Starting phenix.real_space_refine on Sat Jul 4 05:34:57 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7k0o_22605/07_2026/7k0o_22605.cif Found real_map, /net/cci-nas-00/data/ceres_data/7k0o_22605/07_2026/7k0o_22605.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7k0o_22605/07_2026/7k0o_22605.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7k0o_22605/07_2026/7k0o_22605.map" restraint_files = "/net/cci-nas-00/data/ceres_data/7k0o_22605/07_2026/7k0o_22605.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7k0o_22605/07_2026/7k0o_22605.cif" model { file = "/net/cci-nas-00/data/ceres_data/7k0o_22605/07_2026/7k0o_22605.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7k0o_22605/07_2026/7k0o_22605.cif" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.101 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 11986 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 70 residue(s): 0.04s 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: 18558 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: "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: "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: "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: 24 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 24 Unusual residues: {'POV': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 80 Unresolved non-hydrogen angles: 98 Unresolved non-hydrogen dihedrals: 58 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'POV:plan-1': 2, 'POV:plan-2': 2, 'POV:plan-3': 2} Unresolved non-hydrogen planarities: 24 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: 24 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 24 Unusual residues: {'POV': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 80 Unresolved non-hydrogen angles: 98 Unresolved non-hydrogen dihedrals: 58 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'POV:plan-1': 2, 'POV:plan-2': 2, 'POV:plan-3': 2} Unresolved non-hydrogen planarities: 24 Chain: "H" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'POV': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 117 Unresolved non-hydrogen angles: 144 Unresolved non-hydrogen dihedrals: 84 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'POV:plan-2': 3, 'POV:plan-3': 3, 'POV:plan-1': 2} Unresolved non-hydrogen planarities: 31 Chain: "F" Number of atoms: 45 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 45 Unusual residues: {'PLP': 1, 'POV': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 23 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen dihedrals: 21 Planarities with less than four sites: {'POV:plan-1': 1} Unresolved non-hydrogen planarities: 2 Time building chain proxies: 4.27, per 1000 atoms: 0.23 Number of scatterers: 18558 At special positions: 0 Unit cell: (149.745, 135.675, 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 11986 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: 1.95 Conformation dependent library (CDL) restraints added in 916.5 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: 96 helices and 14 sheets defined 54.8% alpha, 8.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.46 Creating SS restraints... Processing helix chain 'A' and resid 10 through 20 removed outlier: 3.520A pdb=" N ALA A 20 " --> pdb=" O ALA A 16 " (cutoff:3.500A) Processing helix chain 'A' and resid 21 through 40 removed outlier: 3.713A pdb=" N LEU A 25 " --> pdb=" O PRO A 21 " (cutoff:3.500A) Processing helix chain 'A' and resid 53 through 64 removed outlier: 3.693A pdb=" N TRP A 64 " --> pdb=" O LEU A 60 " (cutoff:3.500A) Processing helix chain 'A' and resid 77 through 81 Processing helix chain 'A' and resid 114 through 129 Processing helix chain 'A' and resid 142 through 156 removed outlier: 3.666A pdb=" N LEU A 146 " --> pdb=" O PHE A 142 " (cutoff:3.500A) Processing helix chain 'A' and resid 166 through 179 removed outlier: 4.191A 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: 3.749A pdb=" N LEU A 217 " --> pdb=" O ASP A 213 " (cutoff:3.500A) removed outlier: 3.517A 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: 3.535A pdb=" N HIS A 292 " --> pdb=" O GLY A 288 " (cutoff:3.500A) Processing helix chain 'A' and resid 321 through 332 removed outlier: 4.678A pdb=" N HIS A 327 " --> pdb=" O PHE A 323 " (cutoff:3.500A) removed outlier: 4.288A pdb=" N GLN A 328 " --> pdb=" O VAL A 324 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N ARG A 329 " --> pdb=" O ILE A 325 " (cutoff:3.500A) removed outlier: 4.472A 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 Processing helix chain 'A' and resid 360 through 378 removed outlier: 4.298A pdb=" N ALA A 364 " --> pdb=" O PRO A 360 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N GLN A 378 " --> pdb=" O HIS A 374 " (cutoff:3.500A) Processing helix chain 'A' and resid 404 through 422 removed outlier: 3.557A pdb=" N ASP A 408 " --> pdb=" O SER A 404 " (cutoff:3.500A) Processing helix chain 'A' and resid 453 through 473 Processing helix chain 'B' and resid 67 through 94 Processing helix chain 'B' and resid 105 through 109 Processing helix chain 'B' and resid 116 through 119 Processing helix chain 'B' and resid 120 through 126 Processing helix chain 'B' and resid 130 through 134 Processing helix chain 'B' and resid 186 through 200 Processing helix chain 'B' and resid 213 through 228 removed outlier: 3.742A pdb=" N GLU B 217 " --> pdb=" O LEU B 213 " (cutoff:3.500A) Processing helix chain 'B' and resid 237 through 250 removed outlier: 3.708A pdb=" N ASN B 242 " --> pdb=" O GLY B 238 " (cutoff:3.500A) Proline residue: B 247 - end of helix Processing helix chain 'B' and resid 263 through 273 Processing helix chain 'B' and resid 284 through 299 Processing helix chain 'B' and resid 326 through 338 Processing helix chain 'B' and resid 358 through 364 Processing helix chain 'B' and resid 366 through 370 Processing helix chain 'B' and resid 391 through 402 Processing helix chain 'B' and resid 402 through 407 Processing helix chain 'B' and resid 412 through 428 Processing helix chain 'B' and resid 433 through 455 removed outlier: 3.887A pdb=" N VAL B 439 " --> pdb=" O GLY B 435 " (cutoff:3.500A) Processing helix chain 'B' and resid 475 through 489 removed outlier: 4.057A pdb=" N GLY B 480 " --> pdb=" O PRO B 476 " (cutoff:3.500A) Processing helix chain 'B' and resid 517 through 536 Processing helix chain 'C' and resid 9 through 24 Processing helix chain 'C' and resid 30 through 55 Processing helix chain 'C' and resid 58 through 69 Processing helix chain 'D' and resid 11 through 19 removed outlier: 4.704A pdb=" N MET D 17 " --> pdb=" O THR D 14 " (cutoff:3.500A) removed outlier: 3.750A 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 removed outlier: 3.567A pdb=" N GLY D 149 " --> pdb=" O ARG D 146 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ILE D 150 " --> pdb=" O ILE D 147 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 146 through 150' Processing helix chain 'E' and resid 11 through 20 removed outlier: 3.520A pdb=" N ALA E 20 " --> pdb=" O ALA E 16 " (cutoff:3.500A) Processing helix chain 'E' and resid 21 through 40 removed outlier: 3.713A pdb=" N LEU E 25 " --> pdb=" O PRO E 21 " (cutoff:3.500A) Processing helix chain 'E' and resid 53 through 64 removed outlier: 3.694A pdb=" N TRP E 64 " --> pdb=" O LEU E 60 " (cutoff:3.500A) Processing helix chain 'E' and resid 77 through 81 Processing helix chain 'E' and resid 114 through 129 Processing helix chain 'E' and resid 142 through 156 removed outlier: 3.667A pdb=" N LEU E 146 " --> pdb=" O PHE E 142 " (cutoff:3.500A) Processing helix chain 'E' and resid 166 through 179 removed outlier: 4.191A 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: 3.749A pdb=" N LEU E 217 " --> pdb=" O ASP E 213 " (cutoff:3.500A) removed outlier: 3.517A 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: 3.535A pdb=" N HIS E 292 " --> pdb=" O GLY E 288 " (cutoff:3.500A) Processing helix chain 'E' and resid 321 through 332 removed outlier: 4.679A pdb=" N HIS E 327 " --> pdb=" O PHE E 323 " (cutoff:3.500A) removed outlier: 4.288A pdb=" N GLN E 328 " --> pdb=" O VAL E 324 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N ARG E 329 " --> pdb=" O ILE E 325 " (cutoff:3.500A) removed outlier: 4.472A 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 Processing helix chain 'E' and resid 360 through 378 removed outlier: 4.298A pdb=" N ALA E 364 " --> pdb=" O PRO E 360 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N GLN E 378 " --> pdb=" O HIS E 374 " (cutoff:3.500A) Processing helix chain 'E' and resid 404 through 422 removed outlier: 3.557A pdb=" N ASP E 408 " --> pdb=" O SER E 404 " (cutoff:3.500A) Processing helix chain 'E' and resid 453 through 473 Processing helix chain 'G' and resid 9 through 24 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: 4.704A pdb=" N MET H 17 " --> pdb=" O THR H 14 " (cutoff:3.500A) removed outlier: 3.750A 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 removed outlier: 3.567A pdb=" N GLY H 149 " --> pdb=" O ARG H 146 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ILE H 150 " --> pdb=" O ILE H 147 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 146 through 150' 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: 3.741A pdb=" N GLU F 217 " --> pdb=" O LEU F 213 " (cutoff:3.500A) Processing helix chain 'F' and resid 237 through 250 removed outlier: 3.708A pdb=" N ASN F 242 " --> pdb=" O GLY F 238 " (cutoff:3.500A) Proline residue: F 247 - end of helix Processing helix chain 'F' and resid 263 through 273 Processing helix chain 'F' and resid 284 through 299 Processing helix chain 'F' and resid 326 through 338 Processing helix chain 'F' and resid 358 through 364 Processing helix chain 'F' and resid 366 through 370 Processing helix chain 'F' and resid 391 through 402 Processing helix chain 'F' and resid 402 through 407 Processing helix chain 'F' and resid 412 through 428 Processing helix chain 'F' and resid 433 through 455 removed outlier: 3.887A pdb=" N VAL F 439 " --> pdb=" O GLY F 435 " (cutoff:3.500A) Processing helix chain 'F' and resid 475 through 489 removed outlier: 4.058A 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 101 through 102 removed outlier: 6.328A pdb=" N ILE A 101 " --> pdb=" O ALA A 425 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'A' and resid 160 through 164 removed outlier: 7.057A pdb=" N ILE A 271 " --> pdb=" O LEU A 302 " (cutoff:3.500A) removed outlier: 8.400A pdb=" N SER A 304 " --> pdb=" O ILE A 271 " (cutoff:3.500A) removed outlier: 6.592A pdb=" N LEU A 273 " --> pdb=" O SER A 304 " (cutoff:3.500A) removed outlier: 8.818A pdb=" N ASN A 306 " --> pdb=" O LEU A 273 " (cutoff:3.500A) removed outlier: 6.833A pdb=" N ARG A 240 " --> pdb=" O ARG A 270 " (cutoff:3.500A) removed outlier: 7.787A pdb=" N PHE A 272 " --> pdb=" O ARG A 240 " (cutoff:3.500A) removed outlier: 6.129A pdb=" N ILE A 242 " --> pdb=" O PHE A 272 " (cutoff:3.500A) removed outlier: 7.644A pdb=" N GLU A 274 " --> pdb=" O ILE A 242 " (cutoff:3.500A) removed outlier: 6.986A pdb=" N VAL A 244 " --> pdb=" O GLU A 274 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N ASP A 188 " --> pdb=" O VAL A 243 " (cutoff:3.500A) removed outlier: 8.118A pdb=" N GLU A 245 " --> pdb=" O ASP A 188 " (cutoff:3.500A) removed outlier: 6.338A pdb=" N VAL A 185 " --> pdb=" O LYS A 207 " (cutoff:3.500A) removed outlier: 7.554A pdb=" N PHE A 209 " --> pdb=" O VAL A 185 " (cutoff:3.500A) removed outlier: 6.906A pdb=" N VAL A 187 " --> pdb=" O PHE A 209 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 383 through 386 removed outlier: 4.208A pdb=" N THR A 427 " --> pdb=" O ARG A 445 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 145 through 152 removed outlier: 6.986A pdb=" N VAL B 146 " --> pdb=" O ILE B 167 " (cutoff:3.500A) removed outlier: 7.042A pdb=" N ILE B 167 " --> pdb=" O VAL B 146 " (cutoff:3.500A) removed outlier: 7.812A pdb=" N ILE B 148 " --> pdb=" O ASN B 165 " (cutoff:3.500A) removed outlier: 7.925A pdb=" N ASN B 165 " --> pdb=" O ILE B 148 " (cutoff:3.500A) removed outlier: 4.914A pdb=" N GLU B 150 " --> pdb=" O THR B 163 " (cutoff:3.500A) removed outlier: 7.876A pdb=" N GLY B 492 " --> pdb=" O GLY B 169 " (cutoff:3.500A) removed outlier: 6.663A 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: 6.646A pdb=" N ILE B 310 " --> pdb=" O TYR B 340 " (cutoff:3.500A) removed outlier: 7.636A pdb=" N TYR B 342 " --> pdb=" O ILE B 310 " (cutoff:3.500A) removed outlier: 6.151A pdb=" N ILE B 312 " --> pdb=" O TYR B 342 " (cutoff:3.500A) removed outlier: 7.330A pdb=" N ASP B 344 " --> pdb=" O ILE B 312 " (cutoff:3.500A) removed outlier: 6.838A pdb=" N VAL B 314 " --> pdb=" O ASP B 344 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 468 through 472 removed outlier: 3.820A 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 101 through 102 removed outlier: 6.329A pdb=" N ILE E 101 " --> pdb=" O ALA E 425 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'E' and resid 160 through 164 removed outlier: 7.058A pdb=" N ILE E 271 " --> pdb=" O LEU E 302 " (cutoff:3.500A) removed outlier: 8.400A pdb=" N SER E 304 " --> pdb=" O ILE E 271 " (cutoff:3.500A) removed outlier: 6.592A pdb=" N LEU E 273 " --> pdb=" O SER E 304 " (cutoff:3.500A) removed outlier: 8.819A pdb=" N ASN E 306 " --> pdb=" O LEU E 273 " (cutoff:3.500A) removed outlier: 6.833A pdb=" N ARG E 240 " --> pdb=" O ARG E 270 " (cutoff:3.500A) removed outlier: 7.787A pdb=" N PHE E 272 " --> pdb=" O ARG E 240 " (cutoff:3.500A) removed outlier: 6.129A pdb=" N ILE E 242 " --> pdb=" O PHE E 272 " (cutoff:3.500A) removed outlier: 7.643A pdb=" N GLU E 274 " --> pdb=" O ILE E 242 " (cutoff:3.500A) removed outlier: 6.986A pdb=" N VAL E 244 " --> pdb=" O GLU E 274 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N ASP E 188 " --> pdb=" O VAL E 243 " (cutoff:3.500A) removed outlier: 8.118A pdb=" N GLU E 245 " --> pdb=" O ASP E 188 " (cutoff:3.500A) removed outlier: 6.337A pdb=" N VAL E 185 " --> pdb=" O LYS E 207 " (cutoff:3.500A) removed outlier: 7.555A pdb=" N PHE E 209 " --> pdb=" O VAL E 185 " (cutoff:3.500A) removed outlier: 6.906A pdb=" N VAL E 187 " --> pdb=" O PHE E 209 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'E' and resid 383 through 386 removed outlier: 4.207A pdb=" N THR E 427 " --> pdb=" O ARG E 445 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'F' and resid 145 through 152 removed outlier: 6.987A pdb=" N VAL F 146 " --> pdb=" O ILE F 167 " (cutoff:3.500A) removed outlier: 7.042A pdb=" N ILE F 167 " --> pdb=" O VAL F 146 " (cutoff:3.500A) removed outlier: 7.812A pdb=" N ILE F 148 " --> pdb=" O ASN F 165 " (cutoff:3.500A) removed outlier: 7.925A pdb=" N ASN F 165 " --> pdb=" O ILE F 148 " (cutoff:3.500A) removed outlier: 4.914A pdb=" N GLU F 150 " --> pdb=" O THR F 163 " (cutoff:3.500A) removed outlier: 7.877A pdb=" N GLY F 492 " --> pdb=" O GLY F 169 " (cutoff:3.500A) removed outlier: 6.664A 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: 6.646A pdb=" N ILE F 310 " --> pdb=" O TYR F 340 " (cutoff:3.500A) removed outlier: 7.635A pdb=" N TYR F 342 " --> pdb=" O ILE F 310 " (cutoff:3.500A) removed outlier: 6.151A pdb=" N ILE F 312 " --> pdb=" O TYR F 342 " (cutoff:3.500A) removed outlier: 7.328A pdb=" N ASP F 344 " --> pdb=" O ILE F 312 " (cutoff:3.500A) removed outlier: 6.838A pdb=" N VAL F 314 " --> pdb=" O ASP F 344 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'F' and resid 468 through 472 removed outlier: 3.820A pdb=" N VAL F 494 " --> pdb=" O ARG F 509 " (cutoff:3.500A) 953 hydrogen bonds defined for protein. 2727 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: 3.18 Time building geometry restraints manager: 2.50 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 3566 1.33 - 1.45: 4454 1.45 - 1.57: 10754 1.57 - 1.69: 4 1.69 - 1.81: 168 Bond restraints: 18946 Sorted by residual: bond pdb=" C29 POV H 901 " pdb="C210 POV H 901 " ideal model delta sigma weight residual 1.333 1.523 -0.190 2.00e-02 2.50e+03 9.06e+01 bond pdb=" C29 POV D 901 " pdb="C210 POV D 901 " ideal model delta sigma weight residual 1.333 1.523 -0.190 2.00e-02 2.50e+03 8.99e+01 bond pdb=" O12 POV F 601 " pdb=" P POV F 601 " ideal model delta sigma weight residual 1.657 1.742 -0.085 2.00e-02 2.50e+03 1.79e+01 bond pdb=" O12 POV B 602 " pdb=" P POV B 602 " ideal model delta sigma weight residual 1.657 1.742 -0.085 2.00e-02 2.50e+03 1.79e+01 bond pdb=" CA PRO B 413 " pdb=" C PRO B 413 " ideal model delta sigma weight residual 1.517 1.547 -0.029 9.30e-03 1.16e+04 1.00e+01 ... (remaining 18941 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.54: 25475 3.54 - 7.09: 119 7.09 - 10.63: 6 10.63 - 14.17: 0 14.17 - 17.72: 4 Bond angle restraints: 25604 Sorted by residual: angle pdb=" C28 POV D 901 " pdb=" C29 POV D 901 " pdb="C210 POV D 901 " ideal model delta sigma weight residual 127.79 110.07 17.72 3.00e+00 1.11e-01 3.49e+01 angle pdb=" C28 POV H 901 " pdb=" C29 POV H 901 " pdb="C210 POV H 901 " ideal model delta sigma weight residual 127.79 110.08 17.71 3.00e+00 1.11e-01 3.49e+01 angle pdb=" C29 POV H 901 " pdb="C210 POV H 901 " pdb="C211 POV H 901 " ideal model delta sigma weight residual 127.67 110.03 17.64 3.00e+00 1.11e-01 3.46e+01 angle pdb=" C29 POV D 901 " pdb="C210 POV D 901 " pdb="C211 POV D 901 " ideal model delta sigma weight residual 127.67 110.05 17.62 3.00e+00 1.11e-01 3.45e+01 angle pdb=" CA PRO F 413 " pdb=" C PRO F 413 " pdb=" N PRO F 414 " ideal model delta sigma weight residual 117.93 124.26 -6.33 1.20e+00 6.94e-01 2.78e+01 ... (remaining 25599 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.80: 10442 17.80 - 35.60: 742 35.60 - 53.40: 146 53.40 - 71.20: 12 71.20 - 88.99: 12 Dihedral angle restraints: 11354 sinusoidal: 4568 harmonic: 6786 Sorted by residual: dihedral pdb=" CA LYS D 79 " pdb=" C LYS D 79 " pdb=" N ALA D 80 " pdb=" CA ALA D 80 " ideal model delta harmonic sigma weight residual -180.00 -160.38 -19.62 0 5.00e+00 4.00e-02 1.54e+01 dihedral pdb=" CA LYS H 79 " pdb=" C LYS H 79 " pdb=" N ALA H 80 " pdb=" CA ALA H 80 " ideal model delta harmonic sigma weight residual -180.00 -160.39 -19.61 0 5.00e+00 4.00e-02 1.54e+01 dihedral pdb=" CA VAL D 93 " pdb=" C VAL D 93 " pdb=" N GLN D 94 " pdb=" CA GLN D 94 " ideal model delta harmonic sigma weight residual 180.00 -161.18 -18.82 0 5.00e+00 4.00e-02 1.42e+01 ... (remaining 11351 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.038: 1882 0.038 - 0.076: 683 0.076 - 0.114: 227 0.114 - 0.152: 56 0.152 - 0.190: 6 Chirality restraints: 2854 Sorted by residual: 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 2.34 0.19 2.00e-01 2.50e+01 9.01e-01 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 2.34 0.18 2.00e-01 2.50e+01 8.53e-01 chirality pdb=" CA PRO B 413 " pdb=" N PRO B 413 " pdb=" C PRO B 413 " pdb=" CB PRO B 413 " both_signs ideal model delta sigma weight residual False 2.72 2.55 0.17 2.00e-01 2.50e+01 7.25e-01 ... (remaining 2851 not shown) Planarity restraints: 3244 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL F 469 " -0.033 5.00e-02 4.00e+02 5.01e-02 4.02e+00 pdb=" N PRO F 470 " 0.087 5.00e-02 4.00e+02 pdb=" CA PRO F 470 " -0.026 5.00e-02 4.00e+02 pdb=" CD PRO F 470 " -0.028 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL B 469 " 0.033 5.00e-02 4.00e+02 4.98e-02 3.96e+00 pdb=" N PRO B 470 " -0.086 5.00e-02 4.00e+02 pdb=" CA PRO B 470 " 0.026 5.00e-02 4.00e+02 pdb=" CD PRO B 470 " 0.028 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR B 501 " -0.033 5.00e-02 4.00e+02 4.91e-02 3.86e+00 pdb=" N PRO B 502 " 0.085 5.00e-02 4.00e+02 pdb=" CA PRO B 502 " -0.025 5.00e-02 4.00e+02 pdb=" CD PRO B 502 " -0.027 5.00e-02 4.00e+02 ... (remaining 3241 not shown) Histogram of nonbonded interaction distances: 2.16 - 2.71: 516 2.71 - 3.26: 18077 3.26 - 3.80: 28687 3.80 - 4.35: 37141 4.35 - 4.90: 65235 Nonbonded interactions: 149656 Sorted by model distance: nonbonded pdb=" O VAL D 10 " pdb=" OG1 THR D 74 " model vdw 2.161 3.040 nonbonded pdb=" O VAL H 10 " pdb=" OG1 THR H 74 " model vdw 2.161 3.040 nonbonded pdb=" OH TYR B 448 " pdb=" OD1 ASP B 522 " model vdw 2.234 3.040 nonbonded pdb=" OH TYR F 448 " pdb=" OD1 ASP F 522 " model vdw 2.234 3.040 nonbonded pdb=" OH TYR E 178 " pdb=" O VAL E 324 " model vdw 2.266 3.040 ... (remaining 149651 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain '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' and resid 1 through 902) } 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: 0.010 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.810 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.250 Check model and map are aligned: 0.060 Set scattering table: 0.050 Process input model: 18.590 Find NCS groups from input model: 0.360 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:1.510 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.690 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8189 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 : 0.006 0.190 18948 Z= 0.261 Angle : 0.745 17.715 25604 Z= 0.411 Chirality : 0.045 0.190 2854 Planarity : 0.005 0.050 3244 Dihedral : 12.896 88.995 7010 Min Nonbonded Distance : 2.161 Molprobity Statistics. All-atom Clashscore : 5.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Rotamer: Outliers : 0.21 % Allowed : 0.67 % Favored : 99.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.95 (0.17), residues: 2326 helix: 1.76 (0.15), residues: 1092 sheet: -0.25 (0.35), residues: 226 loop : -0.38 (0.19), residues: 1008 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG A 459 TYR 0.029 0.002 TYR E 166 PHE 0.022 0.002 PHE E 168 TRP 0.014 0.001 TRP G 32 HIS 0.007 0.001 HIS E 24 Details of bonding type rmsd/Z covalent geometry : bond 0.00560 / 0.26 (18946) covalent geometry : angle 0.74500 / 0.41 (25604) hydrogen bonds : bond 0.13470 / 9.36 ( 953) hydrogen bonds : angle 5.86448 / 4.43 ( 2727) Misc. bond : bond 0.02896 / 1.45 ( 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 235 residues out of total 2008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 231 time to evaluate : 0.702 Fit side-chains REVERT: A 214 MET cc_start: 0.6571 (mmt) cc_final: 0.6189 (mmt) REVERT: B 285 MET cc_start: 0.8032 (mmt) cc_final: 0.7384 (mmt) REVERT: E 214 MET cc_start: 0.6508 (mmt) cc_final: 0.6166 (mmt) REVERT: F 285 MET cc_start: 0.7993 (mmt) cc_final: 0.7333 (mmt) outliers start: 4 outliers final: 0 residues processed: 233 average time/residue: 0.1541 time to fit residues: 53.4692 Evaluate side-chains 193 residues out of total 2008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 193 time to evaluate : 0.826 ------------------------------------------------------------------------------- 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: 0.9990 chunk 98 optimal weight: 2.9990 chunk 194 optimal weight: 3.9990 chunk 227 optimal weight: 0.0570 chunk 107 optimal weight: 0.9990 chunk 10 optimal weight: 3.9990 chunk 66 optimal weight: 3.9990 chunk 130 optimal weight: 2.9990 chunk 124 optimal weight: 5.9990 chunk 103 optimal weight: 0.7980 chunk 200 optimal weight: 0.8980 overall best weight: 0.7502 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 229 GLN E 229 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3624 r_free = 0.3624 target = 0.140795 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3293 r_free = 0.3293 target = 0.112438 restraints weight = 22490.985| |-----------------------------------------------------------------------------| r_work (start): 0.3258 rms_B_bonded: 1.75 r_work: 0.3121 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.2985 rms_B_bonded: 3.99 restraints_weight: 0.2500 r_work (final): 0.2985 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8293 moved from start: 0.0891 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 18948 Z= 0.129 Angle : 0.516 7.192 25604 Z= 0.277 Chirality : 0.042 0.179 2854 Planarity : 0.005 0.047 3244 Dihedral : 6.236 74.006 2698 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 5.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.76 % Favored : 98.24 % Rotamer: Outliers : 0.62 % Allowed : 6.36 % Favored : 93.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.29 (0.17), residues: 2326 helix: 1.98 (0.15), residues: 1134 sheet: -0.09 (0.35), residues: 226 loop : -0.21 (0.19), residues: 966 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 459 TYR 0.014 0.001 TYR H 26 PHE 0.016 0.001 PHE E 168 TRP 0.013 0.001 TRP G 32 HIS 0.006 0.001 HIS H 143 Details of bonding type rmsd/Z covalent geometry : bond 0.00290 / 0.13 (18946) covalent geometry : angle 0.51617 / 0.28 (25604) hydrogen bonds : bond 0.04586 / 3.12 ( 953) hydrogen bonds : angle 4.61586 / 3.46 ( 2727) Misc. bond : bond 0.00105 / 0.05 ( 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 218 residues out of total 2008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 206 time to evaluate : 0.878 Fit side-chains REVERT: A 55 LYS cc_start: 0.8802 (mtpp) cc_final: 0.8369 (pttp) REVERT: A 150 ASP cc_start: 0.7336 (m-30) cc_final: 0.7117 (m-30) REVERT: B 285 MET cc_start: 0.8197 (mmt) cc_final: 0.7662 (mmt) REVERT: B 423 MET cc_start: 0.8505 (ttm) cc_final: 0.8247 (mtt) REVERT: D 79 LYS cc_start: 0.8395 (mmmm) cc_final: 0.7880 (tppt) REVERT: D 89 MET cc_start: 0.8681 (ttm) cc_final: 0.8459 (ttm) REVERT: E 55 LYS cc_start: 0.8793 (mtpp) cc_final: 0.8352 (pttp) REVERT: E 150 ASP cc_start: 0.7337 (m-30) cc_final: 0.7129 (m-30) REVERT: H 79 LYS cc_start: 0.8379 (mmmm) cc_final: 0.7817 (tppt) REVERT: H 89 MET cc_start: 0.8681 (ttm) cc_final: 0.8441 (ttm) REVERT: F 285 MET cc_start: 0.8159 (mmt) cc_final: 0.7612 (mmt) REVERT: F 423 MET cc_start: 0.8501 (ttm) cc_final: 0.8256 (mtt) outliers start: 12 outliers final: 8 residues processed: 215 average time/residue: 0.1612 time to fit residues: 51.8758 Evaluate side-chains 207 residues out of total 2008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 199 time to evaluate : 0.712 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 94 VAL Chi-restraints excluded: chain B residue 140 SER Chi-restraints excluded: chain B residue 296 ILE Chi-restraints excluded: chain D residue 96 THR Chi-restraints excluded: chain E residue 94 VAL Chi-restraints excluded: chain H residue 96 THR Chi-restraints excluded: chain F residue 140 SER Chi-restraints excluded: chain F residue 296 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 88 optimal weight: 0.9980 chunk 22 optimal weight: 0.8980 chunk 74 optimal weight: 0.7980 chunk 27 optimal weight: 3.9990 chunk 216 optimal weight: 3.9990 chunk 159 optimal weight: 0.9980 chunk 26 optimal weight: 2.9990 chunk 39 optimal weight: 6.9990 chunk 212 optimal weight: 2.9990 chunk 135 optimal weight: 2.9990 chunk 155 optimal weight: 5.9990 overall best weight: 1.3382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 229 GLN B 245 ASN E 229 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3577 r_free = 0.3577 target = 0.135866 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3183 r_free = 0.3183 target = 0.103692 restraints weight = 22932.655| |-----------------------------------------------------------------------------| r_work (start): 0.3184 rms_B_bonded: 2.16 r_work: 0.3056 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.2910 rms_B_bonded: 4.44 restraints_weight: 0.2500 r_work (final): 0.2910 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7770 moved from start: 0.1084 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 18948 Z= 0.176 Angle : 0.539 6.271 25604 Z= 0.288 Chirality : 0.044 0.176 2854 Planarity : 0.005 0.050 3244 Dihedral : 6.097 72.359 2698 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 4.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.89 % Favored : 98.11 % Rotamer: Outliers : 1.09 % Allowed : 8.12 % Favored : 90.80 % 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: 1.13 (0.17), residues: 2326 helix: 1.92 (0.15), residues: 1124 sheet: -0.15 (0.35), residues: 224 loop : -0.38 (0.19), residues: 978 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 136 TYR 0.015 0.002 TYR D 26 PHE 0.016 0.002 PHE E 209 TRP 0.014 0.001 TRP C 32 HIS 0.005 0.001 HIS B 403 Details of bonding type rmsd/Z covalent geometry : bond 0.00428 / 0.18 (18946) covalent geometry : angle 0.53853 / 0.29 (25604) hydrogen bonds : bond 0.04942 / 3.34 ( 953) hydrogen bonds : angle 4.51607 / 3.37 ( 2727) Misc. bond : bond 0.00088 / 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 223 residues out of total 2008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 202 time to evaluate : 0.729 Fit side-chains revert: symmetry clash REVERT: A 150 ASP cc_start: 0.6973 (m-30) cc_final: 0.6728 (m-30) REVERT: B 281 LYS cc_start: 0.8501 (mtpt) cc_final: 0.7685 (mptt) REVERT: H 113 THR cc_start: 0.7808 (t) cc_final: 0.7521 (p) REVERT: F 281 LYS cc_start: 0.8501 (mtpt) cc_final: 0.7683 (mptt) REVERT: F 285 MET cc_start: 0.7796 (mmt) cc_final: 0.7073 (mmt) outliers start: 21 outliers final: 13 residues processed: 215 average time/residue: 0.1465 time to fit residues: 47.7164 Evaluate side-chains 202 residues out of total 2008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 189 time to evaluate : 0.688 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 GLU Chi-restraints excluded: chain B residue 103 THR Chi-restraints excluded: chain B residue 117 ASP Chi-restraints excluded: chain B residue 140 SER Chi-restraints excluded: chain B residue 166 ILE Chi-restraints excluded: chain B residue 296 ILE Chi-restraints excluded: chain D residue 50 THR Chi-restraints excluded: chain D residue 96 THR Chi-restraints excluded: chain H residue 50 THR Chi-restraints excluded: chain H residue 96 THR Chi-restraints excluded: chain F residue 103 THR Chi-restraints excluded: chain F residue 140 SER Chi-restraints excluded: chain F residue 296 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 192 optimal weight: 0.0030 chunk 96 optimal weight: 1.9990 chunk 43 optimal weight: 3.9990 chunk 115 optimal weight: 9.9990 chunk 200 optimal weight: 1.9990 chunk 125 optimal weight: 3.9990 chunk 35 optimal weight: 2.9990 chunk 100 optimal weight: 0.0070 chunk 193 optimal weight: 0.8980 chunk 194 optimal weight: 4.9990 chunk 126 optimal weight: 0.6980 overall best weight: 0.7210 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 229 GLN A 428 GLN E 229 GLN E 428 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3620 r_free = 0.3620 target = 0.140523 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3292 r_free = 0.3292 target = 0.112487 restraints weight = 22749.570| |-----------------------------------------------------------------------------| r_work (start): 0.3269 rms_B_bonded: 1.72 r_work: 0.3133 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.2997 rms_B_bonded: 3.97 restraints_weight: 0.2500 r_work (final): 0.2997 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8295 moved from start: 0.1276 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 18948 Z= 0.118 Angle : 0.484 7.044 25604 Z= 0.260 Chirality : 0.041 0.167 2854 Planarity : 0.004 0.048 3244 Dihedral : 5.837 73.472 2698 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 4.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.46 % Favored : 98.54 % Rotamer: Outliers : 1.34 % Allowed : 9.46 % 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: 1.38 (0.17), residues: 2326 helix: 2.08 (0.15), residues: 1134 sheet: 0.15 (0.32), residues: 250 loop : -0.27 (0.19), residues: 942 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 459 TYR 0.013 0.001 TYR H 26 PHE 0.015 0.001 PHE D 115 TRP 0.014 0.001 TRP C 32 HIS 0.003 0.001 HIS B 403 Details of bonding type rmsd/Z covalent geometry : bond 0.00268 / 0.12 (18946) covalent geometry : angle 0.48386 / 0.26 (25604) hydrogen bonds : bond 0.04077 / 2.77 ( 953) hydrogen bonds : angle 4.33603 / 3.24 ( 2727) Misc. bond : bond 0.00070 / 0.04 ( 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 228 residues out of total 2008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 202 time to evaluate : 0.762 Fit side-chains revert: symmetry clash REVERT: A 407 GLN cc_start: 0.7752 (tp40) cc_final: 0.7284 (tt0) REVERT: B 285 MET cc_start: 0.8133 (mmt) cc_final: 0.7618 (mmt) REVERT: D 79 LYS cc_start: 0.8851 (OUTLIER) cc_final: 0.8355 (tppt) REVERT: D 113 THR cc_start: 0.8108 (t) cc_final: 0.7787 (p) REVERT: E 407 GLN cc_start: 0.7749 (tp40) cc_final: 0.7262 (tt0) REVERT: H 79 LYS cc_start: 0.8870 (OUTLIER) cc_final: 0.8375 (tppt) REVERT: H 113 THR cc_start: 0.8014 (t) cc_final: 0.7711 (p) outliers start: 26 outliers final: 15 residues processed: 222 average time/residue: 0.1522 time to fit residues: 51.4332 Evaluate side-chains 205 residues out of total 2008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 188 time to evaluate : 0.804 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 LEU Chi-restraints excluded: chain A residue 56 GLU Chi-restraints excluded: chain A residue 94 VAL Chi-restraints excluded: chain A residue 213 ASP Chi-restraints excluded: chain B residue 140 SER Chi-restraints excluded: chain D residue 38 LEU Chi-restraints excluded: chain D residue 50 THR Chi-restraints excluded: chain D residue 79 LYS Chi-restraints excluded: chain D residue 96 THR Chi-restraints excluded: chain E residue 52 LEU Chi-restraints excluded: chain E residue 59 GLU Chi-restraints excluded: chain E residue 94 VAL Chi-restraints excluded: chain H residue 38 LEU Chi-restraints excluded: chain H residue 50 THR Chi-restraints excluded: chain H residue 79 LYS Chi-restraints excluded: chain H residue 96 THR Chi-restraints excluded: chain F residue 140 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 141 optimal weight: 0.6980 chunk 146 optimal weight: 4.9990 chunk 68 optimal weight: 1.9990 chunk 132 optimal weight: 0.5980 chunk 103 optimal weight: 0.8980 chunk 83 optimal weight: 0.0370 chunk 231 optimal weight: 0.3980 chunk 133 optimal weight: 0.6980 chunk 130 optimal weight: 2.9990 chunk 177 optimal weight: 5.9990 chunk 117 optimal weight: 0.9990 overall best weight: 0.4858 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... F 245 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3638 r_free = 0.3638 target = 0.142061 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3281 r_free = 0.3281 target = 0.112466 restraints weight = 22536.052| |-----------------------------------------------------------------------------| r_work (start): 0.3280 rms_B_bonded: 1.85 r_work: 0.3170 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.3034 rms_B_bonded: 3.97 restraints_weight: 0.2500 r_work (final): 0.3034 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8229 moved from start: 0.1445 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 18948 Z= 0.101 Angle : 0.462 8.288 25604 Z= 0.248 Chirality : 0.041 0.163 2854 Planarity : 0.004 0.048 3244 Dihedral : 5.594 72.988 2698 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 4.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.50 % Favored : 98.50 % Rotamer: Outliers : 1.50 % Allowed : 10.50 % Favored : 88.00 % 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: 1.57 (0.17), residues: 2326 helix: 2.22 (0.15), residues: 1134 sheet: 0.33 (0.32), residues: 246 loop : -0.19 (0.20), residues: 946 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 151 TYR 0.011 0.001 TYR D 26 PHE 0.012 0.001 PHE E 168 TRP 0.013 0.001 TRP C 32 HIS 0.003 0.000 HIS F 403 Details of bonding type rmsd/Z covalent geometry : bond 0.00220 / 0.10 (18946) covalent geometry : angle 0.46160 / 0.25 (25604) hydrogen bonds : bond 0.03665 / 2.51 ( 953) hydrogen bonds : angle 4.24270 / 3.16 ( 2727) Misc. bond : bond 0.00058 / 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 229 residues out of total 2008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 200 time to evaluate : 0.745 Fit side-chains REVERT: A 407 GLN cc_start: 0.7609 (tp40) cc_final: 0.7088 (tt0) REVERT: B 126 LEU cc_start: 0.8810 (OUTLIER) cc_final: 0.8580 (tt) REVERT: B 285 MET cc_start: 0.8076 (mmt) cc_final: 0.7648 (mmt) REVERT: D 79 LYS cc_start: 0.8772 (OUTLIER) cc_final: 0.8329 (tttm) REVERT: D 113 THR cc_start: 0.8083 (t) cc_final: 0.7763 (p) REVERT: D 119 TYR cc_start: 0.7324 (m-80) cc_final: 0.6739 (m-80) REVERT: E 407 GLN cc_start: 0.7642 (tp40) cc_final: 0.7106 (tt0) REVERT: H 79 LYS cc_start: 0.8768 (OUTLIER) cc_final: 0.8291 (tttm) REVERT: H 113 THR cc_start: 0.8044 (t) cc_final: 0.7743 (p) REVERT: F 126 LEU cc_start: 0.8805 (OUTLIER) cc_final: 0.8572 (tt) REVERT: F 285 MET cc_start: 0.8080 (mmt) cc_final: 0.7613 (mmt) REVERT: F 486 MET cc_start: 0.8863 (mmm) cc_final: 0.8661 (mmm) outliers start: 29 outliers final: 18 residues processed: 218 average time/residue: 0.1508 time to fit residues: 49.9027 Evaluate side-chains 209 residues out of total 2008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 187 time to evaluate : 0.650 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 LEU Chi-restraints excluded: chain A residue 56 GLU Chi-restraints excluded: chain A residue 94 VAL Chi-restraints excluded: chain A residue 213 ASP Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain B residue 103 THR Chi-restraints excluded: chain B residue 126 LEU Chi-restraints excluded: chain B residue 140 SER Chi-restraints excluded: chain D residue 38 LEU Chi-restraints excluded: chain D residue 50 THR Chi-restraints excluded: chain D residue 79 LYS Chi-restraints excluded: chain D residue 96 THR Chi-restraints excluded: chain E residue 56 GLU Chi-restraints excluded: chain E residue 94 VAL Chi-restraints excluded: chain E residue 390 LEU Chi-restraints excluded: chain H residue 38 LEU Chi-restraints excluded: chain H residue 50 THR Chi-restraints excluded: chain H residue 79 LYS Chi-restraints excluded: chain H residue 96 THR Chi-restraints excluded: chain F residue 103 THR Chi-restraints excluded: chain F residue 126 LEU Chi-restraints excluded: chain F residue 140 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 27 optimal weight: 3.9990 chunk 55 optimal weight: 0.9980 chunk 223 optimal weight: 0.9980 chunk 150 optimal weight: 2.9990 chunk 148 optimal weight: 1.9990 chunk 37 optimal weight: 6.9990 chunk 211 optimal weight: 3.9990 chunk 84 optimal weight: 2.9990 chunk 134 optimal weight: 1.9990 chunk 78 optimal weight: 0.7980 chunk 6 optimal weight: 2.9990 overall best weight: 1.3584 ------------------------------------------------------------------------------- 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 = 0.3577 r_free = 0.3577 target = 0.135920 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3180 r_free = 0.3180 target = 0.103590 restraints weight = 22739.727| |-----------------------------------------------------------------------------| r_work (start): 0.3192 rms_B_bonded: 2.17 r_work: 0.3066 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.2924 rms_B_bonded: 4.45 restraints_weight: 0.2500 r_work (final): 0.2924 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7784 moved from start: 0.1401 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 18948 Z= 0.172 Angle : 0.533 8.264 25604 Z= 0.284 Chirality : 0.043 0.169 2854 Planarity : 0.005 0.050 3244 Dihedral : 5.800 75.702 2698 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 4.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % Rotamer: Outliers : 1.55 % Allowed : 11.79 % Favored : 86.66 % 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: 1.32 (0.17), residues: 2326 helix: 2.06 (0.15), residues: 1126 sheet: 0.16 (0.32), residues: 248 loop : -0.35 (0.19), residues: 952 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 151 TYR 0.014 0.002 TYR A 164 PHE 0.016 0.002 PHE A 168 TRP 0.013 0.001 TRP C 32 HIS 0.005 0.001 HIS B 403 Details of bonding type rmsd/Z covalent geometry : bond 0.00419 / 0.17 (18946) covalent geometry : angle 0.53334 / 0.28 (25604) hydrogen bonds : bond 0.04604 / 3.12 ( 953) hydrogen bonds : angle 4.36760 / 3.24 ( 2727) Misc. bond : bond 0.00094 / 0.05 ( 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 225 residues out of total 2008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 195 time to evaluate : 0.769 Fit side-chains REVERT: A 407 GLN cc_start: 0.7400 (tp40) cc_final: 0.6787 (tt0) REVERT: B 126 LEU cc_start: 0.8569 (OUTLIER) cc_final: 0.8310 (tt) REVERT: B 281 LYS cc_start: 0.8474 (mtpt) cc_final: 0.7733 (mptt) REVERT: B 285 MET cc_start: 0.7767 (mmt) cc_final: 0.7353 (mmt) REVERT: D 79 LYS cc_start: 0.8470 (OUTLIER) cc_final: 0.8188 (tttm) REVERT: E 407 GLN cc_start: 0.7413 (tp40) cc_final: 0.6808 (tt0) REVERT: H 79 LYS cc_start: 0.8536 (OUTLIER) cc_final: 0.8259 (tttm) REVERT: H 113 THR cc_start: 0.7926 (t) cc_final: 0.7622 (p) REVERT: F 126 LEU cc_start: 0.8570 (OUTLIER) cc_final: 0.8308 (tt) REVERT: F 281 LYS cc_start: 0.8470 (mtpt) cc_final: 0.7739 (mptt) REVERT: F 285 MET cc_start: 0.7776 (mmt) cc_final: 0.7323 (mmt) outliers start: 30 outliers final: 19 residues processed: 217 average time/residue: 0.1468 time to fit residues: 48.3758 Evaluate side-chains 214 residues out of total 2008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 191 time to evaluate : 0.725 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 GLU Chi-restraints excluded: chain A residue 94 VAL Chi-restraints excluded: chain A residue 213 ASP Chi-restraints excluded: chain B residue 103 THR Chi-restraints excluded: chain B residue 126 LEU Chi-restraints excluded: chain B residue 140 SER Chi-restraints excluded: chain B residue 166 ILE Chi-restraints excluded: chain D residue 38 LEU Chi-restraints excluded: chain D residue 48 VAL Chi-restraints excluded: chain D residue 50 THR Chi-restraints excluded: chain D residue 79 LYS Chi-restraints excluded: chain D residue 96 THR Chi-restraints excluded: chain E residue 94 VAL Chi-restraints excluded: chain H residue 38 LEU Chi-restraints excluded: chain H residue 48 VAL Chi-restraints excluded: chain H residue 50 THR Chi-restraints excluded: chain H residue 79 LYS Chi-restraints excluded: chain H residue 96 THR Chi-restraints excluded: chain F residue 103 THR Chi-restraints excluded: chain F residue 117 ASP Chi-restraints excluded: chain F residue 126 LEU Chi-restraints excluded: chain F residue 140 SER Chi-restraints excluded: chain F residue 296 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 209 optimal weight: 1.9990 chunk 0 optimal weight: 50.0000 chunk 120 optimal weight: 4.9990 chunk 102 optimal weight: 0.8980 chunk 104 optimal weight: 0.0000 chunk 48 optimal weight: 0.6980 chunk 172 optimal weight: 0.3980 chunk 155 optimal weight: 20.0000 chunk 52 optimal weight: 2.9990 chunk 84 optimal weight: 3.9990 chunk 24 optimal weight: 0.6980 overall best weight: 0.5384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 441 GLN F 441 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3630 r_free = 0.3630 target = 0.141344 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3270 r_free = 0.3270 target = 0.111636 restraints weight = 22733.455| |-----------------------------------------------------------------------------| r_work (start): 0.3243 rms_B_bonded: 1.85 r_work: 0.3134 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.2997 rms_B_bonded: 3.97 restraints_weight: 0.2500 r_work (final): 0.2997 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8218 moved from start: 0.1558 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 18948 Z= 0.105 Angle : 0.466 8.443 25604 Z= 0.251 Chirality : 0.041 0.162 2854 Planarity : 0.004 0.049 3244 Dihedral : 5.521 74.613 2698 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 4.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.55 % Favored : 98.45 % Rotamer: Outliers : 1.60 % Allowed : 12.15 % Favored : 86.25 % 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 (0.17), residues: 2326 helix: 2.20 (0.15), residues: 1138 sheet: 0.25 (0.32), residues: 246 loop : -0.24 (0.20), residues: 942 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 459 TYR 0.011 0.001 TYR H 26 PHE 0.012 0.001 PHE E 209 TRP 0.014 0.001 TRP C 32 HIS 0.003 0.001 HIS F 403 Details of bonding type rmsd/Z covalent geometry : bond 0.00236 / 0.11 (18946) covalent geometry : angle 0.46590 / 0.25 (25604) hydrogen bonds : bond 0.03677 / 2.51 ( 953) hydrogen bonds : angle 4.22433 / 3.14 ( 2727) Misc. bond : bond 0.00061 / 0.03 ( 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 231 residues out of total 2008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 200 time to evaluate : 0.725 Fit side-chains revert: symmetry clash REVERT: A 407 GLN cc_start: 0.7622 (tp40) cc_final: 0.7051 (tt0) REVERT: B 126 LEU cc_start: 0.8802 (OUTLIER) cc_final: 0.8541 (tt) REVERT: B 281 LYS cc_start: 0.8892 (mtpt) cc_final: 0.8181 (mmtt) REVERT: B 285 MET cc_start: 0.8023 (mmt) cc_final: 0.7625 (mmt) REVERT: D 79 LYS cc_start: 0.8747 (OUTLIER) cc_final: 0.8418 (tttm) REVERT: D 113 THR cc_start: 0.8061 (t) cc_final: 0.7753 (p) REVERT: E 407 GLN cc_start: 0.7621 (tp40) cc_final: 0.7047 (tt0) REVERT: H 79 LYS cc_start: 0.8773 (OUTLIER) cc_final: 0.8442 (tttm) REVERT: H 113 THR cc_start: 0.8041 (t) cc_final: 0.7740 (p) REVERT: F 126 LEU cc_start: 0.8800 (OUTLIER) cc_final: 0.8540 (tt) REVERT: F 281 LYS cc_start: 0.8898 (mtpt) cc_final: 0.8188 (mmtt) REVERT: F 285 MET cc_start: 0.8034 (mmt) cc_final: 0.7621 (mmt) REVERT: F 486 MET cc_start: 0.8818 (mmm) cc_final: 0.8612 (mmm) outliers start: 31 outliers final: 20 residues processed: 223 average time/residue: 0.1524 time to fit residues: 50.9074 Evaluate side-chains 212 residues out of total 2008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 188 time to evaluate : 0.606 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 GLU Chi-restraints excluded: chain A residue 94 VAL Chi-restraints excluded: chain A residue 213 ASP Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain B residue 103 THR Chi-restraints excluded: chain B residue 126 LEU Chi-restraints excluded: chain B residue 140 SER Chi-restraints excluded: chain D residue 38 LEU Chi-restraints excluded: chain D residue 48 VAL Chi-restraints excluded: chain D residue 50 THR Chi-restraints excluded: chain D residue 79 LYS Chi-restraints excluded: chain D residue 96 THR Chi-restraints excluded: chain E residue 94 VAL Chi-restraints excluded: chain E residue 277 LEU Chi-restraints excluded: chain E residue 390 LEU Chi-restraints excluded: chain H residue 38 LEU Chi-restraints excluded: chain H residue 48 VAL Chi-restraints excluded: chain H residue 50 THR Chi-restraints excluded: chain H residue 79 LYS Chi-restraints excluded: chain H residue 96 THR Chi-restraints excluded: chain F residue 103 THR Chi-restraints excluded: chain F residue 126 LEU Chi-restraints excluded: chain F residue 140 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 89 optimal weight: 0.7980 chunk 21 optimal weight: 0.7980 chunk 218 optimal weight: 3.9990 chunk 144 optimal weight: 0.4980 chunk 136 optimal weight: 4.9990 chunk 124 optimal weight: 0.0870 chunk 78 optimal weight: 0.8980 chunk 65 optimal weight: 0.7980 chunk 47 optimal weight: 0.5980 chunk 33 optimal weight: 0.9980 chunk 226 optimal weight: 0.7980 overall best weight: 0.5558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 441 GLN F 245 ASN F 441 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3634 r_free = 0.3634 target = 0.141688 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3277 r_free = 0.3277 target = 0.112154 restraints weight = 22496.234| |-----------------------------------------------------------------------------| r_work (start): 0.3250 rms_B_bonded: 1.83 r_work: 0.3141 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.3005 rms_B_bonded: 3.93 restraints_weight: 0.2500 r_work (final): 0.3005 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8216 moved from start: 0.1633 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 18948 Z= 0.105 Angle : 0.463 7.837 25604 Z= 0.248 Chirality : 0.041 0.162 2854 Planarity : 0.004 0.048 3244 Dihedral : 5.414 74.424 2698 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 4.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.59 % Favored : 98.41 % Rotamer: Outliers : 1.71 % Allowed : 11.74 % Favored : 86.56 % 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: 1.49 (0.17), residues: 2326 helix: 2.23 (0.15), residues: 1142 sheet: 0.11 (0.35), residues: 220 loop : -0.30 (0.19), residues: 964 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 459 TYR 0.011 0.001 TYR D 26 PHE 0.020 0.001 PHE H 115 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 0.00236 / 0.11 (18946) covalent geometry : angle 0.46349 / 0.25 (25604) hydrogen bonds : bond 0.03662 / 2.51 ( 953) hydrogen bonds : angle 4.17247 / 3.09 ( 2727) Misc. bond : bond 0.00059 / 0.03 ( 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 227 residues out of total 2008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 194 time to evaluate : 0.733 Fit side-chains REVERT: A 407 GLN cc_start: 0.7638 (tp40) cc_final: 0.7035 (tt0) REVERT: B 126 LEU cc_start: 0.8794 (OUTLIER) cc_final: 0.8565 (tt) REVERT: B 281 LYS cc_start: 0.8891 (mtpt) cc_final: 0.8183 (mmtt) REVERT: B 285 MET cc_start: 0.8024 (mmt) cc_final: 0.7731 (mmt) REVERT: D 79 LYS cc_start: 0.8731 (OUTLIER) cc_final: 0.8322 (tttm) REVERT: D 113 THR cc_start: 0.8052 (t) cc_final: 0.7745 (p) REVERT: E 407 GLN cc_start: 0.7692 (tp40) cc_final: 0.7100 (tt0) REVERT: G 13 MET cc_start: 0.6778 (tpt) cc_final: 0.5746 (mpp) REVERT: H 79 LYS cc_start: 0.8728 (OUTLIER) cc_final: 0.8300 (tttm) REVERT: H 113 THR cc_start: 0.8039 (t) cc_final: 0.7740 (p) REVERT: F 126 LEU cc_start: 0.8792 (OUTLIER) cc_final: 0.8564 (tt) REVERT: F 281 LYS cc_start: 0.8888 (mtpt) cc_final: 0.8181 (mmtt) REVERT: F 285 MET cc_start: 0.8060 (mmt) cc_final: 0.7687 (mmt) outliers start: 33 outliers final: 20 residues processed: 223 average time/residue: 0.1394 time to fit residues: 47.3565 Evaluate side-chains 212 residues out of total 2008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 188 time to evaluate : 0.580 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 GLU Chi-restraints excluded: chain A residue 94 VAL Chi-restraints excluded: chain A residue 213 ASP Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain B residue 103 THR Chi-restraints excluded: chain B residue 126 LEU Chi-restraints excluded: chain B residue 140 SER Chi-restraints excluded: chain D residue 38 LEU Chi-restraints excluded: chain D residue 48 VAL Chi-restraints excluded: chain D residue 50 THR Chi-restraints excluded: chain D residue 79 LYS Chi-restraints excluded: chain D residue 96 THR Chi-restraints excluded: chain E residue 94 VAL Chi-restraints excluded: chain E residue 277 LEU Chi-restraints excluded: chain E residue 390 LEU Chi-restraints excluded: chain H residue 38 LEU Chi-restraints excluded: chain H residue 48 VAL Chi-restraints excluded: chain H residue 50 THR Chi-restraints excluded: chain H residue 79 LYS Chi-restraints excluded: chain H residue 96 THR Chi-restraints excluded: chain F residue 103 THR Chi-restraints excluded: chain F residue 126 LEU Chi-restraints excluded: chain F residue 140 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 0 optimal weight: 50.0000 chunk 72 optimal weight: 0.9980 chunk 102 optimal weight: 0.7980 chunk 100 optimal weight: 0.8980 chunk 168 optimal weight: 0.0000 chunk 64 optimal weight: 0.9990 chunk 191 optimal weight: 2.9990 chunk 213 optimal weight: 0.0570 chunk 224 optimal weight: 2.9990 chunk 114 optimal weight: 3.9990 chunk 26 optimal weight: 2.9990 overall best weight: 0.5502 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 441 GLN F 441 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3639 r_free = 0.3639 target = 0.142144 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.112328 restraints weight = 22589.064| |-----------------------------------------------------------------------------| r_work (start): 0.3253 rms_B_bonded: 1.86 r_work: 0.3143 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.3006 rms_B_bonded: 4.00 restraints_weight: 0.2500 r_work (final): 0.3006 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8203 moved from start: 0.1725 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 18948 Z= 0.105 Angle : 0.476 7.504 25604 Z= 0.253 Chirality : 0.041 0.201 2854 Planarity : 0.004 0.056 3244 Dihedral : 5.365 74.428 2698 Min Nonbonded Distance : 2.409 Molprobity Statistics. All-atom Clashscore : 4.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.55 % Favored : 98.45 % Rotamer: Outliers : 1.50 % Allowed : 12.15 % Favored : 86.35 % 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 (0.17), residues: 2326 helix: 2.27 (0.15), residues: 1142 sheet: 0.14 (0.35), residues: 220 loop : -0.30 (0.19), residues: 964 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 459 TYR 0.011 0.001 TYR D 26 PHE 0.014 0.001 PHE E 168 TRP 0.013 0.001 TRP G 32 HIS 0.003 0.001 HIS E 24 Details of bonding type rmsd/Z covalent geometry : bond 0.00234 / 0.10 (18946) covalent geometry : angle 0.47563 / 0.25 (25604) hydrogen bonds : bond 0.03580 / 2.44 ( 953) hydrogen bonds : angle 4.18205 / 3.09 ( 2727) Misc. bond : bond 0.00057 / 0.03 ( 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 223 residues out of total 2008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 194 time to evaluate : 0.736 Fit side-chains revert: symmetry clash REVERT: A 407 GLN cc_start: 0.7637 (tp40) cc_final: 0.7053 (tt0) REVERT: B 126 LEU cc_start: 0.8786 (OUTLIER) cc_final: 0.8551 (tt) REVERT: B 281 LYS cc_start: 0.8888 (mtpt) cc_final: 0.8179 (mmtt) REVERT: B 285 MET cc_start: 0.7982 (mmt) cc_final: 0.7703 (mmt) REVERT: C 13 MET cc_start: 0.6805 (tpt) cc_final: 0.5752 (mpp) REVERT: D 76 ASP cc_start: 0.8751 (p0) cc_final: 0.8464 (p0) REVERT: D 79 LYS cc_start: 0.8663 (OUTLIER) cc_final: 0.8144 (tttm) REVERT: D 113 THR cc_start: 0.8058 (t) cc_final: 0.7748 (p) REVERT: E 407 GLN cc_start: 0.7636 (tp40) cc_final: 0.7047 (tt0) REVERT: G 13 MET cc_start: 0.6789 (tpt) cc_final: 0.5788 (mpp) REVERT: H 76 ASP cc_start: 0.8744 (p0) cc_final: 0.8482 (p0) REVERT: H 79 LYS cc_start: 0.8664 (OUTLIER) cc_final: 0.8129 (tttm) REVERT: H 113 THR cc_start: 0.8012 (t) cc_final: 0.7711 (p) REVERT: F 126 LEU cc_start: 0.8784 (OUTLIER) cc_final: 0.8547 (tt) REVERT: F 281 LYS cc_start: 0.8881 (mtpt) cc_final: 0.8167 (mmtt) REVERT: F 285 MET cc_start: 0.8055 (mmt) cc_final: 0.7671 (mmt) outliers start: 29 outliers final: 21 residues processed: 217 average time/residue: 0.1484 time to fit residues: 48.6057 Evaluate side-chains 218 residues out of total 2008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 193 time to evaluate : 0.870 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 GLU Chi-restraints excluded: chain A residue 94 VAL Chi-restraints excluded: chain A residue 213 ASP Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain B residue 103 THR Chi-restraints excluded: chain B residue 126 LEU Chi-restraints excluded: chain B residue 140 SER Chi-restraints excluded: chain D residue 38 LEU Chi-restraints excluded: chain D residue 48 VAL Chi-restraints excluded: chain D residue 50 THR Chi-restraints excluded: chain D residue 79 LYS Chi-restraints excluded: chain D residue 96 THR Chi-restraints excluded: chain E residue 63 GLU Chi-restraints excluded: chain E residue 94 VAL Chi-restraints excluded: chain E residue 277 LEU Chi-restraints excluded: chain E residue 390 LEU Chi-restraints excluded: chain H residue 38 LEU Chi-restraints excluded: chain H residue 48 VAL Chi-restraints excluded: chain H residue 50 THR Chi-restraints excluded: chain H residue 79 LYS Chi-restraints excluded: chain H residue 96 THR Chi-restraints excluded: chain F residue 103 THR Chi-restraints excluded: chain F residue 126 LEU Chi-restraints excluded: chain F residue 140 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 188 optimal weight: 0.5980 chunk 122 optimal weight: 0.8980 chunk 87 optimal weight: 0.7980 chunk 159 optimal weight: 3.9990 chunk 114 optimal weight: 0.0980 chunk 31 optimal weight: 0.7980 chunk 81 optimal weight: 3.9990 chunk 100 optimal weight: 0.0470 chunk 171 optimal weight: 0.5980 chunk 92 optimal weight: 4.9990 chunk 12 optimal weight: 1.9990 overall best weight: 0.4278 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... F 245 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3701 r_free = 0.3701 target = 0.147470 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.121474 restraints weight = 22453.614| |-----------------------------------------------------------------------------| r_work (start): 0.3270 rms_B_bonded: 1.64 r_work: 0.3150 rms_B_bonded: 2.16 restraints_weight: 0.5000 r_work: 0.3024 rms_B_bonded: 3.57 restraints_weight: 0.2500 r_work (final): 0.3024 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8343 moved from start: 0.1823 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 18948 Z= 0.096 Angle : 0.457 7.458 25604 Z= 0.244 Chirality : 0.041 0.169 2854 Planarity : 0.004 0.053 3244 Dihedral : 5.239 74.037 2698 Min Nonbonded Distance : 2.421 Molprobity Statistics. All-atom Clashscore : 4.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.50 % Favored : 98.50 % Rotamer: Outliers : 1.40 % Allowed : 12.20 % Favored : 86.40 % 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: 1.63 (0.18), residues: 2326 helix: 2.29 (0.15), residues: 1146 sheet: 0.23 (0.33), residues: 250 loop : -0.19 (0.20), residues: 930 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 459 TYR 0.011 0.001 TYR D 26 PHE 0.020 0.001 PHE D 115 TRP 0.013 0.001 TRP G 32 HIS 0.005 0.001 HIS A 24 Details of bonding type rmsd/Z covalent geometry : bond 0.00211 / 0.10 (18946) covalent geometry : angle 0.45658 / 0.24 (25604) hydrogen bonds : bond 0.03356 / 2.30 ( 953) hydrogen bonds : angle 4.13451 / 3.05 ( 2727) Misc. bond : bond 0.00048 / 0.02 ( 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 232 residues out of total 2008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 205 time to evaluate : 0.493 Fit side-chains revert: symmetry clash REVERT: A 25 LEU cc_start: 0.6891 (mm) cc_final: 0.6616 (mp) REVERT: A 407 GLN cc_start: 0.7679 (tp40) cc_final: 0.7213 (tt0) REVERT: B 126 LEU cc_start: 0.8775 (OUTLIER) cc_final: 0.8540 (tt) REVERT: B 281 LYS cc_start: 0.8978 (mtpt) cc_final: 0.8432 (mmtt) REVERT: C 13 MET cc_start: 0.6865 (tpt) cc_final: 0.5867 (mpp) REVERT: D 76 ASP cc_start: 0.8831 (p0) cc_final: 0.8547 (p0) REVERT: D 79 LYS cc_start: 0.8694 (OUTLIER) cc_final: 0.8173 (tttm) REVERT: D 113 THR cc_start: 0.8028 (t) cc_final: 0.7731 (p) REVERT: E 25 LEU cc_start: 0.6862 (mm) cc_final: 0.6569 (mp) REVERT: E 372 GLN cc_start: 0.6911 (mt0) cc_final: 0.6682 (mt0) REVERT: E 407 GLN cc_start: 0.7682 (tp40) cc_final: 0.7204 (tt0) REVERT: G 13 MET cc_start: 0.6857 (tpt) cc_final: 0.5889 (mpp) REVERT: H 76 ASP cc_start: 0.8831 (p0) cc_final: 0.8540 (p0) REVERT: H 79 LYS cc_start: 0.8696 (OUTLIER) cc_final: 0.8141 (tttm) REVERT: H 113 THR cc_start: 0.8008 (t) cc_final: 0.7721 (p) REVERT: F 126 LEU cc_start: 0.8775 (OUTLIER) cc_final: 0.8541 (tt) REVERT: F 244 MET cc_start: 0.8370 (mtt) cc_final: 0.7840 (mtt) REVERT: F 281 LYS cc_start: 0.8974 (mtpt) cc_final: 0.8424 (mmtt) REVERT: F 285 MET cc_start: 0.8036 (mmt) cc_final: 0.7730 (mmt) outliers start: 27 outliers final: 21 residues processed: 227 average time/residue: 0.1510 time to fit residues: 51.8634 Evaluate side-chains 223 residues out of total 2008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 198 time to evaluate : 0.801 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 GLU Chi-restraints excluded: chain A residue 94 VAL Chi-restraints excluded: chain A residue 213 ASP Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain B residue 103 THR Chi-restraints excluded: chain B residue 126 LEU Chi-restraints excluded: chain B residue 140 SER Chi-restraints excluded: chain D residue 38 LEU Chi-restraints excluded: chain D residue 48 VAL Chi-restraints excluded: chain D residue 50 THR Chi-restraints excluded: chain D residue 79 LYS Chi-restraints excluded: chain D residue 96 THR Chi-restraints excluded: chain E residue 63 GLU Chi-restraints excluded: chain E residue 94 VAL Chi-restraints excluded: chain E residue 277 LEU Chi-restraints excluded: chain E residue 390 LEU Chi-restraints excluded: chain H residue 38 LEU Chi-restraints excluded: chain H residue 48 VAL Chi-restraints excluded: chain H residue 50 THR Chi-restraints excluded: chain H residue 79 LYS Chi-restraints excluded: chain H residue 96 THR Chi-restraints excluded: chain F residue 103 THR Chi-restraints excluded: chain F residue 126 LEU Chi-restraints excluded: chain F residue 140 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 101 optimal weight: 3.9990 chunk 94 optimal weight: 0.9980 chunk 169 optimal weight: 0.7980 chunk 125 optimal weight: 2.9990 chunk 190 optimal weight: 0.7980 chunk 200 optimal weight: 1.9990 chunk 5 optimal weight: 0.8980 chunk 217 optimal weight: 0.9980 chunk 183 optimal weight: 0.6980 chunk 176 optimal weight: 0.4980 chunk 85 optimal weight: 1.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3682 r_free = 0.3682 target = 0.145762 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.119451 restraints weight = 22612.691| |-----------------------------------------------------------------------------| r_work (start): 0.3251 rms_B_bonded: 1.49 r_work: 0.3123 rms_B_bonded: 2.16 restraints_weight: 0.5000 r_work: 0.2998 rms_B_bonded: 3.55 restraints_weight: 0.2500 r_work (final): 0.2998 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8352 moved from start: 0.1790 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 18948 Z= 0.118 Angle : 0.479 7.498 25604 Z= 0.256 Chirality : 0.042 0.178 2854 Planarity : 0.004 0.059 3244 Dihedral : 5.323 75.819 2698 Min Nonbonded Distance : 2.375 Molprobity Statistics. All-atom Clashscore : 4.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.63 % Favored : 98.37 % Rotamer: Outliers : 1.40 % Allowed : 12.15 % Favored : 86.45 % 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 (0.17), residues: 2326 helix: 2.24 (0.15), residues: 1148 sheet: -0.02 (0.35), residues: 226 loop : -0.27 (0.19), residues: 952 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 459 TYR 0.011 0.001 TYR D 26 PHE 0.015 0.001 PHE A 168 TRP 0.012 0.001 TRP G 32 HIS 0.005 0.001 HIS E 24 Details of bonding type rmsd/Z covalent geometry : bond 0.00271 / 0.12 (18946) covalent geometry : angle 0.47919 / 0.26 (25604) hydrogen bonds : bond 0.03731 / 2.54 ( 953) hydrogen bonds : angle 4.18857 / 3.09 ( 2727) Misc. bond : bond 0.00063 / 0.03 ( 2) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4993.46 seconds wall clock time: 86 minutes 16.17 seconds (5176.17 seconds total)