Starting phenix.real_space_refine on Wed Mar 12 21:41:47 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8tvg_41641/03_2025/8tvg_41641.cif Found real_map, /net/cci-nas-00/data/ceres_data/8tvg_41641/03_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_41641/03_2025/8tvg_41641.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8tvg_41641/03_2025/8tvg_41641.map" model { file = "/net/cci-nas-00/data/ceres_data/8tvg_41641/03_2025/8tvg_41641.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8tvg_41641/03_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): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/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: 7.24, per 1000 atoms: 0.87 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: 2.39 Conformation dependent library (CDL) restraints added in 1.2 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: 1.24 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: 2.74 Time building geometry restraints manager: 2.82 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: 0.06 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: 8.750 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: 0.330 Check model and map are aligned: 0.050 Set scattering table: 0.090 Process input model: 25.810 Find NCS groups from input model: 0.160 Set up NCS constraints: 0.050 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:3.010 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 38.260 ------------------------------------------------------------------------------- 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 : 0.858 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: 0.1901 time to fit residues: 47.3582 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 : 0.979 ------------------------------------------------------------------------------- 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 = 0.113682 restraints weight = 10716.984| |-----------------------------------------------------------------------------| r_work (start): 0.3298 rms_B_bonded: 2.11 r_work: 0.3160 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.3010 rms_B_bonded: 4.78 restraints_weight: 0.2500 r_work (final): 0.3010 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8186 moved from start: 0.2276 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 : 0.848 Fit side-chains REVERT: A 188 ASP cc_start: 0.7930 (m-30) cc_final: 0.7702 (m-30) REVERT: C 303 TRP cc_start: 0.8739 (m100) cc_final: 0.8389 (m100) outliers start: 19 outliers final: 10 residues processed: 121 average time/residue: 0.1579 time to fit residues: 28.3514 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 : 0.882 ------------------------------------------------------------------------------- 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: 1.9990 chunk 77 optimal weight: 0.0020 chunk 72 optimal weight: 4.9990 chunk 101 optimal weight: 3.9990 chunk 32 optimal weight: 0.7980 chunk 3 optimal weight: 0.9980 chunk 19 optimal weight: 0.8980 chunk 107 optimal weight: 3.9990 chunk 70 optimal weight: 0.7980 chunk 46 optimal weight: 0.6980 overall best weight: 0.6388 ------------------------------------------------------------------------------- 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 = 0.3585 r_free = 0.3585 target = 0.136572 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3285 r_free = 0.3285 target = 0.112415 restraints weight = 10804.534| |-----------------------------------------------------------------------------| r_work (start): 0.3260 rms_B_bonded: 1.96 r_work: 0.3141 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.2991 rms_B_bonded: 4.38 restraints_weight: 0.2500 r_work (final): 0.2991 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8192 moved from start: 0.2904 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 8433 Z= 0.233 Angle : 0.560 7.738 11508 Z= 0.304 Chirality : 0.046 0.174 1437 Planarity : 0.004 0.030 1464 Dihedral : 4.940 27.486 1347 Min Nonbonded Distance : 2.606 Molprobity Statistics. All-atom Clashscore : 3.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.29 % Favored : 95.71 % Rotamer: Outliers : 2.36 % Allowed : 7.59 % Favored : 90.05 % 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: 2.40 (0.27), residues: 405 sheet: 0.95 (0.36), residues: 186 loop : -0.36 (0.25), residues: 528 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP A 303 HIS 0.002 0.001 HIS C 24 PHE 0.011 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 105 residues out of total 1008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 86 time to evaluate : 2.341 Fit side-chains REVERT: A 377 LEU cc_start: 0.8287 (OUTLIER) cc_final: 0.8017 (mm) REVERT: C 303 TRP cc_start: 0.8720 (m100) cc_final: 0.8354 (m100) outliers start: 19 outliers final: 12 residues processed: 98 average time/residue: 0.1826 time to fit residues: 27.4077 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 : 0.889 ------------------------------------------------------------------------------- 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: 1.9990 chunk 87 optimal weight: 0.0980 chunk 77 optimal weight: 1.9990 chunk 101 optimal weight: 4.9990 chunk 37 optimal weight: 2.9990 chunk 97 optimal weight: 3.9990 chunk 45 optimal weight: 0.5980 chunk 5 optimal weight: 1.9990 chunk 52 optimal weight: 2.9990 overall best weight: 0.9984 ------------------------------------------------------------------------------- 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 = 0.3520 r_free = 0.3520 target = 0.131705 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3213 r_free = 0.3213 target = 0.107319 restraints weight = 10747.220| |-----------------------------------------------------------------------------| r_work (start): 0.3193 rms_B_bonded: 1.95 r_work: 0.3066 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.2921 rms_B_bonded: 4.34 restraints_weight: 0.2500 r_work (final): 0.2921 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8289 moved from start: 0.3544 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 8433 Z= 0.316 Angle : 0.582 6.398 11508 Z= 0.313 Chirality : 0.047 0.133 1437 Planarity : 0.004 0.036 1464 Dihedral : 5.027 26.332 1347 Min Nonbonded Distance : 2.615 Molprobity Statistics. All-atom Clashscore : 3.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.27 % Favored : 94.73 % Rotamer: Outliers : 3.11 % Allowed : 9.33 % 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: 0.95 (0.24), residues: 1119 helix: 2.39 (0.26), residues: 405 sheet: 0.63 (0.35), residues: 192 loop : -0.82 (0.24), residues: 522 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP A 303 HIS 0.002 0.001 HIS B 24 PHE 0.013 0.002 PHE A 277 TYR 0.015 0.002 TYR A 202 ARG 0.005 0.001 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 107 residues out of total 1008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 82 time to evaluate : 0.975 Fit side-chains REVERT: A 188 ASP cc_start: 0.7888 (m-30) cc_final: 0.7549 (m-30) REVERT: A 377 LEU cc_start: 0.8356 (OUTLIER) cc_final: 0.8101 (mm) REVERT: B 188 ASP cc_start: 0.8289 (m-30) cc_final: 0.7913 (m-30) REVERT: C 188 ASP cc_start: 0.8306 (OUTLIER) cc_final: 0.8091 (t0) REVERT: C 362 LYS cc_start: 0.8689 (tttt) cc_final: 0.8474 (tttm) outliers start: 25 outliers final: 15 residues processed: 100 average time/residue: 0.1547 time to fit residues: 23.7121 Evaluate side-chains 86 residues out of total 1008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 69 time to evaluate : 1.020 ------------------------------------------------------------------------------- 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 263 ASP 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 188 ASP 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 Chi-restraints excluded: chain C residue 377 LEU 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: 0.9990 chunk 28 optimal weight: 0.0870 chunk 31 optimal weight: 0.0570 chunk 105 optimal weight: 0.1980 chunk 81 optimal weight: 0.0270 chunk 4 optimal weight: 0.3980 chunk 3 optimal weight: 0.9980 chunk 72 optimal weight: 0.9980 chunk 85 optimal weight: 0.5980 overall best weight: 0.1534 ------------------------------------------------------------------------------- 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 = 0.137527 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.114262 restraints weight = 10602.690| |-----------------------------------------------------------------------------| r_work (start): 0.3298 rms_B_bonded: 1.89 r_work: 0.3177 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.3036 rms_B_bonded: 4.32 restraints_weight: 0.2500 r_work (final): 0.3036 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8189 moved from start: 0.3756 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 8433 Z= 0.124 Angle : 0.484 6.756 11508 Z= 0.261 Chirality : 0.044 0.148 1437 Planarity : 0.004 0.031 1464 Dihedral : 4.545 26.999 1347 Min Nonbonded Distance : 2.624 Molprobity Statistics. All-atom Clashscore : 3.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.38 % Favored : 95.62 % Rotamer: Outliers : 2.49 % Allowed : 9.33 % Favored : 88.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.28 (0.25), residues: 1119 helix: 2.67 (0.27), residues: 405 sheet: 0.93 (0.37), residues: 186 loop : -0.68 (0.24), residues: 528 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.003 TRP C 303 HIS 0.002 0.001 HIS C 24 PHE 0.008 0.001 PHE B 230 TYR 0.012 0.001 TYR C 202 ARG 0.002 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 109 residues out of total 1008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 89 time to evaluate : 0.884 Fit side-chains revert: symmetry clash REVERT: A 357 LYS cc_start: 0.6132 (OUTLIER) cc_final: 0.4880 (tppt) REVERT: A 377 LEU cc_start: 0.8317 (OUTLIER) cc_final: 0.8045 (mm) REVERT: B 188 ASP cc_start: 0.8197 (m-30) cc_final: 0.7703 (m-30) REVERT: B 357 LYS cc_start: 0.5881 (OUTLIER) cc_final: 0.4726 (tppt) REVERT: C 207 THR cc_start: 0.8791 (m) cc_final: 0.8376 (m) REVERT: C 303 TRP cc_start: 0.8798 (m100) cc_final: 0.8542 (m100) REVERT: C 357 LYS cc_start: 0.5542 (OUTLIER) cc_final: 0.4217 (tppt) REVERT: C 362 LYS cc_start: 0.8675 (tttt) cc_final: 0.8240 (tttm) outliers start: 20 outliers final: 10 residues processed: 100 average time/residue: 0.1694 time to fit residues: 25.8772 Evaluate side-chains 99 residues out of total 1008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 85 time to evaluate : 0.971 ------------------------------------------------------------------------------- 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 82 LEU Chi-restraints excluded: chain C residue 205 ILE Chi-restraints excluded: chain C residue 247 ASP Chi-restraints excluded: chain C residue 348 ILE Chi-restraints excluded: chain C residue 357 LYS Chi-restraints excluded: chain C residue 366 SER Chi-restraints excluded: chain C residue 445 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 9 optimal weight: 0.0040 chunk 101 optimal weight: 4.9990 chunk 54 optimal weight: 0.9990 chunk 12 optimal weight: 1.9990 chunk 51 optimal weight: 0.0870 chunk 95 optimal weight: 0.4980 chunk 7 optimal weight: 7.9990 chunk 78 optimal weight: 0.9980 chunk 40 optimal weight: 0.4980 chunk 36 optimal weight: 0.9980 chunk 66 optimal weight: 0.7980 overall best weight: 0.3770 ------------------------------------------------------------------------------- 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 = 0.3566 r_free = 0.3566 target = 0.135841 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3281 r_free = 0.3281 target = 0.112400 restraints weight = 10771.295| |-----------------------------------------------------------------------------| r_work (start): 0.3259 rms_B_bonded: 1.91 r_work: 0.3139 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.2998 rms_B_bonded: 4.29 restraints_weight: 0.2500 r_work (final): 0.2998 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8209 moved from start: 0.3858 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 8433 Z= 0.156 Angle : 0.479 6.126 11508 Z= 0.256 Chirality : 0.044 0.131 1437 Planarity : 0.004 0.032 1464 Dihedral : 4.390 26.071 1347 Min Nonbonded Distance : 2.566 Molprobity Statistics. All-atom Clashscore : 3.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.38 % Favored : 95.62 % 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: 1.31 (0.25), residues: 1119 helix: 2.74 (0.27), residues: 405 sheet: 0.91 (0.36), residues: 186 loop : -0.69 (0.25), residues: 528 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP A 303 HIS 0.001 0.000 HIS A 253 PHE 0.009 0.001 PHE B 230 TYR 0.012 0.001 TYR A 202 ARG 0.002 0.000 ARG C 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 102 residues out of total 1008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 84 time to evaluate : 0.891 Fit side-chains revert: symmetry clash REVERT: A 357 LYS cc_start: 0.5738 (OUTLIER) cc_final: 0.4736 (tppt) REVERT: A 377 LEU cc_start: 0.8262 (OUTLIER) cc_final: 0.8001 (mm) REVERT: B 188 ASP cc_start: 0.8235 (m-30) cc_final: 0.7724 (m-30) REVERT: B 247 ASP cc_start: 0.8513 (t0) cc_final: 0.8291 (t0) REVERT: B 357 LYS cc_start: 0.5892 (OUTLIER) cc_final: 0.4804 (ttpt) REVERT: C 207 THR cc_start: 0.8787 (m) cc_final: 0.8377 (m) REVERT: C 357 LYS cc_start: 0.5201 (OUTLIER) cc_final: 0.4186 (ttpt) REVERT: C 362 LYS cc_start: 0.8653 (tttt) cc_final: 0.8231 (tttm) outliers start: 18 outliers final: 8 residues processed: 95 average time/residue: 0.1854 time to fit residues: 26.8033 Evaluate side-chains 95 residues out of total 1008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 83 time to evaluate : 1.601 ------------------------------------------------------------------------------- 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 82 LEU 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: 0.9980 chunk 98 optimal weight: 2.9990 chunk 15 optimal weight: 0.7980 chunk 44 optimal weight: 0.0070 chunk 48 optimal weight: 0.9980 chunk 75 optimal weight: 0.9990 chunk 52 optimal weight: 1.9990 chunk 0 optimal weight: 2.9990 chunk 76 optimal weight: 0.7980 chunk 94 optimal weight: 0.9980 chunk 10 optimal weight: 0.5980 overall best weight: 0.6398 ------------------------------------------------------------------------------- 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 = 0.3546 r_free = 0.3546 target = 0.134419 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3251 r_free = 0.3251 target = 0.110412 restraints weight = 10723.430| |-----------------------------------------------------------------------------| r_work (start): 0.3230 rms_B_bonded: 1.94 r_work: 0.3107 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.2966 rms_B_bonded: 4.35 restraints_weight: 0.2500 r_work (final): 0.2966 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8240 moved from start: 0.3943 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 8433 Z= 0.222 Angle : 0.542 9.734 11508 Z= 0.288 Chirality : 0.046 0.242 1437 Planarity : 0.004 0.036 1464 Dihedral : 4.510 25.579 1347 Min Nonbonded Distance : 2.566 Molprobity Statistics. All-atom Clashscore : 3.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.56 % Favored : 95.44 % Rotamer: Outliers : 1.87 % Allowed : 10.32 % 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: 1.12 (0.25), residues: 1119 helix: 2.49 (0.27), residues: 408 sheet: 0.86 (0.36), residues: 186 loop : -0.76 (0.25), residues: 525 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP C 303 HIS 0.001 0.000 HIS B 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 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 94 residues out of total 1008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 79 time to evaluate : 0.868 Fit side-chains REVERT: A 357 LYS cc_start: 0.5749 (OUTLIER) cc_final: 0.4883 (tppt) REVERT: A 377 LEU cc_start: 0.8314 (OUTLIER) cc_final: 0.8062 (mm) REVERT: B 330 GLU cc_start: 0.7307 (pm20) cc_final: 0.7055 (pm20) REVERT: B 357 LYS cc_start: 0.5768 (OUTLIER) cc_final: 0.4729 (ttpt) REVERT: C 207 THR cc_start: 0.8834 (m) cc_final: 0.8416 (m) REVERT: C 357 LYS cc_start: 0.5296 (OUTLIER) cc_final: 0.4320 (ttpt) REVERT: C 362 LYS cc_start: 0.8641 (tttt) cc_final: 0.8248 (tttm) REVERT: C 390 MET cc_start: 0.7066 (mmp) cc_final: 0.6826 (mmt) outliers start: 15 outliers final: 7 residues processed: 89 average time/residue: 0.1585 time to fit residues: 21.4433 Evaluate side-chains 87 residues out of total 1008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 76 time to evaluate : 0.875 ------------------------------------------------------------------------------- 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 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: 1.9990 chunk 84 optimal weight: 0.9980 chunk 95 optimal weight: 0.5980 chunk 12 optimal weight: 0.8980 chunk 51 optimal weight: 0.7980 chunk 69 optimal weight: 1.9990 chunk 109 optimal weight: 4.9990 chunk 27 optimal weight: 0.9980 chunk 58 optimal weight: 0.4980 chunk 82 optimal weight: 0.5980 chunk 102 optimal weight: 0.6980 overall best weight: 0.6380 ------------------------------------------------------------------------------- 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 = 0.3540 r_free = 0.3540 target = 0.133864 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3247 r_free = 0.3247 target = 0.110071 restraints weight = 10803.586| |-----------------------------------------------------------------------------| r_work (start): 0.3226 rms_B_bonded: 1.92 r_work: 0.3103 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.2962 rms_B_bonded: 4.34 restraints_weight: 0.2500 r_work (final): 0.2962 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8250 moved from start: 0.4043 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 8433 Z= 0.219 Angle : 0.528 9.022 11508 Z= 0.282 Chirality : 0.046 0.192 1437 Planarity : 0.004 0.040 1464 Dihedral : 4.514 25.062 1347 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 3.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.74 % Favored : 95.26 % Rotamer: Outliers : 1.87 % Allowed : 10.32 % 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: 1.06 (0.25), residues: 1119 helix: 2.48 (0.27), residues: 408 sheet: 0.85 (0.36), residues: 186 loop : -0.83 (0.25), residues: 525 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.003 TRP C 303 HIS 0.001 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 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 92 residues out of total 1008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 77 time to evaluate : 0.947 Fit side-chains REVERT: A 357 LYS cc_start: 0.5532 (OUTLIER) cc_final: 0.4725 (tppt) REVERT: A 377 LEU cc_start: 0.8310 (OUTLIER) cc_final: 0.8059 (mm) REVERT: B 330 GLU cc_start: 0.7265 (pm20) cc_final: 0.7023 (pm20) REVERT: B 357 LYS cc_start: 0.5551 (OUTLIER) cc_final: 0.4623 (ttpt) REVERT: C 207 THR cc_start: 0.8857 (m) cc_final: 0.8440 (m) REVERT: C 357 LYS cc_start: 0.5338 (OUTLIER) cc_final: 0.4460 (ttpt) outliers start: 15 outliers final: 7 residues processed: 87 average time/residue: 0.1561 time to fit residues: 20.9350 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 : 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: 0.6980 chunk 65 optimal weight: 0.9990 chunk 86 optimal weight: 1.9990 chunk 4 optimal weight: 0.9980 chunk 43 optimal weight: 0.5980 chunk 107 optimal weight: 0.4980 chunk 91 optimal weight: 1.9990 chunk 12 optimal weight: 0.8980 chunk 7 optimal weight: 0.9980 chunk 67 optimal weight: 5.9990 chunk 89 optimal weight: 0.9980 overall best weight: 0.7380 ------------------------------------------------------------------------------- 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 = 0.3525 r_free = 0.3525 target = 0.132742 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3229 r_free = 0.3229 target = 0.108858 restraints weight = 10846.803| |-----------------------------------------------------------------------------| r_work (start): 0.3209 rms_B_bonded: 1.92 r_work: 0.3083 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.2939 rms_B_bonded: 4.39 restraints_weight: 0.2500 r_work (final): 0.2939 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8272 moved from start: 0.4142 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 8433 Z= 0.243 Angle : 0.539 8.961 11508 Z= 0.288 Chirality : 0.046 0.183 1437 Planarity : 0.004 0.041 1464 Dihedral : 4.591 24.941 1347 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 3.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.83 % Favored : 95.17 % Rotamer: Outliers : 1.62 % Allowed : 10.45 % 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: 0.97 (0.25), residues: 1119 helix: 2.44 (0.27), residues: 408 sheet: 0.82 (0.36), residues: 186 loop : -0.92 (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 B 24 PHE 0.011 0.002 PHE B 230 TYR 0.013 0.001 TYR A 202 ARG 0.003 0.000 ARG B 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 93 residues out of total 1008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 80 time to evaluate : 0.969 Fit side-chains REVERT: A 357 LYS cc_start: 0.5263 (OUTLIER) cc_final: 0.4643 (tppt) REVERT: B 188 ASP cc_start: 0.8301 (m-30) cc_final: 0.8022 (t0) REVERT: B 330 GLU cc_start: 0.7204 (pm20) cc_final: 0.6949 (pm20) REVERT: B 357 LYS cc_start: 0.5440 (OUTLIER) cc_final: 0.4566 (ttpt) REVERT: C 188 ASP cc_start: 0.8247 (m-30) cc_final: 0.8041 (t0) REVERT: C 207 THR cc_start: 0.8884 (m) cc_final: 0.8464 (m) REVERT: C 357 LYS cc_start: 0.5548 (OUTLIER) cc_final: 0.4599 (ttmt) outliers start: 13 outliers final: 7 residues processed: 89 average time/residue: 0.1496 time to fit residues: 20.8012 Evaluate side-chains 86 residues out of total 1008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 76 time to evaluate : 0.964 ------------------------------------------------------------------------------- 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 90 optimal weight: 0.6980 chunk 102 optimal weight: 0.8980 chunk 42 optimal weight: 0.9990 chunk 73 optimal weight: 0.9980 chunk 86 optimal weight: 0.9980 chunk 67 optimal weight: 0.5980 chunk 93 optimal weight: 0.6980 chunk 65 optimal weight: 0.7980 chunk 17 optimal weight: 1.9990 chunk 39 optimal weight: 2.9990 chunk 49 optimal weight: 0.5980 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 = 0.3528 r_free = 0.3528 target = 0.132848 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3227 r_free = 0.3227 target = 0.108771 restraints weight = 10815.568| |-----------------------------------------------------------------------------| r_work (start): 0.3190 rms_B_bonded: 1.94 r_work: 0.3070 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.2927 rms_B_bonded: 4.34 restraints_weight: 0.2500 r_work (final): 0.2927 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8257 moved from start: 0.4205 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 8433 Z= 0.227 Angle : 0.540 9.699 11508 Z= 0.284 Chirality : 0.046 0.177 1437 Planarity : 0.004 0.043 1464 Dihedral : 4.570 24.481 1347 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 3.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.56 % Favored : 95.44 % Rotamer: Outliers : 1.74 % Allowed : 10.57 % Favored : 87.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.00 (0.25), residues: 1119 helix: 2.68 (0.27), residues: 393 sheet: 0.81 (0.36), residues: 186 loop : -0.99 (0.24), residues: 540 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.003 TRP C 303 HIS 0.001 0.000 HIS B 24 PHE 0.011 0.001 PHE B 230 TYR 0.013 0.001 TYR A 202 ARG 0.003 0.000 ARG B 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 91 residues out of total 1008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 77 time to evaluate : 0.922 Fit side-chains REVERT: A 357 LYS cc_start: 0.5329 (OUTLIER) cc_final: 0.4831 (tppt) REVERT: B 188 ASP cc_start: 0.8336 (m-30) cc_final: 0.8082 (t0) REVERT: B 357 LYS cc_start: 0.5301 (OUTLIER) cc_final: 0.4570 (ttpt) REVERT: C 188 ASP cc_start: 0.8235 (m-30) cc_final: 0.8014 (t0) REVERT: C 207 THR cc_start: 0.8882 (m) cc_final: 0.8458 (m) REVERT: C 357 LYS cc_start: 0.5395 (OUTLIER) cc_final: 0.4622 (ttmt) outliers start: 14 outliers final: 8 residues processed: 86 average time/residue: 0.1547 time to fit residues: 21.1136 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 : 0.840 ------------------------------------------------------------------------------- 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 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 52 MET 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: 0.3980 chunk 77 optimal weight: 0.9980 chunk 1 optimal weight: 1.9990 chunk 24 optimal weight: 1.9990 chunk 58 optimal weight: 0.7980 chunk 72 optimal weight: 1.9990 chunk 2 optimal weight: 2.9990 chunk 47 optimal weight: 0.0570 chunk 51 optimal weight: 0.0770 chunk 3 optimal weight: 0.9990 chunk 99 optimal weight: 2.9990 overall best weight: 0.4656 ------------------------------------------------------------------------------- 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 = 0.3542 r_free = 0.3542 target = 0.134057 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3244 r_free = 0.3244 target = 0.110035 restraints weight = 10917.926| |-----------------------------------------------------------------------------| r_work (start): 0.3224 rms_B_bonded: 1.95 r_work: 0.3102 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.2959 rms_B_bonded: 4.42 restraints_weight: 0.2500 r_work (final): 0.2959 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8249 moved from start: 0.4262 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 8433 Z= 0.177 Angle : 0.517 9.213 11508 Z= 0.272 Chirality : 0.045 0.143 1437 Planarity : 0.004 0.044 1464 Dihedral : 4.453 24.610 1347 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 3.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.65 % Favored : 95.35 % Rotamer: Outliers : 1.24 % Allowed : 11.19 % 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: 1.08 (0.25), residues: 1119 helix: 2.74 (0.27), residues: 393 sheet: 0.85 (0.36), residues: 186 loop : -0.94 (0.25), residues: 540 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.003 TRP C 303 HIS 0.001 0.000 HIS B 253 PHE 0.009 0.001 PHE B 230 TYR 0.012 0.001 TYR A 202 ARG 0.002 0.000 ARG C 258 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5274.62 seconds wall clock time: 94 minutes 31.31 seconds (5671.31 seconds total)