Starting phenix.real_space_refine on Fri Oct 10 18:08:20 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8tvg_41641/10_2025/8tvg_41641.cif Found real_map, /net/cci-nas-00/data/ceres_data/8tvg_41641/10_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 { model { file = "/net/cci-nas-00/data/ceres_data/8tvg_41641/10_2025/8tvg_41641.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8tvg_41641/10_2025/8tvg_41641.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8tvg_41641/10_2025/8tvg_41641.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8tvg_41641/10_2025/8tvg_41641.map" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5842/lib/python3.9/site-packages/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: {'ASP:plan': 15, 'ASN:plan1': 3, 'GLU:plan': 5} 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: {'ASP:plan': 15, 'ASN:plan1': 3, 'GLU:plan': 5} 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: {'ASP:plan': 15, 'ASN:plan1': 3, 'GLU:plan': 5} 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: 2.41, per 1000 atoms: 0.29 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: 0.89 Conformation dependent library (CDL) restraints added in 373.3 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 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: 0.39 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: 1.65 Time building geometry restraints manager: 1.16 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: 0.02 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: 11.940 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.160 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 10.600 Find NCS groups from input model: 0.070 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.350 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.200 ------------------------------------------------------------------------------- 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. 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 ARG 0.005 0.001 ARG B 314 TYR 0.035 0.006 TYR C 415 PHE 0.007 0.002 PHE A 277 TRP 0.008 0.004 TRP C 303 HIS 0.003 0.001 HIS C 24 Details of bonding type rmsd covalent geometry : bond 0.01251 ( 8433) covalent geometry : angle 1.35501 (11508) SS BOND : bond 0.06804 ( 15) SS BOND : angle 4.84958 ( 30) hydrogen bonds : bond 0.18323 ( 399) hydrogen bonds : angle 7.65001 ( 1182) link_NAG-ASN : bond 0.06671 ( 6) link_NAG-ASN : angle 2.15995 ( 18) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2238 Ramachandran restraints generated. 1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2238 Ramachandran restraints generated. 1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 1008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 175 time to evaluate : 0.316 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: 0.0956 time to fit residues: 23.8407 Evaluate side-chains 92 residues out of total 1008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 89 time to evaluate : 0.337 ------------------------------------------------------------------------------- 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 108 optimal weight: 1.9990 chunk 49 optimal weight: 0.5980 chunk 97 optimal weight: 0.5980 chunk 53 optimal weight: 0.6980 chunk 5 optimal weight: 0.6980 chunk 33 optimal weight: 0.9980 chunk 65 optimal weight: 2.9990 chunk 62 optimal weight: 0.9980 chunk 51 optimal weight: 0.0060 chunk 100 optimal weight: 0.9980 chunk 106 optimal weight: 0.6980 overall best weight: 0.5196 ------------------------------------------------------------------------------- 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 = 0.3634 r_free = 0.3634 target = 0.140327 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.115212 restraints weight = 10789.349| |-----------------------------------------------------------------------------| r_work (start): 0.3305 rms_B_bonded: 2.12 r_work: 0.3171 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.3022 rms_B_bonded: 4.73 restraints_weight: 0.2500 r_work (final): 0.3022 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8140 moved from start: 0.2322 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 8454 Z= 0.150 Angle : 0.663 7.940 11556 Z= 0.343 Chirality : 0.047 0.157 1437 Planarity : 0.005 0.035 1464 Dihedral : 5.217 26.684 1347 Min Nonbonded Distance : 2.626 Molprobity Statistics. All-atom Clashscore : 3.37 Ramachandran Plot: Outliers : 0.27 % Allowed : 3.22 % Favored : 96.51 % Rotamer: Outliers : 1.99 % Allowed : 6.59 % Favored : 91.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.22 (0.24), residues: 1119 helix: 1.97 (0.25), residues: 393 sheet: 1.06 (0.37), residues: 186 loop : -0.11 (0.24), residues: 540 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG B 325 TYR 0.012 0.001 TYR A 202 PHE 0.010 0.001 PHE B 230 TRP 0.003 0.001 TRP A 303 HIS 0.003 0.001 HIS C 24 Details of bonding type rmsd covalent geometry : bond 0.00340 ( 8433) covalent geometry : angle 0.63889 (11508) SS BOND : bond 0.00338 ( 15) SS BOND : angle 1.65312 ( 30) hydrogen bonds : bond 0.05130 ( 399) hydrogen bonds : angle 4.75117 ( 1182) link_NAG-ASN : bond 0.00975 ( 6) link_NAG-ASN : angle 4.13068 ( 18) *********************** 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 128 residues out of total 1008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 112 time to evaluate : 0.344 Fit side-chains REVERT: A 188 ASP cc_start: 0.8002 (m-30) cc_final: 0.7757 (m-30) REVERT: A 303 TRP cc_start: 0.8683 (m100) cc_final: 0.8480 (m100) REVERT: C 303 TRP cc_start: 0.8704 (m100) cc_final: 0.8310 (m100) outliers start: 16 outliers final: 10 residues processed: 122 average time/residue: 0.0773 time to fit residues: 14.1765 Evaluate side-chains 95 residues out of total 1008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 85 time to evaluate : 0.363 ------------------------------------------------------------------------------- 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 64 optimal weight: 2.9990 chunk 43 optimal weight: 0.8980 chunk 98 optimal weight: 4.9990 chunk 86 optimal weight: 0.2980 chunk 52 optimal weight: 0.8980 chunk 73 optimal weight: 0.7980 chunk 42 optimal weight: 0.6980 chunk 8 optimal weight: 0.6980 chunk 46 optimal weight: 0.6980 chunk 63 optimal weight: 1.9990 chunk 1 optimal weight: 1.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 24 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3586 r_free = 0.3586 target = 0.136701 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3286 r_free = 0.3286 target = 0.112546 restraints weight = 10653.306| |-----------------------------------------------------------------------------| r_work (start): 0.3281 rms_B_bonded: 1.95 r_work: 0.3154 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.3008 rms_B_bonded: 4.42 restraints_weight: 0.2500 r_work (final): 0.3008 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8204 moved from start: 0.2938 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 8454 Z= 0.147 Angle : 0.557 6.608 11556 Z= 0.298 Chirality : 0.046 0.140 1437 Planarity : 0.004 0.029 1464 Dihedral : 4.871 27.018 1347 Min Nonbonded Distance : 2.597 Molprobity Statistics. All-atom Clashscore : 3.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.38 % Favored : 95.62 % Rotamer: Outliers : 2.99 % Allowed : 7.96 % Favored : 89.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.36 (0.25), residues: 1119 helix: 2.45 (0.27), residues: 405 sheet: 0.97 (0.36), residues: 186 loop : -0.36 (0.25), residues: 528 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 232 TYR 0.013 0.001 TYR A 202 PHE 0.011 0.001 PHE A 277 TRP 0.008 0.001 TRP B 303 HIS 0.002 0.001 HIS C 24 Details of bonding type rmsd covalent geometry : bond 0.00349 ( 8433) covalent geometry : angle 0.54446 (11508) SS BOND : bond 0.00182 ( 15) SS BOND : angle 1.12319 ( 30) hydrogen bonds : bond 0.04703 ( 399) hydrogen bonds : angle 4.28096 ( 1182) link_NAG-ASN : bond 0.00889 ( 6) link_NAG-ASN : angle 2.68415 ( 18) *********************** 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 108 residues out of total 1008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 84 time to evaluate : 0.321 Fit side-chains REVERT: A 377 LEU cc_start: 0.8305 (OUTLIER) cc_final: 0.8025 (mm) REVERT: C 207 THR cc_start: 0.8867 (m) cc_final: 0.8434 (m) REVERT: C 303 TRP cc_start: 0.8718 (m100) cc_final: 0.8384 (m100) outliers start: 24 outliers final: 14 residues processed: 98 average time/residue: 0.0724 time to fit residues: 10.9787 Evaluate side-chains 90 residues out of total 1008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 75 time to evaluate : 0.419 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 LEU 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 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 41 optimal weight: 0.5980 chunk 24 optimal weight: 0.0570 chunk 65 optimal weight: 0.9990 chunk 52 optimal weight: 1.9990 chunk 76 optimal weight: 2.9990 chunk 12 optimal weight: 0.9990 chunk 109 optimal weight: 3.9990 chunk 47 optimal weight: 0.5980 chunk 32 optimal weight: 4.9990 chunk 73 optimal weight: 0.6980 chunk 81 optimal weight: 6.9990 overall best weight: 0.5900 ------------------------------------------------------------------------------- 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 = 0.3574 r_free = 0.3574 target = 0.136209 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3275 r_free = 0.3275 target = 0.111861 restraints weight = 10683.326| |-----------------------------------------------------------------------------| r_work (start): 0.3254 rms_B_bonded: 1.96 r_work: 0.3131 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.2986 rms_B_bonded: 4.36 restraints_weight: 0.2500 r_work (final): 0.2986 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8210 moved from start: 0.3315 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 8454 Z= 0.135 Angle : 0.542 8.831 11556 Z= 0.288 Chirality : 0.045 0.165 1437 Planarity : 0.004 0.031 1464 Dihedral : 4.711 26.451 1347 Min Nonbonded Distance : 2.628 Molprobity Statistics. All-atom Clashscore : 3.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.83 % Favored : 95.17 % Rotamer: Outliers : 2.49 % Allowed : 9.58 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.34 (0.25), residues: 1119 helix: 2.78 (0.27), residues: 390 sheet: 0.88 (0.36), residues: 186 loop : -0.55 (0.24), residues: 543 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 258 TYR 0.013 0.001 TYR A 202 PHE 0.011 0.001 PHE B 230 TRP 0.007 0.002 TRP A 303 HIS 0.002 0.000 HIS B 24 Details of bonding type rmsd covalent geometry : bond 0.00322 ( 8433) covalent geometry : angle 0.53051 (11508) SS BOND : bond 0.00210 ( 15) SS BOND : angle 1.64827 ( 30) hydrogen bonds : bond 0.04382 ( 399) hydrogen bonds : angle 4.10538 ( 1182) link_NAG-ASN : bond 0.00483 ( 6) link_NAG-ASN : angle 2.05315 ( 18) *********************** 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 94 residues out of total 1008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 74 time to evaluate : 0.350 Fit side-chains REVERT: A 377 LEU cc_start: 0.8282 (OUTLIER) cc_final: 0.7982 (mm) REVERT: C 188 ASP cc_start: 0.8264 (m-30) cc_final: 0.8061 (t0) REVERT: C 303 TRP cc_start: 0.8814 (m100) cc_final: 0.8543 (m100) REVERT: C 357 LYS cc_start: 0.6192 (OUTLIER) cc_final: 0.4516 (tppt) outliers start: 20 outliers final: 11 residues processed: 88 average time/residue: 0.0724 time to fit residues: 9.9841 Evaluate side-chains 87 residues out of total 1008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 74 time to evaluate : 0.370 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 LEU 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 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 73 optimal weight: 0.4980 chunk 59 optimal weight: 0.8980 chunk 52 optimal weight: 0.7980 chunk 5 optimal weight: 1.9990 chunk 61 optimal weight: 5.9990 chunk 86 optimal weight: 1.9990 chunk 13 optimal weight: 0.2980 chunk 72 optimal weight: 3.9990 chunk 63 optimal weight: 0.6980 chunk 31 optimal weight: 0.0870 chunk 83 optimal weight: 0.9980 overall best weight: 0.4758 ------------------------------------------------------------------------------- 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 = 0.3569 r_free = 0.3569 target = 0.135937 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3275 r_free = 0.3275 target = 0.111972 restraints weight = 10723.371| |-----------------------------------------------------------------------------| r_work (start): 0.3255 rms_B_bonded: 1.95 r_work: 0.3134 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.2990 rms_B_bonded: 4.31 restraints_weight: 0.2500 r_work (final): 0.2990 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8211 moved from start: 0.3556 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 8454 Z= 0.117 Angle : 0.498 6.666 11556 Z= 0.266 Chirality : 0.045 0.141 1437 Planarity : 0.004 0.031 1464 Dihedral : 4.555 26.052 1347 Min Nonbonded Distance : 2.617 Molprobity Statistics. All-atom Clashscore : 3.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.56 % Favored : 95.44 % Rotamer: Outliers : 2.86 % Allowed : 8.96 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.37 (0.25), residues: 1119 helix: 2.90 (0.27), residues: 390 sheet: 0.93 (0.36), residues: 186 loop : -0.63 (0.24), residues: 543 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 258 TYR 0.012 0.001 TYR A 202 PHE 0.009 0.001 PHE B 230 TRP 0.011 0.002 TRP A 303 HIS 0.001 0.000 HIS C 24 Details of bonding type rmsd covalent geometry : bond 0.00271 ( 8433) covalent geometry : angle 0.49125 (11508) SS BOND : bond 0.00346 ( 15) SS BOND : angle 1.05512 ( 30) hydrogen bonds : bond 0.04019 ( 399) hydrogen bonds : angle 3.94746 ( 1182) link_NAG-ASN : bond 0.00608 ( 6) link_NAG-ASN : angle 1.74683 ( 18) *********************** 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 107 residues out of total 1008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 84 time to evaluate : 0.347 Fit side-chains REVERT: A 357 LYS cc_start: 0.5892 (OUTLIER) cc_final: 0.4739 (tppt) REVERT: A 377 LEU cc_start: 0.8314 (OUTLIER) cc_final: 0.8024 (mm) REVERT: B 357 LYS cc_start: 0.5841 (OUTLIER) cc_final: 0.4679 (tppt) REVERT: C 207 THR cc_start: 0.8820 (m) cc_final: 0.8396 (m) REVERT: C 303 TRP cc_start: 0.8782 (m100) cc_final: 0.8556 (m100) REVERT: C 357 LYS cc_start: 0.5813 (OUTLIER) cc_final: 0.4371 (tppt) REVERT: C 362 LYS cc_start: 0.8615 (tttt) cc_final: 0.8276 (tttm) outliers start: 23 outliers final: 9 residues processed: 98 average time/residue: 0.0728 time to fit residues: 11.1324 Evaluate side-chains 92 residues out of total 1008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 79 time to evaluate : 0.417 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 205 ILE Chi-restraints excluded: chain A residue 287 VAL Chi-restraints excluded: chain A residue 357 LYS Chi-restraints excluded: chain A residue 377 LEU Chi-restraints excluded: chain A residue 432 GLU Chi-restraints excluded: chain B residue 205 ILE Chi-restraints excluded: chain B residue 313 THR Chi-restraints excluded: chain B residue 357 LYS Chi-restraints excluded: chain C residue 166 VAL Chi-restraints excluded: chain C residue 205 ILE Chi-restraints excluded: chain C residue 348 ILE Chi-restraints excluded: chain C residue 357 LYS Chi-restraints excluded: chain C residue 445 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 90 optimal weight: 0.9980 chunk 105 optimal weight: 0.9990 chunk 77 optimal weight: 1.9990 chunk 83 optimal weight: 0.8980 chunk 88 optimal weight: 0.6980 chunk 47 optimal weight: 0.2980 chunk 10 optimal weight: 0.5980 chunk 21 optimal weight: 2.9990 chunk 69 optimal weight: 0.5980 chunk 9 optimal weight: 0.6980 chunk 35 optimal weight: 0.9990 overall best weight: 0.5780 ------------------------------------------------------------------------------- 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 = 0.3556 r_free = 0.3556 target = 0.135121 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3259 r_free = 0.3259 target = 0.111004 restraints weight = 10609.110| |-----------------------------------------------------------------------------| r_work (start): 0.3240 rms_B_bonded: 1.95 r_work: 0.3120 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.2974 rms_B_bonded: 4.34 restraints_weight: 0.2500 r_work (final): 0.2974 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8225 moved from start: 0.3752 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 8454 Z= 0.130 Angle : 0.521 8.792 11556 Z= 0.276 Chirality : 0.045 0.194 1437 Planarity : 0.004 0.034 1464 Dihedral : 4.513 25.820 1347 Min Nonbonded Distance : 2.581 Molprobity Statistics. All-atom Clashscore : 3.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.92 % Favored : 95.08 % Rotamer: Outliers : 2.11 % Allowed : 10.45 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.30 (0.25), residues: 1119 helix: 2.89 (0.27), residues: 390 sheet: 0.90 (0.36), residues: 186 loop : -0.72 (0.24), residues: 543 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 258 TYR 0.013 0.001 TYR A 202 PHE 0.010 0.001 PHE B 230 TRP 0.010 0.002 TRP A 303 HIS 0.001 0.000 HIS B 24 Details of bonding type rmsd covalent geometry : bond 0.00312 ( 8433) covalent geometry : angle 0.51212 (11508) SS BOND : bond 0.00303 ( 15) SS BOND : angle 1.44467 ( 30) hydrogen bonds : bond 0.04196 ( 399) hydrogen bonds : angle 3.96360 ( 1182) link_NAG-ASN : bond 0.00497 ( 6) link_NAG-ASN : angle 1.82241 ( 18) *********************** 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 100 residues out of total 1008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 83 time to evaluate : 0.354 Fit side-chains REVERT: A 357 LYS cc_start: 0.5681 (OUTLIER) cc_final: 0.4515 (tppt) REVERT: A 377 LEU cc_start: 0.8281 (OUTLIER) cc_final: 0.8014 (mm) REVERT: B 188 ASP cc_start: 0.7905 (m-30) cc_final: 0.7636 (m-30) REVERT: B 247 ASP cc_start: 0.8565 (t0) cc_final: 0.8295 (t0) REVERT: B 357 LYS cc_start: 0.5897 (OUTLIER) cc_final: 0.4769 (ttpt) REVERT: C 207 THR cc_start: 0.8819 (m) cc_final: 0.8399 (m) REVERT: C 357 LYS cc_start: 0.5393 (OUTLIER) cc_final: 0.4231 (ttpt) REVERT: C 362 LYS cc_start: 0.8659 (tttt) cc_final: 0.8239 (tttm) outliers start: 17 outliers final: 9 residues processed: 92 average time/residue: 0.0762 time to fit residues: 10.6790 Evaluate side-chains 93 residues out of total 1008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 80 time to evaluate : 0.336 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 LEU Chi-restraints excluded: chain A residue 205 ILE Chi-restraints excluded: chain A residue 287 VAL Chi-restraints excluded: chain A residue 357 LYS Chi-restraints excluded: chain A residue 377 LEU Chi-restraints excluded: chain B residue 205 ILE Chi-restraints excluded: chain B residue 313 THR Chi-restraints excluded: chain B residue 357 LYS Chi-restraints excluded: chain C residue 166 VAL Chi-restraints excluded: chain C residue 205 ILE Chi-restraints excluded: chain C residue 348 ILE Chi-restraints excluded: chain C residue 357 LYS Chi-restraints excluded: chain C residue 445 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 77 optimal weight: 0.6980 chunk 67 optimal weight: 3.9990 chunk 24 optimal weight: 0.9990 chunk 46 optimal weight: 0.9980 chunk 15 optimal weight: 1.9990 chunk 71 optimal weight: 2.9990 chunk 106 optimal weight: 5.9990 chunk 69 optimal weight: 4.9990 chunk 12 optimal weight: 0.9990 chunk 13 optimal weight: 1.9990 chunk 48 optimal weight: 1.9990 overall best weight: 1.1386 ------------------------------------------------------------------------------- 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 = 0.3497 r_free = 0.3497 target = 0.130337 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3195 r_free = 0.3195 target = 0.106427 restraints weight = 10885.293| |-----------------------------------------------------------------------------| r_work (start): 0.3174 rms_B_bonded: 1.92 r_work: 0.3054 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.2904 rms_B_bonded: 4.32 restraints_weight: 0.2500 r_work (final): 0.2904 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8302 moved from start: 0.3964 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.057 8454 Z= 0.208 Angle : 0.584 8.301 11556 Z= 0.310 Chirality : 0.048 0.189 1437 Planarity : 0.004 0.042 1464 Dihedral : 4.866 25.445 1347 Min Nonbonded Distance : 2.563 Molprobity Statistics. All-atom Clashscore : 3.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.45 % Favored : 94.55 % Rotamer: Outliers : 2.36 % Allowed : 9.83 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.92 (0.25), residues: 1119 helix: 2.62 (0.27), residues: 393 sheet: 0.76 (0.36), residues: 186 loop : -1.04 (0.24), residues: 540 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG C 258 TYR 0.015 0.002 TYR B 345 PHE 0.014 0.002 PHE B 230 TRP 0.011 0.003 TRP A 303 HIS 0.002 0.001 HIS B 24 Details of bonding type rmsd covalent geometry : bond 0.00524 ( 8433) covalent geometry : angle 0.57391 (11508) SS BOND : bond 0.00592 ( 15) SS BOND : angle 1.75943 ( 30) hydrogen bonds : bond 0.05240 ( 399) hydrogen bonds : angle 4.30869 ( 1182) link_NAG-ASN : bond 0.00621 ( 6) link_NAG-ASN : angle 1.86967 ( 18) *********************** 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 98 residues out of total 1008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 79 time to evaluate : 0.351 Fit side-chains REVERT: B 330 GLU cc_start: 0.7354 (pm20) cc_final: 0.7081 (pm20) REVERT: B 357 LYS cc_start: 0.5858 (OUTLIER) cc_final: 0.4706 (ttpt) REVERT: C 303 TRP cc_start: 0.8876 (m100) cc_final: 0.8666 (m100) REVERT: C 357 LYS cc_start: 0.5485 (OUTLIER) cc_final: 0.4323 (ttpt) outliers start: 19 outliers final: 11 residues processed: 94 average time/residue: 0.0768 time to fit residues: 11.0451 Evaluate side-chains 86 residues out of total 1008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 73 time to evaluate : 0.445 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 LEU Chi-restraints excluded: chain A residue 205 ILE Chi-restraints excluded: chain A residue 287 VAL Chi-restraints excluded: chain A residue 357 LYS Chi-restraints excluded: chain A residue 432 GLU Chi-restraints excluded: chain B residue 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 B residue 412 CYS 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 57 optimal weight: 1.9990 chunk 42 optimal weight: 0.5980 chunk 22 optimal weight: 0.9980 chunk 76 optimal weight: 2.9990 chunk 11 optimal weight: 0.5980 chunk 62 optimal weight: 1.9990 chunk 43 optimal weight: 0.5980 chunk 85 optimal weight: 0.7980 chunk 31 optimal weight: 0.0670 chunk 32 optimal weight: 2.9990 chunk 29 optimal weight: 0.2980 overall best weight: 0.4318 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.134068 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3249 r_free = 0.3249 target = 0.110375 restraints weight = 10773.218| |-----------------------------------------------------------------------------| r_work (start): 0.3227 rms_B_bonded: 1.94 r_work: 0.3106 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.2963 rms_B_bonded: 4.36 restraints_weight: 0.2500 r_work (final): 0.2963 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8241 moved from start: 0.4074 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 8454 Z= 0.113 Angle : 0.505 9.305 11556 Z= 0.266 Chirality : 0.045 0.149 1437 Planarity : 0.004 0.039 1464 Dihedral : 4.544 26.237 1347 Min Nonbonded Distance : 2.598 Molprobity Statistics. All-atom Clashscore : 3.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.29 % Favored : 95.71 % Rotamer: Outliers : 1.87 % Allowed : 9.83 % Favored : 88.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.08 (0.25), residues: 1119 helix: 2.83 (0.27), residues: 393 sheet: 0.83 (0.36), residues: 186 loop : -1.00 (0.24), residues: 540 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 258 TYR 0.018 0.001 TYR B 345 PHE 0.009 0.001 PHE B 230 TRP 0.011 0.002 TRP A 303 HIS 0.001 0.000 HIS C 253 Details of bonding type rmsd covalent geometry : bond 0.00260 ( 8433) covalent geometry : angle 0.49734 (11508) SS BOND : bond 0.00327 ( 15) SS BOND : angle 1.22762 ( 30) hydrogen bonds : bond 0.04056 ( 399) hydrogen bonds : angle 3.96358 ( 1182) link_NAG-ASN : bond 0.00490 ( 6) link_NAG-ASN : angle 1.68553 ( 18) *********************** 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 97 residues out of total 1008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 82 time to evaluate : 0.372 Fit side-chains REVERT: B 188 ASP cc_start: 0.8342 (t0) cc_final: 0.8091 (t0) REVERT: B 357 LYS cc_start: 0.5563 (OUTLIER) cc_final: 0.4620 (ttpt) REVERT: C 207 THR cc_start: 0.8847 (m) cc_final: 0.8430 (m) REVERT: C 357 LYS cc_start: 0.5242 (OUTLIER) cc_final: 0.4381 (ttpt) outliers start: 15 outliers final: 9 residues processed: 92 average time/residue: 0.0694 time to fit residues: 10.0882 Evaluate side-chains 87 residues out of total 1008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 76 time to evaluate : 0.339 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 LEU 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 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 110 optimal weight: 0.9990 chunk 96 optimal weight: 0.9980 chunk 8 optimal weight: 0.5980 chunk 84 optimal weight: 0.6980 chunk 109 optimal weight: 4.9990 chunk 67 optimal weight: 1.9990 chunk 14 optimal weight: 0.9990 chunk 28 optimal weight: 2.9990 chunk 39 optimal weight: 1.9990 chunk 74 optimal weight: 2.9990 chunk 27 optimal weight: 1.9990 overall best weight: 0.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3511 r_free = 0.3511 target = 0.131588 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3209 r_free = 0.3209 target = 0.107634 restraints weight = 10794.376| |-----------------------------------------------------------------------------| r_work (start): 0.3188 rms_B_bonded: 1.93 r_work: 0.3067 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.2922 rms_B_bonded: 4.36 restraints_weight: 0.2500 r_work (final): 0.2922 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8285 moved from start: 0.4151 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.067 8454 Z= 0.169 Angle : 0.580 10.526 11556 Z= 0.305 Chirality : 0.047 0.221 1437 Planarity : 0.004 0.043 1464 Dihedral : 4.701 26.024 1347 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 3.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.92 % Favored : 95.08 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.88 (0.25), residues: 1119 helix: 2.66 (0.27), residues: 393 sheet: 0.77 (0.36), residues: 186 loop : -1.14 (0.24), residues: 540 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 258 TYR 0.018 0.001 TYR B 345 PHE 0.012 0.002 PHE B 230 TRP 0.019 0.003 TRP C 303 HIS 0.001 0.000 HIS B 24 Details of bonding type rmsd covalent geometry : bond 0.00423 ( 8433) covalent geometry : angle 0.56810 (11508) SS BOND : bond 0.00614 ( 15) SS BOND : angle 1.97782 ( 30) hydrogen bonds : bond 0.04719 ( 399) hydrogen bonds : angle 4.14626 ( 1182) link_NAG-ASN : bond 0.00506 ( 6) link_NAG-ASN : angle 1.85412 ( 18) *********************** 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 89 residues out of total 1008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 75 time to evaluate : 0.293 Fit side-chains REVERT: B 357 LYS cc_start: 0.5452 (OUTLIER) cc_final: 0.4619 (ttpt) REVERT: C 357 LYS cc_start: 0.5209 (OUTLIER) cc_final: 0.4341 (ttpt) outliers start: 14 outliers final: 9 residues processed: 85 average time/residue: 0.0694 time to fit residues: 9.2602 Evaluate side-chains 85 residues out of total 1008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 74 time to evaluate : 0.342 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 LEU 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 78 optimal weight: 0.0770 chunk 75 optimal weight: 0.6980 chunk 79 optimal weight: 1.9990 chunk 57 optimal weight: 0.9990 chunk 106 optimal weight: 0.1980 chunk 82 optimal weight: 0.5980 chunk 84 optimal weight: 0.7980 chunk 68 optimal weight: 0.5980 chunk 71 optimal weight: 0.6980 chunk 105 optimal weight: 0.9980 chunk 32 optimal weight: 4.9990 overall best weight: 0.4338 ------------------------------------------------------------------------------- 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 = 0.3544 r_free = 0.3544 target = 0.134367 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3251 r_free = 0.3251 target = 0.110699 restraints weight = 10771.702| |-----------------------------------------------------------------------------| r_work (start): 0.3230 rms_B_bonded: 1.93 r_work: 0.3111 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.2966 rms_B_bonded: 4.39 restraints_weight: 0.2500 r_work (final): 0.2966 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8241 moved from start: 0.4255 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 8454 Z= 0.116 Angle : 0.540 9.963 11556 Z= 0.280 Chirality : 0.045 0.177 1437 Planarity : 0.004 0.042 1464 Dihedral : 4.525 26.660 1347 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 3.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.56 % Favored : 95.44 % Rotamer: Outliers : 1.24 % Allowed : 11.19 % Favored : 87.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.01 (0.25), residues: 1119 helix: 2.74 (0.27), residues: 393 sheet: 0.87 (0.37), residues: 186 loop : -1.05 (0.24), residues: 540 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 258 TYR 0.016 0.001 TYR B 345 PHE 0.008 0.001 PHE B 230 TRP 0.021 0.003 TRP C 303 HIS 0.001 0.000 HIS C 253 Details of bonding type rmsd covalent geometry : bond 0.00270 ( 8433) covalent geometry : angle 0.52781 (11508) SS BOND : bond 0.00339 ( 15) SS BOND : angle 1.93590 ( 30) hydrogen bonds : bond 0.04006 ( 399) hydrogen bonds : angle 3.90093 ( 1182) link_NAG-ASN : bond 0.00435 ( 6) link_NAG-ASN : angle 1.72744 ( 18) ********************** 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 86 residues out of total 1008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 76 time to evaluate : 0.356 Fit side-chains REVERT: B 357 LYS cc_start: 0.5104 (OUTLIER) cc_final: 0.4492 (ttpt) REVERT: C 207 THR cc_start: 0.8853 (m) cc_final: 0.8458 (m) REVERT: C 357 LYS cc_start: 0.5229 (OUTLIER) cc_final: 0.4440 (tppt) outliers start: 10 outliers final: 8 residues processed: 83 average time/residue: 0.0718 time to fit residues: 9.2875 Evaluate side-chains 85 residues out of total 1008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 75 time to evaluate : 0.263 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 LEU 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 B residue 357 LYS Chi-restraints excluded: chain C residue 166 VAL Chi-restraints excluded: chain C residue 205 ILE Chi-restraints excluded: chain C residue 357 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 82 optimal weight: 0.7980 chunk 108 optimal weight: 0.6980 chunk 54 optimal weight: 1.9990 chunk 1 optimal weight: 1.9990 chunk 26 optimal weight: 0.5980 chunk 55 optimal weight: 2.9990 chunk 21 optimal weight: 0.4980 chunk 47 optimal weight: 0.6980 chunk 95 optimal weight: 0.7980 chunk 8 optimal weight: 0.8980 chunk 88 optimal weight: 0.0870 overall best weight: 0.5158 ------------------------------------------------------------------------------- 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 = 0.3538 r_free = 0.3538 target = 0.133924 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3243 r_free = 0.3243 target = 0.110172 restraints weight = 10858.012| |-----------------------------------------------------------------------------| r_work (start): 0.3221 rms_B_bonded: 1.94 r_work: 0.3102 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.2959 rms_B_bonded: 4.36 restraints_weight: 0.2500 r_work (final): 0.2959 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8245 moved from start: 0.4295 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 8454 Z= 0.125 Angle : 0.545 9.517 11556 Z= 0.283 Chirality : 0.045 0.176 1437 Planarity : 0.004 0.043 1464 Dihedral : 4.490 26.624 1347 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 3.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.83 % Favored : 95.17 % Rotamer: Outliers : 1.49 % Allowed : 10.82 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.99 (0.25), residues: 1119 helix: 2.74 (0.27), residues: 393 sheet: 0.83 (0.36), residues: 186 loop : -1.06 (0.25), residues: 540 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 258 TYR 0.017 0.001 TYR B 345 PHE 0.009 0.001 PHE B 230 TRP 0.028 0.003 TRP C 303 HIS 0.001 0.000 HIS A 253 Details of bonding type rmsd covalent geometry : bond 0.00298 ( 8433) covalent geometry : angle 0.53296 (11508) SS BOND : bond 0.00393 ( 15) SS BOND : angle 1.84931 ( 30) hydrogen bonds : bond 0.04102 ( 399) hydrogen bonds : angle 3.89832 ( 1182) link_NAG-ASN : bond 0.00458 ( 6) link_NAG-ASN : angle 1.78136 ( 18) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2325.49 seconds wall clock time: 40 minutes 39.63 seconds (2439.63 seconds total)