Starting phenix.real_space_refine on Thu Sep 18 05:56:28 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9nr8_49725/09_2025/9nr8_49725.cif Found real_map, /net/cci-nas-00/data/ceres_data/9nr8_49725/09_2025/9nr8_49725.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.53 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9nr8_49725/09_2025/9nr8_49725.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9nr8_49725/09_2025/9nr8_49725.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9nr8_49725/09_2025/9nr8_49725.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9nr8_49725/09_2025/9nr8_49725.map" } resolution = 3.53 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= 0.000 sd= 0.024 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 50 5.16 5 C 9167 2.51 5 N 2569 2.21 5 O 2790 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 15 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 14576 Number of models: 1 Model: "" Number of chains: 18 Chain: "A" Number of atoms: 2984 Number of conformers: 1 Conformer: "" Number of residues, atoms: 372, 2984 Classifications: {'peptide': 372} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 13, 'TRANS': 358} Unresolved non-hydrogen bonds: 39 Unresolved non-hydrogen angles: 46 Unresolved non-hydrogen dihedrals: 34 Planarities with less than four sites: {'ASN:plan1': 2, 'PHE:plan': 1, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 27 Chain: "B" Number of atoms: 3020 Number of conformers: 1 Conformer: "" Number of residues, atoms: 378, 3020 Classifications: {'peptide': 378} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 14, 'TRANS': 363} Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 19 Unresolved non-hydrogen dihedrals: 13 Planarities with less than four sites: {'ARG:plan': 2, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 14 Chain: "C" Number of atoms: 2994 Number of conformers: 1 Conformer: "" Number of residues, atoms: 372, 2994 Classifications: {'peptide': 372} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 13, 'TRANS': 358} Unresolved non-hydrogen bonds: 29 Unresolved non-hydrogen angles: 35 Unresolved non-hydrogen dihedrals: 25 Planarities with less than four sites: {'ASN:plan1': 2, 'PHE:plan': 1, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 22 Chain: "D" Number of atoms: 3028 Number of conformers: 1 Conformer: "" Number of residues, atoms: 378, 3028 Classifications: {'peptide': 378} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 14, 'TRANS': 363} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "E" Number of atoms: 1124 Number of conformers: 1 Conformer: "" Number of residues, atoms: 229, 1124 Classifications: {'peptide': 229} Incomplete info: {'truncation_to_alanine': 193} Link IDs: {'PCIS': 3, 'PTRANS': 9, 'TRANS': 216} Chain breaks: 1 Unresolved chain link angles: 12 Unresolved non-hydrogen bonds: 683 Unresolved non-hydrogen angles: 881 Unresolved non-hydrogen dihedrals: 584 Unresolved non-hydrogen chiralities: 59 Planarities with less than four sites: {'GLU:plan': 11, 'GLN:plan1': 11, 'PHE:plan': 7, 'ASP:plan': 13, 'TYR:plan': 12, 'TRP:plan': 5, 'ARG:plan': 10, 'ASN:plan1': 5, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 368 Chain: "F" Number of atoms: 1124 Number of conformers: 1 Conformer: "" Number of residues, atoms: 229, 1124 Classifications: {'peptide': 229} Incomplete info: {'truncation_to_alanine': 193} Link IDs: {'PCIS': 3, 'PTRANS': 9, 'TRANS': 216} Chain breaks: 1 Unresolved chain link angles: 12 Unresolved non-hydrogen bonds: 683 Unresolved non-hydrogen angles: 881 Unresolved non-hydrogen dihedrals: 584 Unresolved non-hydrogen chiralities: 59 Planarities with less than four sites: {'GLU:plan': 11, 'GLN:plan1': 11, 'PHE:plan': 7, 'ASP:plan': 13, 'TYR:plan': 12, 'TRP:plan': 5, 'ARG:plan': 10, 'ASN:plan1': 5, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 368 Chain: "I" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "J" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "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 dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "L" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "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 dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "C" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "D" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 3.75, per 1000 atoms: 0.26 Number of scatterers: 14576 At special positions: 0 Unit cell: (121.26, 219.02, 87.42, 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 50 16.00 O 2790 8.00 N 2569 7.00 C 9167 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS A 57 " - pdb=" SG CYS A 305 " distance=2.03 Simple disulfide: pdb=" SG CYS B 64 " - pdb=" SG CYS B 311 " distance=2.03 Simple disulfide: pdb=" SG CYS C 57 " - pdb=" SG CYS C 305 " distance=2.03 Simple disulfide: pdb=" SG CYS D 64 " - pdb=" SG CYS D 311 " 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 G 1 " - " NAG G 2 " " NAG H 1 " - " NAG H 2 " " NAG I 1 " - " NAG I 2 " " NAG I 2 " - " BMA I 3 " " NAG J 1 " - " NAG J 2 " " NAG J 2 " - " BMA J 3 " " NAG K 1 " - " NAG K 2 " " NAG L 1 " - " NAG L 2 " " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " NAG-ASN " NAG B 401 " - " ASN B 238 " " NAG C 401 " - " ASN C 239 " " NAG D 401 " - " ASN D 238 " " NAG G 1 " - " ASN B 351 " " NAG I 1 " - " ASN A 45 " " NAG J 1 " - " ASN C 45 " " NAG K 1 " - " ASN A 231 " " NAG L 1 " - " ASN C 231 " " NAG N 1 " - " ASN D 351 " Time building additional restraints: 1.17 Conformation dependent library (CDL) restraints added in 680.9 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 3884 Ramachandran restraints generated. 1942 Oldfield, 0 Emsley, 1942 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3636 Finding SS restraints... Secondary structure from input PDB file: 51 helices and 23 sheets defined 32.5% alpha, 18.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.65 Creating SS restraints... Processing helix chain 'A' and resid 18 through 30 Processing helix chain 'A' and resid 48 through 63 removed outlier: 3.552A pdb=" N MET A 52 " --> pdb=" O ASP A 48 " (cutoff:3.500A) Processing helix chain 'A' and resid 75 through 87 Processing helix chain 'A' and resid 113 through 122 Processing helix chain 'A' and resid 133 through 136 removed outlier: 3.899A pdb=" N GLY A 136 " --> pdb=" O ALA A 133 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 133 through 136' Processing helix chain 'A' and resid 137 through 151 Processing helix chain 'A' and resid 163 through 175 Processing helix chain 'A' and resid 187 through 201 removed outlier: 3.904A pdb=" N ALA A 193 " --> pdb=" O GLU A 189 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N LEU A 201 " --> pdb=" O GLN A 197 " (cutoff:3.500A) Processing helix chain 'A' and resid 223 through 227 removed outlier: 3.651A pdb=" N GLU A 227 " --> pdb=" O LYS A 224 " (cutoff:3.500A) Processing helix chain 'A' and resid 242 through 254 Processing helix chain 'A' and resid 269 through 292 removed outlier: 3.929A pdb=" N ALA A 273 " --> pdb=" O LYS A 269 " (cutoff:3.500A) Processing helix chain 'A' and resid 315 through 323 Processing helix chain 'B' and resid 17 through 33 Processing helix chain 'B' and resid 55 through 70 Processing helix chain 'B' and resid 79 through 81 No H-bonds generated for 'chain 'B' and resid 79 through 81' Processing helix chain 'B' and resid 82 through 93 removed outlier: 3.870A pdb=" N LEU B 86 " --> pdb=" O SER B 82 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N LEU B 93 " --> pdb=" O PHE B 89 " (cutoff:3.500A) Processing helix chain 'B' and resid 118 through 129 Processing helix chain 'B' and resid 144 through 158 Processing helix chain 'B' and resid 170 through 184 Processing helix chain 'B' and resid 194 through 209 Processing helix chain 'B' and resid 230 through 236 removed outlier: 3.532A pdb=" N HIS B 234 " --> pdb=" O GLU B 230 " (cutoff:3.500A) Processing helix chain 'B' and resid 249 through 261 Processing helix chain 'B' and resid 275 through 298 Processing helix chain 'B' and resid 321 through 330 removed outlier: 3.696A pdb=" N LYS B 330 " --> pdb=" O GLU B 326 " (cutoff:3.500A) Processing helix chain 'C' and resid 18 through 30 Processing helix chain 'C' and resid 48 through 63 Processing helix chain 'C' and resid 75 through 86 Processing helix chain 'C' and resid 113 through 122 Processing helix chain 'C' and resid 133 through 136 removed outlier: 3.891A pdb=" N GLY C 136 " --> pdb=" O ALA C 133 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 133 through 136' Processing helix chain 'C' and resid 137 through 151 Processing helix chain 'C' and resid 163 through 176 removed outlier: 3.579A pdb=" N LYS C 176 " --> pdb=" O GLN C 172 " (cutoff:3.500A) Processing helix chain 'C' and resid 187 through 202 removed outlier: 3.913A pdb=" N ALA C 193 " --> pdb=" O GLU C 189 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N LEU C 201 " --> pdb=" O GLN C 197 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N GLU C 202 " --> pdb=" O ILE C 198 " (cutoff:3.500A) Processing helix chain 'C' and resid 223 through 227 removed outlier: 3.825A pdb=" N GLU C 227 " --> pdb=" O LYS C 224 " (cutoff:3.500A) Processing helix chain 'C' and resid 242 through 255 Processing helix chain 'C' and resid 269 through 292 removed outlier: 3.751A pdb=" N ALA C 273 " --> pdb=" O LYS C 269 " (cutoff:3.500A) Processing helix chain 'C' and resid 315 through 324 Processing helix chain 'D' and resid 17 through 33 Processing helix chain 'D' and resid 36 through 40 Processing helix chain 'D' and resid 55 through 70 Processing helix chain 'D' and resid 79 through 81 No H-bonds generated for 'chain 'D' and resid 79 through 81' Processing helix chain 'D' and resid 82 through 91 removed outlier: 3.961A pdb=" N LEU D 86 " --> pdb=" O SER D 82 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N THR D 87 " --> pdb=" O VAL D 83 " (cutoff:3.500A) Processing helix chain 'D' and resid 118 through 129 Processing helix chain 'D' and resid 144 through 158 Processing helix chain 'D' and resid 170 through 184 Processing helix chain 'D' and resid 194 through 209 Processing helix chain 'D' and resid 230 through 236 removed outlier: 3.542A pdb=" N HIS D 234 " --> pdb=" O GLU D 230 " (cutoff:3.500A) Processing helix chain 'D' and resid 249 through 262 Processing helix chain 'D' and resid 275 through 298 Processing helix chain 'D' and resid 321 through 330 Processing helix chain 'E' and resid 217 through 221 Processing helix chain 'F' and resid 217 through 221 Processing sheet with id=AA1, first strand: chain 'A' and resid 36 through 43 removed outlier: 10.907A pdb=" N ALA A 66 " --> pdb=" O ASN A 6 " (cutoff:3.500A) removed outlier: 7.449A pdb=" N GLN A 8 " --> pdb=" O ALA A 66 " (cutoff:3.500A) removed outlier: 8.815A pdb=" N PHE A 68 " --> pdb=" O GLN A 8 " (cutoff:3.500A) removed outlier: 6.502A pdb=" N GLY A 10 " --> pdb=" O PHE A 68 " (cutoff:3.500A) removed outlier: 6.407A pdb=" N ILE A 67 " --> pdb=" O ILE A 91 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 153 through 158 removed outlier: 7.238A pdb=" N PHE A 127 " --> pdb=" O THR A 155 " (cutoff:3.500A) removed outlier: 8.023A pdb=" N VAL A 157 " --> pdb=" O PHE A 127 " (cutoff:3.500A) removed outlier: 6.337A pdb=" N TYR A 129 " --> pdb=" O VAL A 157 " (cutoff:3.500A) removed outlier: 4.403A pdb=" N LEU A 181 " --> pdb=" O THR A 126 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N VAL A 182 " --> pdb=" O HIS A 209 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 232 through 236 removed outlier: 3.645A pdb=" N GLY A 362 " --> pdb=" O VAL A 350 " (cutoff:3.500A) removed outlier: 6.398A pdb=" N GLU A 352 " --> pdb=" O LYS A 360 " (cutoff:3.500A) removed outlier: 5.396A pdb=" N LYS A 360 " --> pdb=" O GLU A 352 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 336 through 337 removed outlier: 4.190A pdb=" N GLN A 336 " --> pdb=" O THR A 344 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 48 through 50 removed outlier: 3.650A pdb=" N GLY B 10 " --> pdb=" O ALA B 73 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N PHE B 75 " --> pdb=" O GLY B 10 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 160 through 165 removed outlier: 7.174A pdb=" N PHE B 134 " --> pdb=" O SER B 162 " (cutoff:3.500A) removed outlier: 7.895A pdb=" N ILE B 164 " --> pdb=" O PHE B 134 " (cutoff:3.500A) removed outlier: 6.273A pdb=" N PHE B 136 " --> pdb=" O ILE B 164 " (cutoff:3.500A) removed outlier: 5.309A pdb=" N LYS B 188 " --> pdb=" O CYS B 133 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N PHE B 242 " --> pdb=" O ILE B 219 " (cutoff:3.500A) removed outlier: 4.317A pdb=" N VAL B 239 " --> pdb=" O LEU B 359 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N GLY B 368 " --> pdb=" O VAL B 356 " (cutoff:3.500A) removed outlier: 6.347A pdb=" N GLU B 358 " --> pdb=" O LYS B 366 " (cutoff:3.500A) removed outlier: 6.205A pdb=" N LYS B 366 " --> pdb=" O GLU B 358 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 334 through 336 removed outlier: 3.940A pdb=" N ILE B 334 " --> pdb=" O VAL B 341 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N GLN B 342 " --> pdb=" O VAL B 350 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 36 through 43 removed outlier: 4.325A pdb=" N ALA C 66 " --> pdb=" O GLN C 8 " (cutoff:3.500A) removed outlier: 6.224A pdb=" N ILE C 67 " --> pdb=" O ILE C 91 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 153 through 158 removed outlier: 7.182A pdb=" N THR C 126 " --> pdb=" O LEU C 181 " (cutoff:3.500A) removed outlier: 8.109A pdb=" N VAL C 183 " --> pdb=" O THR C 126 " (cutoff:3.500A) removed outlier: 6.033A pdb=" N VAL C 128 " --> pdb=" O VAL C 183 " (cutoff:3.500A) removed outlier: 7.815A pdb=" N ASP C 185 " --> pdb=" O VAL C 128 " (cutoff:3.500A) removed outlier: 6.623A pdb=" N ILE C 130 " --> pdb=" O ASP C 185 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N VAL C 182 " --> pdb=" O HIS C 209 " (cutoff:3.500A) removed outlier: 6.864A pdb=" N TYR C 210 " --> pdb=" O THR C 233 " (cutoff:3.500A) removed outlier: 8.753A pdb=" N PHE C 235 " --> pdb=" O TYR C 210 " (cutoff:3.500A) removed outlier: 8.114A pdb=" N LEU C 212 " --> pdb=" O PHE C 235 " (cutoff:3.500A) removed outlier: 6.451A pdb=" N LEU C 348 " --> pdb=" O TYR C 363 " (cutoff:3.500A) removed outlier: 4.520A pdb=" N TYR C 363 " --> pdb=" O LEU C 348 " (cutoff:3.500A) removed outlier: 7.023A pdb=" N VAL C 350 " --> pdb=" O ILE C 361 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 329 through 330 Processing sheet with id=AB2, first strand: chain 'C' and resid 336 through 337 removed outlier: 3.953A pdb=" N GLN C 336 " --> pdb=" O THR C 344 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 6 through 7 removed outlier: 3.804A pdb=" N VAL D 7 " --> pdb=" O ASN D 43 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB3 Processing sheet with id=AB4, first strand: chain 'D' and resid 10 through 11 removed outlier: 3.538A pdb=" N PHE D 75 " --> pdb=" O GLY D 10 " (cutoff:3.500A) removed outlier: 6.425A pdb=" N ILE D 74 " --> pdb=" O ILE D 98 " (cutoff:3.500A) removed outlier: 6.680A pdb=" N LEU D 97 " --> pdb=" O LEU D 112 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 160 through 165 removed outlier: 7.196A pdb=" N PHE D 134 " --> pdb=" O SER D 162 " (cutoff:3.500A) removed outlier: 7.901A pdb=" N ILE D 164 " --> pdb=" O PHE D 134 " (cutoff:3.500A) removed outlier: 6.263A pdb=" N PHE D 136 " --> pdb=" O ILE D 164 " (cutoff:3.500A) removed outlier: 5.300A pdb=" N LYS D 188 " --> pdb=" O CYS D 133 " (cutoff:3.500A) removed outlier: 4.087A pdb=" N PHE D 242 " --> pdb=" O ILE D 219 " (cutoff:3.500A) removed outlier: 4.513A pdb=" N VAL D 239 " --> pdb=" O LEU D 359 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N GLY D 368 " --> pdb=" O VAL D 356 " (cutoff:3.500A) removed outlier: 6.276A pdb=" N GLU D 358 " --> pdb=" O LYS D 366 " (cutoff:3.500A) removed outlier: 5.936A pdb=" N LYS D 366 " --> pdb=" O GLU D 358 " (cutoff:3.500A) removed outlier: 6.524A pdb=" N LYS D 360 " --> pdb=" O PRO D 364 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 334 through 336 removed outlier: 3.738A pdb=" N ILE D 334 " --> pdb=" O VAL D 341 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'E' and resid 3 through 5 removed outlier: 3.679A pdb=" N LYS E 3 " --> pdb=" O SER E 25 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N LEU E 20 " --> pdb=" O LEU E 81 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N LEU E 81 " --> pdb=" O LEU E 20 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'E' and resid 45 through 50 removed outlier: 6.232A pdb=" N TRP E 36 " --> pdb=" O ILE E 48 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'E' and resid 138 through 141 Processing sheet with id=AC1, first strand: chain 'E' and resid 144 through 147 removed outlier: 6.842A pdb=" N LEU E 145 " --> pdb=" O GLU E 243 " (cutoff:3.500A) removed outlier: 6.071A pdb=" N GLN E 175 " --> pdb=" O LEU E 184 " (cutoff:3.500A) removed outlier: 5.319A pdb=" N LEU E 184 " --> pdb=" O GLN E 175 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'F' and resid 3 through 6 removed outlier: 3.603A pdb=" N LYS F 3 " --> pdb=" O SER F 25 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N LEU F 20 " --> pdb=" O LEU F 81 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N LEU F 81 " --> pdb=" O LEU F 20 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'F' and resid 45 through 50 removed outlier: 6.425A pdb=" N TRP F 36 " --> pdb=" O ILE F 48 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'F' and resid 138 through 141 removed outlier: 3.670A pdb=" N ILE F 155 " --> pdb=" O LEU F 211 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N LEU F 211 " --> pdb=" O ILE F 155 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'F' and resid 144 through 147 removed outlier: 6.575A pdb=" N LEU F 145 " --> pdb=" O GLU F 243 " (cutoff:3.500A) removed outlier: 6.058A pdb=" N GLN F 175 " --> pdb=" O LEU F 184 " (cutoff:3.500A) removed outlier: 5.331A pdb=" N LEU F 184 " --> pdb=" O GLN F 175 " (cutoff:3.500A) 623 hydrogen bonds defined for protein. 1770 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: 2.31 Time building geometry restraints manager: 1.55 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.33: 4226 1.33 - 1.45: 2448 1.45 - 1.57: 8093 1.57 - 1.69: 1 1.69 - 1.81: 78 Bond restraints: 14846 Sorted by residual: bond pdb=" C1 NAG B 401 " pdb=" O5 NAG B 401 " ideal model delta sigma weight residual 1.406 1.496 -0.090 2.00e-02 2.50e+03 2.03e+01 bond pdb=" C1 NAG D 401 " pdb=" O5 NAG D 401 " ideal model delta sigma weight residual 1.406 1.495 -0.089 2.00e-02 2.50e+03 1.98e+01 bond pdb=" C PRO A 34 " pdb=" N PRO A 35 " ideal model delta sigma weight residual 1.333 1.371 -0.038 1.01e-02 9.80e+03 1.40e+01 bond pdb=" N TRP C 265 " pdb=" CA TRP C 265 " ideal model delta sigma weight residual 1.459 1.492 -0.033 1.06e-02 8.90e+03 9.68e+00 bond pdb=" N ASP C 259 " pdb=" CA ASP C 259 " ideal model delta sigma weight residual 1.457 1.493 -0.036 1.29e-02 6.01e+03 7.70e+00 ... (remaining 14841 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.02: 19718 2.02 - 4.04: 360 4.04 - 6.06: 70 6.06 - 8.09: 36 8.09 - 10.11: 5 Bond angle restraints: 20189 Sorted by residual: angle pdb=" C LEU C 323 " pdb=" N GLN C 324 " pdb=" CA GLN C 324 " ideal model delta sigma weight residual 122.83 115.02 7.81 1.54e+00 4.22e-01 2.57e+01 angle pdb=" C ARG C 267 " pdb=" CA ARG C 267 " pdb=" CB ARG C 267 " ideal model delta sigma weight residual 110.15 115.57 -5.42 1.15e+00 7.56e-01 2.22e+01 angle pdb=" C ARG D 348 " pdb=" CA ARG D 348 " pdb=" CB ARG D 348 " ideal model delta sigma weight residual 110.19 120.30 -10.11 2.18e+00 2.10e-01 2.15e+01 angle pdb=" N GLN C 324 " pdb=" CA GLN C 324 " pdb=" C GLN C 324 " ideal model delta sigma weight residual 112.57 107.47 5.10 1.13e+00 7.83e-01 2.04e+01 angle pdb=" N ARG D 348 " pdb=" CA ARG D 348 " pdb=" CB ARG D 348 " ideal model delta sigma weight residual 110.38 104.28 6.10 1.37e+00 5.33e-01 1.98e+01 ... (remaining 20184 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.15: 8192 22.15 - 44.31: 730 44.31 - 66.46: 85 66.46 - 88.62: 31 88.62 - 110.77: 17 Dihedral angle restraints: 9055 sinusoidal: 3411 harmonic: 5644 Sorted by residual: dihedral pdb=" CB CYS A 57 " pdb=" SG CYS A 57 " pdb=" SG CYS A 305 " pdb=" CB CYS A 305 " ideal model delta sinusoidal sigma weight residual -86.00 -156.61 70.61 1 1.00e+01 1.00e-02 6.41e+01 dihedral pdb=" CA ALA D 54 " pdb=" C ALA D 54 " pdb=" N ASN D 55 " pdb=" CA ASN D 55 " ideal model delta harmonic sigma weight residual 180.00 157.08 22.92 0 5.00e+00 4.00e-02 2.10e+01 dihedral pdb=" CA THR E 207 " pdb=" C THR E 207 " pdb=" N ASP E 208 " pdb=" CA ASP E 208 " ideal model delta harmonic sigma weight residual 180.00 159.93 20.07 0 5.00e+00 4.00e-02 1.61e+01 ... (remaining 9052 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.063: 2007 0.063 - 0.126: 305 0.126 - 0.189: 22 0.189 - 0.252: 7 0.252 - 0.315: 4 Chirality restraints: 2345 Sorted by residual: chirality pdb=" CA ARG A 180 " pdb=" N ARG A 180 " pdb=" C ARG A 180 " pdb=" CB ARG A 180 " both_signs ideal model delta sigma weight residual False 2.51 2.83 -0.32 2.00e-01 2.50e+01 2.49e+00 chirality pdb=" C5 BMA J 3 " pdb=" C4 BMA J 3 " pdb=" C6 BMA J 3 " pdb=" O5 BMA J 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.54 0.26 2.00e-01 2.50e+01 1.75e+00 chirality pdb=" C5 BMA I 3 " pdb=" C4 BMA I 3 " pdb=" C6 BMA I 3 " pdb=" O5 BMA I 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.53 0.26 2.00e-01 2.50e+01 1.69e+00 ... (remaining 2342 not shown) Planarity restraints: 2654 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG D 348 " 0.265 9.50e-02 1.11e+02 1.19e-01 8.64e+00 pdb=" NE ARG D 348 " -0.015 2.00e-02 2.50e+03 pdb=" CZ ARG D 348 " -0.004 2.00e-02 2.50e+03 pdb=" NH1 ARG D 348 " -0.002 2.00e-02 2.50e+03 pdb=" NH2 ARG D 348 " 0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU B 52 " 0.014 2.00e-02 2.50e+03 2.79e-02 7.78e+00 pdb=" C GLU B 52 " -0.048 2.00e-02 2.50e+03 pdb=" O GLU B 52 " 0.018 2.00e-02 2.50e+03 pdb=" N THR B 53 " 0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP B 370 " -0.013 2.00e-02 2.50e+03 1.67e-02 6.95e+00 pdb=" CG TRP B 370 " 0.044 2.00e-02 2.50e+03 pdb=" CD1 TRP B 370 " -0.023 2.00e-02 2.50e+03 pdb=" CD2 TRP B 370 " -0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP B 370 " 0.002 2.00e-02 2.50e+03 pdb=" CE2 TRP B 370 " -0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP B 370 " -0.011 2.00e-02 2.50e+03 pdb=" CZ2 TRP B 370 " 0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP B 370 " 0.001 2.00e-02 2.50e+03 pdb=" CH2 TRP B 370 " 0.000 2.00e-02 2.50e+03 ... (remaining 2651 not shown) Histogram of nonbonded interaction distances: 1.79 - 2.41: 18 2.41 - 3.03: 7975 3.03 - 3.65: 21093 3.65 - 4.28: 29520 4.28 - 4.90: 50387 Nonbonded interactions: 108993 Sorted by model distance: nonbonded pdb=" OD2 ASP D 141 " pdb=" OE2 GLU D 194 " model vdw 1.787 3.040 nonbonded pdb=" O ASP D 141 " pdb=" OD1 ASP D 141 " model vdw 2.240 3.040 nonbonded pdb=" OH TYR A 129 " pdb=" OD2 ASP A 185 " model vdw 2.277 3.040 nonbonded pdb=" OD1 ASP A 48 " pdb=" O6 NAG I 1 " model vdw 2.295 3.040 nonbonded pdb=" OH TYR C 122 " pdb=" OE1 GLU C 352 " model vdw 2.296 3.040 ... (remaining 108988 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = (chain 'C' and (resid 2 through 177 or (resid 178 and (name N or name CA or name \ C or name O or name CB )) or resid 179 or (resid 180 and (name N or name CA or \ name C or name O or name CB )) or resid 181 through 401)) } ncs_group { reference = (chain 'B' and (resid 2 through 298 or (resid 299 and (name N or name CA or name \ C or name O or name CB )) or resid 300 through 401)) selection = (chain 'D' and (resid 2 through 14 or (resid 15 and (name N or name CA or name C \ or name O or name CB )) or resid 16 through 264 or (resid 265 and (name N or na \ me CA or name C or name O or name CB )) or resid 266 through 401)) } ncs_group { reference = chain 'E' selection = chain 'F' } ncs_group { reference = chain 'G' selection = chain 'H' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' } ncs_group { reference = chain 'I' selection = chain 'J' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 6.330 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.240 Check model and map are aligned: 0.050 Set scattering table: 0.030 Process input model: 14.350 Find NCS groups from input model: 0.300 Set up NCS constraints: 0.030 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: 0.010 Load rotamer database and sin/cos tables:1.340 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.690 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7432 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 : 0.004 0.090 14869 Z= 0.215 Angle : 0.722 10.108 20254 Z= 0.381 Chirality : 0.047 0.315 2345 Planarity : 0.006 0.119 2645 Dihedral : 17.136 110.772 5407 Min Nonbonded Distance : 1.787 Molprobity Statistics. All-atom Clashscore : 4.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.46 % Favored : 94.54 % Rotamer: Outliers : 0.15 % Allowed : 18.69 % Favored : 81.16 % Cbeta Deviations : 0.06 % Peptide Plane: Cis-proline : 7.69 % 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 aren not related in a simple way. whole: -0.94 (0.18), residues: 1942 helix: 0.97 (0.20), residues: 596 sheet: -0.70 (0.26), residues: 410 loop : -1.66 (0.19), residues: 936 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG B 327 TYR 0.013 0.001 TYR A 71 PHE 0.035 0.001 PHE A 95 TRP 0.044 0.002 TRP B 370 HIS 0.007 0.001 HIS C 87 Details of bonding type rmsd covalent geometry : bond 0.00400 (14846) covalent geometry : angle 0.71070 (20189) SS BOND : bond 0.00063 ( 4) SS BOND : angle 0.67092 ( 8) hydrogen bonds : bond 0.13714 ( 623) hydrogen bonds : angle 5.70362 ( 1770) link_BETA1-4 : bond 0.00852 ( 10) link_BETA1-4 : angle 1.31917 ( 30) link_NAG-ASN : bond 0.00403 ( 9) link_NAG-ASN : angle 3.39744 ( 27) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3884 Ramachandran restraints generated. 1942 Oldfield, 0 Emsley, 1942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3884 Ramachandran restraints generated. 1942 Oldfield, 0 Emsley, 1942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 1700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 154 time to evaluate : 0.392 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 2 outliers final: 1 residues processed: 156 average time/residue: 0.1215 time to fit residues: 28.3435 Evaluate side-chains 139 residues out of total 1700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 138 time to evaluate : 0.526 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 263 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 98 optimal weight: 0.9990 chunk 107 optimal weight: 0.8980 chunk 10 optimal weight: 0.5980 chunk 66 optimal weight: 1.9990 chunk 130 optimal weight: 1.9990 chunk 124 optimal weight: 0.9990 chunk 103 optimal weight: 1.9990 chunk 77 optimal weight: 2.9990 chunk 122 optimal weight: 0.9980 chunk 91 optimal weight: 5.9990 chunk 149 optimal weight: 0.0040 overall best weight: 0.6994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 21 HIS A 334 ASN C 40 GLN C 324 GLN D 113 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4145 r_free = 0.4145 target = 0.182233 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3855 r_free = 0.3855 target = 0.153885 restraints weight = 17918.176| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3826 r_free = 0.3826 target = 0.151929 restraints weight = 28321.155| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 50)----------------| | r_work = 0.3784 r_free = 0.3784 target = 0.151206 restraints weight = 26198.729| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3744 r_free = 0.3744 target = 0.147361 restraints weight = 20547.226| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3754 r_free = 0.3754 target = 0.148211 restraints weight = 18263.368| |-----------------------------------------------------------------------------| r_work (final): 0.3737 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7654 moved from start: 0.1041 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 14869 Z= 0.140 Angle : 0.559 9.578 20254 Z= 0.277 Chirality : 0.043 0.227 2345 Planarity : 0.004 0.058 2645 Dihedral : 8.510 95.451 2558 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 5.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.48 % Favored : 95.52 % Rotamer: Outliers : 2.47 % Allowed : 15.83 % Favored : 81.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % 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 aren not related in a simple way. whole: -0.45 (0.19), residues: 1942 helix: 1.52 (0.21), residues: 614 sheet: -0.57 (0.26), residues: 406 loop : -1.45 (0.20), residues: 922 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 327 TYR 0.013 0.001 TYR A 71 PHE 0.016 0.001 PHE C 95 TRP 0.016 0.001 TRP B 370 HIS 0.005 0.001 HIS D 211 Details of bonding type rmsd covalent geometry : bond 0.00333 (14846) covalent geometry : angle 0.54235 (20189) SS BOND : bond 0.00092 ( 4) SS BOND : angle 0.60527 ( 8) hydrogen bonds : bond 0.03415 ( 623) hydrogen bonds : angle 4.41490 ( 1770) link_BETA1-4 : bond 0.00695 ( 10) link_BETA1-4 : angle 1.76471 ( 30) link_NAG-ASN : bond 0.00366 ( 9) link_NAG-ASN : angle 3.25191 ( 27) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3884 Ramachandran restraints generated. 1942 Oldfield, 0 Emsley, 1942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3884 Ramachandran restraints generated. 1942 Oldfield, 0 Emsley, 1942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 1700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 143 time to evaluate : 0.491 Fit side-chains revert: symmetry clash REVERT: C 249 MET cc_start: 0.7223 (mmm) cc_final: 0.6846 (mmm) outliers start: 32 outliers final: 20 residues processed: 164 average time/residue: 0.1240 time to fit residues: 30.4424 Evaluate side-chains 148 residues out of total 1700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 128 time to evaluate : 0.565 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 128 VAL Chi-restraints excluded: chain A residue 170 LEU Chi-restraints excluded: chain A residue 305 CYS Chi-restraints excluded: chain B residue 83 VAL Chi-restraints excluded: chain B residue 97 LEU Chi-restraints excluded: chain B residue 334 ILE Chi-restraints excluded: chain B residue 362 THR Chi-restraints excluded: chain B residue 378 LEU Chi-restraints excluded: chain B residue 379 ILE Chi-restraints excluded: chain C residue 61 SER Chi-restraints excluded: chain C residue 101 ASN Chi-restraints excluded: chain C residue 169 MET Chi-restraints excluded: chain C residue 263 VAL Chi-restraints excluded: chain C residue 311 VAL Chi-restraints excluded: chain C residue 353 MET Chi-restraints excluded: chain D residue 97 LEU Chi-restraints excluded: chain D residue 312 LEU Chi-restraints excluded: chain D residue 350 VAL Chi-restraints excluded: chain D residue 378 LEU Chi-restraints excluded: chain D residue 379 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 158 optimal weight: 0.4980 chunk 143 optimal weight: 0.5980 chunk 37 optimal weight: 0.0980 chunk 45 optimal weight: 1.9990 chunk 24 optimal weight: 1.9990 chunk 124 optimal weight: 1.9990 chunk 132 optimal weight: 0.8980 chunk 87 optimal weight: 1.9990 chunk 105 optimal weight: 0.4980 chunk 155 optimal weight: 0.8980 chunk 94 optimal weight: 2.9990 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 113 GLN B 148 GLN B 298 GLN D 113 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4137 r_free = 0.4137 target = 0.181503 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3830 r_free = 0.3830 target = 0.151416 restraints weight = 18073.732| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3820 r_free = 0.3820 target = 0.151055 restraints weight = 24449.682| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3812 r_free = 0.3812 target = 0.150986 restraints weight = 22001.819| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3802 r_free = 0.3802 target = 0.150048 restraints weight = 17679.919| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3814 r_free = 0.3814 target = 0.151378 restraints weight = 15141.603| |-----------------------------------------------------------------------------| r_work (final): 0.3806 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7568 moved from start: 0.1247 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 14869 Z= 0.113 Angle : 0.538 9.947 20254 Z= 0.264 Chirality : 0.042 0.240 2345 Planarity : 0.004 0.057 2645 Dihedral : 7.083 86.558 2558 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 4.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.58 % Favored : 95.42 % Rotamer: Outliers : 1.93 % Allowed : 17.68 % Favored : 80.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % 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 aren not related in a simple way. whole: -0.28 (0.19), residues: 1942 helix: 1.80 (0.21), residues: 618 sheet: -0.56 (0.26), residues: 406 loop : -1.43 (0.20), residues: 918 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG D 348 TYR 0.012 0.001 TYR A 71 PHE 0.016 0.001 PHE C 95 TRP 0.022 0.001 TRP B 370 HIS 0.004 0.001 HIS D 211 Details of bonding type rmsd covalent geometry : bond 0.00267 (14846) covalent geometry : angle 0.52249 (20189) SS BOND : bond 0.00063 ( 4) SS BOND : angle 0.47851 ( 8) hydrogen bonds : bond 0.03076 ( 623) hydrogen bonds : angle 4.18405 ( 1770) link_BETA1-4 : bond 0.00655 ( 10) link_BETA1-4 : angle 1.44777 ( 30) link_NAG-ASN : bond 0.00374 ( 9) link_NAG-ASN : angle 3.21770 ( 27) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3884 Ramachandran restraints generated. 1942 Oldfield, 0 Emsley, 1942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3884 Ramachandran restraints generated. 1942 Oldfield, 0 Emsley, 1942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 1700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 140 time to evaluate : 0.563 Fit side-chains revert: symmetry clash REVERT: B 9 ILE cc_start: 0.5832 (mt) cc_final: 0.5630 (mt) REVERT: C 48 ASP cc_start: 0.7605 (t70) cc_final: 0.7323 (t0) REVERT: C 249 MET cc_start: 0.7196 (mmm) cc_final: 0.6830 (mmm) outliers start: 25 outliers final: 15 residues processed: 158 average time/residue: 0.1208 time to fit residues: 28.8465 Evaluate side-chains 147 residues out of total 1700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 132 time to evaluate : 0.549 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 242 ASP Chi-restraints excluded: chain A residue 305 CYS Chi-restraints excluded: chain A residue 326 VAL Chi-restraints excluded: chain B residue 83 VAL Chi-restraints excluded: chain B residue 378 LEU Chi-restraints excluded: chain B residue 379 ILE Chi-restraints excluded: chain C residue 31 LEU Chi-restraints excluded: chain C residue 101 ASN Chi-restraints excluded: chain C residue 169 MET Chi-restraints excluded: chain C residue 311 VAL Chi-restraints excluded: chain C residue 326 VAL Chi-restraints excluded: chain C residue 353 MET Chi-restraints excluded: chain D residue 97 LEU Chi-restraints excluded: chain D residue 312 LEU Chi-restraints excluded: chain D residue 379 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 186 optimal weight: 0.0030 chunk 107 optimal weight: 0.5980 chunk 70 optimal weight: 2.9990 chunk 182 optimal weight: 1.9990 chunk 75 optimal weight: 3.9990 chunk 38 optimal weight: 2.9990 chunk 36 optimal weight: 0.9990 chunk 96 optimal weight: 3.9990 chunk 24 optimal weight: 2.9990 chunk 141 optimal weight: 2.9990 chunk 55 optimal weight: 2.9990 overall best weight: 1.3196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 260 HIS B 47 HIS C 141 GLN D 19 GLN D 113 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4045 r_free = 0.4045 target = 0.173340 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3649 r_free = 0.3649 target = 0.136552 restraints weight = 18203.122| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3611 r_free = 0.3611 target = 0.134209 restraints weight = 19078.670| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3626 r_free = 0.3626 target = 0.136096 restraints weight = 19936.992| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3628 r_free = 0.3628 target = 0.136292 restraints weight = 12628.431| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3632 r_free = 0.3632 target = 0.136730 restraints weight = 11594.857| |-----------------------------------------------------------------------------| r_work (final): 0.3345 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7540 moved from start: 0.1991 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 14869 Z= 0.214 Angle : 0.623 10.416 20254 Z= 0.308 Chirality : 0.045 0.252 2345 Planarity : 0.004 0.058 2645 Dihedral : 6.479 79.491 2557 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 4.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.36 % Favored : 94.64 % Rotamer: Outliers : 3.78 % Allowed : 16.91 % Favored : 79.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % 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 aren not related in a simple way. whole: -0.43 (0.19), residues: 1942 helix: 1.60 (0.21), residues: 620 sheet: -0.79 (0.25), residues: 424 loop : -1.40 (0.20), residues: 898 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG D 348 TYR 0.019 0.002 TYR D 276 PHE 0.020 0.002 PHE B 24 TRP 0.019 0.002 TRP B 370 HIS 0.008 0.001 HIS D 211 Details of bonding type rmsd covalent geometry : bond 0.00525 (14846) covalent geometry : angle 0.60530 (20189) SS BOND : bond 0.00089 ( 4) SS BOND : angle 0.69973 ( 8) hydrogen bonds : bond 0.03764 ( 623) hydrogen bonds : angle 4.35195 ( 1770) link_BETA1-4 : bond 0.00664 ( 10) link_BETA1-4 : angle 1.40378 ( 30) link_NAG-ASN : bond 0.00527 ( 9) link_NAG-ASN : angle 3.80093 ( 27) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3884 Ramachandran restraints generated. 1942 Oldfield, 0 Emsley, 1942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3884 Ramachandran restraints generated. 1942 Oldfield, 0 Emsley, 1942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 1700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 121 time to evaluate : 0.581 Fit side-chains revert: symmetry clash REVERT: A 197 GLN cc_start: 0.7396 (tm-30) cc_final: 0.7145 (tm-30) REVERT: A 249 MET cc_start: 0.6923 (mmm) cc_final: 0.6699 (mmm) REVERT: B 9 ILE cc_start: 0.6814 (mt) cc_final: 0.6594 (mt) REVERT: B 288 MET cc_start: 0.7677 (OUTLIER) cc_final: 0.7451 (mtp) REVERT: B 325 MET cc_start: 0.8294 (OUTLIER) cc_final: 0.7419 (ttt) REVERT: B 326 GLU cc_start: 0.7727 (OUTLIER) cc_final: 0.7376 (tp30) REVERT: C 249 MET cc_start: 0.7001 (mmm) cc_final: 0.6749 (mmm) outliers start: 49 outliers final: 33 residues processed: 161 average time/residue: 0.1078 time to fit residues: 26.9604 Evaluate side-chains 149 residues out of total 1700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 113 time to evaluate : 0.605 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 LEU Chi-restraints excluded: chain A residue 48 ASP Chi-restraints excluded: chain A residue 76 VAL Chi-restraints excluded: chain A residue 128 VAL Chi-restraints excluded: chain A residue 170 LEU Chi-restraints excluded: chain A residue 206 ILE Chi-restraints excluded: chain A residue 242 ASP Chi-restraints excluded: chain A residue 305 CYS Chi-restraints excluded: chain A residue 326 VAL Chi-restraints excluded: chain A residue 344 THR Chi-restraints excluded: chain B residue 83 VAL Chi-restraints excluded: chain B residue 97 LEU Chi-restraints excluded: chain B residue 99 THR Chi-restraints excluded: chain B residue 222 LEU Chi-restraints excluded: chain B residue 288 MET Chi-restraints excluded: chain B residue 325 MET Chi-restraints excluded: chain B residue 326 GLU Chi-restraints excluded: chain B residue 362 THR Chi-restraints excluded: chain B residue 378 LEU Chi-restraints excluded: chain B residue 379 ILE Chi-restraints excluded: chain C residue 31 LEU Chi-restraints excluded: chain C residue 41 ILE Chi-restraints excluded: chain C residue 61 SER Chi-restraints excluded: chain C residue 76 VAL Chi-restraints excluded: chain C residue 101 ASN Chi-restraints excluded: chain C residue 169 MET Chi-restraints excluded: chain C residue 263 VAL Chi-restraints excluded: chain C residue 311 VAL Chi-restraints excluded: chain C residue 326 VAL Chi-restraints excluded: chain D residue 22 THR Chi-restraints excluded: chain D residue 44 LEU Chi-restraints excluded: chain D residue 97 LEU Chi-restraints excluded: chain D residue 245 VAL Chi-restraints excluded: chain D residue 251 MET Chi-restraints excluded: chain D residue 378 LEU Chi-restraints excluded: chain D residue 379 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 1 optimal weight: 2.9990 chunk 181 optimal weight: 20.0000 chunk 143 optimal weight: 0.5980 chunk 147 optimal weight: 0.9980 chunk 58 optimal weight: 1.9990 chunk 66 optimal weight: 0.7980 chunk 18 optimal weight: 0.8980 chunk 52 optimal weight: 0.7980 chunk 57 optimal weight: 0.6980 chunk 53 optimal weight: 0.8980 chunk 60 optimal weight: 0.5980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 113 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4065 r_free = 0.4065 target = 0.175118 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3693 r_free = 0.3693 target = 0.140236 restraints weight = 18019.708| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3663 r_free = 0.3663 target = 0.138262 restraints weight = 23040.925| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3676 r_free = 0.3676 target = 0.140366 restraints weight = 21435.974| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3669 r_free = 0.3669 target = 0.139716 restraints weight = 14974.945| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3680 r_free = 0.3680 target = 0.140833 restraints weight = 13205.890| |-----------------------------------------------------------------------------| r_work (final): 0.3415 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7552 moved from start: 0.2049 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 14869 Z= 0.131 Angle : 0.569 10.987 20254 Z= 0.276 Chirality : 0.042 0.244 2345 Planarity : 0.004 0.060 2645 Dihedral : 5.614 62.891 2557 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 4.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.74 % Favored : 95.26 % Rotamer: Outliers : 2.78 % Allowed : 18.61 % Favored : 78.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % 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 aren not related in a simple way. whole: -0.27 (0.19), residues: 1942 helix: 1.85 (0.21), residues: 620 sheet: -0.75 (0.25), residues: 424 loop : -1.37 (0.20), residues: 898 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 333 TYR 0.014 0.001 TYR A 71 PHE 0.018 0.001 PHE A 95 TRP 0.017 0.001 TRP B 370 HIS 0.004 0.001 HIS C 87 Details of bonding type rmsd covalent geometry : bond 0.00316 (14846) covalent geometry : angle 0.55034 (20189) SS BOND : bond 0.00053 ( 4) SS BOND : angle 0.58773 ( 8) hydrogen bonds : bond 0.03100 ( 623) hydrogen bonds : angle 4.12364 ( 1770) link_BETA1-4 : bond 0.00627 ( 10) link_BETA1-4 : angle 1.30126 ( 30) link_NAG-ASN : bond 0.00391 ( 9) link_NAG-ASN : angle 3.79242 ( 27) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3884 Ramachandran restraints generated. 1942 Oldfield, 0 Emsley, 1942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3884 Ramachandran restraints generated. 1942 Oldfield, 0 Emsley, 1942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 1700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 125 time to evaluate : 0.564 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 5 ASN cc_start: 0.6657 (p0) cc_final: 0.5811 (t0) REVERT: A 197 GLN cc_start: 0.7519 (tm-30) cc_final: 0.7221 (tm-30) REVERT: B 325 MET cc_start: 0.8238 (OUTLIER) cc_final: 0.7185 (ttt) REVERT: B 326 GLU cc_start: 0.7726 (OUTLIER) cc_final: 0.7475 (tp30) REVERT: C 25 ARG cc_start: 0.7028 (mtp85) cc_final: 0.6765 (mmp-170) REVERT: C 249 MET cc_start: 0.7028 (mmm) cc_final: 0.6718 (mmm) outliers start: 36 outliers final: 22 residues processed: 154 average time/residue: 0.1178 time to fit residues: 27.9425 Evaluate side-chains 143 residues out of total 1700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 119 time to evaluate : 0.559 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 LEU Chi-restraints excluded: chain A residue 48 ASP Chi-restraints excluded: chain A residue 128 VAL Chi-restraints excluded: chain A residue 170 LEU Chi-restraints excluded: chain A residue 184 VAL Chi-restraints excluded: chain A residue 242 ASP Chi-restraints excluded: chain A residue 305 CYS Chi-restraints excluded: chain B residue 83 VAL Chi-restraints excluded: chain B residue 325 MET Chi-restraints excluded: chain B residue 326 GLU Chi-restraints excluded: chain B residue 378 LEU Chi-restraints excluded: chain B residue 379 ILE Chi-restraints excluded: chain C residue 31 LEU Chi-restraints excluded: chain C residue 61 SER Chi-restraints excluded: chain C residue 76 VAL Chi-restraints excluded: chain C residue 101 ASN Chi-restraints excluded: chain C residue 169 MET Chi-restraints excluded: chain C residue 260 HIS Chi-restraints excluded: chain C residue 297 SER Chi-restraints excluded: chain C residue 311 VAL Chi-restraints excluded: chain D residue 97 LEU Chi-restraints excluded: chain D residue 222 LEU Chi-restraints excluded: chain D residue 245 VAL Chi-restraints excluded: chain D residue 379 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 109 optimal weight: 0.7980 chunk 49 optimal weight: 0.9990 chunk 141 optimal weight: 2.9990 chunk 52 optimal weight: 2.9990 chunk 35 optimal weight: 0.6980 chunk 92 optimal weight: 0.9980 chunk 64 optimal weight: 0.5980 chunk 121 optimal weight: 0.5980 chunk 115 optimal weight: 2.9990 chunk 42 optimal weight: 0.7980 chunk 143 optimal weight: 0.8980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 314 ASN D 113 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4059 r_free = 0.4059 target = 0.174424 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3685 r_free = 0.3685 target = 0.139495 restraints weight = 18026.388| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3656 r_free = 0.3656 target = 0.137606 restraints weight = 21312.676| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3674 r_free = 0.3674 target = 0.139743 restraints weight = 21201.591| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3669 r_free = 0.3669 target = 0.139402 restraints weight = 13931.552| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3674 r_free = 0.3674 target = 0.139856 restraints weight = 13134.705| |-----------------------------------------------------------------------------| r_work (final): 0.3662 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7709 moved from start: 0.2219 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 14869 Z= 0.135 Angle : 0.561 9.540 20254 Z= 0.274 Chirality : 0.042 0.245 2345 Planarity : 0.004 0.060 2645 Dihedral : 4.805 57.748 2557 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 4.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.25 % Favored : 94.75 % Rotamer: Outliers : 3.01 % Allowed : 18.92 % Favored : 78.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % 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 aren not related in a simple way. whole: -0.20 (0.19), residues: 1942 helix: 1.96 (0.21), residues: 620 sheet: -0.72 (0.25), residues: 424 loop : -1.35 (0.20), residues: 898 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 333 TYR 0.015 0.001 TYR A 71 PHE 0.019 0.001 PHE A 95 TRP 0.021 0.001 TRP A 265 HIS 0.004 0.001 HIS C 87 Details of bonding type rmsd covalent geometry : bond 0.00327 (14846) covalent geometry : angle 0.53701 (20189) SS BOND : bond 0.00060 ( 4) SS BOND : angle 0.57607 ( 8) hydrogen bonds : bond 0.03051 ( 623) hydrogen bonds : angle 4.03134 ( 1770) link_BETA1-4 : bond 0.00609 ( 10) link_BETA1-4 : angle 1.29244 ( 30) link_NAG-ASN : bond 0.00468 ( 9) link_NAG-ASN : angle 4.28927 ( 27) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3884 Ramachandran restraints generated. 1942 Oldfield, 0 Emsley, 1942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3884 Ramachandran restraints generated. 1942 Oldfield, 0 Emsley, 1942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 1700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 125 time to evaluate : 0.622 Fit side-chains revert: symmetry clash REVERT: A 5 ASN cc_start: 0.6387 (p0) cc_final: 0.5721 (t0) REVERT: A 197 GLN cc_start: 0.7449 (tm-30) cc_final: 0.7094 (tm-30) REVERT: B 266 GLU cc_start: 0.7154 (OUTLIER) cc_final: 0.6868 (tt0) REVERT: B 325 MET cc_start: 0.8215 (OUTLIER) cc_final: 0.7225 (ttt) REVERT: B 326 GLU cc_start: 0.7879 (OUTLIER) cc_final: 0.7664 (tp30) REVERT: C 249 MET cc_start: 0.7105 (mmm) cc_final: 0.6777 (mmm) outliers start: 39 outliers final: 22 residues processed: 157 average time/residue: 0.1180 time to fit residues: 28.3323 Evaluate side-chains 146 residues out of total 1700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 121 time to evaluate : 0.584 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 LEU Chi-restraints excluded: chain A residue 48 ASP Chi-restraints excluded: chain A residue 76 VAL Chi-restraints excluded: chain A residue 128 VAL Chi-restraints excluded: chain A residue 170 LEU Chi-restraints excluded: chain A residue 305 CYS Chi-restraints excluded: chain A residue 326 VAL Chi-restraints excluded: chain B residue 83 VAL Chi-restraints excluded: chain B residue 97 LEU Chi-restraints excluded: chain B residue 266 GLU Chi-restraints excluded: chain B residue 325 MET Chi-restraints excluded: chain B residue 326 GLU Chi-restraints excluded: chain B residue 378 LEU Chi-restraints excluded: chain B residue 379 ILE Chi-restraints excluded: chain C residue 31 LEU Chi-restraints excluded: chain C residue 61 SER Chi-restraints excluded: chain C residue 76 VAL Chi-restraints excluded: chain C residue 101 ASN Chi-restraints excluded: chain C residue 297 SER Chi-restraints excluded: chain C residue 311 VAL Chi-restraints excluded: chain D residue 48 VAL Chi-restraints excluded: chain D residue 97 LEU Chi-restraints excluded: chain D residue 222 LEU Chi-restraints excluded: chain D residue 245 VAL Chi-restraints excluded: chain D residue 379 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 77 optimal weight: 2.9990 chunk 113 optimal weight: 1.9990 chunk 153 optimal weight: 5.9990 chunk 31 optimal weight: 0.8980 chunk 39 optimal weight: 0.7980 chunk 86 optimal weight: 0.5980 chunk 82 optimal weight: 1.9990 chunk 14 optimal weight: 2.9990 chunk 84 optimal weight: 0.9990 chunk 150 optimal weight: 9.9990 chunk 114 optimal weight: 3.9990 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 94 HIS D 113 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4036 r_free = 0.4036 target = 0.172369 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3640 r_free = 0.3640 target = 0.135705 restraints weight = 18048.161| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3596 r_free = 0.3596 target = 0.132634 restraints weight = 19187.963| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3616 r_free = 0.3616 target = 0.135005 restraints weight = 18598.371| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3619 r_free = 0.3619 target = 0.135329 restraints weight = 12083.249| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3621 r_free = 0.3621 target = 0.135548 restraints weight = 11556.156| |-----------------------------------------------------------------------------| r_work (final): 0.3337 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7598 moved from start: 0.2473 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 14869 Z= 0.178 Angle : 0.599 9.501 20254 Z= 0.294 Chirality : 0.043 0.245 2345 Planarity : 0.004 0.061 2645 Dihedral : 4.746 57.823 2557 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 5.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.51 % Favored : 94.49 % Rotamer: Outliers : 3.55 % Allowed : 19.00 % Favored : 77.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % 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 aren not related in a simple way. whole: -0.26 (0.19), residues: 1942 helix: 1.88 (0.20), residues: 620 sheet: -0.72 (0.25), residues: 424 loop : -1.39 (0.20), residues: 898 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 333 TYR 0.016 0.001 TYR A 71 PHE 0.020 0.002 PHE A 95 TRP 0.022 0.001 TRP A 265 HIS 0.006 0.001 HIS D 211 Details of bonding type rmsd covalent geometry : bond 0.00437 (14846) covalent geometry : angle 0.57729 (20189) SS BOND : bond 0.00074 ( 4) SS BOND : angle 0.65640 ( 8) hydrogen bonds : bond 0.03327 ( 623) hydrogen bonds : angle 4.13487 ( 1770) link_BETA1-4 : bond 0.00608 ( 10) link_BETA1-4 : angle 1.31417 ( 30) link_NAG-ASN : bond 0.00545 ( 9) link_NAG-ASN : angle 4.21858 ( 27) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3884 Ramachandran restraints generated. 1942 Oldfield, 0 Emsley, 1942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3884 Ramachandran restraints generated. 1942 Oldfield, 0 Emsley, 1942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 1700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 117 time to evaluate : 0.590 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 5 ASN cc_start: 0.6877 (p0) cc_final: 0.6645 (p0) REVERT: A 197 GLN cc_start: 0.7526 (tm-30) cc_final: 0.7089 (tm-30) REVERT: B 9 ILE cc_start: 0.7116 (mt) cc_final: 0.6885 (mt) REVERT: B 29 PHE cc_start: 0.8430 (t80) cc_final: 0.8129 (t80) REVERT: B 266 GLU cc_start: 0.7165 (OUTLIER) cc_final: 0.6895 (tt0) REVERT: B 325 MET cc_start: 0.8313 (OUTLIER) cc_final: 0.7379 (ttt) REVERT: B 326 GLU cc_start: 0.7733 (OUTLIER) cc_final: 0.7417 (tp30) REVERT: C 249 MET cc_start: 0.6975 (mmm) cc_final: 0.6669 (mmm) REVERT: C 253 ARG cc_start: 0.6440 (OUTLIER) cc_final: 0.5418 (mmt-90) outliers start: 46 outliers final: 32 residues processed: 154 average time/residue: 0.1170 time to fit residues: 27.5378 Evaluate side-chains 151 residues out of total 1700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 115 time to evaluate : 0.573 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 LEU Chi-restraints excluded: chain A residue 41 ILE Chi-restraints excluded: chain A residue 48 ASP Chi-restraints excluded: chain A residue 76 VAL Chi-restraints excluded: chain A residue 128 VAL Chi-restraints excluded: chain A residue 170 LEU Chi-restraints excluded: chain A residue 184 VAL Chi-restraints excluded: chain A residue 194 ILE Chi-restraints excluded: chain A residue 305 CYS Chi-restraints excluded: chain A residue 326 VAL Chi-restraints excluded: chain A residue 344 THR Chi-restraints excluded: chain B residue 83 VAL Chi-restraints excluded: chain B residue 97 LEU Chi-restraints excluded: chain B residue 266 GLU Chi-restraints excluded: chain B residue 325 MET Chi-restraints excluded: chain B residue 326 GLU Chi-restraints excluded: chain B residue 362 THR Chi-restraints excluded: chain B residue 378 LEU Chi-restraints excluded: chain B residue 379 ILE Chi-restraints excluded: chain C residue 31 LEU Chi-restraints excluded: chain C residue 61 SER Chi-restraints excluded: chain C residue 76 VAL Chi-restraints excluded: chain C residue 101 ASN Chi-restraints excluded: chain C residue 169 MET Chi-restraints excluded: chain C residue 253 ARG Chi-restraints excluded: chain C residue 260 HIS Chi-restraints excluded: chain C residue 297 SER Chi-restraints excluded: chain C residue 311 VAL Chi-restraints excluded: chain C residue 353 MET Chi-restraints excluded: chain D residue 22 THR Chi-restraints excluded: chain D residue 48 VAL Chi-restraints excluded: chain D residue 97 LEU Chi-restraints excluded: chain D residue 222 LEU Chi-restraints excluded: chain D residue 245 VAL Chi-restraints excluded: chain D residue 253 THR Chi-restraints excluded: chain D residue 379 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 52 optimal weight: 0.8980 chunk 25 optimal weight: 0.8980 chunk 181 optimal weight: 0.9990 chunk 171 optimal weight: 5.9990 chunk 176 optimal weight: 20.0000 chunk 155 optimal weight: 0.2980 chunk 156 optimal weight: 5.9990 chunk 150 optimal weight: 6.9990 chunk 147 optimal weight: 0.9980 chunk 95 optimal weight: 0.7980 chunk 66 optimal weight: 0.9980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 113 GLN ** D 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4046 r_free = 0.4046 target = 0.173310 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3671 r_free = 0.3671 target = 0.138341 restraints weight = 18023.046| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3638 r_free = 0.3638 target = 0.136121 restraints weight = 20859.152| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3652 r_free = 0.3652 target = 0.137780 restraints weight = 20486.795| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3657 r_free = 0.3657 target = 0.138294 restraints weight = 13543.230| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3659 r_free = 0.3659 target = 0.138581 restraints weight = 12792.648| |-----------------------------------------------------------------------------| r_work (final): 0.3369 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7559 moved from start: 0.2548 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 14869 Z= 0.142 Angle : 0.569 10.182 20254 Z= 0.280 Chirality : 0.042 0.245 2345 Planarity : 0.004 0.061 2645 Dihedral : 4.617 57.993 2557 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 5.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.61 % Favored : 94.39 % Rotamer: Outliers : 2.78 % Allowed : 20.08 % Favored : 77.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % 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 aren not related in a simple way. whole: -0.18 (0.19), residues: 1942 helix: 1.95 (0.21), residues: 620 sheet: -0.66 (0.25), residues: 424 loop : -1.36 (0.20), residues: 898 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 333 TYR 0.015 0.001 TYR A 71 PHE 0.020 0.001 PHE C 95 TRP 0.020 0.001 TRP A 265 HIS 0.003 0.001 HIS D 211 Details of bonding type rmsd covalent geometry : bond 0.00345 (14846) covalent geometry : angle 0.54862 (20189) SS BOND : bond 0.00050 ( 4) SS BOND : angle 0.60571 ( 8) hydrogen bonds : bond 0.03083 ( 623) hydrogen bonds : angle 4.05115 ( 1770) link_BETA1-4 : bond 0.00604 ( 10) link_BETA1-4 : angle 1.27892 ( 30) link_NAG-ASN : bond 0.00428 ( 9) link_NAG-ASN : angle 3.93466 ( 27) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3884 Ramachandran restraints generated. 1942 Oldfield, 0 Emsley, 1942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3884 Ramachandran restraints generated. 1942 Oldfield, 0 Emsley, 1942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 1700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 122 time to evaluate : 0.620 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 5 ASN cc_start: 0.6761 (p0) cc_final: 0.6540 (p0) REVERT: A 197 GLN cc_start: 0.7581 (tm-30) cc_final: 0.7102 (tm-30) REVERT: B 9 ILE cc_start: 0.7124 (mt) cc_final: 0.6879 (mt) REVERT: B 29 PHE cc_start: 0.8418 (t80) cc_final: 0.8158 (t80) REVERT: B 266 GLU cc_start: 0.7170 (OUTLIER) cc_final: 0.6908 (tt0) REVERT: B 325 MET cc_start: 0.8299 (OUTLIER) cc_final: 0.7312 (ttt) REVERT: B 326 GLU cc_start: 0.7712 (OUTLIER) cc_final: 0.7459 (tp30) REVERT: C 249 MET cc_start: 0.6915 (mmm) cc_final: 0.6620 (mmm) REVERT: C 253 ARG cc_start: 0.6555 (OUTLIER) cc_final: 0.5427 (mmt-90) outliers start: 36 outliers final: 27 residues processed: 151 average time/residue: 0.1239 time to fit residues: 28.1713 Evaluate side-chains 146 residues out of total 1700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 115 time to evaluate : 0.574 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 LEU Chi-restraints excluded: chain A residue 48 ASP Chi-restraints excluded: chain A residue 76 VAL Chi-restraints excluded: chain A residue 128 VAL Chi-restraints excluded: chain A residue 170 LEU Chi-restraints excluded: chain A residue 184 VAL Chi-restraints excluded: chain A residue 305 CYS Chi-restraints excluded: chain A residue 326 VAL Chi-restraints excluded: chain A residue 344 THR Chi-restraints excluded: chain B residue 83 VAL Chi-restraints excluded: chain B residue 97 LEU Chi-restraints excluded: chain B residue 266 GLU Chi-restraints excluded: chain B residue 325 MET Chi-restraints excluded: chain B residue 326 GLU Chi-restraints excluded: chain B residue 378 LEU Chi-restraints excluded: chain C residue 31 LEU Chi-restraints excluded: chain C residue 61 SER Chi-restraints excluded: chain C residue 76 VAL Chi-restraints excluded: chain C residue 101 ASN Chi-restraints excluded: chain C residue 169 MET Chi-restraints excluded: chain C residue 253 ARG Chi-restraints excluded: chain C residue 260 HIS Chi-restraints excluded: chain C residue 297 SER Chi-restraints excluded: chain C residue 311 VAL Chi-restraints excluded: chain C residue 353 MET Chi-restraints excluded: chain D residue 44 LEU Chi-restraints excluded: chain D residue 48 VAL Chi-restraints excluded: chain D residue 97 LEU Chi-restraints excluded: chain D residue 222 LEU Chi-restraints excluded: chain D residue 245 VAL Chi-restraints excluded: chain D residue 253 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 15 optimal weight: 1.9990 chunk 171 optimal weight: 50.0000 chunk 20 optimal weight: 2.9990 chunk 173 optimal weight: 20.0000 chunk 186 optimal weight: 40.0000 chunk 189 optimal weight: 9.9990 chunk 152 optimal weight: 30.0000 chunk 169 optimal weight: 20.0000 chunk 56 optimal weight: 0.7980 chunk 146 optimal weight: 0.9980 chunk 180 optimal weight: 30.0000 overall best weight: 3.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 185 GLN B 216 HIS C 153 GLN C 204 ASN D 113 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3942 r_free = 0.3942 target = 0.163837 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3539 r_free = 0.3539 target = 0.127998 restraints weight = 18620.831| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3484 r_free = 0.3484 target = 0.124269 restraints weight = 21659.975| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3500 r_free = 0.3500 target = 0.126021 restraints weight = 22418.312| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3508 r_free = 0.3508 target = 0.126738 restraints weight = 14608.323| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3508 r_free = 0.3508 target = 0.126859 restraints weight = 13192.573| |-----------------------------------------------------------------------------| r_work (final): 0.3235 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7762 moved from start: 0.3367 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.012 0.077 14869 Z= 0.473 Angle : 0.900 9.534 20254 Z= 0.451 Chirality : 0.054 0.273 2345 Planarity : 0.006 0.059 2645 Dihedral : 5.998 59.029 2557 Min Nonbonded Distance : 2.339 Molprobity Statistics. All-atom Clashscore : 7.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.98 % Favored : 92.02 % Rotamer: Outliers : 3.63 % Allowed : 19.38 % Favored : 76.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % 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 aren not related in a simple way. whole: -1.12 (0.18), residues: 1942 helix: 0.84 (0.20), residues: 620 sheet: -1.08 (0.25), residues: 426 loop : -1.71 (0.19), residues: 896 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG D 348 TYR 0.029 0.003 TYR C 71 PHE 0.029 0.003 PHE B 24 TRP 0.044 0.003 TRP A 265 HIS 0.010 0.002 HIS D 211 Details of bonding type rmsd covalent geometry : bond 0.01153 (14846) covalent geometry : angle 0.87806 (20189) SS BOND : bond 0.00490 ( 4) SS BOND : angle 1.27097 ( 8) hydrogen bonds : bond 0.05194 ( 623) hydrogen bonds : angle 4.93308 ( 1770) link_BETA1-4 : bond 0.00734 ( 10) link_BETA1-4 : angle 1.88468 ( 30) link_NAG-ASN : bond 0.01051 ( 9) link_NAG-ASN : angle 5.20231 ( 27) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3884 Ramachandran restraints generated. 1942 Oldfield, 0 Emsley, 1942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3884 Ramachandran restraints generated. 1942 Oldfield, 0 Emsley, 1942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 1700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 127 time to evaluate : 0.687 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 197 GLN cc_start: 0.7818 (tm-30) cc_final: 0.7348 (tm-30) REVERT: B 326 GLU cc_start: 0.7799 (OUTLIER) cc_final: 0.7409 (tp30) REVERT: C 253 ARG cc_start: 0.6555 (OUTLIER) cc_final: 0.5543 (mmt-90) outliers start: 47 outliers final: 33 residues processed: 166 average time/residue: 0.1326 time to fit residues: 32.5220 Evaluate side-chains 150 residues out of total 1700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 115 time to evaluate : 0.594 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 LEU Chi-restraints excluded: chain A residue 41 ILE Chi-restraints excluded: chain A residue 48 ASP Chi-restraints excluded: chain A residue 76 VAL Chi-restraints excluded: chain A residue 128 VAL Chi-restraints excluded: chain A residue 170 LEU Chi-restraints excluded: chain A residue 184 VAL Chi-restraints excluded: chain A residue 194 ILE Chi-restraints excluded: chain A residue 242 ASP Chi-restraints excluded: chain A residue 305 CYS Chi-restraints excluded: chain A residue 326 VAL Chi-restraints excluded: chain A residue 344 THR Chi-restraints excluded: chain B residue 83 VAL Chi-restraints excluded: chain B residue 97 LEU Chi-restraints excluded: chain B residue 325 MET Chi-restraints excluded: chain B residue 326 GLU Chi-restraints excluded: chain B residue 362 THR Chi-restraints excluded: chain C residue 31 LEU Chi-restraints excluded: chain C residue 46 ILE Chi-restraints excluded: chain C residue 61 SER Chi-restraints excluded: chain C residue 76 VAL Chi-restraints excluded: chain C residue 101 ASN Chi-restraints excluded: chain C residue 186 CYS Chi-restraints excluded: chain C residue 253 ARG Chi-restraints excluded: chain C residue 260 HIS Chi-restraints excluded: chain C residue 297 SER Chi-restraints excluded: chain C residue 353 MET Chi-restraints excluded: chain D residue 22 THR Chi-restraints excluded: chain D residue 48 VAL Chi-restraints excluded: chain D residue 97 LEU Chi-restraints excluded: chain D residue 99 THR Chi-restraints excluded: chain D residue 113 GLN Chi-restraints excluded: chain D residue 222 LEU Chi-restraints excluded: chain D residue 245 VAL Chi-restraints excluded: chain D residue 253 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 30 optimal weight: 0.9980 chunk 67 optimal weight: 2.9990 chunk 132 optimal weight: 0.7980 chunk 154 optimal weight: 8.9990 chunk 18 optimal weight: 0.9990 chunk 184 optimal weight: 50.0000 chunk 179 optimal weight: 1.9990 chunk 25 optimal weight: 6.9990 chunk 59 optimal weight: 0.6980 chunk 42 optimal weight: 0.5980 chunk 83 optimal weight: 0.8980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 260 HIS D 113 GLN D 148 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4008 r_free = 0.4008 target = 0.169998 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3633 r_free = 0.3633 target = 0.135628 restraints weight = 18157.441| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3603 r_free = 0.3603 target = 0.133722 restraints weight = 22763.262| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3620 r_free = 0.3620 target = 0.135709 restraints weight = 21833.076| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3615 r_free = 0.3615 target = 0.135344 restraints weight = 14335.658| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3621 r_free = 0.3621 target = 0.135878 restraints weight = 13443.415| |-----------------------------------------------------------------------------| r_work (final): 0.3332 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7607 moved from start: 0.3166 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 14869 Z= 0.159 Angle : 0.630 10.483 20254 Z= 0.313 Chirality : 0.044 0.256 2345 Planarity : 0.004 0.064 2645 Dihedral : 5.355 58.304 2557 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 6.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.51 % Favored : 94.49 % Rotamer: Outliers : 2.24 % Allowed : 20.93 % Favored : 76.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % 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 aren not related in a simple way. whole: -0.66 (0.19), residues: 1942 helix: 1.49 (0.20), residues: 622 sheet: -1.01 (0.25), residues: 426 loop : -1.54 (0.20), residues: 894 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 333 TYR 0.017 0.001 TYR C 208 PHE 0.022 0.001 PHE C 95 TRP 0.021 0.001 TRP A 265 HIS 0.005 0.001 HIS C 87 Details of bonding type rmsd covalent geometry : bond 0.00379 (14846) covalent geometry : angle 0.61014 (20189) SS BOND : bond 0.00093 ( 4) SS BOND : angle 0.86548 ( 8) hydrogen bonds : bond 0.03543 ( 623) hydrogen bonds : angle 4.33180 ( 1770) link_BETA1-4 : bond 0.00675 ( 10) link_BETA1-4 : angle 1.42295 ( 30) link_NAG-ASN : bond 0.00486 ( 9) link_NAG-ASN : angle 4.15039 ( 27) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3884 Ramachandran restraints generated. 1942 Oldfield, 0 Emsley, 1942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3884 Ramachandran restraints generated. 1942 Oldfield, 0 Emsley, 1942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 1700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 115 time to evaluate : 0.617 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 5 ASN cc_start: 0.6878 (p0) cc_final: 0.6052 (t0) REVERT: A 197 GLN cc_start: 0.7592 (tm-30) cc_final: 0.7062 (tm-30) REVERT: B 29 PHE cc_start: 0.8590 (t80) cc_final: 0.8307 (t80) REVERT: C 5 ASN cc_start: 0.6835 (p0) cc_final: 0.6164 (t0) REVERT: C 187 GLU cc_start: 0.8015 (mm-30) cc_final: 0.7781 (mm-30) REVERT: C 249 MET cc_start: 0.6683 (mmm) cc_final: 0.5937 (ttt) outliers start: 29 outliers final: 25 residues processed: 139 average time/residue: 0.1219 time to fit residues: 25.7749 Evaluate side-chains 135 residues out of total 1700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 110 time to evaluate : 0.495 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 LEU Chi-restraints excluded: chain A residue 41 ILE Chi-restraints excluded: chain A residue 48 ASP Chi-restraints excluded: chain A residue 76 VAL Chi-restraints excluded: chain A residue 128 VAL Chi-restraints excluded: chain A residue 170 LEU Chi-restraints excluded: chain A residue 184 VAL Chi-restraints excluded: chain A residue 260 HIS Chi-restraints excluded: chain A residue 305 CYS Chi-restraints excluded: chain A residue 326 VAL Chi-restraints excluded: chain A residue 344 THR Chi-restraints excluded: chain B residue 83 VAL Chi-restraints excluded: chain B residue 97 LEU Chi-restraints excluded: chain B residue 325 MET Chi-restraints excluded: chain C residue 31 LEU Chi-restraints excluded: chain C residue 61 SER Chi-restraints excluded: chain C residue 76 VAL Chi-restraints excluded: chain C residue 101 ASN Chi-restraints excluded: chain C residue 260 HIS Chi-restraints excluded: chain C residue 353 MET Chi-restraints excluded: chain D residue 48 VAL Chi-restraints excluded: chain D residue 97 LEU Chi-restraints excluded: chain D residue 222 LEU Chi-restraints excluded: chain D residue 245 VAL Chi-restraints excluded: chain D residue 253 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 93 optimal weight: 0.1980 chunk 16 optimal weight: 0.8980 chunk 173 optimal weight: 20.0000 chunk 182 optimal weight: 50.0000 chunk 163 optimal weight: 30.0000 chunk 72 optimal weight: 1.9990 chunk 151 optimal weight: 10.0000 chunk 138 optimal weight: 0.0000 chunk 162 optimal weight: 9.9990 chunk 104 optimal weight: 10.0000 chunk 24 optimal weight: 0.9980 overall best weight: 0.8186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 21 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 113 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4014 r_free = 0.4014 target = 0.170440 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3616 r_free = 0.3616 target = 0.133898 restraints weight = 18130.351| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3587 r_free = 0.3587 target = 0.132430 restraints weight = 17781.034| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3593 r_free = 0.3593 target = 0.133394 restraints weight = 18972.458| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3591 r_free = 0.3591 target = 0.133345 restraints weight = 12870.280| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3596 r_free = 0.3596 target = 0.133804 restraints weight = 11782.380| |-----------------------------------------------------------------------------| r_work (final): 0.3330 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7622 moved from start: 0.3141 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 14869 Z= 0.156 Angle : 0.614 10.361 20254 Z= 0.304 Chirality : 0.043 0.249 2345 Planarity : 0.004 0.064 2645 Dihedral : 5.089 58.117 2557 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 6.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.23 % Favored : 93.77 % Rotamer: Outliers : 2.32 % Allowed : 20.54 % Favored : 77.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % 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 aren not related in a simple way. whole: -0.52 (0.19), residues: 1942 helix: 1.65 (0.20), residues: 622 sheet: -0.95 (0.26), residues: 426 loop : -1.50 (0.20), residues: 894 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.021 0.000 ARG A 258 TYR 0.014 0.001 TYR A 71 PHE 0.021 0.001 PHE C 95 TRP 0.023 0.001 TRP A 265 HIS 0.014 0.001 HIS A 260 Details of bonding type rmsd covalent geometry : bond 0.00377 (14846) covalent geometry : angle 0.59422 (20189) SS BOND : bond 0.00081 ( 4) SS BOND : angle 0.74198 ( 8) hydrogen bonds : bond 0.03359 ( 623) hydrogen bonds : angle 4.18972 ( 1770) link_BETA1-4 : bond 0.00599 ( 10) link_BETA1-4 : angle 1.42620 ( 30) link_NAG-ASN : bond 0.00466 ( 9) link_NAG-ASN : angle 4.06689 ( 27) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2353.87 seconds wall clock time: 41 minutes 35.70 seconds (2495.70 seconds total)