Starting phenix.real_space_refine on Sun Mar 17 19:46:47 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ulw_26595/03_2024/7ulw_26595.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ulw_26595/03_2024/7ulw_26595.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ulw_26595/03_2024/7ulw_26595.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ulw_26595/03_2024/7ulw_26595.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ulw_26595/03_2024/7ulw_26595.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ulw_26595/03_2024/7ulw_26595.pdb" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 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 Symmetric amino acids flipped None Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 18766 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 3128 Number of conformers: 1 Conformer: "" Number of residues, atoms: 400, 3128 Classifications: {'peptide': 400} Incomplete info: {'truncation_to_alanine': 16} Link IDs: {'PTRANS': 17, 'TRANS': 382} Chain breaks: 1 Unresolved non-hydrogen bonds: 61 Unresolved non-hydrogen angles: 69 Unresolved non-hydrogen dihedrals: 53 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 7} Unresolved non-hydrogen planarities: 28 Chain: "B" Number of atoms: 3124 Number of conformers: 1 Conformer: "" Number of residues, atoms: 400, 3124 Classifications: {'peptide': 400} Incomplete info: {'truncation_to_alanine': 16} Link IDs: {'PTRANS': 17, 'TRANS': 382} Chain breaks: 1 Unresolved non-hydrogen bonds: 66 Unresolved non-hydrogen angles: 76 Unresolved non-hydrogen dihedrals: 59 Planarities with less than four sites: {'TYR:plan': 1, 'GLU:plan': 7} Unresolved non-hydrogen planarities: 35 Chain: "C" Number of atoms: 3135 Number of conformers: 1 Conformer: "" Number of residues, atoms: 400, 3135 Classifications: {'peptide': 400} Incomplete info: {'truncation_to_alanine': 14} Link IDs: {'PTRANS': 17, 'TRANS': 382} Chain breaks: 1 Unresolved non-hydrogen bonds: 54 Unresolved non-hydrogen angles: 60 Unresolved non-hydrogen dihedrals: 48 Planarities with less than four sites: {'GLU:plan': 6} Unresolved non-hydrogen planarities: 24 Chain: "D" Number of atoms: 3128 Number of conformers: 1 Conformer: "" Number of residues, atoms: 400, 3128 Classifications: {'peptide': 400} Incomplete info: {'truncation_to_alanine': 16} Link IDs: {'PTRANS': 17, 'TRANS': 382} Chain breaks: 1 Unresolved non-hydrogen bonds: 61 Unresolved non-hydrogen angles: 69 Unresolved non-hydrogen dihedrals: 53 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 7} Unresolved non-hydrogen planarities: 28 Chain: "E" Number of atoms: 3127 Number of conformers: 1 Conformer: "" Number of residues, atoms: 400, 3127 Classifications: {'peptide': 400} Incomplete info: {'truncation_to_alanine': 16} Link IDs: {'PTRANS': 17, 'TRANS': 382} Chain breaks: 1 Unresolved non-hydrogen bonds: 62 Unresolved non-hydrogen angles: 70 Unresolved non-hydrogen dihedrals: 54 Planarities with less than four sites: {'GLU:plan': 8} Unresolved non-hydrogen planarities: 32 Chain: "F" Number of atoms: 3124 Number of conformers: 1 Conformer: "" Number of residues, atoms: 400, 3124 Classifications: {'peptide': 400} Incomplete info: {'truncation_to_alanine': 17} Link IDs: {'PTRANS': 17, 'TRANS': 382} Chain breaks: 1 Unresolved non-hydrogen bonds: 65 Unresolved non-hydrogen angles: 74 Unresolved non-hydrogen dihedrals: 56 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 8} Unresolved non-hydrogen planarities: 32 Time building chain proxies: 10.08, per 1000 atoms: 0.54 Number of scatterers: 18766 At special positions: 0 Unit cell: (155.188, 133.839, 142.05, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 102 16.00 O 3453 8.00 N 3180 7.00 C 12031 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 6.96 Conformation dependent library (CDL) restraints added in 3.4 seconds 4752 Ramachandran restraints generated. 2376 Oldfield, 0 Emsley, 2376 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4464 Finding SS restraints... Secondary structure from input PDB file: 90 helices and 24 sheets defined 40.8% alpha, 14.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.30 Creating SS restraints... Processing helix chain 'A' and resid 99 through 104 Processing helix chain 'A' and resid 106 through 123 Processing helix chain 'A' and resid 164 through 180 removed outlier: 3.518A pdb=" N ALA A 180 " --> pdb=" O LYS A 176 " (cutoff:3.500A) Processing helix chain 'A' and resid 188 through 192 Processing helix chain 'A' and resid 209 through 215 Processing helix chain 'A' and resid 226 through 242 Processing helix chain 'A' and resid 300 through 305 removed outlier: 3.537A pdb=" N SER A 304 " --> pdb=" O ASN A 300 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N LEU A 305 " --> pdb=" O SER A 301 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 300 through 305' Processing helix chain 'A' and resid 306 through 308 No H-bonds generated for 'chain 'A' and resid 306 through 308' Processing helix chain 'A' and resid 325 through 340 Processing helix chain 'A' and resid 342 through 354 Processing helix chain 'A' and resid 391 through 395 removed outlier: 4.144A pdb=" N TRP A 395 " --> pdb=" O SER A 392 " (cutoff:3.500A) Processing helix chain 'A' and resid 403 through 424 removed outlier: 4.683A pdb=" N GLY A 421 " --> pdb=" O GLY A 417 " (cutoff:3.500A) removed outlier: 5.265A pdb=" N LEU A 422 " --> pdb=" O TYR A 418 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N PHE A 423 " --> pdb=" O GLN A 419 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N LYS A 424 " --> pdb=" O VAL A 420 " (cutoff:3.500A) Processing helix chain 'A' and resid 436 through 443 Processing helix chain 'A' and resid 506 through 510 Processing helix chain 'A' and resid 530 through 545 Processing helix chain 'B' and resid 100 through 104 Processing helix chain 'B' and resid 106 through 123 Processing helix chain 'B' and resid 164 through 180 removed outlier: 3.518A pdb=" N ALA B 180 " --> pdb=" O LYS B 176 " (cutoff:3.500A) Processing helix chain 'B' and resid 188 through 192 Processing helix chain 'B' and resid 209 through 215 Processing helix chain 'B' and resid 226 through 242 Processing helix chain 'B' and resid 300 through 305 removed outlier: 3.537A pdb=" N SER B 304 " --> pdb=" O ASN B 300 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N LEU B 305 " --> pdb=" O SER B 301 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 300 through 305' Processing helix chain 'B' and resid 306 through 308 No H-bonds generated for 'chain 'B' and resid 306 through 308' Processing helix chain 'B' and resid 325 through 340 Processing helix chain 'B' and resid 342 through 354 Processing helix chain 'B' and resid 391 through 395 removed outlier: 4.144A pdb=" N TRP B 395 " --> pdb=" O SER B 392 " (cutoff:3.500A) Processing helix chain 'B' and resid 403 through 424 removed outlier: 4.683A pdb=" N GLY B 421 " --> pdb=" O GLY B 417 " (cutoff:3.500A) removed outlier: 5.265A pdb=" N LEU B 422 " --> pdb=" O TYR B 418 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N PHE B 423 " --> pdb=" O GLN B 419 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N LYS B 424 " --> pdb=" O VAL B 420 " (cutoff:3.500A) Processing helix chain 'B' and resid 436 through 443 Processing helix chain 'B' and resid 506 through 510 Processing helix chain 'B' and resid 530 through 545 Processing helix chain 'C' and resid 100 through 104 Processing helix chain 'C' and resid 106 through 123 Processing helix chain 'C' and resid 164 through 180 removed outlier: 3.518A pdb=" N ALA C 180 " --> pdb=" O LYS C 176 " (cutoff:3.500A) Processing helix chain 'C' and resid 188 through 192 Processing helix chain 'C' and resid 209 through 215 Processing helix chain 'C' and resid 226 through 242 Processing helix chain 'C' and resid 300 through 305 removed outlier: 3.537A pdb=" N SER C 304 " --> pdb=" O ASN C 300 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N LEU C 305 " --> pdb=" O SER C 301 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 300 through 305' Processing helix chain 'C' and resid 306 through 308 No H-bonds generated for 'chain 'C' and resid 306 through 308' Processing helix chain 'C' and resid 325 through 340 Processing helix chain 'C' and resid 342 through 354 Processing helix chain 'C' and resid 391 through 395 removed outlier: 4.144A pdb=" N TRP C 395 " --> pdb=" O SER C 392 " (cutoff:3.500A) Processing helix chain 'C' and resid 403 through 424 removed outlier: 4.683A pdb=" N GLY C 421 " --> pdb=" O GLY C 417 " (cutoff:3.500A) removed outlier: 5.264A pdb=" N LEU C 422 " --> pdb=" O TYR C 418 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N PHE C 423 " --> pdb=" O GLN C 419 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N LYS C 424 " --> pdb=" O VAL C 420 " (cutoff:3.500A) Processing helix chain 'C' and resid 436 through 443 Processing helix chain 'C' and resid 506 through 510 Processing helix chain 'C' and resid 530 through 545 Processing helix chain 'D' and resid 100 through 104 Processing helix chain 'D' and resid 106 through 123 Processing helix chain 'D' and resid 164 through 180 removed outlier: 3.518A pdb=" N ALA D 180 " --> pdb=" O LYS D 176 " (cutoff:3.500A) Processing helix chain 'D' and resid 188 through 192 Processing helix chain 'D' and resid 209 through 215 Processing helix chain 'D' and resid 226 through 242 Processing helix chain 'D' and resid 300 through 305 removed outlier: 3.537A pdb=" N SER D 304 " --> pdb=" O ASN D 300 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N LEU D 305 " --> pdb=" O SER D 301 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 300 through 305' Processing helix chain 'D' and resid 306 through 308 No H-bonds generated for 'chain 'D' and resid 306 through 308' Processing helix chain 'D' and resid 325 through 340 Processing helix chain 'D' and resid 342 through 354 Processing helix chain 'D' and resid 391 through 395 removed outlier: 4.144A pdb=" N TRP D 395 " --> pdb=" O SER D 392 " (cutoff:3.500A) Processing helix chain 'D' and resid 403 through 424 removed outlier: 4.683A pdb=" N GLY D 421 " --> pdb=" O GLY D 417 " (cutoff:3.500A) removed outlier: 5.264A pdb=" N LEU D 422 " --> pdb=" O TYR D 418 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N PHE D 423 " --> pdb=" O GLN D 419 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N LYS D 424 " --> pdb=" O VAL D 420 " (cutoff:3.500A) Processing helix chain 'D' and resid 436 through 443 Processing helix chain 'D' and resid 506 through 510 Processing helix chain 'D' and resid 530 through 545 Processing helix chain 'E' and resid 100 through 104 Processing helix chain 'E' and resid 106 through 123 Processing helix chain 'E' and resid 164 through 180 removed outlier: 3.519A pdb=" N ALA E 180 " --> pdb=" O LYS E 176 " (cutoff:3.500A) Processing helix chain 'E' and resid 188 through 192 Processing helix chain 'E' and resid 209 through 215 Processing helix chain 'E' and resid 226 through 242 Processing helix chain 'E' and resid 300 through 305 removed outlier: 3.537A pdb=" N SER E 304 " --> pdb=" O ASN E 300 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N LEU E 305 " --> pdb=" O SER E 301 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 300 through 305' Processing helix chain 'E' and resid 306 through 308 No H-bonds generated for 'chain 'E' and resid 306 through 308' Processing helix chain 'E' and resid 325 through 340 Processing helix chain 'E' and resid 342 through 354 Processing helix chain 'E' and resid 391 through 395 removed outlier: 4.143A pdb=" N TRP E 395 " --> pdb=" O SER E 392 " (cutoff:3.500A) Processing helix chain 'E' and resid 403 through 424 removed outlier: 4.683A pdb=" N GLY E 421 " --> pdb=" O GLY E 417 " (cutoff:3.500A) removed outlier: 5.263A pdb=" N LEU E 422 " --> pdb=" O TYR E 418 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N PHE E 423 " --> pdb=" O GLN E 419 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N LYS E 424 " --> pdb=" O VAL E 420 " (cutoff:3.500A) Processing helix chain 'E' and resid 436 through 443 Processing helix chain 'E' and resid 506 through 510 Processing helix chain 'E' and resid 530 through 545 Processing helix chain 'F' and resid 100 through 104 Processing helix chain 'F' and resid 106 through 123 Processing helix chain 'F' and resid 164 through 180 removed outlier: 3.518A pdb=" N ALA F 180 " --> pdb=" O LYS F 176 " (cutoff:3.500A) Processing helix chain 'F' and resid 188 through 192 Processing helix chain 'F' and resid 209 through 215 Processing helix chain 'F' and resid 226 through 242 Processing helix chain 'F' and resid 300 through 305 removed outlier: 3.537A pdb=" N SER F 304 " --> pdb=" O ASN F 300 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N LEU F 305 " --> pdb=" O SER F 301 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 300 through 305' Processing helix chain 'F' and resid 306 through 308 No H-bonds generated for 'chain 'F' and resid 306 through 308' Processing helix chain 'F' and resid 325 through 340 Processing helix chain 'F' and resid 342 through 354 Processing helix chain 'F' and resid 391 through 395 removed outlier: 4.144A pdb=" N TRP F 395 " --> pdb=" O SER F 392 " (cutoff:3.500A) Processing helix chain 'F' and resid 403 through 424 removed outlier: 4.683A pdb=" N GLY F 421 " --> pdb=" O GLY F 417 " (cutoff:3.500A) removed outlier: 5.264A pdb=" N LEU F 422 " --> pdb=" O TYR F 418 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N PHE F 423 " --> pdb=" O GLN F 419 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N LYS F 424 " --> pdb=" O VAL F 420 " (cutoff:3.500A) Processing helix chain 'F' and resid 436 through 443 Processing helix chain 'F' and resid 506 through 510 Processing helix chain 'F' and resid 530 through 545 Processing sheet with id=AA1, first strand: chain 'A' and resid 152 through 153 removed outlier: 7.344A pdb=" N VAL A 131 " --> pdb=" O VAL A 138 " (cutoff:3.500A) removed outlier: 4.650A pdb=" N SER A 140 " --> pdb=" O VAL A 129 " (cutoff:3.500A) removed outlier: 6.999A pdb=" N VAL A 129 " --> pdb=" O SER A 140 " (cutoff:3.500A) removed outlier: 4.613A pdb=" N GLY A 142 " --> pdb=" O ILE A 127 " (cutoff:3.500A) removed outlier: 6.683A pdb=" N ILE A 127 " --> pdb=" O GLY A 142 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N ALA A 492 " --> pdb=" O ALA A 489 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N TRP A 464 " --> pdb=" O ALA A 461 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 160 through 161 Processing sheet with id=AA3, first strand: chain 'A' and resid 200 through 201 Processing sheet with id=AA4, first strand: chain 'A' and resid 375 through 377 Processing sheet with id=AA5, first strand: chain 'B' and resid 152 through 153 removed outlier: 7.344A pdb=" N VAL B 131 " --> pdb=" O VAL B 138 " (cutoff:3.500A) removed outlier: 4.649A pdb=" N SER B 140 " --> pdb=" O VAL B 129 " (cutoff:3.500A) removed outlier: 6.998A pdb=" N VAL B 129 " --> pdb=" O SER B 140 " (cutoff:3.500A) removed outlier: 4.614A pdb=" N GLY B 142 " --> pdb=" O ILE B 127 " (cutoff:3.500A) removed outlier: 6.684A pdb=" N ILE B 127 " --> pdb=" O GLY B 142 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N ALA B 492 " --> pdb=" O ALA B 489 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N TRP B 464 " --> pdb=" O ALA B 461 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 160 through 161 Processing sheet with id=AA7, first strand: chain 'B' and resid 200 through 201 Processing sheet with id=AA8, first strand: chain 'B' and resid 375 through 377 Processing sheet with id=AA9, first strand: chain 'C' and resid 152 through 153 removed outlier: 7.344A pdb=" N VAL C 131 " --> pdb=" O VAL C 138 " (cutoff:3.500A) removed outlier: 4.650A pdb=" N SER C 140 " --> pdb=" O VAL C 129 " (cutoff:3.500A) removed outlier: 6.999A pdb=" N VAL C 129 " --> pdb=" O SER C 140 " (cutoff:3.500A) removed outlier: 4.614A pdb=" N GLY C 142 " --> pdb=" O ILE C 127 " (cutoff:3.500A) removed outlier: 6.685A pdb=" N ILE C 127 " --> pdb=" O GLY C 142 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N ALA C 492 " --> pdb=" O ALA C 489 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N TRP C 464 " --> pdb=" O ALA C 461 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 160 through 161 Processing sheet with id=AB2, first strand: chain 'C' and resid 200 through 201 Processing sheet with id=AB3, first strand: chain 'C' and resid 375 through 377 Processing sheet with id=AB4, first strand: chain 'D' and resid 152 through 153 removed outlier: 7.344A pdb=" N VAL D 131 " --> pdb=" O VAL D 138 " (cutoff:3.500A) removed outlier: 4.651A pdb=" N SER D 140 " --> pdb=" O VAL D 129 " (cutoff:3.500A) removed outlier: 6.998A pdb=" N VAL D 129 " --> pdb=" O SER D 140 " (cutoff:3.500A) removed outlier: 4.614A pdb=" N GLY D 142 " --> pdb=" O ILE D 127 " (cutoff:3.500A) removed outlier: 6.683A pdb=" N ILE D 127 " --> pdb=" O GLY D 142 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N ALA D 492 " --> pdb=" O ALA D 489 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N TRP D 464 " --> pdb=" O ALA D 461 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 160 through 161 Processing sheet with id=AB6, first strand: chain 'D' and resid 200 through 201 Processing sheet with id=AB7, first strand: chain 'D' and resid 375 through 377 Processing sheet with id=AB8, first strand: chain 'E' and resid 152 through 153 removed outlier: 7.344A pdb=" N VAL E 131 " --> pdb=" O VAL E 138 " (cutoff:3.500A) removed outlier: 4.650A pdb=" N SER E 140 " --> pdb=" O VAL E 129 " (cutoff:3.500A) removed outlier: 6.998A pdb=" N VAL E 129 " --> pdb=" O SER E 140 " (cutoff:3.500A) removed outlier: 4.612A pdb=" N GLY E 142 " --> pdb=" O ILE E 127 " (cutoff:3.500A) removed outlier: 6.684A pdb=" N ILE E 127 " --> pdb=" O GLY E 142 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N ALA E 492 " --> pdb=" O ALA E 489 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N TRP E 464 " --> pdb=" O ALA E 461 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'E' and resid 160 through 161 Processing sheet with id=AC1, first strand: chain 'E' and resid 200 through 201 Processing sheet with id=AC2, first strand: chain 'E' and resid 375 through 377 Processing sheet with id=AC3, first strand: chain 'F' and resid 152 through 153 removed outlier: 7.344A pdb=" N VAL F 131 " --> pdb=" O VAL F 138 " (cutoff:3.500A) removed outlier: 4.650A pdb=" N SER F 140 " --> pdb=" O VAL F 129 " (cutoff:3.500A) removed outlier: 6.998A pdb=" N VAL F 129 " --> pdb=" O SER F 140 " (cutoff:3.500A) removed outlier: 4.612A pdb=" N GLY F 142 " --> pdb=" O ILE F 127 " (cutoff:3.500A) removed outlier: 6.684A pdb=" N ILE F 127 " --> pdb=" O GLY F 142 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N ALA F 492 " --> pdb=" O ALA F 489 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N TRP F 464 " --> pdb=" O ALA F 461 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'F' and resid 160 through 161 Processing sheet with id=AC5, first strand: chain 'F' and resid 200 through 201 Processing sheet with id=AC6, first strand: chain 'F' and resid 375 through 377 841 hydrogen bonds defined for protein. 2307 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 5.73 Time building geometry restraints manager: 7.59 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 6010 1.34 - 1.46: 4284 1.46 - 1.58: 8723 1.58 - 1.69: 0 1.69 - 1.81: 168 Bond restraints: 19185 Sorted by residual: bond pdb=" C PRO E 513 " pdb=" N PRO E 514 " ideal model delta sigma weight residual 1.334 1.367 -0.033 2.34e-02 1.83e+03 1.98e+00 bond pdb=" C PRO F 513 " pdb=" N PRO F 514 " ideal model delta sigma weight residual 1.334 1.367 -0.033 2.34e-02 1.83e+03 1.98e+00 bond pdb=" C PRO B 513 " pdb=" N PRO B 514 " ideal model delta sigma weight residual 1.334 1.366 -0.033 2.34e-02 1.83e+03 1.94e+00 bond pdb=" C PRO C 513 " pdb=" N PRO C 514 " ideal model delta sigma weight residual 1.334 1.366 -0.032 2.34e-02 1.83e+03 1.93e+00 bond pdb=" C PRO D 513 " pdb=" N PRO D 514 " ideal model delta sigma weight residual 1.334 1.366 -0.032 2.34e-02 1.83e+03 1.90e+00 ... (remaining 19180 not shown) Histogram of bond angle deviations from ideal: 100.56 - 107.25: 647 107.25 - 113.94: 10694 113.94 - 120.63: 7755 120.63 - 127.32: 6670 127.32 - 134.01: 210 Bond angle restraints: 25976 Sorted by residual: angle pdb=" N PRO F 513 " pdb=" CA PRO F 513 " pdb=" C PRO F 513 " ideal model delta sigma weight residual 110.70 114.03 -3.33 1.22e+00 6.72e-01 7.46e+00 angle pdb=" N PRO D 513 " pdb=" CA PRO D 513 " pdb=" C PRO D 513 " ideal model delta sigma weight residual 110.70 113.99 -3.29 1.22e+00 6.72e-01 7.29e+00 angle pdb=" N PRO A 513 " pdb=" CA PRO A 513 " pdb=" C PRO A 513 " ideal model delta sigma weight residual 110.70 113.99 -3.29 1.22e+00 6.72e-01 7.27e+00 angle pdb=" N PRO E 513 " pdb=" CA PRO E 513 " pdb=" C PRO E 513 " ideal model delta sigma weight residual 110.70 113.98 -3.28 1.22e+00 6.72e-01 7.21e+00 angle pdb=" N PRO B 513 " pdb=" CA PRO B 513 " pdb=" C PRO B 513 " ideal model delta sigma weight residual 110.70 113.96 -3.26 1.22e+00 6.72e-01 7.16e+00 ... (remaining 25971 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.97: 10511 17.97 - 35.95: 844 35.95 - 53.92: 117 53.92 - 71.90: 18 71.90 - 89.87: 24 Dihedral angle restraints: 11514 sinusoidal: 4537 harmonic: 6977 Sorted by residual: dihedral pdb=" CB GLU B 363 " pdb=" CG GLU B 363 " pdb=" CD GLU B 363 " pdb=" OE1 GLU B 363 " ideal model delta sinusoidal sigma weight residual 0.00 89.87 -89.87 1 3.00e+01 1.11e-03 1.06e+01 dihedral pdb=" CB GLU A 363 " pdb=" CG GLU A 363 " pdb=" CD GLU A 363 " pdb=" OE1 GLU A 363 " ideal model delta sinusoidal sigma weight residual 0.00 89.85 -89.85 1 3.00e+01 1.11e-03 1.06e+01 dihedral pdb=" CB GLU C 363 " pdb=" CG GLU C 363 " pdb=" CD GLU C 363 " pdb=" OE1 GLU C 363 " ideal model delta sinusoidal sigma weight residual 0.00 89.80 -89.80 1 3.00e+01 1.11e-03 1.06e+01 ... (remaining 11511 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.028: 1859 0.028 - 0.056: 642 0.056 - 0.085: 183 0.085 - 0.113: 133 0.113 - 0.141: 66 Chirality restraints: 2883 Sorted by residual: chirality pdb=" CA VAL E 376 " pdb=" N VAL E 376 " pdb=" C VAL E 376 " pdb=" CB VAL E 376 " both_signs ideal model delta sigma weight residual False 2.44 2.58 -0.14 2.00e-01 2.50e+01 4.97e-01 chirality pdb=" CA VAL D 376 " pdb=" N VAL D 376 " pdb=" C VAL D 376 " pdb=" CB VAL D 376 " both_signs ideal model delta sigma weight residual False 2.44 2.58 -0.14 2.00e-01 2.50e+01 4.96e-01 chirality pdb=" CA VAL C 376 " pdb=" N VAL C 376 " pdb=" C VAL C 376 " pdb=" CB VAL C 376 " both_signs ideal model delta sigma weight residual False 2.44 2.58 -0.14 2.00e-01 2.50e+01 4.95e-01 ... (remaining 2880 not shown) Planarity restraints: 3292 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PRO B 513 " -0.018 5.00e-02 4.00e+02 2.77e-02 1.23e+00 pdb=" N PRO B 514 " 0.048 5.00e-02 4.00e+02 pdb=" CA PRO B 514 " -0.014 5.00e-02 4.00e+02 pdb=" CD PRO B 514 " -0.016 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO A 513 " -0.018 5.00e-02 4.00e+02 2.76e-02 1.22e+00 pdb=" N PRO A 514 " 0.048 5.00e-02 4.00e+02 pdb=" CA PRO A 514 " -0.014 5.00e-02 4.00e+02 pdb=" CD PRO A 514 " -0.016 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO F 513 " 0.018 5.00e-02 4.00e+02 2.75e-02 1.21e+00 pdb=" N PRO F 514 " -0.048 5.00e-02 4.00e+02 pdb=" CA PRO F 514 " 0.014 5.00e-02 4.00e+02 pdb=" CD PRO F 514 " 0.016 5.00e-02 4.00e+02 ... (remaining 3289 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.77: 3137 2.77 - 3.30: 17435 3.30 - 3.83: 30488 3.83 - 4.37: 34611 4.37 - 4.90: 60990 Nonbonded interactions: 146661 Sorted by model distance: nonbonded pdb=" OE2 GLU D 137 " pdb=" OG SER D 140 " model vdw 2.235 2.440 nonbonded pdb=" OE2 GLU C 137 " pdb=" OG SER C 140 " model vdw 2.236 2.440 nonbonded pdb=" OE2 GLU E 137 " pdb=" OG SER E 140 " model vdw 2.236 2.440 nonbonded pdb=" OE2 GLU F 137 " pdb=" OG SER F 140 " model vdw 2.236 2.440 nonbonded pdb=" OE2 GLU A 137 " pdb=" OG SER A 140 " model vdw 2.236 2.440 ... (remaining 146656 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 99 through 204 or (resid 205 and (name N or name CA or nam \ e C or name O or name CB )) or resid 206 through 231 or (resid 232 through 233 a \ nd (name N or name CA or name C or name O or name CB )) or resid 234 through 235 \ or (resid 236 through 291 and (name N or name CA or name C or name O or name CB \ )) or resid 292 through 298 or (resid 299 and (name N or name CA or name C or n \ ame O or name CB )) or resid 300 through 456 or (resid 457 and (name N or name C \ A or name C or name O or name CB )) or resid 458 through 546)) selection = (chain 'B' and (resid 99 through 120 or (resid 121 and (name N or name CA or nam \ e C or name O or name CB )) or resid 122 through 224 or (resid 225 and (name N o \ r name CA or name C or name O or name CB )) or resid 226 through 238 or (resid 2 \ 39 through 291 and (name N or name CA or name C or name O or name CB )) or resid \ 292 through 450 or (resid 451 and (name N or name CA or name C or name O or nam \ e CB )) or resid 452 through 456 or (resid 457 and (name N or name CA or name C \ or name O or name CB )) or resid 458 through 501 or (resid 502 and (name N or na \ me CA or name C or name O or name CB )) or resid 503 through 546)) selection = (chain 'C' and (resid 99 through 120 or (resid 121 and (name N or name CA or nam \ e C or name O or name CB )) or resid 122 through 204 or (resid 205 and (name N o \ r name CA or name C or name O or name CB )) or resid 206 through 231 or (resid 2 \ 32 through 233 and (name N or name CA or name C or name O or name CB )) or resid \ 234 through 235 or (resid 236 through 291 and (name N or name CA or name C or n \ ame O or name CB )) or resid 292 through 456 or (resid 457 and (name N or name C \ A or name C or name O or name CB )) or resid 458 through 501 or (resid 502 and ( \ name N or name CA or name C or name O or name CB )) or resid 503 through 546)) selection = (chain 'D' and (resid 99 through 120 or (resid 121 and (name N or name CA or nam \ e C or name O or name CB )) or resid 122 through 204 or (resid 205 and (name N o \ r name CA or name C or name O or name CB )) or resid 206 through 231 or (resid 2 \ 32 through 233 and (name N or name CA or name C or name O or name CB )) or resid \ 234 through 235 or (resid 236 through 291 and (name N or name CA or name C or n \ ame O or name CB )) or resid 292 through 456 or (resid 457 and (name N or name C \ A or name C or name O or name CB )) or resid 458 through 546)) selection = (chain 'E' and (resid 99 through 204 or (resid 205 and (name N or name CA or nam \ e C or name O or name CB )) or resid 206 through 231 or (resid 232 through 233 a \ nd (name N or name CA or name C or name O or name CB )) or resid 234 through 235 \ or (resid 236 through 291 and (name N or name CA or name C or name O or name CB \ )) or resid 292 through 456 or (resid 457 and (name N or name CA or name C or n \ ame O or name CB )) or resid 458 through 546)) selection = (chain 'F' and (resid 99 through 120 or (resid 121 and (name N or name CA or nam \ e C or name O or name CB )) or resid 122 through 204 or (resid 205 and (name N o \ r name CA or name C or name O or name CB )) or resid 206 through 231 or (resid 2 \ 32 through 233 and (name N or name CA or name C or name O or name CB )) or resid \ 234 through 235 or (resid 236 through 291 and (name N or name CA or name C or n \ ame O or name CB )) or resid 292 through 546)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators 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: 2.600 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: 0.020 Extract box with map and model: 7.780 Check model and map are aligned: 0.250 Set scattering table: 0.170 Process input model: 50.450 Find NCS groups from input model: 1.630 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.810 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 65.810 ------------------------------------------------------------------------------- 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= 0.106 Angle : 0.406 6.266 25976 Z= 0.224 Chirality : 0.039 0.141 2883 Planarity : 0.003 0.028 3292 Dihedral : 13.471 89.870 7050 Min Nonbonded Distance : 2.235 Molprobity Statistics. All-atom Clashscore : 2.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.26 % Favored : 98.74 % Rotamer: Outliers : 0.00 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.53 (0.18), residues: 2376 helix: 3.16 (0.18), residues: 840 sheet: 0.61 (0.27), residues: 360 loop : 1.06 (0.20), residues: 1176 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP F 454 HIS 0.002 0.000 HIS B 485 PHE 0.006 0.001 PHE A 374 TYR 0.008 0.001 TYR A 328 ARG 0.001 0.000 ARG D 161 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4752 Ramachandran restraints generated. 2376 Oldfield, 0 Emsley, 2376 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4752 Ramachandran restraints generated. 2376 Oldfield, 0 Emsley, 2376 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 827 residues out of total 2094 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 827 time to evaluate : 2.438 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: 0.9090 (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: 0.8502 (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: 0.3660 time to fit residues: 426.5049 Evaluate side-chains 488 residues out of total 2094 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 488 time to evaluate : 2.336 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 202 optimal weight: 3.9990 chunk 181 optimal weight: 8.9990 chunk 100 optimal weight: 0.6980 chunk 62 optimal weight: 0.0980 chunk 122 optimal weight: 0.6980 chunk 97 optimal weight: 7.9990 chunk 188 optimal weight: 8.9990 chunk 72 optimal weight: 1.9990 chunk 114 optimal weight: 9.9990 chunk 140 optimal weight: 6.9990 chunk 217 optimal weight: 10.0000 overall best weight: 1.4984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 320 GLN B 391 ASN C 320 GLN D 320 GLN D 391 ASN E 471 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8263 moved from start: 0.2523 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.077 19185 Z= 0.179 Angle : 0.514 7.477 25976 Z= 0.276 Chirality : 0.041 0.156 2883 Planarity : 0.004 0.049 3292 Dihedral : 3.531 12.998 2627 Min Nonbonded Distance : 2.183 Molprobity Statistics. All-atom Clashscore : 6.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.98 % Favored : 98.02 % Rotamer: Outliers : 1.75 % Allowed : 13.06 % Favored : 85.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.99 (0.18), residues: 2376 helix: 2.57 (0.18), residues: 900 sheet: 0.24 (0.26), residues: 384 loop : 0.80 (0.20), residues: 1092 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 464 HIS 0.008 0.001 HIS B 191 PHE 0.015 0.001 PHE F 541 TYR 0.017 0.001 TYR D 236 ARG 0.006 0.000 ARG F 477 *********************** 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 554 residues out of total 2094 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 519 time to evaluate : 2.360 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 113 ASP cc_start: 0.8811 (t0) cc_final: 0.8599 (t0) REVERT: A 224 GLU cc_start: 0.8696 (tp30) cc_final: 0.8261 (tp30) REVERT: A 236 TYR cc_start: 0.8807 (t80) cc_final: 0.8564 (t80) REVERT: A 348 GLN cc_start: 0.8618 (tp40) cc_final: 0.8357 (tp40) REVERT: A 349 LYS cc_start: 0.9017 (tppt) cc_final: 0.8791 (tppt) REVERT: A 355 ASP cc_start: 0.8585 (t70) cc_final: 0.8310 (t70) REVERT: A 409 LYS cc_start: 0.8591 (mttt) cc_final: 0.8302 (mttt) REVERT: B 117 ARG cc_start: 0.8335 (mtp180) cc_final: 0.6996 (ttt180) REVERT: B 195 GLU cc_start: 0.9113 (mp0) cc_final: 0.8824 (mp0) REVERT: B 296 GLU cc_start: 0.8169 (tm-30) cc_final: 0.7947 (tm-30) REVERT: B 386 THR cc_start: 0.8756 (m) cc_final: 0.8520 (p) REVERT: B 477 ARG cc_start: 0.8580 (ttt90) cc_final: 0.7325 (mtt180) REVERT: C 171 MET cc_start: 0.8818 (tpt) cc_final: 0.8351 (tpt) REVERT: C 228 LYS cc_start: 0.8893 (mmmt) cc_final: 0.8642 (mmmt) REVERT: C 294 LEU cc_start: 0.9000 (mt) cc_final: 0.8797 (mt) REVERT: C 320 GLN cc_start: 0.8625 (tp-100) cc_final: 0.8410 (tp-100) REVERT: C 453 SER cc_start: 0.9379 (t) cc_final: 0.9143 (m) REVERT: C 540 GLU cc_start: 0.8190 (tp30) cc_final: 0.7819 (tp30) REVERT: C 544 ASP cc_start: 0.8058 (t0) cc_final: 0.7671 (t0) REVERT: D 176 LYS cc_start: 0.9141 (tppp) cc_final: 0.8786 (tppt) REVERT: D 343 TYR cc_start: 0.8682 (t80) cc_final: 0.8438 (t80) REVERT: D 348 GLN cc_start: 0.8895 (tp40) cc_final: 0.8464 (tm-30) REVERT: D 449 ASN cc_start: 0.7970 (t0) cc_final: 0.7606 (t0) REVERT: D 473 TYR cc_start: 0.8142 (m-80) cc_final: 0.7858 (m-80) REVERT: D 477 ARG cc_start: 0.7985 (ttt90) cc_final: 0.5493 (mtt-85) REVERT: D 478 LYS cc_start: 0.8998 (tttt) cc_final: 0.8637 (tptt) REVERT: E 111 SER cc_start: 0.9290 (m) cc_final: 0.8922 (p) REVERT: E 120 ASP cc_start: 0.8797 (m-30) cc_final: 0.8581 (m-30) REVERT: E 195 GLU cc_start: 0.8321 (mp0) cc_final: 0.8066 (mp0) REVERT: E 226 ASP cc_start: 0.7549 (t0) cc_final: 0.7153 (t70) REVERT: E 295 ARG cc_start: 0.8908 (tpp80) cc_final: 0.8615 (mtt-85) REVERT: E 297 LYS cc_start: 0.8856 (tttt) cc_final: 0.8513 (tppt) REVERT: E 320 GLN cc_start: 0.8847 (tp40) cc_final: 0.8620 (tp-100) REVERT: E 478 LYS cc_start: 0.8809 (ttmm) cc_final: 0.8605 (tppt) REVERT: F 224 GLU cc_start: 0.8669 (tp30) cc_final: 0.8378 (tp30) REVERT: F 226 ASP cc_start: 0.8268 (t0) cc_final: 0.7876 (t0) REVERT: F 342 LYS cc_start: 0.9028 (mmmm) cc_final: 0.8679 (mmtm) REVERT: F 355 ASP cc_start: 0.8441 (t70) cc_final: 0.7979 (t0) REVERT: F 422 LEU cc_start: 0.9045 (tt) cc_final: 0.8471 (mp) outliers start: 35 outliers final: 19 residues processed: 539 average time/residue: 0.3330 time to fit residues: 261.7502 Evaluate side-chains 475 residues out of total 2094 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 456 time to evaluate : 2.252 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 441 VAL Chi-restraints excluded: chain A residue 466 VAL Chi-restraints excluded: chain A residue 520 SER Chi-restraints excluded: chain B residue 109 GLU Chi-restraints excluded: chain B residue 122 VAL Chi-restraints excluded: chain B residue 325 THR 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 131 VAL Chi-restraints excluded: chain D residue 138 VAL Chi-restraints excluded: chain D residue 470 LYS 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 441 VAL Chi-restraints excluded: chain E residue 466 VAL Chi-restraints excluded: chain F residue 131 VAL Chi-restraints excluded: chain F residue 210 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 121 optimal weight: 0.9980 chunk 67 optimal weight: 7.9990 chunk 181 optimal weight: 10.0000 chunk 148 optimal weight: 6.9990 chunk 60 optimal weight: 0.9990 chunk 218 optimal weight: 10.0000 chunk 235 optimal weight: 0.3980 chunk 194 optimal weight: 8.9990 chunk 216 optimal weight: 7.9990 chunk 74 optimal weight: 9.9990 chunk 175 optimal weight: 1.9990 overall best weight: 2.2786 ------------------------------------------------------------------------------- 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 391 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8326 moved from start: 0.3160 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= 0.223 Angle : 0.509 5.995 25976 Z= 0.274 Chirality : 0.041 0.152 2883 Planarity : 0.004 0.055 3292 Dihedral : 3.707 16.556 2627 Min Nonbonded Distance : 2.198 Molprobity Statistics. All-atom Clashscore : 7.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Rotamer: Outliers : 2.55 % Allowed : 16.01 % Favored : 81.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.84 (0.18), residues: 2376 helix: 2.44 (0.18), residues: 900 sheet: 0.11 (0.26), residues: 384 loop : 0.73 (0.19), residues: 1092 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP E 464 HIS 0.005 0.001 HIS B 191 PHE 0.020 0.001 PHE F 541 TYR 0.014 0.001 TYR E 343 ARG 0.006 0.001 ARG F 477 *********************** 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 503 residues out of total 2094 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 452 time to evaluate : 2.345 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: 0.8797 (t0) cc_final: 0.8569 (t0) REVERT: A 236 TYR cc_start: 0.8775 (t80) cc_final: 0.8539 (t80) REVERT: A 348 GLN cc_start: 0.8699 (tp40) cc_final: 0.8457 (tp40) REVERT: A 349 LYS cc_start: 0.9092 (tppt) cc_final: 0.8869 (tppt) REVERT: A 355 ASP cc_start: 0.8613 (t70) cc_final: 0.8257 (t70) REVERT: B 117 ARG cc_start: 0.8502 (mtp180) cc_final: 0.7064 (ttt180) REVERT: B 120 ASP cc_start: 0.8708 (m-30) cc_final: 0.8297 (m-30) REVERT: B 386 THR cc_start: 0.8791 (m) cc_final: 0.8558 (p) REVERT: B 477 ARG cc_start: 0.8638 (ttt90) cc_final: 0.7390 (mtt180) REVERT: C 106 ARG cc_start: 0.7693 (ptm-80) cc_final: 0.7461 (ptm-80) REVERT: C 204 GLU cc_start: 0.8187 (tm-30) cc_final: 0.7903 (tm-30) REVERT: C 228 LYS cc_start: 0.8954 (mmmt) cc_final: 0.8707 (mmmt) REVERT: C 295 ARG cc_start: 0.9099 (OUTLIER) cc_final: 0.8740 (mtm-85) REVERT: C 453 SER cc_start: 0.9376 (t) cc_final: 0.9137 (m) REVERT: D 218 SER cc_start: 0.9345 (OUTLIER) cc_final: 0.9127 (m) REVERT: D 348 GLN cc_start: 0.8857 (tp40) cc_final: 0.8558 (tm-30) REVERT: D 449 ASN cc_start: 0.8116 (t0) cc_final: 0.7826 (t0) REVERT: D 470 LYS cc_start: 0.8631 (OUTLIER) cc_final: 0.8349 (ttpp) REVERT: D 473 TYR cc_start: 0.8214 (m-80) cc_final: 0.7906 (m-80) REVERT: D 477 ARG cc_start: 0.7820 (ttt90) cc_final: 0.5634 (mtt-85) REVERT: E 111 SER cc_start: 0.9326 (m) cc_final: 0.8990 (p) REVERT: E 226 ASP cc_start: 0.7619 (t0) cc_final: 0.7175 (t0) REVERT: E 297 LYS cc_start: 0.8954 (tttt) cc_final: 0.8580 (tppt) REVERT: E 349 LYS cc_start: 0.9212 (ttmm) cc_final: 0.8970 (mttt) REVERT: E 355 ASP cc_start: 0.8840 (t0) cc_final: 0.8567 (t0) REVERT: F 296 GLU cc_start: 0.7583 (tm-30) cc_final: 0.6910 (tm-30) REVERT: F 355 ASP cc_start: 0.8517 (t70) cc_final: 0.8073 (t0) REVERT: F 422 LEU cc_start: 0.9046 (tt) cc_final: 0.8497 (mp) outliers start: 51 outliers final: 30 residues processed: 481 average time/residue: 0.3632 time to fit residues: 255.7665 Evaluate side-chains 477 residues out of total 2094 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 444 time to evaluate : 2.014 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 215 SER Chi-restraints excluded: chain A residue 386 THR Chi-restraints excluded: chain A residue 402 SER 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 152 VAL Chi-restraints excluded: chain B residue 325 THR Chi-restraints excluded: chain B residue 504 ASP Chi-restraints excluded: chain B residue 543 LYS Chi-restraints excluded: chain C residue 218 SER Chi-restraints excluded: chain C residue 295 ARG Chi-restraints excluded: chain C residue 302 ILE 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 131 VAL Chi-restraints excluded: chain D residue 137 GLU Chi-restraints excluded: chain D residue 138 VAL Chi-restraints excluded: chain D residue 218 SER Chi-restraints excluded: chain D residue 306 ARG Chi-restraints excluded: chain D residue 442 MET Chi-restraints excluded: chain D residue 470 LYS 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 386 THR 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 208 VAL Chi-restraints excluded: chain F residue 210 THR Chi-restraints excluded: chain F residue 354 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 215 optimal weight: 7.9990 chunk 164 optimal weight: 3.9990 chunk 113 optimal weight: 9.9990 chunk 24 optimal weight: 3.9990 chunk 104 optimal weight: 7.9990 chunk 146 optimal weight: 8.9990 chunk 219 optimal weight: 9.9990 chunk 231 optimal weight: 9.9990 chunk 114 optimal weight: 9.9990 chunk 207 optimal weight: 6.9990 chunk 62 optimal weight: 4.9990 overall best weight: 5.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 391 ASN E 216 HIS F 216 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8425 moved from start: 0.3953 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.049 19185 Z= 0.483 Angle : 0.643 6.377 25976 Z= 0.346 Chirality : 0.046 0.170 2883 Planarity : 0.005 0.061 3292 Dihedral : 4.465 20.272 2627 Min Nonbonded Distance : 2.051 Molprobity Statistics. All-atom Clashscore : 8.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % Rotamer: Outliers : 3.30 % Allowed : 17.66 % Favored : 79.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.23 (0.17), residues: 2376 helix: 1.96 (0.18), residues: 900 sheet: -0.21 (0.25), residues: 366 loop : 0.34 (0.19), residues: 1110 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP E 464 HIS 0.004 0.001 HIS E 116 PHE 0.026 0.002 PHE E 541 TYR 0.024 0.002 TYR F 393 ARG 0.007 0.001 ARG D 469 *********************** 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 493 residues out of total 2094 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 427 time to evaluate : 2.181 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 113 ASP cc_start: 0.8814 (t0) cc_final: 0.8612 (t0) REVERT: A 349 LYS cc_start: 0.9195 (tppt) cc_final: 0.8961 (tppt) REVERT: A 355 ASP cc_start: 0.8757 (t70) cc_final: 0.8432 (t70) REVERT: A 478 LYS cc_start: 0.8967 (tptt) cc_final: 0.8618 (ttmm) REVERT: A 525 MET cc_start: 0.8259 (tpp) cc_final: 0.7574 (tpp) REVERT: B 120 ASP cc_start: 0.8847 (m-30) cc_final: 0.8422 (m-30) REVERT: B 225 LYS cc_start: 0.9000 (mmmt) cc_final: 0.8663 (tptm) REVERT: B 296 GLU cc_start: 0.7989 (tm-30) cc_final: 0.7031 (tm-30) REVERT: B 477 ARG cc_start: 0.8708 (ttt90) cc_final: 0.7387 (mtt180) REVERT: C 294 LEU cc_start: 0.9404 (mt) cc_final: 0.9193 (mp) REVERT: C 295 ARG cc_start: 0.9077 (OUTLIER) cc_final: 0.8624 (mtp85) REVERT: C 475 SER cc_start: 0.8624 (m) cc_final: 0.8333 (p) REVERT: C 527 SER cc_start: 0.9113 (m) cc_final: 0.8694 (p) REVERT: C 540 GLU cc_start: 0.8265 (tp30) cc_final: 0.7789 (tp30) REVERT: D 170 THR cc_start: 0.9401 (m) cc_final: 0.9158 (p) REVERT: D 330 LEU cc_start: 0.9438 (OUTLIER) cc_final: 0.9120 (tt) REVERT: D 336 GLU cc_start: 0.9112 (tp30) cc_final: 0.8763 (tp30) REVERT: D 348 GLN cc_start: 0.8861 (tp40) cc_final: 0.8503 (tm-30) REVERT: D 355 ASP cc_start: 0.8805 (t70) cc_final: 0.8502 (t70) REVERT: D 470 LYS cc_start: 0.8573 (OUTLIER) cc_final: 0.8341 (ttpp) REVERT: D 477 ARG cc_start: 0.7981 (ttt90) cc_final: 0.5861 (mtt180) REVERT: D 478 LYS cc_start: 0.9186 (tttt) cc_final: 0.8797 (tppt) REVERT: E 111 SER cc_start: 0.9368 (m) cc_final: 0.9105 (p) REVERT: E 177 LEU cc_start: 0.9251 (OUTLIER) cc_final: 0.9023 (mp) REVERT: E 226 ASP cc_start: 0.7965 (t0) cc_final: 0.7685 (t0) REVERT: E 297 LYS cc_start: 0.9076 (tttt) cc_final: 0.8209 (tppt) REVERT: E 349 LYS cc_start: 0.9292 (ttmm) cc_final: 0.9051 (mttt) REVERT: E 355 ASP cc_start: 0.8960 (t0) cc_final: 0.8669 (t0) REVERT: E 390 ASP cc_start: 0.8127 (t0) cc_final: 0.7898 (t0) REVERT: E 478 LYS cc_start: 0.8833 (ttmm) cc_final: 0.8509 (ttmm) REVERT: F 355 ASP cc_start: 0.8650 (t70) cc_final: 0.8205 (t0) REVERT: F 442 MET cc_start: 0.8799 (tmm) cc_final: 0.8180 (tmm) outliers start: 66 outliers final: 49 residues processed: 469 average time/residue: 0.3495 time to fit residues: 236.5837 Evaluate side-chains 454 residues out of total 2094 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 401 time to evaluate : 2.306 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 215 SER Chi-restraints excluded: chain A residue 367 VAL Chi-restraints excluded: chain A residue 386 THR Chi-restraints excluded: chain A residue 402 SER Chi-restraints excluded: chain A residue 441 VAL Chi-restraints excluded: chain A residue 466 VAL Chi-restraints excluded: chain B residue 208 VAL Chi-restraints excluded: chain B residue 292 LEU Chi-restraints excluded: chain B residue 325 THR Chi-restraints excluded: chain B residue 504 ASP Chi-restraints excluded: chain B residue 543 LYS Chi-restraints excluded: chain C residue 122 VAL Chi-restraints excluded: chain C residue 218 SER Chi-restraints excluded: chain C residue 295 ARG Chi-restraints excluded: chain C residue 330 LEU 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 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 182 LYS Chi-restraints excluded: chain D residue 330 LEU Chi-restraints excluded: chain D residue 353 ASP Chi-restraints excluded: chain D residue 354 LEU Chi-restraints excluded: chain D residue 365 GLU Chi-restraints excluded: chain D residue 367 VAL Chi-restraints excluded: chain D residue 441 VAL Chi-restraints excluded: chain D residue 442 MET Chi-restraints excluded: chain D residue 470 LYS Chi-restraints excluded: chain D residue 486 THR Chi-restraints excluded: chain D residue 522 ILE Chi-restraints excluded: chain E residue 109 GLU Chi-restraints excluded: chain E residue 177 LEU 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 386 THR Chi-restraints excluded: chain E residue 466 VAL Chi-restraints excluded: chain E residue 508 ILE Chi-restraints excluded: chain E residue 518 ILE Chi-restraints excluded: chain F residue 131 VAL Chi-restraints excluded: chain F residue 172 VAL Chi-restraints excluded: chain F residue 208 VAL Chi-restraints excluded: chain F residue 210 THR Chi-restraints excluded: chain F residue 311 ASP Chi-restraints excluded: chain F residue 330 LEU Chi-restraints excluded: chain F residue 354 LEU Chi-restraints excluded: chain F residue 367 VAL Chi-restraints excluded: chain F residue 510 ASN 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 193 optimal weight: 6.9990 chunk 131 optimal weight: 0.9990 chunk 3 optimal weight: 0.9980 chunk 172 optimal weight: 10.0000 chunk 95 optimal weight: 1.9990 chunk 197 optimal weight: 0.8980 chunk 160 optimal weight: 10.0000 chunk 0 optimal weight: 8.9990 chunk 118 optimal weight: 0.7980 chunk 208 optimal weight: 6.9990 chunk 58 optimal weight: 1.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 391 ASN E 216 HIS E 531 ASN F 216 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8335 moved from start: 0.3859 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= 0.155 Angle : 0.499 10.203 25976 Z= 0.267 Chirality : 0.041 0.158 2883 Planarity : 0.004 0.057 3292 Dihedral : 3.995 18.106 2627 Min Nonbonded Distance : 2.100 Molprobity Statistics. All-atom Clashscore : 7.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.98 % Favored : 98.02 % Rotamer: Outliers : 1.80 % Allowed : 20.21 % Favored : 77.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.59 (0.18), residues: 2376 helix: 2.32 (0.18), residues: 900 sheet: 0.00 (0.28), residues: 354 loop : 0.48 (0.19), residues: 1122 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP E 454 HIS 0.003 0.000 HIS B 191 PHE 0.019 0.001 PHE D 308 TYR 0.020 0.001 TYR F 343 ARG 0.006 0.000 ARG F 477 *********************** 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 492 residues out of total 2094 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 456 time to evaluate : 2.443 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 113 ASP cc_start: 0.8758 (t0) cc_final: 0.8521 (t0) REVERT: A 349 LYS cc_start: 0.9113 (tppt) cc_final: 0.8890 (tppt) REVERT: A 355 ASP cc_start: 0.8645 (t70) cc_final: 0.8320 (t70) REVERT: A 478 LYS cc_start: 0.8965 (tptt) cc_final: 0.8653 (ttmm) REVERT: B 120 ASP cc_start: 0.8718 (m-30) cc_final: 0.8266 (m-30) REVERT: B 225 LYS cc_start: 0.8984 (mmmt) cc_final: 0.8688 (tptm) REVERT: B 296 GLU cc_start: 0.8155 (tm-30) cc_final: 0.7905 (tm-30) REVERT: B 477 ARG cc_start: 0.8617 (ttt90) cc_final: 0.7287 (mtt180) REVERT: C 295 ARG cc_start: 0.9072 (OUTLIER) cc_final: 0.8717 (mtm-85) REVERT: C 386 THR cc_start: 0.9126 (m) cc_final: 0.8723 (p) REVERT: C 441 VAL cc_start: 0.9511 (OUTLIER) cc_final: 0.9283 (m) REVERT: C 527 SER cc_start: 0.9220 (m) cc_final: 0.8838 (p) REVERT: C 540 GLU cc_start: 0.8304 (tp30) cc_final: 0.7934 (tp30) REVERT: D 170 THR cc_start: 0.9380 (m) cc_final: 0.9132 (p) REVERT: D 330 LEU cc_start: 0.9406 (OUTLIER) cc_final: 0.9067 (tt) REVERT: D 336 GLU cc_start: 0.9214 (tp30) cc_final: 0.8882 (tp30) REVERT: D 348 GLN cc_start: 0.8771 (tp40) cc_final: 0.8309 (tp40) REVERT: D 355 ASP cc_start: 0.8707 (t70) cc_final: 0.8458 (t70) REVERT: D 453 SER cc_start: 0.9537 (t) cc_final: 0.9144 (m) REVERT: D 470 LYS cc_start: 0.8593 (OUTLIER) cc_final: 0.8345 (ttpp) REVERT: D 471 GLN cc_start: 0.7771 (tp-100) cc_final: 0.7516 (tp-100) REVERT: D 473 TYR cc_start: 0.7928 (m-80) cc_final: 0.7638 (m-80) REVERT: D 477 ARG cc_start: 0.7846 (ttt90) cc_final: 0.5733 (mpt-90) REVERT: E 111 SER cc_start: 0.9265 (m) cc_final: 0.8883 (p) REVERT: E 187 ILE cc_start: 0.9267 (mt) cc_final: 0.8998 (tp) REVERT: E 226 ASP cc_start: 0.7913 (t0) cc_final: 0.7441 (t0) REVERT: E 232 GLU cc_start: 0.8750 (mm-30) cc_final: 0.8446 (mm-30) REVERT: E 349 LYS cc_start: 0.9157 (ttmm) cc_final: 0.8937 (mttt) REVERT: E 355 ASP cc_start: 0.8782 (t0) cc_final: 0.8575 (t0) REVERT: F 355 ASP cc_start: 0.8577 (t70) cc_final: 0.8233 (t70) REVERT: F 422 LEU cc_start: 0.9029 (tt) cc_final: 0.8456 (mp) REVERT: F 452 MET cc_start: 0.7505 (ttt) cc_final: 0.7189 (ttt) outliers start: 36 outliers final: 23 residues processed: 473 average time/residue: 0.3448 time to fit residues: 237.5180 Evaluate side-chains 448 residues out of total 2094 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 421 time to evaluate : 2.299 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 386 THR Chi-restraints excluded: chain A residue 402 SER Chi-restraints excluded: chain B residue 325 THR Chi-restraints excluded: chain B residue 504 ASP Chi-restraints excluded: chain C residue 122 VAL Chi-restraints excluded: chain C residue 295 ARG Chi-restraints excluded: chain C residue 360 VAL Chi-restraints excluded: chain C residue 429 ASN Chi-restraints excluded: chain C residue 441 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 356 MET Chi-restraints excluded: chain D residue 380 LYS Chi-restraints excluded: chain D residue 442 MET Chi-restraints excluded: chain D residue 470 LYS Chi-restraints excluded: chain E residue 109 GLU 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 466 VAL Chi-restraints excluded: chain E residue 530 LEU Chi-restraints excluded: chain F residue 131 VAL Chi-restraints excluded: chain F residue 294 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 78 optimal weight: 4.9990 chunk 208 optimal weight: 3.9990 chunk 45 optimal weight: 3.9990 chunk 136 optimal weight: 5.9990 chunk 57 optimal weight: 9.9990 chunk 232 optimal weight: 4.9990 chunk 192 optimal weight: 0.9990 chunk 107 optimal weight: 0.0170 chunk 19 optimal weight: 0.8980 chunk 76 optimal weight: 1.9990 chunk 121 optimal weight: 3.9990 overall best weight: 1.5824 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8338 moved from start: 0.3913 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 19185 Z= 0.177 Angle : 0.500 9.041 25976 Z= 0.266 Chirality : 0.041 0.152 2883 Planarity : 0.004 0.056 3292 Dihedral : 3.890 18.192 2627 Min Nonbonded Distance : 2.103 Molprobity Statistics. All-atom Clashscore : 6.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 2.15 % Allowed : 20.51 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.68 (0.18), residues: 2376 helix: 2.36 (0.18), residues: 900 sheet: 0.16 (0.27), residues: 378 loop : 0.53 (0.19), residues: 1098 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 454 HIS 0.003 0.000 HIS B 191 PHE 0.010 0.001 PHE E 541 TYR 0.020 0.001 TYR E 236 ARG 0.005 0.000 ARG D 469 *********************** 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 491 residues out of total 2094 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 448 time to evaluate : 2.404 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 113 ASP cc_start: 0.8763 (t0) cc_final: 0.8518 (t0) REVERT: A 349 LYS cc_start: 0.9145 (tppt) cc_final: 0.8930 (tppt) REVERT: A 355 ASP cc_start: 0.8665 (t70) cc_final: 0.8339 (t70) REVERT: A 478 LYS cc_start: 0.8987 (tptt) cc_final: 0.8646 (ttmm) REVERT: B 120 ASP cc_start: 0.8746 (m-30) cc_final: 0.8292 (m-30) REVERT: B 225 LYS cc_start: 0.8977 (mmmt) cc_final: 0.8678 (tptm) REVERT: B 296 GLU cc_start: 0.8141 (tm-30) cc_final: 0.7873 (tm-30) REVERT: B 477 ARG cc_start: 0.8615 (ttt90) cc_final: 0.7199 (mpt-90) REVERT: C 117 ARG cc_start: 0.8856 (mtp85) cc_final: 0.8347 (mtp180) REVERT: C 441 VAL cc_start: 0.9526 (OUTLIER) cc_final: 0.9303 (m) REVERT: C 527 SER cc_start: 0.9156 (m) cc_final: 0.8771 (p) REVERT: C 540 GLU cc_start: 0.8273 (tp30) cc_final: 0.7909 (tp30) REVERT: D 170 THR cc_start: 0.9404 (m) cc_final: 0.9166 (p) REVERT: D 330 LEU cc_start: 0.9387 (OUTLIER) cc_final: 0.9024 (tt) REVERT: D 336 GLU cc_start: 0.9189 (tp30) cc_final: 0.8841 (tp30) REVERT: D 348 GLN cc_start: 0.8753 (tp40) cc_final: 0.8543 (tp40) REVERT: D 355 ASP cc_start: 0.8695 (t70) cc_final: 0.8463 (t70) REVERT: D 453 SER cc_start: 0.9513 (t) cc_final: 0.9130 (m) REVERT: D 470 LYS cc_start: 0.8609 (OUTLIER) cc_final: 0.8239 (ttpp) REVERT: D 471 GLN cc_start: 0.7785 (tp-100) cc_final: 0.7551 (tp40) REVERT: D 477 ARG cc_start: 0.7861 (ttt90) cc_final: 0.5722 (mtt-85) REVERT: E 226 ASP cc_start: 0.7941 (t0) cc_final: 0.7464 (t0) REVERT: E 232 GLU cc_start: 0.8746 (mm-30) cc_final: 0.8429 (mm-30) REVERT: E 349 LYS cc_start: 0.9141 (ttmm) cc_final: 0.8914 (mttt) REVERT: F 171 MET cc_start: 0.8504 (tpp) cc_final: 0.8300 (tpp) REVERT: F 355 ASP cc_start: 0.8574 (t70) cc_final: 0.8226 (t70) REVERT: F 362 GLU cc_start: 0.8453 (tp30) cc_final: 0.8223 (tp30) REVERT: F 422 LEU cc_start: 0.9036 (tt) cc_final: 0.8472 (mp) REVERT: F 442 MET cc_start: 0.8919 (tmm) cc_final: 0.8436 (tmm) REVERT: F 452 MET cc_start: 0.7432 (ttt) cc_final: 0.7130 (ttt) outliers start: 43 outliers final: 32 residues processed: 473 average time/residue: 0.3416 time to fit residues: 236.2095 Evaluate side-chains 468 residues out of total 2094 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 433 time to evaluate : 2.339 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 187 ILE Chi-restraints excluded: chain A residue 367 VAL Chi-restraints excluded: chain A residue 386 THR Chi-restraints excluded: chain A residue 402 SER 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 504 ASP 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 429 ASN Chi-restraints excluded: chain C residue 441 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 138 VAL Chi-restraints excluded: chain D residue 330 LEU Chi-restraints excluded: chain D residue 353 ASP Chi-restraints excluded: chain D residue 365 GLU Chi-restraints excluded: chain D residue 367 VAL Chi-restraints excluded: chain D residue 380 LYS Chi-restraints excluded: chain D residue 442 MET Chi-restraints excluded: chain D residue 470 LYS Chi-restraints excluded: chain D residue 490 VAL Chi-restraints excluded: chain E residue 109 GLU Chi-restraints excluded: chain E residue 294 LEU Chi-restraints excluded: chain E residue 357 LEU Chi-restraints excluded: chain E residue 367 VAL Chi-restraints excluded: chain E residue 386 THR 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 208 VAL Chi-restraints excluded: chain F residue 490 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 223 optimal weight: 0.9990 chunk 26 optimal weight: 1.9990 chunk 132 optimal weight: 0.5980 chunk 169 optimal weight: 0.0670 chunk 131 optimal weight: 7.9990 chunk 195 optimal weight: 8.9990 chunk 129 optimal weight: 2.9990 chunk 231 optimal weight: 9.9990 chunk 144 optimal weight: 0.5980 chunk 141 optimal weight: 8.9990 chunk 106 optimal weight: 5.9990 overall best weight: 0.8522 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8302 moved from start: 0.3947 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 19185 Z= 0.142 Angle : 0.488 8.393 25976 Z= 0.257 Chirality : 0.040 0.147 2883 Planarity : 0.004 0.056 3292 Dihedral : 3.758 17.673 2627 Min Nonbonded Distance : 2.131 Molprobity Statistics. All-atom Clashscore : 6.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.98 % Favored : 98.02 % Rotamer: Outliers : 1.95 % Allowed : 21.46 % Favored : 76.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.75 (0.18), residues: 2376 helix: 2.39 (0.18), residues: 900 sheet: 0.23 (0.27), residues: 378 loop : 0.59 (0.19), residues: 1098 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 454 HIS 0.003 0.000 HIS B 191 PHE 0.018 0.001 PHE D 308 TYR 0.022 0.001 TYR B 343 ARG 0.006 0.000 ARG A 295 *********************** 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 505 residues out of total 2094 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 466 time to evaluate : 2.219 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 113 ASP cc_start: 0.8744 (t0) cc_final: 0.8490 (t0) REVERT: A 355 ASP cc_start: 0.8623 (t70) cc_final: 0.8308 (t70) REVERT: A 478 LYS cc_start: 0.8983 (tptt) cc_final: 0.8651 (ttmm) REVERT: A 540 GLU cc_start: 0.8728 (tp30) cc_final: 0.8293 (tp30) REVERT: B 120 ASP cc_start: 0.8712 (m-30) cc_final: 0.8239 (m-30) REVERT: B 225 LYS cc_start: 0.8967 (mmmt) cc_final: 0.8687 (tptm) REVERT: B 296 GLU cc_start: 0.8144 (tm-30) cc_final: 0.7867 (tm-30) REVERT: B 361 GLN cc_start: 0.9069 (pm20) cc_final: 0.8843 (pm20) REVERT: B 477 ARG cc_start: 0.8582 (ttt90) cc_final: 0.7312 (mtt180) REVERT: C 295 ARG cc_start: 0.8938 (mpp80) cc_final: 0.8595 (mtm-85) REVERT: C 441 VAL cc_start: 0.9529 (OUTLIER) cc_final: 0.9308 (m) REVERT: C 527 SER cc_start: 0.9203 (m) cc_final: 0.8815 (p) REVERT: C 540 GLU cc_start: 0.8228 (tp30) cc_final: 0.7885 (tp30) REVERT: D 170 THR cc_start: 0.9385 (m) cc_final: 0.9151 (p) REVERT: D 296 GLU cc_start: 0.8277 (tt0) cc_final: 0.7998 (tm-30) REVERT: D 330 LEU cc_start: 0.9372 (OUTLIER) cc_final: 0.9009 (tt) REVERT: D 336 GLU cc_start: 0.9197 (tp30) cc_final: 0.8863 (tp30) REVERT: D 348 GLN cc_start: 0.8729 (tp40) cc_final: 0.8268 (tp40) REVERT: D 441 VAL cc_start: 0.9057 (t) cc_final: 0.8795 (p) REVERT: D 453 SER cc_start: 0.9472 (t) cc_final: 0.9102 (m) REVERT: D 471 GLN cc_start: 0.7801 (tp-100) cc_final: 0.7512 (tp-100) REVERT: D 477 ARG cc_start: 0.7825 (ttt90) cc_final: 0.5822 (mtt180) REVERT: E 187 ILE cc_start: 0.9191 (mt) cc_final: 0.8937 (tp) REVERT: E 226 ASP cc_start: 0.7885 (t0) cc_final: 0.7373 (t0) REVERT: E 232 GLU cc_start: 0.8751 (mm-30) cc_final: 0.8413 (mm-30) REVERT: F 355 ASP cc_start: 0.8509 (t70) cc_final: 0.8199 (t70) REVERT: F 422 LEU cc_start: 0.9000 (tt) cc_final: 0.8417 (mp) REVERT: F 452 MET cc_start: 0.7282 (ttt) cc_final: 0.6957 (ttt) outliers start: 39 outliers final: 30 residues processed: 490 average time/residue: 0.3345 time to fit residues: 242.3473 Evaluate side-chains 474 residues out of total 2094 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 442 time to evaluate : 2.323 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 187 ILE Chi-restraints excluded: chain A residue 302 ILE Chi-restraints excluded: chain A residue 367 VAL Chi-restraints excluded: chain A residue 386 THR Chi-restraints excluded: chain B residue 122 VAL Chi-restraints excluded: chain B residue 325 THR Chi-restraints excluded: chain B residue 504 ASP Chi-restraints excluded: chain C residue 360 VAL Chi-restraints excluded: chain C residue 367 VAL Chi-restraints excluded: chain C residue 429 ASN Chi-restraints excluded: chain C residue 441 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 138 VAL 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 442 MET Chi-restraints excluded: chain D residue 490 VAL Chi-restraints excluded: chain E residue 213 LEU Chi-restraints excluded: chain E residue 294 LEU Chi-restraints excluded: chain E residue 367 VAL Chi-restraints excluded: chain E residue 386 THR Chi-restraints excluded: chain E residue 466 VAL Chi-restraints excluded: chain F residue 131 VAL Chi-restraints excluded: chain F residue 208 VAL Chi-restraints excluded: chain F residue 357 LEU 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 143 optimal weight: 0.9980 chunk 92 optimal weight: 10.0000 chunk 138 optimal weight: 6.9990 chunk 69 optimal weight: 2.9990 chunk 45 optimal weight: 0.1980 chunk 44 optimal weight: 1.9990 chunk 147 optimal weight: 4.9990 chunk 157 optimal weight: 6.9990 chunk 114 optimal weight: 10.0000 chunk 21 optimal weight: 1.9990 chunk 181 optimal weight: 5.9990 overall best weight: 1.6386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 531 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 391 ASN D 391 ASN E 391 ASN E 427 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8326 moved from start: 0.4013 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 19185 Z= 0.183 Angle : 0.519 13.423 25976 Z= 0.270 Chirality : 0.041 0.147 2883 Planarity : 0.004 0.056 3292 Dihedral : 3.757 17.847 2627 Min Nonbonded Distance : 2.111 Molprobity Statistics. All-atom Clashscore : 6.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 2.25 % Allowed : 21.86 % Favored : 75.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.75 (0.18), residues: 2376 helix: 2.40 (0.18), residues: 900 sheet: 0.18 (0.27), residues: 378 loop : 0.60 (0.19), residues: 1098 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 454 HIS 0.007 0.001 HIS B 191 PHE 0.019 0.001 PHE D 308 TYR 0.023 0.001 TYR B 343 ARG 0.005 0.000 ARG A 469 *********************** 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 485 residues out of total 2094 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 440 time to evaluate : 2.388 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 113 ASP cc_start: 0.8755 (t0) cc_final: 0.8505 (t0) REVERT: A 355 ASP cc_start: 0.8666 (t70) cc_final: 0.8329 (t70) REVERT: A 478 LYS cc_start: 0.9005 (tptt) cc_final: 0.8652 (ttmm) REVERT: A 540 GLU cc_start: 0.8729 (tp30) cc_final: 0.8490 (tp30) REVERT: B 120 ASP cc_start: 0.8741 (m-30) cc_final: 0.8281 (m-30) REVERT: B 225 LYS cc_start: 0.8971 (mmmt) cc_final: 0.8694 (tptm) REVERT: B 296 GLU cc_start: 0.8145 (tm-30) cc_final: 0.7865 (tm-30) REVERT: B 361 GLN cc_start: 0.9108 (pm20) cc_final: 0.8881 (pm20) REVERT: B 477 ARG cc_start: 0.8610 (ttt90) cc_final: 0.7320 (mtt180) REVERT: C 226 ASP cc_start: 0.7315 (t0) cc_final: 0.6708 (t0) REVERT: C 441 VAL cc_start: 0.9537 (OUTLIER) cc_final: 0.9320 (m) REVERT: C 527 SER cc_start: 0.9167 (m) cc_final: 0.8909 (t) REVERT: C 540 GLU cc_start: 0.8234 (tp30) cc_final: 0.7865 (tp30) REVERT: D 170 THR cc_start: 0.9401 (m) cc_final: 0.9175 (p) REVERT: D 296 GLU cc_start: 0.8263 (tt0) cc_final: 0.8007 (tm-30) REVERT: D 330 LEU cc_start: 0.9378 (OUTLIER) cc_final: 0.9012 (tt) REVERT: D 348 GLN cc_start: 0.8736 (tp40) cc_final: 0.8525 (tp40) REVERT: D 453 SER cc_start: 0.9479 (t) cc_final: 0.9106 (m) REVERT: D 470 LYS cc_start: 0.8533 (OUTLIER) cc_final: 0.8116 (ttpp) REVERT: D 471 GLN cc_start: 0.7778 (tp-100) cc_final: 0.7525 (tp-100) REVERT: D 477 ARG cc_start: 0.7869 (ttt90) cc_final: 0.5848 (mtt180) REVERT: D 478 LYS cc_start: 0.9146 (tttt) cc_final: 0.8796 (tppt) REVERT: E 187 ILE cc_start: 0.9158 (mt) cc_final: 0.8901 (tp) REVERT: E 226 ASP cc_start: 0.7955 (t0) cc_final: 0.7450 (t0) REVERT: E 232 GLU cc_start: 0.8761 (mm-30) cc_final: 0.8422 (mm-30) REVERT: E 442 MET cc_start: 0.9183 (tmm) cc_final: 0.8707 (tmm) REVERT: F 355 ASP cc_start: 0.8601 (t70) cc_final: 0.8275 (t70) REVERT: F 422 LEU cc_start: 0.8996 (tt) cc_final: 0.8422 (mp) REVERT: F 452 MET cc_start: 0.7409 (ttt) cc_final: 0.7118 (ttt) outliers start: 45 outliers final: 38 residues processed: 467 average time/residue: 0.3292 time to fit residues: 225.8030 Evaluate side-chains 474 residues out of total 2094 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 433 time to evaluate : 2.239 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 187 ILE Chi-restraints excluded: chain A residue 215 SER Chi-restraints excluded: chain A residue 302 ILE Chi-restraints excluded: chain A residue 367 VAL Chi-restraints excluded: chain A residue 386 THR 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 504 ASP Chi-restraints excluded: chain C residue 210 THR Chi-restraints excluded: chain C residue 360 VAL Chi-restraints excluded: chain C residue 367 VAL Chi-restraints excluded: chain C residue 429 ASN Chi-restraints excluded: chain C residue 441 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 138 VAL 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 357 LEU Chi-restraints excluded: chain D residue 367 VAL Chi-restraints excluded: chain D residue 442 MET 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 357 LEU Chi-restraints excluded: chain E residue 367 VAL Chi-restraints excluded: chain E residue 386 THR Chi-restraints excluded: chain E residue 441 VAL 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 208 VAL Chi-restraints excluded: chain F residue 218 SER Chi-restraints excluded: chain F residue 367 VAL Chi-restraints excluded: chain F residue 402 SER 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 210 optimal weight: 0.0870 chunk 221 optimal weight: 0.0870 chunk 202 optimal weight: 0.9990 chunk 215 optimal weight: 5.9990 chunk 129 optimal weight: 2.9990 chunk 93 optimal weight: 9.9990 chunk 169 optimal weight: 7.9990 chunk 66 optimal weight: 5.9990 chunk 194 optimal weight: 10.0000 chunk 203 optimal weight: 3.9990 chunk 214 optimal weight: 10.0000 overall best weight: 1.6342 ------------------------------------------------------------------------------- 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 E 216 HIS E 391 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8325 moved from start: 0.4074 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 19185 Z= 0.183 Angle : 0.525 14.222 25976 Z= 0.272 Chirality : 0.041 0.147 2883 Planarity : 0.004 0.057 3292 Dihedral : 3.768 18.488 2627 Min Nonbonded Distance : 2.115 Molprobity Statistics. All-atom Clashscore : 7.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Rotamer: Outliers : 2.35 % Allowed : 22.01 % Favored : 75.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.70 (0.18), residues: 2376 helix: 2.35 (0.18), residues: 900 sheet: 0.17 (0.27), residues: 378 loop : 0.58 (0.19), residues: 1098 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 454 HIS 0.007 0.001 HIS B 191 PHE 0.019 0.001 PHE D 308 TYR 0.023 0.001 TYR C 236 ARG 0.005 0.000 ARG A 469 *********************** 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 487 residues out of total 2094 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 440 time to evaluate : 2.378 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 113 ASP cc_start: 0.8749 (t0) cc_final: 0.8502 (t0) REVERT: A 355 ASP cc_start: 0.8655 (t70) cc_final: 0.8309 (t70) REVERT: A 478 LYS cc_start: 0.9011 (tptt) cc_final: 0.8643 (ttmm) REVERT: A 540 GLU cc_start: 0.8729 (tp30) cc_final: 0.8489 (tp30) REVERT: B 120 ASP cc_start: 0.8731 (m-30) cc_final: 0.8280 (m-30) REVERT: B 225 LYS cc_start: 0.8964 (mmmt) cc_final: 0.8694 (tptm) REVERT: B 296 GLU cc_start: 0.8108 (tm-30) cc_final: 0.7831 (tm-30) REVERT: B 361 GLN cc_start: 0.9132 (pm20) cc_final: 0.8908 (pm20) REVERT: B 477 ARG cc_start: 0.8604 (ttt90) cc_final: 0.7318 (mtt180) REVERT: C 226 ASP cc_start: 0.7312 (t0) cc_final: 0.6724 (t0) REVERT: C 441 VAL cc_start: 0.9539 (OUTLIER) cc_final: 0.9322 (m) REVERT: C 485 HIS cc_start: 0.8511 (OUTLIER) cc_final: 0.7851 (t-90) REVERT: C 527 SER cc_start: 0.9160 (m) cc_final: 0.8902 (t) REVERT: C 540 GLU cc_start: 0.8232 (tp30) cc_final: 0.7828 (tp30) REVERT: C 544 ASP cc_start: 0.8190 (t0) cc_final: 0.7801 (t0) REVERT: D 170 THR cc_start: 0.9382 (m) cc_final: 0.9157 (p) REVERT: D 296 GLU cc_start: 0.8250 (tt0) cc_final: 0.8010 (tm-30) REVERT: D 330 LEU cc_start: 0.9386 (OUTLIER) cc_final: 0.9025 (tt) REVERT: D 336 GLU cc_start: 0.9187 (tp30) cc_final: 0.8839 (tp30) REVERT: D 348 GLN cc_start: 0.8765 (tp40) cc_final: 0.8550 (tp40) REVERT: D 453 SER cc_start: 0.9476 (t) cc_final: 0.9106 (m) REVERT: D 470 LYS cc_start: 0.8526 (OUTLIER) cc_final: 0.8099 (ttpp) REVERT: D 471 GLN cc_start: 0.7758 (tp-100) cc_final: 0.7498 (tp-100) REVERT: D 477 ARG cc_start: 0.7867 (ttt90) cc_final: 0.5847 (mtt180) REVERT: D 478 LYS cc_start: 0.9138 (tttt) cc_final: 0.8792 (tppt) REVERT: E 226 ASP cc_start: 0.7972 (t0) cc_final: 0.7490 (t0) REVERT: E 232 GLU cc_start: 0.8754 (mm-30) cc_final: 0.8461 (mm-30) REVERT: E 442 MET cc_start: 0.9157 (tmm) cc_final: 0.8765 (tmm) REVERT: F 355 ASP cc_start: 0.8633 (t70) cc_final: 0.8296 (t70) REVERT: F 422 LEU cc_start: 0.9002 (tt) cc_final: 0.8430 (mp) REVERT: F 452 MET cc_start: 0.7423 (ttt) cc_final: 0.7142 (ttt) outliers start: 47 outliers final: 38 residues processed: 469 average time/residue: 0.3269 time to fit residues: 225.5926 Evaluate side-chains 476 residues out of total 2094 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 434 time to evaluate : 2.247 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 187 ILE Chi-restraints excluded: chain A residue 215 SER Chi-restraints excluded: chain A residue 302 ILE Chi-restraints excluded: chain A residue 367 VAL Chi-restraints excluded: chain A residue 386 THR 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 504 ASP Chi-restraints excluded: chain B residue 543 LYS Chi-restraints excluded: chain C residue 367 VAL Chi-restraints excluded: chain C residue 429 ASN Chi-restraints excluded: chain C residue 441 VAL Chi-restraints excluded: chain C residue 485 HIS 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 138 VAL 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 357 LEU Chi-restraints excluded: chain D residue 367 VAL Chi-restraints excluded: chain D residue 442 MET 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 357 LEU Chi-restraints excluded: chain E residue 367 VAL Chi-restraints excluded: chain E residue 386 THR Chi-restraints excluded: chain E residue 441 VAL 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 208 VAL Chi-restraints excluded: chain F residue 218 SER Chi-restraints excluded: chain F residue 357 LEU Chi-restraints excluded: chain F residue 367 VAL Chi-restraints excluded: chain F residue 402 SER 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 141 optimal weight: 1.9990 chunk 227 optimal weight: 5.9990 chunk 139 optimal weight: 3.9990 chunk 108 optimal weight: 1.9990 chunk 158 optimal weight: 0.1980 chunk 239 optimal weight: 0.8980 chunk 220 optimal weight: 1.9990 chunk 190 optimal weight: 6.9990 chunk 19 optimal weight: 0.9990 chunk 147 optimal weight: 3.9990 chunk 116 optimal weight: 0.5980 overall best weight: 0.9384 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8298 moved from start: 0.4078 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= 0.151 Angle : 0.514 13.860 25976 Z= 0.265 Chirality : 0.041 0.153 2883 Planarity : 0.004 0.057 3292 Dihedral : 3.687 17.496 2627 Min Nonbonded Distance : 2.132 Molprobity Statistics. All-atom Clashscore : 7.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Rotamer: Outliers : 1.95 % Allowed : 22.26 % Favored : 75.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.74 (0.18), residues: 2376 helix: 2.35 (0.18), residues: 900 sheet: 0.22 (0.27), residues: 378 loop : 0.62 (0.19), residues: 1098 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP E 454 HIS 0.007 0.000 HIS B 191 PHE 0.008 0.001 PHE B 374 TYR 0.025 0.001 TYR B 343 ARG 0.006 0.000 ARG D 469 ********************** 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 490 residues out of total 2094 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 451 time to evaluate : 2.263 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 113 ASP cc_start: 0.8741 (t0) cc_final: 0.8484 (t0) REVERT: A 355 ASP cc_start: 0.8617 (t70) cc_final: 0.8277 (t70) REVERT: A 478 LYS cc_start: 0.9016 (tptt) cc_final: 0.8648 (ttmm) REVERT: A 540 GLU cc_start: 0.8697 (tp30) cc_final: 0.8470 (tp30) REVERT: B 120 ASP cc_start: 0.8709 (m-30) cc_final: 0.8246 (m-30) REVERT: B 225 LYS cc_start: 0.8942 (mmmt) cc_final: 0.8682 (tptm) REVERT: B 296 GLU cc_start: 0.8140 (tm-30) cc_final: 0.7853 (tm-30) REVERT: B 361 GLN cc_start: 0.9122 (pm20) cc_final: 0.8904 (pm20) REVERT: B 477 ARG cc_start: 0.8577 (ttt90) cc_final: 0.7307 (mtt180) REVERT: C 106 ARG cc_start: 0.7601 (ptm-80) cc_final: 0.7370 (ttp80) REVERT: C 226 ASP cc_start: 0.7273 (t0) cc_final: 0.6665 (t0) REVERT: C 386 THR cc_start: 0.9064 (m) cc_final: 0.8611 (p) REVERT: C 441 VAL cc_start: 0.9534 (OUTLIER) cc_final: 0.9317 (m) REVERT: C 485 HIS cc_start: 0.8419 (OUTLIER) cc_final: 0.7761 (t-90) REVERT: C 527 SER cc_start: 0.9174 (m) cc_final: 0.8898 (t) REVERT: C 540 GLU cc_start: 0.8203 (tp30) cc_final: 0.7975 (tp30) REVERT: D 170 THR cc_start: 0.9371 (m) cc_final: 0.9134 (p) REVERT: D 296 GLU cc_start: 0.8235 (tt0) cc_final: 0.7988 (tm-30) REVERT: D 330 LEU cc_start: 0.9347 (OUTLIER) cc_final: 0.8980 (tt) REVERT: D 336 GLU cc_start: 0.9198 (tp30) cc_final: 0.8823 (tp30) REVERT: D 348 GLN cc_start: 0.8729 (tp40) cc_final: 0.8263 (tp40) REVERT: D 441 VAL cc_start: 0.9043 (t) cc_final: 0.8784 (p) REVERT: D 453 SER cc_start: 0.9455 (t) cc_final: 0.9103 (m) REVERT: D 477 ARG cc_start: 0.7827 (ttt90) cc_final: 0.5825 (mtt180) REVERT: D 478 LYS cc_start: 0.9134 (tttt) cc_final: 0.8783 (tptt) REVERT: E 226 ASP cc_start: 0.7970 (t0) cc_final: 0.7464 (t0) REVERT: E 232 GLU cc_start: 0.8777 (mm-30) cc_final: 0.8485 (mm-30) REVERT: E 442 MET cc_start: 0.9058 (tmm) cc_final: 0.8775 (tmm) REVERT: F 355 ASP cc_start: 0.8533 (t70) cc_final: 0.8220 (t70) REVERT: F 422 LEU cc_start: 0.9031 (tt) cc_final: 0.8425 (mp) REVERT: F 452 MET cc_start: 0.7291 (ttt) cc_final: 0.6976 (ttt) outliers start: 39 outliers final: 33 residues processed: 476 average time/residue: 0.3212 time to fit residues: 225.4173 Evaluate side-chains 476 residues out of total 2094 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 440 time to evaluate : 3.442 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 187 ILE Chi-restraints excluded: chain A residue 215 SER Chi-restraints excluded: chain A residue 302 ILE Chi-restraints excluded: chain A residue 367 VAL Chi-restraints excluded: chain A residue 386 THR Chi-restraints excluded: chain B residue 122 VAL Chi-restraints excluded: chain B residue 137 GLU Chi-restraints excluded: chain B residue 325 THR Chi-restraints excluded: chain B residue 504 ASP Chi-restraints excluded: chain C residue 210 THR Chi-restraints excluded: chain C residue 367 VAL Chi-restraints excluded: chain C residue 429 ASN Chi-restraints excluded: chain C residue 441 VAL Chi-restraints excluded: chain C residue 485 HIS 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 138 VAL 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 E residue 213 LEU Chi-restraints excluded: chain E residue 357 LEU Chi-restraints excluded: chain E residue 367 VAL Chi-restraints excluded: chain E residue 386 THR Chi-restraints excluded: chain E residue 441 VAL Chi-restraints excluded: chain E residue 466 VAL Chi-restraints excluded: chain E residue 518 ILE Chi-restraints excluded: chain E residue 530 LEU Chi-restraints excluded: chain F residue 131 VAL Chi-restraints excluded: chain F residue 208 VAL Chi-restraints excluded: chain F residue 218 SER Chi-restraints excluded: chain F residue 357 LEU 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 151 optimal weight: 2.9990 chunk 202 optimal weight: 6.9990 chunk 58 optimal weight: 9.9990 chunk 175 optimal weight: 0.8980 chunk 28 optimal weight: 0.0270 chunk 52 optimal weight: 10.0000 chunk 190 optimal weight: 7.9990 chunk 79 optimal weight: 5.9990 chunk 195 optimal weight: 0.9990 chunk 24 optimal weight: 6.9990 chunk 35 optimal weight: 1.9990 overall best weight: 1.3844 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.111109 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3073 r_free = 0.3073 target = 0.088072 restraints weight = 35839.862| |-----------------------------------------------------------------------------| r_work (start): 0.3067 rms_B_bonded: 3.23 r_work: 0.2930 rms_B_bonded: 3.64 restraints_weight: 0.5000 r_work (final): 0.2930 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8399 moved from start: 0.4119 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 19185 Z= 0.173 Angle : 0.529 15.735 25976 Z= 0.271 Chirality : 0.041 0.147 2883 Planarity : 0.004 0.057 3292 Dihedral : 3.703 17.433 2627 Min Nonbonded Distance : 2.122 Molprobity Statistics. All-atom Clashscore : 7.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Rotamer: Outliers : 1.85 % Allowed : 22.51 % Favored : 75.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.73 (0.18), residues: 2376 helix: 2.37 (0.18), residues: 900 sheet: 0.20 (0.27), residues: 378 loop : 0.58 (0.19), residues: 1098 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 454 HIS 0.006 0.001 HIS B 191 PHE 0.008 0.001 PHE E 423 TYR 0.023 0.001 TYR B 343 ARG 0.005 0.000 ARG D 469 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5486.31 seconds wall clock time: 98 minutes 41.59 seconds (5921.59 seconds total)