Starting phenix.real_space_refine on Thu Sep 18 06:17:56 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8iqf_35660/09_2025/8iqf_35660.cif Found real_map, /net/cci-nas-00/data/ceres_data/8iqf_35660/09_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_35660/09_2025/8iqf_35660.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8iqf_35660/09_2025/8iqf_35660.map" model { file = "/net/cci-nas-00/data/ceres_data/8iqf_35660/09_2025/8iqf_35660.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8iqf_35660/09_2025/8iqf_35660.cif" } resolution = 4.6 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.006 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-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/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, 'ASP:plan': 22, 'GLU:plan': 22, 'ARG:plan': 10, 'PHE:plan': 8, 'ASN:plan1': 3, 'HIS:plan': 4, 'TYR:plan': 3, 'TRP:plan': 6} 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: {'ARG:plan': 15, 'GLN:plan1': 7, 'HIS:plan': 2, 'TYR:plan': 3, 'GLU:plan': 7, 'PHE:plan': 4, 'ASP:plan': 4, 'ASN:plan1': 1} 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: {'ARG:plan': 11, 'ASP:plan': 3, 'ASN:plan1': 2, 'GLN:plan1': 2, 'TYR:plan': 4, 'GLU:plan': 4, 'PHE:plan': 2, 'HIS:plan': 1} 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: {'GLU:plan': 31, 'ARG:plan': 11, 'ASN:plan1': 22, 'TYR:plan': 8, 'TRP:plan': 13, 'PHE:plan': 14, 'ASP:plan': 31, 'HIS:plan': 20, 'GLN:plan1': 12} 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: {'GLU:plan': 17, 'TRP:plan': 8, 'HIS:plan': 10, 'ASN:plan1': 16, 'TYR:plan': 13, 'ASP:plan': 22, 'PHE:plan': 17, 'GLN:plan1': 8, 'ARG:plan': 18} 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, 'ASP:plan': 22, 'GLU:plan': 22, 'ARG:plan': 10, 'PHE:plan': 8, 'ASN:plan1': 3, 'HIS:plan': 4, 'TYR:plan': 3, 'TRP:plan': 6} 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: {'ARG:plan': 15, 'GLN:plan1': 7, 'HIS:plan': 2, 'TYR:plan': 3, 'GLU:plan': 7, 'PHE:plan': 4, 'ASP:plan': 4, 'ASN:plan1': 1} 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: {'ARG:plan': 11, 'ASP:plan': 3, 'ASN:plan1': 2, 'GLN:plan1': 2, 'TYR:plan': 4, 'GLU:plan': 4, 'PHE:plan': 2, 'HIS:plan': 1} 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: {'GLU:plan': 31, 'ARG:plan': 11, 'ASN:plan1': 22, 'TYR:plan': 8, 'TRP:plan': 13, 'PHE:plan': 14, 'ASP:plan': 31, 'HIS:plan': 20, 'GLN:plan1': 12} 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: {'GLU:plan': 17, 'TRP:plan': 8, 'HIS:plan': 10, 'ASN:plan1': 16, 'TYR:plan': 13, 'ASP:plan': 22, 'PHE:plan': 17, 'GLN:plan1': 8, 'ARG:plan': 18} Unresolved non-hydrogen planarities: 705 Time building chain proxies: 2.90, per 1000 atoms: 0.32 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: 1.04 Conformation dependent library (CDL) restraints added in 584.1 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 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: 0.53 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: 1.69 Time building geometry restraints manager: 1.23 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: 0.01 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: 1.090 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.040 Construct map_model_manager: 0.000 Extract box with map and model: 0.170 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 11.760 Find NCS groups from input model: 0.200 Set up NCS constraints: 0.030 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:1.470 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.820 ------------------------------------------------------------------------------- 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. 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 covalent geometry : bond 0.00282 ( 9054) covalent geometry : angle 0.63414 (11286) hydrogen bonds : bond 0.25263 ( 615) hydrogen bonds : angle 8.61227 ( 1749) *********************** 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 : 0.375 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 35 average time/residue: 0.0397 time to fit residues: 3.1594 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 : 0.376 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 222 random chunks: chunk 216 optimal weight: 6.9990 chunk 98 optimal weight: 50.0000 chunk 194 optimal weight: 50.0000 chunk 107 optimal weight: 3.9990 chunk 10 optimal weight: 7.9990 chunk 66 optimal weight: 40.0000 chunk 130 optimal weight: 30.0000 chunk 124 optimal weight: 30.0000 chunk 103 optimal weight: 50.0000 chunk 200 optimal weight: 50.0000 chunk 212 optimal weight: 20.0000 overall best weight: 13.7994 ------------------------------------------------------------------------------- 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 = 0.3104 r_free = 0.3104 target = 0.057317 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2677 r_free = 0.2677 target = 0.041542 restraints weight = 82482.372| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 20)----------------| | r_work = 0.2679 r_free = 0.2679 target = 0.041595 restraints weight = 79901.788| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.2681 r_free = 0.2681 target = 0.041678 restraints weight = 78395.669| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 20)----------------| | r_work = 0.2681 r_free = 0.2681 target = 0.041699 restraints weight = 77192.392| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 17)----------------| | r_work = 0.2682 r_free = 0.2682 target = 0.041709 restraints weight = 76595.455| |-----------------------------------------------------------------------------| r_work (final): 0.2657 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7761 moved from start: 0.7465 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.052 9054 Z= 0.414 Angle : 0.942 8.678 11286 Z= 0.607 Chirality : 0.000 0.000 0 Planarity : 0.006 0.025 2250 Dihedral : 7.556 29.501 2250 Min Nonbonded Distance : 2.343 Molprobity Statistics. All-atom Clashscore : 3.04 Ramachandran Plot: Outliers : 0.09 % Allowed : 6.41 % Favored : 93.50 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.11 (0.17), residues: 2232 helix: 0.99 (0.26), residues: 387 sheet: -0.59 (0.21), residues: 548 loop : -1.37 (0.16), residues: 1297 Details of bonding type rmsd covalent geometry : bond 0.00564 ( 9054) covalent geometry : angle 0.94210 (11286) hydrogen bonds : bond 0.07306 ( 615) hydrogen bonds : angle 7.82331 ( 1749) *********************** 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 : 0.412 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 35 average time/residue: 0.0391 time to fit residues: 3.1875 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 : 0.363 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 222 random chunks: chunk 53 optimal weight: 40.0000 chunk 100 optimal weight: 10.0000 chunk 120 optimal weight: 40.0000 chunk 182 optimal weight: 5.9990 chunk 142 optimal weight: 10.0000 chunk 5 optimal weight: 40.0000 chunk 68 optimal weight: 8.9990 chunk 161 optimal weight: 50.0000 chunk 198 optimal weight: 40.0000 chunk 102 optimal weight: 20.0000 chunk 145 optimal weight: 10.0000 overall best weight: 8.9996 ------------------------------------------------------------------------------- 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 = 0.3077 r_free = 0.3077 target = 0.056070 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2657 r_free = 0.2657 target = 0.040642 restraints weight = 82312.177| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 17)----------------| | r_work = 0.2657 r_free = 0.2657 target = 0.040643 restraints weight = 79723.335| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 17)----------------| | r_work = 0.2660 r_free = 0.2660 target = 0.040720 restraints weight = 79696.502| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.2663 r_free = 0.2663 target = 0.040815 restraints weight = 77729.671| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 18)----------------| | r_work = 0.2663 r_free = 0.2663 target = 0.040818 restraints weight = 76367.965| |-----------------------------------------------------------------------------| r_work (final): 0.2639 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7797 moved from start: 0.8229 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 9054 Z= 0.251 Angle : 0.594 5.561 11286 Z= 0.382 Chirality : 0.000 0.000 0 Planarity : 0.003 0.019 2250 Dihedral : 5.623 22.995 2250 Min Nonbonded Distance : 2.358 Molprobity Statistics. All-atom Clashscore : 1.74 Ramachandran Plot: Outliers : 0.04 % Allowed : 6.77 % Favored : 93.19 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.00 (0.17), residues: 2232 helix: 1.87 (0.26), residues: 400 sheet: -0.74 (0.22), residues: 528 loop : -1.50 (0.16), residues: 1304 Details of bonding type rmsd covalent geometry : bond 0.00342 ( 9054) covalent geometry : angle 0.59418 (11286) hydrogen bonds : bond 0.04366 ( 615) hydrogen bonds : angle 6.18027 ( 1749) *********************** 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 : 0.390 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 35 average time/residue: 0.0398 time to fit residues: 3.1909 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 : 0.392 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 222 random chunks: chunk 165 optimal weight: 50.0000 chunk 191 optimal weight: 9.9990 chunk 14 optimal weight: 50.0000 chunk 193 optimal weight: 10.0000 chunk 91 optimal weight: 30.0000 chunk 107 optimal weight: 0.0570 chunk 89 optimal weight: 10.0000 chunk 34 optimal weight: 20.0000 chunk 183 optimal weight: 9.9990 chunk 62 optimal weight: 50.0000 chunk 180 optimal weight: 30.0000 overall best weight: 8.0110 ------------------------------------------------------------------------------- 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 = 0.3041 r_free = 0.3041 target = 0.054786 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.2618 r_free = 0.2618 target = 0.039534 restraints weight = 84696.321| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.2621 r_free = 0.2621 target = 0.039629 restraints weight = 81330.883| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.2624 r_free = 0.2624 target = 0.039722 restraints weight = 78747.114| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 20)----------------| | r_work = 0.2627 r_free = 0.2627 target = 0.039821 restraints weight = 76755.081| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.2627 r_free = 0.2627 target = 0.039821 restraints weight = 75196.862| |-----------------------------------------------------------------------------| r_work (final): 0.2605 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7840 moved from start: 0.9755 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 9054 Z= 0.238 Angle : 0.582 6.100 11286 Z= 0.375 Chirality : 0.000 0.000 0 Planarity : 0.003 0.013 2250 Dihedral : 5.700 22.892 2250 Min Nonbonded Distance : 2.350 Molprobity Statistics. All-atom Clashscore : 1.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.60 % Favored : 91.40 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.33 (0.18), residues: 2232 helix: 2.07 (0.25), residues: 414 sheet: -1.31 (0.21), residues: 581 loop : -1.75 (0.17), residues: 1237 Details of bonding type rmsd covalent geometry : bond 0.00325 ( 9054) covalent geometry : angle 0.58158 (11286) hydrogen bonds : bond 0.04157 ( 615) hydrogen bonds : angle 6.15813 ( 1749) *********************** 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 : 0.421 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 35 average time/residue: 0.0402 time to fit residues: 3.2409 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 : 0.390 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 222 random chunks: chunk 53 optimal weight: 40.0000 chunk 103 optimal weight: 8.9990 chunk 198 optimal weight: 50.0000 chunk 76 optimal weight: 9.9990 chunk 195 optimal weight: 1.9990 chunk 158 optimal weight: 50.0000 chunk 68 optimal weight: 10.0000 chunk 134 optimal weight: 30.0000 chunk 209 optimal weight: 50.0000 chunk 48 optimal weight: 20.0000 chunk 197 optimal weight: 30.0000 overall best weight: 10.1994 ------------------------------------------------------------------------------- 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 = 0.2995 r_free = 0.2995 target = 0.053319 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2591 r_free = 0.2591 target = 0.038723 restraints weight = 84596.699| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2594 r_free = 0.2594 target = 0.038800 restraints weight = 81961.575| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 14)----------------| | r_work = 0.2595 r_free = 0.2595 target = 0.038830 restraints weight = 80118.021| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 12)----------------| | r_work = 0.2595 r_free = 0.2595 target = 0.038830 restraints weight = 79104.930| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.2595 r_free = 0.2595 target = 0.038830 restraints weight = 79101.088| |-----------------------------------------------------------------------------| r_work (final): 0.2553 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7900 moved from start: 1.0934 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= 0.286 Angle : 0.664 7.048 11286 Z= 0.428 Chirality : 0.000 0.000 0 Planarity : 0.003 0.012 2250 Dihedral : 6.284 22.411 2250 Min Nonbonded Distance : 2.295 Molprobity Statistics. All-atom Clashscore : 3.13 Ramachandran Plot: Outliers : 0.09 % Allowed : 9.95 % Favored : 89.96 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.92 (0.17), residues: 2232 helix: 1.75 (0.25), residues: 406 sheet: -1.87 (0.21), residues: 554 loop : -2.08 (0.17), residues: 1272 Details of bonding type rmsd covalent geometry : bond 0.00392 ( 9054) covalent geometry : angle 0.66418 (11286) hydrogen bonds : bond 0.04614 ( 615) hydrogen bonds : angle 6.89532 ( 1749) *********************** 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 : 0.401 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 35 average time/residue: 0.0396 time to fit residues: 3.2016 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 : 0.417 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 222 random chunks: chunk 185 optimal weight: 40.0000 chunk 144 optimal weight: 9.9990 chunk 22 optimal weight: 20.0000 chunk 95 optimal weight: 50.0000 chunk 12 optimal weight: 50.0000 chunk 78 optimal weight: 20.0000 chunk 47 optimal weight: 40.0000 chunk 0 optimal weight: 90.0000 chunk 112 optimal weight: 40.0000 chunk 194 optimal weight: 50.0000 chunk 16 optimal weight: 40.0000 overall best weight: 25.9998 ------------------------------------------------------------------------------- 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 = 0.2915 r_free = 0.2915 target = 0.050488 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.2511 r_free = 0.2511 target = 0.036584 restraints weight = 86473.043| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.2511 r_free = 0.2511 target = 0.036601 restraints weight = 83653.407| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.2511 r_free = 0.2511 target = 0.036602 restraints weight = 83052.438| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.2511 r_free = 0.2511 target = 0.036602 restraints weight = 83030.058| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.2511 r_free = 0.2511 target = 0.036602 restraints weight = 83030.058| |-----------------------------------------------------------------------------| r_work (final): 0.2474 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8037 moved from start: 1.3035 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.105 9054 Z= 0.612 Angle : 1.166 13.021 11286 Z= 0.760 Chirality : 0.000 0.000 0 Planarity : 0.007 0.042 2250 Dihedral : 9.281 33.223 2250 Min Nonbonded Distance : 2.213 Molprobity Statistics. All-atom Clashscore : 13.65 Ramachandran Plot: Outliers : 0.45 % Allowed : 18.86 % Favored : 80.69 % 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 : 0.33 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.82 (0.16), residues: 2232 helix: -1.03 (0.25), residues: 371 sheet: -2.61 (0.23), residues: 423 loop : -3.12 (0.14), residues: 1438 Details of bonding type rmsd covalent geometry : bond 0.00839 ( 9054) covalent geometry : angle 1.16648 (11286) hydrogen bonds : bond 0.08518 ( 615) hydrogen bonds : angle 10.14924 ( 1749) *********************** 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 : 0.411 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 35 average time/residue: 0.0400 time to fit residues: 3.2318 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 : 0.384 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 222 random chunks: chunk 85 optimal weight: 0.0870 chunk 40 optimal weight: 50.0000 chunk 101 optimal weight: 0.7980 chunk 6 optimal weight: 50.0000 chunk 213 optimal weight: 0.0070 chunk 100 optimal weight: 4.9990 chunk 53 optimal weight: 20.0000 chunk 206 optimal weight: 0.0040 chunk 96 optimal weight: 6.9990 chunk 176 optimal weight: 30.0000 chunk 218 optimal weight: 0.9980 overall best weight: 0.3788 ------------------------------------------------------------------------------- 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 = 0.3047 r_free = 0.3047 target = 0.055350 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2649 r_free = 0.2649 target = 0.040659 restraints weight = 81793.768| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.2654 r_free = 0.2654 target = 0.040819 restraints weight = 76811.352| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 21)----------------| | r_work = 0.2658 r_free = 0.2658 target = 0.040940 restraints weight = 73565.910| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.2658 r_free = 0.2658 target = 0.040940 restraints weight = 71166.747| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.2658 r_free = 0.2658 target = 0.040940 restraints weight = 71166.747| |-----------------------------------------------------------------------------| r_work (final): 0.2619 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7804 moved from start: 1.2027 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.001 0.014 9054 Z= 0.103 Angle : 0.441 6.278 11286 Z= 0.278 Chirality : 0.000 0.000 0 Planarity : 0.002 0.012 2250 Dihedral : 5.224 22.645 2250 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 0.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.90 % Favored : 93.10 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.55 (0.17), residues: 2232 helix: 1.39 (0.25), residues: 414 sheet: -2.52 (0.20), residues: 557 loop : -2.45 (0.16), residues: 1261 Details of bonding type rmsd covalent geometry : bond 0.00139 ( 9054) covalent geometry : angle 0.44076 (11286) hydrogen bonds : bond 0.03026 ( 615) hydrogen bonds : angle 6.10335 ( 1749) *********************** 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 : 0.372 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 35 average time/residue: 0.0392 time to fit residues: 3.1494 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 : 0.372 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 222 random chunks: chunk 178 optimal weight: 50.0000 chunk 63 optimal weight: 9.9990 chunk 170 optimal weight: 0.7980 chunk 44 optimal weight: 40.0000 chunk 14 optimal weight: 50.0000 chunk 167 optimal weight: 7.9990 chunk 50 optimal weight: 40.0000 chunk 190 optimal weight: 9.9990 chunk 35 optimal weight: 9.9990 chunk 141 optimal weight: 9.9990 chunk 112 optimal weight: 30.0000 overall best weight: 7.7588 ------------------------------------------------------------------------------- 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 = 0.2968 r_free = 0.2968 target = 0.052718 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2650 r_free = 0.2650 target = 0.038864 restraints weight = 98028.108| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.2655 r_free = 0.2655 target = 0.039009 restraints weight = 94592.650| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 21)----------------| | r_work = 0.2656 r_free = 0.2656 target = 0.039059 restraints weight = 90339.543| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 15)----------------| | r_work = 0.2657 r_free = 0.2657 target = 0.039101 restraints weight = 88643.133| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 21)----------------| | r_work = 0.2658 r_free = 0.2658 target = 0.039102 restraints weight = 87061.107| |-----------------------------------------------------------------------------| r_work (final): 0.2583 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6391 moved from start: 1.2309 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= 0.215 Angle : 0.531 7.418 11286 Z= 0.341 Chirality : 0.000 0.000 0 Planarity : 0.003 0.010 2250 Dihedral : 5.502 21.883 2250 Min Nonbonded Distance : 2.340 Molprobity Statistics. All-atom Clashscore : 1.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.89 % Favored : 86.11 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.41 (0.17), residues: 2232 helix: 1.59 (0.25), residues: 424 sheet: -2.42 (0.21), residues: 528 loop : -2.46 (0.16), residues: 1280 Details of bonding type rmsd covalent geometry : bond 0.00293 ( 9054) covalent geometry : angle 0.53059 (11286) hydrogen bonds : bond 0.03912 ( 615) hydrogen bonds : angle 6.57293 ( 1749) *********************** 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 : 0.369 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 35 average time/residue: 0.0378 time to fit residues: 3.0322 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 : 0.383 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 222 random chunks: chunk 87 optimal weight: 50.0000 chunk 29 optimal weight: 8.9990 chunk 210 optimal weight: 8.9990 chunk 124 optimal weight: 50.0000 chunk 55 optimal weight: 50.0000 chunk 89 optimal weight: 8.9990 chunk 100 optimal weight: 20.0000 chunk 21 optimal weight: 5.9990 chunk 101 optimal weight: 0.2980 chunk 121 optimal weight: 50.0000 chunk 12 optimal weight: 50.0000 overall best weight: 6.6588 ------------------------------------------------------------------------------- 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 = 0.2974 r_free = 0.2974 target = 0.052854 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2654 r_free = 0.2654 target = 0.038961 restraints weight = 97306.079| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.2657 r_free = 0.2657 target = 0.039042 restraints weight = 93804.156| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 20)----------------| | r_work = 0.2657 r_free = 0.2657 target = 0.039045 restraints weight = 90759.409| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.2659 r_free = 0.2659 target = 0.039136 restraints weight = 90693.435| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.2661 r_free = 0.2661 target = 0.039171 restraints weight = 88707.086| |-----------------------------------------------------------------------------| r_work (final): 0.2592 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6382 moved from start: 1.2431 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= 0.186 Angle : 0.485 6.467 11286 Z= 0.312 Chirality : 0.000 0.000 0 Planarity : 0.002 0.010 2250 Dihedral : 5.263 22.163 2250 Min Nonbonded Distance : 2.371 Molprobity Statistics. All-atom Clashscore : 1.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.72 % Favored : 87.28 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.24 (0.18), residues: 2232 helix: 2.06 (0.26), residues: 412 sheet: -2.42 (0.21), residues: 525 loop : -2.38 (0.16), residues: 1295 Details of bonding type rmsd covalent geometry : bond 0.00254 ( 9054) covalent geometry : angle 0.48550 (11286) hydrogen bonds : bond 0.03521 ( 615) hydrogen bonds : angle 6.31636 ( 1749) *********************** 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 : 0.488 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 35 average time/residue: 0.0395 time to fit residues: 3.3031 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 : 0.483 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 222 random chunks: chunk 113 optimal weight: 50.0000 chunk 221 optimal weight: 40.0000 chunk 110 optimal weight: 40.0000 chunk 188 optimal weight: 20.0000 chunk 159 optimal weight: 50.0000 chunk 73 optimal weight: 30.0000 chunk 152 optimal weight: 7.9990 chunk 74 optimal weight: 20.0000 chunk 125 optimal weight: 50.0000 chunk 137 optimal weight: 20.0000 chunk 9 optimal weight: 50.0000 overall best weight: 19.5998 ------------------------------------------------------------------------------- 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 = 0.2893 r_free = 0.2893 target = 0.050050 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2607 r_free = 0.2607 target = 0.037576 restraints weight = 102690.931| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.2610 r_free = 0.2610 target = 0.037667 restraints weight = 99508.013| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.2612 r_free = 0.2612 target = 0.037699 restraints weight = 96684.487| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 15)----------------| | r_work = 0.2614 r_free = 0.2614 target = 0.037763 restraints weight = 95392.546| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.2614 r_free = 0.2614 target = 0.037773 restraints weight = 92956.712| |-----------------------------------------------------------------------------| r_work (final): 0.2529 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6503 moved from start: 1.3650 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.085 9054 Z= 0.477 Angle : 0.934 10.065 11286 Z= 0.612 Chirality : 0.000 0.000 0 Planarity : 0.005 0.031 2250 Dihedral : 7.945 28.285 2250 Min Nonbonded Distance : 2.247 Molprobity Statistics. All-atom Clashscore : 6.78 Ramachandran Plot: Outliers : 0.27 % Allowed : 20.43 % Favored : 79.30 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.52 (0.16), residues: 2232 helix: -0.08 (0.25), residues: 386 sheet: -2.74 (0.23), residues: 443 loop : -3.04 (0.15), residues: 1403 Details of bonding type rmsd covalent geometry : bond 0.00658 ( 9054) covalent geometry : angle 0.93374 (11286) hydrogen bonds : bond 0.06778 ( 615) hydrogen bonds : angle 9.12233 ( 1749) ********************** 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 : 0.425 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 35 average time/residue: 0.0379 time to fit residues: 3.0237 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 : 0.337 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 222 random chunks: chunk 189 optimal weight: 9.9990 chunk 145 optimal weight: 10.0000 chunk 143 optimal weight: 3.9990 chunk 170 optimal weight: 50.0000 chunk 28 optimal weight: 10.0000 chunk 153 optimal weight: 30.0000 chunk 102 optimal weight: 20.0000 chunk 125 optimal weight: 50.0000 chunk 184 optimal weight: 20.0000 chunk 91 optimal weight: 20.0000 chunk 175 optimal weight: 20.0000 overall best weight: 10.7996 ------------------------------------------------------------------------------- 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 = 0.2941 r_free = 0.2941 target = 0.051379 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2548 r_free = 0.2548 target = 0.037517 restraints weight = 83397.396| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 17)----------------| | r_work = 0.2552 r_free = 0.2552 target = 0.037650 restraints weight = 78878.171| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.2552 r_free = 0.2552 target = 0.037655 restraints weight = 76091.446| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.2552 r_free = 0.2552 target = 0.037655 restraints weight = 75891.209| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.2552 r_free = 0.2552 target = 0.037655 restraints weight = 75891.209| |-----------------------------------------------------------------------------| r_work (final): 0.2532 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7975 moved from start: 1.3529 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 9054 Z= 0.288 Angle : 0.658 6.164 11286 Z= 0.427 Chirality : 0.000 0.000 0 Planarity : 0.004 0.015 2250 Dihedral : 6.713 25.105 2250 Min Nonbonded Distance : 2.311 Molprobity Statistics. All-atom Clashscore : 2.61 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.45 (0.16), residues: 2232 helix: 0.21 (0.25), residues: 401 sheet: -2.78 (0.22), residues: 487 loop : -3.04 (0.15), residues: 1344 Details of bonding type rmsd covalent geometry : bond 0.00396 ( 9054) covalent geometry : angle 0.65786 (11286) hydrogen bonds : bond 0.04866 ( 615) hydrogen bonds : angle 7.87086 ( 1749) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1304.75 seconds wall clock time: 22 minutes 57.28 seconds (1377.28 seconds total)