Starting phenix.real_space_refine (version: 1.21rc1) on Fri Apr 21 22:12:32 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vtk_21380/04_2023/6vtk_21380.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vtk_21380/04_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_21380/04_2023/6vtk_21380.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vtk_21380/04_2023/6vtk_21380.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vtk_21380/04_2023/6vtk_21380.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vtk_21380/04_2023/6vtk_21380.pdb" } resolution = 2.82 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- 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: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4938/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 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 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 chiralities: 2 Time building chain proxies: 5.86, per 1000 atoms: 0.55 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: 4.06 Conformation dependent library (CDL) restraints added in 1.6 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: 0.80 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: 3.07 Time building geometry restraints manager: 4.41 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: 6188 15.13 - 30.27: 292 30.27 - 45.40: 42 45.40 - 60.54: 6 60.54 - 75.67: 9 Dihedral angle restraints: 6537 sinusoidal: 2622 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 6534 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: 2.120 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: 10.610 Check model and map are aligned: 0.160 Set scattering table: 0.090 Process input model: 29.090 Find NCS groups from input model: 0.600 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:13.740 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 56.470 ------------------------------------------------------------------------------- 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 : 8.887 75.671 3966 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 % 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 *********************** 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 : 1.280 Fit side-chains outliers start: 0 outliers final: 1 residues processed: 202 average time/residue: 1.3585 time to fit residues: 293.6520 Evaluate side-chains 97 residues out of total 1167 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 96 time to evaluate : 1.306 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 1 residues processed: 1 average time/residue: 0.2764 time to fit residues: 2.0664 ------------------------------------------------------------------------------- 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: 0.1751 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.043 10935 Z= 0.201 Angle : 0.613 6.719 14823 Z= 0.323 Chirality : 0.042 0.217 1635 Planarity : 0.005 0.046 1920 Dihedral : 5.427 29.553 1458 Min Nonbonded Distance : 2.045 Molprobity Statistics. All-atom Clashscore : 5.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer Outliers : 2.20 % 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: -2.88 (0.20), residues: 1332 helix: -2.80 (0.17), residues: 489 sheet: -1.05 (0.30), residues: 273 loop : -1.27 (0.24), residues: 570 *********************** 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 129 residues out of total 1167 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 104 time to evaluate : 1.123 Fit side-chains outliers start: 25 outliers final: 5 residues processed: 120 average time/residue: 1.2430 time to fit residues: 161.3159 Evaluate side-chains 92 residues out of total 1167 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 87 time to evaluate : 1.281 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 2 residues processed: 3 average time/residue: 0.5648 time to fit residues: 3.7117 ------------------------------------------------------------------------------- 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: 0.6980 chunk 37 optimal weight: 0.9990 chunk 99 optimal weight: 2.9990 chunk 81 optimal weight: 1.9990 chunk 33 optimal weight: 1.9990 chunk 120 optimal weight: 0.9990 chunk 129 optimal weight: 2.9990 chunk 106 optimal weight: 2.9990 chunk 119 optimal weight: 0.8980 chunk 40 optimal weight: 3.9990 chunk 96 optimal weight: 1.9990 overall best weight: 1.1186 ------------------------------------------------------------------------------- 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: 0.7893 moved from start: 0.2260 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.035 10935 Z= 0.322 Angle : 0.628 8.832 14823 Z= 0.326 Chirality : 0.043 0.152 1635 Planarity : 0.005 0.052 1920 Dihedral : 5.283 22.821 1458 Min Nonbonded Distance : 2.074 Molprobity Statistics. All-atom Clashscore : 5.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Rotamer Outliers : 2.02 % 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: -1.83 (0.21), residues: 1332 helix: -1.33 (0.22), residues: 489 sheet: -0.81 (0.30), residues: 273 loop : -1.13 (0.24), residues: 570 *********************** 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 113 residues out of total 1167 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 90 time to evaluate : 1.246 Fit side-chains outliers start: 23 outliers final: 5 residues processed: 105 average time/residue: 1.4236 time to fit residues: 160.6401 Evaluate side-chains 88 residues out of total 1167 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 83 time to evaluate : 1.259 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 4 residues processed: 1 average time/residue: 1.0854 time to fit residues: 2.9060 ------------------------------------------------------------------------------- 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: 0.9990 chunk 62 optimal weight: 1.9990 chunk 13 optimal weight: 0.9980 chunk 57 optimal weight: 0.5980 chunk 80 optimal weight: 1.9990 chunk 120 optimal weight: 0.9980 chunk 127 optimal weight: 1.9990 chunk 114 optimal weight: 0.6980 chunk 34 optimal weight: 0.0870 chunk 106 optimal weight: 1.9990 overall best weight: 0.6758 ------------------------------------------------------------------------------- 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: 0.7873 moved from start: 0.2452 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.030 10935 Z= 0.218 Angle : 0.553 7.202 14823 Z= 0.288 Chirality : 0.041 0.131 1635 Planarity : 0.004 0.054 1920 Dihedral : 4.997 20.861 1458 Min Nonbonded Distance : 2.093 Molprobity Statistics. All-atom Clashscore : 6.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.80 % Favored : 98.20 % Rotamer Outliers : 1.50 % 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: -1.34 (0.22), residues: 1332 helix: -0.64 (0.23), residues: 489 sheet: -0.71 (0.30), residues: 273 loop : -1.03 (0.24), residues: 570 *********************** 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 100 residues out of total 1167 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 83 time to evaluate : 1.295 Fit side-chains outliers start: 17 outliers final: 8 residues processed: 97 average time/residue: 1.3899 time to fit residues: 145.4312 Evaluate side-chains 88 residues out of total 1167 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 80 time to evaluate : 1.225 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 7 residues processed: 1 average time/residue: 1.7877 time to fit residues: 3.5849 ------------------------------------------------------------------------------- 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: 0.9980 chunk 1 optimal weight: 0.9990 chunk 95 optimal weight: 1.9990 chunk 52 optimal weight: 2.9990 chunk 108 optimal weight: 0.8980 chunk 88 optimal weight: 3.9990 chunk 0 optimal weight: 2.9990 chunk 65 optimal weight: 0.3980 chunk 114 optimal weight: 3.9990 chunk 32 optimal weight: 1.9990 chunk 42 optimal weight: 2.9990 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 121 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: 0.2627 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.034 10935 Z= 0.310 Angle : 0.597 8.914 14823 Z= 0.308 Chirality : 0.043 0.169 1635 Planarity : 0.004 0.055 1920 Dihedral : 5.078 21.747 1458 Min Nonbonded Distance : 2.074 Molprobity Statistics. All-atom Clashscore : 6.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Rotamer Outliers : 2.02 % 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: -1.11 (0.22), residues: 1332 helix: -0.38 (0.24), residues: 492 sheet: -0.54 (0.30), residues: 273 loop : -1.00 (0.25), residues: 567 *********************** 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 113 residues out of total 1167 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 90 time to evaluate : 1.287 Fit side-chains outliers start: 23 outliers final: 8 residues processed: 108 average time/residue: 1.3025 time to fit residues: 152.1344 Evaluate side-chains 94 residues out of total 1167 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 86 time to evaluate : 1.142 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 7 residues processed: 1 average time/residue: 1.7094 time to fit residues: 3.4377 ------------------------------------------------------------------------------- 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: 1.9990 chunk 25 optimal weight: 1.9990 chunk 74 optimal weight: 0.9980 chunk 31 optimal weight: 0.3980 chunk 127 optimal weight: 0.8980 chunk 106 optimal weight: 1.9990 chunk 59 optimal weight: 0.6980 chunk 10 optimal weight: 0.4980 chunk 42 optimal weight: 1.9990 chunk 67 optimal weight: 1.9990 chunk 123 optimal weight: 0.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- 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: 0.7881 moved from start: 0.2743 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.030 10935 Z= 0.225 Angle : 0.556 7.717 14823 Z= 0.289 Chirality : 0.041 0.137 1635 Planarity : 0.004 0.064 1920 Dihedral : 4.934 19.689 1458 Min Nonbonded Distance : 2.097 Molprobity Statistics. All-atom Clashscore : 6.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.50 % Favored : 98.50 % Rotamer Outliers : 2.02 % 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: -0.93 (0.22), residues: 1332 helix: -0.17 (0.24), residues: 492 sheet: -0.52 (0.30), residues: 273 loop : -0.92 (0.25), residues: 567 *********************** 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 107 residues out of total 1167 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 84 time to evaluate : 1.226 Fit side-chains outliers start: 23 outliers final: 8 residues processed: 102 average time/residue: 1.3569 time to fit residues: 149.2400 Evaluate side-chains 88 residues out of total 1167 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 80 time to evaluate : 1.277 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 6 residues processed: 2 average time/residue: 1.3744 time to fit residues: 4.6477 ------------------------------------------------------------------------------- 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: 1.9990 chunk 72 optimal weight: 0.8980 chunk 93 optimal weight: 1.9990 chunk 107 optimal weight: 0.9990 chunk 71 optimal weight: 0.0000 chunk 127 optimal weight: 0.8980 chunk 79 optimal weight: 0.7980 chunk 77 optimal weight: 1.9990 chunk 58 optimal weight: 0.9980 chunk 78 optimal weight: 0.9990 chunk 50 optimal weight: 1.9990 overall best weight: 0.7184 ------------------------------------------------------------------------------- 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: 0.2824 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.035 10935 Z= 0.230 Angle : 0.560 7.871 14823 Z= 0.289 Chirality : 0.041 0.139 1635 Planarity : 0.004 0.069 1920 Dihedral : 4.895 19.259 1458 Min Nonbonded Distance : 2.091 Molprobity Statistics. All-atom Clashscore : 6.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer Outliers : 1.67 % 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: -0.77 (0.23), residues: 1332 helix: -0.03 (0.24), residues: 492 sheet: -0.43 (0.30), residues: 273 loop : -0.84 (0.25), residues: 567 *********************** 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 103 residues out of total 1167 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 84 time to evaluate : 1.312 Fit side-chains outliers start: 19 outliers final: 10 residues processed: 98 average time/residue: 1.4007 time to fit residues: 148.6055 Evaluate side-chains 92 residues out of total 1167 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 82 time to evaluate : 1.802 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 8 residues processed: 2 average time/residue: 1.3870 time to fit residues: 4.6878 ------------------------------------------------------------------------------- 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: 0.7980 chunk 38 optimal weight: 1.9990 chunk 24 optimal weight: 0.0570 chunk 80 optimal weight: 0.6980 chunk 86 optimal weight: 2.9990 chunk 62 optimal weight: 1.9990 chunk 11 optimal weight: 0.9980 chunk 100 optimal weight: 0.9980 chunk 115 optimal weight: 0.8980 chunk 121 optimal weight: 0.8980 chunk 111 optimal weight: 0.5980 overall best weight: 0.6098 ------------------------------------------------------------------------------- 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: 0.7871 moved from start: 0.2901 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.037 10935 Z= 0.207 Angle : 0.542 7.502 14823 Z= 0.281 Chirality : 0.041 0.135 1635 Planarity : 0.004 0.055 1920 Dihedral : 4.788 19.168 1458 Min Nonbonded Distance : 2.101 Molprobity Statistics. All-atom Clashscore : 6.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.73 % Favored : 98.27 % Rotamer Outliers : 1.32 % 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: -0.59 (0.23), residues: 1332 helix: 0.15 (0.24), residues: 492 sheet: -0.40 (0.30), residues: 273 loop : -0.73 (0.25), residues: 567 *********************** 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 98 residues out of total 1167 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 83 time to evaluate : 1.364 Fit side-chains outliers start: 15 outliers final: 8 residues processed: 96 average time/residue: 1.4345 time to fit residues: 148.2278 Evaluate side-chains 89 residues out of total 1167 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 81 time to evaluate : 1.271 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 7 residues processed: 1 average time/residue: 1.7560 time to fit residues: 3.6864 ------------------------------------------------------------------------------- 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: 0.6980 chunk 121 optimal weight: 0.9980 chunk 71 optimal weight: 0.4980 chunk 51 optimal weight: 1.9990 chunk 93 optimal weight: 0.9990 chunk 36 optimal weight: 2.9990 chunk 107 optimal weight: 0.0570 chunk 112 optimal weight: 0.3980 chunk 77 optimal weight: 1.9990 chunk 125 optimal weight: 0.6980 chunk 76 optimal weight: 0.5980 overall best weight: 0.4498 ------------------------------------------------------------------------------- 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: 0.7857 moved from start: 0.2965 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= 0.178 Angle : 0.537 7.035 14823 Z= 0.279 Chirality : 0.040 0.151 1635 Planarity : 0.004 0.054 1920 Dihedral : 4.694 21.625 1458 Min Nonbonded Distance : 2.110 Molprobity Statistics. All-atom Clashscore : 6.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.03 % Favored : 97.97 % Rotamer Outliers : 1.32 % 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: -0.41 (0.23), residues: 1332 helix: 0.26 (0.24), residues: 501 sheet: -0.35 (0.31), residues: 273 loop : -0.57 (0.26), residues: 558 *********************** 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 99 residues out of total 1167 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 84 time to evaluate : 1.303 Fit side-chains outliers start: 15 outliers final: 8 residues processed: 97 average time/residue: 1.3673 time to fit residues: 143.1563 Evaluate side-chains 87 residues out of total 1167 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 79 time to evaluate : 1.213 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 8 residues processed: 0 time to fit residues: 1.6922 ------------------------------------------------------------------------------- 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: 0.9980 chunk 121 optimal weight: 0.7980 chunk 104 optimal weight: 0.4980 chunk 10 optimal weight: 0.8980 chunk 80 optimal weight: 2.9990 chunk 64 optimal weight: 1.9990 chunk 83 optimal weight: 0.6980 chunk 111 optimal weight: 0.9980 chunk 32 optimal weight: 0.0770 overall best weight: 0.5538 ------------------------------------------------------------------------------- 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: 0.7862 moved from start: 0.2994 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.052 10935 Z= 0.202 Angle : 0.561 9.657 14823 Z= 0.288 Chirality : 0.040 0.142 1635 Planarity : 0.004 0.062 1920 Dihedral : 4.685 20.592 1458 Min Nonbonded Distance : 2.104 Molprobity Statistics. All-atom Clashscore : 6.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.80 % Favored : 98.20 % Rotamer Outliers : 1.23 % 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: -0.30 (0.23), residues: 1332 helix: 0.39 (0.24), residues: 498 sheet: -0.28 (0.31), residues: 273 loop : -0.55 (0.26), residues: 561 ********************** 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 94 residues out of total 1167 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 80 time to evaluate : 1.221 Fit side-chains outliers start: 14 outliers final: 10 residues processed: 93 average time/residue: 1.4747 time to fit residues: 147.3745 Evaluate side-chains 90 residues out of total 1167 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 80 time to evaluate : 1.275 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 10 residues processed: 0 time to fit residues: 1.7231 ------------------------------------------------------------------------------- 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: 0.7980 chunk 15 optimal weight: 0.7980 chunk 29 optimal weight: 0.9990 chunk 104 optimal weight: 0.0010 chunk 43 optimal weight: 1.9990 chunk 107 optimal weight: 0.2980 chunk 13 optimal weight: 0.9990 chunk 19 optimal weight: 1.9990 chunk 92 optimal weight: 0.7980 chunk 5 optimal weight: 0.9990 chunk 75 optimal weight: 0.9980 overall best weight: 0.5386 ------------------------------------------------------------------------------- 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 = 0.3840 r_free = 0.3840 target = 0.145048 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3548 r_free = 0.3548 target = 0.115534 restraints weight = 13618.533| |-----------------------------------------------------------------------------| r_work (start): 0.3499 rms_B_bonded: 2.53 r_work: 0.3335 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.3195 rms_B_bonded: 4.83 restraints_weight: 0.2500 r_work (final): 0.3195 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8019 moved from start: 0.3021 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.048 10935 Z= 0.197 Angle : 0.551 8.215 14823 Z= 0.284 Chirality : 0.040 0.133 1635 Planarity : 0.004 0.074 1920 Dihedral : 4.661 20.542 1458 Min Nonbonded Distance : 2.103 Molprobity Statistics. All-atom Clashscore : 6.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.80 % Favored : 98.20 % Rotamer Outliers : 1.23 % 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: -0.19 (0.23), residues: 1332 helix: 0.59 (0.25), residues: 489 sheet: -0.26 (0.30), residues: 273 loop : -0.56 (0.26), residues: 570 =============================================================================== Job complete usr+sys time: 3553.34 seconds wall clock time: 63 minutes 52.52 seconds (3832.52 seconds total)