Starting phenix.real_space_refine on Tue Apr 9 03:06:44 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dno_27575/04_2024/8dno_27575.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dno_27575/04_2024/8dno_27575.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dno_27575/04_2024/8dno_27575.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dno_27575/04_2024/8dno_27575.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dno_27575/04_2024/8dno_27575.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dno_27575/04_2024/8dno_27575.pdb" } 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 Symmetric amino acids flipped None Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/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: 7.90, per 1000 atoms: 0.52 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 - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 6.20 Conformation dependent library (CDL) restraints added in 3.0 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: 1.63 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: 5.26 Time building geometry restraints manager: 6.62 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: 100.31 - 107.05: 712 107.05 - 113.78: 8451 113.78 - 120.52: 6680 120.52 - 127.25: 4949 127.25 - 133.99: 180 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 2.520 nonbonded pdb=" O ILE A 401 " pdb=" N GLY A 403 " model vdw 2.298 2.520 nonbonded pdb=" O ILE D 401 " pdb=" N GLY D 403 " model vdw 2.298 2.520 nonbonded pdb=" O ILE B 401 " pdb=" N GLY B 403 " model vdw 2.299 2.520 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 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.50 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.850 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: 4.240 Check model and map are aligned: 0.200 Set scattering table: 0.120 Process input model: 42.620 Find NCS groups from input model: 1.080 Set up NCS constraints: 0.100 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.810 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 52.050 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7218 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.013 0.057 15488 Z= 0.821 Angle : 1.453 9.925 20972 Z= 0.973 Chirality : 0.061 0.205 2324 Planarity : 0.006 0.070 2712 Dihedral : 13.087 89.530 5672 Min Nonbonded Distance : 2.298 Molprobity Statistics. All-atom Clashscore : 40.43 Ramachandran Plot: Outliers : 2.65 % Allowed : 10.39 % Favored : 86.97 % Rotamer: Outliers : 4.71 % Allowed : 9.93 % Favored : 85.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.22 (0.15), residues: 1964 helix: -2.67 (0.14), residues: 784 sheet: -2.45 (0.24), residues: 388 loop : -2.92 (0.19), residues: 792 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP D 29 HIS 0.007 0.002 HIS D 484 PHE 0.018 0.003 PHE B 24 TYR 0.018 0.002 TYR D 154 ARG 0.006 0.001 ARG D 143 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3928 Ramachandran restraints generated. 1964 Oldfield, 0 Emsley, 1964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3928 Ramachandran restraints generated. 1964 Oldfield, 0 Emsley, 1964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 659 residues out of total 1632 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 76 poor density : 583 time to evaluate : 1.762 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: 0.3131 time to fit residues: 271.2461 Evaluate side-chains 488 residues out of total 1632 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 461 time to evaluate : 1.536 ------------------------------------------------------------------------------- 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: 0.8980 chunk 82 optimal weight: 1.9990 chunk 50 optimal weight: 1.9990 chunk 100 optimal weight: 0.9990 chunk 79 optimal weight: 0.6980 chunk 153 optimal weight: 0.9990 chunk 59 optimal weight: 0.5980 chunk 93 optimal weight: 0.9990 chunk 114 optimal weight: 0.6980 chunk 177 optimal weight: 0.5980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 19 GLN ** A 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 293 HIS ** A 299 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 301 GLN A 345 GLN B 19 GLN ** B 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 293 HIS B 301 GLN ** B 345 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 407 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 498 GLN C 19 GLN ** C 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 293 HIS C 301 GLN ** C 345 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 407 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 498 GLN D 19 GLN D 293 HIS D 301 GLN ** D 345 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 498 GLN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7212 moved from start: 0.3497 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 15488 Z= 0.229 Angle : 0.671 10.963 20972 Z= 0.344 Chirality : 0.046 0.259 2324 Planarity : 0.005 0.036 2712 Dihedral : 7.440 59.893 2170 Min Nonbonded Distance : 2.178 Molprobity Statistics. All-atom Clashscore : 18.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.04 % Favored : 94.96 % Rotamer: Outliers : 3.47 % Allowed : 17.99 % Favored : 78.54 % 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: -1.87 (0.18), residues: 1964 helix: -0.34 (0.17), residues: 828 sheet: -1.75 (0.25), residues: 404 loop : -1.81 (0.23), residues: 732 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 29 HIS 0.004 0.001 HIS A 298 PHE 0.021 0.002 PHE A 402 TYR 0.019 0.002 TYR A 351 ARG 0.007 0.000 ARG A 395 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3928 Ramachandran restraints generated. 1964 Oldfield, 0 Emsley, 1964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3928 Ramachandran restraints generated. 1964 Oldfield, 0 Emsley, 1964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 525 residues out of total 1632 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 469 time to evaluate : 1.754 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 158 GLU cc_start: 0.8165 (mt-10) cc_final: 0.7704 (mt-10) REVERT: A 266 VAL cc_start: 0.8189 (OUTLIER) cc_final: 0.7988 (t) REVERT: A 347 ASP cc_start: 0.6485 (p0) cc_final: 0.6200 (m-30) REVERT: A 471 MET cc_start: 0.8466 (mtp) cc_final: 0.8084 (mtp) REVERT: B 53 GLU cc_start: 0.6293 (mt-10) cc_final: 0.6080 (mt-10) REVERT: B 237 MET cc_start: 0.6107 (mmt) cc_final: 0.5298 (mmt) REVERT: B 410 LYS cc_start: 0.7780 (ttpt) cc_final: 0.7502 (tttm) REVERT: B 499 LYS cc_start: 0.6098 (ttpt) cc_final: 0.5890 (ttpt) REVERT: C 237 MET cc_start: 0.6199 (mmt) cc_final: 0.5420 (mmt) REVERT: C 410 LYS cc_start: 0.7769 (ttpt) cc_final: 0.7504 (tttm) REVERT: C 471 MET cc_start: 0.7947 (mtp) cc_final: 0.7556 (mtp) REVERT: D 237 MET cc_start: 0.6125 (mmt) cc_final: 0.5708 (mmt) REVERT: D 273 LYS cc_start: 0.7530 (tptt) cc_final: 0.7215 (tptt) REVERT: D 410 LYS cc_start: 0.7776 (ttpt) cc_final: 0.7505 (tttm) outliers start: 56 outliers final: 40 residues processed: 506 average time/residue: 0.2764 time to fit residues: 204.4650 Evaluate side-chains 429 residues out of total 1632 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 388 time to evaluate : 1.700 ------------------------------------------------------------------------------- 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 266 VAL Chi-restraints excluded: chain A residue 279 LEU Chi-restraints excluded: chain A residue 332 LEU Chi-restraints excluded: chain A residue 445 SER Chi-restraints excluded: chain A residue 460 VAL Chi-restraints excluded: chain B residue 51 GLN 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 185 SER Chi-restraints excluded: chain B residue 222 VAL Chi-restraints excluded: chain B residue 266 VAL Chi-restraints excluded: chain B residue 279 LEU Chi-restraints excluded: chain B residue 299 GLN Chi-restraints excluded: chain B residue 332 LEU Chi-restraints excluded: chain B residue 424 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 185 SER Chi-restraints excluded: chain C residue 222 VAL Chi-restraints excluded: chain C residue 266 VAL Chi-restraints excluded: chain C residue 279 LEU Chi-restraints excluded: chain C residue 299 GLN Chi-restraints excluded: chain C residue 332 LEU Chi-restraints excluded: chain C residue 424 THR 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 185 SER Chi-restraints excluded: chain D residue 222 VAL Chi-restraints excluded: chain D residue 266 VAL Chi-restraints excluded: chain D residue 279 LEU Chi-restraints excluded: chain D residue 299 GLN Chi-restraints excluded: chain D residue 332 LEU Chi-restraints excluded: chain D residue 341 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 98 optimal weight: 10.0000 chunk 55 optimal weight: 0.9980 chunk 148 optimal weight: 0.6980 chunk 121 optimal weight: 0.9980 chunk 49 optimal weight: 10.0000 chunk 178 optimal weight: 5.9990 chunk 192 optimal weight: 0.0170 chunk 158 optimal weight: 4.9990 chunk 176 optimal weight: 5.9990 chunk 60 optimal weight: 4.9990 chunk 143 optimal weight: 0.7980 overall best weight: 0.7018 ------------------------------------------------------------------------------- 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 406 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 448 GLN A 498 GLN ** B 30 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 72 GLN ** B 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 345 GLN ** B 407 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 30 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 51 GLN C 72 GLN ** C 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 345 GLN ** D 30 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 72 GLN D 345 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7251 moved from start: 0.4401 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 15488 Z= 0.221 Angle : 0.603 7.751 20972 Z= 0.309 Chirality : 0.044 0.234 2324 Planarity : 0.004 0.036 2712 Dihedral : 5.981 56.710 2129 Min Nonbonded Distance : 2.219 Molprobity Statistics. All-atom Clashscore : 15.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.70 % Favored : 94.30 % Rotamer: Outliers : 4.84 % Allowed : 20.04 % Favored : 75.12 % 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: -0.94 (0.19), residues: 1964 helix: 0.29 (0.19), residues: 824 sheet: -1.18 (0.25), residues: 396 loop : -1.20 (0.24), residues: 744 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 29 HIS 0.003 0.001 HIS D 30 PHE 0.016 0.002 PHE A 402 TYR 0.016 0.001 TYR A 20 ARG 0.004 0.000 ARG A 395 *********************** 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 493 residues out of total 1632 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 78 poor density : 415 time to evaluate : 1.667 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 158 GLU cc_start: 0.8131 (mt-10) cc_final: 0.7688 (mt-10) REVERT: A 169 TRP cc_start: 0.8644 (p-90) cc_final: 0.8097 (p-90) REVERT: A 177 ILE cc_start: 0.8653 (OUTLIER) cc_final: 0.8334 (mp) REVERT: A 266 VAL cc_start: 0.8035 (OUTLIER) cc_final: 0.7770 (t) REVERT: A 273 LYS cc_start: 0.7932 (tptm) cc_final: 0.7441 (tptt) REVERT: A 471 MET cc_start: 0.8615 (mtp) cc_final: 0.8199 (mtp) REVERT: B 53 GLU cc_start: 0.6626 (mt-10) cc_final: 0.6310 (mt-10) REVERT: B 110 ASN cc_start: 0.7211 (t0) cc_final: 0.6929 (t160) REVERT: B 177 ILE cc_start: 0.8614 (OUTLIER) cc_final: 0.8316 (mp) REVERT: B 237 MET cc_start: 0.6116 (mmt) cc_final: 0.5627 (mmt) REVERT: B 410 LYS cc_start: 0.7880 (ttpt) cc_final: 0.7587 (tttm) REVERT: C 110 ASN cc_start: 0.7203 (t0) cc_final: 0.6957 (t160) REVERT: C 139 LYS cc_start: 0.7522 (mttp) cc_final: 0.7237 (mttm) REVERT: C 237 MET cc_start: 0.6140 (mmt) cc_final: 0.5630 (mmt) REVERT: C 410 LYS cc_start: 0.7848 (ttpt) cc_final: 0.7498 (tttm) REVERT: C 471 MET cc_start: 0.8055 (mtp) cc_final: 0.7628 (mtp) REVERT: D 110 ASN cc_start: 0.7233 (t0) cc_final: 0.6950 (t160) REVERT: D 237 MET cc_start: 0.6055 (mmt) cc_final: 0.5605 (mmt) REVERT: D 410 LYS cc_start: 0.7847 (ttpt) cc_final: 0.7593 (tttm) outliers start: 78 outliers final: 42 residues processed: 460 average time/residue: 0.2977 time to fit residues: 197.1197 Evaluate side-chains 441 residues out of total 1632 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 396 time to evaluate : 1.675 ------------------------------------------------------------------------------- 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 185 SER Chi-restraints excluded: chain A residue 205 VAL Chi-restraints excluded: chain A residue 239 ILE Chi-restraints excluded: chain A residue 266 VAL Chi-restraints excluded: chain A residue 279 LEU Chi-restraints excluded: chain A residue 332 LEU Chi-restraints excluded: chain A residue 424 THR Chi-restraints excluded: chain B residue 79 THR Chi-restraints excluded: chain B residue 177 ILE Chi-restraints excluded: chain B residue 185 SER Chi-restraints excluded: chain B residue 219 VAL Chi-restraints excluded: chain B residue 222 VAL Chi-restraints excluded: chain B residue 248 THR Chi-restraints excluded: chain B residue 261 SER Chi-restraints excluded: chain B residue 266 VAL Chi-restraints excluded: chain B residue 299 GLN Chi-restraints excluded: chain B residue 332 LEU Chi-restraints excluded: chain B residue 424 THR Chi-restraints excluded: chain B residue 494 VAL Chi-restraints excluded: chain C residue 79 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 219 VAL Chi-restraints excluded: chain C residue 248 THR Chi-restraints excluded: chain C residue 266 VAL Chi-restraints excluded: chain C residue 299 GLN Chi-restraints excluded: chain C residue 332 LEU Chi-restraints excluded: chain C residue 424 THR 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 177 ILE Chi-restraints excluded: chain D residue 185 SER Chi-restraints excluded: chain D residue 219 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 424 THR Chi-restraints excluded: chain D residue 494 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 176 optimal weight: 6.9990 chunk 134 optimal weight: 7.9990 chunk 92 optimal weight: 2.9990 chunk 19 optimal weight: 1.9990 chunk 85 optimal weight: 7.9990 chunk 119 optimal weight: 3.9990 chunk 178 optimal weight: 5.9990 chunk 189 optimal weight: 3.9990 chunk 93 optimal weight: 0.8980 chunk 169 optimal weight: 4.9990 chunk 51 optimal weight: 7.9990 overall best weight: 2.7788 ------------------------------------------------------------------------------- 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 298 HIS ** 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 389 ASN ** C 30 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 72 GLN ** D 30 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 72 GLN ** D 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7453 moved from start: 0.4921 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.065 15488 Z= 0.516 Angle : 0.779 9.654 20972 Z= 0.403 Chirality : 0.053 0.305 2324 Planarity : 0.005 0.034 2712 Dihedral : 6.532 60.053 2123 Min Nonbonded Distance : 2.070 Molprobity Statistics. All-atom Clashscore : 17.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.77 % Favored : 93.23 % Rotamer: Outliers : 7.51 % Allowed : 19.23 % Favored : 73.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.25 (0.19), residues: 1964 helix: -0.14 (0.18), residues: 828 sheet: -1.25 (0.26), residues: 396 loop : -1.20 (0.24), residues: 740 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 29 HIS 0.014 0.002 HIS B 292 PHE 0.024 0.003 PHE C 402 TYR 0.017 0.002 TYR B 330 ARG 0.007 0.001 ARG A 85 *********************** 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 550 residues out of total 1632 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 121 poor density : 429 time to evaluate : 1.683 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 20 TYR cc_start: 0.6338 (m-80) cc_final: 0.5803 (m-80) REVERT: A 57 LYS cc_start: 0.7918 (mmtm) cc_final: 0.7693 (tptm) REVERT: A 177 ILE cc_start: 0.8947 (OUTLIER) cc_final: 0.8618 (mp) REVERT: A 273 LYS cc_start: 0.8300 (tptm) cc_final: 0.7782 (tptt) REVERT: A 369 GLU cc_start: 0.6773 (mm-30) cc_final: 0.6556 (mm-30) REVERT: B 177 ILE cc_start: 0.8642 (OUTLIER) cc_final: 0.8418 (mp) REVERT: B 410 LYS cc_start: 0.7940 (ttpt) cc_final: 0.7693 (tttm) REVERT: C 177 ILE cc_start: 0.8596 (OUTLIER) cc_final: 0.8257 (mp) REVERT: C 471 MET cc_start: 0.8176 (mtp) cc_final: 0.7788 (mtp) REVERT: C 480 GLU cc_start: 0.7797 (tt0) cc_final: 0.7252 (tt0) REVERT: D 177 ILE cc_start: 0.8642 (OUTLIER) cc_final: 0.8436 (mp) REVERT: D 273 LYS cc_start: 0.8153 (tptt) cc_final: 0.7846 (tptp) REVERT: D 471 MET cc_start: 0.8307 (mtp) cc_final: 0.8048 (mtp) outliers start: 121 outliers final: 92 residues processed: 481 average time/residue: 0.2926 time to fit residues: 202.1708 Evaluate side-chains 483 residues out of total 1632 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 96 poor density : 387 time to evaluate : 1.681 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 VAL Chi-restraints excluded: chain A residue 79 THR Chi-restraints excluded: chain A residue 83 SER Chi-restraints excluded: chain A residue 114 LEU Chi-restraints excluded: chain A residue 129 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 196 GLU 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 239 ILE Chi-restraints excluded: chain A residue 267 THR Chi-restraints excluded: chain A residue 279 LEU Chi-restraints excluded: chain A residue 303 CYS Chi-restraints excluded: chain A residue 332 LEU Chi-restraints excluded: chain A residue 390 VAL Chi-restraints excluded: chain A residue 424 THR Chi-restraints excluded: chain A residue 442 THR Chi-restraints excluded: chain A residue 451 THR Chi-restraints excluded: chain A residue 494 VAL Chi-restraints excluded: chain B residue 79 THR Chi-restraints excluded: chain B residue 114 LEU Chi-restraints excluded: chain B residue 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 196 GLU Chi-restraints excluded: chain B residue 205 VAL Chi-restraints excluded: chain B residue 219 VAL Chi-restraints excluded: chain B residue 222 VAL Chi-restraints excluded: chain B residue 248 THR Chi-restraints excluded: chain B residue 261 SER 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 303 CYS Chi-restraints excluded: chain B residue 332 LEU Chi-restraints excluded: chain B residue 424 THR Chi-restraints excluded: chain B residue 425 PHE Chi-restraints excluded: chain B residue 441 ILE Chi-restraints excluded: chain B residue 460 VAL Chi-restraints excluded: chain B residue 494 VAL Chi-restraints excluded: chain C residue 40 VAL Chi-restraints excluded: chain C residue 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 167 ILE Chi-restraints excluded: chain C residue 177 ILE Chi-restraints excluded: chain C residue 185 SER Chi-restraints excluded: chain C residue 196 GLU Chi-restraints excluded: chain C residue 205 VAL Chi-restraints excluded: chain C residue 219 VAL Chi-restraints excluded: chain C residue 221 ILE Chi-restraints excluded: chain C residue 222 VAL Chi-restraints excluded: chain C residue 248 THR Chi-restraints excluded: chain C residue 254 ILE Chi-restraints excluded: chain C residue 266 VAL Chi-restraints excluded: chain C residue 299 GLN 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 424 THR 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 79 THR 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 196 GLU Chi-restraints excluded: chain D residue 205 VAL Chi-restraints excluded: chain D residue 219 VAL Chi-restraints excluded: chain D residue 221 ILE Chi-restraints excluded: chain D residue 222 VAL Chi-restraints excluded: chain D residue 248 THR Chi-restraints excluded: chain D residue 266 VAL Chi-restraints excluded: chain D residue 299 GLN 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 424 THR Chi-restraints excluded: chain D residue 441 ILE Chi-restraints excluded: chain D residue 451 THR Chi-restraints excluded: chain D residue 460 VAL Chi-restraints excluded: chain D residue 494 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 157 optimal weight: 2.9990 chunk 107 optimal weight: 3.9990 chunk 2 optimal weight: 8.9990 chunk 141 optimal weight: 0.6980 chunk 78 optimal weight: 0.5980 chunk 161 optimal weight: 0.5980 chunk 130 optimal weight: 6.9990 chunk 0 optimal weight: 10.0000 chunk 96 optimal weight: 1.9990 chunk 170 optimal weight: 0.9990 chunk 47 optimal weight: 0.6980 overall best weight: 0.7182 ------------------------------------------------------------------------------- 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 298 HIS ** 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 204 HIS ** B 406 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 72 GLN C 204 HIS ** C 406 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 72 GLN ** 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7338 moved from start: 0.5397 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 15488 Z= 0.224 Angle : 0.573 6.145 20972 Z= 0.297 Chirality : 0.045 0.277 2324 Planarity : 0.004 0.033 2712 Dihedral : 5.929 58.341 2123 Min Nonbonded Distance : 2.170 Molprobity Statistics. All-atom Clashscore : 15.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.38 % Favored : 95.62 % Rotamer: Outliers : 5.46 % Allowed : 22.46 % 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: -0.79 (0.20), residues: 1964 helix: 0.30 (0.19), residues: 832 sheet: -1.16 (0.25), residues: 404 loop : -0.93 (0.25), residues: 728 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 29 HIS 0.009 0.001 HIS D 292 PHE 0.014 0.002 PHE A 402 TYR 0.014 0.001 TYR D 119 ARG 0.006 0.000 ARG A 395 *********************** 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 480 residues out of total 1632 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 88 poor density : 392 time to evaluate : 1.789 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 169 TRP cc_start: 0.8672 (p-90) cc_final: 0.8236 (p-90) REVERT: A 177 ILE cc_start: 0.8821 (OUTLIER) cc_final: 0.8396 (mp) REVERT: B 169 TRP cc_start: 0.8684 (p-90) cc_final: 0.7932 (p-90) REVERT: B 177 ILE cc_start: 0.8736 (OUTLIER) cc_final: 0.8316 (mp) REVERT: C 169 TRP cc_start: 0.8727 (p-90) cc_final: 0.7951 (p-90) REVERT: C 177 ILE cc_start: 0.8549 (OUTLIER) cc_final: 0.8331 (mp) REVERT: C 237 MET cc_start: 0.6453 (mmt) cc_final: 0.5756 (mmt) REVERT: C 263 LEU cc_start: 0.8289 (mt) cc_final: 0.8067 (mt) REVERT: C 471 MET cc_start: 0.8048 (mtp) cc_final: 0.7672 (mtp) REVERT: C 480 GLU cc_start: 0.7690 (tt0) cc_final: 0.7256 (tt0) REVERT: D 169 TRP cc_start: 0.8683 (p-90) cc_final: 0.7913 (p-90) REVERT: D 177 ILE cc_start: 0.8763 (OUTLIER) cc_final: 0.8312 (mp) REVERT: D 237 MET cc_start: 0.6343 (mmt) cc_final: 0.5337 (mmt) REVERT: D 252 LYS cc_start: 0.7177 (mttt) cc_final: 0.6964 (mttm) REVERT: D 471 MET cc_start: 0.8220 (mtp) cc_final: 0.7986 (mtp) outliers start: 88 outliers final: 56 residues processed: 444 average time/residue: 0.2853 time to fit residues: 184.0433 Evaluate side-chains 438 residues out of total 1632 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 378 time to evaluate : 1.515 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 VAL 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 205 VAL Chi-restraints excluded: chain A residue 239 ILE Chi-restraints excluded: chain A residue 248 THR Chi-restraints excluded: chain A residue 279 LEU Chi-restraints excluded: chain A residue 303 CYS Chi-restraints excluded: chain A residue 308 ARG Chi-restraints excluded: chain A residue 424 THR 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 177 ILE Chi-restraints excluded: chain B residue 185 SER Chi-restraints excluded: chain B residue 205 VAL Chi-restraints excluded: chain B residue 219 VAL Chi-restraints excluded: chain B residue 261 SER Chi-restraints excluded: chain B residue 266 VAL Chi-restraints excluded: chain B residue 303 CYS Chi-restraints excluded: chain B residue 315 ILE Chi-restraints excluded: chain B residue 332 LEU Chi-restraints excluded: chain B residue 424 THR 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 83 SER 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 205 VAL Chi-restraints excluded: chain C residue 219 VAL Chi-restraints excluded: chain C residue 222 VAL Chi-restraints excluded: chain C residue 266 VAL Chi-restraints excluded: chain C residue 315 ILE Chi-restraints excluded: chain C residue 332 LEU Chi-restraints excluded: chain C residue 424 THR 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 83 SER Chi-restraints excluded: chain D residue 114 LEU Chi-restraints excluded: chain D residue 147 ILE Chi-restraints excluded: chain D residue 177 ILE Chi-restraints excluded: chain D residue 185 SER Chi-restraints excluded: chain D residue 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 315 ILE Chi-restraints excluded: chain D residue 332 LEU Chi-restraints excluded: chain D residue 341 THR Chi-restraints excluded: chain D residue 424 THR Chi-restraints excluded: chain D residue 451 THR Chi-restraints excluded: chain D residue 460 VAL Chi-restraints excluded: chain D residue 494 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 63 optimal weight: 3.9990 chunk 170 optimal weight: 0.9990 chunk 37 optimal weight: 0.9990 chunk 111 optimal weight: 3.9990 chunk 46 optimal weight: 0.8980 chunk 189 optimal weight: 0.9980 chunk 157 optimal weight: 4.9990 chunk 87 optimal weight: 7.9990 chunk 15 optimal weight: 1.9990 chunk 62 optimal weight: 0.8980 chunk 99 optimal weight: 3.9990 overall best weight: 0.9584 ------------------------------------------------------------------------------- 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 298 HIS ** 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 298 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 299 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 406 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 72 GLN ** C 298 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 299 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7352 moved from start: 0.5572 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 15488 Z= 0.253 Angle : 0.588 5.170 20972 Z= 0.303 Chirality : 0.046 0.275 2324 Planarity : 0.004 0.037 2712 Dihedral : 5.575 56.270 2112 Min Nonbonded Distance : 2.164 Molprobity Statistics. All-atom Clashscore : 15.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.33 % Favored : 95.67 % Rotamer: Outliers : 6.27 % Allowed : 21.77 % Favored : 71.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.55 (0.20), residues: 1964 helix: 0.43 (0.19), residues: 828 sheet: -0.89 (0.26), residues: 396 loop : -0.81 (0.25), residues: 740 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 29 HIS 0.009 0.001 HIS D 292 PHE 0.014 0.002 PHE A 402 TYR 0.012 0.001 TYR B 119 ARG 0.007 0.000 ARG A 395 *********************** 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 477 residues out of total 1632 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 101 poor density : 376 time to evaluate : 1.697 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 177 ILE cc_start: 0.8776 (OUTLIER) cc_final: 0.8229 (mp) REVERT: A 237 MET cc_start: 0.6527 (OUTLIER) cc_final: 0.6321 (mmp) REVERT: A 402 PHE cc_start: 0.7350 (OUTLIER) cc_final: 0.7000 (t80) REVERT: A 489 VAL cc_start: 0.8748 (OUTLIER) cc_final: 0.8538 (m) REVERT: B 169 TRP cc_start: 0.8728 (p-90) cc_final: 0.7980 (p-90) REVERT: B 177 ILE cc_start: 0.8660 (OUTLIER) cc_final: 0.8158 (mp) REVERT: B 402 PHE cc_start: 0.7309 (OUTLIER) cc_final: 0.7037 (t80) REVERT: C 177 ILE cc_start: 0.8716 (OUTLIER) cc_final: 0.8308 (mp) REVERT: C 402 PHE cc_start: 0.7340 (OUTLIER) cc_final: 0.6992 (t80) REVERT: C 471 MET cc_start: 0.8028 (mtp) cc_final: 0.7655 (mtp) REVERT: C 480 GLU cc_start: 0.7702 (tt0) cc_final: 0.7194 (tt0) REVERT: D 177 ILE cc_start: 0.8687 (OUTLIER) cc_final: 0.8153 (mp) REVERT: D 237 MET cc_start: 0.6422 (mmt) cc_final: 0.5295 (mmt) REVERT: D 402 PHE cc_start: 0.7317 (OUTLIER) cc_final: 0.7007 (t80) outliers start: 101 outliers final: 70 residues processed: 428 average time/residue: 0.2910 time to fit residues: 180.0552 Evaluate side-chains 445 residues out of total 1632 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 80 poor density : 365 time to evaluate : 1.734 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 VAL Chi-restraints excluded: chain A residue 60 VAL 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 237 MET Chi-restraints excluded: chain A residue 239 ILE Chi-restraints excluded: chain A residue 248 THR Chi-restraints excluded: chain A residue 279 LEU Chi-restraints excluded: chain A residue 303 CYS Chi-restraints excluded: chain A residue 308 ARG Chi-restraints excluded: chain A residue 402 PHE Chi-restraints excluded: chain A residue 415 ASP Chi-restraints excluded: chain A residue 424 THR Chi-restraints excluded: chain A residue 460 VAL Chi-restraints excluded: chain A residue 489 VAL Chi-restraints excluded: chain A residue 494 VAL Chi-restraints excluded: chain B residue 79 THR Chi-restraints excluded: chain B residue 155 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 221 ILE Chi-restraints excluded: chain B residue 222 VAL Chi-restraints excluded: chain B residue 248 THR Chi-restraints excluded: chain B residue 261 SER Chi-restraints excluded: chain B residue 266 VAL Chi-restraints excluded: chain B residue 303 CYS Chi-restraints excluded: chain B residue 315 ILE Chi-restraints excluded: chain B residue 332 LEU Chi-restraints excluded: chain B residue 402 PHE Chi-restraints excluded: chain B residue 415 ASP Chi-restraints excluded: chain B residue 424 THR Chi-restraints excluded: chain B residue 460 VAL Chi-restraints excluded: chain B residue 494 VAL Chi-restraints excluded: chain C residue 79 THR Chi-restraints excluded: chain C residue 83 SER 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 196 GLU Chi-restraints excluded: chain C residue 219 VAL Chi-restraints excluded: chain C residue 222 VAL Chi-restraints excluded: chain C residue 239 ILE Chi-restraints excluded: chain C residue 248 THR Chi-restraints excluded: chain C residue 266 VAL Chi-restraints excluded: chain C residue 303 CYS Chi-restraints excluded: chain C residue 315 ILE Chi-restraints excluded: chain C residue 332 LEU Chi-restraints excluded: chain C residue 402 PHE Chi-restraints excluded: chain C residue 424 THR Chi-restraints excluded: chain C residue 451 THR Chi-restraints excluded: chain C residue 460 VAL Chi-restraints excluded: chain C residue 499 LYS Chi-restraints excluded: chain D residue 79 THR Chi-restraints excluded: chain D residue 83 SER Chi-restraints excluded: chain D residue 114 LEU Chi-restraints excluded: chain D residue 147 ILE Chi-restraints excluded: chain D residue 155 THR Chi-restraints excluded: chain D residue 177 ILE Chi-restraints excluded: chain D residue 185 SER Chi-restraints excluded: chain D residue 196 GLU 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 248 THR Chi-restraints excluded: chain D residue 266 VAL Chi-restraints excluded: chain D residue 303 CYS Chi-restraints excluded: chain D residue 315 ILE Chi-restraints excluded: chain D residue 332 LEU Chi-restraints excluded: chain D residue 341 THR Chi-restraints excluded: chain D residue 402 PHE Chi-restraints excluded: chain D residue 424 THR Chi-restraints excluded: chain D residue 460 VAL Chi-restraints excluded: chain D residue 494 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 182 optimal weight: 4.9990 chunk 21 optimal weight: 1.9990 chunk 108 optimal weight: 2.9990 chunk 138 optimal weight: 0.7980 chunk 107 optimal weight: 3.9990 chunk 159 optimal weight: 1.9990 chunk 105 optimal weight: 3.9990 chunk 188 optimal weight: 3.9990 chunk 118 optimal weight: 0.9980 chunk 115 optimal weight: 0.5980 chunk 87 optimal weight: 8.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- 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 298 HIS ** 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 298 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 406 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 72 GLN ** C 298 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 299 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 406 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 72 GLN ** D 298 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 406 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7378 moved from start: 0.5708 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 15488 Z= 0.300 Angle : 0.619 6.975 20972 Z= 0.317 Chirality : 0.047 0.282 2324 Planarity : 0.004 0.039 2712 Dihedral : 5.630 56.378 2112 Min Nonbonded Distance : 2.157 Molprobity Statistics. All-atom Clashscore : 15.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.43 % Favored : 95.57 % Rotamer: Outliers : 6.33 % Allowed : 22.52 % Favored : 71.15 % 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: 0.38 (0.19), residues: 828 sheet: -0.88 (0.26), residues: 396 loop : -0.76 (0.26), residues: 740 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP D 169 HIS 0.009 0.001 HIS D 292 PHE 0.015 0.002 PHE A 402 TYR 0.013 0.001 TYR C 119 ARG 0.006 0.001 ARG A 395 *********************** 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 476 residues out of total 1632 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 102 poor density : 374 time to evaluate : 1.714 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 177 ILE cc_start: 0.8782 (OUTLIER) cc_final: 0.8276 (mp) REVERT: A 316 TYR cc_start: 0.6738 (t80) cc_final: 0.6259 (t80) REVERT: A 402 PHE cc_start: 0.7398 (OUTLIER) cc_final: 0.7051 (t80) REVERT: A 489 VAL cc_start: 0.8775 (OUTLIER) cc_final: 0.8566 (m) REVERT: B 169 TRP cc_start: 0.8712 (p-90) cc_final: 0.7970 (p-90) REVERT: B 177 ILE cc_start: 0.8789 (OUTLIER) cc_final: 0.8277 (mp) REVERT: B 402 PHE cc_start: 0.7380 (OUTLIER) cc_final: 0.7084 (t80) REVERT: C 177 ILE cc_start: 0.8724 (OUTLIER) cc_final: 0.8253 (mp) REVERT: C 273 LYS cc_start: 0.8217 (tptm) cc_final: 0.8010 (tptt) REVERT: C 402 PHE cc_start: 0.7440 (OUTLIER) cc_final: 0.7115 (t80) REVERT: C 415 ASP cc_start: 0.8091 (m-30) cc_final: 0.7863 (m-30) REVERT: C 471 MET cc_start: 0.8030 (mtp) cc_final: 0.7640 (mtp) REVERT: C 480 GLU cc_start: 0.7744 (tt0) cc_final: 0.7213 (tt0) REVERT: D 177 ILE cc_start: 0.8801 (OUTLIER) cc_final: 0.8285 (mp) REVERT: D 237 MET cc_start: 0.6524 (mmt) cc_final: 0.5218 (mmt) REVERT: D 402 PHE cc_start: 0.7463 (OUTLIER) cc_final: 0.7119 (t80) outliers start: 102 outliers final: 82 residues processed: 426 average time/residue: 0.2865 time to fit residues: 177.0110 Evaluate side-chains 456 residues out of total 1632 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 91 poor density : 365 time to evaluate : 1.637 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 VAL Chi-restraints excluded: chain A residue 60 VAL Chi-restraints excluded: chain A residue 79 THR Chi-restraints excluded: chain A residue 123 LEU Chi-restraints excluded: chain A residue 147 ILE Chi-restraints excluded: chain A residue 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 239 ILE Chi-restraints excluded: chain A residue 248 THR Chi-restraints excluded: chain A residue 279 LEU Chi-restraints excluded: chain A residue 303 CYS Chi-restraints excluded: chain A residue 308 ARG Chi-restraints excluded: chain A residue 402 PHE Chi-restraints excluded: chain A residue 415 ASP Chi-restraints excluded: chain A residue 424 THR Chi-restraints excluded: chain A residue 460 VAL Chi-restraints excluded: chain A residue 489 VAL 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 155 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 196 GLU Chi-restraints excluded: chain B residue 205 VAL Chi-restraints excluded: chain B residue 219 VAL Chi-restraints excluded: chain B residue 221 ILE Chi-restraints excluded: chain B residue 222 VAL Chi-restraints excluded: chain B residue 248 THR Chi-restraints excluded: chain B residue 261 SER Chi-restraints excluded: chain B residue 266 VAL Chi-restraints excluded: chain B residue 303 CYS Chi-restraints excluded: chain B residue 315 ILE Chi-restraints excluded: chain B residue 332 LEU Chi-restraints excluded: chain B residue 402 PHE Chi-restraints excluded: chain B residue 451 THR Chi-restraints excluded: chain B residue 460 VAL Chi-restraints excluded: chain B residue 494 VAL Chi-restraints excluded: chain C residue 79 THR Chi-restraints excluded: chain C residue 83 SER Chi-restraints excluded: chain C residue 147 ILE Chi-restraints excluded: chain C residue 155 THR Chi-restraints excluded: chain C residue 167 ILE Chi-restraints excluded: chain C residue 177 ILE Chi-restraints excluded: chain C residue 180 ILE Chi-restraints excluded: chain C residue 185 SER Chi-restraints excluded: chain C residue 205 VAL Chi-restraints excluded: chain C residue 219 VAL Chi-restraints excluded: chain C residue 221 ILE Chi-restraints excluded: chain C residue 222 VAL Chi-restraints excluded: chain C residue 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 424 THR Chi-restraints excluded: chain C residue 451 THR Chi-restraints excluded: chain C residue 460 VAL Chi-restraints excluded: chain C residue 499 LYS Chi-restraints excluded: chain D residue 79 THR Chi-restraints excluded: chain D residue 83 SER Chi-restraints excluded: chain D residue 114 LEU Chi-restraints excluded: chain D residue 147 ILE Chi-restraints excluded: chain D residue 155 THR Chi-restraints excluded: chain D residue 177 ILE Chi-restraints excluded: chain D residue 180 ILE Chi-restraints excluded: chain D residue 185 SER Chi-restraints excluded: chain D residue 196 GLU 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 248 THR Chi-restraints excluded: chain D residue 266 VAL Chi-restraints excluded: chain D residue 279 LEU Chi-restraints excluded: chain D residue 303 CYS Chi-restraints excluded: chain D residue 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 424 THR Chi-restraints excluded: chain D residue 445 SER Chi-restraints excluded: chain D residue 451 THR Chi-restraints excluded: chain D residue 460 VAL Chi-restraints excluded: chain D residue 494 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 116 optimal weight: 2.9990 chunk 75 optimal weight: 3.9990 chunk 112 optimal weight: 2.9990 chunk 56 optimal weight: 0.6980 chunk 37 optimal weight: 0.9990 chunk 36 optimal weight: 6.9990 chunk 120 optimal weight: 3.9990 chunk 128 optimal weight: 2.9990 chunk 93 optimal weight: 0.8980 chunk 17 optimal weight: 0.9980 chunk 148 optimal weight: 0.9980 overall best weight: 0.9182 ------------------------------------------------------------------------------- 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 298 HIS ** 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 298 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 406 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 72 GLN ** C 298 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 406 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7347 moved from start: 0.5870 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 15488 Z= 0.244 Angle : 0.586 9.825 20972 Z= 0.300 Chirality : 0.046 0.275 2324 Planarity : 0.004 0.034 2712 Dihedral : 5.475 55.856 2112 Min Nonbonded Distance : 2.136 Molprobity Statistics. All-atom Clashscore : 14.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.43 % Favored : 95.57 % Rotamer: Outliers : 5.96 % Allowed : 24.01 % Favored : 70.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.50 (0.20), residues: 1964 helix: 0.49 (0.19), residues: 828 sheet: -1.03 (0.25), residues: 420 loop : -0.67 (0.26), residues: 716 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP D 169 HIS 0.007 0.001 HIS D 292 PHE 0.015 0.002 PHE B 411 TYR 0.014 0.001 TYR B 119 ARG 0.006 0.000 ARG A 395 *********************** 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 471 residues out of total 1632 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 96 poor density : 375 time to evaluate : 1.709 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 177 ILE cc_start: 0.8814 (OUTLIER) cc_final: 0.8310 (mp) REVERT: A 316 TYR cc_start: 0.6684 (t80) cc_final: 0.6231 (t80) REVERT: A 369 GLU cc_start: 0.6714 (mm-30) cc_final: 0.5795 (mm-30) REVERT: A 402 PHE cc_start: 0.7303 (OUTLIER) cc_final: 0.6970 (t80) REVERT: B 177 ILE cc_start: 0.8675 (OUTLIER) cc_final: 0.8146 (mp) REVERT: B 402 PHE cc_start: 0.7357 (OUTLIER) cc_final: 0.7048 (t80) REVERT: B 471 MET cc_start: 0.8311 (mtm) cc_final: 0.8086 (mtm) REVERT: C 177 ILE cc_start: 0.8666 (OUTLIER) cc_final: 0.8114 (mp) REVERT: C 237 MET cc_start: 0.6426 (mmt) cc_final: 0.5312 (mmt) REVERT: C 273 LYS cc_start: 0.8116 (tptm) cc_final: 0.7614 (tptt) REVERT: C 402 PHE cc_start: 0.7377 (OUTLIER) cc_final: 0.7032 (t80) REVERT: C 410 LYS cc_start: 0.7806 (ttpt) cc_final: 0.7551 (ptmm) REVERT: C 414 LEU cc_start: 0.7377 (tp) cc_final: 0.7145 (tp) REVERT: C 415 ASP cc_start: 0.8071 (m-30) cc_final: 0.7844 (m-30) REVERT: C 480 GLU cc_start: 0.7768 (tt0) cc_final: 0.7271 (tt0) REVERT: D 169 TRP cc_start: 0.8761 (p-90) cc_final: 0.8484 (p-90) REVERT: D 177 ILE cc_start: 0.8682 (OUTLIER) cc_final: 0.8152 (mp) REVERT: D 237 MET cc_start: 0.6681 (mmt) cc_final: 0.5484 (mmt) REVERT: D 273 LYS cc_start: 0.8135 (tptm) cc_final: 0.7902 (tptt) REVERT: D 402 PHE cc_start: 0.7440 (OUTLIER) cc_final: 0.7059 (t80) REVERT: D 414 LEU cc_start: 0.7558 (tp) cc_final: 0.7274 (tp) outliers start: 96 outliers final: 75 residues processed: 427 average time/residue: 0.2950 time to fit residues: 181.9839 Evaluate side-chains 452 residues out of total 1632 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 83 poor density : 369 time to evaluate : 1.572 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 VAL Chi-restraints excluded: chain A residue 79 THR Chi-restraints excluded: chain A residue 123 LEU Chi-restraints excluded: chain A residue 147 ILE Chi-restraints excluded: chain A residue 177 ILE Chi-restraints excluded: chain A residue 180 ILE Chi-restraints excluded: chain A residue 185 SER Chi-restraints excluded: chain A residue 222 VAL Chi-restraints excluded: chain A residue 239 ILE Chi-restraints excluded: chain A residue 248 THR Chi-restraints excluded: chain A residue 279 LEU Chi-restraints excluded: chain A residue 303 CYS Chi-restraints excluded: chain A residue 398 LYS Chi-restraints excluded: chain A residue 402 PHE Chi-restraints excluded: chain A residue 415 ASP Chi-restraints excluded: chain A residue 424 THR Chi-restraints excluded: chain A residue 460 VAL Chi-restraints excluded: chain A residue 492 VAL Chi-restraints excluded: chain A residue 494 VAL Chi-restraints excluded: chain B residue 79 THR Chi-restraints excluded: chain B residue 177 ILE Chi-restraints excluded: chain B residue 180 ILE Chi-restraints excluded: chain B residue 185 SER Chi-restraints excluded: chain B residue 205 VAL Chi-restraints excluded: chain B residue 219 VAL Chi-restraints excluded: chain B residue 222 VAL Chi-restraints excluded: chain B residue 239 ILE Chi-restraints excluded: chain B residue 248 THR Chi-restraints excluded: chain B residue 261 SER Chi-restraints excluded: chain B residue 266 VAL Chi-restraints excluded: chain B residue 303 CYS Chi-restraints excluded: chain B residue 315 ILE Chi-restraints excluded: chain B residue 332 LEU Chi-restraints excluded: chain B residue 402 PHE Chi-restraints excluded: chain B residue 437 ILE Chi-restraints excluded: chain B residue 451 THR Chi-restraints excluded: chain B residue 460 VAL Chi-restraints excluded: chain B residue 494 VAL Chi-restraints excluded: chain C residue 79 THR Chi-restraints excluded: chain C residue 83 SER Chi-restraints excluded: chain C residue 155 THR Chi-restraints excluded: chain C residue 167 ILE Chi-restraints excluded: chain C residue 177 ILE Chi-restraints excluded: chain C residue 180 ILE Chi-restraints excluded: chain C residue 185 SER Chi-restraints excluded: chain C residue 205 VAL Chi-restraints excluded: chain C residue 219 VAL Chi-restraints excluded: chain C residue 221 ILE Chi-restraints excluded: chain C residue 222 VAL Chi-restraints excluded: chain C residue 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 424 THR Chi-restraints excluded: chain C residue 451 THR Chi-restraints excluded: chain C residue 460 VAL Chi-restraints excluded: chain C residue 499 LYS Chi-restraints excluded: chain D residue 79 THR Chi-restraints excluded: chain D residue 83 SER Chi-restraints excluded: chain D residue 147 ILE Chi-restraints excluded: chain D residue 155 THR Chi-restraints excluded: chain D residue 177 ILE Chi-restraints excluded: chain D residue 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 248 THR Chi-restraints excluded: chain D residue 266 VAL Chi-restraints excluded: chain D residue 279 LEU Chi-restraints excluded: chain D residue 303 CYS Chi-restraints excluded: chain D residue 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 424 THR Chi-restraints excluded: chain D residue 445 SER Chi-restraints excluded: chain D residue 451 THR Chi-restraints excluded: chain D residue 460 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 171 optimal weight: 2.9990 chunk 180 optimal weight: 2.9990 chunk 165 optimal weight: 0.7980 chunk 176 optimal weight: 0.4980 chunk 105 optimal weight: 4.9990 chunk 76 optimal weight: 1.9990 chunk 138 optimal weight: 0.9990 chunk 54 optimal weight: 2.9990 chunk 159 optimal weight: 0.5980 chunk 166 optimal weight: 0.7980 chunk 175 optimal weight: 2.9990 overall best weight: 0.7382 ------------------------------------------------------------------------------- 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 298 HIS ** 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 298 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 406 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 72 GLN ** C 298 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 406 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 298 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 406 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7327 moved from start: 0.6042 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= 0.217 Angle : 0.585 10.847 20972 Z= 0.300 Chirality : 0.045 0.255 2324 Planarity : 0.004 0.033 2712 Dihedral : 5.349 55.114 2112 Min Nonbonded Distance : 2.120 Molprobity Statistics. All-atom Clashscore : 14.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.33 % Favored : 95.67 % Rotamer: Outliers : 5.52 % Allowed : 24.88 % Favored : 69.60 % 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: -0.37 (0.20), residues: 1964 helix: 0.56 (0.19), residues: 828 sheet: -0.90 (0.26), residues: 420 loop : -0.59 (0.26), residues: 716 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP B 169 HIS 0.007 0.001 HIS D 292 PHE 0.014 0.002 PHE B 411 TYR 0.014 0.001 TYR C 119 ARG 0.006 0.000 ARG A 395 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3928 Ramachandran restraints generated. 1964 Oldfield, 0 Emsley, 1964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3928 Ramachandran restraints generated. 1964 Oldfield, 0 Emsley, 1964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 456 residues out of total 1632 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 89 poor density : 367 time to evaluate : 1.620 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 177 ILE cc_start: 0.8761 (OUTLIER) cc_final: 0.8193 (mp) REVERT: A 237 MET cc_start: 0.6495 (OUTLIER) cc_final: 0.6115 (mmp) REVERT: A 316 TYR cc_start: 0.6651 (t80) cc_final: 0.6094 (t80) REVERT: A 369 GLU cc_start: 0.6672 (mm-30) cc_final: 0.5784 (mm-30) REVERT: A 402 PHE cc_start: 0.7307 (OUTLIER) cc_final: 0.6963 (t80) REVERT: B 177 ILE cc_start: 0.8658 (OUTLIER) cc_final: 0.8114 (mp) REVERT: B 402 PHE cc_start: 0.7343 (OUTLIER) cc_final: 0.6995 (t80) REVERT: B 471 MET cc_start: 0.8348 (mtm) cc_final: 0.8064 (mtm) REVERT: C 169 TRP cc_start: 0.8741 (p-90) cc_final: 0.8463 (p-90) REVERT: C 177 ILE cc_start: 0.8599 (OUTLIER) cc_final: 0.8082 (mp) REVERT: C 237 MET cc_start: 0.6583 (mmt) cc_final: 0.5524 (mmt) REVERT: C 402 PHE cc_start: 0.7439 (OUTLIER) cc_final: 0.7078 (t80) REVERT: C 410 LYS cc_start: 0.7721 (ttpt) cc_final: 0.7443 (ptmm) REVERT: C 414 LEU cc_start: 0.7421 (tp) cc_final: 0.7156 (tp) REVERT: C 415 ASP cc_start: 0.8059 (m-30) cc_final: 0.7840 (m-30) REVERT: C 480 GLU cc_start: 0.7723 (tt0) cc_final: 0.7206 (tt0) REVERT: D 169 TRP cc_start: 0.8713 (p-90) cc_final: 0.8467 (p-90) REVERT: D 177 ILE cc_start: 0.8671 (OUTLIER) cc_final: 0.8199 (mp) REVERT: D 252 LYS cc_start: 0.7119 (mttt) cc_final: 0.6827 (ttmt) REVERT: D 316 TYR cc_start: 0.6552 (t80) cc_final: 0.6198 (t80) REVERT: D 402 PHE cc_start: 0.7366 (OUTLIER) cc_final: 0.7034 (t80) REVERT: D 414 LEU cc_start: 0.7557 (tp) cc_final: 0.7243 (tp) outliers start: 89 outliers final: 73 residues processed: 417 average time/residue: 0.2837 time to fit residues: 171.9885 Evaluate side-chains 438 residues out of total 1632 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 82 poor density : 356 time to evaluate : 1.624 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 VAL Chi-restraints excluded: chain A residue 79 THR Chi-restraints excluded: chain A residue 83 SER Chi-restraints excluded: chain A residue 123 LEU Chi-restraints excluded: chain A residue 147 ILE Chi-restraints excluded: chain A residue 177 ILE Chi-restraints excluded: chain A residue 180 ILE Chi-restraints excluded: chain A residue 185 SER Chi-restraints excluded: chain A residue 222 VAL Chi-restraints excluded: chain A residue 237 MET Chi-restraints excluded: chain A residue 239 ILE Chi-restraints excluded: chain A residue 248 THR Chi-restraints excluded: chain A residue 267 THR Chi-restraints excluded: chain A residue 279 LEU Chi-restraints excluded: chain A residue 303 CYS Chi-restraints excluded: chain A residue 398 LYS Chi-restraints excluded: chain A residue 402 PHE Chi-restraints excluded: chain A residue 424 THR Chi-restraints excluded: chain A residue 437 ILE Chi-restraints excluded: chain A residue 460 VAL Chi-restraints excluded: chain A residue 492 VAL Chi-restraints excluded: chain B residue 79 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 248 THR Chi-restraints excluded: chain B residue 261 SER Chi-restraints excluded: chain B residue 266 VAL Chi-restraints excluded: chain B residue 303 CYS Chi-restraints excluded: chain B residue 315 ILE Chi-restraints excluded: chain B residue 332 LEU Chi-restraints excluded: chain B residue 402 PHE Chi-restraints excluded: chain B residue 415 ASP Chi-restraints excluded: chain B residue 451 THR Chi-restraints excluded: chain B residue 460 VAL Chi-restraints excluded: chain C residue 79 THR Chi-restraints excluded: chain C residue 83 SER Chi-restraints excluded: chain C residue 155 THR Chi-restraints excluded: chain C residue 160 ILE Chi-restraints excluded: chain C residue 177 ILE Chi-restraints excluded: chain C residue 180 ILE Chi-restraints excluded: chain C residue 185 SER Chi-restraints excluded: chain C residue 205 VAL Chi-restraints excluded: chain C residue 219 VAL Chi-restraints excluded: chain C residue 222 VAL Chi-restraints excluded: chain C residue 239 ILE Chi-restraints excluded: chain C residue 248 THR Chi-restraints excluded: chain C residue 266 VAL Chi-restraints excluded: chain C residue 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 424 THR Chi-restraints excluded: chain C residue 451 THR Chi-restraints excluded: chain C residue 460 VAL Chi-restraints excluded: chain C residue 499 LYS Chi-restraints excluded: chain D residue 79 THR Chi-restraints excluded: chain D residue 83 SER Chi-restraints excluded: chain D residue 147 ILE Chi-restraints excluded: chain D residue 177 ILE Chi-restraints excluded: chain D residue 180 ILE Chi-restraints excluded: chain D residue 185 SER Chi-restraints excluded: chain D residue 205 VAL Chi-restraints excluded: chain D residue 219 VAL Chi-restraints excluded: chain D residue 221 ILE Chi-restraints excluded: chain D residue 222 VAL Chi-restraints excluded: chain D residue 239 ILE Chi-restraints excluded: chain D residue 248 THR Chi-restraints excluded: chain D residue 266 VAL Chi-restraints excluded: chain D residue 279 LEU Chi-restraints excluded: chain D residue 303 CYS Chi-restraints excluded: chain D residue 315 ILE Chi-restraints excluded: chain D residue 332 LEU Chi-restraints excluded: chain D residue 341 THR Chi-restraints excluded: chain D residue 402 PHE Chi-restraints excluded: chain D residue 424 THR Chi-restraints excluded: chain D residue 437 ILE 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 115 optimal weight: 0.9980 chunk 186 optimal weight: 0.5980 chunk 113 optimal weight: 0.7980 chunk 88 optimal weight: 1.9990 chunk 129 optimal weight: 0.8980 chunk 195 optimal weight: 0.5980 chunk 179 optimal weight: 2.9990 chunk 155 optimal weight: 2.9990 chunk 16 optimal weight: 0.1980 chunk 120 optimal weight: 1.9990 chunk 95 optimal weight: 0.0040 overall best weight: 0.4392 ------------------------------------------------------------------------------- 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 298 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 299 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 298 HIS ** 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 298 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 406 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7278 moved from start: 0.6264 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 15488 Z= 0.179 Angle : 0.566 10.372 20972 Z= 0.288 Chirality : 0.044 0.229 2324 Planarity : 0.004 0.035 2712 Dihedral : 5.141 53.551 2112 Min Nonbonded Distance : 2.122 Molprobity Statistics. All-atom Clashscore : 14.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.77 % Favored : 96.23 % Rotamer: Outliers : 4.16 % Allowed : 25.87 % Favored : 69.98 % 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: -0.22 (0.20), residues: 1964 helix: 0.60 (0.19), residues: 832 sheet: -0.65 (0.26), residues: 404 loop : -0.54 (0.26), residues: 728 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 169 HIS 0.005 0.001 HIS D 292 PHE 0.030 0.001 PHE A 411 TYR 0.014 0.001 TYR D 119 ARG 0.006 0.000 ARG A 395 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3928 Ramachandran restraints generated. 1964 Oldfield, 0 Emsley, 1964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3928 Ramachandran restraints generated. 1964 Oldfield, 0 Emsley, 1964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 460 residues out of total 1632 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 393 time to evaluate : 1.501 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 177 ILE cc_start: 0.8701 (OUTLIER) cc_final: 0.8108 (mp) REVERT: A 237 MET cc_start: 0.6413 (OUTLIER) cc_final: 0.5108 (mmp) REVERT: A 369 GLU cc_start: 0.6633 (mm-30) cc_final: 0.5777 (mm-30) REVERT: A 402 PHE cc_start: 0.7260 (OUTLIER) cc_final: 0.6868 (t80) REVERT: B 177 ILE cc_start: 0.8596 (OUTLIER) cc_final: 0.8132 (mp) REVERT: B 316 TYR cc_start: 0.6461 (t80) cc_final: 0.6075 (t80) REVERT: B 367 LYS cc_start: 0.6409 (tptp) cc_final: 0.5885 (tptt) REVERT: B 402 PHE cc_start: 0.7347 (OUTLIER) cc_final: 0.6987 (t80) REVERT: B 471 MET cc_start: 0.8311 (mtm) cc_final: 0.8051 (mtm) REVERT: C 169 TRP cc_start: 0.8561 (p-90) cc_final: 0.8322 (p-90) REVERT: C 177 ILE cc_start: 0.8561 (OUTLIER) cc_final: 0.8010 (mp) REVERT: C 237 MET cc_start: 0.6549 (mmt) cc_final: 0.5687 (mmp) REVERT: C 316 TYR cc_start: 0.6559 (t80) cc_final: 0.6196 (t80) REVERT: C 402 PHE cc_start: 0.7365 (OUTLIER) cc_final: 0.7001 (t80) REVERT: C 414 LEU cc_start: 0.7465 (tp) cc_final: 0.7186 (tp) REVERT: C 415 ASP cc_start: 0.8040 (m-30) cc_final: 0.7817 (m-30) REVERT: C 480 GLU cc_start: 0.7684 (tt0) cc_final: 0.7181 (tt0) REVERT: D 177 ILE cc_start: 0.8675 (OUTLIER) cc_final: 0.8125 (mp) REVERT: D 237 MET cc_start: 0.6584 (mmt) cc_final: 0.5830 (mmp) REVERT: D 252 LYS cc_start: 0.7055 (mttt) cc_final: 0.6804 (ttmt) REVERT: D 316 TYR cc_start: 0.6498 (t80) cc_final: 0.6155 (t80) REVERT: D 402 PHE cc_start: 0.7326 (OUTLIER) cc_final: 0.6964 (t80) REVERT: D 410 LYS cc_start: 0.7487 (ptmm) cc_final: 0.7253 (tttm) REVERT: D 414 LEU cc_start: 0.7513 (tp) cc_final: 0.7270 (tp) outliers start: 67 outliers final: 47 residues processed: 424 average time/residue: 0.2899 time to fit residues: 177.7182 Evaluate side-chains 429 residues out of total 1632 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 373 time to evaluate : 1.724 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 VAL Chi-restraints excluded: chain A residue 79 THR Chi-restraints excluded: chain A residue 123 LEU Chi-restraints excluded: chain A residue 177 ILE Chi-restraints excluded: chain A residue 180 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 267 THR Chi-restraints excluded: chain A residue 398 LYS Chi-restraints excluded: chain A residue 402 PHE Chi-restraints excluded: chain A residue 424 THR Chi-restraints excluded: chain B residue 79 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 221 ILE Chi-restraints excluded: chain B residue 239 ILE Chi-restraints excluded: chain B residue 248 THR Chi-restraints excluded: chain B residue 266 VAL Chi-restraints excluded: chain B residue 303 CYS Chi-restraints excluded: chain B residue 315 ILE Chi-restraints excluded: chain B residue 332 LEU Chi-restraints excluded: chain B residue 402 PHE Chi-restraints excluded: chain B residue 451 THR Chi-restraints excluded: chain C residue 83 SER Chi-restraints excluded: chain C residue 160 ILE Chi-restraints excluded: chain C residue 177 ILE Chi-restraints excluded: chain C residue 180 ILE Chi-restraints excluded: chain C residue 219 VAL Chi-restraints excluded: chain C residue 222 VAL Chi-restraints excluded: chain C residue 239 ILE Chi-restraints excluded: chain C residue 248 THR Chi-restraints excluded: chain C residue 266 VAL Chi-restraints excluded: chain C residue 303 CYS Chi-restraints excluded: chain C residue 315 ILE Chi-restraints excluded: chain C residue 332 LEU Chi-restraints excluded: chain C residue 402 PHE Chi-restraints excluded: chain C residue 451 THR Chi-restraints excluded: chain C residue 499 LYS Chi-restraints excluded: chain D residue 79 THR Chi-restraints excluded: chain D residue 83 SER Chi-restraints excluded: chain D residue 177 ILE Chi-restraints excluded: chain D residue 180 ILE Chi-restraints excluded: chain D residue 185 SER Chi-restraints excluded: chain D residue 219 VAL Chi-restraints excluded: chain D residue 222 VAL Chi-restraints excluded: chain D residue 239 ILE Chi-restraints excluded: chain D residue 266 VAL Chi-restraints excluded: chain D residue 315 ILE Chi-restraints excluded: chain D residue 332 LEU Chi-restraints excluded: chain D residue 341 THR Chi-restraints excluded: chain D residue 402 PHE Chi-restraints excluded: chain D residue 424 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 123 optimal weight: 4.9990 chunk 165 optimal weight: 1.9990 chunk 47 optimal weight: 0.8980 chunk 143 optimal weight: 2.9990 chunk 22 optimal weight: 3.9990 chunk 43 optimal weight: 1.9990 chunk 155 optimal weight: 2.9990 chunk 65 optimal weight: 0.6980 chunk 159 optimal weight: 0.6980 chunk 19 optimal weight: 0.7980 chunk 28 optimal weight: 4.9990 overall best weight: 1.0182 ------------------------------------------------------------------------------- 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 298 HIS ** 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 298 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 299 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 406 GLN C 72 GLN ** 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: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4035 r_free = 0.4035 target = 0.194530 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3610 r_free = 0.3610 target = 0.155049 restraints weight = 17035.539| |-----------------------------------------------------------------------------| r_work (start): 0.3588 rms_B_bonded: 2.16 r_work: 0.3462 rms_B_bonded: 3.31 restraints_weight: 0.5000 r_work (final): 0.3462 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3441 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3441 r_free = 0.3441 target_work(ls_wunit_k1) = 0.140 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3429 r_free = 0.3429 target_work(ls_wunit_k1) = 0.139 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| r_final: 0.3429 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7514 moved from start: 0.6225 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 15488 Z= 0.255 Angle : 0.620 11.965 20972 Z= 0.316 Chirality : 0.046 0.234 2324 Planarity : 0.004 0.034 2712 Dihedral : 5.215 53.594 2110 Min Nonbonded Distance : 2.131 Molprobity Statistics. All-atom Clashscore : 15.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.28 % Favored : 95.72 % Rotamer: Outliers : 4.16 % Allowed : 26.30 % Favored : 69.54 % 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: -0.24 (0.20), residues: 1964 helix: 0.55 (0.19), residues: 828 sheet: -0.70 (0.26), residues: 404 loop : -0.47 (0.26), residues: 732 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 453 HIS 0.007 0.001 HIS D 292 PHE 0.027 0.002 PHE D 38 TYR 0.013 0.001 TYR D 119 ARG 0.006 0.000 ARG A 395 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4007.65 seconds wall clock time: 73 minutes 47.69 seconds (4427.69 seconds total)