Starting phenix.real_space_refine (version: dev) on Wed Feb 22 23:55:37 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ulw_26595/02_2023/7ulw_26595.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ulw_26595/02_2023/7ulw_26595.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ulw_26595/02_2023/7ulw_26595.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ulw_26595/02_2023/7ulw_26595.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ulw_26595/02_2023/7ulw_26595.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ulw_26595/02_2023/7ulw_26595.pdb" } resolution = 3.1 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 ------------------------------------------------------------------------------- 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= 0.000 sd= 0.001 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Process input model Symmetric amino acids flipped None Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/modules/chem_data/mon_lib" Total number of atoms: 18766 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 3128 Number of conformers: 1 Conformer: "" Number of residues, atoms: 400, 3128 Classifications: {'peptide': 400} Incomplete info: {'truncation_to_alanine': 16} Link IDs: {'PTRANS': 17, 'TRANS': 382} Chain breaks: 1 Unresolved non-hydrogen bonds: 61 Unresolved non-hydrogen angles: 69 Unresolved non-hydrogen dihedrals: 53 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 7} Unresolved non-hydrogen planarities: 28 Chain: "B" Number of atoms: 3124 Number of conformers: 1 Conformer: "" Number of residues, atoms: 400, 3124 Classifications: {'peptide': 400} Incomplete info: {'truncation_to_alanine': 16} Link IDs: {'PTRANS': 17, 'TRANS': 382} Chain breaks: 1 Unresolved non-hydrogen bonds: 66 Unresolved non-hydrogen angles: 76 Unresolved non-hydrogen dihedrals: 59 Planarities with less than four sites: {'TYR:plan': 1, 'GLU:plan': 7} Unresolved non-hydrogen planarities: 35 Chain: "C" Number of atoms: 3135 Number of conformers: 1 Conformer: "" Number of residues, atoms: 400, 3135 Classifications: {'peptide': 400} Incomplete info: {'truncation_to_alanine': 14} Link IDs: {'PTRANS': 17, 'TRANS': 382} Chain breaks: 1 Unresolved non-hydrogen bonds: 54 Unresolved non-hydrogen angles: 60 Unresolved non-hydrogen dihedrals: 48 Planarities with less than four sites: {'GLU:plan': 6} Unresolved non-hydrogen planarities: 24 Chain: "D" Number of atoms: 3128 Number of conformers: 1 Conformer: "" Number of residues, atoms: 400, 3128 Classifications: {'peptide': 400} Incomplete info: {'truncation_to_alanine': 16} Link IDs: {'PTRANS': 17, 'TRANS': 382} Chain breaks: 1 Unresolved non-hydrogen bonds: 61 Unresolved non-hydrogen angles: 69 Unresolved non-hydrogen dihedrals: 53 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 7} Unresolved non-hydrogen planarities: 28 Chain: "E" Number of atoms: 3127 Number of conformers: 1 Conformer: "" Number of residues, atoms: 400, 3127 Classifications: {'peptide': 400} Incomplete info: {'truncation_to_alanine': 16} Link IDs: {'PTRANS': 17, 'TRANS': 382} Chain breaks: 1 Unresolved non-hydrogen bonds: 62 Unresolved non-hydrogen angles: 70 Unresolved non-hydrogen dihedrals: 54 Planarities with less than four sites: {'GLU:plan': 8} Unresolved non-hydrogen planarities: 32 Chain: "F" Number of atoms: 3124 Number of conformers: 1 Conformer: "" Number of residues, atoms: 400, 3124 Classifications: {'peptide': 400} Incomplete info: {'truncation_to_alanine': 17} Link IDs: {'PTRANS': 17, 'TRANS': 382} Chain breaks: 1 Unresolved non-hydrogen bonds: 65 Unresolved non-hydrogen angles: 74 Unresolved non-hydrogen dihedrals: 56 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 8} Unresolved non-hydrogen planarities: 32 Time building chain proxies: 9.88, per 1000 atoms: 0.53 Number of scatterers: 18766 At special positions: 0 Unit cell: (155.188, 133.839, 142.05, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 102 16.00 O 3453 8.00 N 3180 7.00 C 12031 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 - 3.50 Amino acid : False - 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: 7.55 Conformation dependent library (CDL) restraints added in 2.9 seconds 4752 Ramachandran restraints generated. 2376 Oldfield, 0 Emsley, 2376 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4464 Finding SS restraints... Secondary structure from input PDB file: 90 helices and 24 sheets defined 40.8% alpha, 14.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.10 Creating SS restraints... Processing helix chain 'A' and resid 99 through 104 Processing helix chain 'A' and resid 106 through 123 Processing helix chain 'A' and resid 164 through 180 removed outlier: 3.518A pdb=" N ALA A 180 " --> pdb=" O LYS A 176 " (cutoff:3.500A) Processing helix chain 'A' and resid 188 through 192 Processing helix chain 'A' and resid 209 through 215 Processing helix chain 'A' and resid 226 through 242 Processing helix chain 'A' and resid 300 through 305 removed outlier: 3.537A pdb=" N SER A 304 " --> pdb=" O ASN A 300 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N LEU A 305 " --> pdb=" O SER A 301 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 300 through 305' Processing helix chain 'A' and resid 306 through 308 No H-bonds generated for 'chain 'A' and resid 306 through 308' Processing helix chain 'A' and resid 325 through 340 Processing helix chain 'A' and resid 342 through 354 Processing helix chain 'A' and resid 391 through 395 removed outlier: 4.144A pdb=" N TRP A 395 " --> pdb=" O SER A 392 " (cutoff:3.500A) Processing helix chain 'A' and resid 403 through 424 removed outlier: 4.683A pdb=" N GLY A 421 " --> pdb=" O GLY A 417 " (cutoff:3.500A) removed outlier: 5.265A pdb=" N LEU A 422 " --> pdb=" O TYR A 418 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N PHE A 423 " --> pdb=" O GLN A 419 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N LYS A 424 " --> pdb=" O VAL A 420 " (cutoff:3.500A) Processing helix chain 'A' and resid 436 through 443 Processing helix chain 'A' and resid 506 through 510 Processing helix chain 'A' and resid 530 through 545 Processing helix chain 'B' and resid 100 through 104 Processing helix chain 'B' and resid 106 through 123 Processing helix chain 'B' and resid 164 through 180 removed outlier: 3.518A pdb=" N ALA B 180 " --> pdb=" O LYS B 176 " (cutoff:3.500A) Processing helix chain 'B' and resid 188 through 192 Processing helix chain 'B' and resid 209 through 215 Processing helix chain 'B' and resid 226 through 242 Processing helix chain 'B' and resid 300 through 305 removed outlier: 3.537A pdb=" N SER B 304 " --> pdb=" O ASN B 300 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N LEU B 305 " --> pdb=" O SER B 301 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 300 through 305' Processing helix chain 'B' and resid 306 through 308 No H-bonds generated for 'chain 'B' and resid 306 through 308' Processing helix chain 'B' and resid 325 through 340 Processing helix chain 'B' and resid 342 through 354 Processing helix chain 'B' and resid 391 through 395 removed outlier: 4.144A pdb=" N TRP B 395 " --> pdb=" O SER B 392 " (cutoff:3.500A) Processing helix chain 'B' and resid 403 through 424 removed outlier: 4.683A pdb=" N GLY B 421 " --> pdb=" O GLY B 417 " (cutoff:3.500A) removed outlier: 5.265A pdb=" N LEU B 422 " --> pdb=" O TYR B 418 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N PHE B 423 " --> pdb=" O GLN B 419 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N LYS B 424 " --> pdb=" O VAL B 420 " (cutoff:3.500A) Processing helix chain 'B' and resid 436 through 443 Processing helix chain 'B' and resid 506 through 510 Processing helix chain 'B' and resid 530 through 545 Processing helix chain 'C' and resid 100 through 104 Processing helix chain 'C' and resid 106 through 123 Processing helix chain 'C' and resid 164 through 180 removed outlier: 3.518A pdb=" N ALA C 180 " --> pdb=" O LYS C 176 " (cutoff:3.500A) Processing helix chain 'C' and resid 188 through 192 Processing helix chain 'C' and resid 209 through 215 Processing helix chain 'C' and resid 226 through 242 Processing helix chain 'C' and resid 300 through 305 removed outlier: 3.537A pdb=" N SER C 304 " --> pdb=" O ASN C 300 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N LEU C 305 " --> pdb=" O SER C 301 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 300 through 305' Processing helix chain 'C' and resid 306 through 308 No H-bonds generated for 'chain 'C' and resid 306 through 308' Processing helix chain 'C' and resid 325 through 340 Processing helix chain 'C' and resid 342 through 354 Processing helix chain 'C' and resid 391 through 395 removed outlier: 4.144A pdb=" N TRP C 395 " --> pdb=" O SER C 392 " (cutoff:3.500A) Processing helix chain 'C' and resid 403 through 424 removed outlier: 4.683A pdb=" N GLY C 421 " --> pdb=" O GLY C 417 " (cutoff:3.500A) removed outlier: 5.264A pdb=" N LEU C 422 " --> pdb=" O TYR C 418 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N PHE C 423 " --> pdb=" O GLN C 419 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N LYS C 424 " --> pdb=" O VAL C 420 " (cutoff:3.500A) Processing helix chain 'C' and resid 436 through 443 Processing helix chain 'C' and resid 506 through 510 Processing helix chain 'C' and resid 530 through 545 Processing helix chain 'D' and resid 100 through 104 Processing helix chain 'D' and resid 106 through 123 Processing helix chain 'D' and resid 164 through 180 removed outlier: 3.518A pdb=" N ALA D 180 " --> pdb=" O LYS D 176 " (cutoff:3.500A) Processing helix chain 'D' and resid 188 through 192 Processing helix chain 'D' and resid 209 through 215 Processing helix chain 'D' and resid 226 through 242 Processing helix chain 'D' and resid 300 through 305 removed outlier: 3.537A pdb=" N SER D 304 " --> pdb=" O ASN D 300 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N LEU D 305 " --> pdb=" O SER D 301 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 300 through 305' Processing helix chain 'D' and resid 306 through 308 No H-bonds generated for 'chain 'D' and resid 306 through 308' Processing helix chain 'D' and resid 325 through 340 Processing helix chain 'D' and resid 342 through 354 Processing helix chain 'D' and resid 391 through 395 removed outlier: 4.144A pdb=" N TRP D 395 " --> pdb=" O SER D 392 " (cutoff:3.500A) Processing helix chain 'D' and resid 403 through 424 removed outlier: 4.683A pdb=" N GLY D 421 " --> pdb=" O GLY D 417 " (cutoff:3.500A) removed outlier: 5.264A pdb=" N LEU D 422 " --> pdb=" O TYR D 418 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N PHE D 423 " --> pdb=" O GLN D 419 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N LYS D 424 " --> pdb=" O VAL D 420 " (cutoff:3.500A) Processing helix chain 'D' and resid 436 through 443 Processing helix chain 'D' and resid 506 through 510 Processing helix chain 'D' and resid 530 through 545 Processing helix chain 'E' and resid 100 through 104 Processing helix chain 'E' and resid 106 through 123 Processing helix chain 'E' and resid 164 through 180 removed outlier: 3.519A pdb=" N ALA E 180 " --> pdb=" O LYS E 176 " (cutoff:3.500A) Processing helix chain 'E' and resid 188 through 192 Processing helix chain 'E' and resid 209 through 215 Processing helix chain 'E' and resid 226 through 242 Processing helix chain 'E' and resid 300 through 305 removed outlier: 3.537A pdb=" N SER E 304 " --> pdb=" O ASN E 300 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N LEU E 305 " --> pdb=" O SER E 301 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 300 through 305' Processing helix chain 'E' and resid 306 through 308 No H-bonds generated for 'chain 'E' and resid 306 through 308' Processing helix chain 'E' and resid 325 through 340 Processing helix chain 'E' and resid 342 through 354 Processing helix chain 'E' and resid 391 through 395 removed outlier: 4.143A pdb=" N TRP E 395 " --> pdb=" O SER E 392 " (cutoff:3.500A) Processing helix chain 'E' and resid 403 through 424 removed outlier: 4.683A pdb=" N GLY E 421 " --> pdb=" O GLY E 417 " (cutoff:3.500A) removed outlier: 5.263A pdb=" N LEU E 422 " --> pdb=" O TYR E 418 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N PHE E 423 " --> pdb=" O GLN E 419 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N LYS E 424 " --> pdb=" O VAL E 420 " (cutoff:3.500A) Processing helix chain 'E' and resid 436 through 443 Processing helix chain 'E' and resid 506 through 510 Processing helix chain 'E' and resid 530 through 545 Processing helix chain 'F' and resid 100 through 104 Processing helix chain 'F' and resid 106 through 123 Processing helix chain 'F' and resid 164 through 180 removed outlier: 3.518A pdb=" N ALA F 180 " --> pdb=" O LYS F 176 " (cutoff:3.500A) Processing helix chain 'F' and resid 188 through 192 Processing helix chain 'F' and resid 209 through 215 Processing helix chain 'F' and resid 226 through 242 Processing helix chain 'F' and resid 300 through 305 removed outlier: 3.537A pdb=" N SER F 304 " --> pdb=" O ASN F 300 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N LEU F 305 " --> pdb=" O SER F 301 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 300 through 305' Processing helix chain 'F' and resid 306 through 308 No H-bonds generated for 'chain 'F' and resid 306 through 308' Processing helix chain 'F' and resid 325 through 340 Processing helix chain 'F' and resid 342 through 354 Processing helix chain 'F' and resid 391 through 395 removed outlier: 4.144A pdb=" N TRP F 395 " --> pdb=" O SER F 392 " (cutoff:3.500A) Processing helix chain 'F' and resid 403 through 424 removed outlier: 4.683A pdb=" N GLY F 421 " --> pdb=" O GLY F 417 " (cutoff:3.500A) removed outlier: 5.264A pdb=" N LEU F 422 " --> pdb=" O TYR F 418 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N PHE F 423 " --> pdb=" O GLN F 419 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N LYS F 424 " --> pdb=" O VAL F 420 " (cutoff:3.500A) Processing helix chain 'F' and resid 436 through 443 Processing helix chain 'F' and resid 506 through 510 Processing helix chain 'F' and resid 530 through 545 Processing sheet with id=AA1, first strand: chain 'A' and resid 152 through 153 removed outlier: 7.344A pdb=" N VAL A 131 " --> pdb=" O VAL A 138 " (cutoff:3.500A) removed outlier: 4.650A pdb=" N SER A 140 " --> pdb=" O VAL A 129 " (cutoff:3.500A) removed outlier: 6.999A pdb=" N VAL A 129 " --> pdb=" O SER A 140 " (cutoff:3.500A) removed outlier: 4.613A pdb=" N GLY A 142 " --> pdb=" O ILE A 127 " (cutoff:3.500A) removed outlier: 6.683A pdb=" N ILE A 127 " --> pdb=" O GLY A 142 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N ALA A 492 " --> pdb=" O ALA A 489 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N TRP A 464 " --> pdb=" O ALA A 461 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 160 through 161 Processing sheet with id=AA3, first strand: chain 'A' and resid 200 through 201 Processing sheet with id=AA4, first strand: chain 'A' and resid 375 through 377 Processing sheet with id=AA5, first strand: chain 'B' and resid 152 through 153 removed outlier: 7.344A pdb=" N VAL B 131 " --> pdb=" O VAL B 138 " (cutoff:3.500A) removed outlier: 4.649A pdb=" N SER B 140 " --> pdb=" O VAL B 129 " (cutoff:3.500A) removed outlier: 6.998A pdb=" N VAL B 129 " --> pdb=" O SER B 140 " (cutoff:3.500A) removed outlier: 4.614A pdb=" N GLY B 142 " --> pdb=" O ILE B 127 " (cutoff:3.500A) removed outlier: 6.684A pdb=" N ILE B 127 " --> pdb=" O GLY B 142 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N ALA B 492 " --> pdb=" O ALA B 489 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N TRP B 464 " --> pdb=" O ALA B 461 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 160 through 161 Processing sheet with id=AA7, first strand: chain 'B' and resid 200 through 201 Processing sheet with id=AA8, first strand: chain 'B' and resid 375 through 377 Processing sheet with id=AA9, first strand: chain 'C' and resid 152 through 153 removed outlier: 7.344A pdb=" N VAL C 131 " --> pdb=" O VAL C 138 " (cutoff:3.500A) removed outlier: 4.650A pdb=" N SER C 140 " --> pdb=" O VAL C 129 " (cutoff:3.500A) removed outlier: 6.999A pdb=" N VAL C 129 " --> pdb=" O SER C 140 " (cutoff:3.500A) removed outlier: 4.614A pdb=" N GLY C 142 " --> pdb=" O ILE C 127 " (cutoff:3.500A) removed outlier: 6.685A pdb=" N ILE C 127 " --> pdb=" O GLY C 142 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N ALA C 492 " --> pdb=" O ALA C 489 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N TRP C 464 " --> pdb=" O ALA C 461 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 160 through 161 Processing sheet with id=AB2, first strand: chain 'C' and resid 200 through 201 Processing sheet with id=AB3, first strand: chain 'C' and resid 375 through 377 Processing sheet with id=AB4, first strand: chain 'D' and resid 152 through 153 removed outlier: 7.344A pdb=" N VAL D 131 " --> pdb=" O VAL D 138 " (cutoff:3.500A) removed outlier: 4.651A pdb=" N SER D 140 " --> pdb=" O VAL D 129 " (cutoff:3.500A) removed outlier: 6.998A pdb=" N VAL D 129 " --> pdb=" O SER D 140 " (cutoff:3.500A) removed outlier: 4.614A pdb=" N GLY D 142 " --> pdb=" O ILE D 127 " (cutoff:3.500A) removed outlier: 6.683A pdb=" N ILE D 127 " --> pdb=" O GLY D 142 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N ALA D 492 " --> pdb=" O ALA D 489 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N TRP D 464 " --> pdb=" O ALA D 461 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 160 through 161 Processing sheet with id=AB6, first strand: chain 'D' and resid 200 through 201 Processing sheet with id=AB7, first strand: chain 'D' and resid 375 through 377 Processing sheet with id=AB8, first strand: chain 'E' and resid 152 through 153 removed outlier: 7.344A pdb=" N VAL E 131 " --> pdb=" O VAL E 138 " (cutoff:3.500A) removed outlier: 4.650A pdb=" N SER E 140 " --> pdb=" O VAL E 129 " (cutoff:3.500A) removed outlier: 6.998A pdb=" N VAL E 129 " --> pdb=" O SER E 140 " (cutoff:3.500A) removed outlier: 4.612A pdb=" N GLY E 142 " --> pdb=" O ILE E 127 " (cutoff:3.500A) removed outlier: 6.684A pdb=" N ILE E 127 " --> pdb=" O GLY E 142 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N ALA E 492 " --> pdb=" O ALA E 489 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N TRP E 464 " --> pdb=" O ALA E 461 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'E' and resid 160 through 161 Processing sheet with id=AC1, first strand: chain 'E' and resid 200 through 201 Processing sheet with id=AC2, first strand: chain 'E' and resid 375 through 377 Processing sheet with id=AC3, first strand: chain 'F' and resid 152 through 153 removed outlier: 7.344A pdb=" N VAL F 131 " --> pdb=" O VAL F 138 " (cutoff:3.500A) removed outlier: 4.650A pdb=" N SER F 140 " --> pdb=" O VAL F 129 " (cutoff:3.500A) removed outlier: 6.998A pdb=" N VAL F 129 " --> pdb=" O SER F 140 " (cutoff:3.500A) removed outlier: 4.612A pdb=" N GLY F 142 " --> pdb=" O ILE F 127 " (cutoff:3.500A) removed outlier: 6.684A pdb=" N ILE F 127 " --> pdb=" O GLY F 142 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N ALA F 492 " --> pdb=" O ALA F 489 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N TRP F 464 " --> pdb=" O ALA F 461 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'F' and resid 160 through 161 Processing sheet with id=AC5, first strand: chain 'F' and resid 200 through 201 Processing sheet with id=AC6, first strand: chain 'F' and resid 375 through 377 841 hydrogen bonds defined for protein. 2307 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: 5.93 Time building geometry restraints manager: 8.13 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 6010 1.34 - 1.46: 4284 1.46 - 1.58: 8723 1.58 - 1.69: 0 1.69 - 1.81: 168 Bond restraints: 19185 Sorted by residual: bond pdb=" C PRO E 513 " pdb=" N PRO E 514 " ideal model delta sigma weight residual 1.334 1.367 -0.033 2.34e-02 1.83e+03 1.98e+00 bond pdb=" C PRO F 513 " pdb=" N PRO F 514 " ideal model delta sigma weight residual 1.334 1.367 -0.033 2.34e-02 1.83e+03 1.98e+00 bond pdb=" C PRO B 513 " pdb=" N PRO B 514 " ideal model delta sigma weight residual 1.334 1.366 -0.033 2.34e-02 1.83e+03 1.94e+00 bond pdb=" C PRO C 513 " pdb=" N PRO C 514 " ideal model delta sigma weight residual 1.334 1.366 -0.032 2.34e-02 1.83e+03 1.93e+00 bond pdb=" C PRO D 513 " pdb=" N PRO D 514 " ideal model delta sigma weight residual 1.334 1.366 -0.032 2.34e-02 1.83e+03 1.90e+00 ... (remaining 19180 not shown) Histogram of bond angle deviations from ideal: 100.56 - 107.25: 647 107.25 - 113.94: 10694 113.94 - 120.63: 7755 120.63 - 127.32: 6670 127.32 - 134.01: 210 Bond angle restraints: 25976 Sorted by residual: angle pdb=" N PRO F 513 " pdb=" CA PRO F 513 " pdb=" C PRO F 513 " ideal model delta sigma weight residual 110.70 114.03 -3.33 1.22e+00 6.72e-01 7.46e+00 angle pdb=" N PRO D 513 " pdb=" CA PRO D 513 " pdb=" C PRO D 513 " ideal model delta sigma weight residual 110.70 113.99 -3.29 1.22e+00 6.72e-01 7.29e+00 angle pdb=" N PRO A 513 " pdb=" CA PRO A 513 " pdb=" C PRO A 513 " ideal model delta sigma weight residual 110.70 113.99 -3.29 1.22e+00 6.72e-01 7.27e+00 angle pdb=" N PRO E 513 " pdb=" CA PRO E 513 " pdb=" C PRO E 513 " ideal model delta sigma weight residual 110.70 113.98 -3.28 1.22e+00 6.72e-01 7.21e+00 angle pdb=" N PRO B 513 " pdb=" CA PRO B 513 " pdb=" C PRO B 513 " ideal model delta sigma weight residual 110.70 113.96 -3.26 1.22e+00 6.72e-01 7.16e+00 ... (remaining 25971 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.97: 10511 17.97 - 35.95: 844 35.95 - 53.92: 117 53.92 - 71.90: 18 71.90 - 89.87: 24 Dihedral angle restraints: 11514 sinusoidal: 4537 harmonic: 6977 Sorted by residual: dihedral pdb=" CB GLU B 363 " pdb=" CG GLU B 363 " pdb=" CD GLU B 363 " pdb=" OE1 GLU B 363 " ideal model delta sinusoidal sigma weight residual 0.00 89.87 -89.87 1 3.00e+01 1.11e-03 1.06e+01 dihedral pdb=" CB GLU A 363 " pdb=" CG GLU A 363 " pdb=" CD GLU A 363 " pdb=" OE1 GLU A 363 " ideal model delta sinusoidal sigma weight residual 0.00 89.85 -89.85 1 3.00e+01 1.11e-03 1.06e+01 dihedral pdb=" CB GLU C 363 " pdb=" CG GLU C 363 " pdb=" CD GLU C 363 " pdb=" OE1 GLU C 363 " ideal model delta sinusoidal sigma weight residual 0.00 89.80 -89.80 1 3.00e+01 1.11e-03 1.06e+01 ... (remaining 11511 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.028: 1859 0.028 - 0.056: 642 0.056 - 0.085: 183 0.085 - 0.113: 133 0.113 - 0.141: 66 Chirality restraints: 2883 Sorted by residual: chirality pdb=" CA VAL E 376 " pdb=" N VAL E 376 " pdb=" C VAL E 376 " pdb=" CB VAL E 376 " both_signs ideal model delta sigma weight residual False 2.44 2.58 -0.14 2.00e-01 2.50e+01 4.97e-01 chirality pdb=" CA VAL D 376 " pdb=" N VAL D 376 " pdb=" C VAL D 376 " pdb=" CB VAL D 376 " both_signs ideal model delta sigma weight residual False 2.44 2.58 -0.14 2.00e-01 2.50e+01 4.96e-01 chirality pdb=" CA VAL C 376 " pdb=" N VAL C 376 " pdb=" C VAL C 376 " pdb=" CB VAL C 376 " both_signs ideal model delta sigma weight residual False 2.44 2.58 -0.14 2.00e-01 2.50e+01 4.95e-01 ... (remaining 2880 not shown) Planarity restraints: 3292 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PRO B 513 " -0.018 5.00e-02 4.00e+02 2.77e-02 1.23e+00 pdb=" N PRO B 514 " 0.048 5.00e-02 4.00e+02 pdb=" CA PRO B 514 " -0.014 5.00e-02 4.00e+02 pdb=" CD PRO B 514 " -0.016 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO A 513 " -0.018 5.00e-02 4.00e+02 2.76e-02 1.22e+00 pdb=" N PRO A 514 " 0.048 5.00e-02 4.00e+02 pdb=" CA PRO A 514 " -0.014 5.00e-02 4.00e+02 pdb=" CD PRO A 514 " -0.016 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO F 513 " 0.018 5.00e-02 4.00e+02 2.75e-02 1.21e+00 pdb=" N PRO F 514 " -0.048 5.00e-02 4.00e+02 pdb=" CA PRO F 514 " 0.014 5.00e-02 4.00e+02 pdb=" CD PRO F 514 " 0.016 5.00e-02 4.00e+02 ... (remaining 3289 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.77: 3137 2.77 - 3.30: 17435 3.30 - 3.83: 30488 3.83 - 4.37: 34611 4.37 - 4.90: 60990 Nonbonded interactions: 146661 Sorted by model distance: nonbonded pdb=" OE2 GLU D 137 " pdb=" OG SER D 140 " model vdw 2.235 2.440 nonbonded pdb=" OE2 GLU C 137 " pdb=" OG SER C 140 " model vdw 2.236 2.440 nonbonded pdb=" OE2 GLU E 137 " pdb=" OG SER E 140 " model vdw 2.236 2.440 nonbonded pdb=" OE2 GLU F 137 " pdb=" OG SER F 140 " model vdw 2.236 2.440 nonbonded pdb=" OE2 GLU A 137 " pdb=" OG SER A 140 " model vdw 2.236 2.440 ... (remaining 146656 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 99 through 204 or (resid 205 and (name N or name CA or nam \ e C or name O or name CB )) or resid 206 through 231 or (resid 232 through 233 a \ nd (name N or name CA or name C or name O or name CB )) or resid 234 through 235 \ or (resid 236 through 291 and (name N or name CA or name C or name O or name CB \ )) or resid 292 through 298 or (resid 299 and (name N or name CA or name C or n \ ame O or name CB )) or resid 300 through 456 or (resid 457 and (name N or name C \ A or name C or name O or name CB )) or resid 458 through 546)) selection = (chain 'B' and (resid 99 through 120 or (resid 121 and (name N or name CA or nam \ e C or name O or name CB )) or resid 122 through 224 or (resid 225 and (name N o \ r name CA or name C or name O or name CB )) or resid 226 through 238 or (resid 2 \ 39 through 291 and (name N or name CA or name C or name O or name CB )) or resid \ 292 through 450 or (resid 451 and (name N or name CA or name C or name O or nam \ e CB )) or resid 452 through 456 or (resid 457 and (name N or name CA or name C \ or name O or name CB )) or resid 458 through 501 or (resid 502 and (name N or na \ me CA or name C or name O or name CB )) or resid 503 through 546)) selection = (chain 'C' and (resid 99 through 120 or (resid 121 and (name N or name CA or nam \ e C or name O or name CB )) or resid 122 through 204 or (resid 205 and (name N o \ r name CA or name C or name O or name CB )) or resid 206 through 231 or (resid 2 \ 32 through 233 and (name N or name CA or name C or name O or name CB )) or resid \ 234 through 235 or (resid 236 through 291 and (name N or name CA or name C or n \ ame O or name CB )) or resid 292 through 456 or (resid 457 and (name N or name C \ A or name C or name O or name CB )) or resid 458 through 501 or (resid 502 and ( \ name N or name CA or name C or name O or name CB )) or resid 503 through 546)) selection = (chain 'D' and (resid 99 through 120 or (resid 121 and (name N or name CA or nam \ e C or name O or name CB )) or resid 122 through 204 or (resid 205 and (name N o \ r name CA or name C or name O or name CB )) or resid 206 through 231 or (resid 2 \ 32 through 233 and (name N or name CA or name C or name O or name CB )) or resid \ 234 through 235 or (resid 236 through 291 and (name N or name CA or name C or n \ ame O or name CB )) or resid 292 through 456 or (resid 457 and (name N or name C \ A or name C or name O or name CB )) or resid 458 through 546)) selection = (chain 'E' and (resid 99 through 204 or (resid 205 and (name N or name CA or nam \ e C or name O or name CB )) or resid 206 through 231 or (resid 232 through 233 a \ nd (name N or name CA or name C or name O or name CB )) or resid 234 through 235 \ or (resid 236 through 291 and (name N or name CA or name C or name O or name CB \ )) or resid 292 through 456 or (resid 457 and (name N or name CA or name C or n \ ame O or name CB )) or resid 458 through 546)) selection = (chain 'F' and (resid 99 through 120 or (resid 121 and (name N or name CA or nam \ e C or name O or name CB )) or resid 122 through 204 or (resid 205 and (name N o \ r name CA or name C or name O or name CB )) or resid 206 through 231 or (resid 2 \ 32 through 233 and (name N or name CA or name C or name O or name CB )) or resid \ 234 through 235 or (resid 236 through 291 and (name N or name CA or name C or n \ ame O or name CB )) or resid 292 through 546)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 102 5.16 5 C 12031 2.51 5 N 3180 2.21 5 O 3453 1.98 5 sf(0) = scattering factor at diffraction angle 0. Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.460 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 8.730 Check model and map are aligned: 0.270 Process input model: 48.030 Find NCS groups from input model: 1.350 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Set scattering table: 0.180 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:2.870 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 63.980 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8294 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 : 0.002 0.033 19185 Z= 0.106 Angle : 0.406 6.266 25976 Z= 0.224 Chirality : 0.039 0.141 2883 Planarity : 0.003 0.028 3292 Dihedral : 13.471 89.870 7050 Min Nonbonded Distance : 2.235 Molprobity Statistics. All-atom Clashscore : 2.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.26 % Favored : 98.74 % Rotamer Outliers : 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: 2.53 (0.18), residues: 2376 helix: 3.16 (0.18), residues: 840 sheet: 0.61 (0.27), residues: 360 loop : 1.06 (0.20), residues: 1176 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4752 Ramachandran restraints generated. 2376 Oldfield, 0 Emsley, 2376 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4752 Ramachandran restraints generated. 2376 Oldfield, 0 Emsley, 2376 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 827 residues out of total 2094 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 827 time to evaluate : 2.109 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 827 average time/residue: 0.3703 time to fit residues: 432.2036 Evaluate side-chains 469 residues out of total 2094 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 469 time to evaluate : 2.284 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 3.1675 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 202 optimal weight: 3.9990 chunk 181 optimal weight: 10.0000 chunk 100 optimal weight: 0.9980 chunk 62 optimal weight: 0.9990 chunk 122 optimal weight: 0.6980 chunk 97 optimal weight: 7.9990 chunk 188 optimal weight: 8.9990 chunk 72 optimal weight: 1.9990 chunk 114 optimal weight: 9.9990 chunk 140 optimal weight: 7.9990 chunk 217 optimal weight: 8.9990 overall best weight: 1.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 320 GLN B 391 ASN C 320 GLN D 320 GLN D 391 ASN E 471 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8398 moved from start: 0.2701 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.047 19185 Z= 0.198 Angle : 0.530 7.412 25976 Z= 0.286 Chirality : 0.042 0.155 2883 Planarity : 0.004 0.049 3292 Dihedral : 3.533 12.732 2627 Min Nonbonded Distance : 2.180 Molprobity Statistics. All-atom Clashscore : 7.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Rotamer Outliers : 2.00 % 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: 1.98 (0.18), residues: 2376 helix: 2.57 (0.18), residues: 900 sheet: 0.25 (0.26), residues: 384 loop : 0.78 (0.19), residues: 1092 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4752 Ramachandran restraints generated. 2376 Oldfield, 0 Emsley, 2376 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4752 Ramachandran restraints generated. 2376 Oldfield, 0 Emsley, 2376 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 548 residues out of total 2094 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 508 time to evaluate : 2.154 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 40 outliers final: 22 residues processed: 530 average time/residue: 0.3322 time to fit residues: 256.7397 Evaluate side-chains 464 residues out of total 2094 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 442 time to evaluate : 2.370 Switching outliers to nearest non-outliers outliers start: 22 outliers final: 0 residues processed: 22 average time/residue: 0.1798 time to fit residues: 10.4804 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 121 optimal weight: 1.9990 chunk 67 optimal weight: 7.9990 chunk 181 optimal weight: 10.0000 chunk 148 optimal weight: 2.9990 chunk 60 optimal weight: 2.9990 chunk 218 optimal weight: 0.8980 chunk 235 optimal weight: 6.9990 chunk 194 optimal weight: 10.0000 chunk 216 optimal weight: 3.9990 chunk 74 optimal weight: 9.9990 chunk 175 optimal weight: 0.9980 overall best weight: 1.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 391 ASN E 391 ASN E 471 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8435 moved from start: 0.3276 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.065 19185 Z= 0.202 Angle : 0.508 6.089 25976 Z= 0.272 Chirality : 0.041 0.151 2883 Planarity : 0.004 0.054 3292 Dihedral : 3.694 16.110 2627 Min Nonbonded Distance : 2.196 Molprobity Statistics. All-atom Clashscore : 7.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Rotamer Outliers : 1.50 % 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: 1.83 (0.18), residues: 2376 helix: 2.43 (0.18), residues: 900 sheet: 0.13 (0.26), residues: 384 loop : 0.72 (0.19), residues: 1092 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4752 Ramachandran restraints generated. 2376 Oldfield, 0 Emsley, 2376 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4752 Ramachandran restraints generated. 2376 Oldfield, 0 Emsley, 2376 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 481 residues out of total 2094 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 451 time to evaluate : 2.213 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 30 outliers final: 15 residues processed: 468 average time/residue: 0.3434 time to fit residues: 234.2266 Evaluate side-chains 444 residues out of total 2094 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 429 time to evaluate : 2.282 Switching outliers to nearest non-outliers outliers start: 15 outliers final: 0 residues processed: 15 average time/residue: 0.2278 time to fit residues: 8.7876 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 215 optimal weight: 8.9990 chunk 164 optimal weight: 4.9990 chunk 113 optimal weight: 9.9990 chunk 24 optimal weight: 10.0000 chunk 104 optimal weight: 2.9990 chunk 146 optimal weight: 7.9990 chunk 219 optimal weight: 3.9990 chunk 231 optimal weight: 10.0000 chunk 114 optimal weight: 10.0000 chunk 207 optimal weight: 7.9990 chunk 62 optimal weight: 0.9980 overall best weight: 4.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 216 HIS B 391 ASN E 216 HIS E 471 GLN F 216 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8524 moved from start: 0.3951 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.062 19185 Z= 0.368 Angle : 0.594 5.928 25976 Z= 0.320 Chirality : 0.044 0.163 2883 Planarity : 0.005 0.060 3292 Dihedral : 4.247 19.663 2627 Min Nonbonded Distance : 2.068 Molprobity Statistics. All-atom Clashscore : 8.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer Outliers : 1.80 % 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: 1.46 (0.18), residues: 2376 helix: 2.18 (0.18), residues: 900 sheet: -0.17 (0.26), residues: 372 loop : 0.48 (0.19), residues: 1104 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4752 Ramachandran restraints generated. 2376 Oldfield, 0 Emsley, 2376 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4752 Ramachandran restraints generated. 2376 Oldfield, 0 Emsley, 2376 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 461 residues out of total 2094 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 425 time to evaluate : 2.359 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 36 outliers final: 19 residues processed: 448 average time/residue: 0.3503 time to fit residues: 229.0257 Evaluate side-chains 417 residues out of total 2094 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 398 time to evaluate : 2.396 Switching outliers to nearest non-outliers outliers start: 19 outliers final: 0 residues processed: 19 average time/residue: 0.1712 time to fit residues: 9.4068 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 193 optimal weight: 0.8980 chunk 131 optimal weight: 4.9990 chunk 3 optimal weight: 3.9990 chunk 172 optimal weight: 10.0000 chunk 95 optimal weight: 1.9990 chunk 197 optimal weight: 3.9990 chunk 160 optimal weight: 10.0000 chunk 0 optimal weight: 10.0000 chunk 118 optimal weight: 0.5980 chunk 208 optimal weight: 6.9990 chunk 58 optimal weight: 4.9990 overall best weight: 2.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 216 HIS B 391 ASN E 216 HIS E 531 ASN F 216 HIS F 348 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8484 moved from start: 0.3986 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.071 19185 Z= 0.221 Angle : 0.523 7.442 25976 Z= 0.281 Chirality : 0.042 0.175 2883 Planarity : 0.004 0.057 3292 Dihedral : 4.037 17.915 2627 Min Nonbonded Distance : 2.080 Molprobity Statistics. All-atom Clashscore : 7.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Rotamer Outliers : 1.15 % 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: 1.59 (0.18), residues: 2376 helix: 2.28 (0.18), residues: 900 sheet: 0.05 (0.26), residues: 378 loop : 0.50 (0.19), residues: 1098 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4752 Ramachandran restraints generated. 2376 Oldfield, 0 Emsley, 2376 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4752 Ramachandran restraints generated. 2376 Oldfield, 0 Emsley, 2376 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 455 residues out of total 2094 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 432 time to evaluate : 2.467 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 23 outliers final: 12 residues processed: 443 average time/residue: 0.3468 time to fit residues: 224.1592 Evaluate side-chains 422 residues out of total 2094 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 410 time to evaluate : 2.298 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 0 residues processed: 12 average time/residue: 0.1760 time to fit residues: 7.2973 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 78 optimal weight: 5.9990 chunk 208 optimal weight: 6.9990 chunk 45 optimal weight: 0.9990 chunk 136 optimal weight: 6.9990 chunk 57 optimal weight: 8.9990 chunk 232 optimal weight: 5.9990 chunk 192 optimal weight: 0.0670 chunk 107 optimal weight: 8.9990 chunk 19 optimal weight: 1.9990 chunk 76 optimal weight: 0.8980 chunk 121 optimal weight: 2.9990 overall best weight: 1.3924 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 216 HIS B 391 ASN D 391 ASN E 216 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8457 moved from start: 0.4017 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.050 19185 Z= 0.168 Angle : 0.507 6.772 25976 Z= 0.269 Chirality : 0.041 0.152 2883 Planarity : 0.004 0.057 3292 Dihedral : 3.882 17.658 2627 Min Nonbonded Distance : 2.089 Molprobity Statistics. All-atom Clashscore : 7.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.31 % Favored : 97.69 % Rotamer Outliers : 1.00 % 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: 1.68 (0.18), residues: 2376 helix: 2.32 (0.18), residues: 900 sheet: 0.15 (0.26), residues: 378 loop : 0.58 (0.19), residues: 1098 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4752 Ramachandran restraints generated. 2376 Oldfield, 0 Emsley, 2376 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4752 Ramachandran restraints generated. 2376 Oldfield, 0 Emsley, 2376 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 456 residues out of total 2094 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 436 time to evaluate : 2.417 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 20 outliers final: 12 residues processed: 447 average time/residue: 0.3395 time to fit residues: 222.6299 Evaluate side-chains 426 residues out of total 2094 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 414 time to evaluate : 2.272 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 0 residues processed: 12 average time/residue: 0.1929 time to fit residues: 7.3254 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 223 optimal weight: 1.9990 chunk 26 optimal weight: 2.9990 chunk 132 optimal weight: 6.9990 chunk 169 optimal weight: 6.9990 chunk 131 optimal weight: 1.9990 chunk 195 optimal weight: 0.9990 chunk 129 optimal weight: 0.9980 chunk 231 optimal weight: 5.9990 chunk 144 optimal weight: 4.9990 chunk 141 optimal weight: 6.9990 chunk 106 optimal weight: 3.9990 overall best weight: 1.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 216 HIS B 391 ASN D 391 ASN D 485 HIS E 216 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8461 moved from start: 0.4109 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.046 19185 Z= 0.194 Angle : 0.524 9.362 25976 Z= 0.275 Chirality : 0.041 0.163 2883 Planarity : 0.004 0.058 3292 Dihedral : 3.870 17.798 2627 Min Nonbonded Distance : 2.092 Molprobity Statistics. All-atom Clashscore : 7.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer Outliers : 0.65 % 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: 1.77 (0.18), residues: 2376 helix: 2.32 (0.18), residues: 900 sheet: 0.32 (0.29), residues: 318 loop : 0.63 (0.19), residues: 1158 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4752 Ramachandran restraints generated. 2376 Oldfield, 0 Emsley, 2376 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4752 Ramachandran restraints generated. 2376 Oldfield, 0 Emsley, 2376 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 438 residues out of total 2094 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 425 time to evaluate : 2.452 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 13 outliers final: 5 residues processed: 433 average time/residue: 0.3397 time to fit residues: 216.7667 Evaluate side-chains 415 residues out of total 2094 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 410 time to evaluate : 2.431 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.2381 time to fit residues: 5.2853 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 143 optimal weight: 0.8980 chunk 92 optimal weight: 9.9990 chunk 138 optimal weight: 9.9990 chunk 69 optimal weight: 0.8980 chunk 45 optimal weight: 0.3980 chunk 44 optimal weight: 0.8980 chunk 147 optimal weight: 3.9990 chunk 157 optimal weight: 6.9990 chunk 114 optimal weight: 8.9990 chunk 21 optimal weight: 4.9990 chunk 181 optimal weight: 4.9990 overall best weight: 1.4182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 216 HIS ** A 531 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 391 ASN D 391 ASN E 216 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8444 moved from start: 0.4177 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.039 19185 Z= 0.170 Angle : 0.514 9.230 25976 Z= 0.270 Chirality : 0.041 0.176 2883 Planarity : 0.004 0.058 3292 Dihedral : 3.796 17.646 2627 Min Nonbonded Distance : 2.099 Molprobity Statistics. All-atom Clashscore : 7.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % Rotamer Outliers : 0.65 % 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: 1.83 (0.18), residues: 2376 helix: 2.35 (0.18), residues: 900 sheet: 0.37 (0.29), residues: 318 loop : 0.68 (0.19), residues: 1158 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4752 Ramachandran restraints generated. 2376 Oldfield, 0 Emsley, 2376 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4752 Ramachandran restraints generated. 2376 Oldfield, 0 Emsley, 2376 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 444 residues out of total 2094 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 431 time to evaluate : 2.110 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 13 outliers final: 10 residues processed: 436 average time/residue: 0.3368 time to fit residues: 218.3817 Evaluate side-chains 420 residues out of total 2094 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 410 time to evaluate : 2.199 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 0 residues processed: 10 average time/residue: 0.2559 time to fit residues: 6.9797 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 210 optimal weight: 9.9990 chunk 221 optimal weight: 0.8980 chunk 202 optimal weight: 0.9980 chunk 215 optimal weight: 0.8980 chunk 129 optimal weight: 0.0020 chunk 93 optimal weight: 9.9990 chunk 169 optimal weight: 4.9990 chunk 66 optimal weight: 3.9990 chunk 194 optimal weight: 10.0000 chunk 203 optimal weight: 10.0000 chunk 214 optimal weight: 8.9990 overall best weight: 1.3590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 216 HIS A 531 ASN B 391 ASN D 391 ASN E 216 HIS E 427 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8441 moved from start: 0.4201 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.037 19185 Z= 0.170 Angle : 0.521 10.090 25976 Z= 0.273 Chirality : 0.041 0.166 2883 Planarity : 0.004 0.057 3292 Dihedral : 3.761 17.507 2627 Min Nonbonded Distance : 2.100 Molprobity Statistics. All-atom Clashscore : 7.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Rotamer Outliers : 0.20 % 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: 1.86 (0.18), residues: 2376 helix: 2.37 (0.18), residues: 900 sheet: 0.38 (0.30), residues: 318 loop : 0.70 (0.19), residues: 1158 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4752 Ramachandran restraints generated. 2376 Oldfield, 0 Emsley, 2376 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4752 Ramachandran restraints generated. 2376 Oldfield, 0 Emsley, 2376 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 431 residues out of total 2094 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 427 time to evaluate : 2.411 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 4 outliers final: 1 residues processed: 429 average time/residue: 0.3344 time to fit residues: 214.1099 Evaluate side-chains 416 residues out of total 2094 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 415 time to evaluate : 2.537 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.2068 time to fit residues: 3.6338 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 141 optimal weight: 4.9990 chunk 227 optimal weight: 9.9990 chunk 139 optimal weight: 8.9990 chunk 108 optimal weight: 7.9990 chunk 158 optimal weight: 0.9990 chunk 239 optimal weight: 3.9990 chunk 220 optimal weight: 0.9990 chunk 190 optimal weight: 0.9980 chunk 19 optimal weight: 9.9990 chunk 147 optimal weight: 3.9990 chunk 116 optimal weight: 7.9990 overall best weight: 2.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 216 HIS B 391 ASN D 391 ASN E 216 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8467 moved from start: 0.4287 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.040 19185 Z= 0.223 Angle : 0.547 9.986 25976 Z= 0.287 Chirality : 0.042 0.160 2883 Planarity : 0.004 0.058 3292 Dihedral : 3.863 19.351 2627 Min Nonbonded Distance : 2.090 Molprobity Statistics. All-atom Clashscore : 8.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer Outliers : 0.15 % 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: 1.69 (0.18), residues: 2376 helix: 2.36 (0.18), residues: 900 sheet: 0.09 (0.27), residues: 378 loop : 0.59 (0.19), residues: 1098 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4752 Ramachandran restraints generated. 2376 Oldfield, 0 Emsley, 2376 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4752 Ramachandran restraints generated. 2376 Oldfield, 0 Emsley, 2376 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 418 residues out of total 2094 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 415 time to evaluate : 2.444 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 3 outliers final: 2 residues processed: 417 average time/residue: 0.3621 time to fit residues: 222.1697 Evaluate side-chains 411 residues out of total 2094 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 409 time to evaluate : 2.189 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.1772 time to fit residues: 3.5413 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 151 optimal weight: 5.9990 chunk 202 optimal weight: 1.9990 chunk 58 optimal weight: 2.9990 chunk 175 optimal weight: 10.0000 chunk 28 optimal weight: 1.9990 chunk 52 optimal weight: 10.0000 chunk 190 optimal weight: 4.9990 chunk 79 optimal weight: 4.9990 chunk 195 optimal weight: 0.0770 chunk 24 optimal weight: 3.9990 chunk 35 optimal weight: 0.8980 overall best weight: 1.5944 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 216 HIS B 391 ASN D 391 ASN E 216 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.109665 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3056 r_free = 0.3056 target = 0.087192 restraints weight = 36631.133| |-----------------------------------------------------------------------------| r_work (start): 0.3052 rms_B_bonded: 3.24 r_work: 0.2915 rms_B_bonded: 3.61 restraints_weight: 0.5000 r_work (final): 0.2915 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8528 moved from start: 0.4304 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.039 19185 Z= 0.185 Angle : 0.536 10.054 25976 Z= 0.279 Chirality : 0.041 0.157 2883 Planarity : 0.004 0.058 3292 Dihedral : 3.817 18.573 2627 Min Nonbonded Distance : 2.103 Molprobity Statistics. All-atom Clashscore : 7.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % Rotamer Outliers : 0.30 % 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: 1.71 (0.18), residues: 2376 helix: 2.35 (0.18), residues: 900 sheet: 0.15 (0.27), residues: 378 loop : 0.60 (0.19), residues: 1098 =============================================================================== Job complete usr+sys time: 5012.76 seconds wall clock time: 90 minutes 31.69 seconds (5431.69 seconds total)