Starting phenix.real_space_refine on Sat Dec 9 10:00:27 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vtk_21380/12_2023/6vtk_21380.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vtk_21380/12_2023/6vtk_21380.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.82 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vtk_21380/12_2023/6vtk_21380.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vtk_21380/12_2023/6vtk_21380.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vtk_21380/12_2023/6vtk_21380.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vtk_21380/12_2023/6vtk_21380.pdb" } resolution = 2.82 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= 0.066 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 81 5.16 5 C 6846 2.51 5 N 1725 2.21 5 O 2034 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 65": "NH1" <-> "NH2" Residue "A ARG 310": "NH1" <-> "NH2" Residue "A TYR 399": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 65": "NH1" <-> "NH2" Residue "C ARG 310": "NH1" <-> "NH2" Residue "C TYR 399": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 65": "NH1" <-> "NH2" Residue "B ARG 310": "NH1" <-> "NH2" Residue "B TYR 399": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/chem_data/mon_lib" Total number of atoms: 10686 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 3534 Number of conformers: 1 Conformer: "" Number of residues, atoms: 446, 3534 Classifications: {'peptide': 446} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PCIS': 2, 'PTRANS': 18, 'TRANS': 425} Unresolved non-hydrogen bonds: 40 Unresolved non-hydrogen angles: 49 Unresolved non-hydrogen dihedrals: 36 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 1, 'HIS:plan': 1, 'ARG:plan': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 25 Chain: "C" Number of atoms: 3534 Number of conformers: 1 Conformer: "" Number of residues, atoms: 446, 3534 Classifications: {'peptide': 446} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PCIS': 2, 'PTRANS': 18, 'TRANS': 425} Unresolved non-hydrogen bonds: 40 Unresolved non-hydrogen angles: 49 Unresolved non-hydrogen dihedrals: 36 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 1, 'HIS:plan': 1, 'ARG:plan': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 25 Chain: "B" Number of atoms: 3534 Number of conformers: 1 Conformer: "" Number of residues, atoms: 446, 3534 Classifications: {'peptide': 446} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PCIS': 2, 'PTRANS': 18, 'TRANS': 425} Unresolved non-hydrogen bonds: 40 Unresolved non-hydrogen angles: 49 Unresolved non-hydrogen dihedrals: 36 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 1, 'HIS:plan': 1, 'ARG:plan': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 25 Chain: "A" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "C" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Time building chain proxies: 3.37, per 1000 atoms: 0.32 Number of scatterers: 10686 At special positions: 0 Unit cell: (97.544, 94.256, 132.616, 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 81 16.00 O 2034 8.00 N 1725 7.00 C 6846 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=21, symmetry=0 Simple disulfide: pdb=" SG CYS A 94 " - pdb=" SG CYS A 195 " distance=2.02 Simple disulfide: pdb=" SG CYS A 173 " - pdb=" SG CYS A 180 " distance=2.04 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 366 " distance=2.05 Simple disulfide: pdb=" SG CYS A 309 " - pdb=" SG CYS A 362 " distance=2.04 Simple disulfide: pdb=" SG CYS A 313 " - pdb=" SG CYS A 360 " distance=2.04 Simple disulfide: pdb=" SG CYS A 322 " - pdb=" SG CYS A 344 " distance=2.04 Simple disulfide: pdb=" SG CYS A 324 " - pdb=" SG CYS A 336 " distance=2.03 Simple disulfide: pdb=" SG CYS C 94 " - pdb=" SG CYS C 195 " distance=2.02 Simple disulfide: pdb=" SG CYS C 173 " - pdb=" SG CYS C 180 " distance=2.04 Simple disulfide: pdb=" SG CYS C 291 " - pdb=" SG CYS C 366 " distance=2.05 Simple disulfide: pdb=" SG CYS C 309 " - pdb=" SG CYS C 362 " distance=2.04 Simple disulfide: pdb=" SG CYS C 313 " - pdb=" SG CYS C 360 " distance=2.03 Simple disulfide: pdb=" SG CYS C 322 " - pdb=" SG CYS C 344 " distance=2.04 Simple disulfide: pdb=" SG CYS C 324 " - pdb=" SG CYS C 336 " distance=2.03 Simple disulfide: pdb=" SG CYS B 94 " - pdb=" SG CYS B 195 " distance=2.02 Simple disulfide: pdb=" SG CYS B 173 " - pdb=" SG CYS B 180 " distance=2.04 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 366 " distance=2.05 Simple disulfide: pdb=" SG CYS B 309 " - pdb=" SG CYS B 362 " distance=2.04 Simple disulfide: pdb=" SG CYS B 313 " - pdb=" SG CYS B 360 " distance=2.04 Simple disulfide: pdb=" SG CYS B 322 " - pdb=" SG CYS B 344 " distance=2.04 Simple disulfide: pdb=" SG CYS B 324 " - pdb=" SG CYS B 336 " distance=2.03 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 Links applied NAG-ASN " NAG A 601 " - " ASN A 394 " " NAG A 602 " - " ASN A 367 " " NAG B 601 " - " ASN B 394 " " NAG B 602 " - " ASN B 367 " " NAG C 601 " - " ASN C 394 " " NAG C 602 " - " ASN C 367 " Time building additional restraints: 4.45 Conformation dependent library (CDL) restraints added in 2.1 seconds 2664 Ramachandran restraints generated. 1332 Oldfield, 0 Emsley, 1332 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2508 Finding SS restraints... Secondary structure from input PDB file: 57 helices and 12 sheets defined 42.4% alpha, 24.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.22 Creating SS restraints... Processing helix chain 'A' and resid 18 through 26 removed outlier: 3.584A pdb=" N SER A 24 " --> pdb=" O GLN A 20 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N SER A 25 " --> pdb=" O ALA A 21 " (cutoff:3.500A) Processing helix chain 'A' and resid 30 through 35 removed outlier: 3.754A pdb=" N ILE A 34 " --> pdb=" O GLY A 30 " (cutoff:3.500A) Processing helix chain 'A' and resid 41 through 70 removed outlier: 4.120A pdb=" N VAL A 45 " --> pdb=" O SER A 41 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N ALA A 48 " --> pdb=" O ARG A 44 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N LEU A 49 " --> pdb=" O VAL A 45 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N CYS A 50 " --> pdb=" O VAL A 46 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N ALA A 59 " --> pdb=" O LEU A 55 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N LEU A 60 " --> pdb=" O ALA A 56 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N VAL A 61 " --> pdb=" O LEU A 57 " (cutoff:3.500A) Processing helix chain 'A' and resid 100 through 104 removed outlier: 3.570A pdb=" N ARG A 103 " --> pdb=" O ARG A 100 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N VAL A 104 " --> pdb=" O PHE A 101 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 100 through 104' Processing helix chain 'A' and resid 105 through 112 Processing helix chain 'A' and resid 134 through 142 removed outlier: 3.762A pdb=" N LYS A 142 " --> pdb=" O ILE A 138 " (cutoff:3.500A) Processing helix chain 'A' and resid 154 through 163 Processing helix chain 'A' and resid 165 through 170 Processing helix chain 'A' and resid 181 through 183 No H-bonds generated for 'chain 'A' and resid 181 through 183' Processing helix chain 'A' and resid 214 through 217 Processing helix chain 'A' and resid 226 through 230 Processing helix chain 'A' and resid 258 through 263 removed outlier: 3.503A pdb=" N GLY A 263 " --> pdb=" O ILE A 259 " (cutoff:3.500A) Processing helix chain 'A' and resid 305 through 323 removed outlier: 3.723A pdb=" N ASP A 312 " --> pdb=" O ALA A 308 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N CYS A 313 " --> pdb=" O CYS A 309 " (cutoff:3.500A) Processing helix chain 'A' and resid 337 through 344 removed outlier: 3.719A pdb=" N LYS A 342 " --> pdb=" O PRO A 338 " (cutoff:3.500A) Processing helix chain 'A' and resid 344 through 355 removed outlier: 3.548A pdb=" N GLU A 354 " --> pdb=" O ASP A 350 " (cutoff:3.500A) Processing helix chain 'A' and resid 385 through 393 removed outlier: 3.520A pdb=" N LEU A 389 " --> pdb=" O SER A 385 " (cutoff:3.500A) Processing helix chain 'A' and resid 396 through 403 removed outlier: 3.941A pdb=" N GLY A 401 " --> pdb=" O GLU A 397 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N GLU A 402 " --> pdb=" O GLN A 398 " (cutoff:3.500A) Processing helix chain 'A' and resid 426 through 441 removed outlier: 3.588A pdb=" N PHE A 441 " --> pdb=" O GLN A 437 " (cutoff:3.500A) Processing helix chain 'A' and resid 447 through 462 removed outlier: 3.588A pdb=" N ILE A 460 " --> pdb=" O ALA A 456 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N LYS A 461 " --> pdb=" O TYR A 457 " (cutoff:3.500A) Processing helix chain 'C' and resid 18 through 26 removed outlier: 3.584A pdb=" N SER C 24 " --> pdb=" O GLN C 20 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N SER C 25 " --> pdb=" O ALA C 21 " (cutoff:3.500A) Processing helix chain 'C' and resid 30 through 35 removed outlier: 3.753A pdb=" N ILE C 34 " --> pdb=" O GLY C 30 " (cutoff:3.500A) Processing helix chain 'C' and resid 41 through 70 removed outlier: 4.120A pdb=" N VAL C 45 " --> pdb=" O SER C 41 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N ALA C 48 " --> pdb=" O ARG C 44 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N LEU C 49 " --> pdb=" O VAL C 45 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N CYS C 50 " --> pdb=" O VAL C 46 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N ALA C 59 " --> pdb=" O LEU C 55 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N LEU C 60 " --> pdb=" O ALA C 56 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N VAL C 61 " --> pdb=" O LEU C 57 " (cutoff:3.500A) Processing helix chain 'C' and resid 100 through 104 removed outlier: 3.571A pdb=" N ARG C 103 " --> pdb=" O ARG C 100 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N VAL C 104 " --> pdb=" O PHE C 101 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 100 through 104' Processing helix chain 'C' and resid 105 through 112 Processing helix chain 'C' and resid 134 through 142 removed outlier: 3.761A pdb=" N LYS C 142 " --> pdb=" O ILE C 138 " (cutoff:3.500A) Processing helix chain 'C' and resid 154 through 163 Processing helix chain 'C' and resid 165 through 170 Processing helix chain 'C' and resid 181 through 183 No H-bonds generated for 'chain 'C' and resid 181 through 183' Processing helix chain 'C' and resid 214 through 217 Processing helix chain 'C' and resid 226 through 230 Processing helix chain 'C' and resid 258 through 263 removed outlier: 3.503A pdb=" N GLY C 263 " --> pdb=" O ILE C 259 " (cutoff:3.500A) Processing helix chain 'C' and resid 305 through 323 removed outlier: 3.723A pdb=" N ASP C 312 " --> pdb=" O ALA C 308 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N CYS C 313 " --> pdb=" O CYS C 309 " (cutoff:3.500A) Processing helix chain 'C' and resid 337 through 344 removed outlier: 3.718A pdb=" N LYS C 342 " --> pdb=" O PRO C 338 " (cutoff:3.500A) Processing helix chain 'C' and resid 344 through 355 removed outlier: 3.549A pdb=" N GLU C 354 " --> pdb=" O ASP C 350 " (cutoff:3.500A) Processing helix chain 'C' and resid 385 through 393 removed outlier: 3.521A pdb=" N LEU C 389 " --> pdb=" O SER C 385 " (cutoff:3.500A) Processing helix chain 'C' and resid 396 through 403 removed outlier: 3.941A pdb=" N GLY C 401 " --> pdb=" O GLU C 397 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N GLU C 402 " --> pdb=" O GLN C 398 " (cutoff:3.500A) Processing helix chain 'C' and resid 426 through 441 removed outlier: 3.588A pdb=" N PHE C 441 " --> pdb=" O GLN C 437 " (cutoff:3.500A) Processing helix chain 'C' and resid 447 through 462 removed outlier: 3.588A pdb=" N ILE C 460 " --> pdb=" O ALA C 456 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N LYS C 461 " --> pdb=" O TYR C 457 " (cutoff:3.500A) Processing helix chain 'B' and resid 18 through 26 removed outlier: 3.584A pdb=" N SER B 24 " --> pdb=" O GLN B 20 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N SER B 25 " --> pdb=" O ALA B 21 " (cutoff:3.500A) Processing helix chain 'B' and resid 30 through 35 removed outlier: 3.753A pdb=" N ILE B 34 " --> pdb=" O GLY B 30 " (cutoff:3.500A) Processing helix chain 'B' and resid 41 through 70 removed outlier: 4.120A pdb=" N VAL B 45 " --> pdb=" O SER B 41 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N ALA B 48 " --> pdb=" O ARG B 44 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N LEU B 49 " --> pdb=" O VAL B 45 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N CYS B 50 " --> pdb=" O VAL B 46 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N ALA B 59 " --> pdb=" O LEU B 55 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N LEU B 60 " --> pdb=" O ALA B 56 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N VAL B 61 " --> pdb=" O LEU B 57 " (cutoff:3.500A) Processing helix chain 'B' and resid 100 through 104 removed outlier: 3.571A pdb=" N ARG B 103 " --> pdb=" O ARG B 100 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N VAL B 104 " --> pdb=" O PHE B 101 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 100 through 104' Processing helix chain 'B' and resid 105 through 112 Processing helix chain 'B' and resid 134 through 142 removed outlier: 3.762A pdb=" N LYS B 142 " --> pdb=" O ILE B 138 " (cutoff:3.500A) Processing helix chain 'B' and resid 154 through 163 Processing helix chain 'B' and resid 165 through 170 Processing helix chain 'B' and resid 181 through 183 No H-bonds generated for 'chain 'B' and resid 181 through 183' Processing helix chain 'B' and resid 214 through 217 Processing helix chain 'B' and resid 226 through 230 Processing helix chain 'B' and resid 258 through 263 removed outlier: 3.503A pdb=" N GLY B 263 " --> pdb=" O ILE B 259 " (cutoff:3.500A) Processing helix chain 'B' and resid 305 through 323 removed outlier: 3.723A pdb=" N ASP B 312 " --> pdb=" O ALA B 308 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N CYS B 313 " --> pdb=" O CYS B 309 " (cutoff:3.500A) Processing helix chain 'B' and resid 337 through 344 removed outlier: 3.718A pdb=" N LYS B 342 " --> pdb=" O PRO B 338 " (cutoff:3.500A) Processing helix chain 'B' and resid 344 through 355 removed outlier: 3.548A pdb=" N GLU B 354 " --> pdb=" O ASP B 350 " (cutoff:3.500A) Processing helix chain 'B' and resid 385 through 393 removed outlier: 3.521A pdb=" N LEU B 389 " --> pdb=" O SER B 385 " (cutoff:3.500A) Processing helix chain 'B' and resid 396 through 403 removed outlier: 3.941A pdb=" N GLY B 401 " --> pdb=" O GLU B 397 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N GLU B 402 " --> pdb=" O GLN B 398 " (cutoff:3.500A) Processing helix chain 'B' and resid 426 through 441 removed outlier: 3.588A pdb=" N PHE B 441 " --> pdb=" O GLN B 437 " (cutoff:3.500A) Processing helix chain 'B' and resid 447 through 462 removed outlier: 3.588A pdb=" N ILE B 460 " --> pdb=" O ALA B 456 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N LYS B 461 " --> pdb=" O TYR B 457 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 74 through 81 Processing sheet with id=AA2, first strand: chain 'A' and resid 74 through 81 removed outlier: 4.254A pdb=" N PHE A 270 " --> pdb=" O ILE A 404 " (cutoff:3.500A) removed outlier: 8.097A pdb=" N GLU A 278 " --> pdb=" O GLU A 412 " (cutoff:3.500A) removed outlier: 9.215A pdb=" N LEU A 414 " --> pdb=" O GLU A 278 " (cutoff:3.500A) removed outlier: 10.252A pdb=" N ARG A 280 " --> pdb=" O LEU A 414 " (cutoff:3.500A) removed outlier: 9.896A pdb=" N TYR A 416 " --> pdb=" O ARG A 280 " (cutoff:3.500A) removed outlier: 12.557A pdb=" N ILE A 282 " --> pdb=" O TYR A 416 " (cutoff:3.500A) removed outlier: 9.658A pdb=" N THR A 418 " --> pdb=" O ILE A 282 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 86 through 87 Processing sheet with id=AA4, first strand: chain 'A' and resid 185 through 190 removed outlier: 7.085A pdb=" N LYS A 194 " --> pdb=" O ASN A 95 " (cutoff:3.500A) removed outlier: 5.373A pdb=" N ASN A 95 " --> pdb=" O LYS A 194 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 74 through 81 Processing sheet with id=AA6, first strand: chain 'C' and resid 74 through 81 removed outlier: 4.254A pdb=" N PHE C 270 " --> pdb=" O ILE C 404 " (cutoff:3.500A) removed outlier: 8.097A pdb=" N GLU C 278 " --> pdb=" O GLU C 412 " (cutoff:3.500A) removed outlier: 9.215A pdb=" N LEU C 414 " --> pdb=" O GLU C 278 " (cutoff:3.500A) removed outlier: 10.251A pdb=" N ARG C 280 " --> pdb=" O LEU C 414 " (cutoff:3.500A) removed outlier: 9.896A pdb=" N TYR C 416 " --> pdb=" O ARG C 280 " (cutoff:3.500A) removed outlier: 12.556A pdb=" N ILE C 282 " --> pdb=" O TYR C 416 " (cutoff:3.500A) removed outlier: 9.658A pdb=" N THR C 418 " --> pdb=" O ILE C 282 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 86 through 87 Processing sheet with id=AA8, first strand: chain 'C' and resid 185 through 190 removed outlier: 7.085A pdb=" N LYS C 194 " --> pdb=" O ASN C 95 " (cutoff:3.500A) removed outlier: 5.374A pdb=" N ASN C 95 " --> pdb=" O LYS C 194 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 74 through 81 Processing sheet with id=AB1, first strand: chain 'B' and resid 74 through 81 removed outlier: 4.254A pdb=" N PHE B 270 " --> pdb=" O ILE B 404 " (cutoff:3.500A) removed outlier: 8.097A pdb=" N GLU B 278 " --> pdb=" O GLU B 412 " (cutoff:3.500A) removed outlier: 9.215A pdb=" N LEU B 414 " --> pdb=" O GLU B 278 " (cutoff:3.500A) removed outlier: 10.252A pdb=" N ARG B 280 " --> pdb=" O LEU B 414 " (cutoff:3.500A) removed outlier: 9.896A pdb=" N TYR B 416 " --> pdb=" O ARG B 280 " (cutoff:3.500A) removed outlier: 12.557A pdb=" N ILE B 282 " --> pdb=" O TYR B 416 " (cutoff:3.500A) removed outlier: 9.657A pdb=" N THR B 418 " --> pdb=" O ILE B 282 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 86 through 87 Processing sheet with id=AB3, first strand: chain 'B' and resid 185 through 190 removed outlier: 7.086A pdb=" N LYS B 194 " --> pdb=" O ASN B 95 " (cutoff:3.500A) removed outlier: 5.373A pdb=" N ASN B 95 " --> pdb=" O LYS B 194 " (cutoff:3.500A) 486 hydrogen bonds defined for protein. 1350 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: 3.66 Time building geometry restraints manager: 4.49 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 3398 1.34 - 1.46: 2101 1.46 - 1.58: 5325 1.58 - 1.70: 0 1.70 - 1.82: 111 Bond restraints: 10935 Sorted by residual: bond pdb=" C1 NAG C 602 " pdb=" O5 NAG C 602 " ideal model delta sigma weight residual 1.406 1.451 -0.045 2.00e-02 2.50e+03 5.16e+00 bond pdb=" C1 NAG A 602 " pdb=" O5 NAG A 602 " ideal model delta sigma weight residual 1.406 1.451 -0.045 2.00e-02 2.50e+03 5.07e+00 bond pdb=" C1 NAG B 602 " pdb=" O5 NAG B 602 " ideal model delta sigma weight residual 1.406 1.451 -0.045 2.00e-02 2.50e+03 4.95e+00 bond pdb=" C1 NAG B 601 " pdb=" O5 NAG B 601 " ideal model delta sigma weight residual 1.406 1.443 -0.037 2.00e-02 2.50e+03 3.35e+00 bond pdb=" C1 NAG A 601 " pdb=" O5 NAG A 601 " ideal model delta sigma weight residual 1.406 1.443 -0.037 2.00e-02 2.50e+03 3.34e+00 ... (remaining 10930 not shown) Histogram of bond angle deviations from ideal: 99.61 - 106.49: 300 106.49 - 113.36: 5721 113.36 - 120.24: 4215 120.24 - 127.12: 4482 127.12 - 133.99: 105 Bond angle restraints: 14823 Sorted by residual: angle pdb=" C GLN B 202 " pdb=" N ASP B 203 " pdb=" CA ASP B 203 " ideal model delta sigma weight residual 122.40 127.24 -4.84 1.45e+00 4.76e-01 1.11e+01 angle pdb=" C GLN A 202 " pdb=" N ASP A 203 " pdb=" CA ASP A 203 " ideal model delta sigma weight residual 122.40 127.19 -4.79 1.45e+00 4.76e-01 1.09e+01 angle pdb=" C GLN C 202 " pdb=" N ASP C 203 " pdb=" CA ASP C 203 " ideal model delta sigma weight residual 122.40 127.17 -4.77 1.45e+00 4.76e-01 1.08e+01 angle pdb=" N ILE A 442 " pdb=" CA ILE A 442 " pdb=" C ILE A 442 " ideal model delta sigma weight residual 113.53 110.62 2.91 9.80e-01 1.04e+00 8.82e+00 angle pdb=" N ILE C 442 " pdb=" CA ILE C 442 " pdb=" C ILE C 442 " ideal model delta sigma weight residual 113.53 110.66 2.87 9.80e-01 1.04e+00 8.55e+00 ... (remaining 14818 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.13: 6296 15.13 - 30.27: 298 30.27 - 45.40: 48 45.40 - 60.54: 12 60.54 - 75.67: 9 Dihedral angle restraints: 6663 sinusoidal: 2748 harmonic: 3915 Sorted by residual: dihedral pdb=" CB CYS B 313 " pdb=" SG CYS B 313 " pdb=" SG CYS B 360 " pdb=" CB CYS B 360 " ideal model delta sinusoidal sigma weight residual -86.00 -157.90 71.90 1 1.00e+01 1.00e-02 6.62e+01 dihedral pdb=" CB CYS A 313 " pdb=" SG CYS A 313 " pdb=" SG CYS A 360 " pdb=" CB CYS A 360 " ideal model delta sinusoidal sigma weight residual -86.00 -157.87 71.87 1 1.00e+01 1.00e-02 6.61e+01 dihedral pdb=" CB CYS C 313 " pdb=" SG CYS C 313 " pdb=" SG CYS C 360 " pdb=" CB CYS C 360 " ideal model delta sinusoidal sigma weight residual -86.00 -157.84 71.84 1 1.00e+01 1.00e-02 6.61e+01 ... (remaining 6660 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.035: 962 0.035 - 0.070: 461 0.070 - 0.106: 138 0.106 - 0.141: 61 0.141 - 0.176: 13 Chirality restraints: 1635 Sorted by residual: chirality pdb=" CA CYS B 366 " pdb=" N CYS B 366 " pdb=" C CYS B 366 " pdb=" CB CYS B 366 " both_signs ideal model delta sigma weight residual False 2.51 2.33 0.18 2.00e-01 2.50e+01 7.74e-01 chirality pdb=" CA CYS A 366 " pdb=" N CYS A 366 " pdb=" C CYS A 366 " pdb=" CB CYS A 366 " both_signs ideal model delta sigma weight residual False 2.51 2.34 0.17 2.00e-01 2.50e+01 7.51e-01 chirality pdb=" CA CYS C 366 " pdb=" N CYS C 366 " pdb=" C CYS C 366 " pdb=" CB CYS C 366 " both_signs ideal model delta sigma weight residual False 2.51 2.34 0.17 2.00e-01 2.50e+01 7.38e-01 ... (remaining 1632 not shown) Planarity restraints: 1926 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR B 230 " -0.016 2.00e-02 2.50e+03 1.44e-02 4.15e+00 pdb=" CG TYR B 230 " 0.033 2.00e-02 2.50e+03 pdb=" CD1 TYR B 230 " -0.014 2.00e-02 2.50e+03 pdb=" CD2 TYR B 230 " -0.001 2.00e-02 2.50e+03 pdb=" CE1 TYR B 230 " 0.009 2.00e-02 2.50e+03 pdb=" CE2 TYR B 230 " -0.004 2.00e-02 2.50e+03 pdb=" CZ TYR B 230 " -0.003 2.00e-02 2.50e+03 pdb=" OH TYR B 230 " -0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 230 " -0.016 2.00e-02 2.50e+03 1.44e-02 4.12e+00 pdb=" CG TYR A 230 " 0.033 2.00e-02 2.50e+03 pdb=" CD1 TYR A 230 " -0.014 2.00e-02 2.50e+03 pdb=" CD2 TYR A 230 " -0.001 2.00e-02 2.50e+03 pdb=" CE1 TYR A 230 " 0.009 2.00e-02 2.50e+03 pdb=" CE2 TYR A 230 " -0.004 2.00e-02 2.50e+03 pdb=" CZ TYR A 230 " -0.003 2.00e-02 2.50e+03 pdb=" OH TYR A 230 " -0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR C 230 " 0.015 2.00e-02 2.50e+03 1.43e-02 4.09e+00 pdb=" CG TYR C 230 " -0.033 2.00e-02 2.50e+03 pdb=" CD1 TYR C 230 " 0.015 2.00e-02 2.50e+03 pdb=" CD2 TYR C 230 " 0.001 2.00e-02 2.50e+03 pdb=" CE1 TYR C 230 " -0.009 2.00e-02 2.50e+03 pdb=" CE2 TYR C 230 " 0.004 2.00e-02 2.50e+03 pdb=" CZ TYR C 230 " 0.003 2.00e-02 2.50e+03 pdb=" OH TYR C 230 " 0.003 2.00e-02 2.50e+03 ... (remaining 1923 not shown) Histogram of nonbonded interaction distances: 2.29 - 2.81: 3132 2.81 - 3.33: 8418 3.33 - 3.85: 17081 3.85 - 4.38: 20621 4.38 - 4.90: 35915 Nonbonded interactions: 85167 Sorted by model distance: nonbonded pdb=" OG SER C 241 " pdb=" OE1 GLU C 243 " model vdw 2.287 2.440 nonbonded pdb=" OG SER A 241 " pdb=" OE1 GLU A 243 " model vdw 2.288 2.440 nonbonded pdb=" OH TYR C 283 " pdb=" O GLU B 80 " model vdw 2.289 2.440 nonbonded pdb=" OG SER B 241 " pdb=" OE1 GLU B 243 " model vdw 2.289 2.440 nonbonded pdb=" OH TYR A 283 " pdb=" O GLU C 80 " model vdw 2.290 2.440 ... (remaining 85162 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' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 18.450 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: 0.000 Extract box with map and model: 13.380 Check model and map are aligned: 0.000 Set scattering table: 0.000 Process input model: 27.700 Find NCS groups from input model: 0.850 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:16.600 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 77.070 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7818 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 : 0.005 0.055 10935 Z= 0.339 Angle : 0.818 9.518 14823 Z= 0.455 Chirality : 0.048 0.176 1635 Planarity : 0.005 0.049 1920 Dihedral : 9.132 75.671 4092 Min Nonbonded Distance : 2.287 Molprobity Statistics. All-atom Clashscore : 3.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.15 % Favored : 96.85 % Rotamer: Outliers : 0.00 % Allowed : 0.79 % Favored : 99.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % 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: -4.44 (0.18), residues: 1332 helix: -4.97 (0.06), residues: 456 sheet: -1.42 (0.31), residues: 279 loop : -1.80 (0.21), residues: 597 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP A 47 HIS 0.004 0.001 HIS B 164 PHE 0.020 0.002 PHE A 264 TYR 0.033 0.002 TYR B 230 ARG 0.003 0.001 ARG C 65 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2664 Ramachandran restraints generated. 1332 Oldfield, 0 Emsley, 1332 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2664 Ramachandran restraints generated. 1332 Oldfield, 0 Emsley, 1332 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 1167 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 202 time to evaluate : 1.171 Fit side-chains outliers start: 0 outliers final: 1 residues processed: 202 average time/residue: 1.4217 time to fit residues: 306.9012 Evaluate side-chains 97 residues out of total 1167 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 96 time to evaluate : 1.260 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 1 residues processed: 1 average time/residue: 0.2815 time to fit residues: 2.1457 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 111 optimal weight: 0.9990 chunk 100 optimal weight: 3.9990 chunk 55 optimal weight: 0.7980 chunk 34 optimal weight: 2.9990 chunk 67 optimal weight: 0.9980 chunk 53 optimal weight: 0.9990 chunk 103 optimal weight: 0.0980 chunk 40 optimal weight: 1.9990 chunk 62 optimal weight: 0.6980 chunk 77 optimal weight: 0.5980 chunk 119 optimal weight: 0.4980 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 328 HIS A 421 GLN C 120 ASN C 421 GLN B 202 GLN B 421 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7830 moved from start: 0.1764 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 10935 Z= 0.202 Angle : 0.613 6.739 14823 Z= 0.323 Chirality : 0.042 0.213 1635 Planarity : 0.005 0.046 1920 Dihedral : 6.276 52.429 1584 Min Nonbonded Distance : 2.040 Molprobity Statistics. All-atom Clashscore : 6.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer: Outliers : 2.20 % Allowed : 8.00 % Favored : 89.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % 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: -2.89 (0.20), residues: 1332 helix: -2.83 (0.17), residues: 489 sheet: -1.07 (0.30), residues: 273 loop : -1.27 (0.24), residues: 570 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP B 234 HIS 0.002 0.001 HIS B 111 PHE 0.014 0.001 PHE B 148 TYR 0.011 0.001 TYR A 230 ARG 0.009 0.001 ARG B 122 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2664 Ramachandran restraints generated. 1332 Oldfield, 0 Emsley, 1332 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2664 Ramachandran restraints generated. 1332 Oldfield, 0 Emsley, 1332 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 1167 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 103 time to evaluate : 1.128 Fit side-chains outliers start: 25 outliers final: 5 residues processed: 119 average time/residue: 1.2233 time to fit residues: 157.4790 Evaluate side-chains 92 residues out of total 1167 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 87 time to evaluate : 1.094 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 2 residues processed: 3 average time/residue: 0.4914 time to fit residues: 3.2469 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 66 optimal weight: 0.5980 chunk 37 optimal weight: 0.9990 chunk 99 optimal weight: 3.9990 chunk 81 optimal weight: 1.9990 chunk 33 optimal weight: 1.9990 chunk 120 optimal weight: 1.9990 chunk 129 optimal weight: 2.9990 chunk 106 optimal weight: 2.9990 chunk 119 optimal weight: 0.7980 chunk 40 optimal weight: 3.9990 chunk 96 optimal weight: 1.9990 overall best weight: 1.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 120 ASN B 202 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7900 moved from start: 0.2256 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.040 10935 Z= 0.359 Angle : 0.645 9.507 14823 Z= 0.335 Chirality : 0.044 0.162 1635 Planarity : 0.005 0.052 1920 Dihedral : 6.014 49.554 1584 Min Nonbonded Distance : 2.064 Molprobity Statistics. All-atom Clashscore : 6.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 1.85 % Allowed : 10.20 % Favored : 87.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % 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: -1.91 (0.21), residues: 1332 helix: -1.42 (0.22), residues: 489 sheet: -0.80 (0.30), residues: 273 loop : -1.17 (0.24), residues: 570 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 47 HIS 0.004 0.001 HIS C 33 PHE 0.012 0.002 PHE A 93 TYR 0.020 0.002 TYR B 425 ARG 0.012 0.001 ARG B 122 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2664 Ramachandran restraints generated. 1332 Oldfield, 0 Emsley, 1332 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2664 Ramachandran restraints generated. 1332 Oldfield, 0 Emsley, 1332 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 1167 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 91 time to evaluate : 1.245 Fit side-chains outliers start: 21 outliers final: 6 residues processed: 105 average time/residue: 1.5759 time to fit residues: 177.3593 Evaluate side-chains 90 residues out of total 1167 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 84 time to evaluate : 1.187 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 4 residues processed: 2 average time/residue: 1.0706 time to fit residues: 3.9145 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 118 optimal weight: 0.9990 chunk 90 optimal weight: 2.9990 chunk 62 optimal weight: 1.9990 chunk 13 optimal weight: 0.0010 chunk 57 optimal weight: 0.8980 chunk 80 optimal weight: 1.9990 chunk 120 optimal weight: 0.6980 chunk 127 optimal weight: 1.9990 chunk 114 optimal weight: 0.7980 chunk 34 optimal weight: 1.9990 chunk 106 optimal weight: 1.9990 overall best weight: 0.6788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 121 ASN B 202 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7875 moved from start: 0.2448 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 10935 Z= 0.219 Angle : 0.559 7.346 14823 Z= 0.291 Chirality : 0.041 0.131 1635 Planarity : 0.004 0.061 1920 Dihedral : 5.763 50.020 1584 Min Nonbonded Distance : 2.094 Molprobity Statistics. All-atom Clashscore : 6.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.65 % Favored : 98.35 % Rotamer: Outliers : 1.67 % Allowed : 11.43 % Favored : 86.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % 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: -1.40 (0.22), residues: 1332 helix: -0.73 (0.23), residues: 489 sheet: -0.72 (0.30), residues: 273 loop : -1.04 (0.24), residues: 570 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 47 HIS 0.002 0.001 HIS B 111 PHE 0.009 0.001 PHE C 93 TYR 0.015 0.001 TYR C 457 ARG 0.014 0.001 ARG B 122 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2664 Ramachandran restraints generated. 1332 Oldfield, 0 Emsley, 1332 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2664 Ramachandran restraints generated. 1332 Oldfield, 0 Emsley, 1332 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 1167 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 85 time to evaluate : 1.240 Fit side-chains outliers start: 19 outliers final: 9 residues processed: 100 average time/residue: 1.3119 time to fit residues: 141.7028 Evaluate side-chains 92 residues out of total 1167 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 83 time to evaluate : 1.181 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 7 residues processed: 2 average time/residue: 1.4284 time to fit residues: 4.7458 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 72 optimal weight: 0.3980 chunk 1 optimal weight: 0.9980 chunk 95 optimal weight: 1.9990 chunk 52 optimal weight: 2.9990 chunk 108 optimal weight: 0.9980 chunk 88 optimal weight: 3.9990 chunk 0 optimal weight: 2.9990 chunk 65 optimal weight: 0.5980 chunk 114 optimal weight: 3.9990 chunk 32 optimal weight: 1.9990 chunk 42 optimal weight: 0.9980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 121 ASN B 202 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7883 moved from start: 0.2611 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 10935 Z= 0.246 Angle : 0.564 8.019 14823 Z= 0.292 Chirality : 0.041 0.155 1635 Planarity : 0.004 0.054 1920 Dihedral : 5.682 50.152 1584 Min Nonbonded Distance : 2.087 Molprobity Statistics. All-atom Clashscore : 6.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Rotamer: Outliers : 1.85 % Allowed : 12.14 % Favored : 86.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % 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: -1.08 (0.22), residues: 1332 helix: -0.35 (0.24), residues: 492 sheet: -0.56 (0.30), residues: 273 loop : -0.98 (0.25), residues: 567 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP C 234 HIS 0.002 0.001 HIS C 33 PHE 0.009 0.001 PHE A 264 TYR 0.014 0.001 TYR C 457 ARG 0.013 0.001 ARG B 122 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2664 Ramachandran restraints generated. 1332 Oldfield, 0 Emsley, 1332 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2664 Ramachandran restraints generated. 1332 Oldfield, 0 Emsley, 1332 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 1167 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 85 time to evaluate : 1.222 Fit side-chains outliers start: 21 outliers final: 8 residues processed: 101 average time/residue: 1.3690 time to fit residues: 149.0495 Evaluate side-chains 90 residues out of total 1167 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 82 time to evaluate : 1.264 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 7 residues processed: 1 average time/residue: 1.8266 time to fit residues: 3.6070 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 114 optimal weight: 0.7980 chunk 25 optimal weight: 1.9990 chunk 74 optimal weight: 0.8980 chunk 31 optimal weight: 0.9990 chunk 127 optimal weight: 1.9990 chunk 106 optimal weight: 1.9990 chunk 59 optimal weight: 0.9990 chunk 10 optimal weight: 0.0970 chunk 42 optimal weight: 2.9990 chunk 67 optimal weight: 1.9990 chunk 123 optimal weight: 2.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 121 ASN B 202 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7880 moved from start: 0.2727 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 10935 Z= 0.237 Angle : 0.553 7.846 14823 Z= 0.287 Chirality : 0.041 0.133 1635 Planarity : 0.004 0.060 1920 Dihedral : 5.608 49.965 1584 Min Nonbonded Distance : 2.095 Molprobity Statistics. All-atom Clashscore : 6.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.58 % Favored : 98.42 % Rotamer: Outliers : 1.85 % Allowed : 12.66 % Favored : 85.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % 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: -0.86 (0.23), residues: 1332 helix: -0.11 (0.24), residues: 492 sheet: -0.46 (0.30), residues: 273 loop : -0.91 (0.25), residues: 567 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 47 HIS 0.002 0.001 HIS C 111 PHE 0.010 0.001 PHE A 264 TYR 0.012 0.001 TYR C 457 ARG 0.014 0.001 ARG B 122 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2664 Ramachandran restraints generated. 1332 Oldfield, 0 Emsley, 1332 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2664 Ramachandran restraints generated. 1332 Oldfield, 0 Emsley, 1332 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 1167 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 79 time to evaluate : 1.320 Fit side-chains outliers start: 21 outliers final: 8 residues processed: 97 average time/residue: 1.3852 time to fit residues: 144.7661 Evaluate side-chains 85 residues out of total 1167 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 77 time to evaluate : 1.268 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 7 residues processed: 1 average time/residue: 1.6905 time to fit residues: 3.4802 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 14 optimal weight: 0.9980 chunk 72 optimal weight: 0.4980 chunk 93 optimal weight: 0.9980 chunk 107 optimal weight: 0.9980 chunk 71 optimal weight: 0.0470 chunk 127 optimal weight: 0.7980 chunk 79 optimal weight: 2.9990 chunk 77 optimal weight: 1.9990 chunk 58 optimal weight: 0.7980 chunk 78 optimal weight: 0.8980 chunk 50 optimal weight: 2.9990 overall best weight: 0.6078 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 121 ASN B 202 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7869 moved from start: 0.2800 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 10935 Z= 0.203 Angle : 0.536 7.414 14823 Z= 0.278 Chirality : 0.040 0.132 1635 Planarity : 0.004 0.056 1920 Dihedral : 5.529 50.303 1584 Min Nonbonded Distance : 2.097 Molprobity Statistics. All-atom Clashscore : 6.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 1.50 % Allowed : 13.10 % Favored : 85.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % 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: -0.64 (0.23), residues: 1332 helix: 0.12 (0.24), residues: 492 sheet: -0.38 (0.30), residues: 273 loop : -0.79 (0.25), residues: 567 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 47 HIS 0.002 0.001 HIS A 33 PHE 0.009 0.001 PHE C 93 TYR 0.012 0.001 TYR C 457 ARG 0.011 0.001 ARG A 122 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2664 Ramachandran restraints generated. 1332 Oldfield, 0 Emsley, 1332 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2664 Ramachandran restraints generated. 1332 Oldfield, 0 Emsley, 1332 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 1167 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 80 time to evaluate : 1.217 Fit side-chains outliers start: 17 outliers final: 9 residues processed: 94 average time/residue: 1.3527 time to fit residues: 137.0582 Evaluate side-chains 87 residues out of total 1167 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 78 time to evaluate : 1.204 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 7 residues processed: 2 average time/residue: 1.3867 time to fit residues: 4.5785 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 75 optimal weight: 0.8980 chunk 38 optimal weight: 1.9990 chunk 24 optimal weight: 0.7980 chunk 80 optimal weight: 0.6980 chunk 86 optimal weight: 1.9990 chunk 62 optimal weight: 1.9990 chunk 11 optimal weight: 2.9990 chunk 100 optimal weight: 0.5980 chunk 115 optimal weight: 0.0070 chunk 121 optimal weight: 0.9990 chunk 111 optimal weight: 0.5980 overall best weight: 0.5398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 121 ASN B 202 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7861 moved from start: 0.2884 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 10935 Z= 0.191 Angle : 0.530 7.294 14823 Z= 0.275 Chirality : 0.040 0.131 1635 Planarity : 0.004 0.055 1920 Dihedral : 5.453 50.675 1584 Min Nonbonded Distance : 2.106 Molprobity Statistics. All-atom Clashscore : 6.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.65 % Favored : 98.35 % Rotamer: Outliers : 1.58 % Allowed : 13.19 % Favored : 85.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.42 (0.23), residues: 1332 helix: 0.38 (0.25), residues: 489 sheet: -0.32 (0.30), residues: 273 loop : -0.71 (0.26), residues: 570 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP A 47 HIS 0.002 0.001 HIS B 111 PHE 0.010 0.001 PHE C 93 TYR 0.011 0.001 TYR C 457 ARG 0.015 0.001 ARG B 122 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2664 Ramachandran restraints generated. 1332 Oldfield, 0 Emsley, 1332 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2664 Ramachandran restraints generated. 1332 Oldfield, 0 Emsley, 1332 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 1167 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 82 time to evaluate : 1.214 Fit side-chains outliers start: 18 outliers final: 11 residues processed: 99 average time/residue: 1.3722 time to fit residues: 146.3567 Evaluate side-chains 88 residues out of total 1167 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 77 time to evaluate : 1.234 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 10 residues processed: 1 average time/residue: 1.6648 time to fit residues: 3.4096 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 118 optimal weight: 0.8980 chunk 121 optimal weight: 0.9980 chunk 71 optimal weight: 0.0050 chunk 51 optimal weight: 1.9990 chunk 93 optimal weight: 0.8980 chunk 36 optimal weight: 1.9990 chunk 107 optimal weight: 0.7980 chunk 112 optimal weight: 0.0980 chunk 77 optimal weight: 0.8980 chunk 125 optimal weight: 0.8980 chunk 76 optimal weight: 0.7980 overall best weight: 0.5194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 121 ASN ** B 202 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7859 moved from start: 0.2943 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 10935 Z= 0.191 Angle : 0.541 8.129 14823 Z= 0.280 Chirality : 0.040 0.187 1635 Planarity : 0.004 0.057 1920 Dihedral : 5.425 50.712 1584 Min Nonbonded Distance : 2.105 Molprobity Statistics. All-atom Clashscore : 6.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.03 % Favored : 97.97 % Rotamer: Outliers : 1.06 % Allowed : 13.98 % Favored : 84.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % 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: -0.33 (0.23), residues: 1332 helix: 0.42 (0.25), residues: 495 sheet: -0.26 (0.31), residues: 273 loop : -0.63 (0.26), residues: 564 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP B 47 HIS 0.002 0.001 HIS B 111 PHE 0.009 0.001 PHE C 93 TYR 0.011 0.001 TYR C 457 ARG 0.014 0.000 ARG A 122 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2664 Ramachandran restraints generated. 1332 Oldfield, 0 Emsley, 1332 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2664 Ramachandran restraints generated. 1332 Oldfield, 0 Emsley, 1332 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 1167 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 81 time to evaluate : 1.182 Fit side-chains outliers start: 12 outliers final: 9 residues processed: 92 average time/residue: 1.4318 time to fit residues: 141.6495 Evaluate side-chains 84 residues out of total 1167 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 75 time to evaluate : 1.221 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 9 residues processed: 0 time to fit residues: 1.6281 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 59 optimal weight: 0.9990 chunk 87 optimal weight: 0.6980 chunk 131 optimal weight: 0.7980 chunk 121 optimal weight: 1.9990 chunk 104 optimal weight: 2.9990 chunk 10 optimal weight: 0.5980 chunk 80 optimal weight: 2.9990 chunk 64 optimal weight: 1.9990 chunk 83 optimal weight: 0.9980 chunk 111 optimal weight: 0.9990 chunk 32 optimal weight: 0.9980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 121 ASN B 202 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7879 moved from start: 0.2960 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 10935 Z= 0.255 Angle : 0.576 8.361 14823 Z= 0.297 Chirality : 0.041 0.156 1635 Planarity : 0.004 0.079 1920 Dihedral : 5.516 50.137 1584 Min Nonbonded Distance : 2.088 Molprobity Statistics. All-atom Clashscore : 6.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.18 % Favored : 97.82 % Rotamer: Outliers : 1.32 % Allowed : 13.90 % Favored : 84.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % 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: -0.33 (0.23), residues: 1332 helix: 0.45 (0.25), residues: 489 sheet: -0.24 (0.30), residues: 273 loop : -0.67 (0.25), residues: 570 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP A 47 HIS 0.002 0.001 HIS A 111 PHE 0.010 0.001 PHE A 264 TYR 0.011 0.001 TYR C 457 ARG 0.018 0.001 ARG B 122 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2664 Ramachandran restraints generated. 1332 Oldfield, 0 Emsley, 1332 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2664 Ramachandran restraints generated. 1332 Oldfield, 0 Emsley, 1332 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 1167 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 80 time to evaluate : 1.205 Fit side-chains outliers start: 15 outliers final: 9 residues processed: 94 average time/residue: 1.4219 time to fit residues: 143.6309 Evaluate side-chains 88 residues out of total 1167 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 79 time to evaluate : 1.194 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 8 residues processed: 1 average time/residue: 1.6956 time to fit residues: 3.4222 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 96 optimal weight: 0.9990 chunk 15 optimal weight: 0.8980 chunk 29 optimal weight: 0.8980 chunk 104 optimal weight: 0.9980 chunk 43 optimal weight: 1.9990 chunk 107 optimal weight: 0.4980 chunk 13 optimal weight: 0.0980 chunk 19 optimal weight: 0.9990 chunk 92 optimal weight: 0.6980 chunk 5 optimal weight: 0.6980 chunk 75 optimal weight: 0.7980 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 121 ASN ** B 202 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3835 r_free = 0.3835 target = 0.144694 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3544 r_free = 0.3544 target = 0.115181 restraints weight = 13635.642| |-----------------------------------------------------------------------------| r_work (start): 0.3491 rms_B_bonded: 2.53 r_work: 0.3325 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.3185 rms_B_bonded: 4.81 restraints_weight: 0.2500 r_work (final): 0.3185 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8007 moved from start: 0.3000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 10935 Z= 0.200 Angle : 0.559 8.179 14823 Z= 0.287 Chirality : 0.041 0.227 1635 Planarity : 0.004 0.055 1920 Dihedral : 5.459 50.273 1584 Min Nonbonded Distance : 2.104 Molprobity Statistics. All-atom Clashscore : 6.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.03 % Favored : 97.97 % Rotamer: Outliers : 1.06 % Allowed : 14.42 % Favored : 84.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % 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: -0.29 (0.23), residues: 1332 helix: 0.43 (0.25), residues: 495 sheet: -0.25 (0.31), residues: 273 loop : -0.58 (0.26), residues: 564 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 47 HIS 0.002 0.001 HIS B 111 PHE 0.010 0.001 PHE C 93 TYR 0.011 0.001 TYR C 457 ARG 0.009 0.001 ARG C 122 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3565.61 seconds wall clock time: 65 minutes 20.39 seconds (3920.39 seconds total)