Starting phenix.real_space_refine on Wed Feb 4 15:08:46 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9uvc_64532/02_2026/9uvc_64532.cif Found real_map, /net/cci-nas-00/data/ceres_data/9uvc_64532/02_2026/9uvc_64532.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9uvc_64532/02_2026/9uvc_64532.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9uvc_64532/02_2026/9uvc_64532.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9uvc_64532/02_2026/9uvc_64532.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9uvc_64532/02_2026/9uvc_64532.map" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.016 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 27 5.16 5 C 6989 2.51 5 N 1954 2.21 5 O 2146 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 11116 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 3740 Number of conformers: 1 Conformer: "" Number of residues, atoms: 525, 3740 Classifications: {'peptide': 525} Incomplete info: {'truncation_to_alanine': 155} Link IDs: {'PTRANS': 18, 'TRANS': 506} Chain breaks: 3 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 530 Unresolved non-hydrogen angles: 687 Unresolved non-hydrogen dihedrals: 417 Unresolved non-hydrogen chiralities: 68 Planarities with less than four sites: {'ARG:plan': 11, 'GLU:plan': 11, 'ASP:plan': 8, 'GLN:plan1': 7, 'TRP:plan': 1, 'HIS:plan': 3, 'PHE:plan': 3, 'TYR:plan': 8, 'ASN:plan1': 10} Unresolved non-hydrogen planarities: 279 Chain: "B" Number of atoms: 3637 Number of conformers: 1 Conformer: "" Number of residues, atoms: 523, 3637 Classifications: {'peptide': 523} Incomplete info: {'truncation_to_alanine': 178} Link IDs: {'PTRANS': 18, 'TRANS': 504} Chain breaks: 3 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 622 Unresolved non-hydrogen angles: 805 Unresolved non-hydrogen dihedrals: 497 Unresolved non-hydrogen chiralities: 71 Planarities with less than four sites: {'GLU:plan': 14, 'ASP:plan': 10, 'GLN:plan1': 10, 'TRP:plan': 2, 'ARG:plan': 12, 'HIS:plan': 3, 'PHE:plan': 5, 'TYR:plan': 9, 'ASN:plan1': 12} Unresolved non-hydrogen planarities: 348 Chain: "C" Number of atoms: 3739 Number of conformers: 1 Conformer: "" Number of residues, atoms: 524, 3739 Classifications: {'peptide': 524} Incomplete info: {'truncation_to_alanine': 151} Link IDs: {'PTRANS': 18, 'TRANS': 505} Chain breaks: 3 Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 520 Unresolved non-hydrogen angles: 670 Unresolved non-hydrogen dihedrals: 412 Unresolved non-hydrogen chiralities: 59 Planarities with less than four sites: {'ARG:plan': 10, 'GLU:plan': 11, 'ASP:plan': 9, 'HIS:plan': 1, 'PHE:plan': 5, 'GLN:plan1': 9, 'TYR:plan': 9, 'ASN:plan1': 10} Unresolved non-hydrogen planarities: 285 Time building chain proxies: 2.51, per 1000 atoms: 0.23 Number of scatterers: 11116 At special positions: 0 Unit cell: (93.84, 93.84, 181.24, 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 27 16.00 O 2146 8.00 N 1954 7.00 C 6989 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=9, symmetry=0 Simple disulfide: pdb=" SG CYS A 87 " - pdb=" SG CYS A 482 " distance=2.03 Simple disulfide: pdb=" SG CYS A 159 " - pdb=" SG CYS A 224 " distance=2.03 Simple disulfide: pdb=" SG CYS A 317 " - pdb=" SG CYS A 364 " distance=2.03 Simple disulfide: pdb=" SG CYS B 87 " - pdb=" SG CYS B 482 " distance=2.03 Simple disulfide: pdb=" SG CYS B 159 " - pdb=" SG CYS B 224 " distance=2.03 Simple disulfide: pdb=" SG CYS B 317 " - pdb=" SG CYS B 364 " distance=2.03 Simple disulfide: pdb=" SG CYS C 87 " - pdb=" SG CYS C 482 " distance=2.03 Simple disulfide: pdb=" SG CYS C 159 " - pdb=" SG CYS C 224 " distance=2.03 Simple disulfide: pdb=" SG CYS C 317 " - pdb=" SG CYS C 364 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.97 Conformation dependent library (CDL) restraints added in 591.9 milliseconds 3096 Ramachandran restraints generated. 1548 Oldfield, 0 Emsley, 1548 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3020 Finding SS restraints... Secondary structure from input PDB file: 13 helices and 17 sheets defined 16.0% alpha, 25.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.43 Creating SS restraints... Processing helix chain 'A' and resid 147 through 156 Processing helix chain 'A' and resid 365 through 380 Processing helix chain 'A' and resid 451 through 496 removed outlier: 4.048A pdb=" N GLN A 458 " --> pdb=" O LEU A 454 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N ILE A 459 " --> pdb=" O ILE A 455 " (cutoff:3.500A) Processing helix chain 'A' and resid 499 through 508 Processing helix chain 'B' and resid 148 through 157 Processing helix chain 'B' and resid 362 through 380 removed outlier: 4.088A pdb=" N ASP B 367 " --> pdb=" O SER B 363 " (cutoff:3.500A) removed outlier: 4.962A pdb=" N GLN B 368 " --> pdb=" O CYS B 364 " (cutoff:3.500A) Processing helix chain 'B' and resid 451 through 496 removed outlier: 4.034A pdb=" N GLN B 458 " --> pdb=" O LEU B 454 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N ILE B 459 " --> pdb=" O ILE B 455 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N GLN B 460 " --> pdb=" O THR B 456 " (cutoff:3.500A) Processing helix chain 'B' and resid 499 through 508 removed outlier: 3.963A pdb=" N VAL B 503 " --> pdb=" O ASN B 499 " (cutoff:3.500A) Processing helix chain 'C' and resid 147 through 156 removed outlier: 3.895A pdb=" N GLY C 151 " --> pdb=" O GLU C 147 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N ASP C 152 " --> pdb=" O TRP C 148 " (cutoff:3.500A) Processing helix chain 'C' and resid 282 through 286 removed outlier: 3.720A pdb=" N ARG C 286 " --> pdb=" O TYR C 283 " (cutoff:3.500A) Processing helix chain 'C' and resid 365 through 380 Processing helix chain 'C' and resid 451 through 497 removed outlier: 3.995A pdb=" N GLN C 458 " --> pdb=" O LEU C 454 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N ILE C 459 " --> pdb=" O ILE C 455 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N GLN C 460 " --> pdb=" O THR C 456 " (cutoff:3.500A) removed outlier: 4.192A pdb=" N LYS C 497 " --> pdb=" O TYR C 493 " (cutoff:3.500A) Processing helix chain 'C' and resid 499 through 505 Processing sheet with id=AA1, first strand: chain 'A' and resid 520 through 521 removed outlier: 4.079A pdb=" N ALA C 618 " --> pdb=" O THR A 78 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N ARG A 80 " --> pdb=" O ALA C 618 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 347 through 350 removed outlier: 3.635A pdb=" N PHE A 348 " --> pdb=" O PHE A 339 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N TRP A 322 " --> pdb=" O VAL A 102 " (cutoff:3.500A) removed outlier: 7.319A pdb=" N VAL A 102 " --> pdb=" O TRP A 322 " (cutoff:3.500A) removed outlier: 4.822A pdb=" N THR A 324 " --> pdb=" O LEU A 100 " (cutoff:3.500A) removed outlier: 6.683A pdb=" N LEU A 100 " --> pdb=" O THR A 324 " (cutoff:3.500A) removed outlier: 5.898A pdb=" N GLY A 98 " --> pdb=" O PRO A 326 " (cutoff:3.500A) removed outlier: 6.186A pdb=" N ALA A 328 " --> pdb=" O VAL A 96 " (cutoff:3.500A) removed outlier: 6.076A pdb=" N VAL A 96 " --> pdb=" O ALA A 328 " (cutoff:3.500A) removed outlier: 4.330A pdb=" N GLU A 97 " --> pdb=" O LEU A 406 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N TYR A 400 " --> pdb=" O TYR A 103 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 347 through 350 removed outlier: 3.635A pdb=" N PHE A 348 " --> pdb=" O PHE A 339 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N TRP A 322 " --> pdb=" O VAL A 102 " (cutoff:3.500A) removed outlier: 7.319A pdb=" N VAL A 102 " --> pdb=" O TRP A 322 " (cutoff:3.500A) removed outlier: 4.822A pdb=" N THR A 324 " --> pdb=" O LEU A 100 " (cutoff:3.500A) removed outlier: 6.683A pdb=" N LEU A 100 " --> pdb=" O THR A 324 " (cutoff:3.500A) removed outlier: 5.898A pdb=" N GLY A 98 " --> pdb=" O PRO A 326 " (cutoff:3.500A) removed outlier: 6.186A pdb=" N ALA A 328 " --> pdb=" O VAL A 96 " (cutoff:3.500A) removed outlier: 6.076A pdb=" N VAL A 96 " --> pdb=" O ALA A 328 " (cutoff:3.500A) removed outlier: 4.330A pdb=" N GLU A 97 " --> pdb=" O LEU A 406 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N TYR A 400 " --> pdb=" O TYR A 103 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N PHE A 393 " --> pdb=" O LEU A 401 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 197 through 199 removed outlier: 3.697A pdb=" N ILE A 226 " --> pdb=" O TYR A 199 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N ARG A 232 " --> pdb=" O ALA A 241 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N ALA A 241 " --> pdb=" O ARG A 232 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N LEU A 248 " --> pdb=" O ILE A 240 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 197 through 199 removed outlier: 3.697A pdb=" N ILE A 226 " --> pdb=" O TYR A 199 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N ILE A 120 " --> pdb=" O ASN A 223 " (cutoff:3.500A) removed outlier: 4.164A pdb=" N GLU A 225 " --> pdb=" O ARG A 118 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N ARG A 118 " --> pdb=" O GLU A 225 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N PHE A 112 " --> pdb=" O ALA A 231 " (cutoff:3.500A) removed outlier: 4.157A pdb=" N TYR A 110 " --> pdb=" O SER A 233 " (cutoff:3.500A) removed outlier: 7.506A pdb=" N LYS A 113 " --> pdb=" O LYS A 308 " (cutoff:3.500A) removed outlier: 4.319A pdb=" N LYS A 308 " --> pdb=" O LYS A 113 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N THR A 304 " --> pdb=" O TYR A 117 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N PHE A 297 " --> pdb=" O ARG A 271 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N ASP A 269 " --> pdb=" O GLU A 299 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 618 through 619 removed outlier: 6.109A pdb=" N ALA A 618 " --> pdb=" O ARG B 80 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'B' and resid 347 through 350 removed outlier: 3.544A pdb=" N PHE B 348 " --> pdb=" O PHE B 339 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N TYR B 337 " --> pdb=" O THR B 350 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N TRP B 322 " --> pdb=" O VAL B 102 " (cutoff:3.500A) removed outlier: 7.338A pdb=" N VAL B 102 " --> pdb=" O TRP B 322 " (cutoff:3.500A) removed outlier: 4.926A pdb=" N THR B 324 " --> pdb=" O LEU B 100 " (cutoff:3.500A) removed outlier: 6.769A pdb=" N LEU B 100 " --> pdb=" O THR B 324 " (cutoff:3.500A) removed outlier: 5.998A pdb=" N GLY B 98 " --> pdb=" O PRO B 326 " (cutoff:3.500A) removed outlier: 6.317A pdb=" N ALA B 328 " --> pdb=" O VAL B 96 " (cutoff:3.500A) removed outlier: 6.204A pdb=" N VAL B 96 " --> pdb=" O ALA B 328 " (cutoff:3.500A) removed outlier: 4.292A pdb=" N GLU B 97 " --> pdb=" O LEU B 406 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N TYR B 400 " --> pdb=" O TYR B 103 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 347 through 350 removed outlier: 3.544A pdb=" N PHE B 348 " --> pdb=" O PHE B 339 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N TYR B 337 " --> pdb=" O THR B 350 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N TRP B 322 " --> pdb=" O VAL B 102 " (cutoff:3.500A) removed outlier: 7.338A pdb=" N VAL B 102 " --> pdb=" O TRP B 322 " (cutoff:3.500A) removed outlier: 4.926A pdb=" N THR B 324 " --> pdb=" O LEU B 100 " (cutoff:3.500A) removed outlier: 6.769A pdb=" N LEU B 100 " --> pdb=" O THR B 324 " (cutoff:3.500A) removed outlier: 5.998A pdb=" N GLY B 98 " --> pdb=" O PRO B 326 " (cutoff:3.500A) removed outlier: 6.317A pdb=" N ALA B 328 " --> pdb=" O VAL B 96 " (cutoff:3.500A) removed outlier: 6.204A pdb=" N VAL B 96 " --> pdb=" O ALA B 328 " (cutoff:3.500A) removed outlier: 4.292A pdb=" N GLU B 97 " --> pdb=" O LEU B 406 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N TYR B 400 " --> pdb=" O TYR B 103 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N PHE B 393 " --> pdb=" O LEU B 401 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 141 through 142 removed outlier: 3.786A pdb=" N MET B 141 " --> pdb=" O ILE B 121 " (cutoff:3.500A) removed outlier: 4.040A pdb=" N TYR B 110 " --> pdb=" O SER B 233 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N PHE B 112 " --> pdb=" O ALA B 231 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N ARG B 118 " --> pdb=" O GLU B 225 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N GLU B 225 " --> pdb=" O ARG B 118 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N ILE B 120 " --> pdb=" O ASN B 223 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N ASN B 223 " --> pdb=" O ILE B 120 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 141 through 142 removed outlier: 3.786A pdb=" N MET B 141 " --> pdb=" O ILE B 121 " (cutoff:3.500A) removed outlier: 7.247A pdb=" N LYS B 113 " --> pdb=" O LYS B 308 " (cutoff:3.500A) removed outlier: 4.172A pdb=" N LYS B 308 " --> pdb=" O LYS B 113 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 240 through 241 Processing sheet with id=AB3, first strand: chain 'B' and resid 515 through 516 removed outlier: 3.962A pdb=" N TYR B 516 " --> pdb=" O SER B 522 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N SER B 522 " --> pdb=" O TYR B 516 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB3 Processing sheet with id=AB4, first strand: chain 'C' and resid 347 through 350 removed outlier: 3.609A pdb=" N PHE C 348 " --> pdb=" O PHE C 339 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N TRP C 322 " --> pdb=" O VAL C 102 " (cutoff:3.500A) removed outlier: 7.366A pdb=" N VAL C 102 " --> pdb=" O TRP C 322 " (cutoff:3.500A) removed outlier: 4.849A pdb=" N THR C 324 " --> pdb=" O LEU C 100 " (cutoff:3.500A) removed outlier: 6.706A pdb=" N LEU C 100 " --> pdb=" O THR C 324 " (cutoff:3.500A) removed outlier: 5.836A pdb=" N GLY C 98 " --> pdb=" O PRO C 326 " (cutoff:3.500A) removed outlier: 6.133A pdb=" N ALA C 328 " --> pdb=" O VAL C 96 " (cutoff:3.500A) removed outlier: 5.973A pdb=" N VAL C 96 " --> pdb=" O ALA C 328 " (cutoff:3.500A) removed outlier: 4.290A pdb=" N GLU C 97 " --> pdb=" O LEU C 406 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N TYR C 400 " --> pdb=" O TYR C 103 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 347 through 350 removed outlier: 3.609A pdb=" N PHE C 348 " --> pdb=" O PHE C 339 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N TRP C 322 " --> pdb=" O VAL C 102 " (cutoff:3.500A) removed outlier: 7.366A pdb=" N VAL C 102 " --> pdb=" O TRP C 322 " (cutoff:3.500A) removed outlier: 4.849A pdb=" N THR C 324 " --> pdb=" O LEU C 100 " (cutoff:3.500A) removed outlier: 6.706A pdb=" N LEU C 100 " --> pdb=" O THR C 324 " (cutoff:3.500A) removed outlier: 5.836A pdb=" N GLY C 98 " --> pdb=" O PRO C 326 " (cutoff:3.500A) removed outlier: 6.133A pdb=" N ALA C 328 " --> pdb=" O VAL C 96 " (cutoff:3.500A) removed outlier: 5.973A pdb=" N VAL C 96 " --> pdb=" O ALA C 328 " (cutoff:3.500A) removed outlier: 4.290A pdb=" N GLU C 97 " --> pdb=" O LEU C 406 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N TYR C 400 " --> pdb=" O TYR C 103 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 139 through 143 removed outlier: 3.692A pdb=" N THR C 143 " --> pdb=" O LYS C 119 " (cutoff:3.500A) removed outlier: 4.197A pdb=" N LYS C 119 " --> pdb=" O THR C 143 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N TYR C 110 " --> pdb=" O SER C 233 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N PHE C 112 " --> pdb=" O ALA C 231 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N ALA C 231 " --> pdb=" O PHE C 112 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N ARG C 118 " --> pdb=" O GLU C 225 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N GLU C 225 " --> pdb=" O ARG C 118 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N ARG C 232 " --> pdb=" O ALA C 241 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N ALA C 241 " --> pdb=" O ARG C 232 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N LEU C 248 " --> pdb=" O ILE C 240 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 198 through 199 removed outlier: 3.592A pdb=" N ILE C 226 " --> pdb=" O TYR C 199 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N GLU C 225 " --> pdb=" O ARG C 118 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N ARG C 118 " --> pdb=" O GLU C 225 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N ALA C 231 " --> pdb=" O PHE C 112 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N PHE C 112 " --> pdb=" O ALA C 231 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N TYR C 110 " --> pdb=" O SER C 233 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N THR C 304 " --> pdb=" O TYR C 117 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N TRP C 307 " --> pdb=" O THR C 296 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N THR C 296 " --> pdb=" O TRP C 307 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N PHE C 297 " --> pdb=" O ARG C 271 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N ASP C 269 " --> pdb=" O GLU C 299 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 158 through 161 removed outlier: 4.211A pdb=" N TYR C 160 " --> pdb=" O VAL C 184 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N VAL C 184 " --> pdb=" O TYR C 160 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB8 366 hydrogen bonds defined for protein. 1038 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: 1.55 Time building geometry restraints manager: 1.25 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.35: 3757 1.35 - 1.46: 2795 1.46 - 1.58: 4754 1.58 - 1.70: 0 1.70 - 1.82: 36 Bond restraints: 11342 Sorted by residual: bond pdb=" CA ALA B 520 " pdb=" C ALA B 520 " ideal model delta sigma weight residual 1.529 1.509 0.020 1.04e-02 9.25e+03 3.81e+00 bond pdb=" CG ARG C 187 " pdb=" CD ARG C 187 " ideal model delta sigma weight residual 1.520 1.551 -0.031 3.00e-02 1.11e+03 1.08e+00 bond pdb=" N ALA B 520 " pdb=" CA ALA B 520 " ideal model delta sigma weight residual 1.462 1.451 0.011 1.32e-02 5.74e+03 7.56e-01 bond pdb=" CB ARG C 187 " pdb=" CG ARG C 187 " ideal model delta sigma weight residual 1.520 1.545 -0.025 3.00e-02 1.11e+03 6.84e-01 bond pdb=" C ILE C 186 " pdb=" N ARG C 187 " ideal model delta sigma weight residual 1.331 1.347 -0.016 2.07e-02 2.33e+03 5.83e-01 ... (remaining 11337 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.79: 15371 1.79 - 3.58: 112 3.58 - 5.38: 18 5.38 - 7.17: 6 7.17 - 8.96: 3 Bond angle restraints: 15510 Sorted by residual: angle pdb=" N VAL B 69 " pdb=" CA VAL B 69 " pdb=" C VAL B 69 " ideal model delta sigma weight residual 109.34 116.12 -6.78 2.08e+00 2.31e-01 1.06e+01 angle pdb=" N SER B 522 " pdb=" CA SER B 522 " pdb=" C SER B 522 " ideal model delta sigma weight residual 107.23 112.63 -5.40 1.67e+00 3.59e-01 1.04e+01 angle pdb=" CG ARG C 187 " pdb=" CD ARG C 187 " pdb=" NE ARG C 187 " ideal model delta sigma weight residual 112.00 118.88 -6.88 2.20e+00 2.07e-01 9.79e+00 angle pdb=" CB MET B 504 " pdb=" CG MET B 504 " pdb=" SD MET B 504 " ideal model delta sigma weight residual 112.70 121.66 -8.96 3.00e+00 1.11e-01 8.92e+00 angle pdb=" C VAL B 69 " pdb=" CA VAL B 69 " pdb=" CB VAL B 69 " ideal model delta sigma weight residual 111.29 106.42 4.87 1.64e+00 3.72e-01 8.83e+00 ... (remaining 15505 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.28: 5835 15.28 - 30.56: 559 30.56 - 45.85: 230 45.85 - 61.13: 77 61.13 - 76.41: 13 Dihedral angle restraints: 6714 sinusoidal: 2063 harmonic: 4651 Sorted by residual: dihedral pdb=" CB CYS A 317 " pdb=" SG CYS A 317 " pdb=" SG CYS A 364 " pdb=" CB CYS A 364 " ideal model delta sinusoidal sigma weight residual 93.00 47.58 45.42 1 1.00e+01 1.00e-02 2.86e+01 dihedral pdb=" CB CYS B 317 " pdb=" SG CYS B 317 " pdb=" SG CYS B 364 " pdb=" CB CYS B 364 " ideal model delta sinusoidal sigma weight residual 93.00 50.14 42.86 1 1.00e+01 1.00e-02 2.56e+01 dihedral pdb=" CB CYS C 317 " pdb=" SG CYS C 317 " pdb=" SG CYS C 364 " pdb=" CB CYS C 364 " ideal model delta sinusoidal sigma weight residual 93.00 53.86 39.14 1 1.00e+01 1.00e-02 2.15e+01 ... (remaining 6711 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.043: 1400 0.043 - 0.085: 248 0.085 - 0.128: 142 0.128 - 0.171: 1 0.171 - 0.214: 1 Chirality restraints: 1792 Sorted by residual: chirality pdb=" CG LEU B 474 " pdb=" CB LEU B 474 " pdb=" CD1 LEU B 474 " pdb=" CD2 LEU B 474 " both_signs ideal model delta sigma weight residual False -2.59 -2.38 -0.21 2.00e-01 2.50e+01 1.14e+00 chirality pdb=" CA ILE A 576 " pdb=" N ILE A 576 " pdb=" C ILE A 576 " pdb=" CB ILE A 576 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.20e-01 chirality pdb=" CA LEU B 474 " pdb=" N LEU B 474 " pdb=" C LEU B 474 " pdb=" CB LEU B 474 " both_signs ideal model delta sigma weight residual False 2.51 2.38 0.13 2.00e-01 2.50e+01 4.05e-01 ... (remaining 1789 not shown) Planarity restraints: 2043 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLN B 202 " 0.033 5.00e-02 4.00e+02 5.05e-02 4.07e+00 pdb=" N PRO B 203 " -0.087 5.00e-02 4.00e+02 pdb=" CA PRO B 203 " 0.026 5.00e-02 4.00e+02 pdb=" CD PRO B 203 " 0.028 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TRP A 492 " 0.011 2.00e-02 2.50e+03 9.47e-03 2.24e+00 pdb=" CG TRP A 492 " -0.026 2.00e-02 2.50e+03 pdb=" CD1 TRP A 492 " 0.011 2.00e-02 2.50e+03 pdb=" CD2 TRP A 492 " -0.000 2.00e-02 2.50e+03 pdb=" NE1 TRP A 492 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 TRP A 492 " -0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP A 492 " 0.001 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 492 " 0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 492 " 0.002 2.00e-02 2.50e+03 pdb=" CH2 TRP A 492 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE B 156 " 0.005 2.00e-02 2.50e+03 1.07e-02 1.15e+00 pdb=" C ILE B 156 " -0.019 2.00e-02 2.50e+03 pdb=" O ILE B 156 " 0.007 2.00e-02 2.50e+03 pdb=" N TYR B 157 " 0.006 2.00e-02 2.50e+03 ... (remaining 2040 not shown) Histogram of nonbonded interaction distances: 2.32 - 2.84: 3849 2.84 - 3.35: 9235 3.35 - 3.87: 16797 3.87 - 4.38: 16175 4.38 - 4.90: 29525 Nonbonded interactions: 75581 Sorted by model distance: nonbonded pdb=" O THR B 311 " pdb=" OG1 THR B 314 " model vdw 2.321 3.040 nonbonded pdb=" OD1 ASN C 499 " pdb=" OG1 THR C 501 " model vdw 2.334 3.040 nonbonded pdb=" OG SER B 336 " pdb=" OD1 ASN B 349 " model vdw 2.363 3.040 nonbonded pdb=" N ASP A 82 " pdb=" OD1 ASP A 82 " model vdw 2.387 3.120 nonbonded pdb=" OG SER A 201 " pdb=" OD1 ASN A 223 " model vdw 2.401 3.040 ... (remaining 75576 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 67 through 81 or (resid 82 and (name N or name CA or name \ C or name O or name CB )) or resid 83 through 124 or (resid 125 through 128 and \ (name N or name CA or name C or name O or name CB )) or (resid 129 through 136 a \ nd (name N or name CA or name C or name O or name CB )) or resid 137 through 143 \ or (resid 144 through 146 and (name N or name CA or name C or name O or name CB \ )) or resid 147 or (resid 148 through 150 and (name N or name CA or name C or n \ ame O or name CB )) or resid 151 or (resid 152 through 154 and (name N or name C \ A or name C or name O or name CB )) or resid 155 through 157 or (resid 158 and ( \ name N or name CA or name C or name O or name CB )) or resid 159 through 161 or \ (resid 162 through 167 and (name N or name CA or name C or name O or name CB )) \ or resid 168 through 171 or (resid 172 through 175 and (name N or name CA or nam \ e C or name O or name CB )) or resid 176 through 200 or (resid 201 through 202 a \ nd (name N or name CA or name C or name O or name CB )) or resid 203 through 204 \ or (resid 205 through 206 and (name N or name CA or name C or name O or name CB \ )) or resid 207 through 211 or (resid 212 through 220 and (name N or name CA or \ name C or name O or name CB )) or resid 221 or (resid 222 and (name N or name C \ A or name C or name O or name CB )) or resid 223 through 255 or (resid 256 throu \ gh 258 and (name N or name CA or name C or name O or name CB )) or resid 259 thr \ ough 261 or (resid 262 through 264 and (name N or name CA or name C or name O or \ name CB )) or resid 265 through 270 or (resid 271 through 273 and (name N or na \ me CA or name C or name O or name CB )) or resid 274 through 275 or (resid 276 a \ nd (name N or name CA or name C or name O or name CB )) or resid 277 through 278 \ or (resid 279 and (name N or name CA or name C or name O or name CB )) or resid \ 280 or (resid 281 and (name N or name CA or name C or name O or name CB )) or r \ esid 282 through 283 or (resid 284 and (name N or name CA or name C or name O or \ name CB )) or resid 285 or (resid 286 and (name N or name CA or name C or name \ O or name CB )) or resid 287 or (resid 288 through 291 and (name N or name CA or \ name C or name O or name CB )) or resid 292 through 298 or (resid 299 through 3 \ 00 and (name N or name CA or name C or name O or name CB )) or resid 301 through \ 305 or (resid 306 and (name N or name CA or name C or name O or name CB )) or r \ esid 307 through 310 or (resid 311 and (name N or name CA or name C or name O or \ name CB )) or resid 312 through 313 or (resid 314 through 315 and (name N or na \ me CA or name C or name O or name CB )) or resid 316 through 319 or (resid 320 a \ nd (name N or name CA or name C or name O or name CB )) or resid 321 through 333 \ or (resid 334 and (name N or name CA or name C or name O or name CB )) or resid \ 335 through 350 or (resid 351 through 352 and (name N or name CA or name C or n \ ame O or name CB )) or resid 353 through 484 or (resid 485 and (name N or name C \ A or name C or name O or name CB )) or resid 486 through 496 or (resid 497 throu \ gh 501 and (name N or name CA or name C or name O or name CB )) or resid 502 thr \ ough 537 or (resid 538 and (name N or name CA or name C or name O or name CB )) \ or resid 539 through 540 or (resid 554 through 555 and (name N or name CA or nam \ e C or name O or name CB )) or resid 556 through 558 or (resid 559 through 560 a \ nd (name N or name CA or name C or name O or name CB )) or resid 569 through 593 \ or (resid 594 through 596 and (name N or name CA or name C or name O or name CB \ )) or resid 597 through 601 or (resid 602 through 620 and (name N or name CA or \ name C or name O or name CB )) or resid 621 through 648)) selection = (chain 'B' and (resid 67 or (resid 68 through 70 and (name N or name CA or name \ C or name O or name CB )) or (resid 71 through 78 and (name N or name CA or name \ C or name O or name CB )) or resid 79 through 81 or (resid 82 and (name N or na \ me CA or name C or name O or name CB )) or resid 83 through 85 or (resid 86 and \ (name N or name CA or name C or name O or name CB )) or resid 87 through 107 or \ (resid 108 and (name N or name CA or name C or name O or name CB )) or resid 109 \ through 118 or (resid 119 through 128 and (name N or name CA or name C or name \ O or name CB )) or (resid 129 through 136 and (name N or name CA or name C or na \ me O or name CB )) or resid 137 through 157 or (resid 158 and (name N or name CA \ or name C or name O or name CB )) or resid 159 through 165 or (resid 166 throug \ h 167 and (name N or name CA or name C or name O or name CB )) or resid 168 thro \ ugh 169 or (resid 170 through 175 and (name N or name CA or name C or name O or \ name CB )) or resid 176 or (resid 177 through 178 and (name N or name CA or name \ C or name O or name CB )) or resid 179 through 182 or (resid 183 through 184 an \ d (name N or name CA or name C or name O or name CB )) or resid 185 through 200 \ or (resid 201 through 202 and (name N or name CA or name C or name O or name CB \ )) or resid 203 through 204 or (resid 205 through 206 and (name N or name CA or \ name C or name O or name CB )) or resid 207 through 215 or (resid 216 through 22 \ 0 and (name N or name CA or name C or name O or name CB )) or resid 221 or (resi \ d 222 and (name N or name CA or name C or name O or name CB )) or resid 223 thro \ ugh 251 or (resid 252 and (name N or name CA or name C or name O or name CB )) o \ r resid 253 through 259 or (resid 260 through 264 and (name N or name CA or name \ C or name O or name CB )) or resid 265 through 266 or (resid 267 through 268 an \ d (name N or name CA or name C or name O or name CB )) or resid 269 through 289 \ or (resid 290 through 291 and (name N or name CA or name C or name O or name CB \ )) or resid 292 through 308 or (resid 309 through 311 and (name N or name CA or \ name C or name O or name CB )) or resid 312 through 313 or (resid 314 through 31 \ 5 and (name N or name CA or name C or name O or name CB )) or resid 316 through \ 343 or (resid 344 and (name N or name CA or name C or name O or name CB )) or re \ sid 345 through 494 or (resid 495 through 501 and (name N or name CA or name C o \ r name O or name CB )) or resid 502 through 516 or (resid 517 and (name N or nam \ e CA or name C or name O or name CB )) or resid 518 through 593 or (resid 594 th \ rough 596 and (name N or name CA or name C or name O or name CB )) or resid 597 \ through 600 or (resid 601 through 620 and (name N or name CA or name C or name O \ or name CB )) or resid 621 through 648)) selection = (chain 'C' and (resid 67 through 68 or (resid 69 through 70 and (name N or name \ CA or name C or name O or name CB )) or resid 71 or (resid 72 through 75 and (na \ me N or name CA or name C or name O or name CB )) or (resid 76 through 78 and (n \ ame N or name CA or name C or name O or name CB )) or resid 79 through 85 or (re \ sid 86 and (name N or name CA or name C or name O or name CB )) or resid 87 thro \ ugh 107 or (resid 108 and (name N or name CA or name C or name O or name CB )) o \ r resid 109 through 118 or (resid 119 through 128 and (name N or name CA or name \ C or name O or name CB )) or resid 129 or (resid 130 through 136 and (name N or \ name CA or name C or name O or name CB )) or resid 137 through 143 or (resid 14 \ 4 through 146 and (name N or name CA or name C or name O or name CB )) or resid \ 147 or (resid 148 through 150 and (name N or name CA or name C or name O or name \ CB )) or resid 151 or (resid 152 through 154 and (name N or name CA or name C o \ r name O or name CB )) or resid 155 through 160 or (resid 161 through 167 and (n \ ame N or name CA or name C or name O or name CB )) or resid 168 through 176 or ( \ resid 177 through 178 and (name N or name CA or name C or name O or name CB )) o \ r resid 179 through 183 or (resid 184 and (name N or name CA or name C or name O \ or name CB )) or resid 185 through 186 or (resid 187 and (name N or name CA or \ name C or name O or name CB )) or resid 188 through 195 or (resid 196 and (name \ N or name CA or name C or name O or name CB )) or resid 197 through 219 or (resi \ d 220 and (name N or name CA or name C or name O or name CB )) or resid 221 thro \ ugh 256 or (resid 257 through 258 and (name N or name CA or name C or name O or \ name CB )) or resid 259 or (resid 260 through 264 and (name N or name CA or name \ C or name O or name CB )) or resid 265 through 270 or (resid 271 through 273 an \ d (name N or name CA or name C or name O or name CB )) or resid 274 through 275 \ or (resid 276 and (name N or name CA or name C or name O or name CB )) or resid \ 277 or (resid 278 through 279 and (name N or name CA or name C or name O or name \ CB )) or resid 280 or (resid 281 and (name N or name CA or name C or name O or \ name CB )) or resid 282 through 285 or (resid 286 and (name N or name CA or name \ C or name O or name CB )) or resid 287 or (resid 288 through 291 and (name N or \ name CA or name C or name O or name CB )) or resid 292 through 298 or (resid 29 \ 9 through 300 and (name N or name CA or name C or name O or name CB )) or resid \ 301 through 305 or (resid 306 and (name N or name CA or name C or name O or name \ CB )) or resid 307 through 308 or (resid 309 through 311 and (name N or name CA \ or name C or name O or name CB )) or resid 312 through 319 or (resid 320 and (n \ ame N or name CA or name C or name O or name CB )) or resid 321 through 333 or ( \ resid 334 and (name N or name CA or name C or name O or name CB )) or resid 335 \ through 343 or (resid 344 and (name N or name CA or name C or name O or name CB \ )) or resid 345 through 350 or (resid 351 through 352 and (name N or name CA or \ name C or name O or name CB )) or resid 353 through 494 or (resid 495 through 50 \ 1 and (name N or name CA or name C or name O or name CB )) or resid 502 through \ 521 or (resid 522 through 527 and (name N or name CA or name C or name O or name \ CB )) or resid 528 through 536 or (resid 537 through 538 and (name N or name CA \ or name C or name O or name CB )) or resid 539 through 540 or (resid 554 throug \ h 555 and (name N or name CA or name C or name O or name CB )) or resid 556 thro \ ugh 558 or (resid 559 through 560 and (name N or name CA or name C or name O or \ name CB )) or (resid 569 through 570 and (name N or name CA or name C or name O \ or name CB )) or resid 571 through 595 or (resid 596 and (name N or name CA or n \ ame C or name O or name CB )) or resid 597 through 600 or (resid 601 through 620 \ and (name N or name CA or name C or name O or name CB )) or resid 621 through 6 \ 48)) } 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: 1.620 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.180 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 10.790 Find NCS groups from input model: 0.220 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.350 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.270 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7620 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 : 0.001 0.032 11351 Z= 0.080 Angle : 0.433 8.959 15528 Z= 0.222 Chirality : 0.041 0.214 1792 Planarity : 0.002 0.050 2043 Dihedral : 16.078 76.412 3667 Min Nonbonded Distance : 2.321 Molprobity Statistics. All-atom Clashscore : 2.06 Ramachandran Plot: Outliers : 0.06 % Allowed : 7.62 % Favored : 92.31 % Rotamer: Outliers : 0.11 % Allowed : 29.70 % Favored : 70.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.58 (0.22), residues: 1548 helix: 3.59 (0.34), residues: 248 sheet: 1.74 (0.35), residues: 268 loop : -2.20 (0.18), residues: 1032 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 187 TYR 0.004 0.000 TYR A 110 PHE 0.007 0.000 PHE A 594 TRP 0.026 0.001 TRP A 492 HIS 0.000 0.000 HIS C 338 Details of bonding type rmsd covalent geometry : bond 0.00144 (11342) covalent geometry : angle 0.43342 (15510) SS BOND : bond 0.00109 ( 9) SS BOND : angle 0.09429 ( 18) hydrogen bonds : bond 0.20626 ( 309) hydrogen bonds : angle 7.95609 ( 1038) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3096 Ramachandran restraints generated. 1548 Oldfield, 0 Emsley, 1548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3096 Ramachandran restraints generated. 1548 Oldfield, 0 Emsley, 1548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 63 residues out of total 1420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 62 time to evaluate : 0.434 Fit side-chains REVERT: A 200 PHE cc_start: 0.8800 (t80) cc_final: 0.8366 (t80) REVERT: A 276 LYS cc_start: 0.9456 (pttm) cc_final: 0.9131 (tppt) REVERT: B 200 PHE cc_start: 0.9132 (t80) cc_final: 0.8781 (t80) REVERT: B 594 PHE cc_start: 0.7965 (p90) cc_final: 0.7405 (p90) REVERT: C 200 PHE cc_start: 0.9122 (t80) cc_final: 0.8909 (t80) REVERT: C 491 MET cc_start: 0.8284 (tpt) cc_final: 0.8057 (tpp) REVERT: C 508 TYR cc_start: 0.8166 (t80) cc_final: 0.7445 (t80) outliers start: 1 outliers final: 0 residues processed: 63 average time/residue: 0.0748 time to fit residues: 8.0242 Evaluate side-chains 61 residues out of total 1420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 61 time to evaluate : 0.425 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 98 optimal weight: 7.9990 chunk 107 optimal weight: 6.9990 chunk 10 optimal weight: 0.4980 chunk 66 optimal weight: 50.0000 chunk 130 optimal weight: 0.9980 chunk 124 optimal weight: 0.0370 chunk 103 optimal weight: 7.9990 chunk 77 optimal weight: 6.9990 chunk 122 optimal weight: 10.0000 chunk 91 optimal weight: 5.9990 chunk 149 optimal weight: 50.0000 overall best weight: 2.9062 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 144 GLN A 293 GLN A 404 GLN A 633 ASN ** B 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 333 HIS B 404 GLN B 633 ASN C 333 HIS C 404 GLN ** C 633 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3811 r_free = 0.3811 target = 0.077360 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3294 r_free = 0.3294 target = 0.055083 restraints weight = 57459.195| |-----------------------------------------------------------------------------| r_work (start): 0.3208 rms_B_bonded: 4.82 r_work: 0.3109 rms_B_bonded: 4.38 restraints_weight: 0.5000 r_work (final): 0.3109 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8103 moved from start: 0.4079 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 11351 Z= 0.213 Angle : 0.594 6.370 15528 Z= 0.328 Chirality : 0.045 0.165 1792 Planarity : 0.004 0.041 2043 Dihedral : 3.580 16.101 1685 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 5.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.47 % Favored : 89.53 % Rotamer: Outliers : 2.99 % Allowed : 24.36 % Favored : 72.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.13 (0.22), residues: 1548 helix: 2.88 (0.32), residues: 251 sheet: 1.15 (0.36), residues: 245 loop : -2.36 (0.18), residues: 1052 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 232 TYR 0.025 0.002 TYR C 337 PHE 0.019 0.002 PHE B 339 TRP 0.019 0.002 TRP B 492 HIS 0.003 0.001 HIS C 335 Details of bonding type rmsd covalent geometry : bond 0.00475 (11342) covalent geometry : angle 0.59324 (15510) SS BOND : bond 0.00448 ( 9) SS BOND : angle 1.06301 ( 18) hydrogen bonds : bond 0.07959 ( 309) hydrogen bonds : angle 4.77239 ( 1038) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3096 Ramachandran restraints generated. 1548 Oldfield, 0 Emsley, 1548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3096 Ramachandran restraints generated. 1548 Oldfield, 0 Emsley, 1548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 1420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 53 time to evaluate : 0.449 Fit side-chains REVERT: A 115 ARG cc_start: 0.5895 (OUTLIER) cc_final: 0.5679 (tpp80) REVERT: A 200 PHE cc_start: 0.9054 (t80) cc_final: 0.8501 (t80) REVERT: A 491 MET cc_start: 0.8796 (tpp) cc_final: 0.8342 (tpp) REVERT: B 200 PHE cc_start: 0.9128 (t80) cc_final: 0.8819 (t80) REVERT: B 250 LEU cc_start: 0.8902 (mm) cc_final: 0.8566 (tt) REVERT: B 390 THR cc_start: 0.8144 (OUTLIER) cc_final: 0.7844 (p) REVERT: B 491 MET cc_start: 0.8764 (mmt) cc_final: 0.8539 (tpp) REVERT: B 594 PHE cc_start: 0.8221 (p90) cc_final: 0.7507 (p90) REVERT: C 491 MET cc_start: 0.8732 (tpt) cc_final: 0.8202 (tpt) REVERT: C 538 GLN cc_start: 0.5187 (OUTLIER) cc_final: 0.3855 (mp10) outliers start: 28 outliers final: 11 residues processed: 80 average time/residue: 0.0740 time to fit residues: 9.7462 Evaluate side-chains 62 residues out of total 1420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 48 time to evaluate : 0.425 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 CYS Chi-restraints excluded: chain A residue 115 ARG Chi-restraints excluded: chain A residue 364 CYS Chi-restraints excluded: chain A residue 622 THR Chi-restraints excluded: chain B residue 87 CYS Chi-restraints excluded: chain B residue 108 VAL Chi-restraints excluded: chain B residue 247 SER Chi-restraints excluded: chain B residue 349 ASN Chi-restraints excluded: chain B residue 390 THR Chi-restraints excluded: chain B residue 478 SER Chi-restraints excluded: chain C residue 87 CYS Chi-restraints excluded: chain C residue 296 THR Chi-restraints excluded: chain C residue 364 CYS Chi-restraints excluded: chain C residue 538 GLN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 53 optimal weight: 0.6980 chunk 79 optimal weight: 5.9990 chunk 3 optimal weight: 4.9990 chunk 29 optimal weight: 3.9990 chunk 92 optimal weight: 9.9990 chunk 135 optimal weight: 9.9990 chunk 56 optimal weight: 6.9990 chunk 144 optimal weight: 5.9990 chunk 7 optimal weight: 40.0000 chunk 99 optimal weight: 20.0000 chunk 9 optimal weight: 20.0000 overall best weight: 4.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 338 HIS C 633 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3739 r_free = 0.3739 target = 0.077281 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3179 r_free = 0.3179 target = 0.054291 restraints weight = 55742.670| |-----------------------------------------------------------------------------| r_work (start): 0.3015 rms_B_bonded: 5.09 r_work: 0.2876 rms_B_bonded: 4.53 restraints_weight: 0.5000 r_work (final): 0.2876 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8335 moved from start: 0.5821 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.061 11351 Z= 0.262 Angle : 0.601 10.364 15528 Z= 0.332 Chirality : 0.045 0.146 1792 Planarity : 0.004 0.041 2043 Dihedral : 4.124 17.315 1685 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 6.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.95 % Favored : 88.05 % Rotamer: Outliers : 2.99 % Allowed : 23.82 % Favored : 73.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.44 (0.21), residues: 1548 helix: 2.70 (0.32), residues: 256 sheet: 0.08 (0.34), residues: 275 loop : -2.44 (0.18), residues: 1017 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 295 TYR 0.016 0.002 TYR A 392 PHE 0.017 0.002 PHE A 461 TRP 0.008 0.001 TRP A 148 HIS 0.003 0.001 HIS A 335 Details of bonding type rmsd covalent geometry : bond 0.00588 (11342) covalent geometry : angle 0.60052 (15510) SS BOND : bond 0.00336 ( 9) SS BOND : angle 0.86131 ( 18) hydrogen bonds : bond 0.07941 ( 309) hydrogen bonds : angle 4.78318 ( 1038) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3096 Ramachandran restraints generated. 1548 Oldfield, 0 Emsley, 1548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3096 Ramachandran restraints generated. 1548 Oldfield, 0 Emsley, 1548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 70 residues out of total 1420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 42 time to evaluate : 0.426 Fit side-chains revert: symmetry clash REVERT: A 200 PHE cc_start: 0.9044 (t80) cc_final: 0.8493 (t80) REVERT: A 390 THR cc_start: 0.8481 (OUTLIER) cc_final: 0.8199 (p) REVERT: A 487 ARG cc_start: 0.9259 (OUTLIER) cc_final: 0.8365 (mtm-85) REVERT: A 491 MET cc_start: 0.8942 (tpp) cc_final: 0.8467 (tpp) REVERT: B 200 PHE cc_start: 0.9182 (t80) cc_final: 0.8842 (t80) REVERT: B 390 THR cc_start: 0.8406 (OUTLIER) cc_final: 0.8117 (p) REVERT: B 594 PHE cc_start: 0.8228 (p90) cc_final: 0.7601 (p90) REVERT: C 390 THR cc_start: 0.8514 (OUTLIER) cc_final: 0.8240 (p) REVERT: C 491 MET cc_start: 0.8968 (tpt) cc_final: 0.8513 (tpp) outliers start: 28 outliers final: 14 residues processed: 69 average time/residue: 0.0771 time to fit residues: 8.8221 Evaluate side-chains 60 residues out of total 1420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 42 time to evaluate : 0.446 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 CYS Chi-restraints excluded: chain A residue 364 CYS Chi-restraints excluded: chain A residue 382 ASN Chi-restraints excluded: chain A residue 390 THR Chi-restraints excluded: chain A residue 487 ARG Chi-restraints excluded: chain A residue 622 THR Chi-restraints excluded: chain B residue 87 CYS Chi-restraints excluded: chain B residue 108 VAL Chi-restraints excluded: chain B residue 199 TYR Chi-restraints excluded: chain B residue 336 SER Chi-restraints excluded: chain B residue 364 CYS Chi-restraints excluded: chain B residue 382 ASN Chi-restraints excluded: chain B residue 390 THR Chi-restraints excluded: chain C residue 87 CYS Chi-restraints excluded: chain C residue 364 CYS Chi-restraints excluded: chain C residue 382 ASN Chi-restraints excluded: chain C residue 390 THR Chi-restraints excluded: chain C residue 559 PHE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 44 optimal weight: 20.0000 chunk 53 optimal weight: 8.9990 chunk 111 optimal weight: 8.9990 chunk 128 optimal weight: 0.9990 chunk 142 optimal weight: 5.9990 chunk 16 optimal weight: 5.9990 chunk 73 optimal weight: 5.9990 chunk 69 optimal weight: 8.9990 chunk 71 optimal weight: 0.0270 chunk 150 optimal weight: 20.0000 chunk 49 optimal weight: 0.0000 overall best weight: 2.6048 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 185 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3744 r_free = 0.3744 target = 0.077029 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3183 r_free = 0.3183 target = 0.054157 restraints weight = 56062.880| |-----------------------------------------------------------------------------| r_work (start): 0.3039 rms_B_bonded: 5.02 r_work: 0.2900 rms_B_bonded: 4.54 restraints_weight: 0.5000 r_work (final): 0.2900 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8340 moved from start: 0.6145 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 11351 Z= 0.166 Angle : 0.498 6.172 15528 Z= 0.273 Chirality : 0.043 0.143 1792 Planarity : 0.003 0.032 2043 Dihedral : 3.657 17.116 1685 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 4.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.18 % Favored : 88.82 % Rotamer: Outliers : 3.31 % Allowed : 23.72 % Favored : 72.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.43 (0.21), residues: 1548 helix: 3.17 (0.32), residues: 250 sheet: 0.04 (0.34), residues: 275 loop : -2.53 (0.17), residues: 1023 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 573 TYR 0.010 0.001 TYR C 199 PHE 0.013 0.001 PHE A 594 TRP 0.008 0.001 TRP C 481 HIS 0.002 0.000 HIS A 338 Details of bonding type rmsd covalent geometry : bond 0.00371 (11342) covalent geometry : angle 0.49773 (15510) SS BOND : bond 0.00274 ( 9) SS BOND : angle 0.73653 ( 18) hydrogen bonds : bond 0.06723 ( 309) hydrogen bonds : angle 4.27502 ( 1038) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3096 Ramachandran restraints generated. 1548 Oldfield, 0 Emsley, 1548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3096 Ramachandran restraints generated. 1548 Oldfield, 0 Emsley, 1548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 76 residues out of total 1420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 45 time to evaluate : 0.461 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 157 TYR cc_start: 0.8733 (OUTLIER) cc_final: 0.7684 (t80) REVERT: A 200 PHE cc_start: 0.9043 (t80) cc_final: 0.8509 (t80) REVERT: A 283 TYR cc_start: 0.8706 (OUTLIER) cc_final: 0.8481 (m-80) REVERT: A 390 THR cc_start: 0.8401 (OUTLIER) cc_final: 0.8142 (p) REVERT: A 487 ARG cc_start: 0.9221 (OUTLIER) cc_final: 0.8973 (mmm-85) REVERT: A 490 LEU cc_start: 0.9426 (OUTLIER) cc_final: 0.9198 (tt) REVERT: A 491 MET cc_start: 0.8939 (tpp) cc_final: 0.8705 (ttm) REVERT: B 200 PHE cc_start: 0.9163 (t80) cc_final: 0.8798 (t80) REVERT: B 251 SER cc_start: 0.8091 (OUTLIER) cc_final: 0.7678 (m) REVERT: B 390 THR cc_start: 0.8289 (OUTLIER) cc_final: 0.8033 (p) REVERT: B 491 MET cc_start: 0.8721 (tpt) cc_final: 0.8378 (tpt) REVERT: B 594 PHE cc_start: 0.8224 (p90) cc_final: 0.7588 (p90) REVERT: C 390 THR cc_start: 0.8321 (OUTLIER) cc_final: 0.8086 (p) REVERT: C 491 MET cc_start: 0.8855 (tpt) cc_final: 0.8478 (tpt) outliers start: 31 outliers final: 13 residues processed: 74 average time/residue: 0.0921 time to fit residues: 10.3905 Evaluate side-chains 64 residues out of total 1420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 43 time to evaluate : 0.388 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 157 TYR Chi-restraints excluded: chain A residue 253 PHE Chi-restraints excluded: chain A residue 273 ARG Chi-restraints excluded: chain A residue 283 TYR Chi-restraints excluded: chain A residue 364 CYS Chi-restraints excluded: chain A residue 390 THR Chi-restraints excluded: chain A residue 487 ARG Chi-restraints excluded: chain A residue 490 LEU Chi-restraints excluded: chain A residue 559 PHE Chi-restraints excluded: chain A residue 622 THR Chi-restraints excluded: chain B residue 108 VAL Chi-restraints excluded: chain B residue 251 SER Chi-restraints excluded: chain B residue 283 TYR Chi-restraints excluded: chain B residue 336 SER Chi-restraints excluded: chain B residue 364 CYS Chi-restraints excluded: chain B residue 390 THR Chi-restraints excluded: chain C residue 87 CYS Chi-restraints excluded: chain C residue 240 ILE Chi-restraints excluded: chain C residue 296 THR Chi-restraints excluded: chain C residue 364 CYS Chi-restraints excluded: chain C residue 390 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 43 optimal weight: 30.0000 chunk 112 optimal weight: 8.9990 chunk 138 optimal weight: 2.9990 chunk 16 optimal weight: 8.9990 chunk 55 optimal weight: 4.9990 chunk 13 optimal weight: 0.3980 chunk 118 optimal weight: 0.9980 chunk 67 optimal weight: 8.9990 chunk 104 optimal weight: 10.0000 chunk 28 optimal weight: 1.9990 chunk 45 optimal weight: 9.9990 overall best weight: 2.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 185 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3739 r_free = 0.3739 target = 0.076577 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3176 r_free = 0.3176 target = 0.053809 restraints weight = 55315.609| |-----------------------------------------------------------------------------| r_work (start): 0.3089 rms_B_bonded: 5.05 r_work: 0.2964 rms_B_bonded: 4.53 restraints_weight: 0.5000 r_work (final): 0.2964 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8257 moved from start: 0.6428 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 11351 Z= 0.152 Angle : 0.485 5.474 15528 Z= 0.265 Chirality : 0.043 0.140 1792 Planarity : 0.003 0.031 2043 Dihedral : 3.560 15.821 1685 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 4.61 Ramachandran Plot: Outliers : 0.13 % Allowed : 11.43 % Favored : 88.44 % Rotamer: Outliers : 2.88 % Allowed : 25.21 % Favored : 71.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.46 (0.21), residues: 1548 helix: 3.23 (0.32), residues: 250 sheet: 0.07 (0.34), residues: 274 loop : -2.58 (0.17), residues: 1024 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 115 TYR 0.008 0.001 TYR C 199 PHE 0.012 0.001 PHE A 280 TRP 0.006 0.001 TRP C 481 HIS 0.003 0.000 HIS A 338 Details of bonding type rmsd covalent geometry : bond 0.00336 (11342) covalent geometry : angle 0.48493 (15510) SS BOND : bond 0.00256 ( 9) SS BOND : angle 0.67002 ( 18) hydrogen bonds : bond 0.06414 ( 309) hydrogen bonds : angle 4.19013 ( 1038) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3096 Ramachandran restraints generated. 1548 Oldfield, 0 Emsley, 1548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3096 Ramachandran restraints generated. 1548 Oldfield, 0 Emsley, 1548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 70 residues out of total 1420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 43 time to evaluate : 0.446 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 157 TYR cc_start: 0.8649 (OUTLIER) cc_final: 0.7753 (t80) REVERT: A 200 PHE cc_start: 0.9017 (t80) cc_final: 0.8481 (t80) REVERT: A 256 PHE cc_start: 0.9535 (p90) cc_final: 0.9320 (p90) REVERT: A 283 TYR cc_start: 0.8768 (OUTLIER) cc_final: 0.8486 (m-80) REVERT: A 390 THR cc_start: 0.8377 (OUTLIER) cc_final: 0.8104 (p) REVERT: A 487 ARG cc_start: 0.9089 (OUTLIER) cc_final: 0.8887 (mmm-85) REVERT: A 490 LEU cc_start: 0.9365 (OUTLIER) cc_final: 0.9164 (tt) REVERT: A 491 MET cc_start: 0.8876 (tpp) cc_final: 0.8636 (ttm) REVERT: B 200 PHE cc_start: 0.9119 (t80) cc_final: 0.8749 (t80) REVERT: B 390 THR cc_start: 0.8286 (OUTLIER) cc_final: 0.8021 (p) REVERT: B 487 ARG cc_start: 0.9083 (OUTLIER) cc_final: 0.8545 (ttt-90) REVERT: B 491 MET cc_start: 0.8710 (tpt) cc_final: 0.8473 (tpt) REVERT: B 594 PHE cc_start: 0.8121 (p90) cc_final: 0.7548 (p90) REVERT: C 390 THR cc_start: 0.8297 (OUTLIER) cc_final: 0.8039 (p) REVERT: C 491 MET cc_start: 0.8821 (tpt) cc_final: 0.8398 (tpt) outliers start: 27 outliers final: 13 residues processed: 68 average time/residue: 0.0903 time to fit residues: 9.6438 Evaluate side-chains 60 residues out of total 1420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 39 time to evaluate : 0.358 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 CYS Chi-restraints excluded: chain A residue 157 TYR Chi-restraints excluded: chain A residue 253 PHE Chi-restraints excluded: chain A residue 283 TYR Chi-restraints excluded: chain A residue 364 CYS Chi-restraints excluded: chain A residue 390 THR Chi-restraints excluded: chain A residue 487 ARG Chi-restraints excluded: chain A residue 490 LEU Chi-restraints excluded: chain A residue 622 THR Chi-restraints excluded: chain B residue 108 VAL Chi-restraints excluded: chain B residue 283 TYR Chi-restraints excluded: chain B residue 336 SER Chi-restraints excluded: chain B residue 364 CYS Chi-restraints excluded: chain B residue 390 THR Chi-restraints excluded: chain B residue 487 ARG Chi-restraints excluded: chain C residue 87 CYS Chi-restraints excluded: chain C residue 296 THR Chi-restraints excluded: chain C residue 336 SER Chi-restraints excluded: chain C residue 364 CYS Chi-restraints excluded: chain C residue 390 THR Chi-restraints excluded: chain C residue 559 PHE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 0 optimal weight: 30.0000 chunk 103 optimal weight: 3.9990 chunk 133 optimal weight: 0.0570 chunk 148 optimal weight: 5.9990 chunk 155 optimal weight: 4.9990 chunk 122 optimal weight: 9.9990 chunk 143 optimal weight: 10.0000 chunk 30 optimal weight: 7.9990 chunk 66 optimal weight: 0.0020 chunk 46 optimal weight: 40.0000 chunk 15 optimal weight: 20.0000 overall best weight: 3.0112 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 185 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3716 r_free = 0.3716 target = 0.076118 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3154 r_free = 0.3154 target = 0.053425 restraints weight = 55353.210| |-----------------------------------------------------------------------------| r_work (start): 0.3007 rms_B_bonded: 5.04 r_work: 0.2864 rms_B_bonded: 4.58 restraints_weight: 0.5000 r_work (final): 0.2864 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8378 moved from start: 0.6953 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 11351 Z= 0.190 Angle : 0.523 8.143 15528 Z= 0.285 Chirality : 0.043 0.140 1792 Planarity : 0.003 0.030 2043 Dihedral : 3.790 17.498 1685 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 5.69 Ramachandran Plot: Outliers : 0.13 % Allowed : 12.47 % Favored : 87.40 % Rotamer: Outliers : 3.42 % Allowed : 24.89 % Favored : 71.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.61 (0.21), residues: 1548 helix: 3.09 (0.32), residues: 250 sheet: 0.01 (0.34), residues: 270 loop : -2.69 (0.17), residues: 1028 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 487 TYR 0.010 0.001 TYR C 337 PHE 0.013 0.001 PHE A 594 TRP 0.009 0.001 TRP B 481 HIS 0.004 0.001 HIS C 338 Details of bonding type rmsd covalent geometry : bond 0.00428 (11342) covalent geometry : angle 0.52233 (15510) SS BOND : bond 0.00309 ( 9) SS BOND : angle 0.75421 ( 18) hydrogen bonds : bond 0.07035 ( 309) hydrogen bonds : angle 4.31453 ( 1038) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3096 Ramachandran restraints generated. 1548 Oldfield, 0 Emsley, 1548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3096 Ramachandran restraints generated. 1548 Oldfield, 0 Emsley, 1548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 69 residues out of total 1420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 37 time to evaluate : 0.471 Fit side-chains revert: symmetry clash REVERT: A 157 TYR cc_start: 0.8704 (OUTLIER) cc_final: 0.7611 (t80) REVERT: A 200 PHE cc_start: 0.9072 (t80) cc_final: 0.8525 (t80) REVERT: A 283 TYR cc_start: 0.8864 (OUTLIER) cc_final: 0.8575 (m-80) REVERT: A 390 THR cc_start: 0.8411 (OUTLIER) cc_final: 0.8141 (p) REVERT: A 487 ARG cc_start: 0.9206 (OUTLIER) cc_final: 0.8301 (mtm-85) REVERT: A 490 LEU cc_start: 0.9454 (OUTLIER) cc_final: 0.9236 (tt) REVERT: A 491 MET cc_start: 0.8928 (tpp) cc_final: 0.8697 (ttm) REVERT: B 200 PHE cc_start: 0.9120 (t80) cc_final: 0.8725 (t80) REVERT: B 251 SER cc_start: 0.8341 (OUTLIER) cc_final: 0.7988 (m) REVERT: B 390 THR cc_start: 0.8359 (OUTLIER) cc_final: 0.8091 (p) REVERT: B 487 ARG cc_start: 0.9246 (OUTLIER) cc_final: 0.8452 (tmm-80) REVERT: B 491 MET cc_start: 0.8766 (tpt) cc_final: 0.8396 (tpt) REVERT: B 594 PHE cc_start: 0.8181 (p90) cc_final: 0.7979 (p90) REVERT: C 390 THR cc_start: 0.8348 (OUTLIER) cc_final: 0.8099 (p) REVERT: C 491 MET cc_start: 0.8892 (tpt) cc_final: 0.8491 (tpt) outliers start: 32 outliers final: 18 residues processed: 68 average time/residue: 0.0921 time to fit residues: 9.8595 Evaluate side-chains 65 residues out of total 1420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 38 time to evaluate : 0.435 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 CYS Chi-restraints excluded: chain A residue 157 TYR Chi-restraints excluded: chain A residue 229 MET Chi-restraints excluded: chain A residue 253 PHE Chi-restraints excluded: chain A residue 283 TYR Chi-restraints excluded: chain A residue 364 CYS Chi-restraints excluded: chain A residue 382 ASN Chi-restraints excluded: chain A residue 390 THR Chi-restraints excluded: chain A residue 487 ARG Chi-restraints excluded: chain A residue 490 LEU Chi-restraints excluded: chain A residue 559 PHE Chi-restraints excluded: chain A residue 622 THR Chi-restraints excluded: chain B residue 87 CYS Chi-restraints excluded: chain B residue 108 VAL Chi-restraints excluded: chain B residue 251 SER Chi-restraints excluded: chain B residue 283 TYR Chi-restraints excluded: chain B residue 336 SER Chi-restraints excluded: chain B residue 364 CYS Chi-restraints excluded: chain B residue 390 THR Chi-restraints excluded: chain B residue 487 ARG Chi-restraints excluded: chain C residue 87 CYS Chi-restraints excluded: chain C residue 240 ILE Chi-restraints excluded: chain C residue 296 THR Chi-restraints excluded: chain C residue 336 SER Chi-restraints excluded: chain C residue 364 CYS Chi-restraints excluded: chain C residue 390 THR Chi-restraints excluded: chain C residue 559 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 107 optimal weight: 1.9990 chunk 74 optimal weight: 7.9990 chunk 140 optimal weight: 3.9990 chunk 115 optimal weight: 30.0000 chunk 10 optimal weight: 20.0000 chunk 38 optimal weight: 4.9990 chunk 148 optimal weight: 30.0000 chunk 4 optimal weight: 0.9990 chunk 68 optimal weight: 4.9990 chunk 128 optimal weight: 10.0000 chunk 101 optimal weight: 0.7980 overall best weight: 2.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 185 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3712 r_free = 0.3712 target = 0.076719 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3155 r_free = 0.3155 target = 0.053806 restraints weight = 54556.180| |-----------------------------------------------------------------------------| r_work (start): 0.3011 rms_B_bonded: 5.07 r_work: 0.2865 rms_B_bonded: 4.81 restraints_weight: 0.5000 r_work (final): 0.2865 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8278 moved from start: 0.7088 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 11351 Z= 0.161 Angle : 0.495 7.843 15528 Z= 0.270 Chirality : 0.043 0.140 1792 Planarity : 0.003 0.031 2043 Dihedral : 3.673 17.058 1685 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 4.61 Ramachandran Plot: Outliers : 0.13 % Allowed : 12.02 % Favored : 87.86 % Rotamer: Outliers : 3.21 % Allowed : 25.00 % Favored : 71.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.61 (0.21), residues: 1548 helix: 3.26 (0.32), residues: 250 sheet: 0.05 (0.34), residues: 276 loop : -2.76 (0.17), residues: 1022 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 487 TYR 0.008 0.001 TYR C 337 PHE 0.012 0.001 PHE A 280 TRP 0.007 0.001 TRP C 481 HIS 0.003 0.001 HIS A 338 Details of bonding type rmsd covalent geometry : bond 0.00360 (11342) covalent geometry : angle 0.49497 (15510) SS BOND : bond 0.00262 ( 9) SS BOND : angle 0.67823 ( 18) hydrogen bonds : bond 0.06580 ( 309) hydrogen bonds : angle 4.16859 ( 1038) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3096 Ramachandran restraints generated. 1548 Oldfield, 0 Emsley, 1548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3096 Ramachandran restraints generated. 1548 Oldfield, 0 Emsley, 1548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 70 residues out of total 1420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 40 time to evaluate : 0.438 Fit side-chains revert: symmetry clash REVERT: A 157 TYR cc_start: 0.8627 (OUTLIER) cc_final: 0.7630 (t80) REVERT: A 200 PHE cc_start: 0.9041 (t80) cc_final: 0.8486 (t80) REVERT: A 283 TYR cc_start: 0.9034 (OUTLIER) cc_final: 0.8545 (m-80) REVERT: A 390 THR cc_start: 0.8464 (OUTLIER) cc_final: 0.8187 (p) REVERT: A 487 ARG cc_start: 0.9165 (OUTLIER) cc_final: 0.8942 (mmm-85) REVERT: A 490 LEU cc_start: 0.9432 (OUTLIER) cc_final: 0.9221 (tt) REVERT: A 491 MET cc_start: 0.8880 (tpp) cc_final: 0.8315 (tpp) REVERT: A 499 ASN cc_start: 0.8028 (t0) cc_final: 0.7447 (t0) REVERT: B 200 PHE cc_start: 0.9075 (t80) cc_final: 0.8685 (t80) REVERT: B 251 SER cc_start: 0.8284 (OUTLIER) cc_final: 0.7969 (m) REVERT: B 316 THR cc_start: 0.9143 (OUTLIER) cc_final: 0.8908 (p) REVERT: B 390 THR cc_start: 0.8354 (OUTLIER) cc_final: 0.8069 (p) REVERT: B 487 ARG cc_start: 0.9156 (OUTLIER) cc_final: 0.8311 (tmm-80) REVERT: B 491 MET cc_start: 0.8665 (tpt) cc_final: 0.8268 (tpt) REVERT: B 594 PHE cc_start: 0.8249 (p90) cc_final: 0.7739 (p90) REVERT: C 390 THR cc_start: 0.8395 (OUTLIER) cc_final: 0.8146 (p) REVERT: C 491 MET cc_start: 0.8864 (tpt) cc_final: 0.8404 (tpt) outliers start: 30 outliers final: 15 residues processed: 68 average time/residue: 0.0923 time to fit residues: 9.6974 Evaluate side-chains 64 residues out of total 1420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 39 time to evaluate : 0.408 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 CYS Chi-restraints excluded: chain A residue 157 TYR Chi-restraints excluded: chain A residue 229 MET Chi-restraints excluded: chain A residue 253 PHE Chi-restraints excluded: chain A residue 283 TYR Chi-restraints excluded: chain A residue 364 CYS Chi-restraints excluded: chain A residue 390 THR Chi-restraints excluded: chain A residue 487 ARG Chi-restraints excluded: chain A residue 490 LEU Chi-restraints excluded: chain A residue 559 PHE Chi-restraints excluded: chain A residue 622 THR Chi-restraints excluded: chain B residue 108 VAL Chi-restraints excluded: chain B residue 251 SER Chi-restraints excluded: chain B residue 283 TYR Chi-restraints excluded: chain B residue 316 THR Chi-restraints excluded: chain B residue 336 SER Chi-restraints excluded: chain B residue 364 CYS Chi-restraints excluded: chain B residue 390 THR Chi-restraints excluded: chain B residue 487 ARG Chi-restraints excluded: chain C residue 87 CYS Chi-restraints excluded: chain C residue 240 ILE Chi-restraints excluded: chain C residue 296 THR Chi-restraints excluded: chain C residue 364 CYS Chi-restraints excluded: chain C residue 390 THR Chi-restraints excluded: chain C residue 559 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 133 optimal weight: 0.0370 chunk 153 optimal weight: 10.0000 chunk 126 optimal weight: 9.9990 chunk 139 optimal weight: 0.6980 chunk 45 optimal weight: 40.0000 chunk 137 optimal weight: 0.9990 chunk 121 optimal weight: 10.0000 chunk 155 optimal weight: 3.9990 chunk 149 optimal weight: 40.0000 chunk 0 optimal weight: 20.0000 chunk 27 optimal weight: 2.9990 overall best weight: 1.7464 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 185 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3725 r_free = 0.3725 target = 0.076321 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3171 r_free = 0.3171 target = 0.053667 restraints weight = 55695.568| |-----------------------------------------------------------------------------| r_work (start): 0.3027 rms_B_bonded: 5.11 r_work: 0.2890 rms_B_bonded: 4.59 restraints_weight: 0.5000 r_work (final): 0.2890 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8338 moved from start: 0.7063 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 11351 Z= 0.124 Angle : 0.467 7.843 15528 Z= 0.254 Chirality : 0.042 0.138 1792 Planarity : 0.003 0.031 2043 Dihedral : 3.475 16.738 1685 Min Nonbonded Distance : 2.560 Molprobity Statistics. All-atom Clashscore : 4.12 Ramachandran Plot: Outliers : 0.13 % Allowed : 11.11 % Favored : 88.76 % Rotamer: Outliers : 2.78 % Allowed : 25.32 % Favored : 71.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.50 (0.22), residues: 1548 helix: 3.43 (0.32), residues: 250 sheet: 0.17 (0.34), residues: 274 loop : -2.73 (0.17), residues: 1024 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 487 TYR 0.009 0.001 TYR B 199 PHE 0.011 0.001 PHE A 594 TRP 0.007 0.001 TRP B 481 HIS 0.003 0.000 HIS A 338 Details of bonding type rmsd covalent geometry : bond 0.00267 (11342) covalent geometry : angle 0.46719 (15510) SS BOND : bond 0.00219 ( 9) SS BOND : angle 0.58753 ( 18) hydrogen bonds : bond 0.06037 ( 309) hydrogen bonds : angle 4.00241 ( 1038) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3096 Ramachandran restraints generated. 1548 Oldfield, 0 Emsley, 1548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3096 Ramachandran restraints generated. 1548 Oldfield, 0 Emsley, 1548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 67 residues out of total 1420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 41 time to evaluate : 0.403 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 157 TYR cc_start: 0.8716 (OUTLIER) cc_final: 0.7459 (t80) REVERT: A 200 PHE cc_start: 0.9058 (t80) cc_final: 0.8541 (t80) REVERT: A 283 TYR cc_start: 0.9019 (OUTLIER) cc_final: 0.8679 (m-80) REVERT: A 390 THR cc_start: 0.8357 (OUTLIER) cc_final: 0.8110 (p) REVERT: A 491 MET cc_start: 0.8869 (tpp) cc_final: 0.8348 (tpp) REVERT: A 499 ASN cc_start: 0.8104 (t0) cc_final: 0.7528 (t0) REVERT: B 200 PHE cc_start: 0.9001 (t80) cc_final: 0.8627 (t80) REVERT: B 251 SER cc_start: 0.8253 (OUTLIER) cc_final: 0.7978 (m) REVERT: B 316 THR cc_start: 0.9148 (OUTLIER) cc_final: 0.8937 (p) REVERT: B 390 THR cc_start: 0.8298 (OUTLIER) cc_final: 0.8045 (p) REVERT: C 390 THR cc_start: 0.8261 (OUTLIER) cc_final: 0.8030 (p) REVERT: C 491 MET cc_start: 0.8843 (tpt) cc_final: 0.8393 (tpt) outliers start: 26 outliers final: 14 residues processed: 64 average time/residue: 0.0796 time to fit residues: 8.1727 Evaluate side-chains 62 residues out of total 1420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 41 time to evaluate : 0.332 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 157 TYR Chi-restraints excluded: chain A residue 229 MET Chi-restraints excluded: chain A residue 253 PHE Chi-restraints excluded: chain A residue 283 TYR Chi-restraints excluded: chain A residue 364 CYS Chi-restraints excluded: chain A residue 390 THR Chi-restraints excluded: chain A residue 622 THR Chi-restraints excluded: chain B residue 79 PHE Chi-restraints excluded: chain B residue 108 VAL Chi-restraints excluded: chain B residue 251 SER Chi-restraints excluded: chain B residue 283 TYR Chi-restraints excluded: chain B residue 316 THR Chi-restraints excluded: chain B residue 336 SER Chi-restraints excluded: chain B residue 390 THR Chi-restraints excluded: chain B residue 394 LYS Chi-restraints excluded: chain C residue 87 CYS Chi-restraints excluded: chain C residue 240 ILE Chi-restraints excluded: chain C residue 296 THR Chi-restraints excluded: chain C residue 364 CYS Chi-restraints excluded: chain C residue 390 THR Chi-restraints excluded: chain C residue 559 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 58 optimal weight: 50.0000 chunk 109 optimal weight: 5.9990 chunk 45 optimal weight: 0.8980 chunk 41 optimal weight: 4.9990 chunk 106 optimal weight: 9.9990 chunk 143 optimal weight: 8.9990 chunk 30 optimal weight: 7.9990 chunk 155 optimal weight: 6.9990 chunk 76 optimal weight: 3.9990 chunk 42 optimal weight: 7.9990 chunk 94 optimal weight: 7.9990 overall best weight: 4.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 185 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3681 r_free = 0.3681 target = 0.076148 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3108 r_free = 0.3108 target = 0.052944 restraints weight = 54186.306| |-----------------------------------------------------------------------------| r_work (start): 0.2964 rms_B_bonded: 5.21 r_work: 0.2815 rms_B_bonded: 4.85 restraints_weight: 0.5000 r_work (final): 0.2815 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8341 moved from start: 0.7730 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.048 11351 Z= 0.272 Angle : 0.601 8.276 15528 Z= 0.328 Chirality : 0.044 0.145 1792 Planarity : 0.003 0.031 2043 Dihedral : 4.204 19.775 1685 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 6.67 Ramachandran Plot: Outliers : 0.13 % Allowed : 14.60 % Favored : 85.27 % Rotamer: Outliers : 3.21 % Allowed : 24.79 % Favored : 72.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.89 (0.21), residues: 1548 helix: 3.06 (0.31), residues: 244 sheet: -0.09 (0.34), residues: 275 loop : -2.94 (0.17), residues: 1029 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 487 TYR 0.015 0.002 TYR A 392 PHE 0.015 0.002 PHE A 461 TRP 0.009 0.001 TRP B 481 HIS 0.004 0.001 HIS C 338 Details of bonding type rmsd covalent geometry : bond 0.00616 (11342) covalent geometry : angle 0.60024 (15510) SS BOND : bond 0.00457 ( 9) SS BOND : angle 0.99504 ( 18) hydrogen bonds : bond 0.07802 ( 309) hydrogen bonds : angle 4.52505 ( 1038) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3096 Ramachandran restraints generated. 1548 Oldfield, 0 Emsley, 1548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3096 Ramachandran restraints generated. 1548 Oldfield, 0 Emsley, 1548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 69 residues out of total 1420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 39 time to evaluate : 0.437 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 157 TYR cc_start: 0.8710 (OUTLIER) cc_final: 0.7715 (t80) REVERT: A 200 PHE cc_start: 0.9121 (t80) cc_final: 0.8550 (t80) REVERT: A 283 TYR cc_start: 0.9164 (OUTLIER) cc_final: 0.8627 (m-80) REVERT: A 390 THR cc_start: 0.8565 (OUTLIER) cc_final: 0.8240 (p) REVERT: A 491 MET cc_start: 0.8999 (tpp) cc_final: 0.8795 (ttm) REVERT: A 499 ASN cc_start: 0.8137 (t0) cc_final: 0.7556 (t0) REVERT: B 200 PHE cc_start: 0.8963 (t80) cc_final: 0.8442 (t80) REVERT: B 251 SER cc_start: 0.8521 (OUTLIER) cc_final: 0.8205 (m) REVERT: B 316 THR cc_start: 0.9144 (OUTLIER) cc_final: 0.8890 (p) REVERT: B 390 THR cc_start: 0.8551 (OUTLIER) cc_final: 0.8257 (p) REVERT: C 390 THR cc_start: 0.8559 (OUTLIER) cc_final: 0.8291 (p) REVERT: C 487 ARG cc_start: 0.8989 (OUTLIER) cc_final: 0.8711 (ttp80) REVERT: C 491 MET cc_start: 0.8927 (tpt) cc_final: 0.8580 (tpt) outliers start: 30 outliers final: 18 residues processed: 67 average time/residue: 0.0798 time to fit residues: 8.4694 Evaluate side-chains 63 residues out of total 1420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 37 time to evaluate : 0.345 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 CYS Chi-restraints excluded: chain A residue 157 TYR Chi-restraints excluded: chain A residue 229 MET Chi-restraints excluded: chain A residue 253 PHE Chi-restraints excluded: chain A residue 283 TYR Chi-restraints excluded: chain A residue 364 CYS Chi-restraints excluded: chain A residue 390 THR Chi-restraints excluded: chain A residue 622 THR Chi-restraints excluded: chain B residue 108 VAL Chi-restraints excluded: chain B residue 251 SER Chi-restraints excluded: chain B residue 283 TYR Chi-restraints excluded: chain B residue 316 THR Chi-restraints excluded: chain B residue 336 SER Chi-restraints excluded: chain B residue 355 VAL Chi-restraints excluded: chain B residue 364 CYS Chi-restraints excluded: chain B residue 390 THR Chi-restraints excluded: chain C residue 87 CYS Chi-restraints excluded: chain C residue 240 ILE Chi-restraints excluded: chain C residue 296 THR Chi-restraints excluded: chain C residue 364 CYS Chi-restraints excluded: chain C residue 382 ASN Chi-restraints excluded: chain C residue 390 THR Chi-restraints excluded: chain C residue 487 ARG Chi-restraints excluded: chain C residue 498 VAL Chi-restraints excluded: chain C residue 559 PHE Chi-restraints excluded: chain C residue 622 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 70 optimal weight: 0.9990 chunk 64 optimal weight: 30.0000 chunk 114 optimal weight: 30.0000 chunk 37 optimal weight: 2.9990 chunk 81 optimal weight: 0.9990 chunk 29 optimal weight: 0.1980 chunk 119 optimal weight: 9.9990 chunk 77 optimal weight: 5.9990 chunk 75 optimal weight: 6.9990 chunk 45 optimal weight: 40.0000 chunk 154 optimal weight: 1.9990 overall best weight: 1.4388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 185 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3716 r_free = 0.3716 target = 0.076818 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3158 r_free = 0.3158 target = 0.053897 restraints weight = 54369.731| |-----------------------------------------------------------------------------| r_work (start): 0.3015 rms_B_bonded: 5.17 r_work: 0.2873 rms_B_bonded: 4.85 restraints_weight: 0.5000 r_work (final): 0.2873 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8267 moved from start: 0.7477 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 11351 Z= 0.117 Angle : 0.485 7.832 15528 Z= 0.261 Chirality : 0.042 0.138 1792 Planarity : 0.003 0.031 2043 Dihedral : 3.659 17.613 1685 Min Nonbonded Distance : 2.560 Molprobity Statistics. All-atom Clashscore : 3.77 Ramachandran Plot: Outliers : 0.13 % Allowed : 10.92 % Favored : 88.95 % Rotamer: Outliers : 2.56 % Allowed : 25.00 % Favored : 72.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.69 (0.21), residues: 1548 helix: 3.32 (0.33), residues: 250 sheet: 0.13 (0.33), residues: 280 loop : -2.91 (0.17), residues: 1018 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 487 TYR 0.009 0.001 TYR B 199 PHE 0.011 0.001 PHE A 461 TRP 0.007 0.001 TRP C 481 HIS 0.002 0.000 HIS A 338 Details of bonding type rmsd covalent geometry : bond 0.00251 (11342) covalent geometry : angle 0.48513 (15510) SS BOND : bond 0.00217 ( 9) SS BOND : angle 0.68646 ( 18) hydrogen bonds : bond 0.06081 ( 309) hydrogen bonds : angle 4.00200 ( 1038) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3096 Ramachandran restraints generated. 1548 Oldfield, 0 Emsley, 1548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3096 Ramachandran restraints generated. 1548 Oldfield, 0 Emsley, 1548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 65 residues out of total 1420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 41 time to evaluate : 0.445 Fit side-chains REVERT: A 157 TYR cc_start: 0.8611 (OUTLIER) cc_final: 0.7415 (t80) REVERT: A 200 PHE cc_start: 0.9089 (t80) cc_final: 0.8526 (t80) REVERT: A 283 TYR cc_start: 0.9184 (OUTLIER) cc_final: 0.8592 (m-80) REVERT: A 390 THR cc_start: 0.8387 (OUTLIER) cc_final: 0.8121 (p) REVERT: A 499 ASN cc_start: 0.8190 (t0) cc_final: 0.7650 (t0) REVERT: B 200 PHE cc_start: 0.8890 (t80) cc_final: 0.8487 (t80) REVERT: B 251 SER cc_start: 0.8237 (OUTLIER) cc_final: 0.8018 (m) REVERT: B 316 THR cc_start: 0.9146 (OUTLIER) cc_final: 0.8906 (p) REVERT: B 390 THR cc_start: 0.8341 (OUTLIER) cc_final: 0.8078 (p) REVERT: B 594 PHE cc_start: 0.8200 (p90) cc_final: 0.7712 (p90) REVERT: C 390 THR cc_start: 0.8328 (OUTLIER) cc_final: 0.8086 (p) REVERT: C 491 MET cc_start: 0.8804 (tpt) cc_final: 0.8428 (tpt) outliers start: 24 outliers final: 14 residues processed: 64 average time/residue: 0.0698 time to fit residues: 7.6672 Evaluate side-chains 60 residues out of total 1420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 39 time to evaluate : 0.513 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 157 TYR Chi-restraints excluded: chain A residue 229 MET Chi-restraints excluded: chain A residue 253 PHE Chi-restraints excluded: chain A residue 283 TYR Chi-restraints excluded: chain A residue 364 CYS Chi-restraints excluded: chain A residue 390 THR Chi-restraints excluded: chain A residue 622 THR Chi-restraints excluded: chain B residue 108 VAL Chi-restraints excluded: chain B residue 251 SER Chi-restraints excluded: chain B residue 316 THR Chi-restraints excluded: chain B residue 336 SER Chi-restraints excluded: chain B residue 355 VAL Chi-restraints excluded: chain B residue 364 CYS Chi-restraints excluded: chain B residue 390 THR Chi-restraints excluded: chain B residue 394 LYS Chi-restraints excluded: chain C residue 87 CYS Chi-restraints excluded: chain C residue 240 ILE Chi-restraints excluded: chain C residue 336 SER Chi-restraints excluded: chain C residue 364 CYS Chi-restraints excluded: chain C residue 390 THR Chi-restraints excluded: chain C residue 622 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 108 optimal weight: 0.7980 chunk 3 optimal weight: 6.9990 chunk 48 optimal weight: 3.9990 chunk 78 optimal weight: 2.9990 chunk 31 optimal weight: 3.9990 chunk 110 optimal weight: 20.0000 chunk 38 optimal weight: 7.9990 chunk 53 optimal weight: 6.9990 chunk 5 optimal weight: 9.9990 chunk 8 optimal weight: 1.9990 chunk 15 optimal weight: 20.0000 overall best weight: 2.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 185 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3701 r_free = 0.3701 target = 0.076667 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3135 r_free = 0.3135 target = 0.053529 restraints weight = 54514.036| |-----------------------------------------------------------------------------| r_work (start): 0.2966 rms_B_bonded: 5.23 r_work: 0.2829 rms_B_bonded: 4.61 restraints_weight: 0.5000 r_work (final): 0.2829 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8303 moved from start: 0.7658 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 11351 Z= 0.175 Angle : 0.521 8.284 15528 Z= 0.280 Chirality : 0.043 0.140 1792 Planarity : 0.003 0.032 2043 Dihedral : 3.746 17.297 1685 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 5.29 Ramachandran Plot: Outliers : 0.13 % Allowed : 13.50 % Favored : 86.37 % Rotamer: Outliers : 2.14 % Allowed : 25.11 % Favored : 72.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.74 (0.21), residues: 1548 helix: 3.36 (0.32), residues: 244 sheet: 0.11 (0.33), residues: 278 loop : -2.93 (0.17), residues: 1026 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 487 TYR 0.016 0.001 TYR B 283 PHE 0.012 0.001 PHE A 461 TRP 0.013 0.001 TRP A 492 HIS 0.004 0.001 HIS A 338 Details of bonding type rmsd covalent geometry : bond 0.00393 (11342) covalent geometry : angle 0.52124 (15510) SS BOND : bond 0.00279 ( 9) SS BOND : angle 0.57517 ( 18) hydrogen bonds : bond 0.06658 ( 309) hydrogen bonds : angle 4.18402 ( 1038) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2790.86 seconds wall clock time: 48 minutes 24.65 seconds (2904.65 seconds total)