Starting phenix.real_space_refine on Tue Dec 31 07:37:53 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8dno_27575/12_2024/8dno_27575.cif Found real_map, /net/cci-nas-00/data/ceres_data/8dno_27575/12_2024/8dno_27575.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8dno_27575/12_2024/8dno_27575.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8dno_27575/12_2024/8dno_27575.map" model { file = "/net/cci-nas-00/data/ceres_data/8dno_27575/12_2024/8dno_27575.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8dno_27575/12_2024/8dno_27575.cif" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.062 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 76 5.16 5 C 9680 2.51 5 N 2564 2.21 5 O 2840 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/chem_data/mon_lib" Total number of atoms: 15160 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 3790 Number of conformers: 1 Conformer: "" Number of residues, atoms: 493, 3790 Classifications: {'peptide': 493} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 23, 'TRANS': 469} Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "B" Number of atoms: 3790 Number of conformers: 1 Conformer: "" Number of residues, atoms: 493, 3790 Classifications: {'peptide': 493} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 23, 'TRANS': 469} Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "C" Number of atoms: 3790 Number of conformers: 1 Conformer: "" Number of residues, atoms: 493, 3790 Classifications: {'peptide': 493} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 23, 'TRANS': 469} Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "D" Number of atoms: 3790 Number of conformers: 1 Conformer: "" Number of residues, atoms: 493, 3790 Classifications: {'peptide': 493} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 23, 'TRANS': 469} Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 7 Residues with excluded nonbonded symmetry interactions: 8 residue: pdb=" N TYR A 90 " occ=0.50 ... (10 atoms not shown) pdb=" OH TYR A 90 " occ=0.50 residue: pdb=" N CYS A 370 " occ=0.50 ... (4 atoms not shown) pdb=" SG CYS A 370 " occ=0.50 residue: pdb=" N TYR B 90 " occ=0.50 ... (10 atoms not shown) pdb=" OH TYR B 90 " occ=0.50 residue: pdb=" N CYS B 370 " occ=0.50 ... (4 atoms not shown) pdb=" SG CYS B 370 " occ=0.50 residue: pdb=" N TYR C 90 " occ=0.50 ... (10 atoms not shown) pdb=" OH TYR C 90 " occ=0.50 residue: pdb=" N CYS C 370 " occ=0.50 ... (4 atoms not shown) pdb=" SG CYS C 370 " occ=0.50 residue: pdb=" N TYR D 90 " occ=0.50 ... (10 atoms not shown) pdb=" OH TYR D 90 " occ=0.50 residue: pdb=" N CYS D 370 " occ=0.50 ... (4 atoms not shown) pdb=" SG CYS D 370 " occ=0.50 Time building chain proxies: 8.51, per 1000 atoms: 0.56 Number of scatterers: 15160 At special positions: 0 Unit cell: (104.86, 99.51, 99.51, 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 76 16.00 O 2840 8.00 N 2564 7.00 C 9680 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.78 Conformation dependent library (CDL) restraints added in 2.1 seconds 3928 Ramachandran restraints generated. 1964 Oldfield, 0 Emsley, 1964 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3568 Finding SS restraints... Secondary structure from input PDB file: 76 helices and 12 sheets defined 44.6% alpha, 11.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.74 Creating SS restraints... Processing helix chain 'A' and resid 56 through 71 Processing helix chain 'A' and resid 75 through 80 removed outlier: 3.529A pdb=" N THR A 79 " --> pdb=" O SER A 75 " (cutoff:3.500A) Processing helix chain 'A' and resid 81 through 112 removed outlier: 5.264A pdb=" N LEU A 101 " --> pdb=" O GLU A 97 " (cutoff:3.500A) removed outlier: 6.307A pdb=" N LEU A 102 " --> pdb=" O ARG A 98 " (cutoff:3.500A) Processing helix chain 'A' and resid 114 through 120 Processing helix chain 'A' and resid 121 through 135 Processing helix chain 'A' and resid 136 through 140 removed outlier: 3.649A pdb=" N LYS A 139 " --> pdb=" O TRP A 136 " (cutoff:3.500A) removed outlier: 4.157A pdb=" N ILE A 140 " --> pdb=" O ALA A 137 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 136 through 140' Processing helix chain 'A' and resid 173 through 180 Processing helix chain 'A' and resid 181 through 187 Processing helix chain 'A' and resid 199 through 213 removed outlier: 3.511A pdb=" N LEU A 203 " --> pdb=" O PRO A 199 " (cutoff:3.500A) Processing helix chain 'A' and resid 225 through 234 removed outlier: 3.858A pdb=" N ALA A 229 " --> pdb=" O TYR A 225 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N ALA A 232 " --> pdb=" O THR A 228 " (cutoff:3.500A) Processing helix chain 'A' and resid 247 through 260 Processing helix chain 'A' and resid 283 through 297 removed outlier: 3.549A pdb=" N VAL A 295 " --> pdb=" O ALA A 291 " (cutoff:3.500A) Processing helix chain 'A' and resid 315 through 329 removed outlier: 3.513A pdb=" N LYS A 329 " --> pdb=" O GLU A 325 " (cutoff:3.500A) Processing helix chain 'A' and resid 347 through 364 Processing helix chain 'A' and resid 394 through 398 Processing helix chain 'A' and resid 413 through 422 Processing helix chain 'A' and resid 436 through 447 Processing helix chain 'A' and resid 469 through 473 removed outlier: 3.500A pdb=" N GLY A 473 " --> pdb=" O LYS A 470 " (cutoff:3.500A) Processing helix chain 'A' and resid 480 through 484 removed outlier: 3.622A pdb=" N PHE A 483 " --> pdb=" O GLU A 480 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N HIS A 484 " --> pdb=" O TYR A 481 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 480 through 484' Processing helix chain 'B' and resid 56 through 71 Processing helix chain 'B' and resid 75 through 80 removed outlier: 3.528A pdb=" N THR B 79 " --> pdb=" O SER B 75 " (cutoff:3.500A) Processing helix chain 'B' and resid 81 through 112 removed outlier: 5.264A pdb=" N LEU B 101 " --> pdb=" O GLU B 97 " (cutoff:3.500A) removed outlier: 6.308A pdb=" N LEU B 102 " --> pdb=" O ARG B 98 " (cutoff:3.500A) Processing helix chain 'B' and resid 114 through 120 Processing helix chain 'B' and resid 121 through 135 Processing helix chain 'B' and resid 136 through 140 removed outlier: 3.650A pdb=" N LYS B 139 " --> pdb=" O TRP B 136 " (cutoff:3.500A) removed outlier: 4.158A pdb=" N ILE B 140 " --> pdb=" O ALA B 137 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 136 through 140' Processing helix chain 'B' and resid 173 through 180 Processing helix chain 'B' and resid 181 through 187 Processing helix chain 'B' and resid 199 through 213 removed outlier: 3.510A pdb=" N LEU B 203 " --> pdb=" O PRO B 199 " (cutoff:3.500A) Processing helix chain 'B' and resid 225 through 234 removed outlier: 3.858A pdb=" N ALA B 229 " --> pdb=" O TYR B 225 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N ALA B 232 " --> pdb=" O THR B 228 " (cutoff:3.500A) Processing helix chain 'B' and resid 247 through 260 Processing helix chain 'B' and resid 283 through 297 removed outlier: 3.549A pdb=" N VAL B 295 " --> pdb=" O ALA B 291 " (cutoff:3.500A) Processing helix chain 'B' and resid 315 through 329 removed outlier: 3.512A pdb=" N LYS B 329 " --> pdb=" O GLU B 325 " (cutoff:3.500A) Processing helix chain 'B' and resid 347 through 364 Processing helix chain 'B' and resid 394 through 398 Processing helix chain 'B' and resid 413 through 422 Processing helix chain 'B' and resid 436 through 447 Processing helix chain 'B' and resid 469 through 473 removed outlier: 3.501A pdb=" N GLY B 473 " --> pdb=" O LYS B 470 " (cutoff:3.500A) Processing helix chain 'B' and resid 480 through 484 removed outlier: 3.622A pdb=" N PHE B 483 " --> pdb=" O GLU B 480 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N HIS B 484 " --> pdb=" O TYR B 481 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 480 through 484' Processing helix chain 'C' and resid 56 through 71 Processing helix chain 'C' and resid 75 through 80 removed outlier: 3.529A pdb=" N THR C 79 " --> pdb=" O SER C 75 " (cutoff:3.500A) Processing helix chain 'C' and resid 81 through 112 removed outlier: 5.263A pdb=" N LEU C 101 " --> pdb=" O GLU C 97 " (cutoff:3.500A) removed outlier: 6.307A pdb=" N LEU C 102 " --> pdb=" O ARG C 98 " (cutoff:3.500A) Processing helix chain 'C' and resid 114 through 120 Processing helix chain 'C' and resid 121 through 135 Processing helix chain 'C' and resid 136 through 140 removed outlier: 3.649A pdb=" N LYS C 139 " --> pdb=" O TRP C 136 " (cutoff:3.500A) removed outlier: 4.158A pdb=" N ILE C 140 " --> pdb=" O ALA C 137 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 136 through 140' Processing helix chain 'C' and resid 173 through 180 Processing helix chain 'C' and resid 181 through 187 Processing helix chain 'C' and resid 199 through 213 removed outlier: 3.510A pdb=" N LEU C 203 " --> pdb=" O PRO C 199 " (cutoff:3.500A) Processing helix chain 'C' and resid 225 through 234 removed outlier: 3.858A pdb=" N ALA C 229 " --> pdb=" O TYR C 225 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N ALA C 232 " --> pdb=" O THR C 228 " (cutoff:3.500A) Processing helix chain 'C' and resid 247 through 260 Processing helix chain 'C' and resid 283 through 297 removed outlier: 3.549A pdb=" N VAL C 295 " --> pdb=" O ALA C 291 " (cutoff:3.500A) Processing helix chain 'C' and resid 315 through 329 removed outlier: 3.513A pdb=" N LYS C 329 " --> pdb=" O GLU C 325 " (cutoff:3.500A) Processing helix chain 'C' and resid 347 through 364 Processing helix chain 'C' and resid 394 through 398 Processing helix chain 'C' and resid 413 through 422 Processing helix chain 'C' and resid 436 through 447 Processing helix chain 'C' and resid 469 through 473 Processing helix chain 'C' and resid 480 through 484 removed outlier: 3.622A pdb=" N PHE C 483 " --> pdb=" O GLU C 480 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N HIS C 484 " --> pdb=" O TYR C 481 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 480 through 484' Processing helix chain 'D' and resid 56 through 71 Processing helix chain 'D' and resid 75 through 80 removed outlier: 3.529A pdb=" N THR D 79 " --> pdb=" O SER D 75 " (cutoff:3.500A) Processing helix chain 'D' and resid 81 through 112 removed outlier: 5.264A pdb=" N LEU D 101 " --> pdb=" O GLU D 97 " (cutoff:3.500A) removed outlier: 6.307A pdb=" N LEU D 102 " --> pdb=" O ARG D 98 " (cutoff:3.500A) Processing helix chain 'D' and resid 114 through 120 Processing helix chain 'D' and resid 121 through 135 Processing helix chain 'D' and resid 136 through 140 removed outlier: 3.650A pdb=" N LYS D 139 " --> pdb=" O TRP D 136 " (cutoff:3.500A) removed outlier: 4.157A pdb=" N ILE D 140 " --> pdb=" O ALA D 137 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 136 through 140' Processing helix chain 'D' and resid 173 through 180 Processing helix chain 'D' and resid 181 through 187 Processing helix chain 'D' and resid 199 through 213 removed outlier: 3.510A pdb=" N LEU D 203 " --> pdb=" O PRO D 199 " (cutoff:3.500A) Processing helix chain 'D' and resid 225 through 234 removed outlier: 3.858A pdb=" N ALA D 229 " --> pdb=" O TYR D 225 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N ALA D 232 " --> pdb=" O THR D 228 " (cutoff:3.500A) Processing helix chain 'D' and resid 247 through 260 Processing helix chain 'D' and resid 283 through 297 removed outlier: 3.549A pdb=" N VAL D 295 " --> pdb=" O ALA D 291 " (cutoff:3.500A) Processing helix chain 'D' and resid 315 through 329 removed outlier: 3.512A pdb=" N LYS D 329 " --> pdb=" O GLU D 325 " (cutoff:3.500A) Processing helix chain 'D' and resid 347 through 364 Processing helix chain 'D' and resid 394 through 398 Processing helix chain 'D' and resid 413 through 422 Processing helix chain 'D' and resid 436 through 447 Processing helix chain 'D' and resid 469 through 473 removed outlier: 3.500A pdb=" N GLY D 473 " --> pdb=" O LYS D 470 " (cutoff:3.500A) Processing helix chain 'D' and resid 480 through 484 removed outlier: 3.622A pdb=" N PHE D 483 " --> pdb=" O GLU D 480 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N HIS D 484 " --> pdb=" O TYR D 481 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 480 through 484' Processing sheet with id=AA1, first strand: chain 'A' and resid 40 through 41 removed outlier: 6.845A pdb=" N VAL A 40 " --> pdb=" O LEU A 49 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 152 through 159 removed outlier: 7.903A pdb=" N VAL B 452 " --> pdb=" O VAL A 489 " (cutoff:3.500A) removed outlier: 6.199A pdb=" N THR A 491 " --> pdb=" O VAL B 452 " (cutoff:3.500A) removed outlier: 7.520A pdb=" N VAL B 454 " --> pdb=" O THR A 491 " (cutoff:3.500A) removed outlier: 6.509A pdb=" N THR A 493 " --> pdb=" O VAL B 454 " (cutoff:3.500A) removed outlier: 6.371A pdb=" N ALA B 430 " --> pdb=" O TRP B 453 " (cutoff:3.500A) removed outlier: 6.300A pdb=" N CYS B 276 " --> pdb=" O PHE B 310 " (cutoff:3.500A) removed outlier: 7.981A pdb=" N GLU B 312 " --> pdb=" O CYS B 276 " (cutoff:3.500A) removed outlier: 8.188A pdb=" N VAL B 278 " --> pdb=" O GLU B 312 " (cutoff:3.500A) removed outlier: 6.259A pdb=" N VAL B 386 " --> pdb=" O GLU B 369 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 219 through 221 removed outlier: 6.290A pdb=" N VAL A 190 " --> pdb=" O ASN A 220 " (cutoff:3.500A) removed outlier: 6.568A pdb=" N VAL A 162 " --> pdb=" O ILE A 239 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 367 through 370 removed outlier: 6.259A pdb=" N VAL A 386 " --> pdb=" O GLU A 369 " (cutoff:3.500A) removed outlier: 6.300A pdb=" N CYS A 276 " --> pdb=" O PHE A 310 " (cutoff:3.500A) removed outlier: 7.981A pdb=" N GLU A 312 " --> pdb=" O CYS A 276 " (cutoff:3.500A) removed outlier: 8.188A pdb=" N VAL A 278 " --> pdb=" O GLU A 312 " (cutoff:3.500A) removed outlier: 6.370A pdb=" N ALA A 430 " --> pdb=" O TRP A 453 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 40 through 41 removed outlier: 6.845A pdb=" N VAL B 40 " --> pdb=" O LEU B 49 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 219 through 221 removed outlier: 6.290A pdb=" N VAL B 190 " --> pdb=" O ASN B 220 " (cutoff:3.500A) removed outlier: 6.569A pdb=" N VAL B 162 " --> pdb=" O ILE B 239 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 40 through 41 removed outlier: 6.845A pdb=" N VAL C 40 " --> pdb=" O LEU C 49 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 152 through 159 removed outlier: 7.827A pdb=" N VAL D 452 " --> pdb=" O VAL C 489 " (cutoff:3.500A) removed outlier: 6.142A pdb=" N THR C 491 " --> pdb=" O VAL D 452 " (cutoff:3.500A) removed outlier: 7.410A pdb=" N VAL D 454 " --> pdb=" O THR C 491 " (cutoff:3.500A) removed outlier: 6.499A pdb=" N THR C 493 " --> pdb=" O VAL D 454 " (cutoff:3.500A) removed outlier: 6.371A pdb=" N ALA D 430 " --> pdb=" O TRP D 453 " (cutoff:3.500A) removed outlier: 6.300A pdb=" N CYS D 276 " --> pdb=" O PHE D 310 " (cutoff:3.500A) removed outlier: 7.981A pdb=" N GLU D 312 " --> pdb=" O CYS D 276 " (cutoff:3.500A) removed outlier: 8.188A pdb=" N VAL D 278 " --> pdb=" O GLU D 312 " (cutoff:3.500A) removed outlier: 6.259A pdb=" N VAL D 386 " --> pdb=" O GLU D 369 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 219 through 221 removed outlier: 6.290A pdb=" N VAL C 190 " --> pdb=" O ASN C 220 " (cutoff:3.500A) removed outlier: 6.569A pdb=" N VAL C 162 " --> pdb=" O ILE C 239 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 367 through 370 removed outlier: 6.259A pdb=" N VAL C 386 " --> pdb=" O GLU C 369 " (cutoff:3.500A) removed outlier: 6.299A pdb=" N CYS C 276 " --> pdb=" O PHE C 310 " (cutoff:3.500A) removed outlier: 7.981A pdb=" N GLU C 312 " --> pdb=" O CYS C 276 " (cutoff:3.500A) removed outlier: 8.188A pdb=" N VAL C 278 " --> pdb=" O GLU C 312 " (cutoff:3.500A) removed outlier: 6.371A pdb=" N ALA C 430 " --> pdb=" O TRP C 453 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N THR D 493 " --> pdb=" O VAL C 452 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 40 through 41 removed outlier: 6.844A pdb=" N VAL D 40 " --> pdb=" O LEU D 49 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 219 through 221 removed outlier: 6.290A pdb=" N VAL D 190 " --> pdb=" O ASN D 220 " (cutoff:3.500A) removed outlier: 6.568A pdb=" N VAL D 162 " --> pdb=" O ILE D 239 " (cutoff:3.500A) 674 hydrogen bonds defined for protein. 1935 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 5.30 Time building geometry restraints manager: 4.36 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 4277 1.33 - 1.45: 3054 1.45 - 1.57: 8049 1.57 - 1.69: 0 1.69 - 1.81: 108 Bond restraints: 15488 Sorted by residual: bond pdb=" CA CYS C 456 " pdb=" C CYS C 456 " ideal model delta sigma weight residual 1.524 1.466 0.057 1.23e-02 6.61e+03 2.16e+01 bond pdb=" CA CYS D 456 " pdb=" C CYS D 456 " ideal model delta sigma weight residual 1.524 1.466 0.057 1.23e-02 6.61e+03 2.16e+01 bond pdb=" CA CYS B 456 " pdb=" C CYS B 456 " ideal model delta sigma weight residual 1.524 1.466 0.057 1.23e-02 6.61e+03 2.16e+01 bond pdb=" CA CYS A 456 " pdb=" C CYS A 456 " ideal model delta sigma weight residual 1.524 1.467 0.057 1.23e-02 6.61e+03 2.15e+01 bond pdb=" CA THR B 155 " pdb=" C THR B 155 " ideal model delta sigma weight residual 1.523 1.467 0.055 1.28e-02 6.10e+03 1.88e+01 ... (remaining 15483 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.99: 18246 1.99 - 3.97: 2162 3.97 - 5.96: 432 5.96 - 7.94: 110 7.94 - 9.93: 22 Bond angle restraints: 20972 Sorted by residual: angle pdb=" N GLU B 480 " pdb=" CA GLU B 480 " pdb=" C GLU B 480 " ideal model delta sigma weight residual 113.28 104.40 8.88 1.22e+00 6.72e-01 5.30e+01 angle pdb=" N GLU A 480 " pdb=" CA GLU A 480 " pdb=" C GLU A 480 " ideal model delta sigma weight residual 113.28 104.43 8.85 1.22e+00 6.72e-01 5.26e+01 angle pdb=" N GLU D 480 " pdb=" CA GLU D 480 " pdb=" C GLU D 480 " ideal model delta sigma weight residual 113.28 104.44 8.84 1.22e+00 6.72e-01 5.25e+01 angle pdb=" N GLU C 480 " pdb=" CA GLU C 480 " pdb=" C GLU C 480 " ideal model delta sigma weight residual 113.28 104.46 8.82 1.22e+00 6.72e-01 5.23e+01 angle pdb=" N VAL C 190 " pdb=" CA VAL C 190 " pdb=" C VAL C 190 " ideal model delta sigma weight residual 108.53 118.46 -9.93 1.45e+00 4.76e-01 4.69e+01 ... (remaining 20967 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.91: 8458 17.91 - 35.81: 646 35.81 - 53.72: 104 53.72 - 71.62: 20 71.62 - 89.53: 12 Dihedral angle restraints: 9240 sinusoidal: 3640 harmonic: 5600 Sorted by residual: dihedral pdb=" N HIS A 484 " pdb=" C HIS A 484 " pdb=" CA HIS A 484 " pdb=" CB HIS A 484 " ideal model delta harmonic sigma weight residual 122.80 113.73 9.07 0 2.50e+00 1.60e-01 1.32e+01 dihedral pdb=" C PRO D 199 " pdb=" N PRO D 199 " pdb=" CA PRO D 199 " pdb=" CB PRO D 199 " ideal model delta harmonic sigma weight residual -120.70 -112.19 -8.51 0 2.50e+00 1.60e-01 1.16e+01 dihedral pdb=" C PRO C 199 " pdb=" N PRO C 199 " pdb=" CA PRO C 199 " pdb=" CB PRO C 199 " ideal model delta harmonic sigma weight residual -120.70 -112.20 -8.50 0 2.50e+00 1.60e-01 1.15e+01 ... (remaining 9237 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.041: 1326 0.041 - 0.082: 584 0.082 - 0.123: 278 0.123 - 0.164: 100 0.164 - 0.205: 36 Chirality restraints: 2324 Sorted by residual: chirality pdb=" CA VAL D 405 " pdb=" N VAL D 405 " pdb=" C VAL D 405 " pdb=" CB VAL D 405 " both_signs ideal model delta sigma weight residual False 2.44 2.65 -0.21 2.00e-01 2.50e+01 1.05e+00 chirality pdb=" CA VAL B 405 " pdb=" N VAL B 405 " pdb=" C VAL B 405 " pdb=" CB VAL B 405 " both_signs ideal model delta sigma weight residual False 2.44 2.65 -0.20 2.00e-01 2.50e+01 1.05e+00 chirality pdb=" CA VAL A 405 " pdb=" N VAL A 405 " pdb=" C VAL A 405 " pdb=" CB VAL A 405 " both_signs ideal model delta sigma weight residual False 2.44 2.65 -0.20 2.00e-01 2.50e+01 1.04e+00 ... (remaining 2321 not shown) Planarity restraints: 2712 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLU B 158 " 0.046 5.00e-02 4.00e+02 6.96e-02 7.74e+00 pdb=" N PRO B 159 " -0.120 5.00e-02 4.00e+02 pdb=" CA PRO B 159 " 0.035 5.00e-02 4.00e+02 pdb=" CD PRO B 159 " 0.038 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLU D 158 " -0.042 5.00e-02 4.00e+02 6.34e-02 6.43e+00 pdb=" N PRO D 159 " 0.110 5.00e-02 4.00e+02 pdb=" CA PRO D 159 " -0.033 5.00e-02 4.00e+02 pdb=" CD PRO D 159 " -0.034 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLU A 158 " -0.042 5.00e-02 4.00e+02 6.33e-02 6.40e+00 pdb=" N PRO A 159 " 0.109 5.00e-02 4.00e+02 pdb=" CA PRO A 159 " -0.033 5.00e-02 4.00e+02 pdb=" CD PRO A 159 " -0.034 5.00e-02 4.00e+02 ... (remaining 2709 not shown) Histogram of nonbonded interaction distances: 2.30 - 2.82: 6068 2.82 - 3.34: 15788 3.34 - 3.86: 27856 3.86 - 4.38: 35859 4.38 - 4.90: 55321 Nonbonded interactions: 140892 Sorted by model distance: nonbonded pdb=" O ILE C 401 " pdb=" N GLY C 403 " model vdw 2.298 3.120 nonbonded pdb=" O ILE A 401 " pdb=" N GLY A 403 " model vdw 2.298 3.120 nonbonded pdb=" O ILE D 401 " pdb=" N GLY D 403 " model vdw 2.298 3.120 nonbonded pdb=" O ILE B 401 " pdb=" N GLY B 403 " model vdw 2.299 3.120 nonbonded pdb=" OXT SER B 501 " pdb=" CG PRO C 159 " model vdw 2.302 3.440 ... (remaining 140887 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' } 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=0.50 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.770 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.520 Check model and map are aligned: 0.090 Set scattering table: 0.140 Process input model: 34.570 Find NCS groups from input model: 0.450 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: 0.000 Load rotamer database and sin/cos tables:2.710 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 40.330 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7218 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 : 0.013 0.057 15488 Z= 0.821 Angle : 1.453 9.925 20972 Z= 0.973 Chirality : 0.061 0.205 2324 Planarity : 0.006 0.070 2712 Dihedral : 13.087 89.530 5672 Min Nonbonded Distance : 2.298 Molprobity Statistics. All-atom Clashscore : 40.43 Ramachandran Plot: Outliers : 2.65 % Allowed : 10.39 % Favored : 86.97 % Rotamer: Outliers : 4.71 % Allowed : 9.93 % Favored : 85.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.22 (0.15), residues: 1964 helix: -2.67 (0.14), residues: 784 sheet: -2.45 (0.24), residues: 388 loop : -2.92 (0.19), residues: 792 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP D 29 HIS 0.007 0.002 HIS D 484 PHE 0.018 0.003 PHE B 24 TYR 0.018 0.002 TYR D 154 ARG 0.006 0.001 ARG D 143 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3928 Ramachandran restraints generated. 1964 Oldfield, 0 Emsley, 1964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3928 Ramachandran restraints generated. 1964 Oldfield, 0 Emsley, 1964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 659 residues out of total 1632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 583 time to evaluate : 1.813 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 65 LYS cc_start: 0.8820 (tttt) cc_final: 0.8502 (mtpp) REVERT: A 158 GLU cc_start: 0.8256 (mt-10) cc_final: 0.7899 (mt-10) REVERT: A 175 MET cc_start: 0.8069 (OUTLIER) cc_final: 0.7580 (mmp) REVERT: A 292 HIS cc_start: 0.6786 (OUTLIER) cc_final: 0.6443 (t-90) REVERT: A 308 ARG cc_start: 0.7670 (mtm180) cc_final: 0.7428 (mtm180) REVERT: A 471 MET cc_start: 0.8665 (mtp) cc_final: 0.8372 (mtp) REVERT: A 477 GLU cc_start: 0.7683 (mt-10) cc_final: 0.7479 (mt-10) REVERT: B 169 TRP cc_start: 0.8607 (p-90) cc_final: 0.8257 (p-90) REVERT: B 175 MET cc_start: 0.7980 (OUTLIER) cc_final: 0.7511 (mmp) REVERT: B 267 THR cc_start: 0.8060 (p) cc_final: 0.7750 (p) REVERT: B 292 HIS cc_start: 0.5517 (OUTLIER) cc_final: 0.5286 (t-90) REVERT: B 410 LYS cc_start: 0.7945 (ttpt) cc_final: 0.7643 (tttm) REVERT: C 169 TRP cc_start: 0.8579 (p-90) cc_final: 0.8226 (p-90) REVERT: C 175 MET cc_start: 0.8009 (OUTLIER) cc_final: 0.7584 (mmp) REVERT: C 267 THR cc_start: 0.8093 (p) cc_final: 0.7747 (p) REVERT: C 292 HIS cc_start: 0.5600 (OUTLIER) cc_final: 0.5329 (t-90) REVERT: C 410 LYS cc_start: 0.7943 (ttpt) cc_final: 0.7638 (tttm) REVERT: C 415 ASP cc_start: 0.7876 (m-30) cc_final: 0.7091 (m-30) REVERT: D 169 TRP cc_start: 0.8576 (p-90) cc_final: 0.8240 (p-90) REVERT: D 175 MET cc_start: 0.7987 (OUTLIER) cc_final: 0.7568 (mmp) REVERT: D 267 THR cc_start: 0.8103 (p) cc_final: 0.7779 (p) REVERT: D 410 LYS cc_start: 0.7954 (ttpt) cc_final: 0.7661 (tttm) outliers start: 76 outliers final: 20 residues processed: 615 average time/residue: 0.3072 time to fit residues: 268.2485 Evaluate side-chains 488 residues out of total 1632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 461 time to evaluate : 1.632 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 175 MET Chi-restraints excluded: chain A residue 177 ILE Chi-restraints excluded: chain A residue 196 GLU Chi-restraints excluded: chain A residue 279 LEU Chi-restraints excluded: chain A residue 292 HIS Chi-restraints excluded: chain A residue 332 LEU Chi-restraints excluded: chain B residue 175 MET Chi-restraints excluded: chain B residue 177 ILE Chi-restraints excluded: chain B residue 196 GLU Chi-restraints excluded: chain B residue 279 LEU Chi-restraints excluded: chain B residue 292 HIS Chi-restraints excluded: chain B residue 299 GLN Chi-restraints excluded: chain B residue 332 LEU Chi-restraints excluded: chain C residue 51 GLN Chi-restraints excluded: chain C residue 175 MET Chi-restraints excluded: chain C residue 177 ILE Chi-restraints excluded: chain C residue 196 GLU Chi-restraints excluded: chain C residue 279 LEU Chi-restraints excluded: chain C residue 292 HIS Chi-restraints excluded: chain C residue 299 GLN Chi-restraints excluded: chain C residue 332 LEU Chi-restraints excluded: chain D residue 175 MET Chi-restraints excluded: chain D residue 177 ILE Chi-restraints excluded: chain D residue 196 GLU Chi-restraints excluded: chain D residue 279 LEU Chi-restraints excluded: chain D residue 299 GLN Chi-restraints excluded: chain D residue 332 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 165 optimal weight: 0.6980 chunk 148 optimal weight: 0.6980 chunk 82 optimal weight: 1.9990 chunk 50 optimal weight: 0.7980 chunk 100 optimal weight: 5.9990 chunk 79 optimal weight: 0.9980 chunk 153 optimal weight: 0.8980 chunk 59 optimal weight: 0.6980 chunk 93 optimal weight: 0.6980 chunk 114 optimal weight: 0.9990 chunk 177 optimal weight: 0.7980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 19 GLN A 293 HIS ** A 299 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 301 GLN A 345 GLN ** A 407 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 19 GLN ** B 30 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 293 HIS B 301 GLN B 345 GLN ** B 407 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 498 GLN C 19 GLN ** C 30 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 51 GLN ** C 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 293 HIS C 301 GLN C 345 GLN ** C 407 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 498 GLN D 19 GLN ** D 30 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 293 HIS D 301 GLN D 345 GLN ** D 407 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7221 moved from start: 0.3543 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 15488 Z= 0.251 Angle : 0.685 10.709 20972 Z= 0.354 Chirality : 0.046 0.249 2324 Planarity : 0.005 0.037 2712 Dihedral : 7.434 59.734 2170 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 17.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.50 % Favored : 94.50 % Rotamer: Outliers : 3.66 % Allowed : 16.81 % Favored : 79.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.93 (0.18), residues: 1964 helix: -0.39 (0.17), residues: 824 sheet: -1.85 (0.24), residues: 404 loop : -1.79 (0.23), residues: 736 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 29 HIS 0.005 0.001 HIS A 298 PHE 0.025 0.002 PHE A 402 TYR 0.018 0.002 TYR A 351 ARG 0.006 0.001 ARG A 395 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3928 Ramachandran restraints generated. 1964 Oldfield, 0 Emsley, 1964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3928 Ramachandran restraints generated. 1964 Oldfield, 0 Emsley, 1964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 533 residues out of total 1632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 474 time to evaluate : 2.223 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 158 GLU cc_start: 0.8102 (mt-10) cc_final: 0.7646 (mt-10) REVERT: A 273 LYS cc_start: 0.8039 (tptt) cc_final: 0.7812 (tptm) REVERT: A 308 ARG cc_start: 0.7469 (mtm180) cc_final: 0.7215 (mtm180) REVERT: A 347 ASP cc_start: 0.6490 (p0) cc_final: 0.6214 (m-30) REVERT: A 420 ARG cc_start: 0.8648 (mtp180) cc_final: 0.8428 (mtp180) REVERT: A 471 MET cc_start: 0.8459 (mtp) cc_final: 0.8069 (mtp) REVERT: B 53 GLU cc_start: 0.6411 (mt-10) cc_final: 0.6141 (mt-10) REVERT: B 177 ILE cc_start: 0.8412 (OUTLIER) cc_final: 0.8122 (mp) REVERT: B 237 MET cc_start: 0.6029 (mmt) cc_final: 0.5459 (mmt) REVERT: B 410 LYS cc_start: 0.7823 (ttpt) cc_final: 0.7538 (tttm) REVERT: C 177 ILE cc_start: 0.8399 (OUTLIER) cc_final: 0.8105 (mp) REVERT: C 237 MET cc_start: 0.6040 (mmt) cc_final: 0.5507 (mmt) REVERT: C 410 LYS cc_start: 0.7766 (ttpt) cc_final: 0.7479 (tttm) REVERT: D 177 ILE cc_start: 0.8406 (OUTLIER) cc_final: 0.8104 (mp) REVERT: D 273 LYS cc_start: 0.7732 (tptt) cc_final: 0.7214 (tptt) REVERT: D 410 LYS cc_start: 0.7802 (ttpt) cc_final: 0.7500 (tttm) outliers start: 59 outliers final: 37 residues processed: 510 average time/residue: 0.2945 time to fit residues: 219.3879 Evaluate side-chains 427 residues out of total 1632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 387 time to evaluate : 1.781 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 THR Chi-restraints excluded: chain A residue 147 ILE Chi-restraints excluded: chain A residue 185 SER Chi-restraints excluded: chain A residue 205 VAL Chi-restraints excluded: chain A residue 279 LEU Chi-restraints excluded: chain A residue 332 LEU Chi-restraints excluded: chain A residue 460 VAL Chi-restraints excluded: chain B residue 147 ILE Chi-restraints excluded: chain B residue 155 THR Chi-restraints excluded: chain B residue 167 ILE Chi-restraints excluded: chain B residue 177 ILE Chi-restraints excluded: chain B residue 185 SER Chi-restraints excluded: chain B residue 220 ASN Chi-restraints excluded: chain B residue 266 VAL Chi-restraints excluded: chain B residue 279 LEU Chi-restraints excluded: chain B residue 299 GLN Chi-restraints excluded: chain B residue 303 CYS Chi-restraints excluded: chain B residue 332 LEU Chi-restraints excluded: chain C residue 147 ILE Chi-restraints excluded: chain C residue 155 THR Chi-restraints excluded: chain C residue 167 ILE Chi-restraints excluded: chain C residue 177 ILE Chi-restraints excluded: chain C residue 185 SER Chi-restraints excluded: chain C residue 220 ASN Chi-restraints excluded: chain C residue 266 VAL Chi-restraints excluded: chain C residue 279 LEU Chi-restraints excluded: chain C residue 299 GLN Chi-restraints excluded: chain C residue 332 LEU Chi-restraints excluded: chain C residue 494 VAL Chi-restraints excluded: chain D residue 147 ILE Chi-restraints excluded: chain D residue 155 THR Chi-restraints excluded: chain D residue 167 ILE Chi-restraints excluded: chain D residue 177 ILE Chi-restraints excluded: chain D residue 185 SER Chi-restraints excluded: chain D residue 220 ASN Chi-restraints excluded: chain D residue 266 VAL Chi-restraints excluded: chain D residue 279 LEU Chi-restraints excluded: chain D residue 299 GLN Chi-restraints excluded: chain D residue 332 LEU Chi-restraints excluded: chain D residue 341 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 98 optimal weight: 10.0000 chunk 55 optimal weight: 0.9980 chunk 148 optimal weight: 2.9990 chunk 121 optimal weight: 0.7980 chunk 49 optimal weight: 10.0000 chunk 178 optimal weight: 7.9990 chunk 192 optimal weight: 0.0370 chunk 158 optimal weight: 3.9990 chunk 176 optimal weight: 0.9990 chunk 60 optimal weight: 3.9990 chunk 143 optimal weight: 0.5980 overall best weight: 0.6860 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 30 HIS A 72 GLN ** A 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 299 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 406 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 407 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 30 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 72 GLN ** B 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 407 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 30 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 72 GLN ** C 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 407 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 30 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 72 GLN ** D 407 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7251 moved from start: 0.4438 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 15488 Z= 0.219 Angle : 0.606 7.790 20972 Z= 0.314 Chirality : 0.044 0.236 2324 Planarity : 0.004 0.036 2712 Dihedral : 6.035 53.695 2135 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 13.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.65 % Favored : 94.35 % Rotamer: Outliers : 4.71 % Allowed : 18.49 % Favored : 76.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.02 (0.19), residues: 1964 helix: 0.24 (0.19), residues: 836 sheet: -1.37 (0.24), residues: 392 loop : -1.19 (0.24), residues: 736 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 77 HIS 0.008 0.001 HIS B 292 PHE 0.018 0.002 PHE A 402 TYR 0.015 0.001 TYR A 20 ARG 0.004 0.000 ARG A 68 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3928 Ramachandran restraints generated. 1964 Oldfield, 0 Emsley, 1964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3928 Ramachandran restraints generated. 1964 Oldfield, 0 Emsley, 1964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 496 residues out of total 1632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 420 time to evaluate : 1.767 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 57 LYS cc_start: 0.8193 (mmtp) cc_final: 0.7821 (tptm) REVERT: A 158 GLU cc_start: 0.8137 (mt-10) cc_final: 0.7713 (mt-10) REVERT: A 169 TRP cc_start: 0.8640 (p-90) cc_final: 0.8118 (p-90) REVERT: A 273 LYS cc_start: 0.7938 (tptt) cc_final: 0.7456 (tptt) REVERT: A 308 ARG cc_start: 0.7603 (mtm180) cc_final: 0.7277 (mtm180) REVERT: A 471 MET cc_start: 0.8531 (mtp) cc_final: 0.8124 (mtp) REVERT: B 110 ASN cc_start: 0.7130 (t0) cc_final: 0.6877 (t160) REVERT: B 177 ILE cc_start: 0.8666 (OUTLIER) cc_final: 0.8346 (mp) REVERT: C 110 ASN cc_start: 0.7156 (t0) cc_final: 0.6919 (t160) REVERT: C 177 ILE cc_start: 0.8640 (OUTLIER) cc_final: 0.8317 (mp) REVERT: C 237 MET cc_start: 0.5900 (mmt) cc_final: 0.5668 (mmt) REVERT: C 410 LYS cc_start: 0.7837 (ttpt) cc_final: 0.7511 (tttm) REVERT: C 471 MET cc_start: 0.7589 (mtm) cc_final: 0.7304 (mtp) REVERT: C 480 GLU cc_start: 0.7647 (tt0) cc_final: 0.7237 (tt0) REVERT: D 110 ASN cc_start: 0.7278 (t0) cc_final: 0.7050 (t160) REVERT: D 177 ILE cc_start: 0.8641 (OUTLIER) cc_final: 0.8311 (mp) REVERT: D 237 MET cc_start: 0.5168 (mmt) cc_final: 0.4951 (mmt) REVERT: D 238 ASP cc_start: 0.7071 (m-30) cc_final: 0.6821 (m-30) REVERT: D 410 LYS cc_start: 0.7939 (ttpt) cc_final: 0.7594 (tttm) outliers start: 76 outliers final: 47 residues processed: 460 average time/residue: 0.3017 time to fit residues: 205.4861 Evaluate side-chains 445 residues out of total 1632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 395 time to evaluate : 1.762 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 THR Chi-restraints excluded: chain A residue 147 ILE Chi-restraints excluded: chain A residue 185 SER Chi-restraints excluded: chain A residue 205 VAL Chi-restraints excluded: chain A residue 239 ILE Chi-restraints excluded: chain A residue 332 LEU Chi-restraints excluded: chain A residue 445 SER Chi-restraints excluded: chain B residue 79 THR Chi-restraints excluded: chain B residue 177 ILE Chi-restraints excluded: chain B residue 185 SER Chi-restraints excluded: chain B residue 219 VAL Chi-restraints excluded: chain B residue 220 ASN Chi-restraints excluded: chain B residue 222 VAL Chi-restraints excluded: chain B residue 248 THR Chi-restraints excluded: chain B residue 266 VAL Chi-restraints excluded: chain B residue 289 GLU Chi-restraints excluded: chain B residue 299 GLN Chi-restraints excluded: chain B residue 332 LEU Chi-restraints excluded: chain B residue 445 SER Chi-restraints excluded: chain B residue 451 THR Chi-restraints excluded: chain B residue 494 VAL Chi-restraints excluded: chain C residue 79 THR Chi-restraints excluded: chain C residue 147 ILE Chi-restraints excluded: chain C residue 167 ILE Chi-restraints excluded: chain C residue 177 ILE Chi-restraints excluded: chain C residue 185 SER Chi-restraints excluded: chain C residue 198 THR Chi-restraints excluded: chain C residue 219 VAL Chi-restraints excluded: chain C residue 220 ASN Chi-restraints excluded: chain C residue 248 THR Chi-restraints excluded: chain C residue 266 VAL Chi-restraints excluded: chain C residue 299 GLN Chi-restraints excluded: chain C residue 332 LEU Chi-restraints excluded: chain C residue 451 THR Chi-restraints excluded: chain C residue 494 VAL Chi-restraints excluded: chain D residue 79 THR Chi-restraints excluded: chain D residue 147 ILE Chi-restraints excluded: chain D residue 167 ILE Chi-restraints excluded: chain D residue 177 ILE Chi-restraints excluded: chain D residue 185 SER Chi-restraints excluded: chain D residue 198 THR Chi-restraints excluded: chain D residue 219 VAL Chi-restraints excluded: chain D residue 220 ASN Chi-restraints excluded: chain D residue 222 VAL Chi-restraints excluded: chain D residue 248 THR Chi-restraints excluded: chain D residue 266 VAL Chi-restraints excluded: chain D residue 299 GLN Chi-restraints excluded: chain D residue 332 LEU Chi-restraints excluded: chain D residue 390 VAL Chi-restraints excluded: chain D residue 494 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 176 optimal weight: 1.9990 chunk 134 optimal weight: 0.0670 chunk 92 optimal weight: 0.9990 chunk 19 optimal weight: 1.9990 chunk 85 optimal weight: 6.9990 chunk 119 optimal weight: 1.9990 chunk 178 optimal weight: 7.9990 chunk 189 optimal weight: 1.9990 chunk 93 optimal weight: 2.9990 chunk 169 optimal weight: 4.9990 chunk 51 optimal weight: 10.0000 overall best weight: 1.4126 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 299 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 406 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 498 GLN ** B 30 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 72 GLN ** B 406 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 30 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 72 GLN ** D 30 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 72 GLN ** D 406 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7361 moved from start: 0.4968 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.063 15488 Z= 0.312 Angle : 0.646 6.765 20972 Z= 0.335 Chirality : 0.047 0.214 2324 Planarity : 0.004 0.034 2712 Dihedral : 6.234 59.167 2127 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 13.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.65 % Favored : 94.35 % Rotamer: Outliers : 6.58 % Allowed : 19.17 % Favored : 74.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.92 (0.20), residues: 1964 helix: 0.25 (0.18), residues: 832 sheet: -1.18 (0.25), residues: 396 loop : -1.12 (0.24), residues: 736 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 77 HIS 0.012 0.002 HIS B 292 PHE 0.017 0.002 PHE C 402 TYR 0.015 0.002 TYR B 330 ARG 0.003 0.001 ARG A 395 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3928 Ramachandran restraints generated. 1964 Oldfield, 0 Emsley, 1964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3928 Ramachandran restraints generated. 1964 Oldfield, 0 Emsley, 1964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 526 residues out of total 1632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 106 poor density : 420 time to evaluate : 1.657 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 20 TYR cc_start: 0.6231 (m-80) cc_final: 0.5462 (m-80) REVERT: A 57 LYS cc_start: 0.8198 (mmtp) cc_final: 0.7793 (tptm) REVERT: A 169 TRP cc_start: 0.8740 (p-90) cc_final: 0.8292 (p-90) REVERT: A 177 ILE cc_start: 0.8707 (OUTLIER) cc_final: 0.8396 (mp) REVERT: A 471 MET cc_start: 0.8564 (mtp) cc_final: 0.8150 (mtp) REVERT: B 20 TYR cc_start: 0.5967 (m-80) cc_final: 0.5545 (m-80) REVERT: B 53 GLU cc_start: 0.7255 (mt-10) cc_final: 0.6954 (tt0) REVERT: B 169 TRP cc_start: 0.8730 (p-90) cc_final: 0.7955 (p-90) REVERT: B 410 LYS cc_start: 0.7952 (ttpt) cc_final: 0.7624 (tttm) REVERT: B 471 MET cc_start: 0.8244 (OUTLIER) cc_final: 0.7837 (mtp) REVERT: C 158 GLU cc_start: 0.8289 (mt-10) cc_final: 0.8037 (mt-10) REVERT: C 237 MET cc_start: 0.6301 (mmt) cc_final: 0.5746 (mmt) REVERT: C 367 LYS cc_start: 0.5919 (tptp) cc_final: 0.5678 (tptp) REVERT: C 410 LYS cc_start: 0.7878 (ttpt) cc_final: 0.7600 (tttm) REVERT: C 480 GLU cc_start: 0.7733 (tt0) cc_final: 0.7271 (tt0) REVERT: D 53 GLU cc_start: 0.6640 (tt0) cc_final: 0.6424 (tt0) REVERT: D 429 SER cc_start: 0.8944 (t) cc_final: 0.8650 (t) REVERT: D 471 MET cc_start: 0.8008 (mtp) cc_final: 0.7723 (mtp) outliers start: 106 outliers final: 77 residues processed: 468 average time/residue: 0.2852 time to fit residues: 193.9533 Evaluate side-chains 475 residues out of total 1632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 396 time to evaluate : 1.632 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 THR Chi-restraints excluded: chain A residue 114 LEU Chi-restraints excluded: chain A residue 144 THR Chi-restraints excluded: chain A residue 147 ILE Chi-restraints excluded: chain A residue 177 ILE Chi-restraints excluded: chain A residue 180 ILE Chi-restraints excluded: chain A residue 185 SER Chi-restraints excluded: chain A residue 205 VAL Chi-restraints excluded: chain A residue 222 VAL Chi-restraints excluded: chain A residue 239 ILE Chi-restraints excluded: chain A residue 279 LEU Chi-restraints excluded: chain A residue 303 CYS Chi-restraints excluded: chain A residue 390 VAL Chi-restraints excluded: chain A residue 442 THR Chi-restraints excluded: chain A residue 451 THR Chi-restraints excluded: chain A residue 460 VAL Chi-restraints excluded: chain A residue 494 VAL Chi-restraints excluded: chain B residue 60 VAL Chi-restraints excluded: chain B residue 79 THR Chi-restraints excluded: chain B residue 114 LEU Chi-restraints excluded: chain B residue 147 ILE Chi-restraints excluded: chain B residue 155 THR Chi-restraints excluded: chain B residue 177 ILE Chi-restraints excluded: chain B residue 185 SER Chi-restraints excluded: chain B residue 219 VAL Chi-restraints excluded: chain B residue 220 ASN Chi-restraints excluded: chain B residue 221 ILE Chi-restraints excluded: chain B residue 222 VAL Chi-restraints excluded: chain B residue 239 ILE Chi-restraints excluded: chain B residue 248 THR Chi-restraints excluded: chain B residue 266 VAL Chi-restraints excluded: chain B residue 289 GLU Chi-restraints excluded: chain B residue 303 CYS Chi-restraints excluded: chain B residue 332 LEU Chi-restraints excluded: chain B residue 390 VAL Chi-restraints excluded: chain B residue 460 VAL Chi-restraints excluded: chain B residue 471 MET Chi-restraints excluded: chain B residue 494 VAL Chi-restraints excluded: chain C residue 60 VAL Chi-restraints excluded: chain C residue 79 THR Chi-restraints excluded: chain C residue 147 ILE Chi-restraints excluded: chain C residue 155 THR Chi-restraints excluded: chain C residue 167 ILE Chi-restraints excluded: chain C residue 177 ILE Chi-restraints excluded: chain C residue 185 SER Chi-restraints excluded: chain C residue 198 THR Chi-restraints excluded: chain C residue 219 VAL Chi-restraints excluded: chain C residue 220 ASN Chi-restraints excluded: chain C residue 222 VAL Chi-restraints excluded: chain C residue 248 THR Chi-restraints excluded: chain C residue 254 ILE Chi-restraints excluded: chain C residue 266 VAL Chi-restraints excluded: chain C residue 303 CYS Chi-restraints excluded: chain C residue 332 LEU Chi-restraints excluded: chain C residue 341 THR Chi-restraints excluded: chain C residue 390 VAL Chi-restraints excluded: chain C residue 460 VAL Chi-restraints excluded: chain C residue 494 VAL Chi-restraints excluded: chain D residue 79 THR Chi-restraints excluded: chain D residue 114 LEU Chi-restraints excluded: chain D residue 147 ILE Chi-restraints excluded: chain D residue 155 THR Chi-restraints excluded: chain D residue 167 ILE Chi-restraints excluded: chain D residue 177 ILE Chi-restraints excluded: chain D residue 185 SER Chi-restraints excluded: chain D residue 198 THR Chi-restraints excluded: chain D residue 219 VAL Chi-restraints excluded: chain D residue 220 ASN Chi-restraints excluded: chain D residue 221 ILE Chi-restraints excluded: chain D residue 222 VAL Chi-restraints excluded: chain D residue 248 THR Chi-restraints excluded: chain D residue 266 VAL Chi-restraints excluded: chain D residue 332 LEU Chi-restraints excluded: chain D residue 341 THR Chi-restraints excluded: chain D residue 390 VAL Chi-restraints excluded: chain D residue 445 SER Chi-restraints excluded: chain D residue 451 THR Chi-restraints excluded: chain D residue 460 VAL Chi-restraints excluded: chain D residue 494 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 157 optimal weight: 3.9990 chunk 107 optimal weight: 6.9990 chunk 2 optimal weight: 10.0000 chunk 141 optimal weight: 0.8980 chunk 78 optimal weight: 0.5980 chunk 161 optimal weight: 0.2980 chunk 130 optimal weight: 2.9990 chunk 0 optimal weight: 10.0000 chunk 96 optimal weight: 0.6980 chunk 170 optimal weight: 0.6980 chunk 47 optimal weight: 0.6980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 299 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 406 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 72 GLN ** B 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 299 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 406 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 72 GLN ** C 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 204 HIS ** C 299 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 72 GLN ** D 299 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7288 moved from start: 0.5418 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 15488 Z= 0.199 Angle : 0.563 6.260 20972 Z= 0.292 Chirality : 0.044 0.259 2324 Planarity : 0.004 0.034 2712 Dihedral : 5.570 57.892 2116 Min Nonbonded Distance : 2.559 Molprobity Statistics. All-atom Clashscore : 12.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.33 % Favored : 95.67 % Rotamer: Outliers : 5.02 % Allowed : 21.65 % Favored : 73.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.58 (0.20), residues: 1964 helix: 0.47 (0.19), residues: 836 sheet: -0.87 (0.26), residues: 392 loop : -0.94 (0.25), residues: 736 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 453 HIS 0.006 0.001 HIS C 292 PHE 0.014 0.001 PHE B 411 TYR 0.012 0.001 TYR B 119 ARG 0.006 0.000 ARG D 321 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3928 Ramachandran restraints generated. 1964 Oldfield, 0 Emsley, 1964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3928 Ramachandran restraints generated. 1964 Oldfield, 0 Emsley, 1964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 489 residues out of total 1632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 408 time to evaluate : 1.549 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 57 LYS cc_start: 0.8217 (mmtp) cc_final: 0.7843 (tptm) REVERT: A 169 TRP cc_start: 0.8708 (p-90) cc_final: 0.8201 (p-90) REVERT: A 369 GLU cc_start: 0.6704 (mm-30) cc_final: 0.6445 (mm-30) REVERT: A 471 MET cc_start: 0.8565 (mtp) cc_final: 0.8196 (mtp) REVERT: B 20 TYR cc_start: 0.5931 (m-80) cc_final: 0.4994 (m-80) REVERT: B 53 GLU cc_start: 0.7238 (mt-10) cc_final: 0.6969 (tt0) REVERT: B 158 GLU cc_start: 0.8103 (mt-10) cc_final: 0.7860 (mt-10) REVERT: B 169 TRP cc_start: 0.8687 (p-90) cc_final: 0.7855 (p-90) REVERT: B 256 GLU cc_start: 0.7248 (tt0) cc_final: 0.6985 (tt0) REVERT: B 471 MET cc_start: 0.8111 (OUTLIER) cc_final: 0.7840 (mtm) REVERT: C 237 MET cc_start: 0.6071 (mmt) cc_final: 0.5670 (mmt) REVERT: C 480 GLU cc_start: 0.7667 (tt0) cc_final: 0.7282 (tt0) REVERT: D 158 GLU cc_start: 0.8283 (mt-10) cc_final: 0.8044 (mt-10) REVERT: D 252 LYS cc_start: 0.7187 (mttt) cc_final: 0.6850 (ttmt) REVERT: D 295 VAL cc_start: 0.7742 (p) cc_final: 0.7529 (p) REVERT: D 471 MET cc_start: 0.7938 (mtp) cc_final: 0.7655 (mtp) outliers start: 81 outliers final: 47 residues processed: 446 average time/residue: 0.2752 time to fit residues: 179.6263 Evaluate side-chains 443 residues out of total 1632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 395 time to evaluate : 1.697 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 THR Chi-restraints excluded: chain A residue 147 ILE Chi-restraints excluded: chain A residue 180 ILE Chi-restraints excluded: chain A residue 185 SER Chi-restraints excluded: chain A residue 239 ILE Chi-restraints excluded: chain A residue 248 THR Chi-restraints excluded: chain A residue 303 CYS Chi-restraints excluded: chain B residue 79 THR Chi-restraints excluded: chain B residue 114 LEU Chi-restraints excluded: chain B residue 144 THR Chi-restraints excluded: chain B residue 177 ILE Chi-restraints excluded: chain B residue 185 SER Chi-restraints excluded: chain B residue 219 VAL Chi-restraints excluded: chain B residue 220 ASN Chi-restraints excluded: chain B residue 222 VAL Chi-restraints excluded: chain B residue 237 MET Chi-restraints excluded: chain B residue 239 ILE Chi-restraints excluded: chain B residue 266 VAL Chi-restraints excluded: chain B residue 289 GLU Chi-restraints excluded: chain B residue 303 CYS Chi-restraints excluded: chain B residue 332 LEU Chi-restraints excluded: chain B residue 451 THR Chi-restraints excluded: chain B residue 471 MET Chi-restraints excluded: chain B residue 494 VAL Chi-restraints excluded: chain C residue 79 THR Chi-restraints excluded: chain C residue 177 ILE Chi-restraints excluded: chain C residue 185 SER Chi-restraints excluded: chain C residue 219 VAL Chi-restraints excluded: chain C residue 220 ASN Chi-restraints excluded: chain C residue 222 VAL Chi-restraints excluded: chain C residue 248 THR Chi-restraints excluded: chain C residue 266 VAL Chi-restraints excluded: chain C residue 303 CYS Chi-restraints excluded: chain C residue 332 LEU Chi-restraints excluded: chain C residue 451 THR Chi-restraints excluded: chain D residue 79 THR Chi-restraints excluded: chain D residue 147 ILE Chi-restraints excluded: chain D residue 177 ILE Chi-restraints excluded: chain D residue 185 SER Chi-restraints excluded: chain D residue 219 VAL Chi-restraints excluded: chain D residue 220 ASN Chi-restraints excluded: chain D residue 222 VAL Chi-restraints excluded: chain D residue 239 ILE Chi-restraints excluded: chain D residue 266 VAL Chi-restraints excluded: chain D residue 303 CYS Chi-restraints excluded: chain D residue 332 LEU Chi-restraints excluded: chain D residue 341 THR Chi-restraints excluded: chain D residue 451 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 63 optimal weight: 1.9990 chunk 170 optimal weight: 0.9980 chunk 37 optimal weight: 0.8980 chunk 111 optimal weight: 3.9990 chunk 46 optimal weight: 0.0970 chunk 189 optimal weight: 1.9990 chunk 157 optimal weight: 3.9990 chunk 87 optimal weight: 7.9990 chunk 15 optimal weight: 1.9990 chunk 62 optimal weight: 0.8980 chunk 99 optimal weight: 0.1980 overall best weight: 0.6178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 299 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 406 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 72 GLN ** B 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 406 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 72 GLN ** C 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 72 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7285 moved from start: 0.5660 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 15488 Z= 0.207 Angle : 0.578 6.764 20972 Z= 0.297 Chirality : 0.045 0.244 2324 Planarity : 0.004 0.037 2712 Dihedral : 5.419 53.855 2116 Min Nonbonded Distance : 2.572 Molprobity Statistics. All-atom Clashscore : 12.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.74 % Favored : 95.26 % Rotamer: Outliers : 4.84 % Allowed : 21.96 % Favored : 73.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.49 (0.20), residues: 1964 helix: 0.47 (0.19), residues: 836 sheet: -0.69 (0.26), residues: 392 loop : -0.88 (0.25), residues: 736 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 453 HIS 0.006 0.001 HIS C 292 PHE 0.031 0.002 PHE D 38 TYR 0.014 0.001 TYR B 119 ARG 0.009 0.000 ARG C 321 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3928 Ramachandran restraints generated. 1964 Oldfield, 0 Emsley, 1964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3928 Ramachandran restraints generated. 1964 Oldfield, 0 Emsley, 1964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 465 residues out of total 1632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 387 time to evaluate : 1.557 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 57 LYS cc_start: 0.8180 (mmtp) cc_final: 0.7854 (tptm) REVERT: A 369 GLU cc_start: 0.6670 (mm-30) cc_final: 0.6417 (mm-30) REVERT: A 402 PHE cc_start: 0.7339 (OUTLIER) cc_final: 0.6997 (t80) REVERT: A 471 MET cc_start: 0.8490 (mtp) cc_final: 0.8181 (mtp) REVERT: B 20 TYR cc_start: 0.5893 (m-80) cc_final: 0.5086 (m-80) REVERT: B 256 GLU cc_start: 0.7139 (tt0) cc_final: 0.6805 (tm-30) REVERT: B 402 PHE cc_start: 0.7353 (OUTLIER) cc_final: 0.7007 (t80) REVERT: B 471 MET cc_start: 0.8093 (OUTLIER) cc_final: 0.7890 (mtm) REVERT: C 237 MET cc_start: 0.6172 (mmt) cc_final: 0.5710 (mmt) REVERT: C 402 PHE cc_start: 0.7256 (OUTLIER) cc_final: 0.6961 (t80) REVERT: C 429 SER cc_start: 0.8929 (OUTLIER) cc_final: 0.8595 (t) REVERT: C 480 GLU cc_start: 0.7697 (tt0) cc_final: 0.7326 (tt0) REVERT: D 252 LYS cc_start: 0.7150 (mttt) cc_final: 0.6823 (ttmt) REVERT: D 295 VAL cc_start: 0.7728 (p) cc_final: 0.7513 (p) REVERT: D 402 PHE cc_start: 0.7272 (OUTLIER) cc_final: 0.6922 (t80) REVERT: D 471 MET cc_start: 0.7926 (mtp) cc_final: 0.7651 (mtp) outliers start: 78 outliers final: 57 residues processed: 422 average time/residue: 0.2876 time to fit residues: 176.6089 Evaluate side-chains 442 residues out of total 1632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 379 time to evaluate : 1.498 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 THR Chi-restraints excluded: chain A residue 147 ILE Chi-restraints excluded: chain A residue 180 ILE Chi-restraints excluded: chain A residue 185 SER Chi-restraints excluded: chain A residue 239 ILE Chi-restraints excluded: chain A residue 248 THR Chi-restraints excluded: chain A residue 303 CYS Chi-restraints excluded: chain A residue 402 PHE Chi-restraints excluded: chain B residue 79 THR Chi-restraints excluded: chain B residue 114 LEU Chi-restraints excluded: chain B residue 123 LEU Chi-restraints excluded: chain B residue 144 THR Chi-restraints excluded: chain B residue 177 ILE Chi-restraints excluded: chain B residue 180 ILE Chi-restraints excluded: chain B residue 185 SER Chi-restraints excluded: chain B residue 219 VAL Chi-restraints excluded: chain B residue 220 ASN Chi-restraints excluded: chain B residue 222 VAL Chi-restraints excluded: chain B residue 239 ILE Chi-restraints excluded: chain B residue 266 VAL Chi-restraints excluded: chain B residue 289 GLU Chi-restraints excluded: chain B residue 303 CYS Chi-restraints excluded: chain B residue 332 LEU Chi-restraints excluded: chain B residue 402 PHE Chi-restraints excluded: chain B residue 451 THR Chi-restraints excluded: chain B residue 460 VAL Chi-restraints excluded: chain B residue 471 MET Chi-restraints excluded: chain B residue 494 VAL Chi-restraints excluded: chain C residue 79 THR Chi-restraints excluded: chain C residue 147 ILE Chi-restraints excluded: chain C residue 177 ILE Chi-restraints excluded: chain C residue 180 ILE Chi-restraints excluded: chain C residue 185 SER Chi-restraints excluded: chain C residue 219 VAL Chi-restraints excluded: chain C residue 220 ASN Chi-restraints excluded: chain C residue 239 ILE Chi-restraints excluded: chain C residue 248 THR Chi-restraints excluded: chain C residue 266 VAL Chi-restraints excluded: chain C residue 303 CYS Chi-restraints excluded: chain C residue 332 LEU Chi-restraints excluded: chain C residue 402 PHE Chi-restraints excluded: chain C residue 429 SER Chi-restraints excluded: chain C residue 460 VAL Chi-restraints excluded: chain D residue 79 THR Chi-restraints excluded: chain D residue 109 MET Chi-restraints excluded: chain D residue 123 LEU Chi-restraints excluded: chain D residue 147 ILE Chi-restraints excluded: chain D residue 177 ILE Chi-restraints excluded: chain D residue 180 ILE Chi-restraints excluded: chain D residue 185 SER Chi-restraints excluded: chain D residue 219 VAL Chi-restraints excluded: chain D residue 220 ASN Chi-restraints excluded: chain D residue 222 VAL Chi-restraints excluded: chain D residue 239 ILE Chi-restraints excluded: chain D residue 266 VAL Chi-restraints excluded: chain D residue 292 HIS Chi-restraints excluded: chain D residue 303 CYS Chi-restraints excluded: chain D residue 332 LEU Chi-restraints excluded: chain D residue 341 THR Chi-restraints excluded: chain D residue 402 PHE Chi-restraints excluded: chain D residue 451 THR Chi-restraints excluded: chain D residue 460 VAL Chi-restraints excluded: chain D residue 494 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 182 optimal weight: 5.9990 chunk 21 optimal weight: 2.9990 chunk 108 optimal weight: 2.9990 chunk 138 optimal weight: 0.9990 chunk 107 optimal weight: 4.9990 chunk 159 optimal weight: 0.9990 chunk 105 optimal weight: 2.9990 chunk 188 optimal weight: 5.9990 chunk 118 optimal weight: 0.1980 chunk 115 optimal weight: 0.0970 chunk 87 optimal weight: 7.9990 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 72 GLN ** A 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 299 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 406 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 72 GLN ** B 406 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 72 GLN ** C 299 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 72 GLN ** D 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 299 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7332 moved from start: 0.5739 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 15488 Z= 0.261 Angle : 0.606 9.294 20972 Z= 0.311 Chirality : 0.046 0.235 2324 Planarity : 0.004 0.039 2712 Dihedral : 5.495 49.912 2116 Min Nonbonded Distance : 2.573 Molprobity Statistics. All-atom Clashscore : 12.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.89 % Favored : 95.11 % Rotamer: Outliers : 5.40 % Allowed : 21.59 % Favored : 73.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.53 (0.20), residues: 1964 helix: 0.40 (0.19), residues: 832 sheet: -0.71 (0.26), residues: 392 loop : -0.85 (0.25), residues: 740 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 169 HIS 0.007 0.001 HIS C 292 PHE 0.027 0.002 PHE D 38 TYR 0.012 0.001 TYR A 330 ARG 0.006 0.000 ARG B 322 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3928 Ramachandran restraints generated. 1964 Oldfield, 0 Emsley, 1964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3928 Ramachandran restraints generated. 1964 Oldfield, 0 Emsley, 1964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 481 residues out of total 1632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 394 time to evaluate : 1.805 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 57 LYS cc_start: 0.8146 (mmtp) cc_final: 0.7789 (tptm) REVERT: A 402 PHE cc_start: 0.7430 (OUTLIER) cc_final: 0.7092 (t80) REVERT: A 471 MET cc_start: 0.8490 (mtp) cc_final: 0.8073 (mtp) REVERT: A 489 VAL cc_start: 0.8782 (OUTLIER) cc_final: 0.8577 (m) REVERT: B 402 PHE cc_start: 0.7383 (OUTLIER) cc_final: 0.7058 (t80) REVERT: B 471 MET cc_start: 0.8133 (OUTLIER) cc_final: 0.7819 (mtm) REVERT: C 237 MET cc_start: 0.6469 (mmt) cc_final: 0.5818 (mmt) REVERT: C 402 PHE cc_start: 0.7364 (OUTLIER) cc_final: 0.7047 (t80) REVERT: C 429 SER cc_start: 0.8966 (t) cc_final: 0.8625 (t) REVERT: C 480 GLU cc_start: 0.7766 (tt0) cc_final: 0.7341 (tt0) REVERT: D 402 PHE cc_start: 0.7367 (OUTLIER) cc_final: 0.7048 (t80) REVERT: D 471 MET cc_start: 0.7939 (mtp) cc_final: 0.7718 (mtp) outliers start: 87 outliers final: 68 residues processed: 433 average time/residue: 0.2852 time to fit residues: 179.7408 Evaluate side-chains 447 residues out of total 1632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 373 time to evaluate : 1.687 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 THR Chi-restraints excluded: chain A residue 147 ILE Chi-restraints excluded: chain A residue 180 ILE Chi-restraints excluded: chain A residue 185 SER Chi-restraints excluded: chain A residue 222 VAL Chi-restraints excluded: chain A residue 239 ILE Chi-restraints excluded: chain A residue 248 THR Chi-restraints excluded: chain A residue 303 CYS Chi-restraints excluded: chain A residue 402 PHE Chi-restraints excluded: chain A residue 460 VAL Chi-restraints excluded: chain A residue 489 VAL Chi-restraints excluded: chain B residue 79 THR Chi-restraints excluded: chain B residue 114 LEU Chi-restraints excluded: chain B residue 123 LEU Chi-restraints excluded: chain B residue 129 THR Chi-restraints excluded: chain B residue 144 THR Chi-restraints excluded: chain B residue 147 ILE Chi-restraints excluded: chain B residue 155 THR Chi-restraints excluded: chain B residue 177 ILE Chi-restraints excluded: chain B residue 185 SER Chi-restraints excluded: chain B residue 219 VAL Chi-restraints excluded: chain B residue 220 ASN Chi-restraints excluded: chain B residue 221 ILE Chi-restraints excluded: chain B residue 222 VAL Chi-restraints excluded: chain B residue 239 ILE Chi-restraints excluded: chain B residue 248 THR Chi-restraints excluded: chain B residue 266 VAL Chi-restraints excluded: chain B residue 289 GLU Chi-restraints excluded: chain B residue 303 CYS Chi-restraints excluded: chain B residue 332 LEU Chi-restraints excluded: chain B residue 402 PHE Chi-restraints excluded: chain B residue 460 VAL Chi-restraints excluded: chain B residue 471 MET Chi-restraints excluded: chain B residue 494 VAL Chi-restraints excluded: chain C residue 79 THR Chi-restraints excluded: chain C residue 129 THR Chi-restraints excluded: chain C residue 144 THR Chi-restraints excluded: chain C residue 147 ILE Chi-restraints excluded: chain C residue 155 THR Chi-restraints excluded: chain C residue 177 ILE Chi-restraints excluded: chain C residue 180 ILE Chi-restraints excluded: chain C residue 185 SER Chi-restraints excluded: chain C residue 219 VAL Chi-restraints excluded: chain C residue 220 ASN Chi-restraints excluded: chain C residue 222 VAL Chi-restraints excluded: chain C residue 239 ILE Chi-restraints excluded: chain C residue 248 THR Chi-restraints excluded: chain C residue 266 VAL Chi-restraints excluded: chain C residue 303 CYS Chi-restraints excluded: chain C residue 332 LEU Chi-restraints excluded: chain C residue 402 PHE Chi-restraints excluded: chain C residue 460 VAL Chi-restraints excluded: chain D residue 79 THR Chi-restraints excluded: chain D residue 109 MET Chi-restraints excluded: chain D residue 123 LEU Chi-restraints excluded: chain D residue 129 THR Chi-restraints excluded: chain D residue 147 ILE Chi-restraints excluded: chain D residue 177 ILE Chi-restraints excluded: chain D residue 180 ILE Chi-restraints excluded: chain D residue 185 SER Chi-restraints excluded: chain D residue 219 VAL Chi-restraints excluded: chain D residue 220 ASN Chi-restraints excluded: chain D residue 221 ILE Chi-restraints excluded: chain D residue 222 VAL Chi-restraints excluded: chain D residue 239 ILE Chi-restraints excluded: chain D residue 266 VAL Chi-restraints excluded: chain D residue 292 HIS Chi-restraints excluded: chain D residue 303 CYS Chi-restraints excluded: chain D residue 332 LEU Chi-restraints excluded: chain D residue 341 THR Chi-restraints excluded: chain D residue 402 PHE Chi-restraints excluded: chain D residue 451 THR Chi-restraints excluded: chain D residue 460 VAL Chi-restraints excluded: chain D residue 494 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 116 optimal weight: 0.2980 chunk 75 optimal weight: 1.9990 chunk 112 optimal weight: 1.9990 chunk 56 optimal weight: 1.9990 chunk 37 optimal weight: 0.8980 chunk 36 optimal weight: 0.9990 chunk 120 optimal weight: 4.9990 chunk 128 optimal weight: 0.8980 chunk 93 optimal weight: 4.9990 chunk 17 optimal weight: 0.8980 chunk 148 optimal weight: 1.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 72 GLN ** A 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 293 HIS ** A 299 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 406 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 72 GLN ** B 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 299 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 406 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 30 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 72 GLN ** C 299 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 72 GLN ** D 299 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7315 moved from start: 0.5947 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 15488 Z= 0.225 Angle : 0.594 9.457 20972 Z= 0.304 Chirality : 0.045 0.229 2324 Planarity : 0.004 0.035 2712 Dihedral : 5.395 47.630 2116 Min Nonbonded Distance : 2.580 Molprobity Statistics. All-atom Clashscore : 13.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.79 % Favored : 95.21 % Rotamer: Outliers : 5.02 % Allowed : 22.33 % Favored : 72.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.53 (0.20), residues: 1964 helix: 0.42 (0.19), residues: 828 sheet: -0.78 (0.26), residues: 408 loop : -0.82 (0.25), residues: 728 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 169 HIS 0.006 0.001 HIS C 292 PHE 0.030 0.002 PHE B 38 TYR 0.014 0.001 TYR D 119 ARG 0.006 0.000 ARG D 322 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3928 Ramachandran restraints generated. 1964 Oldfield, 0 Emsley, 1964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3928 Ramachandran restraints generated. 1964 Oldfield, 0 Emsley, 1964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 465 residues out of total 1632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 384 time to evaluate : 1.807 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 158 GLU cc_start: 0.8003 (mt-10) cc_final: 0.7674 (mt-10) REVERT: A 402 PHE cc_start: 0.7463 (OUTLIER) cc_final: 0.7114 (t80) REVERT: A 471 MET cc_start: 0.8420 (mtp) cc_final: 0.7994 (mtp) REVERT: A 489 VAL cc_start: 0.8783 (OUTLIER) cc_final: 0.8567 (m) REVERT: B 402 PHE cc_start: 0.7400 (OUTLIER) cc_final: 0.7052 (t80) REVERT: B 471 MET cc_start: 0.8026 (OUTLIER) cc_final: 0.7754 (mtm) REVERT: C 97 GLU cc_start: 0.7652 (tp30) cc_final: 0.7384 (tp30) REVERT: C 237 MET cc_start: 0.6426 (mmt) cc_final: 0.5755 (mmp) REVERT: C 402 PHE cc_start: 0.7355 (OUTLIER) cc_final: 0.7040 (t80) REVERT: C 429 SER cc_start: 0.8953 (OUTLIER) cc_final: 0.8605 (t) REVERT: C 480 GLU cc_start: 0.7721 (tt0) cc_final: 0.7286 (tt0) REVERT: D 252 LYS cc_start: 0.7219 (mttt) cc_final: 0.6877 (ttmt) REVERT: D 402 PHE cc_start: 0.7351 (OUTLIER) cc_final: 0.7033 (t80) REVERT: D 471 MET cc_start: 0.7901 (mtp) cc_final: 0.7633 (mtp) outliers start: 81 outliers final: 63 residues processed: 424 average time/residue: 0.2805 time to fit residues: 174.1620 Evaluate side-chains 451 residues out of total 1632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 381 time to evaluate : 1.750 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 THR Chi-restraints excluded: chain A residue 147 ILE Chi-restraints excluded: chain A residue 180 ILE Chi-restraints excluded: chain A residue 185 SER Chi-restraints excluded: chain A residue 222 VAL Chi-restraints excluded: chain A residue 239 ILE Chi-restraints excluded: chain A residue 248 THR Chi-restraints excluded: chain A residue 303 CYS Chi-restraints excluded: chain A residue 402 PHE Chi-restraints excluded: chain A residue 489 VAL Chi-restraints excluded: chain B residue 79 THR Chi-restraints excluded: chain B residue 109 MET Chi-restraints excluded: chain B residue 114 LEU Chi-restraints excluded: chain B residue 123 LEU Chi-restraints excluded: chain B residue 129 THR Chi-restraints excluded: chain B residue 144 THR Chi-restraints excluded: chain B residue 177 ILE Chi-restraints excluded: chain B residue 185 SER Chi-restraints excluded: chain B residue 219 VAL Chi-restraints excluded: chain B residue 220 ASN Chi-restraints excluded: chain B residue 221 ILE Chi-restraints excluded: chain B residue 222 VAL Chi-restraints excluded: chain B residue 239 ILE Chi-restraints excluded: chain B residue 248 THR Chi-restraints excluded: chain B residue 266 VAL Chi-restraints excluded: chain B residue 303 CYS Chi-restraints excluded: chain B residue 332 LEU Chi-restraints excluded: chain B residue 402 PHE Chi-restraints excluded: chain B residue 460 VAL Chi-restraints excluded: chain B residue 471 MET Chi-restraints excluded: chain B residue 494 VAL Chi-restraints excluded: chain C residue 79 THR Chi-restraints excluded: chain C residue 109 MET Chi-restraints excluded: chain C residue 129 THR Chi-restraints excluded: chain C residue 144 THR Chi-restraints excluded: chain C residue 147 ILE Chi-restraints excluded: chain C residue 160 ILE Chi-restraints excluded: chain C residue 177 ILE Chi-restraints excluded: chain C residue 185 SER Chi-restraints excluded: chain C residue 219 VAL Chi-restraints excluded: chain C residue 220 ASN Chi-restraints excluded: chain C residue 222 VAL Chi-restraints excluded: chain C residue 239 ILE Chi-restraints excluded: chain C residue 248 THR Chi-restraints excluded: chain C residue 266 VAL Chi-restraints excluded: chain C residue 303 CYS Chi-restraints excluded: chain C residue 332 LEU Chi-restraints excluded: chain C residue 402 PHE Chi-restraints excluded: chain C residue 429 SER Chi-restraints excluded: chain C residue 460 VAL Chi-restraints excluded: chain D residue 79 THR Chi-restraints excluded: chain D residue 123 LEU Chi-restraints excluded: chain D residue 129 THR Chi-restraints excluded: chain D residue 147 ILE Chi-restraints excluded: chain D residue 177 ILE Chi-restraints excluded: chain D residue 185 SER Chi-restraints excluded: chain D residue 219 VAL Chi-restraints excluded: chain D residue 220 ASN Chi-restraints excluded: chain D residue 221 ILE Chi-restraints excluded: chain D residue 222 VAL Chi-restraints excluded: chain D residue 239 ILE Chi-restraints excluded: chain D residue 266 VAL Chi-restraints excluded: chain D residue 303 CYS Chi-restraints excluded: chain D residue 315 ILE Chi-restraints excluded: chain D residue 332 LEU Chi-restraints excluded: chain D residue 341 THR Chi-restraints excluded: chain D residue 402 PHE Chi-restraints excluded: chain D residue 451 THR Chi-restraints excluded: chain D residue 460 VAL Chi-restraints excluded: chain D residue 494 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 171 optimal weight: 1.9990 chunk 180 optimal weight: 5.9990 chunk 165 optimal weight: 0.6980 chunk 176 optimal weight: 2.9990 chunk 105 optimal weight: 3.9990 chunk 76 optimal weight: 2.9990 chunk 138 optimal weight: 5.9990 chunk 54 optimal weight: 0.6980 chunk 159 optimal weight: 1.9990 chunk 166 optimal weight: 0.5980 chunk 175 optimal weight: 4.9990 overall best weight: 1.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 72 GLN ** A 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 293 HIS ** A 299 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 406 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 72 GLN ** B 299 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 406 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 72 GLN ** C 299 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 72 GLN ** D 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 298 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 299 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7355 moved from start: 0.5959 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 15488 Z= 0.283 Angle : 0.642 9.793 20972 Z= 0.330 Chirality : 0.047 0.272 2324 Planarity : 0.004 0.034 2712 Dihedral : 5.564 47.136 2116 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 13.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.99 % Favored : 95.01 % Rotamer: Outliers : 5.09 % Allowed : 22.83 % Favored : 72.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.65 (0.20), residues: 1964 helix: 0.24 (0.18), residues: 828 sheet: -0.81 (0.25), residues: 408 loop : -0.80 (0.25), residues: 728 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 169 HIS 0.009 0.001 HIS D 292 PHE 0.028 0.002 PHE B 38 TYR 0.013 0.001 TYR D 297 ARG 0.007 0.001 ARG A 395 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3928 Ramachandran restraints generated. 1964 Oldfield, 0 Emsley, 1964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3928 Ramachandran restraints generated. 1964 Oldfield, 0 Emsley, 1964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 462 residues out of total 1632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 380 time to evaluate : 1.615 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: A 53 GLU cc_start: 0.7640 (mt-10) cc_final: 0.7393 (mt-10) REVERT: A 177 ILE cc_start: 0.8794 (OUTLIER) cc_final: 0.8260 (mp) REVERT: A 316 TYR cc_start: 0.6618 (t80) cc_final: 0.6047 (t80) REVERT: A 369 GLU cc_start: 0.6633 (mm-30) cc_final: 0.6412 (mm-30) REVERT: A 402 PHE cc_start: 0.7537 (OUTLIER) cc_final: 0.7202 (t80) REVERT: A 471 MET cc_start: 0.8451 (mtp) cc_final: 0.8004 (mtp) REVERT: B 402 PHE cc_start: 0.7376 (OUTLIER) cc_final: 0.7051 (t80) REVERT: B 471 MET cc_start: 0.8117 (OUTLIER) cc_final: 0.7818 (mtm) REVERT: C 97 GLU cc_start: 0.7782 (tp30) cc_final: 0.7515 (tp30) REVERT: C 237 MET cc_start: 0.6511 (mmt) cc_final: 0.5726 (mmt) REVERT: C 402 PHE cc_start: 0.7383 (OUTLIER) cc_final: 0.7068 (t80) REVERT: C 429 SER cc_start: 0.8978 (OUTLIER) cc_final: 0.8636 (t) REVERT: C 480 GLU cc_start: 0.7746 (tt0) cc_final: 0.7316 (tt0) REVERT: D 53 GLU cc_start: 0.6710 (tt0) cc_final: 0.6468 (tt0) REVERT: D 402 PHE cc_start: 0.7361 (OUTLIER) cc_final: 0.7058 (t80) REVERT: D 471 MET cc_start: 0.7936 (mtp) cc_final: 0.7704 (mtp) outliers start: 82 outliers final: 69 residues processed: 421 average time/residue: 0.2774 time to fit residues: 172.2133 Evaluate side-chains 442 residues out of total 1632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 366 time to evaluate : 1.658 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 THR Chi-restraints excluded: chain A residue 144 THR Chi-restraints excluded: chain A residue 147 ILE Chi-restraints excluded: chain A residue 177 ILE Chi-restraints excluded: chain A residue 180 ILE Chi-restraints excluded: chain A residue 185 SER Chi-restraints excluded: chain A residue 222 VAL Chi-restraints excluded: chain A residue 239 ILE Chi-restraints excluded: chain A residue 248 THR Chi-restraints excluded: chain A residue 303 CYS Chi-restraints excluded: chain A residue 402 PHE Chi-restraints excluded: chain A residue 460 VAL Chi-restraints excluded: chain B residue 79 THR Chi-restraints excluded: chain B residue 109 MET Chi-restraints excluded: chain B residue 114 LEU Chi-restraints excluded: chain B residue 123 LEU Chi-restraints excluded: chain B residue 129 THR Chi-restraints excluded: chain B residue 144 THR Chi-restraints excluded: chain B residue 147 ILE Chi-restraints excluded: chain B residue 177 ILE Chi-restraints excluded: chain B residue 185 SER Chi-restraints excluded: chain B residue 219 VAL Chi-restraints excluded: chain B residue 220 ASN Chi-restraints excluded: chain B residue 221 ILE Chi-restraints excluded: chain B residue 222 VAL Chi-restraints excluded: chain B residue 239 ILE Chi-restraints excluded: chain B residue 248 THR Chi-restraints excluded: chain B residue 266 VAL Chi-restraints excluded: chain B residue 303 CYS Chi-restraints excluded: chain B residue 332 LEU Chi-restraints excluded: chain B residue 402 PHE Chi-restraints excluded: chain B residue 460 VAL Chi-restraints excluded: chain B residue 471 MET Chi-restraints excluded: chain B residue 494 VAL Chi-restraints excluded: chain C residue 79 THR Chi-restraints excluded: chain C residue 109 MET Chi-restraints excluded: chain C residue 129 THR Chi-restraints excluded: chain C residue 144 THR Chi-restraints excluded: chain C residue 147 ILE Chi-restraints excluded: chain C residue 155 THR Chi-restraints excluded: chain C residue 177 ILE Chi-restraints excluded: chain C residue 185 SER Chi-restraints excluded: chain C residue 219 VAL Chi-restraints excluded: chain C residue 220 ASN Chi-restraints excluded: chain C residue 222 VAL Chi-restraints excluded: chain C residue 239 ILE Chi-restraints excluded: chain C residue 248 THR Chi-restraints excluded: chain C residue 263 LEU Chi-restraints excluded: chain C residue 266 VAL Chi-restraints excluded: chain C residue 303 CYS Chi-restraints excluded: chain C residue 332 LEU Chi-restraints excluded: chain C residue 402 PHE Chi-restraints excluded: chain C residue 429 SER Chi-restraints excluded: chain C residue 460 VAL Chi-restraints excluded: chain D residue 79 THR Chi-restraints excluded: chain D residue 123 LEU Chi-restraints excluded: chain D residue 129 THR Chi-restraints excluded: chain D residue 147 ILE Chi-restraints excluded: chain D residue 155 THR Chi-restraints excluded: chain D residue 177 ILE Chi-restraints excluded: chain D residue 185 SER Chi-restraints excluded: chain D residue 219 VAL Chi-restraints excluded: chain D residue 220 ASN Chi-restraints excluded: chain D residue 221 ILE Chi-restraints excluded: chain D residue 222 VAL Chi-restraints excluded: chain D residue 239 ILE Chi-restraints excluded: chain D residue 248 THR Chi-restraints excluded: chain D residue 266 VAL Chi-restraints excluded: chain D residue 303 CYS Chi-restraints excluded: chain D residue 315 ILE Chi-restraints excluded: chain D residue 332 LEU Chi-restraints excluded: chain D residue 341 THR Chi-restraints excluded: chain D residue 402 PHE Chi-restraints excluded: chain D residue 451 THR Chi-restraints excluded: chain D residue 460 VAL Chi-restraints excluded: chain D residue 494 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 115 optimal weight: 0.6980 chunk 186 optimal weight: 2.9990 chunk 113 optimal weight: 0.6980 chunk 88 optimal weight: 1.9990 chunk 129 optimal weight: 3.9990 chunk 195 optimal weight: 2.9990 chunk 179 optimal weight: 4.9990 chunk 155 optimal weight: 1.9990 chunk 16 optimal weight: 0.8980 chunk 120 optimal weight: 3.9990 chunk 95 optimal weight: 2.9990 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 30 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 72 GLN ** A 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 299 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 406 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 72 GLN ** B 299 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 406 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 30 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 72 GLN ** C 299 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 72 GLN ** D 298 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 299 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7363 moved from start: 0.6023 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.063 15488 Z= 0.297 Angle : 0.660 11.074 20972 Z= 0.340 Chirality : 0.047 0.291 2324 Planarity : 0.004 0.036 2712 Dihedral : 5.673 48.505 2116 Min Nonbonded Distance : 2.574 Molprobity Statistics. All-atom Clashscore : 13.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.94 % Favored : 95.06 % Rotamer: Outliers : 4.96 % Allowed : 23.39 % Favored : 71.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.71 (0.20), residues: 1964 helix: 0.14 (0.18), residues: 828 sheet: -0.80 (0.26), residues: 408 loop : -0.79 (0.25), residues: 728 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 169 HIS 0.008 0.002 HIS D 292 PHE 0.028 0.002 PHE B 38 TYR 0.012 0.001 TYR B 119 ARG 0.008 0.001 ARG A 395 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3928 Ramachandran restraints generated. 1964 Oldfield, 0 Emsley, 1964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3928 Ramachandran restraints generated. 1964 Oldfield, 0 Emsley, 1964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 449 residues out of total 1632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 369 time to evaluate : 1.790 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 53 GLU cc_start: 0.7705 (mt-10) cc_final: 0.7456 (mt-10) REVERT: A 177 ILE cc_start: 0.8772 (OUTLIER) cc_final: 0.8325 (mp) REVERT: A 316 TYR cc_start: 0.6683 (t80) cc_final: 0.6045 (t80) REVERT: A 369 GLU cc_start: 0.6648 (mm-30) cc_final: 0.6429 (mm-30) REVERT: A 402 PHE cc_start: 0.7555 (OUTLIER) cc_final: 0.7201 (t80) REVERT: A 471 MET cc_start: 0.8460 (mtp) cc_final: 0.8000 (mtp) REVERT: B 402 PHE cc_start: 0.7378 (OUTLIER) cc_final: 0.7053 (t80) REVERT: B 471 MET cc_start: 0.8165 (OUTLIER) cc_final: 0.7843 (mtp) REVERT: C 97 GLU cc_start: 0.7785 (tp30) cc_final: 0.7533 (tp30) REVERT: C 237 MET cc_start: 0.6434 (mmt) cc_final: 0.5473 (mmt) REVERT: C 238 ASP cc_start: 0.7855 (m-30) cc_final: 0.7640 (m-30) REVERT: C 402 PHE cc_start: 0.7395 (OUTLIER) cc_final: 0.7083 (t80) REVERT: C 429 SER cc_start: 0.8982 (OUTLIER) cc_final: 0.8634 (t) REVERT: C 480 GLU cc_start: 0.7766 (tt0) cc_final: 0.7299 (tt0) REVERT: D 53 GLU cc_start: 0.6769 (tt0) cc_final: 0.6503 (tt0) REVERT: D 402 PHE cc_start: 0.7397 (OUTLIER) cc_final: 0.7072 (t80) REVERT: D 471 MET cc_start: 0.7957 (mtp) cc_final: 0.7726 (mtp) outliers start: 80 outliers final: 69 residues processed: 410 average time/residue: 0.2715 time to fit residues: 164.0652 Evaluate side-chains 432 residues out of total 1632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 356 time to evaluate : 1.623 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 THR Chi-restraints excluded: chain A residue 144 THR Chi-restraints excluded: chain A residue 147 ILE Chi-restraints excluded: chain A residue 177 ILE Chi-restraints excluded: chain A residue 180 ILE Chi-restraints excluded: chain A residue 185 SER Chi-restraints excluded: chain A residue 222 VAL Chi-restraints excluded: chain A residue 239 ILE Chi-restraints excluded: chain A residue 248 THR Chi-restraints excluded: chain A residue 303 CYS Chi-restraints excluded: chain A residue 402 PHE Chi-restraints excluded: chain A residue 460 VAL Chi-restraints excluded: chain B residue 79 THR Chi-restraints excluded: chain B residue 109 MET Chi-restraints excluded: chain B residue 114 LEU Chi-restraints excluded: chain B residue 123 LEU Chi-restraints excluded: chain B residue 129 THR Chi-restraints excluded: chain B residue 144 THR Chi-restraints excluded: chain B residue 147 ILE Chi-restraints excluded: chain B residue 155 THR Chi-restraints excluded: chain B residue 177 ILE Chi-restraints excluded: chain B residue 185 SER Chi-restraints excluded: chain B residue 219 VAL Chi-restraints excluded: chain B residue 220 ASN Chi-restraints excluded: chain B residue 221 ILE Chi-restraints excluded: chain B residue 222 VAL Chi-restraints excluded: chain B residue 239 ILE Chi-restraints excluded: chain B residue 248 THR Chi-restraints excluded: chain B residue 266 VAL Chi-restraints excluded: chain B residue 303 CYS Chi-restraints excluded: chain B residue 332 LEU Chi-restraints excluded: chain B residue 402 PHE Chi-restraints excluded: chain B residue 460 VAL Chi-restraints excluded: chain B residue 471 MET Chi-restraints excluded: chain B residue 494 VAL Chi-restraints excluded: chain C residue 79 THR Chi-restraints excluded: chain C residue 129 THR Chi-restraints excluded: chain C residue 144 THR Chi-restraints excluded: chain C residue 147 ILE Chi-restraints excluded: chain C residue 155 THR Chi-restraints excluded: chain C residue 177 ILE Chi-restraints excluded: chain C residue 185 SER Chi-restraints excluded: chain C residue 219 VAL Chi-restraints excluded: chain C residue 220 ASN Chi-restraints excluded: chain C residue 222 VAL Chi-restraints excluded: chain C residue 239 ILE Chi-restraints excluded: chain C residue 248 THR Chi-restraints excluded: chain C residue 263 LEU Chi-restraints excluded: chain C residue 266 VAL Chi-restraints excluded: chain C residue 303 CYS Chi-restraints excluded: chain C residue 332 LEU Chi-restraints excluded: chain C residue 402 PHE Chi-restraints excluded: chain C residue 429 SER Chi-restraints excluded: chain C residue 460 VAL Chi-restraints excluded: chain D residue 79 THR Chi-restraints excluded: chain D residue 123 LEU Chi-restraints excluded: chain D residue 129 THR Chi-restraints excluded: chain D residue 147 ILE Chi-restraints excluded: chain D residue 155 THR Chi-restraints excluded: chain D residue 177 ILE Chi-restraints excluded: chain D residue 185 SER Chi-restraints excluded: chain D residue 219 VAL Chi-restraints excluded: chain D residue 220 ASN Chi-restraints excluded: chain D residue 221 ILE Chi-restraints excluded: chain D residue 222 VAL Chi-restraints excluded: chain D residue 239 ILE Chi-restraints excluded: chain D residue 248 THR Chi-restraints excluded: chain D residue 266 VAL Chi-restraints excluded: chain D residue 303 CYS Chi-restraints excluded: chain D residue 315 ILE Chi-restraints excluded: chain D residue 332 LEU Chi-restraints excluded: chain D residue 341 THR Chi-restraints excluded: chain D residue 402 PHE Chi-restraints excluded: chain D residue 451 THR Chi-restraints excluded: chain D residue 460 VAL Chi-restraints excluded: chain D residue 494 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 123 optimal weight: 0.0980 chunk 165 optimal weight: 0.4980 chunk 47 optimal weight: 0.5980 chunk 143 optimal weight: 0.2980 chunk 22 optimal weight: 4.9990 chunk 43 optimal weight: 0.5980 chunk 155 optimal weight: 0.6980 chunk 65 optimal weight: 0.0070 chunk 159 optimal weight: 0.5980 chunk 19 optimal weight: 0.8980 chunk 28 optimal weight: 2.9990 overall best weight: 0.2998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 72 GLN ** A 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 299 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 406 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 30 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 72 GLN ** B 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 299 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 406 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 30 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 72 GLN ** C 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 299 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 30 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 72 GLN ** D 298 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 299 GLN ** 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 = 0.4062 r_free = 0.4062 target = 0.198041 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3662 r_free = 0.3662 target = 0.159928 restraints weight = 16998.819| |-----------------------------------------------------------------------------| r_work (start): 0.3619 rms_B_bonded: 2.04 r_work: 0.3504 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work (final): 0.3504 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3486 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3486 r_free = 0.3486 target_work(ls_wunit_k1) = 0.144 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3472 r_free = 0.3472 target_work(ls_wunit_k1) = 0.143 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| r_final: 0.3472 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7427 moved from start: 0.6363 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 15488 Z= 0.180 Angle : 0.616 12.000 20972 Z= 0.315 Chirality : 0.044 0.240 2324 Planarity : 0.004 0.036 2712 Dihedral : 5.267 45.032 2116 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 12.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.58 % Favored : 95.42 % Rotamer: Outliers : 3.72 % Allowed : 25.43 % Favored : 70.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.53 (0.20), residues: 1964 helix: 0.30 (0.18), residues: 832 sheet: -0.65 (0.26), residues: 408 loop : -0.75 (0.25), residues: 724 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.001 TRP C 169 HIS 0.004 0.001 HIS D 298 PHE 0.026 0.001 PHE B 38 TYR 0.015 0.001 TYR C 119 ARG 0.008 0.000 ARG A 395 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3934.55 seconds wall clock time: 72 minutes 37.46 seconds (4357.46 seconds total)