Starting phenix.real_space_refine on Thu Mar 5 03:28:42 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7ulw_26595/03_2026/7ulw_26595.cif Found real_map, /net/cci-nas-00/data/ceres_data/7ulw_26595/03_2026/7ulw_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 { model { file = "/net/cci-nas-00/data/ceres_data/7ulw_26595/03_2026/7ulw_26595.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7ulw_26595/03_2026/7ulw_26595.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7ulw_26595/03_2026/7ulw_26595.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7ulw_26595/03_2026/7ulw_26595.map" } 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 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= 0.000 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 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. Process input model Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/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: {'GLU:plan': 7, 'TYR:plan': 1} 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: 3.86, per 1000 atoms: 0.21 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 - 3.00 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: 1.08 Conformation dependent library (CDL) restraints added in 817.4 milliseconds 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: 0.76 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: 2.97 Time building geometry restraints manager: 1.54 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: 0.00 - 1.25: 25591 1.25 - 2.51: 261 2.51 - 3.76: 112 3.76 - 5.01: 6 5.01 - 6.27: 6 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 3.040 nonbonded pdb=" OE2 GLU C 137 " pdb=" OG SER C 140 " model vdw 2.236 3.040 nonbonded pdb=" OE2 GLU E 137 " pdb=" OG SER E 140 " model vdw 2.236 3.040 nonbonded pdb=" OE2 GLU F 137 " pdb=" OG SER F 140 " model vdw 2.236 3.040 nonbonded pdb=" OE2 GLU A 137 " pdb=" OG SER A 140 " model vdw 2.236 3.040 ... (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 Time spend for trying shortcut: 0.00 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 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: 2.290 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: 0.350 Check model and map are aligned: 0.050 Set scattering table: 0.050 Process input model: 15.560 Find NCS groups from input model: 0.520 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:1.240 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.010 Total: 20.110 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8159 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= 0.083 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 : 2.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.26 % Favored : 98.74 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % 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 are not related in a simple way. 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 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG D 161 TYR 0.008 0.001 TYR A 328 PHE 0.006 0.001 PHE A 374 TRP 0.006 0.001 TRP F 454 HIS 0.002 0.000 HIS B 485 Details of bonding type rmsd covalent geometry : bond 0.00159 (19185) covalent geometry : angle 0.40610 (25976) hydrogen bonds : bond 0.16863 ( 841) hydrogen bonds : angle 6.37026 ( 2307) *********************** 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 to be fit. rotamer outliers: 0 poor density : 827 time to evaluate : 0.712 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 REVERT: A 215 SER cc_start: 0.9359 (m) cc_final: 0.8916 (p) REVERT: A 224 GLU cc_start: 0.8701 (tp30) cc_final: 0.8207 (tp30) REVERT: A 229 LYS cc_start: 0.9122 (mtpp) cc_final: 0.8854 (mtpp) REVERT: A 236 TYR cc_start: 0.8753 (t80) cc_final: 0.8532 (t80) REVERT: A 303 GLU cc_start: 0.8712 (tt0) cc_final: 0.8448 (tt0) REVERT: A 348 GLN cc_start: 0.8584 (tp40) cc_final: 0.8370 (tp40) REVERT: A 355 ASP cc_start: 0.8533 (t70) cc_final: 0.8305 (t70) REVERT: A 409 LYS cc_start: 0.8499 (mttt) cc_final: 0.8241 (mttt) REVERT: B 117 ARG cc_start: 0.8256 (mtp180) cc_final: 0.6942 (ttt180) REVERT: B 176 LYS cc_start: 0.8673 (tppp) cc_final: 0.8338 (tppp) REVERT: B 195 GLU cc_start: 0.9089 (mp0) cc_final: 0.8810 (mp0) REVERT: B 202 GLU cc_start: 0.8764 (mm-30) cc_final: 0.8561 (mp0) REVERT: B 386 THR cc_start: 0.8650 (m) cc_final: 0.8390 (p) REVERT: B 477 ARG cc_start: 0.8497 (ttt90) cc_final: 0.7227 (mtt180) REVERT: B 540 GLU cc_start: 0.8232 (tp30) cc_final: 0.7698 (tp30) REVERT: B 544 ASP cc_start: 0.7939 (t0) cc_final: 0.7662 (t0) REVERT: C 119 LYS cc_start: 0.8490 (tttm) cc_final: 0.8288 (tttm) REVERT: C 171 MET cc_start: 0.8743 (tpt) cc_final: 0.8420 (tpt) REVERT: C 195 GLU cc_start: 0.8615 (mp0) cc_final: 0.8172 (mp0) REVERT: C 226 ASP cc_start: 0.8151 (t0) cc_final: 0.7583 (t0) REVERT: C 297 LYS cc_start: 0.9141 (tttt) cc_final: 0.8892 (tttt) REVERT: C 303 GLU cc_start: 0.9089 (tt0) cc_final: 0.8586 (tt0) REVERT: C 355 ASP cc_start: 0.8862 (t70) cc_final: 0.8560 (t70) REVERT: C 409 LYS cc_start: 0.8473 (mttt) cc_final: 0.8192 (mttt) REVERT: C 436 LYS cc_start: 0.9120 (mttt) cc_final: 0.8898 (mtpp) REVERT: C 453 SER cc_start: 0.9419 (t) cc_final: 0.9181 (m) REVERT: C 544 ASP cc_start: 0.8151 (t0) cc_final: 0.7907 (t0) REVERT: D 179 GLU cc_start: 0.8635 (mt-10) cc_final: 0.8403 (mt-10) REVERT: D 202 GLU cc_start: 0.8594 (mm-30) cc_final: 0.7930 (mp0) REVERT: D 228 LYS cc_start: 0.8941 (mmtm) cc_final: 0.8730 (mtmm) REVERT: D 348 GLN cc_start: 0.8907 (tp40) cc_final: 0.8503 (tm-30) REVERT: D 449 ASN cc_start: 0.8347 (t0) cc_final: 0.8064 (t0) REVERT: D 473 TYR cc_start: 0.8119 (m-80) cc_final: 0.5944 (t80) REVERT: D 477 ARG cc_start: 0.7573 (ttt90) cc_final: 0.5287 (mpt-90) REVERT: D 478 LYS cc_start: 0.8813 (tttt) cc_final: 0.8443 (tptt) REVERT: D 479 GLN cc_start: 0.7065 (tt0) cc_final: 0.6738 (mt0) REVERT: D 526 GLN cc_start: 0.8041 (pt0) cc_final: 0.7800 (pt0) REVERT: D 536 LYS cc_start: 0.8856 (mttt) cc_final: 0.8654 (mtpt) REVERT: E 111 SER cc_start: 0.9231 (m) cc_final: 0.8830 (p) REVERT: E 120 ASP cc_start: 0.8834 (m-30) cc_final: 0.8597 (m-30) REVERT: E 149 GLU cc_start: 0.8517 (mt-10) cc_final: 0.8241 (mt-10) REVERT: E 226 ASP cc_start: 0.8047 (t0) cc_final: 0.7050 (t0) REVERT: E 297 LYS cc_start: 0.8923 (tttt) cc_final: 0.8566 (tppt) REVERT: E 386 THR cc_start: 0.9094 (m) cc_final: 0.8672 (p) REVERT: F 117 ARG cc_start: 0.8733 (mtp180) cc_final: 0.8455 (mtp85) REVERT: F 195 GLU cc_start: 0.8292 (mp0) cc_final: 0.7506 (mp0) REVERT: F 224 GLU cc_start: 0.8614 (tp30) cc_final: 0.8130 (tp30) REVERT: F 226 ASP cc_start: 0.8484 (t0) cc_final: 0.7629 (t70) REVERT: F 229 LYS cc_start: 0.9265 (mtpp) cc_final: 0.8873 (mttm) REVERT: F 316 LYS cc_start: 0.9435 (ttpp) cc_final: 0.9076 (ttmm) REVERT: F 355 ASP cc_start: 0.8268 (t70) cc_final: 0.8002 (t0) REVERT: F 422 LEU cc_start: 0.9025 (tt) cc_final: 0.8410 (mp) REVERT: F 462 MET cc_start: 0.7099 (mtt) cc_final: 0.6881 (mtt) REVERT: F 544 ASP cc_start: 0.7857 (t0) cc_final: 0.7436 (t70) outliers start: 0 outliers final: 0 residues processed: 827 average time/residue: 0.1653 time to fit residues: 194.8728 Evaluate side-chains 488 residues out of total 2094 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 488 time to evaluate : 0.698 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 216 optimal weight: 5.9990 chunk 98 optimal weight: 3.9990 chunk 194 optimal weight: 10.0000 chunk 227 optimal weight: 3.9990 chunk 107 optimal weight: 0.9980 chunk 10 optimal weight: 4.9990 chunk 66 optimal weight: 3.9990 chunk 130 optimal weight: 4.9990 chunk 124 optimal weight: 2.9990 chunk 103 optimal weight: 0.0980 chunk 235 optimal weight: 6.9990 overall best weight: 2.4186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 320 GLN B 320 GLN B 391 ASN C 320 GLN D 320 GLN D 391 ASN E 471 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.111857 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3084 r_free = 0.3084 target = 0.088075 restraints weight = 35855.453| |-----------------------------------------------------------------------------| r_work (start): 0.3068 rms_B_bonded: 3.26 r_work: 0.2930 rms_B_bonded: 3.70 restraints_weight: 0.5000 r_work (final): 0.2930 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8458 moved from start: 0.2736 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 19185 Z= 0.163 Angle : 0.555 7.576 25976 Z= 0.300 Chirality : 0.043 0.149 2883 Planarity : 0.004 0.050 3292 Dihedral : 3.767 13.699 2627 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 6.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 1.45 % Allowed : 13.86 % Favored : 84.69 % 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 are not related in a simple way. whole: 2.21 (0.18), residues: 2376 helix: 2.80 (0.18), residues: 858 sheet: 0.14 (0.25), residues: 384 loop : 1.06 (0.20), residues: 1134 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG F 477 TYR 0.017 0.001 TYR D 236 PHE 0.019 0.001 PHE F 541 TRP 0.012 0.001 TRP B 464 HIS 0.008 0.001 HIS B 191 Details of bonding type rmsd covalent geometry : bond 0.00380 (19185) covalent geometry : angle 0.55492 (25976) hydrogen bonds : bond 0.04386 ( 841) hydrogen bonds : angle 4.66303 ( 2307) *********************** 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 529 residues out of total 2094 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 500 time to evaluate : 0.714 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 113 ASP cc_start: 0.9088 (t0) cc_final: 0.8881 (t0) REVERT: A 224 GLU cc_start: 0.8796 (tp30) cc_final: 0.8331 (tp30) REVERT: A 236 TYR cc_start: 0.8885 (t80) cc_final: 0.8660 (t80) REVERT: A 348 GLN cc_start: 0.8818 (tp40) cc_final: 0.8582 (tp40) REVERT: A 355 ASP cc_start: 0.8906 (t70) cc_final: 0.8556 (t70) REVERT: B 120 ASP cc_start: 0.9120 (m-30) cc_final: 0.8777 (m-30) REVERT: B 195 GLU cc_start: 0.9277 (mp0) cc_final: 0.9038 (mp0) REVERT: B 373 ARG cc_start: 0.8794 (mmm160) cc_final: 0.8430 (tpp-160) REVERT: B 386 THR cc_start: 0.8920 (m) cc_final: 0.8699 (p) REVERT: B 477 ARG cc_start: 0.8780 (ttt90) cc_final: 0.7412 (mtt90) REVERT: C 228 LYS cc_start: 0.8973 (mmmt) cc_final: 0.8746 (mmmt) REVERT: C 320 GLN cc_start: 0.8703 (tp-100) cc_final: 0.8429 (tp-100) REVERT: C 453 SER cc_start: 0.9387 (t) cc_final: 0.9134 (m) REVERT: C 540 GLU cc_start: 0.8749 (tp30) cc_final: 0.8232 (tp30) REVERT: C 544 ASP cc_start: 0.8348 (t0) cc_final: 0.7949 (t0) REVERT: D 176 LYS cc_start: 0.9222 (tppp) cc_final: 0.8915 (tptt) REVERT: D 348 GLN cc_start: 0.9074 (tp40) cc_final: 0.8635 (tm-30) REVERT: D 449 ASN cc_start: 0.8515 (t0) cc_final: 0.8275 (t0) REVERT: D 473 TYR cc_start: 0.8162 (m-80) cc_final: 0.7895 (m-80) REVERT: D 477 ARG cc_start: 0.8120 (ttt90) cc_final: 0.5526 (mtt-85) REVERT: D 478 LYS cc_start: 0.9092 (tttt) cc_final: 0.8689 (tptt) REVERT: D 540 GLU cc_start: 0.8789 (tp30) cc_final: 0.8552 (tp30) REVERT: E 111 SER cc_start: 0.9361 (m) cc_final: 0.9052 (p) REVERT: E 195 GLU cc_start: 0.8679 (mp0) cc_final: 0.8383 (mp0) REVERT: E 226 ASP cc_start: 0.7624 (t0) cc_final: 0.7386 (t0) REVERT: E 295 ARG cc_start: 0.8893 (tpp80) cc_final: 0.8669 (mtt-85) REVERT: E 297 LYS cc_start: 0.9013 (tttt) cc_final: 0.8614 (tppt) REVERT: E 309 LYS cc_start: 0.8744 (OUTLIER) cc_final: 0.8500 (ptpp) REVERT: E 320 GLN cc_start: 0.9003 (tp40) cc_final: 0.8724 (tp-100) REVERT: E 342 LYS cc_start: 0.9110 (mmmm) cc_final: 0.8886 (mmmm) REVERT: E 386 THR cc_start: 0.9173 (m) cc_final: 0.8704 (p) REVERT: F 224 GLU cc_start: 0.8745 (tp30) cc_final: 0.8416 (tp30) REVERT: F 226 ASP cc_start: 0.8292 (t0) cc_final: 0.7886 (t0) REVERT: F 296 GLU cc_start: 0.7566 (tm-30) cc_final: 0.7125 (tm-30) REVERT: F 342 LYS cc_start: 0.9106 (mmmm) cc_final: 0.8769 (mmtm) REVERT: F 355 ASP cc_start: 0.8680 (t70) cc_final: 0.8175 (t0) REVERT: F 422 LEU cc_start: 0.9087 (tt) cc_final: 0.8537 (mp) REVERT: F 486 THR cc_start: 0.8738 (t) cc_final: 0.8524 (p) REVERT: F 544 ASP cc_start: 0.8101 (t0) cc_final: 0.7841 (t70) outliers start: 29 outliers final: 21 residues processed: 515 average time/residue: 0.1516 time to fit residues: 114.6511 Evaluate side-chains 454 residues out of total 2094 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 432 time to evaluate : 0.767 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 441 VAL Chi-restraints excluded: chain A residue 466 VAL Chi-restraints excluded: chain B residue 109 GLU Chi-restraints excluded: chain B residue 122 VAL Chi-restraints excluded: chain B residue 292 LEU Chi-restraints excluded: chain B residue 325 THR Chi-restraints excluded: chain C residue 122 VAL Chi-restraints excluded: chain C residue 360 VAL Chi-restraints excluded: chain C residue 422 LEU Chi-restraints excluded: chain C residue 503 LEU Chi-restraints excluded: chain D residue 102 ARG Chi-restraints excluded: chain D residue 131 VAL Chi-restraints excluded: chain D residue 138 VAL Chi-restraints excluded: chain D residue 442 MET Chi-restraints excluded: chain E residue 294 LEU Chi-restraints excluded: chain E residue 309 LYS Chi-restraints excluded: chain E residue 441 VAL Chi-restraints excluded: chain E residue 466 VAL Chi-restraints excluded: chain F residue 131 VAL Chi-restraints excluded: chain F residue 137 GLU Chi-restraints excluded: chain F residue 210 THR Chi-restraints excluded: chain F residue 354 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 177 optimal weight: 0.6980 chunk 239 optimal weight: 3.9990 chunk 32 optimal weight: 4.9990 chunk 194 optimal weight: 7.9990 chunk 190 optimal weight: 3.9990 chunk 205 optimal weight: 5.9990 chunk 102 optimal weight: 2.9990 chunk 3 optimal weight: 0.6980 chunk 61 optimal weight: 1.9990 chunk 193 optimal weight: 5.9990 chunk 113 optimal weight: 10.0000 overall best weight: 2.0786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 391 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3425 r_free = 0.3425 target = 0.110272 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3061 r_free = 0.3061 target = 0.086736 restraints weight = 36346.633| |-----------------------------------------------------------------------------| r_work (start): 0.3047 rms_B_bonded: 3.27 r_work: 0.2906 rms_B_bonded: 3.72 restraints_weight: 0.5000 r_work (final): 0.2906 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8471 moved from start: 0.3248 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 19185 Z= 0.139 Angle : 0.511 6.114 25976 Z= 0.275 Chirality : 0.042 0.151 2883 Planarity : 0.004 0.054 3292 Dihedral : 3.848 18.359 2627 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 5.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.94 % Favored : 98.06 % Rotamer: Outliers : 2.10 % Allowed : 15.46 % Favored : 82.44 % 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 are not related in a simple way. whole: 1.78 (0.18), residues: 2376 helix: 2.34 (0.18), residues: 900 sheet: 0.07 (0.26), residues: 384 loop : 0.75 (0.19), residues: 1092 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG F 477 TYR 0.019 0.001 TYR E 343 PHE 0.017 0.001 PHE F 541 TRP 0.010 0.001 TRP E 464 HIS 0.005 0.001 HIS B 191 Details of bonding type rmsd covalent geometry : bond 0.00324 (19185) covalent geometry : angle 0.51091 (25976) hydrogen bonds : bond 0.04029 ( 841) hydrogen bonds : angle 4.49302 ( 2307) *********************** 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 501 residues out of total 2094 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 459 time to evaluate : 0.758 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: A 113 ASP cc_start: 0.9074 (t0) cc_final: 0.8840 (t0) REVERT: A 186 ASP cc_start: 0.8531 (m-30) cc_final: 0.8269 (p0) REVERT: A 236 TYR cc_start: 0.8841 (t80) cc_final: 0.8618 (t80) REVERT: A 348 GLN cc_start: 0.8877 (tp40) cc_final: 0.8637 (tp40) REVERT: A 355 ASP cc_start: 0.8881 (t70) cc_final: 0.8471 (t70) REVERT: B 117 ARG cc_start: 0.8627 (mtp180) cc_final: 0.7158 (ttt180) REVERT: B 120 ASP cc_start: 0.9154 (m-30) cc_final: 0.8764 (m-30) REVERT: B 225 LYS cc_start: 0.8853 (mmmt) cc_final: 0.8627 (tptm) REVERT: B 373 ARG cc_start: 0.8772 (mmm160) cc_final: 0.8400 (tpp-160) REVERT: B 386 THR cc_start: 0.8949 (m) cc_final: 0.8704 (p) REVERT: B 477 ARG cc_start: 0.8820 (ttt90) cc_final: 0.7451 (mtt90) REVERT: C 228 LYS cc_start: 0.9012 (mmmt) cc_final: 0.8773 (mmmt) REVERT: C 379 LYS cc_start: 0.9368 (ttpp) cc_final: 0.9017 (tppt) REVERT: C 453 SER cc_start: 0.9370 (t) cc_final: 0.9113 (m) REVERT: C 527 SER cc_start: 0.9295 (m) cc_final: 0.8857 (p) REVERT: C 540 GLU cc_start: 0.8804 (tp30) cc_final: 0.8385 (tp30) REVERT: D 336 GLU cc_start: 0.9291 (tp30) cc_final: 0.8874 (tp30) REVERT: D 348 GLN cc_start: 0.9049 (tp40) cc_final: 0.8695 (tm-30) REVERT: D 355 ASP cc_start: 0.8897 (t70) cc_final: 0.8628 (t70) REVERT: D 449 ASN cc_start: 0.8554 (t0) cc_final: 0.8300 (t0) REVERT: D 473 TYR cc_start: 0.8067 (m-80) cc_final: 0.7815 (m-80) REVERT: D 477 ARG cc_start: 0.8189 (ttt90) cc_final: 0.5716 (mtt-85) REVERT: D 540 GLU cc_start: 0.8827 (tp30) cc_final: 0.8558 (tp30) REVERT: E 111 SER cc_start: 0.9320 (m) cc_final: 0.8995 (p) REVERT: E 195 GLU cc_start: 0.8716 (mp0) cc_final: 0.8366 (mp0) REVERT: E 226 ASP cc_start: 0.7577 (t0) cc_final: 0.7151 (t0) REVERT: E 297 LYS cc_start: 0.9074 (tttt) cc_final: 0.8592 (tppt) REVERT: E 349 LYS cc_start: 0.9281 (ttmm) cc_final: 0.9023 (mttt) REVERT: E 355 ASP cc_start: 0.9089 (t0) cc_final: 0.8881 (t0) REVERT: E 386 THR cc_start: 0.9181 (m) cc_final: 0.8669 (p) REVERT: E 390 ASP cc_start: 0.8170 (t0) cc_final: 0.7962 (t0) REVERT: F 355 ASP cc_start: 0.8731 (t70) cc_final: 0.8391 (t70) REVERT: F 422 LEU cc_start: 0.9105 (tt) cc_final: 0.8558 (mp) outliers start: 42 outliers final: 20 residues processed: 478 average time/residue: 0.1534 time to fit residues: 106.8024 Evaluate side-chains 455 residues out of total 2094 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 435 time to evaluate : 0.620 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 137 GLU Chi-restraints excluded: chain A residue 441 VAL Chi-restraints excluded: chain A residue 466 VAL Chi-restraints excluded: chain B residue 122 VAL Chi-restraints excluded: chain B residue 218 SER Chi-restraints excluded: chain B residue 325 THR Chi-restraints excluded: chain B residue 543 LYS Chi-restraints excluded: chain C residue 122 VAL Chi-restraints excluded: chain C residue 422 LEU Chi-restraints excluded: chain C residue 503 LEU Chi-restraints excluded: chain D residue 131 VAL Chi-restraints excluded: chain D residue 137 GLU Chi-restraints excluded: chain D residue 138 VAL Chi-restraints excluded: chain E residue 210 THR Chi-restraints excluded: chain E residue 294 LEU Chi-restraints excluded: chain E residue 301 SER Chi-restraints excluded: chain E residue 466 VAL Chi-restraints excluded: chain E residue 518 ILE Chi-restraints excluded: chain F residue 131 VAL Chi-restraints excluded: chain F residue 137 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 57 optimal weight: 10.0000 chunk 227 optimal weight: 7.9990 chunk 158 optimal weight: 2.9990 chunk 153 optimal weight: 4.9990 chunk 122 optimal weight: 5.9990 chunk 88 optimal weight: 10.0000 chunk 50 optimal weight: 7.9990 chunk 51 optimal weight: 2.9990 chunk 58 optimal weight: 1.9990 chunk 33 optimal weight: 10.0000 chunk 90 optimal weight: 20.0000 overall best weight: 3.7990 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.106609 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2994 r_free = 0.2994 target = 0.082881 restraints weight = 36757.857| |-----------------------------------------------------------------------------| r_work (start): 0.2980 rms_B_bonded: 3.24 r_work: 0.2841 rms_B_bonded: 3.64 restraints_weight: 0.5000 r_work (final): 0.2841 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8540 moved from start: 0.3714 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 19185 Z= 0.222 Angle : 0.572 6.483 25976 Z= 0.308 Chirality : 0.044 0.170 2883 Planarity : 0.004 0.059 3292 Dihedral : 4.192 19.013 2627 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 6.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 2.40 % Allowed : 17.36 % Favored : 80.24 % 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 are not related in a simple way. whole: 1.51 (0.18), residues: 2376 helix: 2.19 (0.18), residues: 900 sheet: -0.19 (0.25), residues: 384 loop : 0.59 (0.19), residues: 1092 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG F 477 TYR 0.022 0.002 TYR F 393 PHE 0.021 0.001 PHE E 541 TRP 0.014 0.002 TRP B 464 HIS 0.004 0.001 HIS B 191 Details of bonding type rmsd covalent geometry : bond 0.00521 (19185) covalent geometry : angle 0.57160 (25976) hydrogen bonds : bond 0.05000 ( 841) hydrogen bonds : angle 4.80324 ( 2307) *********************** 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 485 residues out of total 2094 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 437 time to evaluate : 0.567 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 113 ASP cc_start: 0.9075 (t0) cc_final: 0.8857 (t0) REVERT: A 236 TYR cc_start: 0.8840 (t80) cc_final: 0.8633 (t80) REVERT: A 348 GLN cc_start: 0.8972 (tp40) cc_final: 0.8746 (tp40) REVERT: A 355 ASP cc_start: 0.8947 (t70) cc_final: 0.8496 (t70) REVERT: B 120 ASP cc_start: 0.9214 (m-30) cc_final: 0.8808 (m-30) REVERT: B 225 LYS cc_start: 0.8904 (mmmt) cc_final: 0.8663 (tptm) REVERT: B 361 GLN cc_start: 0.9181 (pm20) cc_final: 0.8962 (pm20) REVERT: B 373 ARG cc_start: 0.8737 (mmm160) cc_final: 0.8381 (tpp-160) REVERT: B 477 ARG cc_start: 0.8885 (ttt90) cc_final: 0.7481 (mtt180) REVERT: C 228 LYS cc_start: 0.9105 (mmmt) cc_final: 0.8889 (mmmt) REVERT: C 379 LYS cc_start: 0.9341 (ttpp) cc_final: 0.9028 (tppt) REVERT: C 453 SER cc_start: 0.9396 (t) cc_final: 0.9139 (m) REVERT: C 527 SER cc_start: 0.9235 (m) cc_final: 0.8802 (p) REVERT: C 540 GLU cc_start: 0.8818 (tp30) cc_final: 0.8354 (tp30) REVERT: D 170 THR cc_start: 0.9459 (m) cc_final: 0.9202 (p) REVERT: D 226 ASP cc_start: 0.8409 (t0) cc_final: 0.7944 (t0) REVERT: D 330 LEU cc_start: 0.9448 (OUTLIER) cc_final: 0.9106 (tt) REVERT: D 336 GLU cc_start: 0.9236 (tp30) cc_final: 0.8853 (tp30) REVERT: D 348 GLN cc_start: 0.9027 (tp40) cc_final: 0.8636 (tm-30) REVERT: D 355 ASP cc_start: 0.9024 (t70) cc_final: 0.8386 (t70) REVERT: D 379 LYS cc_start: 0.9410 (ttpt) cc_final: 0.9158 (ttmm) REVERT: D 453 SER cc_start: 0.9575 (t) cc_final: 0.9194 (m) REVERT: D 477 ARG cc_start: 0.8176 (ttt90) cc_final: 0.5875 (mtt-85) REVERT: D 478 LYS cc_start: 0.9164 (tttt) cc_final: 0.8878 (tppt) REVERT: D 540 GLU cc_start: 0.8922 (tp30) cc_final: 0.8559 (tp30) REVERT: E 111 SER cc_start: 0.9346 (m) cc_final: 0.9078 (p) REVERT: E 226 ASP cc_start: 0.7761 (t0) cc_final: 0.7486 (t0) REVERT: E 296 GLU cc_start: 0.8009 (tt0) cc_final: 0.7664 (tm-30) REVERT: E 297 LYS cc_start: 0.9140 (tttt) cc_final: 0.8313 (tppt) REVERT: E 349 LYS cc_start: 0.9283 (ttmm) cc_final: 0.9041 (mttt) REVERT: E 355 ASP cc_start: 0.9175 (t0) cc_final: 0.8940 (t0) REVERT: E 386 THR cc_start: 0.9295 (m) cc_final: 0.8855 (p) REVERT: E 390 ASP cc_start: 0.8162 (t0) cc_final: 0.7941 (t0) REVERT: F 355 ASP cc_start: 0.8900 (t70) cc_final: 0.8561 (t70) REVERT: F 422 LEU cc_start: 0.9118 (tt) cc_final: 0.8648 (mp) REVERT: F 477 ARG cc_start: 0.8833 (ttt90) cc_final: 0.8391 (ttt90) outliers start: 48 outliers final: 37 residues processed: 467 average time/residue: 0.1521 time to fit residues: 103.4362 Evaluate side-chains 445 residues out of total 2094 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 407 time to evaluate : 0.744 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 137 GLU Chi-restraints excluded: chain A residue 367 VAL Chi-restraints excluded: chain A residue 441 VAL Chi-restraints excluded: chain A residue 466 VAL Chi-restraints excluded: chain B residue 122 VAL Chi-restraints excluded: chain B residue 325 THR Chi-restraints excluded: chain B residue 543 LYS Chi-restraints excluded: chain C residue 122 VAL Chi-restraints excluded: chain C residue 330 LEU Chi-restraints excluded: chain C residue 367 VAL Chi-restraints excluded: chain C residue 422 LEU Chi-restraints excluded: chain C residue 457 GLU Chi-restraints excluded: chain C residue 503 LEU Chi-restraints excluded: chain C residue 543 LYS Chi-restraints excluded: chain D residue 131 VAL Chi-restraints excluded: chain D residue 137 GLU Chi-restraints excluded: chain D residue 138 VAL Chi-restraints excluded: chain D residue 182 LYS Chi-restraints excluded: chain D residue 210 THR Chi-restraints excluded: chain D residue 306 ARG Chi-restraints excluded: chain D residue 330 LEU Chi-restraints excluded: chain D residue 353 ASP Chi-restraints excluded: chain D residue 367 VAL Chi-restraints excluded: chain D residue 441 VAL Chi-restraints excluded: chain D residue 470 LYS Chi-restraints excluded: chain D residue 486 THR Chi-restraints excluded: chain E residue 210 THR Chi-restraints excluded: chain E residue 213 LEU Chi-restraints excluded: chain E residue 294 LEU Chi-restraints excluded: chain E residue 301 SER Chi-restraints excluded: chain E residue 443 MET Chi-restraints excluded: chain E residue 466 VAL Chi-restraints excluded: chain E residue 518 ILE Chi-restraints excluded: chain F residue 131 VAL Chi-restraints excluded: chain F residue 137 GLU Chi-restraints excluded: chain F residue 330 LEU Chi-restraints excluded: chain F residue 354 LEU Chi-restraints excluded: chain F residue 512 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 107 optimal weight: 3.9990 chunk 147 optimal weight: 0.0040 chunk 87 optimal weight: 4.9990 chunk 18 optimal weight: 10.0000 chunk 24 optimal weight: 6.9990 chunk 45 optimal weight: 0.9990 chunk 192 optimal weight: 3.9990 chunk 89 optimal weight: 0.9980 chunk 102 optimal weight: 0.7980 chunk 47 optimal weight: 0.9980 chunk 133 optimal weight: 0.0270 overall best weight: 0.5650 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 391 ASN D 391 ASN D 485 HIS E 216 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.111422 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3083 r_free = 0.3083 target = 0.088433 restraints weight = 36060.861| |-----------------------------------------------------------------------------| r_work (start): 0.3070 rms_B_bonded: 3.25 r_work: 0.2931 rms_B_bonded: 3.70 restraints_weight: 0.5000 r_work (final): 0.2931 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8443 moved from start: 0.3708 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.059 19185 Z= 0.094 Angle : 0.491 8.489 25976 Z= 0.263 Chirality : 0.041 0.156 2883 Planarity : 0.004 0.055 3292 Dihedral : 3.896 17.697 2627 Min Nonbonded Distance : 2.572 Molprobity Statistics. All-atom Clashscore : 5.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.22 % Favored : 98.78 % Rotamer: Outliers : 1.35 % Allowed : 19.06 % Favored : 79.59 % 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 are not related in a simple way. whole: 1.72 (0.18), residues: 2376 helix: 2.28 (0.18), residues: 900 sheet: 0.19 (0.26), residues: 378 loop : 0.66 (0.19), residues: 1098 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 477 TYR 0.023 0.001 TYR E 343 PHE 0.010 0.001 PHE B 374 TRP 0.010 0.001 TRP E 454 HIS 0.003 0.000 HIS B 191 Details of bonding type rmsd covalent geometry : bond 0.00208 (19185) covalent geometry : angle 0.49074 (25976) hydrogen bonds : bond 0.03272 ( 841) hydrogen bonds : angle 4.28313 ( 2307) *********************** 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 500 residues out of total 2094 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 473 time to evaluate : 0.700 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 113 ASP cc_start: 0.9034 (t0) cc_final: 0.8786 (t0) REVERT: A 186 ASP cc_start: 0.8575 (m-30) cc_final: 0.8233 (p0) REVERT: A 236 TYR cc_start: 0.8839 (t80) cc_final: 0.8611 (t80) REVERT: A 348 GLN cc_start: 0.8892 (tp40) cc_final: 0.8647 (tp40) REVERT: A 355 ASP cc_start: 0.8809 (t70) cc_final: 0.8322 (t70) REVERT: A 540 GLU cc_start: 0.9147 (tp30) cc_final: 0.8889 (tp30) REVERT: B 117 ARG cc_start: 0.8515 (mtp180) cc_final: 0.7091 (ttt180) REVERT: B 361 GLN cc_start: 0.9169 (pm20) cc_final: 0.8908 (pm20) REVERT: B 363 GLU cc_start: 0.8277 (mm-30) cc_final: 0.8042 (mm-30) REVERT: B 477 ARG cc_start: 0.8760 (ttt90) cc_final: 0.7365 (mtt180) REVERT: C 228 LYS cc_start: 0.9065 (mmmt) cc_final: 0.8859 (mmmt) REVERT: C 379 LYS cc_start: 0.9323 (ttpp) cc_final: 0.8981 (tppt) REVERT: C 386 THR cc_start: 0.9090 (m) cc_final: 0.8645 (p) REVERT: C 453 SER cc_start: 0.9344 (t) cc_final: 0.9104 (m) REVERT: C 527 SER cc_start: 0.9285 (m) cc_final: 0.8856 (p) REVERT: C 540 GLU cc_start: 0.8807 (tp30) cc_final: 0.8367 (tp30) REVERT: C 544 ASP cc_start: 0.8231 (t0) cc_final: 0.7830 (t0) REVERT: D 170 THR cc_start: 0.9420 (m) cc_final: 0.9186 (p) REVERT: D 330 LEU cc_start: 0.9384 (OUTLIER) cc_final: 0.9010 (tt) REVERT: D 336 GLU cc_start: 0.9246 (tp30) cc_final: 0.8885 (tp30) REVERT: D 348 GLN cc_start: 0.8952 (tp40) cc_final: 0.8725 (tp40) REVERT: D 355 ASP cc_start: 0.8907 (t70) cc_final: 0.8625 (t70) REVERT: D 379 LYS cc_start: 0.9324 (ttpt) cc_final: 0.9073 (ttmm) REVERT: D 441 VAL cc_start: 0.9056 (t) cc_final: 0.8783 (p) REVERT: D 442 MET cc_start: 0.9411 (tmm) cc_final: 0.9173 (ppp) REVERT: D 453 SER cc_start: 0.9497 (t) cc_final: 0.9108 (m) REVERT: D 473 TYR cc_start: 0.7923 (m-80) cc_final: 0.7683 (m-80) REVERT: D 477 ARG cc_start: 0.8033 (ttt90) cc_final: 0.5777 (mtt180) REVERT: D 478 LYS cc_start: 0.9132 (tttt) cc_final: 0.8876 (tppt) REVERT: D 540 GLU cc_start: 0.8885 (tp30) cc_final: 0.8600 (tp30) REVERT: E 187 ILE cc_start: 0.9332 (mt) cc_final: 0.9061 (tp) REVERT: E 226 ASP cc_start: 0.7616 (t0) cc_final: 0.7123 (t0) REVERT: E 232 GLU cc_start: 0.8860 (mm-30) cc_final: 0.8543 (mm-30) REVERT: E 297 LYS cc_start: 0.9115 (tttt) cc_final: 0.8632 (tppt) REVERT: E 349 LYS cc_start: 0.9184 (ttmm) cc_final: 0.8898 (mttt) REVERT: E 390 ASP cc_start: 0.8149 (t0) cc_final: 0.7868 (t0) REVERT: F 355 ASP cc_start: 0.8721 (t70) cc_final: 0.8416 (t70) REVERT: F 422 LEU cc_start: 0.9109 (tt) cc_final: 0.8654 (mp) REVERT: F 442 MET cc_start: 0.8937 (tmm) cc_final: 0.8649 (tmm) outliers start: 27 outliers final: 17 residues processed: 485 average time/residue: 0.1477 time to fit residues: 105.1912 Evaluate side-chains 459 residues out of total 2094 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 441 time to evaluate : 0.568 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 137 GLU Chi-restraints excluded: chain B residue 122 VAL Chi-restraints excluded: chain B residue 218 SER Chi-restraints excluded: chain C residue 360 VAL Chi-restraints excluded: chain C residue 503 LEU Chi-restraints excluded: chain D residue 137 GLU Chi-restraints excluded: chain D residue 138 VAL Chi-restraints excluded: chain D residue 330 LEU Chi-restraints excluded: chain D residue 367 VAL Chi-restraints excluded: chain D residue 380 LYS Chi-restraints excluded: chain D residue 470 LYS Chi-restraints excluded: chain E residue 109 GLU Chi-restraints excluded: chain E residue 213 LEU Chi-restraints excluded: chain E residue 367 VAL Chi-restraints excluded: chain E residue 466 VAL Chi-restraints excluded: chain F residue 137 GLU Chi-restraints excluded: chain F residue 294 LEU Chi-restraints excluded: chain F residue 367 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 139 optimal weight: 10.0000 chunk 126 optimal weight: 3.9990 chunk 115 optimal weight: 6.9990 chunk 188 optimal weight: 8.9990 chunk 162 optimal weight: 0.0670 chunk 192 optimal weight: 3.9990 chunk 152 optimal weight: 1.9990 chunk 198 optimal weight: 3.9990 chunk 212 optimal weight: 6.9990 chunk 8 optimal weight: 9.9990 chunk 54 optimal weight: 9.9990 overall best weight: 2.8126 ------------------------------------------------------------------------------- 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 E 391 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.107360 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3013 r_free = 0.3013 target = 0.083769 restraints weight = 36334.273| |-----------------------------------------------------------------------------| r_work (start): 0.3005 rms_B_bonded: 3.26 r_work: 0.2865 rms_B_bonded: 3.67 restraints_weight: 0.5000 r_work (final): 0.2865 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8508 moved from start: 0.3894 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 19185 Z= 0.172 Angle : 0.536 6.826 25976 Z= 0.286 Chirality : 0.042 0.155 2883 Planarity : 0.004 0.058 3292 Dihedral : 4.023 17.953 2627 Min Nonbonded Distance : 2.411 Molprobity Statistics. All-atom Clashscore : 6.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer: Outliers : 1.90 % Allowed : 19.96 % Favored : 78.14 % 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 are not related in a simple way. whole: 1.62 (0.18), residues: 2376 helix: 2.29 (0.18), residues: 900 sheet: 0.02 (0.26), residues: 378 loop : 0.57 (0.19), residues: 1098 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG F 477 TYR 0.023 0.001 TYR E 343 PHE 0.015 0.001 PHE E 541 TRP 0.012 0.001 TRP B 464 HIS 0.004 0.001 HIS F 191 Details of bonding type rmsd covalent geometry : bond 0.00408 (19185) covalent geometry : angle 0.53613 (25976) hydrogen bonds : bond 0.04298 ( 841) hydrogen bonds : angle 4.52182 ( 2307) *********************** 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 462 residues out of total 2094 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 424 time to evaluate : 0.658 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 113 ASP cc_start: 0.9058 (t0) cc_final: 0.8819 (t0) REVERT: A 236 TYR cc_start: 0.8825 (t80) cc_final: 0.8604 (t80) REVERT: A 348 GLN cc_start: 0.8945 (tp40) cc_final: 0.8722 (tp40) REVERT: A 355 ASP cc_start: 0.8922 (t70) cc_final: 0.8449 (t70) REVERT: B 361 GLN cc_start: 0.9169 (pm20) cc_final: 0.8922 (pm20) REVERT: B 363 GLU cc_start: 0.8285 (mm-30) cc_final: 0.8062 (mm-30) REVERT: B 373 ARG cc_start: 0.8739 (mmm160) cc_final: 0.8366 (tpp-160) REVERT: B 477 ARG cc_start: 0.8849 (ttt90) cc_final: 0.7460 (mtt180) REVERT: C 106 ARG cc_start: 0.8317 (ptm-80) cc_final: 0.8075 (ptm-80) REVERT: C 117 ARG cc_start: 0.8979 (mtp85) cc_final: 0.8473 (mtp180) REVERT: C 379 LYS cc_start: 0.9332 (ttpp) cc_final: 0.9011 (tppt) REVERT: C 453 SER cc_start: 0.9361 (t) cc_final: 0.9100 (m) REVERT: D 170 THR cc_start: 0.9460 (m) cc_final: 0.9236 (p) REVERT: D 226 ASP cc_start: 0.8382 (t0) cc_final: 0.7966 (t0) REVERT: D 330 LEU cc_start: 0.9429 (OUTLIER) cc_final: 0.9027 (tt) REVERT: D 336 GLU cc_start: 0.9242 (tp30) cc_final: 0.8876 (tp30) REVERT: D 348 GLN cc_start: 0.8987 (tp40) cc_final: 0.8597 (tm-30) REVERT: D 355 ASP cc_start: 0.9021 (t70) cc_final: 0.8557 (t70) REVERT: D 379 LYS cc_start: 0.9382 (ttpt) cc_final: 0.9145 (ttmm) REVERT: D 453 SER cc_start: 0.9532 (t) cc_final: 0.9160 (m) REVERT: D 473 TYR cc_start: 0.7852 (m-80) cc_final: 0.7637 (m-80) REVERT: D 477 ARG cc_start: 0.8091 (ttt90) cc_final: 0.5814 (mtt180) REVERT: D 478 LYS cc_start: 0.9148 (tttt) cc_final: 0.8872 (tppt) REVERT: D 540 GLU cc_start: 0.8922 (tp30) cc_final: 0.8568 (tp30) REVERT: E 111 SER cc_start: 0.9272 (m) cc_final: 0.8792 (p) REVERT: E 187 ILE cc_start: 0.9346 (mt) cc_final: 0.9074 (tp) REVERT: E 226 ASP cc_start: 0.7708 (t0) cc_final: 0.7342 (t0) REVERT: E 232 GLU cc_start: 0.8878 (mm-30) cc_final: 0.8564 (mm-30) REVERT: E 296 GLU cc_start: 0.7916 (tt0) cc_final: 0.7511 (tm-30) REVERT: E 297 LYS cc_start: 0.9138 (tttt) cc_final: 0.8317 (tppt) REVERT: E 349 LYS cc_start: 0.9247 (ttmm) cc_final: 0.9025 (mttt) REVERT: E 390 ASP cc_start: 0.8071 (t0) cc_final: 0.7827 (t0) REVERT: E 471 GLN cc_start: 0.8536 (OUTLIER) cc_final: 0.7132 (tp40) REVERT: E 478 LYS cc_start: 0.8683 (mmtt) cc_final: 0.8175 (mmtm) REVERT: F 355 ASP cc_start: 0.8924 (t70) cc_final: 0.8600 (t70) REVERT: F 362 GLU cc_start: 0.8638 (tp30) cc_final: 0.8408 (tp30) REVERT: F 422 LEU cc_start: 0.9089 (tt) cc_final: 0.8659 (mp) REVERT: F 442 MET cc_start: 0.8986 (tmm) cc_final: 0.8746 (tmm) outliers start: 38 outliers final: 31 residues processed: 445 average time/residue: 0.1490 time to fit residues: 97.7706 Evaluate side-chains 447 residues out of total 2094 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 414 time to evaluate : 0.668 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 137 GLU Chi-restraints excluded: chain A residue 367 VAL Chi-restraints excluded: chain A residue 466 VAL Chi-restraints excluded: chain B residue 122 VAL Chi-restraints excluded: chain B residue 325 THR Chi-restraints excluded: chain B residue 543 LYS Chi-restraints excluded: chain C residue 360 VAL Chi-restraints excluded: chain C residue 367 VAL Chi-restraints excluded: chain C residue 422 LEU Chi-restraints excluded: chain C residue 490 VAL Chi-restraints excluded: chain C residue 503 LEU Chi-restraints excluded: chain D residue 131 VAL Chi-restraints excluded: chain D residue 137 GLU Chi-restraints excluded: chain D residue 138 VAL Chi-restraints excluded: chain D residue 330 LEU Chi-restraints excluded: chain D residue 353 ASP Chi-restraints excluded: chain D residue 367 VAL Chi-restraints excluded: chain D residue 380 LYS Chi-restraints excluded: chain D residue 470 LYS Chi-restraints excluded: chain E residue 109 GLU Chi-restraints excluded: chain E residue 210 THR Chi-restraints excluded: chain E residue 213 LEU Chi-restraints excluded: chain E residue 367 VAL Chi-restraints excluded: chain E residue 386 THR Chi-restraints excluded: chain E residue 443 MET Chi-restraints excluded: chain E residue 466 VAL Chi-restraints excluded: chain E residue 471 GLN Chi-restraints excluded: chain E residue 490 VAL Chi-restraints excluded: chain E residue 518 ILE Chi-restraints excluded: chain F residue 131 VAL Chi-restraints excluded: chain F residue 137 GLU Chi-restraints excluded: chain F residue 301 SER Chi-restraints excluded: chain F residue 367 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 152 optimal weight: 5.9990 chunk 226 optimal weight: 4.9990 chunk 63 optimal weight: 3.9990 chunk 40 optimal weight: 10.0000 chunk 37 optimal weight: 9.9990 chunk 61 optimal weight: 10.0000 chunk 230 optimal weight: 8.9990 chunk 221 optimal weight: 5.9990 chunk 165 optimal weight: 0.5980 chunk 231 optimal weight: 6.9990 chunk 100 optimal weight: 0.9990 overall best weight: 3.3188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 391 ASN D 391 ASN E 216 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.106934 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2994 r_free = 0.2994 target = 0.083563 restraints weight = 36235.296| |-----------------------------------------------------------------------------| r_work (start): 0.2982 rms_B_bonded: 3.19 r_work: 0.2845 rms_B_bonded: 3.58 restraints_weight: 0.5000 r_work (final): 0.2845 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8477 moved from start: 0.4073 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 19185 Z= 0.194 Angle : 0.556 6.747 25976 Z= 0.299 Chirality : 0.043 0.153 2883 Planarity : 0.004 0.060 3292 Dihedral : 4.191 18.951 2627 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 6.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.57 % Favored : 97.43 % Rotamer: Outliers : 2.45 % Allowed : 20.21 % Favored : 77.34 % 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 are not related in a simple way. whole: 1.48 (0.18), residues: 2376 helix: 2.20 (0.18), residues: 900 sheet: -0.11 (0.26), residues: 378 loop : 0.47 (0.19), residues: 1098 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 477 TYR 0.035 0.001 TYR F 343 PHE 0.013 0.001 PHE E 541 TRP 0.012 0.001 TRP B 464 HIS 0.004 0.001 HIS A 216 Details of bonding type rmsd covalent geometry : bond 0.00460 (19185) covalent geometry : angle 0.55620 (25976) hydrogen bonds : bond 0.04618 ( 841) hydrogen bonds : angle 4.68312 ( 2307) *********************** 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 469 residues out of total 2094 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 420 time to evaluate : 0.721 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 113 ASP cc_start: 0.9014 (t0) cc_final: 0.8780 (t0) REVERT: A 236 TYR cc_start: 0.8827 (t80) cc_final: 0.8607 (t80) REVERT: A 348 GLN cc_start: 0.9020 (tp40) cc_final: 0.8790 (tp40) REVERT: A 355 ASP cc_start: 0.9000 (t70) cc_final: 0.8491 (t70) REVERT: B 361 GLN cc_start: 0.9137 (pm20) cc_final: 0.8878 (pm20) REVERT: B 363 GLU cc_start: 0.8209 (mm-30) cc_final: 0.7990 (mm-30) REVERT: B 373 ARG cc_start: 0.8752 (mmm160) cc_final: 0.8312 (tpp-160) REVERT: B 477 ARG cc_start: 0.8821 (ttt90) cc_final: 0.7403 (mtt180) REVERT: C 106 ARG cc_start: 0.8339 (ptm-80) cc_final: 0.8063 (ptm-80) REVERT: C 226 ASP cc_start: 0.7351 (t0) cc_final: 0.6847 (t0) REVERT: C 379 LYS cc_start: 0.9367 (ttpp) cc_final: 0.9039 (tppt) REVERT: C 453 SER cc_start: 0.9367 (t) cc_final: 0.9096 (m) REVERT: C 475 SER cc_start: 0.8719 (m) cc_final: 0.8479 (p) REVERT: D 170 THR cc_start: 0.9479 (m) cc_final: 0.9273 (p) REVERT: D 226 ASP cc_start: 0.8387 (t0) cc_final: 0.7913 (t0) REVERT: D 296 GLU cc_start: 0.8519 (tt0) cc_final: 0.8130 (tm-30) REVERT: D 330 LEU cc_start: 0.9426 (OUTLIER) cc_final: 0.9066 (tt) REVERT: D 348 GLN cc_start: 0.9008 (tp40) cc_final: 0.8789 (tp40) REVERT: D 355 ASP cc_start: 0.9146 (t70) cc_final: 0.8629 (t70) REVERT: D 379 LYS cc_start: 0.9408 (ttpt) cc_final: 0.9161 (ttmm) REVERT: D 453 SER cc_start: 0.9545 (t) cc_final: 0.9175 (m) REVERT: D 477 ARG cc_start: 0.8071 (ttt90) cc_final: 0.5836 (mtt180) REVERT: D 478 LYS cc_start: 0.9188 (tttt) cc_final: 0.8844 (tppt) REVERT: D 540 GLU cc_start: 0.8937 (tp30) cc_final: 0.8465 (tp30) REVERT: E 226 ASP cc_start: 0.7796 (t0) cc_final: 0.7505 (t0) REVERT: E 232 GLU cc_start: 0.8882 (mm-30) cc_final: 0.8613 (mm-30) REVERT: E 297 LYS cc_start: 0.9110 (tttt) cc_final: 0.8394 (tppt) REVERT: E 349 LYS cc_start: 0.9284 (ttmm) cc_final: 0.9004 (mttt) REVERT: E 390 ASP cc_start: 0.8098 (t0) cc_final: 0.7791 (t0) REVERT: E 471 GLN cc_start: 0.8520 (OUTLIER) cc_final: 0.7111 (tp40) REVERT: E 478 LYS cc_start: 0.8730 (mmtt) cc_final: 0.8096 (mptt) REVERT: E 540 GLU cc_start: 0.8967 (tp30) cc_final: 0.8686 (tp30) REVERT: F 355 ASP cc_start: 0.8992 (t70) cc_final: 0.8645 (t70) REVERT: F 362 GLU cc_start: 0.8577 (tp30) cc_final: 0.8331 (tp30) REVERT: F 422 LEU cc_start: 0.9087 (tt) cc_final: 0.8668 (mp) outliers start: 49 outliers final: 35 residues processed: 445 average time/residue: 0.1458 time to fit residues: 96.6644 Evaluate side-chains 450 residues out of total 2094 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 413 time to evaluate : 0.552 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 137 GLU Chi-restraints excluded: chain A residue 367 VAL Chi-restraints excluded: chain B residue 122 VAL Chi-restraints excluded: chain B residue 182 LYS Chi-restraints excluded: chain B residue 325 THR Chi-restraints excluded: chain B residue 453 SER Chi-restraints excluded: chain B residue 543 LYS Chi-restraints excluded: chain C residue 122 VAL Chi-restraints excluded: chain C residue 360 VAL Chi-restraints excluded: chain C residue 367 VAL Chi-restraints excluded: chain C residue 422 LEU Chi-restraints excluded: chain C residue 457 GLU Chi-restraints excluded: chain C residue 490 VAL Chi-restraints excluded: chain C residue 503 LEU Chi-restraints excluded: chain D residue 131 VAL Chi-restraints excluded: chain D residue 137 GLU Chi-restraints excluded: chain D residue 138 VAL Chi-restraints excluded: chain D residue 330 LEU Chi-restraints excluded: chain D residue 353 ASP Chi-restraints excluded: chain D residue 367 VAL Chi-restraints excluded: chain D residue 380 LYS Chi-restraints excluded: chain D residue 470 LYS Chi-restraints excluded: chain E residue 109 GLU Chi-restraints excluded: chain E residue 210 THR Chi-restraints excluded: chain E residue 213 LEU Chi-restraints excluded: chain E residue 294 LEU Chi-restraints excluded: chain E residue 301 SER Chi-restraints excluded: chain E residue 367 VAL Chi-restraints excluded: chain E residue 386 THR Chi-restraints excluded: chain E residue 443 MET Chi-restraints excluded: chain E residue 466 VAL Chi-restraints excluded: chain E residue 471 GLN Chi-restraints excluded: chain E residue 518 ILE Chi-restraints excluded: chain F residue 131 VAL Chi-restraints excluded: chain F residue 137 GLU Chi-restraints excluded: chain F residue 367 VAL Chi-restraints excluded: chain F residue 490 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 186 optimal weight: 3.9990 chunk 98 optimal weight: 8.9990 chunk 142 optimal weight: 3.9990 chunk 229 optimal weight: 7.9990 chunk 99 optimal weight: 3.9990 chunk 139 optimal weight: 10.0000 chunk 117 optimal weight: 9.9990 chunk 238 optimal weight: 1.9990 chunk 64 optimal weight: 0.7980 chunk 130 optimal weight: 8.9990 chunk 210 optimal weight: 0.2980 overall best weight: 2.2186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 352 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 = 0.3390 r_free = 0.3390 target = 0.108419 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3021 r_free = 0.3021 target = 0.085077 restraints weight = 36172.707| |-----------------------------------------------------------------------------| r_work (start): 0.3012 rms_B_bonded: 3.18 r_work: 0.2876 rms_B_bonded: 3.59 restraints_weight: 0.5000 r_work (final): 0.2876 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8452 moved from start: 0.4098 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 19185 Z= 0.144 Angle : 0.534 8.933 25976 Z= 0.284 Chirality : 0.042 0.151 2883 Planarity : 0.004 0.059 3292 Dihedral : 4.085 18.871 2627 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 5.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 2.00 % Allowed : 20.91 % Favored : 77.09 % 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 are not related in a simple way. whole: 1.53 (0.18), residues: 2376 helix: 2.25 (0.18), residues: 900 sheet: -0.04 (0.26), residues: 378 loop : 0.49 (0.19), residues: 1098 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 477 TYR 0.026 0.001 TYR B 343 PHE 0.010 0.001 PHE E 541 TRP 0.013 0.001 TRP A 454 HIS 0.004 0.001 HIS F 191 Details of bonding type rmsd covalent geometry : bond 0.00339 (19185) covalent geometry : angle 0.53444 (25976) hydrogen bonds : bond 0.03984 ( 841) hydrogen bonds : angle 4.50466 ( 2307) *********************** 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 469 residues out of total 2094 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 429 time to evaluate : 0.776 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 113 ASP cc_start: 0.8985 (t0) cc_final: 0.8736 (t0) REVERT: A 236 TYR cc_start: 0.8830 (t80) cc_final: 0.8610 (t80) REVERT: A 348 GLN cc_start: 0.8965 (tp40) cc_final: 0.8719 (tp40) REVERT: A 355 ASP cc_start: 0.8937 (t70) cc_final: 0.8432 (t70) REVERT: B 361 GLN cc_start: 0.9146 (pm20) cc_final: 0.8898 (pm20) REVERT: B 363 GLU cc_start: 0.8194 (mm-30) cc_final: 0.7990 (mm-30) REVERT: B 373 ARG cc_start: 0.8744 (mmm160) cc_final: 0.8307 (tpp-160) REVERT: B 477 ARG cc_start: 0.8842 (ttt90) cc_final: 0.7416 (mtt90) REVERT: C 117 ARG cc_start: 0.8950 (mtp85) cc_final: 0.8481 (mtp180) REVERT: C 226 ASP cc_start: 0.7437 (t0) cc_final: 0.6854 (t0) REVERT: C 379 LYS cc_start: 0.9347 (ttpp) cc_final: 0.8990 (tppt) REVERT: C 453 SER cc_start: 0.9343 (t) cc_final: 0.9082 (m) REVERT: C 475 SER cc_start: 0.8727 (m) cc_final: 0.8505 (p) REVERT: C 540 GLU cc_start: 0.8811 (tp30) cc_final: 0.8339 (tp30) REVERT: D 170 THR cc_start: 0.9479 (m) cc_final: 0.9266 (p) REVERT: D 226 ASP cc_start: 0.8419 (t0) cc_final: 0.7943 (t0) REVERT: D 296 GLU cc_start: 0.8546 (tt0) cc_final: 0.8142 (tm-30) REVERT: D 297 LYS cc_start: 0.9239 (ttmt) cc_final: 0.8964 (ttmt) REVERT: D 330 LEU cc_start: 0.9418 (OUTLIER) cc_final: 0.9061 (tt) REVERT: D 348 GLN cc_start: 0.8979 (tp40) cc_final: 0.8548 (tp40) REVERT: D 355 ASP cc_start: 0.9117 (t70) cc_final: 0.8648 (t70) REVERT: D 379 LYS cc_start: 0.9375 (ttpt) cc_final: 0.9131 (ttmm) REVERT: D 453 SER cc_start: 0.9511 (t) cc_final: 0.9133 (m) REVERT: D 477 ARG cc_start: 0.7998 (ttt90) cc_final: 0.5811 (mtt-85) REVERT: D 478 LYS cc_start: 0.9173 (tttt) cc_final: 0.8847 (tppt) REVERT: D 540 GLU cc_start: 0.8922 (tp30) cc_final: 0.8436 (tp30) REVERT: E 111 SER cc_start: 0.9322 (m) cc_final: 0.8804 (p) REVERT: E 226 ASP cc_start: 0.7761 (t0) cc_final: 0.7391 (t0) REVERT: E 232 GLU cc_start: 0.8864 (mm-30) cc_final: 0.8589 (mm-30) REVERT: E 296 GLU cc_start: 0.7516 (tm-30) cc_final: 0.7162 (tm-30) REVERT: E 297 LYS cc_start: 0.8925 (tttt) cc_final: 0.8498 (tppt) REVERT: E 349 LYS cc_start: 0.9253 (ttmm) cc_final: 0.8970 (mttt) REVERT: E 390 ASP cc_start: 0.8115 (t0) cc_final: 0.7856 (t0) REVERT: E 540 GLU cc_start: 0.8962 (tp30) cc_final: 0.8717 (tp30) REVERT: F 355 ASP cc_start: 0.8959 (t70) cc_final: 0.8624 (t70) REVERT: F 422 LEU cc_start: 0.9110 (tt) cc_final: 0.8682 (mp) outliers start: 40 outliers final: 33 residues processed: 453 average time/residue: 0.1447 time to fit residues: 97.5669 Evaluate side-chains 459 residues out of total 2094 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 425 time to evaluate : 0.747 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 137 GLU Chi-restraints excluded: chain A residue 367 VAL Chi-restraints excluded: chain A residue 466 VAL Chi-restraints excluded: chain B residue 122 VAL Chi-restraints excluded: chain B residue 182 LYS Chi-restraints excluded: chain B residue 325 THR Chi-restraints excluded: chain B residue 453 SER Chi-restraints excluded: chain C residue 360 VAL Chi-restraints excluded: chain C residue 367 VAL Chi-restraints excluded: chain C residue 422 LEU Chi-restraints excluded: chain C residue 490 VAL Chi-restraints excluded: chain C residue 503 LEU Chi-restraints excluded: chain D residue 131 VAL Chi-restraints excluded: chain D residue 137 GLU Chi-restraints excluded: chain D residue 138 VAL Chi-restraints excluded: chain D residue 210 THR Chi-restraints excluded: chain D residue 330 LEU Chi-restraints excluded: chain D residue 353 ASP Chi-restraints excluded: chain D residue 367 VAL Chi-restraints excluded: chain D residue 380 LYS Chi-restraints excluded: chain D residue 470 LYS Chi-restraints excluded: chain D residue 490 VAL Chi-restraints excluded: chain E residue 210 THR Chi-restraints excluded: chain E residue 213 LEU Chi-restraints excluded: chain E residue 294 LEU Chi-restraints excluded: chain E residue 301 SER Chi-restraints excluded: chain E residue 367 VAL Chi-restraints excluded: chain E residue 386 THR Chi-restraints excluded: chain E residue 443 MET Chi-restraints excluded: chain E residue 466 VAL Chi-restraints excluded: chain F residue 131 VAL Chi-restraints excluded: chain F residue 137 GLU Chi-restraints excluded: chain F residue 367 VAL Chi-restraints excluded: chain F residue 490 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 63 optimal weight: 1.9990 chunk 106 optimal weight: 2.9990 chunk 20 optimal weight: 2.9990 chunk 65 optimal weight: 6.9990 chunk 131 optimal weight: 5.9990 chunk 27 optimal weight: 4.9990 chunk 138 optimal weight: 0.9990 chunk 156 optimal weight: 4.9990 chunk 38 optimal weight: 10.0000 chunk 52 optimal weight: 10.0000 chunk 78 optimal weight: 5.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 150 ASN ** 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.107437 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3004 r_free = 0.3004 target = 0.084121 restraints weight = 36141.019| |-----------------------------------------------------------------------------| r_work (start): 0.2995 rms_B_bonded: 3.20 r_work: 0.2858 rms_B_bonded: 3.60 restraints_weight: 0.5000 r_work (final): 0.2858 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8468 moved from start: 0.4163 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 19185 Z= 0.171 Angle : 0.552 9.543 25976 Z= 0.294 Chirality : 0.042 0.150 2883 Planarity : 0.004 0.060 3292 Dihedral : 4.150 18.922 2627 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 6.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer: Outliers : 2.35 % Allowed : 20.91 % Favored : 76.74 % 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 are not related in a simple way. whole: 1.48 (0.18), residues: 2376 helix: 2.23 (0.18), residues: 900 sheet: -0.08 (0.26), residues: 378 loop : 0.44 (0.19), residues: 1098 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 477 TYR 0.024 0.001 TYR B 343 PHE 0.011 0.001 PHE E 541 TRP 0.012 0.001 TRP A 454 HIS 0.003 0.001 HIS A 216 Details of bonding type rmsd covalent geometry : bond 0.00405 (19185) covalent geometry : angle 0.55233 (25976) hydrogen bonds : bond 0.04336 ( 841) hydrogen bonds : angle 4.58443 ( 2307) *********************** 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 473 residues out of total 2094 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 426 time to evaluate : 0.664 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 113 ASP cc_start: 0.9007 (t0) cc_final: 0.8762 (t0) REVERT: A 236 TYR cc_start: 0.8830 (t80) cc_final: 0.8609 (t80) REVERT: A 348 GLN cc_start: 0.8987 (tp40) cc_final: 0.8738 (tp40) REVERT: A 355 ASP cc_start: 0.8979 (t70) cc_final: 0.8476 (t70) REVERT: B 361 GLN cc_start: 0.9154 (pm20) cc_final: 0.8900 (pm20) REVERT: B 373 ARG cc_start: 0.8755 (mmm160) cc_final: 0.8319 (tpp-160) REVERT: B 477 ARG cc_start: 0.8834 (ttt90) cc_final: 0.7396 (mtt90) REVERT: C 106 ARG cc_start: 0.8322 (ptm-80) cc_final: 0.8059 (ttp80) REVERT: C 117 ARG cc_start: 0.8967 (mtp85) cc_final: 0.8469 (mtp180) REVERT: C 226 ASP cc_start: 0.7424 (t0) cc_final: 0.6775 (t0) REVERT: C 379 LYS cc_start: 0.9369 (ttpp) cc_final: 0.9022 (tppt) REVERT: C 453 SER cc_start: 0.9341 (t) cc_final: 0.9078 (m) REVERT: C 475 SER cc_start: 0.8713 (m) cc_final: 0.8486 (p) REVERT: D 170 THR cc_start: 0.9491 (m) cc_final: 0.9283 (p) REVERT: D 226 ASP cc_start: 0.8415 (t0) cc_final: 0.7935 (t0) REVERT: D 295 ARG cc_start: 0.9236 (tpp80) cc_final: 0.8988 (mmt90) REVERT: D 296 GLU cc_start: 0.8484 (tt0) cc_final: 0.7859 (tm-30) REVERT: D 297 LYS cc_start: 0.9253 (ttmt) cc_final: 0.8782 (ttmt) REVERT: D 330 LEU cc_start: 0.9424 (OUTLIER) cc_final: 0.9055 (tt) REVERT: D 355 ASP cc_start: 0.9123 (t70) cc_final: 0.8772 (t70) REVERT: D 379 LYS cc_start: 0.9375 (ttpt) cc_final: 0.9138 (ttmm) REVERT: D 441 VAL cc_start: 0.9145 (OUTLIER) cc_final: 0.8877 (p) REVERT: D 453 SER cc_start: 0.9529 (t) cc_final: 0.9158 (m) REVERT: D 477 ARG cc_start: 0.8050 (ttt90) cc_final: 0.5866 (mtt180) REVERT: D 478 LYS cc_start: 0.9190 (tttt) cc_final: 0.8845 (tppt) REVERT: D 540 GLU cc_start: 0.8946 (tp30) cc_final: 0.8439 (tp30) REVERT: E 111 SER cc_start: 0.9344 (m) cc_final: 0.8843 (p) REVERT: E 226 ASP cc_start: 0.7838 (t0) cc_final: 0.7366 (t0) REVERT: E 232 GLU cc_start: 0.8884 (mm-30) cc_final: 0.8607 (mm-30) REVERT: E 296 GLU cc_start: 0.7554 (tm-30) cc_final: 0.7229 (tm-30) REVERT: E 297 LYS cc_start: 0.8941 (tttt) cc_final: 0.8504 (tppt) REVERT: E 349 LYS cc_start: 0.9264 (ttmm) cc_final: 0.8991 (mttt) REVERT: E 355 ASP cc_start: 0.9222 (t0) cc_final: 0.8904 (t0) REVERT: E 390 ASP cc_start: 0.8128 (t0) cc_final: 0.7849 (t0) REVERT: E 540 GLU cc_start: 0.8965 (tp30) cc_final: 0.8708 (tp30) REVERT: F 355 ASP cc_start: 0.8971 (t70) cc_final: 0.8619 (t70) REVERT: F 422 LEU cc_start: 0.9117 (tt) cc_final: 0.8695 (mp) outliers start: 47 outliers final: 39 residues processed: 456 average time/residue: 0.1474 time to fit residues: 99.8548 Evaluate side-chains 460 residues out of total 2094 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 419 time to evaluate : 0.499 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 367 VAL Chi-restraints excluded: chain A residue 466 VAL Chi-restraints excluded: chain B residue 122 VAL Chi-restraints excluded: chain B residue 152 VAL Chi-restraints excluded: chain B residue 182 LYS Chi-restraints excluded: chain B residue 292 LEU Chi-restraints excluded: chain B residue 325 THR Chi-restraints excluded: chain B residue 453 SER Chi-restraints excluded: chain C residue 122 VAL Chi-restraints excluded: chain C residue 360 VAL Chi-restraints excluded: chain C residue 367 VAL Chi-restraints excluded: chain C residue 422 LEU Chi-restraints excluded: chain C residue 457 GLU Chi-restraints excluded: chain C residue 490 VAL Chi-restraints excluded: chain C residue 503 LEU Chi-restraints excluded: chain D residue 131 VAL Chi-restraints excluded: chain D residue 137 GLU Chi-restraints excluded: chain D residue 138 VAL Chi-restraints excluded: chain D residue 210 THR Chi-restraints excluded: chain D residue 294 LEU Chi-restraints excluded: chain D residue 330 LEU Chi-restraints excluded: chain D residue 353 ASP Chi-restraints excluded: chain D residue 367 VAL Chi-restraints excluded: chain D residue 380 LYS Chi-restraints excluded: chain D residue 441 VAL Chi-restraints excluded: chain D residue 470 LYS Chi-restraints excluded: chain D residue 490 VAL Chi-restraints excluded: chain E residue 210 THR Chi-restraints excluded: chain E residue 213 LEU Chi-restraints excluded: chain E residue 294 LEU Chi-restraints excluded: chain E residue 301 SER Chi-restraints excluded: chain E residue 367 VAL Chi-restraints excluded: chain E residue 386 THR Chi-restraints excluded: chain E residue 443 MET Chi-restraints excluded: chain E residue 466 VAL Chi-restraints excluded: chain E residue 490 VAL Chi-restraints excluded: chain E residue 518 ILE Chi-restraints excluded: chain F residue 131 VAL Chi-restraints excluded: chain F residue 301 SER Chi-restraints excluded: chain F residue 367 VAL Chi-restraints excluded: chain F residue 490 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 133 optimal weight: 0.0370 chunk 144 optimal weight: 2.9990 chunk 212 optimal weight: 8.9990 chunk 188 optimal weight: 3.9990 chunk 72 optimal weight: 1.9990 chunk 62 optimal weight: 0.9980 chunk 96 optimal weight: 0.2980 chunk 121 optimal weight: 0.9980 chunk 127 optimal weight: 0.9990 chunk 75 optimal weight: 0.1980 chunk 125 optimal weight: 7.9990 overall best weight: 0.5058 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 531 ASN B 391 ASN D 391 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.112553 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3093 r_free = 0.3093 target = 0.089215 restraints weight = 35618.651| |-----------------------------------------------------------------------------| r_work (start): 0.3084 rms_B_bonded: 3.23 r_work: 0.2952 rms_B_bonded: 3.64 restraints_weight: 0.5000 r_work (final): 0.2952 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8385 moved from start: 0.4134 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.052 19185 Z= 0.097 Angle : 0.524 10.896 25976 Z= 0.274 Chirality : 0.041 0.153 2883 Planarity : 0.004 0.058 3292 Dihedral : 3.839 18.490 2627 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 5.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.81 % Favored : 98.19 % Rotamer: Outliers : 1.50 % Allowed : 22.11 % Favored : 76.39 % 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 are not related in a simple way. whole: 1.60 (0.18), residues: 2376 helix: 2.25 (0.18), residues: 900 sheet: 0.05 (0.28), residues: 354 loop : 0.54 (0.19), residues: 1122 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 477 TYR 0.026 0.001 TYR B 343 PHE 0.011 0.001 PHE B 374 TRP 0.015 0.001 TRP E 454 HIS 0.003 0.001 HIS F 191 Details of bonding type rmsd covalent geometry : bond 0.00223 (19185) covalent geometry : angle 0.52424 (25976) hydrogen bonds : bond 0.02950 ( 841) hydrogen bonds : angle 4.17602 ( 2307) ********************** 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 506 residues out of total 2094 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 476 time to evaluate : 0.566 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 348 GLN cc_start: 0.8905 (tp40) cc_final: 0.8653 (tp40) REVERT: A 355 ASP cc_start: 0.8761 (t70) cc_final: 0.8288 (t70) REVERT: A 386 THR cc_start: 0.8772 (p) cc_final: 0.8513 (p) REVERT: A 422 LEU cc_start: 0.9127 (tt) cc_final: 0.8881 (mt) REVERT: A 540 GLU cc_start: 0.9158 (tp30) cc_final: 0.8605 (tp30) REVERT: B 106 ARG cc_start: 0.8364 (ptm-80) cc_final: 0.8127 (ptm-80) REVERT: B 117 ARG cc_start: 0.8422 (mtp180) cc_final: 0.6999 (ttt180) REVERT: B 477 ARG cc_start: 0.8735 (ttt90) cc_final: 0.7294 (mtt180) REVERT: C 106 ARG cc_start: 0.8294 (ptm-80) cc_final: 0.7897 (ttp80) REVERT: C 204 GLU cc_start: 0.8309 (tm-30) cc_final: 0.8063 (tm-30) REVERT: C 226 ASP cc_start: 0.7183 (t0) cc_final: 0.6640 (t0) REVERT: C 379 LYS cc_start: 0.9313 (ttpp) cc_final: 0.8954 (tppt) REVERT: C 386 THR cc_start: 0.9136 (m) cc_final: 0.8655 (p) REVERT: C 453 SER cc_start: 0.9268 (t) cc_final: 0.9036 (m) REVERT: C 540 GLU cc_start: 0.8773 (tp30) cc_final: 0.8348 (tp30) REVERT: D 226 ASP cc_start: 0.8337 (t0) cc_final: 0.7839 (t0) REVERT: D 295 ARG cc_start: 0.9236 (tpp80) cc_final: 0.8978 (mmt90) REVERT: D 296 GLU cc_start: 0.8547 (tt0) cc_final: 0.8062 (tm-30) REVERT: D 297 LYS cc_start: 0.9271 (ttmt) cc_final: 0.8787 (ttmt) REVERT: D 330 LEU cc_start: 0.9409 (OUTLIER) cc_final: 0.9039 (tt) REVERT: D 355 ASP cc_start: 0.8996 (t70) cc_final: 0.8771 (t70) REVERT: D 379 LYS cc_start: 0.9309 (ttpt) cc_final: 0.9062 (ttmm) REVERT: D 441 VAL cc_start: 0.9053 (t) cc_final: 0.8783 (p) REVERT: D 453 SER cc_start: 0.9463 (t) cc_final: 0.9105 (m) REVERT: D 477 ARG cc_start: 0.8021 (ttt90) cc_final: 0.5815 (mtt180) REVERT: D 478 LYS cc_start: 0.9118 (tttt) cc_final: 0.8829 (tppt) REVERT: D 540 GLU cc_start: 0.8943 (tp30) cc_final: 0.8558 (tp30) REVERT: E 187 ILE cc_start: 0.9224 (mt) cc_final: 0.8958 (tp) REVERT: E 226 ASP cc_start: 0.7732 (t0) cc_final: 0.7230 (t0) REVERT: E 232 GLU cc_start: 0.8887 (mm-30) cc_final: 0.8590 (mm-30) REVERT: E 296 GLU cc_start: 0.7772 (tm-30) cc_final: 0.7379 (tm-30) REVERT: E 297 LYS cc_start: 0.8949 (tttt) cc_final: 0.8490 (tppt) REVERT: E 345 ASP cc_start: 0.9282 (p0) cc_final: 0.9048 (p0) REVERT: E 355 ASP cc_start: 0.9031 (t0) cc_final: 0.8810 (t0) REVERT: E 390 ASP cc_start: 0.7991 (t0) cc_final: 0.7591 (t0) REVERT: F 355 ASP cc_start: 0.8797 (t70) cc_final: 0.8482 (t70) REVERT: F 422 LEU cc_start: 0.9164 (tt) cc_final: 0.8759 (mp) outliers start: 30 outliers final: 24 residues processed: 497 average time/residue: 0.1402 time to fit residues: 103.9701 Evaluate side-chains 475 residues out of total 2094 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 450 time to evaluate : 0.493 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 367 VAL Chi-restraints excluded: chain B residue 122 VAL Chi-restraints excluded: chain B residue 325 THR Chi-restraints excluded: chain B residue 453 SER Chi-restraints excluded: chain C residue 360 VAL Chi-restraints excluded: chain C residue 367 VAL Chi-restraints excluded: chain C residue 490 VAL Chi-restraints excluded: chain C residue 503 LEU Chi-restraints excluded: chain D residue 131 VAL Chi-restraints excluded: chain D residue 137 GLU Chi-restraints excluded: chain D residue 138 VAL Chi-restraints excluded: chain D residue 294 LEU Chi-restraints excluded: chain D residue 330 LEU Chi-restraints excluded: chain D residue 367 VAL Chi-restraints excluded: chain D residue 470 LYS Chi-restraints excluded: chain E residue 210 THR Chi-restraints excluded: chain E residue 213 LEU Chi-restraints excluded: chain E residue 367 VAL Chi-restraints excluded: chain E residue 466 VAL Chi-restraints excluded: chain E residue 490 VAL Chi-restraints excluded: chain E residue 518 ILE Chi-restraints excluded: chain F residue 131 VAL Chi-restraints excluded: chain F residue 301 SER Chi-restraints excluded: chain F residue 367 VAL Chi-restraints excluded: chain F residue 490 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 26 optimal weight: 6.9990 chunk 166 optimal weight: 4.9990 chunk 165 optimal weight: 6.9990 chunk 148 optimal weight: 0.3980 chunk 129 optimal weight: 3.9990 chunk 1 optimal weight: 5.9990 chunk 167 optimal weight: 6.9990 chunk 19 optimal weight: 0.9980 chunk 89 optimal weight: 2.9990 chunk 188 optimal weight: 3.9990 chunk 234 optimal weight: 0.8980 overall best weight: 1.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 391 ASN D 391 ASN E 391 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.109264 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3046 r_free = 0.3046 target = 0.086069 restraints weight = 35865.889| |-----------------------------------------------------------------------------| r_work (start): 0.3039 rms_B_bonded: 3.20 r_work: 0.2905 rms_B_bonded: 3.60 restraints_weight: 0.5000 r_work (final): 0.2905 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8439 moved from start: 0.4185 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= 0.133 Angle : 0.549 9.655 25976 Z= 0.288 Chirality : 0.042 0.191 2883 Planarity : 0.004 0.058 3292 Dihedral : 3.874 18.005 2627 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 6.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 1.35 % Allowed : 22.26 % Favored : 76.39 % 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 are not related in a simple way. whole: 1.66 (0.18), residues: 2376 helix: 2.32 (0.18), residues: 900 sheet: 0.09 (0.26), residues: 378 loop : 0.56 (0.19), residues: 1098 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG E 295 TYR 0.024 0.001 TYR B 343 PHE 0.009 0.001 PHE B 374 TRP 0.010 0.001 TRP F 454 HIS 0.007 0.001 HIS B 191 Details of bonding type rmsd covalent geometry : bond 0.00317 (19185) covalent geometry : angle 0.54867 (25976) hydrogen bonds : bond 0.03629 ( 841) hydrogen bonds : angle 4.33786 ( 2307) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4620.28 seconds wall clock time: 80 minutes 35.71 seconds (4835.71 seconds total)