Starting phenix.real_space_refine on Tue Oct 15 01:13:01 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7t6o_25721/10_2024/7t6o_25721.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7t6o_25721/10_2024/7t6o_25721.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7t6o_25721/10_2024/7t6o_25721.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7t6o_25721/10_2024/7t6o_25721.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7t6o_25721/10_2024/7t6o_25721.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7t6o_25721/10_2024/7t6o_25721.cif" } resolution = 2.6 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= 0.002 sd= 0.048 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: 4 Type Number sf(0) Gaussians S 140 5.16 5 C 12548 2.51 5 N 3284 2.21 5 O 3440 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 34 residue(s): 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5477/modules/chem_data/mon_lib" Total number of atoms: 19412 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 4853 Number of conformers: 1 Conformer: "" Number of residues, atoms: 606, 4853 Classifications: {'peptide': 606} Link IDs: {'PTRANS': 24, 'TRANS': 581} Chain breaks: 1 Chain: "B" Number of atoms: 4853 Number of conformers: 1 Conformer: "" Number of residues, atoms: 606, 4853 Classifications: {'peptide': 606} Link IDs: {'PTRANS': 24, 'TRANS': 581} Chain breaks: 1 Chain: "C" Number of atoms: 4853 Number of conformers: 1 Conformer: "" Number of residues, atoms: 606, 4853 Classifications: {'peptide': 606} Link IDs: {'PTRANS': 24, 'TRANS': 581} Chain breaks: 1 Chain: "D" Number of atoms: 4853 Number of conformers: 1 Conformer: "" Number of residues, atoms: 606, 4853 Classifications: {'peptide': 606} Link IDs: {'PTRANS': 24, 'TRANS': 581} Chain breaks: 1 Time building chain proxies: 11.49, per 1000 atoms: 0.59 Number of scatterers: 19412 At special positions: 0 Unit cell: (143.59, 143.59, 119.52, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 140 16.00 O 3440 8.00 N 3284 7.00 C 12548 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=0, symmetry=0 Time building additional restraints: 4.73 Conformation dependent library (CDL) restraints added in 2.7 seconds 4816 Ramachandran restraints generated. 2408 Oldfield, 0 Emsley, 2408 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4576 Finding SS restraints... Secondary structure from input PDB file: 136 helices and 8 sheets defined 70.0% alpha, 4.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.06 Creating SS restraints... Processing helix chain 'A' and resid 29 through 47 Processing helix chain 'A' and resid 47 through 55 Processing helix chain 'A' and resid 57 through 66 removed outlier: 3.633A pdb=" N LEU A 61 " --> pdb=" O ASP A 57 " (cutoff:3.500A) Processing helix chain 'A' and resid 81 through 89 Processing helix chain 'A' and resid 91 through 102 Processing helix chain 'A' and resid 103 through 107 removed outlier: 3.792A pdb=" N ALA A 106 " --> pdb=" O PRO A 103 " (cutoff:3.500A) Processing helix chain 'A' and resid 112 through 116 removed outlier: 4.106A pdb=" N VAL A 116 " --> pdb=" O GLU A 113 " (cutoff:3.500A) Processing helix chain 'A' and resid 119 through 127 removed outlier: 3.528A pdb=" N ILE A 123 " --> pdb=" O THR A 119 " (cutoff:3.500A) Processing helix chain 'A' and resid 129 through 139 removed outlier: 3.627A pdb=" N ARG A 139 " --> pdb=" O ALA A 135 " (cutoff:3.500A) Processing helix chain 'A' and resid 165 through 174 removed outlier: 3.506A pdb=" N GLY A 174 " --> pdb=" O ALA A 170 " (cutoff:3.500A) Processing helix chain 'A' and resid 175 through 185 Processing helix chain 'A' and resid 198 through 205 Processing helix chain 'A' and resid 208 through 221 removed outlier: 4.000A pdb=" N CYS A 213 " --> pdb=" O LYS A 209 " (cutoff:3.500A) removed outlier: 4.282A pdb=" N GLN A 214 " --> pdb=" O THR A 210 " (cutoff:3.500A) Processing helix chain 'A' and resid 231 through 235 Processing helix chain 'A' and resid 242 through 250 Processing helix chain 'A' and resid 252 through 262 removed outlier: 3.931A pdb=" N LYS A 262 " --> pdb=" O HIS A 258 " (cutoff:3.500A) Processing helix chain 'A' and resid 280 through 285 removed outlier: 3.932A pdb=" N SER A 285 " --> pdb=" O THR A 281 " (cutoff:3.500A) Processing helix chain 'A' and resid 291 through 298 Processing helix chain 'A' and resid 302 through 309 removed outlier: 3.847A pdb=" N ARG A 305 " --> pdb=" O ARG A 302 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N GLU A 309 " --> pdb=" O GLN A 306 " (cutoff:3.500A) Processing helix chain 'A' and resid 310 through 324 removed outlier: 3.982A pdb=" N GLU A 315 " --> pdb=" O THR A 311 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N LEU A 316 " --> pdb=" O PRO A 312 " (cutoff:3.500A) Processing helix chain 'A' and resid 324 through 349 Processing helix chain 'A' and resid 379 through 410 Proline residue: A 405 - end of helix removed outlier: 3.693A pdb=" N VAL A 410 " --> pdb=" O ASP A 406 " (cutoff:3.500A) Processing helix chain 'A' and resid 411 through 418 removed outlier: 3.683A pdb=" N GLN A 418 " --> pdb=" O ARG A 414 " (cutoff:3.500A) Processing helix chain 'A' and resid 422 through 445 Processing helix chain 'A' and resid 450 through 464 Processing helix chain 'A' and resid 465 through 472 removed outlier: 3.608A pdb=" N GLY A 471 " --> pdb=" O PHE A 468 " (cutoff:3.500A) Processing helix chain 'A' and resid 474 through 487 removed outlier: 4.283A pdb=" N PHE A 478 " --> pdb=" O MET A 474 " (cutoff:3.500A) Processing helix chain 'A' and resid 488 through 512 removed outlier: 3.587A pdb=" N ARG A 492 " --> pdb=" O GLY A 488 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N TRP A 495 " --> pdb=" O MET A 491 " (cutoff:3.500A) removed outlier: 4.173A pdb=" N LEU A 496 " --> pdb=" O ARG A 492 " (cutoff:3.500A) Processing helix chain 'A' and resid 525 through 538 Processing helix chain 'A' and resid 552 through 566 removed outlier: 3.547A pdb=" N CYS A 556 " --> pdb=" O PRO A 552 " (cutoff:3.500A) Processing helix chain 'A' and resid 569 through 585 Processing helix chain 'A' and resid 585 through 608 Processing helix chain 'A' and resid 609 through 613 Processing helix chain 'A' and resid 621 through 624 removed outlier: 3.744A pdb=" N GLY A 624 " --> pdb=" O TYR A 621 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 621 through 624' Processing helix chain 'B' and resid 30 through 47 Processing helix chain 'B' and resid 47 through 55 Processing helix chain 'B' and resid 57 through 66 removed outlier: 3.628A pdb=" N LEU B 61 " --> pdb=" O ASP B 57 " (cutoff:3.500A) Processing helix chain 'B' and resid 81 through 89 Processing helix chain 'B' and resid 91 through 102 Processing helix chain 'B' and resid 103 through 107 removed outlier: 3.794A pdb=" N ALA B 106 " --> pdb=" O PRO B 103 " (cutoff:3.500A) Processing helix chain 'B' and resid 112 through 116 removed outlier: 4.108A pdb=" N VAL B 116 " --> pdb=" O GLU B 113 " (cutoff:3.500A) Processing helix chain 'B' and resid 119 through 127 removed outlier: 3.519A pdb=" N ILE B 123 " --> pdb=" O THR B 119 " (cutoff:3.500A) Processing helix chain 'B' and resid 129 through 139 removed outlier: 3.633A pdb=" N ARG B 139 " --> pdb=" O ALA B 135 " (cutoff:3.500A) Processing helix chain 'B' and resid 165 through 174 removed outlier: 3.504A pdb=" N GLY B 174 " --> pdb=" O ALA B 170 " (cutoff:3.500A) Processing helix chain 'B' and resid 175 through 185 Processing helix chain 'B' and resid 198 through 205 Processing helix chain 'B' and resid 208 through 221 removed outlier: 4.003A pdb=" N CYS B 213 " --> pdb=" O LYS B 209 " (cutoff:3.500A) removed outlier: 4.285A pdb=" N GLN B 214 " --> pdb=" O THR B 210 " (cutoff:3.500A) Processing helix chain 'B' and resid 231 through 235 Processing helix chain 'B' and resid 242 through 250 Processing helix chain 'B' and resid 252 through 262 removed outlier: 3.931A pdb=" N LYS B 262 " --> pdb=" O HIS B 258 " (cutoff:3.500A) Processing helix chain 'B' and resid 280 through 285 removed outlier: 3.912A pdb=" N SER B 285 " --> pdb=" O THR B 281 " (cutoff:3.500A) Processing helix chain 'B' and resid 291 through 298 Processing helix chain 'B' and resid 302 through 309 removed outlier: 3.847A pdb=" N ARG B 305 " --> pdb=" O ARG B 302 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N GLU B 309 " --> pdb=" O GLN B 306 " (cutoff:3.500A) Processing helix chain 'B' and resid 310 through 324 removed outlier: 3.983A pdb=" N GLU B 315 " --> pdb=" O THR B 311 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N LEU B 316 " --> pdb=" O PRO B 312 " (cutoff:3.500A) Processing helix chain 'B' and resid 324 through 349 Processing helix chain 'B' and resid 379 through 410 Proline residue: B 405 - end of helix removed outlier: 3.694A pdb=" N VAL B 410 " --> pdb=" O ASP B 406 " (cutoff:3.500A) Processing helix chain 'B' and resid 411 through 418 removed outlier: 3.684A pdb=" N GLN B 418 " --> pdb=" O ARG B 414 " (cutoff:3.500A) Processing helix chain 'B' and resid 422 through 445 Processing helix chain 'B' and resid 450 through 464 Processing helix chain 'B' and resid 465 through 472 removed outlier: 3.608A pdb=" N GLY B 471 " --> pdb=" O PHE B 468 " (cutoff:3.500A) Processing helix chain 'B' and resid 474 through 487 removed outlier: 4.283A pdb=" N PHE B 478 " --> pdb=" O MET B 474 " (cutoff:3.500A) Processing helix chain 'B' and resid 488 through 512 removed outlier: 3.592A pdb=" N ARG B 492 " --> pdb=" O GLY B 488 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N TRP B 495 " --> pdb=" O MET B 491 " (cutoff:3.500A) removed outlier: 4.174A pdb=" N LEU B 496 " --> pdb=" O ARG B 492 " (cutoff:3.500A) Processing helix chain 'B' and resid 525 through 538 Processing helix chain 'B' and resid 552 through 566 removed outlier: 3.548A pdb=" N CYS B 556 " --> pdb=" O PRO B 552 " (cutoff:3.500A) Processing helix chain 'B' and resid 569 through 585 Processing helix chain 'B' and resid 585 through 608 Processing helix chain 'B' and resid 609 through 613 Processing helix chain 'B' and resid 621 through 624 removed outlier: 3.747A pdb=" N GLY B 624 " --> pdb=" O TYR B 621 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 621 through 624' Processing helix chain 'C' and resid 30 through 47 Processing helix chain 'C' and resid 47 through 55 Processing helix chain 'C' and resid 57 through 66 removed outlier: 3.628A pdb=" N LEU C 61 " --> pdb=" O ASP C 57 " (cutoff:3.500A) Processing helix chain 'C' and resid 81 through 89 Processing helix chain 'C' and resid 91 through 102 Processing helix chain 'C' and resid 103 through 107 removed outlier: 3.790A pdb=" N ALA C 106 " --> pdb=" O PRO C 103 " (cutoff:3.500A) Processing helix chain 'C' and resid 112 through 116 removed outlier: 4.106A pdb=" N VAL C 116 " --> pdb=" O GLU C 113 " (cutoff:3.500A) Processing helix chain 'C' and resid 119 through 127 removed outlier: 3.529A pdb=" N ILE C 123 " --> pdb=" O THR C 119 " (cutoff:3.500A) Processing helix chain 'C' and resid 129 through 139 removed outlier: 3.630A pdb=" N ARG C 139 " --> pdb=" O ALA C 135 " (cutoff:3.500A) Processing helix chain 'C' and resid 165 through 174 removed outlier: 3.519A pdb=" N GLY C 174 " --> pdb=" O ALA C 170 " (cutoff:3.500A) Processing helix chain 'C' and resid 175 through 185 Processing helix chain 'C' and resid 198 through 205 Processing helix chain 'C' and resid 208 through 221 removed outlier: 3.999A pdb=" N CYS C 213 " --> pdb=" O LYS C 209 " (cutoff:3.500A) removed outlier: 4.282A pdb=" N GLN C 214 " --> pdb=" O THR C 210 " (cutoff:3.500A) Processing helix chain 'C' and resid 231 through 235 Processing helix chain 'C' and resid 242 through 250 Processing helix chain 'C' and resid 252 through 262 removed outlier: 3.923A pdb=" N LYS C 262 " --> pdb=" O HIS C 258 " (cutoff:3.500A) Processing helix chain 'C' and resid 280 through 285 removed outlier: 3.906A pdb=" N SER C 285 " --> pdb=" O THR C 281 " (cutoff:3.500A) Processing helix chain 'C' and resid 291 through 298 Processing helix chain 'C' and resid 302 through 309 removed outlier: 3.847A pdb=" N ARG C 305 " --> pdb=" O ARG C 302 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N GLU C 309 " --> pdb=" O GLN C 306 " (cutoff:3.500A) Processing helix chain 'C' and resid 310 through 324 removed outlier: 4.005A pdb=" N GLU C 315 " --> pdb=" O THR C 311 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N LEU C 316 " --> pdb=" O PRO C 312 " (cutoff:3.500A) Processing helix chain 'C' and resid 324 through 349 Processing helix chain 'C' and resid 379 through 410 Proline residue: C 405 - end of helix removed outlier: 3.693A pdb=" N VAL C 410 " --> pdb=" O ASP C 406 " (cutoff:3.500A) Processing helix chain 'C' and resid 411 through 418 removed outlier: 3.684A pdb=" N GLN C 418 " --> pdb=" O ARG C 414 " (cutoff:3.500A) Processing helix chain 'C' and resid 422 through 445 Processing helix chain 'C' and resid 450 through 464 Processing helix chain 'C' and resid 465 through 472 removed outlier: 3.608A pdb=" N GLY C 471 " --> pdb=" O PHE C 468 " (cutoff:3.500A) Processing helix chain 'C' and resid 474 through 487 removed outlier: 4.278A pdb=" N PHE C 478 " --> pdb=" O MET C 474 " (cutoff:3.500A) Processing helix chain 'C' and resid 488 through 512 removed outlier: 3.608A pdb=" N ARG C 492 " --> pdb=" O GLY C 488 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N TRP C 495 " --> pdb=" O MET C 491 " (cutoff:3.500A) removed outlier: 4.159A pdb=" N LEU C 496 " --> pdb=" O ARG C 492 " (cutoff:3.500A) Processing helix chain 'C' and resid 525 through 538 Processing helix chain 'C' and resid 552 through 566 removed outlier: 3.599A pdb=" N CYS C 556 " --> pdb=" O PRO C 552 " (cutoff:3.500A) Processing helix chain 'C' and resid 569 through 585 Processing helix chain 'C' and resid 585 through 608 Processing helix chain 'C' and resid 609 through 613 Processing helix chain 'C' and resid 621 through 624 removed outlier: 3.759A pdb=" N GLY C 624 " --> pdb=" O TYR C 621 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 621 through 624' Processing helix chain 'D' and resid 30 through 47 Processing helix chain 'D' and resid 47 through 55 Processing helix chain 'D' and resid 57 through 66 removed outlier: 3.633A pdb=" N LEU D 61 " --> pdb=" O ASP D 57 " (cutoff:3.500A) Processing helix chain 'D' and resid 81 through 89 Processing helix chain 'D' and resid 91 through 102 Processing helix chain 'D' and resid 103 through 107 removed outlier: 3.793A pdb=" N ALA D 106 " --> pdb=" O PRO D 103 " (cutoff:3.500A) Processing helix chain 'D' and resid 112 through 116 removed outlier: 4.106A pdb=" N VAL D 116 " --> pdb=" O GLU D 113 " (cutoff:3.500A) Processing helix chain 'D' and resid 119 through 127 removed outlier: 3.528A pdb=" N ILE D 123 " --> pdb=" O THR D 119 " (cutoff:3.500A) Processing helix chain 'D' and resid 129 through 139 removed outlier: 3.629A pdb=" N ARG D 139 " --> pdb=" O ALA D 135 " (cutoff:3.500A) Processing helix chain 'D' and resid 165 through 174 removed outlier: 3.506A pdb=" N GLY D 174 " --> pdb=" O ALA D 170 " (cutoff:3.500A) Processing helix chain 'D' and resid 175 through 185 Processing helix chain 'D' and resid 198 through 205 Processing helix chain 'D' and resid 208 through 221 removed outlier: 4.000A pdb=" N CYS D 213 " --> pdb=" O LYS D 209 " (cutoff:3.500A) removed outlier: 4.283A pdb=" N GLN D 214 " --> pdb=" O THR D 210 " (cutoff:3.500A) Processing helix chain 'D' and resid 231 through 235 Processing helix chain 'D' and resid 242 through 250 Processing helix chain 'D' and resid 252 through 262 removed outlier: 3.927A pdb=" N LYS D 262 " --> pdb=" O HIS D 258 " (cutoff:3.500A) Processing helix chain 'D' and resid 280 through 285 removed outlier: 3.941A pdb=" N SER D 285 " --> pdb=" O THR D 281 " (cutoff:3.500A) Processing helix chain 'D' and resid 291 through 298 Processing helix chain 'D' and resid 302 through 309 removed outlier: 3.846A pdb=" N ARG D 305 " --> pdb=" O ARG D 302 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N GLU D 309 " --> pdb=" O GLN D 306 " (cutoff:3.500A) Processing helix chain 'D' and resid 310 through 324 removed outlier: 3.985A pdb=" N GLU D 315 " --> pdb=" O THR D 311 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N LEU D 316 " --> pdb=" O PRO D 312 " (cutoff:3.500A) Processing helix chain 'D' and resid 324 through 349 Processing helix chain 'D' and resid 379 through 410 Proline residue: D 405 - end of helix removed outlier: 3.693A pdb=" N VAL D 410 " --> pdb=" O ASP D 406 " (cutoff:3.500A) Processing helix chain 'D' and resid 411 through 418 removed outlier: 3.683A pdb=" N GLN D 418 " --> pdb=" O ARG D 414 " (cutoff:3.500A) Processing helix chain 'D' and resid 422 through 445 Processing helix chain 'D' and resid 450 through 464 Processing helix chain 'D' and resid 465 through 472 removed outlier: 3.609A pdb=" N GLY D 471 " --> pdb=" O PHE D 468 " (cutoff:3.500A) Processing helix chain 'D' and resid 474 through 487 removed outlier: 4.284A pdb=" N PHE D 478 " --> pdb=" O MET D 474 " (cutoff:3.500A) Processing helix chain 'D' and resid 488 through 512 removed outlier: 3.618A pdb=" N ARG D 492 " --> pdb=" O GLY D 488 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N TRP D 495 " --> pdb=" O MET D 491 " (cutoff:3.500A) removed outlier: 4.165A pdb=" N LEU D 496 " --> pdb=" O ARG D 492 " (cutoff:3.500A) Processing helix chain 'D' and resid 525 through 538 Processing helix chain 'D' and resid 552 through 566 removed outlier: 3.546A pdb=" N CYS D 556 " --> pdb=" O PRO D 552 " (cutoff:3.500A) Processing helix chain 'D' and resid 569 through 585 Processing helix chain 'D' and resid 585 through 608 Processing helix chain 'D' and resid 609 through 613 Processing helix chain 'D' and resid 621 through 624 removed outlier: 3.740A pdb=" N GLY D 624 " --> pdb=" O TYR D 621 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 621 through 624' Processing sheet with id=AA1, first strand: chain 'A' and resid 264 through 270 removed outlier: 6.706A pdb=" N SER A 275 " --> pdb=" O GLN A 267 " (cutoff:3.500A) removed outlier: 4.385A pdb=" N THR A 269 " --> pdb=" O LEU A 273 " (cutoff:3.500A) removed outlier: 6.425A pdb=" N LEU A 273 " --> pdb=" O THR A 269 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 352 through 354 Processing sheet with id=AA3, first strand: chain 'B' and resid 264 through 270 removed outlier: 6.706A pdb=" N SER B 275 " --> pdb=" O GLN B 267 " (cutoff:3.500A) removed outlier: 4.386A pdb=" N THR B 269 " --> pdb=" O LEU B 273 " (cutoff:3.500A) removed outlier: 6.424A pdb=" N LEU B 273 " --> pdb=" O THR B 269 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 352 through 354 Processing sheet with id=AA5, first strand: chain 'C' and resid 264 through 270 removed outlier: 6.697A pdb=" N SER C 275 " --> pdb=" O GLN C 267 " (cutoff:3.500A) removed outlier: 4.387A pdb=" N THR C 269 " --> pdb=" O LEU C 273 " (cutoff:3.500A) removed outlier: 6.427A pdb=" N LEU C 273 " --> pdb=" O THR C 269 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 352 through 354 Processing sheet with id=AA7, first strand: chain 'D' and resid 264 through 270 removed outlier: 6.703A pdb=" N SER D 275 " --> pdb=" O GLN D 267 " (cutoff:3.500A) removed outlier: 4.383A pdb=" N THR D 269 " --> pdb=" O LEU D 273 " (cutoff:3.500A) removed outlier: 6.424A pdb=" N LEU D 273 " --> pdb=" O THR D 269 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 352 through 354 1129 hydrogen bonds defined for protein. 3219 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: 6.40 Time building geometry restraints manager: 5.38 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: 6195 1.34 - 1.46: 4253 1.46 - 1.58: 9184 1.58 - 1.70: 0 1.70 - 1.82: 228 Bond restraints: 19860 Sorted by residual: bond pdb=" C THR A 311 " pdb=" N PRO A 312 " ideal model delta sigma weight residual 1.337 1.367 -0.030 1.24e-02 6.50e+03 5.85e+00 bond pdb=" C THR B 311 " pdb=" N PRO B 312 " ideal model delta sigma weight residual 1.337 1.367 -0.030 1.24e-02 6.50e+03 5.81e+00 bond pdb=" C THR C 311 " pdb=" N PRO C 312 " ideal model delta sigma weight residual 1.337 1.367 -0.029 1.24e-02 6.50e+03 5.62e+00 bond pdb=" C THR D 311 " pdb=" N PRO D 312 " ideal model delta sigma weight residual 1.337 1.366 -0.029 1.24e-02 6.50e+03 5.38e+00 bond pdb=" C VAL B 452 " pdb=" N PRO B 453 " ideal model delta sigma weight residual 1.336 1.358 -0.023 1.23e-02 6.61e+03 3.38e+00 ... (remaining 19855 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.77: 25931 1.77 - 3.53: 828 3.53 - 5.30: 124 5.30 - 7.07: 64 7.07 - 8.83: 17 Bond angle restraints: 26964 Sorted by residual: angle pdb=" N GLU C 591 " pdb=" CA GLU C 591 " pdb=" CB GLU C 591 " ideal model delta sigma weight residual 110.28 117.34 -7.06 1.55e+00 4.16e-01 2.07e+01 angle pdb=" N GLU A 591 " pdb=" CA GLU A 591 " pdb=" CB GLU A 591 " ideal model delta sigma weight residual 110.28 117.31 -7.03 1.55e+00 4.16e-01 2.06e+01 angle pdb=" N GLU D 591 " pdb=" CA GLU D 591 " pdb=" CB GLU D 591 " ideal model delta sigma weight residual 110.28 117.28 -7.00 1.55e+00 4.16e-01 2.04e+01 angle pdb=" N GLU B 591 " pdb=" CA GLU B 591 " pdb=" CB GLU B 591 " ideal model delta sigma weight residual 110.28 117.28 -7.00 1.55e+00 4.16e-01 2.04e+01 angle pdb=" CA GLU B 591 " pdb=" CB GLU B 591 " pdb=" CG GLU B 591 " ideal model delta sigma weight residual 114.10 121.29 -7.19 2.00e+00 2.50e-01 1.29e+01 ... (remaining 26959 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.04: 10669 17.04 - 34.07: 903 34.07 - 51.11: 168 51.11 - 68.15: 44 68.15 - 85.18: 28 Dihedral angle restraints: 11812 sinusoidal: 4732 harmonic: 7080 Sorted by residual: dihedral pdb=" CA MET C 474 " pdb=" C MET C 474 " pdb=" N LEU C 475 " pdb=" CA LEU C 475 " ideal model delta harmonic sigma weight residual -180.00 -163.71 -16.29 0 5.00e+00 4.00e-02 1.06e+01 dihedral pdb=" CA MET B 474 " pdb=" C MET B 474 " pdb=" N LEU B 475 " pdb=" CA LEU B 475 " ideal model delta harmonic sigma weight residual -180.00 -163.77 -16.23 0 5.00e+00 4.00e-02 1.05e+01 dihedral pdb=" CA MET A 474 " pdb=" C MET A 474 " pdb=" N LEU A 475 " pdb=" CA LEU A 475 " ideal model delta harmonic sigma weight residual -180.00 -163.80 -16.20 0 5.00e+00 4.00e-02 1.05e+01 ... (remaining 11809 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.074: 2716 0.074 - 0.148: 333 0.148 - 0.223: 19 0.223 - 0.297: 0 0.297 - 0.371: 4 Chirality restraints: 3072 Sorted by residual: chirality pdb=" CB VAL D 297 " pdb=" CA VAL D 297 " pdb=" CG1 VAL D 297 " pdb=" CG2 VAL D 297 " both_signs ideal model delta sigma weight residual False -2.63 -2.26 -0.37 2.00e-01 2.50e+01 3.44e+00 chirality pdb=" CB VAL A 297 " pdb=" CA VAL A 297 " pdb=" CG1 VAL A 297 " pdb=" CG2 VAL A 297 " both_signs ideal model delta sigma weight residual False -2.63 -2.26 -0.37 2.00e-01 2.50e+01 3.44e+00 chirality pdb=" CB VAL B 297 " pdb=" CA VAL B 297 " pdb=" CG1 VAL B 297 " pdb=" CG2 VAL B 297 " both_signs ideal model delta sigma weight residual False -2.63 -2.26 -0.37 2.00e-01 2.50e+01 3.39e+00 ... (remaining 3069 not shown) Planarity restraints: 3416 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLY B 476 " -0.036 5.00e-02 4.00e+02 5.46e-02 4.77e+00 pdb=" N PRO B 477 " 0.094 5.00e-02 4.00e+02 pdb=" CA PRO B 477 " -0.028 5.00e-02 4.00e+02 pdb=" CD PRO B 477 " -0.031 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY D 476 " -0.036 5.00e-02 4.00e+02 5.44e-02 4.74e+00 pdb=" N PRO D 477 " 0.094 5.00e-02 4.00e+02 pdb=" CA PRO D 477 " -0.028 5.00e-02 4.00e+02 pdb=" CD PRO D 477 " -0.030 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY C 476 " 0.036 5.00e-02 4.00e+02 5.44e-02 4.73e+00 pdb=" N PRO C 477 " -0.094 5.00e-02 4.00e+02 pdb=" CA PRO C 477 " 0.028 5.00e-02 4.00e+02 pdb=" CD PRO C 477 " 0.030 5.00e-02 4.00e+02 ... (remaining 3413 not shown) Histogram of nonbonded interaction distances: 2.30 - 2.82: 5632 2.82 - 3.34: 18026 3.34 - 3.86: 34068 3.86 - 4.38: 40083 4.38 - 4.90: 67034 Nonbonded interactions: 164843 Sorted by model distance: nonbonded pdb=" OH TYR B 161 " pdb=" OD2 ASP B 193 " model vdw 2.302 3.040 nonbonded pdb=" OH TYR A 161 " pdb=" OD2 ASP A 193 " model vdw 2.302 3.040 nonbonded pdb=" OH TYR C 161 " pdb=" OD2 ASP C 193 " model vdw 2.302 3.040 nonbonded pdb=" OH TYR D 161 " pdb=" OD2 ASP D 193 " model vdw 2.303 3.040 nonbonded pdb=" O PRO B 544 " pdb=" OH TYR B 555 " model vdw 2.342 3.040 ... (remaining 164838 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 'B' selection = chain 'C' selection = chain 'D' } 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: 3.160 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: 0.800 Check model and map are aligned: 0.140 Set scattering table: 0.200 Process input model: 43.790 Find NCS groups from input model: 0.620 Set up NCS constraints: 0.090 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:13.220 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.010 Total: 62.060 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8143 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 19860 Z= 0.275 Angle : 0.793 8.831 26964 Z= 0.430 Chirality : 0.048 0.371 3072 Planarity : 0.007 0.065 3416 Dihedral : 14.057 85.182 7236 Min Nonbonded Distance : 2.302 Molprobity Statistics. All-atom Clashscore : 2.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.33 % Favored : 98.67 % Rotamer: Outliers : 0.00 % Allowed : 0.48 % Favored : 99.52 % 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: -1.56 (0.15), residues: 2408 helix: -0.80 (0.11), residues: 1484 sheet: -1.14 (0.45), residues: 128 loop : -1.16 (0.20), residues: 796 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP B 593 HIS 0.005 0.001 HIS D 201 PHE 0.022 0.002 PHE B 553 TYR 0.013 0.002 TYR A 623 ARG 0.015 0.001 ARG B 35 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4816 Ramachandran restraints generated. 2408 Oldfield, 0 Emsley, 2408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4816 Ramachandran restraints generated. 2408 Oldfield, 0 Emsley, 2408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 370 residues out of total 2096 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 370 time to evaluate : 2.426 Fit side-chains REVERT: A 233 GLU cc_start: 0.7625 (tt0) cc_final: 0.6999 (mm-30) REVERT: B 139 ARG cc_start: 0.7122 (mtp180) cc_final: 0.6908 (mmm160) REVERT: B 233 GLU cc_start: 0.7624 (tt0) cc_final: 0.6993 (mm-30) REVERT: C 139 ARG cc_start: 0.7132 (mtp180) cc_final: 0.6903 (mmm160) REVERT: C 233 GLU cc_start: 0.7638 (tt0) cc_final: 0.7003 (mm-30) REVERT: D 233 GLU cc_start: 0.7623 (tt0) cc_final: 0.6997 (mm-30) outliers start: 0 outliers final: 0 residues processed: 370 average time/residue: 1.3946 time to fit residues: 576.8246 Evaluate side-chains 310 residues out of total 2096 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 310 time to evaluate : 2.696 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 202 optimal weight: 3.9990 chunk 181 optimal weight: 5.9990 chunk 100 optimal weight: 0.1980 chunk 62 optimal weight: 9.9990 chunk 122 optimal weight: 1.9990 chunk 97 optimal weight: 9.9990 chunk 188 optimal weight: 1.9990 chunk 72 optimal weight: 5.9990 chunk 114 optimal weight: 0.5980 chunk 140 optimal weight: 0.9980 chunk 217 optimal weight: 0.6980 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 131 ASN A 208 ASN A 587 GLN B 131 ASN B 208 ASN B 587 GLN C 131 ASN C 208 ASN C 587 GLN D 131 ASN D 208 ASN D 587 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8230 moved from start: 0.1310 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 19860 Z= 0.189 Angle : 0.505 5.911 26964 Z= 0.267 Chirality : 0.039 0.130 3072 Planarity : 0.005 0.043 3416 Dihedral : 4.125 15.837 2644 Min Nonbonded Distance : 2.608 Molprobity Statistics. All-atom Clashscore : 4.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.50 % Favored : 99.50 % Rotamer: Outliers : 2.19 % Allowed : 6.82 % Favored : 90.98 % 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: 0.21 (0.16), residues: 2408 helix: 0.71 (0.13), residues: 1496 sheet: -1.20 (0.45), residues: 128 loop : -0.56 (0.22), residues: 784 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP D 593 HIS 0.004 0.001 HIS C 258 PHE 0.018 0.002 PHE C 537 TYR 0.014 0.001 TYR D 555 ARG 0.005 0.000 ARG D 302 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4816 Ramachandran restraints generated. 2408 Oldfield, 0 Emsley, 2408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4816 Ramachandran restraints generated. 2408 Oldfield, 0 Emsley, 2408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 367 residues out of total 2096 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 321 time to evaluate : 2.375 Fit side-chains REVERT: A 35 ARG cc_start: 0.6931 (tpt90) cc_final: 0.6638 (tpt170) REVERT: A 38 MET cc_start: 0.7615 (OUTLIER) cc_final: 0.7375 (ttm) REVERT: A 302 ARG cc_start: 0.7052 (ttt-90) cc_final: 0.6852 (ttt90) REVERT: A 491 MET cc_start: 0.7449 (tpp) cc_final: 0.7205 (tpt) REVERT: A 589 ARG cc_start: 0.7886 (ttp80) cc_final: 0.7296 (ttm170) REVERT: B 35 ARG cc_start: 0.6941 (tpt90) cc_final: 0.6658 (tpt170) REVERT: B 38 MET cc_start: 0.7628 (OUTLIER) cc_final: 0.7412 (ttm) REVERT: B 129 ASN cc_start: 0.7895 (OUTLIER) cc_final: 0.7452 (m-40) REVERT: B 302 ARG cc_start: 0.7050 (ttt-90) cc_final: 0.6849 (ttt90) REVERT: B 491 MET cc_start: 0.7465 (tpp) cc_final: 0.7227 (tpt) REVERT: B 589 ARG cc_start: 0.7883 (ttp80) cc_final: 0.7290 (ttm170) REVERT: C 35 ARG cc_start: 0.6938 (tpt90) cc_final: 0.6645 (tpt170) REVERT: C 38 MET cc_start: 0.7629 (OUTLIER) cc_final: 0.7381 (ttm) REVERT: C 139 ARG cc_start: 0.7283 (mtp180) cc_final: 0.7080 (mmm160) REVERT: C 302 ARG cc_start: 0.7055 (ttt-90) cc_final: 0.6851 (ttt90) REVERT: C 589 ARG cc_start: 0.7884 (ttp80) cc_final: 0.7301 (ttm170) REVERT: D 35 ARG cc_start: 0.6939 (tpt90) cc_final: 0.6651 (tpt170) REVERT: D 38 MET cc_start: 0.7623 (OUTLIER) cc_final: 0.7373 (ttm) REVERT: D 302 ARG cc_start: 0.7050 (ttt-90) cc_final: 0.6846 (ttt90) REVERT: D 491 MET cc_start: 0.7491 (tpp) cc_final: 0.7255 (tpt) REVERT: D 589 ARG cc_start: 0.7874 (ttp80) cc_final: 0.7278 (ttm170) outliers start: 46 outliers final: 1 residues processed: 350 average time/residue: 1.3442 time to fit residues: 529.3703 Evaluate side-chains 322 residues out of total 2096 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 316 time to evaluate : 2.343 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 MET Chi-restraints excluded: chain B residue 38 MET Chi-restraints excluded: chain B residue 43 ARG Chi-restraints excluded: chain B residue 129 ASN Chi-restraints excluded: chain C residue 38 MET Chi-restraints excluded: chain D residue 38 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 121 optimal weight: 0.9980 chunk 67 optimal weight: 4.9990 chunk 181 optimal weight: 1.9990 chunk 148 optimal weight: 0.6980 chunk 60 optimal weight: 7.9990 chunk 218 optimal weight: 6.9990 chunk 235 optimal weight: 5.9990 chunk 194 optimal weight: 0.6980 chunk 216 optimal weight: 0.9990 chunk 74 optimal weight: 0.9980 chunk 175 optimal weight: 5.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 31 GLN A 131 ASN B 31 GLN B 131 ASN C 31 GLN C 131 ASN D 31 GLN D 131 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8246 moved from start: 0.1539 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 19860 Z= 0.186 Angle : 0.485 5.846 26964 Z= 0.254 Chirality : 0.039 0.128 3072 Planarity : 0.004 0.039 3416 Dihedral : 3.967 14.714 2644 Min Nonbonded Distance : 2.623 Molprobity Statistics. All-atom Clashscore : 4.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.83 % Favored : 99.17 % Rotamer: Outliers : 2.19 % Allowed : 9.83 % Favored : 87.98 % 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: 0.91 (0.17), residues: 2408 helix: 1.33 (0.13), residues: 1500 sheet: -1.23 (0.45), residues: 128 loop : -0.38 (0.23), residues: 780 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP D 593 HIS 0.004 0.001 HIS C 258 PHE 0.015 0.001 PHE C 537 TYR 0.012 0.001 TYR B 555 ARG 0.004 0.000 ARG C 302 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4816 Ramachandran restraints generated. 2408 Oldfield, 0 Emsley, 2408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4816 Ramachandran restraints generated. 2408 Oldfield, 0 Emsley, 2408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 360 residues out of total 2096 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 314 time to evaluate : 2.385 Fit side-chains REVERT: A 326 ARG cc_start: 0.7918 (OUTLIER) cc_final: 0.7411 (ttm110) REVERT: A 491 MET cc_start: 0.7528 (tpp) cc_final: 0.7302 (tpt) REVERT: A 578 MET cc_start: 0.8310 (ttm) cc_final: 0.8067 (mtm) REVERT: B 129 ASN cc_start: 0.8033 (OUTLIER) cc_final: 0.7567 (m-40) REVERT: C 139 ARG cc_start: 0.7382 (mtp180) cc_final: 0.7113 (mmm160) REVERT: C 326 ARG cc_start: 0.7917 (OUTLIER) cc_final: 0.7403 (ttm110) REVERT: C 578 MET cc_start: 0.8256 (OUTLIER) cc_final: 0.8007 (mtm) REVERT: D 326 ARG cc_start: 0.7921 (OUTLIER) cc_final: 0.7415 (ttm110) REVERT: D 491 MET cc_start: 0.7531 (tpp) cc_final: 0.7318 (tpt) outliers start: 46 outliers final: 17 residues processed: 340 average time/residue: 1.5325 time to fit residues: 580.3445 Evaluate side-chains 336 residues out of total 2096 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 314 time to evaluate : 2.615 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 157 HIS Chi-restraints excluded: chain A residue 326 ARG Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 401 LEU Chi-restraints excluded: chain A residue 474 MET Chi-restraints excluded: chain B residue 43 ARG Chi-restraints excluded: chain B residue 129 ASN Chi-restraints excluded: chain B residue 157 HIS Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain B residue 401 LEU Chi-restraints excluded: chain B residue 474 MET Chi-restraints excluded: chain C residue 157 HIS Chi-restraints excluded: chain C residue 326 ARG Chi-restraints excluded: chain C residue 335 LEU Chi-restraints excluded: chain C residue 401 LEU Chi-restraints excluded: chain C residue 474 MET Chi-restraints excluded: chain C residue 578 MET Chi-restraints excluded: chain D residue 157 HIS Chi-restraints excluded: chain D residue 326 ARG Chi-restraints excluded: chain D residue 335 LEU Chi-restraints excluded: chain D residue 401 LEU Chi-restraints excluded: chain D residue 474 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 215 optimal weight: 0.9990 chunk 164 optimal weight: 1.9990 chunk 113 optimal weight: 1.9990 chunk 24 optimal weight: 6.9990 chunk 104 optimal weight: 0.9980 chunk 146 optimal weight: 4.9990 chunk 219 optimal weight: 0.6980 chunk 231 optimal weight: 0.9990 chunk 114 optimal weight: 3.9990 chunk 207 optimal weight: 0.9980 chunk 62 optimal weight: 4.9990 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 131 ASN B 131 ASN C 31 GLN C 131 ASN D 31 GLN D 131 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8255 moved from start: 0.1715 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 19860 Z= 0.195 Angle : 0.488 5.839 26964 Z= 0.256 Chirality : 0.039 0.130 3072 Planarity : 0.004 0.057 3416 Dihedral : 3.913 15.364 2644 Min Nonbonded Distance : 2.618 Molprobity Statistics. All-atom Clashscore : 4.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.83 % Favored : 99.17 % Rotamer: Outliers : 1.91 % Allowed : 11.55 % Favored : 86.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.15 (0.17), residues: 2408 helix: 1.54 (0.13), residues: 1500 sheet: -1.19 (0.45), residues: 128 loop : -0.30 (0.23), residues: 780 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 593 HIS 0.004 0.001 HIS A 201 PHE 0.013 0.001 PHE A 472 TYR 0.013 0.001 TYR A 555 ARG 0.008 0.000 ARG D 302 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4816 Ramachandran restraints generated. 2408 Oldfield, 0 Emsley, 2408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4816 Ramachandran restraints generated. 2408 Oldfield, 0 Emsley, 2408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 366 residues out of total 2096 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 326 time to evaluate : 2.135 Fit side-chains REVERT: A 35 ARG cc_start: 0.6945 (tpt90) cc_final: 0.6454 (mtt90) REVERT: A 591 GLU cc_start: 0.7687 (mt-10) cc_final: 0.7481 (mt-10) REVERT: B 35 ARG cc_start: 0.6937 (tpt90) cc_final: 0.6506 (mtt90) REVERT: B 129 ASN cc_start: 0.8090 (OUTLIER) cc_final: 0.7616 (m-40) REVERT: B 326 ARG cc_start: 0.7946 (OUTLIER) cc_final: 0.7415 (ttm110) REVERT: B 591 GLU cc_start: 0.7644 (mt-10) cc_final: 0.7420 (mt-10) REVERT: C 35 ARG cc_start: 0.6953 (tpt90) cc_final: 0.6503 (mtt90) REVERT: C 139 ARG cc_start: 0.7417 (mtp180) cc_final: 0.7120 (mmm160) REVERT: C 326 ARG cc_start: 0.7956 (OUTLIER) cc_final: 0.7404 (ttm110) REVERT: C 578 MET cc_start: 0.8273 (OUTLIER) cc_final: 0.7993 (mtm) REVERT: C 591 GLU cc_start: 0.7652 (mt-10) cc_final: 0.7431 (mt-10) REVERT: D 35 ARG cc_start: 0.6956 (tpt90) cc_final: 0.6520 (mtt90) REVERT: D 591 GLU cc_start: 0.7671 (mt-10) cc_final: 0.7457 (mt-10) outliers start: 40 outliers final: 15 residues processed: 352 average time/residue: 1.3776 time to fit residues: 543.6675 Evaluate side-chains 327 residues out of total 2096 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 308 time to evaluate : 2.212 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 297 VAL Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 401 LEU Chi-restraints excluded: chain A residue 499 VAL Chi-restraints excluded: chain B residue 43 ARG Chi-restraints excluded: chain B residue 129 ASN Chi-restraints excluded: chain B residue 297 VAL Chi-restraints excluded: chain B residue 326 ARG Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain B residue 499 VAL Chi-restraints excluded: chain C residue 297 VAL Chi-restraints excluded: chain C residue 326 ARG Chi-restraints excluded: chain C residue 335 LEU Chi-restraints excluded: chain C residue 499 VAL Chi-restraints excluded: chain C residue 578 MET Chi-restraints excluded: chain D residue 297 VAL Chi-restraints excluded: chain D residue 335 LEU Chi-restraints excluded: chain D residue 401 LEU Chi-restraints excluded: chain D residue 499 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 193 optimal weight: 1.9990 chunk 131 optimal weight: 9.9990 chunk 3 optimal weight: 10.0000 chunk 172 optimal weight: 1.9990 chunk 95 optimal weight: 1.9990 chunk 197 optimal weight: 2.9990 chunk 160 optimal weight: 0.7980 chunk 0 optimal weight: 7.9990 chunk 118 optimal weight: 3.9990 chunk 208 optimal weight: 1.9990 chunk 58 optimal weight: 2.9990 overall best weight: 1.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 31 GLN A 131 ASN B 31 GLN B 131 ASN C 31 GLN C 131 ASN D 31 GLN D 131 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8305 moved from start: 0.1934 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 19860 Z= 0.303 Angle : 0.555 5.997 26964 Z= 0.291 Chirality : 0.043 0.142 3072 Planarity : 0.004 0.040 3416 Dihedral : 4.185 17.011 2644 Min Nonbonded Distance : 2.580 Molprobity Statistics. All-atom Clashscore : 5.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.87 % Favored : 99.13 % Rotamer: Outliers : 2.00 % Allowed : 12.12 % Favored : 85.88 % 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: 1.11 (0.17), residues: 2408 helix: 1.47 (0.13), residues: 1500 sheet: -1.14 (0.46), residues: 128 loop : -0.25 (0.23), residues: 780 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A 593 HIS 0.004 0.001 HIS C 258 PHE 0.015 0.002 PHE B 472 TYR 0.014 0.002 TYR A 555 ARG 0.009 0.000 ARG A 302 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4816 Ramachandran restraints generated. 2408 Oldfield, 0 Emsley, 2408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4816 Ramachandran restraints generated. 2408 Oldfield, 0 Emsley, 2408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 355 residues out of total 2096 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 313 time to evaluate : 2.329 Fit side-chains REVERT: A 326 ARG cc_start: 0.7974 (OUTLIER) cc_final: 0.7440 (ttm110) REVERT: A 381 GLN cc_start: 0.5279 (tp40) cc_final: 0.4924 (mm-40) REVERT: A 485 MET cc_start: 0.7802 (mmt) cc_final: 0.7560 (mmt) REVERT: A 578 MET cc_start: 0.8331 (OUTLIER) cc_final: 0.7985 (mtm) REVERT: B 129 ASN cc_start: 0.8315 (OUTLIER) cc_final: 0.7807 (m-40) REVERT: B 326 ARG cc_start: 0.7973 (OUTLIER) cc_final: 0.7432 (ttm110) REVERT: B 381 GLN cc_start: 0.5316 (tp40) cc_final: 0.4936 (mm-40) REVERT: C 129 ASN cc_start: 0.8204 (OUTLIER) cc_final: 0.7738 (m-40) REVERT: C 139 ARG cc_start: 0.7542 (mtp180) cc_final: 0.7180 (mmm160) REVERT: C 326 ARG cc_start: 0.7966 (OUTLIER) cc_final: 0.7437 (ttm110) REVERT: C 381 GLN cc_start: 0.5324 (tp40) cc_final: 0.4940 (mm-40) REVERT: C 578 MET cc_start: 0.8331 (OUTLIER) cc_final: 0.8045 (mtm) REVERT: D 326 ARG cc_start: 0.7975 (OUTLIER) cc_final: 0.7440 (ttm110) REVERT: D 381 GLN cc_start: 0.5286 (tp40) cc_final: 0.4931 (mm-40) outliers start: 42 outliers final: 19 residues processed: 343 average time/residue: 1.3708 time to fit residues: 528.0243 Evaluate side-chains 340 residues out of total 2096 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 313 time to evaluate : 2.527 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 157 HIS Chi-restraints excluded: chain A residue 297 VAL Chi-restraints excluded: chain A residue 326 ARG Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 499 VAL Chi-restraints excluded: chain A residue 578 MET Chi-restraints excluded: chain B residue 43 ARG Chi-restraints excluded: chain B residue 129 ASN Chi-restraints excluded: chain B residue 157 HIS Chi-restraints excluded: chain B residue 297 VAL Chi-restraints excluded: chain B residue 326 ARG Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain B residue 499 VAL Chi-restraints excluded: chain C residue 129 ASN Chi-restraints excluded: chain C residue 157 HIS Chi-restraints excluded: chain C residue 297 VAL Chi-restraints excluded: chain C residue 326 ARG Chi-restraints excluded: chain C residue 335 LEU Chi-restraints excluded: chain C residue 499 VAL Chi-restraints excluded: chain C residue 578 MET Chi-restraints excluded: chain C residue 580 ASP Chi-restraints excluded: chain D residue 157 HIS Chi-restraints excluded: chain D residue 297 VAL Chi-restraints excluded: chain D residue 326 ARG Chi-restraints excluded: chain D residue 335 LEU Chi-restraints excluded: chain D residue 401 LEU Chi-restraints excluded: chain D residue 499 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 78 optimal weight: 2.9990 chunk 208 optimal weight: 0.7980 chunk 45 optimal weight: 2.9990 chunk 136 optimal weight: 7.9990 chunk 57 optimal weight: 1.9990 chunk 232 optimal weight: 0.6980 chunk 192 optimal weight: 5.9990 chunk 107 optimal weight: 0.9980 chunk 19 optimal weight: 4.9990 chunk 76 optimal weight: 7.9990 chunk 121 optimal weight: 0.7980 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 31 GLN A 131 ASN B 31 GLN B 131 ASN C 31 GLN C 131 ASN D 31 GLN D 131 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8277 moved from start: 0.1868 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 19860 Z= 0.209 Angle : 0.502 5.881 26964 Z= 0.263 Chirality : 0.040 0.132 3072 Planarity : 0.004 0.042 3416 Dihedral : 3.979 15.577 2644 Min Nonbonded Distance : 2.617 Molprobity Statistics. All-atom Clashscore : 4.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.87 % Favored : 99.13 % Rotamer: Outliers : 2.10 % Allowed : 11.78 % Favored : 86.12 % 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: 1.31 (0.17), residues: 2408 helix: 1.63 (0.13), residues: 1500 sheet: -1.42 (0.45), residues: 136 loop : -0.09 (0.24), residues: 772 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 593 HIS 0.004 0.001 HIS A 201 PHE 0.011 0.002 PHE A 472 TYR 0.013 0.002 TYR A 555 ARG 0.011 0.000 ARG B 302 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4816 Ramachandran restraints generated. 2408 Oldfield, 0 Emsley, 2408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4816 Ramachandran restraints generated. 2408 Oldfield, 0 Emsley, 2408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 351 residues out of total 2096 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 307 time to evaluate : 2.309 Fit side-chains REVERT: A 326 ARG cc_start: 0.7975 (OUTLIER) cc_final: 0.7434 (ttm110) REVERT: A 381 GLN cc_start: 0.5276 (tp40) cc_final: 0.4940 (mm-40) REVERT: A 578 MET cc_start: 0.8293 (OUTLIER) cc_final: 0.8012 (mtm) REVERT: B 129 ASN cc_start: 0.8279 (OUTLIER) cc_final: 0.7784 (m-40) REVERT: B 326 ARG cc_start: 0.7926 (OUTLIER) cc_final: 0.7406 (ttm110) REVERT: B 381 GLN cc_start: 0.5279 (tp40) cc_final: 0.4909 (mm-40) REVERT: C 129 ASN cc_start: 0.8203 (OUTLIER) cc_final: 0.7734 (m-40) REVERT: C 139 ARG cc_start: 0.7510 (mtp180) cc_final: 0.7213 (mmt-90) REVERT: C 326 ARG cc_start: 0.7957 (OUTLIER) cc_final: 0.7427 (ttm110) REVERT: C 381 GLN cc_start: 0.5306 (tp40) cc_final: 0.4924 (mm-40) REVERT: C 578 MET cc_start: 0.8323 (OUTLIER) cc_final: 0.8049 (mtm) REVERT: D 326 ARG cc_start: 0.7965 (OUTLIER) cc_final: 0.7425 (ttm110) REVERT: D 381 GLN cc_start: 0.5283 (tp40) cc_final: 0.4949 (mm-40) outliers start: 44 outliers final: 20 residues processed: 338 average time/residue: 1.4197 time to fit residues: 537.7480 Evaluate side-chains 336 residues out of total 2096 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 308 time to evaluate : 2.246 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 297 VAL Chi-restraints excluded: chain A residue 326 ARG Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 401 LEU Chi-restraints excluded: chain A residue 499 VAL Chi-restraints excluded: chain A residue 578 MET Chi-restraints excluded: chain B residue 43 ARG Chi-restraints excluded: chain B residue 129 ASN Chi-restraints excluded: chain B residue 297 VAL Chi-restraints excluded: chain B residue 326 ARG Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain B residue 401 LEU Chi-restraints excluded: chain B residue 474 MET Chi-restraints excluded: chain B residue 499 VAL Chi-restraints excluded: chain C residue 129 ASN Chi-restraints excluded: chain C residue 297 VAL Chi-restraints excluded: chain C residue 326 ARG Chi-restraints excluded: chain C residue 335 LEU Chi-restraints excluded: chain C residue 401 LEU Chi-restraints excluded: chain C residue 474 MET Chi-restraints excluded: chain C residue 499 VAL Chi-restraints excluded: chain C residue 578 MET Chi-restraints excluded: chain D residue 297 VAL Chi-restraints excluded: chain D residue 326 ARG Chi-restraints excluded: chain D residue 335 LEU Chi-restraints excluded: chain D residue 401 LEU Chi-restraints excluded: chain D residue 474 MET Chi-restraints excluded: chain D residue 499 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 223 optimal weight: 0.7980 chunk 26 optimal weight: 3.9990 chunk 132 optimal weight: 4.9990 chunk 169 optimal weight: 0.5980 chunk 131 optimal weight: 8.9990 chunk 195 optimal weight: 0.6980 chunk 129 optimal weight: 0.6980 chunk 231 optimal weight: 0.0980 chunk 144 optimal weight: 2.9990 chunk 141 optimal weight: 1.9990 chunk 106 optimal weight: 2.9990 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 31 GLN A 131 ASN B 131 ASN C 131 ASN D 131 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8239 moved from start: 0.1916 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 19860 Z= 0.153 Angle : 0.473 5.799 26964 Z= 0.246 Chirality : 0.038 0.122 3072 Planarity : 0.004 0.044 3416 Dihedral : 3.755 14.061 2644 Min Nonbonded Distance : 2.629 Molprobity Statistics. All-atom Clashscore : 4.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.96 % Favored : 99.04 % Rotamer: Outliers : 1.00 % Allowed : 13.17 % Favored : 85.83 % 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: 1.48 (0.17), residues: 2408 helix: 1.81 (0.13), residues: 1504 sheet: -1.39 (0.44), residues: 136 loop : -0.12 (0.24), residues: 768 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 593 HIS 0.003 0.001 HIS A 201 PHE 0.011 0.001 PHE C 534 TYR 0.012 0.001 TYR B 555 ARG 0.014 0.000 ARG A 302 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4816 Ramachandran restraints generated. 2408 Oldfield, 0 Emsley, 2408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4816 Ramachandran restraints generated. 2408 Oldfield, 0 Emsley, 2408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 328 residues out of total 2096 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 307 time to evaluate : 2.333 Fit side-chains REVERT: A 233 GLU cc_start: 0.7642 (tt0) cc_final: 0.7033 (mm-30) REVERT: A 326 ARG cc_start: 0.7948 (OUTLIER) cc_final: 0.7464 (ttm110) REVERT: A 381 GLN cc_start: 0.5266 (tp40) cc_final: 0.4825 (mp10) REVERT: B 233 GLU cc_start: 0.7641 (tt0) cc_final: 0.7024 (mm-30) REVERT: B 326 ARG cc_start: 0.7953 (OUTLIER) cc_final: 0.7504 (ttm110) REVERT: B 381 GLN cc_start: 0.5235 (tp40) cc_final: 0.4772 (mp10) REVERT: C 139 ARG cc_start: 0.7435 (mtp180) cc_final: 0.7144 (mmt-90) REVERT: C 233 GLU cc_start: 0.7645 (tt0) cc_final: 0.7034 (mm-30) REVERT: C 381 GLN cc_start: 0.5262 (tp40) cc_final: 0.4761 (mp10) REVERT: C 578 MET cc_start: 0.8323 (ttm) cc_final: 0.8071 (mtm) REVERT: D 233 GLU cc_start: 0.7640 (tt0) cc_final: 0.7032 (mm-30) REVERT: D 326 ARG cc_start: 0.7951 (OUTLIER) cc_final: 0.7466 (ttm110) REVERT: D 381 GLN cc_start: 0.5277 (tp40) cc_final: 0.4826 (mp10) outliers start: 21 outliers final: 13 residues processed: 321 average time/residue: 1.0448 time to fit residues: 378.2937 Evaluate side-chains 319 residues out of total 2096 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 303 time to evaluate : 1.378 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 326 ARG Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 474 MET Chi-restraints excluded: chain A residue 499 VAL Chi-restraints excluded: chain B residue 43 ARG Chi-restraints excluded: chain B residue 326 ARG Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain B residue 474 MET Chi-restraints excluded: chain B residue 499 VAL Chi-restraints excluded: chain C residue 335 LEU Chi-restraints excluded: chain C residue 474 MET Chi-restraints excluded: chain C residue 499 VAL Chi-restraints excluded: chain D residue 326 ARG Chi-restraints excluded: chain D residue 335 LEU Chi-restraints excluded: chain D residue 474 MET Chi-restraints excluded: chain D residue 499 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 143 optimal weight: 1.9990 chunk 92 optimal weight: 1.9990 chunk 138 optimal weight: 5.9990 chunk 69 optimal weight: 5.9990 chunk 45 optimal weight: 0.8980 chunk 44 optimal weight: 0.0980 chunk 147 optimal weight: 1.9990 chunk 157 optimal weight: 4.9990 chunk 114 optimal weight: 0.6980 chunk 21 optimal weight: 0.8980 chunk 181 optimal weight: 4.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Sorry: Reduce crashed with command 'molprobity.reduce -quiet -trim -'. Dumping stdin to file 'reduce_failure.pdb'. Return code: -15 Dumping stderr: