN E 67 " -0.009 2.00e-02 2.50e+03 pdb=" ND2 ASN E 67 " -0.069 2.00e-02 2.50e+03 pdb=" C1 NAG E 602 " 0.055 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 67 " 0.045 2.00e-02 2.50e+03 4.54e-02 2.58e+01 pdb=" CG ASN A 67 " -0.022 2.00e-02 2.50e+03 pdb=" OD1 ASN A 67 " -0.009 2.00e-02 2.50e+03 pdb=" ND2 ASN A 67 " -0.068 2.00e-02 2.50e+03 pdb=" C1 NAG A 602 " 0.055 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN B 67 " -0.045 2.00e-02 2.50e+03 4.53e-02 2.56e+01 pdb=" CG ASN B 67 " 0.022 2.00e-02 2.50e+03 pdb=" OD1 ASN B 67 " 0.010 2.00e-02 2.50e+03 pdb=" ND2 ASN B 67 " 0.068 2.00e-02 2.50e+03 pdb=" C1 NAG B 602 " -0.055 2.00e-02 2.50e+03 ... (remaining 2661 not shown) Histogram of nonbonded interaction distances: 2.35 - 2.86: 5224 2.86 - 3.37: 14212 3.37 - 3.88: 27455 3.88 - 4.39: 31711 4.39 - 4.90: 53008 Nonbonded interactions: 131610 Sorted by model distance: nonbonded pdb=" OG SER B 50 " pdb=" OG1 THR B 286 " model vdw 2.351 3.040 nonbonded pdb=" OG SER E 50 " pdb=" OG1 THR E 286 " model vdw 2.352 3.040 nonbonded pdb=" OG SER A 50 " pdb=" OG1 THR A 286 " model vdw 2.352 3.040 nonbonded pdb=" CG PRO A 347 " pdb=" O LEU B 367 " model vdw 2.427 3.440 nonbonded pdb=" O LEU A 367 " pdb=" CG PRO E 347 " model vdw 2.427 3.440 ... (remaining 131605 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 'B' selection = chain 'E' } ncs_group { reference = chain 'C' selection = chain 'F' selection = chain 'L' } ncs_group { reference = chain 'D' selection = chain 'G' selection = chain 'H' } ncs_group { reference = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'M' selection = chain 'N' selection = chain 'O' } 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 individual isotropic 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: 3.980 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.250 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 13.480 Find NCS groups from input model: 0.320 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:8.560 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.720 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8062 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 : 0.014 0.094 15774 Z= 0.734 Angle : 1.389 8.968 21510 Z= 0.929 Chirality : 0.093 0.421 2595 Planarity : 0.006 0.032 2652 Dihedral : 11.115 86.808 5526 Min Nonbonded Distance : 2.351 Molprobity Statistics. All-atom Clashscore : 2.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.22 % Favored : 98.78 % Rotamer: Outliers : 0.17 % Allowed : 1.22 % Favored : 98.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.00 % 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: 0.21 (0.18), residues: 1962 helix: -0.45 (0.21), residues: 438 sheet: 0.45 (0.21), residues: 528 loop : 0.43 (0.19), residues: 996 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG B 365 TYR 0.038 0.005 TYR B 46 PHE 0.023 0.004 PHE D 79 TRP 0.023 0.006 TRP B 308 HIS 0.002 0.001 HIS C 33 Details of bonding type rmsd/Z covalent geometry : bond 0.01373 / 0.73 (15735) covalent geometry : angle 1.37902 / 0.93 (21414) SS BOND : bond 0.02289 / 1.36 ( 21) SS BOND : angle 2.83483 / 2.07 ( 42) hydrogen bonds : bond 0.16286 / 10.67 ( 644) hydrogen bonds : angle 7.72580 / 5.40 ( 1815) link_BETA1-4 : bond 0.05557 / 3.72 ( 6) link_BETA1-4 : angle 2.65973 / 1.56 ( 18) link_NAG-ASN : bond 0.05771 / 3.68 ( 12) link_NAG-ASN : angle 3.01484 / 2.13 ( 36) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3924 Ramachandran restraints generated. 1962 Oldfield, 0 Emsley, 1962 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3924 Ramachandran restraints generated. 1962 Oldfield, 0 Emsley, 1962 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 401 residues out of total 1749 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 398 time to evaluate : 0.433 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 244 ARG cc_start: 0.8086 (ttp-170) cc_final: 0.7848 (ttm-80) REVERT: H 45 LYS cc_start: 0.8261 (tmmt) cc_final: 0.8061 (pmtt) REVERT: B 138 MET cc_start: 0.8075 (mmm) cc_final: 0.7645 (mmm) REVERT: B 155 ASN cc_start: 0.7583 (p0) cc_final: 0.6947 (t0) REVERT: E 138 MET cc_start: 0.7992 (mmm) cc_final: 0.7422 (mmm) REVERT: E 244 ARG cc_start: 0.7921 (ttp-170) cc_final: 0.7721 (ttp-170) REVERT: F 31 TYR cc_start: 0.8598 (m-80) cc_final: 0.8334 (m-80) outliers start: 3 outliers final: 1 residues processed: 401 average time/residue: 0.4377 time to fit residues: 198.3296 Evaluate side-chains 228 residues out of total 1749 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 227 time to evaluate : 0.628 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 220 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 98 optimal weight: 0.8980 chunk 107 optimal weight: 2.9990 chunk 10 optimal weight: 0.9980 chunk 66 optimal weight: 4.9990 chunk 130 optimal weight: 1.9990 chunk 124 optimal weight: 0.9980 chunk 103 optimal weight: 0.8980 chunk 77 optimal weight: 0.9990 chunk 122 optimal weight: 0.9980 chunk 91 optimal weight: 0.8980 chunk 149 optimal weight: 0.7980 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 303 ASN A 393 GLN A 395 GLN H 77 ASN B 100 ASN B 127 GLN B 395 GLN D 77 ASN E 100 ASN E 127 GLN E 182 ASN E 194 GLN E 219 GLN E 395 GLN G 77 ASN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3576 r_free = 0.3576 target = 0.144425 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3374 r_free = 0.3374 target = 0.128782 restraints weight = 18121.517| |-----------------------------------------------------------------------------| r_work (start): 0.3384 rms_B_bonded: 1.24 r_work: 0.3285 rms_B_bonded: 1.61 restraints_weight: 0.5000 r_work: 0.3179 rms_B_bonded: 2.74 restraints_weight: 0.2500 r_work (final): 0.3179 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8341 moved from start: 0.2101 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.059 15774 Z= 0.205 Angle : 0.664 9.695 21510 Z= 0.355 Chirality : 0.050 0.337 2595 Planarity : 0.004 0.030 2652 Dihedral : 5.207 34.144 2132 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 4.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.38 % Favored : 98.62 % Rotamer: Outliers : 3.26 % Allowed : 9.21 % Favored : 87.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.00 % 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: 0.31 (0.18), residues: 1962 helix: 0.57 (0.23), residues: 444 sheet: 0.12 (0.20), residues: 606 loop : 0.27 (0.20), residues: 912 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG E 365 TYR 0.019 0.002 TYR E 432 PHE 0.014 0.002 PHE A 212 TRP 0.022 0.002 TRP G 109 HIS 0.004 0.002 HIS L 33 Details of bonding type rmsd/Z covalent geometry : bond 0.00479 / 0.20 (15735) covalent geometry : angle 0.64457 / 0.35 (21414) SS BOND : bond 0.00256 / 0.16 ( 21) SS BOND : angle 1.75350 / 1.23 ( 42) hydrogen bonds : bond 0.04725 / 3.17 ( 644) hydrogen bonds : angle 5.73300 / 4.04 ( 1815) link_BETA1-4 : bond 0.00591 / 0.39 ( 6) link_BETA1-4 : angle 1.58374 / 0.98 ( 18) link_NAG-ASN : bond 0.00954 / 0.68 ( 12) link_NAG-ASN : angle 3.40010 / 2.24 ( 36) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3924 Ramachandran restraints generated. 1962 Oldfield, 0 Emsley, 1962 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3924 Ramachandran restraints generated. 1962 Oldfield, 0 Emsley, 1962 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 295 residues out of total 1749 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 239 time to evaluate : 0.610 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 45 LYS cc_start: 0.8789 (OUTLIER) cc_final: 0.8260 (ptmt) REVERT: A 56 ASP cc_start: 0.7740 (m-30) cc_final: 0.7517 (m-30) REVERT: A 135 TYR cc_start: 0.8722 (t80) cc_final: 0.8332 (t80) REVERT: A 244 ARG cc_start: 0.8627 (ttp-170) cc_final: 0.7926 (ttm-80) REVERT: A 304 ASP cc_start: 0.7045 (t0) cc_final: 0.6799 (t0) REVERT: A 425 ILE cc_start: 0.8522 (OUTLIER) cc_final: 0.8168 (mp) REVERT: A 453 LYS cc_start: 0.7383 (OUTLIER) cc_final: 0.6695 (pttp) REVERT: L 31 TYR cc_start: 0.8579 (m-80) cc_final: 0.8366 (m-80) REVERT: B 139 LYS cc_start: 0.7467 (mmmt) cc_final: 0.7184 (mppt) REVERT: B 155 ASN cc_start: 0.8113 (p0) cc_final: 0.7130 (t0) REVERT: B 156 GLU cc_start: 0.7946 (OUTLIER) cc_final: 0.7717 (tp30) REVERT: B 220 ASP cc_start: 0.8126 (OUTLIER) cc_final: 0.7722 (m-30) REVERT: B 306 SER cc_start: 0.8785 (OUTLIER) cc_final: 0.8519 (t) REVERT: C 19 ILE cc_start: 0.8525 (OUTLIER) cc_final: 0.8320 (OUTLIER) REVERT: C 31 TYR cc_start: 0.8538 (m-80) cc_final: 0.8305 (m-80) REVERT: C 102 LYS cc_start: 0.8300 (ttmm) cc_final: 0.7837 (ttpt) REVERT: D 45 LYS cc_start: 0.8640 (tmtm) cc_final: 0.7974 (ptpp) REVERT: E 32 LYS cc_start: 0.8899 (OUTLIER) cc_final: 0.8379 (mttp) REVERT: E 138 MET cc_start: 0.8088 (mmm) cc_final: 0.7683 (mmm) REVERT: E 166 GLU cc_start: 0.7776 (OUTLIER) cc_final: 0.7015 (mt-10) REVERT: E 220 ASP cc_start: 0.8195 (OUTLIER) cc_final: 0.7739 (t0) REVERT: E 244 ARG cc_start: 0.8482 (ttp-170) cc_final: 0.7631 (tpp-160) REVERT: F 11 MET cc_start: 0.7300 (mtp) cc_final: 0.6817 (ttm) REVERT: F 44 LYS cc_start: 0.8137 (tttt) cc_final: 0.7882 (ttpp) REVERT: F 86 TYR cc_start: 0.9021 (m-80) cc_final: 0.8747 (m-80) REVERT: G 45 LYS cc_start: 0.8058 (ptpp) cc_final: 0.7740 (ptmm) REVERT: G 73 ASP cc_start: 0.7741 (t0) cc_final: 0.7213 (t70) outliers start: 56 outliers final: 20 residues processed: 276 average time/residue: 0.4657 time to fit residues: 145.0815 Evaluate side-chains 239 residues out of total 1749 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 210 time to evaluate : 0.560 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 LYS Chi-restraints excluded: chain A residue 72 THR Chi-restraints excluded: chain A residue 153 SER Chi-restraints excluded: chain A residue 156 GLU Chi-restraints excluded: chain A residue 306 SER Chi-restraints excluded: chain A residue 425 ILE Chi-restraints excluded: chain A residue 453 LYS Chi-restraints excluded: chain L residue 22 THR Chi-restraints excluded: chain H residue 88 SER Chi-restraints excluded: chain B residue 72 THR Chi-restraints excluded: chain B residue 153 SER Chi-restraints excluded: chain B residue 156 GLU Chi-restraints excluded: chain B residue 220 ASP Chi-restraints excluded: chain B residue 306 SER Chi-restraints excluded: chain B residue 375 ARG Chi-restraints excluded: chain B residue 397 THR Chi-restraints excluded: chain B residue 416 THR Chi-restraints excluded: chain C residue 19 ILE Chi-restraints excluded: chain D residue 88 SER Chi-restraints excluded: chain E residue 32 LYS Chi-restraints excluded: chain E residue 72 THR Chi-restraints excluded: chain E residue 153 SER Chi-restraints excluded: chain E residue 166 GLU Chi-restraints excluded: chain E residue 186 THR Chi-restraints excluded: chain E residue 220 ASP Chi-restraints excluded: chain E residue 306 SER Chi-restraints excluded: chain E residue 397 THR Chi-restraints excluded: chain F residue 22 THR Chi-restraints excluded: chain G residue 88 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 52 optimal weight: 1.9990 chunk 71 optimal weight: 1.9990 chunk 13 optimal weight: 2.9990 chunk 72 optimal weight: 2.9990 chunk 144 optimal weight: 0.5980 chunk 66 optimal weight: 3.9990 chunk 19 optimal weight: 0.3980 chunk 149 optimal weight: 1.9990 chunk 21 optimal weight: 2.9990 chunk 96 optimal weight: 0.9990 chunk 105 optimal weight: 1.9990 overall best weight: 1.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 393 GLN L 52 ASN H 77 ASN B 194 GLN B 393 GLN C 52 ASN D 77 ASN E 162 GLN E 194 GLN F 52 ASN G 77 ASN G 78 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3539 r_free = 0.3539 target = 0.141332 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.125758 restraints weight = 18236.731| |-----------------------------------------------------------------------------| r_work (start): 0.3346 rms_B_bonded: 1.19 r_work: 0.3246 rms_B_bonded: 1.57 restraints_weight: 0.5000 r_work: 0.3139 rms_B_bonded: 2.68 restraints_weight: 0.2500 r_work (final): 0.3139 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8379 moved from start: 0.2632 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.095 15774 Z= 0.230 Angle : 0.659 8.494 21510 Z= 0.346 Chirality : 0.050 0.352 2595 Planarity : 0.004 0.035 2652 Dihedral : 5.055 16.486 2130 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 5.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.94 % Favored : 98.06 % Rotamer: Outliers : 3.21 % Allowed : 11.13 % Favored : 85.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.00 % 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: 0.11 (0.18), residues: 1962 helix: 0.72 (0.23), residues: 450 sheet: -0.10 (0.20), residues: 600 loop : 0.02 (0.20), residues: 912 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG B 365 TYR 0.016 0.002 TYR E 438 PHE 0.018 0.002 PHE A 212 TRP 0.021 0.002 TRP G 109 HIS 0.008 0.002 HIS B 29 Details of bonding type rmsd/Z covalent geometry : bond 0.00548 / 0.23 (15735) covalent geometry : angle 0.64656 / 0.34 (21414) SS BOND : bond 0.00413 / 0.26 ( 21) SS BOND : angle 1.85486 / 1.39 ( 42) hydrogen bonds : bond 0.04320 / 2.88 ( 644) hydrogen bonds : angle 5.46638 / 3.85 ( 1815) link_BETA1-4 : bond 0.00610 / 0.40 ( 6) link_BETA1-4 : angle 1.26772 / 0.82 ( 18) link_NAG-ASN : bond 0.00441 / 0.32 ( 12) link_NAG-ASN : angle 2.52418 / 1.74 ( 36) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3924 Ramachandran restraints generated. 1962 Oldfield, 0 Emsley, 1962 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3924 Ramachandran restraints generated. 1962 Oldfield, 0 Emsley, 1962 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 289 residues out of total 1749 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 234 time to evaluate : 0.545 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 67 ASN cc_start: 0.7956 (m-40) cc_final: 0.7549 (t160) REVERT: A 135 TYR cc_start: 0.8740 (t80) cc_final: 0.8322 (t80) REVERT: A 220 ASP cc_start: 0.8012 (OUTLIER) cc_final: 0.7584 (t0) REVERT: A 244 ARG cc_start: 0.8549 (ttp-170) cc_final: 0.7951 (ttm-80) REVERT: A 304 ASP cc_start: 0.7271 (t0) cc_final: 0.6863 (t0) REVERT: A 425 ILE cc_start: 0.8659 (OUTLIER) cc_final: 0.8266 (mp) REVERT: A 453 LYS cc_start: 0.7427 (OUTLIER) cc_final: 0.6808 (pttp) REVERT: B 139 LYS cc_start: 0.7571 (mmmt) cc_final: 0.7289 (mppt) REVERT: B 155 ASN cc_start: 0.8064 (p0) cc_final: 0.7115 (t0) REVERT: B 156 GLU cc_start: 0.8026 (OUTLIER) cc_final: 0.7751 (tp30) REVERT: B 161 LEU cc_start: 0.9027 (mt) cc_final: 0.8748 (mp) REVERT: B 220 ASP cc_start: 0.8265 (OUTLIER) cc_final: 0.7761 (m-30) REVERT: B 304 ASP cc_start: 0.7166 (t0) cc_final: 0.6936 (t0) REVERT: B 306 SER cc_start: 0.8745 (OUTLIER) cc_final: 0.8503 (t) REVERT: B 390 VAL cc_start: 0.8373 (m) cc_final: 0.7969 (p) REVERT: C 31 TYR cc_start: 0.8574 (m-80) cc_final: 0.8298 (m-80) REVERT: C 71 SER cc_start: 0.8720 (p) cc_final: 0.8380 (t) REVERT: C 102 LYS cc_start: 0.8247 (ttmm) cc_final: 0.7819 (ttpt) REVERT: D 113 THR cc_start: 0.8535 (OUTLIER) cc_final: 0.8299 (p) REVERT: E 32 LYS cc_start: 0.8919 (OUTLIER) cc_final: 0.8431 (mttp) REVERT: E 76 MET cc_start: 0.8819 (mmm) cc_final: 0.8599 (mmm) REVERT: E 138 MET cc_start: 0.8092 (mmm) cc_final: 0.7741 (mmm) REVERT: E 139 LYS cc_start: 0.7947 (mppt) cc_final: 0.7671 (mppt) REVERT: E 220 ASP cc_start: 0.8334 (OUTLIER) cc_final: 0.7891 (t0) REVERT: E 244 ARG cc_start: 0.8485 (ttp-170) cc_final: 0.7758 (ttp-170) REVERT: E 304 ASP cc_start: 0.7101 (t0) cc_final: 0.6827 (t0) REVERT: F 44 LYS cc_start: 0.8263 (tttt) cc_final: 0.7760 (ptpp) REVERT: F 86 TYR cc_start: 0.9047 (m-80) cc_final: 0.8799 (m-80) REVERT: G 45 LYS cc_start: 0.8112 (ptpp) cc_final: 0.7796 (ptmm) outliers start: 55 outliers final: 31 residues processed: 270 average time/residue: 0.4494 time to fit residues: 137.1812 Evaluate side-chains 253 residues out of total 1749 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 213 time to evaluate : 0.592 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 THR Chi-restraints excluded: chain A residue 153 SER Chi-restraints excluded: chain A residue 156 GLU Chi-restraints excluded: chain A residue 220 ASP Chi-restraints excluded: chain A residue 306 SER Chi-restraints excluded: chain A residue 397 THR Chi-restraints excluded: chain A residue 422 LEU Chi-restraints excluded: chain A residue 425 ILE Chi-restraints excluded: chain A residue 453 LYS Chi-restraints excluded: chain L residue 22 THR Chi-restraints excluded: chain H residue 29 ILE Chi-restraints excluded: chain H residue 88 SER Chi-restraints excluded: chain H residue 114 SER Chi-restraints excluded: chain H residue 116 THR Chi-restraints excluded: chain B residue 49 LYS Chi-restraints excluded: chain B residue 72 THR Chi-restraints excluded: chain B residue 153 SER Chi-restraints excluded: chain B residue 156 GLU Chi-restraints excluded: chain B residue 220 ASP Chi-restraints excluded: chain B residue 306 SER Chi-restraints excluded: chain B residue 375 ARG Chi-restraints excluded: chain B residue 397 THR Chi-restraints excluded: chain B residue 422 LEU Chi-restraints excluded: chain C residue 5 THR Chi-restraints excluded: chain C residue 19 ILE Chi-restraints excluded: chain C residue 22 THR Chi-restraints excluded: chain D residue 88 SER Chi-restraints excluded: chain D residue 113 THR Chi-restraints excluded: chain D residue 116 THR Chi-restraints excluded: chain E residue 32 LYS Chi-restraints excluded: chain E residue 72 THR Chi-restraints excluded: chain E residue 149 SER Chi-restraints excluded: chain E residue 153 SER Chi-restraints excluded: chain E residue 186 THR Chi-restraints excluded: chain E residue 220 ASP Chi-restraints excluded: chain E residue 306 SER Chi-restraints excluded: chain E residue 397 THR Chi-restraints excluded: chain F residue 22 THR Chi-restraints excluded: chain F residue 53 LEU Chi-restraints excluded: chain G residue 88 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 180 optimal weight: 0.8980 chunk 158 optimal weight: 1.9990 chunk 106 optimal weight: 3.9990 chunk 159 optimal weight: 1.9990 chunk 32 optimal weight: 0.0970 chunk 171 optimal weight: 1.9990 chunk 50 optimal weight: 0.6980 chunk 37 optimal weight: 1.9990 chunk 80 optimal weight: 0.6980 chunk 162 optimal weight: 0.1980 chunk 173 optimal weight: 3.9990 overall best weight: 0.5178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 393 GLN B 393 GLN D 77 ASN E 393 GLN G 77 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3578 r_free = 0.3578 target = 0.144312 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.129438 restraints weight = 18497.248| |-----------------------------------------------------------------------------| r_work (start): 0.3383 rms_B_bonded: 1.16 r_work: 0.3284 rms_B_bonded: 1.54 restraints_weight: 0.5000 r_work: 0.3180 rms_B_bonded: 2.63 restraints_weight: 0.2500 r_work (final): 0.3180 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8352 moved from start: 0.2828 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 15774 Z= 0.133 Angle : 0.543 7.362 21510 Z= 0.286 Chirality : 0.046 0.316 2595 Planarity : 0.004 0.035 2652 Dihedral : 4.772 16.862 2130 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 5.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.58 % Favored : 98.42 % Rotamer: Outliers : 3.21 % Allowed : 11.89 % Favored : 84.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.00 % 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: 0.25 (0.19), residues: 1962 helix: 1.09 (0.24), residues: 450 sheet: -0.11 (0.20), residues: 597 loop : 0.03 (0.20), residues: 915 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG G 72 TYR 0.013 0.001 TYR E 274 PHE 0.023 0.002 PHE A 212 TRP 0.017 0.001 TRP G 35 HIS 0.002 0.001 HIS B 29 Details of bonding type rmsd/Z covalent geometry : bond 0.00308 / 0.13 (15735) covalent geometry : angle 0.53521 / 0.28 (21414) SS BOND : bond 0.00239 / 0.13 ( 21) SS BOND : angle 1.17772 / 0.91 ( 42) hydrogen bonds : bond 0.03468 / 2.35 ( 644) hydrogen bonds : angle 5.15474 / 3.63 ( 1815) link_BETA1-4 : bond 0.00467 / 0.31 ( 6) link_BETA1-4 : angle 1.09121 / 0.71 ( 18) link_NAG-ASN : bond 0.00365 / 0.26 ( 12) link_NAG-ASN : angle 1.84714 / 1.24 ( 36) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3924 Ramachandran restraints generated. 1962 Oldfield, 0 Emsley, 1962 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3924 Ramachandran restraints generated. 1962 Oldfield, 0 Emsley, 1962 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 301 residues out of total 1749 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 246 time to evaluate : 0.579 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 67 ASN cc_start: 0.7848 (m-40) cc_final: 0.7474 (t160) REVERT: A 115 MET cc_start: 0.8161 (OUTLIER) cc_final: 0.7862 (mmm) REVERT: A 135 TYR cc_start: 0.8711 (t80) cc_final: 0.8324 (t80) REVERT: A 220 ASP cc_start: 0.8135 (OUTLIER) cc_final: 0.7781 (t0) REVERT: A 244 ARG cc_start: 0.8511 (ttp-170) cc_final: 0.7916 (ttm-80) REVERT: A 304 ASP cc_start: 0.6982 (t0) cc_final: 0.6576 (t0) REVERT: A 390 VAL cc_start: 0.8328 (m) cc_final: 0.7933 (p) REVERT: A 425 ILE cc_start: 0.8678 (OUTLIER) cc_final: 0.8268 (mp) REVERT: A 453 LYS cc_start: 0.7394 (OUTLIER) cc_final: 0.6824 (pttp) REVERT: L 31 TYR cc_start: 0.8486 (m-80) cc_final: 0.8235 (m-80) REVERT: H 16 GLN cc_start: 0.7628 (mt0) cc_final: 0.7399 (mt0) REVERT: B 45 LYS cc_start: 0.8832 (OUTLIER) cc_final: 0.8520 (ptpp) REVERT: B 139 LYS cc_start: 0.7542 (mmmt) cc_final: 0.7268 (mppt) REVERT: B 155 ASN cc_start: 0.8016 (p0) cc_final: 0.7110 (t0) REVERT: B 156 GLU cc_start: 0.7968 (OUTLIER) cc_final: 0.7668 (tp30) REVERT: B 161 LEU cc_start: 0.8991 (mt) cc_final: 0.8700 (mp) REVERT: B 212 PHE cc_start: 0.7696 (t80) cc_final: 0.7494 (t80) REVERT: B 220 ASP cc_start: 0.8262 (OUTLIER) cc_final: 0.7704 (t0) REVERT: B 244 ARG cc_start: 0.8014 (ttm-80) cc_final: 0.7175 (ttt180) REVERT: B 390 VAL cc_start: 0.8336 (m) cc_final: 0.7964 (p) REVERT: C 31 TYR cc_start: 0.8454 (m-80) cc_final: 0.8151 (m-80) REVERT: C 71 SER cc_start: 0.8715 (p) cc_final: 0.8431 (t) REVERT: C 102 LYS cc_start: 0.8258 (ttmm) cc_final: 0.7849 (ttpt) REVERT: E 32 LYS cc_start: 0.8848 (OUTLIER) cc_final: 0.8360 (mttp) REVERT: E 138 MET cc_start: 0.8088 (mmm) cc_final: 0.7736 (mmm) REVERT: E 220 ASP cc_start: 0.8324 (OUTLIER) cc_final: 0.7902 (t0) REVERT: E 244 ARG cc_start: 0.8429 (ttp-170) cc_final: 0.7685 (ttp-170) REVERT: E 304 ASP cc_start: 0.7166 (t0) cc_final: 0.6860 (t0) REVERT: E 427 ILE cc_start: 0.8556 (OUTLIER) cc_final: 0.8100 (mt) REVERT: F 44 LYS cc_start: 0.8231 (tttt) cc_final: 0.7731 (ptpp) REVERT: F 86 TYR cc_start: 0.8954 (m-80) cc_final: 0.8710 (m-80) REVERT: G 45 LYS cc_start: 0.8015 (ptpp) cc_final: 0.7803 (ptmm) outliers start: 55 outliers final: 24 residues processed: 286 average time/residue: 0.4367 time to fit residues: 141.7187 Evaluate side-chains 253 residues out of total 1749 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 219 time to evaluate : 0.626 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 THR Chi-restraints excluded: chain A residue 115 MET Chi-restraints excluded: chain A residue 153 SER Chi-restraints excluded: chain A residue 220 ASP Chi-restraints excluded: chain A residue 306 SER Chi-restraints excluded: chain A residue 312 VAL Chi-restraints excluded: chain A residue 397 THR Chi-restraints excluded: chain A residue 422 LEU Chi-restraints excluded: chain A residue 425 ILE Chi-restraints excluded: chain A residue 445 VAL Chi-restraints excluded: chain A residue 453 LYS Chi-restraints excluded: chain L residue 71 SER Chi-restraints excluded: chain H residue 88 SER Chi-restraints excluded: chain H residue 114 SER Chi-restraints excluded: chain H residue 116 THR Chi-restraints excluded: chain B residue 45 LYS Chi-restraints excluded: chain B residue 72 THR Chi-restraints excluded: chain B residue 153 SER Chi-restraints excluded: chain B residue 156 GLU Chi-restraints excluded: chain B residue 220 ASP Chi-restraints excluded: chain B residue 397 THR Chi-restraints excluded: chain B residue 417 CYS Chi-restraints excluded: chain B residue 422 LEU Chi-restraints excluded: chain D residue 88 SER Chi-restraints excluded: chain D residue 116 THR Chi-restraints excluded: chain E residue 32 LYS Chi-restraints excluded: chain E residue 72 THR Chi-restraints excluded: chain E residue 153 SER Chi-restraints excluded: chain E residue 220 ASP Chi-restraints excluded: chain E residue 306 SER Chi-restraints excluded: chain E residue 397 THR Chi-restraints excluded: chain E residue 427 ILE Chi-restraints excluded: chain F residue 53 LEU Chi-restraints excluded: chain G residue 88 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 121 optimal weight: 0.9990 chunk 7 optimal weight: 0.9980 chunk 181 optimal weight: 4.9990 chunk 3 optimal weight: 0.7980 chunk 74 optimal weight: 3.9990 chunk 58 optimal weight: 1.9990 chunk 53 optimal weight: 3.9990 chunk 182 optimal weight: 0.0770 chunk 172 optimal weight: 1.9990 chunk 129 optimal weight: 1.9990 chunk 169 optimal weight: 3.9990 overall best weight: 0.9742 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 162 GLN A 393 GLN H 77 ASN B 162 GLN D 77 ASN G 77 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3555 r_free = 0.3555 target = 0.142393 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.127470 restraints weight = 18708.899| |-----------------------------------------------------------------------------| r_work (start): 0.3361 rms_B_bonded: 1.16 r_work: 0.3263 rms_B_bonded: 1.54 restraints_weight: 0.5000 r_work: 0.3156 rms_B_bonded: 2.63 restraints_weight: 0.2500 r_work (final): 0.3156 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8378 moved from start: 0.2994 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.061 15774 Z= 0.190 Angle : 0.600 8.955 21510 Z= 0.314 Chirality : 0.048 0.421 2595 Planarity : 0.004 0.039 2652 Dihedral : 4.838 17.835 2130 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 5.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.09 % Favored : 97.91 % Rotamer: Outliers : 3.85 % Allowed : 11.60 % Favored : 84.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.00 % 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: 0.18 (0.19), residues: 1962 helix: 1.10 (0.25), residues: 444 sheet: -0.17 (0.21), residues: 600 loop : -0.02 (0.20), residues: 918 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 60 TYR 0.015 0.002 TYR D 51 PHE 0.016 0.002 PHE H 79 TRP 0.016 0.002 TRP G 35 HIS 0.004 0.001 HIS B 29 Details of bonding type rmsd/Z covalent geometry : bond 0.00452 / 0.19 (15735) covalent geometry : angle 0.58378 / 0.31 (21414) SS BOND : bond 0.00465 / 0.29 ( 21) SS BOND : angle 2.69297 / 1.95 ( 42) hydrogen bonds : bond 0.03729 / 2.51 ( 644) hydrogen bonds : angle 5.18440 / 3.65 ( 1815) link_BETA1-4 : bond 0.00465 / 0.31 ( 6) link_BETA1-4 : angle 1.16951 / 0.77 ( 18) link_NAG-ASN : bond 0.00346 / 0.24 ( 12) link_NAG-ASN : angle 1.79786 / 1.16 ( 36) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3924 Ramachandran restraints generated. 1962 Oldfield, 0 Emsley, 1962 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3924 Ramachandran restraints generated. 1962 Oldfield, 0 Emsley, 1962 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 294 residues out of total 1749 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 228 time to evaluate : 0.516 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 115 MET cc_start: 0.8200 (OUTLIER) cc_final: 0.7869 (mmm) REVERT: A 135 TYR cc_start: 0.8707 (t80) cc_final: 0.8279 (t80) REVERT: A 220 ASP cc_start: 0.8150 (OUTLIER) cc_final: 0.7801 (t0) REVERT: A 244 ARG cc_start: 0.8526 (ttp-170) cc_final: 0.7713 (tpp-160) REVERT: A 304 ASP cc_start: 0.7157 (t0) cc_final: 0.6738 (t0) REVERT: A 390 VAL cc_start: 0.8246 (m) cc_final: 0.7860 (p) REVERT: A 425 ILE cc_start: 0.8739 (OUTLIER) cc_final: 0.8367 (mp) REVERT: A 453 LYS cc_start: 0.7461 (OUTLIER) cc_final: 0.6850 (pttp) REVERT: B 45 LYS cc_start: 0.8858 (OUTLIER) cc_final: 0.8559 (ptpp) REVERT: B 139 LYS cc_start: 0.7588 (mmmt) cc_final: 0.7310 (mppt) REVERT: B 155 ASN cc_start: 0.8036 (p0) cc_final: 0.7135 (t0) REVERT: B 156 GLU cc_start: 0.7954 (OUTLIER) cc_final: 0.7686 (tp30) REVERT: B 161 LEU cc_start: 0.8941 (mt) cc_final: 0.8652 (mp) REVERT: B 212 PHE cc_start: 0.7655 (t80) cc_final: 0.7294 (t80) REVERT: B 220 ASP cc_start: 0.8235 (OUTLIER) cc_final: 0.7699 (t0) REVERT: B 258 GLU cc_start: 0.8154 (OUTLIER) cc_final: 0.7462 (mp0) REVERT: B 390 VAL cc_start: 0.8270 (m) cc_final: 0.7864 (p) REVERT: C 31 TYR cc_start: 0.8589 (m-80) cc_final: 0.8311 (m-80) REVERT: C 71 SER cc_start: 0.8699 (p) cc_final: 0.8418 (t) REVERT: C 102 LYS cc_start: 0.8286 (ttmm) cc_final: 0.7857 (ttpt) REVERT: E 32 LYS cc_start: 0.8894 (OUTLIER) cc_final: 0.8418 (mttp) REVERT: E 138 MET cc_start: 0.8117 (mmm) cc_final: 0.7740 (mmm) REVERT: E 139 LYS cc_start: 0.7827 (mppt) cc_final: 0.7614 (mppt) REVERT: E 220 ASP cc_start: 0.8387 (OUTLIER) cc_final: 0.7955 (t0) REVERT: E 244 ARG cc_start: 0.8480 (ttp-170) cc_final: 0.7724 (ttp-170) REVERT: E 304 ASP cc_start: 0.7259 (t0) cc_final: 0.6954 (t0) REVERT: E 427 ILE cc_start: 0.8571 (OUTLIER) cc_final: 0.8114 (mt) REVERT: F 44 LYS cc_start: 0.8254 (tttt) cc_final: 0.7729 (ptpp) REVERT: F 86 TYR cc_start: 0.9008 (m-80) cc_final: 0.8760 (m-80) REVERT: G 45 LYS cc_start: 0.8089 (ptpp) cc_final: 0.7815 (ptmm) outliers start: 66 outliers final: 38 residues processed: 272 average time/residue: 0.4472 time to fit residues: 137.8693 Evaluate side-chains 268 residues out of total 1749 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 219 time to evaluate : 0.590 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 LYS Chi-restraints excluded: chain A residue 72 THR Chi-restraints excluded: chain A residue 115 MET Chi-restraints excluded: chain A residue 153 SER Chi-restraints excluded: chain A residue 187 ILE Chi-restraints excluded: chain A residue 220 ASP Chi-restraints excluded: chain A residue 306 SER Chi-restraints excluded: chain A residue 312 VAL Chi-restraints excluded: chain A residue 355 CYS Chi-restraints excluded: chain A residue 397 THR Chi-restraints excluded: chain A residue 422 LEU Chi-restraints excluded: chain A residue 425 ILE Chi-restraints excluded: chain A residue 453 LYS Chi-restraints excluded: chain L residue 11 MET Chi-restraints excluded: chain L residue 22 THR Chi-restraints excluded: chain L residue 71 SER Chi-restraints excluded: chain L residue 84 ASP Chi-restraints excluded: chain H residue 88 SER Chi-restraints excluded: chain H residue 114 SER Chi-restraints excluded: chain H residue 116 THR Chi-restraints excluded: chain B residue 45 LYS Chi-restraints excluded: chain B residue 72 THR Chi-restraints excluded: chain B residue 153 SER Chi-restraints excluded: chain B residue 156 GLU Chi-restraints excluded: chain B residue 187 ILE Chi-restraints excluded: chain B residue 220 ASP Chi-restraints excluded: chain B residue 258 GLU Chi-restraints excluded: chain B residue 306 SER Chi-restraints excluded: chain B residue 375 ARG Chi-restraints excluded: chain B residue 397 THR Chi-restraints excluded: chain B residue 417 CYS Chi-restraints excluded: chain B residue 422 LEU Chi-restraints excluded: chain C residue 19 ILE Chi-restraints excluded: chain C residue 22 THR Chi-restraints excluded: chain D residue 88 SER Chi-restraints excluded: chain D residue 116 THR Chi-restraints excluded: chain E residue 32 LYS Chi-restraints excluded: chain E residue 72 THR Chi-restraints excluded: chain E residue 153 SER Chi-restraints excluded: chain E residue 220 ASP Chi-restraints excluded: chain E residue 306 SER Chi-restraints excluded: chain E residue 355 CYS Chi-restraints excluded: chain E residue 397 THR Chi-restraints excluded: chain E residue 427 ILE Chi-restraints excluded: chain F residue 22 THR Chi-restraints excluded: chain F residue 27 SER Chi-restraints excluded: chain F residue 53 LEU Chi-restraints excluded: chain F residue 84 ASP Chi-restraints excluded: chain G residue 88 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 45 optimal weight: 4.9990 chunk 13 optimal weight: 3.9990 chunk 127 optimal weight: 0.6980 chunk 150 optimal weight: 2.9990 chunk 178 optimal weight: 1.9990 chunk 36 optimal weight: 0.4980 chunk 5 optimal weight: 0.8980 chunk 148 optimal weight: 1.9990 chunk 186 optimal weight: 0.9990 chunk 159 optimal weight: 0.6980 chunk 92 optimal weight: 0.6980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 393 GLN H 16 GLN D 77 ASN F 88 HIS G 77 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.143513 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.128746 restraints weight = 18530.263| |-----------------------------------------------------------------------------| r_work (start): 0.3372 rms_B_bonded: 1.15 r_work: 0.3275 rms_B_bonded: 1.53 restraints_weight: 0.5000 r_work: 0.3169 rms_B_bonded: 2.62 restraints_weight: 0.2500 r_work (final): 0.3169 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8362 moved from start: 0.3099 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 15774 Z= 0.152 Angle : 0.567 10.317 21510 Z= 0.295 Chirality : 0.048 0.523 2595 Planarity : 0.004 0.043 2652 Dihedral : 4.747 17.544 2130 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 5.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.73 % Favored : 98.27 % Rotamer: Outliers : 3.96 % Allowed : 11.83 % Favored : 84.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.00 % 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: 0.22 (0.19), residues: 1962 helix: 1.22 (0.25), residues: 444 sheet: -0.17 (0.21), residues: 600 loop : -0.02 (0.21), residues: 918 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 60 TYR 0.014 0.001 TYR A 438 PHE 0.027 0.002 PHE A 212 TRP 0.016 0.001 TRP G 35 HIS 0.003 0.001 HIS B 29 Details of bonding type rmsd/Z covalent geometry : bond 0.00356 / 0.15 (15735) covalent geometry : angle 0.55173 / 0.29 (21414) SS BOND : bond 0.00269 / 0.16 ( 21) SS BOND : angle 2.13152 / 1.56 ( 42) hydrogen bonds : bond 0.03449 / 2.34 ( 644) hydrogen bonds : angle 5.08612 / 3.57 ( 1815) link_BETA1-4 : bond 0.00410 / 0.28 ( 6) link_BETA1-4 : angle 1.11337 / 0.73 ( 18) link_NAG-ASN : bond 0.00805 / 0.51 ( 12) link_NAG-ASN : angle 2.31151 / 1.97 ( 36) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3924 Ramachandran restraints generated. 1962 Oldfield, 0 Emsley, 1962 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3924 Ramachandran restraints generated. 1962 Oldfield, 0 Emsley, 1962 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 300 residues out of total 1749 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 232 time to evaluate : 0.591 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 115 MET cc_start: 0.8199 (OUTLIER) cc_final: 0.7887 (mmm) REVERT: A 135 TYR cc_start: 0.8684 (t80) cc_final: 0.8293 (t80) REVERT: A 155 ASN cc_start: 0.8115 (p0) cc_final: 0.7176 (t0) REVERT: A 220 ASP cc_start: 0.8191 (OUTLIER) cc_final: 0.7798 (t0) REVERT: A 244 ARG cc_start: 0.8458 (ttp-170) cc_final: 0.7664 (tpp-160) REVERT: A 304 ASP cc_start: 0.7140 (t0) cc_final: 0.6713 (t0) REVERT: A 390 VAL cc_start: 0.8290 (m) cc_final: 0.7924 (p) REVERT: A 425 ILE cc_start: 0.8700 (OUTLIER) cc_final: 0.8300 (mp) REVERT: A 453 LYS cc_start: 0.7499 (OUTLIER) cc_final: 0.6843 (pttp) REVERT: B 45 LYS cc_start: 0.8850 (OUTLIER) cc_final: 0.8552 (ptpp) REVERT: B 139 LYS cc_start: 0.7592 (mmmt) cc_final: 0.7315 (mppt) REVERT: B 155 ASN cc_start: 0.8015 (p0) cc_final: 0.7152 (t0) REVERT: B 156 GLU cc_start: 0.7911 (OUTLIER) cc_final: 0.7647 (tp30) REVERT: B 161 LEU cc_start: 0.8922 (mt) cc_final: 0.8631 (mp) REVERT: B 212 PHE cc_start: 0.7686 (t80) cc_final: 0.7400 (t80) REVERT: B 220 ASP cc_start: 0.8226 (OUTLIER) cc_final: 0.7695 (t0) REVERT: B 244 ARG cc_start: 0.8065 (ttm-80) cc_final: 0.7195 (ttt180) REVERT: B 258 GLU cc_start: 0.8244 (OUTLIER) cc_final: 0.7597 (mp0) REVERT: B 390 VAL cc_start: 0.8251 (m) cc_final: 0.7865 (p) REVERT: C 31 TYR cc_start: 0.8542 (m-80) cc_final: 0.8203 (m-80) REVERT: C 71 SER cc_start: 0.8653 (p) cc_final: 0.8405 (t) REVERT: C 102 LYS cc_start: 0.8289 (ttmm) cc_final: 0.7874 (ttpt) REVERT: E 32 LYS cc_start: 0.8862 (OUTLIER) cc_final: 0.8381 (mttp) REVERT: E 138 MET cc_start: 0.8069 (mmm) cc_final: 0.7682 (mmm) REVERT: E 220 ASP cc_start: 0.8385 (OUTLIER) cc_final: 0.7978 (t0) REVERT: E 244 ARG cc_start: 0.8434 (ttp-170) cc_final: 0.7698 (ttp-170) REVERT: E 304 ASP cc_start: 0.7247 (t0) cc_final: 0.6927 (t0) REVERT: E 329 LYS cc_start: 0.8545 (OUTLIER) cc_final: 0.8168 (ptpt) REVERT: E 427 ILE cc_start: 0.8570 (OUTLIER) cc_final: 0.8112 (mt) REVERT: F 44 LYS cc_start: 0.8242 (tttt) cc_final: 0.7748 (ptpp) REVERT: F 86 TYR cc_start: 0.8951 (m-80) cc_final: 0.8699 (m-80) REVERT: G 45 LYS cc_start: 0.8032 (ptpp) cc_final: 0.7782 (ptmm) outliers start: 68 outliers final: 38 residues processed: 275 average time/residue: 0.4644 time to fit residues: 144.3709 Evaluate side-chains 273 residues out of total 1749 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 223 time to evaluate : 0.541 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 LYS Chi-restraints excluded: chain A residue 72 THR Chi-restraints excluded: chain A residue 115 MET Chi-restraints excluded: chain A residue 187 ILE Chi-restraints excluded: chain A residue 220 ASP Chi-restraints excluded: chain A residue 306 SER Chi-restraints excluded: chain A residue 312 VAL Chi-restraints excluded: chain A residue 355 CYS Chi-restraints excluded: chain A residue 397 THR Chi-restraints excluded: chain A residue 422 LEU Chi-restraints excluded: chain A residue 425 ILE Chi-restraints excluded: chain A residue 445 VAL Chi-restraints excluded: chain A residue 453 LYS Chi-restraints excluded: chain L residue 22 THR Chi-restraints excluded: chain L residue 27 SER Chi-restraints excluded: chain L residue 71 SER Chi-restraints excluded: chain L residue 84 ASP Chi-restraints excluded: chain H residue 88 SER Chi-restraints excluded: chain H residue 114 SER Chi-restraints excluded: chain H residue 116 THR Chi-restraints excluded: chain B residue 45 LYS Chi-restraints excluded: chain B residue 72 THR Chi-restraints excluded: chain B residue 153 SER Chi-restraints excluded: chain B residue 156 GLU Chi-restraints excluded: chain B residue 187 ILE Chi-restraints excluded: chain B residue 220 ASP Chi-restraints excluded: chain B residue 258 GLU Chi-restraints excluded: chain B residue 355 CYS Chi-restraints excluded: chain B residue 375 ARG Chi-restraints excluded: chain B residue 397 THR Chi-restraints excluded: chain B residue 417 CYS Chi-restraints excluded: chain B residue 445 VAL Chi-restraints excluded: chain C residue 22 THR Chi-restraints excluded: chain D residue 25 THR Chi-restraints excluded: chain D residue 88 SER Chi-restraints excluded: chain D residue 116 THR Chi-restraints excluded: chain E residue 32 LYS Chi-restraints excluded: chain E residue 72 THR Chi-restraints excluded: chain E residue 153 SER Chi-restraints excluded: chain E residue 187 ILE Chi-restraints excluded: chain E residue 220 ASP Chi-restraints excluded: chain E residue 329 LYS Chi-restraints excluded: chain E residue 355 CYS Chi-restraints excluded: chain E residue 397 THR Chi-restraints excluded: chain E residue 427 ILE Chi-restraints excluded: chain F residue 22 THR Chi-restraints excluded: chain F residue 27 SER Chi-restraints excluded: chain F residue 53 LEU Chi-restraints excluded: chain F residue 71 SER Chi-restraints excluded: chain G residue 88 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 79 optimal weight: 0.0870 chunk 12 optimal weight: 2.9990 chunk 119 optimal weight: 3.9990 chunk 3 optimal weight: 0.9980 chunk 142 optimal weight: 0.9980 chunk 91 optimal weight: 2.9990 chunk 45 optimal weight: 5.9990 chunk 127 optimal weight: 0.0010 chunk 59 optimal weight: 0.8980 chunk 116 skipped: trial refinement blew up (Bond distance > max_reasonable_bond_distance: 62.1394 > 50:) chunk 145 optimal weight: 0.6980 overall best weight: 0.5364 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 393 GLN H 16 GLN D 77 ASN E 393 GLN G 77 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3577 r_free = 0.3577 target = 0.144325 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.129512 restraints weight = 18483.486| |-----------------------------------------------------------------------------| r_work (start): 0.3383 rms_B_bonded: 1.16 r_work: 0.3287 rms_B_bonded: 1.53 restraints_weight: 0.5000 r_work: 0.3182 rms_B_bonded: 2.63 restraints_weight: 0.2500 r_work (final): 0.3182 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8351 moved from start: 0.3201 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 15774 Z= 0.133 Angle : 0.559 12.987 21510 Z= 0.290 Chirality : 0.047 0.437 2595 Planarity : 0.004 0.041 2652 Dihedral : 4.634 17.537 2130 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 5.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.99 % Favored : 98.01 % Rotamer: Outliers : 3.79 % Allowed : 12.47 % Favored : 83.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.00 % 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: 0.27 (0.19), residues: 1962 helix: 1.21 (0.25), residues: 456 sheet: -0.06 (0.21), residues: 579 loop : -0.05 (0.20), residues: 927 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 72 TYR 0.013 0.001 TYR A 438 PHE 0.023 0.002 PHE A 212 TRP 0.015 0.001 TRP G 35 HIS 0.002 0.001 HIS B 29 Details of bonding type rmsd/Z covalent geometry : bond 0.00307 / 0.13 (15735) covalent geometry : angle 0.53539 / 0.28 (21414) SS BOND : bond 0.00211 / 0.13 ( 21) SS BOND : angle 2.86230 / 2.03 ( 42) hydrogen bonds : bond 0.03289 / 2.25 ( 644) hydrogen bonds : angle 4.99905 / 3.52 ( 1815) link_BETA1-4 : bond 0.00419 / 0.28 ( 6) link_BETA1-4 : angle 1.07515 / 0.70 ( 18) link_NAG-ASN : bond 0.00552 / 0.36 ( 12) link_NAG-ASN : angle 2.47250 / 2.18 ( 36) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3924 Ramachandran restraints generated. 1962 Oldfield, 0 Emsley, 1962 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3924 Ramachandran restraints generated. 1962 Oldfield, 0 Emsley, 1962 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 301 residues out of total 1749 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 236 time to evaluate : 0.442 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 115 MET cc_start: 0.8208 (OUTLIER) cc_final: 0.7894 (mmm) REVERT: A 135 TYR cc_start: 0.8710 (t80) cc_final: 0.8272 (t80) REVERT: A 155 ASN cc_start: 0.8074 (p0) cc_final: 0.7173 (t0) REVERT: A 220 ASP cc_start: 0.8135 (OUTLIER) cc_final: 0.7783 (t0) REVERT: A 244 ARG cc_start: 0.8432 (ttp-170) cc_final: 0.7656 (tpp-160) REVERT: A 304 ASP cc_start: 0.7132 (t0) cc_final: 0.6728 (t0) REVERT: A 390 VAL cc_start: 0.8293 (m) cc_final: 0.7951 (p) REVERT: A 416 THR cc_start: 0.8047 (t) cc_final: 0.7642 (t) REVERT: A 425 ILE cc_start: 0.8710 (OUTLIER) cc_final: 0.8294 (mp) REVERT: A 453 LYS cc_start: 0.7513 (OUTLIER) cc_final: 0.6852 (pttp) REVERT: L 31 TYR cc_start: 0.8504 (m-80) cc_final: 0.8251 (m-80) REVERT: H 16 GLN cc_start: 0.7440 (mt0) cc_final: 0.7213 (mt0) REVERT: B 45 LYS cc_start: 0.8839 (OUTLIER) cc_final: 0.8528 (ptpp) REVERT: B 139 LYS cc_start: 0.7574 (mmmt) cc_final: 0.7305 (mppt) REVERT: B 155 ASN cc_start: 0.7997 (p0) cc_final: 0.7190 (t0) REVERT: B 156 GLU cc_start: 0.7841 (OUTLIER) cc_final: 0.7553 (tp30) REVERT: B 161 LEU cc_start: 0.8877 (mt) cc_final: 0.8585 (mp) REVERT: B 212 PHE cc_start: 0.7667 (t80) cc_final: 0.7367 (t80) REVERT: B 220 ASP cc_start: 0.8271 (OUTLIER) cc_final: 0.7777 (t0) REVERT: B 244 ARG cc_start: 0.8020 (ttm-80) cc_final: 0.7149 (ttt180) REVERT: B 390 VAL cc_start: 0.8208 (m) cc_final: 0.7834 (p) REVERT: C 31 TYR cc_start: 0.8519 (m-80) cc_final: 0.8173 (m-80) REVERT: C 71 SER cc_start: 0.8615 (p) cc_final: 0.8379 (t) REVERT: C 102 LYS cc_start: 0.8279 (ttmm) cc_final: 0.7867 (ttpt) REVERT: E 32 LYS cc_start: 0.8865 (OUTLIER) cc_final: 0.8400 (mttp) REVERT: E 138 MET cc_start: 0.8077 (mmm) cc_final: 0.7691 (mmm) REVERT: E 220 ASP cc_start: 0.8350 (OUTLIER) cc_final: 0.7987 (t0) REVERT: E 244 ARG cc_start: 0.8423 (ttp-170) cc_final: 0.7697 (ttp-170) REVERT: E 304 ASP cc_start: 0.7265 (t0) cc_final: 0.6927 (t0) REVERT: E 329 LYS cc_start: 0.8555 (OUTLIER) cc_final: 0.8177 (ptpt) REVERT: E 427 ILE cc_start: 0.8561 (OUTLIER) cc_final: 0.8100 (mt) REVERT: F 44 LYS cc_start: 0.8233 (tttt) cc_final: 0.7731 (ptpp) REVERT: F 86 TYR cc_start: 0.8973 (m-80) cc_final: 0.8718 (m-80) REVERT: G 45 LYS cc_start: 0.7979 (ptpp) cc_final: 0.7760 (ptmm) outliers start: 65 outliers final: 38 residues processed: 279 average time/residue: 0.4555 time to fit residues: 143.8766 Evaluate side-chains 271 residues out of total 1749 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 222 time to evaluate : 0.565 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 LYS Chi-restraints excluded: chain A residue 72 THR Chi-restraints excluded: chain A residue 115 MET Chi-restraints excluded: chain A residue 153 SER Chi-restraints excluded: chain A residue 187 ILE Chi-restraints excluded: chain A residue 220 ASP Chi-restraints excluded: chain A residue 306 SER Chi-restraints excluded: chain A residue 312 VAL Chi-restraints excluded: chain A residue 355 CYS Chi-restraints excluded: chain A residue 397 THR Chi-restraints excluded: chain A residue 422 LEU Chi-restraints excluded: chain A residue 425 ILE Chi-restraints excluded: chain A residue 445 VAL Chi-restraints excluded: chain A residue 453 LYS Chi-restraints excluded: chain A residue 461 SER Chi-restraints excluded: chain L residue 22 THR Chi-restraints excluded: chain L residue 27 SER Chi-restraints excluded: chain L residue 71 SER Chi-restraints excluded: chain H residue 88 SER Chi-restraints excluded: chain H residue 114 SER Chi-restraints excluded: chain B residue 45 LYS Chi-restraints excluded: chain B residue 72 THR Chi-restraints excluded: chain B residue 153 SER Chi-restraints excluded: chain B residue 156 GLU Chi-restraints excluded: chain B residue 187 ILE Chi-restraints excluded: chain B residue 220 ASP Chi-restraints excluded: chain B residue 355 CYS Chi-restraints excluded: chain B residue 375 ARG Chi-restraints excluded: chain B residue 397 THR Chi-restraints excluded: chain B residue 417 CYS Chi-restraints excluded: chain B residue 445 VAL Chi-restraints excluded: chain C residue 22 THR Chi-restraints excluded: chain D residue 25 THR Chi-restraints excluded: chain D residue 88 SER Chi-restraints excluded: chain D residue 116 THR Chi-restraints excluded: chain E residue 32 LYS Chi-restraints excluded: chain E residue 45 LYS Chi-restraints excluded: chain E residue 72 THR Chi-restraints excluded: chain E residue 153 SER Chi-restraints excluded: chain E residue 220 ASP Chi-restraints excluded: chain E residue 306 SER Chi-restraints excluded: chain E residue 329 LYS Chi-restraints excluded: chain E residue 355 CYS Chi-restraints excluded: chain E residue 397 THR Chi-restraints excluded: chain E residue 427 ILE Chi-restraints excluded: chain F residue 22 THR Chi-restraints excluded: chain F residue 27 SER Chi-restraints excluded: chain F residue 71 SER Chi-restraints excluded: chain G residue 88 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 50 optimal weight: 0.1980 chunk 16 optimal weight: 0.6980 chunk 103 optimal weight: 3.9990 chunk 164 optimal weight: 0.0270 chunk 151 optimal weight: 0.9980 chunk 117 optimal weight: 3.9990 chunk 101 optimal weight: 0.6980 chunk 38 optimal weight: 3.9990 chunk 138 optimal weight: 1.9990 chunk 165 optimal weight: 2.9990 chunk 171 optimal weight: 1.9990 overall best weight: 0.5238 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 393 GLN B 393 GLN D 77 ASN E 393 GLN G 77 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3582 r_free = 0.3582 target = 0.144777 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.129896 restraints weight = 18719.817| |-----------------------------------------------------------------------------| r_work (start): 0.3389 rms_B_bonded: 1.16 r_work: 0.3291 rms_B_bonded: 1.55 restraints_weight: 0.5000 r_work: 0.3188 rms_B_bonded: 2.64 restraints_weight: 0.2500 r_work (final): 0.3188 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8346 moved from start: 0.3277 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 15774 Z= 0.130 Angle : 0.557 13.326 21510 Z= 0.289 Chirality : 0.047 0.584 2595 Planarity : 0.004 0.039 2652 Dihedral : 4.591 18.789 2130 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 5.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.89 % Favored : 98.11 % Rotamer: Outliers : 3.73 % Allowed : 12.59 % Favored : 83.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.00 % 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: 0.28 (0.19), residues: 1962 helix: 1.23 (0.25), residues: 456 sheet: -0.06 (0.21), residues: 579 loop : -0.05 (0.20), residues: 927 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 72 TYR 0.012 0.001 TYR A 438 PHE 0.025 0.002 PHE A 212 TRP 0.015 0.001 TRP G 35 HIS 0.002 0.001 HIS B 29 Details of bonding type rmsd/Z covalent geometry : bond 0.00301 / 0.13 (15735) covalent geometry : angle 0.53059 / 0.28 (21414) SS BOND : bond 0.00173 / 0.10 ( 21) SS BOND : angle 2.76981 / 1.95 ( 42) hydrogen bonds : bond 0.03269 / 2.24 ( 644) hydrogen bonds : angle 4.96877 / 3.49 ( 1815) link_BETA1-4 : bond 0.00442 / 0.29 ( 6) link_BETA1-4 : angle 1.07277 / 0.70 ( 18) link_NAG-ASN : bond 0.00556 / 0.36 ( 12) link_NAG-ASN : angle 2.91236 / 2.51 ( 36) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3924 Ramachandran restraints generated. 1962 Oldfield, 0 Emsley, 1962 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3924 Ramachandran restraints generated. 1962 Oldfield, 0 Emsley, 1962 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 299 residues out of total 1749 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 235 time to evaluate : 0.585 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 115 MET cc_start: 0.8214 (OUTLIER) cc_final: 0.7909 (mmm) REVERT: A 135 TYR cc_start: 0.8693 (t80) cc_final: 0.8280 (t80) REVERT: A 155 ASN cc_start: 0.8054 (p0) cc_final: 0.7178 (t0) REVERT: A 220 ASP cc_start: 0.8221 (OUTLIER) cc_final: 0.7902 (t0) REVERT: A 244 ARG cc_start: 0.8422 (ttp-170) cc_final: 0.7650 (tpp-160) REVERT: A 304 ASP cc_start: 0.7113 (t0) cc_final: 0.6715 (t0) REVERT: A 390 VAL cc_start: 0.8302 (m) cc_final: 0.7955 (p) REVERT: A 416 THR cc_start: 0.8020 (t) cc_final: 0.7621 (t) REVERT: A 425 ILE cc_start: 0.8707 (OUTLIER) cc_final: 0.8302 (mp) REVERT: A 453 LYS cc_start: 0.7530 (OUTLIER) cc_final: 0.6863 (pttp) REVERT: L 31 TYR cc_start: 0.8488 (m-80) cc_final: 0.8228 (m-80) REVERT: B 45 LYS cc_start: 0.8848 (OUTLIER) cc_final: 0.8590 (ptpp) REVERT: B 139 LYS cc_start: 0.7597 (mmmt) cc_final: 0.7316 (mppt) REVERT: B 155 ASN cc_start: 0.7980 (p0) cc_final: 0.7188 (t0) REVERT: B 156 GLU cc_start: 0.7836 (OUTLIER) cc_final: 0.7548 (tp30) REVERT: B 161 LEU cc_start: 0.8860 (mt) cc_final: 0.8570 (mp) REVERT: B 212 PHE cc_start: 0.7686 (t80) cc_final: 0.7451 (t80) REVERT: B 220 ASP cc_start: 0.8326 (OUTLIER) cc_final: 0.7812 (t70) REVERT: B 244 ARG cc_start: 0.8014 (ttm-80) cc_final: 0.7144 (ttt180) REVERT: B 258 GLU cc_start: 0.8244 (OUTLIER) cc_final: 0.7762 (mp0) REVERT: B 390 VAL cc_start: 0.8126 (m) cc_final: 0.7748 (p) REVERT: C 31 TYR cc_start: 0.8528 (m-80) cc_final: 0.8184 (m-80) REVERT: C 71 SER cc_start: 0.8605 (p) cc_final: 0.8388 (t) REVERT: C 102 LYS cc_start: 0.8253 (ttmm) cc_final: 0.7882 (ttpt) REVERT: E 138 MET cc_start: 0.8098 (mmm) cc_final: 0.7701 (mmm) REVERT: E 155 ASN cc_start: 0.7905 (p0) cc_final: 0.7082 (t0) REVERT: E 220 ASP cc_start: 0.8298 (OUTLIER) cc_final: 0.7958 (t0) REVERT: E 244 ARG cc_start: 0.8405 (ttp-170) cc_final: 0.7678 (ttp-170) REVERT: E 304 ASP cc_start: 0.7209 (t0) cc_final: 0.6903 (t0) REVERT: E 329 LYS cc_start: 0.8598 (OUTLIER) cc_final: 0.8202 (ptpt) REVERT: E 427 ILE cc_start: 0.8569 (OUTLIER) cc_final: 0.8116 (mt) REVERT: F 44 LYS cc_start: 0.8218 (tttt) cc_final: 0.7726 (ptpp) REVERT: F 86 TYR cc_start: 0.8961 (m-80) cc_final: 0.8710 (m-80) REVERT: G 45 LYS cc_start: 0.7966 (ptpp) cc_final: 0.7744 (ptmm) outliers start: 64 outliers final: 41 residues processed: 277 average time/residue: 0.4473 time to fit residues: 140.3046 Evaluate side-chains 281 residues out of total 1749 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 229 time to evaluate : 0.539 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 LYS Chi-restraints excluded: chain A residue 67 ASN Chi-restraints excluded: chain A residue 72 THR Chi-restraints excluded: chain A residue 115 MET Chi-restraints excluded: chain A residue 187 ILE Chi-restraints excluded: chain A residue 220 ASP Chi-restraints excluded: chain A residue 306 SER Chi-restraints excluded: chain A residue 309 ILE Chi-restraints excluded: chain A residue 312 VAL Chi-restraints excluded: chain A residue 355 CYS Chi-restraints excluded: chain A residue 397 THR Chi-restraints excluded: chain A residue 422 LEU Chi-restraints excluded: chain A residue 425 ILE Chi-restraints excluded: chain A residue 445 VAL Chi-restraints excluded: chain A residue 453 LYS Chi-restraints excluded: chain A residue 461 SER Chi-restraints excluded: chain L residue 22 THR Chi-restraints excluded: chain L residue 27 SER Chi-restraints excluded: chain L residue 71 SER Chi-restraints excluded: chain L residue 84 ASP Chi-restraints excluded: chain H residue 86 VAL Chi-restraints excluded: chain H residue 88 SER Chi-restraints excluded: chain H residue 114 SER Chi-restraints excluded: chain B residue 45 LYS Chi-restraints excluded: chain B residue 72 THR Chi-restraints excluded: chain B residue 153 SER Chi-restraints excluded: chain B residue 156 GLU Chi-restraints excluded: chain B residue 187 ILE Chi-restraints excluded: chain B residue 220 ASP Chi-restraints excluded: chain B residue 258 GLU Chi-restraints excluded: chain B residue 355 CYS Chi-restraints excluded: chain B residue 375 ARG Chi-restraints excluded: chain B residue 397 THR Chi-restraints excluded: chain B residue 417 CYS Chi-restraints excluded: chain B residue 445 VAL Chi-restraints excluded: chain C residue 22 THR Chi-restraints excluded: chain D residue 11 LEU Chi-restraints excluded: chain D residue 88 SER Chi-restraints excluded: chain D residue 114 SER Chi-restraints excluded: chain D residue 116 THR Chi-restraints excluded: chain E residue 45 LYS Chi-restraints excluded: chain E residue 72 THR Chi-restraints excluded: chain E residue 220 ASP Chi-restraints excluded: chain E residue 306 SER Chi-restraints excluded: chain E residue 329 LYS Chi-restraints excluded: chain E residue 355 CYS Chi-restraints excluded: chain E residue 397 THR Chi-restraints excluded: chain E residue 427 ILE Chi-restraints excluded: chain F residue 22 THR Chi-restraints excluded: chain F residue 27 SER Chi-restraints excluded: chain F residue 71 SER Chi-restraints excluded: chain G residue 88 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 35 optimal weight: 0.8980 chunk 73 optimal weight: 2.9990 chunk 159 optimal weight: 0.9980 chunk 46 optimal weight: 1.9990 chunk 95 optimal weight: 0.7980 chunk 8 optimal weight: 3.9990 chunk 154 optimal weight: 0.7980 chunk 75 optimal weight: 0.3980 chunk 6 optimal weight: 0.5980 chunk 178 optimal weight: 0.3980 chunk 143 optimal weight: 0.0670 overall best weight: 0.4518 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 393 GLN H 16 GLN D 77 ASN E 393 GLN G 77 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3591 r_free = 0.3591 target = 0.145534 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.130742 restraints weight = 18534.030| |-----------------------------------------------------------------------------| r_work (start): 0.3399 rms_B_bonded: 1.16 r_work: 0.3302 rms_B_bonded: 1.55 restraints_weight: 0.5000 r_work: 0.3200 rms_B_bonded: 2.63 restraints_weight: 0.2500 r_work (final): 0.3200 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8331 moved from start: 0.3366 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 15774 Z= 0.120 Angle : 0.543 11.478 21510 Z= 0.280 Chirality : 0.047 0.520 2595 Planarity : 0.004 0.037 2652 Dihedral : 4.508 17.600 2130 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 5.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.99 % Favored : 98.01 % Rotamer: Outliers : 3.26 % Allowed : 13.17 % Favored : 83.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.00 % 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: 0.35 (0.19), residues: 1962 helix: 1.23 (0.25), residues: 456 sheet: 0.02 (0.22), residues: 564 loop : -0.01 (0.20), residues: 942 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 72 TYR 0.014 0.001 TYR B 135 PHE 0.014 0.001 PHE H 79 TRP 0.015 0.001 TRP G 35 HIS 0.002 0.001 HIS E 29 Details of bonding type rmsd/Z covalent geometry : bond 0.00275 / 0.12 (15735) covalent geometry : angle 0.52348 / 0.27 (21414) SS BOND : bond 0.00168 / 0.10 ( 21) SS BOND : angle 2.40804 / 1.70 ( 42) hydrogen bonds : bond 0.03169 / 2.18 ( 644) hydrogen bonds : angle 4.89032 / 3.45 ( 1815) link_BETA1-4 : bond 0.00427 / 0.29 ( 6) link_BETA1-4 : angle 1.04918 / 0.68 ( 18) link_NAG-ASN : bond 0.00428 / 0.28 ( 12) link_NAG-ASN : angle 2.36204 / 1.89 ( 36) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3924 Ramachandran restraints generated. 1962 Oldfield, 0 Emsley, 1962 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3924 Ramachandran restraints generated. 1962 Oldfield, 0 Emsley, 1962 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 304 residues out of total 1749 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 248 time to evaluate : 0.594 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 115 MET cc_start: 0.8225 (OUTLIER) cc_final: 0.7931 (mmm) REVERT: A 135 TYR cc_start: 0.8683 (t80) cc_final: 0.8311 (t80) REVERT: A 155 ASN cc_start: 0.8040 (p0) cc_final: 0.7190 (t0) REVERT: A 166 GLU cc_start: 0.6053 (mp0) cc_final: 0.5762 (mp0) REVERT: A 220 ASP cc_start: 0.8290 (OUTLIER) cc_final: 0.7994 (t0) REVERT: A 244 ARG cc_start: 0.8402 (ttp-170) cc_final: 0.7602 (tpp-160) REVERT: A 304 ASP cc_start: 0.7143 (t0) cc_final: 0.6737 (t0) REVERT: A 390 VAL cc_start: 0.8291 (m) cc_final: 0.7949 (p) REVERT: A 416 THR cc_start: 0.7993 (t) cc_final: 0.7594 (t) REVERT: A 425 ILE cc_start: 0.8684 (OUTLIER) cc_final: 0.8303 (mp) REVERT: A 453 LYS cc_start: 0.7526 (OUTLIER) cc_final: 0.6852 (pttp) REVERT: L 31 TYR cc_start: 0.8468 (m-80) cc_final: 0.8199 (m-80) REVERT: H 32 ASP cc_start: 0.8050 (t0) cc_final: 0.7826 (t0) REVERT: B 45 LYS cc_start: 0.8684 (OUTLIER) cc_final: 0.8391 (ptpp) REVERT: B 139 LYS cc_start: 0.7583 (mmmt) cc_final: 0.7298 (mppt) REVERT: B 155 ASN cc_start: 0.7950 (p0) cc_final: 0.7171 (t0) REVERT: B 156 GLU cc_start: 0.7886 (OUTLIER) cc_final: 0.7606 (tp30) REVERT: B 161 LEU cc_start: 0.8824 (mt) cc_final: 0.8544 (mp) REVERT: B 212 PHE cc_start: 0.7698 (t80) cc_final: 0.7479 (t80) REVERT: B 220 ASP cc_start: 0.8256 (OUTLIER) cc_final: 0.7965 (t70) REVERT: B 244 ARG cc_start: 0.8020 (ttm-80) cc_final: 0.7155 (ttt180) REVERT: B 258 GLU cc_start: 0.8202 (OUTLIER) cc_final: 0.7946 (mp0) REVERT: B 390 VAL cc_start: 0.8056 (m) cc_final: 0.7678 (p) REVERT: C 31 TYR cc_start: 0.8420 (m-80) cc_final: 0.8083 (m-80) REVERT: C 71 SER cc_start: 0.8606 (p) cc_final: 0.8391 (t) REVERT: C 102 LYS cc_start: 0.8239 (ttmm) cc_final: 0.7886 (ttpt) REVERT: E 138 MET cc_start: 0.8044 (mmm) cc_final: 0.7651 (mmm) REVERT: E 155 ASN cc_start: 0.7914 (p0) cc_final: 0.7109 (t0) REVERT: E 220 ASP cc_start: 0.8312 (OUTLIER) cc_final: 0.7989 (t0) REVERT: E 244 ARG cc_start: 0.8393 (ttp-170) cc_final: 0.7627 (ttp-170) REVERT: E 251 GLU cc_start: 0.7594 (tt0) cc_final: 0.7311 (mt-10) REVERT: E 304 ASP cc_start: 0.7204 (t0) cc_final: 0.6902 (t0) REVERT: E 329 LYS cc_start: 0.8592 (OUTLIER) cc_final: 0.8185 (ptpt) REVERT: E 427 ILE cc_start: 0.8558 (OUTLIER) cc_final: 0.8109 (mt) REVERT: F 44 LYS cc_start: 0.8219 (tttt) cc_final: 0.7751 (ptpp) REVERT: F 86 TYR cc_start: 0.8943 (m-80) cc_final: 0.8687 (m-80) REVERT: G 45 LYS cc_start: 0.7964 (ptpp) cc_final: 0.7708 (ptmt) outliers start: 56 outliers final: 40 residues processed: 282 average time/residue: 0.4565 time to fit residues: 145.4561 Evaluate side-chains 290 residues out of total 1749 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 239 time to evaluate : 0.562 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 LYS Chi-restraints excluded: chain A residue 72 THR Chi-restraints excluded: chain A residue 115 MET Chi-restraints excluded: chain A residue 153 SER Chi-restraints excluded: chain A residue 187 ILE Chi-restraints excluded: chain A residue 220 ASP Chi-restraints excluded: chain A residue 306 SER Chi-restraints excluded: chain A residue 309 ILE Chi-restraints excluded: chain A residue 312 VAL Chi-restraints excluded: chain A residue 355 CYS Chi-restraints excluded: chain A residue 397 THR Chi-restraints excluded: chain A residue 422 LEU Chi-restraints excluded: chain A residue 425 ILE Chi-restraints excluded: chain A residue 445 VAL Chi-restraints excluded: chain A residue 453 LYS Chi-restraints excluded: chain A residue 461 SER Chi-restraints excluded: chain L residue 22 THR Chi-restraints excluded: chain L residue 27 SER Chi-restraints excluded: chain L residue 71 SER Chi-restraints excluded: chain L residue 84 ASP Chi-restraints excluded: chain H residue 86 VAL Chi-restraints excluded: chain H residue 88 SER Chi-restraints excluded: chain H residue 114 SER Chi-restraints excluded: chain B residue 45 LYS Chi-restraints excluded: chain B residue 72 THR Chi-restraints excluded: chain B residue 156 GLU Chi-restraints excluded: chain B residue 187 ILE Chi-restraints excluded: chain B residue 220 ASP Chi-restraints excluded: chain B residue 258 GLU Chi-restraints excluded: chain B residue 355 CYS Chi-restraints excluded: chain B residue 375 ARG Chi-restraints excluded: chain B residue 397 THR Chi-restraints excluded: chain B residue 417 CYS Chi-restraints excluded: chain B residue 445 VAL Chi-restraints excluded: chain C residue 22 THR Chi-restraints excluded: chain D residue 11 LEU Chi-restraints excluded: chain D residue 88 SER Chi-restraints excluded: chain D residue 114 SER Chi-restraints excluded: chain D residue 116 THR Chi-restraints excluded: chain E residue 45 LYS Chi-restraints excluded: chain E residue 72 THR Chi-restraints excluded: chain E residue 187 ILE Chi-restraints excluded: chain E residue 220 ASP Chi-restraints excluded: chain E residue 306 SER Chi-restraints excluded: chain E residue 329 LYS Chi-restraints excluded: chain E residue 355 CYS Chi-restraints excluded: chain E residue 397 THR Chi-restraints excluded: chain E residue 427 ILE Chi-restraints excluded: chain F residue 22 THR Chi-restraints excluded: chain F residue 27 SER Chi-restraints excluded: chain G residue 88 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 135 optimal weight: 2.9990 chunk 109 optimal weight: 4.9990 chunk 65 optimal weight: 0.8980 chunk 86 optimal weight: 2.9990 chunk 139 optimal weight: 2.9990 chunk 75 optimal weight: 0.5980 chunk 42 optimal weight: 2.9990 chunk 12 optimal weight: 1.9990 chunk 159 optimal weight: 0.9980 chunk 126 optimal weight: 0.9990 chunk 87 optimal weight: 3.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 393 GLN H 77 ASN B 194 GLN D 77 ASN E 393 GLN G 77 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3552 r_free = 0.3552 target = 0.142279 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.127333 restraints weight = 18685.557| |-----------------------------------------------------------------------------| r_work (start): 0.3356 rms_B_bonded: 1.15 r_work: 0.3257 rms_B_bonded: 1.55 restraints_weight: 0.5000 r_work: 0.3153 rms_B_bonded: 2.64 restraints_weight: 0.2500 r_work (final): 0.3153 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8383 moved from start: 0.3400 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.065 15774 Z= 0.207 Angle : 0.627 10.572 21510 Z= 0.323 Chirality : 0.051 0.682 2595 Planarity : 0.004 0.039 2652 Dihedral : 4.815 18.381 2130 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 6.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % Rotamer: Outliers : 3.38 % Allowed : 13.29 % Favored : 83.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.00 % 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: -0.05 (0.19), residues: 1962 helix: 0.73 (0.24), residues: 468 sheet: -0.07 (0.21), residues: 573 loop : -0.27 (0.20), residues: 921 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG E 244 TYR 0.018 0.002 TYR E 135 PHE 0.030 0.002 PHE A 212 TRP 0.013 0.002 TRP G 35 HIS 0.004 0.002 HIS B 29 Details of bonding type rmsd/Z covalent geometry : bond 0.00497 / 0.21 (15735) covalent geometry : angle 0.60766 / 0.32 (21414) SS BOND : bond 0.00271 / 0.16 ( 21) SS BOND : angle 2.43799 / 1.73 ( 42) hydrogen bonds : bond 0.03724 / 2.51 ( 644) hydrogen bonds : angle 5.14150 / 3.62 ( 1815) link_BETA1-4 : bond 0.00410 / 0.27 ( 6) link_BETA1-4 : angle 1.21071 / 0.78 ( 18) link_NAG-ASN : bond 0.00436 / 0.29 ( 12) link_NAG-ASN : angle 2.80159 / 2.19 ( 36) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3924 Ramachandran restraints generated. 1962 Oldfield, 0 Emsley, 1962 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3924 Ramachandran restraints generated. 1962 Oldfield, 0 Emsley, 1962 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 293 residues out of total 1749 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 235 time to evaluate : 0.615 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 115 MET cc_start: 0.8221 (OUTLIER) cc_final: 0.7889 (mmm) REVERT: A 135 TYR cc_start: 0.8658 (t80) cc_final: 0.8233 (t80) REVERT: A 155 ASN cc_start: 0.8019 (p0) cc_final: 0.7164 (t0) REVERT: A 220 ASP cc_start: 0.8255 (OUTLIER) cc_final: 0.7909 (t0) REVERT: A 244 ARG cc_start: 0.8451 (ttp-170) cc_final: 0.7682 (tpp-160) REVERT: A 304 ASP cc_start: 0.7194 (t0) cc_final: 0.6781 (t0) REVERT: A 390 VAL cc_start: 0.8309 (m) cc_final: 0.7896 (p) REVERT: A 416 THR cc_start: 0.8029 (t) cc_final: 0.7621 (t) REVERT: A 425 ILE cc_start: 0.8768 (OUTLIER) cc_final: 0.8387 (mp) REVERT: A 453 LYS cc_start: 0.7568 (OUTLIER) cc_final: 0.6848 (pttp) REVERT: B 45 LYS cc_start: 0.8880 (OUTLIER) cc_final: 0.8506 (ptpp) REVERT: B 139 LYS cc_start: 0.7653 (mmmt) cc_final: 0.7344 (mppt) REVERT: B 155 ASN cc_start: 0.8031 (p0) cc_final: 0.7252 (t0) REVERT: B 161 LEU cc_start: 0.8857 (mt) cc_final: 0.8591 (mp) REVERT: B 189 GLN cc_start: 0.8461 (mt0) cc_final: 0.8198 (mt0) REVERT: B 212 PHE cc_start: 0.7736 (t80) cc_final: 0.7411 (t80) REVERT: B 220 ASP cc_start: 0.8273 (OUTLIER) cc_final: 0.7756 (t70) REVERT: B 244 ARG cc_start: 0.8033 (ttm-80) cc_final: 0.7162 (ttt180) REVERT: B 258 GLU cc_start: 0.8234 (OUTLIER) cc_final: 0.7751 (mp0) REVERT: B 390 VAL cc_start: 0.8102 (m) cc_final: 0.7646 (p) REVERT: C 71 SER cc_start: 0.8609 (p) cc_final: 0.8347 (t) REVERT: C 102 LYS cc_start: 0.8391 (ttmm) cc_final: 0.7938 (ttpt) REVERT: E 138 MET cc_start: 0.8086 (mmm) cc_final: 0.7689 (mmm) REVERT: E 155 ASN cc_start: 0.7948 (p0) cc_final: 0.7168 (t0) REVERT: E 220 ASP cc_start: 0.8347 (OUTLIER) cc_final: 0.7974 (t0) REVERT: E 244 ARG cc_start: 0.8431 (ttp-170) cc_final: 0.7722 (ttp-170) REVERT: E 304 ASP cc_start: 0.7267 (t0) cc_final: 0.7032 (t0) REVERT: E 329 LYS cc_start: 0.8594 (OUTLIER) cc_final: 0.8191 (ptpt) REVERT: E 411 MET cc_start: 0.8597 (tmm) cc_final: 0.8392 (tmm) REVERT: E 427 ILE cc_start: 0.8590 (OUTLIER) cc_final: 0.8127 (mt) REVERT: F 44 LYS cc_start: 0.8281 (tttt) cc_final: 0.7785 (ptpp) REVERT: F 86 TYR cc_start: 0.9040 (m-80) cc_final: 0.8799 (m-80) REVERT: G 45 LYS cc_start: 0.7942 (ptpp) cc_final: 0.7712 (ptmm) outliers start: 58 outliers final: 40 residues processed: 271 average time/residue: 0.4406 time to fit residues: 134.9637 Evaluate side-chains 283 residues out of total 1749 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 233 time to evaluate : 0.554 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 LYS Chi-restraints excluded: chain A residue 72 THR Chi-restraints excluded: chain A residue 115 MET Chi-restraints excluded: chain A residue 153 SER Chi-restraints excluded: chain A residue 187 ILE Chi-restraints excluded: chain A residue 220 ASP Chi-restraints excluded: chain A residue 306 SER Chi-restraints excluded: chain A residue 312 VAL Chi-restraints excluded: chain A residue 355 CYS Chi-restraints excluded: chain A residue 397 THR Chi-restraints excluded: chain A residue 422 LEU Chi-restraints excluded: chain A residue 425 ILE Chi-restraints excluded: chain A residue 445 VAL Chi-restraints excluded: chain A residue 453 LYS Chi-restraints excluded: chain A residue 461 SER Chi-restraints excluded: chain L residue 22 THR Chi-restraints excluded: chain L residue 27 SER Chi-restraints excluded: chain L residue 71 SER Chi-restraints excluded: chain L residue 84 ASP Chi-restraints excluded: chain H residue 86 VAL Chi-restraints excluded: chain H residue 88 SER Chi-restraints excluded: chain H residue 114 SER Chi-restraints excluded: chain B residue 45 LYS Chi-restraints excluded: chain B residue 72 THR Chi-restraints excluded: chain B residue 153 SER Chi-restraints excluded: chain B residue 187 ILE Chi-restraints excluded: chain B residue 220 ASP Chi-restraints excluded: chain B residue 258 GLU Chi-restraints excluded: chain B residue 355 CYS Chi-restraints excluded: chain B residue 375 ARG Chi-restraints excluded: chain B residue 397 THR Chi-restraints excluded: chain B residue 417 CYS Chi-restraints excluded: chain B residue 422 LEU Chi-restraints excluded: chain B residue 445 VAL Chi-restraints excluded: chain C residue 22 THR Chi-restraints excluded: chain D residue 88 SER Chi-restraints excluded: chain D residue 114 SER Chi-restraints excluded: chain D residue 116 THR Chi-restraints excluded: chain E residue 45 LYS Chi-restraints excluded: chain E residue 72 THR Chi-restraints excluded: chain E residue 187 ILE Chi-restraints excluded: chain E residue 220 ASP Chi-restraints excluded: chain E residue 306 SER Chi-restraints excluded: chain E residue 329 LYS Chi-restraints excluded: chain E residue 355 CYS Chi-restraints excluded: chain E residue 397 THR Chi-restraints excluded: chain E residue 427 ILE Chi-restraints excluded: chain F residue 22 THR Chi-restraints excluded: chain F residue 27 SER Chi-restraints excluded: chain G residue 88 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 37 optimal weight: 0.0370 chunk 2 optimal weight: 1.9990 chunk 94 optimal weight: 3.9990 chunk 164 optimal weight: 3.9990 chunk 177 optimal weight: 2.9990 chunk 73 optimal weight: 1.9990 chunk 169 optimal weight: 0.0980 chunk 183 optimal weight: 4.9990 chunk 69 optimal weight: 0.9990 chunk 103 optimal weight: 2.9990 chunk 140 optimal weight: 0.6980 overall best weight: 0.7662 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 393 GLN H 16 GLN B 189 GLN B 393 GLN D 77 ASN E 393 GLN G 77 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3565 r_free = 0.3565 target = 0.143381 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3374 r_free = 0.3374 target = 0.128493 restraints weight = 18428.869| |-----------------------------------------------------------------------------| r_work (start): 0.3371 rms_B_bonded: 1.16 r_work: 0.3273 rms_B_bonded: 1.55 restraints_weight: 0.5000 r_work: 0.3169 rms_B_bonded: 2.64 restraints_weight: 0.2500 r_work (final): 0.3169 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8366 moved from start: 0.3449 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 15774 Z= 0.159 Angle : 0.585 11.270 21510 Z= 0.301 Chirality : 0.049 0.533 2595 Planarity : 0.004 0.041 2652 Dihedral : 4.722 18.077 2130 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 6.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.78 % Favored : 98.22 % Rotamer: Outliers : 3.21 % Allowed : 13.64 % Favored : 83.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.00 % 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: -0.04 (0.19), residues: 1962 helix: 0.80 (0.25), residues: 468 sheet: -0.10 (0.21), residues: 573 loop : -0.29 (0.20), residues: 921 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG L 60 TYR 0.016 0.001 TYR E 135 PHE 0.030 0.002 PHE A 212 TRP 0.016 0.001 TRP G 35 HIS 0.002 0.001 HIS B 29 Details of bonding type rmsd/Z covalent geometry : bond 0.00378 / 0.16 (15735) covalent geometry : angle 0.56782 / 0.30 (21414) SS BOND : bond 0.00223 / 0.13 ( 21) SS BOND : angle 2.21976 / 1.58 ( 42) hydrogen bonds : bond 0.03448 / 2.34 ( 644) hydrogen bonds : angle 5.05428 / 3.56 ( 1815) link_BETA1-4 : bond 0.00401 / 0.27 ( 6) link_BETA1-4 : angle 1.15243 / 0.74 ( 18) link_NAG-ASN : bond 0.00411 / 0.27 ( 12) link_NAG-ASN : angle 2.45353 / 1.86 ( 36) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4616.80 seconds wall clock time: 79 minutes 45.05 seconds (4785.05 seconds total)