Starting phenix.real_space_refine on Sat Aug 23 22:37:49 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8dno_27575/08_2025/8dno_27575.cif Found real_map, /net/cci-nas-00/data/ceres_data/8dno_27575/08_2025/8dno_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 { model { file = "/net/cci-nas-00/data/ceres_data/8dno_27575/08_2025/8dno_27575.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8dno_27575/08_2025/8dno_27575.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8dno_27575/08_2025/8dno_27575.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8dno_27575/08_2025/8dno_27575.map" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.062 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-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/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: {'ASP:plan': 1, 'GLU: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: {'ASP:plan': 1, 'GLU: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: {'ASP:plan': 1, 'GLU: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: {'ASP:plan': 1, 'GLU: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: 3.51, per 1000 atoms: 0.23 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: 1.32 Conformation dependent library (CDL) restraints added in 647.4 milliseconds Enol-peptide restraints added in 238.4 nanoseconds 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: 0.36 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: 2.12 Time building geometry restraints manager: 1.73 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: 0.05 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: 1.000 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: 0.140 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 13.520 Find NCS groups from input model: 0.130 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.330 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.230 ------------------------------------------------------------------------------- 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= 0.949 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. 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 ARG 0.006 0.001 ARG D 143 TYR 0.018 0.002 TYR D 154 PHE 0.018 0.003 PHE B 24 TRP 0.014 0.002 TRP D 29 HIS 0.007 0.002 HIS D 484 Details of bonding type rmsd covalent geometry : bond 0.01259 (15488) covalent geometry : angle 1.45281 (20972) hydrogen bonds : bond 0.24263 ( 674) hydrogen bonds : angle 9.27791 ( 1935) *********************** 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 : 0.593 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: 0.8501 (mtpp) REVERT: A 158 GLU cc_start: 0.8256 (mt-10) cc_final: 0.7897 (mt-10) REVERT: A 175 MET cc_start: 0.8069 (OUTLIER) cc_final: 0.7578 (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: 0.7427 (mtm180) REVERT: A 471 MET cc_start: 0.8665 (mtp) cc_final: 0.8373 (mtp) REVERT: A 477 GLU cc_start: 0.7683 (mt-10) cc_final: 0.7480 (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: 0.7512 (mmp) REVERT: B 267 THR cc_start: 0.8060 (p) cc_final: 0.7746 (p) REVERT: B 292 HIS cc_start: 0.5517 (OUTLIER) cc_final: 0.5285 (t-90) REVERT: B 410 LYS cc_start: 0.7945 (ttpt) cc_final: 0.7644 (tttm) REVERT: C 169 TRP cc_start: 0.8579 (p-90) cc_final: 0.8227 (p-90) REVERT: C 175 MET cc_start: 0.8009 (OUTLIER) cc_final: 0.7583 (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: 0.5330 (t-90) REVERT: C 410 LYS cc_start: 0.7943 (ttpt) cc_final: 0.7639 (tttm) REVERT: C 415 ASP cc_start: 0.7876 (m-30) cc_final: 0.7090 (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: 0.7660 (tttm) outliers start: 76 outliers final: 20 residues processed: 615 average time/residue: 0.1159 time to fit residues: 101.9788 Evaluate side-chains 487 residues out of total 1632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 460 time to evaluate : 0.411 ------------------------------------------------------------------------------- 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 98 optimal weight: 8.9990 chunk 194 optimal weight: 0.9980 chunk 107 optimal weight: 1.9990 chunk 10 optimal weight: 0.8980 chunk 66 optimal weight: 0.6980 chunk 130 optimal weight: 0.9990 chunk 124 optimal weight: 0.9990 chunk 103 optimal weight: 0.9990 chunk 77 optimal weight: 0.9990 chunk 122 optimal weight: 0.8980 chunk 91 optimal weight: 0.8980 overall best weight: 0.8780 ------------------------------------------------------------------------------- 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** 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** 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: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4055 r_free = 0.4055 target = 0.197884 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3641 r_free = 0.3641 target = 0.158351 restraints weight = 17086.044| |-----------------------------------------------------------------------------| r_work (start): 0.3595 rms_B_bonded: 2.16 r_work: 0.3474 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work (final): 0.3474 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3467 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3467 r_free = 0.3467 target_work(ls_wunit_k1) = 0.143 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3455 r_free = 0.3455 target_work(ls_wunit_k1) = 0.142 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| r_final: 0.3455 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7410 moved from start: 0.3726 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 15488 Z= 0.173 Angle : 0.690 10.769 20972 Z= 0.356 Chirality : 0.047 0.256 2324 Planarity : 0.005 0.038 2712 Dihedral : 7.437 59.479 2170 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 15.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.50 % Favored : 94.50 % Rotamer: Outliers : 4.22 % Allowed : 16.32 % Favored : 79.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.94 (0.18), residues: 1964 helix: -0.42 (0.17), residues: 824 sheet: -1.84 (0.24), residues: 404 loop : -1.80 (0.23), residues: 736 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 395 TYR 0.018 0.002 TYR A 351 PHE 0.022 0.002 PHE A 402 TRP 0.009 0.001 TRP B 29 HIS 0.005 0.001 HIS A 298 Details of bonding type rmsd covalent geometry : bond 0.00395 (15488) covalent geometry : angle 0.69027 (20972) hydrogen bonds : bond 0.04139 ( 674) hydrogen bonds : angle 5.25821 ( 1935) *********************** 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 542 residues out of total 1632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 474 time to evaluate : 0.626 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 65 LYS cc_start: 0.8396 (tttt) cc_final: 0.8180 (mtpp) REVERT: A 158 GLU cc_start: 0.8434 (mt-10) cc_final: 0.8004 (mt-10) REVERT: A 260 LYS cc_start: 0.6995 (tttt) cc_final: 0.6754 (pttp) REVERT: A 308 ARG cc_start: 0.7677 (mtm180) cc_final: 0.7136 (mtm180) REVERT: A 347 ASP cc_start: 0.7173 (p0) cc_final: 0.6336 (m-30) REVERT: A 420 ARG cc_start: 0.8783 (mtp180) cc_final: 0.8528 (mtp180) REVERT: A 471 MET cc_start: 0.8853 (mtp) cc_final: 0.8464 (mtp) REVERT: A 498 GLN cc_start: 0.6424 (mp10) cc_final: 0.6178 (mp10) REVERT: B 30 HIS cc_start: 0.5081 (m-70) cc_final: 0.4748 (m-70) REVERT: B 53 GLU cc_start: 0.7290 (mt-10) cc_final: 0.7085 (mt-10) REVERT: B 177 ILE cc_start: 0.8661 (OUTLIER) cc_final: 0.8405 (mp) REVERT: B 237 MET cc_start: 0.7261 (mmt) cc_final: 0.6675 (mmt) REVERT: B 341 THR cc_start: 0.8188 (p) cc_final: 0.7986 (p) REVERT: B 398 LYS cc_start: 0.7060 (mtpt) cc_final: 0.6847 (mtpp) REVERT: B 410 LYS cc_start: 0.7873 (ttpt) cc_final: 0.7347 (tttm) REVERT: B 499 LYS cc_start: 0.6349 (ttpt) cc_final: 0.6142 (ttpt) REVERT: C 20 TYR cc_start: 0.6013 (m-80) cc_final: 0.5487 (m-80) REVERT: C 30 HIS cc_start: 0.4944 (m-70) cc_final: 0.4668 (m-70) REVERT: C 177 ILE cc_start: 0.8651 (OUTLIER) cc_final: 0.8401 (mp) REVERT: C 237 MET cc_start: 0.7221 (mmt) cc_final: 0.6566 (mmt) REVERT: C 341 THR cc_start: 0.8259 (p) cc_final: 0.8048 (p) REVERT: C 410 LYS cc_start: 0.7774 (ttpt) cc_final: 0.7241 (tttm) REVERT: C 471 MET cc_start: 0.8528 (mtp) cc_final: 0.8322 (mtm) REVERT: D 30 HIS cc_start: 0.5034 (m-70) cc_final: 0.4663 (m-70) REVERT: D 57 LYS cc_start: 0.7705 (mmtp) cc_final: 0.7473 (mmmm) REVERT: D 177 ILE cc_start: 0.8652 (OUTLIER) cc_final: 0.8415 (mp) REVERT: D 237 MET cc_start: 0.7399 (mmt) cc_final: 0.6999 (mmt) REVERT: D 273 LYS cc_start: 0.7867 (tptt) cc_final: 0.7404 (tptt) REVERT: D 308 ARG cc_start: 0.7260 (mtm180) cc_final: 0.6809 (ttm170) REVERT: D 410 LYS cc_start: 0.7819 (ttpt) cc_final: 0.7271 (tttm) REVERT: D 499 LYS cc_start: 0.6423 (ttpt) cc_final: 0.6163 (ttpt) outliers start: 68 outliers final: 41 residues processed: 514 average time/residue: 0.1362 time to fit residues: 102.4792 Evaluate side-chains 439 residues out of total 1632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 395 time to evaluate : 0.581 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 303 CYS Chi-restraints excluded: chain A residue 332 LEU Chi-restraints excluded: chain A residue 445 SER 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 332 LEU Chi-restraints excluded: chain B residue 390 VAL Chi-restraints excluded: chain B residue 451 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 220 ASN Chi-restraints excluded: chain C residue 248 THR Chi-restraints excluded: chain C residue 266 VAL Chi-restraints excluded: chain C residue 279 LEU Chi-restraints excluded: chain C residue 332 LEU Chi-restraints excluded: chain C residue 390 VAL Chi-restraints excluded: chain C residue 494 VAL 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 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 Chi-restraints excluded: chain D residue 390 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 38 optimal weight: 8.9990 chunk 10 optimal weight: 4.9990 chunk 57 optimal weight: 1.9990 chunk 61 optimal weight: 0.9980 chunk 107 optimal weight: 5.9990 chunk 143 optimal weight: 4.9990 chunk 54 optimal weight: 4.9990 chunk 106 optimal weight: 1.9990 chunk 16 optimal weight: 0.1980 chunk 2 optimal weight: 10.0000 chunk 103 optimal weight: 4.9990 overall best weight: 2.0386 ------------------------------------------------------------------------------- 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 298 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 299 GLN ** A 406 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 30 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 72 GLN ** C 30 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 72 GLN ** C 299 GLN ** 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3945 r_free = 0.3945 target = 0.187146 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3509 r_free = 0.3509 target = 0.146506 restraints weight = 17284.991| |-----------------------------------------------------------------------------| r_work (start): 0.3464 rms_B_bonded: 2.13 r_work: 0.3341 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work (final): 0.3341 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3337 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3337 r_free = 0.3337 target_work(ls_wunit_k1) = 0.132 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3336 r_free = 0.3336 target_work(ls_wunit_k1) = 0.132 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| r_final: 0.3336 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7558 moved from start: 0.4634 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.072 15488 Z= 0.276 Angle : 0.731 9.114 20972 Z= 0.379 Chirality : 0.049 0.255 2324 Planarity : 0.005 0.033 2712 Dihedral : 6.719 52.451 2132 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 14.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.89 % Favored : 92.11 % Rotamer: Outliers : 6.33 % Allowed : 18.42 % Favored : 75.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.54 (0.19), residues: 1964 helix: -0.21 (0.17), residues: 832 sheet: -1.59 (0.25), residues: 400 loop : -1.46 (0.24), residues: 732 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG D 85 TYR 0.015 0.002 TYR A 297 PHE 0.022 0.003 PHE A 402 TRP 0.011 0.002 TRP C 77 HIS 0.014 0.002 HIS B 292 Details of bonding type rmsd covalent geometry : bond 0.00644 (15488) covalent geometry : angle 0.73137 (20972) hydrogen bonds : bond 0.04690 ( 674) hydrogen bonds : angle 5.13516 ( 1935) *********************** 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 541 residues out of total 1632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 102 poor density : 439 time to evaluate : 0.584 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 20 TYR cc_start: 0.6351 (m-80) cc_final: 0.5455 (m-80) REVERT: A 57 LYS cc_start: 0.8171 (mmtp) cc_final: 0.7576 (tptm) REVERT: A 101 LEU cc_start: 0.7769 (mt) cc_final: 0.7439 (mp) REVERT: A 158 GLU cc_start: 0.8436 (mt-10) cc_final: 0.8151 (mt-10) REVERT: A 169 TRP cc_start: 0.8777 (p-90) cc_final: 0.8167 (p-90) REVERT: A 268 LEU cc_start: 0.8268 (mt) cc_final: 0.8058 (mp) REVERT: A 299 GLN cc_start: 0.7536 (OUTLIER) cc_final: 0.7125 (mt0) REVERT: A 395 ARG cc_start: 0.7779 (mmm-85) cc_final: 0.7441 (mmm-85) REVERT: A 471 MET cc_start: 0.8903 (mtp) cc_final: 0.8426 (mtp) REVERT: B 30 HIS cc_start: 0.5417 (m-70) cc_final: 0.5097 (m-70) REVERT: B 57 LYS cc_start: 0.8154 (mmtp) cc_final: 0.7525 (mmtm) REVERT: B 169 TRP cc_start: 0.8893 (p-90) cc_final: 0.8099 (p-90) REVERT: B 177 ILE cc_start: 0.8936 (OUTLIER) cc_final: 0.8565 (mp) REVERT: B 398 LYS cc_start: 0.7353 (mtpt) cc_final: 0.6998 (mtpp) REVERT: B 410 LYS cc_start: 0.8051 (ttpt) cc_final: 0.7526 (tttm) REVERT: C 30 HIS cc_start: 0.5120 (m-70) cc_final: 0.4845 (m-70) REVERT: C 57 LYS cc_start: 0.7800 (mmtm) cc_final: 0.7381 (mmtm) REVERT: C 177 ILE cc_start: 0.8950 (OUTLIER) cc_final: 0.8552 (mp) REVERT: C 256 GLU cc_start: 0.7179 (tt0) cc_final: 0.6977 (mt-10) REVERT: C 341 THR cc_start: 0.8234 (p) cc_final: 0.8031 (p) REVERT: C 410 LYS cc_start: 0.7940 (ttpt) cc_final: 0.7496 (tttm) REVERT: C 471 MET cc_start: 0.8597 (mtp) cc_final: 0.8173 (mtp) REVERT: C 480 GLU cc_start: 0.7990 (tt0) cc_final: 0.7492 (tt0) REVERT: D 30 HIS cc_start: 0.5182 (m-70) cc_final: 0.4915 (m-70) REVERT: D 57 LYS cc_start: 0.7888 (mmtp) cc_final: 0.7483 (mmtp) REVERT: D 177 ILE cc_start: 0.8945 (OUTLIER) cc_final: 0.8553 (mp) REVERT: D 237 MET cc_start: 0.7552 (mmt) cc_final: 0.6688 (mmt) REVERT: D 256 GLU cc_start: 0.7149 (tt0) cc_final: 0.6907 (mt-10) REVERT: D 410 LYS cc_start: 0.8009 (ttpt) cc_final: 0.7477 (tttm) outliers start: 102 outliers final: 75 residues processed: 484 average time/residue: 0.1179 time to fit residues: 83.8374 Evaluate side-chains 484 residues out of total 1632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 405 time to evaluate : 0.567 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 VAL 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 167 ILE Chi-restraints excluded: chain A residue 177 ILE Chi-restraints excluded: chain A residue 185 SER Chi-restraints excluded: chain A residue 205 VAL Chi-restraints excluded: chain A residue 221 ILE Chi-restraints excluded: chain A residue 239 ILE Chi-restraints excluded: chain A residue 279 LEU Chi-restraints excluded: chain A residue 299 GLN Chi-restraints excluded: chain A residue 303 CYS Chi-restraints excluded: chain A residue 332 LEU Chi-restraints excluded: chain A residue 442 THR Chi-restraints excluded: chain A residue 445 SER 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 114 LEU 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 167 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 222 VAL Chi-restraints excluded: chain B residue 248 THR Chi-restraints excluded: chain B residue 254 ILE Chi-restraints excluded: chain B residue 266 VAL Chi-restraints excluded: chain B residue 279 LEU 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 445 SER Chi-restraints excluded: chain B residue 451 THR Chi-restraints excluded: chain B residue 460 VAL Chi-restraints excluded: chain B residue 494 VAL Chi-restraints excluded: chain C residue 40 VAL Chi-restraints excluded: chain C residue 114 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 198 THR Chi-restraints excluded: chain C residue 219 VAL 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 279 LEU Chi-restraints excluded: chain C residue 303 CYS Chi-restraints excluded: chain C residue 332 LEU Chi-restraints excluded: chain C residue 390 VAL Chi-restraints excluded: chain C residue 445 SER Chi-restraints excluded: chain C residue 451 THR Chi-restraints excluded: chain C residue 460 VAL Chi-restraints excluded: chain C residue 494 VAL 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 219 VAL 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 279 LEU 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 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 146 optimal weight: 0.0670 chunk 52 optimal weight: 3.9990 chunk 45 optimal weight: 0.3980 chunk 122 optimal weight: 1.9990 chunk 181 optimal weight: 0.9990 chunk 7 optimal weight: 0.9990 chunk 177 optimal weight: 0.9990 chunk 112 optimal weight: 0.9980 chunk 67 optimal weight: 0.6980 chunk 167 optimal weight: 1.9990 chunk 60 optimal weight: 0.9980 overall best weight: 0.6318 ------------------------------------------------------------------------------- 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 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 298 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 299 GLN ** A 406 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 30 HIS B 72 GLN ** B 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 204 HIS ** B 299 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 406 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 30 HIS 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 30 HIS D 72 GLN ** D 299 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4026 r_free = 0.4026 target = 0.195171 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3597 r_free = 0.3597 target = 0.154264 restraints weight = 17152.776| |-----------------------------------------------------------------------------| r_work (start): 0.3552 rms_B_bonded: 2.13 r_work: 0.3437 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work (final): 0.3437 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3423 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3423 r_free = 0.3423 target_work(ls_wunit_k1) = 0.139 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3423 r_free = 0.3423 target_work(ls_wunit_k1) = 0.139 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| r_final: 0.3423 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7462 moved from start: 0.5203 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= 0.135 Angle : 0.586 6.421 20972 Z= 0.304 Chirality : 0.045 0.265 2324 Planarity : 0.004 0.034 2712 Dihedral : 6.039 53.426 2126 Min Nonbonded Distance : 2.563 Molprobity Statistics. All-atom Clashscore : 12.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.30 % Favored : 94.70 % Rotamer: Outliers : 4.53 % Allowed : 21.22 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.98 (0.20), residues: 1964 helix: 0.32 (0.19), residues: 832 sheet: -1.43 (0.25), residues: 400 loop : -1.16 (0.24), residues: 732 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 321 TYR 0.014 0.001 TYR B 119 PHE 0.015 0.002 PHE A 402 TRP 0.008 0.001 TRP C 29 HIS 0.007 0.001 HIS B 292 Details of bonding type rmsd covalent geometry : bond 0.00324 (15488) covalent geometry : angle 0.58588 (20972) hydrogen bonds : bond 0.03528 ( 674) hydrogen bonds : angle 4.77103 ( 1935) *********************** 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 493 residues out of total 1632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 420 time to evaluate : 0.459 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 20 TYR cc_start: 0.6278 (m-80) cc_final: 0.5192 (m-80) REVERT: A 23 ILE cc_start: 0.6792 (OUTLIER) cc_final: 0.6552 (mm) REVERT: A 57 LYS cc_start: 0.8130 (mmtp) cc_final: 0.7897 (mmtm) REVERT: A 101 LEU cc_start: 0.7792 (mt) cc_final: 0.7525 (mp) REVERT: A 169 TRP cc_start: 0.8777 (p-90) cc_final: 0.7893 (p-90) REVERT: A 177 ILE cc_start: 0.8811 (OUTLIER) cc_final: 0.8567 (mp) REVERT: A 260 LYS cc_start: 0.6993 (ttmt) cc_final: 0.6716 (pttt) REVERT: A 268 LEU cc_start: 0.8295 (mt) cc_final: 0.8071 (mp) REVERT: A 299 GLN cc_start: 0.7252 (OUTLIER) cc_final: 0.6918 (mt0) REVERT: A 318 GLU cc_start: 0.6733 (tp30) cc_final: 0.6503 (tp30) REVERT: A 347 ASP cc_start: 0.7007 (p0) cc_final: 0.6417 (m-30) REVERT: A 459 VAL cc_start: 0.7074 (t) cc_final: 0.6863 (m) REVERT: A 471 MET cc_start: 0.8868 (mtp) cc_final: 0.8491 (mtp) REVERT: B 25 ILE cc_start: 0.7686 (mt) cc_final: 0.7385 (mp) REVERT: B 57 LYS cc_start: 0.8011 (mmtp) cc_final: 0.7710 (mmtm) REVERT: B 169 TRP cc_start: 0.8772 (p-90) cc_final: 0.7655 (p-90) REVERT: B 177 ILE cc_start: 0.8779 (OUTLIER) cc_final: 0.8379 (mp) REVERT: B 237 MET cc_start: 0.7396 (mmt) cc_final: 0.6778 (mmt) REVERT: B 318 GLU cc_start: 0.6851 (tp30) cc_final: 0.6520 (tp30) REVERT: B 398 LYS cc_start: 0.7328 (mtpt) cc_final: 0.6988 (mtpp) REVERT: B 406 GLN cc_start: 0.7520 (tt0) cc_final: 0.7294 (tt0) REVERT: C 25 ILE cc_start: 0.7749 (mt) cc_final: 0.7469 (mp) REVERT: C 53 GLU cc_start: 0.7856 (mt-10) cc_final: 0.6931 (tt0) REVERT: C 158 GLU cc_start: 0.8553 (mt-10) cc_final: 0.8174 (mt-10) REVERT: C 177 ILE cc_start: 0.8737 (OUTLIER) cc_final: 0.8229 (mp) REVERT: C 237 MET cc_start: 0.7391 (mmt) cc_final: 0.6768 (mmt) REVERT: C 322 ARG cc_start: 0.6315 (mmp80) cc_final: 0.5658 (mmp80) REVERT: C 341 THR cc_start: 0.8191 (p) cc_final: 0.7983 (p) REVERT: C 471 MET cc_start: 0.8492 (mtp) cc_final: 0.8078 (mtp) REVERT: C 480 GLU cc_start: 0.7916 (tt0) cc_final: 0.7444 (tt0) REVERT: D 25 ILE cc_start: 0.7790 (mt) cc_final: 0.7473 (mp) REVERT: D 30 HIS cc_start: 0.4698 (m90) cc_final: 0.4496 (m90) REVERT: D 177 ILE cc_start: 0.8743 (OUTLIER) cc_final: 0.8243 (mp) REVERT: D 237 MET cc_start: 0.7409 (mmt) cc_final: 0.6850 (mmt) REVERT: D 322 ARG cc_start: 0.6276 (mmp80) cc_final: 0.5785 (mmp80) outliers start: 73 outliers final: 47 residues processed: 463 average time/residue: 0.1142 time to fit residues: 78.0408 Evaluate side-chains 455 residues out of total 1632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 402 time to evaluate : 0.516 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 ILE Chi-restraints excluded: chain A residue 79 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 279 LEU Chi-restraints excluded: chain A residue 299 GLN Chi-restraints excluded: chain A residue 445 SER Chi-restraints excluded: chain A residue 451 THR Chi-restraints excluded: chain B residue 79 THR Chi-restraints excluded: chain B residue 147 ILE Chi-restraints excluded: chain B residue 167 ILE 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 266 VAL Chi-restraints excluded: chain B residue 279 LEU Chi-restraints excluded: chain B residue 303 CYS Chi-restraints excluded: chain B residue 332 LEU Chi-restraints excluded: chain C residue 79 THR Chi-restraints excluded: chain C residue 114 LEU 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 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 266 VAL Chi-restraints excluded: chain C residue 279 LEU 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 167 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 266 VAL Chi-restraints excluded: chain D residue 279 LEU Chi-restraints excluded: chain D residue 303 CYS Chi-restraints excluded: chain D residue 332 LEU Chi-restraints excluded: chain D residue 451 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 139 optimal weight: 3.9990 chunk 60 optimal weight: 1.9990 chunk 90 optimal weight: 4.9990 chunk 83 optimal weight: 0.9980 chunk 172 optimal weight: 2.9990 chunk 135 optimal weight: 2.9990 chunk 8 optimal weight: 1.9990 chunk 111 optimal weight: 0.6980 chunk 57 optimal weight: 0.9980 chunk 118 optimal weight: 2.9990 chunk 54 optimal weight: 4.9990 overall best weight: 1.3384 ------------------------------------------------------------------------------- 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 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 299 GLN ** A 406 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 72 GLN ** B 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 298 HIS ** 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 298 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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** D 448 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3974 r_free = 0.3974 target = 0.189278 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3549 r_free = 0.3549 target = 0.150572 restraints weight = 17290.083| |-----------------------------------------------------------------------------| r_work (start): 0.3532 rms_B_bonded: 2.06 r_work: 0.3414 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work (final): 0.3414 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3408 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3408 r_free = 0.3408 target_work(ls_wunit_k1) = 0.138 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3408 r_free = 0.3408 target_work(ls_wunit_k1) = 0.138 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| r_final: 0.3408 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7518 moved from start: 0.5373 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.059 15488 Z= 0.194 Angle : 0.619 5.736 20972 Z= 0.321 Chirality : 0.047 0.272 2324 Planarity : 0.004 0.034 2712 Dihedral : 6.229 59.859 2124 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 12.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.11 % Favored : 93.89 % Rotamer: Outliers : 6.58 % Allowed : 19.29 % Favored : 74.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.94 (0.20), residues: 1964 helix: 0.30 (0.18), residues: 832 sheet: -1.31 (0.25), residues: 404 loop : -1.12 (0.25), residues: 728 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 85 TYR 0.011 0.001 TYR A 297 PHE 0.030 0.002 PHE D 38 TRP 0.015 0.002 TRP D 169 HIS 0.008 0.001 HIS B 292 Details of bonding type rmsd covalent geometry : bond 0.00464 (15488) covalent geometry : angle 0.61899 (20972) hydrogen bonds : bond 0.03717 ( 674) hydrogen bonds : angle 4.76575 ( 1935) *********************** 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 518 residues out of total 1632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 106 poor density : 412 time to evaluate : 0.521 Fit side-chains 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: 0.7774 (tptm) REVERT: A 101 LEU cc_start: 0.7812 (mt) cc_final: 0.7516 (mp) REVERT: A 298 HIS cc_start: 0.7285 (t-90) cc_final: 0.6396 (t-90) REVERT: A 299 GLN cc_start: 0.7282 (OUTLIER) cc_final: 0.6849 (mt0) REVERT: A 318 GLU cc_start: 0.6734 (tp30) cc_final: 0.6423 (tp30) REVERT: A 347 ASP cc_start: 0.7054 (p0) cc_final: 0.6277 (m-30) REVERT: A 402 PHE cc_start: 0.7740 (OUTLIER) cc_final: 0.7190 (t80) REVERT: A 471 MET cc_start: 0.8784 (mtp) cc_final: 0.8385 (mtp) REVERT: B 57 LYS cc_start: 0.8018 (mmtp) cc_final: 0.7718 (mmtm) REVERT: B 169 TRP cc_start: 0.8815 (p-90) cc_final: 0.7776 (p-90) REVERT: B 237 MET cc_start: 0.7478 (mmt) cc_final: 0.6778 (mmt) REVERT: B 318 GLU cc_start: 0.6930 (tp30) cc_final: 0.6646 (tp30) REVERT: B 367 LYS cc_start: 0.5747 (tptp) cc_final: 0.5539 (tptp) REVERT: B 398 LYS cc_start: 0.7362 (mtpt) cc_final: 0.6963 (mtpp) REVERT: B 429 SER cc_start: 0.9186 (t) cc_final: 0.8902 (t) REVERT: C 169 TRP cc_start: 0.8913 (p-90) cc_final: 0.8551 (p-90) REVERT: C 177 ILE cc_start: 0.8739 (OUTLIER) cc_final: 0.8331 (mp) REVERT: C 237 MET cc_start: 0.7470 (mmt) cc_final: 0.6759 (mmt) REVERT: C 260 LYS cc_start: 0.7140 (pttt) cc_final: 0.6756 (pttp) REVERT: C 322 ARG cc_start: 0.6366 (mmp80) cc_final: 0.5997 (mmp80) REVERT: C 341 THR cc_start: 0.8288 (p) cc_final: 0.8088 (p) REVERT: C 367 LYS cc_start: 0.5682 (tptp) cc_final: 0.5459 (tptp) REVERT: C 410 LYS cc_start: 0.8091 (ttpt) cc_final: 0.7638 (tttm) REVERT: C 480 GLU cc_start: 0.8032 (tt0) cc_final: 0.7514 (tt0) REVERT: D 25 ILE cc_start: 0.7813 (mt) cc_final: 0.7524 (mp) REVERT: D 57 LYS cc_start: 0.8062 (mmtp) cc_final: 0.7789 (mmtm) REVERT: D 169 TRP cc_start: 0.8921 (p-90) cc_final: 0.8547 (p-90) REVERT: D 177 ILE cc_start: 0.8735 (OUTLIER) cc_final: 0.8342 (mp) REVERT: D 237 MET cc_start: 0.7413 (mmt) cc_final: 0.6638 (mmt) REVERT: D 322 ARG cc_start: 0.6299 (mmp80) cc_final: 0.5703 (mmp80) REVERT: D 367 LYS cc_start: 0.5653 (tptp) cc_final: 0.5428 (tptp) REVERT: D 429 SER cc_start: 0.9154 (OUTLIER) cc_final: 0.8867 (t) outliers start: 106 outliers final: 67 residues processed: 469 average time/residue: 0.1183 time to fit residues: 81.0149 Evaluate side-chains 466 residues out of total 1632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 394 time to evaluate : 0.341 ------------------------------------------------------------------------------- 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 279 LEU Chi-restraints excluded: chain A residue 299 GLN 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 494 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 167 ILE 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 248 THR Chi-restraints excluded: chain B residue 266 VAL Chi-restraints excluded: chain B residue 279 LEU Chi-restraints excluded: chain B residue 303 CYS Chi-restraints excluded: chain B residue 315 ILE Chi-restraints excluded: chain B residue 332 LEU Chi-restraints excluded: chain B residue 460 VAL Chi-restraints excluded: chain B residue 494 VAL Chi-restraints excluded: chain C residue 79 THR Chi-restraints excluded: chain C residue 114 LEU 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 167 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 222 VAL Chi-restraints excluded: chain C residue 248 THR Chi-restraints excluded: chain C residue 266 VAL Chi-restraints excluded: chain C residue 279 LEU Chi-restraints excluded: chain C residue 303 CYS Chi-restraints excluded: chain C residue 315 ILE Chi-restraints excluded: chain C residue 332 LEU 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 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 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 248 THR Chi-restraints excluded: chain D residue 279 LEU 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 429 SER Chi-restraints excluded: chain D residue 460 VAL Chi-restraints excluded: chain D residue 494 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 99 optimal weight: 0.9990 chunk 112 optimal weight: 2.9990 chunk 96 optimal weight: 1.9990 chunk 45 optimal weight: 0.0970 chunk 5 optimal weight: 0.9980 chunk 140 optimal weight: 1.9990 chunk 186 optimal weight: 0.6980 chunk 21 optimal weight: 0.9980 chunk 182 optimal weight: 0.6980 chunk 87 optimal weight: 7.9990 chunk 4 optimal weight: 1.9990 overall best weight: 0.6978 ------------------------------------------------------------------------------- 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 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 299 GLN ** A 406 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 72 GLN ** B 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 298 HIS ** 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 298 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4005 r_free = 0.4005 target = 0.192371 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3597 r_free = 0.3597 target = 0.154611 restraints weight = 17156.692| |-----------------------------------------------------------------------------| r_work (start): 0.3548 rms_B_bonded: 2.04 r_work: 0.3432 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work (final): 0.3432 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3440 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3440 r_free = 0.3440 target_work(ls_wunit_k1) = 0.141 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3440 r_free = 0.3440 target_work(ls_wunit_k1) = 0.141 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| r_final: 0.3440 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7475 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 0.046 15488 Z= 0.134 Angle : 0.572 5.505 20972 Z= 0.296 Chirality : 0.045 0.268 2324 Planarity : 0.004 0.033 2712 Dihedral : 5.905 58.387 2124 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 12.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.79 % Favored : 95.21 % Rotamer: Outliers : 5.15 % Allowed : 21.15 % Favored : 73.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.75 (0.20), residues: 1964 helix: 0.39 (0.19), residues: 832 sheet: -1.07 (0.25), residues: 400 loop : -1.02 (0.25), residues: 732 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 68 TYR 0.015 0.001 TYR B 119 PHE 0.023 0.002 PHE D 38 TRP 0.013 0.001 TRP B 136 HIS 0.006 0.001 HIS D 292 Details of bonding type rmsd covalent geometry : bond 0.00327 (15488) covalent geometry : angle 0.57153 (20972) hydrogen bonds : bond 0.03222 ( 674) hydrogen bonds : angle 4.72485 ( 1935) *********************** 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 478 residues out of total 1632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 395 time to evaluate : 0.496 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 57 LYS cc_start: 0.8288 (mmtp) cc_final: 0.7830 (tptm) REVERT: A 101 LEU cc_start: 0.7842 (mt) cc_final: 0.7491 (mp) REVERT: A 298 HIS cc_start: 0.7129 (t-90) cc_final: 0.6720 (t-90) REVERT: A 299 GLN cc_start: 0.7231 (OUTLIER) cc_final: 0.6722 (mt0) REVERT: A 318 GLU cc_start: 0.6554 (tp30) cc_final: 0.6291 (tp30) REVERT: A 347 ASP cc_start: 0.7078 (p0) cc_final: 0.6184 (m-30) REVERT: A 402 PHE cc_start: 0.7620 (OUTLIER) cc_final: 0.7125 (t80) REVERT: A 471 MET cc_start: 0.8760 (mtp) cc_final: 0.8353 (mtp) REVERT: B 22 LYS cc_start: 0.7284 (mttt) cc_final: 0.6902 (mppt) REVERT: B 53 GLU cc_start: 0.8116 (mt-10) cc_final: 0.7787 (mt-10) REVERT: B 237 MET cc_start: 0.7447 (mmt) cc_final: 0.6724 (mmt) REVERT: B 367 LYS cc_start: 0.5761 (tptp) cc_final: 0.5429 (tptp) REVERT: B 398 LYS cc_start: 0.7366 (mtpt) cc_final: 0.6985 (mtpp) REVERT: B 402 PHE cc_start: 0.7678 (OUTLIER) cc_final: 0.7260 (t80) REVERT: B 429 SER cc_start: 0.9159 (t) cc_final: 0.8867 (t) REVERT: C 22 LYS cc_start: 0.7220 (mttt) cc_final: 0.6881 (mppt) REVERT: C 169 TRP cc_start: 0.8933 (p-90) cc_final: 0.8640 (p-90) REVERT: C 177 ILE cc_start: 0.8710 (OUTLIER) cc_final: 0.8384 (mp) REVERT: C 237 MET cc_start: 0.7388 (mmt) cc_final: 0.6681 (mmt) REVERT: C 260 LYS cc_start: 0.6973 (pttt) cc_final: 0.6678 (pttp) REVERT: C 367 LYS cc_start: 0.5671 (tptp) cc_final: 0.5341 (tptp) REVERT: C 402 PHE cc_start: 0.7715 (OUTLIER) cc_final: 0.7231 (t80) REVERT: C 410 LYS cc_start: 0.8048 (ttpt) cc_final: 0.7636 (tttm) REVERT: C 480 GLU cc_start: 0.7996 (tt0) cc_final: 0.7562 (tt0) REVERT: D 169 TRP cc_start: 0.8916 (p-90) cc_final: 0.8631 (p-90) REVERT: D 177 ILE cc_start: 0.8708 (OUTLIER) cc_final: 0.8373 (mp) REVERT: D 237 MET cc_start: 0.7428 (mmt) cc_final: 0.6681 (mmt) REVERT: D 252 LYS cc_start: 0.6792 (mttt) cc_final: 0.6457 (ttmt) REVERT: D 322 ARG cc_start: 0.6429 (mmp80) cc_final: 0.6102 (mmp80) REVERT: D 402 PHE cc_start: 0.7583 (OUTLIER) cc_final: 0.7071 (t80) REVERT: D 429 SER cc_start: 0.9088 (OUTLIER) cc_final: 0.8805 (t) outliers start: 83 outliers final: 65 residues processed: 443 average time/residue: 0.1268 time to fit residues: 82.5238 Evaluate side-chains 461 residues out of total 1632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 388 time to evaluate : 0.504 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 THR Chi-restraints excluded: chain A residue 123 LEU Chi-restraints excluded: chain A residue 147 ILE Chi-restraints excluded: chain A residue 167 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 261 SER Chi-restraints excluded: chain A residue 279 LEU Chi-restraints excluded: chain A residue 299 GLN 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 109 MET Chi-restraints excluded: chain B residue 123 LEU Chi-restraints excluded: chain B residue 147 ILE Chi-restraints excluded: chain B residue 167 ILE 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 205 VAL 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 279 LEU Chi-restraints excluded: chain B residue 303 CYS Chi-restraints excluded: chain B residue 315 ILE 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 494 VAL Chi-restraints excluded: chain C residue 79 THR Chi-restraints excluded: chain C residue 114 LEU Chi-restraints excluded: chain C residue 123 LEU Chi-restraints excluded: chain C residue 144 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 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 248 THR Chi-restraints excluded: chain C residue 266 VAL Chi-restraints excluded: chain C residue 279 LEU Chi-restraints excluded: chain C residue 315 ILE Chi-restraints excluded: chain C residue 332 LEU Chi-restraints excluded: chain C residue 402 PHE 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 167 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 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 429 SER 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 3 optimal weight: 0.3980 chunk 177 optimal weight: 2.9990 chunk 179 optimal weight: 8.9990 chunk 162 optimal weight: 4.9990 chunk 18 optimal weight: 2.9990 chunk 66 optimal weight: 0.9980 chunk 98 optimal weight: 10.0000 chunk 138 optimal weight: 5.9990 chunk 41 optimal weight: 4.9990 chunk 78 optimal weight: 1.9990 chunk 73 optimal weight: 3.9990 overall best weight: 1.8786 ------------------------------------------------------------------------------- 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 ** A 406 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 72 GLN ** B 298 HIS ** 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 298 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3940 r_free = 0.3940 target = 0.185990 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.147411 restraints weight = 17057.124| |-----------------------------------------------------------------------------| r_work (start): 0.3507 rms_B_bonded: 2.05 r_work: 0.3390 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work (final): 0.3390 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3377 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3377 r_free = 0.3377 target_work(ls_wunit_k1) = 0.135 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3377 r_free = 0.3377 target_work(ls_wunit_k1) = 0.135 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| r_final: 0.3377 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7555 moved from start: 0.5654 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.067 15488 Z= 0.247 Angle : 0.674 7.380 20972 Z= 0.348 Chirality : 0.049 0.286 2324 Planarity : 0.005 0.076 2712 Dihedral : 6.398 57.561 2122 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 12.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.06 % Favored : 93.94 % Rotamer: Outliers : 6.51 % Allowed : 21.53 % Favored : 71.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.92 (0.20), residues: 1964 helix: 0.14 (0.18), residues: 832 sheet: -1.08 (0.26), residues: 400 loop : -1.03 (0.25), residues: 732 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 321 TYR 0.016 0.002 TYR A 330 PHE 0.032 0.002 PHE B 38 TRP 0.021 0.002 TRP B 169 HIS 0.010 0.002 HIS B 292 Details of bonding type rmsd covalent geometry : bond 0.00595 (15488) covalent geometry : angle 0.67359 (20972) hydrogen bonds : bond 0.04002 ( 674) hydrogen bonds : angle 4.89844 ( 1935) *********************** 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 508 residues out of total 1632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 105 poor density : 403 time to evaluate : 0.517 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: 0.8159 (mmtp) cc_final: 0.7701 (tptm) REVERT: A 298 HIS cc_start: 0.7259 (t-90) cc_final: 0.6827 (t-90) REVERT: A 299 GLN cc_start: 0.7467 (OUTLIER) cc_final: 0.7027 (mt0) REVERT: A 316 TYR cc_start: 0.7160 (t80) cc_final: 0.6284 (t80) REVERT: A 318 GLU cc_start: 0.6722 (tp30) cc_final: 0.5513 (tp30) REVERT: A 402 PHE cc_start: 0.7806 (OUTLIER) cc_final: 0.7306 (t80) REVERT: A 471 MET cc_start: 0.8788 (mtp) cc_final: 0.8357 (mtp) REVERT: B 22 LYS cc_start: 0.7461 (mttt) cc_final: 0.7017 (mppt) REVERT: B 53 GLU cc_start: 0.8277 (mt-10) cc_final: 0.8017 (mt-10) REVERT: B 318 GLU cc_start: 0.7102 (tp30) cc_final: 0.6534 (tp30) REVERT: B 322 ARG cc_start: 0.6486 (mmp80) cc_final: 0.6206 (mmp80) REVERT: B 398 LYS cc_start: 0.7456 (mtpt) cc_final: 0.7054 (mtpp) REVERT: B 402 PHE cc_start: 0.7739 (OUTLIER) cc_final: 0.7340 (t80) REVERT: B 429 SER cc_start: 0.9211 (t) cc_final: 0.8923 (t) REVERT: C 22 LYS cc_start: 0.7438 (mttt) cc_final: 0.7024 (mppt) REVERT: C 169 TRP cc_start: 0.8903 (p-90) cc_final: 0.8496 (p-90) REVERT: C 260 LYS cc_start: 0.6970 (pttt) cc_final: 0.6711 (pttp) REVERT: C 322 ARG cc_start: 0.5871 (mmp80) cc_final: 0.5444 (mmp80) REVERT: C 399 GLU cc_start: 0.6131 (mt-10) cc_final: 0.5836 (mt-10) REVERT: C 402 PHE cc_start: 0.7761 (OUTLIER) cc_final: 0.7334 (t80) REVERT: C 480 GLU cc_start: 0.8010 (tt0) cc_final: 0.7503 (tt0) REVERT: D 53 GLU cc_start: 0.8301 (mt-10) cc_final: 0.8096 (mt-10) REVERT: D 169 TRP cc_start: 0.8910 (p-90) cc_final: 0.8491 (p-90) REVERT: D 237 MET cc_start: 0.7400 (mmt) cc_final: 0.6448 (mmt) REVERT: D 273 LYS cc_start: 0.8361 (tptm) cc_final: 0.8079 (tptt) REVERT: D 318 GLU cc_start: 0.7178 (tp30) cc_final: 0.6317 (tp30) REVERT: D 322 ARG cc_start: 0.6666 (mmp80) cc_final: 0.6264 (mmp80) REVERT: D 367 LYS cc_start: 0.5748 (tptp) cc_final: 0.5529 (tptp) REVERT: D 402 PHE cc_start: 0.7707 (OUTLIER) cc_final: 0.7329 (t80) REVERT: D 429 SER cc_start: 0.9181 (t) cc_final: 0.8882 (t) outliers start: 105 outliers final: 94 residues processed: 463 average time/residue: 0.1299 time to fit residues: 88.0407 Evaluate side-chains 485 residues out of total 1632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 99 poor density : 386 time to evaluate : 0.544 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 THR Chi-restraints excluded: chain A residue 123 LEU Chi-restraints excluded: chain A residue 144 THR Chi-restraints excluded: chain A residue 147 ILE Chi-restraints excluded: chain A residue 167 ILE Chi-restraints excluded: chain A residue 180 ILE Chi-restraints excluded: chain A residue 185 SER Chi-restraints excluded: chain A residue 196 GLU Chi-restraints excluded: chain A residue 221 ILE 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 261 SER Chi-restraints excluded: chain A residue 279 LEU Chi-restraints excluded: chain A residue 299 GLN Chi-restraints excluded: chain A residue 303 CYS Chi-restraints excluded: chain A residue 402 PHE Chi-restraints excluded: chain A residue 424 THR Chi-restraints excluded: chain A residue 442 THR Chi-restraints excluded: chain A residue 445 SER Chi-restraints excluded: chain A residue 460 VAL Chi-restraints excluded: chain A residue 492 VAL Chi-restraints excluded: chain A residue 494 VAL Chi-restraints excluded: chain B residue 79 THR Chi-restraints excluded: chain B residue 109 MET 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 167 ILE 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 196 GLU Chi-restraints excluded: chain B residue 205 VAL Chi-restraints excluded: chain B residue 219 VAL 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 279 LEU Chi-restraints excluded: chain B residue 303 CYS Chi-restraints excluded: chain B residue 315 ILE Chi-restraints excluded: chain B residue 332 LEU Chi-restraints excluded: chain B residue 402 PHE Chi-restraints excluded: chain B residue 415 ASP Chi-restraints excluded: chain B residue 437 ILE Chi-restraints excluded: chain B residue 451 THR Chi-restraints excluded: chain B residue 460 VAL Chi-restraints excluded: chain B residue 494 VAL Chi-restraints excluded: chain C residue 79 THR Chi-restraints excluded: chain C residue 114 LEU Chi-restraints excluded: chain C residue 123 LEU 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 167 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 221 ILE 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 279 LEU Chi-restraints excluded: chain C residue 303 CYS Chi-restraints excluded: chain C residue 315 ILE Chi-restraints excluded: chain C residue 332 LEU Chi-restraints excluded: chain C residue 402 PHE Chi-restraints excluded: chain C residue 437 ILE 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 144 THR 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 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 248 THR 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 425 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 26 optimal weight: 0.5980 chunk 49 optimal weight: 10.0000 chunk 98 optimal weight: 10.0000 chunk 134 optimal weight: 0.8980 chunk 141 optimal weight: 0.5980 chunk 32 optimal weight: 0.9990 chunk 36 optimal weight: 5.9990 chunk 172 optimal weight: 3.9990 chunk 33 optimal weight: 0.7980 chunk 190 optimal weight: 1.9990 chunk 84 optimal weight: 1.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- 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 293 HIS A 299 GLN B 72 GLN ** B 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 298 HIS ** 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 298 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 299 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 72 GLN ** D 298 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3993 r_free = 0.3993 target = 0.191289 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3587 r_free = 0.3587 target = 0.153464 restraints weight = 17150.718| |-----------------------------------------------------------------------------| r_work (start): 0.3550 rms_B_bonded: 2.04 r_work: 0.3430 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work (final): 0.3430 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3423 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3423 r_free = 0.3423 target_work(ls_wunit_k1) = 0.139 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3423 r_free = 0.3423 target_work(ls_wunit_k1) = 0.139 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| r_final: 0.3423 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7498 moved from start: 0.5921 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 15488 Z= 0.142 Angle : 0.591 8.834 20972 Z= 0.303 Chirality : 0.046 0.284 2324 Planarity : 0.004 0.061 2712 Dihedral : 5.951 59.146 2122 Min Nonbonded Distance : 2.603 Molprobity Statistics. All-atom Clashscore : 12.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.09 % Favored : 94.91 % Rotamer: Outliers : 5.46 % Allowed : 23.57 % Favored : 70.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.71 (0.20), residues: 1964 helix: 0.34 (0.19), residues: 832 sheet: -0.93 (0.26), residues: 400 loop : -0.98 (0.25), residues: 732 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 321 TYR 0.015 0.001 TYR A 330 PHE 0.026 0.002 PHE B 38 TRP 0.017 0.001 TRP B 169 HIS 0.005 0.001 HIS D 292 Details of bonding type rmsd covalent geometry : bond 0.00346 (15488) covalent geometry : angle 0.59060 (20972) hydrogen bonds : bond 0.03297 ( 674) hydrogen bonds : angle 4.73303 ( 1935) *********************** 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 484 residues out of total 1632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 396 time to evaluate : 0.596 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: 0.8218 (mt-10) cc_final: 0.7854 (mt-10) REVERT: A 57 LYS cc_start: 0.8156 (mmtp) cc_final: 0.7730 (tptm) REVERT: A 101 LEU cc_start: 0.7764 (mt) cc_final: 0.7422 (mp) REVERT: A 298 HIS cc_start: 0.7013 (t-90) cc_final: 0.6049 (t-90) REVERT: A 299 GLN cc_start: 0.7277 (OUTLIER) cc_final: 0.6888 (mt0) REVERT: A 316 TYR cc_start: 0.6986 (t80) cc_final: 0.6282 (t80) REVERT: A 402 PHE cc_start: 0.7697 (OUTLIER) cc_final: 0.7237 (t80) REVERT: A 412 LYS cc_start: 0.7592 (tptp) cc_final: 0.7379 (tptp) REVERT: A 459 VAL cc_start: 0.7248 (t) cc_final: 0.7045 (m) REVERT: A 471 MET cc_start: 0.8739 (mtp) cc_final: 0.8271 (mtp) REVERT: B 22 LYS cc_start: 0.7302 (mttt) cc_final: 0.6878 (mppt) REVERT: B 53 GLU cc_start: 0.8194 (mt-10) cc_final: 0.7900 (mt-10) REVERT: B 237 MET cc_start: 0.7487 (mmt) cc_final: 0.6710 (mmp) REVERT: B 318 GLU cc_start: 0.6952 (tp30) cc_final: 0.6296 (tp30) REVERT: B 322 ARG cc_start: 0.6549 (mmp80) cc_final: 0.6326 (mmp80) REVERT: B 367 LYS cc_start: 0.5771 (tptp) cc_final: 0.5566 (tptp) REVERT: B 398 LYS cc_start: 0.7426 (mtpt) cc_final: 0.7054 (mtpp) REVERT: B 402 PHE cc_start: 0.7661 (OUTLIER) cc_final: 0.7268 (t80) REVERT: C 22 LYS cc_start: 0.7281 (mttt) cc_final: 0.6875 (mppt) REVERT: C 53 GLU cc_start: 0.8205 (mt-10) cc_final: 0.7812 (mt-10) REVERT: C 237 MET cc_start: 0.7448 (mmt) cc_final: 0.6653 (mmp) REVERT: C 260 LYS cc_start: 0.6911 (pttt) cc_final: 0.6680 (pttp) REVERT: C 318 GLU cc_start: 0.7200 (tp30) cc_final: 0.6759 (tp30) REVERT: C 322 ARG cc_start: 0.6025 (mmp80) cc_final: 0.5538 (mmp80) REVERT: C 402 PHE cc_start: 0.7678 (OUTLIER) cc_final: 0.7268 (t80) REVERT: C 415 ASP cc_start: 0.8350 (m-30) cc_final: 0.8036 (m-30) REVERT: C 480 GLU cc_start: 0.7953 (tt0) cc_final: 0.7509 (tt0) REVERT: D 22 LYS cc_start: 0.7293 (mttt) cc_final: 0.6915 (mppt) REVERT: D 53 GLU cc_start: 0.8197 (mt-10) cc_final: 0.7956 (mt-10) REVERT: D 237 MET cc_start: 0.7484 (mmt) cc_final: 0.6702 (mmp) REVERT: D 322 ARG cc_start: 0.6715 (mmp80) cc_final: 0.6344 (mmp80) REVERT: D 367 LYS cc_start: 0.5719 (tptp) cc_final: 0.5491 (tptp) REVERT: D 402 PHE cc_start: 0.7619 (OUTLIER) cc_final: 0.7199 (t80) outliers start: 88 outliers final: 74 residues processed: 446 average time/residue: 0.1228 time to fit residues: 80.5644 Evaluate side-chains 466 residues out of total 1632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 387 time to evaluate : 0.593 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 THR Chi-restraints excluded: chain A residue 123 LEU 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 299 GLN Chi-restraints excluded: chain A residue 303 CYS Chi-restraints excluded: chain A residue 402 PHE Chi-restraints excluded: chain A residue 445 SER Chi-restraints excluded: chain A residue 492 VAL Chi-restraints excluded: chain B residue 79 THR Chi-restraints excluded: chain B residue 109 MET 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 167 ILE 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 205 VAL Chi-restraints excluded: chain B residue 219 VAL 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 279 LEU Chi-restraints excluded: chain B residue 303 CYS Chi-restraints excluded: chain B residue 315 ILE Chi-restraints excluded: chain B residue 332 LEU Chi-restraints excluded: chain B residue 402 PHE Chi-restraints excluded: chain B residue 415 ASP Chi-restraints excluded: chain B residue 451 THR Chi-restraints excluded: chain B residue 460 VAL Chi-restraints excluded: chain B residue 494 VAL Chi-restraints excluded: chain C residue 79 THR Chi-restraints excluded: chain C residue 114 LEU Chi-restraints excluded: chain C residue 123 LEU Chi-restraints excluded: chain C residue 144 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 180 ILE Chi-restraints excluded: chain C residue 185 SER Chi-restraints excluded: chain C residue 205 VAL Chi-restraints excluded: chain C residue 219 VAL 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 279 LEU Chi-restraints excluded: chain C residue 303 CYS Chi-restraints excluded: chain C residue 315 ILE 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 147 ILE Chi-restraints excluded: chain D residue 167 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 279 LEU 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 460 VAL Chi-restraints excluded: chain D residue 492 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 173 optimal weight: 0.0170 chunk 51 optimal weight: 7.9990 chunk 165 optimal weight: 0.9980 chunk 109 optimal weight: 1.9990 chunk 132 optimal weight: 2.9990 chunk 49 optimal weight: 10.0000 chunk 124 optimal weight: 2.9990 chunk 72 optimal weight: 0.0970 chunk 29 optimal weight: 4.9990 chunk 142 optimal weight: 0.9990 chunk 153 optimal weight: 0.0070 overall best weight: 0.4236 ------------------------------------------------------------------------------- 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 ** A 406 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 72 GLN ** B 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 298 HIS ** 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 298 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 299 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 72 GLN ** D 298 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4028 r_free = 0.4028 target = 0.194544 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3622 r_free = 0.3622 target = 0.156392 restraints weight = 17020.187| |-----------------------------------------------------------------------------| r_work (start): 0.3586 rms_B_bonded: 2.06 r_work: 0.3468 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work (final): 0.3468 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3466 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3466 r_free = 0.3466 target_work(ls_wunit_k1) = 0.143 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3465 r_free = 0.3465 target_work(ls_wunit_k1) = 0.143 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| r_final: 0.3465 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7454 moved from start: 0.6176 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 15488 Z= 0.117 Angle : 0.574 8.869 20972 Z= 0.296 Chirality : 0.045 0.249 2324 Planarity : 0.004 0.052 2712 Dihedral : 5.518 55.633 2120 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 11.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.58 % Favored : 95.42 % Rotamer: Outliers : 4.34 % Allowed : 25.12 % Favored : 70.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.55 (0.20), residues: 1964 helix: 0.41 (0.19), residues: 836 sheet: -0.73 (0.27), residues: 400 loop : -0.88 (0.25), residues: 728 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 322 TYR 0.014 0.001 TYR B 119 PHE 0.024 0.001 PHE B 38 TRP 0.016 0.001 TRP D 169 HIS 0.004 0.001 HIS A 30 Details of bonding type rmsd covalent geometry : bond 0.00280 (15488) covalent geometry : angle 0.57385 (20972) hydrogen bonds : bond 0.02976 ( 674) hydrogen bonds : angle 4.70990 ( 1935) *********************** 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 475 residues out of total 1632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 405 time to evaluate : 0.577 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 53 GLU cc_start: 0.8203 (mt-10) cc_final: 0.7832 (mt-10) REVERT: A 57 LYS cc_start: 0.8157 (mmtp) cc_final: 0.7848 (tppt) REVERT: A 101 LEU cc_start: 0.7767 (mt) cc_final: 0.7425 (mp) REVERT: A 260 LYS cc_start: 0.6969 (pttt) cc_final: 0.6509 (pttm) REVERT: A 298 HIS cc_start: 0.6864 (t-90) cc_final: 0.6137 (t-90) REVERT: A 299 GLN cc_start: 0.7636 (OUTLIER) cc_final: 0.7431 (mt0) REVERT: A 318 GLU cc_start: 0.6795 (tp30) cc_final: 0.6291 (tp30) REVERT: A 402 PHE cc_start: 0.7657 (OUTLIER) cc_final: 0.7159 (t80) REVERT: A 459 VAL cc_start: 0.7306 (t) cc_final: 0.7097 (m) REVERT: A 471 MET cc_start: 0.8708 (mtp) cc_final: 0.8236 (mtp) REVERT: B 22 LYS cc_start: 0.7272 (mttt) cc_final: 0.6803 (mppt) REVERT: B 53 GLU cc_start: 0.8197 (mt-10) cc_final: 0.7906 (mt-10) REVERT: B 237 MET cc_start: 0.7399 (mmt) cc_final: 0.6698 (mmp) REVERT: B 318 GLU cc_start: 0.6966 (tp30) cc_final: 0.6278 (tp30) REVERT: B 367 LYS cc_start: 0.5798 (tptp) cc_final: 0.5164 (tptp) REVERT: B 369 GLU cc_start: 0.7156 (mm-30) cc_final: 0.6911 (mm-30) REVERT: B 398 LYS cc_start: 0.7419 (mtpt) cc_final: 0.7029 (mtpp) REVERT: B 402 PHE cc_start: 0.7652 (OUTLIER) cc_final: 0.7239 (t80) REVERT: C 22 LYS cc_start: 0.7187 (mttt) cc_final: 0.6836 (mppt) REVERT: C 53 GLU cc_start: 0.8146 (mt-10) cc_final: 0.7919 (mt-10) REVERT: C 237 MET cc_start: 0.7379 (mmt) cc_final: 0.6640 (mmp) REVERT: C 260 LYS cc_start: 0.6888 (pttt) cc_final: 0.6623 (pttp) REVERT: C 322 ARG cc_start: 0.6090 (mmp80) cc_final: 0.5882 (mmp80) REVERT: C 402 PHE cc_start: 0.7659 (OUTLIER) cc_final: 0.7201 (t80) REVERT: C 415 ASP cc_start: 0.8359 (m-30) cc_final: 0.8067 (m-30) REVERT: C 480 GLU cc_start: 0.7953 (tt0) cc_final: 0.7524 (tt0) REVERT: D 22 LYS cc_start: 0.7212 (mttt) cc_final: 0.6840 (mppt) REVERT: D 53 GLU cc_start: 0.8198 (mt-10) cc_final: 0.7919 (mt-10) REVERT: D 237 MET cc_start: 0.7442 (mmt) cc_final: 0.6727 (mmp) REVERT: D 318 GLU cc_start: 0.7180 (tp30) cc_final: 0.6328 (tp30) REVERT: D 322 ARG cc_start: 0.6749 (mmp80) cc_final: 0.6345 (mmp80) REVERT: D 367 LYS cc_start: 0.5750 (tptp) cc_final: 0.5522 (tptp) REVERT: D 402 PHE cc_start: 0.7632 (OUTLIER) cc_final: 0.7181 (t80) outliers start: 70 outliers final: 51 residues processed: 444 average time/residue: 0.1355 time to fit residues: 87.9613 Evaluate side-chains 449 residues out of total 1632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 393 time to evaluate : 0.562 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 THR Chi-restraints excluded: chain A residue 123 LEU 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 279 LEU Chi-restraints excluded: chain A residue 299 GLN Chi-restraints excluded: chain A residue 303 CYS Chi-restraints excluded: chain A residue 402 PHE Chi-restraints excluded: chain A residue 445 SER Chi-restraints excluded: chain A residue 492 VAL Chi-restraints excluded: chain B residue 79 THR Chi-restraints excluded: chain B residue 109 MET Chi-restraints excluded: chain B residue 123 LEU Chi-restraints excluded: chain B residue 129 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 205 VAL Chi-restraints excluded: chain B residue 219 VAL 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 303 CYS Chi-restraints excluded: chain B residue 332 LEU Chi-restraints excluded: chain B residue 402 PHE Chi-restraints excluded: chain B residue 494 VAL Chi-restraints excluded: chain C residue 79 THR Chi-restraints excluded: chain C residue 123 LEU Chi-restraints excluded: chain C residue 144 THR Chi-restraints excluded: chain C residue 180 ILE Chi-restraints excluded: chain C residue 185 SER Chi-restraints excluded: chain C residue 205 VAL Chi-restraints excluded: chain C residue 219 VAL Chi-restraints excluded: chain C residue 222 VAL Chi-restraints excluded: chain C residue 239 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 402 PHE 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 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 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 460 VAL Chi-restraints excluded: chain D residue 492 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 118 optimal weight: 2.9990 chunk 146 optimal weight: 0.9980 chunk 95 optimal weight: 3.9990 chunk 152 optimal weight: 0.9980 chunk 61 optimal weight: 1.9990 chunk 168 optimal weight: 0.9990 chunk 55 optimal weight: 0.5980 chunk 116 optimal weight: 0.9980 chunk 135 optimal weight: 0.0770 chunk 138 optimal weight: 3.9990 chunk 107 optimal weight: 5.9990 overall best weight: 0.7338 ------------------------------------------------------------------------------- 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 B 72 GLN ** B 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 298 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 299 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 72 GLN ** C 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 298 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: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4020 r_free = 0.4020 target = 0.193527 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3608 r_free = 0.3608 target = 0.155132 restraints weight = 17132.402| |-----------------------------------------------------------------------------| r_work (start): 0.3603 rms_B_bonded: 2.07 r_work: 0.3485 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work (final): 0.3485 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3478 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3478 r_free = 0.3478 target_work(ls_wunit_k1) = 0.143 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3478 r_free = 0.3478 target_work(ls_wunit_k1) = 0.143 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| r_final: 0.3478 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7469 moved from start: 0.6231 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 15488 Z= 0.141 Angle : 0.627 11.528 20972 Z= 0.319 Chirality : 0.046 0.242 2324 Planarity : 0.004 0.063 2712 Dihedral : 5.091 42.824 2112 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 12.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.99 % Favored : 95.01 % Rotamer: Outliers : 3.60 % Allowed : 26.36 % Favored : 70.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.56 (0.20), residues: 1964 helix: 0.33 (0.18), residues: 836 sheet: -0.66 (0.27), residues: 400 loop : -0.84 (0.25), residues: 728 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG A 322 TYR 0.014 0.001 TYR A 330 PHE 0.024 0.002 PHE B 38 TRP 0.014 0.001 TRP D 169 HIS 0.005 0.001 HIS B 292 Details of bonding type rmsd covalent geometry : bond 0.00348 (15488) covalent geometry : angle 0.62674 (20972) hydrogen bonds : bond 0.03191 ( 674) hydrogen bonds : angle 4.74705 ( 1935) ********************** 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 445 residues out of total 1632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 387 time to evaluate : 0.625 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 53 GLU cc_start: 0.8129 (mt-10) cc_final: 0.7714 (mt-10) REVERT: A 57 LYS cc_start: 0.8183 (mmtp) cc_final: 0.7869 (tppt) REVERT: A 101 LEU cc_start: 0.7775 (mt) cc_final: 0.7424 (mp) REVERT: A 260 LYS cc_start: 0.7046 (pttt) cc_final: 0.6592 (pttm) REVERT: A 298 HIS cc_start: 0.6871 (t-90) cc_final: 0.6329 (t-90) REVERT: A 299 GLN cc_start: 0.7230 (OUTLIER) cc_final: 0.6842 (mt0) REVERT: A 369 GLU cc_start: 0.7299 (mm-30) cc_final: 0.6624 (mm-30) REVERT: A 395 ARG cc_start: 0.7597 (mmm-85) cc_final: 0.7242 (mmm-85) REVERT: A 402 PHE cc_start: 0.7676 (OUTLIER) cc_final: 0.7190 (t80) REVERT: A 459 VAL cc_start: 0.7418 (t) cc_final: 0.7201 (m) REVERT: A 471 MET cc_start: 0.8725 (mtp) cc_final: 0.8249 (mtp) REVERT: B 22 LYS cc_start: 0.7247 (mttt) cc_final: 0.6811 (mppt) REVERT: B 53 GLU cc_start: 0.8132 (mt-10) cc_final: 0.7843 (mt-10) REVERT: B 169 TRP cc_start: 0.8732 (p-90) cc_final: 0.7633 (p-90) REVERT: B 237 MET cc_start: 0.7480 (mmt) cc_final: 0.6732 (mmp) REVERT: B 318 GLU cc_start: 0.6988 (tp30) cc_final: 0.6667 (tp30) REVERT: B 367 LYS cc_start: 0.5830 (tptp) cc_final: 0.5613 (tptp) REVERT: B 398 LYS cc_start: 0.7395 (mtpt) cc_final: 0.7016 (mtpp) REVERT: B 402 PHE cc_start: 0.7672 (OUTLIER) cc_final: 0.7181 (t80) REVERT: C 22 LYS cc_start: 0.7091 (mttt) cc_final: 0.6768 (mppt) REVERT: C 177 ILE cc_start: 0.8846 (OUTLIER) cc_final: 0.8406 (mp) REVERT: C 237 MET cc_start: 0.7399 (mmt) cc_final: 0.6649 (mmp) REVERT: C 260 LYS cc_start: 0.6884 (pttt) cc_final: 0.6625 (pttp) REVERT: C 318 GLU cc_start: 0.7241 (tp30) cc_final: 0.6718 (tp30) REVERT: C 322 ARG cc_start: 0.6165 (mmp80) cc_final: 0.5690 (mmp80) REVERT: C 402 PHE cc_start: 0.7743 (OUTLIER) cc_final: 0.7285 (t80) REVERT: C 410 LYS cc_start: 0.8011 (ttpt) cc_final: 0.7684 (tttm) REVERT: C 415 ASP cc_start: 0.8374 (m-30) cc_final: 0.8081 (m-30) REVERT: C 480 GLU cc_start: 0.7952 (tt0) cc_final: 0.7551 (tt0) REVERT: D 22 LYS cc_start: 0.7207 (mttt) cc_final: 0.6843 (mppt) REVERT: D 53 GLU cc_start: 0.8175 (mt-10) cc_final: 0.7938 (mt-10) REVERT: D 57 LYS cc_start: 0.7801 (mmmt) cc_final: 0.7592 (mmmt) REVERT: D 169 TRP cc_start: 0.8726 (p-90) cc_final: 0.8300 (p-90) REVERT: D 237 MET cc_start: 0.7651 (mmt) cc_final: 0.6926 (mmp) REVERT: D 318 GLU cc_start: 0.7202 (tp30) cc_final: 0.6318 (tp30) REVERT: D 322 ARG cc_start: 0.6769 (mmp80) cc_final: 0.6365 (mmp80) REVERT: D 367 LYS cc_start: 0.5778 (tptp) cc_final: 0.5540 (tptp) REVERT: D 402 PHE cc_start: 0.7683 (OUTLIER) cc_final: 0.7237 (t80) outliers start: 58 outliers final: 50 residues processed: 423 average time/residue: 0.1367 time to fit residues: 84.3128 Evaluate side-chains 443 residues out of total 1632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 387 time to evaluate : 0.611 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 THR Chi-restraints excluded: chain A residue 123 LEU 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 279 LEU Chi-restraints excluded: chain A residue 299 GLN Chi-restraints excluded: chain A residue 303 CYS Chi-restraints excluded: chain A residue 402 PHE Chi-restraints excluded: chain A residue 492 VAL Chi-restraints excluded: chain B residue 79 THR Chi-restraints excluded: chain B residue 123 LEU Chi-restraints excluded: chain B residue 129 THR Chi-restraints excluded: chain B residue 177 ILE Chi-restraints excluded: chain B residue 185 SER Chi-restraints excluded: chain B residue 205 VAL Chi-restraints excluded: chain B residue 219 VAL 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 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 494 VAL Chi-restraints excluded: chain C residue 79 THR Chi-restraints excluded: chain C residue 123 LEU Chi-restraints excluded: chain C residue 144 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 205 VAL Chi-restraints excluded: chain C residue 219 VAL 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 123 LEU 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 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 460 VAL Chi-restraints excluded: chain D residue 492 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 167 optimal weight: 0.5980 chunk 87 optimal weight: 0.0030 chunk 80 optimal weight: 0.7980 chunk 172 optimal weight: 5.9990 chunk 8 optimal weight: 2.9990 chunk 5 optimal weight: 3.9990 chunk 34 optimal weight: 1.9990 chunk 142 optimal weight: 2.9990 chunk 72 optimal weight: 1.9990 chunk 50 optimal weight: 0.9990 chunk 119 optimal weight: 0.6980 overall best weight: 0.6192 ------------------------------------------------------------------------------- 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 B 72 GLN ** B 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 298 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 299 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 72 GLN ** C 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 298 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: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4021 r_free = 0.4021 target = 0.195093 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3605 r_free = 0.3605 target = 0.155068 restraints weight = 16855.231| |-----------------------------------------------------------------------------| r_work (start): 0.3565 rms_B_bonded: 2.06 r_work: 0.3445 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work (final): 0.3445 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3422 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3422 r_free = 0.3422 target_work(ls_wunit_k1) = 0.139 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3422 r_free = 0.3422 target_work(ls_wunit_k1) = 0.139 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| r_final: 0.3422 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7458 moved from start: 0.6327 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= 0.132 Angle : 0.617 11.184 20972 Z= 0.314 Chirality : 0.045 0.227 2324 Planarity : 0.004 0.053 2712 Dihedral : 5.035 40.117 2112 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 12.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.79 % Favored : 95.21 % Rotamer: Outliers : 3.72 % Allowed : 26.24 % Favored : 70.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.50 (0.20), residues: 1964 helix: 0.35 (0.18), residues: 836 sheet: -0.60 (0.27), residues: 400 loop : -0.79 (0.25), residues: 728 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 395 TYR 0.015 0.001 TYR B 119 PHE 0.024 0.002 PHE B 38 TRP 0.012 0.001 TRP B 169 HIS 0.004 0.001 HIS B 292 Details of bonding type rmsd covalent geometry : bond 0.00325 (15488) covalent geometry : angle 0.61684 (20972) hydrogen bonds : bond 0.03078 ( 674) hydrogen bonds : angle 4.70770 ( 1935) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3346.84 seconds wall clock time: 58 minutes 33.93 seconds (3513.93 seconds total)