Starting phenix.real_space_refine on Fri Jun 13 15:17:40 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8dno_27575/06_2025/8dno_27575.cif Found real_map, /net/cci-nas-00/data/ceres_data/8dno_27575/06_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8dno_27575/06_2025/8dno_27575.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8dno_27575/06_2025/8dno_27575.map" model { file = "/net/cci-nas-00/data/ceres_data/8dno_27575/06_2025/8dno_27575.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8dno_27575/06_2025/8dno_27575.cif" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.062 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 76 5.16 5 C 9680 2.51 5 N 2564 2.21 5 O 2840 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 15160 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 3790 Number of conformers: 1 Conformer: "" Number of residues, atoms: 493, 3790 Classifications: {'peptide': 493} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 23, 'TRANS': 469} Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "B" Number of atoms: 3790 Number of conformers: 1 Conformer: "" Number of residues, atoms: 493, 3790 Classifications: {'peptide': 493} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 23, 'TRANS': 469} Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "C" Number of atoms: 3790 Number of conformers: 1 Conformer: "" Number of residues, atoms: 493, 3790 Classifications: {'peptide': 493} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 23, 'TRANS': 469} Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "D" Number of atoms: 3790 Number of conformers: 1 Conformer: "" Number of residues, atoms: 493, 3790 Classifications: {'peptide': 493} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 23, 'TRANS': 469} Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 7 Residues with excluded nonbonded symmetry interactions: 8 residue: pdb=" N TYR A 90 " occ=0.50 ... (10 atoms not shown) pdb=" OH TYR A 90 " occ=0.50 residue: pdb=" N CYS A 370 " occ=0.50 ... (4 atoms not shown) pdb=" SG CYS A 370 " occ=0.50 residue: pdb=" N TYR B 90 " occ=0.50 ... (10 atoms not shown) pdb=" OH TYR B 90 " occ=0.50 residue: pdb=" N CYS B 370 " occ=0.50 ... (4 atoms not shown) pdb=" SG CYS B 370 " occ=0.50 residue: pdb=" N TYR C 90 " occ=0.50 ... (10 atoms not shown) pdb=" OH TYR C 90 " occ=0.50 residue: pdb=" N CYS C 370 " occ=0.50 ... (4 atoms not shown) pdb=" SG CYS C 370 " occ=0.50 residue: pdb=" N TYR D 90 " occ=0.50 ... (10 atoms not shown) pdb=" OH TYR D 90 " occ=0.50 residue: pdb=" N CYS D 370 " occ=0.50 ... (4 atoms not shown) pdb=" SG CYS D 370 " occ=0.50 Time building chain proxies: 9.01, per 1000 atoms: 0.59 Number of scatterers: 15160 At special positions: 0 Unit cell: (104.86, 99.51, 99.51, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 76 16.00 O 2840 8.00 N 2564 7.00 C 9680 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.93 Conformation dependent library (CDL) restraints added in 2.0 seconds 3928 Ramachandran restraints generated. 1964 Oldfield, 0 Emsley, 1964 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3568 Finding SS restraints... Secondary structure from input PDB file: 76 helices and 12 sheets defined 44.6% alpha, 11.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.70 Creating SS restraints... Processing helix chain 'A' and resid 56 through 71 Processing helix chain 'A' and resid 75 through 80 removed outlier: 3.529A pdb=" N THR A 79 " --> pdb=" O SER A 75 " (cutoff:3.500A) Processing helix chain 'A' and resid 81 through 112 removed outlier: 5.264A pdb=" N LEU A 101 " --> pdb=" O GLU A 97 " (cutoff:3.500A) removed outlier: 6.307A pdb=" N LEU A 102 " --> pdb=" O ARG A 98 " (cutoff:3.500A) Processing helix chain 'A' and resid 114 through 120 Processing helix chain 'A' and resid 121 through 135 Processing helix chain 'A' and resid 136 through 140 removed outlier: 3.649A pdb=" N LYS A 139 " --> pdb=" O TRP A 136 " (cutoff:3.500A) removed outlier: 4.157A pdb=" N ILE A 140 " --> pdb=" O ALA A 137 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 136 through 140' Processing helix chain 'A' and resid 173 through 180 Processing helix chain 'A' and resid 181 through 187 Processing helix chain 'A' and resid 199 through 213 removed outlier: 3.511A pdb=" N LEU A 203 " --> pdb=" O PRO A 199 " (cutoff:3.500A) Processing helix chain 'A' and resid 225 through 234 removed outlier: 3.858A pdb=" N ALA A 229 " --> pdb=" O TYR A 225 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N ALA A 232 " --> pdb=" O THR A 228 " (cutoff:3.500A) Processing helix chain 'A' and resid 247 through 260 Processing helix chain 'A' and resid 283 through 297 removed outlier: 3.549A pdb=" N VAL A 295 " --> pdb=" O ALA A 291 " (cutoff:3.500A) Processing helix chain 'A' and resid 315 through 329 removed outlier: 3.513A pdb=" N LYS A 329 " --> pdb=" O GLU A 325 " (cutoff:3.500A) Processing helix chain 'A' and resid 347 through 364 Processing helix chain 'A' and resid 394 through 398 Processing helix chain 'A' and resid 413 through 422 Processing helix chain 'A' and resid 436 through 447 Processing helix chain 'A' and resid 469 through 473 removed outlier: 3.500A pdb=" N GLY A 473 " --> pdb=" O LYS A 470 " (cutoff:3.500A) Processing helix chain 'A' and resid 480 through 484 removed outlier: 3.622A pdb=" N PHE A 483 " --> pdb=" O GLU A 480 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N HIS A 484 " --> pdb=" O TYR A 481 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 480 through 484' Processing helix chain 'B' and resid 56 through 71 Processing helix chain 'B' and resid 75 through 80 removed outlier: 3.528A pdb=" N THR B 79 " --> pdb=" O SER B 75 " (cutoff:3.500A) Processing helix chain 'B' and resid 81 through 112 removed outlier: 5.264A pdb=" N LEU B 101 " --> pdb=" O GLU B 97 " (cutoff:3.500A) removed outlier: 6.308A pdb=" N LEU B 102 " --> pdb=" O ARG B 98 " (cutoff:3.500A) Processing helix chain 'B' and resid 114 through 120 Processing helix chain 'B' and resid 121 through 135 Processing helix chain 'B' and resid 136 through 140 removed outlier: 3.650A pdb=" N LYS B 139 " --> pdb=" O TRP B 136 " (cutoff:3.500A) removed outlier: 4.158A pdb=" N ILE B 140 " --> pdb=" O ALA B 137 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 136 through 140' Processing helix chain 'B' and resid 173 through 180 Processing helix chain 'B' and resid 181 through 187 Processing helix chain 'B' and resid 199 through 213 removed outlier: 3.510A pdb=" N LEU B 203 " --> pdb=" O PRO B 199 " (cutoff:3.500A) Processing helix chain 'B' and resid 225 through 234 removed outlier: 3.858A pdb=" N ALA B 229 " --> pdb=" O TYR B 225 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N ALA B 232 " --> pdb=" O THR B 228 " (cutoff:3.500A) Processing helix chain 'B' and resid 247 through 260 Processing helix chain 'B' and resid 283 through 297 removed outlier: 3.549A pdb=" N VAL B 295 " --> pdb=" O ALA B 291 " (cutoff:3.500A) Processing helix chain 'B' and resid 315 through 329 removed outlier: 3.512A pdb=" N LYS B 329 " --> pdb=" O GLU B 325 " (cutoff:3.500A) Processing helix chain 'B' and resid 347 through 364 Processing helix chain 'B' and resid 394 through 398 Processing helix chain 'B' and resid 413 through 422 Processing helix chain 'B' and resid 436 through 447 Processing helix chain 'B' and resid 469 through 473 removed outlier: 3.501A pdb=" N GLY B 473 " --> pdb=" O LYS B 470 " (cutoff:3.500A) Processing helix chain 'B' and resid 480 through 484 removed outlier: 3.622A pdb=" N PHE B 483 " --> pdb=" O GLU B 480 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N HIS B 484 " --> pdb=" O TYR B 481 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 480 through 484' Processing helix chain 'C' and resid 56 through 71 Processing helix chain 'C' and resid 75 through 80 removed outlier: 3.529A pdb=" N THR C 79 " --> pdb=" O SER C 75 " (cutoff:3.500A) Processing helix chain 'C' and resid 81 through 112 removed outlier: 5.263A pdb=" N LEU C 101 " --> pdb=" O GLU C 97 " (cutoff:3.500A) removed outlier: 6.307A pdb=" N LEU C 102 " --> pdb=" O ARG C 98 " (cutoff:3.500A) Processing helix chain 'C' and resid 114 through 120 Processing helix chain 'C' and resid 121 through 135 Processing helix chain 'C' and resid 136 through 140 removed outlier: 3.649A pdb=" N LYS C 139 " --> pdb=" O TRP C 136 " (cutoff:3.500A) removed outlier: 4.158A pdb=" N ILE C 140 " --> pdb=" O ALA C 137 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 136 through 140' Processing helix chain 'C' and resid 173 through 180 Processing helix chain 'C' and resid 181 through 187 Processing helix chain 'C' and resid 199 through 213 removed outlier: 3.510A pdb=" N LEU C 203 " --> pdb=" O PRO C 199 " (cutoff:3.500A) Processing helix chain 'C' and resid 225 through 234 removed outlier: 3.858A pdb=" N ALA C 229 " --> pdb=" O TYR C 225 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N ALA C 232 " --> pdb=" O THR C 228 " (cutoff:3.500A) Processing helix chain 'C' and resid 247 through 260 Processing helix chain 'C' and resid 283 through 297 removed outlier: 3.549A pdb=" N VAL C 295 " --> pdb=" O ALA C 291 " (cutoff:3.500A) Processing helix chain 'C' and resid 315 through 329 removed outlier: 3.513A pdb=" N LYS C 329 " --> pdb=" O GLU C 325 " (cutoff:3.500A) Processing helix chain 'C' and resid 347 through 364 Processing helix chain 'C' and resid 394 through 398 Processing helix chain 'C' and resid 413 through 422 Processing helix chain 'C' and resid 436 through 447 Processing helix chain 'C' and resid 469 through 473 Processing helix chain 'C' and resid 480 through 484 removed outlier: 3.622A pdb=" N PHE C 483 " --> pdb=" O GLU C 480 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N HIS C 484 " --> pdb=" O TYR C 481 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 480 through 484' Processing helix chain 'D' and resid 56 through 71 Processing helix chain 'D' and resid 75 through 80 removed outlier: 3.529A pdb=" N THR D 79 " --> pdb=" O SER D 75 " (cutoff:3.500A) Processing helix chain 'D' and resid 81 through 112 removed outlier: 5.264A pdb=" N LEU D 101 " --> pdb=" O GLU D 97 " (cutoff:3.500A) removed outlier: 6.307A pdb=" N LEU D 102 " --> pdb=" O ARG D 98 " (cutoff:3.500A) Processing helix chain 'D' and resid 114 through 120 Processing helix chain 'D' and resid 121 through 135 Processing helix chain 'D' and resid 136 through 140 removed outlier: 3.650A pdb=" N LYS D 139 " --> pdb=" O TRP D 136 " (cutoff:3.500A) removed outlier: 4.157A pdb=" N ILE D 140 " --> pdb=" O ALA D 137 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 136 through 140' Processing helix chain 'D' and resid 173 through 180 Processing helix chain 'D' and resid 181 through 187 Processing helix chain 'D' and resid 199 through 213 removed outlier: 3.510A pdb=" N LEU D 203 " --> pdb=" O PRO D 199 " (cutoff:3.500A) Processing helix chain 'D' and resid 225 through 234 removed outlier: 3.858A pdb=" N ALA D 229 " --> pdb=" O TYR D 225 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N ALA D 232 " --> pdb=" O THR D 228 " (cutoff:3.500A) Processing helix chain 'D' and resid 247 through 260 Processing helix chain 'D' and resid 283 through 297 removed outlier: 3.549A pdb=" N VAL D 295 " --> pdb=" O ALA D 291 " (cutoff:3.500A) Processing helix chain 'D' and resid 315 through 329 removed outlier: 3.512A pdb=" N LYS D 329 " --> pdb=" O GLU D 325 " (cutoff:3.500A) Processing helix chain 'D' and resid 347 through 364 Processing helix chain 'D' and resid 394 through 398 Processing helix chain 'D' and resid 413 through 422 Processing helix chain 'D' and resid 436 through 447 Processing helix chain 'D' and resid 469 through 473 removed outlier: 3.500A pdb=" N GLY D 473 " --> pdb=" O LYS D 470 " (cutoff:3.500A) Processing helix chain 'D' and resid 480 through 484 removed outlier: 3.622A pdb=" N PHE D 483 " --> pdb=" O GLU D 480 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N HIS D 484 " --> pdb=" O TYR D 481 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 480 through 484' Processing sheet with id=AA1, first strand: chain 'A' and resid 40 through 41 removed outlier: 6.845A pdb=" N VAL A 40 " --> pdb=" O LEU A 49 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 152 through 159 removed outlier: 7.903A pdb=" N VAL B 452 " --> pdb=" O VAL A 489 " (cutoff:3.500A) removed outlier: 6.199A pdb=" N THR A 491 " --> pdb=" O VAL B 452 " (cutoff:3.500A) removed outlier: 7.520A pdb=" N VAL B 454 " --> pdb=" O THR A 491 " (cutoff:3.500A) removed outlier: 6.509A pdb=" N THR A 493 " --> pdb=" O VAL B 454 " (cutoff:3.500A) removed outlier: 6.371A pdb=" N ALA B 430 " --> pdb=" O TRP B 453 " (cutoff:3.500A) removed outlier: 6.300A pdb=" N CYS B 276 " --> pdb=" O PHE B 310 " (cutoff:3.500A) removed outlier: 7.981A pdb=" N GLU B 312 " --> pdb=" O CYS B 276 " (cutoff:3.500A) removed outlier: 8.188A pdb=" N VAL B 278 " --> pdb=" O GLU B 312 " (cutoff:3.500A) removed outlier: 6.259A pdb=" N VAL B 386 " --> pdb=" O GLU B 369 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 219 through 221 removed outlier: 6.290A pdb=" N VAL A 190 " --> pdb=" O ASN A 220 " (cutoff:3.500A) removed outlier: 6.568A pdb=" N VAL A 162 " --> pdb=" O ILE A 239 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 367 through 370 removed outlier: 6.259A pdb=" N VAL A 386 " --> pdb=" O GLU A 369 " (cutoff:3.500A) removed outlier: 6.300A pdb=" N CYS A 276 " --> pdb=" O PHE A 310 " (cutoff:3.500A) removed outlier: 7.981A pdb=" N GLU A 312 " --> pdb=" O CYS A 276 " (cutoff:3.500A) removed outlier: 8.188A pdb=" N VAL A 278 " --> pdb=" O GLU A 312 " (cutoff:3.500A) removed outlier: 6.370A pdb=" N ALA A 430 " --> pdb=" O TRP A 453 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 40 through 41 removed outlier: 6.845A pdb=" N VAL B 40 " --> pdb=" O LEU B 49 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 219 through 221 removed outlier: 6.290A pdb=" N VAL B 190 " --> pdb=" O ASN B 220 " (cutoff:3.500A) removed outlier: 6.569A pdb=" N VAL B 162 " --> pdb=" O ILE B 239 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 40 through 41 removed outlier: 6.845A pdb=" N VAL C 40 " --> pdb=" O LEU C 49 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 152 through 159 removed outlier: 7.827A pdb=" N VAL D 452 " --> pdb=" O VAL C 489 " (cutoff:3.500A) removed outlier: 6.142A pdb=" N THR C 491 " --> pdb=" O VAL D 452 " (cutoff:3.500A) removed outlier: 7.410A pdb=" N VAL D 454 " --> pdb=" O THR C 491 " (cutoff:3.500A) removed outlier: 6.499A pdb=" N THR C 493 " --> pdb=" O VAL D 454 " (cutoff:3.500A) removed outlier: 6.371A pdb=" N ALA D 430 " --> pdb=" O TRP D 453 " (cutoff:3.500A) removed outlier: 6.300A pdb=" N CYS D 276 " --> pdb=" O PHE D 310 " (cutoff:3.500A) removed outlier: 7.981A pdb=" N GLU D 312 " --> pdb=" O CYS D 276 " (cutoff:3.500A) removed outlier: 8.188A pdb=" N VAL D 278 " --> pdb=" O GLU D 312 " (cutoff:3.500A) removed outlier: 6.259A pdb=" N VAL D 386 " --> pdb=" O GLU D 369 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 219 through 221 removed outlier: 6.290A pdb=" N VAL C 190 " --> pdb=" O ASN C 220 " (cutoff:3.500A) removed outlier: 6.569A pdb=" N VAL C 162 " --> pdb=" O ILE C 239 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 367 through 370 removed outlier: 6.259A pdb=" N VAL C 386 " --> pdb=" O GLU C 369 " (cutoff:3.500A) removed outlier: 6.299A pdb=" N CYS C 276 " --> pdb=" O PHE C 310 " (cutoff:3.500A) removed outlier: 7.981A pdb=" N GLU C 312 " --> pdb=" O CYS C 276 " (cutoff:3.500A) removed outlier: 8.188A pdb=" N VAL C 278 " --> pdb=" O GLU C 312 " (cutoff:3.500A) removed outlier: 6.371A pdb=" N ALA C 430 " --> pdb=" O TRP C 453 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N THR D 493 " --> pdb=" O VAL C 452 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 40 through 41 removed outlier: 6.844A pdb=" N VAL D 40 " --> pdb=" O LEU D 49 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 219 through 221 removed outlier: 6.290A pdb=" N VAL D 190 " --> pdb=" O ASN D 220 " (cutoff:3.500A) removed outlier: 6.568A pdb=" N VAL D 162 " --> pdb=" O ILE D 239 " (cutoff:3.500A) 674 hydrogen bonds defined for protein. 1935 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 5.19 Time building geometry restraints manager: 4.62 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: 0.11 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'B' 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: 1.020 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.620 Check model and map are aligned: 0.110 Set scattering table: 0.160 Process input model: 36.180 Find NCS groups from input model: 0.330 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.860 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 41.390 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.22 (0.15), residues: 1964 helix: -2.67 (0.14), residues: 784 sheet: -2.45 (0.24), residues: 388 loop : -2.92 (0.19), residues: 792 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP D 29 HIS 0.007 0.002 HIS D 484 PHE 0.018 0.003 PHE B 24 TYR 0.018 0.002 TYR D 154 ARG 0.006 0.001 ARG D 143 Details of bonding type rmsd hydrogen bonds : bond 0.24263 ( 674) hydrogen bonds : angle 9.27791 ( 1935) covalent geometry : bond 0.01259 (15488) covalent geometry : angle 1.45281 (20972) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3928 Ramachandran restraints generated. 1964 Oldfield, 0 Emsley, 1964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3928 Ramachandran restraints generated. 1964 Oldfield, 0 Emsley, 1964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 659 residues out of total 1632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 583 time to evaluate : 1.566 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 65 LYS cc_start: 0.8820 (tttt) cc_final: 0.8502 (mtpp) REVERT: A 158 GLU cc_start: 0.8256 (mt-10) cc_final: 0.7899 (mt-10) REVERT: A 175 MET cc_start: 0.8069 (OUTLIER) cc_final: 0.7580 (mmp) REVERT: A 292 HIS cc_start: 0.6786 (OUTLIER) cc_final: 0.6443 (t-90) REVERT: A 308 ARG cc_start: 0.7670 (mtm180) cc_final: 0.7428 (mtm180) REVERT: A 471 MET cc_start: 0.8665 (mtp) cc_final: 0.8372 (mtp) REVERT: A 477 GLU cc_start: 0.7683 (mt-10) cc_final: 0.7479 (mt-10) REVERT: B 169 TRP cc_start: 0.8607 (p-90) cc_final: 0.8257 (p-90) REVERT: B 175 MET cc_start: 0.7980 (OUTLIER) cc_final: 0.7511 (mmp) REVERT: B 267 THR cc_start: 0.8060 (p) cc_final: 0.7750 (p) REVERT: B 292 HIS cc_start: 0.5517 (OUTLIER) cc_final: 0.5286 (t-90) REVERT: B 410 LYS cc_start: 0.7945 (ttpt) cc_final: 0.7643 (tttm) REVERT: C 169 TRP cc_start: 0.8579 (p-90) cc_final: 0.8226 (p-90) REVERT: C 175 MET cc_start: 0.8009 (OUTLIER) cc_final: 0.7584 (mmp) REVERT: C 267 THR cc_start: 0.8093 (p) cc_final: 0.7747 (p) REVERT: C 292 HIS cc_start: 0.5600 (OUTLIER) cc_final: 0.5329 (t-90) REVERT: C 410 LYS cc_start: 0.7943 (ttpt) cc_final: 0.7638 (tttm) REVERT: C 415 ASP cc_start: 0.7876 (m-30) cc_final: 0.7091 (m-30) REVERT: D 169 TRP cc_start: 0.8576 (p-90) cc_final: 0.8240 (p-90) REVERT: D 175 MET cc_start: 0.7987 (OUTLIER) cc_final: 0.7568 (mmp) REVERT: D 267 THR cc_start: 0.8103 (p) cc_final: 0.7779 (p) REVERT: D 410 LYS cc_start: 0.7954 (ttpt) cc_final: 0.7661 (tttm) outliers start: 76 outliers final: 20 residues processed: 615 average time/residue: 0.3028 time to fit residues: 264.0220 Evaluate side-chains 488 residues out of total 1632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 461 time to evaluate : 1.525 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 175 MET Chi-restraints excluded: chain A residue 177 ILE Chi-restraints excluded: chain A residue 196 GLU Chi-restraints excluded: chain A residue 279 LEU Chi-restraints excluded: chain A residue 292 HIS Chi-restraints excluded: chain A residue 332 LEU Chi-restraints excluded: chain B residue 175 MET Chi-restraints excluded: chain B residue 177 ILE Chi-restraints excluded: chain B residue 196 GLU Chi-restraints excluded: chain B residue 279 LEU Chi-restraints excluded: chain B residue 292 HIS Chi-restraints excluded: chain B residue 299 GLN Chi-restraints excluded: chain B residue 332 LEU Chi-restraints excluded: chain C residue 51 GLN Chi-restraints excluded: chain C residue 175 MET Chi-restraints excluded: chain C residue 177 ILE Chi-restraints excluded: chain C residue 196 GLU Chi-restraints excluded: chain C residue 279 LEU Chi-restraints excluded: chain C residue 292 HIS Chi-restraints excluded: chain C residue 299 GLN Chi-restraints excluded: chain C residue 332 LEU Chi-restraints excluded: chain D residue 175 MET Chi-restraints excluded: chain D residue 177 ILE Chi-restraints excluded: chain D residue 196 GLU Chi-restraints excluded: chain D residue 279 LEU Chi-restraints excluded: chain D residue 299 GLN Chi-restraints excluded: chain D residue 332 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 165 optimal weight: 0.6980 chunk 148 optimal weight: 0.6980 chunk 82 optimal weight: 1.9990 chunk 50 optimal weight: 0.7980 chunk 100 optimal weight: 5.9990 chunk 79 optimal weight: 0.9980 chunk 153 optimal weight: 0.8980 chunk 59 optimal weight: 0.6980 chunk 93 optimal weight: 0.6980 chunk 114 optimal weight: 0.9990 chunk 177 optimal weight: 0.7980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 19 GLN A 293 HIS ** A 299 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 301 GLN A 345 GLN ** A 407 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 19 GLN ** B 30 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 293 HIS B 301 GLN B 345 GLN ** B 407 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 498 GLN C 19 GLN ** C 30 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 51 GLN ** C 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 293 HIS C 301 GLN C 345 GLN ** C 407 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 498 GLN D 19 GLN ** D 30 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 293 HIS D 301 GLN D 345 GLN ** D 407 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4079 r_free = 0.4079 target = 0.200215 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3668 r_free = 0.3668 target = 0.160727 restraints weight = 17077.200| |-----------------------------------------------------------------------------| r_work (start): 0.3621 rms_B_bonded: 2.16 r_work: 0.3508 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work (final): 0.3508 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3508 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3508 r_free = 0.3508 target_work(ls_wunit_k1) = 0.146 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3496 r_free = 0.3496 target_work(ls_wunit_k1) = 0.145 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| r_final: 0.3496 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7360 moved from start: 0.3543 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 15488 Z= 0.170 Angle : 0.685 10.708 20972 Z= 0.354 Chirality : 0.046 0.249 2324 Planarity : 0.005 0.037 2712 Dihedral : 7.434 59.735 2170 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 17.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.50 % Favored : 94.50 % Rotamer: Outliers : 3.66 % Allowed : 16.81 % Favored : 79.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.93 (0.18), residues: 1964 helix: -0.39 (0.17), residues: 824 sheet: -1.85 (0.24), residues: 404 loop : -1.79 (0.23), residues: 736 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 29 HIS 0.005 0.001 HIS A 298 PHE 0.025 0.002 PHE A 402 TYR 0.018 0.002 TYR A 351 ARG 0.006 0.001 ARG A 395 Details of bonding type rmsd hydrogen bonds : bond 0.04218 ( 674) hydrogen bonds : angle 5.26527 ( 1935) covalent geometry : bond 0.00387 (15488) covalent geometry : angle 0.68544 (20972) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3928 Ramachandran restraints generated. 1964 Oldfield, 0 Emsley, 1964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3928 Ramachandran restraints generated. 1964 Oldfield, 0 Emsley, 1964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 533 residues out of total 1632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 474 time to evaluate : 1.606 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 65 LYS cc_start: 0.8413 (tttt) cc_final: 0.8164 (mtpp) REVERT: A 158 GLU cc_start: 0.8419 (mt-10) cc_final: 0.7994 (mt-10) REVERT: A 260 LYS cc_start: 0.6953 (tttt) cc_final: 0.6709 (pttp) REVERT: A 273 LYS cc_start: 0.8153 (tptt) cc_final: 0.7943 (tptm) REVERT: A 308 ARG cc_start: 0.7618 (mtm180) cc_final: 0.7050 (mtm180) REVERT: A 347 ASP cc_start: 0.7117 (p0) cc_final: 0.6395 (m-30) REVERT: A 420 ARG cc_start: 0.8788 (mtp180) cc_final: 0.8517 (mtp180) REVERT: A 471 MET cc_start: 0.8833 (mtp) cc_final: 0.8457 (mtp) REVERT: A 498 GLN cc_start: 0.6433 (mp10) cc_final: 0.6198 (mp10) REVERT: B 30 HIS cc_start: 0.5060 (m-70) cc_final: 0.4761 (m-70) REVERT: B 53 GLU cc_start: 0.7236 (mt-10) cc_final: 0.7028 (mt-10) REVERT: B 177 ILE cc_start: 0.8605 (OUTLIER) cc_final: 0.8319 (mp) REVERT: B 237 MET cc_start: 0.7179 (mmt) cc_final: 0.6530 (mmt) REVERT: B 292 HIS cc_start: 0.5380 (OUTLIER) cc_final: 0.5175 (t-90) REVERT: B 410 LYS cc_start: 0.7879 (ttpt) cc_final: 0.7342 (tttm) REVERT: C 30 HIS cc_start: 0.4951 (m-70) cc_final: 0.4677 (m-70) REVERT: C 177 ILE cc_start: 0.8590 (OUTLIER) cc_final: 0.8299 (mp) REVERT: C 237 MET cc_start: 0.7161 (mmt) cc_final: 0.6515 (mmt) REVERT: C 318 GLU cc_start: 0.6703 (tp30) cc_final: 0.6496 (tp30) REVERT: C 341 THR cc_start: 0.8100 (p) cc_final: 0.7900 (p) REVERT: C 410 LYS cc_start: 0.7763 (ttpt) cc_final: 0.7220 (tttm) REVERT: D 30 HIS cc_start: 0.5202 (m-70) cc_final: 0.4754 (m-70) REVERT: D 57 LYS cc_start: 0.7672 (mmtp) cc_final: 0.7449 (mmmm) REVERT: D 177 ILE cc_start: 0.8604 (OUTLIER) cc_final: 0.8306 (mp) REVERT: D 237 MET cc_start: 0.7249 (mmt) cc_final: 0.7015 (mmt) REVERT: D 273 LYS cc_start: 0.7934 (tptt) cc_final: 0.7472 (tptt) REVERT: D 308 ARG cc_start: 0.7221 (mtm180) cc_final: 0.6791 (ttm170) REVERT: D 410 LYS cc_start: 0.7803 (ttpt) cc_final: 0.7251 (tttm) REVERT: D 499 LYS cc_start: 0.6548 (ttpt) cc_final: 0.6305 (ttpt) outliers start: 59 outliers final: 37 residues processed: 510 average time/residue: 0.2753 time to fit residues: 203.5905 Evaluate side-chains 430 residues out of total 1632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 389 time to evaluate : 1.630 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 THR Chi-restraints excluded: chain A residue 147 ILE Chi-restraints excluded: chain A residue 185 SER Chi-restraints excluded: chain A residue 205 VAL Chi-restraints excluded: chain A residue 279 LEU Chi-restraints excluded: chain A residue 332 LEU Chi-restraints excluded: chain A residue 460 VAL Chi-restraints excluded: chain B residue 147 ILE Chi-restraints excluded: chain B residue 155 THR Chi-restraints excluded: chain B residue 167 ILE Chi-restraints excluded: chain B residue 177 ILE Chi-restraints excluded: chain B residue 185 SER Chi-restraints excluded: chain B residue 220 ASN Chi-restraints excluded: chain B residue 266 VAL Chi-restraints excluded: chain B residue 279 LEU Chi-restraints excluded: chain B residue 292 HIS Chi-restraints excluded: chain B residue 299 GLN Chi-restraints excluded: chain B residue 303 CYS Chi-restraints excluded: chain B residue 332 LEU Chi-restraints excluded: chain C residue 147 ILE Chi-restraints excluded: chain C residue 155 THR Chi-restraints excluded: chain C residue 167 ILE Chi-restraints excluded: chain C residue 177 ILE Chi-restraints excluded: chain C residue 185 SER Chi-restraints excluded: chain C residue 220 ASN Chi-restraints excluded: chain C residue 266 VAL Chi-restraints excluded: chain C residue 279 LEU Chi-restraints excluded: chain C residue 299 GLN Chi-restraints excluded: chain C residue 332 LEU Chi-restraints excluded: chain C residue 494 VAL Chi-restraints excluded: chain D residue 147 ILE Chi-restraints excluded: chain D residue 155 THR Chi-restraints excluded: chain D residue 167 ILE Chi-restraints excluded: chain D residue 177 ILE Chi-restraints excluded: chain D residue 185 SER Chi-restraints excluded: chain D residue 220 ASN Chi-restraints excluded: chain D residue 266 VAL Chi-restraints excluded: chain D residue 279 LEU Chi-restraints excluded: chain D residue 299 GLN Chi-restraints excluded: chain D residue 332 LEU Chi-restraints excluded: chain D residue 341 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 98 optimal weight: 10.0000 chunk 34 optimal weight: 10.0000 chunk 28 optimal weight: 6.9990 chunk 86 optimal weight: 3.9990 chunk 107 optimal weight: 2.9990 chunk 194 optimal weight: 0.9980 chunk 122 optimal weight: 0.8980 chunk 190 optimal weight: 0.7980 chunk 185 optimal weight: 4.9990 chunk 71 optimal weight: 0.4980 chunk 68 optimal weight: 0.5980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 30 HIS A 72 GLN ** A 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 299 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 406 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 407 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 30 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 72 GLN ** B 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 407 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 30 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 72 GLN ** C 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 407 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 30 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 72 GLN ** D 407 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4049 r_free = 0.4049 target = 0.197342 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3626 r_free = 0.3626 target = 0.156937 restraints weight = 17078.464| |-----------------------------------------------------------------------------| r_work (start): 0.3572 rms_B_bonded: 2.15 r_work: 0.3454 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work (final): 0.3454 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3451 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3451 r_free = 0.3451 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 = 0.3450 r_free = 0.3450 target_work(ls_wunit_k1) = 0.141 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 10 | |-----------------------------------------------------------------------------| r_final: 0.3450 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7415 moved from start: 0.4408 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.072 15488 Z= 0.148 Angle : 0.604 7.869 20972 Z= 0.312 Chirality : 0.044 0.234 2324 Planarity : 0.004 0.036 2712 Dihedral : 6.132 53.735 2137 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 13.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.91 % Favored : 94.09 % Rotamer: Outliers : 4.59 % Allowed : 18.61 % Favored : 76.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.05 (0.19), residues: 1964 helix: 0.23 (0.18), residues: 836 sheet: -1.37 (0.25), residues: 392 loop : -1.23 (0.24), residues: 736 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 77 HIS 0.003 0.001 HIS C 292 PHE 0.018 0.002 PHE A 402 TYR 0.012 0.001 TYR A 20 ARG 0.004 0.000 ARG A 68 Details of bonding type rmsd hydrogen bonds : bond 0.03671 ( 674) hydrogen bonds : angle 4.79110 ( 1935) covalent geometry : bond 0.00359 (15488) covalent geometry : angle 0.60402 (20972) *********************** 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 497 residues out of total 1632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 423 time to evaluate : 1.699 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 51 GLN cc_start: 0.7696 (mm110) cc_final: 0.7419 (tp40) REVERT: A 57 LYS cc_start: 0.8142 (mmtp) cc_final: 0.7616 (tptm) REVERT: A 101 LEU cc_start: 0.7655 (mt) cc_final: 0.7321 (mp) REVERT: A 158 GLU cc_start: 0.8479 (mt-10) cc_final: 0.8059 (mt-10) REVERT: A 169 TRP cc_start: 0.8643 (p-90) cc_final: 0.8297 (p-90) REVERT: A 256 GLU cc_start: 0.7808 (mt-10) cc_final: 0.7581 (mt-10) REVERT: A 273 LYS cc_start: 0.8076 (tptt) cc_final: 0.7655 (tptt) REVERT: A 299 GLN cc_start: 0.7515 (mt0) cc_final: 0.7051 (mt0) REVERT: A 308 ARG cc_start: 0.7801 (mtm180) cc_final: 0.7200 (mtm180) REVERT: A 341 THR cc_start: 0.8172 (p) cc_final: 0.7970 (p) REVERT: A 347 ASP cc_start: 0.6985 (p0) cc_final: 0.6248 (m-30) REVERT: A 471 MET cc_start: 0.8840 (mtp) cc_final: 0.8472 (mtp) REVERT: B 30 HIS cc_start: 0.4830 (m-70) cc_final: 0.4450 (m-70) REVERT: B 57 LYS cc_start: 0.7785 (mmmm) cc_final: 0.7548 (mmtm) REVERT: B 169 TRP cc_start: 0.8962 (p-90) cc_final: 0.8702 (p-90) REVERT: B 177 ILE cc_start: 0.8897 (OUTLIER) cc_final: 0.8535 (mp) REVERT: B 196 GLU cc_start: 0.6603 (OUTLIER) cc_final: 0.6350 (pm20) REVERT: B 237 MET cc_start: 0.7123 (mmt) cc_final: 0.6730 (mmt) REVERT: C 53 GLU cc_start: 0.7538 (mt-10) cc_final: 0.6801 (tt0) REVERT: C 169 TRP cc_start: 0.8975 (p-90) cc_final: 0.8713 (p-90) REVERT: C 177 ILE cc_start: 0.8882 (OUTLIER) cc_final: 0.8527 (mp) REVERT: C 237 MET cc_start: 0.7194 (mmt) cc_final: 0.6740 (mmt) REVERT: C 312 GLU cc_start: 0.6778 (OUTLIER) cc_final: 0.6481 (mm-30) REVERT: C 318 GLU cc_start: 0.6841 (tp30) cc_final: 0.6617 (tp30) REVERT: C 410 LYS cc_start: 0.7772 (ttpt) cc_final: 0.7218 (tttm) REVERT: C 419 LYS cc_start: 0.8117 (mttm) cc_final: 0.7732 (mmtp) REVERT: C 471 MET cc_start: 0.8250 (mtm) cc_final: 0.7868 (mtp) REVERT: C 480 GLU cc_start: 0.7951 (tt0) cc_final: 0.7354 (tt0) REVERT: D 53 GLU cc_start: 0.7666 (mt-10) cc_final: 0.6812 (tt0) REVERT: D 169 TRP cc_start: 0.8968 (p-90) cc_final: 0.8702 (p-90) REVERT: D 177 ILE cc_start: 0.8879 (OUTLIER) cc_final: 0.8511 (mp) REVERT: D 237 MET cc_start: 0.7227 (mmt) cc_final: 0.6830 (mmt) REVERT: D 273 LYS cc_start: 0.7880 (tptt) cc_final: 0.7582 (tptm) REVERT: D 308 ARG cc_start: 0.7465 (mtm180) cc_final: 0.6832 (ttm170) REVERT: D 410 LYS cc_start: 0.7965 (ttpt) cc_final: 0.7386 (tttm) outliers start: 74 outliers final: 48 residues processed: 462 average time/residue: 0.2765 time to fit residues: 186.5802 Evaluate side-chains 452 residues out of total 1632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 399 time to evaluate : 1.764 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 THR Chi-restraints excluded: chain A residue 114 LEU Chi-restraints excluded: chain A residue 147 ILE Chi-restraints excluded: chain A residue 185 SER Chi-restraints excluded: chain A residue 205 VAL Chi-restraints excluded: chain A residue 239 ILE Chi-restraints excluded: chain A residue 332 LEU Chi-restraints excluded: chain A residue 494 VAL 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 185 SER Chi-restraints excluded: chain B residue 196 GLU Chi-restraints excluded: chain B residue 219 VAL Chi-restraints excluded: chain B residue 220 ASN Chi-restraints excluded: chain B residue 222 VAL Chi-restraints excluded: chain B residue 248 THR Chi-restraints excluded: chain B residue 266 VAL Chi-restraints excluded: chain B residue 289 GLU Chi-restraints excluded: chain B residue 299 GLN Chi-restraints excluded: chain B residue 332 LEU Chi-restraints excluded: chain B residue 451 THR Chi-restraints excluded: chain B residue 494 VAL Chi-restraints excluded: chain C residue 79 THR Chi-restraints excluded: chain C residue 147 ILE Chi-restraints excluded: chain C residue 167 ILE Chi-restraints excluded: chain C residue 177 ILE Chi-restraints excluded: chain C residue 185 SER Chi-restraints excluded: chain C residue 198 THR Chi-restraints excluded: chain C residue 219 VAL Chi-restraints excluded: chain C residue 220 ASN Chi-restraints excluded: chain C residue 248 THR Chi-restraints excluded: chain C residue 266 VAL Chi-restraints excluded: chain C residue 299 GLN Chi-restraints excluded: chain C residue 312 GLU Chi-restraints excluded: chain C residue 332 LEU Chi-restraints excluded: chain C residue 451 THR Chi-restraints excluded: chain C residue 494 VAL Chi-restraints excluded: chain D residue 79 THR Chi-restraints excluded: chain D residue 147 ILE Chi-restraints excluded: chain D residue 167 ILE Chi-restraints excluded: chain D residue 177 ILE Chi-restraints excluded: chain D residue 185 SER Chi-restraints excluded: chain D residue 198 THR Chi-restraints excluded: chain D residue 219 VAL Chi-restraints excluded: chain D residue 220 ASN Chi-restraints excluded: chain D residue 222 VAL Chi-restraints excluded: chain D residue 248 THR Chi-restraints excluded: chain D residue 266 VAL Chi-restraints excluded: chain D residue 299 GLN Chi-restraints excluded: chain D residue 332 LEU Chi-restraints excluded: chain D residue 494 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 100 optimal weight: 7.9990 chunk 0 optimal weight: 10.0000 chunk 55 optimal weight: 3.9990 chunk 158 optimal weight: 1.9990 chunk 7 optimal weight: 2.9990 chunk 91 optimal weight: 3.9990 chunk 45 optimal weight: 3.9990 chunk 106 optimal weight: 2.9990 chunk 63 optimal weight: 1.9990 chunk 131 optimal weight: 2.9990 chunk 6 optimal weight: 1.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 299 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 406 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 498 GLN ** B 30 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 72 GLN ** B 406 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 30 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 72 GLN ** C 406 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 72 GLN ** D 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 406 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 407 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 498 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3927 r_free = 0.3927 target = 0.184883 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3474 r_free = 0.3474 target = 0.143558 restraints weight = 17230.995| |-----------------------------------------------------------------------------| r_work (start): 0.3441 rms_B_bonded: 2.13 r_work: 0.3317 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work (final): 0.3317 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3308 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3308 r_free = 0.3308 target_work(ls_wunit_k1) = 0.130 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 10 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3307 r_free = 0.3307 target_work(ls_wunit_k1) = 0.130 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 10 | |-----------------------------------------------------------------------------| r_final: 0.3307 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7585 moved from start: 0.5022 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.075 15488 Z= 0.304 Angle : 0.750 8.269 20972 Z= 0.388 Chirality : 0.052 0.233 2324 Planarity : 0.005 0.033 2712 Dihedral : 6.441 52.566 2127 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 14.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.82 % Favored : 93.18 % Rotamer: Outliers : 7.26 % Allowed : 18.55 % Favored : 74.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.31 (0.19), residues: 1964 helix: -0.12 (0.18), residues: 832 sheet: -1.46 (0.25), residues: 416 loop : -1.17 (0.25), residues: 716 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP A 77 HIS 0.007 0.002 HIS B 292 PHE 0.023 0.003 PHE C 402 TYR 0.018 0.002 TYR C 330 ARG 0.006 0.001 ARG A 85 Details of bonding type rmsd hydrogen bonds : bond 0.04716 ( 674) hydrogen bonds : angle 5.08830 ( 1935) covalent geometry : bond 0.00718 (15488) covalent geometry : angle 0.75020 (20972) *********************** 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 534 residues out of total 1632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 117 poor density : 417 time to evaluate : 1.561 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 23 ILE cc_start: 0.6585 (OUTLIER) cc_final: 0.6332 (mm) REVERT: A 57 LYS cc_start: 0.8121 (mmtp) cc_final: 0.7576 (tptm) REVERT: A 269 GLU cc_start: 0.7483 (tm-30) cc_final: 0.7266 (tm-30) REVERT: A 299 GLN cc_start: 0.7636 (mp10) cc_final: 0.7017 (mt0) REVERT: A 420 ARG cc_start: 0.8788 (mtp180) cc_final: 0.8545 (mtp180) REVERT: A 471 MET cc_start: 0.8934 (mtp) cc_final: 0.8476 (mtp) REVERT: B 57 LYS cc_start: 0.7960 (mmmm) cc_final: 0.7630 (mmtp) REVERT: B 169 TRP cc_start: 0.8872 (p-90) cc_final: 0.8205 (p-90) REVERT: B 318 GLU cc_start: 0.6985 (tp30) cc_final: 0.6737 (tp30) REVERT: B 341 THR cc_start: 0.8242 (p) cc_final: 0.8036 (p) REVERT: B 499 LYS cc_start: 0.6668 (ttpt) cc_final: 0.6349 (ttpt) REVERT: C 57 LYS cc_start: 0.7828 (mmtm) cc_final: 0.7567 (mmtm) REVERT: C 169 TRP cc_start: 0.8876 (p-90) cc_final: 0.8191 (p-90) REVERT: C 318 GLU cc_start: 0.6999 (tp30) cc_final: 0.6604 (tp30) REVERT: C 410 LYS cc_start: 0.8013 (ttpt) cc_final: 0.7524 (tttm) REVERT: C 499 LYS cc_start: 0.6685 (ttpt) cc_final: 0.6370 (ttpt) REVERT: D 57 LYS cc_start: 0.8095 (mmtp) cc_final: 0.7548 (mmtm) REVERT: D 169 TRP cc_start: 0.8881 (p-90) cc_final: 0.8207 (p-90) REVERT: D 256 GLU cc_start: 0.7231 (tt0) cc_final: 0.6927 (mt-10) REVERT: D 318 GLU cc_start: 0.6928 (tp30) cc_final: 0.6672 (tp30) REVERT: D 471 MET cc_start: 0.8615 (mtp) cc_final: 0.8360 (mtp) outliers start: 117 outliers final: 88 residues processed: 476 average time/residue: 0.2825 time to fit residues: 194.2355 Evaluate side-chains 478 residues out of total 1632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 389 time to evaluate : 1.720 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 ILE Chi-restraints excluded: chain A residue 60 VAL Chi-restraints excluded: chain A residue 79 THR Chi-restraints excluded: chain A residue 83 SER Chi-restraints excluded: chain A residue 114 LEU Chi-restraints excluded: chain A residue 129 THR 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 180 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 222 VAL Chi-restraints excluded: chain A residue 237 MET Chi-restraints excluded: chain A residue 239 ILE Chi-restraints excluded: chain A residue 279 LEU Chi-restraints excluded: chain A residue 303 CYS Chi-restraints excluded: chain A residue 415 ASP Chi-restraints excluded: chain A residue 442 THR Chi-restraints excluded: chain A residue 451 THR Chi-restraints excluded: chain A residue 460 VAL Chi-restraints excluded: chain A residue 494 VAL Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 79 THR Chi-restraints excluded: chain B residue 83 SER 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 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 266 VAL Chi-restraints excluded: chain B residue 289 GLU Chi-restraints excluded: chain B residue 303 CYS Chi-restraints excluded: chain B residue 332 LEU Chi-restraints excluded: chain B residue 390 VAL Chi-restraints excluded: chain B residue 425 PHE Chi-restraints excluded: chain B residue 445 SER 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 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 185 SER Chi-restraints excluded: chain C residue 198 THR Chi-restraints excluded: chain C residue 219 VAL Chi-restraints excluded: chain C residue 220 ASN Chi-restraints excluded: chain C residue 222 VAL Chi-restraints excluded: chain C residue 248 THR Chi-restraints excluded: chain C residue 254 ILE Chi-restraints excluded: chain C residue 266 VAL Chi-restraints excluded: chain C residue 303 CYS Chi-restraints excluded: chain C residue 332 LEU Chi-restraints excluded: chain C residue 390 VAL Chi-restraints excluded: chain C residue 445 SER Chi-restraints excluded: chain C residue 460 VAL Chi-restraints excluded: chain C residue 494 VAL Chi-restraints excluded: chain D residue 40 VAL Chi-restraints excluded: chain D residue 79 THR Chi-restraints excluded: chain D residue 114 LEU Chi-restraints excluded: chain D residue 129 THR Chi-restraints excluded: chain D residue 147 ILE Chi-restraints excluded: chain D residue 155 THR Chi-restraints excluded: chain D residue 167 ILE Chi-restraints excluded: chain D residue 177 ILE Chi-restraints excluded: chain D residue 185 SER Chi-restraints excluded: chain D residue 198 THR Chi-restraints excluded: chain D residue 219 VAL Chi-restraints excluded: chain D residue 220 ASN Chi-restraints excluded: chain D residue 222 VAL Chi-restraints excluded: chain D residue 248 THR Chi-restraints excluded: chain D residue 266 VAL Chi-restraints excluded: chain D residue 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 460 VAL Chi-restraints excluded: chain D residue 494 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 161 optimal weight: 0.6980 chunk 145 optimal weight: 0.9990 chunk 185 optimal weight: 5.9990 chunk 55 optimal weight: 0.0870 chunk 139 optimal weight: 2.9990 chunk 14 optimal weight: 0.9990 chunk 114 optimal weight: 0.7980 chunk 50 optimal weight: 0.8980 chunk 179 optimal weight: 0.8980 chunk 60 optimal weight: 1.9990 chunk 40 optimal weight: 0.7980 overall best weight: 0.6558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 299 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 406 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 30 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 72 GLN ** B 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 204 HIS ** 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 204 HIS ** C 298 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 299 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 406 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 406 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.4003 r_free = 0.4003 target = 0.192107 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3586 r_free = 0.3586 target = 0.153938 restraints weight = 17263.155| |-----------------------------------------------------------------------------| r_work (start): 0.3577 rms_B_bonded: 2.06 r_work: 0.3458 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work (final): 0.3458 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3456 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3456 r_free = 0.3456 target_work(ls_wunit_k1) = 0.142 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 10 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3456 r_free = 0.3456 target_work(ls_wunit_k1) = 0.142 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 10 | |-----------------------------------------------------------------------------| r_final: 0.3456 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7478 moved from start: 0.5469 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= 0.133 Angle : 0.575 5.891 20972 Z= 0.298 Chirality : 0.045 0.273 2324 Planarity : 0.004 0.035 2712 Dihedral : 5.496 45.392 2116 Min Nonbonded Distance : 2.599 Molprobity Statistics. All-atom Clashscore : 13.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.79 % Favored : 95.21 % Rotamer: Outliers : 4.96 % Allowed : 21.09 % Favored : 73.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.92 (0.20), residues: 1964 helix: 0.25 (0.19), residues: 832 sheet: -1.25 (0.25), residues: 408 loop : -1.06 (0.25), residues: 724 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 29 HIS 0.004 0.001 HIS D 298 PHE 0.015 0.002 PHE A 402 TYR 0.012 0.001 TYR B 119 ARG 0.007 0.000 ARG A 395 Details of bonding type rmsd hydrogen bonds : bond 0.03361 ( 674) hydrogen bonds : angle 4.80000 ( 1935) covalent geometry : bond 0.00318 (15488) covalent geometry : angle 0.57495 (20972) *********************** 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 484 residues out of total 1632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 404 time to evaluate : 1.639 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 57 LYS cc_start: 0.8173 (mmtp) cc_final: 0.7753 (tptm) REVERT: A 101 LEU cc_start: 0.7751 (mt) cc_final: 0.7416 (mp) REVERT: A 252 LYS cc_start: 0.7021 (mttm) cc_final: 0.6818 (mttt) REVERT: A 260 LYS cc_start: 0.7039 (ttmt) cc_final: 0.6676 (pttm) REVERT: A 299 GLN cc_start: 0.7573 (mp10) cc_final: 0.7007 (mt0) REVERT: A 318 GLU cc_start: 0.6667 (tp30) cc_final: 0.6173 (tp30) REVERT: A 347 ASP cc_start: 0.7017 (p0) cc_final: 0.6197 (m-30) REVERT: A 402 PHE cc_start: 0.7665 (OUTLIER) cc_final: 0.7277 (t80) REVERT: B 237 MET cc_start: 0.7440 (mmt) cc_final: 0.6719 (mmt) REVERT: B 499 LYS cc_start: 0.6653 (ttpt) cc_final: 0.6356 (ttpt) REVERT: C 237 MET cc_start: 0.7443 (mmt) cc_final: 0.6705 (mmt) REVERT: C 318 GLU cc_start: 0.6853 (tp30) cc_final: 0.6629 (tp30) REVERT: C 367 LYS cc_start: 0.5631 (tptp) cc_final: 0.5408 (tptp) REVERT: C 480 GLU cc_start: 0.7902 (tt0) cc_final: 0.7338 (tt0) REVERT: D 57 LYS cc_start: 0.8005 (mmtp) cc_final: 0.7728 (mmtm) REVERT: D 158 GLU cc_start: 0.8563 (mt-10) cc_final: 0.8232 (mt-10) REVERT: D 237 MET cc_start: 0.7325 (mmt) cc_final: 0.6683 (mmt) REVERT: D 471 MET cc_start: 0.8522 (mtp) cc_final: 0.8267 (mtp) outliers start: 80 outliers final: 54 residues processed: 449 average time/residue: 0.2769 time to fit residues: 181.2902 Evaluate side-chains 443 residues out of total 1632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 388 time to evaluate : 1.495 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 THR Chi-restraints excluded: chain A residue 147 ILE Chi-restraints excluded: chain A residue 180 ILE Chi-restraints excluded: chain A residue 185 SER Chi-restraints excluded: chain A residue 239 ILE Chi-restraints excluded: chain A residue 303 CYS Chi-restraints excluded: chain A residue 402 PHE 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 114 LEU Chi-restraints excluded: chain B residue 129 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 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 289 GLU Chi-restraints excluded: chain B residue 303 CYS Chi-restraints excluded: chain B residue 332 LEU Chi-restraints excluded: chain B residue 445 SER Chi-restraints excluded: chain C residue 79 THR Chi-restraints excluded: chain C residue 129 THR Chi-restraints excluded: chain C residue 147 ILE Chi-restraints excluded: chain C residue 155 THR Chi-restraints excluded: chain C residue 177 ILE Chi-restraints excluded: chain C residue 185 SER Chi-restraints excluded: chain C residue 198 THR Chi-restraints excluded: chain C residue 205 VAL Chi-restraints excluded: chain C residue 219 VAL Chi-restraints excluded: chain C residue 220 ASN Chi-restraints excluded: chain C residue 222 VAL Chi-restraints excluded: chain C residue 248 THR Chi-restraints excluded: chain C residue 266 VAL Chi-restraints excluded: chain C residue 303 CYS Chi-restraints excluded: chain C residue 332 LEU Chi-restraints excluded: chain C residue 451 THR Chi-restraints excluded: chain D residue 79 THR Chi-restraints excluded: chain D residue 129 THR Chi-restraints excluded: chain D residue 147 ILE Chi-restraints excluded: chain D residue 167 ILE Chi-restraints excluded: chain D residue 177 ILE Chi-restraints excluded: chain D residue 185 SER Chi-restraints excluded: chain D residue 198 THR Chi-restraints excluded: chain D residue 205 VAL Chi-restraints excluded: chain D residue 219 VAL Chi-restraints excluded: chain D residue 222 VAL Chi-restraints excluded: chain D residue 266 VAL Chi-restraints excluded: chain D residue 332 LEU Chi-restraints excluded: chain D residue 341 THR Chi-restraints excluded: chain D residue 451 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 184 optimal weight: 0.5980 chunk 74 optimal weight: 5.9990 chunk 109 optimal weight: 2.9990 chunk 110 optimal weight: 0.8980 chunk 91 optimal weight: 2.9990 chunk 117 optimal weight: 0.9990 chunk 78 optimal weight: 2.9990 chunk 57 optimal weight: 1.9990 chunk 183 optimal weight: 0.5980 chunk 62 optimal weight: 2.9990 chunk 155 optimal weight: 2.9990 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 299 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 406 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 72 GLN ** B 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 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** ** C 406 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 406 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3974 r_free = 0.3974 target = 0.189263 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3552 r_free = 0.3552 target = 0.150856 restraints weight = 17096.616| |-----------------------------------------------------------------------------| r_work (start): 0.3539 rms_B_bonded: 2.05 r_work: 0.3421 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work (final): 0.3421 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3426 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3426 r_free = 0.3426 target_work(ls_wunit_k1) = 0.140 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 10 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3426 r_free = 0.3426 target_work(ls_wunit_k1) = 0.140 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 10 | |-----------------------------------------------------------------------------| r_final: 0.3426 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7503 moved from start: 0.5631 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 15488 Z= 0.162 Angle : 0.597 6.464 20972 Z= 0.309 Chirality : 0.046 0.267 2324 Planarity : 0.004 0.037 2712 Dihedral : 5.497 45.405 2116 Min Nonbonded Distance : 2.597 Molprobity Statistics. All-atom Clashscore : 13.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.04 % Favored : 94.96 % Rotamer: Outliers : 4.90 % Allowed : 22.15 % Favored : 72.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.79 (0.20), residues: 1964 helix: 0.26 (0.18), residues: 828 sheet: -1.04 (0.26), residues: 408 loop : -0.96 (0.25), residues: 728 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 77 HIS 0.005 0.001 HIS A 30 PHE 0.030 0.002 PHE C 38 TYR 0.013 0.001 TYR B 426 ARG 0.005 0.000 ARG A 395 Details of bonding type rmsd hydrogen bonds : bond 0.03446 ( 674) hydrogen bonds : angle 4.78220 ( 1935) covalent geometry : bond 0.00392 (15488) covalent geometry : angle 0.59737 (20972) *********************** 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 464 residues out of total 1632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 385 time to evaluate : 1.527 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 57 LYS cc_start: 0.8238 (mmtp) cc_final: 0.7833 (tptm) REVERT: A 101 LEU cc_start: 0.7787 (mt) cc_final: 0.7448 (mp) REVERT: A 177 ILE cc_start: 0.8920 (OUTLIER) cc_final: 0.8413 (mp) REVERT: A 237 MET cc_start: 0.7298 (OUTLIER) cc_final: 0.6457 (mmp) REVERT: A 260 LYS cc_start: 0.7097 (ttmt) cc_final: 0.6784 (pttm) REVERT: A 299 GLN cc_start: 0.7591 (mp10) cc_final: 0.7170 (mt0) REVERT: A 347 ASP cc_start: 0.7094 (p0) cc_final: 0.6198 (m-30) REVERT: A 402 PHE cc_start: 0.7694 (OUTLIER) cc_final: 0.7294 (t80) REVERT: A 429 SER cc_start: 0.9150 (t) cc_final: 0.8883 (t) REVERT: B 22 LYS cc_start: 0.7318 (mttt) cc_final: 0.6915 (mppt) REVERT: B 237 MET cc_start: 0.7546 (mmt) cc_final: 0.6779 (mmp) REVERT: B 367 LYS cc_start: 0.5770 (tptp) cc_final: 0.5533 (tptp) REVERT: B 402 PHE cc_start: 0.7625 (OUTLIER) cc_final: 0.7235 (t80) REVERT: B 499 LYS cc_start: 0.6711 (ttpt) cc_final: 0.6408 (ttpt) REVERT: C 22 LYS cc_start: 0.7173 (mttt) cc_final: 0.6828 (mppt) REVERT: C 237 MET cc_start: 0.7497 (mmt) cc_final: 0.6756 (mmp) REVERT: C 402 PHE cc_start: 0.7640 (OUTLIER) cc_final: 0.7252 (t80) REVERT: C 429 SER cc_start: 0.9156 (t) cc_final: 0.8851 (t) REVERT: C 480 GLU cc_start: 0.7925 (tt0) cc_final: 0.7391 (tt0) REVERT: C 499 LYS cc_start: 0.7049 (ttpt) cc_final: 0.6708 (ttpt) REVERT: D 158 GLU cc_start: 0.8554 (mt-10) cc_final: 0.8295 (mt-10) REVERT: D 237 MET cc_start: 0.7538 (mmt) cc_final: 0.6786 (mmt) REVERT: D 367 LYS cc_start: 0.5756 (tptp) cc_final: 0.5540 (tptp) REVERT: D 402 PHE cc_start: 0.7477 (OUTLIER) cc_final: 0.7093 (t80) REVERT: D 471 MET cc_start: 0.8531 (mtp) cc_final: 0.8309 (mtp) outliers start: 79 outliers final: 62 residues processed: 430 average time/residue: 0.2697 time to fit residues: 170.2362 Evaluate side-chains 444 residues out of total 1632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 376 time to evaluate : 1.524 ------------------------------------------------------------------------------- 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 177 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 222 VAL Chi-restraints excluded: chain A residue 237 MET Chi-restraints excluded: chain A residue 239 ILE Chi-restraints excluded: chain A residue 248 THR Chi-restraints excluded: chain A residue 303 CYS Chi-restraints excluded: chain A residue 402 PHE Chi-restraints excluded: chain A residue 445 SER Chi-restraints excluded: chain B residue 79 THR Chi-restraints excluded: chain B residue 129 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 239 ILE Chi-restraints excluded: chain B residue 248 THR Chi-restraints excluded: chain B residue 266 VAL Chi-restraints excluded: chain B residue 289 GLU Chi-restraints excluded: chain B residue 303 CYS Chi-restraints excluded: chain B residue 332 LEU Chi-restraints excluded: chain B residue 402 PHE Chi-restraints excluded: chain B residue 460 VAL Chi-restraints excluded: chain B residue 494 VAL Chi-restraints excluded: chain C residue 79 THR Chi-restraints excluded: chain C residue 129 THR Chi-restraints excluded: chain C residue 147 ILE Chi-restraints excluded: chain C residue 155 THR Chi-restraints excluded: chain C residue 177 ILE Chi-restraints excluded: chain C residue 185 SER Chi-restraints excluded: chain C residue 205 VAL Chi-restraints excluded: chain C residue 219 VAL Chi-restraints excluded: chain C residue 220 ASN Chi-restraints excluded: chain C residue 222 VAL Chi-restraints excluded: chain C residue 239 ILE Chi-restraints excluded: chain C residue 248 THR Chi-restraints excluded: chain C residue 266 VAL Chi-restraints excluded: chain C residue 303 CYS Chi-restraints excluded: chain C residue 315 ILE Chi-restraints excluded: chain C residue 332 LEU Chi-restraints excluded: chain C residue 402 PHE Chi-restraints excluded: chain C residue 445 SER Chi-restraints excluded: chain C residue 460 VAL Chi-restraints excluded: chain D residue 79 THR Chi-restraints excluded: chain D residue 123 LEU Chi-restraints excluded: chain D residue 129 THR Chi-restraints excluded: chain D residue 147 ILE Chi-restraints excluded: chain D residue 155 THR Chi-restraints excluded: chain D residue 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 239 ILE Chi-restraints excluded: chain D residue 266 VAL Chi-restraints excluded: chain D residue 303 CYS Chi-restraints excluded: chain D residue 332 LEU Chi-restraints excluded: chain D residue 341 THR Chi-restraints excluded: chain D residue 402 PHE 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 9 optimal weight: 5.9990 chunk 48 optimal weight: 1.9990 chunk 71 optimal weight: 3.9990 chunk 31 optimal weight: 0.9980 chunk 124 optimal weight: 1.9990 chunk 115 optimal weight: 0.6980 chunk 149 optimal weight: 6.9990 chunk 118 optimal weight: 1.9990 chunk 27 optimal weight: 3.9990 chunk 97 optimal weight: 0.6980 chunk 86 optimal weight: 0.8980 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 299 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 406 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 72 GLN ** B 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 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** ** C 406 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: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3984 r_free = 0.3984 target = 0.190295 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3558 r_free = 0.3558 target = 0.151562 restraints weight = 17247.719| |-----------------------------------------------------------------------------| r_work (start): 0.3530 rms_B_bonded: 2.09 r_work: 0.3411 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work (final): 0.3411 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3415 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3415 r_free = 0.3415 target_work(ls_wunit_k1) = 0.139 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 10 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3415 r_free = 0.3415 target_work(ls_wunit_k1) = 0.139 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 10 | |-----------------------------------------------------------------------------| r_final: 0.3415 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7510 moved from start: 0.5798 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 15488 Z= 0.164 Angle : 0.600 6.779 20972 Z= 0.310 Chirality : 0.046 0.276 2324 Planarity : 0.004 0.073 2712 Dihedral : 5.491 44.250 2116 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 12.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.84 % Favored : 95.16 % Rotamer: Outliers : 5.27 % Allowed : 22.64 % Favored : 72.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.73 (0.20), residues: 1964 helix: 0.28 (0.18), residues: 832 sheet: -0.98 (0.26), residues: 408 loop : -0.89 (0.26), residues: 724 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP D 169 HIS 0.009 0.001 HIS D 292 PHE 0.025 0.002 PHE C 38 TYR 0.014 0.001 TYR A 330 ARG 0.012 0.000 ARG D 321 Details of bonding type rmsd hydrogen bonds : bond 0.03431 ( 674) hydrogen bonds : angle 4.73776 ( 1935) covalent geometry : bond 0.00400 (15488) covalent geometry : angle 0.59986 (20972) *********************** 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 466 residues out of total 1632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 381 time to evaluate : 2.298 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: 0.8271 (mmtp) cc_final: 0.7823 (tptm) REVERT: A 101 LEU cc_start: 0.7817 (mt) cc_final: 0.7480 (mp) REVERT: A 177 ILE cc_start: 0.8909 (OUTLIER) cc_final: 0.8470 (mp) REVERT: A 237 MET cc_start: 0.7344 (OUTLIER) cc_final: 0.6545 (mmp) REVERT: A 260 LYS cc_start: 0.7137 (ttmt) cc_final: 0.6889 (pttt) REVERT: A 299 GLN cc_start: 0.7581 (mp10) cc_final: 0.6983 (mt0) REVERT: A 402 PHE cc_start: 0.7716 (OUTLIER) cc_final: 0.7294 (t80) REVERT: A 429 SER cc_start: 0.9162 (t) cc_final: 0.8860 (t) REVERT: B 22 LYS cc_start: 0.7410 (mttt) cc_final: 0.7008 (mppt) REVERT: B 237 MET cc_start: 0.7476 (mmt) cc_final: 0.6709 (mmp) REVERT: B 367 LYS cc_start: 0.5776 (tptp) cc_final: 0.5542 (tptp) REVERT: B 402 PHE cc_start: 0.7698 (OUTLIER) cc_final: 0.7273 (t80) REVERT: B 499 LYS cc_start: 0.6679 (ttpt) cc_final: 0.6343 (ttpt) REVERT: C 22 LYS cc_start: 0.7303 (mttt) cc_final: 0.6905 (mppt) REVERT: C 237 MET cc_start: 0.7488 (mmt) cc_final: 0.6719 (mmp) REVERT: C 402 PHE cc_start: 0.7682 (OUTLIER) cc_final: 0.7267 (t80) REVERT: C 429 SER cc_start: 0.9149 (OUTLIER) cc_final: 0.8845 (t) REVERT: C 480 GLU cc_start: 0.7944 (tt0) cc_final: 0.7391 (tt0) REVERT: C 499 LYS cc_start: 0.7044 (ttpt) cc_final: 0.6709 (ttpt) REVERT: D 53 GLU cc_start: 0.8238 (mt-10) cc_final: 0.7990 (mt-10) REVERT: D 237 MET cc_start: 0.7567 (mmt) cc_final: 0.6802 (mmp) REVERT: D 316 TYR cc_start: 0.6967 (t80) cc_final: 0.6427 (t80) REVERT: D 322 ARG cc_start: 0.6466 (mmp80) cc_final: 0.6250 (mmp80) REVERT: D 367 LYS cc_start: 0.5767 (tptp) cc_final: 0.5525 (tptp) REVERT: D 402 PHE cc_start: 0.7531 (OUTLIER) cc_final: 0.7114 (t80) REVERT: D 471 MET cc_start: 0.8523 (mtp) cc_final: 0.8295 (mtp) outliers start: 85 outliers final: 71 residues processed: 428 average time/residue: 0.2743 time to fit residues: 172.8684 Evaluate side-chains 455 residues out of total 1632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 377 time to evaluate : 1.641 ------------------------------------------------------------------------------- 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 177 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 222 VAL Chi-restraints excluded: chain A residue 237 MET Chi-restraints excluded: chain A residue 239 ILE Chi-restraints excluded: chain A residue 248 THR Chi-restraints excluded: chain A residue 303 CYS Chi-restraints excluded: chain A residue 402 PHE Chi-restraints excluded: chain A residue 445 SER Chi-restraints excluded: chain A residue 460 VAL Chi-restraints excluded: chain B residue 79 THR 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 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 289 GLU Chi-restraints excluded: chain B residue 303 CYS Chi-restraints excluded: chain B residue 332 LEU Chi-restraints excluded: chain B residue 402 PHE Chi-restraints excluded: chain B residue 415 ASP 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 129 THR Chi-restraints excluded: chain C residue 147 ILE Chi-restraints excluded: chain C residue 155 THR Chi-restraints excluded: chain C residue 177 ILE Chi-restraints excluded: chain C residue 180 ILE Chi-restraints excluded: chain C residue 185 SER Chi-restraints excluded: chain C residue 205 VAL Chi-restraints excluded: chain C residue 219 VAL Chi-restraints excluded: chain C residue 220 ASN Chi-restraints excluded: chain C residue 222 VAL Chi-restraints excluded: chain C residue 239 ILE Chi-restraints excluded: chain C residue 248 THR Chi-restraints excluded: chain C residue 266 VAL Chi-restraints excluded: chain C residue 303 CYS Chi-restraints excluded: chain C residue 315 ILE Chi-restraints excluded: chain C residue 332 LEU Chi-restraints excluded: chain C residue 402 PHE Chi-restraints excluded: chain C residue 429 SER Chi-restraints excluded: chain C residue 445 SER Chi-restraints excluded: chain C residue 451 THR Chi-restraints excluded: chain C residue 460 VAL Chi-restraints excluded: chain D residue 79 THR Chi-restraints excluded: chain D residue 123 LEU Chi-restraints excluded: chain D residue 129 THR Chi-restraints excluded: chain D residue 147 ILE Chi-restraints excluded: chain D residue 155 THR Chi-restraints excluded: chain D residue 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 205 VAL Chi-restraints excluded: chain D residue 219 VAL Chi-restraints excluded: chain D residue 222 VAL Chi-restraints excluded: chain D residue 239 ILE Chi-restraints excluded: chain D residue 266 VAL Chi-restraints excluded: chain D residue 303 CYS Chi-restraints excluded: chain D residue 315 ILE Chi-restraints excluded: chain D residue 332 LEU Chi-restraints excluded: chain D residue 341 THR Chi-restraints excluded: chain D residue 402 PHE Chi-restraints excluded: chain D residue 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 71 optimal weight: 3.9990 chunk 189 optimal weight: 1.9990 chunk 124 optimal weight: 0.8980 chunk 101 optimal weight: 0.0870 chunk 179 optimal weight: 7.9990 chunk 54 optimal weight: 0.9990 chunk 47 optimal weight: 0.0050 chunk 87 optimal weight: 7.9990 chunk 16 optimal weight: 0.9980 chunk 55 optimal weight: 0.6980 chunk 113 optimal weight: 0.9980 overall best weight: 0.5372 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 72 GLN ** A 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 293 HIS ** A 299 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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** ** D 30 HIS ** 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 = 0.4017 r_free = 0.4017 target = 0.193553 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3607 r_free = 0.3607 target = 0.155395 restraints weight = 17110.354| |-----------------------------------------------------------------------------| r_work (start): 0.3581 rms_B_bonded: 2.07 r_work: 0.3463 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work (final): 0.3463 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3452 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3452 r_free = 0.3452 target_work(ls_wunit_k1) = 0.142 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 10 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3452 r_free = 0.3452 target_work(ls_wunit_k1) = 0.142 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 10 | |-----------------------------------------------------------------------------| r_final: 0.3452 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7458 moved from start: 0.6033 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 15488 Z= 0.120 Angle : 0.575 9.391 20972 Z= 0.296 Chirality : 0.045 0.247 2324 Planarity : 0.004 0.075 2712 Dihedral : 5.234 41.345 2116 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 11.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.74 % Favored : 95.26 % Rotamer: Outliers : 4.16 % Allowed : 24.01 % Favored : 71.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.56 (0.20), residues: 1964 helix: 0.42 (0.19), residues: 828 sheet: -0.80 (0.26), residues: 408 loop : -0.86 (0.25), residues: 728 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP C 169 HIS 0.006 0.001 HIS D 292 PHE 0.023 0.001 PHE B 38 TYR 0.014 0.001 TYR A 330 ARG 0.007 0.000 ARG D 322 Details of bonding type rmsd hydrogen bonds : bond 0.03071 ( 674) hydrogen bonds : angle 4.61693 ( 1935) covalent geometry : bond 0.00292 (15488) covalent geometry : angle 0.57511 (20972) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3928 Ramachandran restraints generated. 1964 Oldfield, 0 Emsley, 1964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3928 Ramachandran restraints generated. 1964 Oldfield, 0 Emsley, 1964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 465 residues out of total 1632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 398 time to evaluate : 1.564 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 53 GLU cc_start: 0.8152 (mt-10) cc_final: 0.7841 (mt-10) REVERT: A 57 LYS cc_start: 0.8256 (mmtp) cc_final: 0.7968 (tppt) REVERT: A 101 LEU cc_start: 0.7922 (mt) cc_final: 0.7586 (mp) REVERT: A 177 ILE cc_start: 0.8939 (OUTLIER) cc_final: 0.8448 (mp) REVERT: A 237 MET cc_start: 0.7325 (OUTLIER) cc_final: 0.6567 (mmp) REVERT: A 260 LYS cc_start: 0.7108 (ttmt) cc_final: 0.6855 (pttt) REVERT: A 299 GLN cc_start: 0.7576 (mp10) cc_final: 0.7148 (mt0) REVERT: A 347 ASP cc_start: 0.7109 (p0) cc_final: 0.6117 (m-30) REVERT: A 402 PHE cc_start: 0.7698 (OUTLIER) cc_final: 0.7369 (t80) REVERT: A 414 LEU cc_start: 0.6934 (tp) cc_final: 0.6624 (tp) REVERT: B 22 LYS cc_start: 0.7295 (mttt) cc_final: 0.6863 (mppt) REVERT: B 53 GLU cc_start: 0.8174 (mt-10) cc_final: 0.7762 (mt-10) REVERT: B 169 TRP cc_start: 0.8768 (p-90) cc_final: 0.8442 (p-90) REVERT: B 237 MET cc_start: 0.7445 (mmt) cc_final: 0.6709 (mmp) REVERT: B 316 TYR cc_start: 0.6956 (t80) cc_final: 0.6283 (t80) REVERT: B 318 GLU cc_start: 0.6835 (tp30) cc_final: 0.6561 (tp30) REVERT: B 367 LYS cc_start: 0.5795 (tptp) cc_final: 0.5477 (tptp) REVERT: B 402 PHE cc_start: 0.7612 (OUTLIER) cc_final: 0.7149 (t80) REVERT: B 499 LYS cc_start: 0.6637 (ttpt) cc_final: 0.6291 (ttpt) REVERT: C 22 LYS cc_start: 0.7129 (mttt) cc_final: 0.6691 (mppt) REVERT: C 53 GLU cc_start: 0.8056 (mt-10) cc_final: 0.7730 (mt-10) REVERT: C 169 TRP cc_start: 0.8804 (p-90) cc_final: 0.8469 (p-90) REVERT: C 237 MET cc_start: 0.7421 (mmt) cc_final: 0.6677 (mmp) REVERT: C 318 GLU cc_start: 0.7247 (tp30) cc_final: 0.6645 (tp30) REVERT: C 322 ARG cc_start: 0.5450 (mmp80) cc_final: 0.5096 (mmp80) REVERT: C 402 PHE cc_start: 0.7617 (OUTLIER) cc_final: 0.7173 (t80) REVERT: C 415 ASP cc_start: 0.8310 (m-30) cc_final: 0.8096 (m-30) REVERT: C 429 SER cc_start: 0.9138 (OUTLIER) cc_final: 0.8817 (t) REVERT: C 480 GLU cc_start: 0.7900 (tt0) cc_final: 0.7351 (tt0) REVERT: D 22 LYS cc_start: 0.7168 (mttt) cc_final: 0.6782 (mppt) REVERT: D 53 GLU cc_start: 0.8130 (mt-10) cc_final: 0.7885 (mt-10) REVERT: D 158 GLU cc_start: 0.8548 (mt-10) cc_final: 0.8342 (mt-10) REVERT: D 237 MET cc_start: 0.7520 (mmt) cc_final: 0.6801 (mmp) REVERT: D 252 LYS cc_start: 0.6908 (mttm) cc_final: 0.6483 (ttmt) REVERT: D 316 TYR cc_start: 0.6957 (t80) cc_final: 0.6225 (t80) REVERT: D 367 LYS cc_start: 0.5807 (tptp) cc_final: 0.5561 (tptp) REVERT: D 402 PHE cc_start: 0.7540 (OUTLIER) cc_final: 0.7083 (t80) REVERT: D 471 MET cc_start: 0.8472 (mtp) cc_final: 0.8231 (mtp) outliers start: 67 outliers final: 51 residues processed: 435 average time/residue: 0.2790 time to fit residues: 178.6373 Evaluate side-chains 436 residues out of total 1632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 378 time to evaluate : 1.580 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 THR Chi-restraints excluded: chain A residue 144 THR Chi-restraints excluded: chain A residue 177 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 222 VAL Chi-restraints excluded: chain A residue 237 MET Chi-restraints excluded: chain A residue 239 ILE Chi-restraints excluded: chain A residue 248 THR Chi-restraints excluded: chain A residue 266 VAL 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 B residue 79 THR Chi-restraints excluded: chain B residue 129 THR 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 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 129 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 220 ASN Chi-restraints excluded: chain C residue 222 VAL Chi-restraints excluded: chain C residue 239 ILE Chi-restraints excluded: chain C residue 248 THR Chi-restraints excluded: chain C residue 266 VAL Chi-restraints excluded: chain C residue 303 CYS Chi-restraints excluded: chain C residue 332 LEU Chi-restraints excluded: chain C residue 402 PHE Chi-restraints excluded: chain C residue 429 SER Chi-restraints excluded: chain C residue 460 VAL Chi-restraints excluded: chain D residue 79 THR Chi-restraints excluded: chain D residue 110 ASN Chi-restraints excluded: chain D residue 123 LEU Chi-restraints excluded: chain D residue 129 THR Chi-restraints excluded: chain D residue 180 ILE Chi-restraints excluded: chain D residue 185 SER Chi-restraints excluded: chain D residue 205 VAL Chi-restraints excluded: chain D residue 219 VAL Chi-restraints excluded: chain D residue 222 VAL Chi-restraints excluded: chain D residue 239 ILE Chi-restraints excluded: chain D residue 266 VAL Chi-restraints excluded: chain D residue 303 CYS Chi-restraints excluded: chain D residue 315 ILE Chi-restraints excluded: chain D residue 332 LEU Chi-restraints excluded: chain D residue 341 THR Chi-restraints excluded: chain D residue 402 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 65 optimal weight: 0.6980 chunk 115 optimal weight: 0.0070 chunk 136 optimal weight: 3.9990 chunk 32 optimal weight: 0.8980 chunk 164 optimal weight: 0.0870 chunk 142 optimal weight: 1.9990 chunk 183 optimal weight: 3.9990 chunk 188 optimal weight: 7.9990 chunk 90 optimal weight: 5.9990 chunk 53 optimal weight: 5.9990 chunk 156 optimal weight: 0.9980 overall best weight: 0.5376 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 72 GLN ** A 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 293 HIS ** A 299 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 406 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 30 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 72 GLN ** D 298 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 299 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4036 r_free = 0.4036 target = 0.195333 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3637 r_free = 0.3637 target = 0.157900 restraints weight = 16969.069| |-----------------------------------------------------------------------------| r_work (start): 0.3610 rms_B_bonded: 2.01 r_work: 0.3491 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work (final): 0.3491 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3470 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3470 r_free = 0.3470 target_work(ls_wunit_k1) = 0.143 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 10 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3470 r_free = 0.3470 target_work(ls_wunit_k1) = 0.143 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 10 | |-----------------------------------------------------------------------------| r_final: 0.3470 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7455 moved from start: 0.6193 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 15488 Z= 0.121 Angle : 0.582 10.312 20972 Z= 0.300 Chirality : 0.045 0.238 2324 Planarity : 0.004 0.037 2712 Dihedral : 4.910 40.031 2110 Min Nonbonded Distance : 2.566 Molprobity Statistics. All-atom Clashscore : 11.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.79 % Favored : 95.21 % Rotamer: Outliers : 4.16 % Allowed : 24.57 % Favored : 71.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.49 (0.20), residues: 1964 helix: 0.46 (0.19), residues: 828 sheet: -0.71 (0.26), residues: 408 loop : -0.84 (0.25), residues: 728 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP D 136 HIS 0.005 0.001 HIS D 292 PHE 0.023 0.001 PHE B 38 TYR 0.014 0.001 TYR C 119 ARG 0.004 0.000 ARG A 395 Details of bonding type rmsd hydrogen bonds : bond 0.03029 ( 674) hydrogen bonds : angle 4.64205 ( 1935) covalent geometry : bond 0.00293 (15488) covalent geometry : angle 0.58153 (20972) *********************** 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 452 residues out of total 1632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 385 time to evaluate : 1.611 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 53 GLU cc_start: 0.8253 (mt-10) cc_final: 0.7895 (mt-10) REVERT: A 57 LYS cc_start: 0.8243 (mmtp) cc_final: 0.7946 (tppt) REVERT: A 101 LEU cc_start: 0.7829 (mt) cc_final: 0.7482 (mp) REVERT: A 177 ILE cc_start: 0.8926 (OUTLIER) cc_final: 0.8442 (mp) REVERT: A 237 MET cc_start: 0.7279 (OUTLIER) cc_final: 0.6610 (mmp) REVERT: A 267 THR cc_start: 0.8505 (p) cc_final: 0.8253 (p) REVERT: A 299 GLN cc_start: 0.7530 (mp10) cc_final: 0.7122 (mt0) REVERT: A 395 ARG cc_start: 0.7545 (mmm-85) cc_final: 0.7152 (mmm-85) REVERT: A 402 PHE cc_start: 0.7684 (OUTLIER) cc_final: 0.7351 (t80) REVERT: B 22 LYS cc_start: 0.7265 (mttt) cc_final: 0.6879 (mppt) REVERT: B 53 GLU cc_start: 0.8118 (mt-10) cc_final: 0.7740 (mt-10) REVERT: B 169 TRP cc_start: 0.8671 (p-90) cc_final: 0.7699 (p-90) REVERT: B 237 MET cc_start: 0.7427 (mmt) cc_final: 0.6706 (mmp) REVERT: B 316 TYR cc_start: 0.6942 (t80) cc_final: 0.6196 (t80) REVERT: B 367 LYS cc_start: 0.5814 (tptp) cc_final: 0.5094 (tptp) REVERT: B 369 GLU cc_start: 0.7062 (mm-30) cc_final: 0.6777 (mm-30) REVERT: B 402 PHE cc_start: 0.7636 (OUTLIER) cc_final: 0.7164 (t80) REVERT: B 499 LYS cc_start: 0.6638 (ttpt) cc_final: 0.6302 (ttpt) REVERT: C 22 LYS cc_start: 0.7140 (mttt) cc_final: 0.6725 (mppt) REVERT: C 53 GLU cc_start: 0.8076 (mt-10) cc_final: 0.7747 (mt-10) REVERT: C 169 TRP cc_start: 0.8762 (p-90) cc_final: 0.8475 (p-90) REVERT: C 237 MET cc_start: 0.7393 (mmt) cc_final: 0.6657 (mmp) REVERT: C 318 GLU cc_start: 0.7299 (tp30) cc_final: 0.7019 (tp30) REVERT: C 402 PHE cc_start: 0.7623 (OUTLIER) cc_final: 0.7163 (t80) REVERT: C 410 LYS cc_start: 0.7882 (ttpt) cc_final: 0.7589 (ptmm) REVERT: C 429 SER cc_start: 0.9129 (OUTLIER) cc_final: 0.8799 (t) REVERT: C 438 ASP cc_start: 0.6834 (t0) cc_final: 0.6595 (t0) REVERT: C 480 GLU cc_start: 0.7915 (tt0) cc_final: 0.7398 (tt0) REVERT: D 22 LYS cc_start: 0.7101 (mttt) cc_final: 0.6684 (mppt) REVERT: D 169 TRP cc_start: 0.8669 (p-90) cc_final: 0.7690 (p-90) REVERT: D 237 MET cc_start: 0.7505 (mmt) cc_final: 0.6773 (mmp) REVERT: D 252 LYS cc_start: 0.6878 (mttm) cc_final: 0.6490 (ttmt) REVERT: D 402 PHE cc_start: 0.7554 (OUTLIER) cc_final: 0.7086 (t80) REVERT: D 471 MET cc_start: 0.8402 (mtp) cc_final: 0.8135 (mtp) outliers start: 67 outliers final: 52 residues processed: 423 average time/residue: 0.2695 time to fit residues: 168.4150 Evaluate side-chains 443 residues out of total 1632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 384 time to evaluate : 1.581 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 THR Chi-restraints excluded: chain A residue 144 THR Chi-restraints excluded: chain A residue 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 237 MET Chi-restraints excluded: chain A residue 239 ILE Chi-restraints excluded: chain A residue 248 THR Chi-restraints excluded: chain A residue 303 CYS Chi-restraints excluded: chain A residue 402 PHE Chi-restraints excluded: chain A residue 445 SER Chi-restraints excluded: chain B residue 79 THR 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 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 460 VAL Chi-restraints excluded: chain B residue 494 VAL Chi-restraints excluded: chain C residue 79 THR Chi-restraints excluded: chain C residue 110 ASN Chi-restraints excluded: chain C residue 123 LEU Chi-restraints excluded: chain C residue 129 THR Chi-restraints excluded: chain C residue 160 ILE Chi-restraints excluded: chain C residue 177 ILE Chi-restraints excluded: chain C residue 185 SER Chi-restraints excluded: chain C residue 219 VAL Chi-restraints excluded: chain C residue 220 ASN Chi-restraints excluded: chain C residue 222 VAL Chi-restraints excluded: chain C residue 239 ILE Chi-restraints excluded: chain C residue 248 THR Chi-restraints excluded: chain C residue 266 VAL Chi-restraints excluded: chain C residue 303 CYS Chi-restraints excluded: chain C residue 332 LEU Chi-restraints excluded: chain C residue 402 PHE Chi-restraints excluded: chain C residue 429 SER Chi-restraints excluded: chain C residue 460 VAL Chi-restraints excluded: chain D residue 79 THR Chi-restraints excluded: chain D residue 123 LEU Chi-restraints excluded: chain D residue 129 THR Chi-restraints excluded: chain D residue 160 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 239 ILE Chi-restraints excluded: chain D residue 266 VAL Chi-restraints excluded: chain D residue 303 CYS Chi-restraints excluded: chain D residue 315 ILE Chi-restraints excluded: chain D residue 332 LEU Chi-restraints excluded: chain D residue 341 THR Chi-restraints excluded: chain D residue 402 PHE Chi-restraints excluded: chain D residue 451 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 70 optimal weight: 0.9990 chunk 190 optimal weight: 1.9990 chunk 121 optimal weight: 0.9990 chunk 137 optimal weight: 0.5980 chunk 1 optimal weight: 0.0170 chunk 187 optimal weight: 3.9990 chunk 3 optimal weight: 0.0970 chunk 46 optimal weight: 2.9990 chunk 33 optimal weight: 0.6980 chunk 153 optimal weight: 0.0870 chunk 0 optimal weight: 9.9990 overall best weight: 0.2994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 72 GLN A 293 HIS ** A 299 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** 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 30 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 72 GLN ** D 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 298 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 299 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4056 r_free = 0.4056 target = 0.198884 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3656 r_free = 0.3656 target = 0.159663 restraints weight = 16939.286| |-----------------------------------------------------------------------------| r_work (start): 0.3607 rms_B_bonded: 2.05 r_work: 0.3487 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work (final): 0.3487 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3480 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3480 r_free = 0.3480 target_work(ls_wunit_k1) = 0.144 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 10 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3480 r_free = 0.3480 target_work(ls_wunit_k1) = 0.144 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 10 | |-----------------------------------------------------------------------------| r_final: 0.3480 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7411 moved from start: 0.6398 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= 0.111 Angle : 0.593 11.399 20972 Z= 0.304 Chirality : 0.044 0.201 2324 Planarity : 0.004 0.039 2712 Dihedral : 4.789 39.635 2110 Min Nonbonded Distance : 2.596 Molprobity Statistics. All-atom Clashscore : 11.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.48 % Favored : 95.52 % Rotamer: Outliers : 3.16 % Allowed : 25.99 % Favored : 70.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.40 (0.20), residues: 1964 helix: 0.48 (0.19), residues: 832 sheet: -0.56 (0.26), residues: 408 loop : -0.79 (0.25), residues: 724 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP D 136 HIS 0.004 0.001 HIS A 30 PHE 0.022 0.001 PHE B 38 TYR 0.015 0.001 TYR B 119 ARG 0.008 0.000 ARG B 321 Details of bonding type rmsd hydrogen bonds : bond 0.02960 ( 674) hydrogen bonds : angle 4.57109 ( 1935) covalent geometry : bond 0.00269 (15488) covalent geometry : angle 0.59265 (20972) ********************** 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 436 residues out of total 1632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 385 time to evaluate : 1.621 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: 0.8054 (mt-10) cc_final: 0.7729 (mt-10) REVERT: A 57 LYS cc_start: 0.8131 (mmtp) cc_final: 0.7927 (tppt) REVERT: A 101 LEU cc_start: 0.7805 (mt) cc_final: 0.7454 (mp) REVERT: A 177 ILE cc_start: 0.8827 (OUTLIER) cc_final: 0.8400 (mp) REVERT: A 237 MET cc_start: 0.7199 (OUTLIER) cc_final: 0.6458 (mmp) REVERT: A 267 THR cc_start: 0.8567 (p) cc_final: 0.8136 (p) REVERT: A 299 GLN cc_start: 0.7583 (mp10) cc_final: 0.7235 (mt0) REVERT: A 367 LYS cc_start: 0.5695 (mmtm) cc_final: 0.5445 (tppt) REVERT: A 395 ARG cc_start: 0.7540 (mmm-85) cc_final: 0.7146 (mmm-85) REVERT: A 402 PHE cc_start: 0.7715 (OUTLIER) cc_final: 0.7342 (t80) REVERT: B 22 LYS cc_start: 0.7161 (mttt) cc_final: 0.6762 (mppt) REVERT: B 53 GLU cc_start: 0.8047 (mt-10) cc_final: 0.7708 (mt-10) REVERT: B 158 GLU cc_start: 0.8564 (mt-10) cc_final: 0.8344 (mt-10) REVERT: B 237 MET cc_start: 0.7324 (mmt) cc_final: 0.6683 (mmt) REVERT: B 299 GLN cc_start: 0.7593 (mp10) cc_final: 0.7283 (mt0) REVERT: B 318 GLU cc_start: 0.7032 (tp30) cc_final: 0.6415 (tp30) REVERT: B 322 ARG cc_start: 0.5699 (mmp80) cc_final: 0.5196 (mmp80) REVERT: B 367 LYS cc_start: 0.5940 (tptp) cc_final: 0.5163 (tptp) REVERT: B 369 GLU cc_start: 0.7167 (mm-30) cc_final: 0.6887 (mm-30) REVERT: B 402 PHE cc_start: 0.7587 (OUTLIER) cc_final: 0.7127 (t80) REVERT: B 499 LYS cc_start: 0.6627 (ttpt) cc_final: 0.6291 (ttpt) REVERT: C 22 LYS cc_start: 0.7054 (mttt) cc_final: 0.6675 (mppt) REVERT: C 53 GLU cc_start: 0.8007 (mt-10) cc_final: 0.7680 (mt-10) REVERT: C 237 MET cc_start: 0.7451 (mmt) cc_final: 0.6785 (mmp) REVERT: C 318 GLU cc_start: 0.7336 (tp30) cc_final: 0.7008 (tp30) REVERT: C 402 PHE cc_start: 0.7556 (OUTLIER) cc_final: 0.7104 (t80) REVERT: C 410 LYS cc_start: 0.7764 (ttpt) cc_final: 0.7492 (ptmm) REVERT: C 429 SER cc_start: 0.9106 (OUTLIER) cc_final: 0.8762 (t) REVERT: C 480 GLU cc_start: 0.7950 (tt0) cc_final: 0.7412 (tt0) REVERT: D 22 LYS cc_start: 0.7044 (mttt) cc_final: 0.6626 (mppt) REVERT: D 237 MET cc_start: 0.7436 (mmt) cc_final: 0.6709 (mmp) REVERT: D 252 LYS cc_start: 0.6901 (mttm) cc_final: 0.6546 (ttmt) REVERT: D 318 GLU cc_start: 0.7152 (tp30) cc_final: 0.6750 (tp30) REVERT: D 402 PHE cc_start: 0.7583 (OUTLIER) cc_final: 0.7061 (t80) REVERT: D 471 MET cc_start: 0.8344 (mtp) cc_final: 0.8117 (mtp) outliers start: 51 outliers final: 41 residues processed: 414 average time/residue: 0.3004 time to fit residues: 184.0692 Evaluate side-chains 422 residues out of total 1632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 374 time to evaluate : 1.729 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 THR Chi-restraints excluded: chain A residue 177 ILE Chi-restraints excluded: chain A residue 222 VAL Chi-restraints excluded: chain A residue 237 MET Chi-restraints excluded: chain A residue 239 ILE Chi-restraints excluded: chain A residue 248 THR Chi-restraints excluded: chain A residue 303 CYS Chi-restraints excluded: chain A residue 402 PHE Chi-restraints excluded: chain B residue 79 THR Chi-restraints excluded: chain B residue 129 THR 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 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 C residue 79 THR Chi-restraints excluded: chain C residue 123 LEU Chi-restraints excluded: chain C residue 129 THR Chi-restraints excluded: chain C residue 160 ILE Chi-restraints excluded: chain C residue 185 SER Chi-restraints excluded: chain C residue 219 VAL Chi-restraints excluded: chain C residue 220 ASN Chi-restraints excluded: chain C residue 222 VAL Chi-restraints excluded: chain C residue 239 ILE Chi-restraints excluded: chain C residue 266 VAL Chi-restraints excluded: chain C residue 303 CYS Chi-restraints excluded: chain C residue 332 LEU Chi-restraints excluded: chain C residue 402 PHE Chi-restraints excluded: chain C residue 429 SER Chi-restraints excluded: chain D residue 79 THR Chi-restraints excluded: chain D residue 123 LEU Chi-restraints excluded: chain D residue 129 THR Chi-restraints excluded: chain D residue 160 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 239 ILE Chi-restraints excluded: chain D residue 266 VAL Chi-restraints excluded: chain D residue 303 CYS Chi-restraints excluded: chain D residue 315 ILE Chi-restraints excluded: chain D residue 332 LEU Chi-restraints excluded: chain D residue 341 THR Chi-restraints excluded: chain D residue 402 PHE Chi-restraints excluded: chain D residue 451 THR Chi-restraints excluded: chain D residue 460 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 27 optimal weight: 3.9990 chunk 142 optimal weight: 0.9990 chunk 84 optimal weight: 2.9990 chunk 16 optimal weight: 0.8980 chunk 124 optimal weight: 0.7980 chunk 155 optimal weight: 3.9990 chunk 193 optimal weight: 4.9990 chunk 180 optimal weight: 0.6980 chunk 136 optimal weight: 6.9990 chunk 52 optimal weight: 0.0070 chunk 187 optimal weight: 6.9990 overall best weight: 0.6800 ------------------------------------------------------------------------------- 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 ** 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** 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 Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4014 r_free = 0.4014 target = 0.194537 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3594 r_free = 0.3594 target = 0.154328 restraints weight = 16891.250| |-----------------------------------------------------------------------------| r_work (start): 0.3582 rms_B_bonded: 2.07 r_work: 0.3462 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work (final): 0.3462 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3451 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3451 r_free = 0.3451 target_work(ls_wunit_k1) = 0.142 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 10 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3451 r_free = 0.3451 target_work(ls_wunit_k1) = 0.142 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 10 | |-----------------------------------------------------------------------------| r_final: 0.3451 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7448 moved from start: 0.6409 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.073 15488 Z= 0.134 Angle : 0.615 11.906 20972 Z= 0.314 Chirality : 0.045 0.196 2324 Planarity : 0.004 0.041 2712 Dihedral : 4.873 40.205 2110 Min Nonbonded Distance : 2.600 Molprobity Statistics. All-atom Clashscore : 12.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.33 % Favored : 95.67 % Rotamer: Outliers : 3.41 % Allowed : 26.05 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.42 (0.20), residues: 1964 helix: 0.44 (0.19), residues: 832 sheet: -0.60 (0.26), residues: 408 loop : -0.76 (0.25), residues: 724 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 136 HIS 0.005 0.001 HIS D 292 PHE 0.021 0.002 PHE C 38 TYR 0.014 0.001 TYR A 119 ARG 0.010 0.001 ARG B 322 Details of bonding type rmsd hydrogen bonds : bond 0.03097 ( 674) hydrogen bonds : angle 4.56654 ( 1935) covalent geometry : bond 0.00332 (15488) covalent geometry : angle 0.61498 (20972) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7299.62 seconds wall clock time: 126 minutes 50.14 seconds (7610.14 seconds total)