Starting phenix.real_space_refine on Sat Jul 4 05:47:56 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7k0m_22602/07_2026/7k0m_22602.cif Found real_map, /net/cci-nas-00/data/ceres_data/7k0m_22602/07_2026/7k0m_22602.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7k0m_22602/07_2026/7k0m_22602.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7k0m_22602/07_2026/7k0m_22602.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7k0m_22602/07_2026/7k0m_22602.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7k0m_22602/07_2026/7k0m_22602.map" restraint_files = "/net/cci-nas-00/data/ceres_data/7k0m_22602/07_2026/7k0m_22602.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7k0m_22602/07_2026/7k0m_22602.cif" } resolution = 2.9 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.121 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 12006 2.51 5 N 3116 2.21 5 O 3352 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 76 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: 18578 Number of models: 1 Model: "" Number of chains: 14 Chain: "A" Number of atoms: 3582 Number of conformers: 1 Conformer: "" Number of residues, atoms: 464, 3582 Classifications: {'peptide': 464} Incomplete info: {'truncation_to_alanine': 16} Link IDs: {'PTRANS': 22, 'TRANS': 441} Unresolved non-hydrogen bonds: 57 Unresolved non-hydrogen angles: 71 Unresolved non-hydrogen dihedrals: 46 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLU:plan': 3, 'GLN:plan1': 1, 'TYR:plan': 1, 'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 31 Chain: "B" Number of atoms: 3883 Number of conformers: 1 Conformer: "" Number of residues, atoms: 492, 3883 Classifications: {'peptide': 492} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 17, 'TRANS': 474} Unresolved non-hydrogen bonds: 21 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 9 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: "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: "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: "E" Number of atoms: 3582 Number of conformers: 1 Conformer: "" Number of residues, atoms: 464, 3582 Classifications: {'peptide': 464} Incomplete info: {'truncation_to_alanine': 16} Link IDs: {'PTRANS': 22, 'TRANS': 441} Unresolved non-hydrogen bonds: 57 Unresolved non-hydrogen angles: 71 Unresolved non-hydrogen dihedrals: 46 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLU:plan': 3, 'GLN:plan1': 1, 'TYR:plan': 1, 'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 31 Chain: "F" Number of atoms: 3883 Number of conformers: 1 Conformer: "" Number of residues, atoms: 492, 3883 Classifications: {'peptide': 492} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 17, 'TRANS': 474} Unresolved non-hydrogen bonds: 21 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "B" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 56 Unusual residues: {'PLP': 1, 'POV': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 64 Unresolved non-hydrogen angles: 76 Unresolved non-hydrogen dihedrals: 51 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: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'POV': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 76 Unresolved non-hydrogen angles: 94 Unresolved non-hydrogen dihedrals: 54 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'POV:plan-2': 2, 'POV:plan-3': 2, 'POV:plan-1': 1} Unresolved non-hydrogen planarities: 19 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: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'POV': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 76 Unresolved non-hydrogen angles: 94 Unresolved non-hydrogen dihedrals: 54 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'POV:plan-2': 2, 'POV:plan-3': 2, 'POV:plan-1': 1} Unresolved non-hydrogen planarities: 19 Chain: "F" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 56 Unusual residues: {'PLP': 1, 'POV': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 64 Unresolved non-hydrogen angles: 76 Unresolved non-hydrogen dihedrals: 51 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: 4.02, per 1000 atoms: 0.22 Number of scatterers: 18578 At special positions: 0 Unit cell: (151.755, 101.505, 118.59, 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 3352 8.00 N 3116 7.00 C 12006 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: 1.29 Conformation dependent library (CDL) restraints added in 574.8 milliseconds 4652 Ramachandran restraints generated. 2326 Oldfield, 0 Emsley, 2326 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4344 Finding SS restraints... Secondary structure from input PDB file: 100 helices and 14 sheets defined 55.0% alpha, 8.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.51 Creating SS restraints... Processing helix chain 'A' and resid 10 through 19 Processing helix chain 'A' and resid 21 through 40 Processing helix chain 'A' and resid 53 through 64 Processing helix chain 'A' and resid 77 through 81 removed outlier: 3.573A pdb=" N ASN A 81 " --> pdb=" O PRO A 78 " (cutoff:3.500A) Processing helix chain 'A' and resid 114 through 128 Processing helix chain 'A' and resid 142 through 156 removed outlier: 3.680A pdb=" N LEU A 146 " --> pdb=" O PHE A 142 " (cutoff:3.500A) Processing helix chain 'A' and resid 166 through 179 removed outlier: 4.155A pdb=" N ILE A 171 " --> pdb=" O GLY A 167 " (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: 3.587A pdb=" N LYS A 230 " --> pdb=" O ILE A 226 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N ASN A 231 " --> pdb=" O GLU A 227 " (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 removed outlier: 3.672A pdb=" N HIS A 292 " --> pdb=" O GLY A 288 " (cutoff:3.500A) Processing helix chain 'A' and resid 296 through 300 Processing helix chain 'A' and resid 321 through 332 removed outlier: 4.769A pdb=" N HIS A 327 " --> pdb=" O PHE A 323 " (cutoff:3.500A) removed outlier: 4.232A pdb=" N GLN A 328 " --> pdb=" O VAL A 324 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N ARG A 329 " --> pdb=" O ILE A 325 " (cutoff:3.500A) removed outlier: 4.320A pdb=" N LEU A 330 " --> pdb=" O ASP A 326 " (cutoff:3.500A) Processing helix chain 'A' and resid 332 through 337 Processing helix chain 'A' and resid 342 through 359 removed outlier: 3.586A pdb=" N ASN A 359 " --> pdb=" O ILE A 355 " (cutoff:3.500A) Processing helix chain 'A' and resid 360 through 378 removed outlier: 4.307A pdb=" N ALA A 364 " --> pdb=" O PRO A 360 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N GLN A 378 " --> pdb=" O HIS A 374 " (cutoff:3.500A) Processing helix chain 'A' and resid 404 through 421 removed outlier: 4.002A pdb=" N ASP A 408 " --> pdb=" O SER A 404 " (cutoff:3.500A) Processing helix chain 'A' and resid 453 through 473 removed outlier: 3.670A pdb=" N LEU A 473 " --> pdb=" O GLN A 469 " (cutoff:3.500A) 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 130 through 134 Processing helix chain 'B' and resid 186 through 200 Processing helix chain 'B' and resid 213 through 228 removed outlier: 3.727A pdb=" N GLU B 217 " --> pdb=" O LEU B 213 " (cutoff:3.500A) Processing helix chain 'B' and resid 237 through 250 removed outlier: 3.726A 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 363 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 removed outlier: 3.529A pdb=" N ALA B 408 " --> pdb=" O SER B 404 " (cutoff:3.500A) Processing helix chain 'B' and resid 412 through 428 Processing helix chain 'B' and resid 436 through 455 Processing helix chain 'B' and resid 475 through 489 removed outlier: 4.091A 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 25 through 29 removed outlier: 3.687A pdb=" N MET C 28 " --> pdb=" O ALA C 25 " (cutoff:3.500A) Processing helix chain 'C' and resid 30 through 55 Processing helix chain 'C' and resid 58 through 69 Processing helix chain 'D' and resid 11 through 19 removed outlier: 3.927A pdb=" N VAL D 16 " --> pdb=" O ASN D 13 " (cutoff:3.500A) removed outlier: 5.215A pdb=" N MET D 17 " --> pdb=" O THR D 14 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N SER D 19 " --> pdb=" O VAL D 16 " (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 146 through 150 Processing helix chain 'G' and resid 9 through 24 Processing helix chain 'G' and resid 25 through 29 removed outlier: 3.686A pdb=" N MET G 28 " --> pdb=" O ALA G 25 " (cutoff:3.500A) Processing helix chain 'G' and resid 30 through 55 Processing helix chain 'G' and resid 58 through 69 Processing helix chain 'H' and resid 11 through 19 removed outlier: 3.927A pdb=" N VAL H 16 " --> pdb=" O ASN H 13 " (cutoff:3.500A) removed outlier: 5.215A pdb=" N MET H 17 " --> pdb=" O THR H 14 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N SER H 19 " --> pdb=" O VAL H 16 " (cutoff:3.500A) 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 146 through 150 Processing helix chain 'E' and resid 11 through 19 Processing helix chain 'E' and resid 21 through 40 Processing helix chain 'E' and resid 53 through 64 Processing helix chain 'E' and resid 77 through 81 removed outlier: 3.573A pdb=" N ASN E 81 " --> pdb=" O PRO E 78 " (cutoff:3.500A) Processing helix chain 'E' and resid 114 through 128 Processing helix chain 'E' and resid 142 through 156 removed outlier: 3.680A pdb=" N LEU E 146 " --> pdb=" O PHE E 142 " (cutoff:3.500A) Processing helix chain 'E' and resid 166 through 179 removed outlier: 4.155A pdb=" N ILE E 171 " --> pdb=" O GLY E 167 " (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: 3.587A pdb=" N LYS E 230 " --> pdb=" O ILE E 226 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N ASN E 231 " --> pdb=" O GLU E 227 " (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 removed outlier: 3.671A pdb=" N HIS E 292 " --> pdb=" O GLY E 288 " (cutoff:3.500A) Processing helix chain 'E' and resid 296 through 300 Processing helix chain 'E' and resid 321 through 332 removed outlier: 4.768A pdb=" N HIS E 327 " --> pdb=" O PHE E 323 " (cutoff:3.500A) removed outlier: 4.233A pdb=" N GLN E 328 " --> pdb=" O VAL E 324 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N ARG E 329 " --> pdb=" O ILE E 325 " (cutoff:3.500A) removed outlier: 4.320A pdb=" N LEU E 330 " --> pdb=" O ASP E 326 " (cutoff:3.500A) Processing helix chain 'E' and resid 332 through 337 Processing helix chain 'E' and resid 342 through 359 removed outlier: 3.587A pdb=" N ASN E 359 " --> pdb=" O ILE E 355 " (cutoff:3.500A) Processing helix chain 'E' and resid 360 through 378 removed outlier: 4.307A pdb=" N ALA E 364 " --> pdb=" O PRO E 360 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N GLN E 378 " --> pdb=" O HIS E 374 " (cutoff:3.500A) Processing helix chain 'E' and resid 404 through 421 removed outlier: 4.002A pdb=" N ASP E 408 " --> pdb=" O SER E 404 " (cutoff:3.500A) Processing helix chain 'E' and resid 453 through 473 removed outlier: 3.670A pdb=" N LEU E 473 " --> pdb=" O GLN E 469 " (cutoff:3.500A) 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 130 through 134 Processing helix chain 'F' and resid 186 through 200 Processing helix chain 'F' and resid 213 through 228 removed outlier: 3.727A pdb=" N GLU F 217 " --> pdb=" O LEU F 213 " (cutoff:3.500A) Processing helix chain 'F' and resid 237 through 250 removed outlier: 3.725A 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 363 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 removed outlier: 3.529A pdb=" N ALA F 408 " --> pdb=" O SER F 404 " (cutoff:3.500A) Processing helix chain 'F' and resid 412 through 428 Processing helix chain 'F' and resid 436 through 455 Processing helix chain 'F' and resid 475 through 489 removed outlier: 4.090A 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: 6.971A pdb=" N ILE A 271 " --> pdb=" O LEU A 302 " (cutoff:3.500A) removed outlier: 8.294A pdb=" N SER A 304 " --> pdb=" O ILE A 271 " (cutoff:3.500A) removed outlier: 6.634A pdb=" N LEU A 273 " --> pdb=" O SER A 304 " (cutoff:3.500A) removed outlier: 8.806A pdb=" N ASN A 306 " --> pdb=" O LEU A 273 " (cutoff:3.500A) removed outlier: 6.839A pdb=" N ARG A 240 " --> pdb=" O ARG A 270 " (cutoff:3.500A) removed outlier: 7.794A pdb=" N PHE A 272 " --> pdb=" O ARG A 240 " (cutoff:3.500A) removed outlier: 6.287A pdb=" N ILE A 242 " --> pdb=" O PHE A 272 " (cutoff:3.500A) removed outlier: 7.602A pdb=" N GLU A 274 " --> pdb=" O ILE A 242 " (cutoff:3.500A) removed outlier: 6.880A pdb=" N VAL A 244 " --> pdb=" O GLU A 274 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N ASP A 188 " --> pdb=" O VAL A 243 " (cutoff:3.500A) removed outlier: 7.959A pdb=" N GLU A 245 " --> pdb=" O ASP A 188 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 383 through 386 removed outlier: 4.179A pdb=" N THR A 427 " --> pdb=" O ARG A 445 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 61 through 62 removed outlier: 3.542A pdb=" N ALA B 62 " --> pdb=" O GLY B 462 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N GLY B 462 " --> pdb=" O ALA B 62 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'B' and resid 145 through 152 removed outlier: 7.042A pdb=" N VAL B 146 " --> pdb=" O ILE B 167 " (cutoff:3.500A) removed outlier: 7.112A pdb=" N ILE B 167 " --> pdb=" O VAL B 146 " (cutoff:3.500A) removed outlier: 7.629A pdb=" N ILE B 148 " --> pdb=" O ASN B 165 " (cutoff:3.500A) removed outlier: 7.811A pdb=" N ASN B 165 " --> pdb=" O ILE B 148 " (cutoff:3.500A) removed outlier: 4.980A pdb=" N GLU B 150 " --> pdb=" O THR B 163 " (cutoff:3.500A) removed outlier: 7.816A pdb=" N GLY B 492 " --> pdb=" O GLY B 169 " (cutoff:3.500A) removed outlier: 6.651A pdb=" N ILE B 171 " --> pdb=" O GLY B 492 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 231 through 235 removed outlier: 6.405A pdb=" N LEU B 341 " --> pdb=" O VAL B 372 " (cutoff:3.500A) removed outlier: 7.451A pdb=" N MET B 374 " --> pdb=" O LEU B 341 " (cutoff:3.500A) removed outlier: 6.190A pdb=" N LEU B 343 " --> pdb=" O MET B 374 " (cutoff:3.500A) removed outlier: 8.076A pdb=" N THR B 376 " --> pdb=" O LEU B 343 " (cutoff:3.500A) removed outlier: 6.690A pdb=" N ILE B 310 " --> pdb=" O TYR B 340 " (cutoff:3.500A) removed outlier: 7.620A pdb=" N TYR B 342 " --> pdb=" O ILE B 310 " (cutoff:3.500A) removed outlier: 6.097A pdb=" N ILE B 312 " --> pdb=" O TYR B 342 " (cutoff:3.500A) removed outlier: 7.207A pdb=" N ASP B 344 " --> pdb=" O ILE B 312 " (cutoff:3.500A) removed outlier: 6.699A pdb=" N VAL B 314 " --> pdb=" O ASP B 344 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N ASP B 259 " --> pdb=" O LEU B 313 " (cutoff:3.500A) removed outlier: 8.439A pdb=" N GLU B 315 " --> pdb=" O ASP B 259 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 468 through 472 removed outlier: 3.795A 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: 3.662A pdb=" N LEU E 302 " --> pdb=" O ILE E 271 " (cutoff:3.500A) removed outlier: 6.839A pdb=" N ARG E 240 " --> pdb=" O ARG E 270 " (cutoff:3.500A) removed outlier: 7.794A pdb=" N PHE E 272 " --> pdb=" O ARG E 240 " (cutoff:3.500A) removed outlier: 6.289A pdb=" N ILE E 242 " --> pdb=" O PHE E 272 " (cutoff:3.500A) removed outlier: 7.601A pdb=" N GLU E 274 " --> pdb=" O ILE E 242 " (cutoff:3.500A) removed outlier: 6.880A pdb=" N VAL E 244 " --> pdb=" O GLU E 274 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N ASP E 188 " --> pdb=" O VAL E 243 " (cutoff:3.500A) removed outlier: 7.959A pdb=" N GLU E 245 " --> pdb=" O ASP E 188 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'E' and resid 383 through 386 removed outlier: 4.179A pdb=" N THR E 427 " --> pdb=" O ARG E 445 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'F' and resid 61 through 62 removed outlier: 3.541A pdb=" N ALA F 62 " --> pdb=" O GLY F 462 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N GLY F 462 " --> pdb=" O ALA F 62 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'F' and resid 145 through 152 removed outlier: 7.041A pdb=" N VAL F 146 " --> pdb=" O ILE F 167 " (cutoff:3.500A) removed outlier: 7.111A pdb=" N ILE F 167 " --> pdb=" O VAL F 146 " (cutoff:3.500A) removed outlier: 7.629A pdb=" N ILE F 148 " --> pdb=" O ASN F 165 " (cutoff:3.500A) removed outlier: 7.811A pdb=" N ASN F 165 " --> pdb=" O ILE F 148 " (cutoff:3.500A) removed outlier: 4.979A pdb=" N GLU F 150 " --> pdb=" O THR F 163 " (cutoff:3.500A) removed outlier: 7.816A pdb=" N GLY F 492 " --> pdb=" O GLY F 169 " (cutoff:3.500A) removed outlier: 6.651A pdb=" N ILE F 171 " --> pdb=" O GLY F 492 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'F' and resid 231 through 235 removed outlier: 6.406A pdb=" N LEU F 341 " --> pdb=" O VAL F 372 " (cutoff:3.500A) removed outlier: 7.452A pdb=" N MET F 374 " --> pdb=" O LEU F 341 " (cutoff:3.500A) removed outlier: 6.190A pdb=" N LEU F 343 " --> pdb=" O MET F 374 " (cutoff:3.500A) removed outlier: 8.075A pdb=" N THR F 376 " --> pdb=" O LEU F 343 " (cutoff:3.500A) removed outlier: 6.690A pdb=" N ILE F 310 " --> pdb=" O TYR F 340 " (cutoff:3.500A) removed outlier: 7.619A pdb=" N TYR F 342 " --> pdb=" O ILE F 310 " (cutoff:3.500A) removed outlier: 6.096A pdb=" N ILE F 312 " --> pdb=" O TYR F 342 " (cutoff:3.500A) removed outlier: 7.207A pdb=" N ASP F 344 " --> pdb=" O ILE F 312 " (cutoff:3.500A) removed outlier: 6.699A pdb=" N VAL F 314 " --> pdb=" O ASP F 344 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N ASP F 259 " --> pdb=" O LEU F 313 " (cutoff:3.500A) removed outlier: 8.438A pdb=" N GLU F 315 " --> pdb=" O ASP F 259 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'F' and resid 468 through 472 removed outlier: 3.795A pdb=" N VAL F 494 " --> pdb=" O ARG F 509 " (cutoff:3.500A) 957 hydrogen bonds defined for protein. 2721 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: 3.48 Time building geometry restraints manager: 1.70 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: 5932 1.34 - 1.46: 4212 1.46 - 1.58: 8648 1.58 - 1.70: 2 1.70 - 1.82: 170 Bond restraints: 18964 Sorted by residual: bond pdb=" O4P PLP F 603 " pdb=" P PLP F 603 " ideal model delta sigma weight residual 1.610 1.823 -0.213 2.00e-02 2.50e+03 1.14e+02 bond pdb=" O4P PLP B 601 " pdb=" P PLP B 601 " ideal model delta sigma weight residual 1.610 1.823 -0.213 2.00e-02 2.50e+03 1.13e+02 bond pdb=" C29 POV D 901 " pdb="C210 POV D 901 " ideal model delta sigma weight residual 1.333 1.522 -0.189 2.00e-02 2.50e+03 8.89e+01 bond pdb=" C29 POV H 901 " pdb="C210 POV H 901 " ideal model delta sigma weight residual 1.333 1.520 -0.187 2.00e-02 2.50e+03 8.79e+01 bond pdb=" O12 POV F 601 " pdb=" P POV F 601 " ideal model delta sigma weight residual 1.657 1.741 -0.084 2.00e-02 2.50e+03 1.78e+01 ... (remaining 18959 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.62: 25529 3.62 - 7.24: 73 7.24 - 10.86: 12 10.86 - 14.48: 2 14.48 - 18.11: 4 Bond angle restraints: 25620 Sorted by residual: angle pdb=" C29 POV D 901 " pdb="C210 POV D 901 " pdb="C211 POV D 901 " ideal model delta sigma weight residual 127.67 109.56 18.11 3.00e+00 1.11e-01 3.64e+01 angle pdb=" C29 POV H 901 " pdb="C210 POV H 901 " pdb="C211 POV H 901 " ideal model delta sigma weight residual 127.67 109.59 18.08 3.00e+00 1.11e-01 3.63e+01 angle pdb=" C28 POV D 901 " pdb=" C29 POV D 901 " pdb="C210 POV D 901 " ideal model delta sigma weight residual 127.79 110.42 17.37 3.00e+00 1.11e-01 3.35e+01 angle pdb=" C28 POV H 901 " pdb=" C29 POV H 901 " pdb="C210 POV H 901 " ideal model delta sigma weight residual 127.79 110.43 17.36 3.00e+00 1.11e-01 3.35e+01 angle pdb=" O3P PLP F 603 " pdb=" P PLP F 603 " pdb=" O4P PLP F 603 " ideal model delta sigma weight residual 109.50 95.51 13.99 3.00e+00 1.11e-01 2.17e+01 ... (remaining 25615 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.30: 10825 23.30 - 46.61: 491 46.61 - 69.91: 34 69.91 - 93.21: 16 93.21 - 116.52: 2 Dihedral angle restraints: 11368 sinusoidal: 4582 harmonic: 6786 Sorted by residual: 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 -167.06 -116.52 1 2.00e+01 2.50e-03 3.47e+01 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 -167.07 -116.51 1 2.00e+01 2.50e-03 3.47e+01 dihedral pdb=" CA THR B 501 " pdb=" C THR B 501 " pdb=" N PRO B 502 " pdb=" CA PRO B 502 " ideal model delta harmonic sigma weight residual 180.00 160.80 19.20 0 5.00e+00 4.00e-02 1.47e+01 ... (remaining 11365 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.039: 2022 0.039 - 0.078: 596 0.078 - 0.117: 204 0.117 - 0.156: 28 0.156 - 0.195: 4 Chirality restraints: 2854 Sorted by residual: chirality pdb=" CA THR D 105 " pdb=" N THR D 105 " pdb=" C THR D 105 " pdb=" CB THR D 105 " both_signs ideal model delta sigma weight residual False 2.53 2.33 0.20 2.00e-01 2.50e+01 9.53e-01 chirality pdb=" CA THR H 105 " pdb=" N THR H 105 " pdb=" C THR H 105 " pdb=" CB THR H 105 " both_signs ideal model delta sigma weight residual False 2.53 2.33 0.19 2.00e-01 2.50e+01 9.18e-01 chirality pdb=" CA GLU E 400 " pdb=" N GLU E 400 " pdb=" C GLU E 400 " pdb=" CB GLU E 400 " both_signs ideal model delta sigma weight residual False 2.51 2.68 -0.17 2.00e-01 2.50e+01 7.59e-01 ... (remaining 2851 not shown) Planarity restraints: 3244 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C28 POV D 901 " -0.033 2.00e-02 2.50e+03 3.30e-02 1.09e+01 pdb=" C29 POV D 901 " 0.034 2.00e-02 2.50e+03 pdb="C210 POV D 901 " 0.032 2.00e-02 2.50e+03 pdb="C211 POV D 901 " -0.033 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C28 POV H 901 " 0.033 2.00e-02 2.50e+03 3.30e-02 1.09e+01 pdb=" C29 POV H 901 " -0.034 2.00e-02 2.50e+03 pdb="C210 POV H 901 " -0.032 2.00e-02 2.50e+03 pdb="C211 POV H 901 " 0.033 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU E 398 " 0.012 2.00e-02 2.50e+03 2.36e-02 5.56e+00 pdb=" C LEU E 398 " -0.041 2.00e-02 2.50e+03 pdb=" O LEU E 398 " 0.015 2.00e-02 2.50e+03 pdb=" N GLU E 399 " 0.014 2.00e-02 2.50e+03 ... (remaining 3241 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.75: 2674 2.75 - 3.29: 17170 3.29 - 3.83: 29651 3.83 - 4.36: 35730 4.36 - 4.90: 64292 Nonbonded interactions: 149517 Sorted by model distance: nonbonded pdb=" OH TYR A 178 " pdb=" O VAL A 324 " model vdw 2.218 3.040 nonbonded pdb=" OH TYR E 178 " pdb=" O VAL E 324 " model vdw 2.219 3.040 nonbonded pdb=" NZ LYS E 264 " pdb=" O ASP E 299 " model vdw 2.226 3.120 nonbonded pdb=" NZ LYS A 264 " pdb=" O ASP A 299 " model vdw 2.226 3.120 nonbonded pdb=" OG1 THR D 84 " pdb=" OE1 GLU D 87 " model vdw 2.253 3.040 ... (remaining 149512 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 544) selection = (chain 'F' and resid 53 through 544) } 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: 3.630 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.330 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 15.950 Find NCS groups from input model: 0.370 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:8.530 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.960 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7879 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.213 18966 Z= 0.234 Angle : 0.686 18.105 25620 Z= 0.345 Chirality : 0.043 0.195 2854 Planarity : 0.004 0.053 3244 Dihedral : 12.846 116.518 7024 Min Nonbonded Distance : 2.218 Molprobity Statistics. All-atom Clashscore : 4.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % 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: 1.05 (0.18), residues: 2326 helix: 1.88 (0.16), residues: 1122 sheet: 0.35 (0.34), residues: 226 loop : -0.60 (0.20), residues: 978 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG F 450 TYR 0.029 0.001 TYR A 166 PHE 0.015 0.001 PHE A 168 TRP 0.013 0.001 TRP C 32 HIS 0.005 0.001 HIS E 24 Details of bonding type rmsd/Z covalent geometry : bond 0.00477 / 0.23 (18964) covalent geometry : angle 0.68613 / 0.35 (25620) hydrogen bonds : bond 0.14414 / 9.91 ( 957) hydrogen bonds : angle 5.19092 / 3.68 ( 2721) Misc. bond : bond 0.02839 / 1.43 ( 2) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4652 Ramachandran restraints generated. 2326 Oldfield, 0 Emsley, 2326 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4652 Ramachandran restraints generated. 2326 Oldfield, 0 Emsley, 2326 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 253 residues out of total 2008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 253 time to evaluate : 0.573 Fit side-chains REVERT: A 81 ASN cc_start: 0.7322 (m-40) cc_final: 0.6844 (m-40) REVERT: A 205 ASP cc_start: 0.7173 (m-30) cc_final: 0.6956 (m-30) REVERT: A 230 LYS cc_start: 0.7071 (mtpt) cc_final: 0.6719 (mptt) REVERT: A 417 ASP cc_start: 0.6944 (m-30) cc_final: 0.6672 (m-30) REVERT: B 95 ARG cc_start: 0.7806 (mmm160) cc_final: 0.7567 (mpp-170) REVERT: B 149 MET cc_start: 0.8215 (mtp) cc_final: 0.7977 (mtp) REVERT: B 221 GLU cc_start: 0.6733 (pp20) cc_final: 0.6513 (pp20) REVERT: B 271 ARG cc_start: 0.7447 (mmt90) cc_final: 0.7162 (mtp180) REVERT: B 281 LYS cc_start: 0.8035 (tttm) cc_final: 0.7749 (mtpp) REVERT: B 286 GLN cc_start: 0.7636 (mp10) cc_final: 0.7345 (mp10) REVERT: B 290 LYS cc_start: 0.7356 (tttp) cc_final: 0.6910 (ttmm) REVERT: B 436 LYS cc_start: 0.7269 (tppt) cc_final: 0.6794 (ttpt) REVERT: E 81 ASN cc_start: 0.7364 (m-40) cc_final: 0.6902 (m-40) REVERT: E 417 ASP cc_start: 0.6969 (m-30) cc_final: 0.6652 (m-30) REVERT: F 95 ARG cc_start: 0.7805 (mmm160) cc_final: 0.7577 (mpp-170) REVERT: F 149 MET cc_start: 0.8271 (mtp) cc_final: 0.8023 (mtp) REVERT: F 221 GLU cc_start: 0.6734 (pp20) cc_final: 0.6506 (pp20) REVERT: F 271 ARG cc_start: 0.7437 (mmt90) cc_final: 0.7160 (mtp180) REVERT: F 281 LYS cc_start: 0.8047 (tttm) cc_final: 0.7759 (mtpp) REVERT: F 286 GLN cc_start: 0.7663 (mp10) cc_final: 0.7368 (mp10) REVERT: F 290 LYS cc_start: 0.7343 (tttp) cc_final: 0.6880 (ttmm) REVERT: F 436 LYS cc_start: 0.7264 (tppt) cc_final: 0.6708 (ttpt) outliers start: 0 outliers final: 0 residues processed: 253 average time/residue: 0.7059 time to fit residues: 195.9878 Evaluate side-chains 190 residues out of total 2008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 190 time to evaluate : 0.438 ------------------------------------------------------------------------------- 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: 4.9990 chunk 98 optimal weight: 1.9990 chunk 194 optimal weight: 0.2980 chunk 227 optimal weight: 1.9990 chunk 107 optimal weight: 3.9990 chunk 10 optimal weight: 2.9990 chunk 66 optimal weight: 3.9990 chunk 130 optimal weight: 0.6980 chunk 124 optimal weight: 0.9990 chunk 103 optimal weight: 0.8980 chunk 200 optimal weight: 1.9990 overall best weight: 0.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 77 HIS A 372 GLN B 429 GLN E 77 HIS E 372 GLN F 429 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.132995 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3216 r_free = 0.3216 target = 0.102977 restraints weight = 22420.025| |-----------------------------------------------------------------------------| r_work (start): 0.3154 rms_B_bonded: 2.37 r_work: 0.3009 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.2864 rms_B_bonded: 4.68 restraints_weight: 0.2500 r_work (final): 0.2864 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8109 moved from start: 0.0877 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 18966 Z= 0.143 Angle : 0.528 6.462 25620 Z= 0.280 Chirality : 0.043 0.195 2854 Planarity : 0.005 0.051 3244 Dihedral : 7.078 91.701 2712 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 3.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % Rotamer: Outliers : 1.45 % Allowed : 6.98 % Favored : 91.57 % 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: 1.16 (0.18), residues: 2326 helix: 1.82 (0.15), residues: 1160 sheet: 0.59 (0.32), residues: 260 loop : -0.55 (0.20), residues: 906 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 20 TYR 0.013 0.001 TYR E 166 PHE 0.017 0.002 PHE A 209 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 0.00336 / 0.14 (18964) covalent geometry : angle 0.52842 / 0.28 (25620) hydrogen bonds : bond 0.04756 / 3.15 ( 957) hydrogen bonds : angle 4.26744 / 3.06 ( 2721) Misc. bond : bond 0.00062 / 0.03 ( 2) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4652 Ramachandran restraints generated. 2326 Oldfield, 0 Emsley, 2326 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4652 Ramachandran restraints generated. 2326 Oldfield, 0 Emsley, 2326 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 230 residues out of total 2008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 202 time to evaluate : 0.511 Fit side-chains revert: symmetry clash REVERT: A 46 LEU cc_start: 0.7892 (OUTLIER) cc_final: 0.7527 (tt) REVERT: A 81 ASN cc_start: 0.7584 (m-40) cc_final: 0.7082 (m-40) REVERT: A 205 ASP cc_start: 0.7521 (m-30) cc_final: 0.7283 (m-30) REVERT: A 230 LYS cc_start: 0.7000 (mtpt) cc_final: 0.6587 (mptt) REVERT: A 417 ASP cc_start: 0.7031 (m-30) cc_final: 0.6787 (m-30) REVERT: B 95 ARG cc_start: 0.7926 (mmm160) cc_final: 0.7413 (mpp-170) REVERT: B 149 MET cc_start: 0.8840 (mtp) cc_final: 0.8626 (mtp) REVERT: B 159 SER cc_start: 0.8727 (m) cc_final: 0.8465 (p) REVERT: B 271 ARG cc_start: 0.8081 (mmt90) cc_final: 0.7363 (mtp180) REVERT: B 281 LYS cc_start: 0.8280 (tttm) cc_final: 0.7995 (mtpp) REVERT: B 286 GLN cc_start: 0.7786 (mp10) cc_final: 0.7521 (mp10) REVERT: B 290 LYS cc_start: 0.7704 (tttp) cc_final: 0.7226 (ttmm) REVERT: B 436 LYS cc_start: 0.7213 (tppt) cc_final: 0.6771 (ttpt) REVERT: C 13 MET cc_start: 0.6616 (OUTLIER) cc_final: 0.6205 (mmm) REVERT: C 28 MET cc_start: 0.8755 (OUTLIER) cc_final: 0.8468 (mtm) REVERT: E 46 LEU cc_start: 0.7891 (OUTLIER) cc_final: 0.7505 (tt) REVERT: E 81 ASN cc_start: 0.7600 (m-40) cc_final: 0.7104 (m-40) REVERT: E 230 LYS cc_start: 0.7001 (mtpt) cc_final: 0.6552 (mptt) REVERT: E 413 GLN cc_start: 0.7506 (tp40) cc_final: 0.6944 (mm-40) REVERT: E 417 ASP cc_start: 0.7084 (m-30) cc_final: 0.6672 (m-30) REVERT: F 95 ARG cc_start: 0.7927 (mmm160) cc_final: 0.7410 (mpp-170) REVERT: F 149 MET cc_start: 0.8854 (mtp) cc_final: 0.8645 (mtp) REVERT: F 159 SER cc_start: 0.8733 (m) cc_final: 0.8478 (p) REVERT: F 271 ARG cc_start: 0.8106 (mmt90) cc_final: 0.7373 (mtp180) REVERT: F 281 LYS cc_start: 0.8284 (tttm) cc_final: 0.7989 (mtpp) REVERT: F 286 GLN cc_start: 0.7819 (mp10) cc_final: 0.7542 (mp10) REVERT: F 290 LYS cc_start: 0.7686 (tttp) cc_final: 0.7201 (ttmm) REVERT: F 436 LYS cc_start: 0.7092 (tppt) cc_final: 0.6697 (ttpt) outliers start: 28 outliers final: 9 residues processed: 216 average time/residue: 0.6694 time to fit residues: 160.1754 Evaluate side-chains 199 residues out of total 2008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 186 time to evaluate : 0.612 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 LEU Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 411 LEU Chi-restraints excluded: chain B residue 140 SER Chi-restraints excluded: chain B residue 360 VAL Chi-restraints excluded: chain C residue 13 MET Chi-restraints excluded: chain C residue 28 MET Chi-restraints excluded: chain D residue 38 LEU Chi-restraints excluded: chain H residue 38 LEU Chi-restraints excluded: chain E residue 46 LEU Chi-restraints excluded: chain E residue 390 LEU Chi-restraints excluded: chain E residue 411 LEU Chi-restraints excluded: chain F residue 360 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 152 optimal weight: 1.9990 chunk 184 optimal weight: 0.7980 chunk 211 optimal weight: 3.9990 chunk 187 optimal weight: 9.9990 chunk 61 optimal weight: 2.9990 chunk 205 optimal weight: 0.9990 chunk 221 optimal weight: 5.9990 chunk 158 optimal weight: 0.9990 chunk 44 optimal weight: 2.9990 chunk 103 optimal weight: 0.7980 chunk 5 optimal weight: 0.9980 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 77 HIS A 372 GLN E 77 HIS E 372 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3570 r_free = 0.3570 target = 0.133296 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3220 r_free = 0.3220 target = 0.103152 restraints weight = 22619.594| |-----------------------------------------------------------------------------| r_work (start): 0.3185 rms_B_bonded: 2.40 r_work: 0.3030 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.2883 rms_B_bonded: 4.76 restraints_weight: 0.2500 r_work (final): 0.2883 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8084 moved from start: 0.1087 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 18966 Z= 0.132 Angle : 0.503 6.485 25620 Z= 0.266 Chirality : 0.042 0.184 2854 Planarity : 0.004 0.049 3244 Dihedral : 6.372 63.861 2712 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 3.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.06 % Favored : 97.94 % Rotamer: Outliers : 1.65 % Allowed : 9.15 % Favored : 89.19 % 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: 1.20 (0.18), residues: 2326 helix: 1.93 (0.15), residues: 1160 sheet: 0.41 (0.32), residues: 268 loop : -0.57 (0.20), residues: 898 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 233 TYR 0.011 0.001 TYR E 166 PHE 0.017 0.001 PHE B 239 TRP 0.013 0.001 TRP G 32 HIS 0.004 0.001 HIS F 403 Details of bonding type rmsd/Z covalent geometry : bond 0.00313 / 0.13 (18964) covalent geometry : angle 0.50295 / 0.27 (25620) hydrogen bonds : bond 0.04427 / 2.93 ( 957) hydrogen bonds : angle 4.08317 / 2.94 ( 2721) Misc. bond : bond 0.00081 / 0.04 ( 2) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4652 Ramachandran restraints generated. 2326 Oldfield, 0 Emsley, 2326 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4652 Ramachandran restraints generated. 2326 Oldfield, 0 Emsley, 2326 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 235 residues out of total 2008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 203 time to evaluate : 0.720 Fit side-chains revert: symmetry clash REVERT: A 30 ILE cc_start: 0.7825 (tt) cc_final: 0.7530 (tp) REVERT: A 46 LEU cc_start: 0.7831 (OUTLIER) cc_final: 0.7535 (tt) REVERT: A 81 ASN cc_start: 0.7571 (m-40) cc_final: 0.7072 (m-40) REVERT: A 205 ASP cc_start: 0.7443 (m-30) cc_final: 0.7208 (m-30) REVERT: A 230 LYS cc_start: 0.6995 (mtpt) cc_final: 0.6582 (mptt) REVERT: A 414 GLU cc_start: 0.7939 (tp30) cc_final: 0.7689 (tp30) REVERT: A 417 ASP cc_start: 0.7011 (m-30) cc_final: 0.6721 (m-30) REVERT: A 420 MET cc_start: 0.6790 (OUTLIER) cc_final: 0.6381 (tpp) REVERT: B 95 ARG cc_start: 0.7872 (mmm160) cc_final: 0.7391 (mpp-170) REVERT: B 245 ASN cc_start: 0.8687 (m-40) cc_final: 0.8357 (m-40) REVERT: B 271 ARG cc_start: 0.8055 (mmt90) cc_final: 0.7295 (mtp180) REVERT: B 281 LYS cc_start: 0.8170 (tttm) cc_final: 0.7885 (mtpp) REVERT: B 286 GLN cc_start: 0.7755 (mp10) cc_final: 0.7468 (mp10) REVERT: B 290 LYS cc_start: 0.7665 (tttp) cc_final: 0.7243 (ttmm) REVERT: B 436 LYS cc_start: 0.7057 (tppt) cc_final: 0.6628 (ttpt) REVERT: C 13 MET cc_start: 0.6580 (OUTLIER) cc_final: 0.6187 (mmm) REVERT: E 30 ILE cc_start: 0.7825 (tt) cc_final: 0.7530 (tp) REVERT: E 46 LEU cc_start: 0.7863 (OUTLIER) cc_final: 0.7553 (tt) REVERT: E 81 ASN cc_start: 0.7580 (m-40) cc_final: 0.7076 (t0) REVERT: E 230 LYS cc_start: 0.6924 (mtpt) cc_final: 0.6511 (mptt) REVERT: E 413 GLN cc_start: 0.7440 (tp40) cc_final: 0.6838 (mm-40) REVERT: E 414 GLU cc_start: 0.7953 (tp30) cc_final: 0.7703 (tp30) REVERT: E 417 ASP cc_start: 0.7081 (m-30) cc_final: 0.6662 (m-30) REVERT: F 95 ARG cc_start: 0.7859 (mmm160) cc_final: 0.7354 (mpp-170) REVERT: F 245 ASN cc_start: 0.8691 (m-40) cc_final: 0.8340 (m-40) REVERT: F 271 ARG cc_start: 0.8056 (mmt90) cc_final: 0.7305 (mtp180) REVERT: F 281 LYS cc_start: 0.8181 (tttm) cc_final: 0.7928 (mtpp) REVERT: F 286 GLN cc_start: 0.7778 (mp10) cc_final: 0.7495 (mp10) REVERT: F 290 LYS cc_start: 0.7662 (tttp) cc_final: 0.7239 (ttmm) REVERT: F 436 LYS cc_start: 0.7053 (tppt) cc_final: 0.6624 (ttpt) outliers start: 32 outliers final: 11 residues processed: 219 average time/residue: 0.6932 time to fit residues: 167.5203 Evaluate side-chains 207 residues out of total 2008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 192 time to evaluate : 0.687 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 LEU Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 411 LEU Chi-restraints excluded: chain A residue 420 MET Chi-restraints excluded: chain B residue 140 SER Chi-restraints excluded: chain B residue 360 VAL Chi-restraints excluded: chain C residue 13 MET Chi-restraints excluded: chain D residue 38 LEU Chi-restraints excluded: chain G residue 13 MET Chi-restraints excluded: chain H residue 38 LEU Chi-restraints excluded: chain E residue 39 LEU Chi-restraints excluded: chain E residue 46 LEU Chi-restraints excluded: chain E residue 390 LEU Chi-restraints excluded: chain E residue 411 LEU Chi-restraints excluded: chain F residue 140 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 189 optimal weight: 2.9990 chunk 207 optimal weight: 2.9990 chunk 224 optimal weight: 2.9990 chunk 169 optimal weight: 1.9990 chunk 25 optimal weight: 1.9990 chunk 72 optimal weight: 3.9990 chunk 190 optimal weight: 1.9990 chunk 225 optimal weight: 0.8980 chunk 49 optimal weight: 0.7980 chunk 44 optimal weight: 2.9990 chunk 171 optimal weight: 2.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 77 HIS A 372 GLN B 108 GLN D 85 HIS E 77 HIS E 372 GLN F 108 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3539 r_free = 0.3539 target = 0.130765 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3182 r_free = 0.3182 target = 0.100652 restraints weight = 22776.313| |-----------------------------------------------------------------------------| r_work (start): 0.3149 rms_B_bonded: 2.37 r_work: 0.2995 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.2849 rms_B_bonded: 4.70 restraints_weight: 0.2500 r_work (final): 0.2849 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8128 moved from start: 0.1285 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 18966 Z= 0.189 Angle : 0.556 6.745 25620 Z= 0.291 Chirality : 0.044 0.186 2854 Planarity : 0.005 0.051 3244 Dihedral : 6.211 66.585 2712 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 3.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.79 % Favored : 97.21 % Rotamer: Outliers : 2.17 % Allowed : 11.12 % Favored : 86.71 % 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: 1.04 (0.17), residues: 2326 helix: 1.83 (0.15), residues: 1148 sheet: 0.35 (0.32), residues: 268 loop : -0.67 (0.20), residues: 910 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG F 151 TYR 0.012 0.002 TYR A 164 PHE 0.018 0.002 PHE A 209 TRP 0.015 0.001 TRP G 32 HIS 0.004 0.001 HIS F 403 Details of bonding type rmsd/Z covalent geometry : bond 0.00469 / 0.19 (18964) covalent geometry : angle 0.55565 / 0.29 (25620) hydrogen bonds : bond 0.05070 / 3.34 ( 957) hydrogen bonds : angle 4.11984 / 2.97 ( 2721) Misc. bond : bond 0.00099 / 0.05 ( 2) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4652 Ramachandran restraints generated. 2326 Oldfield, 0 Emsley, 2326 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4652 Ramachandran restraints generated. 2326 Oldfield, 0 Emsley, 2326 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 240 residues out of total 2008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 198 time to evaluate : 0.644 Fit side-chains revert: symmetry clash REVERT: A 30 ILE cc_start: 0.7625 (tt) cc_final: 0.7340 (tp) REVERT: A 46 LEU cc_start: 0.7902 (OUTLIER) cc_final: 0.7639 (tt) REVERT: A 81 ASN cc_start: 0.7582 (m-40) cc_final: 0.7065 (t0) REVERT: A 205 ASP cc_start: 0.7536 (m-30) cc_final: 0.7287 (m-30) REVERT: A 230 LYS cc_start: 0.7002 (mtpt) cc_final: 0.6558 (mptt) REVERT: A 406 GLU cc_start: 0.7359 (mp0) cc_final: 0.6978 (mp0) REVERT: A 414 GLU cc_start: 0.7925 (tp30) cc_final: 0.7484 (tp30) REVERT: A 417 ASP cc_start: 0.7118 (m-30) cc_final: 0.6854 (m-30) REVERT: B 95 ARG cc_start: 0.7924 (mmm160) cc_final: 0.7330 (mpp-170) REVERT: B 159 SER cc_start: 0.8831 (m) cc_final: 0.8577 (p) REVERT: B 162 TYR cc_start: 0.8631 (m-80) cc_final: 0.7742 (m-80) REVERT: B 271 ARG cc_start: 0.8034 (mmt90) cc_final: 0.7208 (mtp180) REVERT: B 281 LYS cc_start: 0.8250 (tttm) cc_final: 0.7964 (mtpp) REVERT: B 286 GLN cc_start: 0.7736 (mp10) cc_final: 0.7490 (mp10) REVERT: B 290 LYS cc_start: 0.7728 (tttp) cc_final: 0.7295 (ttmm) REVERT: B 436 LYS cc_start: 0.7147 (tppt) cc_final: 0.6666 (ttpt) REVERT: B 441 GLN cc_start: 0.7481 (mt0) cc_final: 0.7182 (tt0) REVERT: C 13 MET cc_start: 0.6587 (OUTLIER) cc_final: 0.6222 (mmm) REVERT: D 15 ARG cc_start: 0.7252 (mmt180) cc_final: 0.6954 (mmt-90) REVERT: E 30 ILE cc_start: 0.7640 (tt) cc_final: 0.7353 (tp) REVERT: E 46 LEU cc_start: 0.7903 (OUTLIER) cc_final: 0.7609 (tt) REVERT: E 81 ASN cc_start: 0.7597 (m-40) cc_final: 0.7087 (t0) REVERT: E 230 LYS cc_start: 0.6924 (mtpt) cc_final: 0.6469 (mptt) REVERT: E 414 GLU cc_start: 0.7949 (tp30) cc_final: 0.7493 (tp30) REVERT: E 417 ASP cc_start: 0.7138 (m-30) cc_final: 0.6867 (m-30) REVERT: F 95 ARG cc_start: 0.7881 (mmm160) cc_final: 0.7321 (mpp-170) REVERT: F 159 SER cc_start: 0.8834 (m) cc_final: 0.8586 (p) REVERT: F 162 TYR cc_start: 0.8626 (m-80) cc_final: 0.7748 (m-80) REVERT: F 271 ARG cc_start: 0.8033 (mmt90) cc_final: 0.7210 (mtp180) REVERT: F 281 LYS cc_start: 0.8258 (tttm) cc_final: 0.7973 (mtpp) REVERT: F 286 GLN cc_start: 0.7755 (mp10) cc_final: 0.7513 (mp10) REVERT: F 290 LYS cc_start: 0.7742 (tttp) cc_final: 0.7304 (ttmm) REVERT: F 436 LYS cc_start: 0.7132 (tppt) cc_final: 0.6673 (ttpt) REVERT: F 441 GLN cc_start: 0.7444 (mt0) cc_final: 0.7149 (tt0) outliers start: 42 outliers final: 15 residues processed: 223 average time/residue: 0.7049 time to fit residues: 173.5218 Evaluate side-chains 204 residues out of total 2008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 186 time to evaluate : 0.624 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 LEU Chi-restraints excluded: chain A residue 39 LEU Chi-restraints excluded: chain A residue 46 LEU Chi-restraints excluded: chain A residue 150 ASP Chi-restraints excluded: chain B residue 140 SER Chi-restraints excluded: chain B residue 505 GLU Chi-restraints excluded: chain C residue 13 MET Chi-restraints excluded: chain D residue 10 VAL Chi-restraints excluded: chain D residue 38 LEU Chi-restraints excluded: chain G residue 13 MET Chi-restraints excluded: chain H residue 10 VAL Chi-restraints excluded: chain H residue 38 LEU Chi-restraints excluded: chain E residue 38 LEU Chi-restraints excluded: chain E residue 39 LEU Chi-restraints excluded: chain E residue 46 LEU Chi-restraints excluded: chain E residue 150 ASP Chi-restraints excluded: chain F residue 140 SER Chi-restraints excluded: chain F residue 505 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 76 optimal weight: 0.8980 chunk 212 optimal weight: 0.8980 chunk 215 optimal weight: 0.9980 chunk 224 optimal weight: 1.9990 chunk 7 optimal weight: 0.3980 chunk 63 optimal weight: 2.9990 chunk 163 optimal weight: 3.9990 chunk 118 optimal weight: 0.9980 chunk 108 optimal weight: 0.9980 chunk 80 optimal weight: 0.9990 chunk 11 optimal weight: 0.6980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 77 HIS A 372 GLN B 108 GLN H 85 HIS E 77 HIS E 372 GLN F 108 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3568 r_free = 0.3568 target = 0.133275 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3216 r_free = 0.3216 target = 0.103105 restraints weight = 22451.738| |-----------------------------------------------------------------------------| r_work (start): 0.3151 rms_B_bonded: 2.37 r_work: 0.3006 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.2861 rms_B_bonded: 4.71 restraints_weight: 0.2500 r_work (final): 0.2861 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8116 moved from start: 0.1368 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 18966 Z= 0.121 Angle : 0.484 6.498 25620 Z= 0.257 Chirality : 0.041 0.177 2854 Planarity : 0.004 0.048 3244 Dihedral : 5.881 63.027 2712 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 3.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % Rotamer: Outliers : 1.76 % Allowed : 12.31 % Favored : 85.94 % 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: 2326 helix: 1.97 (0.15), residues: 1162 sheet: 0.50 (0.32), residues: 266 loop : -0.62 (0.20), residues: 898 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 233 TYR 0.009 0.001 TYR F 342 PHE 0.016 0.001 PHE E 209 TRP 0.014 0.001 TRP G 32 HIS 0.003 0.001 HIS F 347 Details of bonding type rmsd/Z covalent geometry : bond 0.00284 / 0.12 (18964) covalent geometry : angle 0.48413 / 0.26 (25620) hydrogen bonds : bond 0.04132 / 2.73 ( 957) hydrogen bonds : angle 3.98524 / 2.87 ( 2721) Misc. bond : bond 0.00059 / 0.03 ( 2) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4652 Ramachandran restraints generated. 2326 Oldfield, 0 Emsley, 2326 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4652 Ramachandran restraints generated. 2326 Oldfield, 0 Emsley, 2326 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 225 residues out of total 2008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 191 time to evaluate : 0.581 Fit side-chains revert: symmetry clash REVERT: A 46 LEU cc_start: 0.7897 (OUTLIER) cc_final: 0.7647 (tt) REVERT: A 81 ASN cc_start: 0.7535 (m-40) cc_final: 0.7027 (t0) REVERT: A 205 ASP cc_start: 0.7461 (m-30) cc_final: 0.7232 (m-30) REVERT: A 230 LYS cc_start: 0.6921 (mtpt) cc_final: 0.6508 (mptt) REVERT: A 406 GLU cc_start: 0.7353 (mp0) cc_final: 0.6946 (mp0) REVERT: A 414 GLU cc_start: 0.7784 (tp30) cc_final: 0.7451 (tp30) REVERT: A 417 ASP cc_start: 0.7124 (m-30) cc_final: 0.6846 (m-30) REVERT: B 95 ARG cc_start: 0.7919 (mmm160) cc_final: 0.7351 (mpp-170) REVERT: B 159 SER cc_start: 0.8810 (m) cc_final: 0.8548 (p) REVERT: B 162 TYR cc_start: 0.8554 (m-80) cc_final: 0.7710 (m-80) REVERT: B 245 ASN cc_start: 0.8690 (m-40) cc_final: 0.8330 (m-40) REVERT: B 271 ARG cc_start: 0.8068 (mmt90) cc_final: 0.7259 (mtp180) REVERT: B 281 LYS cc_start: 0.8192 (tttm) cc_final: 0.7914 (mtpp) REVERT: B 286 GLN cc_start: 0.7746 (mp10) cc_final: 0.7545 (mp10) REVERT: B 290 LYS cc_start: 0.7728 (tttp) cc_final: 0.7291 (ttmm) REVERT: B 436 LYS cc_start: 0.6975 (tppt) cc_final: 0.6558 (ttpt) REVERT: C 13 MET cc_start: 0.6705 (OUTLIER) cc_final: 0.6327 (mmm) REVERT: H 15 ARG cc_start: 0.7079 (mmt180) cc_final: 0.6797 (mmt180) REVERT: E 30 ILE cc_start: 0.7649 (tt) cc_final: 0.7368 (tp) REVERT: E 46 LEU cc_start: 0.7936 (OUTLIER) cc_final: 0.7692 (tt) REVERT: E 81 ASN cc_start: 0.7549 (m-40) cc_final: 0.7034 (t0) REVERT: E 230 LYS cc_start: 0.6919 (mtpt) cc_final: 0.6506 (mptt) REVERT: E 413 GLN cc_start: 0.7550 (tp40) cc_final: 0.6999 (mm-40) REVERT: E 414 GLU cc_start: 0.7760 (tp30) cc_final: 0.7461 (tp30) REVERT: E 417 ASP cc_start: 0.7158 (m-30) cc_final: 0.6769 (m-30) REVERT: F 95 ARG cc_start: 0.7933 (mmm160) cc_final: 0.7358 (mpp-170) REVERT: F 159 SER cc_start: 0.8811 (m) cc_final: 0.8552 (p) REVERT: F 162 TYR cc_start: 0.8550 (m-80) cc_final: 0.7712 (m-80) REVERT: F 245 ASN cc_start: 0.8710 (m-40) cc_final: 0.8338 (m-40) REVERT: F 271 ARG cc_start: 0.8093 (mmt90) cc_final: 0.7275 (mtp180) REVERT: F 281 LYS cc_start: 0.8206 (tttm) cc_final: 0.7932 (mtpp) REVERT: F 286 GLN cc_start: 0.7749 (mp10) cc_final: 0.7509 (mp10) REVERT: F 290 LYS cc_start: 0.7711 (tttp) cc_final: 0.7265 (ttmm) REVERT: F 436 LYS cc_start: 0.6950 (tppt) cc_final: 0.6560 (ttpt) outliers start: 34 outliers final: 21 residues processed: 213 average time/residue: 0.6931 time to fit residues: 163.2996 Evaluate side-chains 205 residues out of total 2008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 181 time to evaluate : 0.501 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 LEU Chi-restraints excluded: chain A residue 46 LEU Chi-restraints excluded: chain A residue 150 ASP Chi-restraints excluded: chain A residue 166 TYR Chi-restraints excluded: chain B residue 120 ASN Chi-restraints excluded: chain B residue 140 SER Chi-restraints excluded: chain B residue 360 VAL Chi-restraints excluded: chain B residue 447 ARG Chi-restraints excluded: chain B residue 505 GLU Chi-restraints excluded: chain C residue 13 MET Chi-restraints excluded: chain C residue 28 MET Chi-restraints excluded: chain D residue 38 LEU Chi-restraints excluded: chain G residue 13 MET Chi-restraints excluded: chain G residue 28 MET Chi-restraints excluded: chain H residue 38 LEU Chi-restraints excluded: chain E residue 38 LEU Chi-restraints excluded: chain E residue 39 LEU Chi-restraints excluded: chain E residue 46 LEU Chi-restraints excluded: chain E residue 150 ASP Chi-restraints excluded: chain E residue 166 TYR Chi-restraints excluded: chain F residue 120 ASN Chi-restraints excluded: chain F residue 140 SER Chi-restraints excluded: chain F residue 360 VAL Chi-restraints excluded: chain F residue 505 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 45 optimal weight: 0.9980 chunk 56 optimal weight: 4.9990 chunk 215 optimal weight: 1.9990 chunk 98 optimal weight: 0.8980 chunk 97 optimal weight: 0.7980 chunk 19 optimal weight: 3.9990 chunk 218 optimal weight: 1.9990 chunk 159 optimal weight: 6.9990 chunk 52 optimal weight: 1.9990 chunk 126 optimal weight: 0.9980 chunk 37 optimal weight: 1.9990 overall best weight: 1.1382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 372 GLN B 108 GLN E 372 GLN F 108 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3555 r_free = 0.3555 target = 0.132100 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3197 r_free = 0.3197 target = 0.101610 restraints weight = 22539.504| |-----------------------------------------------------------------------------| r_work (start): 0.3165 rms_B_bonded: 2.41 r_work: 0.3009 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.2862 rms_B_bonded: 4.76 restraints_weight: 0.2500 r_work (final): 0.2862 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8100 moved from start: 0.1433 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 18966 Z= 0.151 Angle : 0.511 6.501 25620 Z= 0.269 Chirality : 0.042 0.134 2854 Planarity : 0.004 0.050 3244 Dihedral : 5.883 63.384 2712 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 3.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Rotamer: Outliers : 1.91 % Allowed : 12.67 % Favored : 85.42 % 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: 1.19 (0.18), residues: 2326 helix: 1.95 (0.15), residues: 1162 sheet: 0.52 (0.33), residues: 254 loop : -0.66 (0.20), residues: 910 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG F 543 TYR 0.011 0.001 TYR E 164 PHE 0.017 0.002 PHE A 209 TRP 0.014 0.001 TRP G 32 HIS 0.003 0.001 HIS F 401 Details of bonding type rmsd/Z covalent geometry : bond 0.00367 / 0.15 (18964) covalent geometry : angle 0.51077 / 0.27 (25620) hydrogen bonds : bond 0.04493 / 2.97 ( 957) hydrogen bonds : angle 3.99912 / 2.88 ( 2721) Misc. bond : bond 0.00046 / 0.02 ( 2) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4652 Ramachandran restraints generated. 2326 Oldfield, 0 Emsley, 2326 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4652 Ramachandran restraints generated. 2326 Oldfield, 0 Emsley, 2326 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 226 residues out of total 2008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 189 time to evaluate : 0.688 Fit side-chains revert: symmetry clash REVERT: A 46 LEU cc_start: 0.7897 (OUTLIER) cc_final: 0.7648 (tt) REVERT: A 81 ASN cc_start: 0.7520 (m-40) cc_final: 0.7006 (t0) REVERT: A 205 ASP cc_start: 0.7487 (m-30) cc_final: 0.7255 (m-30) REVERT: A 230 LYS cc_start: 0.6887 (mtpt) cc_final: 0.6459 (mptt) REVERT: A 406 GLU cc_start: 0.7327 (mp0) cc_final: 0.6906 (mp0) REVERT: A 413 GLN cc_start: 0.7540 (tp40) cc_final: 0.6986 (mm-40) REVERT: A 414 GLU cc_start: 0.7622 (tp30) cc_final: 0.7306 (tp30) REVERT: A 417 ASP cc_start: 0.7084 (m-30) cc_final: 0.6699 (m-30) REVERT: B 95 ARG cc_start: 0.7858 (mmm160) cc_final: 0.7273 (mpp-170) REVERT: B 159 SER cc_start: 0.8797 (m) cc_final: 0.8525 (p) REVERT: B 162 TYR cc_start: 0.8561 (m-80) cc_final: 0.7784 (m-80) REVERT: B 245 ASN cc_start: 0.8690 (m-40) cc_final: 0.8338 (m-40) REVERT: B 271 ARG cc_start: 0.8071 (mmt90) cc_final: 0.7213 (mtp180) REVERT: B 281 LYS cc_start: 0.8214 (tttm) cc_final: 0.7915 (mtpp) REVERT: B 286 GLN cc_start: 0.7738 (mp10) cc_final: 0.7526 (mp10) REVERT: B 290 LYS cc_start: 0.7726 (tttp) cc_final: 0.7288 (ttmm) REVERT: B 374 MET cc_start: 0.8888 (tmt) cc_final: 0.8580 (tmt) REVERT: B 436 LYS cc_start: 0.6939 (tppt) cc_final: 0.6543 (ttpt) REVERT: C 13 MET cc_start: 0.6611 (OUTLIER) cc_final: 0.6228 (mmm) REVERT: D 15 ARG cc_start: 0.7287 (mmt180) cc_final: 0.7063 (mmt-90) REVERT: H 15 ARG cc_start: 0.7255 (mmt180) cc_final: 0.7006 (mmt180) REVERT: E 46 LEU cc_start: 0.7892 (OUTLIER) cc_final: 0.7647 (tt) REVERT: E 81 ASN cc_start: 0.7600 (m-40) cc_final: 0.7080 (t0) REVERT: E 230 LYS cc_start: 0.6901 (mtpt) cc_final: 0.6459 (mptt) REVERT: E 406 GLU cc_start: 0.7315 (mp0) cc_final: 0.6896 (mp0) REVERT: E 413 GLN cc_start: 0.7530 (tp40) cc_final: 0.6979 (mm-40) REVERT: E 414 GLU cc_start: 0.7595 (tp30) cc_final: 0.7290 (tp30) REVERT: E 417 ASP cc_start: 0.7105 (m-30) cc_final: 0.6723 (m-30) REVERT: F 95 ARG cc_start: 0.7859 (mmm160) cc_final: 0.7269 (mpp-170) REVERT: F 159 SER cc_start: 0.8796 (m) cc_final: 0.8527 (p) REVERT: F 162 TYR cc_start: 0.8561 (m-80) cc_final: 0.7789 (m-80) REVERT: F 245 ASN cc_start: 0.8735 (m-40) cc_final: 0.8342 (m-40) REVERT: F 271 ARG cc_start: 0.8068 (mmt90) cc_final: 0.7198 (mtp180) REVERT: F 281 LYS cc_start: 0.8217 (tttm) cc_final: 0.7939 (mtpp) REVERT: F 286 GLN cc_start: 0.7743 (mp10) cc_final: 0.7533 (mp10) REVERT: F 290 LYS cc_start: 0.7694 (tttp) cc_final: 0.7256 (ttmm) REVERT: F 436 LYS cc_start: 0.6951 (tppt) cc_final: 0.6540 (ttpt) outliers start: 37 outliers final: 20 residues processed: 212 average time/residue: 0.6679 time to fit residues: 156.7744 Evaluate side-chains 204 residues out of total 2008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 181 time to evaluate : 0.574 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 LEU Chi-restraints excluded: chain A residue 39 LEU Chi-restraints excluded: chain A residue 46 LEU Chi-restraints excluded: chain A residue 150 ASP Chi-restraints excluded: chain B residue 120 ASN Chi-restraints excluded: chain B residue 140 SER Chi-restraints excluded: chain B residue 360 VAL Chi-restraints excluded: chain B residue 505 GLU Chi-restraints excluded: chain C residue 13 MET Chi-restraints excluded: chain D residue 10 VAL Chi-restraints excluded: chain D residue 38 LEU Chi-restraints excluded: chain G residue 13 MET Chi-restraints excluded: chain H residue 1 MET Chi-restraints excluded: chain H residue 10 VAL Chi-restraints excluded: chain H residue 38 LEU Chi-restraints excluded: chain E residue 38 LEU Chi-restraints excluded: chain E residue 39 LEU Chi-restraints excluded: chain E residue 46 LEU Chi-restraints excluded: chain E residue 150 ASP Chi-restraints excluded: chain F residue 120 ASN Chi-restraints excluded: chain F residue 140 SER Chi-restraints excluded: chain F residue 360 VAL Chi-restraints excluded: chain F residue 505 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 133 optimal weight: 0.5980 chunk 162 optimal weight: 2.9990 chunk 169 optimal weight: 0.4980 chunk 138 optimal weight: 4.9990 chunk 221 optimal weight: 3.9990 chunk 110 optimal weight: 4.9990 chunk 89 optimal weight: 0.0170 chunk 112 optimal weight: 3.9990 chunk 90 optimal weight: 3.9990 chunk 153 optimal weight: 0.4980 chunk 40 optimal weight: 0.7980 overall best weight: 0.4818 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 372 GLN B 108 GLN E 372 GLN F 108 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3590 r_free = 0.3590 target = 0.135162 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3241 r_free = 0.3241 target = 0.104800 restraints weight = 22560.336| |-----------------------------------------------------------------------------| r_work (start): 0.3208 rms_B_bonded: 2.42 r_work: 0.3054 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.2906 rms_B_bonded: 4.79 restraints_weight: 0.2500 r_work (final): 0.2906 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8032 moved from start: 0.1539 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 18966 Z= 0.099 Angle : 0.455 6.497 25620 Z= 0.242 Chirality : 0.040 0.128 2854 Planarity : 0.004 0.048 3244 Dihedral : 5.524 61.879 2712 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 3.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.72 % Favored : 98.28 % Rotamer: Outliers : 1.60 % Allowed : 13.39 % Favored : 85.01 % 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: 1.41 (0.18), residues: 2326 helix: 2.14 (0.15), residues: 1164 sheet: 0.54 (0.33), residues: 268 loop : -0.55 (0.20), residues: 894 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 450 TYR 0.008 0.001 TYR B 122 PHE 0.019 0.001 PHE F 239 TRP 0.013 0.001 TRP C 32 HIS 0.002 0.000 HIS E 77 Details of bonding type rmsd/Z covalent geometry : bond 0.00221 / 0.10 (18964) covalent geometry : angle 0.45548 / 0.24 (25620) hydrogen bonds : bond 0.03562 / 2.37 ( 957) hydrogen bonds : angle 3.87748 / 2.79 ( 2721) Misc. bond : bond 0.00032 / 0.02 ( 2) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4652 Ramachandran restraints generated. 2326 Oldfield, 0 Emsley, 2326 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4652 Ramachandran restraints generated. 2326 Oldfield, 0 Emsley, 2326 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 223 residues out of total 2008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 192 time to evaluate : 0.660 Fit side-chains revert: symmetry clash REVERT: A 81 ASN cc_start: 0.7487 (m-40) cc_final: 0.6968 (t0) REVERT: A 205 ASP cc_start: 0.7330 (m-30) cc_final: 0.7101 (m-30) REVERT: A 230 LYS cc_start: 0.6836 (mtpt) cc_final: 0.6424 (mptt) REVERT: A 406 GLU cc_start: 0.7306 (mp0) cc_final: 0.6952 (mp0) REVERT: A 414 GLU cc_start: 0.7368 (tp30) cc_final: 0.7096 (tp30) REVERT: A 417 ASP cc_start: 0.6998 (m-30) cc_final: 0.6696 (m-30) REVERT: B 95 ARG cc_start: 0.7791 (mmm160) cc_final: 0.7221 (mpp-170) REVERT: B 162 TYR cc_start: 0.8455 (m-80) cc_final: 0.7653 (m-80) REVERT: B 245 ASN cc_start: 0.8688 (m-40) cc_final: 0.8328 (m-40) REVERT: B 271 ARG cc_start: 0.8127 (mmt90) cc_final: 0.7285 (mtp180) REVERT: B 281 LYS cc_start: 0.8072 (tttm) cc_final: 0.7773 (mtpp) REVERT: B 290 LYS cc_start: 0.7634 (tttp) cc_final: 0.7184 (ttmm) REVERT: B 374 MET cc_start: 0.8816 (tmt) cc_final: 0.8525 (tmt) REVERT: B 436 LYS cc_start: 0.6838 (tppt) cc_final: 0.6552 (ttpt) REVERT: C 13 MET cc_start: 0.6644 (OUTLIER) cc_final: 0.6261 (mmm) REVERT: D 15 ARG cc_start: 0.7320 (mmt180) cc_final: 0.7092 (mmt-90) REVERT: H 15 ARG cc_start: 0.7285 (mmt180) cc_final: 0.7047 (mmt180) REVERT: E 81 ASN cc_start: 0.7530 (m-40) cc_final: 0.7023 (t0) REVERT: E 230 LYS cc_start: 0.6821 (mtpt) cc_final: 0.6404 (mptt) REVERT: E 414 GLU cc_start: 0.7440 (tp30) cc_final: 0.7184 (tp30) REVERT: E 417 ASP cc_start: 0.7007 (m-30) cc_final: 0.6705 (m-30) REVERT: F 95 ARG cc_start: 0.7806 (mmm160) cc_final: 0.7229 (mpp-170) REVERT: F 162 TYR cc_start: 0.8466 (m-80) cc_final: 0.7649 (m-80) REVERT: F 245 ASN cc_start: 0.8681 (m-40) cc_final: 0.8330 (m-40) REVERT: F 271 ARG cc_start: 0.8140 (mmt90) cc_final: 0.7293 (mtp180) REVERT: F 281 LYS cc_start: 0.8166 (tttm) cc_final: 0.7872 (mtpp) REVERT: F 290 LYS cc_start: 0.7620 (tttp) cc_final: 0.7179 (ttmm) REVERT: F 436 LYS cc_start: 0.6849 (tppt) cc_final: 0.6545 (ttpt) REVERT: F 530 GLU cc_start: 0.6194 (tt0) cc_final: 0.5861 (mt-10) outliers start: 31 outliers final: 16 residues processed: 210 average time/residue: 0.6782 time to fit residues: 157.9293 Evaluate side-chains 195 residues out of total 2008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 178 time to evaluate : 0.625 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 150 ASP Chi-restraints excluded: chain A residue 166 TYR Chi-restraints excluded: chain B residue 120 ASN Chi-restraints excluded: chain B residue 360 VAL Chi-restraints excluded: chain B residue 504 ILE Chi-restraints excluded: chain B residue 505 GLU Chi-restraints excluded: chain C residue 13 MET Chi-restraints excluded: chain C residue 28 MET Chi-restraints excluded: chain G residue 13 MET Chi-restraints excluded: chain G residue 28 MET Chi-restraints excluded: chain H residue 10 VAL Chi-restraints excluded: chain E residue 150 ASP Chi-restraints excluded: chain E residue 166 TYR Chi-restraints excluded: chain F residue 120 ASN Chi-restraints excluded: chain F residue 360 VAL Chi-restraints excluded: chain F residue 504 ILE Chi-restraints excluded: chain F residue 505 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 10 optimal weight: 2.9990 chunk 217 optimal weight: 0.9980 chunk 61 optimal weight: 2.9990 chunk 221 optimal weight: 3.9990 chunk 202 optimal weight: 0.0870 chunk 54 optimal weight: 0.9990 chunk 90 optimal weight: 0.0040 chunk 107 optimal weight: 4.9990 chunk 24 optimal weight: 0.8980 chunk 52 optimal weight: 1.9990 chunk 88 optimal weight: 0.5980 overall best weight: 0.5170 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 372 GLN E 372 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3592 r_free = 0.3592 target = 0.135342 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3244 r_free = 0.3244 target = 0.105062 restraints weight = 22480.628| |-----------------------------------------------------------------------------| r_work (start): 0.3212 rms_B_bonded: 2.41 r_work: 0.3058 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.2911 rms_B_bonded: 4.78 restraints_weight: 0.2500 r_work (final): 0.2911 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8028 moved from start: 0.1616 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 18966 Z= 0.100 Angle : 0.456 6.485 25620 Z= 0.240 Chirality : 0.040 0.129 2854 Planarity : 0.004 0.049 3244 Dihedral : 5.350 60.005 2712 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 3.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.93 % Favored : 98.07 % Rotamer: Outliers : 1.60 % Allowed : 14.06 % Favored : 84.33 % 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: 1.53 (0.18), residues: 2326 helix: 2.19 (0.15), residues: 1168 sheet: 0.69 (0.33), residues: 264 loop : -0.47 (0.21), residues: 894 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG F 450 TYR 0.008 0.001 TYR B 122 PHE 0.015 0.001 PHE A 209 TRP 0.012 0.001 TRP G 32 HIS 0.003 0.000 HIS E 77 Details of bonding type rmsd/Z covalent geometry : bond 0.00224 / 0.10 (18964) covalent geometry : angle 0.45595 / 0.24 (25620) hydrogen bonds : bond 0.03604 / 2.39 ( 957) hydrogen bonds : angle 3.82118 / 2.75 ( 2721) Misc. bond : bond 0.00025 / 0.01 ( 2) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4652 Ramachandran restraints generated. 2326 Oldfield, 0 Emsley, 2326 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4652 Ramachandran restraints generated. 2326 Oldfield, 0 Emsley, 2326 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 222 residues out of total 2008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 191 time to evaluate : 0.734 Fit side-chains revert: symmetry clash REVERT: A 81 ASN cc_start: 0.7497 (m-40) cc_final: 0.6988 (t0) REVERT: A 205 ASP cc_start: 0.7330 (m-30) cc_final: 0.7085 (m-30) REVERT: A 230 LYS cc_start: 0.6784 (mtpt) cc_final: 0.6367 (mptt) REVERT: A 406 GLU cc_start: 0.7238 (mp0) cc_final: 0.6862 (mp0) REVERT: A 414 GLU cc_start: 0.7368 (tp30) cc_final: 0.7126 (tp30) REVERT: A 417 ASP cc_start: 0.6974 (m-30) cc_final: 0.6685 (m-30) REVERT: B 95 ARG cc_start: 0.7684 (mmm160) cc_final: 0.7145 (mpp-170) REVERT: B 162 TYR cc_start: 0.8433 (m-80) cc_final: 0.7626 (m-80) REVERT: B 245 ASN cc_start: 0.8701 (m-40) cc_final: 0.8316 (m-40) REVERT: B 271 ARG cc_start: 0.8148 (mmt90) cc_final: 0.7297 (mtp180) REVERT: B 281 LYS cc_start: 0.8064 (tttm) cc_final: 0.7768 (mtpp) REVERT: B 290 LYS cc_start: 0.7606 (tttp) cc_final: 0.7163 (ttmm) REVERT: B 436 LYS cc_start: 0.6774 (tppt) cc_final: 0.6466 (ttpt) REVERT: C 13 MET cc_start: 0.6649 (OUTLIER) cc_final: 0.6260 (mmm) REVERT: H 15 ARG cc_start: 0.7337 (mmt180) cc_final: 0.7082 (mmt-90) REVERT: E 81 ASN cc_start: 0.7521 (m-40) cc_final: 0.7012 (t0) REVERT: E 230 LYS cc_start: 0.6790 (mtpt) cc_final: 0.6375 (mptt) REVERT: E 414 GLU cc_start: 0.7384 (tp30) cc_final: 0.7149 (tp30) REVERT: E 417 ASP cc_start: 0.6996 (m-30) cc_final: 0.6696 (m-30) REVERT: F 95 ARG cc_start: 0.7720 (mmm160) cc_final: 0.7188 (mpp-170) REVERT: F 162 TYR cc_start: 0.8422 (m-80) cc_final: 0.7612 (m-80) REVERT: F 245 ASN cc_start: 0.8685 (m-40) cc_final: 0.8346 (m-40) REVERT: F 271 ARG cc_start: 0.8140 (mmt90) cc_final: 0.7288 (mtp180) REVERT: F 281 LYS cc_start: 0.8216 (tttm) cc_final: 0.7923 (mtpp) REVERT: F 290 LYS cc_start: 0.7612 (tttp) cc_final: 0.7169 (ttmm) REVERT: F 436 LYS cc_start: 0.6824 (tppt) cc_final: 0.6524 (ttpt) REVERT: F 456 MET cc_start: 0.7820 (OUTLIER) cc_final: 0.7465 (mtp) outliers start: 31 outliers final: 19 residues processed: 211 average time/residue: 0.6455 time to fit residues: 151.6241 Evaluate side-chains 204 residues out of total 2008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 183 time to evaluate : 0.482 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 150 ASP Chi-restraints excluded: chain A residue 166 TYR Chi-restraints excluded: chain B residue 120 ASN Chi-restraints excluded: chain B residue 360 VAL Chi-restraints excluded: chain B residue 504 ILE Chi-restraints excluded: chain B residue 505 GLU Chi-restraints excluded: chain C residue 13 MET Chi-restraints excluded: chain C residue 28 MET Chi-restraints excluded: chain D residue 1 MET Chi-restraints excluded: chain D residue 96 THR Chi-restraints excluded: chain G residue 13 MET Chi-restraints excluded: chain G residue 28 MET Chi-restraints excluded: chain H residue 10 VAL Chi-restraints excluded: chain E residue 38 LEU Chi-restraints excluded: chain E residue 150 ASP Chi-restraints excluded: chain E residue 166 TYR Chi-restraints excluded: chain F residue 120 ASN Chi-restraints excluded: chain F residue 360 VAL Chi-restraints excluded: chain F residue 456 MET Chi-restraints excluded: chain F residue 504 ILE Chi-restraints excluded: chain F residue 505 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 196 optimal weight: 3.9990 chunk 69 optimal weight: 0.8980 chunk 133 optimal weight: 0.7980 chunk 13 optimal weight: 0.4980 chunk 47 optimal weight: 2.9990 chunk 102 optimal weight: 0.5980 chunk 48 optimal weight: 0.6980 chunk 174 optimal weight: 6.9990 chunk 197 optimal weight: 2.9990 chunk 85 optimal weight: 0.9990 chunk 207 optimal weight: 1.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 372 GLN E 372 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3583 r_free = 0.3583 target = 0.134480 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3233 r_free = 0.3233 target = 0.104224 restraints weight = 22449.388| |-----------------------------------------------------------------------------| r_work (start): 0.3201 rms_B_bonded: 2.40 r_work: 0.3046 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.2900 rms_B_bonded: 4.77 restraints_weight: 0.2500 r_work (final): 0.2900 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8041 moved from start: 0.1628 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 18966 Z= 0.113 Angle : 0.474 6.767 25620 Z= 0.249 Chirality : 0.041 0.130 2854 Planarity : 0.004 0.049 3244 Dihedral : 5.359 59.232 2712 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 3.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.85 % Favored : 98.15 % Rotamer: Outliers : 1.60 % Allowed : 14.53 % Favored : 83.87 % 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: 1.52 (0.18), residues: 2326 helix: 2.19 (0.15), residues: 1168 sheet: 0.65 (0.33), residues: 266 loop : -0.47 (0.21), residues: 892 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 450 TYR 0.008 0.001 TYR E 164 PHE 0.015 0.001 PHE A 209 TRP 0.012 0.001 TRP C 32 HIS 0.003 0.001 HIS A 77 Details of bonding type rmsd/Z covalent geometry : bond 0.00263 / 0.11 (18964) covalent geometry : angle 0.47406 / 0.25 (25620) hydrogen bonds : bond 0.03758 / 2.49 ( 957) hydrogen bonds : angle 3.82468 / 2.76 ( 2721) Misc. bond : bond 0.00022 / 0.01 ( 2) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4652 Ramachandran restraints generated. 2326 Oldfield, 0 Emsley, 2326 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4652 Ramachandran restraints generated. 2326 Oldfield, 0 Emsley, 2326 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 227 residues out of total 2008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 196 time to evaluate : 0.511 Fit side-chains revert: symmetry clash REVERT: A 81 ASN cc_start: 0.7452 (m-40) cc_final: 0.6986 (t0) REVERT: A 205 ASP cc_start: 0.7355 (m-30) cc_final: 0.7109 (m-30) REVERT: A 230 LYS cc_start: 0.6812 (mtpt) cc_final: 0.6393 (mptt) REVERT: A 406 GLU cc_start: 0.7260 (mp0) cc_final: 0.6879 (mp0) REVERT: A 414 GLU cc_start: 0.7385 (tp30) cc_final: 0.7145 (tp30) REVERT: A 417 ASP cc_start: 0.7002 (m-30) cc_final: 0.6706 (m-30) REVERT: B 95 ARG cc_start: 0.7724 (mmm160) cc_final: 0.7195 (mpp-170) REVERT: B 162 TYR cc_start: 0.8410 (m-80) cc_final: 0.7595 (m-80) REVERT: B 245 ASN cc_start: 0.8677 (m-40) cc_final: 0.8320 (m-40) REVERT: B 271 ARG cc_start: 0.8119 (mmt90) cc_final: 0.7247 (mtp180) REVERT: B 281 LYS cc_start: 0.8095 (tttm) cc_final: 0.7795 (mtpp) REVERT: B 290 LYS cc_start: 0.7617 (tttp) cc_final: 0.7179 (ttmm) REVERT: B 436 LYS cc_start: 0.6759 (tppt) cc_final: 0.6457 (ttpt) REVERT: C 13 MET cc_start: 0.6668 (OUTLIER) cc_final: 0.6282 (mmm) REVERT: H 15 ARG cc_start: 0.7378 (mmt180) cc_final: 0.7164 (mmt-90) REVERT: E 81 ASN cc_start: 0.7469 (m-40) cc_final: 0.7006 (t0) REVERT: E 230 LYS cc_start: 0.6811 (mtpt) cc_final: 0.6388 (mptt) REVERT: E 413 GLN cc_start: 0.7474 (tp40) cc_final: 0.7092 (tp40) REVERT: E 414 GLU cc_start: 0.7375 (tp30) cc_final: 0.7149 (tp30) REVERT: E 417 ASP cc_start: 0.7023 (m-30) cc_final: 0.6623 (m-30) REVERT: F 95 ARG cc_start: 0.7733 (mmm160) cc_final: 0.7204 (mpp-170) REVERT: F 162 TYR cc_start: 0.8413 (m-80) cc_final: 0.7602 (m-80) REVERT: F 245 ASN cc_start: 0.8648 (m-40) cc_final: 0.8315 (m-40) REVERT: F 271 ARG cc_start: 0.8156 (mmt90) cc_final: 0.7304 (mtp180) REVERT: F 281 LYS cc_start: 0.8162 (tttm) cc_final: 0.7859 (mtpp) REVERT: F 290 LYS cc_start: 0.7634 (tttp) cc_final: 0.7190 (ttmm) REVERT: F 436 LYS cc_start: 0.6792 (tppt) cc_final: 0.6479 (ttpt) outliers start: 31 outliers final: 19 residues processed: 214 average time/residue: 0.6668 time to fit residues: 158.0177 Evaluate side-chains 204 residues out of total 2008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 184 time to evaluate : 0.554 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 150 ASP Chi-restraints excluded: chain A residue 166 TYR Chi-restraints excluded: chain B residue 120 ASN Chi-restraints excluded: chain B residue 360 VAL Chi-restraints excluded: chain B residue 504 ILE Chi-restraints excluded: chain B residue 505 GLU Chi-restraints excluded: chain C residue 13 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 G residue 13 MET Chi-restraints excluded: chain G residue 28 MET Chi-restraints excluded: chain H residue 10 VAL Chi-restraints excluded: chain E residue 38 LEU Chi-restraints excluded: chain E residue 150 ASP Chi-restraints excluded: chain E residue 166 TYR Chi-restraints excluded: chain F residue 120 ASN Chi-restraints excluded: chain F residue 360 VAL Chi-restraints excluded: chain F residue 504 ILE Chi-restraints excluded: chain F residue 505 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 78 optimal weight: 0.9990 chunk 142 optimal weight: 2.9990 chunk 107 optimal weight: 4.9990 chunk 13 optimal weight: 0.5980 chunk 10 optimal weight: 2.9990 chunk 129 optimal weight: 0.9980 chunk 207 optimal weight: 0.7980 chunk 60 optimal weight: 0.9980 chunk 137 optimal weight: 10.0000 chunk 154 optimal weight: 0.9980 chunk 213 optimal weight: 0.8980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 372 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3574 r_free = 0.3574 target = 0.133772 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3221 r_free = 0.3221 target = 0.103503 restraints weight = 22508.868| |-----------------------------------------------------------------------------| r_work (start): 0.3191 rms_B_bonded: 2.38 r_work: 0.3037 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.2890 rms_B_bonded: 4.73 restraints_weight: 0.2500 r_work (final): 0.2890 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8078 moved from start: 0.1620 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 18966 Z= 0.125 Angle : 0.491 6.605 25620 Z= 0.258 Chirality : 0.041 0.131 2854 Planarity : 0.004 0.049 3244 Dihedral : 5.433 59.072 2712 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 3.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 1.40 % Allowed : 14.89 % Favored : 83.71 % 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: 1.50 (0.18), residues: 2326 helix: 2.16 (0.15), residues: 1168 sheet: 0.63 (0.33), residues: 266 loop : -0.47 (0.21), residues: 892 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 15 TYR 0.009 0.001 TYR E 164 PHE 0.016 0.001 PHE A 209 TRP 0.012 0.001 TRP C 32 HIS 0.003 0.001 HIS E 77 Details of bonding type rmsd/Z covalent geometry : bond 0.00298 / 0.13 (18964) covalent geometry : angle 0.49145 / 0.26 (25620) hydrogen bonds : bond 0.03971 / 2.63 ( 957) hydrogen bonds : angle 3.85704 / 2.78 ( 2721) Misc. bond : bond 0.00023 / 0.01 ( 2) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4652 Ramachandran restraints generated. 2326 Oldfield, 0 Emsley, 2326 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4652 Ramachandran restraints generated. 2326 Oldfield, 0 Emsley, 2326 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 210 residues out of total 2008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 183 time to evaluate : 0.801 Fit side-chains revert: symmetry clash REVERT: A 81 ASN cc_start: 0.7450 (m-40) cc_final: 0.6991 (t0) REVERT: A 205 ASP cc_start: 0.7384 (m-30) cc_final: 0.7143 (m-30) REVERT: A 230 LYS cc_start: 0.6814 (mtpt) cc_final: 0.6399 (mptt) REVERT: A 400 GLU cc_start: 0.7385 (mp0) cc_final: 0.7058 (mp0) REVERT: A 406 GLU cc_start: 0.7278 (mp0) cc_final: 0.6897 (mp0) REVERT: A 414 GLU cc_start: 0.7392 (tp30) cc_final: 0.7147 (tp30) REVERT: A 417 ASP cc_start: 0.7030 (m-30) cc_final: 0.6734 (m-30) REVERT: B 95 ARG cc_start: 0.7731 (mmm160) cc_final: 0.7167 (mpp-170) REVERT: B 162 TYR cc_start: 0.8405 (m-80) cc_final: 0.7606 (m-80) REVERT: B 245 ASN cc_start: 0.8684 (m-40) cc_final: 0.8350 (m-40) REVERT: B 271 ARG cc_start: 0.8178 (mmt90) cc_final: 0.7328 (mtp180) REVERT: B 281 LYS cc_start: 0.8230 (tttm) cc_final: 0.7934 (mtpp) REVERT: B 290 LYS cc_start: 0.7666 (tttp) cc_final: 0.7220 (ttmm) REVERT: B 436 LYS cc_start: 0.6808 (tppt) cc_final: 0.6508 (ttpt) REVERT: C 13 MET cc_start: 0.6673 (OUTLIER) cc_final: 0.6285 (mmm) REVERT: H 15 ARG cc_start: 0.7450 (mmt180) cc_final: 0.7243 (mmt-90) REVERT: E 81 ASN cc_start: 0.7499 (m-40) cc_final: 0.7032 (t0) REVERT: E 230 LYS cc_start: 0.6820 (mtpt) cc_final: 0.6402 (mptt) REVERT: E 400 GLU cc_start: 0.7348 (mp0) cc_final: 0.7074 (mp0) REVERT: E 413 GLN cc_start: 0.7475 (tp40) cc_final: 0.6943 (mm-40) REVERT: E 414 GLU cc_start: 0.7395 (tp30) cc_final: 0.7144 (tp30) REVERT: E 417 ASP cc_start: 0.7044 (m-30) cc_final: 0.6656 (m-30) REVERT: F 95 ARG cc_start: 0.7746 (mmm160) cc_final: 0.7175 (mpp-170) REVERT: F 159 SER cc_start: 0.8738 (m) cc_final: 0.8436 (p) REVERT: F 162 TYR cc_start: 0.8387 (m-80) cc_final: 0.7587 (m-80) REVERT: F 245 ASN cc_start: 0.8660 (m-40) cc_final: 0.8332 (m-40) REVERT: F 271 ARG cc_start: 0.8175 (mmt90) cc_final: 0.7330 (mtp180) REVERT: F 281 LYS cc_start: 0.8261 (tttm) cc_final: 0.7960 (mtpp) REVERT: F 290 LYS cc_start: 0.7688 (tttp) cc_final: 0.7240 (ttmm) REVERT: F 436 LYS cc_start: 0.6840 (tppt) cc_final: 0.6536 (ttpt) outliers start: 27 outliers final: 20 residues processed: 201 average time/residue: 0.6673 time to fit residues: 149.1516 Evaluate side-chains 202 residues out of total 2008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 181 time to evaluate : 0.688 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 LEU Chi-restraints excluded: chain A residue 39 LEU Chi-restraints excluded: chain A residue 150 ASP Chi-restraints excluded: chain B residue 120 ASN Chi-restraints excluded: chain B residue 360 VAL Chi-restraints excluded: chain B residue 504 ILE Chi-restraints excluded: chain B residue 505 GLU Chi-restraints excluded: chain C residue 13 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 G residue 13 MET Chi-restraints excluded: chain G residue 28 MET Chi-restraints excluded: chain H residue 10 VAL Chi-restraints excluded: chain E residue 38 LEU Chi-restraints excluded: chain E residue 45 LYS Chi-restraints excluded: chain E residue 150 ASP Chi-restraints excluded: chain F residue 120 ASN Chi-restraints excluded: chain F residue 360 VAL Chi-restraints excluded: chain F residue 504 ILE Chi-restraints excluded: chain F residue 505 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 194 optimal weight: 4.9990 chunk 59 optimal weight: 1.9990 chunk 67 optimal weight: 1.9990 chunk 115 optimal weight: 1.9990 chunk 88 optimal weight: 0.9990 chunk 228 optimal weight: 0.9990 chunk 227 optimal weight: 0.4980 chunk 203 optimal weight: 2.9990 chunk 133 optimal weight: 0.6980 chunk 51 optimal weight: 0.6980 chunk 216 optimal weight: 3.9990 overall best weight: 0.7784 ------------------------------------------------------------------------------- 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 = 0.3578 r_free = 0.3578 target = 0.134062 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3225 r_free = 0.3225 target = 0.103731 restraints weight = 22605.155| |-----------------------------------------------------------------------------| r_work (start): 0.3195 rms_B_bonded: 2.41 r_work: 0.3040 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.2894 rms_B_bonded: 4.77 restraints_weight: 0.2500 r_work (final): 0.2894 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8050 moved from start: 0.1639 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 18966 Z= 0.120 Angle : 0.486 6.555 25620 Z= 0.256 Chirality : 0.041 0.131 2854 Planarity : 0.004 0.049 3244 Dihedral : 5.424 58.879 2712 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 3.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.06 % Favored : 97.94 % Rotamer: Outliers : 1.40 % Allowed : 14.74 % Favored : 83.87 % 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: 1.51 (0.18), residues: 2326 helix: 2.17 (0.15), residues: 1168 sheet: 0.63 (0.33), residues: 266 loop : -0.46 (0.21), residues: 892 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG F 450 TYR 0.009 0.001 TYR E 164 PHE 0.016 0.001 PHE A 209 TRP 0.012 0.001 TRP G 32 HIS 0.003 0.001 HIS E 77 Details of bonding type rmsd/Z covalent geometry : bond 0.00282 / 0.12 (18964) covalent geometry : angle 0.48633 / 0.26 (25620) hydrogen bonds : bond 0.03879 / 2.57 ( 957) hydrogen bonds : angle 3.85194 / 2.78 ( 2721) Misc. bond : bond 0.00022 / 0.01 ( 2) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5752.94 seconds wall clock time: 98 minutes 57.57 seconds (5937.57 seconds total)