Starting phenix.real_space_refine on Fri Jun 5 06:34:20 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7k0p_22606/06_2026/7k0p_22606.cif Found real_map, /net/cci-nas-00/data/ceres_data/7k0p_22606/06_2026/7k0p_22606.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7k0p_22606/06_2026/7k0p_22606.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7k0p_22606/06_2026/7k0p_22606.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7k0p_22606/06_2026/7k0p_22606.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7k0p_22606/06_2026/7k0p_22606.map" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.094 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 12000 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 88 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6079/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 18572 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: "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: "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: 1236 Number of conformers: 1 Conformer: "" Number of residues, atoms: 153, 1236 Classifications: {'peptide': 153} Link IDs: {'PTRANS': 8, 'TRANS': 144} Chain: "B" Number of atoms: 54 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 54 Unusual residues: {'PLP': 1, 'POV': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 66 Unresolved non-hydrogen angles: 78 Unresolved non-hydrogen dihedrals: 60 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PLP:plan-2': 1, 'POV:plan-1': 2, 'POV:plan-2': 1, 'POV:plan-3': 1} Unresolved non-hydrogen planarities: 15 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: 70 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: 66 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'POV:plan-2': 2, 'POV:plan-3': 2, 'POV:plan-1': 1} Unresolved non-hydrogen planarities: 19 Chain: "F" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 56 Unusual residues: {'PLP': 1, 'POV': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 64 Unresolved non-hydrogen angles: 76 Unresolved non-hydrogen dihedrals: 58 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PLP:plan-2': 1, 'POV:plan-1': 2, 'POV:plan-2': 1, 'POV:plan-3': 1} Unresolved non-hydrogen planarities: 15 Chain: "G" Number of atoms: 34 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 34 Unusual residues: {'POV': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 122 Unresolved non-hydrogen angles: 149 Unresolved non-hydrogen dihedrals: 107 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'POV:plan-1': 3, 'POV:plan-2': 3, 'POV:plan-3': 3} Unresolved non-hydrogen planarities: 36 Chain: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'POV': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 76 Unresolved non-hydrogen angles: 94 Unresolved non-hydrogen dihedrals: 66 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 Time building chain proxies: 4.53, per 1000 atoms: 0.24 Number of scatterers: 18572 At special positions: 0 Unit cell: (92.46, 120.6, 153.765, 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 12000 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: 1.81 Conformation dependent library (CDL) restraints added in 808.0 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: 98 helices and 12 sheets defined 55.3% alpha, 8.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.56 Creating SS restraints... Processing helix chain 'A' and resid 10 through 20 Processing helix chain 'A' and resid 21 through 40 removed outlier: 3.603A pdb=" N LEU A 25 " --> pdb=" O PRO A 21 " (cutoff:3.500A) Processing helix chain 'A' and resid 53 through 64 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: 3.677A pdb=" N LEU A 146 " --> pdb=" O PHE A 142 " (cutoff:3.500A) Processing helix chain 'A' and resid 166 through 179 removed outlier: 4.122A 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 Processing helix chain 'A' and resid 231 through 237 removed outlier: 3.907A pdb=" N VAL A 237 " --> pdb=" O ARG A 233 " (cutoff:3.500A) Processing helix chain 'A' and resid 256 through 268 Processing helix chain 'A' and resid 288 through 294 Processing helix chain 'A' and resid 321 through 332 removed outlier: 4.706A pdb=" N HIS A 327 " --> pdb=" O PHE A 323 " (cutoff:3.500A) removed outlier: 4.192A pdb=" N GLN A 328 " --> pdb=" O VAL A 324 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N ARG A 329 " --> pdb=" O ILE A 325 " (cutoff:3.500A) removed outlier: 4.372A pdb=" N LEU A 330 " --> pdb=" O ASP A 326 " (cutoff:3.500A) Processing helix chain 'A' and resid 332 through 337 Processing helix chain 'A' and resid 342 through 359 removed outlier: 3.568A pdb=" N ASN A 359 " --> pdb=" O ILE A 355 " (cutoff:3.500A) Processing helix chain 'A' and resid 361 through 378 removed outlier: 3.715A pdb=" N GLN A 378 " --> pdb=" O HIS A 374 " (cutoff:3.500A) Processing helix chain 'A' and resid 404 through 421 removed outlier: 3.730A 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 removed outlier: 3.652A pdb=" N LYS B 109 " --> pdb=" O GLU B 106 " (cutoff:3.500A) Processing helix chain 'B' and resid 116 through 119 Processing helix chain 'B' and resid 120 through 126 Processing helix chain 'B' and resid 127 through 134 removed outlier: 5.463A pdb=" N ASP B 132 " --> pdb=" O ARG B 129 " (cutoff:3.500A) Processing helix chain 'B' and resid 186 through 200 removed outlier: 3.636A pdb=" N GLU B 198 " --> pdb=" O LYS B 194 " (cutoff:3.500A) Processing helix chain 'B' and resid 213 through 228 removed outlier: 3.871A pdb=" N GLU B 217 " --> pdb=" O LEU B 213 " (cutoff:3.500A) Processing helix chain 'B' and resid 237 through 250 removed outlier: 3.761A 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 347 through 352 removed outlier: 4.036A pdb=" N ALA B 351 " --> pdb=" O HIS B 347 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N LEU B 352 " --> pdb=" O SER B 348 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 347 through 352' Processing helix chain 'B' and resid 358 through 364 removed outlier: 3.716A pdb=" N TYR B 362 " --> pdb=" O GLY B 358 " (cutoff:3.500A) Processing helix chain 'B' and resid 391 through 401 Processing helix chain 'B' and resid 402 through 408 removed outlier: 3.590A pdb=" N ALA B 408 " --> pdb=" O SER B 404 " (cutoff:3.500A) Processing helix chain 'B' and resid 412 through 428 Processing helix chain 'B' and resid 436 through 455 removed outlier: 3.765A pdb=" N GLN B 440 " --> pdb=" O LYS B 436 " (cutoff:3.500A) Processing helix chain 'B' and resid 475 through 489 removed outlier: 3.909A 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 removed outlier: 3.531A pdb=" N ALA C 62 " --> pdb=" O GLN C 58 " (cutoff:3.500A) Processing helix chain 'D' and resid 11 through 19 removed outlier: 4.694A pdb=" N MET D 17 " --> pdb=" O THR D 14 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N SER D 19 " --> pdb=" O VAL D 16 " (cutoff:3.500A) Processing helix chain 'D' and resid 21 through 40 removed outlier: 3.780A pdb=" N ILE D 40 " --> pdb=" O VAL D 36 " (cutoff:3.500A) 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 116 Proline residue: D 106 - end of helix Processing helix chain 'D' and resid 120 through 136 removed outlier: 3.781A pdb=" N LEU D 126 " --> pdb=" O ILE D 122 " (cutoff:3.500A) Processing helix chain 'D' and resid 139 through 143 removed outlier: 3.512A pdb=" N HIS D 143 " --> pdb=" O PRO D 140 " (cutoff:3.500A) Processing helix chain 'D' and resid 146 through 150 removed outlier: 3.706A pdb=" N GLY D 149 " --> pdb=" O ARG D 146 " (cutoff:3.500A) Processing helix chain 'E' and resid 11 through 19 Processing helix chain 'E' and resid 21 through 40 Processing helix chain 'E' and resid 53 through 64 Processing helix chain 'E' and resid 77 through 81 Processing helix chain 'E' and resid 114 through 129 Processing helix chain 'E' and resid 142 through 156 removed outlier: 3.637A pdb=" N LEU E 146 " --> pdb=" O PHE E 142 " (cutoff:3.500A) Processing helix chain 'E' and resid 166 through 179 removed outlier: 4.152A 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 Processing helix chain 'E' and resid 231 through 237 Processing helix chain 'E' and resid 256 through 268 Processing helix chain 'E' and resid 288 through 294 Processing helix chain 'E' and resid 321 through 332 removed outlier: 4.772A pdb=" N HIS E 327 " --> pdb=" O PHE E 323 " (cutoff:3.500A) removed outlier: 4.261A pdb=" N GLN E 328 " --> pdb=" O VAL E 324 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N ARG E 329 " --> pdb=" O ILE E 325 " (cutoff:3.500A) removed outlier: 4.292A 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: 4.254A pdb=" N ALA E 364 " --> pdb=" O PRO E 360 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N GLN E 378 " --> pdb=" O HIS E 374 " (cutoff:3.500A) Processing helix chain 'E' and resid 404 through 422 removed outlier: 3.949A pdb=" N ASP E 408 " --> pdb=" O SER E 404 " (cutoff:3.500A) Processing helix chain 'E' and resid 453 through 473 Processing helix chain 'F' and resid 67 through 94 Processing helix chain 'F' and resid 105 through 109 Processing helix chain 'F' and resid 116 through 119 Processing helix chain 'F' and resid 120 through 126 Processing helix chain 'F' and resid 127 through 134 removed outlier: 3.684A pdb=" N ARG F 131 " --> pdb=" O MET F 128 " (cutoff:3.500A) removed outlier: 5.464A pdb=" N ASP F 132 " --> pdb=" O ARG F 129 " (cutoff:3.500A) Processing helix chain 'F' and resid 186 through 200 Processing helix chain 'F' and resid 213 through 228 removed outlier: 3.583A pdb=" N GLU F 217 " --> pdb=" O LEU F 213 " (cutoff:3.500A) Processing helix chain 'F' and resid 237 through 250 Proline residue: F 247 - end of helix removed outlier: 3.530A pdb=" N VAL F 250 " --> pdb=" O ILE F 246 " (cutoff:3.500A) 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 347 through 352 removed outlier: 3.904A pdb=" N ALA F 351 " --> pdb=" O HIS F 347 " (cutoff:3.500A) Processing helix chain 'F' and resid 358 through 364 Processing helix chain 'F' and resid 391 through 401 Processing helix chain 'F' and resid 402 through 408 Processing helix chain 'F' and resid 412 through 428 Processing helix chain 'F' and resid 435 through 457 removed outlier: 3.549A pdb=" N VAL F 439 " --> pdb=" O GLY F 435 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N GLY F 457 " --> pdb=" O LEU F 453 " (cutoff:3.500A) Processing helix chain 'F' and resid 475 through 489 removed outlier: 3.975A pdb=" N GLY F 480 " --> pdb=" O PRO F 476 " (cutoff:3.500A) Processing helix chain 'F' and resid 517 through 536 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: 4.766A pdb=" N MET H 17 " --> pdb=" O THR H 14 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N SER H 19 " --> pdb=" O VAL H 16 " (cutoff:3.500A) Processing helix chain 'H' and resid 21 through 40 removed outlier: 3.639A pdb=" N ILE H 40 " --> pdb=" O VAL H 36 " (cutoff:3.500A) Processing helix chain 'H' and resid 44 through 65 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 removed outlier: 3.799A pdb=" N LEU H 126 " --> pdb=" O ILE H 122 " (cutoff:3.500A) Processing helix chain 'H' and resid 137 through 139 No H-bonds generated for 'chain 'H' and resid 137 through 139' Processing helix chain 'H' and resid 146 through 150 Processing sheet with id=AA1, first strand: chain 'A' and resid 93 through 95 removed outlier: 7.063A pdb=" N ALA A 425 " --> pdb=" O GLU A 99 " (cutoff:3.500A) removed outlier: 6.361A pdb=" N ILE A 101 " --> pdb=" O ALA A 425 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 160 through 164 removed outlier: 6.872A pdb=" N ILE A 271 " --> pdb=" O LEU A 302 " (cutoff:3.500A) removed outlier: 8.216A pdb=" N SER A 304 " --> pdb=" O ILE A 271 " (cutoff:3.500A) removed outlier: 6.638A pdb=" N LEU A 273 " --> pdb=" O SER A 304 " (cutoff:3.500A) removed outlier: 6.747A pdb=" N ARG A 240 " --> pdb=" O ARG A 270 " (cutoff:3.500A) removed outlier: 7.707A pdb=" N PHE A 272 " --> pdb=" O ARG A 240 " (cutoff:3.500A) removed outlier: 6.187A pdb=" N ILE A 242 " --> pdb=" O PHE A 272 " (cutoff:3.500A) removed outlier: 7.510A pdb=" N GLU A 274 " --> pdb=" O ILE A 242 " (cutoff:3.500A) removed outlier: 6.941A pdb=" N VAL A 244 " --> pdb=" O GLU A 274 " (cutoff:3.500A) removed outlier: 7.998A pdb=" N GLU A 245 " --> pdb=" O ASP A 188 " (cutoff:3.500A) removed outlier: 6.123A pdb=" N VAL A 185 " --> pdb=" O LYS A 207 " (cutoff:3.500A) removed outlier: 7.295A pdb=" N PHE A 209 " --> pdb=" O VAL A 185 " (cutoff:3.500A) removed outlier: 6.845A pdb=" N VAL A 187 " --> pdb=" O PHE A 209 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 383 through 386 removed outlier: 4.275A pdb=" N THR A 427 " --> pdb=" O ARG A 445 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 145 through 152 removed outlier: 6.961A pdb=" N VAL B 146 " --> pdb=" O ILE B 167 " (cutoff:3.500A) removed outlier: 7.060A pdb=" N ILE B 167 " --> pdb=" O VAL B 146 " (cutoff:3.500A) removed outlier: 7.869A pdb=" N ILE B 148 " --> pdb=" O ASN B 165 " (cutoff:3.500A) removed outlier: 7.939A pdb=" N ASN B 165 " --> pdb=" O ILE B 148 " (cutoff:3.500A) removed outlier: 5.064A pdb=" N GLU B 150 " --> pdb=" O THR B 163 " (cutoff:3.500A) removed outlier: 7.986A pdb=" N GLY B 492 " --> pdb=" O GLY B 169 " (cutoff:3.500A) removed outlier: 6.775A pdb=" N ILE B 171 " --> pdb=" O GLY B 492 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 231 through 235 removed outlier: 6.672A pdb=" N ILE B 310 " --> pdb=" O TYR B 340 " (cutoff:3.500A) removed outlier: 7.695A pdb=" N TYR B 342 " --> pdb=" O ILE B 310 " (cutoff:3.500A) removed outlier: 6.209A pdb=" N ILE B 312 " --> pdb=" O TYR B 342 " (cutoff:3.500A) removed outlier: 7.335A pdb=" N ASP B 344 " --> pdb=" O ILE B 312 " (cutoff:3.500A) removed outlier: 6.893A pdb=" N VAL B 314 " --> pdb=" O ASP B 344 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 468 through 472 removed outlier: 3.822A pdb=" N VAL B 494 " --> pdb=" O ARG B 509 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'E' and resid 85 through 86 removed outlier: 4.276A pdb=" N VAL E 94 " --> pdb=" O SER E 86 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'E' and resid 160 through 164 removed outlier: 3.756A pdb=" N LEU E 302 " --> pdb=" O ILE E 271 " (cutoff:3.500A) removed outlier: 6.864A pdb=" N ARG E 240 " --> pdb=" O ARG E 270 " (cutoff:3.500A) removed outlier: 7.751A pdb=" N PHE E 272 " --> pdb=" O ARG E 240 " (cutoff:3.500A) removed outlier: 6.137A pdb=" N ILE E 242 " --> pdb=" O PHE E 272 " (cutoff:3.500A) removed outlier: 7.647A pdb=" N GLU E 274 " --> pdb=" O ILE E 242 " (cutoff:3.500A) removed outlier: 6.947A pdb=" N VAL E 244 " --> pdb=" O GLU E 274 " (cutoff:3.500A) removed outlier: 6.592A pdb=" N ILE E 184 " --> pdb=" O PHE E 241 " (cutoff:3.500A) removed outlier: 7.657A pdb=" N VAL E 243 " --> pdb=" O ILE E 184 " (cutoff:3.500A) removed outlier: 6.579A pdb=" N PHE E 186 " --> pdb=" O VAL E 243 " (cutoff:3.500A) removed outlier: 8.527A pdb=" N GLU E 245 " --> pdb=" O PHE E 186 " (cutoff:3.500A) removed outlier: 8.571A pdb=" N ASP E 188 " --> pdb=" O GLU E 245 " (cutoff:3.500A) removed outlier: 6.556A pdb=" N VAL E 185 " --> pdb=" O LYS E 207 " (cutoff:3.500A) removed outlier: 7.509A pdb=" N PHE E 209 " --> pdb=" O VAL E 185 " (cutoff:3.500A) removed outlier: 6.922A pdb=" N VAL E 187 " --> pdb=" O PHE E 209 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'E' and resid 383 through 386 removed outlier: 4.235A pdb=" N THR E 427 " --> pdb=" O ARG E 445 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'F' and resid 145 through 152 removed outlier: 7.146A pdb=" N VAL F 146 " --> pdb=" O ILE F 167 " (cutoff:3.500A) removed outlier: 7.184A pdb=" N ILE F 167 " --> pdb=" O VAL F 146 " (cutoff:3.500A) removed outlier: 7.654A pdb=" N ILE F 148 " --> pdb=" O ASN F 165 " (cutoff:3.500A) removed outlier: 7.764A pdb=" N ASN F 165 " --> pdb=" O ILE F 148 " (cutoff:3.500A) removed outlier: 4.624A pdb=" N GLU F 150 " --> pdb=" O THR F 163 " (cutoff:3.500A) removed outlier: 7.914A pdb=" N GLY F 492 " --> pdb=" O GLY F 169 " (cutoff:3.500A) removed outlier: 6.736A pdb=" N ILE F 171 " --> pdb=" O GLY F 492 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'F' and resid 231 through 235 removed outlier: 6.643A pdb=" N ILE F 310 " --> pdb=" O TYR F 340 " (cutoff:3.500A) removed outlier: 7.664A pdb=" N TYR F 342 " --> pdb=" O ILE F 310 " (cutoff:3.500A) removed outlier: 6.254A pdb=" N ILE F 312 " --> pdb=" O TYR F 342 " (cutoff:3.500A) removed outlier: 7.261A pdb=" N ASP F 344 " --> pdb=" O ILE F 312 " (cutoff:3.500A) removed outlier: 6.956A pdb=" N VAL F 314 " --> pdb=" O ASP F 344 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'F' and resid 468 through 472 removed outlier: 3.505A pdb=" N ARG F 507 " --> pdb=" O VAL F 496 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N VAL F 494 " --> pdb=" O ARG F 509 " (cutoff:3.500A) 960 hydrogen bonds defined for protein. 2739 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: 3.36 Time building geometry restraints manager: 2.26 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 5891 1.34 - 1.46: 2690 1.46 - 1.57: 10207 1.57 - 1.69: 4 1.69 - 1.81: 168 Bond restraints: 18960 Sorted by residual: bond pdb=" C29 POV D 901 " pdb="C210 POV D 901 " ideal model delta sigma weight residual 1.333 1.520 -0.187 2.00e-02 2.50e+03 8.78e+01 bond pdb=" C29 POV H 901 " pdb="C210 POV H 901 " ideal model delta sigma weight residual 1.333 1.520 -0.187 2.00e-02 2.50e+03 8.73e+01 bond pdb=" O12 POV B 602 " pdb=" P POV B 602 " ideal model delta sigma weight residual 1.657 1.740 -0.083 2.00e-02 2.50e+03 1.73e+01 bond pdb=" O12 POV F 602 " pdb=" P POV F 602 " ideal model delta sigma weight residual 1.657 1.740 -0.083 2.00e-02 2.50e+03 1.72e+01 bond pdb=" O4P PLP B 601 " pdb=" P PLP B 601 " ideal model delta sigma weight residual 1.687 1.606 0.081 2.00e-02 2.50e+03 1.63e+01 ... (remaining 18955 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.58: 25499 3.58 - 7.15: 112 7.15 - 10.73: 4 10.73 - 14.30: 0 14.30 - 17.88: 4 Bond angle restraints: 25619 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 127.79 109.91 17.88 3.00e+00 1.11e-01 3.55e+01 angle pdb=" C28 POV H 901 " pdb=" C29 POV H 901 " pdb="C210 POV H 901 " ideal model delta sigma weight residual 127.79 109.94 17.85 3.00e+00 1.11e-01 3.54e+01 angle pdb=" C29 POV D 901 " pdb="C210 POV D 901 " pdb="C211 POV D 901 " ideal model delta sigma weight residual 127.67 110.20 17.47 3.00e+00 1.11e-01 3.39e+01 angle pdb=" C29 POV H 901 " pdb="C210 POV H 901 " pdb="C211 POV H 901 " ideal model delta sigma weight residual 127.67 110.22 17.45 3.00e+00 1.11e-01 3.38e+01 angle pdb=" N GLU E 414 " pdb=" CA GLU E 414 " pdb=" CB GLU E 414 " ideal model delta sigma weight residual 110.28 116.82 -6.54 1.55e+00 4.16e-01 1.78e+01 ... (remaining 25614 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.99: 10370 17.99 - 35.98: 829 35.98 - 53.97: 128 53.97 - 71.96: 36 71.96 - 89.95: 16 Dihedral angle restraints: 11379 sinusoidal: 4593 harmonic: 6786 Sorted by residual: 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 -159.61 -20.39 0 5.00e+00 4.00e-02 1.66e+01 dihedral pdb=" CA THR B 501 " pdb=" C THR B 501 " pdb=" N PRO B 502 " pdb=" CA PRO B 502 " ideal model delta harmonic sigma weight residual 180.00 161.80 18.20 0 5.00e+00 4.00e-02 1.33e+01 dihedral pdb=" CA ASP B 465 " pdb=" CB ASP B 465 " pdb=" CG ASP B 465 " pdb=" OD1 ASP B 465 " ideal model delta sinusoidal sigma weight residual -30.00 -83.24 53.24 1 2.00e+01 2.50e-03 9.64e+00 ... (remaining 11376 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.038: 2006 0.038 - 0.076: 591 0.076 - 0.113: 216 0.113 - 0.151: 38 0.151 - 0.189: 3 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 8.92e-01 chirality pdb=" CA PHE F 498 " pdb=" N PHE F 498 " pdb=" C PHE F 498 " pdb=" CB PHE F 498 " both_signs ideal model delta sigma weight residual False 2.51 2.33 0.18 2.00e-01 2.50e+01 7.73e-01 chirality pdb=" CB THR D 74 " pdb=" CA THR D 74 " pdb=" OG1 THR D 74 " pdb=" CG2 THR D 74 " both_signs ideal model delta sigma weight residual False 2.55 2.40 0.15 2.00e-01 2.50e+01 5.99e-01 ... (remaining 2851 not shown) Planarity restraints: 3245 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 PLP B 601 " 0.025 2.00e-02 2.50e+03 1.76e-01 7.75e+02 pdb=" C2A PLP B 601 " 0.082 2.00e-02 2.50e+03 pdb=" C3 PLP B 601 " -0.122 2.00e-02 2.50e+03 pdb=" C4 PLP B 601 " -0.161 2.00e-02 2.50e+03 pdb=" C4A PLP B 601 " 0.421 2.00e-02 2.50e+03 pdb=" C5 PLP B 601 " -0.079 2.00e-02 2.50e+03 pdb=" C5A PLP B 601 " -0.138 2.00e-02 2.50e+03 pdb=" C6 PLP B 601 " 0.062 2.00e-02 2.50e+03 pdb=" N1 PLP B 601 " 0.116 2.00e-02 2.50e+03 pdb=" O3 PLP B 601 " -0.206 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 PLP F 601 " 0.024 2.00e-02 2.50e+03 1.58e-01 6.21e+02 pdb=" C2A PLP F 601 " 0.075 2.00e-02 2.50e+03 pdb=" C3 PLP F 601 " -0.108 2.00e-02 2.50e+03 pdb=" C4 PLP F 601 " -0.145 2.00e-02 2.50e+03 pdb=" C4A PLP F 601 " 0.376 2.00e-02 2.50e+03 pdb=" C5 PLP F 601 " -0.070 2.00e-02 2.50e+03 pdb=" C5A PLP F 601 " -0.125 2.00e-02 2.50e+03 pdb=" C6 PLP F 601 " 0.056 2.00e-02 2.50e+03 pdb=" N1 PLP F 601 " 0.103 2.00e-02 2.50e+03 pdb=" O3 PLP F 601 " -0.185 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C SER B 412 " 0.046 5.00e-02 4.00e+02 6.94e-02 7.70e+00 pdb=" N PRO B 413 " -0.120 5.00e-02 4.00e+02 pdb=" CA PRO B 413 " 0.036 5.00e-02 4.00e+02 pdb=" CD PRO B 413 " 0.038 5.00e-02 4.00e+02 ... (remaining 3242 not shown) Histogram of nonbonded interaction distances: 2.18 - 2.73: 945 2.73 - 3.27: 18036 3.27 - 3.81: 29317 3.81 - 4.36: 35595 4.36 - 4.90: 63976 Nonbonded interactions: 147869 Sorted by model distance: nonbonded pdb=" OH TYR E 178 " pdb=" O VAL E 324 " model vdw 2.183 3.040 nonbonded pdb=" OE2 GLU A 56 " pdb=" NH2 ARG F 302 " model vdw 2.213 3.120 nonbonded pdb=" OD2 ASP F 259 " pdb=" OH TYR F 318 " model vdw 2.218 3.040 nonbonded pdb=" OG1 THR B 355 " pdb=" OE2 GLU B 361 " model vdw 2.220 3.040 nonbonded pdb=" OE2 GLU H 9 " pdb=" OH TYR H 91 " model vdw 2.230 3.040 ... (remaining 147864 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' selection = (chain 'F' and (resid 53 through 601 or (resid 602 and (name C1 or name C2 or na \ me C21 or name C22 or name C23 or name C24 or name C25 or name C26 or name C27 o \ r name C28 or name C29 or name C3 or name C31 or name C32 or name C33 or name C3 \ 4 or name C35 or name C36 or name C37 or name O11 or name O12 or name O13 or nam \ e O14 or name O21 or name O22 or name O31 or name O32 or name P )) or resid 603) \ ) } ncs_group { reference = chain 'C' selection = (chain 'G' and resid 8 through 102) } ncs_group { reference = chain 'D' selection = (chain 'H' and (resid 1 through 147 or (resid 148 and (name N or name CA or name \ C or name O or name CB )) or resid 149 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: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.050 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: 0.210 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 18.030 Find NCS groups from input model: 0.520 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: 0.010 Load rotamer database and sin/cos tables:1.260 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.200 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7895 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.187 18962 Z= 0.238 Angle : 0.724 17.880 25619 Z= 0.388 Chirality : 0.043 0.189 2854 Planarity : 0.006 0.176 3245 Dihedral : 13.649 89.952 7035 Min Nonbonded Distance : 2.183 Molprobity Statistics. All-atom Clashscore : 5.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.45 % Favored : 97.55 % Rotamer: Outliers : 0.00 % Allowed : 0.21 % Favored : 99.79 % 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: 0.92 (0.17), residues: 2326 helix: 1.83 (0.16), residues: 1109 sheet: -0.56 (0.39), residues: 182 loop : -0.49 (0.18), residues: 1035 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 95 TYR 0.023 0.002 TYR E 166 PHE 0.018 0.002 PHE E 209 TRP 0.013 0.001 TRP G 32 HIS 0.006 0.001 HIS E 292 Details of bonding type rmsd/Z covalent geometry : bond 0.00506 / 0.24 (18960) covalent geometry : angle 0.72416 / 0.39 (25619) hydrogen bonds : bond 0.14396 / 9.62 ( 960) hydrogen bonds : angle 5.68832 / 4.19 ( 2739) Misc. bond : bond 0.02872 / 1.44 ( 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 212 residues out of total 2008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 212 time to evaluate : 0.702 Fit side-chains REVERT: E 236 ARG cc_start: 0.7318 (ttp-110) cc_final: 0.6760 (tpt170) REVERT: F 161 LYS cc_start: 0.8287 (mttt) cc_final: 0.7528 (mmtt) outliers start: 0 outliers final: 0 residues processed: 212 average time/residue: 0.1550 time to fit residues: 49.3024 Evaluate side-chains 173 residues out of total 2008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 173 time to evaluate : 0.723 ------------------------------------------------------------------------------- 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: 10.0000 chunk 98 optimal weight: 4.9990 chunk 194 optimal weight: 0.9990 chunk 227 optimal weight: 0.7980 chunk 107 optimal weight: 2.9990 chunk 10 optimal weight: 0.9980 chunk 66 optimal weight: 0.9980 chunk 130 optimal weight: 0.9990 chunk 124 optimal weight: 5.9990 chunk 103 optimal weight: 2.9990 chunk 200 optimal weight: 5.9990 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 245 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 77 HIS F 154 HIS H 94 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3795 r_free = 0.3795 target = 0.138683 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3466 r_free = 0.3466 target = 0.112494 restraints weight = 25180.622| |-----------------------------------------------------------------------------| r_work (start): 0.3476 rms_B_bonded: 2.34 r_work: 0.3375 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.3236 rms_B_bonded: 4.67 restraints_weight: 0.2500 r_work (final): 0.3236 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7967 moved from start: 0.0746 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 18962 Z= 0.141 Angle : 0.529 6.704 25619 Z= 0.281 Chirality : 0.042 0.183 2854 Planarity : 0.005 0.064 3245 Dihedral : 6.500 60.619 2721 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 3.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.02 % Favored : 97.98 % Rotamer: Outliers : 0.57 % Allowed : 4.24 % Favored : 95.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.20 (0.17), residues: 2326 helix: 2.05 (0.15), residues: 1129 sheet: -0.08 (0.37), residues: 219 loop : -0.45 (0.19), residues: 978 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG F 509 TYR 0.015 0.001 TYR D 26 PHE 0.020 0.002 PHE F 90 TRP 0.011 0.001 TRP G 32 HIS 0.005 0.001 HIS E 24 Details of bonding type rmsd/Z covalent geometry : bond 0.00328 / 0.14 (18960) covalent geometry : angle 0.52874 / 0.28 (25619) hydrogen bonds : bond 0.04839 / 3.32 ( 960) hydrogen bonds : angle 4.54954 / 3.36 ( 2739) Misc. bond : bond 0.00281 / 0.14 ( 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 207 residues out of total 2008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 196 time to evaluate : 0.832 Fit side-chains revert: symmetry clash REVERT: B 155 ASP cc_start: 0.7913 (t0) cc_final: 0.7686 (t0) REVERT: C 47 MET cc_start: 0.6149 (tmm) cc_final: 0.5853 (tmm) REVERT: E 236 ARG cc_start: 0.7676 (ttp-110) cc_final: 0.6816 (tpt170) REVERT: F 161 LYS cc_start: 0.8206 (mttt) cc_final: 0.7274 (mmtt) REVERT: F 320 MET cc_start: 0.8829 (mmt) cc_final: 0.8625 (mmt) REVERT: H 96 THR cc_start: 0.7744 (m) cc_final: 0.7368 (p) outliers start: 11 outliers final: 9 residues processed: 203 average time/residue: 0.1451 time to fit residues: 45.0081 Evaluate side-chains 182 residues out of total 2008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 173 time to evaluate : 0.787 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 LEU Chi-restraints excluded: chain A residue 60 LEU Chi-restraints excluded: chain A residue 113 ASP Chi-restraints excluded: chain B residue 65 GLU Chi-restraints excluded: chain C residue 24 THR Chi-restraints excluded: chain F residue 60 ASN Chi-restraints excluded: chain F residue 384 SER Chi-restraints excluded: chain G residue 42 VAL Chi-restraints excluded: chain H residue 38 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 40 optimal weight: 2.9990 chunk 124 optimal weight: 4.9990 chunk 115 optimal weight: 0.8980 chunk 63 optimal weight: 0.7980 chunk 43 optimal weight: 0.6980 chunk 162 optimal weight: 0.0370 chunk 152 optimal weight: 0.0270 chunk 184 optimal weight: 1.9990 chunk 211 optimal weight: 0.7980 chunk 187 optimal weight: 3.9990 chunk 61 optimal weight: 0.4980 overall best weight: 0.4116 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 177 ASN B 245 ASN E 77 HIS E 91 HIS F 154 HIS ** F 284 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3837 r_free = 0.3837 target = 0.141999 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3524 r_free = 0.3524 target = 0.116363 restraints weight = 25143.690| |-----------------------------------------------------------------------------| r_work (start): 0.3532 rms_B_bonded: 2.27 r_work: 0.3438 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.3302 rms_B_bonded: 4.55 restraints_weight: 0.2500 r_work (final): 0.3302 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8010 moved from start: 0.1096 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 18962 Z= 0.098 Angle : 0.465 6.579 25619 Z= 0.248 Chirality : 0.040 0.173 2854 Planarity : 0.004 0.051 3245 Dihedral : 5.930 61.129 2721 Min Nonbonded Distance : 2.364 Molprobity Statistics. All-atom Clashscore : 3.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.68 % Favored : 98.32 % Rotamer: Outliers : 0.67 % Allowed : 6.41 % Favored : 92.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.44 (0.18), residues: 2326 helix: 2.25 (0.16), residues: 1149 sheet: -0.16 (0.39), residues: 200 loop : -0.36 (0.19), residues: 977 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 95 TYR 0.013 0.001 TYR D 26 PHE 0.013 0.001 PHE E 168 TRP 0.010 0.001 TRP G 32 HIS 0.005 0.001 HIS E 24 Details of bonding type rmsd/Z covalent geometry : bond 0.00213 / 0.10 (18960) covalent geometry : angle 0.46528 / 0.25 (25619) hydrogen bonds : bond 0.03774 / 2.59 ( 960) hydrogen bonds : angle 4.19343 / 3.09 ( 2739) Misc. bond : bond 0.00072 / 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 214 residues out of total 2008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 201 time to evaluate : 0.722 Fit side-chains revert: symmetry clash REVERT: B 155 ASP cc_start: 0.7959 (t0) cc_final: 0.7687 (t0) REVERT: B 285 MET cc_start: 0.7981 (mmm) cc_final: 0.7678 (mmp) REVERT: C 47 MET cc_start: 0.6175 (tmm) cc_final: 0.5966 (tmm) REVERT: E 236 ARG cc_start: 0.7677 (ttp-110) cc_final: 0.6898 (tpt170) REVERT: F 161 LYS cc_start: 0.8258 (mttt) cc_final: 0.7336 (mmtt) REVERT: F 252 LYS cc_start: 0.8705 (tppt) cc_final: 0.8464 (tttt) REVERT: F 487 LEU cc_start: 0.8087 (tp) cc_final: 0.7793 (tp) REVERT: H 76 ASP cc_start: 0.8808 (p0) cc_final: 0.8528 (p0) REVERT: H 96 THR cc_start: 0.7713 (m) cc_final: 0.7366 (p) outliers start: 13 outliers final: 5 residues processed: 209 average time/residue: 0.1435 time to fit residues: 46.4574 Evaluate side-chains 188 residues out of total 2008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 183 time to evaluate : 0.716 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 LEU Chi-restraints excluded: chain A residue 54 VAL Chi-restraints excluded: chain A residue 60 LEU Chi-restraints excluded: chain B residue 65 GLU Chi-restraints excluded: chain C residue 24 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 130 optimal weight: 0.9980 chunk 168 optimal weight: 0.4980 chunk 198 optimal weight: 0.8980 chunk 23 optimal weight: 4.9990 chunk 137 optimal weight: 1.9990 chunk 102 optimal weight: 2.9990 chunk 148 optimal weight: 0.9980 chunk 188 optimal weight: 1.9990 chunk 87 optimal weight: 0.1980 chunk 108 optimal weight: 0.8980 chunk 48 optimal weight: 0.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 177 ASN E 77 HIS F 154 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3825 r_free = 0.3825 target = 0.140937 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3506 r_free = 0.3506 target = 0.115185 restraints weight = 25128.923| |-----------------------------------------------------------------------------| r_work (start): 0.3527 rms_B_bonded: 2.28 r_work: 0.3429 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.3292 rms_B_bonded: 4.60 restraints_weight: 0.2500 r_work (final): 0.3292 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8011 moved from start: 0.1195 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 18962 Z= 0.112 Angle : 0.466 6.568 25619 Z= 0.246 Chirality : 0.040 0.174 2854 Planarity : 0.004 0.050 3245 Dihedral : 5.712 60.878 2721 Min Nonbonded Distance : 2.315 Molprobity Statistics. All-atom Clashscore : 3.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.68 % Favored : 98.32 % Rotamer: Outliers : 1.03 % Allowed : 7.55 % Favored : 91.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.53 (0.18), residues: 2326 helix: 2.38 (0.16), residues: 1133 sheet: -0.14 (0.39), residues: 199 loop : -0.33 (0.19), residues: 994 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG F 95 TYR 0.020 0.001 TYR A 23 PHE 0.026 0.001 PHE F 90 TRP 0.010 0.001 TRP G 32 HIS 0.004 0.001 HIS E 24 Details of bonding type rmsd/Z covalent geometry : bond 0.00260 / 0.11 (18960) covalent geometry : angle 0.46595 / 0.25 (25619) hydrogen bonds : bond 0.03782 / 2.62 ( 960) hydrogen bonds : angle 4.06728 / 2.99 ( 2739) Misc. bond : bond 0.00100 / 0.05 ( 2) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4652 Ramachandran restraints generated. 2326 Oldfield, 0 Emsley, 2326 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4652 Ramachandran restraints generated. 2326 Oldfield, 0 Emsley, 2326 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 218 residues out of total 2008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 198 time to evaluate : 0.714 Fit side-chains REVERT: B 155 ASP cc_start: 0.8067 (t0) cc_final: 0.7826 (t0) REVERT: B 285 MET cc_start: 0.8090 (mmm) cc_final: 0.7749 (mmp) REVERT: C 47 MET cc_start: 0.6082 (OUTLIER) cc_final: 0.5803 (tmm) REVERT: F 95 ARG cc_start: 0.8078 (tpt90) cc_final: 0.7596 (mmm160) REVERT: F 161 LYS cc_start: 0.8211 (mttt) cc_final: 0.7293 (mmtt) REVERT: F 252 LYS cc_start: 0.8698 (tppt) cc_final: 0.8449 (tttt) REVERT: H 73 GLU cc_start: 0.7914 (tt0) cc_final: 0.7701 (tt0) REVERT: H 76 ASP cc_start: 0.8821 (p0) cc_final: 0.8536 (p0) REVERT: H 96 THR cc_start: 0.7722 (OUTLIER) cc_final: 0.7385 (p) outliers start: 20 outliers final: 11 residues processed: 210 average time/residue: 0.1436 time to fit residues: 46.2510 Evaluate side-chains 200 residues out of total 2008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 187 time to evaluate : 0.714 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 LEU Chi-restraints excluded: chain A residue 54 VAL Chi-restraints excluded: chain A residue 60 LEU Chi-restraints excluded: chain B residue 65 GLU Chi-restraints excluded: chain B residue 388 ILE Chi-restraints excluded: chain C residue 24 THR Chi-restraints excluded: chain C residue 40 MET Chi-restraints excluded: chain C residue 47 MET Chi-restraints excluded: chain F residue 384 SER Chi-restraints excluded: chain F residue 388 ILE Chi-restraints excluded: chain H residue 96 THR Chi-restraints excluded: chain H residue 112 LEU Chi-restraints excluded: chain H residue 142 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 138 optimal weight: 0.8980 chunk 223 optimal weight: 3.9990 chunk 200 optimal weight: 0.9990 chunk 28 optimal weight: 0.9980 chunk 169 optimal weight: 3.9990 chunk 120 optimal weight: 0.8980 chunk 7 optimal weight: 2.9990 chunk 38 optimal weight: 3.9990 chunk 27 optimal weight: 0.8980 chunk 15 optimal weight: 2.9990 chunk 19 optimal weight: 0.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 177 ASN E 77 HIS E 114 ASN F 154 HIS H 2 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3810 r_free = 0.3810 target = 0.139850 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3488 r_free = 0.3488 target = 0.114090 restraints weight = 25070.098| |-----------------------------------------------------------------------------| r_work (start): 0.3513 rms_B_bonded: 2.26 r_work: 0.3413 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.3278 rms_B_bonded: 4.56 restraints_weight: 0.2500 r_work (final): 0.3278 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8031 moved from start: 0.1258 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 18962 Z= 0.127 Angle : 0.476 6.577 25619 Z= 0.252 Chirality : 0.041 0.174 2854 Planarity : 0.004 0.051 3245 Dihedral : 5.629 61.344 2721 Min Nonbonded Distance : 2.298 Molprobity Statistics. All-atom Clashscore : 4.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.68 % Favored : 98.32 % Rotamer: Outliers : 1.34 % Allowed : 8.53 % Favored : 90.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.51 (0.18), residues: 2326 helix: 2.37 (0.16), residues: 1137 sheet: -0.18 (0.39), residues: 199 loop : -0.35 (0.19), residues: 990 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 450 TYR 0.014 0.001 TYR D 26 PHE 0.015 0.001 PHE E 209 TRP 0.010 0.001 TRP G 32 HIS 0.004 0.001 HIS E 24 Details of bonding type rmsd/Z covalent geometry : bond 0.00304 / 0.13 (18960) covalent geometry : angle 0.47647 / 0.25 (25619) hydrogen bonds : bond 0.03941 / 2.73 ( 960) hydrogen bonds : angle 4.03225 / 2.96 ( 2739) Misc. bond : bond 0.00115 / 0.06 ( 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 215 residues out of total 2008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 189 time to evaluate : 0.682 Fit side-chains REVERT: A 432 LEU cc_start: 0.8936 (OUTLIER) cc_final: 0.8520 (mp) REVERT: B 155 ASP cc_start: 0.8031 (t0) cc_final: 0.7634 (t0) REVERT: B 285 MET cc_start: 0.8163 (mmm) cc_final: 0.7822 (mmp) REVERT: B 472 MET cc_start: 0.8540 (mmm) cc_final: 0.8264 (mmt) REVERT: C 47 MET cc_start: 0.6117 (OUTLIER) cc_final: 0.5831 (tmm) REVERT: F 95 ARG cc_start: 0.8087 (tpt90) cc_final: 0.7636 (mmm160) REVERT: F 161 LYS cc_start: 0.8239 (mttt) cc_final: 0.7341 (mmtt) REVERT: F 252 LYS cc_start: 0.8709 (tppt) cc_final: 0.8433 (tttt) REVERT: F 487 LEU cc_start: 0.8169 (tp) cc_final: 0.7856 (tp) REVERT: H 73 GLU cc_start: 0.7845 (tt0) cc_final: 0.7630 (tt0) REVERT: H 76 ASP cc_start: 0.8812 (p0) cc_final: 0.8540 (p0) REVERT: H 96 THR cc_start: 0.7793 (OUTLIER) cc_final: 0.7449 (p) outliers start: 26 outliers final: 15 residues processed: 208 average time/residue: 0.1421 time to fit residues: 45.5986 Evaluate side-chains 201 residues out of total 2008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 183 time to evaluate : 0.680 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 LEU Chi-restraints excluded: chain A residue 54 VAL Chi-restraints excluded: chain A residue 60 LEU Chi-restraints excluded: chain A residue 432 LEU Chi-restraints excluded: chain B residue 65 GLU Chi-restraints excluded: chain B residue 113 SER Chi-restraints excluded: chain B residue 388 ILE Chi-restraints excluded: chain C residue 24 THR Chi-restraints excluded: chain C residue 40 MET Chi-restraints excluded: chain C residue 47 MET Chi-restraints excluded: chain E residue 237 VAL Chi-restraints excluded: chain F residue 60 ASN Chi-restraints excluded: chain F residue 384 SER Chi-restraints excluded: chain F residue 388 ILE Chi-restraints excluded: chain F residue 491 ILE Chi-restraints excluded: chain H residue 96 THR Chi-restraints excluded: chain H residue 112 LEU Chi-restraints excluded: chain H residue 142 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 209 optimal weight: 0.7980 chunk 70 optimal weight: 0.7980 chunk 175 optimal weight: 0.0030 chunk 58 optimal weight: 0.4980 chunk 0 optimal weight: 50.0000 chunk 59 optimal weight: 4.9990 chunk 99 optimal weight: 2.9990 chunk 41 optimal weight: 0.9980 chunk 98 optimal weight: 0.9980 chunk 168 optimal weight: 1.9990 chunk 121 optimal weight: 5.9990 overall best weight: 0.6190 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 177 ASN E 77 HIS E 114 ASN F 154 HIS ** F 284 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3826 r_free = 0.3826 target = 0.141137 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3506 r_free = 0.3506 target = 0.115353 restraints weight = 24986.790| |-----------------------------------------------------------------------------| r_work (start): 0.3535 rms_B_bonded: 2.27 r_work: 0.3440 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.3305 rms_B_bonded: 4.56 restraints_weight: 0.2500 r_work (final): 0.3305 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8031 moved from start: 0.1372 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 18962 Z= 0.104 Angle : 0.453 6.539 25619 Z= 0.241 Chirality : 0.040 0.198 2854 Planarity : 0.004 0.049 3245 Dihedral : 5.459 62.442 2721 Min Nonbonded Distance : 2.272 Molprobity Statistics. All-atom Clashscore : 3.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.63 % Favored : 98.37 % Rotamer: Outliers : 1.34 % Allowed : 8.89 % Favored : 89.77 % 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: 1.60 (0.18), residues: 2326 helix: 2.41 (0.16), residues: 1151 sheet: -0.20 (0.39), residues: 199 loop : -0.30 (0.19), residues: 976 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 450 TYR 0.017 0.001 TYR A 23 PHE 0.027 0.001 PHE F 90 TRP 0.010 0.001 TRP G 32 HIS 0.004 0.001 HIS E 24 Details of bonding type rmsd/Z covalent geometry : bond 0.00240 / 0.10 (18960) covalent geometry : angle 0.45320 / 0.24 (25619) hydrogen bonds : bond 0.03572 / 2.47 ( 960) hydrogen bonds : angle 3.94789 / 2.91 ( 2739) Misc. bond : bond 0.00087 / 0.04 ( 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 216 residues out of total 2008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 190 time to evaluate : 0.723 Fit side-chains REVERT: A 432 LEU cc_start: 0.8934 (OUTLIER) cc_final: 0.8529 (mp) REVERT: B 155 ASP cc_start: 0.8135 (t0) cc_final: 0.7757 (t0) REVERT: B 285 MET cc_start: 0.8097 (mmm) cc_final: 0.7736 (mmp) REVERT: B 472 MET cc_start: 0.8578 (mmm) cc_final: 0.8254 (mmt) REVERT: C 47 MET cc_start: 0.6163 (OUTLIER) cc_final: 0.5878 (tmm) REVERT: F 95 ARG cc_start: 0.8109 (tpt90) cc_final: 0.7684 (mmm160) REVERT: F 161 LYS cc_start: 0.8227 (mttt) cc_final: 0.7333 (mmtt) REVERT: F 252 LYS cc_start: 0.8676 (tppt) cc_final: 0.8428 (tttt) REVERT: H 73 GLU cc_start: 0.7912 (tt0) cc_final: 0.7688 (tt0) REVERT: H 76 ASP cc_start: 0.8770 (p0) cc_final: 0.8518 (p0) REVERT: H 96 THR cc_start: 0.7733 (OUTLIER) cc_final: 0.7407 (p) outliers start: 26 outliers final: 15 residues processed: 210 average time/residue: 0.1448 time to fit residues: 46.5966 Evaluate side-chains 201 residues out of total 2008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 183 time to evaluate : 0.707 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 VAL Chi-restraints excluded: chain A residue 60 LEU Chi-restraints excluded: chain A residue 432 LEU Chi-restraints excluded: chain B residue 65 GLU Chi-restraints excluded: chain B residue 113 SER Chi-restraints excluded: chain B residue 141 VAL Chi-restraints excluded: chain B residue 254 CYS Chi-restraints excluded: chain B residue 388 ILE Chi-restraints excluded: chain C residue 24 THR Chi-restraints excluded: chain C residue 47 MET Chi-restraints excluded: chain D residue 96 THR Chi-restraints excluded: chain E residue 114 ASN Chi-restraints excluded: chain E residue 237 VAL Chi-restraints excluded: chain F residue 384 SER Chi-restraints excluded: chain F residue 388 ILE Chi-restraints excluded: chain H residue 19 SER Chi-restraints excluded: chain H residue 96 THR Chi-restraints excluded: chain H residue 142 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 98 optimal weight: 3.9990 chunk 226 optimal weight: 6.9990 chunk 77 optimal weight: 2.9990 chunk 64 optimal weight: 2.9990 chunk 4 optimal weight: 6.9990 chunk 188 optimal weight: 3.9990 chunk 106 optimal weight: 2.9990 chunk 212 optimal weight: 0.6980 chunk 202 optimal weight: 2.9990 chunk 191 optimal weight: 0.8980 chunk 121 optimal weight: 5.9990 overall best weight: 2.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 177 ASN E 77 HIS E 428 GLN F 154 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3759 r_free = 0.3759 target = 0.135646 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3422 r_free = 0.3422 target = 0.109408 restraints weight = 25428.481| |-----------------------------------------------------------------------------| r_work (start): 0.3445 rms_B_bonded: 2.33 r_work: 0.3345 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.3208 rms_B_bonded: 4.60 restraints_weight: 0.2500 r_work (final): 0.3208 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8069 moved from start: 0.1284 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.040 18962 Z= 0.238 Angle : 0.593 6.782 25619 Z= 0.312 Chirality : 0.045 0.181 2854 Planarity : 0.005 0.056 3245 Dihedral : 5.892 63.766 2721 Min Nonbonded Distance : 2.210 Molprobity Statistics. All-atom Clashscore : 4.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Rotamer: Outliers : 1.55 % Allowed : 9.46 % Favored : 88.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.18 (0.17), residues: 2326 helix: 2.14 (0.15), residues: 1143 sheet: -0.54 (0.40), residues: 182 loop : -0.57 (0.18), residues: 1001 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG F 151 TYR 0.022 0.002 TYR E 82 PHE 0.022 0.002 PHE E 209 TRP 0.010 0.001 TRP G 32 HIS 0.007 0.001 HIS F 403 Details of bonding type rmsd/Z covalent geometry : bond 0.00589 / 0.24 (18960) covalent geometry : angle 0.59326 / 0.31 (25619) hydrogen bonds : bond 0.05234 / 3.63 ( 960) hydrogen bonds : angle 4.21892 / 3.09 ( 2739) Misc. bond : bond 0.00210 / 0.11 ( 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 227 residues out of total 2008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 197 time to evaluate : 0.770 Fit side-chains REVERT: A 150 ASP cc_start: 0.8198 (t0) cc_final: 0.7844 (t0) REVERT: A 227 GLU cc_start: 0.7830 (tp30) cc_final: 0.7390 (mm-30) REVERT: A 390 LEU cc_start: 0.8761 (OUTLIER) cc_final: 0.8558 (pp) REVERT: A 432 LEU cc_start: 0.8972 (OUTLIER) cc_final: 0.8540 (mp) REVERT: B 392 LYS cc_start: 0.7865 (tttm) cc_final: 0.7590 (tttp) REVERT: C 47 MET cc_start: 0.6108 (OUTLIER) cc_final: 0.5810 (tmm) REVERT: F 57 ARG cc_start: 0.6971 (ptm160) cc_final: 0.6699 (ptm160) REVERT: F 95 ARG cc_start: 0.8084 (tpt90) cc_final: 0.7649 (mmm160) REVERT: F 161 LYS cc_start: 0.8229 (mttt) cc_final: 0.7339 (mmtt) REVERT: H 73 GLU cc_start: 0.7891 (tt0) cc_final: 0.7633 (tt0) REVERT: H 76 ASP cc_start: 0.8719 (p0) cc_final: 0.8447 (p0) REVERT: H 96 THR cc_start: 0.7861 (OUTLIER) cc_final: 0.7496 (p) outliers start: 30 outliers final: 21 residues processed: 218 average time/residue: 0.1513 time to fit residues: 49.7650 Evaluate side-chains 204 residues out of total 2008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 179 time to evaluate : 0.559 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 LEU Chi-restraints excluded: chain A residue 54 VAL Chi-restraints excluded: chain A residue 60 LEU Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 432 LEU Chi-restraints excluded: chain B residue 65 GLU Chi-restraints excluded: chain B residue 66 THR Chi-restraints excluded: chain B residue 113 SER Chi-restraints excluded: chain B residue 141 VAL Chi-restraints excluded: chain B residue 254 CYS Chi-restraints excluded: chain B residue 388 ILE Chi-restraints excluded: chain C residue 24 THR Chi-restraints excluded: chain C residue 40 MET Chi-restraints excluded: chain C residue 47 MET Chi-restraints excluded: chain D residue 96 THR Chi-restraints excluded: chain E residue 237 VAL Chi-restraints excluded: chain E residue 281 VAL Chi-restraints excluded: chain F residue 60 ASN Chi-restraints excluded: chain F residue 355 THR Chi-restraints excluded: chain F residue 384 SER Chi-restraints excluded: chain F residue 388 ILE Chi-restraints excluded: chain G residue 42 VAL Chi-restraints excluded: chain H residue 96 THR Chi-restraints excluded: chain H residue 112 LEU Chi-restraints excluded: chain H residue 142 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 90 optimal weight: 1.9990 chunk 101 optimal weight: 0.9990 chunk 177 optimal weight: 0.0980 chunk 220 optimal weight: 5.9990 chunk 219 optimal weight: 0.9980 chunk 94 optimal weight: 0.9980 chunk 181 optimal weight: 0.4980 chunk 123 optimal weight: 0.8980 chunk 67 optimal weight: 0.8980 chunk 215 optimal weight: 2.9990 chunk 66 optimal weight: 0.9980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 177 ASN E 77 HIS F 154 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3883 r_free = 0.3883 target = 0.138178 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3530 r_free = 0.3530 target = 0.111371 restraints weight = 24612.691| |-----------------------------------------------------------------------------| r_work (start): 0.3564 rms_B_bonded: 2.40 r_work: 0.3398 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work (final): 0.3398 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7935 moved from start: 0.1389 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 18962 Z= 0.112 Angle : 0.480 6.983 25619 Z= 0.256 Chirality : 0.040 0.170 2854 Planarity : 0.004 0.052 3245 Dihedral : 5.636 62.828 2721 Min Nonbonded Distance : 2.169 Molprobity Statistics. All-atom Clashscore : 4.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.42 % Favored : 98.58 % Rotamer: Outliers : 1.29 % Allowed : 10.08 % Favored : 88.63 % 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: 1.43 (0.18), residues: 2326 helix: 2.33 (0.15), residues: 1149 sheet: -0.34 (0.39), residues: 199 loop : -0.44 (0.19), residues: 978 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 95 TYR 0.017 0.001 TYR E 44 PHE 0.014 0.001 PHE E 168 TRP 0.012 0.001 TRP G 32 HIS 0.007 0.001 HIS E 24 Details of bonding type rmsd/Z covalent geometry : bond 0.00260 / 0.11 (18960) covalent geometry : angle 0.47985 / 0.26 (25619) hydrogen bonds : bond 0.03831 / 2.63 ( 960) hydrogen bonds : angle 3.97644 / 2.93 ( 2739) Misc. bond : bond 0.00089 / 0.05 ( 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 216 residues out of total 2008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 191 time to evaluate : 0.725 Fit side-chains REVERT: A 150 ASP cc_start: 0.8045 (t0) cc_final: 0.7712 (t0) REVERT: A 432 LEU cc_start: 0.8860 (OUTLIER) cc_final: 0.8467 (mp) REVERT: B 155 ASP cc_start: 0.7772 (t0) cc_final: 0.7442 (t0) REVERT: B 285 MET cc_start: 0.7856 (mmm) cc_final: 0.7265 (mmp) REVERT: B 472 MET cc_start: 0.8533 (mmm) cc_final: 0.8126 (mmt) REVERT: C 47 MET cc_start: 0.5980 (OUTLIER) cc_final: 0.5688 (tmm) REVERT: F 57 ARG cc_start: 0.7031 (ptm160) cc_final: 0.6765 (ptm160) REVERT: F 95 ARG cc_start: 0.8081 (tpt90) cc_final: 0.7668 (mmm160) REVERT: F 161 LYS cc_start: 0.8179 (mttt) cc_final: 0.7291 (mmtt) REVERT: F 252 LYS cc_start: 0.8611 (tppt) cc_final: 0.8402 (tttt) REVERT: F 487 LEU cc_start: 0.7977 (tp) cc_final: 0.7755 (tp) REVERT: H 73 GLU cc_start: 0.7876 (tt0) cc_final: 0.7651 (tt0) REVERT: H 74 THR cc_start: 0.8378 (OUTLIER) cc_final: 0.8069 (t) REVERT: H 96 THR cc_start: 0.7647 (OUTLIER) cc_final: 0.7314 (p) outliers start: 25 outliers final: 17 residues processed: 209 average time/residue: 0.1507 time to fit residues: 47.6892 Evaluate side-chains 201 residues out of total 2008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 180 time to evaluate : 0.745 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 VAL Chi-restraints excluded: chain A residue 60 LEU Chi-restraints excluded: chain A residue 432 LEU Chi-restraints excluded: chain B residue 65 GLU Chi-restraints excluded: chain B residue 66 THR Chi-restraints excluded: chain B residue 113 SER Chi-restraints excluded: chain B residue 141 VAL Chi-restraints excluded: chain B residue 254 CYS Chi-restraints excluded: chain B residue 388 ILE Chi-restraints excluded: chain C residue 24 THR Chi-restraints excluded: chain C residue 47 MET Chi-restraints excluded: chain D residue 96 THR Chi-restraints excluded: chain E residue 402 THR Chi-restraints excluded: chain F residue 286 GLN Chi-restraints excluded: chain F residue 355 THR Chi-restraints excluded: chain F residue 384 SER Chi-restraints excluded: chain F residue 388 ILE Chi-restraints excluded: chain H residue 19 SER Chi-restraints excluded: chain H residue 74 THR Chi-restraints excluded: chain H residue 96 THR Chi-restraints excluded: chain H residue 142 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 60 optimal weight: 2.9990 chunk 230 optimal weight: 1.9990 chunk 187 optimal weight: 3.9990 chunk 155 optimal weight: 4.9990 chunk 156 optimal weight: 0.9990 chunk 213 optimal weight: 0.8980 chunk 188 optimal weight: 0.5980 chunk 164 optimal weight: 2.9990 chunk 71 optimal weight: 3.9990 chunk 121 optimal weight: 0.0570 chunk 129 optimal weight: 2.9990 overall best weight: 0.9102 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 177 ASN E 77 HIS F 154 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3875 r_free = 0.3875 target = 0.137579 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3521 r_free = 0.3521 target = 0.110753 restraints weight = 24732.394| |-----------------------------------------------------------------------------| r_work (start): 0.3552 rms_B_bonded: 2.40 r_work: 0.3387 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work (final): 0.3387 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7943 moved from start: 0.1441 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 18962 Z= 0.128 Angle : 0.493 7.196 25619 Z= 0.261 Chirality : 0.041 0.172 2854 Planarity : 0.004 0.052 3245 Dihedral : 5.574 63.036 2721 Min Nonbonded Distance : 2.142 Molprobity Statistics. All-atom Clashscore : 4.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 1.24 % Allowed : 10.70 % Favored : 88.06 % 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: 1.46 (0.18), residues: 2326 helix: 2.35 (0.15), residues: 1149 sheet: -0.38 (0.39), residues: 199 loop : -0.41 (0.19), residues: 978 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 95 TYR 0.017 0.001 TYR B 93 PHE 0.015 0.001 PHE E 209 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 0.00306 / 0.13 (18960) covalent geometry : angle 0.49280 / 0.26 (25619) hydrogen bonds : bond 0.03946 / 2.73 ( 960) hydrogen bonds : angle 3.96348 / 2.92 ( 2739) Misc. bond : bond 0.00109 / 0.06 ( 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 210 residues out of total 2008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 186 time to evaluate : 0.703 Fit side-chains REVERT: A 150 ASP cc_start: 0.8052 (t0) cc_final: 0.7720 (t0) REVERT: A 390 LEU cc_start: 0.8730 (OUTLIER) cc_final: 0.8527 (pp) REVERT: A 432 LEU cc_start: 0.8839 (OUTLIER) cc_final: 0.8435 (mp) REVERT: B 155 ASP cc_start: 0.7783 (t0) cc_final: 0.7438 (t0) REVERT: B 285 MET cc_start: 0.7905 (mmm) cc_final: 0.7321 (mmp) REVERT: B 472 MET cc_start: 0.8548 (mmm) cc_final: 0.8134 (mmt) REVERT: C 47 MET cc_start: 0.5995 (OUTLIER) cc_final: 0.5705 (tmm) REVERT: F 57 ARG cc_start: 0.7036 (ptm160) cc_final: 0.6767 (ptm160) REVERT: F 95 ARG cc_start: 0.8067 (tpt90) cc_final: 0.7643 (mmm160) REVERT: F 161 LYS cc_start: 0.8180 (mttt) cc_final: 0.7295 (mmtt) REVERT: F 252 LYS cc_start: 0.8697 (tppt) cc_final: 0.8474 (tttt) REVERT: F 487 LEU cc_start: 0.8020 (tp) cc_final: 0.7796 (tp) REVERT: H 96 THR cc_start: 0.7671 (OUTLIER) cc_final: 0.7350 (p) outliers start: 24 outliers final: 17 residues processed: 205 average time/residue: 0.1437 time to fit residues: 45.1382 Evaluate side-chains 202 residues out of total 2008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 181 time to evaluate : 0.549 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 VAL Chi-restraints excluded: chain A residue 60 LEU Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 432 LEU Chi-restraints excluded: chain A residue 472 LEU Chi-restraints excluded: chain B residue 65 GLU Chi-restraints excluded: chain B residue 66 THR Chi-restraints excluded: chain B residue 113 SER Chi-restraints excluded: chain B residue 141 VAL Chi-restraints excluded: chain B residue 254 CYS Chi-restraints excluded: chain B residue 388 ILE Chi-restraints excluded: chain C residue 24 THR Chi-restraints excluded: chain C residue 47 MET Chi-restraints excluded: chain D residue 96 THR Chi-restraints excluded: chain E residue 402 THR Chi-restraints excluded: chain F residue 355 THR Chi-restraints excluded: chain F residue 384 SER Chi-restraints excluded: chain F residue 388 ILE Chi-restraints excluded: chain H residue 19 SER Chi-restraints excluded: chain H residue 96 THR Chi-restraints excluded: chain H residue 142 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 96 optimal weight: 0.5980 chunk 2 optimal weight: 1.9990 chunk 221 optimal weight: 0.0060 chunk 106 optimal weight: 3.9990 chunk 213 optimal weight: 0.9990 chunk 125 optimal weight: 2.9990 chunk 68 optimal weight: 0.0010 chunk 179 optimal weight: 2.9990 chunk 225 optimal weight: 3.9990 chunk 94 optimal weight: 0.8980 chunk 105 optimal weight: 1.9990 overall best weight: 0.5004 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 77 HIS F 154 HIS ** F 284 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3914 r_free = 0.3914 target = 0.141900 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3560 r_free = 0.3560 target = 0.114215 restraints weight = 24815.261| |-----------------------------------------------------------------------------| r_work (start): 0.3578 rms_B_bonded: 2.48 r_work: 0.3422 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work (final): 0.3422 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7903 moved from start: 0.1596 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 18962 Z= 0.099 Angle : 0.460 7.381 25619 Z= 0.244 Chirality : 0.040 0.170 2854 Planarity : 0.004 0.050 3245 Dihedral : 5.389 66.335 2721 Min Nonbonded Distance : 2.399 Molprobity Statistics. All-atom Clashscore : 4.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.72 % Favored : 98.28 % Rotamer: Outliers : 0.93 % Allowed : 11.01 % Favored : 88.06 % 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 (0.18), residues: 2326 helix: 2.42 (0.16), residues: 1157 sheet: -0.22 (0.39), residues: 187 loop : -0.38 (0.19), residues: 982 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 95 TYR 0.015 0.001 TYR B 93 PHE 0.011 0.001 PHE E 168 TRP 0.012 0.001 TRP G 32 HIS 0.005 0.000 HIS E 24 Details of bonding type rmsd/Z covalent geometry : bond 0.00229 / 0.10 (18960) covalent geometry : angle 0.46006 / 0.24 (25619) hydrogen bonds : bond 0.03343 / 2.30 ( 960) hydrogen bonds : angle 3.85530 / 2.84 ( 2739) Misc. bond : bond 0.00063 / 0.03 ( 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 206 residues out of total 2008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 188 time to evaluate : 0.762 Fit side-chains REVERT: A 432 LEU cc_start: 0.8825 (OUTLIER) cc_final: 0.8443 (mp) REVERT: B 155 ASP cc_start: 0.7765 (t0) cc_final: 0.7504 (t0) REVERT: B 285 MET cc_start: 0.7890 (mmm) cc_final: 0.7384 (mmp) REVERT: B 472 MET cc_start: 0.8556 (mmm) cc_final: 0.8130 (mmt) REVERT: C 47 MET cc_start: 0.6010 (OUTLIER) cc_final: 0.5743 (tmm) REVERT: F 57 ARG cc_start: 0.7024 (ptm160) cc_final: 0.6758 (ptm160) REVERT: F 95 ARG cc_start: 0.8032 (tpt90) cc_final: 0.7620 (mmm160) REVERT: F 161 LYS cc_start: 0.8177 (mttt) cc_final: 0.7315 (mmtt) REVERT: F 252 LYS cc_start: 0.8713 (tppt) cc_final: 0.8463 (tttt) REVERT: H 96 THR cc_start: 0.7631 (OUTLIER) cc_final: 0.7330 (p) outliers start: 18 outliers final: 12 residues processed: 202 average time/residue: 0.1437 time to fit residues: 44.4609 Evaluate side-chains 196 residues out of total 2008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 181 time to evaluate : 0.748 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 VAL Chi-restraints excluded: chain A residue 60 LEU Chi-restraints excluded: chain A residue 432 LEU Chi-restraints excluded: chain B residue 65 GLU Chi-restraints excluded: chain B residue 113 SER Chi-restraints excluded: chain B residue 141 VAL Chi-restraints excluded: chain B residue 388 ILE Chi-restraints excluded: chain C residue 24 THR Chi-restraints excluded: chain C residue 47 MET Chi-restraints excluded: chain D residue 96 THR Chi-restraints excluded: chain F residue 355 THR Chi-restraints excluded: chain F residue 384 SER Chi-restraints excluded: chain F residue 388 ILE Chi-restraints excluded: chain H residue 96 THR Chi-restraints excluded: chain H residue 142 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 42 optimal weight: 3.9990 chunk 146 optimal weight: 5.9990 chunk 145 optimal weight: 0.7980 chunk 227 optimal weight: 0.9990 chunk 10 optimal weight: 1.9990 chunk 121 optimal weight: 0.9990 chunk 159 optimal weight: 0.8980 chunk 134 optimal weight: 2.9990 chunk 119 optimal weight: 2.9990 chunk 23 optimal weight: 4.9990 chunk 201 optimal weight: 3.9990 overall best weight: 1.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 88 GLN F 154 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3879 r_free = 0.3879 target = 0.139086 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3516 r_free = 0.3516 target = 0.111204 restraints weight = 25265.636| |-----------------------------------------------------------------------------| r_work (start): 0.3538 rms_B_bonded: 2.50 r_work: 0.3384 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work: 0.3240 rms_B_bonded: 4.99 restraints_weight: 0.2500 r_work (final): 0.3240 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7951 moved from start: 0.1519 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 18962 Z= 0.145 Angle : 0.505 8.778 25619 Z= 0.266 Chirality : 0.041 0.172 2854 Planarity : 0.004 0.052 3245 Dihedral : 5.490 65.769 2721 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 4.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.45 % Favored : 97.55 % Rotamer: Outliers : 1.03 % Allowed : 11.21 % Favored : 87.75 % 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: 1.46 (0.18), residues: 2326 helix: 2.34 (0.15), residues: 1155 sheet: -0.31 (0.39), residues: 189 loop : -0.43 (0.19), residues: 982 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 95 TYR 0.018 0.001 TYR B 93 PHE 0.031 0.001 PHE F 90 TRP 0.010 0.001 TRP G 32 HIS 0.004 0.001 HIS E 24 Details of bonding type rmsd/Z covalent geometry : bond 0.00353 / 0.15 (18960) covalent geometry : angle 0.50489 / 0.27 (25619) hydrogen bonds : bond 0.04033 / 2.79 ( 960) hydrogen bonds : angle 3.93885 / 2.90 ( 2739) Misc. bond : bond 0.00126 / 0.06 ( 2) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4359.82 seconds wall clock time: 75 minutes 33.27 seconds (4533.27 seconds total)