Starting phenix.real_space_refine on Fri Jun 13 03:50:13 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8iqf_35660/06_2025/8iqf_35660.cif Found real_map, /net/cci-nas-00/data/ceres_data/8iqf_35660/06_2025/8iqf_35660.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8iqf_35660/06_2025/8iqf_35660.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8iqf_35660/06_2025/8iqf_35660.map" model { file = "/net/cci-nas-00/data/ceres_data/8iqf_35660/06_2025/8iqf_35660.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8iqf_35660/06_2025/8iqf_35660.cif" } resolution = 4.6 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= 0.006 sd= 1.207 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 6984 atoms to isotropic. 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: 3 Type Number sf(0) Gaussians C 4536 2.51 5 N 2268 2.21 5 O 2268 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 9072 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 700 Number of conformers: 1 Conformer: "" Number of residues, atoms: 175, 700 Classifications: {'peptide': 175} Incomplete info: {'backbone_only': 164} Link IDs: {'PTRANS': 7, 'TRANS': 167} Chain breaks: 1 Unresolved chain link angles: 7 Unresolved non-hydrogen bonds: 765 Unresolved non-hydrogen angles: 1096 Unresolved non-hydrogen dihedrals: 516 Unresolved non-hydrogen chiralities: 195 Planarities with less than four sites: {'GLN:plan1': 9, 'HIS:plan': 4, 'TYR:plan': 3, 'ASN:plan1': 3, 'TRP:plan': 6, 'ASP:plan': 22, 'PHE:plan': 8, 'GLU:plan': 22, 'ARG:plan': 10} Unresolved non-hydrogen planarities: 438 Chain: "D" Number of atoms: 436 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 436 Classifications: {'peptide': 109} Incomplete info: {'backbone_only': 106} Link IDs: {'PTRANS': 4, 'TRANS': 104} Chain breaks: 1 Unresolved chain link angles: 4 Unresolved non-hydrogen bonds: 471 Unresolved non-hydrogen angles: 667 Unresolved non-hydrogen dihedrals: 300 Unresolved non-hydrogen chiralities: 137 Planarities with less than four sites: {'GLN:plan1': 7, 'ASP:plan': 4, 'TYR:plan': 3, 'ASN:plan1': 1, 'HIS:plan': 2, 'PHE:plan': 4, 'GLU:plan': 7, 'ARG:plan': 15} Unresolved non-hydrogen planarities: 215 Chain: "E" Number of atoms: 316 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 316 Classifications: {'peptide': 79} Incomplete info: {'backbone_only': 71} Link IDs: {'PTRANS': 1, 'TRANS': 77} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 325 Unresolved non-hydrogen angles: 464 Unresolved non-hydrogen dihedrals: 205 Unresolved non-hydrogen chiralities: 98 Planarities with less than four sites: {'GLN:plan1': 2, 'HIS:plan': 1, 'TYR:plan': 4, 'ASN:plan1': 2, 'ASP:plan': 3, 'PHE:plan': 2, 'GLU:plan': 4, 'ARG:plan': 11} Unresolved non-hydrogen planarities: 151 Chain: "C" Number of atoms: 1604 Number of conformers: 1 Conformer: "" Number of residues, atoms: 401, 1604 Classifications: {'peptide': 401} Incomplete info: {'backbone_only': 379} Link IDs: {'PTRANS': 22, 'TRANS': 378} Unresolved chain link angles: 22 Unresolved non-hydrogen bonds: 1675 Unresolved non-hydrogen angles: 2443 Unresolved non-hydrogen dihedrals: 1112 Unresolved non-hydrogen chiralities: 482 Planarities with less than four sites: {'GLN:plan1': 12, 'HIS:plan': 20, 'TYR:plan': 8, 'ASN:plan1': 22, 'TRP:plan': 13, 'ASP:plan': 31, 'PHE:plan': 14, 'GLU:plan': 31, 'ARG:plan': 11} Unresolved non-hydrogen planarities: 851 Chain: "B" Number of atoms: 1480 Number of conformers: 1 Conformer: "" Number of residues, atoms: 370, 1480 Classifications: {'peptide': 370} Incomplete info: {'backbone_only': 348} Link IDs: {'PTRANS': 15, 'TRANS': 354} Chain breaks: 2 Unresolved chain link angles: 15 Unresolved non-hydrogen bonds: 1508 Unresolved non-hydrogen angles: 2194 Unresolved non-hydrogen dihedrals: 986 Unresolved non-hydrogen chiralities: 457 Planarities with less than four sites: {'GLN:plan1': 8, 'ARG:plan': 18, 'TYR:plan': 13, 'ASN:plan1': 16, 'TRP:plan': 8, 'ASP:plan': 22, 'PHE:plan': 17, 'GLU:plan': 17, 'HIS:plan': 10} Unresolved non-hydrogen planarities: 705 Chain: "F" Number of atoms: 700 Number of conformers: 1 Conformer: "" Number of residues, atoms: 175, 700 Classifications: {'peptide': 175} Incomplete info: {'backbone_only': 164} Link IDs: {'PTRANS': 7, 'TRANS': 167} Chain breaks: 1 Unresolved chain link angles: 7 Unresolved non-hydrogen bonds: 763 Unresolved non-hydrogen angles: 1094 Unresolved non-hydrogen dihedrals: 514 Unresolved non-hydrogen chiralities: 196 Planarities with less than four sites: {'GLN:plan1': 8, 'HIS:plan': 4, 'TYR:plan': 3, 'ASN:plan1': 3, 'TRP:plan': 6, 'ASP:plan': 22, 'PHE:plan': 8, 'GLU:plan': 22, 'ARG:plan': 10} Unresolved non-hydrogen planarities: 434 Chain: "I" Number of atoms: 436 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 436 Classifications: {'peptide': 109} Incomplete info: {'backbone_only': 106} Link IDs: {'PTRANS': 4, 'TRANS': 104} Chain breaks: 1 Unresolved chain link angles: 4 Unresolved non-hydrogen bonds: 471 Unresolved non-hydrogen angles: 667 Unresolved non-hydrogen dihedrals: 300 Unresolved non-hydrogen chiralities: 137 Planarities with less than four sites: {'GLN:plan1': 7, 'ASP:plan': 4, 'TYR:plan': 3, 'ASN:plan1': 1, 'HIS:plan': 2, 'PHE:plan': 4, 'GLU:plan': 7, 'ARG:plan': 15} Unresolved non-hydrogen planarities: 215 Chain: "J" Number of atoms: 316 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 316 Classifications: {'peptide': 79} Incomplete info: {'backbone_only': 71} Link IDs: {'PTRANS': 1, 'TRANS': 77} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 325 Unresolved non-hydrogen angles: 464 Unresolved non-hydrogen dihedrals: 205 Unresolved non-hydrogen chiralities: 98 Planarities with less than four sites: {'GLN:plan1': 2, 'HIS:plan': 1, 'TYR:plan': 4, 'ASN:plan1': 2, 'ASP:plan': 3, 'PHE:plan': 2, 'GLU:plan': 4, 'ARG:plan': 11} Unresolved non-hydrogen planarities: 151 Chain: "H" Number of atoms: 1604 Number of conformers: 1 Conformer: "" Number of residues, atoms: 401, 1604 Classifications: {'peptide': 401} Incomplete info: {'backbone_only': 379} Link IDs: {'PTRANS': 22, 'TRANS': 378} Unresolved chain link angles: 22 Unresolved non-hydrogen bonds: 1675 Unresolved non-hydrogen angles: 2443 Unresolved non-hydrogen dihedrals: 1112 Unresolved non-hydrogen chiralities: 482 Planarities with less than four sites: {'GLN:plan1': 12, 'HIS:plan': 20, 'TYR:plan': 8, 'ASN:plan1': 22, 'TRP:plan': 13, 'ASP:plan': 31, 'PHE:plan': 14, 'GLU:plan': 31, 'ARG:plan': 11} Unresolved non-hydrogen planarities: 851 Chain: "G" Number of atoms: 1480 Number of conformers: 1 Conformer: "" Number of residues, atoms: 370, 1480 Classifications: {'peptide': 370} Incomplete info: {'backbone_only': 348} Link IDs: {'PTRANS': 15, 'TRANS': 354} Chain breaks: 2 Unresolved chain link angles: 15 Unresolved non-hydrogen bonds: 1505 Unresolved non-hydrogen angles: 2191 Unresolved non-hydrogen dihedrals: 983 Unresolved non-hydrogen chiralities: 457 Planarities with less than four sites: {'GLN:plan1': 8, 'ARG:plan': 18, 'TYR:plan': 13, 'ASN:plan1': 16, 'TRP:plan': 8, 'ASP:plan': 22, 'PHE:plan': 17, 'GLU:plan': 17, 'HIS:plan': 10} Unresolved non-hydrogen planarities: 705 Time building chain proxies: 7.11, per 1000 atoms: 0.78 Number of scatterers: 9072 At special positions: 0 Unit cell: (173, 87, 118, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 3 Type Number sf(0) O 2268 8.00 N 2268 7.00 C 4536 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: 2.53 Conformation dependent library (CDL) restraints added in 2.0 seconds 4464 Ramachandran restraints generated. 2232 Oldfield, 0 Emsley, 2232 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 0 Finding SS restraints... Secondary structure from input PDB file: 36 helices and 31 sheets defined 19.8% alpha, 25.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.85 Creating SS restraints... Processing helix chain 'A' and resid 491 through 500 Processing helix chain 'A' and resid 550 through 555 Processing helix chain 'A' and resid 599 through 604 Processing helix chain 'A' and resid 635 through 647 Processing helix chain 'A' and resid 652 through 674 Processing helix chain 'A' and resid 675 through 677 No H-bonds generated for 'chain 'A' and resid 675 through 677' Processing helix chain 'A' and resid 697 through 707 Processing helix chain 'D' and resid 63 through 79 removed outlier: 3.639A pdb=" N PHE D 67 " --> pdb=" O ARG D 63 " (cutoff:3.500A) Processing helix chain 'D' and resid 85 through 114 Processing helix chain 'D' and resid 120 through 132 Processing helix chain 'E' and resid 25 through 29 removed outlier: 4.255A pdb=" N ILE E 29 " --> pdb=" O ILE E 26 " (cutoff:3.500A) Processing helix chain 'E' and resid 30 through 42 Processing helix chain 'E' and resid 49 through 76 removed outlier: 4.048A pdb=" N GLU E 53 " --> pdb=" O LEU E 49 " (cutoff:3.500A) Processing helix chain 'E' and resid 82 through 94 Processing helix chain 'C' and resid 12 through 31 Proline residue: C 29 - end of helix Processing helix chain 'C' and resid 89 through 93 Processing helix chain 'C' and resid 355 through 359 Processing helix chain 'C' and resid 406 through 411 Processing helix chain 'F' and resid 492 through 499 Processing helix chain 'F' and resid 550 through 555 Processing helix chain 'F' and resid 599 through 604 Processing helix chain 'F' and resid 635 through 647 Processing helix chain 'F' and resid 652 through 674 Processing helix chain 'F' and resid 675 through 677 No H-bonds generated for 'chain 'F' and resid 675 through 677' Processing helix chain 'F' and resid 697 through 707 removed outlier: 3.564A pdb=" N LEU F 701 " --> pdb=" O ALA F 697 " (cutoff:3.500A) Processing helix chain 'I' and resid 63 through 79 removed outlier: 3.587A pdb=" N PHE I 67 " --> pdb=" O ARG I 63 " (cutoff:3.500A) Processing helix chain 'I' and resid 85 through 114 Processing helix chain 'I' and resid 120 through 132 removed outlier: 3.559A pdb=" N ILE I 124 " --> pdb=" O MET I 120 " (cutoff:3.500A) Processing helix chain 'J' and resid 25 through 29 removed outlier: 4.099A pdb=" N ILE J 29 " --> pdb=" O ILE J 26 " (cutoff:3.500A) Processing helix chain 'J' and resid 30 through 42 Processing helix chain 'J' and resid 49 through 76 removed outlier: 4.188A pdb=" N GLU J 53 " --> pdb=" O LEU J 49 " (cutoff:3.500A) Processing helix chain 'J' and resid 82 through 94 removed outlier: 3.531A pdb=" N VAL J 86 " --> pdb=" O THR J 82 " (cutoff:3.500A) Processing helix chain 'H' and resid 12 through 28 Processing helix chain 'H' and resid 88 through 93 removed outlier: 3.924A pdb=" N PHE H 93 " --> pdb=" O ASP H 89 " (cutoff:3.500A) Processing helix chain 'H' and resid 355 through 359 Processing helix chain 'H' and resid 406 through 411 Processing sheet with id=AA1, first strand: chain 'A' and resid 570 through 571 removed outlier: 6.301A pdb=" N LEU A 559 " --> pdb=" O VAL C 35 " (cutoff:3.500A) removed outlier: 8.157A pdb=" N THR C 37 " --> pdb=" O LEU A 559 " (cutoff:3.500A) removed outlier: 6.257A pdb=" N GLN A 561 " --> pdb=" O THR C 37 " (cutoff:3.500A) removed outlier: 8.320A pdb=" N ALA C 39 " --> pdb=" O GLN A 561 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N ILE C 398 " --> pdb=" O SER C 394 " (cutoff:3.500A) removed outlier: 7.113A pdb=" N CYS C 391 " --> pdb=" O PHE C 380 " (cutoff:3.500A) removed outlier: 4.417A pdb=" N PHE C 380 " --> pdb=" O CYS C 391 " (cutoff:3.500A) removed outlier: 6.606A pdb=" N VAL C 393 " --> pdb=" O SER C 378 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 684 through 686 removed outlier: 4.055A pdb=" N VAL A 684 " --> pdb=" O SER B 342 " (cutoff:3.500A) removed outlier: 4.244A pdb=" N SER B 342 " --> pdb=" O VAL A 684 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N ILE A 686 " --> pdb=" O TYR B 340 " (cutoff:3.500A) removed outlier: 4.502A pdb=" N TYR B 340 " --> pdb=" O ILE A 686 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N GLY B 339 " --> pdb=" O LEU B 329 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 47 through 48 removed outlier: 3.803A pdb=" N ASN C 77 " --> pdb=" O HIS C 123 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N ILE C 119 " --> pdb=" O ILE C 81 " (cutoff:3.500A) removed outlier: 6.027A pdb=" N SER C 83 " --> pdb=" O ILE C 117 " (cutoff:3.500A) removed outlier: 4.970A pdb=" N ILE C 117 " --> pdb=" O SER C 83 " (cutoff:3.500A) removed outlier: 6.980A pdb=" N GLN C 85 " --> pdb=" O ILE C 115 " (cutoff:3.500A) removed outlier: 5.865A pdb=" N ILE C 115 " --> pdb=" O GLN C 85 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 130 through 132 removed outlier: 3.620A pdb=" N VAL C 149 " --> pdb=" O LEU C 173 " (cutoff:3.500A) removed outlier: 6.798A pdb=" N ARG C 172 " --> pdb=" O VAL C 217 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 182 through 185 removed outlier: 3.671A pdb=" N GLY C 182 " --> pdb=" O ALA C 196 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 230 through 235 removed outlier: 3.804A pdb=" N ALA C 247 " --> pdb=" O LYS C 251 " (cutoff:3.500A) removed outlier: 4.269A pdb=" N LYS C 251 " --> pdb=" O ALA C 247 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 276 through 281 removed outlier: 4.136A pdb=" N CYS C 278 " --> pdb=" O GLY C 292 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N GLY C 292 " --> pdb=" O CYS C 278 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N THR C 291 " --> pdb=" O ALA C 299 " (cutoff:3.500A) removed outlier: 4.358A pdb=" N THR C 297 " --> pdb=" O SER C 293 " (cutoff:3.500A) removed outlier: 6.390A pdb=" N ASP C 302 " --> pdb=" O LYS C 309 " (cutoff:3.500A) removed outlier: 7.353A pdb=" N LYS C 309 " --> pdb=" O ASP C 302 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 320 through 325 removed outlier: 3.589A pdb=" N ALA C 334 " --> pdb=" O GLN C 324 " (cutoff:3.500A) removed outlier: 5.885A pdb=" N ASP C 346 " --> pdb=" O LEU C 366 " (cutoff:3.500A) removed outlier: 5.813A pdb=" N LEU C 366 " --> pdb=" O ASP C 346 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 2 through 6 removed outlier: 3.979A pdb=" N CYS B 370 " --> pdb=" O CYS B 6 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 16 through 20 removed outlier: 6.354A pdb=" N ALA B 35 " --> pdb=" O TYR B 17 " (cutoff:3.500A) removed outlier: 4.252A pdb=" N LEU B 19 " --> pdb=" O ALA B 33 " (cutoff:3.500A) removed outlier: 6.686A pdb=" N ALA B 33 " --> pdb=" O LEU B 19 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N ARG B 42 " --> pdb=" O SER B 34 " (cutoff:3.500A) removed outlier: 6.210A pdb=" N VAL B 41 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 4.127A pdb=" N ASN B 61 " --> pdb=" O VAL B 41 " (cutoff:3.500A) removed outlier: 6.297A pdb=" N ILE B 43 " --> pdb=" O LEU B 59 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 69 through 74 removed outlier: 3.884A pdb=" N VAL B 71 " --> pdb=" O GLY B 84 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N GLY B 84 " --> pdb=" O VAL B 71 " (cutoff:3.500A) removed outlier: 6.786A pdb=" N ILE B 90 " --> pdb=" O THR B 124 " (cutoff:3.500A) removed outlier: 4.744A pdb=" N THR B 124 " --> pdb=" O ILE B 90 " (cutoff:3.500A) removed outlier: 6.188A pdb=" N LEU B 92 " --> pdb=" O VAL B 122 " (cutoff:3.500A) removed outlier: 4.861A pdb=" N ASN B 118 " --> pdb=" O ASN B 96 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 132 through 137 removed outlier: 4.021A pdb=" N SER B 146 " --> pdb=" O ILE B 154 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N ILE B 154 " --> pdb=" O SER B 146 " (cutoff:3.500A) removed outlier: 6.484A pdb=" N ASP B 157 " --> pdb=" O LYS B 163 " (cutoff:3.500A) removed outlier: 6.425A pdb=" N LYS B 163 " --> pdb=" O ASP B 157 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 176 through 179 removed outlier: 4.713A pdb=" N GLY B 176 " --> pdb=" O LEU B 189 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N LEU B 189 " --> pdb=" O GLY B 176 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N VAL B 194 " --> pdb=" O SER B 190 " (cutoff:3.500A) removed outlier: 6.250A pdb=" N SER B 199 " --> pdb=" O VAL B 205 " (cutoff:3.500A) removed outlier: 6.748A pdb=" N VAL B 205 " --> pdb=" O SER B 199 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 211 through 213 Processing sheet with id=AB6, first strand: chain 'B' and resid 248 through 256 removed outlier: 3.515A pdb=" N ALA B 253 " --> pdb=" O THR B 265 " (cutoff:3.500A) removed outlier: 6.035A pdb=" N THR B 265 " --> pdb=" O ALA B 253 " (cutoff:3.500A) removed outlier: 4.167A pdb=" N CYS B 255 " --> pdb=" O MET B 263 " (cutoff:3.500A) removed outlier: 5.931A pdb=" N MET B 263 " --> pdb=" O CYS B 255 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N ALA B 279 " --> pdb=" O VAL B 268 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'F' and resid 558 through 560 Processing sheet with id=AB8, first strand: chain 'F' and resid 684 through 686 removed outlier: 3.577A pdb=" N VAL F 684 " --> pdb=" O SER G 342 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N SER G 342 " --> pdb=" O VAL F 684 " (cutoff:3.500A) removed outlier: 4.280A pdb=" N TYR G 340 " --> pdb=" O ILE F 686 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N GLY G 339 " --> pdb=" O LEU G 329 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N VAL G 341 " --> pdb=" O VAL G 327 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N VAL G 327 " --> pdb=" O VAL G 341 " (cutoff:3.500A) removed outlier: 7.692A pdb=" N ARG G 316 " --> pdb=" O VAL G 296 " (cutoff:3.500A) removed outlier: 7.682A pdb=" N VAL G 296 " --> pdb=" O ARG G 316 " (cutoff:3.500A) removed outlier: 5.412A pdb=" N VAL G 318 " --> pdb=" O CYS G 294 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'H' and resid 32 through 39 removed outlier: 3.700A pdb=" N ILE H 398 " --> pdb=" O SER H 394 " (cutoff:3.500A) removed outlier: 6.628A pdb=" N CYS H 391 " --> pdb=" O PHE H 380 " (cutoff:3.500A) removed outlier: 4.220A pdb=" N PHE H 380 " --> pdb=" O CYS H 391 " (cutoff:3.500A) removed outlier: 6.719A pdb=" N VAL H 393 " --> pdb=" O SER H 378 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'H' and resid 47 through 48 removed outlier: 3.766A pdb=" N ASN H 77 " --> pdb=" O HIS H 123 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N ILE H 119 " --> pdb=" O ILE H 81 " (cutoff:3.500A) removed outlier: 6.067A pdb=" N SER H 83 " --> pdb=" O ILE H 117 " (cutoff:3.500A) removed outlier: 4.884A pdb=" N ILE H 117 " --> pdb=" O SER H 83 " (cutoff:3.500A) removed outlier: 6.907A pdb=" N GLN H 85 " --> pdb=" O ILE H 115 " (cutoff:3.500A) removed outlier: 6.004A pdb=" N ILE H 115 " --> pdb=" O GLN H 85 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'H' and resid 130 through 133 removed outlier: 5.659A pdb=" N ILE H 139 " --> pdb=" O MET H 133 " (cutoff:3.500A) removed outlier: 6.874A pdb=" N ARG H 172 " --> pdb=" O VAL H 217 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'H' and resid 182 through 185 removed outlier: 3.657A pdb=" N GLY H 182 " --> pdb=" O ALA H 196 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'H' and resid 230 through 235 removed outlier: 3.812A pdb=" N ALA H 247 " --> pdb=" O LYS H 251 " (cutoff:3.500A) removed outlier: 4.264A pdb=" N LYS H 251 " --> pdb=" O ALA H 247 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'H' and resid 276 through 281 removed outlier: 4.157A pdb=" N CYS H 278 " --> pdb=" O GLY H 292 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N GLY H 292 " --> pdb=" O CYS H 278 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N THR H 291 " --> pdb=" O ALA H 299 " (cutoff:3.500A) removed outlier: 4.349A pdb=" N THR H 297 " --> pdb=" O SER H 293 " (cutoff:3.500A) removed outlier: 6.376A pdb=" N ASP H 302 " --> pdb=" O LYS H 309 " (cutoff:3.500A) removed outlier: 7.320A pdb=" N LYS H 309 " --> pdb=" O ASP H 302 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'H' and resid 320 through 325 removed outlier: 5.995A pdb=" N ASP H 346 " --> pdb=" O LEU H 366 " (cutoff:3.500A) removed outlier: 5.790A pdb=" N LEU H 366 " --> pdb=" O ASP H 346 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'G' and resid 2 through 5 Processing sheet with id=AC8, first strand: chain 'G' and resid 16 through 20 removed outlier: 6.146A pdb=" N ALA G 35 " --> pdb=" O TYR G 17 " (cutoff:3.500A) removed outlier: 4.263A pdb=" N LEU G 19 " --> pdb=" O ALA G 33 " (cutoff:3.500A) removed outlier: 6.644A pdb=" N ALA G 33 " --> pdb=" O LEU G 19 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N ARG G 42 " --> pdb=" O SER G 34 " (cutoff:3.500A) removed outlier: 4.846A pdb=" N LYS G 45 " --> pdb=" O PHE G 58 " (cutoff:3.500A) removed outlier: 5.066A pdb=" N PHE G 58 " --> pdb=" O LYS G 45 " (cutoff:3.500A) removed outlier: 6.969A pdb=" N GLU G 47 " --> pdb=" O VAL G 56 " (cutoff:3.500A) removed outlier: 5.239A pdb=" N VAL G 56 " --> pdb=" O GLU G 47 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'G' and resid 69 through 74 removed outlier: 3.831A pdb=" N VAL G 71 " --> pdb=" O GLY G 84 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N GLY G 84 " --> pdb=" O VAL G 71 " (cutoff:3.500A) removed outlier: 6.895A pdb=" N ILE G 90 " --> pdb=" O THR G 124 " (cutoff:3.500A) removed outlier: 4.838A pdb=" N THR G 124 " --> pdb=" O ILE G 90 " (cutoff:3.500A) removed outlier: 6.221A pdb=" N LEU G 92 " --> pdb=" O VAL G 122 " (cutoff:3.500A) removed outlier: 4.871A pdb=" N ASN G 118 " --> pdb=" O ASN G 96 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'G' and resid 132 through 137 removed outlier: 3.837A pdb=" N SER G 146 " --> pdb=" O ILE G 154 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N ILE G 154 " --> pdb=" O SER G 146 " (cutoff:3.500A) removed outlier: 6.440A pdb=" N ASP G 157 " --> pdb=" O LYS G 163 " (cutoff:3.500A) removed outlier: 6.297A pdb=" N LYS G 163 " --> pdb=" O ASP G 157 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'G' and resid 176 through 179 removed outlier: 4.667A pdb=" N GLY G 176 " --> pdb=" O LEU G 189 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N VAL G 194 " --> pdb=" O SER G 190 " (cutoff:3.500A) removed outlier: 6.332A pdb=" N SER G 199 " --> pdb=" O VAL G 205 " (cutoff:3.500A) removed outlier: 6.772A pdb=" N VAL G 205 " --> pdb=" O SER G 199 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'G' and resid 211 through 213 Processing sheet with id=AD4, first strand: chain 'G' and resid 248 through 256 removed outlier: 5.882A pdb=" N THR G 265 " --> pdb=" O ALA G 253 " (cutoff:3.500A) removed outlier: 4.221A pdb=" N CYS G 255 " --> pdb=" O MET G 263 " (cutoff:3.500A) removed outlier: 5.950A pdb=" N MET G 263 " --> pdb=" O CYS G 255 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N ALA G 279 " --> pdb=" O VAL G 268 " (cutoff:3.500A) 615 hydrogen bonds defined for protein. 1749 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: 4.62 Time building geometry restraints manager: 2.91 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.29: 2268 1.29 - 1.35: 2248 1.35 - 1.41: 2 1.41 - 1.47: 2262 1.47 - 1.53: 2274 Bond restraints: 9054 Sorted by residual: bond pdb=" C GLU G 7 " pdb=" N ILE G 8 " ideal model delta sigma weight residual 1.335 1.310 0.025 1.41e-02 5.03e+03 3.22e+00 bond pdb=" N PHE I 104 " pdb=" CA PHE I 104 " ideal model delta sigma weight residual 1.459 1.443 0.015 1.24e-02 6.50e+03 1.50e+00 bond pdb=" C VAL C 401 " pdb=" N TRP C 402 " ideal model delta sigma weight residual 1.331 1.317 0.014 1.30e-02 5.92e+03 1.23e+00 bond pdb=" C LEU C 86 " pdb=" O LEU C 86 " ideal model delta sigma weight residual 1.244 1.228 0.015 1.41e-02 5.03e+03 1.19e+00 bond pdb=" N GLN H 250 " pdb=" CA GLN H 250 " ideal model delta sigma weight residual 1.457 1.471 -0.014 1.29e-02 6.01e+03 1.15e+00 ... (remaining 9049 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.53: 10902 1.53 - 3.06: 334 3.06 - 4.60: 41 4.60 - 6.13: 8 6.13 - 7.66: 1 Bond angle restraints: 11286 Sorted by residual: angle pdb=" C GLN C 48 " pdb=" N TRP C 49 " pdb=" CA TRP C 49 " ideal model delta sigma weight residual 121.54 129.20 -7.66 1.91e+00 2.74e-01 1.61e+01 angle pdb=" N PHE J 100 " pdb=" CA PHE J 100 " pdb=" C PHE J 100 " ideal model delta sigma weight residual 114.62 110.62 4.00 1.14e+00 7.69e-01 1.23e+01 angle pdb=" C GLN H 48 " pdb=" N TRP H 49 " pdb=" CA TRP H 49 " ideal model delta sigma weight residual 121.29 126.39 -5.10 1.74e+00 3.30e-01 8.58e+00 angle pdb=" N SER C 326 " pdb=" CA SER C 326 " pdb=" C SER C 326 " ideal model delta sigma weight residual 109.15 113.99 -4.84 1.67e+00 3.59e-01 8.40e+00 angle pdb=" CA PHE J 100 " pdb=" C PHE J 100 " pdb=" N GLY J 101 " ideal model delta sigma weight residual 119.71 116.38 3.33 1.17e+00 7.31e-01 8.10e+00 ... (remaining 11281 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 5.44: 1721 5.44 - 10.87: 449 10.87 - 16.31: 72 16.31 - 21.74: 3 21.74 - 27.18: 5 Dihedral angle restraints: 2250 sinusoidal: 0 harmonic: 2250 Sorted by residual: dihedral pdb=" CA ASN F 565 " pdb=" C ASN F 565 " pdb=" N HIS F 566 " pdb=" CA HIS F 566 " ideal model delta harmonic sigma weight residual 180.00 152.82 27.18 0 5.00e+00 4.00e-02 2.96e+01 dihedral pdb=" CA ASN A 565 " pdb=" C ASN A 565 " pdb=" N HIS A 566 " pdb=" CA HIS A 566 " ideal model delta harmonic sigma weight residual 180.00 155.45 24.55 0 5.00e+00 4.00e-02 2.41e+01 dihedral pdb=" CA VAL B 149 " pdb=" C VAL B 149 " pdb=" N ASP B 150 " pdb=" CA ASP B 150 " ideal model delta harmonic sigma weight residual -180.00 -155.67 -24.33 0 5.00e+00 4.00e-02 2.37e+01 ... (remaining 2247 not shown) Chirality restraints: 0 Planarity restraints: 2250 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLY I 102 " -0.009 2.00e-02 2.50e+03 1.74e-02 3.02e+00 pdb=" C GLY I 102 " 0.030 2.00e-02 2.50e+03 pdb=" O GLY I 102 " -0.011 2.00e-02 2.50e+03 pdb=" N LEU I 103 " -0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLY D 102 " -0.007 2.00e-02 2.50e+03 1.40e-02 1.97e+00 pdb=" C GLY D 102 " 0.024 2.00e-02 2.50e+03 pdb=" O GLY D 102 " -0.009 2.00e-02 2.50e+03 pdb=" N LEU D 103 " -0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA CYS C 391 " 0.007 2.00e-02 2.50e+03 1.39e-02 1.93e+00 pdb=" C CYS C 391 " -0.024 2.00e-02 2.50e+03 pdb=" O CYS C 391 " 0.009 2.00e-02 2.50e+03 pdb=" N SER C 392 " 0.008 2.00e-02 2.50e+03 ... (remaining 2247 not shown) Histogram of nonbonded interaction distances: 2.00 - 2.58: 49 2.58 - 3.16: 7367 3.16 - 3.74: 9007 3.74 - 4.32: 12501 4.32 - 4.90: 18664 Nonbonded interactions: 47588 Sorted by model distance: nonbonded pdb=" O VAL I 46 " pdb=" N ALA G 9 " model vdw 1.995 3.120 nonbonded pdb=" N LEU H 40 " pdb=" O ASN H 397 " model vdw 2.182 3.120 nonbonded pdb=" N LEU C 40 " pdb=" O ASN C 397 " model vdw 2.221 3.120 nonbonded pdb=" O MET B 227 " pdb=" N CYS B 255 " model vdw 2.224 3.120 nonbonded pdb=" O TRP F 571 " pdb=" O GLY H 107 " model vdw 2.252 3.040 ... (remaining 47583 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.03 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 491 through 499 or resid 549 through 713)) selection = (chain 'F' and (resid 491 through 499 or resid 549 through 713)) } ncs_group { reference = (chain 'B' and resid 1 through 391) selection = (chain 'G' and (resid 1 through 97 or resid 113 through 391)) } ncs_group { reference = chain 'C' selection = chain 'H' } ncs_group { reference = chain 'D' selection = chain 'I' } ncs_group { reference = chain 'E' selection = chain 'J' } 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 group one per residue 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: 1.220 Set stop_for_unknowns flag: 0.010 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.090 Construct map_model_manager: 0.010 Extract box with map and model: 0.340 Check model and map are aligned: 0.060 Set scattering table: 0.080 Process input model: 28.920 Find NCS groups from input model: 0.530 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: 0.010 Load rotamer database and sin/cos tables:3.140 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.480 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6121 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 : 0.003 0.025 9054 Z= 0.213 Angle : 0.634 7.662 11286 Z= 0.425 Chirality : 0.000 0.000 0 Planarity : 0.003 0.017 2250 Dihedral : 4.926 27.180 2250 Min Nonbonded Distance : 1.995 Molprobity Statistics. All-atom Clashscore : 4.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.17 % Favored : 95.83 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.27 (0.17), residues: 2232 helix: 1.21 (0.26), residues: 390 sheet: 0.13 (0.20), residues: 618 loop : -0.79 (0.17), residues: 1224 Details of bonding type rmsd hydrogen bonds : bond 0.25263 ( 615) hydrogen bonds : angle 8.61227 ( 1749) covalent geometry : bond 0.00282 ( 9054) covalent geometry : angle 0.63414 (11286) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4464 Ramachandran restraints generated. 2232 Oldfield, 0 Emsley, 2232 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4464 Ramachandran restraints generated. 2232 Oldfield, 0 Emsley, 2232 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 35 residues out of total 1985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 35 time to evaluate : 1.220 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 35 average time/residue: 0.0812 time to fit residues: 6.9953 Evaluate side-chains 35 residues out of total 1985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 35 time to evaluate : 1.153 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 222 random chunks: chunk 187 optimal weight: 10.0000 chunk 168 optimal weight: 30.0000 chunk 93 optimal weight: 40.0000 chunk 57 optimal weight: 6.9990 chunk 113 optimal weight: 30.0000 chunk 89 optimal weight: 40.0000 chunk 174 optimal weight: 50.0000 chunk 67 optimal weight: 10.0000 chunk 105 optimal weight: 8.9990 chunk 129 optimal weight: 9.9990 chunk 201 optimal weight: 40.0000 overall best weight: 9.1994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3156 r_free = 0.3156 target = 0.059500 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2724 r_free = 0.2724 target = 0.043113 restraints weight = 79830.884| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 20)----------------| | r_work = 0.2724 r_free = 0.2724 target = 0.043113 restraints weight = 78029.222| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 20)----------------| | r_work = 0.2724 r_free = 0.2724 target = 0.043113 restraints weight = 78027.955| |-----------------------------------------------------------------------------| r_work (final): 0.2697 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7700 moved from start: 0.6142 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 9054 Z= 0.306 Angle : 0.749 7.219 11286 Z= 0.483 Chirality : 0.000 0.000 0 Planarity : 0.004 0.016 2250 Dihedral : 6.204 25.296 2250 Min Nonbonded Distance : 2.304 Molprobity Statistics. All-atom Clashscore : 1.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.79 % Favored : 95.21 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.66 (0.17), residues: 2232 helix: 1.45 (0.26), residues: 396 sheet: -0.38 (0.20), residues: 611 loop : -1.11 (0.17), residues: 1225 Details of bonding type rmsd hydrogen bonds : bond 0.05602 ( 615) hydrogen bonds : angle 6.79780 ( 1749) covalent geometry : bond 0.00417 ( 9054) covalent geometry : angle 0.74858 (11286) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4464 Ramachandran restraints generated. 2232 Oldfield, 0 Emsley, 2232 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4464 Ramachandran restraints generated. 2232 Oldfield, 0 Emsley, 2232 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 35 residues out of total 1985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 35 time to evaluate : 1.075 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 35 average time/residue: 0.0776 time to fit residues: 6.8453 Evaluate side-chains 35 residues out of total 1985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 35 time to evaluate : 1.150 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 222 random chunks: chunk 212 optimal weight: 50.0000 chunk 32 optimal weight: 20.0000 chunk 41 optimal weight: 10.0000 chunk 118 optimal weight: 0.9990 chunk 143 optimal weight: 8.9990 chunk 108 optimal weight: 6.9990 chunk 26 optimal weight: 30.0000 chunk 44 optimal weight: 8.9990 chunk 100 optimal weight: 40.0000 chunk 128 optimal weight: 50.0000 chunk 193 optimal weight: 20.0000 overall best weight: 7.1992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3112 r_free = 0.3112 target = 0.057440 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2697 r_free = 0.2697 target = 0.041860 restraints weight = 83178.741| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 20)----------------| | r_work = 0.2699 r_free = 0.2699 target = 0.041929 restraints weight = 80273.882| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 19)----------------| | r_work = 0.2702 r_free = 0.2702 target = 0.042036 restraints weight = 78281.653| |-----------------------------------------------------------------------------| r_work (final): 0.2676 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7743 moved from start: 0.7521 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 9054 Z= 0.215 Angle : 0.524 5.275 11286 Z= 0.336 Chirality : 0.000 0.000 0 Planarity : 0.003 0.016 2250 Dihedral : 4.944 20.289 2250 Min Nonbonded Distance : 2.372 Molprobity Statistics. All-atom Clashscore : 1.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.47 % Favored : 94.53 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.40 (0.18), residues: 2232 helix: 2.44 (0.25), residues: 408 sheet: -0.22 (0.22), residues: 537 loop : -1.23 (0.17), residues: 1287 Details of bonding type rmsd hydrogen bonds : bond 0.03780 ( 615) hydrogen bonds : angle 5.52382 ( 1749) covalent geometry : bond 0.00293 ( 9054) covalent geometry : angle 0.52352 (11286) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4464 Ramachandran restraints generated. 2232 Oldfield, 0 Emsley, 2232 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4464 Ramachandran restraints generated. 2232 Oldfield, 0 Emsley, 2232 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 35 residues out of total 1985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 35 time to evaluate : 1.035 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 35 average time/residue: 0.0772 time to fit residues: 6.9089 Evaluate side-chains 35 residues out of total 1985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 35 time to evaluate : 1.157 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 222 random chunks: chunk 103 optimal weight: 50.0000 chunk 126 optimal weight: 20.0000 chunk 48 optimal weight: 50.0000 chunk 170 optimal weight: 50.0000 chunk 122 optimal weight: 40.0000 chunk 75 optimal weight: 30.0000 chunk 221 optimal weight: 20.0000 chunk 4 optimal weight: 10.0000 chunk 198 optimal weight: 50.0000 chunk 163 optimal weight: 7.9990 chunk 28 optimal weight: 20.0000 overall best weight: 15.5998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2989 r_free = 0.2989 target = 0.053206 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.2571 r_free = 0.2571 target = 0.038309 restraints weight = 84151.709| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 21)----------------| | r_work = 0.2572 r_free = 0.2572 target = 0.038340 restraints weight = 82856.549| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 16)----------------| | r_work = 0.2573 r_free = 0.2573 target = 0.038377 restraints weight = 81888.067| |-----------------------------------------------------------------------------| r_work (final): 0.2532 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7920 moved from start: 1.0319 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.051 9054 Z= 0.417 Angle : 0.906 9.605 11286 Z= 0.585 Chirality : 0.000 0.000 0 Planarity : 0.005 0.025 2250 Dihedral : 7.776 27.512 2250 Min Nonbonded Distance : 2.265 Molprobity Statistics. All-atom Clashscore : 5.74 Ramachandran Plot: Outliers : 0.13 % Allowed : 11.02 % Favored : 88.84 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -2.14 (0.17), residues: 2232 helix: 0.53 (0.25), residues: 419 sheet: -1.39 (0.23), residues: 474 loop : -2.17 (0.15), residues: 1339 Details of bonding type rmsd hydrogen bonds : bond 0.06200 ( 615) hydrogen bonds : angle 8.03224 ( 1749) covalent geometry : bond 0.00566 ( 9054) covalent geometry : angle 0.90583 (11286) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4464 Ramachandran restraints generated. 2232 Oldfield, 0 Emsley, 2232 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4464 Ramachandran restraints generated. 2232 Oldfield, 0 Emsley, 2232 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 35 residues out of total 1985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 35 time to evaluate : 0.995 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 35 average time/residue: 0.0736 time to fit residues: 6.3877 Evaluate side-chains 35 residues out of total 1985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 35 time to evaluate : 1.000 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 222 random chunks: chunk 77 optimal weight: 50.0000 chunk 206 optimal weight: 10.0000 chunk 120 optimal weight: 50.0000 chunk 200 optimal weight: 7.9990 chunk 54 optimal weight: 50.0000 chunk 183 optimal weight: 30.0000 chunk 137 optimal weight: 20.0000 chunk 78 optimal weight: 6.9990 chunk 192 optimal weight: 20.0000 chunk 217 optimal weight: 50.0000 chunk 211 optimal weight: 10.0000 overall best weight: 10.9996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2994 r_free = 0.2994 target = 0.053279 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2588 r_free = 0.2588 target = 0.038725 restraints weight = 84146.535| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 20)----------------| | r_work = 0.2591 r_free = 0.2591 target = 0.038800 restraints weight = 82161.546| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.2591 r_free = 0.2591 target = 0.038800 restraints weight = 80316.249| |-----------------------------------------------------------------------------| r_work (final): 0.2550 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7896 moved from start: 1.0730 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 9054 Z= 0.286 Angle : 0.661 6.620 11286 Z= 0.425 Chirality : 0.000 0.000 0 Planarity : 0.004 0.016 2250 Dihedral : 6.335 23.580 2250 Min Nonbonded Distance : 2.349 Molprobity Statistics. All-atom Clashscore : 2.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.48 % Favored : 89.52 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -2.17 (0.17), residues: 2232 helix: 1.15 (0.26), residues: 394 sheet: -1.77 (0.21), residues: 551 loop : -2.21 (0.16), residues: 1287 Details of bonding type rmsd hydrogen bonds : bond 0.04705 ( 615) hydrogen bonds : angle 6.87595 ( 1749) covalent geometry : bond 0.00394 ( 9054) covalent geometry : angle 0.66102 (11286) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4464 Ramachandran restraints generated. 2232 Oldfield, 0 Emsley, 2232 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4464 Ramachandran restraints generated. 2232 Oldfield, 0 Emsley, 2232 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 35 residues out of total 1985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 35 time to evaluate : 1.009 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 35 average time/residue: 0.0773 time to fit residues: 6.5850 Evaluate side-chains 35 residues out of total 1985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 35 time to evaluate : 1.013 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 222 random chunks: chunk 131 optimal weight: 4.9990 chunk 31 optimal weight: 10.0000 chunk 37 optimal weight: 50.0000 chunk 14 optimal weight: 50.0000 chunk 215 optimal weight: 20.0000 chunk 107 optimal weight: 20.0000 chunk 154 optimal weight: 20.0000 chunk 147 optimal weight: 20.0000 chunk 12 optimal weight: 50.0000 chunk 43 optimal weight: 30.0000 chunk 30 optimal weight: 20.0000 overall best weight: 14.9998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2958 r_free = 0.2958 target = 0.052038 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2546 r_free = 0.2546 target = 0.037568 restraints weight = 83906.168| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 22)----------------| | r_work = 0.2546 r_free = 0.2546 target = 0.037568 restraints weight = 80460.639| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.2546 r_free = 0.2546 target = 0.037568 restraints weight = 80457.658| |-----------------------------------------------------------------------------| r_work (final): 0.2525 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7982 moved from start: 1.2231 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.066 9054 Z= 0.392 Angle : 0.839 9.931 11286 Z= 0.542 Chirality : 0.000 0.000 0 Planarity : 0.005 0.024 2250 Dihedral : 7.701 26.071 2250 Min Nonbonded Distance : 2.263 Molprobity Statistics. All-atom Clashscore : 4.61 Ramachandran Plot: Outliers : 0.09 % Allowed : 16.49 % Favored : 83.42 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -2.97 (0.17), residues: 2232 helix: 0.32 (0.26), residues: 397 sheet: -2.28 (0.21), residues: 551 loop : -2.69 (0.16), residues: 1284 Details of bonding type rmsd hydrogen bonds : bond 0.06078 ( 615) hydrogen bonds : angle 8.37438 ( 1749) covalent geometry : bond 0.00537 ( 9054) covalent geometry : angle 0.83881 (11286) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4464 Ramachandran restraints generated. 2232 Oldfield, 0 Emsley, 2232 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4464 Ramachandran restraints generated. 2232 Oldfield, 0 Emsley, 2232 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 35 residues out of total 1985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 35 time to evaluate : 1.041 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 35 average time/residue: 0.0760 time to fit residues: 6.5213 Evaluate side-chains 35 residues out of total 1985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 35 time to evaluate : 1.039 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 222 random chunks: chunk 66 optimal weight: 40.0000 chunk 43 optimal weight: 40.0000 chunk 26 optimal weight: 6.9990 chunk 196 optimal weight: 20.0000 chunk 217 optimal weight: 50.0000 chunk 181 optimal weight: 20.0000 chunk 188 optimal weight: 20.0000 chunk 67 optimal weight: 20.0000 chunk 163 optimal weight: 0.0030 chunk 80 optimal weight: 40.0000 chunk 204 optimal weight: 10.0000 overall best weight: 11.4004 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2970 r_free = 0.2970 target = 0.052388 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2563 r_free = 0.2563 target = 0.037994 restraints weight = 84652.335| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 20)----------------| | r_work = 0.2564 r_free = 0.2564 target = 0.038038 restraints weight = 81034.469| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 16)----------------| | r_work = 0.2564 r_free = 0.2564 target = 0.038038 restraints weight = 79424.414| |-----------------------------------------------------------------------------| r_work (final): 0.2524 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7953 moved from start: 1.2376 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 9054 Z= 0.293 Angle : 0.660 6.918 11286 Z= 0.427 Chirality : 0.000 0.000 0 Planarity : 0.003 0.016 2250 Dihedral : 6.620 23.544 2250 Min Nonbonded Distance : 2.326 Molprobity Statistics. All-atom Clashscore : 2.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.84 % Favored : 86.16 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -2.88 (0.17), residues: 2232 helix: 0.57 (0.26), residues: 409 sheet: -2.38 (0.21), residues: 548 loop : -2.64 (0.16), residues: 1275 Details of bonding type rmsd hydrogen bonds : bond 0.04806 ( 615) hydrogen bonds : angle 7.53172 ( 1749) covalent geometry : bond 0.00401 ( 9054) covalent geometry : angle 0.66002 (11286) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4464 Ramachandran restraints generated. 2232 Oldfield, 0 Emsley, 2232 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4464 Ramachandran restraints generated. 2232 Oldfield, 0 Emsley, 2232 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 35 residues out of total 1985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 35 time to evaluate : 0.998 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 35 average time/residue: 0.0786 time to fit residues: 6.5638 Evaluate side-chains 35 residues out of total 1985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 35 time to evaluate : 0.982 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 222 random chunks: chunk 162 optimal weight: 30.0000 chunk 157 optimal weight: 30.0000 chunk 17 optimal weight: 0.0020 chunk 149 optimal weight: 20.0000 chunk 79 optimal weight: 10.0000 chunk 127 optimal weight: 40.0000 chunk 29 optimal weight: 20.0000 chunk 19 optimal weight: 20.0000 chunk 173 optimal weight: 50.0000 chunk 168 optimal weight: 8.9990 chunk 54 optimal weight: 50.0000 overall best weight: 11.8002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2926 r_free = 0.2926 target = 0.051194 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2614 r_free = 0.2614 target = 0.037892 restraints weight = 101854.775| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.2618 r_free = 0.2618 target = 0.037994 restraints weight = 96859.835| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 21)----------------| | r_work = 0.2619 r_free = 0.2619 target = 0.038023 restraints weight = 93570.578| |-----------------------------------------------------------------------------| r_work (final): 0.2540 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6532 moved from start: 1.2986 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 9054 Z= 0.313 Angle : 0.703 7.440 11286 Z= 0.456 Chirality : 0.000 0.000 0 Planarity : 0.004 0.016 2250 Dihedral : 6.903 24.129 2250 Min Nonbonded Distance : 2.297 Molprobity Statistics. All-atom Clashscore : 3.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 18.19 % Favored : 81.81 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -3.16 (0.17), residues: 2232 helix: 0.54 (0.26), residues: 402 sheet: -2.60 (0.21), residues: 534 loop : -2.86 (0.16), residues: 1296 Details of bonding type rmsd hydrogen bonds : bond 0.05151 ( 615) hydrogen bonds : angle 7.92161 ( 1749) covalent geometry : bond 0.00428 ( 9054) covalent geometry : angle 0.70297 (11286) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4464 Ramachandran restraints generated. 2232 Oldfield, 0 Emsley, 2232 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4464 Ramachandran restraints generated. 2232 Oldfield, 0 Emsley, 2232 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 35 residues out of total 1985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 35 time to evaluate : 0.996 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 35 average time/residue: 0.0762 time to fit residues: 6.5903 Evaluate side-chains 35 residues out of total 1985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 35 time to evaluate : 1.108 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 222 random chunks: chunk 169 optimal weight: 50.0000 chunk 89 optimal weight: 40.0000 chunk 47 optimal weight: 50.0000 chunk 6 optimal weight: 50.0000 chunk 212 optimal weight: 50.0000 chunk 148 optimal weight: 40.0000 chunk 152 optimal weight: 30.0000 chunk 134 optimal weight: 8.9990 chunk 39 optimal weight: 30.0000 chunk 110 optimal weight: 40.0000 chunk 38 optimal weight: 5.9990 overall best weight: 22.9996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2899 r_free = 0.2899 target = 0.049788 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2509 r_free = 0.2509 target = 0.036429 restraints weight = 86651.583| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 22)----------------| | r_work = 0.2509 r_free = 0.2509 target = 0.036430 restraints weight = 82699.313| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.2509 r_free = 0.2509 target = 0.036430 restraints weight = 82684.605| |-----------------------------------------------------------------------------| r_work (final): 0.2472 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8051 moved from start: 1.4142 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.097 9054 Z= 0.560 Angle : 1.073 10.916 11286 Z= 0.704 Chirality : 0.000 0.000 0 Planarity : 0.006 0.039 2250 Dihedral : 8.997 33.788 2250 Min Nonbonded Distance : 2.219 Molprobity Statistics. All-atom Clashscore : 11.65 Ramachandran Plot: Outliers : 0.09 % Allowed : 22.76 % Favored : 77.15 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.19 % 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: -4.19 (0.16), residues: 2232 helix: -1.17 (0.24), residues: 385 sheet: -2.94 (0.23), residues: 399 loop : -3.41 (0.14), residues: 1448 Details of bonding type rmsd hydrogen bonds : bond 0.08058 ( 615) hydrogen bonds : angle 10.25069 ( 1749) covalent geometry : bond 0.00771 ( 9054) covalent geometry : angle 1.07312 (11286) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4464 Ramachandran restraints generated. 2232 Oldfield, 0 Emsley, 2232 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4464 Ramachandran restraints generated. 2232 Oldfield, 0 Emsley, 2232 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 35 residues out of total 1985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 35 time to evaluate : 1.018 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 35 average time/residue: 0.0757 time to fit residues: 6.5450 Evaluate side-chains 35 residues out of total 1985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 35 time to evaluate : 1.068 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 222 random chunks: chunk 204 optimal weight: 8.9990 chunk 121 optimal weight: 50.0000 chunk 142 optimal weight: 7.9990 chunk 97 optimal weight: 0.0570 chunk 73 optimal weight: 1.9990 chunk 160 optimal weight: 30.0000 chunk 175 optimal weight: 50.0000 chunk 55 optimal weight: 20.0000 chunk 213 optimal weight: 30.0000 chunk 210 optimal weight: 2.9990 chunk 206 optimal weight: 30.0000 overall best weight: 4.4106 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2975 r_free = 0.2975 target = 0.052660 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.2583 r_free = 0.2583 target = 0.038615 restraints weight = 85094.989| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 21)----------------| | r_work = 0.2586 r_free = 0.2586 target = 0.038697 restraints weight = 79809.667| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.2591 r_free = 0.2591 target = 0.038874 restraints weight = 77124.138| |-----------------------------------------------------------------------------| r_work (final): 0.2553 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7915 moved from start: 1.3483 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 9054 Z= 0.152 Angle : 0.489 4.200 11286 Z= 0.311 Chirality : 0.000 0.000 0 Planarity : 0.002 0.014 2250 Dihedral : 5.925 22.901 2250 Min Nonbonded Distance : 2.398 Molprobity Statistics. All-atom Clashscore : 1.48 Ramachandran Plot: Outliers : 0.04 % Allowed : 12.37 % Favored : 87.59 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -3.29 (0.17), residues: 2232 helix: 0.56 (0.25), residues: 414 sheet: -2.96 (0.20), residues: 525 loop : -2.89 (0.16), residues: 1293 Details of bonding type rmsd hydrogen bonds : bond 0.03450 ( 615) hydrogen bonds : angle 7.05625 ( 1749) covalent geometry : bond 0.00206 ( 9054) covalent geometry : angle 0.48862 (11286) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4464 Ramachandran restraints generated. 2232 Oldfield, 0 Emsley, 2232 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4464 Ramachandran restraints generated. 2232 Oldfield, 0 Emsley, 2232 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 35 residues out of total 1985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 35 time to evaluate : 1.181 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 35 average time/residue: 0.0855 time to fit residues: 8.0676 Evaluate side-chains 35 residues out of total 1985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 35 time to evaluate : 1.112 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 222 random chunks: chunk 172 optimal weight: 40.0000 chunk 129 optimal weight: 10.0000 chunk 107 optimal weight: 9.9990 chunk 68 optimal weight: 5.9990 chunk 151 optimal weight: 20.0000 chunk 83 optimal weight: 50.0000 chunk 11 optimal weight: 6.9990 chunk 193 optimal weight: 8.9990 chunk 137 optimal weight: 30.0000 chunk 166 optimal weight: 50.0000 chunk 206 optimal weight: 1.9990 overall best weight: 6.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2960 r_free = 0.2960 target = 0.052123 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2571 r_free = 0.2571 target = 0.038160 restraints weight = 84037.474| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 22)----------------| | r_work = 0.2571 r_free = 0.2571 target = 0.038160 restraints weight = 79547.623| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.2571 r_free = 0.2571 target = 0.038160 restraints weight = 79547.622| |-----------------------------------------------------------------------------| r_work (final): 0.2529 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7945 moved from start: 1.3532 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 9054 Z= 0.191 Angle : 0.508 5.226 11286 Z= 0.328 Chirality : 0.000 0.000 0 Planarity : 0.002 0.011 2250 Dihedral : 5.708 23.332 2250 Min Nonbonded Distance : 2.352 Molprobity Statistics. All-atom Clashscore : 1.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 16.76 % Favored : 83.24 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -3.01 (0.17), residues: 2232 helix: 1.08 (0.26), residues: 423 sheet: -2.82 (0.21), residues: 490 loop : -2.85 (0.16), residues: 1319 Details of bonding type rmsd hydrogen bonds : bond 0.03684 ( 615) hydrogen bonds : angle 6.94712 ( 1749) covalent geometry : bond 0.00261 ( 9054) covalent geometry : angle 0.50825 (11286) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2251.35 seconds wall clock time: 39 minutes 39.03 seconds (2379.03 seconds total)