Starting phenix.real_space_refine on Fri Feb 6 20:32:09 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9lh3_63083/02_2026/9lh3_63083.cif Found real_map, /net/cci-nas-00/data/ceres_data/9lh3_63083/02_2026/9lh3_63083.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.51 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9lh3_63083/02_2026/9lh3_63083.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9lh3_63083/02_2026/9lh3_63083.map" model { file = "/net/cci-nas-00/data/ceres_data/9lh3_63083/02_2026/9lh3_63083.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9lh3_63083/02_2026/9lh3_63083.cif" } resolution = 3.51 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.010 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 56 5.16 5 C 17073 2.51 5 N 4802 2.21 5 O 5383 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 27314 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 3902 Number of conformers: 1 Conformer: "" Number of residues, atoms: 505, 3902 Classifications: {'peptide': 505} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 26} Link IDs: {'PTRANS': 13, 'TRANS': 491} Chain breaks: 10 Unresolved non-hydrogen bonds: 120 Unresolved non-hydrogen angles: 144 Unresolved non-hydrogen dihedrals: 108 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASN:plan1': 1, 'GLU:plan': 2, 'ASP:plan': 1, 'ARG:plan': 3, 'PHE:plan': 1, 'GLN:plan1': 6, 'TYR:plan': 1, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 75 Chain: "B" Number of atoms: 3902 Number of conformers: 1 Conformer: "" Number of residues, atoms: 505, 3902 Classifications: {'peptide': 505} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 26} Link IDs: {'PTRANS': 13, 'TRANS': 491} Chain breaks: 10 Unresolved non-hydrogen bonds: 120 Unresolved non-hydrogen angles: 144 Unresolved non-hydrogen dihedrals: 108 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASN:plan1': 1, 'GLU:plan': 2, 'ASP:plan': 1, 'ARG:plan': 3, 'PHE:plan': 1, 'GLN:plan1': 6, 'TYR:plan': 1, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 75 Chain: "C" Number of atoms: 3902 Number of conformers: 1 Conformer: "" Number of residues, atoms: 505, 3902 Classifications: {'peptide': 505} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 26} Link IDs: {'PTRANS': 13, 'TRANS': 491} Chain breaks: 10 Unresolved non-hydrogen bonds: 120 Unresolved non-hydrogen angles: 144 Unresolved non-hydrogen dihedrals: 108 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASN:plan1': 1, 'GLU:plan': 2, 'ASP:plan': 1, 'ARG:plan': 3, 'PHE:plan': 1, 'GLN:plan1': 6, 'TYR:plan': 1, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 75 Chain: "D" Number of atoms: 3902 Number of conformers: 1 Conformer: "" Number of residues, atoms: 505, 3902 Classifications: {'peptide': 505} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 26} Link IDs: {'PTRANS': 13, 'TRANS': 491} Chain breaks: 10 Unresolved non-hydrogen bonds: 120 Unresolved non-hydrogen angles: 144 Unresolved non-hydrogen dihedrals: 108 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASN:plan1': 1, 'GLU:plan': 2, 'ASP:plan': 1, 'ARG:plan': 3, 'PHE:plan': 1, 'GLN:plan1': 6, 'TYR:plan': 1, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 75 Chain: "E" Number of atoms: 3902 Number of conformers: 1 Conformer: "" Number of residues, atoms: 505, 3902 Classifications: {'peptide': 505} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 26} Link IDs: {'PTRANS': 13, 'TRANS': 491} Chain breaks: 10 Unresolved non-hydrogen bonds: 120 Unresolved non-hydrogen angles: 144 Unresolved non-hydrogen dihedrals: 108 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASN:plan1': 1, 'GLU:plan': 2, 'ASP:plan': 1, 'ARG:plan': 3, 'PHE:plan': 1, 'GLN:plan1': 6, 'TYR:plan': 1, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 75 Chain: "F" Number of atoms: 3902 Number of conformers: 1 Conformer: "" Number of residues, atoms: 505, 3902 Classifications: {'peptide': 505} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 26} Link IDs: {'PTRANS': 13, 'TRANS': 491} Chain breaks: 10 Unresolved non-hydrogen bonds: 120 Unresolved non-hydrogen angles: 144 Unresolved non-hydrogen dihedrals: 108 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASN:plan1': 1, 'GLU:plan': 2, 'ASP:plan': 1, 'ARG:plan': 3, 'PHE:plan': 1, 'GLN:plan1': 6, 'TYR:plan': 1, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 75 Chain: "G" Number of atoms: 3902 Number of conformers: 1 Conformer: "" Number of residues, atoms: 505, 3902 Classifications: {'peptide': 505} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 26} Link IDs: {'PTRANS': 13, 'TRANS': 491} Chain breaks: 10 Unresolved non-hydrogen bonds: 120 Unresolved non-hydrogen angles: 144 Unresolved non-hydrogen dihedrals: 108 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASN:plan1': 1, 'GLU:plan': 2, 'ASP:plan': 1, 'ARG:plan': 3, 'PHE:plan': 1, 'GLN:plan1': 6, 'TYR:plan': 1, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 75 Time building chain proxies: 6.95, per 1000 atoms: 0.25 Number of scatterers: 27314 At special positions: 0 Unit cell: (153.64, 152.72, 122.36, 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 56 16.00 O 5383 8.00 N 4802 7.00 C 17073 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=14, symmetry=0 Simple disulfide: pdb=" SG CYS A 472 " - pdb=" SG CYS A 486 " distance=2.47 Simple disulfide: pdb=" SG CYS B 157 " - pdb=" SG CYS B 175 " distance=2.55 Simple disulfide: pdb=" SG CYS B 472 " - pdb=" SG CYS B 486 " distance=2.47 Simple disulfide: pdb=" SG CYS C 472 " - pdb=" SG CYS C 486 " distance=2.47 Simple disulfide: pdb=" SG CYS C 512 " - pdb=" SG CYS C 524 " distance=2.97 Simple disulfide: pdb=" SG CYS D 157 " - pdb=" SG CYS D 175 " distance=2.55 Simple disulfide: pdb=" SG CYS D 472 " - pdb=" SG CYS D 486 " distance=2.47 Simple disulfide: pdb=" SG CYS D 512 " - pdb=" SG CYS D 524 " distance=2.98 Simple disulfide: pdb=" SG CYS E 472 " - pdb=" SG CYS E 486 " distance=2.46 Simple disulfide: pdb=" SG CYS E 512 " - pdb=" SG CYS E 524 " distance=2.98 Simple disulfide: pdb=" SG CYS F 472 " - pdb=" SG CYS F 486 " distance=2.47 Simple disulfide: pdb=" SG CYS F 512 " - pdb=" SG CYS F 524 " distance=2.97 Simple disulfide: pdb=" SG CYS G 472 " - pdb=" SG CYS G 486 " distance=2.47 Simple disulfide: pdb=" SG CYS G 512 " - pdb=" SG CYS G 524 " distance=2.98 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.57 Conformation dependent library (CDL) restraints added in 1.2 seconds 6762 Ramachandran restraints generated. 3381 Oldfield, 0 Emsley, 3381 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6622 Finding SS restraints... Secondary structure from input PDB file: 28 helices and 106 sheets defined 4.4% alpha, 26.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.26 Creating SS restraints... Processing helix chain 'A' and resid 153 through 158 Processing helix chain 'A' and resid 374 through 379 removed outlier: 3.741A pdb=" N TYR A 378 " --> pdb=" O SER A 374 " (cutoff:3.500A) Processing helix chain 'A' and resid 452 through 457 removed outlier: 3.504A pdb=" N PHE A 455 " --> pdb=" O HIS A 452 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N THR A 456 " --> pdb=" O PRO A 453 " (cutoff:3.500A) removed outlier: 4.324A pdb=" N GLY A 457 " --> pdb=" O VAL A 454 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 452 through 457' Processing helix chain 'A' and resid 490 through 493 Processing helix chain 'B' and resid 153 through 158 Processing helix chain 'B' and resid 374 through 379 removed outlier: 3.742A pdb=" N TYR B 378 " --> pdb=" O SER B 374 " (cutoff:3.500A) Processing helix chain 'B' and resid 452 through 457 removed outlier: 3.503A pdb=" N PHE B 455 " --> pdb=" O HIS B 452 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N THR B 456 " --> pdb=" O PRO B 453 " (cutoff:3.500A) removed outlier: 4.325A pdb=" N GLY B 457 " --> pdb=" O VAL B 454 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 452 through 457' Processing helix chain 'B' and resid 490 through 493 Processing helix chain 'C' and resid 153 through 158 Processing helix chain 'C' and resid 374 through 379 removed outlier: 3.741A pdb=" N TYR C 378 " --> pdb=" O SER C 374 " (cutoff:3.500A) Processing helix chain 'C' and resid 452 through 457 removed outlier: 3.504A pdb=" N PHE C 455 " --> pdb=" O HIS C 452 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N THR C 456 " --> pdb=" O PRO C 453 " (cutoff:3.500A) removed outlier: 4.325A pdb=" N GLY C 457 " --> pdb=" O VAL C 454 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 452 through 457' Processing helix chain 'C' and resid 490 through 493 Processing helix chain 'D' and resid 153 through 158 Processing helix chain 'D' and resid 374 through 379 removed outlier: 3.741A pdb=" N TYR D 378 " --> pdb=" O SER D 374 " (cutoff:3.500A) Processing helix chain 'D' and resid 452 through 457 removed outlier: 3.504A pdb=" N PHE D 455 " --> pdb=" O HIS D 452 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N THR D 456 " --> pdb=" O PRO D 453 " (cutoff:3.500A) removed outlier: 4.324A pdb=" N GLY D 457 " --> pdb=" O VAL D 454 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 452 through 457' Processing helix chain 'D' and resid 490 through 493 Processing helix chain 'E' and resid 153 through 158 Processing helix chain 'E' and resid 374 through 379 removed outlier: 3.741A pdb=" N TYR E 378 " --> pdb=" O SER E 374 " (cutoff:3.500A) Processing helix chain 'E' and resid 452 through 457 removed outlier: 3.504A pdb=" N PHE E 455 " --> pdb=" O HIS E 452 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N THR E 456 " --> pdb=" O PRO E 453 " (cutoff:3.500A) removed outlier: 4.324A pdb=" N GLY E 457 " --> pdb=" O VAL E 454 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 452 through 457' Processing helix chain 'E' and resid 490 through 493 Processing helix chain 'F' and resid 153 through 158 Processing helix chain 'F' and resid 374 through 379 removed outlier: 3.741A pdb=" N TYR F 378 " --> pdb=" O SER F 374 " (cutoff:3.500A) Processing helix chain 'F' and resid 452 through 457 removed outlier: 3.504A pdb=" N PHE F 455 " --> pdb=" O HIS F 452 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N THR F 456 " --> pdb=" O PRO F 453 " (cutoff:3.500A) removed outlier: 4.324A pdb=" N GLY F 457 " --> pdb=" O VAL F 454 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 452 through 457' Processing helix chain 'F' and resid 490 through 493 Processing helix chain 'G' and resid 153 through 158 Processing helix chain 'G' and resid 374 through 379 removed outlier: 3.742A pdb=" N TYR G 378 " --> pdb=" O SER G 374 " (cutoff:3.500A) Processing helix chain 'G' and resid 452 through 457 removed outlier: 3.504A pdb=" N PHE G 455 " --> pdb=" O HIS G 452 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N THR G 456 " --> pdb=" O PRO G 453 " (cutoff:3.500A) removed outlier: 4.323A pdb=" N GLY G 457 " --> pdb=" O VAL G 454 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 452 through 457' Processing helix chain 'G' and resid 490 through 493 Processing sheet with id=AA1, first strand: chain 'A' and resid 141 through 146 removed outlier: 3.521A pdb=" N LEU A 188 " --> pdb=" O VAL A 142 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N PHE A 144 " --> pdb=" O VAL A 186 " (cutoff:3.500A) removed outlier: 4.119A pdb=" N VAL A 186 " --> pdb=" O PHE A 144 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ILE A 146 " --> pdb=" O TYR A 184 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N TYR A 184 " --> pdb=" O ILE A 146 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 150 through 152 removed outlier: 4.408A pdb=" N ALA A 178 " --> pdb=" O ILE A 152 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 159 through 160 removed outlier: 4.050A pdb=" N PHE A 159 " --> pdb=" O ARG A 172 " (cutoff:3.500A) removed outlier: 4.040A pdb=" N ARG A 172 " --> pdb=" O PHE A 159 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'A' and resid 230 through 232 removed outlier: 3.718A pdb=" N GLU A 244 " --> pdb=" O PHE A 231 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 247 through 251 removed outlier: 6.030A pdb=" N ASP A 248 " --> pdb=" O ILE A 412 " (cutoff:3.500A) removed outlier: 5.055A pdb=" N ILE A 412 " --> pdb=" O ASP A 248 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N ILE A 440 " --> pdb=" O VAL A 407 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 329 through 334 removed outlier: 6.530A pdb=" N ALA A 337 " --> pdb=" O LYS A 333 " (cutoff:3.500A) removed outlier: 4.378A pdb=" N VAL A 257 " --> pdb=" O ASP A 404 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 329 through 334 removed outlier: 6.530A pdb=" N ALA A 337 " --> pdb=" O LYS A 333 " (cutoff:3.500A) removed outlier: 4.378A pdb=" N VAL A 257 " --> pdb=" O ASP A 404 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N THR A 399 " --> pdb=" O VAL A 448 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N VAL A 448 " --> pdb=" O THR A 399 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 266 through 270 removed outlier: 6.820A pdb=" N ILE A 388 " --> pdb=" O LEU A 268 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 281 through 292 removed outlier: 3.621A pdb=" N GLU A 281 " --> pdb=" O THR A 320 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N LYS A 283 " --> pdb=" O TRP A 318 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N SER A 312 " --> pdb=" O GLU A 289 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N GLU C 281 " --> pdb=" O THR C 320 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N LYS C 283 " --> pdb=" O TRP C 318 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N SER C 312 " --> pdb=" O GLU C 289 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N GLU B 281 " --> pdb=" O THR B 320 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N LYS B 283 " --> pdb=" O TRP B 318 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N SER B 312 " --> pdb=" O GLU B 289 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N GLU F 281 " --> pdb=" O THR F 320 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N LYS F 283 " --> pdb=" O TRP F 318 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N SER F 312 " --> pdb=" O GLU F 289 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N GLU E 281 " --> pdb=" O THR E 320 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N LYS E 283 " --> pdb=" O TRP E 318 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N SER E 312 " --> pdb=" O GLU E 289 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N GLU D 281 " --> pdb=" O THR D 320 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N LYS D 283 " --> pdb=" O TRP D 318 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N SER D 312 " --> pdb=" O GLU D 289 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N GLU G 281 " --> pdb=" O THR G 320 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N LYS G 283 " --> pdb=" O TRP G 318 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N SER G 312 " --> pdb=" O GLU G 289 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 415 through 416 Processing sheet with id=AB2, first strand: chain 'A' and resid 472 through 473 removed outlier: 3.636A pdb=" N ASN A 484 " --> pdb=" O CYS A 472 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 495 through 497 removed outlier: 3.796A pdb=" N VAL A 504 " --> pdb=" O ILE A 496 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 616 through 621 Processing sheet with id=AB5, first strand: chain 'A' and resid 644 through 645 Processing sheet with id=AB6, first strand: chain 'A' and resid 663 through 664 Processing sheet with id=AB7, first strand: chain 'A' and resid 698 through 699 removed outlier: 4.057A pdb=" N GLN A 698 " --> pdb=" O ASP A 714 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N ASP A 714 " --> pdb=" O GLN A 698 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB7 Processing sheet with id=AB8, first strand: chain 'B' and resid 141 through 146 removed outlier: 3.521A pdb=" N LEU B 188 " --> pdb=" O VAL B 142 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N PHE B 144 " --> pdb=" O VAL B 186 " (cutoff:3.500A) removed outlier: 4.118A pdb=" N VAL B 186 " --> pdb=" O PHE B 144 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ILE B 146 " --> pdb=" O TYR B 184 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N TYR B 184 " --> pdb=" O ILE B 146 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 150 through 152 removed outlier: 4.408A pdb=" N ALA B 178 " --> pdb=" O ILE B 152 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 159 through 160 removed outlier: 4.051A pdb=" N PHE B 159 " --> pdb=" O ARG B 172 " (cutoff:3.500A) removed outlier: 4.040A pdb=" N ARG B 172 " --> pdb=" O PHE B 159 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC1 Processing sheet with id=AC2, first strand: chain 'B' and resid 230 through 232 removed outlier: 3.718A pdb=" N GLU B 244 " --> pdb=" O PHE B 231 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 247 through 251 removed outlier: 6.031A pdb=" N ASP B 248 " --> pdb=" O ILE B 412 " (cutoff:3.500A) removed outlier: 5.055A pdb=" N ILE B 412 " --> pdb=" O ASP B 248 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N ILE B 440 " --> pdb=" O VAL B 407 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 329 through 334 removed outlier: 6.529A pdb=" N ALA B 337 " --> pdb=" O LYS B 333 " (cutoff:3.500A) removed outlier: 4.379A pdb=" N VAL B 257 " --> pdb=" O ASP B 404 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 329 through 334 removed outlier: 6.529A pdb=" N ALA B 337 " --> pdb=" O LYS B 333 " (cutoff:3.500A) removed outlier: 4.379A pdb=" N VAL B 257 " --> pdb=" O ASP B 404 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N THR B 399 " --> pdb=" O VAL B 448 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N VAL B 448 " --> pdb=" O THR B 399 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 266 through 270 removed outlier: 6.820A pdb=" N ILE B 388 " --> pdb=" O LEU B 268 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 415 through 416 Processing sheet with id=AC8, first strand: chain 'B' and resid 472 through 473 removed outlier: 3.636A pdb=" N ASN B 484 " --> pdb=" O CYS B 472 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 495 through 497 removed outlier: 3.796A pdb=" N VAL B 504 " --> pdb=" O ILE B 496 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 616 through 621 Processing sheet with id=AD2, first strand: chain 'B' and resid 644 through 645 Processing sheet with id=AD3, first strand: chain 'B' and resid 663 through 664 Processing sheet with id=AD4, first strand: chain 'B' and resid 698 through 699 removed outlier: 4.057A pdb=" N GLN B 698 " --> pdb=" O ASP B 714 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N ASP B 714 " --> pdb=" O GLN B 698 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD4 Processing sheet with id=AD5, first strand: chain 'C' and resid 141 through 146 removed outlier: 3.521A pdb=" N LEU C 188 " --> pdb=" O VAL C 142 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N PHE C 144 " --> pdb=" O VAL C 186 " (cutoff:3.500A) removed outlier: 4.119A pdb=" N VAL C 186 " --> pdb=" O PHE C 144 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ILE C 146 " --> pdb=" O TYR C 184 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N TYR C 184 " --> pdb=" O ILE C 146 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 150 through 152 removed outlier: 4.407A pdb=" N ALA C 178 " --> pdb=" O ILE C 152 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 159 through 160 removed outlier: 4.049A pdb=" N PHE C 159 " --> pdb=" O ARG C 172 " (cutoff:3.500A) removed outlier: 4.040A pdb=" N ARG C 172 " --> pdb=" O PHE C 159 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD7 Processing sheet with id=AD8, first strand: chain 'C' and resid 230 through 232 removed outlier: 3.718A pdb=" N GLU C 244 " --> pdb=" O PHE C 231 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 247 through 251 removed outlier: 6.030A pdb=" N ASP C 248 " --> pdb=" O ILE C 412 " (cutoff:3.500A) removed outlier: 5.055A pdb=" N ILE C 412 " --> pdb=" O ASP C 248 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N ILE C 440 " --> pdb=" O VAL C 407 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 329 through 334 removed outlier: 6.530A pdb=" N ALA C 337 " --> pdb=" O LYS C 333 " (cutoff:3.500A) removed outlier: 4.378A pdb=" N VAL C 257 " --> pdb=" O ASP C 404 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 329 through 334 removed outlier: 6.530A pdb=" N ALA C 337 " --> pdb=" O LYS C 333 " (cutoff:3.500A) removed outlier: 4.378A pdb=" N VAL C 257 " --> pdb=" O ASP C 404 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N THR C 399 " --> pdb=" O VAL C 448 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N VAL C 448 " --> pdb=" O THR C 399 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 266 through 270 removed outlier: 6.821A pdb=" N ILE C 388 " --> pdb=" O LEU C 268 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 415 through 416 Processing sheet with id=AE5, first strand: chain 'C' and resid 472 through 473 removed outlier: 3.636A pdb=" N ASN C 484 " --> pdb=" O CYS C 472 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 495 through 497 removed outlier: 3.796A pdb=" N VAL C 504 " --> pdb=" O ILE C 496 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'C' and resid 616 through 621 Processing sheet with id=AE8, first strand: chain 'C' and resid 644 through 645 Processing sheet with id=AE9, first strand: chain 'C' and resid 663 through 664 Processing sheet with id=AF1, first strand: chain 'C' and resid 698 through 699 removed outlier: 4.058A pdb=" N GLN C 698 " --> pdb=" O ASP C 714 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N ASP C 714 " --> pdb=" O GLN C 698 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF1 Processing sheet with id=AF2, first strand: chain 'D' and resid 141 through 146 removed outlier: 3.521A pdb=" N LEU D 188 " --> pdb=" O VAL D 142 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N PHE D 144 " --> pdb=" O VAL D 186 " (cutoff:3.500A) removed outlier: 4.119A pdb=" N VAL D 186 " --> pdb=" O PHE D 144 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ILE D 146 " --> pdb=" O TYR D 184 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N TYR D 184 " --> pdb=" O ILE D 146 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'D' and resid 150 through 152 removed outlier: 4.407A pdb=" N ALA D 178 " --> pdb=" O ILE D 152 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'D' and resid 159 through 160 removed outlier: 4.050A pdb=" N PHE D 159 " --> pdb=" O ARG D 172 " (cutoff:3.500A) removed outlier: 4.040A pdb=" N ARG D 172 " --> pdb=" O PHE D 159 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF4 Processing sheet with id=AF5, first strand: chain 'D' and resid 230 through 232 removed outlier: 3.718A pdb=" N GLU D 244 " --> pdb=" O PHE D 231 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'D' and resid 247 through 251 removed outlier: 6.031A pdb=" N ASP D 248 " --> pdb=" O ILE D 412 " (cutoff:3.500A) removed outlier: 5.055A pdb=" N ILE D 412 " --> pdb=" O ASP D 248 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N ILE D 440 " --> pdb=" O VAL D 407 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'D' and resid 329 through 334 removed outlier: 6.530A pdb=" N ALA D 337 " --> pdb=" O LYS D 333 " (cutoff:3.500A) removed outlier: 4.378A pdb=" N VAL D 257 " --> pdb=" O ASP D 404 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'D' and resid 329 through 334 removed outlier: 6.530A pdb=" N ALA D 337 " --> pdb=" O LYS D 333 " (cutoff:3.500A) removed outlier: 4.378A pdb=" N VAL D 257 " --> pdb=" O ASP D 404 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N THR D 399 " --> pdb=" O VAL D 448 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N VAL D 448 " --> pdb=" O THR D 399 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'D' and resid 266 through 270 removed outlier: 6.820A pdb=" N ILE D 388 " --> pdb=" O LEU D 268 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'D' and resid 415 through 416 Processing sheet with id=AG2, first strand: chain 'D' and resid 472 through 473 removed outlier: 3.635A pdb=" N ASN D 484 " --> pdb=" O CYS D 472 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'D' and resid 495 through 497 removed outlier: 3.796A pdb=" N VAL D 504 " --> pdb=" O ILE D 496 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'D' and resid 616 through 621 Processing sheet with id=AG5, first strand: chain 'D' and resid 644 through 645 Processing sheet with id=AG6, first strand: chain 'D' and resid 663 through 664 Processing sheet with id=AG7, first strand: chain 'D' and resid 698 through 699 removed outlier: 4.057A pdb=" N GLN D 698 " --> pdb=" O ASP D 714 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N ASP D 714 " --> pdb=" O GLN D 698 " (cutoff:3.500A) No H-bonds generated for sheet with id=AG7 Processing sheet with id=AG8, first strand: chain 'E' and resid 141 through 146 removed outlier: 3.521A pdb=" N LEU E 188 " --> pdb=" O VAL E 142 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N PHE E 144 " --> pdb=" O VAL E 186 " (cutoff:3.500A) removed outlier: 4.119A pdb=" N VAL E 186 " --> pdb=" O PHE E 144 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ILE E 146 " --> pdb=" O TYR E 184 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N TYR E 184 " --> pdb=" O ILE E 146 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'E' and resid 150 through 152 removed outlier: 4.408A pdb=" N ALA E 178 " --> pdb=" O ILE E 152 " (cutoff:3.500A) Processing sheet with id=AH1, first strand: chain 'E' and resid 159 through 160 removed outlier: 4.049A pdb=" N PHE E 159 " --> pdb=" O ARG E 172 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N ARG E 172 " --> pdb=" O PHE E 159 " (cutoff:3.500A) No H-bonds generated for sheet with id=AH1 Processing sheet with id=AH2, first strand: chain 'E' and resid 230 through 232 removed outlier: 3.718A pdb=" N GLU E 244 " --> pdb=" O PHE E 231 " (cutoff:3.500A) Processing sheet with id=AH3, first strand: chain 'E' and resid 247 through 251 removed outlier: 6.030A pdb=" N ASP E 248 " --> pdb=" O ILE E 412 " (cutoff:3.500A) removed outlier: 5.055A pdb=" N ILE E 412 " --> pdb=" O ASP E 248 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N ILE E 440 " --> pdb=" O VAL E 407 " (cutoff:3.500A) Processing sheet with id=AH4, first strand: chain 'E' and resid 329 through 334 removed outlier: 6.530A pdb=" N ALA E 337 " --> pdb=" O LYS E 333 " (cutoff:3.500A) removed outlier: 4.378A pdb=" N VAL E 257 " --> pdb=" O ASP E 404 " (cutoff:3.500A) Processing sheet with id=AH5, first strand: chain 'E' and resid 329 through 334 removed outlier: 6.530A pdb=" N ALA E 337 " --> pdb=" O LYS E 333 " (cutoff:3.500A) removed outlier: 4.378A pdb=" N VAL E 257 " --> pdb=" O ASP E 404 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N THR E 399 " --> pdb=" O VAL E 448 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N VAL E 448 " --> pdb=" O THR E 399 " (cutoff:3.500A) Processing sheet with id=AH6, first strand: chain 'E' and resid 266 through 270 removed outlier: 6.819A pdb=" N ILE E 388 " --> pdb=" O LEU E 268 " (cutoff:3.500A) Processing sheet with id=AH7, first strand: chain 'E' and resid 415 through 416 Processing sheet with id=AH8, first strand: chain 'E' and resid 472 through 473 removed outlier: 3.636A pdb=" N ASN E 484 " --> pdb=" O CYS E 472 " (cutoff:3.500A) Processing sheet with id=AH9, first strand: chain 'E' and resid 495 through 497 removed outlier: 3.796A pdb=" N VAL E 504 " --> pdb=" O ILE E 496 " (cutoff:3.500A) Processing sheet with id=AI1, first strand: chain 'E' and resid 616 through 621 Processing sheet with id=AI2, first strand: chain 'E' and resid 644 through 645 Processing sheet with id=AI3, first strand: chain 'E' and resid 663 through 664 Processing sheet with id=AI4, first strand: chain 'E' and resid 698 through 699 removed outlier: 4.057A pdb=" N GLN E 698 " --> pdb=" O ASP E 714 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N ASP E 714 " --> pdb=" O GLN E 698 " (cutoff:3.500A) No H-bonds generated for sheet with id=AI4 Processing sheet with id=AI5, first strand: chain 'F' and resid 141 through 146 removed outlier: 3.522A pdb=" N LEU F 188 " --> pdb=" O VAL F 142 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N PHE F 144 " --> pdb=" O VAL F 186 " (cutoff:3.500A) removed outlier: 4.119A pdb=" N VAL F 186 " --> pdb=" O PHE F 144 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ILE F 146 " --> pdb=" O TYR F 184 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N TYR F 184 " --> pdb=" O ILE F 146 " (cutoff:3.500A) Processing sheet with id=AI6, first strand: chain 'F' and resid 150 through 152 removed outlier: 4.408A pdb=" N ALA F 178 " --> pdb=" O ILE F 152 " (cutoff:3.500A) Processing sheet with id=AI7, first strand: chain 'F' and resid 159 through 160 removed outlier: 4.050A pdb=" N PHE F 159 " --> pdb=" O ARG F 172 " (cutoff:3.500A) removed outlier: 4.040A pdb=" N ARG F 172 " --> pdb=" O PHE F 159 " (cutoff:3.500A) No H-bonds generated for sheet with id=AI7 Processing sheet with id=AI8, first strand: chain 'F' and resid 230 through 232 removed outlier: 3.718A pdb=" N GLU F 244 " --> pdb=" O PHE F 231 " (cutoff:3.500A) Processing sheet with id=AI9, first strand: chain 'F' and resid 247 through 251 removed outlier: 6.030A pdb=" N ASP F 248 " --> pdb=" O ILE F 412 " (cutoff:3.500A) removed outlier: 5.055A pdb=" N ILE F 412 " --> pdb=" O ASP F 248 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N ILE F 440 " --> pdb=" O VAL F 407 " (cutoff:3.500A) Processing sheet with id=AJ1, first strand: chain 'F' and resid 329 through 334 removed outlier: 6.529A pdb=" N ALA F 337 " --> pdb=" O LYS F 333 " (cutoff:3.500A) removed outlier: 4.378A pdb=" N VAL F 257 " --> pdb=" O ASP F 404 " (cutoff:3.500A) Processing sheet with id=AJ2, first strand: chain 'F' and resid 329 through 334 removed outlier: 6.529A pdb=" N ALA F 337 " --> pdb=" O LYS F 333 " (cutoff:3.500A) removed outlier: 4.378A pdb=" N VAL F 257 " --> pdb=" O ASP F 404 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N THR F 399 " --> pdb=" O VAL F 448 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N VAL F 448 " --> pdb=" O THR F 399 " (cutoff:3.500A) Processing sheet with id=AJ3, first strand: chain 'F' and resid 266 through 270 removed outlier: 6.819A pdb=" N ILE F 388 " --> pdb=" O LEU F 268 " (cutoff:3.500A) Processing sheet with id=AJ4, first strand: chain 'F' and resid 415 through 416 Processing sheet with id=AJ5, first strand: chain 'F' and resid 472 through 473 removed outlier: 3.636A pdb=" N ASN F 484 " --> pdb=" O CYS F 472 " (cutoff:3.500A) Processing sheet with id=AJ6, first strand: chain 'F' and resid 495 through 497 removed outlier: 3.797A pdb=" N VAL F 504 " --> pdb=" O ILE F 496 " (cutoff:3.500A) Processing sheet with id=AJ7, first strand: chain 'F' and resid 616 through 621 Processing sheet with id=AJ8, first strand: chain 'F' and resid 644 through 645 Processing sheet with id=AJ9, first strand: chain 'F' and resid 663 through 664 Processing sheet with id=AK1, first strand: chain 'F' and resid 698 through 699 removed outlier: 4.058A pdb=" N GLN F 698 " --> pdb=" O ASP F 714 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N ASP F 714 " --> pdb=" O GLN F 698 " (cutoff:3.500A) No H-bonds generated for sheet with id=AK1 Processing sheet with id=AK2, first strand: chain 'G' and resid 141 through 146 removed outlier: 3.521A pdb=" N LEU G 188 " --> pdb=" O VAL G 142 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N PHE G 144 " --> pdb=" O VAL G 186 " (cutoff:3.500A) removed outlier: 4.119A pdb=" N VAL G 186 " --> pdb=" O PHE G 144 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ILE G 146 " --> pdb=" O TYR G 184 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N TYR G 184 " --> pdb=" O ILE G 146 " (cutoff:3.500A) Processing sheet with id=AK3, first strand: chain 'G' and resid 150 through 152 removed outlier: 4.408A pdb=" N ALA G 178 " --> pdb=" O ILE G 152 " (cutoff:3.500A) Processing sheet with id=AK4, first strand: chain 'G' and resid 159 through 160 removed outlier: 4.050A pdb=" N PHE G 159 " --> pdb=" O ARG G 172 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N ARG G 172 " --> pdb=" O PHE G 159 " (cutoff:3.500A) No H-bonds generated for sheet with id=AK4 Processing sheet with id=AK5, first strand: chain 'G' and resid 230 through 232 removed outlier: 3.718A pdb=" N GLU G 244 " --> pdb=" O PHE G 231 " (cutoff:3.500A) Processing sheet with id=AK6, first strand: chain 'G' and resid 247 through 251 removed outlier: 6.031A pdb=" N ASP G 248 " --> pdb=" O ILE G 412 " (cutoff:3.500A) removed outlier: 5.055A pdb=" N ILE G 412 " --> pdb=" O ASP G 248 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N ILE G 440 " --> pdb=" O VAL G 407 " (cutoff:3.500A) Processing sheet with id=AK7, first strand: chain 'G' and resid 329 through 334 removed outlier: 6.529A pdb=" N ALA G 337 " --> pdb=" O LYS G 333 " (cutoff:3.500A) removed outlier: 4.379A pdb=" N VAL G 257 " --> pdb=" O ASP G 404 " (cutoff:3.500A) Processing sheet with id=AK8, first strand: chain 'G' and resid 329 through 334 removed outlier: 6.529A pdb=" N ALA G 337 " --> pdb=" O LYS G 333 " (cutoff:3.500A) removed outlier: 4.379A pdb=" N VAL G 257 " --> pdb=" O ASP G 404 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N THR G 399 " --> pdb=" O VAL G 448 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N VAL G 448 " --> pdb=" O THR G 399 " (cutoff:3.500A) Processing sheet with id=AK9, first strand: chain 'G' and resid 266 through 270 removed outlier: 6.820A pdb=" N ILE G 388 " --> pdb=" O LEU G 268 " (cutoff:3.500A) Processing sheet with id=AL1, first strand: chain 'G' and resid 415 through 416 Processing sheet with id=AL2, first strand: chain 'G' and resid 472 through 473 removed outlier: 3.636A pdb=" N ASN G 484 " --> pdb=" O CYS G 472 " (cutoff:3.500A) Processing sheet with id=AL3, first strand: chain 'G' and resid 495 through 497 removed outlier: 3.796A pdb=" N VAL G 504 " --> pdb=" O ILE G 496 " (cutoff:3.500A) Processing sheet with id=AL4, first strand: chain 'G' and resid 616 through 621 Processing sheet with id=AL5, first strand: chain 'G' and resid 644 through 645 Processing sheet with id=AL6, first strand: chain 'G' and resid 663 through 664 Processing sheet with id=AL7, first strand: chain 'G' and resid 698 through 699 removed outlier: 4.058A pdb=" N GLN G 698 " --> pdb=" O ASP G 714 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N ASP G 714 " --> pdb=" O GLN G 698 " (cutoff:3.500A) No H-bonds generated for sheet with id=AL7 574 hydrogen bonds defined for protein. 1428 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: 6.66 Time building geometry restraints manager: 3.34 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 9239 1.34 - 1.46: 6627 1.46 - 1.58: 11896 1.58 - 1.70: 0 1.70 - 1.81: 70 Bond restraints: 27832 Sorted by residual: bond pdb=" C PRO E 411 " pdb=" N ILE E 412 " ideal model delta sigma weight residual 1.334 1.317 0.017 1.29e-02 6.01e+03 1.82e+00 bond pdb=" C PRO G 411 " pdb=" N ILE G 412 " ideal model delta sigma weight residual 1.334 1.317 0.017 1.29e-02 6.01e+03 1.74e+00 bond pdb=" C PRO A 411 " pdb=" N ILE A 412 " ideal model delta sigma weight residual 1.334 1.317 0.017 1.29e-02 6.01e+03 1.74e+00 bond pdb=" C PRO D 411 " pdb=" N ILE D 412 " ideal model delta sigma weight residual 1.334 1.317 0.017 1.29e-02 6.01e+03 1.71e+00 bond pdb=" C PRO C 411 " pdb=" N ILE C 412 " ideal model delta sigma weight residual 1.334 1.317 0.017 1.29e-02 6.01e+03 1.69e+00 ... (remaining 27827 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.40: 36339 1.40 - 2.81: 1204 2.81 - 4.21: 222 4.21 - 5.62: 35 5.62 - 7.02: 14 Bond angle restraints: 37814 Sorted by residual: angle pdb=" N VAL B 674 " pdb=" CA VAL B 674 " pdb=" C VAL B 674 " ideal model delta sigma weight residual 106.21 110.11 -3.90 1.07e+00 8.73e-01 1.33e+01 angle pdb=" N VAL C 674 " pdb=" CA VAL C 674 " pdb=" C VAL C 674 " ideal model delta sigma weight residual 106.21 110.08 -3.87 1.07e+00 8.73e-01 1.31e+01 angle pdb=" N VAL F 674 " pdb=" CA VAL F 674 " pdb=" C VAL F 674 " ideal model delta sigma weight residual 106.21 110.08 -3.87 1.07e+00 8.73e-01 1.31e+01 angle pdb=" N VAL A 674 " pdb=" CA VAL A 674 " pdb=" C VAL A 674 " ideal model delta sigma weight residual 106.21 110.07 -3.86 1.07e+00 8.73e-01 1.30e+01 angle pdb=" N VAL D 674 " pdb=" CA VAL D 674 " pdb=" C VAL D 674 " ideal model delta sigma weight residual 106.21 110.05 -3.84 1.07e+00 8.73e-01 1.29e+01 ... (remaining 37809 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.44: 14742 17.44 - 34.88: 1286 34.88 - 52.31: 210 52.31 - 69.75: 35 69.75 - 87.19: 37 Dihedral angle restraints: 16310 sinusoidal: 6076 harmonic: 10234 Sorted by residual: dihedral pdb=" CB CYS B 157 " pdb=" SG CYS B 157 " pdb=" SG CYS B 175 " pdb=" CB CYS B 175 " ideal model delta sinusoidal sigma weight residual 93.00 165.24 -72.24 1 1.00e+01 1.00e-02 6.67e+01 dihedral pdb=" CB CYS D 157 " pdb=" SG CYS D 157 " pdb=" SG CYS D 175 " pdb=" CB CYS D 175 " ideal model delta sinusoidal sigma weight residual 93.00 165.22 -72.22 1 1.00e+01 1.00e-02 6.67e+01 dihedral pdb=" CB CYS D 472 " pdb=" SG CYS D 472 " pdb=" SG CYS D 486 " pdb=" CB CYS D 486 " ideal model delta sinusoidal sigma weight residual -86.00 -146.48 60.48 1 1.00e+01 1.00e-02 4.87e+01 ... (remaining 16307 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.035: 2783 0.035 - 0.070: 959 0.070 - 0.105: 382 0.105 - 0.140: 90 0.140 - 0.175: 7 Chirality restraints: 4221 Sorted by residual: chirality pdb=" CA ILE G 496 " pdb=" N ILE G 496 " pdb=" C ILE G 496 " pdb=" CB ILE G 496 " both_signs ideal model delta sigma weight residual False 2.43 2.61 -0.18 2.00e-01 2.50e+01 7.66e-01 chirality pdb=" CA ILE B 496 " pdb=" N ILE B 496 " pdb=" C ILE B 496 " pdb=" CB ILE B 496 " both_signs ideal model delta sigma weight residual False 2.43 2.61 -0.17 2.00e-01 2.50e+01 7.56e-01 chirality pdb=" CA ILE E 496 " pdb=" N ILE E 496 " pdb=" C ILE E 496 " pdb=" CB ILE E 496 " both_signs ideal model delta sigma weight residual False 2.43 2.61 -0.17 2.00e-01 2.50e+01 7.50e-01 ... (remaining 4218 not shown) Planarity restraints: 4963 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C HIS B 452 " -0.035 5.00e-02 4.00e+02 5.24e-02 4.40e+00 pdb=" N PRO B 453 " 0.091 5.00e-02 4.00e+02 pdb=" CA PRO B 453 " -0.027 5.00e-02 4.00e+02 pdb=" CD PRO B 453 " -0.029 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C HIS G 452 " 0.035 5.00e-02 4.00e+02 5.24e-02 4.39e+00 pdb=" N PRO G 453 " -0.091 5.00e-02 4.00e+02 pdb=" CA PRO G 453 " 0.027 5.00e-02 4.00e+02 pdb=" CD PRO G 453 " 0.029 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C HIS E 452 " -0.035 5.00e-02 4.00e+02 5.23e-02 4.38e+00 pdb=" N PRO E 453 " 0.091 5.00e-02 4.00e+02 pdb=" CA PRO E 453 " -0.027 5.00e-02 4.00e+02 pdb=" CD PRO E 453 " -0.029 5.00e-02 4.00e+02 ... (remaining 4960 not shown) Histogram of nonbonded interaction distances: 2.09 - 2.65: 571 2.65 - 3.21: 25671 3.21 - 3.78: 41174 3.78 - 4.34: 56503 4.34 - 4.90: 90495 Nonbonded interactions: 214414 Sorted by model distance: nonbonded pdb=" OH TYR F 503 " pdb=" O TRP F 532 " model vdw 2.089 3.040 nonbonded pdb=" OH TYR D 503 " pdb=" O TRP D 532 " model vdw 2.089 3.040 nonbonded pdb=" OH TYR G 503 " pdb=" O TRP G 532 " model vdw 2.089 3.040 nonbonded pdb=" OH TYR A 503 " pdb=" O TRP A 532 " model vdw 2.089 3.040 nonbonded pdb=" OH TYR C 503 " pdb=" O TRP C 532 " model vdw 2.089 3.040 ... (remaining 214409 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.02 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.670 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.020 Extract box with map and model: 0.430 Check model and map are aligned: 0.080 Set scattering table: 0.050 Process input model: 28.400 Find NCS groups from input model: 0.510 Set up NCS constraints: 0.070 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:1.610 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.860 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5131 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 : 0.015 0.945 27846 Z= 0.767 Angle : 0.983 36.875 37842 Z= 0.507 Chirality : 0.042 0.175 4221 Planarity : 0.004 0.052 4963 Dihedral : 13.857 87.188 9646 Min Nonbonded Distance : 2.089 Molprobity Statistics. All-atom Clashscore : 19.92 Ramachandran Plot: Outliers : 0.21 % Allowed : 6.74 % Favored : 93.05 % Rotamer: Outliers : 0.00 % Allowed : 0.25 % Favored : 99.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.30 (0.13), residues: 3381 helix: -4.45 (0.23), residues: 126 sheet: -1.53 (0.19), residues: 763 loop : -2.47 (0.12), residues: 2492 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG G 439 TYR 0.016 0.001 TYR D 389 PHE 0.009 0.001 PHE B 455 TRP 0.008 0.001 TRP B 342 HIS 0.004 0.001 HIS E 221 Details of bonding type rmsd covalent geometry : bond 0.00282 (27832) covalent geometry : angle 0.62979 (37814) SS BOND : bond 0.67158 ( 14) SS BOND : angle 27.76473 ( 28) hydrogen bonds : bond 0.32598 ( 490) hydrogen bonds : angle 13.41473 ( 1428) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6762 Ramachandran restraints generated. 3381 Oldfield, 0 Emsley, 3381 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6762 Ramachandran restraints generated. 3381 Oldfield, 0 Emsley, 3381 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 580 residues out of total 3031 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 580 time to evaluate : 1.025 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: 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 245 TRP cc_start: 0.7551 (m-90) cc_final: 0.6878 (m100) REVERT: A 526 GLN cc_start: 0.6625 (mm-40) cc_final: 0.5216 (tp40) REVERT: A 577 TYR cc_start: 0.4262 (m-80) cc_final: 0.2936 (m-80) REVERT: B 192 LEU cc_start: 0.6891 (tp) cc_final: 0.6441 (tp) REVERT: B 245 TRP cc_start: 0.7560 (m-90) cc_final: 0.7187 (m100) REVERT: B 446 PHE cc_start: 0.6242 (p90) cc_final: 0.5936 (t80) REVERT: B 503 TYR cc_start: 0.3906 (m-10) cc_final: 0.3640 (m-80) REVERT: B 526 GLN cc_start: 0.6315 (mm-40) cc_final: 0.5661 (tp40) REVERT: B 577 TYR cc_start: 0.4468 (m-80) cc_final: 0.3188 (m-80) REVERT: C 253 ASP cc_start: 0.6209 (p0) cc_final: 0.5994 (p0) REVERT: C 430 HIS cc_start: 0.5645 (m90) cc_final: 0.4754 (p90) REVERT: C 503 TYR cc_start: 0.4530 (m-10) cc_final: 0.4259 (m-80) REVERT: C 577 TYR cc_start: 0.4330 (m-80) cc_final: 0.2967 (m-80) REVERT: D 245 TRP cc_start: 0.6995 (m-90) cc_final: 0.6434 (m100) REVERT: D 385 MET cc_start: 0.6576 (pmm) cc_final: 0.6211 (pmm) REVERT: D 417 TYR cc_start: 0.5879 (t80) cc_final: 0.4904 (t80) REVERT: D 429 TYR cc_start: 0.3711 (m-80) cc_final: 0.3269 (m-80) REVERT: D 503 TYR cc_start: 0.4361 (m-10) cc_final: 0.3650 (m-80) REVERT: D 577 TYR cc_start: 0.4329 (m-80) cc_final: 0.4002 (m-10) REVERT: E 385 MET cc_start: 0.6397 (pmm) cc_final: 0.5885 (pmm) REVERT: E 503 TYR cc_start: 0.4295 (m-10) cc_final: 0.3525 (m-80) REVERT: E 526 GLN cc_start: 0.6526 (mm-40) cc_final: 0.5811 (tp40) REVERT: F 253 ASP cc_start: 0.6596 (p0) cc_final: 0.6320 (p0) REVERT: F 385 MET cc_start: 0.6389 (pmm) cc_final: 0.5979 (pmm) REVERT: F 503 TYR cc_start: 0.4381 (m-10) cc_final: 0.3752 (m-80) REVERT: F 526 GLN cc_start: 0.6271 (mm-40) cc_final: 0.5628 (tp40) REVERT: G 245 TRP cc_start: 0.7373 (m-90) cc_final: 0.7150 (m100) REVERT: G 385 MET cc_start: 0.6508 (pmm) cc_final: 0.6202 (pmm) REVERT: G 417 TYR cc_start: 0.5831 (t80) cc_final: 0.4916 (t80) REVERT: G 502 ARG cc_start: 0.5010 (mtm110) cc_final: 0.4785 (ptp90) REVERT: G 503 TYR cc_start: 0.4512 (m-10) cc_final: 0.3891 (m-80) REVERT: G 577 TYR cc_start: 0.4435 (m-80) cc_final: 0.3965 (m-10) outliers start: 0 outliers final: 0 residues processed: 580 average time/residue: 0.1967 time to fit residues: 175.8302 Evaluate side-chains 355 residues out of total 3031 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 355 time to evaluate : 0.924 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 350 random chunks: chunk 197 optimal weight: 30.0000 chunk 215 optimal weight: 20.0000 chunk 20 optimal weight: 10.0000 chunk 132 optimal weight: 9.9990 chunk 261 optimal weight: 1.9990 chunk 248 optimal weight: 8.9990 chunk 207 optimal weight: 3.9990 chunk 155 optimal weight: 10.0000 chunk 244 optimal weight: 9.9990 chunk 183 optimal weight: 1.9990 chunk 298 optimal weight: 7.9990 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 221 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 223 ASN ** A 484 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 525 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 526 GLN ** A 530 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 552 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 221 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 223 ASN B 331 ASN ** B 525 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 526 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 530 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 552 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 221 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 223 ASN C 408 ASN ** C 525 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 552 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 221 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 223 ASN D 259 ASN D 315 GLN D 345 GLN ** D 525 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 552 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 221 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 223 ASN E 259 ASN E 371 ASN ** E 525 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 552 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 221 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 223 ASN ** F 525 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 552 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 149 ASN ** G 221 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 223 ASN G 259 ASN ** G 525 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 526 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 552 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4816 r_free = 0.4816 target = 0.219872 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.4498 r_free = 0.4498 target = 0.186933 restraints weight = 39710.551| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.4523 r_free = 0.4523 target = 0.189117 restraints weight = 27318.693| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.4534 r_free = 0.4534 target = 0.190282 restraints weight = 22004.719| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.4546 r_free = 0.4546 target = 0.191583 restraints weight = 18038.942| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.4548 r_free = 0.4548 target = 0.191744 restraints weight = 16922.920| |-----------------------------------------------------------------------------| r_work (final): 0.4545 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5888 moved from start: 0.4237 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.073 27846 Z= 0.342 Angle : 0.941 13.106 37842 Z= 0.513 Chirality : 0.055 0.206 4221 Planarity : 0.008 0.070 4963 Dihedral : 7.666 45.844 3808 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 21.10 Ramachandran Plot: Outliers : 0.27 % Allowed : 10.59 % Favored : 89.15 % Rotamer: Outliers : 2.81 % Allowed : 15.55 % Favored : 81.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.18 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.92 (0.13), residues: 3381 helix: -4.48 (0.20), residues: 168 sheet: -2.17 (0.17), residues: 868 loop : -2.81 (0.11), residues: 2345 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG G 327 TYR 0.034 0.004 TYR E 254 PHE 0.026 0.003 PHE C 256 TRP 0.040 0.004 TRP C 702 HIS 0.010 0.002 HIS C 221 Details of bonding type rmsd covalent geometry : bond 0.00784 (27832) covalent geometry : angle 0.93944 (37814) SS BOND : bond 0.00356 ( 14) SS BOND : angle 2.06574 ( 28) hydrogen bonds : bond 0.05515 ( 490) hydrogen bonds : angle 9.71803 ( 1428) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6762 Ramachandran restraints generated. 3381 Oldfield, 0 Emsley, 3381 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6762 Ramachandran restraints generated. 3381 Oldfield, 0 Emsley, 3381 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 445 residues out of total 3031 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 365 time to evaluate : 1.155 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 577 TYR cc_start: 0.4526 (m-80) cc_final: 0.3211 (m-80) REVERT: B 329 GLU cc_start: 0.5792 (OUTLIER) cc_final: 0.5023 (tt0) REVERT: B 577 TYR cc_start: 0.4567 (m-80) cc_final: 0.3307 (m-80) REVERT: B 597 MET cc_start: 0.6342 (ptp) cc_final: 0.6120 (ptp) REVERT: C 385 MET cc_start: 0.6845 (OUTLIER) cc_final: 0.6388 (ptm) REVERT: C 577 TYR cc_start: 0.4539 (m-80) cc_final: 0.3425 (m-80) REVERT: C 597 MET cc_start: 0.6086 (ptp) cc_final: 0.5803 (ptp) REVERT: D 253 ASP cc_start: 0.7166 (p0) cc_final: 0.6894 (p0) REVERT: D 369 ASP cc_start: 0.7650 (t0) cc_final: 0.6628 (m-30) REVERT: D 484 ASN cc_start: 0.3196 (m-40) cc_final: 0.2930 (m-40) REVERT: D 577 TYR cc_start: 0.4317 (m-80) cc_final: 0.3196 (m-80) REVERT: E 577 TYR cc_start: 0.4164 (m-10) cc_final: 0.3622 (m-10) REVERT: E 700 LYS cc_start: 0.6470 (mptt) cc_final: 0.5787 (tttp) REVERT: F 484 ASN cc_start: 0.3185 (m-40) cc_final: 0.2813 (m-40) REVERT: G 447 THR cc_start: 0.7313 (m) cc_final: 0.7058 (m) REVERT: G 577 TYR cc_start: 0.4546 (m-80) cc_final: 0.3516 (m-80) REVERT: G 597 MET cc_start: 0.5867 (ptt) cc_final: 0.4670 (ptm) outliers start: 80 outliers final: 45 residues processed: 421 average time/residue: 0.2026 time to fit residues: 132.2009 Evaluate side-chains 338 residues out of total 3031 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 291 time to evaluate : 0.986 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 138 THR Chi-restraints excluded: chain A residue 156 GLU Chi-restraints excluded: chain A residue 281 GLU Chi-restraints excluded: chain A residue 445 SER Chi-restraints excluded: chain A residue 463 LEU Chi-restraints excluded: chain A residue 468 PHE Chi-restraints excluded: chain A residue 502 ARG Chi-restraints excluded: chain A residue 512 CYS Chi-restraints excluded: chain B residue 152 ILE Chi-restraints excluded: chain B residue 156 GLU Chi-restraints excluded: chain B residue 329 GLU Chi-restraints excluded: chain B residue 445 SER Chi-restraints excluded: chain B residue 463 LEU Chi-restraints excluded: chain B residue 473 ILE Chi-restraints excluded: chain B residue 503 TYR Chi-restraints excluded: chain B residue 512 CYS Chi-restraints excluded: chain B residue 699 LEU Chi-restraints excluded: chain C residue 156 GLU Chi-restraints excluded: chain C residue 385 MET Chi-restraints excluded: chain C residue 463 LEU Chi-restraints excluded: chain C residue 503 TYR Chi-restraints excluded: chain C residue 699 LEU Chi-restraints excluded: chain D residue 138 THR Chi-restraints excluded: chain D residue 286 SER Chi-restraints excluded: chain D residue 320 THR Chi-restraints excluded: chain D residue 345 GLN Chi-restraints excluded: chain D residue 502 ARG Chi-restraints excluded: chain D residue 503 TYR Chi-restraints excluded: chain D residue 699 LEU Chi-restraints excluded: chain E residue 138 THR Chi-restraints excluded: chain E residue 156 GLU Chi-restraints excluded: chain E residue 289 GLU Chi-restraints excluded: chain E residue 320 THR Chi-restraints excluded: chain E residue 445 SER Chi-restraints excluded: chain E residue 502 ARG Chi-restraints excluded: chain E residue 503 TYR Chi-restraints excluded: chain F residue 156 GLU Chi-restraints excluded: chain F residue 286 SER Chi-restraints excluded: chain F residue 463 LEU Chi-restraints excluded: chain F residue 503 TYR Chi-restraints excluded: chain F residue 699 LEU Chi-restraints excluded: chain G residue 138 THR Chi-restraints excluded: chain G residue 253 ASP Chi-restraints excluded: chain G residue 365 THR Chi-restraints excluded: chain G residue 445 SER Chi-restraints excluded: chain G residue 503 TYR Chi-restraints excluded: chain G residue 699 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 350 random chunks: chunk 7 optimal weight: 1.9990 chunk 240 optimal weight: 20.0000 chunk 343 optimal weight: 30.0000 chunk 105 optimal weight: 1.9990 chunk 78 optimal weight: 0.8980 chunk 199 optimal weight: 4.9990 chunk 29 optimal weight: 0.9980 chunk 217 optimal weight: 0.4980 chunk 154 optimal weight: 0.8980 chunk 115 optimal weight: 20.0000 chunk 24 optimal weight: 0.8980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 221 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 552 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 712 GLN ** B 221 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 530 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 552 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 600 GLN ** C 187 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 408 ASN ** C 552 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 682 ASN ** D 552 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 484 ASN ** E 552 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 193 GLN ** F 221 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 530 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 552 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 187 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 552 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 600 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4861 r_free = 0.4861 target = 0.225788 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.4539 r_free = 0.4539 target = 0.190924 restraints weight = 41569.960| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 57)----------------| | r_work = 0.4573 r_free = 0.4573 target = 0.194446 restraints weight = 26650.779| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 52)----------------| | r_work = 0.4597 r_free = 0.4597 target = 0.196948 restraints weight = 19580.387| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 54)----------------| | r_work = 0.4613 r_free = 0.4613 target = 0.198620 restraints weight = 15855.291| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.4622 r_free = 0.4622 target = 0.199625 restraints weight = 13781.187| |-----------------------------------------------------------------------------| r_work (final): 0.4640 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5473 moved from start: 0.4368 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 27846 Z= 0.126 Angle : 0.604 9.303 37842 Z= 0.331 Chirality : 0.045 0.206 4221 Planarity : 0.005 0.050 4963 Dihedral : 6.059 42.646 3808 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 11.97 Ramachandran Plot: Outliers : 0.21 % Allowed : 7.78 % Favored : 92.01 % Rotamer: Outliers : 2.63 % Allowed : 17.23 % Favored : 80.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.74 (0.13), residues: 3381 helix: -4.70 (0.13), residues: 168 sheet: -2.11 (0.17), residues: 931 loop : -2.61 (0.12), residues: 2282 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 531 TYR 0.030 0.002 TYR B 378 PHE 0.024 0.002 PHE F 288 TRP 0.024 0.002 TRP G 702 HIS 0.004 0.001 HIS A 141 Details of bonding type rmsd covalent geometry : bond 0.00274 (27832) covalent geometry : angle 0.60260 (37814) SS BOND : bond 0.00195 ( 14) SS BOND : angle 1.48938 ( 28) hydrogen bonds : bond 0.03736 ( 490) hydrogen bonds : angle 8.18461 ( 1428) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6762 Ramachandran restraints generated. 3381 Oldfield, 0 Emsley, 3381 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6762 Ramachandran restraints generated. 3381 Oldfield, 0 Emsley, 3381 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 437 residues out of total 3031 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 362 time to evaluate : 1.069 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 329 GLU cc_start: 0.5453 (OUTLIER) cc_final: 0.4462 (tt0) REVERT: A 512 CYS cc_start: 0.6829 (OUTLIER) cc_final: 0.6438 (m) REVERT: A 577 TYR cc_start: 0.4232 (m-80) cc_final: 0.2968 (m-80) REVERT: A 597 MET cc_start: 0.6226 (ptt) cc_final: 0.4977 (ptm) REVERT: B 403 ILE cc_start: 0.7232 (OUTLIER) cc_final: 0.6569 (mm) REVERT: B 484 ASN cc_start: 0.2681 (m-40) cc_final: 0.2119 (m110) REVERT: B 577 TYR cc_start: 0.4149 (m-80) cc_final: 0.2998 (m-80) REVERT: C 253 ASP cc_start: 0.6895 (p0) cc_final: 0.6623 (p0) REVERT: C 329 GLU cc_start: 0.5698 (OUTLIER) cc_final: 0.4735 (tt0) REVERT: C 385 MET cc_start: 0.6831 (pmm) cc_final: 0.6418 (mtm) REVERT: C 403 ILE cc_start: 0.7395 (OUTLIER) cc_final: 0.7127 (mt) REVERT: C 447 THR cc_start: 0.6932 (m) cc_final: 0.6676 (m) REVERT: C 514 ASP cc_start: 0.6954 (OUTLIER) cc_final: 0.5661 (m-30) REVERT: C 577 TYR cc_start: 0.4316 (m-80) cc_final: 0.3114 (m-80) REVERT: D 177 ASP cc_start: 0.6579 (t0) cc_final: 0.6317 (t0) REVERT: D 220 ILE cc_start: 0.8368 (tp) cc_final: 0.7725 (mp) REVERT: D 253 ASP cc_start: 0.7039 (p0) cc_final: 0.6668 (p0) REVERT: D 259 ASN cc_start: 0.7682 (t0) cc_final: 0.7175 (t0) REVERT: D 369 ASP cc_start: 0.7892 (t0) cc_final: 0.6765 (m-30) REVERT: D 484 ASN cc_start: 0.3127 (m-40) cc_final: 0.2708 (m-40) REVERT: D 502 ARG cc_start: 0.5271 (OUTLIER) cc_final: 0.5034 (ptp90) REVERT: D 577 TYR cc_start: 0.4132 (m-80) cc_final: 0.2971 (m-80) REVERT: E 259 ASN cc_start: 0.7684 (t0) cc_final: 0.7220 (t0) REVERT: E 403 ILE cc_start: 0.6993 (OUTLIER) cc_final: 0.6519 (mm) REVERT: E 577 TYR cc_start: 0.4085 (m-10) cc_final: 0.3432 (m-10) REVERT: F 220 ILE cc_start: 0.8408 (tp) cc_final: 0.8156 (tp) REVERT: F 329 GLU cc_start: 0.5751 (OUTLIER) cc_final: 0.4651 (tt0) REVERT: F 403 ILE cc_start: 0.7180 (OUTLIER) cc_final: 0.6770 (mt) REVERT: F 484 ASN cc_start: 0.2799 (m-40) cc_final: 0.2490 (m-40) REVERT: F 597 MET cc_start: 0.5084 (ptt) cc_final: 0.4863 (ptp) REVERT: G 577 TYR cc_start: 0.4378 (m-80) cc_final: 0.3361 (m-80) REVERT: G 597 MET cc_start: 0.5740 (ptt) cc_final: 0.4494 (ptm) outliers start: 75 outliers final: 42 residues processed: 405 average time/residue: 0.1963 time to fit residues: 124.2841 Evaluate side-chains 359 residues out of total 3031 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 307 time to evaluate : 0.974 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 138 THR Chi-restraints excluded: chain A residue 285 VAL Chi-restraints excluded: chain A residue 329 GLU Chi-restraints excluded: chain A residue 445 SER Chi-restraints excluded: chain A residue 463 LEU Chi-restraints excluded: chain A residue 468 PHE Chi-restraints excluded: chain A residue 512 CYS Chi-restraints excluded: chain A residue 589 ILE Chi-restraints excluded: chain A residue 674 VAL Chi-restraints excluded: chain B residue 156 GLU Chi-restraints excluded: chain B residue 220 ILE Chi-restraints excluded: chain B residue 385 MET Chi-restraints excluded: chain B residue 403 ILE Chi-restraints excluded: chain B residue 445 SER Chi-restraints excluded: chain B residue 463 LEU Chi-restraints excluded: chain B residue 502 ARG Chi-restraints excluded: chain B residue 503 TYR Chi-restraints excluded: chain B residue 512 CYS Chi-restraints excluded: chain B residue 699 LEU Chi-restraints excluded: chain C residue 220 ILE Chi-restraints excluded: chain C residue 268 LEU Chi-restraints excluded: chain C residue 329 GLU Chi-restraints excluded: chain C residue 403 ILE Chi-restraints excluded: chain C residue 463 LEU Chi-restraints excluded: chain C residue 503 TYR Chi-restraints excluded: chain C residue 514 ASP Chi-restraints excluded: chain D residue 138 THR Chi-restraints excluded: chain D residue 385 MET Chi-restraints excluded: chain D residue 463 LEU Chi-restraints excluded: chain D residue 502 ARG Chi-restraints excluded: chain D residue 503 TYR Chi-restraints excluded: chain D residue 699 LEU Chi-restraints excluded: chain E residue 138 THR Chi-restraints excluded: chain E residue 220 ILE Chi-restraints excluded: chain E residue 285 VAL Chi-restraints excluded: chain E residue 388 ILE Chi-restraints excluded: chain E residue 403 ILE Chi-restraints excluded: chain E residue 445 SER Chi-restraints excluded: chain E residue 447 THR Chi-restraints excluded: chain E residue 503 TYR Chi-restraints excluded: chain E residue 699 LEU Chi-restraints excluded: chain F residue 329 GLU Chi-restraints excluded: chain F residue 351 GLU Chi-restraints excluded: chain F residue 403 ILE Chi-restraints excluded: chain F residue 463 LEU Chi-restraints excluded: chain F residue 503 TYR Chi-restraints excluded: chain G residue 138 THR Chi-restraints excluded: chain G residue 220 ILE Chi-restraints excluded: chain G residue 445 SER Chi-restraints excluded: chain G residue 463 LEU Chi-restraints excluded: chain G residue 503 TYR Chi-restraints excluded: chain G residue 699 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 350 random chunks: chunk 320 optimal weight: 6.9990 chunk 311 optimal weight: 5.9990 chunk 228 optimal weight: 4.9990 chunk 188 optimal weight: 3.9990 chunk 32 optimal weight: 10.0000 chunk 234 optimal weight: 9.9990 chunk 77 optimal weight: 6.9990 chunk 47 optimal weight: 40.0000 chunk 13 optimal weight: 6.9990 chunk 56 optimal weight: 0.3980 chunk 201 optimal weight: 8.9990 overall best weight: 4.4788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 221 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 484 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 525 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 552 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 221 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 525 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 552 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 187 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 221 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 223 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 552 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 658 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 221 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 259 ASN ** D 525 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 552 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 600 GLN ** E 221 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 522 GLN ** E 552 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 600 GLN F 522 GLN ** F 552 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 658 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 187 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 221 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 552 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4773 r_free = 0.4773 target = 0.214817 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4464 r_free = 0.4464 target = 0.182489 restraints weight = 41874.542| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.4468 r_free = 0.4468 target = 0.183967 restraints weight = 31288.459| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.4476 r_free = 0.4476 target = 0.184787 restraints weight = 23516.319| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.4479 r_free = 0.4479 target = 0.185278 restraints weight = 20640.934| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.4484 r_free = 0.4484 target = 0.185723 restraints weight = 20162.964| |-----------------------------------------------------------------------------| r_work (final): 0.4495 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5907 moved from start: 0.5451 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.053 27846 Z= 0.296 Angle : 0.800 10.631 37842 Z= 0.441 Chirality : 0.049 0.205 4221 Planarity : 0.007 0.090 4963 Dihedral : 7.276 45.117 3808 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 19.77 Ramachandran Plot: Outliers : 0.21 % Allowed : 11.06 % Favored : 88.73 % Rotamer: Outliers : 6.35 % Allowed : 17.23 % Favored : 76.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.83 (0.13), residues: 3381 helix: -4.68 (0.19), residues: 168 sheet: -2.17 (0.17), residues: 938 loop : -2.69 (0.12), residues: 2275 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG D 502 TYR 0.028 0.003 TYR E 254 PHE 0.028 0.003 PHE G 256 TRP 0.040 0.003 TRP C 702 HIS 0.006 0.002 HIS C 452 Details of bonding type rmsd covalent geometry : bond 0.00683 (27832) covalent geometry : angle 0.79827 (37814) SS BOND : bond 0.01007 ( 14) SS BOND : angle 2.13535 ( 28) hydrogen bonds : bond 0.05039 ( 490) hydrogen bonds : angle 8.67627 ( 1428) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6762 Ramachandran restraints generated. 3381 Oldfield, 0 Emsley, 3381 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6762 Ramachandran restraints generated. 3381 Oldfield, 0 Emsley, 3381 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 503 residues out of total 3031 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 181 poor density : 322 time to evaluate : 0.952 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: symmetry clash revert: symmetry clash REVERT: A 152 ILE cc_start: 0.4634 (OUTLIER) cc_final: 0.4395 (mt) REVERT: A 255 ARG cc_start: 0.6207 (ttm170) cc_final: 0.5769 (mtt180) REVERT: A 329 GLU cc_start: 0.5735 (OUTLIER) cc_final: 0.4863 (tt0) REVERT: A 497 TYR cc_start: 0.5938 (OUTLIER) cc_final: 0.5016 (t80) REVERT: A 577 TYR cc_start: 0.4523 (m-80) cc_final: 0.3317 (m-80) REVERT: A 597 MET cc_start: 0.6065 (ptt) cc_final: 0.4751 (ptm) REVERT: A 712 GLN cc_start: 0.7286 (OUTLIER) cc_final: 0.6770 (tp-100) REVERT: B 255 ARG cc_start: 0.5900 (ttm170) cc_final: 0.5540 (mtt180) REVERT: B 259 ASN cc_start: 0.7915 (t0) cc_final: 0.7558 (t0) REVERT: B 403 ILE cc_start: 0.7640 (OUTLIER) cc_final: 0.7250 (mt) REVERT: B 497 TYR cc_start: 0.5759 (OUTLIER) cc_final: 0.3929 (t80) REVERT: B 577 TYR cc_start: 0.4414 (m-80) cc_final: 0.3304 (m-80) REVERT: B 597 MET cc_start: 0.5389 (ptp) cc_final: 0.4191 (ptm) REVERT: B 702 TRP cc_start: 0.6384 (t60) cc_final: 0.6168 (t-100) REVERT: C 252 GLN cc_start: 0.7101 (OUTLIER) cc_final: 0.6760 (tp40) REVERT: C 255 ARG cc_start: 0.6194 (ttm170) cc_final: 0.5958 (mtp180) REVERT: C 329 GLU cc_start: 0.5718 (OUTLIER) cc_final: 0.4698 (tt0) REVERT: C 385 MET cc_start: 0.6994 (OUTLIER) cc_final: 0.6354 (ptm) REVERT: C 403 ILE cc_start: 0.7866 (OUTLIER) cc_final: 0.7650 (mt) REVERT: C 447 THR cc_start: 0.7127 (m) cc_final: 0.6812 (m) REVERT: C 497 TYR cc_start: 0.5963 (OUTLIER) cc_final: 0.4675 (t80) REVERT: C 577 TYR cc_start: 0.4420 (m-80) cc_final: 0.3386 (m-80) REVERT: C 597 MET cc_start: 0.4895 (ptt) cc_final: 0.4185 (ptm) REVERT: C 616 ILE cc_start: 0.1234 (OUTLIER) cc_final: 0.0980 (mt) REVERT: C 713 PHE cc_start: 0.6132 (m-80) cc_final: 0.5770 (m-80) REVERT: D 329 GLU cc_start: 0.5934 (OUTLIER) cc_final: 0.4866 (tt0) REVERT: D 354 LEU cc_start: 0.6447 (OUTLIER) cc_final: 0.6084 (mm) REVERT: D 403 ILE cc_start: 0.7540 (OUTLIER) cc_final: 0.6859 (mm) REVERT: D 497 TYR cc_start: 0.5819 (OUTLIER) cc_final: 0.3850 (t80) REVERT: D 577 TYR cc_start: 0.4509 (m-80) cc_final: 0.3232 (m-10) REVERT: D 700 LYS cc_start: 0.5654 (mmtm) cc_final: 0.5378 (tttp) REVERT: D 702 TRP cc_start: 0.5184 (m-10) cc_final: 0.4806 (m-10) REVERT: E 252 GLN cc_start: 0.7137 (OUTLIER) cc_final: 0.6752 (tp40) REVERT: E 329 GLU cc_start: 0.5504 (OUTLIER) cc_final: 0.4765 (tt0) REVERT: E 403 ILE cc_start: 0.7533 (OUTLIER) cc_final: 0.7172 (mt) REVERT: E 497 TYR cc_start: 0.5693 (OUTLIER) cc_final: 0.3427 (t80) REVERT: E 577 TYR cc_start: 0.4250 (m-10) cc_final: 0.3636 (m-10) REVERT: E 597 MET cc_start: 0.5334 (ptp) cc_final: 0.4154 (ptm) REVERT: F 152 ILE cc_start: 0.4361 (OUTLIER) cc_final: 0.4050 (mt) REVERT: F 220 ILE cc_start: 0.8779 (OUTLIER) cc_final: 0.8557 (tp) REVERT: F 252 GLN cc_start: 0.6883 (OUTLIER) cc_final: 0.6327 (tp40) REVERT: F 253 ASP cc_start: 0.7269 (p0) cc_final: 0.6888 (p0) REVERT: F 329 GLU cc_start: 0.5936 (OUTLIER) cc_final: 0.4933 (tt0) REVERT: F 403 ILE cc_start: 0.7661 (OUTLIER) cc_final: 0.7263 (mt) REVERT: F 497 TYR cc_start: 0.5804 (OUTLIER) cc_final: 0.3793 (t80) REVERT: F 597 MET cc_start: 0.5251 (ptt) cc_final: 0.3832 (ptm) REVERT: F 713 PHE cc_start: 0.6292 (m-80) cc_final: 0.5792 (m-80) REVERT: G 177 ASP cc_start: 0.7295 (t0) cc_final: 0.7025 (t0) REVERT: G 329 GLU cc_start: 0.5835 (OUTLIER) cc_final: 0.4906 (tt0) REVERT: G 385 MET cc_start: 0.6735 (OUTLIER) cc_final: 0.6313 (ptm) REVERT: G 403 ILE cc_start: 0.7463 (OUTLIER) cc_final: 0.6779 (mm) REVERT: G 497 TYR cc_start: 0.5790 (OUTLIER) cc_final: 0.3590 (t80) REVERT: G 577 TYR cc_start: 0.4415 (m-80) cc_final: 0.3510 (m-80) REVERT: G 597 MET cc_start: 0.5799 (ptt) cc_final: 0.4809 (ptm) outliers start: 181 outliers final: 82 residues processed: 454 average time/residue: 0.1942 time to fit residues: 139.1587 Evaluate side-chains 406 residues out of total 3031 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 112 poor density : 294 time to evaluate : 1.032 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 138 THR Chi-restraints excluded: chain A residue 152 ILE Chi-restraints excluded: chain A residue 156 GLU Chi-restraints excluded: chain A residue 285 VAL Chi-restraints excluded: chain A residue 286 SER Chi-restraints excluded: chain A residue 329 GLU Chi-restraints excluded: chain A residue 365 THR Chi-restraints excluded: chain A residue 385 MET Chi-restraints excluded: chain A residue 407 VAL Chi-restraints excluded: chain A residue 409 ILE Chi-restraints excluded: chain A residue 417 TYR Chi-restraints excluded: chain A residue 445 SER Chi-restraints excluded: chain A residue 463 LEU Chi-restraints excluded: chain A residue 468 PHE Chi-restraints excluded: chain A residue 497 TYR Chi-restraints excluded: chain A residue 512 CYS Chi-restraints excluded: chain A residue 589 ILE Chi-restraints excluded: chain A residue 600 GLN Chi-restraints excluded: chain A residue 712 GLN Chi-restraints excluded: chain B residue 156 GLU Chi-restraints excluded: chain B residue 201 THR Chi-restraints excluded: chain B residue 220 ILE Chi-restraints excluded: chain B residue 285 VAL Chi-restraints excluded: chain B residue 365 THR Chi-restraints excluded: chain B residue 382 VAL Chi-restraints excluded: chain B residue 385 MET Chi-restraints excluded: chain B residue 403 ILE Chi-restraints excluded: chain B residue 445 SER Chi-restraints excluded: chain B residue 463 LEU Chi-restraints excluded: chain B residue 497 TYR Chi-restraints excluded: chain B residue 502 ARG Chi-restraints excluded: chain B residue 503 TYR Chi-restraints excluded: chain B residue 512 CYS Chi-restraints excluded: chain B residue 531 ARG Chi-restraints excluded: chain B residue 699 LEU Chi-restraints excluded: chain C residue 156 GLU Chi-restraints excluded: chain C residue 220 ILE Chi-restraints excluded: chain C residue 252 GLN Chi-restraints excluded: chain C residue 268 LEU Chi-restraints excluded: chain C residue 285 VAL Chi-restraints excluded: chain C residue 286 SER Chi-restraints excluded: chain C residue 329 GLU Chi-restraints excluded: chain C residue 365 THR Chi-restraints excluded: chain C residue 382 VAL Chi-restraints excluded: chain C residue 385 MET Chi-restraints excluded: chain C residue 403 ILE Chi-restraints excluded: chain C residue 407 VAL Chi-restraints excluded: chain C residue 409 ILE Chi-restraints excluded: chain C residue 448 VAL Chi-restraints excluded: chain C residue 497 TYR Chi-restraints excluded: chain C residue 503 TYR Chi-restraints excluded: chain C residue 616 ILE Chi-restraints excluded: chain D residue 138 THR Chi-restraints excluded: chain D residue 220 ILE Chi-restraints excluded: chain D residue 286 SER Chi-restraints excluded: chain D residue 329 GLU Chi-restraints excluded: chain D residue 354 LEU Chi-restraints excluded: chain D residue 365 THR Chi-restraints excluded: chain D residue 385 MET Chi-restraints excluded: chain D residue 403 ILE Chi-restraints excluded: chain D residue 407 VAL Chi-restraints excluded: chain D residue 409 ILE Chi-restraints excluded: chain D residue 463 LEU Chi-restraints excluded: chain D residue 497 TYR Chi-restraints excluded: chain D residue 502 ARG Chi-restraints excluded: chain D residue 503 TYR Chi-restraints excluded: chain D residue 699 LEU Chi-restraints excluded: chain E residue 138 THR Chi-restraints excluded: chain E residue 152 ILE Chi-restraints excluded: chain E residue 220 ILE Chi-restraints excluded: chain E residue 245 TRP Chi-restraints excluded: chain E residue 252 GLN Chi-restraints excluded: chain E residue 285 VAL Chi-restraints excluded: chain E residue 320 THR Chi-restraints excluded: chain E residue 329 GLU Chi-restraints excluded: chain E residue 365 THR Chi-restraints excluded: chain E residue 382 VAL Chi-restraints excluded: chain E residue 388 ILE Chi-restraints excluded: chain E residue 403 ILE Chi-restraints excluded: chain E residue 445 SER Chi-restraints excluded: chain E residue 463 LEU Chi-restraints excluded: chain E residue 497 TYR Chi-restraints excluded: chain E residue 503 TYR Chi-restraints excluded: chain E residue 699 LEU Chi-restraints excluded: chain F residue 152 ILE Chi-restraints excluded: chain F residue 220 ILE Chi-restraints excluded: chain F residue 252 GLN Chi-restraints excluded: chain F residue 285 VAL Chi-restraints excluded: chain F residue 329 GLU Chi-restraints excluded: chain F residue 365 THR Chi-restraints excluded: chain F residue 403 ILE Chi-restraints excluded: chain F residue 409 ILE Chi-restraints excluded: chain F residue 463 LEU Chi-restraints excluded: chain F residue 497 TYR Chi-restraints excluded: chain F residue 503 TYR Chi-restraints excluded: chain G residue 138 THR Chi-restraints excluded: chain G residue 152 ILE Chi-restraints excluded: chain G residue 208 ARG Chi-restraints excluded: chain G residue 220 ILE Chi-restraints excluded: chain G residue 286 SER Chi-restraints excluded: chain G residue 329 GLU Chi-restraints excluded: chain G residue 365 THR Chi-restraints excluded: chain G residue 385 MET Chi-restraints excluded: chain G residue 403 ILE Chi-restraints excluded: chain G residue 407 VAL Chi-restraints excluded: chain G residue 445 SER Chi-restraints excluded: chain G residue 463 LEU Chi-restraints excluded: chain G residue 473 ILE Chi-restraints excluded: chain G residue 497 TYR Chi-restraints excluded: chain G residue 503 TYR Chi-restraints excluded: chain G residue 600 GLN Chi-restraints excluded: chain G residue 699 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 350 random chunks: chunk 212 optimal weight: 5.9990 chunk 106 optimal weight: 2.9990 chunk 162 optimal weight: 0.8980 chunk 36 optimal weight: 7.9990 chunk 64 optimal weight: 7.9990 chunk 119 optimal weight: 2.9990 chunk 154 optimal weight: 2.9990 chunk 339 optimal weight: 3.9990 chunk 333 optimal weight: 2.9990 chunk 171 optimal weight: 0.6980 chunk 26 optimal weight: 3.9990 overall best weight: 2.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 221 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 223 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 484 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 508 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 552 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 552 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 221 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 223 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 552 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 658 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 221 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 345 GLN ** D 552 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 600 GLN ** E 221 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 552 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 600 GLN ** F 223 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 427 GLN ** F 552 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 658 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 221 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 552 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4808 r_free = 0.4808 target = 0.219113 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4487 r_free = 0.4487 target = 0.185543 restraints weight = 42325.237| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.4508 r_free = 0.4508 target = 0.188142 restraints weight = 28211.701| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.4522 r_free = 0.4522 target = 0.189767 restraints weight = 19916.532| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.4524 r_free = 0.4524 target = 0.190155 restraints weight = 17730.246| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.4527 r_free = 0.4527 target = 0.190349 restraints weight = 16929.973| |-----------------------------------------------------------------------------| r_work (final): 0.4533 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5786 moved from start: 0.5681 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 27846 Z= 0.171 Angle : 0.641 9.616 37842 Z= 0.353 Chirality : 0.046 0.200 4221 Planarity : 0.005 0.075 4963 Dihedral : 6.514 43.299 3808 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 15.20 Ramachandran Plot: Outliers : 0.21 % Allowed : 8.67 % Favored : 91.13 % Rotamer: Outliers : 4.42 % Allowed : 20.01 % Favored : 75.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.83 (0.13), residues: 3381 helix: -4.69 (0.18), residues: 168 sheet: -2.36 (0.16), residues: 1015 loop : -2.57 (0.13), residues: 2198 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 502 TYR 0.019 0.002 TYR E 429 PHE 0.027 0.002 PHE B 288 TRP 0.034 0.002 TRP C 702 HIS 0.005 0.001 HIS A 141 Details of bonding type rmsd covalent geometry : bond 0.00388 (27832) covalent geometry : angle 0.64068 (37814) SS BOND : bond 0.00515 ( 14) SS BOND : angle 1.34752 ( 28) hydrogen bonds : bond 0.03839 ( 490) hydrogen bonds : angle 7.78068 ( 1428) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6762 Ramachandran restraints generated. 3381 Oldfield, 0 Emsley, 3381 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6762 Ramachandran restraints generated. 3381 Oldfield, 0 Emsley, 3381 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 440 residues out of total 3031 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 126 poor density : 314 time to evaluate : 1.102 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 177 ASP cc_start: 0.6868 (t0) cc_final: 0.6668 (t0) REVERT: A 220 ILE cc_start: 0.8352 (OUTLIER) cc_final: 0.8146 (tp) REVERT: A 255 ARG cc_start: 0.5867 (ttm170) cc_final: 0.5559 (mtt180) REVERT: A 329 GLU cc_start: 0.5503 (OUTLIER) cc_final: 0.4792 (tt0) REVERT: A 403 ILE cc_start: 0.7398 (OUTLIER) cc_final: 0.7118 (mt) REVERT: A 511 LEU cc_start: 0.4501 (OUTLIER) cc_final: 0.4107 (tp) REVERT: A 577 TYR cc_start: 0.4497 (m-80) cc_final: 0.3143 (m-80) REVERT: A 597 MET cc_start: 0.5842 (ptt) cc_final: 0.4602 (ptm) REVERT: A 712 GLN cc_start: 0.7197 (OUTLIER) cc_final: 0.6615 (tp-100) REVERT: B 329 GLU cc_start: 0.5967 (OUTLIER) cc_final: 0.4945 (tt0) REVERT: B 403 ILE cc_start: 0.7568 (OUTLIER) cc_final: 0.7243 (mt) REVERT: B 531 ARG cc_start: 0.4679 (OUTLIER) cc_final: 0.3552 (mtt90) REVERT: B 577 TYR cc_start: 0.4414 (m-80) cc_final: 0.3152 (m-80) REVERT: B 597 MET cc_start: 0.4932 (ptp) cc_final: 0.3654 (ptm) REVERT: B 702 TRP cc_start: 0.6205 (t60) cc_final: 0.5838 (t-100) REVERT: B 713 PHE cc_start: 0.6151 (m-80) cc_final: 0.5709 (m-80) REVERT: C 177 ASP cc_start: 0.6973 (t0) cc_final: 0.6688 (t0) REVERT: C 329 GLU cc_start: 0.5802 (OUTLIER) cc_final: 0.4839 (tt0) REVERT: C 447 THR cc_start: 0.7005 (m) cc_final: 0.6760 (m) REVERT: C 577 TYR cc_start: 0.4395 (m-80) cc_final: 0.3207 (m-80) REVERT: C 597 MET cc_start: 0.5111 (ptt) cc_final: 0.4335 (ptm) REVERT: C 713 PHE cc_start: 0.6045 (m-80) cc_final: 0.5545 (m-80) REVERT: D 253 ASP cc_start: 0.7220 (p0) cc_final: 0.6888 (p0) REVERT: D 329 GLU cc_start: 0.5745 (OUTLIER) cc_final: 0.4734 (tt0) REVERT: D 342 TRP cc_start: 0.7385 (m-90) cc_final: 0.7044 (m-90) REVERT: D 354 LEU cc_start: 0.6087 (OUTLIER) cc_final: 0.5821 (mm) REVERT: D 403 ILE cc_start: 0.7474 (OUTLIER) cc_final: 0.6925 (mm) REVERT: D 577 TYR cc_start: 0.4403 (m-80) cc_final: 0.2979 (m-10) REVERT: D 597 MET cc_start: 0.4988 (ptp) cc_final: 0.4299 (ptm) REVERT: D 713 PHE cc_start: 0.6611 (m-80) cc_final: 0.5905 (m-80) REVERT: E 329 GLU cc_start: 0.5670 (OUTLIER) cc_final: 0.4811 (tt0) REVERT: E 403 ILE cc_start: 0.7468 (OUTLIER) cc_final: 0.7132 (mt) REVERT: E 577 TYR cc_start: 0.4419 (m-10) cc_final: 0.3596 (m-10) REVERT: E 597 MET cc_start: 0.4971 (ptp) cc_final: 0.4003 (ptm) REVERT: E 713 PHE cc_start: 0.6719 (m-80) cc_final: 0.5958 (m-80) REVERT: F 220 ILE cc_start: 0.8754 (OUTLIER) cc_final: 0.8485 (tp) REVERT: F 252 GLN cc_start: 0.6664 (OUTLIER) cc_final: 0.6364 (tp40) REVERT: F 329 GLU cc_start: 0.6008 (OUTLIER) cc_final: 0.4941 (tt0) REVERT: F 403 ILE cc_start: 0.7547 (OUTLIER) cc_final: 0.7142 (mt) REVERT: F 597 MET cc_start: 0.5156 (ptt) cc_final: 0.3795 (ptm) REVERT: F 698 GLN cc_start: 0.6653 (pm20) cc_final: 0.6340 (pm20) REVERT: F 713 PHE cc_start: 0.6122 (m-80) cc_final: 0.5714 (m-80) REVERT: G 177 ASP cc_start: 0.7226 (t0) cc_final: 0.7003 (t0) REVERT: G 329 GLU cc_start: 0.5761 (OUTLIER) cc_final: 0.4822 (tt0) REVERT: G 403 ILE cc_start: 0.7424 (OUTLIER) cc_final: 0.6800 (mm) REVERT: G 577 TYR cc_start: 0.4461 (m-80) cc_final: 0.3353 (m-80) REVERT: G 597 MET cc_start: 0.5479 (ptt) cc_final: 0.4136 (ptm) REVERT: G 699 LEU cc_start: 0.5423 (OUTLIER) cc_final: 0.5023 (pp) outliers start: 126 outliers final: 64 residues processed: 398 average time/residue: 0.1974 time to fit residues: 123.1550 Evaluate side-chains 368 residues out of total 3031 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 283 time to evaluate : 1.064 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 138 THR Chi-restraints excluded: chain A residue 156 GLU Chi-restraints excluded: chain A residue 220 ILE Chi-restraints excluded: chain A residue 285 VAL Chi-restraints excluded: chain A residue 286 SER Chi-restraints excluded: chain A residue 329 GLU Chi-restraints excluded: chain A residue 351 GLU Chi-restraints excluded: chain A residue 385 MET Chi-restraints excluded: chain A residue 403 ILE Chi-restraints excluded: chain A residue 445 SER Chi-restraints excluded: chain A residue 463 LEU Chi-restraints excluded: chain A residue 468 PHE Chi-restraints excluded: chain A residue 503 TYR Chi-restraints excluded: chain A residue 504 VAL Chi-restraints excluded: chain A residue 511 LEU Chi-restraints excluded: chain A residue 512 CYS Chi-restraints excluded: chain A residue 589 ILE Chi-restraints excluded: chain A residue 712 GLN Chi-restraints excluded: chain B residue 156 GLU Chi-restraints excluded: chain B residue 220 ILE Chi-restraints excluded: chain B residue 285 VAL Chi-restraints excluded: chain B residue 329 GLU Chi-restraints excluded: chain B residue 351 GLU Chi-restraints excluded: chain B residue 354 LEU Chi-restraints excluded: chain B residue 385 MET Chi-restraints excluded: chain B residue 403 ILE Chi-restraints excluded: chain B residue 445 SER Chi-restraints excluded: chain B residue 463 LEU Chi-restraints excluded: chain B residue 468 PHE Chi-restraints excluded: chain B residue 503 TYR Chi-restraints excluded: chain B residue 512 CYS Chi-restraints excluded: chain B residue 531 ARG Chi-restraints excluded: chain B residue 674 VAL Chi-restraints excluded: chain B residue 699 LEU Chi-restraints excluded: chain C residue 220 ILE Chi-restraints excluded: chain C residue 268 LEU Chi-restraints excluded: chain C residue 285 VAL Chi-restraints excluded: chain C residue 286 SER Chi-restraints excluded: chain C residue 329 GLU Chi-restraints excluded: chain C residue 354 LEU Chi-restraints excluded: chain C residue 385 MET Chi-restraints excluded: chain C residue 407 VAL Chi-restraints excluded: chain C residue 468 PHE Chi-restraints excluded: chain C residue 503 TYR Chi-restraints excluded: chain C residue 674 VAL Chi-restraints excluded: chain D residue 138 THR Chi-restraints excluded: chain D residue 220 ILE Chi-restraints excluded: chain D residue 286 SER Chi-restraints excluded: chain D residue 329 GLU Chi-restraints excluded: chain D residue 345 GLN Chi-restraints excluded: chain D residue 354 LEU Chi-restraints excluded: chain D residue 385 MET Chi-restraints excluded: chain D residue 403 ILE Chi-restraints excluded: chain D residue 463 LEU Chi-restraints excluded: chain D residue 500 LEU Chi-restraints excluded: chain D residue 503 TYR Chi-restraints excluded: chain E residue 138 THR Chi-restraints excluded: chain E residue 220 ILE Chi-restraints excluded: chain E residue 285 VAL Chi-restraints excluded: chain E residue 329 GLU Chi-restraints excluded: chain E residue 388 ILE Chi-restraints excluded: chain E residue 403 ILE Chi-restraints excluded: chain E residue 445 SER Chi-restraints excluded: chain E residue 503 TYR Chi-restraints excluded: chain E residue 600 GLN Chi-restraints excluded: chain F residue 220 ILE Chi-restraints excluded: chain F residue 252 GLN Chi-restraints excluded: chain F residue 285 VAL Chi-restraints excluded: chain F residue 329 GLU Chi-restraints excluded: chain F residue 351 GLU Chi-restraints excluded: chain F residue 403 ILE Chi-restraints excluded: chain F residue 409 ILE Chi-restraints excluded: chain F residue 463 LEU Chi-restraints excluded: chain F residue 503 TYR Chi-restraints excluded: chain G residue 138 THR Chi-restraints excluded: chain G residue 220 ILE Chi-restraints excluded: chain G residue 286 SER Chi-restraints excluded: chain G residue 329 GLU Chi-restraints excluded: chain G residue 385 MET Chi-restraints excluded: chain G residue 403 ILE Chi-restraints excluded: chain G residue 445 SER Chi-restraints excluded: chain G residue 463 LEU Chi-restraints excluded: chain G residue 503 TYR Chi-restraints excluded: chain G residue 600 GLN Chi-restraints excluded: chain G residue 699 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 350 random chunks: chunk 252 optimal weight: 10.0000 chunk 198 optimal weight: 0.7980 chunk 70 optimal weight: 4.9990 chunk 237 optimal weight: 10.0000 chunk 343 optimal weight: 50.0000 chunk 300 optimal weight: 1.9990 chunk 178 optimal weight: 0.8980 chunk 72 optimal weight: 0.6980 chunk 249 optimal weight: 9.9990 chunk 124 optimal weight: 2.9990 chunk 111 optimal weight: 0.9980 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 223 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 508 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 552 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 223 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 552 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 221 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 552 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 658 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 223 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 414 ASN ** D 552 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 552 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 600 GLN ** F 223 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 552 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 658 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 552 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4828 r_free = 0.4828 target = 0.222164 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4527 r_free = 0.4527 target = 0.189982 restraints weight = 44113.347| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.4547 r_free = 0.4547 target = 0.192432 restraints weight = 29056.060| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.4557 r_free = 0.4557 target = 0.193587 restraints weight = 21902.492| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.4561 r_free = 0.4561 target = 0.194206 restraints weight = 18960.424| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.4564 r_free = 0.4564 target = 0.194455 restraints weight = 18930.830| |-----------------------------------------------------------------------------| r_work (final): 0.4565 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5660 moved from start: 0.5853 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 27846 Z= 0.125 Angle : 0.581 9.651 37842 Z= 0.316 Chirality : 0.044 0.196 4221 Planarity : 0.005 0.063 4963 Dihedral : 5.933 41.238 3808 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 13.26 Ramachandran Plot: Outliers : 0.21 % Allowed : 8.22 % Favored : 91.57 % Rotamer: Outliers : 3.30 % Allowed : 21.24 % Favored : 75.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.79 (0.13), residues: 3381 helix: -4.44 (0.16), residues: 210 sheet: -2.21 (0.16), residues: 1043 loop : -2.58 (0.13), residues: 2128 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 502 TYR 0.028 0.002 TYR B 378 PHE 0.019 0.001 PHE B 159 TRP 0.038 0.001 TRP C 702 HIS 0.006 0.001 HIS A 141 Details of bonding type rmsd covalent geometry : bond 0.00280 (27832) covalent geometry : angle 0.57986 (37814) SS BOND : bond 0.00166 ( 14) SS BOND : angle 1.20438 ( 28) hydrogen bonds : bond 0.03350 ( 490) hydrogen bonds : angle 7.25862 ( 1428) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6762 Ramachandran restraints generated. 3381 Oldfield, 0 Emsley, 3381 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6762 Ramachandran restraints generated. 3381 Oldfield, 0 Emsley, 3381 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 413 residues out of total 3031 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 319 time to evaluate : 1.212 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: A 255 ARG cc_start: 0.5863 (ttm170) cc_final: 0.5569 (mtt180) REVERT: A 318 TRP cc_start: 0.7168 (m-10) cc_final: 0.6913 (m-10) REVERT: A 329 GLU cc_start: 0.5350 (OUTLIER) cc_final: 0.4563 (tt0) REVERT: A 403 ILE cc_start: 0.7573 (OUTLIER) cc_final: 0.7364 (mt) REVERT: A 511 LEU cc_start: 0.4341 (OUTLIER) cc_final: 0.3974 (tp) REVERT: A 577 TYR cc_start: 0.4494 (m-80) cc_final: 0.3153 (m-80) REVERT: A 597 MET cc_start: 0.5783 (ptt) cc_final: 0.4582 (ptm) REVERT: B 329 GLU cc_start: 0.5878 (OUTLIER) cc_final: 0.4920 (tt0) REVERT: B 354 LEU cc_start: 0.7471 (OUTLIER) cc_final: 0.6828 (mm) REVERT: B 385 MET cc_start: 0.7049 (OUTLIER) cc_final: 0.6448 (mtm) REVERT: B 403 ILE cc_start: 0.7609 (OUTLIER) cc_final: 0.7184 (mt) REVERT: B 531 ARG cc_start: 0.4816 (OUTLIER) cc_final: 0.3684 (mtt90) REVERT: B 577 TYR cc_start: 0.4356 (m-80) cc_final: 0.3223 (m-80) REVERT: B 713 PHE cc_start: 0.6020 (m-80) cc_final: 0.5655 (m-80) REVERT: C 329 GLU cc_start: 0.5724 (OUTLIER) cc_final: 0.4839 (tt0) REVERT: C 577 TYR cc_start: 0.4324 (m-80) cc_final: 0.3120 (m-80) REVERT: C 597 MET cc_start: 0.5113 (ptt) cc_final: 0.4161 (ttt) REVERT: C 687 ARG cc_start: 0.7297 (ttt-90) cc_final: 0.6729 (ttt180) REVERT: C 713 PHE cc_start: 0.6053 (m-80) cc_final: 0.5680 (m-80) REVERT: D 159 PHE cc_start: 0.5984 (m-10) cc_final: 0.5682 (t80) REVERT: D 208 ARG cc_start: 0.6026 (ptt180) cc_final: 0.5825 (ptt-90) REVERT: D 329 GLU cc_start: 0.5612 (OUTLIER) cc_final: 0.4651 (tt0) REVERT: D 342 TRP cc_start: 0.7234 (m-90) cc_final: 0.6851 (m-90) REVERT: D 369 ASP cc_start: 0.7890 (t0) cc_final: 0.6582 (m-30) REVERT: D 385 MET cc_start: 0.7032 (OUTLIER) cc_final: 0.6036 (mtm) REVERT: D 403 ILE cc_start: 0.7331 (OUTLIER) cc_final: 0.6878 (mt) REVERT: D 577 TYR cc_start: 0.4357 (m-80) cc_final: 0.2906 (m-10) REVERT: D 597 MET cc_start: 0.4924 (ptp) cc_final: 0.4131 (ptm) REVERT: D 713 PHE cc_start: 0.6483 (m-80) cc_final: 0.5919 (m-80) REVERT: E 252 GLN cc_start: 0.6733 (OUTLIER) cc_final: 0.6363 (tp40) REVERT: E 329 GLU cc_start: 0.5891 (OUTLIER) cc_final: 0.5004 (tt0) REVERT: E 403 ILE cc_start: 0.7291 (OUTLIER) cc_final: 0.7005 (mt) REVERT: E 427 GLN cc_start: 0.7052 (tt0) cc_final: 0.6538 (pt0) REVERT: E 577 TYR cc_start: 0.4387 (m-10) cc_final: 0.3470 (m-10) REVERT: E 597 MET cc_start: 0.4746 (ptp) cc_final: 0.3867 (ptm) REVERT: E 600 GLN cc_start: 0.6087 (OUTLIER) cc_final: 0.5762 (tm-30) REVERT: E 713 PHE cc_start: 0.6571 (m-80) cc_final: 0.5942 (m-80) REVERT: F 220 ILE cc_start: 0.8654 (OUTLIER) cc_final: 0.8367 (tp) REVERT: F 329 GLU cc_start: 0.5786 (OUTLIER) cc_final: 0.4724 (tt0) REVERT: F 342 TRP cc_start: 0.7368 (m-90) cc_final: 0.6979 (m100) REVERT: F 403 ILE cc_start: 0.7499 (OUTLIER) cc_final: 0.7109 (mt) REVERT: F 597 MET cc_start: 0.5040 (ptt) cc_final: 0.3585 (ptm) REVERT: F 698 GLN cc_start: 0.6667 (pm20) cc_final: 0.6360 (pm20) REVERT: F 713 PHE cc_start: 0.6007 (m-80) cc_final: 0.5633 (m-80) REVERT: G 177 ASP cc_start: 0.7114 (t0) cc_final: 0.6887 (t0) REVERT: G 329 GLU cc_start: 0.5572 (OUTLIER) cc_final: 0.4598 (tt0) REVERT: G 403 ILE cc_start: 0.7360 (OUTLIER) cc_final: 0.7077 (mt) REVERT: G 512 CYS cc_start: 0.5384 (p) cc_final: 0.5038 (p) REVERT: G 577 TYR cc_start: 0.4412 (m-80) cc_final: 0.3269 (m-80) REVERT: G 597 MET cc_start: 0.5356 (ptt) cc_final: 0.4533 (ptm) REVERT: G 702 TRP cc_start: 0.5237 (m-10) cc_final: 0.4911 (m-10) outliers start: 94 outliers final: 53 residues processed: 381 average time/residue: 0.1894 time to fit residues: 114.5154 Evaluate side-chains 359 residues out of total 3031 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 285 time to evaluate : 0.990 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 138 THR Chi-restraints excluded: chain A residue 220 ILE Chi-restraints excluded: chain A residue 285 VAL Chi-restraints excluded: chain A residue 286 SER Chi-restraints excluded: chain A residue 329 GLU Chi-restraints excluded: chain A residue 351 GLU Chi-restraints excluded: chain A residue 385 MET Chi-restraints excluded: chain A residue 403 ILE Chi-restraints excluded: chain A residue 445 SER Chi-restraints excluded: chain A residue 463 LEU Chi-restraints excluded: chain A residue 468 PHE Chi-restraints excluded: chain A residue 511 LEU Chi-restraints excluded: chain A residue 512 CYS Chi-restraints excluded: chain A residue 589 ILE Chi-restraints excluded: chain B residue 156 GLU Chi-restraints excluded: chain B residue 158 THR Chi-restraints excluded: chain B residue 220 ILE Chi-restraints excluded: chain B residue 285 VAL Chi-restraints excluded: chain B residue 329 GLU Chi-restraints excluded: chain B residue 351 GLU Chi-restraints excluded: chain B residue 354 LEU Chi-restraints excluded: chain B residue 385 MET Chi-restraints excluded: chain B residue 403 ILE Chi-restraints excluded: chain B residue 463 LEU Chi-restraints excluded: chain B residue 468 PHE Chi-restraints excluded: chain B residue 503 TYR Chi-restraints excluded: chain B residue 512 CYS Chi-restraints excluded: chain B residue 531 ARG Chi-restraints excluded: chain B residue 674 VAL Chi-restraints excluded: chain B residue 699 LEU Chi-restraints excluded: chain C residue 220 ILE Chi-restraints excluded: chain C residue 268 LEU Chi-restraints excluded: chain C residue 286 SER Chi-restraints excluded: chain C residue 329 GLU Chi-restraints excluded: chain C residue 354 LEU Chi-restraints excluded: chain C residue 365 THR Chi-restraints excluded: chain C residue 385 MET Chi-restraints excluded: chain C residue 503 TYR Chi-restraints excluded: chain D residue 138 THR Chi-restraints excluded: chain D residue 220 ILE Chi-restraints excluded: chain D residue 286 SER Chi-restraints excluded: chain D residue 329 GLU Chi-restraints excluded: chain D residue 385 MET Chi-restraints excluded: chain D residue 403 ILE Chi-restraints excluded: chain D residue 463 LEU Chi-restraints excluded: chain D residue 500 LEU Chi-restraints excluded: chain D residue 503 TYR Chi-restraints excluded: chain E residue 138 THR Chi-restraints excluded: chain E residue 220 ILE Chi-restraints excluded: chain E residue 252 GLN Chi-restraints excluded: chain E residue 270 THR Chi-restraints excluded: chain E residue 285 VAL Chi-restraints excluded: chain E residue 329 GLU Chi-restraints excluded: chain E residue 403 ILE Chi-restraints excluded: chain E residue 445 SER Chi-restraints excluded: chain E residue 503 TYR Chi-restraints excluded: chain E residue 600 GLN Chi-restraints excluded: chain F residue 220 ILE Chi-restraints excluded: chain F residue 285 VAL Chi-restraints excluded: chain F residue 329 GLU Chi-restraints excluded: chain F residue 351 GLU Chi-restraints excluded: chain F residue 403 ILE Chi-restraints excluded: chain F residue 409 ILE Chi-restraints excluded: chain F residue 463 LEU Chi-restraints excluded: chain F residue 503 TYR Chi-restraints excluded: chain F residue 674 VAL Chi-restraints excluded: chain G residue 138 THR Chi-restraints excluded: chain G residue 220 ILE Chi-restraints excluded: chain G residue 329 GLU Chi-restraints excluded: chain G residue 385 MET Chi-restraints excluded: chain G residue 403 ILE Chi-restraints excluded: chain G residue 463 LEU Chi-restraints excluded: chain G residue 503 TYR Chi-restraints excluded: chain G residue 699 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 350 random chunks: chunk 72 optimal weight: 4.9990 chunk 141 optimal weight: 6.9990 chunk 272 optimal weight: 0.8980 chunk 338 optimal weight: 9.9990 chunk 335 optimal weight: 9.9990 chunk 66 optimal weight: 1.9990 chunk 135 optimal weight: 0.0070 chunk 315 optimal weight: 9.9990 chunk 103 optimal weight: 6.9990 chunk 227 optimal weight: 5.9990 chunk 170 optimal weight: 7.9990 overall best weight: 2.7804 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 221 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 223 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 223 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 331 ASN ** C 221 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 223 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 552 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 658 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 193 GLN ** D 221 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 223 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 345 GLN ** D 414 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 552 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 221 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 223 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 371 ASN ** F 221 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 223 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 658 GLN ** G 221 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 600 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4768 r_free = 0.4768 target = 0.215116 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4477 r_free = 0.4477 target = 0.184112 restraints weight = 44495.248| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.4463 r_free = 0.4463 target = 0.184270 restraints weight = 33117.795| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.4475 r_free = 0.4475 target = 0.185486 restraints weight = 27808.759| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.4479 r_free = 0.4479 target = 0.185951 restraints weight = 24086.756| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.4482 r_free = 0.4482 target = 0.186200 restraints weight = 23193.717| |-----------------------------------------------------------------------------| r_work (final): 0.4495 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5902 moved from start: 0.6251 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 27846 Z= 0.203 Angle : 0.684 10.616 37842 Z= 0.374 Chirality : 0.047 0.242 4221 Planarity : 0.005 0.066 4963 Dihedral : 6.524 42.341 3808 Min Nonbonded Distance : 2.364 Molprobity Statistics. All-atom Clashscore : 17.08 Ramachandran Plot: Outliers : 0.21 % Allowed : 9.67 % Favored : 90.12 % Rotamer: Outliers : 4.67 % Allowed : 21.48 % Favored : 73.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.64 (0.14), residues: 3381 helix: -4.21 (0.35), residues: 84 sheet: -2.20 (0.16), residues: 994 loop : -2.60 (0.12), residues: 2303 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 438 TYR 0.022 0.003 TYR C 241 PHE 0.023 0.002 PHE F 231 TRP 0.028 0.002 TRP C 702 HIS 0.005 0.001 HIS G 452 Details of bonding type rmsd covalent geometry : bond 0.00464 (27832) covalent geometry : angle 0.68353 (37814) SS BOND : bond 0.00154 ( 14) SS BOND : angle 1.32435 ( 28) hydrogen bonds : bond 0.04256 ( 490) hydrogen bonds : angle 7.57824 ( 1428) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6762 Ramachandran restraints generated. 3381 Oldfield, 0 Emsley, 3381 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6762 Ramachandran restraints generated. 3381 Oldfield, 0 Emsley, 3381 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 443 residues out of total 3031 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 133 poor density : 310 time to evaluate : 1.223 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: symmetry clash REVERT: A 255 ARG cc_start: 0.6003 (ttm170) cc_final: 0.5710 (mtt180) REVERT: A 270 THR cc_start: 0.6179 (OUTLIER) cc_final: 0.5569 (m) REVERT: A 329 GLU cc_start: 0.5783 (OUTLIER) cc_final: 0.4908 (tt0) REVERT: A 403 ILE cc_start: 0.7719 (OUTLIER) cc_final: 0.7495 (mt) REVERT: A 577 TYR cc_start: 0.4563 (m-80) cc_final: 0.3295 (m-80) REVERT: A 597 MET cc_start: 0.5883 (ptt) cc_final: 0.4730 (ptm) REVERT: A 687 ARG cc_start: 0.7052 (tmm-80) cc_final: 0.6331 (tmm-80) REVERT: A 712 GLN cc_start: 0.7280 (OUTLIER) cc_final: 0.6717 (tp-100) REVERT: B 329 GLU cc_start: 0.5897 (OUTLIER) cc_final: 0.5044 (tt0) REVERT: B 403 ILE cc_start: 0.7737 (OUTLIER) cc_final: 0.7402 (mt) REVERT: B 497 TYR cc_start: 0.5477 (OUTLIER) cc_final: 0.3720 (t80) REVERT: B 577 TYR cc_start: 0.4514 (m-80) cc_final: 0.3279 (m-80) REVERT: B 713 PHE cc_start: 0.6137 (m-80) cc_final: 0.5815 (m-80) REVERT: C 329 GLU cc_start: 0.5923 (OUTLIER) cc_final: 0.5016 (tt0) REVERT: C 497 TYR cc_start: 0.5535 (OUTLIER) cc_final: 0.4124 (t80) REVERT: C 512 CYS cc_start: 0.5792 (p) cc_final: 0.5475 (p) REVERT: C 577 TYR cc_start: 0.4383 (m-80) cc_final: 0.3134 (m-80) REVERT: C 597 MET cc_start: 0.4716 (ptt) cc_final: 0.3533 (ttt) REVERT: C 713 PHE cc_start: 0.6024 (m-80) cc_final: 0.5641 (m-80) REVERT: D 329 GLU cc_start: 0.5803 (OUTLIER) cc_final: 0.4832 (tt0) REVERT: D 342 TRP cc_start: 0.7462 (m-90) cc_final: 0.6848 (m-90) REVERT: D 369 ASP cc_start: 0.7812 (t0) cc_final: 0.6537 (m-30) REVERT: D 385 MET cc_start: 0.6958 (OUTLIER) cc_final: 0.6388 (mtm) REVERT: D 403 ILE cc_start: 0.7578 (OUTLIER) cc_final: 0.7090 (mm) REVERT: D 497 TYR cc_start: 0.5409 (OUTLIER) cc_final: 0.3401 (t80) REVERT: D 577 TYR cc_start: 0.4481 (m-80) cc_final: 0.2985 (m-10) REVERT: D 597 MET cc_start: 0.5203 (ptp) cc_final: 0.4213 (ptm) REVERT: D 713 PHE cc_start: 0.6413 (m-80) cc_final: 0.5898 (m-80) REVERT: E 329 GLU cc_start: 0.5561 (OUTLIER) cc_final: 0.4772 (tt0) REVERT: E 403 ILE cc_start: 0.7593 (OUTLIER) cc_final: 0.7277 (mt) REVERT: E 577 TYR cc_start: 0.4552 (m-10) cc_final: 0.3677 (m-10) REVERT: E 597 MET cc_start: 0.5216 (ptp) cc_final: 0.4250 (ptm) REVERT: E 712 GLN cc_start: 0.6829 (tm-30) cc_final: 0.5505 (mt0) REVERT: E 713 PHE cc_start: 0.6676 (m-80) cc_final: 0.5772 (m-80) REVERT: F 229 ARG cc_start: 0.7223 (ttm110) cc_final: 0.6462 (tpt170) REVERT: F 255 ARG cc_start: 0.6692 (mtp180) cc_final: 0.6352 (mtp180) REVERT: F 329 GLU cc_start: 0.6048 (OUTLIER) cc_final: 0.5102 (tt0) REVERT: F 403 ILE cc_start: 0.7656 (OUTLIER) cc_final: 0.7262 (mt) REVERT: F 497 TYR cc_start: 0.5690 (OUTLIER) cc_final: 0.3974 (t80) REVERT: F 597 MET cc_start: 0.5227 (ptt) cc_final: 0.3768 (ptm) REVERT: F 687 ARG cc_start: 0.7341 (ttt180) cc_final: 0.7111 (tmt170) REVERT: F 713 PHE cc_start: 0.6031 (m-80) cc_final: 0.5678 (m-80) REVERT: G 177 ASP cc_start: 0.7150 (t0) cc_final: 0.6946 (t0) REVERT: G 329 GLU cc_start: 0.5857 (OUTLIER) cc_final: 0.4923 (tt0) REVERT: G 403 ILE cc_start: 0.7502 (OUTLIER) cc_final: 0.7225 (mt) REVERT: G 497 TYR cc_start: 0.5274 (OUTLIER) cc_final: 0.3405 (t80) REVERT: G 577 TYR cc_start: 0.4479 (m-80) cc_final: 0.3355 (m-80) REVERT: G 597 MET cc_start: 0.5562 (ptt) cc_final: 0.4330 (ptm) outliers start: 133 outliers final: 79 residues processed: 397 average time/residue: 0.1881 time to fit residues: 116.8822 Evaluate side-chains 396 residues out of total 3031 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 100 poor density : 296 time to evaluate : 1.069 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 138 THR Chi-restraints excluded: chain A residue 220 ILE Chi-restraints excluded: chain A residue 270 THR Chi-restraints excluded: chain A residue 285 VAL Chi-restraints excluded: chain A residue 286 SER Chi-restraints excluded: chain A residue 329 GLU Chi-restraints excluded: chain A residue 351 GLU Chi-restraints excluded: chain A residue 365 THR Chi-restraints excluded: chain A residue 385 MET Chi-restraints excluded: chain A residue 403 ILE Chi-restraints excluded: chain A residue 445 SER Chi-restraints excluded: chain A residue 463 LEU Chi-restraints excluded: chain A residue 468 PHE Chi-restraints excluded: chain A residue 503 TYR Chi-restraints excluded: chain A residue 512 CYS Chi-restraints excluded: chain A residue 589 ILE Chi-restraints excluded: chain A residue 712 GLN Chi-restraints excluded: chain B residue 156 GLU Chi-restraints excluded: chain B residue 158 THR Chi-restraints excluded: chain B residue 220 ILE Chi-restraints excluded: chain B residue 285 VAL Chi-restraints excluded: chain B residue 329 GLU Chi-restraints excluded: chain B residue 351 GLU Chi-restraints excluded: chain B residue 354 LEU Chi-restraints excluded: chain B residue 365 THR Chi-restraints excluded: chain B residue 385 MET Chi-restraints excluded: chain B residue 403 ILE Chi-restraints excluded: chain B residue 445 SER Chi-restraints excluded: chain B residue 463 LEU Chi-restraints excluded: chain B residue 468 PHE Chi-restraints excluded: chain B residue 497 TYR Chi-restraints excluded: chain B residue 503 TYR Chi-restraints excluded: chain B residue 512 CYS Chi-restraints excluded: chain B residue 531 ARG Chi-restraints excluded: chain B residue 674 VAL Chi-restraints excluded: chain B residue 699 LEU Chi-restraints excluded: chain C residue 156 GLU Chi-restraints excluded: chain C residue 220 ILE Chi-restraints excluded: chain C residue 268 LEU Chi-restraints excluded: chain C residue 286 SER Chi-restraints excluded: chain C residue 329 GLU Chi-restraints excluded: chain C residue 354 LEU Chi-restraints excluded: chain C residue 365 THR Chi-restraints excluded: chain C residue 382 VAL Chi-restraints excluded: chain C residue 385 MET Chi-restraints excluded: chain C residue 407 VAL Chi-restraints excluded: chain C residue 409 ILE Chi-restraints excluded: chain C residue 443 SER Chi-restraints excluded: chain C residue 464 GLN Chi-restraints excluded: chain C residue 497 TYR Chi-restraints excluded: chain C residue 503 TYR Chi-restraints excluded: chain C residue 589 ILE Chi-restraints excluded: chain D residue 138 THR Chi-restraints excluded: chain D residue 220 ILE Chi-restraints excluded: chain D residue 286 SER Chi-restraints excluded: chain D residue 329 GLU Chi-restraints excluded: chain D residue 333 LYS Chi-restraints excluded: chain D residue 345 GLN Chi-restraints excluded: chain D residue 365 THR Chi-restraints excluded: chain D residue 385 MET Chi-restraints excluded: chain D residue 403 ILE Chi-restraints excluded: chain D residue 414 ASN Chi-restraints excluded: chain D residue 463 LEU Chi-restraints excluded: chain D residue 497 TYR Chi-restraints excluded: chain D residue 503 TYR Chi-restraints excluded: chain E residue 138 THR Chi-restraints excluded: chain E residue 152 ILE Chi-restraints excluded: chain E residue 220 ILE Chi-restraints excluded: chain E residue 270 THR Chi-restraints excluded: chain E residue 285 VAL Chi-restraints excluded: chain E residue 329 GLU Chi-restraints excluded: chain E residue 371 ASN Chi-restraints excluded: chain E residue 403 ILE Chi-restraints excluded: chain E residue 445 SER Chi-restraints excluded: chain E residue 503 TYR Chi-restraints excluded: chain E residue 688 PHE Chi-restraints excluded: chain F residue 220 ILE Chi-restraints excluded: chain F residue 245 TRP Chi-restraints excluded: chain F residue 285 VAL Chi-restraints excluded: chain F residue 329 GLU Chi-restraints excluded: chain F residue 351 GLU Chi-restraints excluded: chain F residue 354 LEU Chi-restraints excluded: chain F residue 403 ILE Chi-restraints excluded: chain F residue 409 ILE Chi-restraints excluded: chain F residue 463 LEU Chi-restraints excluded: chain F residue 468 PHE Chi-restraints excluded: chain F residue 497 TYR Chi-restraints excluded: chain F residue 503 TYR Chi-restraints excluded: chain F residue 592 TYR Chi-restraints excluded: chain F residue 674 VAL Chi-restraints excluded: chain G residue 138 THR Chi-restraints excluded: chain G residue 220 ILE Chi-restraints excluded: chain G residue 286 SER Chi-restraints excluded: chain G residue 329 GLU Chi-restraints excluded: chain G residue 385 MET Chi-restraints excluded: chain G residue 403 ILE Chi-restraints excluded: chain G residue 445 SER Chi-restraints excluded: chain G residue 463 LEU Chi-restraints excluded: chain G residue 497 TYR Chi-restraints excluded: chain G residue 503 TYR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 350 random chunks: chunk 313 optimal weight: 0.7980 chunk 238 optimal weight: 1.9990 chunk 235 optimal weight: 3.9990 chunk 180 optimal weight: 7.9990 chunk 57 optimal weight: 6.9990 chunk 261 optimal weight: 3.9990 chunk 151 optimal weight: 3.9990 chunk 247 optimal weight: 4.9990 chunk 67 optimal weight: 0.0050 chunk 5 optimal weight: 1.9990 chunk 167 optimal weight: 0.6980 overall best weight: 1.0998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 223 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 414 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 552 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 223 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 427 GLN ** B 508 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 552 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 223 ASN ** C 552 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 658 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 414 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 552 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 252 GLN E 427 GLN ** E 552 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 223 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 252 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 552 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 343 ASN ** G 414 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4820 r_free = 0.4820 target = 0.221021 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4530 r_free = 0.4530 target = 0.188916 restraints weight = 44109.134| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.4536 r_free = 0.4536 target = 0.190931 restraints weight = 30925.480| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.4541 r_free = 0.4541 target = 0.191883 restraints weight = 21902.064| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.4549 r_free = 0.4549 target = 0.192693 restraints weight = 20798.033| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.4550 r_free = 0.4550 target = 0.192875 restraints weight = 18430.243| |-----------------------------------------------------------------------------| r_work (final): 0.4553 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5700 moved from start: 0.6373 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 27846 Z= 0.124 Angle : 0.591 9.838 37842 Z= 0.319 Chirality : 0.045 0.204 4221 Planarity : 0.004 0.058 4963 Dihedral : 5.890 40.528 3808 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 13.45 Ramachandran Plot: Outliers : 0.21 % Allowed : 7.69 % Favored : 92.10 % Rotamer: Outliers : 3.12 % Allowed : 23.52 % Favored : 73.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.73 (0.13), residues: 3381 helix: -4.30 (0.21), residues: 168 sheet: -2.12 (0.16), residues: 1057 loop : -2.63 (0.12), residues: 2156 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG E 372 TYR 0.026 0.002 TYR B 241 PHE 0.017 0.001 PHE A 381 TRP 0.032 0.002 TRP D 702 HIS 0.005 0.001 HIS A 141 Details of bonding type rmsd covalent geometry : bond 0.00280 (27832) covalent geometry : angle 0.59017 (37814) SS BOND : bond 0.00333 ( 14) SS BOND : angle 1.23843 ( 28) hydrogen bonds : bond 0.03320 ( 490) hydrogen bonds : angle 7.07869 ( 1428) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6762 Ramachandran restraints generated. 3381 Oldfield, 0 Emsley, 3381 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6762 Ramachandran restraints generated. 3381 Oldfield, 0 Emsley, 3381 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 402 residues out of total 3031 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 313 time to evaluate : 0.866 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: A 177 ASP cc_start: 0.6665 (t0) cc_final: 0.6446 (t0) REVERT: A 255 ARG cc_start: 0.5897 (ttm170) cc_final: 0.5572 (mtt180) REVERT: A 270 THR cc_start: 0.5952 (OUTLIER) cc_final: 0.5302 (m) REVERT: A 329 GLU cc_start: 0.5464 (OUTLIER) cc_final: 0.4560 (tt0) REVERT: A 497 TYR cc_start: 0.5379 (OUTLIER) cc_final: 0.4469 (t80) REVERT: A 503 TYR cc_start: 0.2876 (OUTLIER) cc_final: 0.2407 (m-80) REVERT: A 577 TYR cc_start: 0.4396 (m-80) cc_final: 0.3126 (m-80) REVERT: A 597 MET cc_start: 0.5861 (ptt) cc_final: 0.4720 (ptm) REVERT: A 687 ARG cc_start: 0.7140 (tmm-80) cc_final: 0.6583 (tmm-80) REVERT: B 329 GLU cc_start: 0.5762 (OUTLIER) cc_final: 0.4883 (tt0) REVERT: B 342 TRP cc_start: 0.7164 (m-90) cc_final: 0.6748 (m-90) REVERT: B 403 ILE cc_start: 0.7471 (OUTLIER) cc_final: 0.7269 (mt) REVERT: B 427 GLN cc_start: 0.6844 (tt0) cc_final: 0.6201 (pt0) REVERT: B 531 ARG cc_start: 0.5029 (OUTLIER) cc_final: 0.4757 (mmt-90) REVERT: B 577 TYR cc_start: 0.4399 (m-80) cc_final: 0.3224 (m-80) REVERT: B 687 ARG cc_start: 0.7037 (ttt-90) cc_final: 0.6726 (tpt-90) REVERT: B 702 TRP cc_start: 0.6419 (t-100) cc_final: 0.6207 (t-100) REVERT: C 329 GLU cc_start: 0.5758 (OUTLIER) cc_final: 0.4905 (tt0) REVERT: C 342 TRP cc_start: 0.7251 (m-90) cc_final: 0.6971 (m-90) REVERT: C 385 MET cc_start: 0.7019 (OUTLIER) cc_final: 0.6166 (mtm) REVERT: C 577 TYR cc_start: 0.4332 (m-80) cc_final: 0.3106 (m-80) REVERT: C 597 MET cc_start: 0.4261 (ptt) cc_final: 0.3310 (ttt) REVERT: C 712 GLN cc_start: 0.6885 (tm-30) cc_final: 0.5342 (mt0) REVERT: C 713 PHE cc_start: 0.5911 (m-80) cc_final: 0.5375 (m-80) REVERT: D 187 ASN cc_start: 0.5865 (m-40) cc_final: 0.5551 (t0) REVERT: D 329 GLU cc_start: 0.5685 (OUTLIER) cc_final: 0.4784 (tt0) REVERT: D 342 TRP cc_start: 0.7241 (m-90) cc_final: 0.6824 (m-90) REVERT: D 369 ASP cc_start: 0.7748 (t0) cc_final: 0.6637 (m-30) REVERT: D 385 MET cc_start: 0.6946 (OUTLIER) cc_final: 0.6120 (mtm) REVERT: D 403 ILE cc_start: 0.7475 (OUTLIER) cc_final: 0.7238 (mt) REVERT: D 577 TYR cc_start: 0.4375 (m-80) cc_final: 0.2872 (m-10) REVERT: D 597 MET cc_start: 0.5241 (ptp) cc_final: 0.4544 (ptm) REVERT: D 713 PHE cc_start: 0.6383 (m-80) cc_final: 0.5878 (m-80) REVERT: E 329 GLU cc_start: 0.5896 (OUTLIER) cc_final: 0.4973 (tt0) REVERT: E 403 ILE cc_start: 0.7388 (OUTLIER) cc_final: 0.7131 (mt) REVERT: E 577 TYR cc_start: 0.4520 (m-10) cc_final: 0.3574 (m-10) REVERT: E 597 MET cc_start: 0.4932 (ptp) cc_final: 0.4081 (ptm) REVERT: E 713 PHE cc_start: 0.6604 (m-80) cc_final: 0.6011 (m-80) REVERT: F 229 ARG cc_start: 0.7087 (ttm110) cc_final: 0.6394 (tpt170) REVERT: F 255 ARG cc_start: 0.6368 (mtp180) cc_final: 0.6078 (mmm-85) REVERT: F 329 GLU cc_start: 0.5734 (OUTLIER) cc_final: 0.4754 (tt0) REVERT: F 385 MET cc_start: 0.6891 (OUTLIER) cc_final: 0.6484 (mtm) REVERT: F 403 ILE cc_start: 0.7394 (OUTLIER) cc_final: 0.7109 (mt) REVERT: F 597 MET cc_start: 0.5253 (ptt) cc_final: 0.3852 (ptm) REVERT: F 687 ARG cc_start: 0.7236 (ttt180) cc_final: 0.6992 (tmt170) REVERT: F 698 GLN cc_start: 0.6703 (pm20) cc_final: 0.6382 (pm20) REVERT: F 713 PHE cc_start: 0.6089 (m-80) cc_final: 0.5652 (m-80) REVERT: G 177 ASP cc_start: 0.7054 (t0) cc_final: 0.6848 (t0) REVERT: G 216 THR cc_start: 0.6961 (p) cc_final: 0.6752 (p) REVERT: G 329 GLU cc_start: 0.5569 (OUTLIER) cc_final: 0.4802 (tt0) REVERT: G 385 MET cc_start: 0.6899 (OUTLIER) cc_final: 0.6159 (mtm) REVERT: G 577 TYR cc_start: 0.4486 (m-80) cc_final: 0.3296 (m-10) REVERT: G 597 MET cc_start: 0.5487 (ptt) cc_final: 0.4726 (ptm) REVERT: G 702 TRP cc_start: 0.5288 (m-10) cc_final: 0.4792 (m-10) outliers start: 89 outliers final: 54 residues processed: 366 average time/residue: 0.1825 time to fit residues: 105.4360 Evaluate side-chains 362 residues out of total 3031 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 289 time to evaluate : 0.881 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 138 THR Chi-restraints excluded: chain A residue 220 ILE Chi-restraints excluded: chain A residue 270 THR Chi-restraints excluded: chain A residue 285 VAL Chi-restraints excluded: chain A residue 286 SER Chi-restraints excluded: chain A residue 329 GLU Chi-restraints excluded: chain A residue 351 GLU Chi-restraints excluded: chain A residue 385 MET Chi-restraints excluded: chain A residue 445 SER Chi-restraints excluded: chain A residue 463 LEU Chi-restraints excluded: chain A residue 497 TYR Chi-restraints excluded: chain A residue 503 TYR Chi-restraints excluded: chain A residue 589 ILE Chi-restraints excluded: chain B residue 156 GLU Chi-restraints excluded: chain B residue 158 THR Chi-restraints excluded: chain B residue 220 ILE Chi-restraints excluded: chain B residue 285 VAL Chi-restraints excluded: chain B residue 329 GLU Chi-restraints excluded: chain B residue 351 GLU Chi-restraints excluded: chain B residue 365 THR Chi-restraints excluded: chain B residue 385 MET Chi-restraints excluded: chain B residue 403 ILE Chi-restraints excluded: chain B residue 445 SER Chi-restraints excluded: chain B residue 463 LEU Chi-restraints excluded: chain B residue 468 PHE Chi-restraints excluded: chain B residue 503 TYR Chi-restraints excluded: chain B residue 512 CYS Chi-restraints excluded: chain B residue 531 ARG Chi-restraints excluded: chain B residue 674 VAL Chi-restraints excluded: chain B residue 699 LEU Chi-restraints excluded: chain C residue 220 ILE Chi-restraints excluded: chain C residue 268 LEU Chi-restraints excluded: chain C residue 286 SER Chi-restraints excluded: chain C residue 329 GLU Chi-restraints excluded: chain C residue 365 THR Chi-restraints excluded: chain C residue 385 MET Chi-restraints excluded: chain C residue 443 SER Chi-restraints excluded: chain C residue 503 TYR Chi-restraints excluded: chain D residue 138 THR Chi-restraints excluded: chain D residue 220 ILE Chi-restraints excluded: chain D residue 286 SER Chi-restraints excluded: chain D residue 329 GLU Chi-restraints excluded: chain D residue 385 MET Chi-restraints excluded: chain D residue 403 ILE Chi-restraints excluded: chain D residue 463 LEU Chi-restraints excluded: chain D residue 503 TYR Chi-restraints excluded: chain E residue 138 THR Chi-restraints excluded: chain E residue 220 ILE Chi-restraints excluded: chain E residue 270 THR Chi-restraints excluded: chain E residue 285 VAL Chi-restraints excluded: chain E residue 329 GLU Chi-restraints excluded: chain E residue 403 ILE Chi-restraints excluded: chain E residue 445 SER Chi-restraints excluded: chain E residue 463 LEU Chi-restraints excluded: chain E residue 503 TYR Chi-restraints excluded: chain F residue 220 ILE Chi-restraints excluded: chain F residue 245 TRP Chi-restraints excluded: chain F residue 285 VAL Chi-restraints excluded: chain F residue 329 GLU Chi-restraints excluded: chain F residue 351 GLU Chi-restraints excluded: chain F residue 385 MET Chi-restraints excluded: chain F residue 403 ILE Chi-restraints excluded: chain F residue 409 ILE Chi-restraints excluded: chain F residue 463 LEU Chi-restraints excluded: chain F residue 503 TYR Chi-restraints excluded: chain F residue 674 VAL Chi-restraints excluded: chain G residue 138 THR Chi-restraints excluded: chain G residue 220 ILE Chi-restraints excluded: chain G residue 286 SER Chi-restraints excluded: chain G residue 329 GLU Chi-restraints excluded: chain G residue 385 MET Chi-restraints excluded: chain G residue 463 LEU Chi-restraints excluded: chain G residue 503 TYR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 350 random chunks: chunk 137 optimal weight: 10.0000 chunk 191 optimal weight: 7.9990 chunk 100 optimal weight: 5.9990 chunk 94 optimal weight: 20.0000 chunk 233 optimal weight: 6.9990 chunk 208 optimal weight: 7.9990 chunk 237 optimal weight: 8.9990 chunk 263 optimal weight: 5.9990 chunk 54 optimal weight: 2.9990 chunk 235 optimal weight: 10.0000 chunk 22 optimal weight: 0.7980 overall best weight: 4.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 193 GLN ** A 221 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 223 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 336 GLN A 343 ASN ** A 414 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 484 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 187 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 223 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 526 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 221 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 371 ASN ** C 658 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 221 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 223 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 343 ASN D 345 GLN ** D 525 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 221 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 223 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 371 ASN E 427 GLN ** F 221 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 223 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 252 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 525 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 187 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 221 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4725 r_free = 0.4725 target = 0.209423 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.4368 r_free = 0.4368 target = 0.173960 restraints weight = 43148.154| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 61)----------------| | r_work = 0.4399 r_free = 0.4399 target = 0.176765 restraints weight = 29499.653| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 68)----------------| | r_work = 0.4420 r_free = 0.4420 target = 0.178680 restraints weight = 22815.781| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 66)----------------| | r_work = 0.4433 r_free = 0.4433 target = 0.179954 restraints weight = 19253.299| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.4439 r_free = 0.4439 target = 0.180589 restraints weight = 17244.135| |-----------------------------------------------------------------------------| r_work (final): 0.4458 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6008 moved from start: 0.6951 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.080 27846 Z= 0.297 Angle : 0.820 11.899 37842 Z= 0.448 Chirality : 0.051 0.265 4221 Planarity : 0.007 0.068 4963 Dihedral : 7.317 43.677 3808 Min Nonbonded Distance : 2.308 Molprobity Statistics. All-atom Clashscore : 20.44 Ramachandran Plot: Outliers : 0.21 % Allowed : 11.86 % Favored : 87.93 % Rotamer: Outliers : 4.46 % Allowed : 23.48 % Favored : 72.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.96 (0.13), residues: 3381 helix: -4.24 (0.38), residues: 84 sheet: -2.36 (0.16), residues: 1036 loop : -2.85 (0.12), residues: 2261 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG F 502 TYR 0.030 0.003 TYR G 497 PHE 0.035 0.003 PHE E 256 TRP 0.033 0.003 TRP D 702 HIS 0.008 0.002 HIS D 141 Details of bonding type rmsd covalent geometry : bond 0.00682 (27832) covalent geometry : angle 0.81939 (37814) SS BOND : bond 0.00251 ( 14) SS BOND : angle 1.41544 ( 28) hydrogen bonds : bond 0.05331 ( 490) hydrogen bonds : angle 8.18445 ( 1428) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6762 Ramachandran restraints generated. 3381 Oldfield, 0 Emsley, 3381 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6762 Ramachandran restraints generated. 3381 Oldfield, 0 Emsley, 3381 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 462 residues out of total 3031 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 127 poor density : 335 time to evaluate : 0.977 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: A 255 ARG cc_start: 0.6288 (ttm170) cc_final: 0.5961 (mtt180) REVERT: A 329 GLU cc_start: 0.5912 (OUTLIER) cc_final: 0.5036 (tt0) REVERT: A 497 TYR cc_start: 0.5782 (OUTLIER) cc_final: 0.4518 (t80) REVERT: A 503 TYR cc_start: 0.3668 (OUTLIER) cc_final: 0.2573 (m-80) REVERT: A 577 TYR cc_start: 0.4735 (m-80) cc_final: 0.3394 (m-80) REVERT: A 597 MET cc_start: 0.6054 (ptt) cc_final: 0.4911 (ptm) REVERT: A 687 ARG cc_start: 0.7252 (tmm-80) cc_final: 0.6359 (tmm-80) REVERT: A 712 GLN cc_start: 0.7529 (OUTLIER) cc_final: 0.6850 (tp-100) REVERT: A 713 PHE cc_start: 0.6370 (m-80) cc_final: 0.5906 (m-80) REVERT: B 154 ASP cc_start: 0.3684 (OUTLIER) cc_final: 0.3289 (t0) REVERT: B 229 ARG cc_start: 0.7221 (ttm110) cc_final: 0.6868 (tpt170) REVERT: B 329 GLU cc_start: 0.6011 (OUTLIER) cc_final: 0.5152 (tt0) REVERT: B 385 MET cc_start: 0.7254 (OUTLIER) cc_final: 0.7016 (mtm) REVERT: B 403 ILE cc_start: 0.7791 (OUTLIER) cc_final: 0.7487 (mt) REVERT: B 577 TYR cc_start: 0.4599 (m-80) cc_final: 0.3260 (m-10) REVERT: B 713 PHE cc_start: 0.6411 (m-80) cc_final: 0.5957 (m-80) REVERT: C 283 LYS cc_start: 0.7483 (mtmt) cc_final: 0.7214 (mtmt) REVERT: C 329 GLU cc_start: 0.5761 (OUTLIER) cc_final: 0.4880 (tt0) REVERT: C 497 TYR cc_start: 0.5627 (OUTLIER) cc_final: 0.4067 (t80) REVERT: C 577 TYR cc_start: 0.4343 (m-80) cc_final: 0.3215 (m-80) REVERT: C 597 MET cc_start: 0.4732 (ptt) cc_final: 0.3850 (ptm) REVERT: C 713 PHE cc_start: 0.6257 (m-80) cc_final: 0.5966 (m-80) REVERT: D 187 ASN cc_start: 0.6079 (m-40) cc_final: 0.5820 (t0) REVERT: D 329 GLU cc_start: 0.6034 (OUTLIER) cc_final: 0.4918 (tt0) REVERT: D 342 TRP cc_start: 0.7552 (m-90) cc_final: 0.7175 (m-90) REVERT: D 403 ILE cc_start: 0.7748 (OUTLIER) cc_final: 0.7309 (mm) REVERT: D 503 TYR cc_start: 0.4701 (OUTLIER) cc_final: 0.2938 (m-80) REVERT: D 577 TYR cc_start: 0.4615 (m-80) cc_final: 0.3189 (m-80) REVERT: D 597 MET cc_start: 0.5641 (ptp) cc_final: 0.4833 (ptm) REVERT: D 713 PHE cc_start: 0.6561 (m-80) cc_final: 0.6016 (m-80) REVERT: E 329 GLU cc_start: 0.5599 (OUTLIER) cc_final: 0.4733 (tt0) REVERT: E 403 ILE cc_start: 0.7695 (OUTLIER) cc_final: 0.7358 (mt) REVERT: E 497 TYR cc_start: 0.5570 (OUTLIER) cc_final: 0.3963 (t80) REVERT: E 533 GLU cc_start: 0.5509 (tt0) cc_final: 0.4930 (mm-30) REVERT: E 597 MET cc_start: 0.5390 (ptp) cc_final: 0.4570 (ptm) REVERT: E 713 PHE cc_start: 0.6750 (m-80) cc_final: 0.6173 (m-80) REVERT: F 229 ARG cc_start: 0.7240 (ttm110) cc_final: 0.6562 (tpt170) REVERT: F 255 ARG cc_start: 0.6661 (mtp180) cc_final: 0.6459 (mtp180) REVERT: F 329 GLU cc_start: 0.6108 (OUTLIER) cc_final: 0.5153 (tt0) REVERT: F 403 ILE cc_start: 0.7711 (OUTLIER) cc_final: 0.7364 (mt) REVERT: F 503 TYR cc_start: 0.4208 (OUTLIER) cc_final: 0.2774 (m-80) REVERT: F 597 MET cc_start: 0.5563 (ptt) cc_final: 0.4338 (ptm) REVERT: F 652 PHE cc_start: 0.3109 (t80) cc_final: 0.2551 (t80) REVERT: F 687 ARG cc_start: 0.7292 (ttt180) cc_final: 0.7065 (tmt170) REVERT: F 712 GLN cc_start: 0.7030 (tm-30) cc_final: 0.5648 (mt0) REVERT: F 713 PHE cc_start: 0.6171 (m-80) cc_final: 0.5625 (m-80) REVERT: G 177 ASP cc_start: 0.7359 (t0) cc_final: 0.7140 (t0) REVERT: G 329 GLU cc_start: 0.5743 (OUTLIER) cc_final: 0.4964 (tt0) REVERT: G 385 MET cc_start: 0.7031 (OUTLIER) cc_final: 0.6570 (ptm) REVERT: G 497 TYR cc_start: 0.5585 (OUTLIER) cc_final: 0.3630 (t80) REVERT: G 577 TYR cc_start: 0.4483 (m-80) cc_final: 0.3370 (m-80) REVERT: G 597 MET cc_start: 0.5697 (ptt) cc_final: 0.4498 (ptm) REVERT: G 712 GLN cc_start: 0.7046 (tm-30) cc_final: 0.6785 (tm-30) outliers start: 127 outliers final: 86 residues processed: 414 average time/residue: 0.1865 time to fit residues: 122.1093 Evaluate side-chains 422 residues out of total 3031 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 108 poor density : 314 time to evaluate : 1.076 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 138 THR Chi-restraints excluded: chain A residue 220 ILE Chi-restraints excluded: chain A residue 270 THR Chi-restraints excluded: chain A residue 285 VAL Chi-restraints excluded: chain A residue 286 SER Chi-restraints excluded: chain A residue 329 GLU Chi-restraints excluded: chain A residue 343 ASN Chi-restraints excluded: chain A residue 365 THR Chi-restraints excluded: chain A residue 385 MET Chi-restraints excluded: chain A residue 445 SER Chi-restraints excluded: chain A residue 463 LEU Chi-restraints excluded: chain A residue 464 GLN Chi-restraints excluded: chain A residue 497 TYR Chi-restraints excluded: chain A residue 503 TYR Chi-restraints excluded: chain A residue 512 CYS Chi-restraints excluded: chain A residue 589 ILE Chi-restraints excluded: chain A residue 712 GLN Chi-restraints excluded: chain B residue 154 ASP Chi-restraints excluded: chain B residue 156 GLU Chi-restraints excluded: chain B residue 158 THR Chi-restraints excluded: chain B residue 220 ILE Chi-restraints excluded: chain B residue 270 THR Chi-restraints excluded: chain B residue 285 VAL Chi-restraints excluded: chain B residue 329 GLU Chi-restraints excluded: chain B residue 351 GLU Chi-restraints excluded: chain B residue 365 THR Chi-restraints excluded: chain B residue 385 MET Chi-restraints excluded: chain B residue 403 ILE Chi-restraints excluded: chain B residue 445 SER Chi-restraints excluded: chain B residue 463 LEU Chi-restraints excluded: chain B residue 468 PHE Chi-restraints excluded: chain B residue 503 TYR Chi-restraints excluded: chain B residue 512 CYS Chi-restraints excluded: chain B residue 531 ARG Chi-restraints excluded: chain B residue 699 LEU Chi-restraints excluded: chain C residue 156 GLU Chi-restraints excluded: chain C residue 220 ILE Chi-restraints excluded: chain C residue 268 LEU Chi-restraints excluded: chain C residue 286 SER Chi-restraints excluded: chain C residue 329 GLU Chi-restraints excluded: chain C residue 333 LYS Chi-restraints excluded: chain C residue 365 THR Chi-restraints excluded: chain C residue 382 VAL Chi-restraints excluded: chain C residue 385 MET Chi-restraints excluded: chain C residue 407 VAL Chi-restraints excluded: chain C residue 409 ILE Chi-restraints excluded: chain C residue 443 SER Chi-restraints excluded: chain C residue 464 GLN Chi-restraints excluded: chain C residue 468 PHE Chi-restraints excluded: chain C residue 497 TYR Chi-restraints excluded: chain C residue 503 TYR Chi-restraints excluded: chain C residue 589 ILE Chi-restraints excluded: chain D residue 138 THR Chi-restraints excluded: chain D residue 209 ILE Chi-restraints excluded: chain D residue 220 ILE Chi-restraints excluded: chain D residue 270 THR Chi-restraints excluded: chain D residue 286 SER Chi-restraints excluded: chain D residue 329 GLU Chi-restraints excluded: chain D residue 343 ASN Chi-restraints excluded: chain D residue 345 GLN Chi-restraints excluded: chain D residue 365 THR Chi-restraints excluded: chain D residue 385 MET Chi-restraints excluded: chain D residue 403 ILE Chi-restraints excluded: chain D residue 414 ASN Chi-restraints excluded: chain D residue 463 LEU Chi-restraints excluded: chain D residue 503 TYR Chi-restraints excluded: chain E residue 138 THR Chi-restraints excluded: chain E residue 152 ILE Chi-restraints excluded: chain E residue 220 ILE Chi-restraints excluded: chain E residue 285 VAL Chi-restraints excluded: chain E residue 329 GLU Chi-restraints excluded: chain E residue 403 ILE Chi-restraints excluded: chain E residue 407 VAL Chi-restraints excluded: chain E residue 445 SER Chi-restraints excluded: chain E residue 463 LEU Chi-restraints excluded: chain E residue 497 TYR Chi-restraints excluded: chain E residue 503 TYR Chi-restraints excluded: chain E residue 589 ILE Chi-restraints excluded: chain F residue 209 ILE Chi-restraints excluded: chain F residue 220 ILE Chi-restraints excluded: chain F residue 245 TRP Chi-restraints excluded: chain F residue 285 VAL Chi-restraints excluded: chain F residue 329 GLU Chi-restraints excluded: chain F residue 385 MET Chi-restraints excluded: chain F residue 403 ILE Chi-restraints excluded: chain F residue 407 VAL Chi-restraints excluded: chain F residue 409 ILE Chi-restraints excluded: chain F residue 443 SER Chi-restraints excluded: chain F residue 463 LEU Chi-restraints excluded: chain F residue 468 PHE Chi-restraints excluded: chain F residue 503 TYR Chi-restraints excluded: chain F residue 592 TYR Chi-restraints excluded: chain F residue 674 VAL Chi-restraints excluded: chain G residue 138 THR Chi-restraints excluded: chain G residue 220 ILE Chi-restraints excluded: chain G residue 270 THR Chi-restraints excluded: chain G residue 286 SER Chi-restraints excluded: chain G residue 320 THR Chi-restraints excluded: chain G residue 329 GLU Chi-restraints excluded: chain G residue 333 LYS Chi-restraints excluded: chain G residue 385 MET Chi-restraints excluded: chain G residue 407 VAL Chi-restraints excluded: chain G residue 445 SER Chi-restraints excluded: chain G residue 447 THR Chi-restraints excluded: chain G residue 463 LEU Chi-restraints excluded: chain G residue 497 TYR Chi-restraints excluded: chain G residue 503 TYR Chi-restraints excluded: chain G residue 699 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 350 random chunks: chunk 281 optimal weight: 8.9990 chunk 110 optimal weight: 0.7980 chunk 287 optimal weight: 9.9990 chunk 158 optimal weight: 0.9990 chunk 143 optimal weight: 30.0000 chunk 132 optimal weight: 3.9990 chunk 222 optimal weight: 2.9990 chunk 238 optimal weight: 3.9990 chunk 95 optimal weight: 10.0000 chunk 14 optimal weight: 9.9990 chunk 275 optimal weight: 1.9990 overall best weight: 2.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 221 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 223 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 414 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 484 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 187 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 223 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 427 GLN ** B 526 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 221 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 658 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 221 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 223 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 345 GLN D 427 GLN ** D 525 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 221 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 223 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 427 GLN ** E 552 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 223 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 252 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 187 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 221 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4725 r_free = 0.4725 target = 0.210002 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.4373 r_free = 0.4373 target = 0.174705 restraints weight = 43463.870| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.4403 r_free = 0.4403 target = 0.177494 restraints weight = 29768.064| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 50)----------------| | r_work = 0.4424 r_free = 0.4424 target = 0.179397 restraints weight = 23062.398| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 50)----------------| | r_work = 0.4437 r_free = 0.4437 target = 0.180683 restraints weight = 19489.232| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.4443 r_free = 0.4443 target = 0.181308 restraints weight = 17455.945| |-----------------------------------------------------------------------------| r_work (final): 0.4451 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6002 moved from start: 0.7000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.300 27846 Z= 0.306 Angle : 1.015 59.198 37842 Z= 0.584 Chirality : 0.051 0.545 4221 Planarity : 0.007 0.155 4963 Dihedral : 7.317 43.670 3808 Min Nonbonded Distance : 1.986 Molprobity Statistics. All-atom Clashscore : 22.66 Ramachandran Plot: Outliers : 0.21 % Allowed : 12.07 % Favored : 87.73 % Rotamer: Outliers : 4.18 % Allowed : 23.73 % Favored : 72.10 % Cbeta Deviations : 0.06 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.00 (0.13), residues: 3381 helix: -4.26 (0.37), residues: 84 sheet: -2.40 (0.16), residues: 1036 loop : -2.88 (0.12), residues: 2261 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG D 327 TYR 0.027 0.003 TYR G 497 PHE 0.039 0.003 PHE A 688 TRP 0.028 0.003 TRP D 702 HIS 0.013 0.002 HIS E 552 Details of bonding type rmsd covalent geometry : bond 0.00685 (27832) covalent geometry : angle 1.01100 (37814) SS BOND : bond 0.01622 ( 14) SS BOND : angle 3.55715 ( 28) hydrogen bonds : bond 0.05162 ( 490) hydrogen bonds : angle 8.16289 ( 1428) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6762 Ramachandran restraints generated. 3381 Oldfield, 0 Emsley, 3381 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6762 Ramachandran restraints generated. 3381 Oldfield, 0 Emsley, 3381 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 435 residues out of total 3031 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 119 poor density : 316 time to evaluate : 0.935 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 255 ARG cc_start: 0.6274 (ttm170) cc_final: 0.5939 (mtt180) REVERT: A 329 GLU cc_start: 0.5788 (OUTLIER) cc_final: 0.5008 (tt0) REVERT: A 497 TYR cc_start: 0.5761 (OUTLIER) cc_final: 0.4495 (t80) REVERT: A 503 TYR cc_start: 0.3647 (OUTLIER) cc_final: 0.2557 (m-80) REVERT: A 577 TYR cc_start: 0.4708 (m-80) cc_final: 0.3394 (m-80) REVERT: A 597 MET cc_start: 0.5970 (ptt) cc_final: 0.4958 (ptm) REVERT: A 687 ARG cc_start: 0.7284 (tmm-80) cc_final: 0.6351 (tmm-80) REVERT: A 712 GLN cc_start: 0.7504 (OUTLIER) cc_final: 0.6834 (tp-100) REVERT: A 713 PHE cc_start: 0.6415 (m-80) cc_final: 0.5896 (m-80) REVERT: B 154 ASP cc_start: 0.3666 (OUTLIER) cc_final: 0.3272 (t0) REVERT: B 229 ARG cc_start: 0.7196 (ttm110) cc_final: 0.6861 (tpt170) REVERT: B 329 GLU cc_start: 0.6005 (OUTLIER) cc_final: 0.5153 (tt0) REVERT: B 385 MET cc_start: 0.7249 (OUTLIER) cc_final: 0.6998 (mtm) REVERT: B 403 ILE cc_start: 0.7773 (OUTLIER) cc_final: 0.7478 (mt) REVERT: B 497 TYR cc_start: 0.5564 (OUTLIER) cc_final: 0.3888 (t80) REVERT: B 577 TYR cc_start: 0.4573 (m-80) cc_final: 0.3253 (m-10) REVERT: B 713 PHE cc_start: 0.6423 (m-80) cc_final: 0.5967 (m-80) REVERT: C 329 GLU cc_start: 0.5832 (OUTLIER) cc_final: 0.4853 (tt0) REVERT: C 497 TYR cc_start: 0.5611 (OUTLIER) cc_final: 0.4049 (t80) REVERT: C 577 TYR cc_start: 0.4311 (m-80) cc_final: 0.3208 (m-80) REVERT: C 597 MET cc_start: 0.4858 (ptt) cc_final: 0.3878 (ptm) REVERT: C 713 PHE cc_start: 0.6238 (m-80) cc_final: 0.5954 (m-80) REVERT: D 329 GLU cc_start: 0.5900 (OUTLIER) cc_final: 0.4912 (tt0) REVERT: D 342 TRP cc_start: 0.7583 (m-90) cc_final: 0.7142 (m-90) REVERT: D 369 ASP cc_start: 0.7853 (t0) cc_final: 0.6663 (m-30) REVERT: D 403 ILE cc_start: 0.7763 (OUTLIER) cc_final: 0.7336 (mm) REVERT: D 497 TYR cc_start: 0.5459 (OUTLIER) cc_final: 0.3632 (t80) REVERT: D 503 TYR cc_start: 0.4667 (OUTLIER) cc_final: 0.2905 (m-80) REVERT: D 577 TYR cc_start: 0.4568 (m-80) cc_final: 0.3183 (m-80) REVERT: D 597 MET cc_start: 0.5713 (ptp) cc_final: 0.4888 (ptm) REVERT: D 713 PHE cc_start: 0.6595 (m-80) cc_final: 0.6034 (m-80) REVERT: E 329 GLU cc_start: 0.5583 (OUTLIER) cc_final: 0.4734 (tt0) REVERT: E 403 ILE cc_start: 0.7686 (OUTLIER) cc_final: 0.7347 (mt) REVERT: E 497 TYR cc_start: 0.5560 (OUTLIER) cc_final: 0.3948 (t80) REVERT: E 533 GLU cc_start: 0.5510 (tt0) cc_final: 0.4933 (mm-30) REVERT: E 597 MET cc_start: 0.5365 (ptp) cc_final: 0.4588 (ptm) REVERT: E 713 PHE cc_start: 0.6723 (m-80) cc_final: 0.6166 (m-80) REVERT: F 229 ARG cc_start: 0.7227 (ttm110) cc_final: 0.6553 (tpt170) REVERT: F 255 ARG cc_start: 0.6645 (mtp180) cc_final: 0.6436 (mtp180) REVERT: F 329 GLU cc_start: 0.6095 (OUTLIER) cc_final: 0.5149 (tt0) REVERT: F 403 ILE cc_start: 0.7710 (OUTLIER) cc_final: 0.7374 (mt) REVERT: F 497 TYR cc_start: 0.5886 (OUTLIER) cc_final: 0.4106 (t80) REVERT: F 503 TYR cc_start: 0.4171 (OUTLIER) cc_final: 0.2740 (m-80) REVERT: F 597 MET cc_start: 0.5565 (ptt) cc_final: 0.4324 (ptm) REVERT: F 652 PHE cc_start: 0.3112 (t80) cc_final: 0.2546 (t80) REVERT: F 687 ARG cc_start: 0.7286 (ttt180) cc_final: 0.7065 (tmt170) REVERT: F 712 GLN cc_start: 0.7026 (tm-30) cc_final: 0.5637 (mt0) REVERT: F 713 PHE cc_start: 0.6146 (m-80) cc_final: 0.5616 (m-80) REVERT: G 177 ASP cc_start: 0.7319 (t0) cc_final: 0.7108 (t0) REVERT: G 329 GLU cc_start: 0.5740 (OUTLIER) cc_final: 0.4932 (tt0) REVERT: G 497 TYR cc_start: 0.5570 (OUTLIER) cc_final: 0.3623 (t80) REVERT: G 577 TYR cc_start: 0.4482 (m-80) cc_final: 0.3303 (m-80) REVERT: G 597 MET cc_start: 0.5519 (ptt) cc_final: 0.4523 (ptm) REVERT: G 712 GLN cc_start: 0.7036 (tm-30) cc_final: 0.6778 (tm-30) outliers start: 119 outliers final: 93 residues processed: 389 average time/residue: 0.1837 time to fit residues: 112.2691 Evaluate side-chains 428 residues out of total 3031 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 117 poor density : 311 time to evaluate : 0.884 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 138 THR Chi-restraints excluded: chain A residue 220 ILE Chi-restraints excluded: chain A residue 266 GLN Chi-restraints excluded: chain A residue 270 THR Chi-restraints excluded: chain A residue 285 VAL Chi-restraints excluded: chain A residue 286 SER Chi-restraints excluded: chain A residue 329 GLU Chi-restraints excluded: chain A residue 365 THR Chi-restraints excluded: chain A residue 385 MET Chi-restraints excluded: chain A residue 445 SER Chi-restraints excluded: chain A residue 463 LEU Chi-restraints excluded: chain A residue 464 GLN Chi-restraints excluded: chain A residue 497 TYR Chi-restraints excluded: chain A residue 503 TYR Chi-restraints excluded: chain A residue 512 CYS Chi-restraints excluded: chain A residue 589 ILE Chi-restraints excluded: chain A residue 674 VAL Chi-restraints excluded: chain A residue 712 GLN Chi-restraints excluded: chain B residue 154 ASP Chi-restraints excluded: chain B residue 156 GLU Chi-restraints excluded: chain B residue 158 THR Chi-restraints excluded: chain B residue 220 ILE Chi-restraints excluded: chain B residue 270 THR Chi-restraints excluded: chain B residue 285 VAL Chi-restraints excluded: chain B residue 329 GLU Chi-restraints excluded: chain B residue 351 GLU Chi-restraints excluded: chain B residue 365 THR Chi-restraints excluded: chain B residue 385 MET Chi-restraints excluded: chain B residue 403 ILE Chi-restraints excluded: chain B residue 445 SER Chi-restraints excluded: chain B residue 463 LEU Chi-restraints excluded: chain B residue 468 PHE Chi-restraints excluded: chain B residue 497 TYR Chi-restraints excluded: chain B residue 503 TYR Chi-restraints excluded: chain B residue 512 CYS Chi-restraints excluded: chain B residue 531 ARG Chi-restraints excluded: chain B residue 699 LEU Chi-restraints excluded: chain C residue 156 GLU Chi-restraints excluded: chain C residue 220 ILE Chi-restraints excluded: chain C residue 268 LEU Chi-restraints excluded: chain C residue 286 SER Chi-restraints excluded: chain C residue 329 GLU Chi-restraints excluded: chain C residue 365 THR Chi-restraints excluded: chain C residue 382 VAL Chi-restraints excluded: chain C residue 385 MET Chi-restraints excluded: chain C residue 409 ILE Chi-restraints excluded: chain C residue 443 SER Chi-restraints excluded: chain C residue 448 VAL Chi-restraints excluded: chain C residue 464 GLN Chi-restraints excluded: chain C residue 468 PHE Chi-restraints excluded: chain C residue 497 TYR Chi-restraints excluded: chain C residue 503 TYR Chi-restraints excluded: chain C residue 529 THR Chi-restraints excluded: chain C residue 589 ILE Chi-restraints excluded: chain C residue 592 TYR Chi-restraints excluded: chain D residue 138 THR Chi-restraints excluded: chain D residue 158 THR Chi-restraints excluded: chain D residue 209 ILE Chi-restraints excluded: chain D residue 220 ILE Chi-restraints excluded: chain D residue 270 THR Chi-restraints excluded: chain D residue 286 SER Chi-restraints excluded: chain D residue 329 GLU Chi-restraints excluded: chain D residue 333 LYS Chi-restraints excluded: chain D residue 365 THR Chi-restraints excluded: chain D residue 385 MET Chi-restraints excluded: chain D residue 403 ILE Chi-restraints excluded: chain D residue 414 ASN Chi-restraints excluded: chain D residue 463 LEU Chi-restraints excluded: chain D residue 468 PHE Chi-restraints excluded: chain D residue 497 TYR Chi-restraints excluded: chain D residue 503 TYR Chi-restraints excluded: chain E residue 138 THR Chi-restraints excluded: chain E residue 152 ILE Chi-restraints excluded: chain E residue 220 ILE Chi-restraints excluded: chain E residue 268 LEU Chi-restraints excluded: chain E residue 285 VAL Chi-restraints excluded: chain E residue 329 GLU Chi-restraints excluded: chain E residue 403 ILE Chi-restraints excluded: chain E residue 407 VAL Chi-restraints excluded: chain E residue 445 SER Chi-restraints excluded: chain E residue 463 LEU Chi-restraints excluded: chain E residue 497 TYR Chi-restraints excluded: chain E residue 503 TYR Chi-restraints excluded: chain E residue 589 ILE Chi-restraints excluded: chain F residue 209 ILE Chi-restraints excluded: chain F residue 220 ILE Chi-restraints excluded: chain F residue 245 TRP Chi-restraints excluded: chain F residue 285 VAL Chi-restraints excluded: chain F residue 329 GLU Chi-restraints excluded: chain F residue 354 LEU Chi-restraints excluded: chain F residue 385 MET Chi-restraints excluded: chain F residue 403 ILE Chi-restraints excluded: chain F residue 407 VAL Chi-restraints excluded: chain F residue 409 ILE Chi-restraints excluded: chain F residue 443 SER Chi-restraints excluded: chain F residue 463 LEU Chi-restraints excluded: chain F residue 468 PHE Chi-restraints excluded: chain F residue 497 TYR Chi-restraints excluded: chain F residue 503 TYR Chi-restraints excluded: chain F residue 592 TYR Chi-restraints excluded: chain F residue 674 VAL Chi-restraints excluded: chain G residue 138 THR Chi-restraints excluded: chain G residue 220 ILE Chi-restraints excluded: chain G residue 270 THR Chi-restraints excluded: chain G residue 286 SER Chi-restraints excluded: chain G residue 320 THR Chi-restraints excluded: chain G residue 329 GLU Chi-restraints excluded: chain G residue 333 LYS Chi-restraints excluded: chain G residue 385 MET Chi-restraints excluded: chain G residue 407 VAL Chi-restraints excluded: chain G residue 445 SER Chi-restraints excluded: chain G residue 447 THR Chi-restraints excluded: chain G residue 463 LEU Chi-restraints excluded: chain G residue 497 TYR Chi-restraints excluded: chain G residue 503 TYR Chi-restraints excluded: chain G residue 589 ILE Chi-restraints excluded: chain G residue 699 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 350 random chunks: chunk 25 optimal weight: 0.8980 chunk 243 optimal weight: 40.0000 chunk 105 optimal weight: 0.9990 chunk 326 optimal weight: 5.9990 chunk 309 optimal weight: 0.0770 chunk 325 optimal weight: 1.9990 chunk 67 optimal weight: 0.8980 chunk 18 optimal weight: 9.9990 chunk 94 optimal weight: 9.9990 chunk 113 optimal weight: 0.9990 chunk 156 optimal weight: 0.9980 overall best weight: 0.7740 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 221 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 223 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 414 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 484 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 187 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 223 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 526 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 221 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 658 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 221 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 223 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 525 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 221 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 223 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 552 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 223 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 252 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 187 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 221 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4726 r_free = 0.4726 target = 0.209979 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.4374 r_free = 0.4374 target = 0.174702 restraints weight = 43116.441| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.4404 r_free = 0.4404 target = 0.177459 restraints weight = 29598.337| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 50)----------------| | r_work = 0.4425 r_free = 0.4425 target = 0.179357 restraints weight = 22972.936| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 56)----------------| | r_work = 0.4438 r_free = 0.4438 target = 0.180619 restraints weight = 19428.036| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 18)----------------| | r_work = 0.4442 r_free = 0.4442 target = 0.181105 restraints weight = 17409.931| |-----------------------------------------------------------------------------| r_work (final): 0.4450 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6005 moved from start: 0.7015 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.682 27846 Z= 0.368 Angle : 1.027 59.198 37842 Z= 0.589 Chirality : 0.051 0.545 4221 Planarity : 0.007 0.155 4963 Dihedral : 7.317 43.670 3808 Min Nonbonded Distance : 1.918 Molprobity Statistics. All-atom Clashscore : 23.21 Ramachandran Plot: Outliers : 0.21 % Allowed : 12.07 % Favored : 87.73 % Rotamer: Outliers : 4.11 % Allowed : 23.80 % Favored : 72.10 % Cbeta Deviations : 0.06 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.00 (0.13), residues: 3381 helix: -4.26 (0.37), residues: 84 sheet: -2.40 (0.16), residues: 1036 loop : -2.88 (0.12), residues: 2261 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG D 327 TYR 0.027 0.003 TYR G 497 PHE 0.039 0.003 PHE A 688 TRP 0.028 0.003 TRP D 702 HIS 0.013 0.002 HIS E 552 Details of bonding type rmsd covalent geometry : bond 0.00685 (27832) covalent geometry : angle 1.01099 (37814) SS BOND : bond 0.18269 ( 14) SS BOND : angle 6.75278 ( 28) hydrogen bonds : bond 0.05162 ( 490) hydrogen bonds : angle 8.16289 ( 1428) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4972.67 seconds wall clock time: 86 minutes 57.17 seconds (5217.17 seconds total)