Starting phenix.real_space_refine on Tue Apr 29 03:42:31 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8tvg_41641/04_2025/8tvg_41641.cif Found real_map, /net/cci-nas-00/data/ceres_data/8tvg_41641/04_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_41641/04_2025/8tvg_41641.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8tvg_41641/04_2025/8tvg_41641.map" model { file = "/net/cci-nas-00/data/ceres_data/8tvg_41641/04_2025/8tvg_41641.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8tvg_41641/04_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): 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/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: 7.82, per 1000 atoms: 0.94 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: 2.44 Conformation dependent library (CDL) restraints added in 1.1 seconds 2238 Ramachandran restraints generated. 1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2112 Finding SS restraints... Secondary structure from input PDB file: 27 helices and 18 sheets defined 36.9% alpha, 34.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.16 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: 2.87 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: 140.690 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: 0.370 Check model and map are aligned: 0.070 Set scattering table: 0.090 Process input model: 26.800 Find NCS groups from input model: 0.170 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:2.990 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 171.220 ------------------------------------------------------------------------------- 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 0.151 8454 Z= 0.698 Angle : 1.377 10.244 11556 Z= 0.940 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 Details of bonding type rmsd link_NAG-ASN : bond 0.06671 ( 6) link_NAG-ASN : angle 2.15995 ( 18) hydrogen bonds : bond 0.18323 ( 399) hydrogen bonds : angle 7.65001 ( 1182) SS BOND : bond 0.06804 ( 15) SS BOND : angle 4.84958 ( 30) covalent geometry : bond 0.01251 ( 8433) covalent geometry : angle 1.35501 (11508) *********************** 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 : 1.042 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: 0.2223 time to fit residues: 55.5031 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 : 1.202 ------------------------------------------------------------------------------- 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 8454 Z= 0.171 Angle : 0.689 7.998 11556 Z= 0.356 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 Details of bonding type rmsd link_NAG-ASN : bond 0.01737 ( 6) link_NAG-ASN : angle 4.74145 ( 18) hydrogen bonds : bond 0.05564 ( 399) hydrogen bonds : angle 4.85364 ( 1182) SS BOND : bond 0.00359 ( 15) SS BOND : angle 1.74724 ( 30) covalent geometry : bond 0.00399 ( 8433) covalent geometry : angle 0.65869 (11508) *********************** 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 : 0.943 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: 0.1688 time to fit residues: 30.1200 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 : 0.990 ------------------------------------------------------------------------------- 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 8454 Z= 0.153 Angle : 0.576 7.738 11556 Z= 0.308 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 Details of bonding type rmsd link_NAG-ASN : bond 0.01210 ( 6) link_NAG-ASN : angle 2.89479 ( 18) hydrogen bonds : bond 0.04780 ( 399) hydrogen bonds : angle 4.33600 ( 1182) SS BOND : bond 0.00430 ( 15) SS BOND : angle 1.56943 ( 30) covalent geometry : bond 0.00363 ( 8433) covalent geometry : angle 0.56046 (11508) *********************** 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 : 1.554 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: 0.2292 time to fit residues: 35.0132 Evaluate side-chains 90 residues out of total 1008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 77 time to evaluate : 1.176 ------------------------------------------------------------------------------- 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 8454 Z= 0.193 Angle : 0.592 6.398 11556 Z= 0.315 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 Details of bonding type rmsd link_NAG-ASN : bond 0.00662 ( 6) link_NAG-ASN : angle 2.36257 ( 18) hydrogen bonds : bond 0.05192 ( 399) hydrogen bonds : angle 4.40247 ( 1182) SS BOND : bond 0.00467 ( 15) SS BOND : angle 1.28156 ( 30) covalent geometry : bond 0.00481 ( 8433) covalent geometry : angle 0.58170 (11508) *********************** 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 : 0.970 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: 0.1503 time to fit residues: 23.1090 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 : 0.935 ------------------------------------------------------------------------------- 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: 0.0570 chunk 3 optimal weight: 0.8980 chunk 72 optimal weight: 0.8980 chunk 85 optimal weight: 0.5980 overall best weight: 0.0852 ------------------------------------------------------------------------------- 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 = 0.3591 r_free = 0.3591 target = 0.137870 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.114596 restraints weight = 10606.061| |-----------------------------------------------------------------------------| r_work (start): 0.3305 rms_B_bonded: 1.90 r_work: 0.3186 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.3045 rms_B_bonded: 4.31 restraints_weight: 0.2500 r_work (final): 0.3045 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8178 moved from start: 0.3754 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.047 8454 Z= 0.097 Angle : 0.493 6.999 11556 Z= 0.262 Chirality : 0.044 0.149 1437 Planarity : 0.004 0.031 1464 Dihedral : 4.528 27.072 1347 Min Nonbonded Distance : 2.625 Molprobity Statistics. All-atom Clashscore : 3.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.29 % Favored : 95.71 % 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: 1.30 (0.25), residues: 1119 helix: 2.68 (0.27), residues: 405 sheet: 0.95 (0.37), residues: 186 loop : -0.66 (0.24), residues: 528 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.003 TRP C 303 HIS 0.002 0.001 HIS C 24 PHE 0.007 0.001 PHE B 230 TYR 0.011 0.001 TYR C 202 ARG 0.002 0.000 ARG B 258 Details of bonding type rmsd link_NAG-ASN : bond 0.00587 ( 6) link_NAG-ASN : angle 2.15418 ( 18) hydrogen bonds : bond 0.03608 ( 399) hydrogen bonds : angle 3.83874 ( 1182) SS BOND : bond 0.00189 ( 15) SS BOND : angle 1.24211 ( 30) covalent geometry : bond 0.00190 ( 8433) covalent geometry : angle 0.48286 (11508) *********************** 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 111 residues out of total 1008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 91 time to evaluate : 1.031 Fit side-chains revert: symmetry clash REVERT: A 357 LYS cc_start: 0.6050 (OUTLIER) cc_final: 0.4820 (tppt) REVERT: A 377 LEU cc_start: 0.8286 (OUTLIER) cc_final: 0.8005 (mm) REVERT: B 188 ASP cc_start: 0.8207 (m-30) cc_final: 0.7709 (m-30) REVERT: B 357 LYS cc_start: 0.5892 (OUTLIER) cc_final: 0.4736 (tppt) REVERT: C 207 THR cc_start: 0.8789 (m) cc_final: 0.8369 (m) REVERT: C 303 TRP cc_start: 0.8765 (m100) cc_final: 0.8556 (m100) REVERT: C 357 LYS cc_start: 0.5522 (OUTLIER) cc_final: 0.4210 (tppt) REVERT: C 362 LYS cc_start: 0.8651 (tttt) cc_final: 0.8275 (tttm) outliers start: 20 outliers final: 10 residues processed: 102 average time/residue: 0.2000 time to fit residues: 30.6690 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 : 1.173 ------------------------------------------------------------------------------- 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: 0.5980 chunk 101 optimal weight: 4.9990 chunk 54 optimal weight: 1.9990 chunk 12 optimal weight: 1.9990 chunk 51 optimal weight: 0.9980 chunk 95 optimal weight: 5.9990 chunk 7 optimal weight: 6.9990 chunk 78 optimal weight: 0.9980 chunk 40 optimal weight: 0.4980 chunk 36 optimal weight: 1.9990 chunk 66 optimal weight: 0.9980 overall best weight: 0.8180 ------------------------------------------------------------------------------- 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 = 0.3523 r_free = 0.3523 target = 0.132396 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3226 r_free = 0.3226 target = 0.108540 restraints weight = 10798.447| |-----------------------------------------------------------------------------| r_work (start): 0.3203 rms_B_bonded: 1.93 r_work: 0.3084 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.2938 rms_B_bonded: 4.30 restraints_weight: 0.2500 r_work (final): 0.2938 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8264 moved from start: 0.3869 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 8454 Z= 0.159 Angle : 0.539 6.694 11556 Z= 0.285 Chirality : 0.046 0.140 1437 Planarity : 0.004 0.037 1464 Dihedral : 4.588 25.814 1347 Min Nonbonded Distance : 2.559 Molprobity Statistics. All-atom Clashscore : 3.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.00 % Favored : 95.00 % Rotamer: Outliers : 2.36 % Allowed : 10.20 % Favored : 87.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.14 (0.25), residues: 1119 helix: 2.56 (0.27), residues: 408 sheet: 0.82 (0.36), residues: 186 loop : -0.77 (0.25), residues: 525 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A 303 HIS 0.001 0.000 HIS B 24 PHE 0.012 0.002 PHE B 230 TYR 0.014 0.001 TYR A 202 ARG 0.003 0.000 ARG B 258 Details of bonding type rmsd link_NAG-ASN : bond 0.00562 ( 6) link_NAG-ASN : angle 2.15028 ( 18) hydrogen bonds : bond 0.04570 ( 399) hydrogen bonds : angle 4.08056 ( 1182) SS BOND : bond 0.00429 ( 15) SS BOND : angle 1.25151 ( 30) covalent geometry : bond 0.00396 ( 8433) covalent geometry : angle 0.52998 (11508) *********************** 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 99 residues out of total 1008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 80 time to evaluate : 0.915 Fit side-chains REVERT: A 357 LYS cc_start: 0.5786 (OUTLIER) cc_final: 0.4686 (tppt) REVERT: A 377 LEU cc_start: 0.8283 (OUTLIER) cc_final: 0.8039 (mm) REVERT: B 188 ASP cc_start: 0.8292 (m-30) cc_final: 0.7754 (m-30) REVERT: B 247 ASP cc_start: 0.8580 (t0) cc_final: 0.8380 (t0) REVERT: B 357 LYS cc_start: 0.5834 (OUTLIER) cc_final: 0.4725 (ttpt) REVERT: C 207 THR cc_start: 0.8871 (m) cc_final: 0.8443 (m) REVERT: C 357 LYS cc_start: 0.5343 (OUTLIER) cc_final: 0.4133 (ttpt) REVERT: C 362 LYS cc_start: 0.8667 (tttt) cc_final: 0.8236 (tttm) outliers start: 19 outliers final: 8 residues processed: 93 average time/residue: 0.1800 time to fit residues: 25.4124 Evaluate side-chains 88 residues out of total 1008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 76 time to evaluate : 0.982 ------------------------------------------------------------------------------- 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 263 ASP Chi-restraints excluded: chain B residue 313 THR Chi-restraints excluded: chain B residue 357 LYS Chi-restraints excluded: chain B residue 432 GLU Chi-restraints excluded: chain C residue 205 ILE 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 17 optimal weight: 0.9990 chunk 98 optimal weight: 4.9990 chunk 15 optimal weight: 0.1980 chunk 44 optimal weight: 6.9990 chunk 48 optimal weight: 0.9990 chunk 75 optimal weight: 0.9980 chunk 52 optimal weight: 1.9990 chunk 0 optimal weight: 2.9990 chunk 76 optimal weight: 2.9990 chunk 94 optimal weight: 0.8980 chunk 10 optimal weight: 0.5980 overall best weight: 0.7382 ------------------------------------------------------------------------------- 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 = 0.3526 r_free = 0.3526 target = 0.132780 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3229 r_free = 0.3229 target = 0.108843 restraints weight = 10749.924| |-----------------------------------------------------------------------------| r_work (start): 0.3209 rms_B_bonded: 1.93 r_work: 0.3085 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.2941 rms_B_bonded: 4.35 restraints_weight: 0.2500 r_work (final): 0.2941 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8266 moved from start: 0.3974 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 8454 Z= 0.152 Angle : 0.551 8.531 11556 Z= 0.292 Chirality : 0.046 0.216 1437 Planarity : 0.004 0.036 1464 Dihedral : 4.606 26.382 1347 Min Nonbonded Distance : 2.565 Molprobity Statistics. All-atom Clashscore : 3.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.83 % Favored : 95.17 % Rotamer: Outliers : 2.11 % Allowed : 9.95 % Favored : 87.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.98 (0.25), residues: 1119 helix: 2.46 (0.27), residues: 408 sheet: 0.79 (0.37), residues: 186 loop : -0.92 (0.24), residues: 525 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 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 427 ARG 0.003 0.000 ARG C 258 Details of bonding type rmsd link_NAG-ASN : bond 0.00464 ( 6) link_NAG-ASN : angle 2.28399 ( 18) hydrogen bonds : bond 0.04503 ( 399) hydrogen bonds : angle 4.09283 ( 1182) SS BOND : bond 0.00403 ( 15) SS BOND : angle 1.90976 ( 30) covalent geometry : bond 0.00373 ( 8433) covalent geometry : angle 0.53597 (11508) *********************** 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 95 residues out of total 1008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 78 time to evaluate : 0.939 Fit side-chains REVERT: A 377 LEU cc_start: 0.8305 (OUTLIER) cc_final: 0.8056 (mm) REVERT: B 188 ASP cc_start: 0.8270 (m-30) cc_final: 0.7956 (m-30) REVERT: B 330 GLU cc_start: 0.7319 (pm20) cc_final: 0.7064 (pm20) REVERT: B 357 LYS cc_start: 0.5857 (OUTLIER) cc_final: 0.4756 (ttpt) REVERT: C 357 LYS cc_start: 0.5251 (OUTLIER) cc_final: 0.4212 (ttpt) REVERT: C 362 LYS cc_start: 0.8655 (tttt) cc_final: 0.8308 (tttm) outliers start: 17 outliers final: 9 residues processed: 91 average time/residue: 0.1810 time to fit residues: 26.0670 Evaluate side-chains 90 residues out of total 1008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 78 time to evaluate : 1.037 ------------------------------------------------------------------------------- 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 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 205 ILE Chi-restraints excluded: chain C residue 357 LYS Chi-restraints excluded: chain C residue 366 SER 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: 0.5980 chunk 95 optimal weight: 6.9990 chunk 12 optimal weight: 0.9980 chunk 51 optimal weight: 0.3980 chunk 69 optimal weight: 3.9990 chunk 109 optimal weight: 3.9990 chunk 27 optimal weight: 2.9990 chunk 58 optimal weight: 0.0970 chunk 82 optimal weight: 0.5980 chunk 102 optimal weight: 1.9990 overall best weight: 0.5378 ------------------------------------------------------------------------------- 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 = 0.3535 r_free = 0.3535 target = 0.133551 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3235 r_free = 0.3235 target = 0.109315 restraints weight = 10886.292| |-----------------------------------------------------------------------------| r_work (start): 0.3197 rms_B_bonded: 1.97 r_work: 0.3081 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.2936 rms_B_bonded: 4.33 restraints_weight: 0.2500 r_work (final): 0.2936 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8246 moved from start: 0.4069 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 8454 Z= 0.126 Angle : 0.520 7.665 11556 Z= 0.275 Chirality : 0.045 0.157 1437 Planarity : 0.004 0.037 1464 Dihedral : 4.499 26.415 1347 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 3.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.74 % Favored : 95.26 % 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: 1.08 (0.25), residues: 1119 helix: 2.78 (0.27), residues: 393 sheet: 0.82 (0.36), residues: 186 loop : -0.95 (0.24), residues: 540 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.003 TRP C 303 HIS 0.001 0.000 HIS A 253 PHE 0.010 0.001 PHE B 230 TYR 0.013 0.001 TYR A 202 ARG 0.002 0.000 ARG C 258 Details of bonding type rmsd link_NAG-ASN : bond 0.00679 ( 6) link_NAG-ASN : angle 2.27066 ( 18) hydrogen bonds : bond 0.04200 ( 399) hydrogen bonds : angle 3.98277 ( 1182) SS BOND : bond 0.00597 ( 15) SS BOND : angle 1.42366 ( 30) covalent geometry : bond 0.00298 ( 8433) covalent geometry : angle 0.50847 (11508) *********************** 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 95 residues out of total 1008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 81 time to evaluate : 0.938 Fit side-chains REVERT: A 377 LEU cc_start: 0.8274 (OUTLIER) cc_final: 0.8033 (mm) REVERT: B 330 GLU cc_start: 0.7213 (pm20) cc_final: 0.6965 (pm20) REVERT: B 357 LYS cc_start: 0.5608 (OUTLIER) cc_final: 0.4646 (ttpt) REVERT: C 207 THR cc_start: 0.8845 (m) cc_final: 0.8428 (m) REVERT: C 357 LYS cc_start: 0.5324 (OUTLIER) cc_final: 0.4301 (ttpt) outliers start: 14 outliers final: 7 residues processed: 90 average time/residue: 0.1534 time to fit residues: 21.2405 Evaluate side-chains 87 residues out of total 1008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 77 time to evaluate : 1.011 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 205 ILE Chi-restraints excluded: chain A residue 287 VAL Chi-restraints excluded: chain A residue 357 LYS Chi-restraints excluded: chain A residue 377 LEU Chi-restraints excluded: chain B residue 205 ILE Chi-restraints excluded: chain B residue 313 THR Chi-restraints excluded: chain B residue 357 LYS Chi-restraints excluded: chain C residue 166 VAL Chi-restraints excluded: chain C residue 205 ILE Chi-restraints excluded: chain C residue 357 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 54 optimal weight: 0.8980 chunk 65 optimal weight: 0.4980 chunk 86 optimal weight: 1.9990 chunk 4 optimal weight: 0.7980 chunk 43 optimal weight: 0.7980 chunk 107 optimal weight: 0.6980 chunk 91 optimal weight: 1.9990 chunk 12 optimal weight: 0.9990 chunk 7 optimal weight: 0.0670 chunk 67 optimal weight: 5.9990 chunk 89 optimal weight: 0.7980 overall best weight: 0.5718 ------------------------------------------------------------------------------- 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 = 0.3534 r_free = 0.3534 target = 0.133375 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3236 r_free = 0.3236 target = 0.109448 restraints weight = 10938.889| |-----------------------------------------------------------------------------| r_work (start): 0.3230 rms_B_bonded: 1.95 r_work: 0.3115 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.2973 rms_B_bonded: 4.30 restraints_weight: 0.2500 r_work (final): 0.2973 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8260 moved from start: 0.4171 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 8454 Z= 0.128 Angle : 0.522 8.924 11556 Z= 0.273 Chirality : 0.045 0.163 1437 Planarity : 0.004 0.040 1464 Dihedral : 4.446 26.689 1347 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 3.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.00 % Favored : 95.00 % Rotamer: Outliers : 1.74 % Allowed : 10.32 % 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: 1.05 (0.25), residues: 1119 helix: 2.76 (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 0.026 0.003 TRP C 303 HIS 0.001 0.000 HIS A 253 PHE 0.010 0.001 PHE B 230 TYR 0.013 0.001 TYR A 202 ARG 0.002 0.000 ARG B 258 Details of bonding type rmsd link_NAG-ASN : bond 0.00572 ( 6) link_NAG-ASN : angle 2.07747 ( 18) hydrogen bonds : bond 0.04165 ( 399) hydrogen bonds : angle 3.95680 ( 1182) SS BOND : bond 0.00505 ( 15) SS BOND : angle 1.36938 ( 30) covalent geometry : bond 0.00307 ( 8433) covalent geometry : angle 0.51153 (11508) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2238 Ramachandran restraints generated. 1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2238 Ramachandran restraints generated. 1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 1008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 78 time to evaluate : 0.997 Fit side-chains REVERT: A 377 LEU cc_start: 0.8345 (OUTLIER) cc_final: 0.8100 (mm) REVERT: B 330 GLU cc_start: 0.7152 (pm20) cc_final: 0.6896 (pm20) REVERT: B 357 LYS cc_start: 0.5302 (OUTLIER) cc_final: 0.4562 (ttpt) REVERT: C 207 THR cc_start: 0.8832 (m) cc_final: 0.8413 (m) REVERT: C 357 LYS cc_start: 0.5203 (OUTLIER) cc_final: 0.4423 (ttpt) outliers start: 14 outliers final: 8 residues processed: 88 average time/residue: 0.1507 time to fit residues: 20.5974 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 : 0.980 ------------------------------------------------------------------------------- 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 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 90 optimal weight: 1.9990 chunk 102 optimal weight: 0.6980 chunk 42 optimal weight: 0.8980 chunk 73 optimal weight: 1.9990 chunk 86 optimal weight: 1.9990 chunk 67 optimal weight: 0.9990 chunk 93 optimal weight: 1.9990 chunk 65 optimal weight: 0.1980 chunk 17 optimal weight: 0.9990 chunk 39 optimal weight: 2.9990 chunk 49 optimal weight: 0.9980 overall best weight: 0.7582 ------------------------------------------------------------------------------- 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 = 0.3521 r_free = 0.3521 target = 0.132363 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3222 r_free = 0.3222 target = 0.108488 restraints weight = 10809.860| |-----------------------------------------------------------------------------| r_work (start): 0.3217 rms_B_bonded: 1.93 r_work: 0.3101 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.2959 rms_B_bonded: 4.27 restraints_weight: 0.2500 r_work (final): 0.2959 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8278 moved from start: 0.4226 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 8454 Z= 0.153 Angle : 0.550 9.158 11556 Z= 0.288 Chirality : 0.046 0.178 1437 Planarity : 0.004 0.041 1464 Dihedral : 4.578 26.527 1347 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 3.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.65 % Favored : 95.35 % 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: 0.94 (0.25), residues: 1119 helix: 2.68 (0.27), residues: 393 sheet: 0.78 (0.37), residues: 186 loop : -1.07 (0.24), residues: 540 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 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 Details of bonding type rmsd link_NAG-ASN : bond 0.00489 ( 6) link_NAG-ASN : angle 1.87572 ( 18) hydrogen bonds : bond 0.04467 ( 399) hydrogen bonds : angle 4.05607 ( 1182) SS BOND : bond 0.00492 ( 15) SS BOND : angle 1.74361 ( 30) covalent geometry : bond 0.00378 ( 8433) covalent geometry : angle 0.53907 (11508) ********************** 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 89 residues out of total 1008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 74 time to evaluate : 1.047 Fit side-chains REVERT: A 377 LEU cc_start: 0.8376 (OUTLIER) cc_final: 0.8174 (mm) REVERT: B 188 ASP cc_start: 0.8367 (m-30) cc_final: 0.7923 (t0) REVERT: B 357 LYS cc_start: 0.5286 (OUTLIER) cc_final: 0.4592 (ttpt) REVERT: C 188 ASP cc_start: 0.8341 (m-30) cc_final: 0.8127 (t0) REVERT: C 207 THR cc_start: 0.8869 (m) cc_final: 0.8440 (m) REVERT: C 357 LYS cc_start: 0.5153 (OUTLIER) cc_final: 0.4407 (tppt) outliers start: 15 outliers final: 9 residues processed: 85 average time/residue: 0.1630 time to fit residues: 21.2874 Evaluate side-chains 85 residues out of total 1008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 73 time to evaluate : 1.055 ------------------------------------------------------------------------------- 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 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 Chi-restraints excluded: chain C residue 366 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 10 optimal weight: 0.5980 chunk 77 optimal weight: 0.9980 chunk 1 optimal weight: 1.9990 chunk 24 optimal weight: 3.9990 chunk 58 optimal weight: 0.6980 chunk 72 optimal weight: 1.9990 chunk 2 optimal weight: 1.9990 chunk 47 optimal weight: 0.5980 chunk 51 optimal weight: 0.0370 chunk 3 optimal weight: 0.7980 chunk 99 optimal weight: 2.9990 overall best weight: 0.5458 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3533 r_free = 0.3533 target = 0.133356 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3241 r_free = 0.3241 target = 0.109851 restraints weight = 10877.526| |-----------------------------------------------------------------------------| r_work (start): 0.3221 rms_B_bonded: 1.92 r_work: 0.3099 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.2956 rms_B_bonded: 4.37 restraints_weight: 0.2500 r_work (final): 0.2956 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8258 moved from start: 0.4297 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 8454 Z= 0.126 Angle : 0.529 8.912 11556 Z= 0.277 Chirality : 0.045 0.158 1437 Planarity : 0.004 0.042 1464 Dihedral : 4.491 26.683 1347 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 3.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.65 % Favored : 95.35 % Rotamer: Outliers : 1.49 % Allowed : 10.70 % 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: 1.00 (0.25), residues: 1119 helix: 2.74 (0.27), residues: 393 sheet: 0.81 (0.37), residues: 186 loop : -1.05 (0.25), residues: 540 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.003 TRP C 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 B 258 Details of bonding type rmsd link_NAG-ASN : bond 0.00454 ( 6) link_NAG-ASN : angle 1.84679 ( 18) hydrogen bonds : bond 0.04108 ( 399) hydrogen bonds : angle 3.94735 ( 1182) SS BOND : bond 0.00384 ( 15) SS BOND : angle 1.73150 ( 30) covalent geometry : bond 0.00300 ( 8433) covalent geometry : angle 0.51771 (11508) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5612.77 seconds wall clock time: 100 minutes 3.27 seconds (6003.27 seconds total)