Starting phenix.real_space_refine on Sat Aug 3 14:35:39 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tvg_41641/08_2024/8tvg_41641.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tvg_41641/08_2024/8tvg_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tvg_41641/08_2024/8tvg_41641.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tvg_41641/08_2024/8tvg_41641.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tvg_41641/08_2024/8tvg_41641.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tvg_41641/08_2024/8tvg_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 Residue "A TYR 39": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 64": "NH1" <-> "NH2" Residue "A PHE 371": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 39": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 64": "NH1" <-> "NH2" Residue "B PHE 371": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 39": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 64": "NH1" <-> "NH2" Residue "C PHE 371": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/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: 6.47, per 1000 atoms: 0.78 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 - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied NAG-ASN " NAG A 601 " - " ASN A 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: 3.10 Conformation dependent library (CDL) restraints added in 1.8 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: 1.31 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: 2.61 Time building geometry restraints manager: 3.43 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: 97.76 - 104.94: 177 104.94 - 112.11: 4139 112.11 - 119.29: 2806 119.29 - 126.46: 4362 126.46 - 133.63: 24 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: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 9.000 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.390 Check model and map are aligned: 0.060 Set scattering table: 0.090 Process input model: 28.590 Find NCS groups from input model: 0.300 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:2.610 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 41.080 ------------------------------------------------------------------------------- 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 fitting. rotamer outliers: 6 poor density : 175 time to evaluate : 0.981 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: 0.2048 time to fit residues: 50.7624 Evaluate side-chains 92 residues out of total 1008 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 89 time to evaluate : 0.907 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7778 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 fitting. rotamer outliers: 19 poor density : 108 time to evaluate : 1.007 Fit side-chains REVERT: A 188 ASP cc_start: 0.7320 (m-30) cc_final: 0.7119 (m-30) REVERT: C 303 TRP cc_start: 0.8528 (m100) cc_final: 0.8293 (m100) outliers start: 19 outliers final: 10 residues processed: 121 average time/residue: 0.1651 time to fit residues: 29.5432 Evaluate side-chains 92 residues out of total 1008 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 82 time to evaluate : 1.014 ------------------------------------------------------------------------------- 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 56 optimal weight: 0.0970 chunk 31 optimal weight: 7.9990 chunk 83 optimal weight: 0.9990 chunk 68 optimal weight: 7.9990 chunk 27 optimal weight: 0.0270 chunk 100 optimal weight: 0.7980 chunk 109 optimal weight: 0.0020 chunk 89 optimal weight: 0.9980 chunk 34 optimal weight: 2.9990 chunk 81 optimal weight: 6.9990 chunk 99 optimal weight: 0.9980 overall best weight: 0.3844 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7777 moved from start: 0.2830 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 8433 Z= 0.174 Angle : 0.534 6.963 11508 Z= 0.291 Chirality : 0.045 0.152 1437 Planarity : 0.004 0.029 1464 Dihedral : 4.825 27.306 1347 Min Nonbonded Distance : 2.602 Molprobity Statistics. All-atom Clashscore : 3.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.84 % Favored : 96.16 % 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: 1.41 (0.25), residues: 1119 helix: 2.50 (0.27), residues: 402 sheet: 1.01 (0.36), residues: 186 loop : -0.32 (0.25), residues: 531 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP A 303 HIS 0.002 0.001 HIS C 24 PHE 0.008 0.001 PHE B 230 TYR 0.013 0.001 TYR A 202 ARG 0.002 0.000 ARG B 64 *********************** 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 110 residues out of total 1008 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 91 time to evaluate : 1.008 Fit side-chains REVERT: C 207 THR cc_start: 0.8680 (m) cc_final: 0.8219 (m) REVERT: C 303 TRP cc_start: 0.8458 (m100) cc_final: 0.8204 (m100) outliers start: 19 outliers final: 12 residues processed: 102 average time/residue: 0.1573 time to fit residues: 24.4954 Evaluate side-chains 93 residues out of total 1008 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 81 time to evaluate : 0.923 ------------------------------------------------------------------------------- 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 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 75 optimal weight: 1.9990 chunk 52 optimal weight: 0.0270 chunk 11 optimal weight: 0.4980 chunk 48 optimal weight: 0.9990 chunk 67 optimal weight: 3.9990 chunk 101 optimal weight: 4.9990 chunk 107 optimal weight: 1.9990 chunk 96 optimal weight: 0.8980 chunk 28 optimal weight: 2.9990 chunk 89 optimal weight: 1.9990 chunk 60 optimal weight: 1.9990 overall best weight: 0.8842 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7887 moved from start: 0.3389 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 8433 Z= 0.286 Angle : 0.569 6.590 11508 Z= 0.306 Chirality : 0.047 0.134 1437 Planarity : 0.004 0.034 1464 Dihedral : 4.896 26.484 1347 Min Nonbonded Distance : 2.610 Molprobity Statistics. All-atom Clashscore : 3.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.45 % Favored : 94.55 % Rotamer: Outliers : 2.61 % Allowed : 9.45 % 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: 1.18 (0.25), residues: 1119 helix: 2.51 (0.26), residues: 405 sheet: 0.78 (0.36), residues: 186 loop : -0.62 (0.24), residues: 528 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP A 303 HIS 0.002 0.001 HIS B 24 PHE 0.013 0.002 PHE A 277 TYR 0.014 0.001 TYR A 202 ARG 0.003 0.001 ARG A 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 102 residues out of total 1008 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 81 time to evaluate : 0.950 Fit side-chains REVERT: A 188 ASP cc_start: 0.7482 (m-30) cc_final: 0.7152 (m-30) outliers start: 21 outliers final: 14 residues processed: 93 average time/residue: 0.1479 time to fit residues: 21.3008 Evaluate side-chains 88 residues out of total 1008 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 74 time to evaluate : 1.021 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 MET Chi-restraints excluded: chain A residue 205 ILE Chi-restraints excluded: chain A residue 263 ASP Chi-restraints excluded: chain A residue 287 VAL Chi-restraints excluded: chain A residue 357 LYS 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 1 optimal weight: 1.9990 chunk 79 optimal weight: 0.5980 chunk 44 optimal weight: 0.0270 chunk 91 optimal weight: 0.9980 chunk 74 optimal weight: 2.9990 chunk 0 optimal weight: 1.9990 chunk 54 optimal weight: 0.6980 chunk 96 optimal weight: 1.9990 chunk 27 optimal weight: 3.9990 chunk 36 optimal weight: 1.9990 chunk 21 optimal weight: 0.8980 overall best weight: 0.6438 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7869 moved from start: 0.3638 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= 0.214 Angle : 0.518 7.173 11508 Z= 0.278 Chirality : 0.046 0.181 1437 Planarity : 0.004 0.034 1464 Dihedral : 4.710 26.800 1347 Min Nonbonded Distance : 2.615 Molprobity Statistics. All-atom Clashscore : 3.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.65 % Favored : 95.35 % 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: 1.22 (0.25), residues: 1119 helix: 2.64 (0.27), residues: 405 sheet: 0.80 (0.36), residues: 186 loop : -0.68 (0.25), residues: 528 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP A 303 HIS 0.001 0.000 HIS C 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 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 98 residues out of total 1008 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 78 time to evaluate : 0.974 Fit side-chains REVERT: B 247 ASP cc_start: 0.7789 (t0) cc_final: 0.7580 (t0) REVERT: B 330 GLU cc_start: 0.7212 (pm20) cc_final: 0.6886 (pm20) REVERT: B 357 LYS cc_start: 0.4581 (OUTLIER) cc_final: 0.4377 (tppt) REVERT: C 357 LYS cc_start: 0.4592 (OUTLIER) cc_final: 0.4227 (tppt) outliers start: 20 outliers final: 12 residues processed: 90 average time/residue: 0.1507 time to fit residues: 20.9192 Evaluate side-chains 88 residues out of total 1008 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 74 time to evaluate : 0.968 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 MET Chi-restraints excluded: chain A residue 205 ILE Chi-restraints excluded: chain A residue 263 ASP 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 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 Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 62 optimal weight: 2.9990 chunk 26 optimal weight: 1.9990 chunk 107 optimal weight: 0.9990 chunk 89 optimal weight: 1.9990 chunk 49 optimal weight: 0.8980 chunk 8 optimal weight: 0.3980 chunk 35 optimal weight: 2.9990 chunk 56 optimal weight: 0.9980 chunk 103 optimal weight: 2.9990 chunk 12 optimal weight: 0.9990 chunk 61 optimal weight: 2.9990 overall best weight: 0.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7910 moved from start: 0.3876 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 8433 Z= 0.273 Angle : 0.539 6.876 11508 Z= 0.287 Chirality : 0.046 0.144 1437 Planarity : 0.004 0.037 1464 Dihedral : 4.715 25.530 1347 Min Nonbonded Distance : 2.619 Molprobity Statistics. All-atom Clashscore : 3.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.18 % Favored : 94.82 % Rotamer: Outliers : 2.36 % Allowed : 10.32 % Favored : 87.31 % 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: 1.10 (0.25), residues: 1119 helix: 2.76 (0.27), residues: 393 sheet: 0.73 (0.37), residues: 186 loop : -0.88 (0.24), residues: 540 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 0.012 0.002 PHE B 230 TYR 0.014 0.001 TYR A 202 ARG 0.004 0.001 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 101 residues out of total 1008 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 82 time to evaluate : 1.066 Fit side-chains REVERT: A 52 MET cc_start: 0.7888 (OUTLIER) cc_final: 0.7438 (ttm) REVERT: A 357 LYS cc_start: 0.5176 (OUTLIER) cc_final: 0.4806 (tppt) REVERT: B 330 GLU cc_start: 0.7283 (pm20) cc_final: 0.6963 (pm20) REVERT: C 357 LYS cc_start: 0.4248 (OUTLIER) cc_final: 0.3957 (ttpt) outliers start: 19 outliers final: 8 residues processed: 93 average time/residue: 0.1702 time to fit residues: 24.1989 Evaluate side-chains 87 residues out of total 1008 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 76 time to evaluate : 1.041 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 MET 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 313 THR 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 357 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 78 optimal weight: 0.4980 chunk 60 optimal weight: 0.6980 chunk 90 optimal weight: 1.9990 chunk 59 optimal weight: 0.6980 chunk 106 optimal weight: 4.9990 chunk 66 optimal weight: 3.9990 chunk 65 optimal weight: 0.7980 chunk 49 optimal weight: 0.9990 chunk 42 optimal weight: 0.7980 chunk 63 optimal weight: 0.5980 chunk 32 optimal weight: 5.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7893 moved from start: 0.3998 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 8433 Z= 0.222 Angle : 0.530 9.081 11508 Z= 0.284 Chirality : 0.046 0.196 1437 Planarity : 0.004 0.038 1464 Dihedral : 4.578 25.174 1343 Min Nonbonded Distance : 2.580 Molprobity Statistics. All-atom Clashscore : 3.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.47 % Favored : 95.53 % Rotamer: Outliers : 2.11 % Allowed : 9.83 % 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: 0.99 (0.25), residues: 1119 helix: 2.49 (0.27), residues: 408 sheet: 0.74 (0.36), residues: 186 loop : -0.91 (0.25), residues: 525 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.003 TRP C 303 HIS 0.001 0.000 HIS B 24 PHE 0.010 0.001 PHE B 230 TYR 0.019 0.001 TYR A 427 ARG 0.003 0.000 ARG C 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 99 residues out of total 1008 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 82 time to evaluate : 0.991 Fit side-chains REVERT: A 52 MET cc_start: 0.7872 (OUTLIER) cc_final: 0.7433 (ttm) REVERT: B 330 GLU cc_start: 0.7213 (pm20) cc_final: 0.6936 (pm20) outliers start: 17 outliers final: 8 residues processed: 91 average time/residue: 0.1409 time to fit residues: 20.3813 Evaluate side-chains 86 residues out of total 1008 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 77 time to evaluate : 0.971 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 MET Chi-restraints excluded: chain A residue 205 ILE Chi-restraints excluded: chain A residue 287 VAL Chi-restraints excluded: chain B residue 205 ILE Chi-restraints excluded: chain B residue 313 THR Chi-restraints excluded: chain C residue 166 VAL Chi-restraints excluded: chain C residue 205 ILE Chi-restraints excluded: chain C residue 366 SER 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 21 optimal weight: 1.9990 chunk 20 optimal weight: 0.8980 chunk 68 optimal weight: 0.4980 chunk 72 optimal weight: 4.9990 chunk 52 optimal weight: 0.8980 chunk 9 optimal weight: 0.9990 chunk 84 optimal weight: 0.9990 chunk 97 optimal weight: 2.9990 chunk 102 optimal weight: 0.9980 chunk 93 optimal weight: 0.6980 chunk 99 optimal weight: 2.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7912 moved from start: 0.4155 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 8433 Z= 0.256 Angle : 0.541 8.638 11508 Z= 0.287 Chirality : 0.046 0.182 1437 Planarity : 0.004 0.042 1464 Dihedral : 4.445 17.781 1335 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 2.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.00 % Favored : 95.00 % Rotamer: Outliers : 1.87 % Allowed : 10.07 % 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: 0.86 (0.25), residues: 1119 helix: 2.43 (0.27), residues: 408 sheet: 0.71 (0.37), residues: 186 loop : -1.05 (0.24), residues: 525 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.003 TRP C 303 HIS 0.001 0.000 HIS B 24 PHE 0.011 0.002 PHE B 230 TYR 0.014 0.001 TYR A 202 ARG 0.003 0.000 ARG B 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 94 residues out of total 1008 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 79 time to evaluate : 0.972 Fit side-chains REVERT: B 330 GLU cc_start: 0.7276 (pm20) cc_final: 0.6977 (pm20) outliers start: 15 outliers final: 8 residues processed: 86 average time/residue: 0.1291 time to fit residues: 18.2572 Evaluate side-chains 85 residues out of total 1008 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 77 time to evaluate : 0.990 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 MET Chi-restraints excluded: chain A residue 205 ILE Chi-restraints excluded: chain A residue 287 VAL Chi-restraints excluded: chain B residue 205 ILE Chi-restraints excluded: chain B residue 313 THR Chi-restraints excluded: chain C residue 166 VAL Chi-restraints excluded: chain C residue 205 ILE Chi-restraints excluded: chain C residue 366 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 102 optimal weight: 0.0030 chunk 60 optimal weight: 0.8980 chunk 43 optimal weight: 0.6980 chunk 78 optimal weight: 0.9980 chunk 30 optimal weight: 3.9990 chunk 90 optimal weight: 1.9990 chunk 94 optimal weight: 1.9990 chunk 99 optimal weight: 0.1980 chunk 65 optimal weight: 1.9990 chunk 105 optimal weight: 0.7980 chunk 64 optimal weight: 0.0980 overall best weight: 0.3590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7858 moved from start: 0.4248 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 8433 Z= 0.152 Angle : 0.503 8.832 11508 Z= 0.263 Chirality : 0.045 0.137 1437 Planarity : 0.004 0.040 1464 Dihedral : 4.200 15.187 1335 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 3.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.38 % Favored : 95.62 % Rotamer: Outliers : 0.87 % Allowed : 11.07 % 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: 1.04 (0.25), residues: 1119 helix: 2.54 (0.27), residues: 408 sheet: 0.81 (0.37), residues: 186 loop : -0.91 (0.25), residues: 525 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.003 TRP C 303 HIS 0.002 0.001 HIS C 253 PHE 0.007 0.001 PHE B 230 TYR 0.020 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 88 residues out of total 1008 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 81 time to evaluate : 0.977 Fit side-chains REVERT: B 330 GLU cc_start: 0.7179 (pm20) cc_final: 0.6878 (pm20) REVERT: C 207 THR cc_start: 0.8690 (m) cc_final: 0.8242 (m) outliers start: 7 outliers final: 7 residues processed: 83 average time/residue: 0.1360 time to fit residues: 18.2937 Evaluate side-chains 84 residues out of total 1008 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 77 time to evaluate : 0.896 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 MET Chi-restraints excluded: chain A residue 205 ILE Chi-restraints excluded: chain A residue 287 VAL Chi-restraints excluded: chain B residue 205 ILE Chi-restraints excluded: chain B residue 313 THR Chi-restraints excluded: chain C residue 52 MET Chi-restraints excluded: chain C residue 205 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 50 optimal weight: 0.7980 chunk 73 optimal weight: 0.9980 chunk 110 optimal weight: 1.9990 chunk 101 optimal weight: 0.9990 chunk 88 optimal weight: 0.8980 chunk 9 optimal weight: 0.2980 chunk 68 optimal weight: 0.0970 chunk 53 optimal weight: 1.9990 chunk 69 optimal weight: 0.2980 chunk 93 optimal weight: 0.6980 chunk 26 optimal weight: 0.8980 overall best weight: 0.4378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7867 moved from start: 0.4316 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= 0.169 Angle : 0.507 8.782 11508 Z= 0.265 Chirality : 0.045 0.145 1437 Planarity : 0.004 0.043 1464 Dihedral : 4.117 14.775 1335 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 2.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.74 % Favored : 95.26 % Rotamer: Outliers : 1.12 % Allowed : 10.70 % 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: 1.04 (0.25), residues: 1119 helix: 2.52 (0.27), residues: 408 sheet: 0.85 (0.37), residues: 186 loop : -0.90 (0.25), residues: 525 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP C 303 HIS 0.001 0.000 HIS C 253 PHE 0.009 0.001 PHE B 230 TYR 0.017 0.001 TYR B 345 ARG 0.002 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 87 residues out of total 1008 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 78 time to evaluate : 1.032 Fit side-chains REVERT: B 330 GLU cc_start: 0.7255 (pm20) cc_final: 0.6947 (pm20) REVERT: C 207 THR cc_start: 0.8668 (m) cc_final: 0.8235 (m) outliers start: 9 outliers final: 7 residues processed: 82 average time/residue: 0.1323 time to fit residues: 17.7833 Evaluate side-chains 85 residues out of total 1008 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 78 time to evaluate : 1.020 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 MET Chi-restraints excluded: chain A residue 205 ILE Chi-restraints excluded: chain A residue 287 VAL Chi-restraints excluded: chain B residue 205 ILE Chi-restraints excluded: chain B residue 313 THR Chi-restraints excluded: chain C residue 52 MET Chi-restraints excluded: chain C residue 205 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 81 optimal weight: 7.9990 chunk 13 optimal weight: 0.6980 chunk 24 optimal weight: 0.7980 chunk 88 optimal weight: 0.8980 chunk 36 optimal weight: 0.8980 chunk 90 optimal weight: 0.5980 chunk 11 optimal weight: 1.9990 chunk 16 optimal weight: 0.8980 chunk 77 optimal weight: 1.9990 chunk 5 optimal weight: 0.6980 chunk 63 optimal weight: 0.9990 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 = 0.3428 r_free = 0.3428 target = 0.126793 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3129 r_free = 0.3129 target = 0.103133 restraints weight = 10666.572| |-----------------------------------------------------------------------------| r_work (start): 0.3121 rms_B_bonded: 1.87 r_work: 0.3005 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.2866 rms_B_bonded: 4.21 restraints_weight: 0.2500 r_work (final): 0.2866 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8261 moved from start: 0.4326 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 8433 Z= 0.237 Angle : 0.533 8.746 11508 Z= 0.280 Chirality : 0.046 0.151 1437 Planarity : 0.004 0.045 1464 Dihedral : 4.265 15.625 1335 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 2.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.74 % Favored : 95.26 % Rotamer: Outliers : 1.12 % Allowed : 10.70 % 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: 0.93 (0.25), residues: 1119 helix: 2.46 (0.27), residues: 408 sheet: 0.76 (0.36), residues: 186 loop : -0.98 (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 0.011 0.002 PHE B 230 TYR 0.018 0.001 TYR B 345 ARG 0.002 0.000 ARG B 258 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2046.02 seconds wall clock time: 37 minutes 7.87 seconds (2227.87 seconds total)