Starting phenix.real_space_refine on Wed Feb 12 20:54:28 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8tvg_41641/02_2025/8tvg_41641.cif Found real_map, /net/cci-nas-00/data/ceres_data/8tvg_41641/02_2025/8tvg_41641.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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8tvg_41641/02_2025/8tvg_41641.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8tvg_41641/02_2025/8tvg_41641.map" model { file = "/net/cci-nas-00/data/ceres_data/8tvg_41641/02_2025/8tvg_41641.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8tvg_41641/02_2025/8tvg_41641.cif" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.039 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 48 5.16 5 C 5337 2.51 5 N 1410 2.21 5 O 1515 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 9 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib" Total number of atoms: 8310 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 2742 Number of conformers: 1 Conformer: "" Number of residues, atoms: 377, 2742 Classifications: {'peptide': 377} Incomplete info: {'truncation_to_alanine': 68} Link IDs: {'PTRANS': 15, 'TRANS': 361} Chain breaks: 1 Unresolved non-hydrogen bonds: 155 Unresolved non-hydrogen angles: 200 Unresolved non-hydrogen dihedrals: 110 Unresolved non-hydrogen chiralities: 22 Planarities with less than four sites: {'GLU:plan': 5, 'ASN:plan1': 3, 'ASP:plan': 15} Unresolved non-hydrogen planarities: 74 Chain: "B" Number of atoms: 2742 Number of conformers: 1 Conformer: "" Number of residues, atoms: 377, 2742 Classifications: {'peptide': 377} Incomplete info: {'truncation_to_alanine': 68} Link IDs: {'PTRANS': 15, 'TRANS': 361} Chain breaks: 1 Unresolved non-hydrogen bonds: 155 Unresolved non-hydrogen angles: 200 Unresolved non-hydrogen dihedrals: 110 Unresolved non-hydrogen chiralities: 22 Planarities with less than four sites: {'GLU:plan': 5, 'ASN:plan1': 3, 'ASP:plan': 15} Unresolved non-hydrogen planarities: 74 Chain: "C" Number of atoms: 2742 Number of conformers: 1 Conformer: "" Number of residues, atoms: 377, 2742 Classifications: {'peptide': 377} Incomplete info: {'truncation_to_alanine': 68} Link IDs: {'PTRANS': 15, 'TRANS': 361} Chain breaks: 1 Unresolved non-hydrogen bonds: 155 Unresolved non-hydrogen angles: 200 Unresolved non-hydrogen dihedrals: 110 Unresolved non-hydrogen chiralities: 22 Planarities with less than four sites: {'GLU:plan': 5, 'ASN:plan1': 3, 'ASP:plan': 15} Unresolved non-hydrogen planarities: 74 Chain: "A" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "C" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Time building chain proxies: 6.83, per 1000 atoms: 0.82 Number of scatterers: 8310 At special positions: 0 Unit cell: (87.5315, 84.581, 142.608, 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 48 16.00 O 1515 8.00 N 1410 7.00 C 5337 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=15, symmetry=0 Simple disulfide: pdb=" SG CYS A 66 " - pdb=" SG CYS A 187 " distance=2.18 Simple disulfide: pdb=" SG CYS A 326 " - pdb=" SG CYS A 335 " distance=2.03 Simple disulfide: pdb=" SG CYS A 350 " - pdb=" SG CYS A 358 " distance=2.04 Simple disulfide: pdb=" SG CYS A 382 " - pdb=" SG CYS A 387 " distance=2.04 Simple disulfide: pdb=" SG CYS A 389 " - pdb=" SG CYS A 412 " distance=2.04 Simple disulfide: pdb=" SG CYS B 66 " - pdb=" SG CYS B 187 " distance=2.18 Simple disulfide: pdb=" SG CYS B 326 " - pdb=" SG CYS B 335 " distance=2.03 Simple disulfide: pdb=" SG CYS B 350 " - pdb=" SG CYS B 358 " distance=2.05 Simple disulfide: pdb=" SG CYS B 382 " - pdb=" SG CYS B 387 " distance=2.04 Simple disulfide: pdb=" SG CYS B 389 " - pdb=" SG CYS B 412 " distance=2.04 Simple disulfide: pdb=" SG CYS C 66 " - pdb=" SG CYS C 187 " distance=2.18 Simple disulfide: pdb=" SG CYS C 326 " - pdb=" SG CYS C 335 " distance=2.03 Simple disulfide: pdb=" SG CYS C 350 " - pdb=" SG CYS C 358 " distance=2.05 Simple disulfide: pdb=" SG CYS C 382 " - pdb=" SG CYS C 387 " distance=2.04 Simple disulfide: pdb=" SG CYS C 389 " - pdb=" SG CYS C 412 " distance=2.04 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 Links applied NAG-ASN " NAG A 601 " - " ASN A 65 " " NAG A 602 " - " ASN A 459 " " NAG B 601 " - " ASN B 65 " " NAG B 602 " - " ASN B 459 " " NAG C 601 " - " ASN C 65 " " NAG C 602 " - " ASN C 459 " Time building additional restraints: 2.18 Conformation dependent library (CDL) restraints added in 1.1 seconds 2238 Ramachandran restraints generated. 1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2112 Finding SS restraints... Secondary structure from input PDB file: 27 helices and 18 sheets defined 36.9% alpha, 34.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.22 Creating SS restraints... Processing helix chain 'A' and resid 25 through 30 removed outlier: 4.190A pdb=" N LYS A 30 " --> pdb=" O ASP A 26 " (cutoff:3.500A) Processing helix chain 'A' and resid 63 through 92 removed outlier: 3.521A pdb=" N THR A 67 " --> pdb=" O VAL A 63 " (cutoff:3.500A) removed outlier: 5.925A pdb=" N LYS A 69 " --> pdb=" O ASN A 65 " (cutoff:3.500A) removed outlier: 6.190A pdb=" N GLN A 70 " --> pdb=" O CYS A 66 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N PHE A 71 " --> pdb=" O THR A 67 " (cutoff:3.500A) Proline residue: A 84 - end of helix Processing helix chain 'A' and resid 160 through 177 Processing helix chain 'A' and resid 177 through 215 removed outlier: 3.552A pdb=" N CYS A 187 " --> pdb=" O ASN A 183 " (cutoff:3.500A) Proline residue: A 211 - end of helix Processing helix chain 'A' and resid 222 through 230 Processing helix chain 'A' and resid 233 through 242 Processing helix chain 'A' and resid 244 through 255 Processing helix chain 'A' and resid 344 through 352 Processing helix chain 'A' and resid 451 through 456 Processing helix chain 'B' and resid 25 through 30 removed outlier: 4.190A pdb=" N LYS B 30 " --> pdb=" O ASP B 26 " (cutoff:3.500A) Processing helix chain 'B' and resid 63 through 92 removed outlier: 3.521A pdb=" N THR B 67 " --> pdb=" O VAL B 63 " (cutoff:3.500A) removed outlier: 5.925A pdb=" N LYS B 69 " --> pdb=" O ASN B 65 " (cutoff:3.500A) removed outlier: 6.191A pdb=" N GLN B 70 " --> pdb=" O CYS B 66 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N PHE B 71 " --> pdb=" O THR B 67 " (cutoff:3.500A) Proline residue: B 84 - end of helix Processing helix chain 'B' and resid 160 through 177 Processing helix chain 'B' and resid 177 through 215 removed outlier: 3.553A pdb=" N CYS B 187 " --> pdb=" O ASN B 183 " (cutoff:3.500A) Proline residue: B 211 - end of helix Processing helix chain 'B' and resid 222 through 230 Processing helix chain 'B' and resid 233 through 242 Processing helix chain 'B' and resid 244 through 255 Processing helix chain 'B' and resid 344 through 352 Processing helix chain 'B' and resid 451 through 456 Processing helix chain 'C' and resid 25 through 30 removed outlier: 4.189A pdb=" N LYS C 30 " --> pdb=" O ASP C 26 " (cutoff:3.500A) Processing helix chain 'C' and resid 63 through 92 removed outlier: 3.520A pdb=" N THR C 67 " --> pdb=" O VAL C 63 " (cutoff:3.500A) removed outlier: 5.925A pdb=" N LYS C 69 " --> pdb=" O ASN C 65 " (cutoff:3.500A) removed outlier: 6.191A pdb=" N GLN C 70 " --> pdb=" O CYS C 66 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N PHE C 71 " --> pdb=" O THR C 67 " (cutoff:3.500A) Proline residue: C 84 - end of helix Processing helix chain 'C' and resid 160 through 177 Processing helix chain 'C' and resid 177 through 215 removed outlier: 3.552A pdb=" N CYS C 187 " --> pdb=" O ASN C 183 " (cutoff:3.500A) Proline residue: C 211 - end of helix Processing helix chain 'C' and resid 222 through 230 Processing helix chain 'C' and resid 233 through 242 Processing helix chain 'C' and resid 244 through 255 Processing helix chain 'C' and resid 344 through 352 Processing helix chain 'C' and resid 451 through 456 Processing sheet with id=AA1, first strand: chain 'A' and resid 219 through 220 removed outlier: 6.996A pdb=" N ALA A 272 " --> pdb=" O ILE A 262 " (cutoff:3.500A) removed outlier: 4.725A pdb=" N VAL A 264 " --> pdb=" O TYR A 270 " (cutoff:3.500A) removed outlier: 6.775A pdb=" N TYR A 270 " --> pdb=" O VAL A 264 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N ASN A 279 " --> pdb=" O SER A 46 " (cutoff:3.500A) removed outlier: 5.158A pdb=" N SER A 46 " --> pdb=" O ASN A 279 " (cutoff:3.500A) removed outlier: 6.911A pdb=" N THR A 281 " --> pdb=" O LYS A 44 " (cutoff:3.500A) removed outlier: 5.489A pdb=" N LYS A 44 " --> pdb=" O THR A 281 " (cutoff:3.500A) removed outlier: 6.715A pdb=" N VAL A 283 " --> pdb=" O LYS A 42 " (cutoff:3.500A) removed outlier: 6.414A pdb=" N LYS A 42 " --> pdb=" O VAL A 283 " (cutoff:3.500A) removed outlier: 9.714A pdb=" N ASN A 285 " --> pdb=" O ASN A 40 " (cutoff:3.500A) removed outlier: 8.775A pdb=" N ASN A 40 " --> pdb=" O ASN A 285 " (cutoff:3.500A) removed outlier: 8.999A pdb=" N VAL A 287 " --> pdb=" O THR A 38 " (cutoff:3.500A) removed outlier: 8.537A pdb=" N THR A 38 " --> pdb=" O VAL A 287 " (cutoff:3.500A) removed outlier: 7.420A pdb=" N GLN A 289 " --> pdb=" O GLY A 36 " (cutoff:3.500A) removed outlier: 6.666A pdb=" N GLY A 36 " --> pdb=" O GLN A 289 " (cutoff:3.500A) removed outlier: 4.838A pdb=" N LEU A 291 " --> pdb=" O ILE A 34 " (cutoff:3.500A) removed outlier: 6.336A pdb=" N ILE A 34 " --> pdb=" O LEU A 291 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 33 through 55 current: chain 'A' and resid 318 through 320 Processing sheet with id=AA2, first strand: chain 'A' and resid 327 through 328 removed outlier: 6.336A pdb=" N ILE A 34 " --> pdb=" O LEU A 291 " (cutoff:3.500A) removed outlier: 4.838A pdb=" N LEU A 291 " --> pdb=" O ILE A 34 " (cutoff:3.500A) removed outlier: 6.666A pdb=" N GLY A 36 " --> pdb=" O GLN A 289 " (cutoff:3.500A) removed outlier: 7.420A pdb=" N GLN A 289 " --> pdb=" O GLY A 36 " (cutoff:3.500A) removed outlier: 8.537A pdb=" N THR A 38 " --> pdb=" O VAL A 287 " (cutoff:3.500A) removed outlier: 8.999A pdb=" N VAL A 287 " --> pdb=" O THR A 38 " (cutoff:3.500A) removed outlier: 8.775A pdb=" N ASN A 40 " --> pdb=" O ASN A 285 " (cutoff:3.500A) removed outlier: 9.714A pdb=" N ASN A 285 " --> pdb=" O ASN A 40 " (cutoff:3.500A) removed outlier: 6.414A pdb=" N LYS A 42 " --> pdb=" O VAL A 283 " (cutoff:3.500A) removed outlier: 6.715A pdb=" N VAL A 283 " --> pdb=" O LYS A 42 " (cutoff:3.500A) removed outlier: 5.489A pdb=" N LYS A 44 " --> pdb=" O THR A 281 " (cutoff:3.500A) removed outlier: 6.911A pdb=" N THR A 281 " --> pdb=" O LYS A 44 " (cutoff:3.500A) removed outlier: 5.158A pdb=" N SER A 46 " --> pdb=" O ASN A 279 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N ASN A 279 " --> pdb=" O SER A 46 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 60 through 61 Processing sheet with id=AA4, first strand: chain 'A' and resid 296 through 297 Processing sheet with id=AA5, first strand: chain 'A' and resid 371 through 374 removed outlier: 4.849A pdb=" N VAL A 378 " --> pdb=" O LEU A 407 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 394 through 396 removed outlier: 4.634A pdb=" N CYS A 387 " --> pdb=" O ILE A 396 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 427 through 433 removed outlier: 4.495A pdb=" N LEU C 51 " --> pdb=" O LEU A 428 " (cutoff:3.500A) removed outlier: 4.387A pdb=" N GLU A 430 " --> pdb=" O LEU C 51 " (cutoff:3.500A) removed outlier: 7.270A pdb=" N VAL C 53 " --> pdb=" O GLU A 430 " (cutoff:3.500A) removed outlier: 4.496A pdb=" N GLU A 432 " --> pdb=" O VAL C 53 " (cutoff:3.500A) removed outlier: 7.398A pdb=" N LYS C 55 " --> pdb=" O GLU A 432 " (cutoff:3.500A) removed outlier: 6.336A pdb=" N ILE C 34 " --> pdb=" O LEU C 291 " (cutoff:3.500A) removed outlier: 4.838A pdb=" N LEU C 291 " --> pdb=" O ILE C 34 " (cutoff:3.500A) removed outlier: 6.665A pdb=" N GLY C 36 " --> pdb=" O GLN C 289 " (cutoff:3.500A) removed outlier: 7.419A pdb=" N GLN C 289 " --> pdb=" O GLY C 36 " (cutoff:3.500A) removed outlier: 8.538A pdb=" N THR C 38 " --> pdb=" O VAL C 287 " (cutoff:3.500A) removed outlier: 8.998A pdb=" N VAL C 287 " --> pdb=" O THR C 38 " (cutoff:3.500A) removed outlier: 8.775A pdb=" N ASN C 40 " --> pdb=" O ASN C 285 " (cutoff:3.500A) removed outlier: 9.712A pdb=" N ASN C 285 " --> pdb=" O ASN C 40 " (cutoff:3.500A) removed outlier: 6.413A pdb=" N LYS C 42 " --> pdb=" O VAL C 283 " (cutoff:3.500A) removed outlier: 6.716A pdb=" N VAL C 283 " --> pdb=" O LYS C 42 " (cutoff:3.500A) removed outlier: 5.488A pdb=" N LYS C 44 " --> pdb=" O THR C 281 " (cutoff:3.500A) removed outlier: 6.912A pdb=" N THR C 281 " --> pdb=" O LYS C 44 " (cutoff:3.500A) removed outlier: 5.158A pdb=" N SER C 46 " --> pdb=" O ASN C 279 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N ASN C 279 " --> pdb=" O SER C 46 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 270 through 293 current: chain 'C' and resid 327 through 328 Processing sheet with id=AA8, first strand: chain 'C' and resid 219 through 220 removed outlier: 6.996A pdb=" N ALA C 272 " --> pdb=" O ILE C 262 " (cutoff:3.500A) removed outlier: 4.724A pdb=" N VAL C 264 " --> pdb=" O TYR C 270 " (cutoff:3.500A) removed outlier: 6.775A pdb=" N TYR C 270 " --> pdb=" O VAL C 264 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N ASN C 279 " --> pdb=" O SER C 46 " (cutoff:3.500A) removed outlier: 5.158A pdb=" N SER C 46 " --> pdb=" O ASN C 279 " (cutoff:3.500A) removed outlier: 6.912A pdb=" N THR C 281 " --> pdb=" O LYS C 44 " (cutoff:3.500A) removed outlier: 5.488A pdb=" N LYS C 44 " --> pdb=" O THR C 281 " (cutoff:3.500A) removed outlier: 6.716A pdb=" N VAL C 283 " --> pdb=" O LYS C 42 " (cutoff:3.500A) removed outlier: 6.413A pdb=" N LYS C 42 " --> pdb=" O VAL C 283 " (cutoff:3.500A) removed outlier: 9.712A pdb=" N ASN C 285 " --> pdb=" O ASN C 40 " (cutoff:3.500A) removed outlier: 8.775A pdb=" N ASN C 40 " --> pdb=" O ASN C 285 " (cutoff:3.500A) removed outlier: 8.998A pdb=" N VAL C 287 " --> pdb=" O THR C 38 " (cutoff:3.500A) removed outlier: 8.538A pdb=" N THR C 38 " --> pdb=" O VAL C 287 " (cutoff:3.500A) removed outlier: 7.419A pdb=" N GLN C 289 " --> pdb=" O GLY C 36 " (cutoff:3.500A) removed outlier: 6.665A pdb=" N GLY C 36 " --> pdb=" O GLN C 289 " (cutoff:3.500A) removed outlier: 4.838A pdb=" N LEU C 291 " --> pdb=" O ILE C 34 " (cutoff:3.500A) removed outlier: 6.336A pdb=" N ILE C 34 " --> pdb=" O LEU C 291 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 33 through 55 current: chain 'C' and resid 318 through 320 Processing sheet with id=AA9, first strand: chain 'A' and resid 438 through 439 removed outlier: 6.360A pdb=" N VAL A 438 " --> pdb=" O ASP C 61 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'B' and resid 219 through 220 removed outlier: 6.996A pdb=" N ALA B 272 " --> pdb=" O ILE B 262 " (cutoff:3.500A) removed outlier: 4.725A pdb=" N VAL B 264 " --> pdb=" O TYR B 270 " (cutoff:3.500A) removed outlier: 6.775A pdb=" N TYR B 270 " --> pdb=" O VAL B 264 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N ASN B 279 " --> pdb=" O SER B 46 " (cutoff:3.500A) removed outlier: 5.158A pdb=" N SER B 46 " --> pdb=" O ASN B 279 " (cutoff:3.500A) removed outlier: 6.912A pdb=" N THR B 281 " --> pdb=" O LYS B 44 " (cutoff:3.500A) removed outlier: 5.488A pdb=" N LYS B 44 " --> pdb=" O THR B 281 " (cutoff:3.500A) removed outlier: 6.715A pdb=" N VAL B 283 " --> pdb=" O LYS B 42 " (cutoff:3.500A) removed outlier: 6.413A pdb=" N LYS B 42 " --> pdb=" O VAL B 283 " (cutoff:3.500A) removed outlier: 9.712A pdb=" N ASN B 285 " --> pdb=" O ASN B 40 " (cutoff:3.500A) removed outlier: 8.775A pdb=" N ASN B 40 " --> pdb=" O ASN B 285 " (cutoff:3.500A) removed outlier: 8.999A pdb=" N VAL B 287 " --> pdb=" O THR B 38 " (cutoff:3.500A) removed outlier: 8.537A pdb=" N THR B 38 " --> pdb=" O VAL B 287 " (cutoff:3.500A) removed outlier: 7.419A pdb=" N GLN B 289 " --> pdb=" O GLY B 36 " (cutoff:3.500A) removed outlier: 6.665A pdb=" N GLY B 36 " --> pdb=" O GLN B 289 " (cutoff:3.500A) removed outlier: 4.838A pdb=" N LEU B 291 " --> pdb=" O ILE B 34 " (cutoff:3.500A) removed outlier: 6.336A pdb=" N ILE B 34 " --> pdb=" O LEU B 291 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 33 through 55 current: chain 'B' and resid 318 through 320 Processing sheet with id=AB2, first strand: chain 'B' and resid 327 through 328 removed outlier: 6.336A pdb=" N ILE B 34 " --> pdb=" O LEU B 291 " (cutoff:3.500A) removed outlier: 4.838A pdb=" N LEU B 291 " --> pdb=" O ILE B 34 " (cutoff:3.500A) removed outlier: 6.665A pdb=" N GLY B 36 " --> pdb=" O GLN B 289 " (cutoff:3.500A) removed outlier: 7.419A pdb=" N GLN B 289 " --> pdb=" O GLY B 36 " (cutoff:3.500A) removed outlier: 8.537A pdb=" N THR B 38 " --> pdb=" O VAL B 287 " (cutoff:3.500A) removed outlier: 8.999A pdb=" N VAL B 287 " --> pdb=" O THR B 38 " (cutoff:3.500A) removed outlier: 8.775A pdb=" N ASN B 40 " --> pdb=" O ASN B 285 " (cutoff:3.500A) removed outlier: 9.712A pdb=" N ASN B 285 " --> pdb=" O ASN B 40 " (cutoff:3.500A) removed outlier: 6.413A pdb=" N LYS B 42 " --> pdb=" O VAL B 283 " (cutoff:3.500A) removed outlier: 6.715A pdb=" N VAL B 283 " --> pdb=" O LYS B 42 " (cutoff:3.500A) removed outlier: 5.488A pdb=" N LYS B 44 " --> pdb=" O THR B 281 " (cutoff:3.500A) removed outlier: 6.912A pdb=" N THR B 281 " --> pdb=" O LYS B 44 " (cutoff:3.500A) removed outlier: 5.158A pdb=" N SER B 46 " --> pdb=" O ASN B 279 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N ASN B 279 " --> pdb=" O SER B 46 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 60 through 61 Processing sheet with id=AB4, first strand: chain 'B' and resid 296 through 297 Processing sheet with id=AB5, first strand: chain 'B' and resid 371 through 374 removed outlier: 4.849A pdb=" N VAL B 378 " --> pdb=" O LEU B 407 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 394 through 396 removed outlier: 4.633A pdb=" N CYS B 387 " --> pdb=" O ILE B 396 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 296 through 297 Processing sheet with id=AB8, first strand: chain 'C' and resid 371 through 374 removed outlier: 4.849A pdb=" N VAL C 378 " --> pdb=" O LEU C 407 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 394 through 396 removed outlier: 4.633A pdb=" N CYS C 387 " --> pdb=" O ILE C 396 " (cutoff:3.500A) 423 hydrogen bonds defined for protein. 1182 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: 2.75 Time building geometry restraints manager: 2.55 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 1780 1.32 - 1.45: 1804 1.45 - 1.58: 4774 1.58 - 1.70: 9 1.70 - 1.83: 66 Bond restraints: 8433 Sorted by residual: bond pdb=" CB LEU B 23 " pdb=" CG LEU B 23 " ideal model delta sigma weight residual 1.530 1.608 -0.078 2.00e-02 2.50e+03 1.53e+01 bond pdb=" CB LEU C 23 " pdb=" CG LEU C 23 " ideal model delta sigma weight residual 1.530 1.608 -0.078 2.00e-02 2.50e+03 1.53e+01 bond pdb=" CB LEU A 23 " pdb=" CG LEU A 23 " ideal model delta sigma weight residual 1.530 1.608 -0.078 2.00e-02 2.50e+03 1.51e+01 bond pdb=" C5 NAG A 601 " pdb=" O5 NAG A 601 " ideal model delta sigma weight residual 1.413 1.480 -0.067 2.00e-02 2.50e+03 1.14e+01 bond pdb=" C5 NAG B 601 " pdb=" O5 NAG B 601 " ideal model delta sigma weight residual 1.413 1.480 -0.067 2.00e-02 2.50e+03 1.12e+01 ... (remaining 8428 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.05: 10285 2.05 - 4.10: 1028 4.10 - 6.15: 177 6.15 - 8.20: 15 8.20 - 10.24: 3 Bond angle restraints: 11508 Sorted by residual: angle pdb=" N THR A 392 " pdb=" CA THR A 392 " pdb=" C THR A 392 " ideal model delta sigma weight residual 114.12 103.88 10.24 1.39e+00 5.18e-01 5.43e+01 angle pdb=" N THR B 392 " pdb=" CA THR B 392 " pdb=" C THR B 392 " ideal model delta sigma weight residual 114.12 103.91 10.21 1.39e+00 5.18e-01 5.40e+01 angle pdb=" N THR C 392 " pdb=" CA THR C 392 " pdb=" C THR C 392 " ideal model delta sigma weight residual 114.12 103.93 10.19 1.39e+00 5.18e-01 5.38e+01 angle pdb=" C PRO C 442 " pdb=" N PRO C 443 " pdb=" CA PRO C 443 " ideal model delta sigma weight residual 120.03 126.71 -6.68 9.90e-01 1.02e+00 4.55e+01 angle pdb=" C PRO A 442 " pdb=" N PRO A 443 " pdb=" CA PRO A 443 " ideal model delta sigma weight residual 120.03 126.69 -6.66 9.90e-01 1.02e+00 4.53e+01 ... (remaining 11503 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 12.68: 4913 12.68 - 25.36: 205 25.36 - 38.05: 54 38.05 - 50.73: 21 50.73 - 63.41: 21 Dihedral angle restraints: 5214 sinusoidal: 1926 harmonic: 3288 Sorted by residual: dihedral pdb=" CB CYS A 389 " pdb=" SG CYS A 389 " pdb=" SG CYS A 412 " pdb=" CB CYS A 412 " ideal model delta sinusoidal sigma weight residual -86.00 -141.15 55.15 1 1.00e+01 1.00e-02 4.11e+01 dihedral pdb=" CB CYS C 389 " pdb=" SG CYS C 389 " pdb=" SG CYS C 412 " pdb=" CB CYS C 412 " ideal model delta sinusoidal sigma weight residual -86.00 -141.14 55.14 1 1.00e+01 1.00e-02 4.11e+01 dihedral pdb=" CB CYS B 389 " pdb=" SG CYS B 389 " pdb=" SG CYS B 412 " pdb=" CB CYS B 412 " ideal model delta sinusoidal sigma weight residual -86.00 -141.14 55.14 1 1.00e+01 1.00e-02 4.11e+01 ... (remaining 5211 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.075: 972 0.075 - 0.150: 394 0.150 - 0.226: 53 0.226 - 0.301: 9 0.301 - 0.376: 9 Chirality restraints: 1437 Sorted by residual: chirality pdb=" C2 NAG B 602 " pdb=" C1 NAG B 602 " pdb=" C3 NAG B 602 " pdb=" N2 NAG B 602 " both_signs ideal model delta sigma weight residual False -2.49 -2.87 0.38 2.00e-01 2.50e+01 3.53e+00 chirality pdb=" C2 NAG C 602 " pdb=" C1 NAG C 602 " pdb=" C3 NAG C 602 " pdb=" N2 NAG C 602 " both_signs ideal model delta sigma weight residual False -2.49 -2.87 0.38 2.00e-01 2.50e+01 3.53e+00 chirality pdb=" C2 NAG A 602 " pdb=" C1 NAG A 602 " pdb=" C3 NAG A 602 " pdb=" N2 NAG A 602 " both_signs ideal model delta sigma weight residual False -2.49 -2.87 0.38 2.00e-01 2.50e+01 3.52e+00 ... (remaining 1434 not shown) Planarity restraints: 1470 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN C 459 " -0.028 2.00e-02 2.50e+03 2.90e-02 1.05e+01 pdb=" CG ASN C 459 " 0.013 2.00e-02 2.50e+03 pdb=" OD1 ASN C 459 " 0.006 2.00e-02 2.50e+03 pdb=" ND2 ASN C 459 " 0.045 2.00e-02 2.50e+03 pdb=" C1 NAG C 602 " -0.035 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 459 " 0.028 2.00e-02 2.50e+03 2.89e-02 1.05e+01 pdb=" CG ASN A 459 " -0.013 2.00e-02 2.50e+03 pdb=" OD1 ASN A 459 " -0.006 2.00e-02 2.50e+03 pdb=" ND2 ASN A 459 " -0.044 2.00e-02 2.50e+03 pdb=" C1 NAG A 602 " 0.035 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN B 459 " -0.028 2.00e-02 2.50e+03 2.89e-02 1.05e+01 pdb=" CG ASN B 459 " 0.013 2.00e-02 2.50e+03 pdb=" OD1 ASN B 459 " 0.006 2.00e-02 2.50e+03 pdb=" ND2 ASN B 459 " 0.044 2.00e-02 2.50e+03 pdb=" C1 NAG B 602 " -0.035 2.00e-02 2.50e+03 ... (remaining 1467 not shown) Histogram of nonbonded interaction distances: 2.40 - 2.90: 3113 2.90 - 3.40: 7535 3.40 - 3.90: 13183 3.90 - 4.40: 14427 4.40 - 4.90: 24287 Nonbonded interactions: 62545 Sorted by model distance: nonbonded pdb=" N THR A 392 " pdb=" N ASP A 393 " model vdw 2.402 2.560 nonbonded pdb=" N THR C 392 " pdb=" N ASP C 393 " model vdw 2.402 2.560 nonbonded pdb=" N THR B 392 " pdb=" N ASP B 393 " model vdw 2.402 2.560 nonbonded pdb=" NZ LYS B 42 " pdb=" OD1 ASP B 247 " model vdw 2.451 3.120 nonbonded pdb=" NZ LYS C 42 " pdb=" OD1 ASP C 247 " model vdw 2.452 3.120 ... (remaining 62540 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: 0.05 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'B' } 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: 6.780 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: 0.320 Check model and map are aligned: 0.060 Set scattering table: 0.080 Process input model: 24.130 Find NCS groups from input model: 0.130 Set up NCS constraints: 0.040 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:2.850 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.400 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7669 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.013 0.093 8433 Z= 0.821 Angle : 1.355 10.244 11508 Z= 0.934 Chirality : 0.082 0.376 1437 Planarity : 0.005 0.018 1464 Dihedral : 8.917 63.411 3057 Min Nonbonded Distance : 2.402 Molprobity Statistics. All-atom Clashscore : 1.16 Ramachandran Plot: Outliers : 0.54 % Allowed : 2.68 % Favored : 96.78 % Rotamer: Outliers : 0.75 % Allowed : 0.75 % Favored : 98.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.61 (0.23), residues: 1119 helix: 0.53 (0.24), residues: 396 sheet: 1.22 (0.36), residues: 192 loop : 0.14 (0.24), residues: 531 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.004 TRP C 303 HIS 0.003 0.001 HIS C 24 PHE 0.007 0.002 PHE A 277 TYR 0.035 0.006 TYR C 415 ARG 0.005 0.001 ARG B 314 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2238 Ramachandran restraints generated. 1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2238 Ramachandran restraints generated. 1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 1008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 175 time to evaluate : 0.926 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 303 TRP cc_start: 0.8110 (m100) cc_final: 0.7903 (m100) REVERT: C 303 TRP cc_start: 0.8249 (m100) cc_final: 0.7943 (m100) outliers start: 6 outliers final: 3 residues processed: 181 average time/residue: 0.2018 time to fit residues: 50.5214 Evaluate side-chains 92 residues out of total 1008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 89 time to evaluate : 0.968 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 357 LYS Chi-restraints excluded: chain B residue 357 LYS Chi-restraints excluded: chain C residue 357 LYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 93 optimal weight: 0.9990 chunk 84 optimal weight: 0.4980 chunk 46 optimal weight: 0.9990 chunk 28 optimal weight: 1.9990 chunk 56 optimal weight: 0.6980 chunk 44 optimal weight: 0.6980 chunk 87 optimal weight: 0.9990 chunk 33 optimal weight: 0.8980 chunk 52 optimal weight: 1.9990 chunk 64 optimal weight: 1.9990 chunk 100 optimal weight: 0.5980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 24 HIS A 95 ASN B 24 HIS B 95 ASN C 95 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3616 r_free = 0.3616 target = 0.138815 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3308 r_free = 0.3308 target = 0.113681 restraints weight = 10717.016| |-----------------------------------------------------------------------------| r_work (start): 0.3298 rms_B_bonded: 2.11 r_work: 0.3161 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.3011 rms_B_bonded: 4.77 restraints_weight: 0.2500 r_work (final): 0.3011 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8188 moved from start: 0.2275 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 8433 Z= 0.262 Angle : 0.659 7.998 11508 Z= 0.348 Chirality : 0.048 0.188 1437 Planarity : 0.005 0.038 1464 Dihedral : 5.291 27.444 1347 Min Nonbonded Distance : 2.606 Molprobity Statistics. All-atom Clashscore : 3.12 Ramachandran Plot: Outliers : 0.27 % Allowed : 3.22 % Favored : 96.51 % Rotamer: Outliers : 2.36 % Allowed : 6.34 % Favored : 91.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.18 (0.24), residues: 1119 helix: 1.97 (0.25), residues: 393 sheet: 0.97 (0.36), residues: 192 loop : -0.15 (0.24), residues: 534 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP C 303 HIS 0.002 0.001 HIS C 24 PHE 0.011 0.002 PHE A 277 TYR 0.012 0.001 TYR A 202 ARG 0.003 0.001 ARG B 325 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2238 Ramachandran restraints generated. 1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2238 Ramachandran restraints generated. 1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 1008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 108 time to evaluate : 0.883 Fit side-chains REVERT: A 188 ASP cc_start: 0.7934 (m-30) cc_final: 0.7707 (m-30) REVERT: C 303 TRP cc_start: 0.8747 (m100) cc_final: 0.8398 (m100) outliers start: 19 outliers final: 10 residues processed: 121 average time/residue: 0.1594 time to fit residues: 28.6118 Evaluate side-chains 92 residues out of total 1008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 82 time to evaluate : 0.915 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 ASN Chi-restraints excluded: chain A residue 205 ILE Chi-restraints excluded: chain A residue 287 VAL Chi-restraints excluded: chain A residue 357 LYS Chi-restraints excluded: chain B residue 205 ILE Chi-restraints excluded: chain B residue 357 LYS Chi-restraints excluded: chain C residue 166 VAL Chi-restraints excluded: chain C residue 205 ILE Chi-restraints excluded: chain C residue 348 ILE Chi-restraints excluded: chain C residue 357 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 68 optimal weight: 7.9990 chunk 26 optimal weight: 0.9990 chunk 77 optimal weight: 0.8980 chunk 72 optimal weight: 4.9990 chunk 101 optimal weight: 4.9990 chunk 32 optimal weight: 3.9990 chunk 3 optimal weight: 0.0870 chunk 19 optimal weight: 0.2980 chunk 107 optimal weight: 3.9990 chunk 70 optimal weight: 0.7980 chunk 46 optimal weight: 0.8980 overall best weight: 0.5958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 24 HIS B 24 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3589 r_free = 0.3589 target = 0.136927 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3290 r_free = 0.3290 target = 0.112830 restraints weight = 10794.861| |-----------------------------------------------------------------------------| r_work (start): 0.3265 rms_B_bonded: 1.95 r_work: 0.3146 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.2998 rms_B_bonded: 4.36 restraints_weight: 0.2500 r_work (final): 0.2998 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8183 moved from start: 0.2915 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 8433 Z= 0.221 Angle : 0.555 7.107 11508 Z= 0.302 Chirality : 0.046 0.155 1437 Planarity : 0.004 0.030 1464 Dihedral : 4.927 27.495 1347 Min Nonbonded Distance : 2.611 Molprobity Statistics. All-atom Clashscore : 3.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.11 % Favored : 95.89 % Rotamer: Outliers : 2.36 % Allowed : 7.46 % Favored : 90.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.33 (0.25), residues: 1119 helix: 2.42 (0.27), residues: 405 sheet: 0.96 (0.36), residues: 186 loop : -0.36 (0.25), residues: 528 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP A 303 HIS 0.002 0.001 HIS C 24 PHE 0.010 0.001 PHE A 277 TYR 0.013 0.001 TYR A 202 ARG 0.002 0.000 ARG A 232 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2238 Ramachandran restraints generated. 1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2238 Ramachandran restraints generated. 1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 1008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 88 time to evaluate : 1.008 Fit side-chains REVERT: A 377 LEU cc_start: 0.8283 (OUTLIER) cc_final: 0.8014 (mm) REVERT: C 303 TRP cc_start: 0.8713 (m100) cc_final: 0.8360 (m100) outliers start: 19 outliers final: 12 residues processed: 99 average time/residue: 0.1529 time to fit residues: 23.4021 Evaluate side-chains 90 residues out of total 1008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 77 time to evaluate : 1.013 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 205 ILE Chi-restraints excluded: chain A residue 287 VAL Chi-restraints excluded: chain A residue 357 LYS Chi-restraints excluded: chain A residue 377 LEU Chi-restraints excluded: chain B residue 23 LEU Chi-restraints excluded: chain B residue 205 ILE Chi-restraints excluded: chain B residue 313 THR Chi-restraints excluded: chain B residue 357 LYS Chi-restraints excluded: chain C residue 166 VAL Chi-restraints excluded: chain C residue 205 ILE Chi-restraints excluded: chain C residue 313 THR Chi-restraints excluded: chain C residue 348 ILE Chi-restraints excluded: chain C residue 357 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 83 optimal weight: 0.2980 chunk 32 optimal weight: 4.9990 chunk 68 optimal weight: 0.0020 chunk 87 optimal weight: 0.0470 chunk 77 optimal weight: 1.9990 chunk 101 optimal weight: 4.9990 chunk 37 optimal weight: 2.9990 chunk 97 optimal weight: 2.9990 chunk 45 optimal weight: 0.5980 chunk 5 optimal weight: 1.9990 chunk 52 optimal weight: 2.9990 overall best weight: 0.5888 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 184 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.135493 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3273 r_free = 0.3273 target = 0.111628 restraints weight = 10688.750| |-----------------------------------------------------------------------------| r_work (start): 0.3249 rms_B_bonded: 1.93 r_work: 0.3128 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.2983 rms_B_bonded: 4.29 restraints_weight: 0.2500 r_work (final): 0.2983 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8218 moved from start: 0.3324 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 8433 Z= 0.210 Angle : 0.519 6.128 11508 Z= 0.280 Chirality : 0.045 0.131 1437 Planarity : 0.004 0.031 1464 Dihedral : 4.701 26.344 1347 Min Nonbonded Distance : 2.622 Molprobity Statistics. All-atom Clashscore : 3.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.74 % Favored : 95.26 % Rotamer: Outliers : 2.11 % Allowed : 9.95 % Favored : 87.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.33 (0.25), residues: 1119 helix: 2.60 (0.27), residues: 405 sheet: 0.92 (0.36), residues: 186 loop : -0.53 (0.24), residues: 528 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP A 303 HIS 0.002 0.000 HIS B 24 PHE 0.010 0.001 PHE B 230 TYR 0.013 0.001 TYR A 202 ARG 0.002 0.000 ARG B 258 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2238 Ramachandran restraints generated. 1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2238 Ramachandran restraints generated. 1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 1008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 79 time to evaluate : 1.019 Fit side-chains REVERT: A 377 LEU cc_start: 0.8294 (OUTLIER) cc_final: 0.8017 (mm) REVERT: C 188 ASP cc_start: 0.8252 (m-30) cc_final: 0.8025 (t0) REVERT: C 303 TRP cc_start: 0.8803 (m100) cc_final: 0.8535 (m100) REVERT: C 357 LYS cc_start: 0.6185 (OUTLIER) cc_final: 0.4528 (tppt) outliers start: 17 outliers final: 9 residues processed: 90 average time/residue: 0.1519 time to fit residues: 21.2351 Evaluate side-chains 86 residues out of total 1008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 75 time to evaluate : 1.007 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 205 ILE Chi-restraints excluded: chain A residue 287 VAL Chi-restraints excluded: chain A residue 357 LYS Chi-restraints excluded: chain A residue 377 LEU Chi-restraints excluded: chain B residue 205 ILE Chi-restraints excluded: chain B residue 313 THR Chi-restraints excluded: chain B residue 357 LYS Chi-restraints excluded: chain C residue 166 VAL Chi-restraints excluded: chain C residue 205 ILE Chi-restraints excluded: chain C residue 348 ILE Chi-restraints excluded: chain C residue 357 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 0 optimal weight: 2.9990 chunk 27 optimal weight: 3.9990 chunk 87 optimal weight: 1.9990 chunk 28 optimal weight: 0.3980 chunk 31 optimal weight: 0.9980 chunk 105 optimal weight: 7.9990 chunk 81 optimal weight: 0.0170 chunk 4 optimal weight: 0.0980 chunk 3 optimal weight: 0.9990 chunk 72 optimal weight: 0.9990 chunk 85 optimal weight: 1.9990 overall best weight: 0.5020 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3563 r_free = 0.3563 target = 0.135530 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.111572 restraints weight = 10558.404| |-----------------------------------------------------------------------------| r_work (start): 0.3249 rms_B_bonded: 1.93 r_work: 0.3129 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.2987 rms_B_bonded: 4.29 restraints_weight: 0.2500 r_work (final): 0.2987 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8210 moved from start: 0.3563 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 8433 Z= 0.186 Angle : 0.503 7.905 11508 Z= 0.271 Chirality : 0.045 0.188 1437 Planarity : 0.004 0.031 1464 Dihedral : 4.554 26.132 1347 Min Nonbonded Distance : 2.614 Molprobity Statistics. All-atom Clashscore : 2.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.74 % Favored : 95.26 % Rotamer: Outliers : 2.49 % Allowed : 9.45 % Favored : 88.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.32 (0.25), residues: 1119 helix: 2.66 (0.27), residues: 405 sheet: 0.94 (0.36), residues: 186 loop : -0.60 (0.24), residues: 528 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 303 HIS 0.001 0.000 HIS C 24 PHE 0.010 0.001 PHE B 230 TYR 0.013 0.001 TYR A 202 ARG 0.003 0.000 ARG B 258 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2238 Ramachandran restraints generated. 1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2238 Ramachandran restraints generated. 1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 1008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 83 time to evaluate : 0.961 Fit side-chains REVERT: A 357 LYS cc_start: 0.6091 (OUTLIER) cc_final: 0.4737 (tppt) REVERT: A 377 LEU cc_start: 0.8328 (OUTLIER) cc_final: 0.8038 (mm) REVERT: B 357 LYS cc_start: 0.5991 (OUTLIER) cc_final: 0.4736 (tppt) REVERT: C 303 TRP cc_start: 0.8777 (m100) cc_final: 0.8560 (m100) REVERT: C 357 LYS cc_start: 0.5848 (OUTLIER) cc_final: 0.4386 (tppt) REVERT: C 362 LYS cc_start: 0.8618 (tttt) cc_final: 0.8372 (tttm) outliers start: 20 outliers final: 9 residues processed: 98 average time/residue: 0.1506 time to fit residues: 22.7716 Evaluate side-chains 95 residues out of total 1008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 82 time to evaluate : 0.966 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 205 ILE Chi-restraints excluded: chain A residue 287 VAL Chi-restraints excluded: chain A residue 357 LYS Chi-restraints excluded: chain A residue 377 LEU Chi-restraints excluded: chain A residue 432 GLU Chi-restraints excluded: chain B residue 23 LEU Chi-restraints excluded: chain B residue 205 ILE Chi-restraints excluded: chain B residue 313 THR Chi-restraints excluded: chain B residue 357 LYS Chi-restraints excluded: chain C residue 166 VAL Chi-restraints excluded: chain C residue 205 ILE Chi-restraints excluded: chain C residue 348 ILE Chi-restraints excluded: chain C residue 357 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 9 optimal weight: 0.0870 chunk 101 optimal weight: 4.9990 chunk 54 optimal weight: 1.9990 chunk 12 optimal weight: 0.9990 chunk 51 optimal weight: 0.5980 chunk 95 optimal weight: 0.6980 chunk 7 optimal weight: 6.9990 chunk 78 optimal weight: 1.9990 chunk 40 optimal weight: 0.5980 chunk 36 optimal weight: 0.7980 chunk 66 optimal weight: 3.9990 overall best weight: 0.5558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3552 r_free = 0.3552 target = 0.134633 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3259 r_free = 0.3259 target = 0.110930 restraints weight = 10714.113| |-----------------------------------------------------------------------------| r_work (start): 0.3254 rms_B_bonded: 1.92 r_work: 0.3137 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.2995 rms_B_bonded: 4.25 restraints_weight: 0.2500 r_work (final): 0.2995 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8235 moved from start: 0.3773 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 8433 Z= 0.199 Angle : 0.504 7.071 11508 Z= 0.269 Chirality : 0.045 0.144 1437 Planarity : 0.004 0.033 1464 Dihedral : 4.462 26.214 1347 Min Nonbonded Distance : 2.574 Molprobity Statistics. All-atom Clashscore : 2.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.74 % Favored : 95.26 % Rotamer: Outliers : 1.99 % Allowed : 10.45 % Favored : 87.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.30 (0.25), residues: 1119 helix: 2.65 (0.27), residues: 408 sheet: 0.90 (0.36), residues: 186 loop : -0.63 (0.25), residues: 525 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP A 303 HIS 0.001 0.000 HIS B 24 PHE 0.010 0.001 PHE B 230 TYR 0.012 0.001 TYR A 202 ARG 0.003 0.000 ARG B 258 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2238 Ramachandran restraints generated. 1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2238 Ramachandran restraints generated. 1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 1008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 87 time to evaluate : 1.032 Fit side-chains revert: symmetry clash REVERT: A 357 LYS cc_start: 0.5669 (OUTLIER) cc_final: 0.4697 (tppt) REVERT: A 377 LEU cc_start: 0.8314 (OUTLIER) cc_final: 0.8039 (mm) REVERT: B 247 ASP cc_start: 0.8481 (t0) cc_final: 0.8218 (t0) REVERT: B 357 LYS cc_start: 0.5976 (OUTLIER) cc_final: 0.4918 (ttpt) REVERT: C 207 THR cc_start: 0.8826 (m) cc_final: 0.8383 (m) REVERT: C 357 LYS cc_start: 0.5365 (OUTLIER) cc_final: 0.4241 (ttpt) outliers start: 16 outliers final: 9 residues processed: 96 average time/residue: 0.1673 time to fit residues: 24.2471 Evaluate side-chains 94 residues out of total 1008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 81 time to evaluate : 0.934 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 205 ILE Chi-restraints excluded: chain A residue 287 VAL Chi-restraints excluded: chain A residue 357 LYS Chi-restraints excluded: chain A residue 377 LEU Chi-restraints excluded: chain A residue 432 GLU Chi-restraints excluded: chain B residue 205 ILE Chi-restraints excluded: chain B residue 313 THR Chi-restraints excluded: chain B residue 357 LYS Chi-restraints excluded: chain C residue 166 VAL Chi-restraints excluded: chain C residue 205 ILE Chi-restraints excluded: chain C residue 348 ILE Chi-restraints excluded: chain C residue 357 LYS Chi-restraints excluded: chain C residue 445 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 17 optimal weight: 0.7980 chunk 98 optimal weight: 0.8980 chunk 15 optimal weight: 0.4980 chunk 44 optimal weight: 0.2980 chunk 48 optimal weight: 1.9990 chunk 75 optimal weight: 0.9980 chunk 52 optimal weight: 1.9990 chunk 0 optimal weight: 2.9990 chunk 76 optimal weight: 2.9990 chunk 94 optimal weight: 0.8980 chunk 10 optimal weight: 0.9980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3533 r_free = 0.3533 target = 0.133152 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3237 r_free = 0.3237 target = 0.109327 restraints weight = 10736.720| |-----------------------------------------------------------------------------| r_work (start): 0.3217 rms_B_bonded: 1.93 r_work: 0.3094 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.2951 rms_B_bonded: 4.31 restraints_weight: 0.2500 r_work (final): 0.2951 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8257 moved from start: 0.3934 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 8433 Z= 0.226 Angle : 0.509 6.541 11508 Z= 0.272 Chirality : 0.045 0.134 1437 Planarity : 0.004 0.039 1464 Dihedral : 4.471 26.541 1347 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 3.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.74 % Favored : 95.26 % Rotamer: Outliers : 2.24 % Allowed : 9.95 % Favored : 87.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.17 (0.25), residues: 1119 helix: 2.63 (0.27), residues: 408 sheet: 0.83 (0.36), residues: 186 loop : -0.80 (0.25), residues: 525 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A 303 HIS 0.001 0.000 HIS B 24 PHE 0.011 0.002 PHE B 230 TYR 0.015 0.001 TYR B 345 ARG 0.004 0.000 ARG B 258 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2238 Ramachandran restraints generated. 1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2238 Ramachandran restraints generated. 1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 1008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 84 time to evaluate : 0.950 Fit side-chains REVERT: A 377 LEU cc_start: 0.8329 (OUTLIER) cc_final: 0.8072 (mm) REVERT: B 247 ASP cc_start: 0.8519 (t0) cc_final: 0.8317 (t0) REVERT: B 357 LYS cc_start: 0.5788 (OUTLIER) cc_final: 0.4690 (ttpt) REVERT: C 207 THR cc_start: 0.8866 (m) cc_final: 0.8441 (m) REVERT: C 357 LYS cc_start: 0.5383 (OUTLIER) cc_final: 0.4423 (ttpt) outliers start: 18 outliers final: 9 residues processed: 95 average time/residue: 0.1565 time to fit residues: 23.0905 Evaluate side-chains 91 residues out of total 1008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 79 time to evaluate : 0.973 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 205 ILE Chi-restraints excluded: chain A residue 287 VAL Chi-restraints excluded: chain A residue 357 LYS Chi-restraints excluded: chain A residue 377 LEU Chi-restraints excluded: chain A residue 432 GLU Chi-restraints excluded: chain B residue 205 ILE Chi-restraints excluded: chain B residue 313 THR Chi-restraints excluded: chain B residue 357 LYS Chi-restraints excluded: chain C residue 166 VAL Chi-restraints excluded: chain C residue 205 ILE Chi-restraints excluded: chain C residue 357 LYS Chi-restraints excluded: chain C residue 445 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 66 optimal weight: 3.9990 chunk 84 optimal weight: 0.9980 chunk 95 optimal weight: 0.5980 chunk 12 optimal weight: 0.9980 chunk 51 optimal weight: 0.6980 chunk 69 optimal weight: 2.9990 chunk 109 optimal weight: 3.9990 chunk 27 optimal weight: 1.9990 chunk 58 optimal weight: 2.9990 chunk 82 optimal weight: 0.9980 chunk 102 optimal weight: 0.9980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.131996 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3216 r_free = 0.3216 target = 0.107949 restraints weight = 10862.148| |-----------------------------------------------------------------------------| r_work (start): 0.3196 rms_B_bonded: 1.94 r_work: 0.3071 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.2928 rms_B_bonded: 4.37 restraints_weight: 0.2500 r_work (final): 0.2928 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8279 moved from start: 0.4038 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 8433 Z= 0.271 Angle : 0.553 9.093 11508 Z= 0.296 Chirality : 0.047 0.223 1437 Planarity : 0.004 0.043 1464 Dihedral : 4.605 26.428 1347 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 3.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.83 % Favored : 95.17 % Rotamer: Outliers : 1.87 % Allowed : 10.20 % Favored : 87.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.95 (0.25), residues: 1119 helix: 2.44 (0.27), residues: 408 sheet: 0.77 (0.36), residues: 186 loop : -0.93 (0.24), residues: 525 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.003 TRP C 303 HIS 0.001 0.000 HIS B 24 PHE 0.011 0.002 PHE B 230 TYR 0.020 0.001 TYR B 345 ARG 0.004 0.000 ARG C 258 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2238 Ramachandran restraints generated. 1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2238 Ramachandran restraints generated. 1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 1008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 78 time to evaluate : 0.949 Fit side-chains REVERT: A 377 LEU cc_start: 0.8343 (OUTLIER) cc_final: 0.8098 (mm) REVERT: B 357 LYS cc_start: 0.5423 (OUTLIER) cc_final: 0.4479 (ttpt) REVERT: C 357 LYS cc_start: 0.5580 (OUTLIER) cc_final: 0.4599 (ttpt) outliers start: 15 outliers final: 8 residues processed: 88 average time/residue: 0.1545 time to fit residues: 21.2004 Evaluate side-chains 88 residues out of total 1008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 77 time to evaluate : 0.957 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 205 ILE Chi-restraints excluded: chain A residue 287 VAL Chi-restraints excluded: chain A residue 357 LYS Chi-restraints excluded: chain A residue 377 LEU Chi-restraints excluded: chain A residue 432 GLU Chi-restraints excluded: chain B residue 205 ILE Chi-restraints excluded: chain B residue 313 THR Chi-restraints excluded: chain B residue 357 LYS Chi-restraints excluded: chain C residue 166 VAL Chi-restraints excluded: chain C residue 205 ILE Chi-restraints excluded: chain C residue 357 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 54 optimal weight: 0.5980 chunk 65 optimal weight: 0.0980 chunk 86 optimal weight: 1.9990 chunk 4 optimal weight: 0.6980 chunk 43 optimal weight: 0.1980 chunk 107 optimal weight: 0.0870 chunk 91 optimal weight: 1.9990 chunk 12 optimal weight: 0.6980 chunk 7 optimal weight: 6.9990 chunk 67 optimal weight: 5.9990 chunk 89 optimal weight: 0.9980 overall best weight: 0.3358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3537 r_free = 0.3537 target = 0.134046 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3248 r_free = 0.3248 target = 0.110296 restraints weight = 10845.812| |-----------------------------------------------------------------------------| r_work (start): 0.3241 rms_B_bonded: 1.94 r_work: 0.3121 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.2978 rms_B_bonded: 4.40 restraints_weight: 0.2500 r_work (final): 0.2978 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8224 moved from start: 0.4145 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 8433 Z= 0.151 Angle : 0.516 9.382 11508 Z= 0.270 Chirality : 0.045 0.194 1437 Planarity : 0.004 0.041 1464 Dihedral : 4.402 26.991 1347 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 3.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.47 % Favored : 95.53 % Rotamer: Outliers : 1.37 % Allowed : 10.70 % Favored : 87.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.08 (0.25), residues: 1119 helix: 2.54 (0.27), residues: 408 sheet: 0.88 (0.37), residues: 186 loop : -0.87 (0.25), residues: 525 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.003 TRP C 303 HIS 0.001 0.000 HIS A 253 PHE 0.008 0.001 PHE B 230 TYR 0.017 0.001 TYR B 345 ARG 0.002 0.000 ARG C 258 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2238 Ramachandran restraints generated. 1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2238 Ramachandran restraints generated. 1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 1008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 81 time to evaluate : 0.956 Fit side-chains REVERT: A 377 LEU cc_start: 0.8334 (OUTLIER) cc_final: 0.8067 (mm) REVERT: B 357 LYS cc_start: 0.5280 (OUTLIER) cc_final: 0.4541 (ttpt) REVERT: C 207 THR cc_start: 0.8832 (m) cc_final: 0.8431 (m) REVERT: C 357 LYS cc_start: 0.5317 (OUTLIER) cc_final: 0.4474 (ttmt) outliers start: 11 outliers final: 7 residues processed: 88 average time/residue: 0.1587 time to fit residues: 21.6857 Evaluate side-chains 89 residues out of total 1008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 79 time to evaluate : 1.019 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 205 ILE Chi-restraints excluded: chain A residue 287 VAL Chi-restraints excluded: chain A residue 357 LYS Chi-restraints excluded: chain A residue 377 LEU Chi-restraints excluded: chain B residue 205 ILE Chi-restraints excluded: chain B residue 313 THR Chi-restraints excluded: chain B residue 357 LYS Chi-restraints excluded: chain C residue 166 VAL Chi-restraints excluded: chain C residue 205 ILE Chi-restraints excluded: chain C residue 357 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 90 optimal weight: 1.9990 chunk 102 optimal weight: 0.9980 chunk 42 optimal weight: 0.9980 chunk 73 optimal weight: 0.8980 chunk 86 optimal weight: 0.6980 chunk 67 optimal weight: 0.7980 chunk 93 optimal weight: 0.9980 chunk 65 optimal weight: 0.0470 chunk 17 optimal weight: 1.9990 chunk 39 optimal weight: 2.9990 chunk 49 optimal weight: 0.5980 overall best weight: 0.6078 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3537 r_free = 0.3537 target = 0.133722 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3242 r_free = 0.3242 target = 0.109842 restraints weight = 10796.895| |-----------------------------------------------------------------------------| r_work (start): 0.3201 rms_B_bonded: 1.94 r_work: 0.3085 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.2942 rms_B_bonded: 4.30 restraints_weight: 0.2500 r_work (final): 0.2942 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8242 moved from start: 0.4195 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 8433 Z= 0.207 Angle : 0.533 9.418 11508 Z= 0.278 Chirality : 0.045 0.169 1437 Planarity : 0.004 0.044 1464 Dihedral : 4.412 26.996 1347 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 2.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.65 % Favored : 95.35 % Rotamer: Outliers : 1.49 % Allowed : 10.57 % Favored : 87.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.08 (0.25), residues: 1119 helix: 2.76 (0.27), residues: 393 sheet: 0.87 (0.37), residues: 186 loop : -0.96 (0.24), residues: 540 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.004 TRP C 303 HIS 0.001 0.000 HIS B 24 PHE 0.010 0.001 PHE B 230 TYR 0.018 0.001 TYR B 345 ARG 0.003 0.000 ARG C 258 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2238 Ramachandran restraints generated. 1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2238 Ramachandran restraints generated. 1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 1008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 78 time to evaluate : 0.826 Fit side-chains REVERT: A 377 LEU cc_start: 0.8317 (OUTLIER) cc_final: 0.8072 (mm) REVERT: B 357 LYS cc_start: 0.5146 (OUTLIER) cc_final: 0.4551 (ttpt) REVERT: C 207 THR cc_start: 0.8831 (m) cc_final: 0.8415 (m) REVERT: C 357 LYS cc_start: 0.5520 (OUTLIER) cc_final: 0.4599 (mtmt) outliers start: 12 outliers final: 7 residues processed: 87 average time/residue: 0.1523 time to fit residues: 20.5932 Evaluate side-chains 88 residues out of total 1008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 78 time to evaluate : 0.967 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 205 ILE Chi-restraints excluded: chain A residue 287 VAL Chi-restraints excluded: chain A residue 357 LYS Chi-restraints excluded: chain A residue 377 LEU Chi-restraints excluded: chain B residue 205 ILE Chi-restraints excluded: chain B residue 313 THR Chi-restraints excluded: chain B residue 357 LYS Chi-restraints excluded: chain C residue 166 VAL Chi-restraints excluded: chain C residue 205 ILE Chi-restraints excluded: chain C residue 357 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 10 optimal weight: 0.5980 chunk 77 optimal weight: 0.0470 chunk 1 optimal weight: 1.9990 chunk 24 optimal weight: 4.9990 chunk 58 optimal weight: 0.1980 chunk 72 optimal weight: 0.6980 chunk 2 optimal weight: 2.9990 chunk 47 optimal weight: 0.5980 chunk 51 optimal weight: 0.0050 chunk 3 optimal weight: 0.8980 chunk 99 optimal weight: 0.0370 overall best weight: 0.1770 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3587 r_free = 0.3587 target = 0.137633 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3307 r_free = 0.3307 target = 0.114570 restraints weight = 10831.299| |-----------------------------------------------------------------------------| r_work (start): 0.3279 rms_B_bonded: 1.90 r_work: 0.3173 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.3035 rms_B_bonded: 4.18 restraints_weight: 0.2500 r_work (final): 0.3035 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8158 moved from start: 0.4333 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 8433 Z= 0.120 Angle : 0.489 9.280 11508 Z= 0.254 Chirality : 0.044 0.152 1437 Planarity : 0.004 0.040 1464 Dihedral : 4.142 28.016 1347 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 3.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.11 % Favored : 95.89 % Rotamer: Outliers : 1.24 % Allowed : 10.82 % Favored : 87.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.23 (0.25), residues: 1119 helix: 2.82 (0.27), residues: 393 sheet: 1.07 (0.37), residues: 186 loop : -0.86 (0.25), residues: 540 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.003 TRP C 303 HIS 0.002 0.001 HIS C 253 PHE 0.006 0.001 PHE B 230 TYR 0.016 0.001 TYR B 345 ARG 0.004 0.000 ARG C 360 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4103.80 seconds wall clock time: 73 minutes 30.33 seconds (4410.33 seconds total)