Starting phenix.real_space_refine on Tue Nov 19 06:24:00 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7k0o_22605/11_2024/7k0o_22605.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7k0o_22605/11_2024/7k0o_22605.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7k0o_22605/11_2024/7k0o_22605.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7k0o_22605/11_2024/7k0o_22605.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7k0o_22605/11_2024/7k0o_22605.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7k0o_22605/11_2024/7k0o_22605.cif" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.101 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 4 5.49 5 S 100 5.16 5 C 11986 2.51 5 N 3116 2.21 5 O 3352 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 70 residue(s): 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/chem_data/mon_lib" Total number of atoms: 18558 Number of models: 1 Model: "" Number of chains: 9 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: {'GLN:plan1': 1, 'GLU:plan': 3, 'ARG:plan': 1, 'ASP:plan': 1, 'TYR: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: {'GLN:plan1': 1, 'TYR:plan': 1, 'HIS:plan': 2, 'PHE:plan': 1, 'GLU:plan': 1, 'ARG: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: "B" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 56 Unusual residues: {'PLP': 1, 'POV': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 64 Unresolved non-hydrogen angles: 76 Unresolved non-hydrogen dihedrals: 57 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'POV:plan-3': 1, 'POV:plan-2': 1, 'POV:plan-1': 2} Unresolved non-hydrogen planarities: 14 Chain: "C" Number of atoms: 24 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 24 Unusual residues: {'POV': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 80 Unresolved non-hydrogen angles: 98 Unresolved non-hydrogen dihedrals: 70 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'POV:plan-3': 2, 'POV:plan-2': 2, 'POV:plan-1': 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-3': 2, 'POV:plan-2': 2, 'POV:plan-1': 1} Unresolved non-hydrogen planarities: 19 Chain: "H" Number of atoms: 11 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 11 Unusual residues: {'POV': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 41 Unresolved non-hydrogen angles: 50 Unresolved non-hydrogen dihedrals: 36 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'POV:plan-3': 1, 'POV:plan-2': 1, 'POV:plan-1': 1} Unresolved non-hydrogen planarities: 12 Chain: "F" Number of atoms: 45 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 45 Unusual residues: {'PLP': 1, 'POV': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 23 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen dihedrals: 21 Planarities with less than four sites: {'POV:plan-1': 1} Unresolved non-hydrogen planarities: 2 Restraints were copied for chains: E, F, G, H Time building chain proxies: 15.28, per 1000 atoms: 0.82 Number of scatterers: 18558 At special positions: 0 Unit cell: (149.745, 135.675, 118.59, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 100 16.00 P 4 15.00 O 3352 8.00 N 3116 7.00 C 11986 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=2, symmetry=0 Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 5.49 Conformation dependent library (CDL) restraints added in 2.5 seconds 4652 Ramachandran restraints generated. 2326 Oldfield, 0 Emsley, 2326 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4344 Finding SS restraints... Secondary structure from input PDB file: 96 helices and 14 sheets defined 54.8% alpha, 8.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.15 Creating SS restraints... Processing helix chain 'A' and resid 10 through 20 removed outlier: 3.520A pdb=" N ALA A 20 " --> pdb=" O ALA A 16 " (cutoff:3.500A) Processing helix chain 'A' and resid 21 through 40 removed outlier: 3.713A pdb=" N LEU A 25 " --> pdb=" O PRO A 21 " (cutoff:3.500A) Processing helix chain 'A' and resid 53 through 64 removed outlier: 3.693A pdb=" N TRP A 64 " --> pdb=" O LEU A 60 " (cutoff:3.500A) Processing helix chain 'A' and resid 77 through 81 Processing helix chain 'A' and resid 114 through 129 Processing helix chain 'A' and resid 142 through 156 removed outlier: 3.666A pdb=" N LEU A 146 " --> pdb=" O PHE A 142 " (cutoff:3.500A) Processing helix chain 'A' and resid 166 through 179 removed outlier: 4.191A pdb=" N ILE A 171 " --> pdb=" O GLY A 167 " (cutoff:3.500A) Proline residue: A 176 - end of helix Processing helix chain 'A' and resid 192 through 202 Processing helix chain 'A' and resid 213 through 231 removed outlier: 3.749A pdb=" N LEU A 217 " --> pdb=" O ASP A 213 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ASN A 231 " --> pdb=" O GLU A 227 " (cutoff:3.500A) Processing helix chain 'A' and resid 231 through 236 Processing helix chain 'A' and resid 256 through 268 Processing helix chain 'A' and resid 288 through 294 removed outlier: 3.535A pdb=" N HIS A 292 " --> pdb=" O GLY A 288 " (cutoff:3.500A) Processing helix chain 'A' and resid 321 through 332 removed outlier: 4.678A pdb=" N HIS A 327 " --> pdb=" O PHE A 323 " (cutoff:3.500A) removed outlier: 4.288A pdb=" N GLN A 328 " --> pdb=" O VAL A 324 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N ARG A 329 " --> pdb=" O ILE A 325 " (cutoff:3.500A) removed outlier: 4.472A pdb=" N LEU A 330 " --> pdb=" O ASP A 326 " (cutoff:3.500A) Processing helix chain 'A' and resid 332 through 337 Processing helix chain 'A' and resid 342 through 359 Processing helix chain 'A' and resid 360 through 378 removed outlier: 4.298A pdb=" N ALA A 364 " --> pdb=" O PRO A 360 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N GLN A 378 " --> pdb=" O HIS A 374 " (cutoff:3.500A) Processing helix chain 'A' and resid 404 through 422 removed outlier: 3.557A pdb=" N ASP A 408 " --> pdb=" O SER A 404 " (cutoff:3.500A) Processing helix chain 'A' and resid 453 through 473 Processing helix chain 'B' and resid 67 through 94 Processing helix chain 'B' and resid 105 through 109 Processing helix chain 'B' and resid 116 through 119 Processing helix chain 'B' and resid 120 through 126 Processing helix chain 'B' and resid 130 through 134 Processing helix chain 'B' and resid 186 through 200 Processing helix chain 'B' and resid 213 through 228 removed outlier: 3.742A pdb=" N GLU B 217 " --> pdb=" O LEU B 213 " (cutoff:3.500A) Processing helix chain 'B' and resid 237 through 250 removed outlier: 3.708A pdb=" N ASN B 242 " --> pdb=" O GLY B 238 " (cutoff:3.500A) Proline residue: B 247 - end of helix Processing helix chain 'B' and resid 263 through 273 Processing helix chain 'B' and resid 284 through 299 Processing helix chain 'B' and resid 326 through 338 Processing helix chain 'B' and resid 358 through 364 Processing helix chain 'B' and resid 366 through 370 Processing helix chain 'B' and resid 391 through 402 Processing helix chain 'B' and resid 402 through 407 Processing helix chain 'B' and resid 412 through 428 Processing helix chain 'B' and resid 433 through 455 removed outlier: 3.887A pdb=" N VAL B 439 " --> pdb=" O GLY B 435 " (cutoff:3.500A) Processing helix chain 'B' and resid 475 through 489 removed outlier: 4.057A pdb=" N GLY B 480 " --> pdb=" O PRO B 476 " (cutoff:3.500A) Processing helix chain 'B' and resid 517 through 536 Processing helix chain 'C' and resid 9 through 24 Processing helix chain 'C' and resid 30 through 55 Processing helix chain 'C' and resid 58 through 69 Processing helix chain 'D' and resid 11 through 19 removed outlier: 4.704A pdb=" N MET D 17 " --> pdb=" O THR D 14 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N SER D 19 " --> pdb=" O VAL D 16 " (cutoff:3.500A) Processing helix chain 'D' and resid 21 through 39 Processing helix chain 'D' and resid 44 through 66 Processing helix chain 'D' and resid 84 through 89 Processing helix chain 'D' and resid 90 through 93 Processing helix chain 'D' and resid 96 through 117 Proline residue: D 106 - end of helix Processing helix chain 'D' and resid 120 through 136 Processing helix chain 'D' and resid 146 through 150 removed outlier: 3.567A pdb=" N GLY D 149 " --> pdb=" O ARG D 146 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ILE D 150 " --> pdb=" O ILE D 147 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 146 through 150' Processing helix chain 'E' and resid 11 through 20 removed outlier: 3.520A pdb=" N ALA E 20 " --> pdb=" O ALA E 16 " (cutoff:3.500A) Processing helix chain 'E' and resid 21 through 40 removed outlier: 3.713A pdb=" N LEU E 25 " --> pdb=" O PRO E 21 " (cutoff:3.500A) Processing helix chain 'E' and resid 53 through 64 removed outlier: 3.694A pdb=" N TRP E 64 " --> pdb=" O LEU E 60 " (cutoff:3.500A) Processing helix chain 'E' and resid 77 through 81 Processing helix chain 'E' and resid 114 through 129 Processing helix chain 'E' and resid 142 through 156 removed outlier: 3.667A pdb=" N LEU E 146 " --> pdb=" O PHE E 142 " (cutoff:3.500A) Processing helix chain 'E' and resid 166 through 179 removed outlier: 4.191A pdb=" N ILE E 171 " --> pdb=" O GLY E 167 " (cutoff:3.500A) Proline residue: E 176 - end of helix Processing helix chain 'E' and resid 192 through 202 Processing helix chain 'E' and resid 213 through 231 removed outlier: 3.749A pdb=" N LEU E 217 " --> pdb=" O ASP E 213 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ASN E 231 " --> pdb=" O GLU E 227 " (cutoff:3.500A) Processing helix chain 'E' and resid 231 through 236 Processing helix chain 'E' and resid 256 through 268 Processing helix chain 'E' and resid 288 through 294 removed outlier: 3.535A pdb=" N HIS E 292 " --> pdb=" O GLY E 288 " (cutoff:3.500A) Processing helix chain 'E' and resid 321 through 332 removed outlier: 4.679A pdb=" N HIS E 327 " --> pdb=" O PHE E 323 " (cutoff:3.500A) removed outlier: 4.288A pdb=" N GLN E 328 " --> pdb=" O VAL E 324 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N ARG E 329 " --> pdb=" O ILE E 325 " (cutoff:3.500A) removed outlier: 4.472A pdb=" N LEU E 330 " --> pdb=" O ASP E 326 " (cutoff:3.500A) Processing helix chain 'E' and resid 332 through 337 Processing helix chain 'E' and resid 342 through 359 Processing helix chain 'E' and resid 360 through 378 removed outlier: 4.298A pdb=" N ALA E 364 " --> pdb=" O PRO E 360 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N GLN E 378 " --> pdb=" O HIS E 374 " (cutoff:3.500A) Processing helix chain 'E' and resid 404 through 422 removed outlier: 3.557A pdb=" N ASP E 408 " --> pdb=" O SER E 404 " (cutoff:3.500A) Processing helix chain 'E' and resid 453 through 473 Processing helix chain 'G' and resid 9 through 24 Processing helix chain 'G' and resid 30 through 55 Processing helix chain 'G' and resid 58 through 69 Processing helix chain 'H' and resid 11 through 19 removed outlier: 4.704A pdb=" N MET H 17 " --> pdb=" O THR H 14 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N SER H 19 " --> pdb=" O VAL H 16 " (cutoff:3.500A) Processing helix chain 'H' and resid 21 through 39 Processing helix chain 'H' and resid 44 through 66 Processing helix chain 'H' and resid 84 through 89 Processing helix chain 'H' and resid 90 through 93 Processing helix chain 'H' and resid 96 through 117 Proline residue: H 106 - end of helix Processing helix chain 'H' and resid 120 through 136 Processing helix chain 'H' and resid 146 through 150 removed outlier: 3.567A pdb=" N GLY H 149 " --> pdb=" O ARG H 146 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ILE H 150 " --> pdb=" O ILE H 147 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 146 through 150' Processing helix chain 'F' and resid 67 through 94 Processing helix chain 'F' and resid 105 through 109 Processing helix chain 'F' and resid 116 through 119 Processing helix chain 'F' and resid 120 through 126 Processing helix chain 'F' and resid 130 through 134 Processing helix chain 'F' and resid 186 through 200 Processing helix chain 'F' and resid 213 through 228 removed outlier: 3.741A pdb=" N GLU F 217 " --> pdb=" O LEU F 213 " (cutoff:3.500A) Processing helix chain 'F' and resid 237 through 250 removed outlier: 3.708A pdb=" N ASN F 242 " --> pdb=" O GLY F 238 " (cutoff:3.500A) Proline residue: F 247 - end of helix Processing helix chain 'F' and resid 263 through 273 Processing helix chain 'F' and resid 284 through 299 Processing helix chain 'F' and resid 326 through 338 Processing helix chain 'F' and resid 358 through 364 Processing helix chain 'F' and resid 366 through 370 Processing helix chain 'F' and resid 391 through 402 Processing helix chain 'F' and resid 402 through 407 Processing helix chain 'F' and resid 412 through 428 Processing helix chain 'F' and resid 433 through 455 removed outlier: 3.887A pdb=" N VAL F 439 " --> pdb=" O GLY F 435 " (cutoff:3.500A) Processing helix chain 'F' and resid 475 through 489 removed outlier: 4.058A pdb=" N GLY F 480 " --> pdb=" O PRO F 476 " (cutoff:3.500A) Processing helix chain 'F' and resid 517 through 536 Processing sheet with id=AA1, first strand: chain 'A' and resid 94 through 95 Processing sheet with id=AA2, first strand: chain 'A' and resid 101 through 102 removed outlier: 6.328A pdb=" N ILE A 101 " --> pdb=" O ALA A 425 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'A' and resid 160 through 164 removed outlier: 7.057A pdb=" N ILE A 271 " --> pdb=" O LEU A 302 " (cutoff:3.500A) removed outlier: 8.400A pdb=" N SER A 304 " --> pdb=" O ILE A 271 " (cutoff:3.500A) removed outlier: 6.592A pdb=" N LEU A 273 " --> pdb=" O SER A 304 " (cutoff:3.500A) removed outlier: 8.818A pdb=" N ASN A 306 " --> pdb=" O LEU A 273 " (cutoff:3.500A) removed outlier: 6.833A pdb=" N ARG A 240 " --> pdb=" O ARG A 270 " (cutoff:3.500A) removed outlier: 7.787A pdb=" N PHE A 272 " --> pdb=" O ARG A 240 " (cutoff:3.500A) removed outlier: 6.129A pdb=" N ILE A 242 " --> pdb=" O PHE A 272 " (cutoff:3.500A) removed outlier: 7.644A pdb=" N GLU A 274 " --> pdb=" O ILE A 242 " (cutoff:3.500A) removed outlier: 6.986A pdb=" N VAL A 244 " --> pdb=" O GLU A 274 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N ASP A 188 " --> pdb=" O VAL A 243 " (cutoff:3.500A) removed outlier: 8.118A pdb=" N GLU A 245 " --> pdb=" O ASP A 188 " (cutoff:3.500A) removed outlier: 6.338A pdb=" N VAL A 185 " --> pdb=" O LYS A 207 " (cutoff:3.500A) removed outlier: 7.554A pdb=" N PHE A 209 " --> pdb=" O VAL A 185 " (cutoff:3.500A) removed outlier: 6.906A pdb=" N VAL A 187 " --> pdb=" O PHE A 209 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 383 through 386 removed outlier: 4.208A pdb=" N THR A 427 " --> pdb=" O ARG A 445 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 145 through 152 removed outlier: 6.986A pdb=" N VAL B 146 " --> pdb=" O ILE B 167 " (cutoff:3.500A) removed outlier: 7.042A pdb=" N ILE B 167 " --> pdb=" O VAL B 146 " (cutoff:3.500A) removed outlier: 7.812A pdb=" N ILE B 148 " --> pdb=" O ASN B 165 " (cutoff:3.500A) removed outlier: 7.925A pdb=" N ASN B 165 " --> pdb=" O ILE B 148 " (cutoff:3.500A) removed outlier: 4.914A pdb=" N GLU B 150 " --> pdb=" O THR B 163 " (cutoff:3.500A) removed outlier: 7.876A pdb=" N GLY B 492 " --> pdb=" O GLY B 169 " (cutoff:3.500A) removed outlier: 6.663A pdb=" N ILE B 171 " --> pdb=" O GLY B 492 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 231 through 235 removed outlier: 6.646A pdb=" N ILE B 310 " --> pdb=" O TYR B 340 " (cutoff:3.500A) removed outlier: 7.636A pdb=" N TYR B 342 " --> pdb=" O ILE B 310 " (cutoff:3.500A) removed outlier: 6.151A pdb=" N ILE B 312 " --> pdb=" O TYR B 342 " (cutoff:3.500A) removed outlier: 7.330A pdb=" N ASP B 344 " --> pdb=" O ILE B 312 " (cutoff:3.500A) removed outlier: 6.838A pdb=" N VAL B 314 " --> pdb=" O ASP B 344 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 468 through 472 removed outlier: 3.820A pdb=" N VAL B 494 " --> pdb=" O ARG B 509 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'E' and resid 94 through 95 Processing sheet with id=AA9, first strand: chain 'E' and resid 101 through 102 removed outlier: 6.329A pdb=" N ILE E 101 " --> pdb=" O ALA E 425 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'E' and resid 160 through 164 removed outlier: 7.058A pdb=" N ILE E 271 " --> pdb=" O LEU E 302 " (cutoff:3.500A) removed outlier: 8.400A pdb=" N SER E 304 " --> pdb=" O ILE E 271 " (cutoff:3.500A) removed outlier: 6.592A pdb=" N LEU E 273 " --> pdb=" O SER E 304 " (cutoff:3.500A) removed outlier: 8.819A pdb=" N ASN E 306 " --> pdb=" O LEU E 273 " (cutoff:3.500A) removed outlier: 6.833A pdb=" N ARG E 240 " --> pdb=" O ARG E 270 " (cutoff:3.500A) removed outlier: 7.787A pdb=" N PHE E 272 " --> pdb=" O ARG E 240 " (cutoff:3.500A) removed outlier: 6.129A pdb=" N ILE E 242 " --> pdb=" O PHE E 272 " (cutoff:3.500A) removed outlier: 7.643A pdb=" N GLU E 274 " --> pdb=" O ILE E 242 " (cutoff:3.500A) removed outlier: 6.986A pdb=" N VAL E 244 " --> pdb=" O GLU E 274 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N ASP E 188 " --> pdb=" O VAL E 243 " (cutoff:3.500A) removed outlier: 8.118A pdb=" N GLU E 245 " --> pdb=" O ASP E 188 " (cutoff:3.500A) removed outlier: 6.337A pdb=" N VAL E 185 " --> pdb=" O LYS E 207 " (cutoff:3.500A) removed outlier: 7.555A pdb=" N PHE E 209 " --> pdb=" O VAL E 185 " (cutoff:3.500A) removed outlier: 6.906A pdb=" N VAL E 187 " --> pdb=" O PHE E 209 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'E' and resid 383 through 386 removed outlier: 4.207A pdb=" N THR E 427 " --> pdb=" O ARG E 445 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'F' and resid 145 through 152 removed outlier: 6.987A pdb=" N VAL F 146 " --> pdb=" O ILE F 167 " (cutoff:3.500A) removed outlier: 7.042A pdb=" N ILE F 167 " --> pdb=" O VAL F 146 " (cutoff:3.500A) removed outlier: 7.812A pdb=" N ILE F 148 " --> pdb=" O ASN F 165 " (cutoff:3.500A) removed outlier: 7.925A pdb=" N ASN F 165 " --> pdb=" O ILE F 148 " (cutoff:3.500A) removed outlier: 4.914A pdb=" N GLU F 150 " --> pdb=" O THR F 163 " (cutoff:3.500A) removed outlier: 7.877A pdb=" N GLY F 492 " --> pdb=" O GLY F 169 " (cutoff:3.500A) removed outlier: 6.664A pdb=" N ILE F 171 " --> pdb=" O GLY F 492 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'F' and resid 231 through 235 removed outlier: 6.646A pdb=" N ILE F 310 " --> pdb=" O TYR F 340 " (cutoff:3.500A) removed outlier: 7.635A pdb=" N TYR F 342 " --> pdb=" O ILE F 310 " (cutoff:3.500A) removed outlier: 6.151A pdb=" N ILE F 312 " --> pdb=" O TYR F 342 " (cutoff:3.500A) removed outlier: 7.328A pdb=" N ASP F 344 " --> pdb=" O ILE F 312 " (cutoff:3.500A) removed outlier: 6.838A pdb=" N VAL F 314 " --> pdb=" O ASP F 344 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'F' and resid 468 through 472 removed outlier: 3.820A pdb=" N VAL F 494 " --> pdb=" O ARG F 509 " (cutoff:3.500A) 953 hydrogen bonds defined for protein. 2727 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 6.14 Time building geometry restraints manager: 5.88 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 3566 1.33 - 1.45: 4454 1.45 - 1.57: 10754 1.57 - 1.69: 4 1.69 - 1.81: 168 Bond restraints: 18946 Sorted by residual: bond pdb=" C29 POV H 901 " pdb="C210 POV H 901 " ideal model delta sigma weight residual 1.333 1.523 -0.190 2.00e-02 2.50e+03 9.06e+01 bond pdb=" C29 POV D 901 " pdb="C210 POV D 901 " ideal model delta sigma weight residual 1.333 1.523 -0.190 2.00e-02 2.50e+03 8.99e+01 bond pdb=" O12 POV F 601 " pdb=" P POV F 601 " ideal model delta sigma weight residual 1.657 1.742 -0.085 2.00e-02 2.50e+03 1.79e+01 bond pdb=" O12 POV B 602 " pdb=" P POV B 602 " ideal model delta sigma weight residual 1.657 1.742 -0.085 2.00e-02 2.50e+03 1.79e+01 bond pdb=" CA PRO B 413 " pdb=" C PRO B 413 " ideal model delta sigma weight residual 1.517 1.547 -0.029 9.30e-03 1.16e+04 1.00e+01 ... (remaining 18941 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.54: 25475 3.54 - 7.09: 119 7.09 - 10.63: 6 10.63 - 14.17: 0 14.17 - 17.72: 4 Bond angle restraints: 25604 Sorted by residual: angle pdb=" C28 POV D 901 " pdb=" C29 POV D 901 " pdb="C210 POV D 901 " ideal model delta sigma weight residual 127.79 110.07 17.72 3.00e+00 1.11e-01 3.49e+01 angle pdb=" C28 POV H 901 " pdb=" C29 POV H 901 " pdb="C210 POV H 901 " ideal model delta sigma weight residual 127.79 110.08 17.71 3.00e+00 1.11e-01 3.49e+01 angle pdb=" C29 POV H 901 " pdb="C210 POV H 901 " pdb="C211 POV H 901 " ideal model delta sigma weight residual 127.67 110.03 17.64 3.00e+00 1.11e-01 3.46e+01 angle pdb=" C29 POV D 901 " pdb="C210 POV D 901 " pdb="C211 POV D 901 " ideal model delta sigma weight residual 127.67 110.05 17.62 3.00e+00 1.11e-01 3.45e+01 angle pdb=" CA PRO F 413 " pdb=" C PRO F 413 " pdb=" N PRO F 414 " ideal model delta sigma weight residual 117.93 124.26 -6.33 1.20e+00 6.94e-01 2.78e+01 ... (remaining 25599 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.80: 10442 17.80 - 35.60: 746 35.60 - 53.40: 152 53.40 - 71.20: 12 71.20 - 88.99: 14 Dihedral angle restraints: 11366 sinusoidal: 4580 harmonic: 6786 Sorted by residual: dihedral pdb=" CA LYS D 79 " pdb=" C LYS D 79 " pdb=" N ALA D 80 " pdb=" CA ALA D 80 " ideal model delta harmonic sigma weight residual -180.00 -160.38 -19.62 0 5.00e+00 4.00e-02 1.54e+01 dihedral pdb=" CA LYS H 79 " pdb=" C LYS H 79 " pdb=" N ALA H 80 " pdb=" CA ALA H 80 " ideal model delta harmonic sigma weight residual -180.00 -160.39 -19.61 0 5.00e+00 4.00e-02 1.54e+01 dihedral pdb=" CA VAL D 93 " pdb=" C VAL D 93 " pdb=" N GLN D 94 " pdb=" CA GLN D 94 " ideal model delta harmonic sigma weight residual 180.00 -161.18 -18.82 0 5.00e+00 4.00e-02 1.42e+01 ... (remaining 11363 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.038: 1882 0.038 - 0.076: 683 0.076 - 0.114: 227 0.114 - 0.152: 56 0.152 - 0.190: 6 Chirality restraints: 2854 Sorted by residual: chirality pdb=" CA THR H 105 " pdb=" N THR H 105 " pdb=" C THR H 105 " pdb=" CB THR H 105 " both_signs ideal model delta sigma weight residual False 2.53 2.34 0.19 2.00e-01 2.50e+01 9.01e-01 chirality pdb=" CA THR D 105 " pdb=" N THR D 105 " pdb=" C THR D 105 " pdb=" CB THR D 105 " both_signs ideal model delta sigma weight residual False 2.53 2.34 0.18 2.00e-01 2.50e+01 8.53e-01 chirality pdb=" CA PRO B 413 " pdb=" N PRO B 413 " pdb=" C PRO B 413 " pdb=" CB PRO B 413 " both_signs ideal model delta sigma weight residual False 2.72 2.55 0.17 2.00e-01 2.50e+01 7.25e-01 ... (remaining 2851 not shown) Planarity restraints: 3244 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL F 469 " -0.033 5.00e-02 4.00e+02 5.01e-02 4.02e+00 pdb=" N PRO F 470 " 0.087 5.00e-02 4.00e+02 pdb=" CA PRO F 470 " -0.026 5.00e-02 4.00e+02 pdb=" CD PRO F 470 " -0.028 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL B 469 " 0.033 5.00e-02 4.00e+02 4.98e-02 3.96e+00 pdb=" N PRO B 470 " -0.086 5.00e-02 4.00e+02 pdb=" CA PRO B 470 " 0.026 5.00e-02 4.00e+02 pdb=" CD PRO B 470 " 0.028 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR B 501 " -0.033 5.00e-02 4.00e+02 4.91e-02 3.86e+00 pdb=" N PRO B 502 " 0.085 5.00e-02 4.00e+02 pdb=" CA PRO B 502 " -0.025 5.00e-02 4.00e+02 pdb=" CD PRO B 502 " -0.027 5.00e-02 4.00e+02 ... (remaining 3241 not shown) Histogram of nonbonded interaction distances: 2.16 - 2.71: 516 2.71 - 3.26: 18077 3.26 - 3.80: 28687 3.80 - 4.35: 37141 4.35 - 4.90: 65235 Nonbonded interactions: 149656 Sorted by model distance: nonbonded pdb=" O VAL D 10 " pdb=" OG1 THR D 74 " model vdw 2.161 3.040 nonbonded pdb=" O VAL H 10 " pdb=" OG1 THR H 74 " model vdw 2.161 3.040 nonbonded pdb=" OH TYR B 448 " pdb=" OD1 ASP B 522 " model vdw 2.234 3.040 nonbonded pdb=" OH TYR F 448 " pdb=" OD1 ASP F 522 " model vdw 2.234 3.040 nonbonded pdb=" OH TYR E 178 " pdb=" O VAL E 324 " model vdw 2.266 3.040 ... (remaining 149651 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'E' } ncs_group { reference = (chain 'B' and resid 53 through 544) selection = (chain 'F' and resid 53 through 544) } ncs_group { reference = chain 'C' selection = chain 'G' } ncs_group { reference = chain 'D' selection = (chain 'H' and (resid 1 through 153 or resid 901 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: 2.140 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.710 Check model and map are aligned: 0.120 Set scattering table: 0.160 Process input model: 46.720 Find NCS groups from input model: 0.770 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.940 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 53.650 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7872 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.190 18946 Z= 0.363 Angle : 0.745 17.715 25604 Z= 0.411 Chirality : 0.045 0.190 2854 Planarity : 0.005 0.050 3244 Dihedral : 13.026 88.995 7022 Min Nonbonded Distance : 2.161 Molprobity Statistics. All-atom Clashscore : 5.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Rotamer: Outliers : 0.21 % Allowed : 0.67 % Favored : 99.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.95 (0.17), residues: 2326 helix: 1.76 (0.15), residues: 1092 sheet: -0.25 (0.35), residues: 226 loop : -0.38 (0.19), residues: 1008 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP G 32 HIS 0.007 0.001 HIS E 24 PHE 0.022 0.002 PHE E 168 TYR 0.029 0.002 TYR E 166 ARG 0.014 0.001 ARG A 459 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4652 Ramachandran restraints generated. 2326 Oldfield, 0 Emsley, 2326 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4652 Ramachandran restraints generated. 2326 Oldfield, 0 Emsley, 2326 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 235 residues out of total 2008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 231 time to evaluate : 2.277 Fit side-chains REVERT: A 214 MET cc_start: 0.6571 (mmt) cc_final: 0.6189 (mmt) REVERT: B 285 MET cc_start: 0.8032 (mmt) cc_final: 0.7384 (mmt) REVERT: E 214 MET cc_start: 0.6508 (mmt) cc_final: 0.6166 (mmt) REVERT: F 285 MET cc_start: 0.7993 (mmt) cc_final: 0.7333 (mmt) outliers start: 4 outliers final: 0 residues processed: 233 average time/residue: 0.3553 time to fit residues: 122.2600 Evaluate side-chains 193 residues out of total 2008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 193 time to evaluate : 2.300 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 195 optimal weight: 2.9990 chunk 175 optimal weight: 0.5980 chunk 97 optimal weight: 2.9990 chunk 60 optimal weight: 1.9990 chunk 118 optimal weight: 1.9990 chunk 93 optimal weight: 0.9990 chunk 181 optimal weight: 0.9980 chunk 70 optimal weight: 0.0040 chunk 110 optimal weight: 1.9990 chunk 135 optimal weight: 1.9990 chunk 210 optimal weight: 0.9980 overall best weight: 0.7194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 229 GLN E 229 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7836 moved from start: 0.0891 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 18946 Z= 0.184 Angle : 0.514 7.093 25604 Z= 0.277 Chirality : 0.042 0.179 2854 Planarity : 0.005 0.046 3244 Dihedral : 6.897 74.179 2710 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 5.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.63 % Favored : 98.37 % Rotamer: Outliers : 0.57 % Allowed : 6.41 % Favored : 93.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.29 (0.17), residues: 2326 helix: 1.98 (0.15), residues: 1134 sheet: -0.08 (0.35), residues: 226 loop : -0.21 (0.19), residues: 966 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP G 32 HIS 0.005 0.001 HIS H 143 PHE 0.016 0.001 PHE E 168 TYR 0.014 0.001 TYR D 26 ARG 0.003 0.000 ARG A 459 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4652 Ramachandran restraints generated. 2326 Oldfield, 0 Emsley, 2326 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4652 Ramachandran restraints generated. 2326 Oldfield, 0 Emsley, 2326 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 218 residues out of total 2008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 207 time to evaluate : 2.012 Fit side-chains REVERT: A 55 LYS cc_start: 0.8709 (mtpp) cc_final: 0.8435 (pttp) REVERT: B 233 MET cc_start: 0.8261 (ttt) cc_final: 0.8040 (ttt) REVERT: B 285 MET cc_start: 0.7867 (mmt) cc_final: 0.7216 (mmt) REVERT: D 79 LYS cc_start: 0.8366 (mmmm) cc_final: 0.8011 (tppt) REVERT: E 55 LYS cc_start: 0.8705 (mtpp) cc_final: 0.8429 (pttp) REVERT: H 79 LYS cc_start: 0.8356 (mmmm) cc_final: 0.7922 (tppt) REVERT: F 233 MET cc_start: 0.8265 (ttt) cc_final: 0.8049 (ttt) REVERT: F 285 MET cc_start: 0.7866 (mmt) cc_final: 0.7178 (mmt) outliers start: 11 outliers final: 6 residues processed: 214 average time/residue: 0.3693 time to fit residues: 116.4779 Evaluate side-chains 202 residues out of total 2008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 196 time to evaluate : 2.490 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 140 SER Chi-restraints excluded: chain B residue 296 ILE Chi-restraints excluded: chain D residue 96 THR Chi-restraints excluded: chain H residue 96 THR Chi-restraints excluded: chain F residue 140 SER Chi-restraints excluded: chain F residue 296 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 117 optimal weight: 0.8980 chunk 65 optimal weight: 0.8980 chunk 175 optimal weight: 0.0980 chunk 143 optimal weight: 3.9990 chunk 58 optimal weight: 3.9990 chunk 211 optimal weight: 1.9990 chunk 228 optimal weight: 0.8980 chunk 187 optimal weight: 10.0000 chunk 209 optimal weight: 0.5980 chunk 71 optimal weight: 3.9990 chunk 169 optimal weight: 2.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 229 GLN E 229 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7831 moved from start: 0.1104 Sorry: Reduce crashed with command 'molprobity.reduce -quiet -trim -'. Dumping stdin to file 'reduce_fail.pdb'. Return code: -15 Dumping stderr: