Starting phenix.real_space_refine on Fri Sep 27 01:42:57 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8iqf_35660/09_2024/8iqf_35660.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8iqf_35660/09_2024/8iqf_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8iqf_35660/09_2024/8iqf_35660.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8iqf_35660/09_2024/8iqf_35660.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8iqf_35660/09_2024/8iqf_35660.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8iqf_35660/09_2024/8iqf_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-5461/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: 6.89, per 1000 atoms: 0.76 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: 2.55 Conformation dependent library (CDL) restraints added in 1.9 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: 1.66 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: 3.40 Time building geometry restraints manager: 2.87 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: 0.00 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: 1.130 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.090 Construct map_model_manager: 0.000 Extract box with map and model: 0.340 Check model and map are aligned: 0.070 Set scattering table: 0.080 Process input model: 26.730 Find NCS groups from input model: 0.430 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.760 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.690 ------------------------------------------------------------------------------- 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 *********************** 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 fitting. rotamer outliers: 0 poor density : 35 time to evaluate : 0.971 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 35 average time/residue: 0.0748 time to fit residues: 6.4565 Evaluate side-chains 35 residues out of total 1985 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 35 time to evaluate : 1.114 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6846 moved from start: 0.6188 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 9054 Z= 0.319 Angle : 0.752 7.318 11286 Z= 0.489 Chirality : 0.000 0.000 0 Planarity : 0.004 0.017 2250 Dihedral : 6.207 24.974 2250 Min Nonbonded Distance : 2.310 Molprobity Statistics. All-atom Clashscore : 1.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.88 % Favored : 95.12 % 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: 1.46 (0.26), residues: 396 sheet: -0.38 (0.20), residues: 611 loop : -1.11 (0.17), residues: 1225 *********************** 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 fitting. rotamer outliers: 0 poor density : 35 time to evaluate : 1.062 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 35 average time/residue: 0.0751 time to fit residues: 6.6375 Evaluate side-chains 35 residues out of total 1985 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 35 time to evaluate : 1.065 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 222 random chunks: chunk 112 optimal weight: 40.0000 chunk 62 optimal weight: 20.0000 chunk 167 optimal weight: 10.0000 chunk 137 optimal weight: 40.0000 chunk 55 optimal weight: 50.0000 chunk 201 optimal weight: 40.0000 chunk 218 optimal weight: 8.9990 chunk 179 optimal weight: 5.9990 chunk 200 optimal weight: 30.0000 chunk 68 optimal weight: 7.9990 chunk 162 optimal weight: 30.0000 overall best weight: 10.5994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7027 moved from start: 0.8745 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 9054 Z= 0.321 Angle : 0.716 7.003 11286 Z= 0.461 Chirality : 0.000 0.000 0 Planarity : 0.004 0.023 2250 Dihedral : 6.354 25.240 2250 Min Nonbonded Distance : 2.321 Molprobity Statistics. All-atom Clashscore : 2.26 Ramachandran Plot: Outliers : 0.04 % Allowed : 7.62 % Favored : 92.34 % 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: -1.16 (0.17), residues: 2232 helix: 1.57 (0.25), residues: 403 sheet: -0.72 (0.22), residues: 526 loop : -1.61 (0.16), residues: 1303 *********************** 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 fitting. rotamer outliers: 0 poor density : 35 time to evaluate : 1.134 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 35 average time/residue: 0.0744 time to fit residues: 6.5905 Evaluate side-chains 35 residues out of total 1985 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 35 time to evaluate : 1.117 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 222 random chunks: chunk 199 optimal weight: 30.0000 chunk 151 optimal weight: 20.0000 chunk 104 optimal weight: 30.0000 chunk 22 optimal weight: 6.9990 chunk 96 optimal weight: 10.0000 chunk 135 optimal weight: 9.9990 chunk 202 optimal weight: 40.0000 chunk 214 optimal weight: 30.0000 chunk 105 optimal weight: 9.9990 chunk 192 optimal weight: 50.0000 chunk 57 optimal weight: 50.0000 overall best weight: 11.3994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7106 moved from start: 1.0320 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 9054 Z= 0.325 Angle : 0.701 6.822 11286 Z= 0.456 Chirality : 0.000 0.000 0 Planarity : 0.004 0.015 2250 Dihedral : 6.633 24.374 2250 Min Nonbonded Distance : 2.346 Molprobity Statistics. All-atom Clashscore : 2.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.41 % Favored : 90.59 % 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: -1.81 (0.17), residues: 2232 helix: 1.26 (0.25), residues: 414 sheet: -1.43 (0.21), residues: 546 loop : -2.02 (0.16), residues: 1272 *********************** 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 fitting. rotamer outliers: 0 poor density : 35 time to evaluate : 1.048 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 35 average time/residue: 0.0761 time to fit residues: 6.6245 Evaluate side-chains 35 residues out of total 1985 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 35 time to evaluate : 1.034 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 222 random chunks: chunk 178 optimal weight: 50.0000 chunk 121 optimal weight: 40.0000 chunk 3 optimal weight: 50.0000 chunk 159 optimal weight: 40.0000 chunk 88 optimal weight: 40.0000 chunk 183 optimal weight: 40.0000 chunk 148 optimal weight: 50.0000 chunk 0 optimal weight: 100.0000 chunk 109 optimal weight: 6.9990 chunk 192 optimal weight: 20.0000 chunk 54 optimal weight: 50.0000 overall best weight: 29.3998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7299 moved from start: 1.3161 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 0.122 9054 Z= 0.733 Angle : 1.343 15.946 11286 Z= 0.869 Chirality : 0.000 0.000 0 Planarity : 0.008 0.049 2250 Dihedral : 10.481 37.083 2250 Min Nonbonded Distance : 2.161 Molprobity Statistics. All-atom Clashscore : 20.61 Ramachandran Plot: Outliers : 0.67 % Allowed : 19.58 % Favored : 79.75 % 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 : 0.79 % 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: -4.06 (0.15), residues: 2232 helix: -1.72 (0.24), residues: 361 sheet: -2.65 (0.24), residues: 395 loop : -3.16 (0.14), residues: 1476 *********************** 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 fitting. rotamer outliers: 0 poor density : 35 time to evaluate : 1.047 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 35 average time/residue: 0.0777 time to fit residues: 6.7477 Evaluate side-chains 35 residues out of total 1985 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 35 time to evaluate : 1.091 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 222 random chunks: chunk 72 optimal weight: 7.9990 chunk 193 optimal weight: 6.9990 chunk 42 optimal weight: 50.0000 chunk 125 optimal weight: 50.0000 chunk 52 optimal weight: 0.0870 chunk 214 optimal weight: 8.9990 chunk 178 optimal weight: 6.9990 chunk 99 optimal weight: 4.9990 chunk 17 optimal weight: 0.9990 chunk 71 optimal weight: 10.0000 chunk 112 optimal weight: 30.0000 overall best weight: 4.0166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7127 moved from start: 1.2204 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 9054 Z= 0.153 Angle : 0.516 6.115 11286 Z= 0.328 Chirality : 0.000 0.000 0 Planarity : 0.003 0.013 2250 Dihedral : 6.119 23.854 2250 Min Nonbonded Distance : 2.403 Molprobity Statistics. All-atom Clashscore : 1.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.78 % Favored : 91.22 % 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: -2.91 (0.17), residues: 2232 helix: 0.58 (0.25), residues: 399 sheet: -2.35 (0.21), residues: 517 loop : -2.68 (0.16), residues: 1316 *********************** 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 fitting. rotamer outliers: 0 poor density : 35 time to evaluate : 1.083 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 35 average time/residue: 0.1062 time to fit residues: 8.8710 Evaluate side-chains 35 residues out of total 1985 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 35 time to evaluate : 1.155 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 222 random chunks: chunk 207 optimal weight: 10.0000 chunk 24 optimal weight: 20.0000 chunk 122 optimal weight: 30.0000 chunk 156 optimal weight: 50.0000 chunk 121 optimal weight: 40.0000 chunk 180 optimal weight: 20.0000 chunk 119 optimal weight: 50.0000 chunk 213 optimal weight: 0.3980 chunk 133 optimal weight: 30.0000 chunk 130 optimal weight: 7.9990 chunk 98 optimal weight: 30.0000 overall best weight: 11.6794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7225 moved from start: 1.2708 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 9054 Z= 0.313 Angle : 0.694 7.702 11286 Z= 0.449 Chirality : 0.000 0.000 0 Planarity : 0.004 0.017 2250 Dihedral : 6.888 24.738 2250 Min Nonbonded Distance : 2.297 Molprobity Statistics. All-atom Clashscore : 3.04 Ramachandran Plot: Outliers : 0.13 % Allowed : 17.38 % Favored : 82.48 % 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: -3.20 (0.17), residues: 2232 helix: 0.52 (0.25), residues: 401 sheet: -2.69 (0.20), residues: 547 loop : -2.85 (0.16), residues: 1284 *********************** 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 fitting. rotamer outliers: 0 poor density : 35 time to evaluate : 1.080 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 35 average time/residue: 0.0757 time to fit residues: 6.6059 Evaluate side-chains 35 residues out of total 1985 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 35 time to evaluate : 1.169 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 222 random chunks: chunk 132 optimal weight: 6.9990 chunk 85 optimal weight: 10.0000 chunk 127 optimal weight: 40.0000 chunk 64 optimal weight: 20.0000 chunk 42 optimal weight: 50.0000 chunk 41 optimal weight: 10.0000 chunk 136 optimal weight: 1.9990 chunk 145 optimal weight: 20.0000 chunk 105 optimal weight: 7.9990 chunk 19 optimal weight: 0.1980 chunk 168 optimal weight: 7.9990 overall best weight: 5.0388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7156 moved from start: 1.2477 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 9054 Z= 0.158 Angle : 0.471 4.347 11286 Z= 0.301 Chirality : 0.000 0.000 0 Planarity : 0.002 0.012 2250 Dihedral : 5.542 22.453 2250 Min Nonbonded Distance : 2.388 Molprobity Statistics. All-atom Clashscore : 1.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.89 % Favored : 89.11 % 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: -2.54 (0.17), residues: 2232 helix: 1.73 (0.26), residues: 399 sheet: -2.52 (0.21), residues: 510 loop : -2.55 (0.16), residues: 1323 *********************** 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 fitting. rotamer outliers: 0 poor density : 35 time to evaluate : 1.156 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 35 average time/residue: 0.0806 time to fit residues: 6.9719 Evaluate side-chains 35 residues out of total 1985 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 35 time to evaluate : 1.200 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 222 random chunks: chunk 194 optimal weight: 40.0000 chunk 204 optimal weight: 20.0000 chunk 187 optimal weight: 10.0000 chunk 199 optimal weight: 40.0000 chunk 120 optimal weight: 50.0000 chunk 86 optimal weight: 9.9990 chunk 156 optimal weight: 30.0000 chunk 61 optimal weight: 20.0000 chunk 180 optimal weight: 20.0000 chunk 188 optimal weight: 40.0000 chunk 198 optimal weight: 50.0000 overall best weight: 15.9998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7267 moved from start: 1.3391 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.070 9054 Z= 0.417 Angle : 0.820 8.786 11286 Z= 0.535 Chirality : 0.000 0.000 0 Planarity : 0.005 0.026 2250 Dihedral : 7.501 26.412 2250 Min Nonbonded Distance : 2.256 Molprobity Statistics. All-atom Clashscore : 4.87 Ramachandran Plot: Outliers : 0.18 % Allowed : 20.39 % Favored : 79.44 % 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: -3.49 (0.16), residues: 2232 helix: 0.09 (0.25), residues: 400 sheet: -2.84 (0.22), residues: 486 loop : -3.02 (0.15), residues: 1346 *********************** 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 fitting. rotamer outliers: 0 poor density : 35 time to evaluate : 1.111 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 35 average time/residue: 0.0770 time to fit residues: 6.7139 Evaluate side-chains 35 residues out of total 1985 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 35 time to evaluate : 1.103 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 222 random chunks: chunk 130 optimal weight: 0.3980 chunk 210 optimal weight: 10.0000 chunk 128 optimal weight: 50.0000 chunk 100 optimal weight: 9.9990 chunk 146 optimal weight: 9.9990 chunk 221 optimal weight: 40.0000 chunk 203 optimal weight: 30.0000 chunk 176 optimal weight: 7.9990 chunk 18 optimal weight: 20.0000 chunk 136 optimal weight: 9.9990 chunk 107 optimal weight: 6.9990 overall best weight: 7.0788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7197 moved from start: 1.3144 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 9054 Z= 0.206 Angle : 0.532 5.064 11286 Z= 0.341 Chirality : 0.000 0.000 0 Planarity : 0.003 0.013 2250 Dihedral : 5.981 22.669 2250 Min Nonbonded Distance : 2.359 Molprobity Statistics. All-atom Clashscore : 1.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 14.02 % Favored : 85.98 % 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: -2.96 (0.17), residues: 2232 helix: 1.17 (0.26), residues: 397 sheet: -2.71 (0.22), residues: 491 loop : -2.80 (0.16), residues: 1344 ********************** 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 fitting. rotamer outliers: 0 poor density : 35 time to evaluate : 1.110 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 35 average time/residue: 0.0772 time to fit residues: 6.7696 Evaluate side-chains 35 residues out of total 1985 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 35 time to evaluate : 1.081 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 222 random chunks: chunk 139 optimal weight: 20.0000 chunk 187 optimal weight: 10.0000 chunk 53 optimal weight: 50.0000 chunk 162 optimal weight: 30.0000 chunk 26 optimal weight: 0.9990 chunk 48 optimal weight: 40.0000 chunk 176 optimal weight: 0.0570 chunk 73 optimal weight: 20.0000 chunk 181 optimal weight: 50.0000 chunk 22 optimal weight: 30.0000 chunk 32 optimal weight: 10.0000 overall best weight: 8.2112 ------------------------------------------------------------------------------- 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 = 0.2931 r_free = 0.2931 target = 0.051478 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2633 r_free = 0.2633 target = 0.038307 restraints weight = 96605.785| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.2633 r_free = 0.2633 target = 0.038326 restraints weight = 92862.560| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.2633 r_free = 0.2633 target = 0.038326 restraints weight = 92243.817| |-----------------------------------------------------------------------------| r_work (final): 0.2549 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6537 moved from start: 1.3358 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 9054 Z= 0.230 Angle : 0.548 5.551 11286 Z= 0.355 Chirality : 0.000 0.000 0 Planarity : 0.003 0.012 2250 Dihedral : 5.922 22.629 2250 Min Nonbonded Distance : 2.332 Molprobity Statistics. All-atom Clashscore : 1.74 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: -2.88 (0.17), residues: 2232 helix: 1.40 (0.26), residues: 399 sheet: -2.71 (0.22), residues: 479 loop : -2.79 (0.16), residues: 1354 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1379.89 seconds wall clock time: 25 minutes 2.94 seconds (1502.94 seconds total)