Starting phenix.real_space_refine on Sat Jul 4 05:26:09 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7k0n_22604/07_2026/7k0n_22604.cif Found real_map, /net/cci-nas-00/data/ceres_data/7k0n_22604/07_2026/7k0n_22604.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7k0n_22604/07_2026/7k0n_22604.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7k0n_22604/07_2026/7k0n_22604.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/7k0n_22604/07_2026/7k0n_22604.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7k0n_22604/07_2026/7k0n_22604.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7k0n_22604/07_2026/7k0n_22604.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7k0n_22604/07_2026/7k0n_22604.map" } resolution = 3.1 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= 0.001 sd= 0.103 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: 5 Type Number sf(0) Gaussians P 4 5.49 5 S 100 5.16 5 C 11952 2.51 5 N 3090 2.21 5 O 3324 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 67 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 18470 Number of models: 1 Model: "" Number of chains: 14 Chain: "A" Number of atoms: 3550 Number of conformers: 1 Conformer: "" Number of residues, atoms: 464, 3550 Classifications: {'peptide': 464} Incomplete info: {'truncation_to_alanine': 26} Link IDs: {'PTRANS': 22, 'TRANS': 441} Unresolved non-hydrogen bonds: 89 Unresolved non-hydrogen angles: 111 Unresolved non-hydrogen dihedrals: 70 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'GLU:plan': 6, 'GLN:plan1': 1, 'TYR:plan': 1, 'ARG:plan': 2, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 51 Chain: "B" Number of atoms: 3857 Number of conformers: 1 Conformer: "" Number of residues, atoms: 491, 3857 Classifications: {'peptide': 491} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 17, 'TRANS': 473} Unresolved non-hydrogen bonds: 40 Unresolved non-hydrogen angles: 49 Unresolved non-hydrogen dihedrals: 35 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1, 'HIS:plan': 2, 'ASP:plan': 1, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 27 Chain: "C" Number of atoms: 476 Number of conformers: 1 Conformer: "" Number of residues, atoms: 62, 476 Classifications: {'peptide': 62} Incomplete info: {'truncation_to_alanine': 14} Link IDs: {'PTRANS': 2, 'TRANS': 59} Unresolved non-hydrogen bonds: 63 Unresolved non-hydrogen angles: 79 Unresolved non-hydrogen dihedrals: 56 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'ARG:plan': 1, 'GLN:plan1': 1, 'HIS:plan': 2, 'TYR:plan': 1, 'PHE:plan': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 36 Chain: "D" Number of atoms: 1230 Number of conformers: 1 Conformer: "" Number of residues, atoms: 153, 1230 Classifications: {'peptide': 153} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 8, 'TRANS': 144} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'PHE:plan': 1} Unresolved non-hydrogen planarities: 6 Chain: "H" Number of atoms: 1230 Number of conformers: 1 Conformer: "" Number of residues, atoms: 153, 1230 Classifications: {'peptide': 153} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 8, 'TRANS': 144} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'PHE:plan': 1} Unresolved non-hydrogen planarities: 6 Chain: "G" Number of atoms: 476 Number of conformers: 1 Conformer: "" Number of residues, atoms: 62, 476 Classifications: {'peptide': 62} Incomplete info: {'truncation_to_alanine': 14} Link IDs: {'PTRANS': 2, 'TRANS': 59} Unresolved non-hydrogen bonds: 63 Unresolved non-hydrogen angles: 79 Unresolved non-hydrogen dihedrals: 56 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'ARG:plan': 1, 'GLN:plan1': 1, 'HIS:plan': 2, 'TYR:plan': 1, 'PHE:plan': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 36 Chain: "E" Number of atoms: 3550 Number of conformers: 1 Conformer: "" Number of residues, atoms: 464, 3550 Classifications: {'peptide': 464} Incomplete info: {'truncation_to_alanine': 26} Link IDs: {'PTRANS': 22, 'TRANS': 441} Unresolved non-hydrogen bonds: 89 Unresolved non-hydrogen angles: 111 Unresolved non-hydrogen dihedrals: 70 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'GLU:plan': 6, 'GLN:plan1': 1, 'TYR:plan': 1, 'ARG:plan': 2, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 51 Chain: "F" Number of atoms: 3857 Number of conformers: 1 Conformer: "" Number of residues, atoms: 491, 3857 Classifications: {'peptide': 491} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 17, 'TRANS': 473} Unresolved non-hydrogen bonds: 40 Unresolved non-hydrogen angles: 49 Unresolved non-hydrogen dihedrals: 35 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1, 'HIS:plan': 2, 'ASP:plan': 1, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 27 Chain: "B" Number of atoms: 52 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 52 Unusual residues: {'PLP': 1, 'POV': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 68 Unresolved non-hydrogen angles: 80 Unresolved non-hydrogen dihedrals: 55 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'POV:plan-1': 2, 'POV:plan-2': 1, 'POV:plan-3': 1} Unresolved non-hydrogen planarities: 14 Chain: "C" Number of atoms: 34 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 34 Unusual residues: {'POV': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 122 Unresolved non-hydrogen angles: 149 Unresolved non-hydrogen dihedrals: 89 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'POV:plan-1': 3, 'POV:plan-2': 3, 'POV:plan-3': 3} Unresolved non-hydrogen planarities: 36 Chain: "D" Number of atoms: 36 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 36 Unusual residues: {'POV': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 120 Unresolved non-hydrogen angles: 147 Unresolved non-hydrogen dihedrals: 87 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'POV:plan-1': 2, 'POV:plan-2': 3, 'POV:plan-3': 3} Unresolved non-hydrogen planarities: 31 Chain: "H" Number of atoms: 36 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 36 Unusual residues: {'POV': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 120 Unresolved non-hydrogen angles: 147 Unresolved non-hydrogen dihedrals: 87 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'POV:plan-1': 2, 'POV:plan-2': 3, 'POV:plan-3': 3} Unresolved non-hydrogen planarities: 31 Chain: "G" Number of atoms: 34 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 34 Unusual residues: {'POV': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 122 Unresolved non-hydrogen angles: 149 Unresolved non-hydrogen dihedrals: 89 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'POV:plan-1': 3, 'POV:plan-2': 3, 'POV:plan-3': 3} Unresolved non-hydrogen planarities: 36 Chain: "F" Number of atoms: 52 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 52 Unusual residues: {'PLP': 1, 'POV': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 68 Unresolved non-hydrogen angles: 80 Unresolved non-hydrogen dihedrals: 55 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'POV:plan-1': 2, 'POV:plan-2': 1, 'POV:plan-3': 1} Unresolved non-hydrogen planarities: 14 Time building chain proxies: 3.87, per 1000 atoms: 0.21 Number of scatterers: 18470 At special positions: 0 Unit cell: (151.755, 115.575, 117.585, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 100 16.00 P 4 15.00 O 3324 8.00 N 3090 7.00 C 11952 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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=2, symmetry=0 Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 1.46 Conformation dependent library (CDL) restraints added in 562.0 milliseconds 4648 Ramachandran restraints generated. 2324 Oldfield, 0 Emsley, 2324 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4340 Finding SS restraints... Secondary structure from input PDB file: 98 helices and 14 sheets defined 54.1% alpha, 7.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.59 Creating SS restraints... Processing helix chain 'A' and resid 10 through 20 Processing helix chain 'A' and resid 21 through 41 removed outlier: 3.764A pdb=" N LEU A 25 " --> pdb=" O PRO A 21 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N PHE A 40 " --> pdb=" O ILE A 36 " (cutoff:3.500A) Processing helix chain 'A' and resid 53 through 64 Processing helix chain 'A' and resid 114 through 129 removed outlier: 3.579A pdb=" N LYS A 127 " --> pdb=" O ALA A 123 " (cutoff:3.500A) Processing helix chain 'A' and resid 142 through 156 removed outlier: 3.572A pdb=" N LEU A 146 " --> pdb=" O PHE A 142 " (cutoff:3.500A) Processing helix chain 'A' and resid 168 through 179 removed outlier: 3.787A pdb=" N ALA A 172 " --> pdb=" O PHE A 168 " (cutoff:3.500A) Proline residue: A 176 - end of helix Processing helix chain 'A' and resid 192 through 202 Processing helix chain 'A' and resid 213 through 231 removed outlier: 3.839A pdb=" N LEU A 217 " --> pdb=" O ASP A 213 " (cutoff:3.500A) Processing helix chain 'A' and resid 231 through 236 Processing helix chain 'A' and resid 256 through 268 Processing helix chain 'A' and resid 288 through 294 Processing helix chain 'A' and resid 296 through 300 Processing helix chain 'A' and resid 321 through 326 Processing helix chain 'A' and resid 327 through 332 Processing helix chain 'A' and resid 332 through 337 Processing helix chain 'A' and resid 342 through 359 Processing helix chain 'A' and resid 360 through 377 removed outlier: 4.283A pdb=" N ALA A 364 " --> pdb=" O PRO A 360 " (cutoff:3.500A) Processing helix chain 'A' and resid 404 through 421 removed outlier: 3.511A pdb=" N ASP A 408 " --> pdb=" O SER A 404 " (cutoff:3.500A) Processing helix chain 'A' and resid 453 through 473 Processing helix chain 'B' and resid 67 through 94 Processing helix chain 'B' and resid 105 through 109 Processing helix chain 'B' and resid 116 through 119 Processing helix chain 'B' and resid 120 through 126 Processing helix chain 'B' and resid 127 through 134 removed outlier: 3.551A pdb=" N ARG B 131 " --> pdb=" O MET B 128 " (cutoff:3.500A) removed outlier: 5.406A pdb=" N ASP B 132 " --> pdb=" O ARG B 129 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N TRP B 134 " --> pdb=" O ARG B 131 " (cutoff:3.500A) Processing helix chain 'B' and resid 186 through 199 removed outlier: 3.624A pdb=" N GLU B 190 " --> pdb=" O GLY B 186 " (cutoff:3.500A) Processing helix chain 'B' and resid 213 through 228 Processing helix chain 'B' and resid 237 through 250 removed outlier: 3.674A pdb=" N ASN B 242 " --> pdb=" O GLY B 238 " (cutoff:3.500A) Proline residue: B 247 - end of helix Processing helix chain 'B' and resid 263 through 273 Processing helix chain 'B' and resid 284 through 299 Processing helix chain 'B' and resid 326 through 338 Processing helix chain 'B' and resid 358 through 364 Processing helix chain 'B' and resid 366 through 370 Processing helix chain 'B' and resid 391 through 401 Processing helix chain 'B' and resid 402 through 408 Processing helix chain 'B' and resid 412 through 427 Processing helix chain 'B' and resid 433 through 456 removed outlier: 3.722A pdb=" N VAL B 439 " --> pdb=" O GLY B 435 " (cutoff:3.500A) Processing helix chain 'B' and resid 475 through 489 removed outlier: 4.165A pdb=" N GLY B 480 " --> pdb=" O PRO B 476 " (cutoff:3.500A) Processing helix chain 'B' and resid 517 through 536 Processing helix chain 'C' and resid 9 through 24 Processing helix chain 'C' and resid 30 through 55 Processing helix chain 'C' and resid 59 through 69 removed outlier: 3.843A pdb=" N ILE C 63 " --> pdb=" O HIS C 59 " (cutoff:3.500A) Processing helix chain 'D' and resid 21 through 39 Processing helix chain 'D' and resid 44 through 66 Processing helix chain 'D' and resid 84 through 89 Processing helix chain 'D' and resid 90 through 93 Processing helix chain 'D' and resid 96 through 117 Proline residue: D 106 - end of helix Processing helix chain 'D' and resid 120 through 136 Processing helix chain 'D' and resid 137 through 139 No H-bonds generated for 'chain 'D' and resid 137 through 139' Processing helix chain 'D' and resid 146 through 150 Processing helix chain 'H' and resid 21 through 39 Processing helix chain 'H' and resid 44 through 66 Processing helix chain 'H' and resid 84 through 89 Processing helix chain 'H' and resid 90 through 93 Processing helix chain 'H' and resid 96 through 117 Proline residue: H 106 - end of helix Processing helix chain 'H' and resid 120 through 136 Processing helix chain 'H' and resid 137 through 139 No H-bonds generated for 'chain 'H' and resid 137 through 139' Processing helix chain 'H' and resid 146 through 150 Processing helix chain 'G' and resid 9 through 24 Processing helix chain 'G' and resid 30 through 55 Processing helix chain 'G' and resid 59 through 69 removed outlier: 3.843A pdb=" N ILE G 63 " --> pdb=" O HIS G 59 " (cutoff:3.500A) Processing helix chain 'E' and resid 11 through 20 Processing helix chain 'E' and resid 21 through 41 removed outlier: 3.763A pdb=" N LEU E 25 " --> pdb=" O PRO E 21 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N PHE E 40 " --> pdb=" O ILE E 36 " (cutoff:3.500A) Processing helix chain 'E' and resid 53 through 64 Processing helix chain 'E' and resid 114 through 129 removed outlier: 3.580A pdb=" N LYS E 127 " --> pdb=" O ALA E 123 " (cutoff:3.500A) Processing helix chain 'E' and resid 142 through 156 removed outlier: 3.572A pdb=" N LEU E 146 " --> pdb=" O PHE E 142 " (cutoff:3.500A) Processing helix chain 'E' and resid 168 through 179 removed outlier: 3.787A pdb=" N ALA E 172 " --> pdb=" O PHE E 168 " (cutoff:3.500A) Proline residue: E 176 - end of helix Processing helix chain 'E' and resid 192 through 202 Processing helix chain 'E' and resid 213 through 231 removed outlier: 3.839A pdb=" N LEU E 217 " --> pdb=" O ASP E 213 " (cutoff:3.500A) Processing helix chain 'E' and resid 231 through 236 Processing helix chain 'E' and resid 256 through 268 Processing helix chain 'E' and resid 288 through 294 Processing helix chain 'E' and resid 296 through 300 Processing helix chain 'E' and resid 321 through 326 Processing helix chain 'E' and resid 327 through 332 Processing helix chain 'E' and resid 332 through 337 Processing helix chain 'E' and resid 342 through 359 Processing helix chain 'E' and resid 360 through 377 removed outlier: 4.282A pdb=" N ALA E 364 " --> pdb=" O PRO E 360 " (cutoff:3.500A) Processing helix chain 'E' and resid 404 through 421 removed outlier: 3.510A pdb=" N ASP E 408 " --> pdb=" O SER E 404 " (cutoff:3.500A) Processing helix chain 'E' and resid 453 through 473 Processing helix chain 'F' and resid 67 through 94 Processing helix chain 'F' and resid 105 through 109 Processing helix chain 'F' and resid 116 through 119 Processing helix chain 'F' and resid 120 through 126 Processing helix chain 'F' and resid 127 through 134 removed outlier: 3.551A pdb=" N ARG F 131 " --> pdb=" O MET F 128 " (cutoff:3.500A) removed outlier: 5.406A pdb=" N ASP F 132 " --> pdb=" O ARG F 129 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N TRP F 134 " --> pdb=" O ARG F 131 " (cutoff:3.500A) Processing helix chain 'F' and resid 186 through 199 removed outlier: 3.624A pdb=" N GLU F 190 " --> pdb=" O GLY F 186 " (cutoff:3.500A) Processing helix chain 'F' and resid 213 through 228 Processing helix chain 'F' and resid 237 through 250 removed outlier: 3.675A pdb=" N ASN F 242 " --> pdb=" O GLY F 238 " (cutoff:3.500A) Proline residue: F 247 - end of helix Processing helix chain 'F' and resid 263 through 273 Processing helix chain 'F' and resid 284 through 299 Processing helix chain 'F' and resid 326 through 338 Processing helix chain 'F' and resid 358 through 364 Processing helix chain 'F' and resid 366 through 370 Processing helix chain 'F' and resid 391 through 401 Processing helix chain 'F' and resid 402 through 408 Processing helix chain 'F' and resid 412 through 427 Processing helix chain 'F' and resid 433 through 456 removed outlier: 3.722A pdb=" N VAL F 439 " --> pdb=" O GLY F 435 " (cutoff:3.500A) Processing helix chain 'F' and resid 475 through 489 removed outlier: 4.166A pdb=" N GLY F 480 " --> pdb=" O PRO F 476 " (cutoff:3.500A) Processing helix chain 'F' and resid 517 through 536 Processing sheet with id=AA1, first strand: chain 'A' and resid 94 through 95 Processing sheet with id=AA2, first strand: chain 'A' and resid 160 through 164 removed outlier: 6.959A pdb=" N ILE A 271 " --> pdb=" O LEU A 302 " (cutoff:3.500A) removed outlier: 8.270A pdb=" N SER A 304 " --> pdb=" O ILE A 271 " (cutoff:3.500A) removed outlier: 6.717A pdb=" N LEU A 273 " --> pdb=" O SER A 304 " (cutoff:3.500A) removed outlier: 8.899A pdb=" N ASN A 306 " --> pdb=" O LEU A 273 " (cutoff:3.500A) removed outlier: 6.813A pdb=" N ARG A 240 " --> pdb=" O ARG A 270 " (cutoff:3.500A) removed outlier: 7.687A pdb=" N PHE A 272 " --> pdb=" O ARG A 240 " (cutoff:3.500A) removed outlier: 6.139A pdb=" N ILE A 242 " --> pdb=" O PHE A 272 " (cutoff:3.500A) removed outlier: 7.663A pdb=" N GLU A 274 " --> pdb=" O ILE A 242 " (cutoff:3.500A) removed outlier: 7.062A pdb=" N VAL A 244 " --> pdb=" O GLU A 274 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N ASP A 188 " --> pdb=" O VAL A 243 " (cutoff:3.500A) removed outlier: 8.014A pdb=" N GLU A 245 " --> pdb=" O ASP A 188 " (cutoff:3.500A) removed outlier: 6.185A pdb=" N VAL A 185 " --> pdb=" O LYS A 207 " (cutoff:3.500A) removed outlier: 7.396A pdb=" N PHE A 209 " --> pdb=" O VAL A 185 " (cutoff:3.500A) removed outlier: 6.900A pdb=" N VAL A 187 " --> pdb=" O PHE A 209 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 383 through 384 removed outlier: 4.183A pdb=" N THR A 427 " --> pdb=" O ARG A 445 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 145 through 146 removed outlier: 6.784A pdb=" N ILE B 171 " --> pdb=" O GLY B 492 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 149 through 152 removed outlier: 5.343A pdb=" N GLU B 150 " --> pdb=" O THR B 163 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N THR B 163 " --> pdb=" O GLU B 150 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 231 through 235 removed outlier: 6.568A pdb=" N ILE B 310 " --> pdb=" O TYR B 340 " (cutoff:3.500A) removed outlier: 7.600A pdb=" N TYR B 342 " --> pdb=" O ILE B 310 " (cutoff:3.500A) removed outlier: 6.151A pdb=" N ILE B 312 " --> pdb=" O TYR B 342 " (cutoff:3.500A) removed outlier: 7.456A pdb=" N ASP B 344 " --> pdb=" O ILE B 312 " (cutoff:3.500A) removed outlier: 7.235A pdb=" N VAL B 314 " --> pdb=" O ASP B 344 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 468 through 472 removed outlier: 3.819A pdb=" N VAL B 494 " --> pdb=" O ARG B 509 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'E' and resid 94 through 95 Processing sheet with id=AA9, first strand: chain 'E' and resid 160 through 164 removed outlier: 6.959A pdb=" N ILE E 271 " --> pdb=" O LEU E 302 " (cutoff:3.500A) removed outlier: 8.271A pdb=" N SER E 304 " --> pdb=" O ILE E 271 " (cutoff:3.500A) removed outlier: 6.717A pdb=" N LEU E 273 " --> pdb=" O SER E 304 " (cutoff:3.500A) removed outlier: 8.898A pdb=" N ASN E 306 " --> pdb=" O LEU E 273 " (cutoff:3.500A) removed outlier: 6.813A pdb=" N ARG E 240 " --> pdb=" O ARG E 270 " (cutoff:3.500A) removed outlier: 7.688A pdb=" N PHE E 272 " --> pdb=" O ARG E 240 " (cutoff:3.500A) removed outlier: 6.140A pdb=" N ILE E 242 " --> pdb=" O PHE E 272 " (cutoff:3.500A) removed outlier: 7.664A pdb=" N GLU E 274 " --> pdb=" O ILE E 242 " (cutoff:3.500A) removed outlier: 7.062A pdb=" N VAL E 244 " --> pdb=" O GLU E 274 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N ASP E 188 " --> pdb=" O VAL E 243 " (cutoff:3.500A) removed outlier: 8.014A pdb=" N GLU E 245 " --> pdb=" O ASP E 188 " (cutoff:3.500A) removed outlier: 6.185A pdb=" N VAL E 185 " --> pdb=" O LYS E 207 " (cutoff:3.500A) removed outlier: 7.397A pdb=" N PHE E 209 " --> pdb=" O VAL E 185 " (cutoff:3.500A) removed outlier: 6.900A pdb=" N VAL E 187 " --> pdb=" O PHE E 209 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'E' and resid 383 through 384 removed outlier: 4.184A pdb=" N THR E 427 " --> pdb=" O ARG E 445 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'F' and resid 145 through 146 removed outlier: 6.783A pdb=" N ILE F 171 " --> pdb=" O GLY F 492 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'F' and resid 149 through 152 removed outlier: 5.343A pdb=" N GLU F 150 " --> pdb=" O THR F 163 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N THR F 163 " --> pdb=" O GLU F 150 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'F' and resid 231 through 235 removed outlier: 6.570A pdb=" N ILE F 310 " --> pdb=" O TYR F 340 " (cutoff:3.500A) removed outlier: 7.600A pdb=" N TYR F 342 " --> pdb=" O ILE F 310 " (cutoff:3.500A) removed outlier: 6.151A pdb=" N ILE F 312 " --> pdb=" O TYR F 342 " (cutoff:3.500A) removed outlier: 7.456A pdb=" N ASP F 344 " --> pdb=" O ILE F 312 " (cutoff:3.500A) removed outlier: 7.236A pdb=" N VAL F 314 " --> pdb=" O ASP F 344 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'F' and resid 468 through 472 removed outlier: 3.820A pdb=" N VAL F 494 " --> pdb=" O ARG F 509 " (cutoff:3.500A) 947 hydrogen bonds defined for protein. 2715 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: 2.43 Time building geometry restraints manager: 1.78 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 5793 1.34 - 1.46: 2665 1.46 - 1.57: 10222 1.57 - 1.69: 4 1.69 - 1.81: 168 Bond restraints: 18852 Sorted by residual: bond pdb=" C29 POV H 903 " pdb="C210 POV H 903 " ideal model delta sigma weight residual 1.333 1.523 -0.190 2.00e-02 2.50e+03 8.98e+01 bond pdb=" C29 POV D 903 " pdb="C210 POV D 903 " ideal model delta sigma weight residual 1.333 1.522 -0.189 2.00e-02 2.50e+03 8.94e+01 bond pdb=" O12 POV B 602 " pdb=" P POV B 602 " ideal model delta sigma weight residual 1.657 1.742 -0.085 2.00e-02 2.50e+03 1.80e+01 bond pdb=" O12 POV F 602 " pdb=" P POV F 602 " ideal model delta sigma weight residual 1.657 1.741 -0.084 2.00e-02 2.50e+03 1.78e+01 bond pdb=" N ASN F 120 " pdb=" CA ASN F 120 " ideal model delta sigma weight residual 1.456 1.489 -0.033 1.26e-02 6.30e+03 6.95e+00 ... (remaining 18847 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.62: 25381 3.62 - 7.23: 89 7.23 - 10.85: 2 10.85 - 14.47: 0 14.47 - 18.09: 4 Bond angle restraints: 25476 Sorted by residual: angle pdb=" C29 POV D 903 " pdb="C210 POV D 903 " pdb="C211 POV D 903 " ideal model delta sigma weight residual 127.67 109.58 18.09 3.00e+00 1.11e-01 3.63e+01 angle pdb=" C29 POV H 903 " pdb="C210 POV H 903 " pdb="C211 POV H 903 " ideal model delta sigma weight residual 127.67 109.60 18.07 3.00e+00 1.11e-01 3.63e+01 angle pdb=" C28 POV H 903 " pdb=" C29 POV H 903 " pdb="C210 POV H 903 " ideal model delta sigma weight residual 127.79 110.40 17.39 3.00e+00 1.11e-01 3.36e+01 angle pdb=" C28 POV D 903 " pdb=" C29 POV D 903 " pdb="C210 POV D 903 " ideal model delta sigma weight residual 127.79 110.42 17.37 3.00e+00 1.11e-01 3.35e+01 angle pdb=" N VAL E 450 " pdb=" CA VAL E 450 " pdb=" C VAL E 450 " ideal model delta sigma weight residual 112.80 108.66 4.14 1.15e+00 7.56e-01 1.29e+01 ... (remaining 25471 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.97: 10604 22.97 - 45.93: 600 45.93 - 68.90: 58 68.90 - 91.87: 22 91.87 - 114.84: 2 Dihedral angle restraints: 11286 sinusoidal: 4506 harmonic: 6780 Sorted by residual: dihedral pdb=" C5A PLP F 603 " pdb=" O4P PLP F 603 " pdb=" P PLP F 603 " pdb=" O1P PLP F 603 " ideal model delta sinusoidal sigma weight residual 76.43 -168.74 -114.84 1 2.00e+01 2.50e-03 3.41e+01 dihedral pdb=" C5A PLP B 601 " pdb=" O4P PLP B 601 " pdb=" P PLP B 601 " pdb=" O1P PLP B 601 " ideal model delta sinusoidal sigma weight residual 76.43 -168.74 -114.83 1 2.00e+01 2.50e-03 3.41e+01 dihedral pdb=" CA ASN B 133 " pdb=" C ASN B 133 " pdb=" N TRP B 134 " pdb=" CA TRP B 134 " ideal model delta harmonic sigma weight residual -180.00 -161.37 -18.63 0 5.00e+00 4.00e-02 1.39e+01 ... (remaining 11283 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.029: 1757 0.029 - 0.058: 651 0.058 - 0.087: 246 0.087 - 0.117: 161 0.117 - 0.146: 31 Chirality restraints: 2846 Sorted by residual: chirality pdb=" CB THR H 52 " pdb=" CA THR H 52 " pdb=" OG1 THR H 52 " pdb=" CG2 THR H 52 " both_signs ideal model delta sigma weight residual False 2.55 2.41 0.15 2.00e-01 2.50e+01 5.31e-01 chirality pdb=" CB THR D 52 " pdb=" CA THR D 52 " pdb=" OG1 THR D 52 " pdb=" CG2 THR D 52 " both_signs ideal model delta sigma weight residual False 2.55 2.41 0.14 2.00e-01 2.50e+01 5.19e-01 chirality pdb=" CA ILE E 242 " pdb=" N ILE E 242 " pdb=" C ILE E 242 " pdb=" CB ILE E 242 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.85e-01 ... (remaining 2843 not shown) Planarity restraints: 3224 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C28 POV H 903 " 0.080 2.00e-02 2.50e+03 8.01e-02 6.42e+01 pdb=" C29 POV H 903 " -0.082 2.00e-02 2.50e+03 pdb="C210 POV H 903 " -0.079 2.00e-02 2.50e+03 pdb="C211 POV H 903 " 0.080 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C28 POV D 903 " -0.080 2.00e-02 2.50e+03 8.01e-02 6.42e+01 pdb=" C29 POV D 903 " 0.082 2.00e-02 2.50e+03 pdb="C210 POV D 903 " 0.079 2.00e-02 2.50e+03 pdb="C211 POV D 903 " -0.080 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C SER B 412 " 0.036 5.00e-02 4.00e+02 5.52e-02 4.88e+00 pdb=" N PRO B 413 " -0.095 5.00e-02 4.00e+02 pdb=" CA PRO B 413 " 0.029 5.00e-02 4.00e+02 pdb=" CD PRO B 413 " 0.030 5.00e-02 4.00e+02 ... (remaining 3221 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.76: 3038 2.76 - 3.30: 17050 3.30 - 3.83: 29412 3.83 - 4.37: 35584 4.37 - 4.90: 63009 Nonbonded interactions: 148093 Sorted by model distance: nonbonded pdb=" O TRP E 64 " pdb=" NZ LYS F 338 " model vdw 2.227 3.120 nonbonded pdb=" O VAL H 10 " pdb=" OG1 THR H 74 " model vdw 2.232 3.040 nonbonded pdb=" O VAL D 10 " pdb=" OG1 THR D 74 " model vdw 2.232 3.040 nonbonded pdb=" OH TYR E 178 " pdb=" O VAL E 324 " model vdw 2.242 3.040 nonbonded pdb=" OH TYR A 178 " pdb=" O VAL A 324 " model vdw 2.243 3.040 ... (remaining 148088 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: 0.03 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'E' } ncs_group { reference = (chain 'B' and (resid 53 through 543 or resid 602)) selection = (chain 'F' and (resid 53 through 543 or resid 602)) } ncs_group { reference = chain 'C' selection = chain 'G' } ncs_group { reference = chain 'D' selection = chain 'H' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.010 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: 0.330 Check model and map are aligned: 0.050 Set scattering table: 0.050 Process input model: 15.260 Find NCS groups from input model: 0.380 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: 0.000 Load rotamer database and sin/cos tables:1.030 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.150 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8239 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 0.190 18854 Z= 0.195 Angle : 0.688 18.087 25476 Z= 0.378 Chirality : 0.042 0.146 2846 Planarity : 0.004 0.080 3224 Dihedral : 13.943 114.836 6946 Min Nonbonded Distance : 2.227 Molprobity Statistics. All-atom Clashscore : 6.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 0.32 % Allowed : 0.47 % Favored : 99.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.72 (0.17), residues: 2324 helix: 1.74 (0.15), residues: 1116 sheet: -0.44 (0.36), residues: 220 loop : -0.76 (0.19), residues: 988 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 95 TYR 0.020 0.001 TYR A 166 PHE 0.011 0.001 PHE F 239 TRP 0.016 0.001 TRP C 32 HIS 0.008 0.001 HIS E 24 Details of bonding type rmsd/Z covalent geometry : bond 0.00365 / 0.19 (18852) covalent geometry : angle 0.68770 / 0.38 (25476) hydrogen bonds : bond 0.14642 / 10.28 ( 947) hydrogen bonds : angle 5.67409 / 4.09 ( 2715) Misc. bond : bond 0.02956 / 1.48 ( 2) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4648 Ramachandran restraints generated. 2324 Oldfield, 0 Emsley, 2324 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4648 Ramachandran restraints generated. 2324 Oldfield, 0 Emsley, 2324 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 228 residues out of total 2006 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 222 time to evaluate : 0.634 Fit side-chains outliers start: 6 outliers final: 0 residues processed: 224 average time/residue: 0.1352 time to fit residues: 45.6065 Evaluate side-chains 179 residues out of total 2006 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 179 time to evaluate : 0.439 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 216 optimal weight: 6.9990 chunk 98 optimal weight: 0.8980 chunk 194 optimal weight: 0.9980 chunk 227 optimal weight: 1.9990 chunk 107 optimal weight: 3.9990 chunk 10 optimal weight: 2.9990 chunk 66 optimal weight: 4.9990 chunk 130 optimal weight: 2.9990 chunk 124 optimal weight: 1.9990 chunk 103 optimal weight: 2.9990 chunk 200 optimal weight: 1.9990 overall best weight: 1.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 469 GLN B 189 GLN D 77 GLN H 77 GLN E 469 GLN ** F 189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4053 r_free = 0.4053 target = 0.160002 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3749 r_free = 0.3749 target = 0.136171 restraints weight = 22821.474| |-----------------------------------------------------------------------------| r_work (start): 0.3788 rms_B_bonded: 1.82 r_work: 0.3638 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.3502 rms_B_bonded: 4.22 restraints_weight: 0.2500 r_work (final): 0.3502 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8467 moved from start: 0.1056 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 18854 Z= 0.200 Angle : 0.602 8.853 25476 Z= 0.318 Chirality : 0.045 0.162 2846 Planarity : 0.005 0.053 3224 Dihedral : 7.645 88.167 2706 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 5.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 1.42 % Allowed : 6.99 % Favored : 91.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.70 (0.17), residues: 2324 helix: 1.62 (0.15), residues: 1154 sheet: -0.45 (0.36), residues: 220 loop : -0.73 (0.19), residues: 950 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG H 20 TYR 0.024 0.002 TYR A 166 PHE 0.018 0.002 PHE A 138 TRP 0.017 0.002 TRP C 32 HIS 0.007 0.001 HIS F 403 Details of bonding type rmsd/Z covalent geometry : bond 0.00491 / 0.20 (18852) covalent geometry : angle 0.60185 / 0.32 (25476) hydrogen bonds : bond 0.05379 / 3.67 ( 947) hydrogen bonds : angle 4.61465 / 3.33 ( 2715) Misc. bond : bond 0.00017 / 0.01 ( 2) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4648 Ramachandran restraints generated. 2324 Oldfield, 0 Emsley, 2324 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4648 Ramachandran restraints generated. 2324 Oldfield, 0 Emsley, 2324 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 225 residues out of total 2006 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 198 time to evaluate : 0.516 Fit side-chains REVERT: B 111 PHE cc_start: 0.8569 (m-80) cc_final: 0.7947 (m-80) REVERT: C 50 TYR cc_start: 0.7193 (t80) cc_final: 0.6798 (t80) REVERT: D 87 GLU cc_start: 0.8956 (mt-10) cc_final: 0.8732 (mt-10) REVERT: H 87 GLU cc_start: 0.8946 (mt-10) cc_final: 0.8737 (mt-10) REVERT: G 50 TYR cc_start: 0.7293 (t80) cc_final: 0.6869 (t80) outliers start: 27 outliers final: 15 residues processed: 212 average time/residue: 0.1301 time to fit residues: 41.4847 Evaluate side-chains 203 residues out of total 2006 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 188 time to evaluate : 0.537 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 LEU Chi-restraints excluded: chain A residue 281 VAL Chi-restraints excluded: chain A residue 434 LYS Chi-restraints excluded: chain B residue 110 ASP Chi-restraints excluded: chain B residue 205 SER Chi-restraints excluded: chain C residue 14 SER Chi-restraints excluded: chain D residue 10 VAL Chi-restraints excluded: chain H residue 10 VAL Chi-restraints excluded: chain G residue 14 SER Chi-restraints excluded: chain E residue 33 LEU Chi-restraints excluded: chain E residue 36 ILE Chi-restraints excluded: chain E residue 39 LEU Chi-restraints excluded: chain E residue 281 VAL Chi-restraints excluded: chain F residue 110 ASP Chi-restraints excluded: chain F residue 205 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 228 optimal weight: 2.9990 chunk 112 optimal weight: 0.9990 chunk 83 optimal weight: 0.6980 chunk 213 optimal weight: 1.9990 chunk 138 optimal weight: 0.9980 chunk 73 optimal weight: 0.7980 chunk 103 optimal weight: 0.9980 chunk 189 optimal weight: 2.9990 chunk 177 optimal weight: 0.6980 chunk 123 optimal weight: 0.7980 chunk 219 optimal weight: 0.6980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4086 r_free = 0.4086 target = 0.163336 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3793 r_free = 0.3793 target = 0.140003 restraints weight = 22953.016| |-----------------------------------------------------------------------------| r_work (start): 0.3837 rms_B_bonded: 1.78 r_work: 0.3688 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.3555 rms_B_bonded: 4.21 restraints_weight: 0.2500 r_work (final): 0.3555 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8423 moved from start: 0.1171 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 18854 Z= 0.117 Angle : 0.494 8.079 25476 Z= 0.260 Chirality : 0.041 0.134 2846 Planarity : 0.004 0.052 3224 Dihedral : 7.016 89.481 2706 Min Nonbonded Distance : 2.583 Molprobity Statistics. All-atom Clashscore : 5.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.81 % Favored : 98.19 % Rotamer: Outliers : 1.37 % Allowed : 8.61 % Favored : 90.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.94 (0.17), residues: 2324 helix: 1.86 (0.15), residues: 1154 sheet: -0.41 (0.37), residues: 224 loop : -0.65 (0.19), residues: 946 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 271 TYR 0.017 0.001 TYR C 27 PHE 0.013 0.001 PHE F 280 TRP 0.015 0.001 TRP C 32 HIS 0.005 0.001 HIS E 24 Details of bonding type rmsd/Z covalent geometry : bond 0.00273 / 0.12 (18852) covalent geometry : angle 0.49438 / 0.26 (25476) hydrogen bonds : bond 0.04175 / 2.88 ( 947) hydrogen bonds : angle 4.30017 / 3.12 ( 2715) Misc. bond : bond 0.00021 / 0.01 ( 2) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4648 Ramachandran restraints generated. 2324 Oldfield, 0 Emsley, 2324 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4648 Ramachandran restraints generated. 2324 Oldfield, 0 Emsley, 2324 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 222 residues out of total 2006 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 196 time to evaluate : 0.760 Fit side-chains REVERT: A 469 GLN cc_start: 0.7643 (OUTLIER) cc_final: 0.6463 (mp-120) REVERT: B 111 PHE cc_start: 0.8515 (m-80) cc_final: 0.7869 (m-80) REVERT: B 155 ASP cc_start: 0.8483 (t0) cc_final: 0.8269 (t0) REVERT: C 50 TYR cc_start: 0.7207 (t80) cc_final: 0.6839 (t80) REVERT: D 87 GLU cc_start: 0.8929 (mt-10) cc_final: 0.8704 (mt-10) REVERT: G 50 TYR cc_start: 0.7344 (t80) cc_final: 0.6995 (t80) REVERT: E 469 GLN cc_start: 0.7657 (OUTLIER) cc_final: 0.6474 (mp-120) outliers start: 26 outliers final: 19 residues processed: 210 average time/residue: 0.1312 time to fit residues: 42.2675 Evaluate side-chains 203 residues out of total 2006 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 182 time to evaluate : 0.761 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 LEU Chi-restraints excluded: chain A residue 158 THR Chi-restraints excluded: chain A residue 281 VAL Chi-restraints excluded: chain A residue 434 LYS Chi-restraints excluded: chain A residue 469 GLN Chi-restraints excluded: chain B residue 110 ASP Chi-restraints excluded: chain B residue 284 ASN Chi-restraints excluded: chain B residue 355 THR Chi-restraints excluded: chain C residue 47 MET Chi-restraints excluded: chain D residue 10 VAL Chi-restraints excluded: chain H residue 1 MET Chi-restraints excluded: chain H residue 10 VAL Chi-restraints excluded: chain E residue 33 LEU Chi-restraints excluded: chain E residue 36 ILE Chi-restraints excluded: chain E residue 39 LEU Chi-restraints excluded: chain E residue 158 THR Chi-restraints excluded: chain E residue 281 VAL Chi-restraints excluded: chain E residue 469 GLN Chi-restraints excluded: chain F residue 110 ASP Chi-restraints excluded: chain F residue 284 ASN Chi-restraints excluded: chain F residue 355 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 43 optimal weight: 0.0050 chunk 190 optimal weight: 3.9990 chunk 153 optimal weight: 0.5980 chunk 215 optimal weight: 0.7980 chunk 99 optimal weight: 1.9990 chunk 76 optimal weight: 1.9990 chunk 103 optimal weight: 1.9990 chunk 229 optimal weight: 0.1980 chunk 173 optimal weight: 2.9990 chunk 134 optimal weight: 0.7980 chunk 87 optimal weight: 0.9980 overall best weight: 0.4794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4106 r_free = 0.4106 target = 0.164985 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3816 r_free = 0.3816 target = 0.141755 restraints weight = 22962.230| |-----------------------------------------------------------------------------| r_work (start): 0.3859 rms_B_bonded: 1.78 r_work: 0.3710 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.3577 rms_B_bonded: 4.24 restraints_weight: 0.2500 r_work (final): 0.3577 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8398 moved from start: 0.1360 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 18854 Z= 0.098 Angle : 0.468 8.483 25476 Z= 0.245 Chirality : 0.041 0.129 2846 Planarity : 0.004 0.050 3224 Dihedral : 6.633 85.424 2706 Min Nonbonded Distance : 2.591 Molprobity Statistics. All-atom Clashscore : 4.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer: Outliers : 1.58 % Allowed : 9.19 % Favored : 89.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.14 (0.18), residues: 2324 helix: 2.05 (0.15), residues: 1154 sheet: -0.26 (0.38), residues: 222 loop : -0.61 (0.19), residues: 948 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 271 TYR 0.018 0.001 TYR C 27 PHE 0.010 0.001 PHE F 280 TRP 0.013 0.001 TRP G 32 HIS 0.004 0.001 HIS A 24 Details of bonding type rmsd/Z covalent geometry : bond 0.00220 / 0.10 (18852) covalent geometry : angle 0.46762 / 0.25 (25476) hydrogen bonds : bond 0.03689 / 2.55 ( 947) hydrogen bonds : angle 4.14022 / 3.01 ( 2715) Misc. bond : bond 0.00015 / 0.01 ( 2) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4648 Ramachandran restraints generated. 2324 Oldfield, 0 Emsley, 2324 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4648 Ramachandran restraints generated. 2324 Oldfield, 0 Emsley, 2324 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 216 residues out of total 2006 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 186 time to evaluate : 0.718 Fit side-chains REVERT: A 126 LYS cc_start: 0.8394 (mmtt) cc_final: 0.8103 (mtmt) REVERT: A 469 GLN cc_start: 0.7608 (OUTLIER) cc_final: 0.6368 (mp-120) REVERT: B 155 ASP cc_start: 0.8446 (t0) cc_final: 0.8146 (t0) REVERT: B 271 ARG cc_start: 0.8433 (mmt90) cc_final: 0.8035 (mtm110) REVERT: C 50 TYR cc_start: 0.7169 (t80) cc_final: 0.6855 (t80) REVERT: D 87 GLU cc_start: 0.8913 (mt-10) cc_final: 0.8708 (mt-10) REVERT: G 50 TYR cc_start: 0.7301 (t80) cc_final: 0.6993 (t80) REVERT: E 356 MET cc_start: 0.8697 (mtp) cc_final: 0.8396 (ttm) REVERT: E 469 GLN cc_start: 0.7625 (OUTLIER) cc_final: 0.6382 (mp-120) REVERT: F 271 ARG cc_start: 0.8425 (mmt90) cc_final: 0.8024 (mtm110) outliers start: 30 outliers final: 22 residues processed: 205 average time/residue: 0.1420 time to fit residues: 44.6657 Evaluate side-chains 202 residues out of total 2006 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 178 time to evaluate : 0.616 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 LEU Chi-restraints excluded: chain A residue 39 LEU Chi-restraints excluded: chain A residue 158 THR Chi-restraints excluded: chain A residue 281 VAL Chi-restraints excluded: chain A residue 434 LYS Chi-restraints excluded: chain A residue 469 GLN Chi-restraints excluded: chain B residue 205 SER Chi-restraints excluded: chain B residue 284 ASN Chi-restraints excluded: chain B residue 355 THR Chi-restraints excluded: chain C residue 47 MET Chi-restraints excluded: chain D residue 1 MET Chi-restraints excluded: chain D residue 10 VAL Chi-restraints excluded: chain H residue 1 MET Chi-restraints excluded: chain H residue 10 VAL Chi-restraints excluded: chain E residue 33 LEU Chi-restraints excluded: chain E residue 36 ILE Chi-restraints excluded: chain E residue 39 LEU Chi-restraints excluded: chain E residue 158 THR Chi-restraints excluded: chain E residue 281 VAL Chi-restraints excluded: chain E residue 434 LYS Chi-restraints excluded: chain E residue 469 GLN Chi-restraints excluded: chain F residue 205 SER Chi-restraints excluded: chain F residue 284 ASN Chi-restraints excluded: chain F residue 355 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 119 optimal weight: 2.9990 chunk 79 optimal weight: 6.9990 chunk 123 optimal weight: 2.9990 chunk 89 optimal weight: 0.2980 chunk 12 optimal weight: 0.0570 chunk 160 optimal weight: 3.9990 chunk 1 optimal weight: 0.8980 chunk 13 optimal weight: 0.4980 chunk 10 optimal weight: 1.9990 chunk 195 optimal weight: 2.9990 chunk 96 optimal weight: 0.8980 overall best weight: 0.5298 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4105 r_free = 0.4105 target = 0.165182 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3814 r_free = 0.3814 target = 0.142005 restraints weight = 22776.676| |-----------------------------------------------------------------------------| r_work (start): 0.3863 rms_B_bonded: 1.78 r_work: 0.3716 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.3581 rms_B_bonded: 4.22 restraints_weight: 0.2500 r_work (final): 0.3581 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8393 moved from start: 0.1475 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 18854 Z= 0.099 Angle : 0.458 9.351 25476 Z= 0.240 Chirality : 0.040 0.126 2846 Planarity : 0.004 0.050 3224 Dihedral : 6.330 81.723 2706 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 4.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.98 % Favored : 98.02 % Rotamer: Outliers : 1.47 % Allowed : 10.98 % Favored : 87.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.23 (0.18), residues: 2324 helix: 2.14 (0.15), residues: 1152 sheet: -0.20 (0.38), residues: 222 loop : -0.59 (0.19), residues: 950 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 271 TYR 0.018 0.001 TYR C 27 PHE 0.014 0.001 PHE B 111 TRP 0.013 0.001 TRP G 32 HIS 0.003 0.001 HIS F 403 Details of bonding type rmsd/Z covalent geometry : bond 0.00225 / 0.10 (18852) covalent geometry : angle 0.45750 / 0.24 (25476) hydrogen bonds : bond 0.03593 / 2.48 ( 947) hydrogen bonds : angle 4.09161 / 2.97 ( 2715) Misc. bond : bond 0.00005 / 0.00 ( 2) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4648 Ramachandran restraints generated. 2324 Oldfield, 0 Emsley, 2324 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4648 Ramachandran restraints generated. 2324 Oldfield, 0 Emsley, 2324 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 220 residues out of total 2006 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 192 time to evaluate : 0.769 Fit side-chains REVERT: A 126 LYS cc_start: 0.8390 (mmtt) cc_final: 0.8118 (mtmt) REVERT: A 469 GLN cc_start: 0.7743 (OUTLIER) cc_final: 0.6486 (mp-120) REVERT: B 155 ASP cc_start: 0.8487 (t0) cc_final: 0.8147 (t0) REVERT: B 271 ARG cc_start: 0.8442 (mmt90) cc_final: 0.8060 (mtm110) REVERT: C 50 TYR cc_start: 0.7138 (t80) cc_final: 0.6821 (t80) REVERT: D 87 GLU cc_start: 0.8893 (mt-10) cc_final: 0.8690 (mt-10) REVERT: G 50 TYR cc_start: 0.7268 (t80) cc_final: 0.7035 (t80) REVERT: E 126 LYS cc_start: 0.8417 (mmtt) cc_final: 0.8111 (mtmt) REVERT: E 356 MET cc_start: 0.8796 (mtp) cc_final: 0.8580 (ttm) REVERT: E 469 GLN cc_start: 0.7713 (OUTLIER) cc_final: 0.6432 (mp-120) REVERT: F 271 ARG cc_start: 0.8461 (mmt90) cc_final: 0.8067 (mtm110) outliers start: 28 outliers final: 25 residues processed: 209 average time/residue: 0.1341 time to fit residues: 42.9432 Evaluate side-chains 212 residues out of total 2006 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 185 time to evaluate : 0.636 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 LEU Chi-restraints excluded: chain A residue 39 LEU Chi-restraints excluded: chain A residue 158 THR Chi-restraints excluded: chain A residue 281 VAL Chi-restraints excluded: chain A residue 434 LYS Chi-restraints excluded: chain A residue 469 GLN Chi-restraints excluded: chain B residue 110 ASP Chi-restraints excluded: chain B residue 205 SER Chi-restraints excluded: chain B residue 284 ASN Chi-restraints excluded: chain B residue 355 THR Chi-restraints excluded: chain C residue 47 MET Chi-restraints excluded: chain D residue 1 MET Chi-restraints excluded: chain D residue 10 VAL Chi-restraints excluded: chain H residue 1 MET Chi-restraints excluded: chain H residue 10 VAL Chi-restraints excluded: chain G residue 28 MET Chi-restraints excluded: chain E residue 33 LEU Chi-restraints excluded: chain E residue 36 ILE Chi-restraints excluded: chain E residue 39 LEU Chi-restraints excluded: chain E residue 158 THR Chi-restraints excluded: chain E residue 281 VAL Chi-restraints excluded: chain E residue 434 LYS Chi-restraints excluded: chain E residue 469 GLN Chi-restraints excluded: chain F residue 110 ASP Chi-restraints excluded: chain F residue 205 SER Chi-restraints excluded: chain F residue 284 ASN Chi-restraints excluded: chain F residue 355 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 60 optimal weight: 2.9990 chunk 25 optimal weight: 0.5980 chunk 223 optimal weight: 0.8980 chunk 185 optimal weight: 0.5980 chunk 5 optimal weight: 3.9990 chunk 2 optimal weight: 1.9990 chunk 84 optimal weight: 1.9990 chunk 98 optimal weight: 0.8980 chunk 118 optimal weight: 2.9990 chunk 178 optimal weight: 3.9990 chunk 67 optimal weight: 2.9990 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4079 r_free = 0.4079 target = 0.162514 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3781 r_free = 0.3781 target = 0.138971 restraints weight = 22835.516| |-----------------------------------------------------------------------------| r_work (start): 0.3823 rms_B_bonded: 1.80 r_work: 0.3674 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.3543 rms_B_bonded: 4.21 restraints_weight: 0.2500 r_work (final): 0.3543 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8433 moved from start: 0.1513 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 18854 Z= 0.137 Angle : 0.498 7.871 25476 Z= 0.261 Chirality : 0.042 0.139 2846 Planarity : 0.004 0.052 3224 Dihedral : 6.438 83.511 2706 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 4.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Rotamer: Outliers : 1.89 % Allowed : 11.34 % Favored : 86.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.10 (0.17), residues: 2324 helix: 2.04 (0.15), residues: 1158 sheet: -0.36 (0.37), residues: 224 loop : -0.65 (0.19), residues: 942 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 484 TYR 0.020 0.001 TYR C 27 PHE 0.012 0.002 PHE A 317 TRP 0.013 0.001 TRP C 32 HIS 0.005 0.001 HIS F 403 Details of bonding type rmsd/Z covalent geometry : bond 0.00332 / 0.14 (18852) covalent geometry : angle 0.49753 / 0.26 (25476) hydrogen bonds : bond 0.04228 / 2.90 ( 947) hydrogen bonds : angle 4.15264 / 3.01 ( 2715) Misc. bond : bond 0.00006 / 0.00 ( 2) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4648 Ramachandran restraints generated. 2324 Oldfield, 0 Emsley, 2324 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4648 Ramachandran restraints generated. 2324 Oldfield, 0 Emsley, 2324 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 224 residues out of total 2006 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 188 time to evaluate : 0.798 Fit side-chains REVERT: A 126 LYS cc_start: 0.8391 (mmtt) cc_final: 0.8117 (mtmt) REVERT: A 469 GLN cc_start: 0.7806 (OUTLIER) cc_final: 0.6545 (mp-120) REVERT: B 155 ASP cc_start: 0.8634 (t0) cc_final: 0.8270 (t0) REVERT: B 271 ARG cc_start: 0.8408 (mmt90) cc_final: 0.8001 (mtm110) REVERT: C 50 TYR cc_start: 0.7256 (t80) cc_final: 0.6994 (t80) REVERT: E 126 LYS cc_start: 0.8411 (mmtt) cc_final: 0.8117 (mtmt) REVERT: E 469 GLN cc_start: 0.7815 (OUTLIER) cc_final: 0.6559 (mp-120) REVERT: F 271 ARG cc_start: 0.8426 (mmt90) cc_final: 0.8008 (mtm110) outliers start: 36 outliers final: 26 residues processed: 209 average time/residue: 0.1567 time to fit residues: 49.5526 Evaluate side-chains 212 residues out of total 2006 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 184 time to evaluate : 0.733 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 LEU Chi-restraints excluded: chain A residue 39 LEU Chi-restraints excluded: chain A residue 158 THR Chi-restraints excluded: chain A residue 281 VAL Chi-restraints excluded: chain A residue 386 VAL Chi-restraints excluded: chain A residue 434 LYS Chi-restraints excluded: chain A residue 469 GLN Chi-restraints excluded: chain B residue 110 ASP Chi-restraints excluded: chain B residue 205 SER Chi-restraints excluded: chain B residue 284 ASN Chi-restraints excluded: chain B residue 355 THR Chi-restraints excluded: chain C residue 47 MET Chi-restraints excluded: chain D residue 1 MET Chi-restraints excluded: chain D residue 10 VAL Chi-restraints excluded: chain H residue 1 MET Chi-restraints excluded: chain H residue 10 VAL Chi-restraints excluded: chain G residue 28 MET Chi-restraints excluded: chain E residue 33 LEU Chi-restraints excluded: chain E residue 39 LEU Chi-restraints excluded: chain E residue 158 THR Chi-restraints excluded: chain E residue 281 VAL Chi-restraints excluded: chain E residue 386 VAL Chi-restraints excluded: chain E residue 434 LYS Chi-restraints excluded: chain E residue 469 GLN Chi-restraints excluded: chain F residue 110 ASP Chi-restraints excluded: chain F residue 205 SER Chi-restraints excluded: chain F residue 284 ASN Chi-restraints excluded: chain F residue 355 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 97 optimal weight: 2.9990 chunk 32 optimal weight: 1.9990 chunk 108 optimal weight: 0.0030 chunk 150 optimal weight: 1.9990 chunk 28 optimal weight: 2.9990 chunk 123 optimal weight: 0.1980 chunk 82 optimal weight: 0.5980 chunk 23 optimal weight: 1.9990 chunk 62 optimal weight: 0.9980 chunk 190 optimal weight: 1.9990 chunk 22 optimal weight: 1.9990 overall best weight: 0.7592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 114 ASN E 114 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4098 r_free = 0.4098 target = 0.163813 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3804 r_free = 0.3804 target = 0.140406 restraints weight = 22932.890| |-----------------------------------------------------------------------------| r_work (start): 0.3845 rms_B_bonded: 1.79 r_work: 0.3694 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.3561 rms_B_bonded: 4.23 restraints_weight: 0.2500 r_work (final): 0.3561 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8420 moved from start: 0.1565 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 18854 Z= 0.115 Angle : 0.475 9.664 25476 Z= 0.249 Chirality : 0.041 0.133 2846 Planarity : 0.004 0.051 3224 Dihedral : 6.338 80.694 2706 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 4.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.37 % Favored : 97.63 % Rotamer: Outliers : 1.84 % Allowed : 11.87 % Favored : 86.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.17 (0.17), residues: 2324 helix: 2.11 (0.15), residues: 1152 sheet: -0.25 (0.38), residues: 222 loop : -0.65 (0.19), residues: 950 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG F 484 TYR 0.020 0.001 TYR C 27 PHE 0.011 0.001 PHE B 280 TRP 0.014 0.001 TRP C 32 HIS 0.004 0.001 HIS F 403 Details of bonding type rmsd/Z covalent geometry : bond 0.00274 / 0.12 (18852) covalent geometry : angle 0.47517 / 0.25 (25476) hydrogen bonds : bond 0.03895 / 2.68 ( 947) hydrogen bonds : angle 4.12015 / 2.99 ( 2715) Misc. bond : bond 0.00002 / 0.00 ( 2) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4648 Ramachandran restraints generated. 2324 Oldfield, 0 Emsley, 2324 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4648 Ramachandran restraints generated. 2324 Oldfield, 0 Emsley, 2324 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 221 residues out of total 2006 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 186 time to evaluate : 0.737 Fit side-chains REVERT: A 126 LYS cc_start: 0.8374 (mmtt) cc_final: 0.8119 (mtmt) REVERT: A 469 GLN cc_start: 0.7821 (OUTLIER) cc_final: 0.6572 (mp-120) REVERT: B 155 ASP cc_start: 0.8666 (t0) cc_final: 0.8285 (t0) REVERT: B 271 ARG cc_start: 0.8447 (mmt90) cc_final: 0.8043 (mtm110) REVERT: E 126 LYS cc_start: 0.8377 (mmtt) cc_final: 0.8106 (mtmt) REVERT: E 356 MET cc_start: 0.8754 (mtp) cc_final: 0.8371 (ttm) REVERT: E 469 GLN cc_start: 0.7833 (OUTLIER) cc_final: 0.6587 (mp-120) REVERT: F 271 ARG cc_start: 0.8462 (mmt90) cc_final: 0.8041 (mtm110) outliers start: 35 outliers final: 30 residues processed: 209 average time/residue: 0.1550 time to fit residues: 49.0272 Evaluate side-chains 214 residues out of total 2006 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 182 time to evaluate : 0.752 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 LEU Chi-restraints excluded: chain A residue 39 LEU Chi-restraints excluded: chain A residue 114 ASN Chi-restraints excluded: chain A residue 158 THR Chi-restraints excluded: chain A residue 162 ILE Chi-restraints excluded: chain A residue 281 VAL Chi-restraints excluded: chain A residue 362 ILE Chi-restraints excluded: chain A residue 434 LYS Chi-restraints excluded: chain A residue 469 GLN Chi-restraints excluded: chain B residue 110 ASP Chi-restraints excluded: chain B residue 205 SER Chi-restraints excluded: chain B residue 284 ASN Chi-restraints excluded: chain B residue 355 THR Chi-restraints excluded: chain C residue 47 MET Chi-restraints excluded: chain D residue 1 MET Chi-restraints excluded: chain D residue 10 VAL Chi-restraints excluded: chain H residue 1 MET Chi-restraints excluded: chain H residue 10 VAL Chi-restraints excluded: chain H residue 96 THR Chi-restraints excluded: chain G residue 28 MET Chi-restraints excluded: chain E residue 33 LEU Chi-restraints excluded: chain E residue 39 LEU Chi-restraints excluded: chain E residue 114 ASN Chi-restraints excluded: chain E residue 158 THR Chi-restraints excluded: chain E residue 162 ILE Chi-restraints excluded: chain E residue 281 VAL Chi-restraints excluded: chain E residue 434 LYS Chi-restraints excluded: chain E residue 469 GLN Chi-restraints excluded: chain F residue 110 ASP Chi-restraints excluded: chain F residue 205 SER Chi-restraints excluded: chain F residue 284 ASN Chi-restraints excluded: chain F residue 355 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 170 optimal weight: 0.6980 chunk 177 optimal weight: 0.9990 chunk 112 optimal weight: 1.9990 chunk 129 optimal weight: 1.9990 chunk 127 optimal weight: 3.9990 chunk 78 optimal weight: 0.9990 chunk 32 optimal weight: 0.8980 chunk 61 optimal weight: 0.9990 chunk 212 optimal weight: 3.9990 chunk 66 optimal weight: 4.9990 chunk 126 optimal weight: 2.9990 overall best weight: 0.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 114 ASN D 85 HIS E 114 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4086 r_free = 0.4086 target = 0.162973 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3791 r_free = 0.3791 target = 0.139549 restraints weight = 22743.823| |-----------------------------------------------------------------------------| r_work (start): 0.3833 rms_B_bonded: 1.79 r_work: 0.3684 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.3551 rms_B_bonded: 4.21 restraints_weight: 0.2500 r_work (final): 0.3551 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8428 moved from start: 0.1592 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 18854 Z= 0.128 Angle : 0.487 9.504 25476 Z= 0.255 Chirality : 0.041 0.136 2846 Planarity : 0.004 0.052 3224 Dihedral : 6.338 79.673 2706 Min Nonbonded Distance : 2.557 Molprobity Statistics. All-atom Clashscore : 4.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % Rotamer: Outliers : 2.05 % Allowed : 11.92 % Favored : 86.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.10 (0.17), residues: 2324 helix: 2.06 (0.15), residues: 1156 sheet: -0.34 (0.37), residues: 224 loop : -0.68 (0.19), residues: 944 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG F 484 TYR 0.021 0.001 TYR C 27 PHE 0.011 0.001 PHE B 280 TRP 0.013 0.001 TRP G 32 HIS 0.005 0.001 HIS B 403 Details of bonding type rmsd/Z covalent geometry : bond 0.00310 / 0.13 (18852) covalent geometry : angle 0.48745 / 0.26 (25476) hydrogen bonds : bond 0.04036 / 2.77 ( 947) hydrogen bonds : angle 4.13202 / 3.00 ( 2715) Misc. bond : bond 0.00003 / 0.00 ( 2) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4648 Ramachandran restraints generated. 2324 Oldfield, 0 Emsley, 2324 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4648 Ramachandran restraints generated. 2324 Oldfield, 0 Emsley, 2324 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 224 residues out of total 2006 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 185 time to evaluate : 0.813 Fit side-chains REVERT: A 126 LYS cc_start: 0.8369 (mmtt) cc_final: 0.8121 (mtmt) REVERT: A 469 GLN cc_start: 0.7809 (OUTLIER) cc_final: 0.6522 (mp-120) REVERT: B 155 ASP cc_start: 0.8684 (t0) cc_final: 0.8293 (t0) REVERT: B 271 ARG cc_start: 0.8454 (mmt90) cc_final: 0.8031 (mtm110) REVERT: E 126 LYS cc_start: 0.8395 (mmtt) cc_final: 0.8117 (mtmt) REVERT: E 356 MET cc_start: 0.8799 (mtp) cc_final: 0.8442 (ttm) REVERT: E 469 GLN cc_start: 0.7820 (OUTLIER) cc_final: 0.6538 (mp-120) REVERT: F 271 ARG cc_start: 0.8436 (mmt90) cc_final: 0.8025 (mtm110) outliers start: 39 outliers final: 35 residues processed: 212 average time/residue: 0.1524 time to fit residues: 49.2066 Evaluate side-chains 220 residues out of total 2006 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 183 time to evaluate : 0.734 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 LEU Chi-restraints excluded: chain A residue 39 LEU Chi-restraints excluded: chain A residue 114 ASN Chi-restraints excluded: chain A residue 158 THR Chi-restraints excluded: chain A residue 162 ILE Chi-restraints excluded: chain A residue 281 VAL Chi-restraints excluded: chain A residue 362 ILE Chi-restraints excluded: chain A residue 386 VAL Chi-restraints excluded: chain A residue 469 GLN Chi-restraints excluded: chain B residue 110 ASP Chi-restraints excluded: chain B residue 205 SER Chi-restraints excluded: chain B residue 284 ASN Chi-restraints excluded: chain B residue 355 THR Chi-restraints excluded: chain B residue 388 ILE Chi-restraints excluded: chain C residue 47 MET Chi-restraints excluded: chain D residue 1 MET Chi-restraints excluded: chain D residue 10 VAL Chi-restraints excluded: chain D residue 96 THR Chi-restraints excluded: chain H residue 1 MET Chi-restraints excluded: chain H residue 10 VAL Chi-restraints excluded: chain H residue 96 THR Chi-restraints excluded: chain G residue 28 MET Chi-restraints excluded: chain E residue 33 LEU Chi-restraints excluded: chain E residue 39 LEU Chi-restraints excluded: chain E residue 114 ASN Chi-restraints excluded: chain E residue 158 THR Chi-restraints excluded: chain E residue 162 ILE Chi-restraints excluded: chain E residue 281 VAL Chi-restraints excluded: chain E residue 362 ILE Chi-restraints excluded: chain E residue 386 VAL Chi-restraints excluded: chain E residue 434 LYS Chi-restraints excluded: chain E residue 469 GLN Chi-restraints excluded: chain F residue 110 ASP Chi-restraints excluded: chain F residue 205 SER Chi-restraints excluded: chain F residue 284 ASN Chi-restraints excluded: chain F residue 355 THR Chi-restraints excluded: chain F residue 388 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 93 optimal weight: 1.9990 chunk 47 optimal weight: 0.9980 chunk 17 optimal weight: 0.4980 chunk 22 optimal weight: 3.9990 chunk 36 optimal weight: 0.9980 chunk 230 optimal weight: 0.8980 chunk 25 optimal weight: 0.7980 chunk 163 optimal weight: 3.9990 chunk 101 optimal weight: 5.9990 chunk 49 optimal weight: 1.9990 chunk 161 optimal weight: 0.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... H 85 HIS E 114 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4088 r_free = 0.4088 target = 0.163136 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3794 r_free = 0.3794 target = 0.139726 restraints weight = 22826.973| |-----------------------------------------------------------------------------| r_work (start): 0.3835 rms_B_bonded: 1.79 r_work: 0.3686 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.3553 rms_B_bonded: 4.21 restraints_weight: 0.2500 r_work (final): 0.3553 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8426 moved from start: 0.1614 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 18854 Z= 0.122 Angle : 0.487 11.471 25476 Z= 0.254 Chirality : 0.041 0.134 2846 Planarity : 0.004 0.052 3224 Dihedral : 6.309 77.662 2706 Min Nonbonded Distance : 2.564 Molprobity Statistics. All-atom Clashscore : 4.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Rotamer: Outliers : 1.89 % Allowed : 12.18 % Favored : 85.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.11 (0.17), residues: 2324 helix: 2.07 (0.15), residues: 1156 sheet: -0.34 (0.38), residues: 224 loop : -0.67 (0.19), residues: 944 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 116 TYR 0.021 0.001 TYR C 27 PHE 0.011 0.001 PHE B 280 TRP 0.014 0.001 TRP C 32 HIS 0.004 0.001 HIS F 403 Details of bonding type rmsd/Z covalent geometry : bond 0.00293 / 0.12 (18852) covalent geometry : angle 0.48694 / 0.25 (25476) hydrogen bonds : bond 0.03977 / 2.73 ( 947) hydrogen bonds : angle 4.11697 / 2.98 ( 2715) Misc. bond : bond 0.00002 / 0.00 ( 2) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4648 Ramachandran restraints generated. 2324 Oldfield, 0 Emsley, 2324 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4648 Ramachandran restraints generated. 2324 Oldfield, 0 Emsley, 2324 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 224 residues out of total 2006 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 188 time to evaluate : 0.769 Fit side-chains REVERT: A 126 LYS cc_start: 0.8382 (mmtt) cc_final: 0.8119 (mtmt) REVERT: A 469 GLN cc_start: 0.7798 (OUTLIER) cc_final: 0.6514 (mp-120) REVERT: B 155 ASP cc_start: 0.8661 (t0) cc_final: 0.8274 (t0) REVERT: B 271 ARG cc_start: 0.8441 (mmt90) cc_final: 0.8012 (mtm110) REVERT: E 126 LYS cc_start: 0.8385 (mmtt) cc_final: 0.8111 (mtmt) REVERT: E 356 MET cc_start: 0.8821 (mtp) cc_final: 0.8461 (ttm) REVERT: E 469 GLN cc_start: 0.7808 (OUTLIER) cc_final: 0.6530 (mp-120) REVERT: F 155 ASP cc_start: 0.8609 (t0) cc_final: 0.8249 (t0) REVERT: F 271 ARG cc_start: 0.8443 (mmt90) cc_final: 0.8033 (mtm110) outliers start: 36 outliers final: 34 residues processed: 212 average time/residue: 0.1502 time to fit residues: 48.5749 Evaluate side-chains 221 residues out of total 2006 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 185 time to evaluate : 0.729 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 LEU Chi-restraints excluded: chain A residue 39 LEU Chi-restraints excluded: chain A residue 158 THR Chi-restraints excluded: chain A residue 162 ILE Chi-restraints excluded: chain A residue 281 VAL Chi-restraints excluded: chain A residue 362 ILE Chi-restraints excluded: chain A residue 386 VAL Chi-restraints excluded: chain A residue 469 GLN Chi-restraints excluded: chain B residue 110 ASP Chi-restraints excluded: chain B residue 205 SER Chi-restraints excluded: chain B residue 284 ASN Chi-restraints excluded: chain B residue 355 THR Chi-restraints excluded: chain B residue 388 ILE Chi-restraints excluded: chain C residue 47 MET Chi-restraints excluded: chain D residue 1 MET Chi-restraints excluded: chain D residue 10 VAL Chi-restraints excluded: chain D residue 96 THR Chi-restraints excluded: chain H residue 1 MET Chi-restraints excluded: chain H residue 10 VAL Chi-restraints excluded: chain H residue 96 THR Chi-restraints excluded: chain G residue 28 MET Chi-restraints excluded: chain E residue 33 LEU Chi-restraints excluded: chain E residue 39 LEU Chi-restraints excluded: chain E residue 114 ASN Chi-restraints excluded: chain E residue 158 THR Chi-restraints excluded: chain E residue 162 ILE Chi-restraints excluded: chain E residue 281 VAL Chi-restraints excluded: chain E residue 362 ILE Chi-restraints excluded: chain E residue 386 VAL Chi-restraints excluded: chain E residue 434 LYS Chi-restraints excluded: chain E residue 469 GLN Chi-restraints excluded: chain F residue 110 ASP Chi-restraints excluded: chain F residue 205 SER Chi-restraints excluded: chain F residue 284 ASN Chi-restraints excluded: chain F residue 355 THR Chi-restraints excluded: chain F residue 388 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 157 optimal weight: 0.6980 chunk 113 optimal weight: 3.9990 chunk 155 optimal weight: 0.7980 chunk 222 optimal weight: 0.6980 chunk 212 optimal weight: 3.9990 chunk 24 optimal weight: 0.9990 chunk 95 optimal weight: 1.9990 chunk 22 optimal weight: 0.1980 chunk 141 optimal weight: 5.9990 chunk 61 optimal weight: 2.9990 chunk 228 optimal weight: 2.9990 overall best weight: 0.6782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 114 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4096 r_free = 0.4096 target = 0.163839 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3804 r_free = 0.3804 target = 0.140550 restraints weight = 22755.852| |-----------------------------------------------------------------------------| r_work (start): 0.3840 rms_B_bonded: 1.77 r_work: 0.3693 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.3566 rms_B_bonded: 4.15 restraints_weight: 0.2500 r_work (final): 0.3566 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8417 moved from start: 0.1640 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 18854 Z= 0.110 Angle : 0.475 8.648 25476 Z= 0.248 Chirality : 0.041 0.130 2846 Planarity : 0.004 0.051 3224 Dihedral : 6.216 73.480 2706 Min Nonbonded Distance : 2.568 Molprobity Statistics. All-atom Clashscore : 4.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer: Outliers : 1.89 % Allowed : 12.29 % Favored : 85.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.18 (0.17), residues: 2324 helix: 2.14 (0.15), residues: 1152 sheet: -0.28 (0.38), residues: 222 loop : -0.64 (0.19), residues: 950 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 15 TYR 0.022 0.001 TYR C 27 PHE 0.011 0.001 PHE B 280 TRP 0.014 0.001 TRP C 32 HIS 0.004 0.001 HIS F 403 Details of bonding type rmsd/Z covalent geometry : bond 0.00258 / 0.11 (18852) covalent geometry : angle 0.47475 / 0.25 (25476) hydrogen bonds : bond 0.03806 / 2.62 ( 947) hydrogen bonds : angle 4.07618 / 2.95 ( 2715) Misc. bond : bond 0.00000 / 0.00 ( 2) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4648 Ramachandran restraints generated. 2324 Oldfield, 0 Emsley, 2324 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4648 Ramachandran restraints generated. 2324 Oldfield, 0 Emsley, 2324 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 229 residues out of total 2006 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 193 time to evaluate : 0.749 Fit side-chains REVERT: A 126 LYS cc_start: 0.8370 (mmtt) cc_final: 0.8115 (mtmt) REVERT: A 469 GLN cc_start: 0.7819 (OUTLIER) cc_final: 0.6540 (mp-120) REVERT: B 155 ASP cc_start: 0.8675 (t0) cc_final: 0.8347 (t0) REVERT: B 271 ARG cc_start: 0.8453 (mmt90) cc_final: 0.8006 (mtm110) REVERT: E 126 LYS cc_start: 0.8378 (mmtt) cc_final: 0.8114 (mtmt) REVERT: E 356 MET cc_start: 0.8826 (mtp) cc_final: 0.8481 (ttm) REVERT: E 469 GLN cc_start: 0.7822 (OUTLIER) cc_final: 0.6549 (mp-120) REVERT: F 155 ASP cc_start: 0.8623 (t0) cc_final: 0.8272 (t0) REVERT: F 271 ARG cc_start: 0.8448 (mmt90) cc_final: 0.8035 (mtm110) outliers start: 36 outliers final: 32 residues processed: 217 average time/residue: 0.1497 time to fit residues: 49.5225 Evaluate side-chains 221 residues out of total 2006 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 187 time to evaluate : 1.024 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 LEU Chi-restraints excluded: chain A residue 39 LEU Chi-restraints excluded: chain A residue 114 ASN Chi-restraints excluded: chain A residue 158 THR Chi-restraints excluded: chain A residue 162 ILE Chi-restraints excluded: chain A residue 281 VAL Chi-restraints excluded: chain A residue 362 ILE Chi-restraints excluded: chain A residue 386 VAL Chi-restraints excluded: chain A residue 469 GLN Chi-restraints excluded: chain B residue 110 ASP Chi-restraints excluded: chain B residue 205 SER Chi-restraints excluded: chain B residue 284 ASN Chi-restraints excluded: chain B residue 355 THR Chi-restraints excluded: chain C residue 47 MET Chi-restraints excluded: chain D residue 1 MET Chi-restraints excluded: chain D residue 10 VAL Chi-restraints excluded: chain D residue 96 THR Chi-restraints excluded: chain H residue 1 MET Chi-restraints excluded: chain H residue 10 VAL Chi-restraints excluded: chain H residue 96 THR Chi-restraints excluded: chain G residue 28 MET Chi-restraints excluded: chain E residue 33 LEU Chi-restraints excluded: chain E residue 39 LEU Chi-restraints excluded: chain E residue 158 THR Chi-restraints excluded: chain E residue 162 ILE Chi-restraints excluded: chain E residue 281 VAL Chi-restraints excluded: chain E residue 362 ILE Chi-restraints excluded: chain E residue 386 VAL Chi-restraints excluded: chain E residue 434 LYS Chi-restraints excluded: chain E residue 469 GLN Chi-restraints excluded: chain F residue 110 ASP Chi-restraints excluded: chain F residue 205 SER Chi-restraints excluded: chain F residue 284 ASN Chi-restraints excluded: chain F residue 355 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 231 optimal weight: 0.0030 chunk 143 optimal weight: 0.0040 chunk 118 optimal weight: 0.9990 chunk 207 optimal weight: 0.8980 chunk 76 optimal weight: 0.7980 chunk 203 optimal weight: 0.0370 chunk 57 optimal weight: 2.9990 chunk 135 optimal weight: 5.9990 chunk 166 optimal weight: 2.9990 chunk 0 optimal weight: 30.0000 chunk 81 optimal weight: 4.9990 overall best weight: 0.3480 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 114 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4099 r_free = 0.4099 target = 0.164031 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3806 r_free = 0.3806 target = 0.140659 restraints weight = 22847.198| |-----------------------------------------------------------------------------| r_work (start): 0.3841 rms_B_bonded: 1.78 r_work: 0.3692 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.3574 rms_B_bonded: 4.10 restraints_weight: 0.2500 r_work (final): 0.3574 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8415 moved from start: 0.1647 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.065 18854 Z= 0.122 Angle : 0.680 59.187 25476 Z= 0.389 Chirality : 0.041 0.410 2846 Planarity : 0.004 0.051 3224 Dihedral : 6.225 73.391 2706 Min Nonbonded Distance : 2.274 Molprobity Statistics. All-atom Clashscore : 4.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer: Outliers : 1.84 % Allowed : 12.45 % Favored : 85.71 % Cbeta Deviations : 0.05 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.20 (0.18), residues: 2324 helix: 2.15 (0.15), residues: 1152 sheet: -0.29 (0.38), residues: 222 loop : -0.63 (0.19), residues: 950 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 15 TYR 0.021 0.001 TYR C 27 PHE 0.011 0.001 PHE B 280 TRP 0.014 0.001 TRP C 32 HIS 0.004 0.001 HIS F 403 Details of bonding type rmsd/Z covalent geometry : bond 0.00250 / 0.12 (18852) covalent geometry : angle 0.67964 / 0.39 (25476) hydrogen bonds : bond 0.03792 / 2.60 ( 947) hydrogen bonds : angle 4.07663 / 2.95 ( 2715) Misc. bond : bond 0.00001 / 0.00 ( 2) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4577.00 seconds wall clock time: 79 minutes 17.50 seconds (4757.50 seconds total)