Starting phenix.real_space_refine on Fri Jul 3 10:16:07 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8tp2_41464/07_2026/8tp2_41464.cif Found real_map, /net/cci-nas-00/data/ceres_data/8tp2_41464/07_2026/8tp2_41464.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/cci-nas-00/data/ceres_data/8tp2_41464/07_2026/8tp2_41464.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8tp2_41464/07_2026/8tp2_41464.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8tp2_41464/07_2026/8tp2_41464.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8tp2_41464/07_2026/8tp2_41464.map" model { file = "/net/cci-nas-00/data/ceres_data/8tp2_41464/07_2026/8tp2_41464.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8tp2_41464/07_2026/8tp2_41464.cif" } resolution = 3.1 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= 0.000 sd= 0.002 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 77 5.16 5 C 8448 2.51 5 N 2286 2.21 5 O 2674 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 72 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 13485 Number of models: 1 Model: "" Number of chains: 11 Chain: "H" Number of atoms: 959 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 959 Classifications: {'peptide': 126} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 118} Chain: "L" Number of atoms: 814 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 814 Classifications: {'peptide': 107} Modifications used: {'COO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 4, 'TRANS': 100} Chain: "C" Number of atoms: 3821 Number of conformers: 1 Conformer: "" Number of residues, atoms: 482, 3821 Classifications: {'peptide': 482} Link IDs: {'PTRANS': 19, 'TRANS': 462} Chain breaks: 1 Chain: "A" Number of atoms: 3816 Number of conformers: 1 Conformer: "" Number of residues, atoms: 481, 3816 Classifications: {'peptide': 481} Link IDs: {'PTRANS': 19, 'TRANS': 461} Chain breaks: 1 Chain: "B" Number of atoms: 3821 Number of conformers: 1 Conformer: "" Number of residues, atoms: 482, 3821 Classifications: {'peptide': 482} Link IDs: {'PTRANS': 19, 'TRANS': 462} Chain breaks: 1 Chain: "D" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 38 Unusual residues: {'FUC': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "E" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 38 Unusual residues: {'FUC': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "F" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 38 Unusual residues: {'FUC': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "C" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'NAG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen chiralities: 4 Chain: "A" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "B" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Time building chain proxies: 2.99, per 1000 atoms: 0.22 Number of scatterers: 13485 At special positions: 0 Unit cell: (108.1, 94.3, 177.1, 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 77 16.00 O 2674 8.00 N 2286 7.00 C 8448 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=20, symmetry=0 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 92 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.04 Simple disulfide: pdb=" SG CYS C 14 " - pdb=" SG CYS C 466 " distance=2.02 Simple disulfide: pdb=" SG CYS C 52 " - pdb=" SG CYS C 277 " distance=2.03 Simple disulfide: pdb=" SG CYS C 64 " - pdb=" SG CYS C 76 " distance=2.03 Simple disulfide: pdb=" SG CYS C 97 " - pdb=" SG CYS C 139 " distance=2.06 Simple disulfide: pdb=" SG CYS C 281 " - pdb=" SG CYS C 305 " distance=2.03 Simple disulfide: pdb=" SG CYS C 473 " - pdb=" SG CYS C 477 " distance=2.04 Simple disulfide: pdb=" SG CYS A 14 " - pdb=" SG CYS A 466 " distance=2.03 Simple disulfide: pdb=" SG CYS A 52 " - pdb=" SG CYS A 277 " distance=2.03 Simple disulfide: pdb=" SG CYS A 64 " - pdb=" SG CYS A 76 " distance=2.03 Simple disulfide: pdb=" SG CYS A 97 " - pdb=" SG CYS A 139 " distance=2.05 Simple disulfide: pdb=" SG CYS A 281 " - pdb=" SG CYS A 305 " distance=2.02 Simple disulfide: pdb=" SG CYS A 473 " - pdb=" SG CYS A 477 " distance=2.04 Simple disulfide: pdb=" SG CYS B 14 " - pdb=" SG CYS B 466 " distance=2.03 Simple disulfide: pdb=" SG CYS B 52 " - pdb=" SG CYS B 277 " distance=2.04 Simple disulfide: pdb=" SG CYS B 64 " - pdb=" SG CYS B 76 " distance=2.03 Simple disulfide: pdb=" SG CYS B 97 " - pdb=" SG CYS B 139 " distance=2.05 Simple disulfide: pdb=" SG CYS B 281 " - pdb=" SG CYS B 305 " distance=2.02 Simple disulfide: pdb=" SG CYS B 473 " - pdb=" SG CYS B 477 " distance=2.05 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 BETA1-4 " NAG D 1 " - " NAG D 2 " " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " BETA1-6 " NAG D 1 " - " FUC D 3 " ~> Even though FUC is an alpha isomer, a beta linkage is required... " NAG E 1 " - " FUC E 3 " " NAG F 1 " - " FUC F 3 " NAG-ASN " NAG A 501 " - " ASN A 21 " " NAG A 502 " - " ASN A 33 " " NAG A 503 " - " ASN A 289 " " NAG B 501 " - " ASN B 21 " " NAG B 502 " - " ASN B 33 " " NAG B 503 " - " ASN B 289 " " NAG C 501 " - " ASN C 33 " " NAG C 502 " - " ASN C 289 " " NAG C 503 " - " ASN C 483 " " NAG C 504 " - " ASN C 21 " " NAG D 1 " - " ASN C 169 " " NAG E 1 " - " ASN A 169 " " NAG F 1 " - " ASN B 169 " Time building additional restraints: 1.10 Conformation dependent library (CDL) restraints added in 599.7 milliseconds 3324 Ramachandran restraints generated. 1662 Oldfield, 0 Emsley, 1662 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3060 Finding SS restraints... Secondary structure from input PDB file: 29 helices and 39 sheets defined 23.9% alpha, 28.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.49 Creating SS restraints... Processing helix chain 'H' and resid 61 through 65 removed outlier: 3.695A pdb=" N ARG H 64 " --> pdb=" O PRO H 61 " (cutoff:3.500A) removed outlier: 5.360A pdb=" N SER H 65 " --> pdb=" O SER H 62 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 61 through 65' Processing helix chain 'L' and resid 79 through 83 Processing helix chain 'C' and resid 65 through 72 Processing helix chain 'C' and resid 73 through 80 removed outlier: 3.981A pdb=" N ASP C 77 " --> pdb=" O PRO C 74 " (cutoff:3.500A) removed outlier: 5.426A pdb=" N ARG C 78 " --> pdb=" O GLU C 75 " (cutoff:3.500A) Processing helix chain 'C' and resid 104 through 112 Processing helix chain 'C' and resid 125 through 127 Processing helix chain 'C' and resid 187 through 196 Processing helix chain 'C' and resid 366 through 387 Processing helix chain 'C' and resid 403 through 456 removed outlier: 3.654A pdb=" N GLN C 454 " --> pdb=" O LYS C 450 " (cutoff:3.500A) Processing helix chain 'C' and resid 474 through 483 Processing helix chain 'C' and resid 488 through 492 Processing helix chain 'A' and resid 65 through 72 Processing helix chain 'A' and resid 73 through 80 removed outlier: 3.960A pdb=" N ASP A 77 " --> pdb=" O PRO A 74 " (cutoff:3.500A) removed outlier: 5.397A pdb=" N ARG A 78 " --> pdb=" O GLU A 75 " (cutoff:3.500A) Processing helix chain 'A' and resid 104 through 112 Processing helix chain 'A' and resid 125 through 127 Processing helix chain 'A' and resid 187 through 196 Processing helix chain 'A' and resid 366 through 387 Processing helix chain 'A' and resid 403 through 456 removed outlier: 3.654A pdb=" N GLN A 454 " --> pdb=" O LYS A 450 " (cutoff:3.500A) Processing helix chain 'A' and resid 474 through 482 removed outlier: 3.563A pdb=" N SER A 480 " --> pdb=" O GLU A 476 " (cutoff:3.500A) Processing helix chain 'A' and resid 487 through 491 Processing helix chain 'B' and resid 65 through 72 Processing helix chain 'B' and resid 73 through 80 removed outlier: 3.968A pdb=" N ASP B 77 " --> pdb=" O PRO B 74 " (cutoff:3.500A) removed outlier: 5.330A pdb=" N ARG B 78 " --> pdb=" O GLU B 75 " (cutoff:3.500A) Processing helix chain 'B' and resid 104 through 112 Processing helix chain 'B' and resid 125 through 127 Processing helix chain 'B' and resid 187 through 196 Processing helix chain 'B' and resid 366 through 387 Processing helix chain 'B' and resid 403 through 456 removed outlier: 3.658A pdb=" N GLN B 454 " --> pdb=" O LYS B 450 " (cutoff:3.500A) Processing helix chain 'B' and resid 476 through 484 Processing helix chain 'B' and resid 487 through 491 Processing sheet with id=AA1, first strand: chain 'H' and resid 3 through 7 removed outlier: 6.168A pdb=" N LEU H 18 " --> pdb=" O THR H 82A" (cutoff:3.500A) removed outlier: 5.331A pdb=" N THR H 82A" --> pdb=" O LEU H 18 " (cutoff:3.500A) removed outlier: 7.649A pdb=" N LEU H 20 " --> pdb=" O LYS H 81 " (cutoff:3.500A) removed outlier: 5.360A pdb=" N LYS H 81 " --> pdb=" O LEU H 20 " (cutoff:3.500A) removed outlier: 7.035A pdb=" N CYS H 22 " --> pdb=" O SER H 79 " (cutoff:3.500A) removed outlier: 5.538A pdb=" N SER H 79 " --> pdb=" O CYS H 22 " (cutoff:3.500A) removed outlier: 7.032A pdb=" N LEU H 24 " --> pdb=" O GLN H 77 " (cutoff:3.500A) removed outlier: 6.223A pdb=" N GLN H 77 " --> pdb=" O LEU H 24 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'H' and resid 11 through 12 removed outlier: 5.299A pdb=" N TYR H 33 " --> pdb=" O ASP H 95 " (cutoff:3.500A) removed outlier: 6.231A pdb=" N TRP H 34 " --> pdb=" O ASN H 50 " (cutoff:3.500A) removed outlier: 4.293A pdb=" N ASN H 50 " --> pdb=" O TRP H 34 " (cutoff:3.500A) removed outlier: 6.655A pdb=" N TRP H 36 " --> pdb=" O ILE H 48 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'H' and resid 11 through 12 Processing sheet with id=AA4, first strand: chain 'H' and resid 100B through 100C removed outlier: 7.424A pdb=" N ALA C 138 " --> pdb=" O ASN C 144 " (cutoff:3.500A) removed outlier: 10.081A pdb=" N ASN C 144 " --> pdb=" O ALA C 138 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'L' and resid 4 through 7 Processing sheet with id=AA6, first strand: chain 'L' and resid 10 through 11 removed outlier: 6.391A pdb=" N LEU L 33 " --> pdb=" O TYR L 49 " (cutoff:3.500A) removed outlier: 4.487A pdb=" N TYR L 49 " --> pdb=" O LEU L 33 " (cutoff:3.500A) removed outlier: 6.573A pdb=" N TRP L 35 " --> pdb=" O LEU L 47 " (cutoff:3.500A) removed outlier: 5.458A pdb=" N LYS L 39 " --> pdb=" O ALA L 43 " (cutoff:3.500A) removed outlier: 5.266A pdb=" N ALA L 43 " --> pdb=" O LYS L 39 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'L' and resid 10 through 11 Processing sheet with id=AA8, first strand: chain 'C' and resid 361 through 365 Processing sheet with id=AA9, first strand: chain 'C' and resid 24 through 26 removed outlier: 4.310A pdb=" N GLU C 24 " --> pdb=" O VAL C 36 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 39 through 41 Processing sheet with id=AB2, first strand: chain 'C' and resid 43 through 44 Processing sheet with id=AB3, first strand: chain 'C' and resid 51 through 54 removed outlier: 7.059A pdb=" N LEU C 51 " --> pdb=" O GLU C 275 " (cutoff:3.500A) removed outlier: 5.018A pdb=" N CYS C 277 " --> pdb=" O LEU C 51 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 59 through 60 removed outlier: 6.452A pdb=" N LEU C 59 " --> pdb=" O MET C 88 " (cutoff:3.500A) removed outlier: 6.234A pdb=" N ILE C 87 " --> pdb=" O MET C 268 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB4 Processing sheet with id=AB5, first strand: chain 'C' and resid 100 through 102 removed outlier: 6.505A pdb=" N SER C 101 " --> pdb=" O PHE C 232 " (cutoff:3.500A) removed outlier: 8.757A pdb=" N TRP C 234 " --> pdb=" O SER C 101 " (cutoff:3.500A) removed outlier: 5.243A pdb=" N ILE C 179 " --> pdb=" O TYR C 256 " (cutoff:3.500A) removed outlier: 6.872A pdb=" N TYR C 256 " --> pdb=" O ILE C 179 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 100 through 102 removed outlier: 6.505A pdb=" N SER C 101 " --> pdb=" O PHE C 232 " (cutoff:3.500A) removed outlier: 8.757A pdb=" N TRP C 234 " --> pdb=" O SER C 101 " (cutoff:3.500A) removed outlier: 7.790A pdb=" N ILE C 179 " --> pdb=" O PRO C 254 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 164 through 169 Processing sheet with id=AB8, first strand: chain 'C' and resid 286 through 287 Processing sheet with id=AB9, first strand: chain 'A' and resid 361 through 365 Processing sheet with id=AC1, first strand: chain 'A' and resid 24 through 26 removed outlier: 4.197A pdb=" N GLU A 24 " --> pdb=" O VAL A 36 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'A' and resid 39 through 41 Processing sheet with id=AC3, first strand: chain 'A' and resid 43 through 44 Processing sheet with id=AC4, first strand: chain 'A' and resid 51 through 54 removed outlier: 7.175A pdb=" N LEU A 51 " --> pdb=" O GLU A 275 " (cutoff:3.500A) removed outlier: 4.966A pdb=" N CYS A 277 " --> pdb=" O LEU A 51 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'A' and resid 59 through 60 removed outlier: 6.551A pdb=" N LEU A 59 " --> pdb=" O MET A 88 " (cutoff:3.500A) removed outlier: 6.194A pdb=" N ILE A 87 " --> pdb=" O MET A 268 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC5 Processing sheet with id=AC6, first strand: chain 'A' and resid 100 through 102 removed outlier: 6.478A pdb=" N SER A 101 " --> pdb=" O PHE A 232 " (cutoff:3.500A) removed outlier: 8.707A pdb=" N TRP A 234 " --> pdb=" O SER A 101 " (cutoff:3.500A) removed outlier: 5.247A pdb=" N ILE A 179 " --> pdb=" O TYR A 256 " (cutoff:3.500A) removed outlier: 6.853A pdb=" N TYR A 256 " --> pdb=" O ILE A 179 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'A' and resid 100 through 102 removed outlier: 6.478A pdb=" N SER A 101 " --> pdb=" O PHE A 232 " (cutoff:3.500A) removed outlier: 8.707A pdb=" N TRP A 234 " --> pdb=" O SER A 101 " (cutoff:3.500A) removed outlier: 7.806A pdb=" N ILE A 179 " --> pdb=" O PRO A 254 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'A' and resid 136 through 141 removed outlier: 7.374A pdb=" N ALA A 138 " --> pdb=" O ASN A 144 " (cutoff:3.500A) removed outlier: 9.966A pdb=" N ASN A 144 " --> pdb=" O ALA A 138 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'A' and resid 164 through 169 Processing sheet with id=AD1, first strand: chain 'A' and resid 286 through 287 Processing sheet with id=AD2, first strand: chain 'B' and resid 361 through 365 Processing sheet with id=AD3, first strand: chain 'B' and resid 24 through 26 removed outlier: 4.379A pdb=" N GLU B 24 " --> pdb=" O VAL B 36 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 39 through 41 Processing sheet with id=AD5, first strand: chain 'B' and resid 43 through 44 Processing sheet with id=AD6, first strand: chain 'B' and resid 51 through 54 removed outlier: 7.026A pdb=" N LEU B 51 " --> pdb=" O GLU B 275 " (cutoff:3.500A) removed outlier: 5.121A pdb=" N CYS B 277 " --> pdb=" O LEU B 51 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'B' and resid 59 through 60 removed outlier: 6.414A pdb=" N LEU B 59 " --> pdb=" O MET B 88 " (cutoff:3.500A) removed outlier: 6.191A pdb=" N ILE B 87 " --> pdb=" O MET B 268 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD7 Processing sheet with id=AD8, first strand: chain 'B' and resid 100 through 102 removed outlier: 6.506A pdb=" N SER B 101 " --> pdb=" O PHE B 232 " (cutoff:3.500A) removed outlier: 8.734A pdb=" N TRP B 234 " --> pdb=" O SER B 101 " (cutoff:3.500A) removed outlier: 5.267A pdb=" N ILE B 179 " --> pdb=" O TYR B 256 " (cutoff:3.500A) removed outlier: 6.845A pdb=" N TYR B 256 " --> pdb=" O ILE B 179 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'B' and resid 100 through 102 removed outlier: 6.506A pdb=" N SER B 101 " --> pdb=" O PHE B 232 " (cutoff:3.500A) removed outlier: 8.734A pdb=" N TRP B 234 " --> pdb=" O SER B 101 " (cutoff:3.500A) removed outlier: 7.750A pdb=" N ILE B 179 " --> pdb=" O PRO B 254 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'B' and resid 136 through 141 removed outlier: 7.386A pdb=" N ALA B 138 " --> pdb=" O ASN B 144 " (cutoff:3.500A) removed outlier: 9.971A pdb=" N ASN B 144 " --> pdb=" O ALA B 138 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'B' and resid 164 through 169 Processing sheet with id=AE3, first strand: chain 'B' and resid 286 through 287 581 hydrogen bonds defined for protein. 1533 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: 2.59 Time building geometry restraints manager: 1.46 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.32: 2924 1.32 - 1.46: 4486 1.46 - 1.59: 6253 1.59 - 1.73: 15 1.73 - 1.87: 110 Bond restraints: 13788 Sorted by residual: bond pdb=" NE1 TRP H 34 " pdb=" CE2 TRP H 34 " ideal model delta sigma weight residual 1.370 1.310 0.060 1.10e-02 8.26e+03 2.95e+01 bond pdb=" CA SER B 265 " pdb=" CB SER B 265 " ideal model delta sigma weight residual 1.542 1.499 0.043 8.90e-03 1.26e+04 2.34e+01 bond pdb=" CB HIS C 47 " pdb=" CG HIS C 47 " ideal model delta sigma weight residual 1.497 1.433 0.064 1.40e-02 5.10e+03 2.12e+01 bond pdb=" CA ASN B 322 " pdb=" C ASN B 322 " ideal model delta sigma weight residual 1.524 1.466 0.058 1.27e-02 6.20e+03 2.08e+01 bond pdb=" CA ASN A 322 " pdb=" C ASN A 322 " ideal model delta sigma weight residual 1.524 1.466 0.058 1.27e-02 6.20e+03 2.07e+01 ... (remaining 13783 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.25: 15905 2.25 - 4.51: 2319 4.51 - 6.76: 376 6.76 - 9.01: 65 9.01 - 11.27: 10 Bond angle restraints: 18675 Sorted by residual: angle pdb=" N THR A 318 " pdb=" CA THR A 318 " pdb=" C THR A 318 " ideal model delta sigma weight residual 114.04 103.82 10.22 1.24e+00 6.50e-01 6.80e+01 angle pdb=" C LYS H 13 " pdb=" N PRO H 14 " pdb=" CA PRO H 14 " ideal model delta sigma weight residual 119.82 127.90 -8.08 9.80e-01 1.04e+00 6.79e+01 angle pdb=" C PRO B 57 " pdb=" N PRO B 58 " pdb=" CA PRO B 58 " ideal model delta sigma weight residual 120.21 127.92 -7.71 9.60e-01 1.09e+00 6.45e+01 angle pdb=" C PRO C 57 " pdb=" N PRO C 58 " pdb=" CA PRO C 58 " ideal model delta sigma weight residual 120.21 127.81 -7.60 9.60e-01 1.09e+00 6.26e+01 angle pdb=" N THR B 318 " pdb=" CA THR B 318 " pdb=" C THR B 318 " ideal model delta sigma weight residual 114.04 104.27 9.77 1.24e+00 6.50e-01 6.21e+01 ... (remaining 18670 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.08: 7796 18.08 - 36.16: 213 36.16 - 54.24: 33 54.24 - 72.32: 32 72.32 - 90.40: 18 Dihedral angle restraints: 8092 sinusoidal: 3294 harmonic: 4798 Sorted by residual: dihedral pdb=" CB CYS B 64 " pdb=" SG CYS B 64 " pdb=" SG CYS B 76 " pdb=" CB CYS B 76 " ideal model delta sinusoidal sigma weight residual -86.00 -124.84 38.84 1 1.00e+01 1.00e-02 2.12e+01 dihedral pdb=" CB CYS C 64 " pdb=" SG CYS C 64 " pdb=" SG CYS C 76 " pdb=" CB CYS C 76 " ideal model delta sinusoidal sigma weight residual -86.00 -121.97 35.97 1 1.00e+01 1.00e-02 1.83e+01 dihedral pdb=" CB CYS A 64 " pdb=" SG CYS A 64 " pdb=" SG CYS A 76 " pdb=" CB CYS A 76 " ideal model delta sinusoidal sigma weight residual -86.00 -121.69 35.69 1 1.00e+01 1.00e-02 1.80e+01 ... (remaining 8089 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.096: 1487 0.096 - 0.192: 441 0.192 - 0.289: 97 0.289 - 0.385: 25 0.385 - 0.481: 12 Chirality restraints: 2062 Sorted by residual: chirality pdb=" C1 NAG E 2 " pdb=" O4 NAG E 1 " pdb=" C2 NAG E 2 " pdb=" O5 NAG E 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.63 0.23 2.00e-02 2.50e+03 1.30e+02 chirality pdb=" C1 NAG F 2 " pdb=" O4 NAG F 1 " pdb=" C2 NAG F 2 " pdb=" O5 NAG F 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.60 0.20 2.00e-02 2.50e+03 9.75e+01 chirality pdb=" C1 NAG D 2 " pdb=" O4 NAG D 1 " pdb=" C2 NAG D 2 " pdb=" O5 NAG D 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.59 0.19 2.00e-02 2.50e+03 8.79e+01 ... (remaining 2059 not shown) Planarity restraints: 2412 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG C 503 " -0.349 2.00e-02 2.50e+03 3.01e-01 1.13e+03 pdb=" C7 NAG C 503 " 0.082 2.00e-02 2.50e+03 pdb=" C8 NAG C 503 " -0.112 2.00e-02 2.50e+03 pdb=" N2 NAG C 503 " 0.537 2.00e-02 2.50e+03 pdb=" O7 NAG C 503 " -0.158 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN B 21 " 0.072 2.00e-02 2.50e+03 7.64e-02 7.30e+01 pdb=" CG ASN B 21 " -0.030 2.00e-02 2.50e+03 pdb=" OD1 ASN B 21 " -0.016 2.00e-02 2.50e+03 pdb=" ND2 ASN B 21 " -0.119 2.00e-02 2.50e+03 pdb=" C1 NAG B 501 " 0.093 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 21 " 0.064 2.00e-02 2.50e+03 6.82e-02 5.81e+01 pdb=" CG ASN A 21 " -0.025 2.00e-02 2.50e+03 pdb=" OD1 ASN A 21 " -0.016 2.00e-02 2.50e+03 pdb=" ND2 ASN A 21 " -0.106 2.00e-02 2.50e+03 pdb=" C1 NAG A 501 " 0.083 2.00e-02 2.50e+03 ... (remaining 2409 not shown) Histogram of nonbonded interaction distances: 2.01 - 2.59: 83 2.59 - 3.17: 11168 3.17 - 3.74: 20349 3.74 - 4.32: 31035 4.32 - 4.90: 49663 Nonbonded interactions: 112298 Sorted by model distance: nonbonded pdb=" OD1 ASP H 95 " pdb=" CE1 PHE H 100J" model vdw 2.009 3.340 nonbonded pdb=" OG SER A 136 " pdb=" NE2 GLN A 226 " model vdw 2.116 3.120 nonbonded pdb=" OG SER C 136 " pdb=" NE2 GLN C 226 " model vdw 2.164 3.120 nonbonded pdb=" OG SER B 136 " pdb=" NE2 GLN B 226 " model vdw 2.257 3.120 nonbonded pdb=" OD2 ASP B 487 " pdb=" NZ LYS B 490 " model vdw 2.391 3.120 ... (remaining 112293 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = (chain 'B' and (resid 11 through 324 or resid 335 through 503)) selection = (chain 'C' and (resid 11 through 324 or resid 335 through 503)) } ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'F' } 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: 2.060 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: 0.230 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 13.510 Find NCS groups from input model: 0.360 Set up NCS constraints: 0.030 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:1.110 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.390 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8489 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 : 0.021 0.121 13827 Z= 1.121 Angle : 1.705 11.265 18772 Z= 1.134 Chirality : 0.103 0.481 2062 Planarity : 0.010 0.301 2399 Dihedral : 10.766 90.404 4972 Min Nonbonded Distance : 2.009 Molprobity Statistics. All-atom Clashscore : 1.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 0.00 % Allowed : 0.34 % Favored : 99.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % 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 are not related in a simple way. whole: 0.79 (0.19), residues: 1662 helix: 0.98 (0.26), residues: 335 sheet: 1.14 (0.25), residues: 388 loop : 0.18 (0.19), residues: 939 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 93 TYR 0.064 0.008 TYR A 486 PHE 0.048 0.006 PHE B 118 TRP 0.052 0.007 TRP A 84 HIS 0.012 0.003 HIS C 183 Details of bonding type rmsd/Z covalent geometry : bond 0.02072 / 1.12 (13788) covalent geometry : angle 1.69412 / 1.13 (18675) SS BOND : bond 0.01174 / 0.69 ( 20) SS BOND : angle 2.98721 / 1.83 ( 40) hydrogen bonds : bond 0.13596 / 9.12 ( 543) hydrogen bonds : angle 7.00594 / 4.86 ( 1533) link_BETA1-4 : bond 0.06935 / 3.45 ( 3) link_BETA1-4 : angle 4.99765 / 2.97 ( 9) link_BETA1-6 : bond 0.05584 / 2.79 ( 3) link_BETA1-6 : angle 2.55582 / 1.53 ( 9) link_NAG-ASN : bond 0.06937 / 4.05 ( 13) link_NAG-ASN : angle 2.83322 / 1.72 ( 39) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3324 Ramachandran restraints generated. 1662 Oldfield, 0 Emsley, 1662 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3324 Ramachandran restraints generated. 1662 Oldfield, 0 Emsley, 1662 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 349 residues out of total 1465 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 349 time to evaluate : 0.528 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: H 47 TYR cc_start: 0.8848 (t80) cc_final: 0.8641 (t80) REVERT: L 83 PHE cc_start: 0.7366 (m-80) cc_final: 0.7152 (m-80) REVERT: L 90 GLN cc_start: 0.8395 (tm130) cc_final: 0.8070 (tm-30) REVERT: C 435 ARG cc_start: 0.7909 (mmm160) cc_final: 0.7684 (mmp-170) REVERT: C 441 ASP cc_start: 0.8129 (m-30) cc_final: 0.7924 (m-30) REVERT: C 445 LYS cc_start: 0.8499 (tptp) cc_final: 0.8231 (ttmm) REVERT: C 450 LYS cc_start: 0.8961 (tttt) cc_final: 0.8625 (ttpp) REVERT: A 132 THR cc_start: 0.8426 (p) cc_final: 0.8213 (p) REVERT: A 160 ASN cc_start: 0.7250 (m-40) cc_final: 0.6810 (t0) REVERT: A 335 ILE cc_start: 0.6682 (pt) cc_final: 0.6120 (tt) REVERT: A 402 LEU cc_start: 0.9146 (mt) cc_final: 0.8922 (mt) REVERT: B 27 ASP cc_start: 0.7654 (m-30) cc_final: 0.7424 (m-30) REVERT: B 190 GLU cc_start: 0.6994 (tt0) cc_final: 0.6606 (tt0) REVERT: B 275 GLU cc_start: 0.7523 (mm-30) cc_final: 0.7233 (mp0) REVERT: B 366 ASP cc_start: 0.8447 (t0) cc_final: 0.8218 (t70) outliers start: 0 outliers final: 0 residues processed: 349 average time/residue: 0.1361 time to fit residues: 65.2167 Evaluate side-chains 173 residues out of total 1465 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 173 time to evaluate : 0.472 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 98 optimal weight: 0.7980 chunk 107 optimal weight: 1.9990 chunk 10 optimal weight: 0.9990 chunk 66 optimal weight: 2.9990 chunk 130 optimal weight: 0.4980 chunk 124 optimal weight: 0.8980 chunk 103 optimal weight: 0.6980 chunk 77 optimal weight: 0.8980 chunk 122 optimal weight: 0.5980 chunk 91 optimal weight: 0.6980 chunk 149 optimal weight: 0.9980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... H 5 GLN L 92 ASN C 355 HIS C 391 GLN A 196 GLN A 210 ASN B 12 GLN B 130 HIS B 175 GLN B 183 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3525 r_free = 0.3525 target = 0.125429 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3237 r_free = 0.3237 target = 0.104662 restraints weight = 18439.240| |-----------------------------------------------------------------------------| r_work (start): 0.3235 rms_B_bonded: 1.82 r_work: 0.3113 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.2981 rms_B_bonded: 3.84 restraints_weight: 0.2500 r_work (final): 0.2981 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8581 moved from start: 0.2504 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 13827 Z= 0.158 Angle : 0.635 6.054 18772 Z= 0.347 Chirality : 0.043 0.190 2062 Planarity : 0.004 0.064 2399 Dihedral : 5.079 31.634 1800 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 4.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.47 % Favored : 97.53 % Rotamer: Outliers : 1.37 % Allowed : 6.28 % Favored : 92.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % 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 are not related in a simple way. whole: 0.79 (0.20), residues: 1662 helix: 2.34 (0.28), residues: 332 sheet: 0.79 (0.26), residues: 380 loop : -0.21 (0.19), residues: 950 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG C 262a TYR 0.017 0.002 TYR H 98 PHE 0.024 0.002 PHE L 83 TRP 0.015 0.002 TRP L 96 HIS 0.012 0.001 HIS C 355 Details of bonding type rmsd/Z covalent geometry : bond 0.00351 / 0.16 (13788) covalent geometry : angle 0.62903 / 0.35 (18675) SS BOND : bond 0.00461 / 0.35 ( 20) SS BOND : angle 0.98831 / 0.57 ( 40) hydrogen bonds : bond 0.05462 / 3.73 ( 543) hydrogen bonds : angle 5.58023 / 3.83 ( 1533) link_BETA1-4 : bond 0.00087 / 0.04 ( 3) link_BETA1-4 : angle 1.95952 / 1.13 ( 9) link_BETA1-6 : bond 0.00752 / 0.38 ( 3) link_BETA1-6 : angle 0.88821 / 0.64 ( 9) link_NAG-ASN : bond 0.00268 / 0.17 ( 13) link_NAG-ASN : angle 1.58557 / 0.95 ( 39) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3324 Ramachandran restraints generated. 1662 Oldfield, 0 Emsley, 1662 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3324 Ramachandran restraints generated. 1662 Oldfield, 0 Emsley, 1662 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 217 residues out of total 1465 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 197 time to evaluate : 0.553 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: L 54 ARG cc_start: 0.8071 (mtm110) cc_final: 0.7804 (mmm-85) REVERT: L 92 ASN cc_start: 0.8744 (t0) cc_final: 0.8338 (t0) REVERT: C 160 ASN cc_start: 0.8540 (m110) cc_final: 0.8251 (t0) REVERT: C 435 ARG cc_start: 0.7980 (mmm160) cc_final: 0.7601 (mmp-170) REVERT: C 445 LYS cc_start: 0.8698 (tptp) cc_final: 0.8237 (ttmm) REVERT: A 24 GLU cc_start: 0.7805 (mm-30) cc_final: 0.7464 (mt-10) REVERT: A 50 LYS cc_start: 0.7908 (mttt) cc_final: 0.7522 (mtpt) REVERT: A 129 GLN cc_start: 0.7690 (mt0) cc_final: 0.7384 (mm110) REVERT: A 487 ASP cc_start: 0.7730 (t0) cc_final: 0.7155 (t70) REVERT: B 27 ASP cc_start: 0.8011 (m-30) cc_final: 0.7806 (m-30) REVERT: B 239 MET cc_start: 0.8144 (OUTLIER) cc_final: 0.7711 (mtm) REVERT: B 275 GLU cc_start: 0.7809 (mm-30) cc_final: 0.7100 (mp0) REVERT: B 401 ASN cc_start: 0.8674 (m-40) cc_final: 0.8298 (p0) outliers start: 20 outliers final: 11 residues processed: 210 average time/residue: 0.1262 time to fit residues: 38.2940 Evaluate side-chains 171 residues out of total 1465 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 159 time to evaluate : 0.499 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 7 SER Chi-restraints excluded: chain H residue 68 THR Chi-restraints excluded: chain H residue 82 THR Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain C residue 11 ASP Chi-restraints excluded: chain C residue 82 VAL Chi-restraints excluded: chain C residue 291 THR Chi-restraints excluded: chain A residue 165 LYS Chi-restraints excluded: chain A residue 291 THR Chi-restraints excluded: chain B residue 155 THR Chi-restraints excluded: chain B residue 239 MET Chi-restraints excluded: chain B residue 457 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 2 optimal weight: 5.9990 chunk 149 optimal weight: 3.9990 chunk 41 optimal weight: 3.9990 chunk 39 optimal weight: 3.9990 chunk 3 optimal weight: 3.9990 chunk 32 optimal weight: 2.9990 chunk 47 optimal weight: 2.9990 chunk 74 optimal weight: 0.8980 chunk 55 optimal weight: 3.9990 chunk 146 optimal weight: 4.9990 chunk 155 optimal weight: 4.9990 overall best weight: 2.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** L 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 117 HIS A 117 HIS A 191 GLN A 210 ASN A 354 HIS B 117 HIS B 196 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3350 r_free = 0.3350 target = 0.113101 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3041 r_free = 0.3041 target = 0.092044 restraints weight = 19000.115| |-----------------------------------------------------------------------------| r_work (start): 0.3041 rms_B_bonded: 1.85 r_work: 0.2917 rms_B_bonded: 2.26 restraints_weight: 0.5000 r_work: 0.2783 rms_B_bonded: 3.75 restraints_weight: 0.2500 r_work (final): 0.2783 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8714 moved from start: 0.3371 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.096 13827 Z= 0.351 Angle : 0.754 8.181 18772 Z= 0.398 Chirality : 0.050 0.252 2062 Planarity : 0.006 0.069 2399 Dihedral : 5.384 28.850 1800 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 5.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.71 % Favored : 97.29 % Rotamer: Outliers : 1.91 % Allowed : 8.81 % Favored : 89.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % 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 are not related in a simple way. whole: 0.13 (0.19), residues: 1662 helix: 1.69 (0.27), residues: 333 sheet: 0.48 (0.25), residues: 398 loop : -0.69 (0.18), residues: 931 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 405 TYR 0.020 0.003 TYR B 17 PHE 0.059 0.004 PHE A 118 TRP 0.017 0.003 TRP A 84 HIS 0.009 0.002 HIS B 183 Details of bonding type rmsd/Z covalent geometry : bond 0.00860 / 0.35 (13788) covalent geometry : angle 0.74789 / 0.40 (18675) SS BOND : bond 0.00516 / 0.34 ( 20) SS BOND : angle 1.17584 / 0.66 ( 40) hydrogen bonds : bond 0.05612 / 3.83 ( 543) hydrogen bonds : angle 5.55410 / 3.83 ( 1533) link_BETA1-4 : bond 0.00329 / 0.16 ( 3) link_BETA1-4 : angle 1.62889 / 1.00 ( 9) link_BETA1-6 : bond 0.00974 / 0.49 ( 3) link_BETA1-6 : angle 0.82044 / 0.54 ( 9) link_NAG-ASN : bond 0.00631 / 0.41 ( 13) link_NAG-ASN : angle 1.82708 / 1.12 ( 39) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3324 Ramachandran restraints generated. 1662 Oldfield, 0 Emsley, 1662 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3324 Ramachandran restraints generated. 1662 Oldfield, 0 Emsley, 1662 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 205 residues out of total 1465 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 177 time to evaluate : 0.578 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: L 90 GLN cc_start: 0.8776 (tm-30) cc_final: 0.8528 (pp30) REVERT: L 92 ASN cc_start: 0.8897 (t0) cc_final: 0.8524 (t0) REVERT: C 112 LEU cc_start: 0.8416 (mt) cc_final: 0.8213 (mt) REVERT: C 160 ASN cc_start: 0.8620 (m110) cc_final: 0.8284 (t0) REVERT: C 188 GLU cc_start: 0.8323 (mm-30) cc_final: 0.7909 (mt-10) REVERT: C 348 ASP cc_start: 0.6557 (m-30) cc_final: 0.6193 (m-30) REVERT: C 435 ARG cc_start: 0.8144 (mmm160) cc_final: 0.7550 (mmp-170) REVERT: C 445 LYS cc_start: 0.8634 (tptp) cc_final: 0.8110 (ttmm) REVERT: C 478 MET cc_start: 0.7736 (mmt) cc_final: 0.7106 (mmt) REVERT: A 24 GLU cc_start: 0.7856 (mm-30) cc_final: 0.7394 (mt-10) REVERT: A 160 ASN cc_start: 0.6870 (t0) cc_final: 0.6584 (t0) REVERT: A 313 LYS cc_start: 0.8397 (pttt) cc_final: 0.8183 (ptmt) REVERT: A 335 ILE cc_start: 0.5696 (OUTLIER) cc_final: 0.5474 (mt) REVERT: A 367 LYS cc_start: 0.8268 (mttp) cc_final: 0.8011 (mptt) REVERT: A 487 ASP cc_start: 0.7949 (t0) cc_final: 0.7400 (t70) REVERT: B 27 ASP cc_start: 0.8322 (m-30) cc_final: 0.8079 (m-30) REVERT: B 239 MET cc_start: 0.8271 (OUTLIER) cc_final: 0.8001 (mtm) REVERT: B 275 GLU cc_start: 0.7948 (mm-30) cc_final: 0.7131 (mp0) REVERT: B 435 ARG cc_start: 0.8443 (mtp180) cc_final: 0.8055 (mtt180) outliers start: 28 outliers final: 18 residues processed: 200 average time/residue: 0.1288 time to fit residues: 36.6149 Evaluate side-chains 179 residues out of total 1465 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 159 time to evaluate : 0.412 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 20 LEU Chi-restraints excluded: chain H residue 68 THR Chi-restraints excluded: chain H residue 82 THR Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 21 LEU Chi-restraints excluded: chain L residue 85 VAL Chi-restraints excluded: chain C residue 82 VAL Chi-restraints excluded: chain C residue 125 ASP Chi-restraints excluded: chain C residue 219 THR Chi-restraints excluded: chain C residue 273 THR Chi-restraints excluded: chain C residue 291 THR Chi-restraints excluded: chain A residue 273 THR Chi-restraints excluded: chain A residue 291 THR Chi-restraints excluded: chain A residue 335 ILE Chi-restraints excluded: chain A residue 490 LYS Chi-restraints excluded: chain B residue 118 PHE Chi-restraints excluded: chain B residue 155 THR Chi-restraints excluded: chain B residue 239 MET Chi-restraints excluded: chain B residue 457 ASP Chi-restraints excluded: chain B residue 477 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 72 optimal weight: 1.9990 chunk 63 optimal weight: 0.9980 chunk 98 optimal weight: 1.9990 chunk 142 optimal weight: 7.9990 chunk 124 optimal weight: 0.6980 chunk 113 optimal weight: 0.7980 chunk 2 optimal weight: 0.9990 chunk 77 optimal weight: 0.6980 chunk 153 optimal weight: 4.9990 chunk 71 optimal weight: 0.8980 chunk 126 optimal weight: 0.7980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... H 5 GLN ** L 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 196 GLN B 483 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3424 r_free = 0.3424 target = 0.117725 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3131 r_free = 0.3131 target = 0.097445 restraints weight = 18613.285| |-----------------------------------------------------------------------------| r_work (start): 0.3126 rms_B_bonded: 1.77 r_work: 0.3001 rms_B_bonded: 2.22 restraints_weight: 0.5000 r_work: 0.2868 rms_B_bonded: 3.74 restraints_weight: 0.2500 r_work (final): 0.2868 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8675 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 : 0.003 0.044 13827 Z= 0.133 Angle : 0.565 13.553 18772 Z= 0.299 Chirality : 0.042 0.228 2062 Planarity : 0.004 0.042 2399 Dihedral : 4.913 29.012 1800 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 5.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 1.84 % Allowed : 9.49 % Favored : 88.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % 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 are not related in a simple way. whole: 0.27 (0.20), residues: 1662 helix: 2.17 (0.27), residues: 333 sheet: 0.45 (0.26), residues: 401 loop : -0.69 (0.19), residues: 928 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG L 61 TYR 0.017 0.001 TYR L 49 PHE 0.026 0.002 PHE A 118 TRP 0.016 0.001 TRP C 84 HIS 0.003 0.001 HIS B 117 Details of bonding type rmsd/Z covalent geometry : bond 0.00299 / 0.13 (13788) covalent geometry : angle 0.54757 / 0.30 (18675) SS BOND : bond 0.00238 / 0.16 ( 20) SS BOND : angle 0.65397 / 0.35 ( 40) hydrogen bonds : bond 0.04582 / 3.14 ( 543) hydrogen bonds : angle 5.26049 / 3.63 ( 1533) link_BETA1-4 : bond 0.00292 / 0.14 ( 3) link_BETA1-4 : angle 1.12079 / 0.69 ( 9) link_BETA1-6 : bond 0.00571 / 0.28 ( 3) link_BETA1-6 : angle 0.94154 / 0.61 ( 9) link_NAG-ASN : bond 0.00575 / 0.41 ( 13) link_NAG-ASN : angle 3.02479 / 2.49 ( 39) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3324 Ramachandran restraints generated. 1662 Oldfield, 0 Emsley, 1662 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3324 Ramachandran restraints generated. 1662 Oldfield, 0 Emsley, 1662 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 1465 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 177 time to evaluate : 0.519 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: H 100 PHE cc_start: 0.8838 (OUTLIER) cc_final: 0.8630 (m-80) REVERT: L 49 TYR cc_start: 0.8586 (p90) cc_final: 0.8385 (p90) REVERT: L 90 GLN cc_start: 0.8803 (tm-30) cc_final: 0.8533 (pp30) REVERT: L 92 ASN cc_start: 0.8789 (t0) cc_final: 0.8484 (t0) REVERT: C 112 LEU cc_start: 0.8123 (mt) cc_final: 0.7867 (mt) REVERT: C 160 ASN cc_start: 0.8565 (m110) cc_final: 0.8315 (t0) REVERT: C 188 GLU cc_start: 0.8297 (mm-30) cc_final: 0.7896 (mt-10) REVERT: C 348 ASP cc_start: 0.6609 (m-30) cc_final: 0.6300 (m-30) REVERT: C 445 LYS cc_start: 0.8601 (tptp) cc_final: 0.8076 (ttmm) REVERT: A 24 GLU cc_start: 0.7778 (mm-30) cc_final: 0.7400 (mt-10) REVERT: A 129 GLN cc_start: 0.7770 (mt0) cc_final: 0.7436 (mm110) REVERT: A 174 GLU cc_start: 0.7260 (tp30) cc_final: 0.6784 (tt0) REVERT: A 367 LYS cc_start: 0.8188 (mttp) cc_final: 0.7928 (mmtm) REVERT: A 487 ASP cc_start: 0.7630 (t0) cc_final: 0.7126 (t70) REVERT: B 27 ASP cc_start: 0.8239 (m-30) cc_final: 0.8009 (m-30) REVERT: B 435 ARG cc_start: 0.8399 (mtp180) cc_final: 0.8015 (mtt180) outliers start: 27 outliers final: 16 residues processed: 196 average time/residue: 0.1331 time to fit residues: 36.3737 Evaluate side-chains 175 residues out of total 1465 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 158 time to evaluate : 0.445 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 7 SER Chi-restraints excluded: chain H residue 20 LEU Chi-restraints excluded: chain H residue 82 THR Chi-restraints excluded: chain H residue 100 PHE Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 21 LEU Chi-restraints excluded: chain L residue 85 VAL Chi-restraints excluded: chain C residue 118 PHE Chi-restraints excluded: chain C residue 125 ASP Chi-restraints excluded: chain C residue 291 THR Chi-restraints excluded: chain A residue 291 THR Chi-restraints excluded: chain A residue 335 ILE Chi-restraints excluded: chain A residue 442 SER Chi-restraints excluded: chain B residue 118 PHE Chi-restraints excluded: chain B residue 323 VAL Chi-restraints excluded: chain B residue 335 ILE Chi-restraints excluded: chain B residue 457 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 122 optimal weight: 2.9990 chunk 17 optimal weight: 10.0000 chunk 43 optimal weight: 0.9990 chunk 158 optimal weight: 3.9990 chunk 75 optimal weight: 2.9990 chunk 66 optimal weight: 6.9990 chunk 76 optimal weight: 0.6980 chunk 134 optimal weight: 4.9990 chunk 153 optimal weight: 6.9990 chunk 116 optimal weight: 4.9990 chunk 47 optimal weight: 3.9990 overall best weight: 2.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** L 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 160 ASN A 210 ASN B 483 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.114767 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3079 r_free = 0.3079 target = 0.094056 restraints weight = 18892.589| |-----------------------------------------------------------------------------| r_work (start): 0.3079 rms_B_bonded: 1.79 r_work: 0.2954 rms_B_bonded: 2.21 restraints_weight: 0.5000 r_work: 0.2819 rms_B_bonded: 3.72 restraints_weight: 0.2500 r_work (final): 0.2819 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8724 moved from start: 0.3745 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.088 13827 Z= 0.281 Angle : 0.687 18.035 18772 Z= 0.353 Chirality : 0.046 0.238 2062 Planarity : 0.005 0.056 2399 Dihedral : 5.070 25.984 1800 Min Nonbonded Distance : 2.235 Molprobity Statistics. All-atom Clashscore : 5.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 2.66 % Allowed : 9.76 % Favored : 87.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % 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 are not related in a simple way. whole: 0.02 (0.20), residues: 1662 helix: 1.88 (0.27), residues: 333 sheet: 0.25 (0.26), residues: 395 loop : -0.80 (0.19), residues: 934 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 262a TYR 0.013 0.002 TYR L 49 PHE 0.041 0.003 PHE A 118 TRP 0.013 0.002 TRP H 103 HIS 0.009 0.002 HIS B 183 Details of bonding type rmsd/Z covalent geometry : bond 0.00685 / 0.28 (13788) covalent geometry : angle 0.65727 / 0.35 (18675) SS BOND : bond 0.00354 / 0.23 ( 20) SS BOND : angle 1.02078 / 0.71 ( 40) hydrogen bonds : bond 0.05092 / 3.49 ( 543) hydrogen bonds : angle 5.48508 / 3.79 ( 1533) link_BETA1-4 : bond 0.00253 / 0.12 ( 3) link_BETA1-4 : angle 1.33678 / 0.83 ( 9) link_BETA1-6 : bond 0.00797 / 0.40 ( 3) link_BETA1-6 : angle 0.86791 / 0.58 ( 9) link_NAG-ASN : bond 0.00404 / 0.24 ( 13) link_NAG-ASN : angle 4.35273 / 3.43 ( 39) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3324 Ramachandran restraints generated. 1662 Oldfield, 0 Emsley, 1662 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3324 Ramachandran restraints generated. 1662 Oldfield, 0 Emsley, 1662 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 1465 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 158 time to evaluate : 0.572 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: H 100 PHE cc_start: 0.8889 (OUTLIER) cc_final: 0.8610 (m-80) REVERT: L 92 ASN cc_start: 0.8877 (t0) cc_final: 0.8561 (t0) REVERT: C 112 LEU cc_start: 0.8247 (mt) cc_final: 0.8014 (mt) REVERT: C 188 GLU cc_start: 0.8329 (mm-30) cc_final: 0.7930 (mt-10) REVERT: C 348 ASP cc_start: 0.6729 (m-30) cc_final: 0.6310 (m-30) REVERT: C 435 ARG cc_start: 0.8150 (mtp85) cc_final: 0.7639 (mmp-170) REVERT: C 441 ASP cc_start: 0.8708 (m-30) cc_final: 0.8388 (m-30) REVERT: C 445 LYS cc_start: 0.8601 (tptp) cc_final: 0.8068 (ttmm) REVERT: C 478 MET cc_start: 0.7768 (mmt) cc_final: 0.7083 (mmt) REVERT: A 24 GLU cc_start: 0.7778 (mm-30) cc_final: 0.7355 (mt-10) REVERT: A 174 GLU cc_start: 0.7426 (tp30) cc_final: 0.6809 (tt0) REVERT: A 367 LYS cc_start: 0.8286 (mttp) cc_final: 0.8023 (mmtm) REVERT: A 487 ASP cc_start: 0.7757 (t0) cc_final: 0.7304 (t70) REVERT: B 27 ASP cc_start: 0.8306 (m-30) cc_final: 0.8057 (m-30) REVERT: B 59 LEU cc_start: 0.8836 (OUTLIER) cc_final: 0.8549 (tp) REVERT: B 348 ASP cc_start: 0.7205 (t0) cc_final: 0.6914 (t0) REVERT: B 435 ARG cc_start: 0.8417 (mtp180) cc_final: 0.8058 (mtt180) outliers start: 39 outliers final: 29 residues processed: 192 average time/residue: 0.1403 time to fit residues: 37.8837 Evaluate side-chains 182 residues out of total 1465 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 151 time to evaluate : 0.581 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 7 SER Chi-restraints excluded: chain H residue 20 LEU Chi-restraints excluded: chain H residue 82 THR Chi-restraints excluded: chain H residue 100 PHE Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 12 SER Chi-restraints excluded: chain L residue 21 LEU Chi-restraints excluded: chain L residue 85 VAL Chi-restraints excluded: chain C residue 82 VAL Chi-restraints excluded: chain C residue 118 PHE Chi-restraints excluded: chain C residue 125 ASP Chi-restraints excluded: chain C residue 273 THR Chi-restraints excluded: chain C residue 277 CYS Chi-restraints excluded: chain C residue 291 THR Chi-restraints excluded: chain C residue 369 SER Chi-restraints excluded: chain C residue 389 ASN Chi-restraints excluded: chain C residue 442 SER Chi-restraints excluded: chain A residue 118 PHE Chi-restraints excluded: chain A residue 137 ARG Chi-restraints excluded: chain A residue 291 THR Chi-restraints excluded: chain A residue 442 SER Chi-restraints excluded: chain A residue 490 LYS Chi-restraints excluded: chain B residue 59 LEU Chi-restraints excluded: chain B residue 82 VAL Chi-restraints excluded: chain B residue 93 ARG Chi-restraints excluded: chain B residue 118 PHE Chi-restraints excluded: chain B residue 155 THR Chi-restraints excluded: chain B residue 323 VAL Chi-restraints excluded: chain B residue 335 ILE Chi-restraints excluded: chain B residue 457 ASP Chi-restraints excluded: chain B residue 477 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 10 optimal weight: 3.9990 chunk 99 optimal weight: 1.9990 chunk 165 optimal weight: 2.9990 chunk 83 optimal weight: 0.0060 chunk 60 optimal weight: 1.9990 chunk 44 optimal weight: 0.7980 chunk 144 optimal weight: 0.9990 chunk 47 optimal weight: 0.7980 chunk 153 optimal weight: 5.9990 chunk 33 optimal weight: 0.7980 chunk 49 optimal weight: 0.9990 overall best weight: 0.6798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... H 5 GLN ** L 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 454 GLN A 160 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3453 r_free = 0.3453 target = 0.119743 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3163 r_free = 0.3163 target = 0.099320 restraints weight = 18553.633| |-----------------------------------------------------------------------------| r_work (start): 0.3161 rms_B_bonded: 1.77 r_work: 0.3043 rms_B_bonded: 2.15 restraints_weight: 0.5000 r_work: 0.2914 rms_B_bonded: 3.61 restraints_weight: 0.2500 r_work (final): 0.2914 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8651 moved from start: 0.3887 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 13827 Z= 0.123 Angle : 0.552 16.369 18772 Z= 0.286 Chirality : 0.041 0.223 2062 Planarity : 0.004 0.037 2399 Dihedral : 4.610 22.787 1800 Min Nonbonded Distance : 2.348 Molprobity Statistics. All-atom Clashscore : 5.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.47 % Favored : 97.53 % Rotamer: Outliers : 1.77 % Allowed : 11.19 % Favored : 87.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % 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 are not related in a simple way. whole: 0.30 (0.20), residues: 1662 helix: 2.30 (0.27), residues: 333 sheet: 0.38 (0.27), residues: 405 loop : -0.68 (0.19), residues: 924 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 262a TYR 0.008 0.001 TYR B 17 PHE 0.021 0.002 PHE C 118 TRP 0.014 0.001 TRP A 84 HIS 0.009 0.001 HIS B 355 Details of bonding type rmsd/Z covalent geometry : bond 0.00281 / 0.12 (13788) covalent geometry : angle 0.52061 / 0.28 (18675) SS BOND : bond 0.00204 / 0.14 ( 20) SS BOND : angle 0.94055 / 0.76 ( 40) hydrogen bonds : bond 0.04302 / 2.95 ( 543) hydrogen bonds : angle 5.19337 / 3.59 ( 1533) link_BETA1-4 : bond 0.00209 / 0.10 ( 3) link_BETA1-4 : angle 0.99689 / 0.62 ( 9) link_BETA1-6 : bond 0.00586 / 0.29 ( 3) link_BETA1-6 : angle 1.06001 / 0.69 ( 9) link_NAG-ASN : bond 0.00382 / 0.27 ( 13) link_NAG-ASN : angle 3.94920 / 3.11 ( 39) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3324 Ramachandran restraints generated. 1662 Oldfield, 0 Emsley, 1662 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3324 Ramachandran restraints generated. 1662 Oldfield, 0 Emsley, 1662 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 1465 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 167 time to evaluate : 0.518 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 93 ASN cc_start: 0.8996 (t0) cc_final: 0.8749 (t0) REVERT: C 112 LEU cc_start: 0.8091 (mt) cc_final: 0.7820 (mt) REVERT: C 188 GLU cc_start: 0.8377 (mm-30) cc_final: 0.7981 (mt-10) REVERT: C 280 LYS cc_start: 0.7767 (tptt) cc_final: 0.7556 (ttmm) REVERT: C 348 ASP cc_start: 0.6690 (m-30) cc_final: 0.6282 (m-30) REVERT: C 445 LYS cc_start: 0.8508 (tptp) cc_final: 0.7947 (mttp) REVERT: A 24 GLU cc_start: 0.7851 (mm-30) cc_final: 0.7404 (mt-10) REVERT: A 129 GLN cc_start: 0.7738 (mt0) cc_final: 0.7388 (mm110) REVERT: A 174 GLU cc_start: 0.7267 (tp30) cc_final: 0.6846 (tt0) REVERT: A 230 MET cc_start: 0.8741 (mtt) cc_final: 0.8462 (mtt) REVERT: A 367 LYS cc_start: 0.8162 (mttp) cc_final: 0.7948 (mmtm) REVERT: A 487 ASP cc_start: 0.7638 (t0) cc_final: 0.7143 (t70) REVERT: B 27 ASP cc_start: 0.8307 (m-30) cc_final: 0.8065 (m-30) REVERT: B 435 ARG cc_start: 0.8366 (mtp180) cc_final: 0.7941 (mtt180) outliers start: 26 outliers final: 20 residues processed: 189 average time/residue: 0.1382 time to fit residues: 36.8627 Evaluate side-chains 175 residues out of total 1465 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 155 time to evaluate : 0.515 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 20 LEU Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 21 LEU Chi-restraints excluded: chain L residue 85 VAL Chi-restraints excluded: chain C residue 63 ASP Chi-restraints excluded: chain C residue 82 VAL Chi-restraints excluded: chain C residue 118 PHE Chi-restraints excluded: chain C residue 125 ASP Chi-restraints excluded: chain C residue 291 THR Chi-restraints excluded: chain A residue 277 CYS Chi-restraints excluded: chain A residue 291 THR Chi-restraints excluded: chain A residue 351 TYR Chi-restraints excluded: chain B residue 93 ARG Chi-restraints excluded: chain B residue 118 PHE Chi-restraints excluded: chain B residue 155 THR Chi-restraints excluded: chain B residue 277 CYS Chi-restraints excluded: chain B residue 323 VAL Chi-restraints excluded: chain B residue 335 ILE Chi-restraints excluded: chain B residue 457 ASP Chi-restraints excluded: chain B residue 477 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 137 optimal weight: 4.9990 chunk 164 optimal weight: 5.9990 chunk 132 optimal weight: 2.9990 chunk 75 optimal weight: 3.9990 chunk 3 optimal weight: 3.9990 chunk 148 optimal weight: 0.7980 chunk 122 optimal weight: 0.5980 chunk 29 optimal weight: 0.6980 chunk 81 optimal weight: 3.9990 chunk 39 optimal weight: 0.9990 chunk 67 optimal weight: 5.9990 overall best weight: 1.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 354 HIS B 483 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.118903 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3143 r_free = 0.3143 target = 0.098143 restraints weight = 18687.153| |-----------------------------------------------------------------------------| r_work (start): 0.3138 rms_B_bonded: 1.80 r_work: 0.3021 rms_B_bonded: 2.16 restraints_weight: 0.5000 r_work: 0.2891 rms_B_bonded: 3.63 restraints_weight: 0.2500 r_work (final): 0.2891 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8671 moved from start: 0.3963 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 13827 Z= 0.168 Angle : 0.571 16.116 18772 Z= 0.297 Chirality : 0.043 0.244 2062 Planarity : 0.004 0.042 2399 Dihedral : 4.587 21.035 1800 Min Nonbonded Distance : 2.373 Molprobity Statistics. All-atom Clashscore : 4.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.01 % Favored : 96.99 % Rotamer: Outliers : 1.84 % Allowed : 11.81 % Favored : 86.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % 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 are not related in a simple way. whole: 0.31 (0.20), residues: 1662 helix: 2.33 (0.27), residues: 333 sheet: 0.50 (0.27), residues: 391 loop : -0.72 (0.19), residues: 938 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG L 54 TYR 0.021 0.002 TYR L 49 PHE 0.032 0.002 PHE A 118 TRP 0.011 0.001 TRP C 84 HIS 0.005 0.001 HIS B 183 Details of bonding type rmsd/Z covalent geometry : bond 0.00401 / 0.17 (13788) covalent geometry : angle 0.54721 / 0.29 (18675) SS BOND : bond 0.00236 / 0.16 ( 20) SS BOND : angle 0.84963 / 0.66 ( 40) hydrogen bonds : bond 0.04473 / 3.06 ( 543) hydrogen bonds : angle 5.17517 / 3.59 ( 1533) link_BETA1-4 : bond 0.00246 / 0.12 ( 3) link_BETA1-4 : angle 1.15664 / 0.71 ( 9) link_BETA1-6 : bond 0.00615 / 0.30 ( 3) link_BETA1-6 : angle 0.94500 / 0.62 ( 9) link_NAG-ASN : bond 0.00591 / 0.42 ( 13) link_NAG-ASN : angle 3.46936 / 2.86 ( 39) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3324 Ramachandran restraints generated. 1662 Oldfield, 0 Emsley, 1662 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3324 Ramachandran restraints generated. 1662 Oldfield, 0 Emsley, 1662 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 1465 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 159 time to evaluate : 0.568 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 112 LEU cc_start: 0.8119 (mt) cc_final: 0.7850 (mt) REVERT: C 188 GLU cc_start: 0.8423 (mm-30) cc_final: 0.8027 (mt-10) REVERT: C 348 ASP cc_start: 0.6763 (m-30) cc_final: 0.6308 (m-30) REVERT: C 435 ARG cc_start: 0.8063 (mtp85) cc_final: 0.7843 (mtt-85) REVERT: C 445 LYS cc_start: 0.8519 (tptp) cc_final: 0.7938 (ttmm) REVERT: A 24 GLU cc_start: 0.7839 (mm-30) cc_final: 0.7386 (mt-10) REVERT: A 129 GLN cc_start: 0.7772 (mt0) cc_final: 0.7405 (mm110) REVERT: A 160 ASN cc_start: 0.6589 (t0) cc_final: 0.6335 (t0) REVERT: A 174 GLU cc_start: 0.7327 (tp30) cc_final: 0.6883 (tt0) REVERT: A 186 ASN cc_start: 0.7383 (t0) cc_final: 0.7104 (t0) REVERT: A 367 LYS cc_start: 0.8196 (mttp) cc_final: 0.7989 (mptt) REVERT: A 487 ASP cc_start: 0.7630 (t0) cc_final: 0.7160 (t70) REVERT: B 27 ASP cc_start: 0.8336 (m-30) cc_final: 0.8099 (m-30) REVERT: B 435 ARG cc_start: 0.8367 (mtp180) cc_final: 0.7878 (mtt180) outliers start: 27 outliers final: 24 residues processed: 180 average time/residue: 0.1368 time to fit residues: 34.9631 Evaluate side-chains 180 residues out of total 1465 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 156 time to evaluate : 0.540 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 20 LEU Chi-restraints excluded: chain H residue 82 THR Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 21 LEU Chi-restraints excluded: chain L residue 85 VAL Chi-restraints excluded: chain C residue 63 ASP Chi-restraints excluded: chain C residue 82 VAL Chi-restraints excluded: chain C residue 118 PHE Chi-restraints excluded: chain C residue 125 ASP Chi-restraints excluded: chain C residue 160 ASN Chi-restraints excluded: chain C residue 277 CYS Chi-restraints excluded: chain C residue 291 THR Chi-restraints excluded: chain C residue 323 VAL Chi-restraints excluded: chain C residue 389 ASN Chi-restraints excluded: chain C residue 442 SER Chi-restraints excluded: chain C residue 483 ASN Chi-restraints excluded: chain A residue 277 CYS Chi-restraints excluded: chain A residue 291 THR Chi-restraints excluded: chain B residue 118 PHE Chi-restraints excluded: chain B residue 155 THR Chi-restraints excluded: chain B residue 277 CYS Chi-restraints excluded: chain B residue 323 VAL Chi-restraints excluded: chain B residue 335 ILE Chi-restraints excluded: chain B residue 477 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 68 optimal weight: 2.9990 chunk 37 optimal weight: 1.9990 chunk 32 optimal weight: 0.9990 chunk 84 optimal weight: 2.9990 chunk 85 optimal weight: 0.9980 chunk 11 optimal weight: 1.9990 chunk 63 optimal weight: 2.9990 chunk 74 optimal weight: 2.9990 chunk 51 optimal weight: 3.9990 chunk 138 optimal weight: 2.9990 chunk 8 optimal weight: 0.3980 overall best weight: 1.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... L 42 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3430 r_free = 0.3430 target = 0.118062 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3137 r_free = 0.3137 target = 0.097751 restraints weight = 18466.649| |-----------------------------------------------------------------------------| r_work (start): 0.3143 rms_B_bonded: 1.75 r_work: 0.3022 rms_B_bonded: 2.16 restraints_weight: 0.5000 r_work: 0.2891 rms_B_bonded: 3.61 restraints_weight: 0.2500 r_work (final): 0.2891 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8674 moved from start: 0.4042 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 13827 Z= 0.169 Angle : 0.562 10.770 18772 Z= 0.294 Chirality : 0.043 0.215 2062 Planarity : 0.004 0.034 2399 Dihedral : 4.563 19.666 1800 Min Nonbonded Distance : 2.335 Molprobity Statistics. All-atom Clashscore : 5.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer: Outliers : 1.91 % Allowed : 11.88 % Favored : 86.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % 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 are not related in a simple way. whole: 0.34 (0.20), residues: 1662 helix: 2.35 (0.27), residues: 333 sheet: 0.54 (0.28), residues: 381 loop : -0.70 (0.19), residues: 948 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG L 54 TYR 0.011 0.001 TYR A 17 PHE 0.030 0.002 PHE A 118 TRP 0.011 0.001 TRP A 84 HIS 0.004 0.001 HIS A 130 Details of bonding type rmsd/Z covalent geometry : bond 0.00404 / 0.17 (13788) covalent geometry : angle 0.54354 / 0.29 (18675) SS BOND : bond 0.00246 / 0.17 ( 20) SS BOND : angle 0.93910 / 0.76 ( 40) hydrogen bonds : bond 0.04438 / 3.04 ( 543) hydrogen bonds : angle 5.15760 / 3.58 ( 1533) link_BETA1-4 : bond 0.00277 / 0.14 ( 3) link_BETA1-4 : angle 1.11106 / 0.70 ( 9) link_BETA1-6 : bond 0.00607 / 0.30 ( 3) link_BETA1-6 : angle 0.97284 / 0.64 ( 9) link_NAG-ASN : bond 0.00197 / 0.12 ( 13) link_NAG-ASN : angle 3.03616 / 2.23 ( 39) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3324 Ramachandran restraints generated. 1662 Oldfield, 0 Emsley, 1662 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3324 Ramachandran restraints generated. 1662 Oldfield, 0 Emsley, 1662 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 1465 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 163 time to evaluate : 0.542 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 100 PHE cc_start: 0.8970 (OUTLIER) cc_final: 0.8713 (m-80) REVERT: L 54 ARG cc_start: 0.8078 (mtm180) cc_final: 0.7736 (mmm-85) REVERT: C 112 LEU cc_start: 0.8126 (mt) cc_final: 0.7856 (mt) REVERT: C 188 GLU cc_start: 0.8448 (mm-30) cc_final: 0.8051 (mt-10) REVERT: C 280 LYS cc_start: 0.7803 (tptt) cc_final: 0.7594 (ttmm) REVERT: C 445 LYS cc_start: 0.8551 (tptp) cc_final: 0.7949 (mttp) REVERT: A 24 GLU cc_start: 0.7836 (mm-30) cc_final: 0.7374 (mt-10) REVERT: A 129 GLN cc_start: 0.7765 (mt0) cc_final: 0.7400 (mm110) REVERT: A 160 ASN cc_start: 0.6602 (t0) cc_final: 0.6354 (t0) REVERT: A 174 GLU cc_start: 0.7327 (tp30) cc_final: 0.6881 (tt0) REVERT: A 186 ASN cc_start: 0.7351 (t0) cc_final: 0.7080 (t0) REVERT: A 367 LYS cc_start: 0.8210 (mttp) cc_final: 0.8009 (mptt) REVERT: A 487 ASP cc_start: 0.7656 (t0) cc_final: 0.7209 (t70) REVERT: B 27 ASP cc_start: 0.8334 (m-30) cc_final: 0.8110 (m-30) REVERT: B 435 ARG cc_start: 0.8363 (mtp180) cc_final: 0.8010 (mtt180) outliers start: 28 outliers final: 26 residues processed: 186 average time/residue: 0.1342 time to fit residues: 35.4746 Evaluate side-chains 186 residues out of total 1465 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 159 time to evaluate : 0.546 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 20 LEU Chi-restraints excluded: chain H residue 82 THR Chi-restraints excluded: chain H residue 100 PHE Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 21 LEU Chi-restraints excluded: chain L residue 38 GLN Chi-restraints excluded: chain L residue 85 VAL Chi-restraints excluded: chain C residue 63 ASP Chi-restraints excluded: chain C residue 82 VAL Chi-restraints excluded: chain C residue 118 PHE Chi-restraints excluded: chain C residue 125 ASP Chi-restraints excluded: chain C residue 160 ASN Chi-restraints excluded: chain C residue 273 THR Chi-restraints excluded: chain C residue 277 CYS Chi-restraints excluded: chain C residue 291 THR Chi-restraints excluded: chain C residue 323 VAL Chi-restraints excluded: chain C residue 442 SER Chi-restraints excluded: chain A residue 277 CYS Chi-restraints excluded: chain A residue 291 THR Chi-restraints excluded: chain A residue 442 SER Chi-restraints excluded: chain B residue 118 PHE Chi-restraints excluded: chain B residue 155 THR Chi-restraints excluded: chain B residue 277 CYS Chi-restraints excluded: chain B residue 323 VAL Chi-restraints excluded: chain B residue 335 ILE Chi-restraints excluded: chain B residue 457 ASP Chi-restraints excluded: chain B residue 477 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 137 optimal weight: 3.9990 chunk 140 optimal weight: 2.9990 chunk 56 optimal weight: 1.9990 chunk 65 optimal weight: 1.9990 chunk 108 optimal weight: 2.9990 chunk 27 optimal weight: 0.9990 chunk 144 optimal weight: 2.9990 chunk 87 optimal weight: 0.8980 chunk 1 optimal weight: 0.1980 chunk 36 optimal weight: 0.6980 chunk 85 optimal weight: 0.0980 overall best weight: 0.5782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 483 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.117267 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3105 r_free = 0.3105 target = 0.096320 restraints weight = 18749.463| |-----------------------------------------------------------------------------| r_work (start): 0.3097 rms_B_bonded: 1.84 r_work: 0.2978 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.2846 rms_B_bonded: 3.77 restraints_weight: 0.2500 r_work (final): 0.2846 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8649 moved from start: 0.4116 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 13827 Z= 0.111 Angle : 0.509 9.352 18772 Z= 0.270 Chirality : 0.040 0.205 2062 Planarity : 0.004 0.035 2399 Dihedral : 4.302 17.505 1800 Min Nonbonded Distance : 2.375 Molprobity Statistics. All-atom Clashscore : 5.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Rotamer: Outliers : 1.91 % Allowed : 12.08 % Favored : 86.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % 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 are not related in a simple way. whole: 0.52 (0.21), residues: 1662 helix: 2.58 (0.27), residues: 333 sheet: 0.62 (0.27), residues: 398 loop : -0.62 (0.20), residues: 931 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG L 61 TYR 0.022 0.001 TYR L 49 PHE 0.019 0.001 PHE C 118 TRP 0.011 0.001 TRP A 84 HIS 0.003 0.001 HIS B 354 Details of bonding type rmsd/Z covalent geometry : bond 0.00252 / 0.11 (13788) covalent geometry : angle 0.49438 / 0.27 (18675) SS BOND : bond 0.00207 / 0.15 ( 20) SS BOND : angle 0.77076 / 0.63 ( 40) hydrogen bonds : bond 0.04108 / 2.82 ( 543) hydrogen bonds : angle 5.00448 / 3.47 ( 1533) link_BETA1-4 : bond 0.00316 / 0.16 ( 3) link_BETA1-4 : angle 1.03026 / 0.64 ( 9) link_BETA1-6 : bond 0.00453 / 0.22 ( 3) link_BETA1-6 : angle 1.05248 / 0.68 ( 9) link_NAG-ASN : bond 0.00154 / 0.10 ( 13) link_NAG-ASN : angle 2.54594 / 1.86 ( 39) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3324 Ramachandran restraints generated. 1662 Oldfield, 0 Emsley, 1662 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3324 Ramachandran restraints generated. 1662 Oldfield, 0 Emsley, 1662 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 199 residues out of total 1465 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 171 time to evaluate : 0.579 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 100 PHE cc_start: 0.8806 (OUTLIER) cc_final: 0.8549 (m-80) REVERT: L 54 ARG cc_start: 0.8064 (mtm180) cc_final: 0.7705 (mmm-85) REVERT: C 112 LEU cc_start: 0.7954 (mt) cc_final: 0.7644 (mt) REVERT: C 188 GLU cc_start: 0.8513 (mm-30) cc_final: 0.8123 (mt-10) REVERT: C 490 LYS cc_start: 0.8535 (mtpp) cc_final: 0.8285 (ttmt) REVERT: A 24 GLU cc_start: 0.7905 (mm-30) cc_final: 0.7452 (mt-10) REVERT: A 129 GLN cc_start: 0.7805 (mt0) cc_final: 0.7405 (mm110) REVERT: A 160 ASN cc_start: 0.6602 (t0) cc_final: 0.6383 (t0) REVERT: A 174 GLU cc_start: 0.7234 (tp30) cc_final: 0.6828 (tt0) REVERT: A 487 ASP cc_start: 0.7589 (t0) cc_final: 0.7133 (t70) REVERT: B 27 ASP cc_start: 0.8448 (m-30) cc_final: 0.8246 (m-30) REVERT: B 435 ARG cc_start: 0.8258 (mtp180) cc_final: 0.7922 (mtt180) outliers start: 28 outliers final: 25 residues processed: 192 average time/residue: 0.1338 time to fit residues: 36.5916 Evaluate side-chains 181 residues out of total 1465 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 155 time to evaluate : 0.530 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 20 LEU Chi-restraints excluded: chain H residue 82 THR Chi-restraints excluded: chain H residue 100 PHE Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 21 LEU Chi-restraints excluded: chain L residue 38 GLN Chi-restraints excluded: chain L residue 85 VAL Chi-restraints excluded: chain C residue 82 VAL Chi-restraints excluded: chain C residue 118 PHE Chi-restraints excluded: chain C residue 125 ASP Chi-restraints excluded: chain C residue 160 ASN Chi-restraints excluded: chain C residue 273 THR Chi-restraints excluded: chain C residue 277 CYS Chi-restraints excluded: chain C residue 291 THR Chi-restraints excluded: chain C residue 323 VAL Chi-restraints excluded: chain A residue 118 PHE Chi-restraints excluded: chain A residue 277 CYS Chi-restraints excluded: chain A residue 291 THR Chi-restraints excluded: chain A residue 442 SER Chi-restraints excluded: chain B residue 118 PHE Chi-restraints excluded: chain B residue 155 THR Chi-restraints excluded: chain B residue 277 CYS Chi-restraints excluded: chain B residue 323 VAL Chi-restraints excluded: chain B residue 335 ILE Chi-restraints excluded: chain B residue 346 MET Chi-restraints excluded: chain B residue 477 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 21 optimal weight: 0.8980 chunk 20 optimal weight: 4.9990 chunk 125 optimal weight: 2.9990 chunk 133 optimal weight: 0.0070 chunk 12 optimal weight: 4.9990 chunk 136 optimal weight: 3.9990 chunk 72 optimal weight: 4.9990 chunk 140 optimal weight: 0.9980 chunk 68 optimal weight: 0.9990 chunk 75 optimal weight: 2.9990 chunk 102 optimal weight: 3.9990 overall best weight: 1.1802 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 401 ASN B 483 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3450 r_free = 0.3450 target = 0.119525 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3151 r_free = 0.3151 target = 0.098730 restraints weight = 18529.343| |-----------------------------------------------------------------------------| r_work (start): 0.3142 rms_B_bonded: 1.81 r_work: 0.3023 rms_B_bonded: 2.18 restraints_weight: 0.5000 r_work: 0.2891 rms_B_bonded: 3.67 restraints_weight: 0.2500 r_work (final): 0.2891 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8668 moved from start: 0.4132 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 13827 Z= 0.159 Angle : 0.552 8.546 18772 Z= 0.289 Chirality : 0.042 0.253 2062 Planarity : 0.004 0.035 2399 Dihedral : 4.433 18.455 1800 Min Nonbonded Distance : 2.361 Molprobity Statistics. All-atom Clashscore : 5.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.13 % Favored : 96.87 % Rotamer: Outliers : 2.05 % Allowed : 12.56 % Favored : 85.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % 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 are not related in a simple way. whole: 0.49 (0.21), residues: 1662 helix: 2.51 (0.27), residues: 333 sheet: 0.59 (0.27), residues: 398 loop : -0.62 (0.20), residues: 931 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG L 61 TYR 0.010 0.001 TYR A 17 PHE 0.028 0.002 PHE A 118 TRP 0.009 0.001 TRP H 103 HIS 0.004 0.001 HIS A 130 Details of bonding type rmsd/Z covalent geometry : bond 0.00380 / 0.16 (13788) covalent geometry : angle 0.53686 / 0.29 (18675) SS BOND : bond 0.00222 / 0.15 ( 20) SS BOND : angle 0.85363 / 0.69 ( 40) hydrogen bonds : bond 0.04327 / 2.96 ( 543) hydrogen bonds : angle 5.07722 / 3.53 ( 1533) link_BETA1-4 : bond 0.00261 / 0.13 ( 3) link_BETA1-4 : angle 1.09524 / 0.68 ( 9) link_BETA1-6 : bond 0.00590 / 0.29 ( 3) link_BETA1-6 : angle 0.97443 / 0.64 ( 9) link_NAG-ASN : bond 0.00300 / 0.17 ( 13) link_NAG-ASN : angle 2.74952 / 1.88 ( 39) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3324 Ramachandran restraints generated. 1662 Oldfield, 0 Emsley, 1662 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3324 Ramachandran restraints generated. 1662 Oldfield, 0 Emsley, 1662 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 1465 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 157 time to evaluate : 0.709 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 100 PHE cc_start: 0.8844 (OUTLIER) cc_final: 0.8588 (m-80) REVERT: L 54 ARG cc_start: 0.8126 (mtm180) cc_final: 0.7800 (mmm-85) REVERT: C 112 LEU cc_start: 0.8092 (mt) cc_final: 0.7825 (mt) REVERT: C 188 GLU cc_start: 0.8480 (mm-30) cc_final: 0.8099 (mt-10) REVERT: C 490 LYS cc_start: 0.8564 (mtpp) cc_final: 0.8299 (ttmt) REVERT: A 24 GLU cc_start: 0.7875 (mm-30) cc_final: 0.7420 (mt-10) REVERT: A 129 GLN cc_start: 0.7754 (mt0) cc_final: 0.7380 (mm110) REVERT: A 160 ASN cc_start: 0.6566 (t0) cc_final: 0.6338 (t0) REVERT: A 174 GLU cc_start: 0.7341 (tp30) cc_final: 0.6840 (tt0) REVERT: A 186 ASN cc_start: 0.7399 (t0) cc_final: 0.7167 (t0) REVERT: A 280 LYS cc_start: 0.7931 (ttmt) cc_final: 0.7472 (mtpt) REVERT: A 487 ASP cc_start: 0.7636 (t0) cc_final: 0.7198 (t70) REVERT: B 27 ASP cc_start: 0.8411 (m-30) cc_final: 0.8200 (m-30) REVERT: B 435 ARG cc_start: 0.8322 (mtp180) cc_final: 0.7977 (mtt180) outliers start: 30 outliers final: 27 residues processed: 179 average time/residue: 0.1279 time to fit residues: 32.9246 Evaluate side-chains 180 residues out of total 1465 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 152 time to evaluate : 0.475 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 20 LEU Chi-restraints excluded: chain H residue 77 GLN Chi-restraints excluded: chain H residue 82 THR Chi-restraints excluded: chain H residue 100 PHE Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 21 LEU Chi-restraints excluded: chain L residue 85 VAL Chi-restraints excluded: chain C residue 63 ASP Chi-restraints excluded: chain C residue 82 VAL Chi-restraints excluded: chain C residue 118 PHE Chi-restraints excluded: chain C residue 125 ASP Chi-restraints excluded: chain C residue 160 ASN Chi-restraints excluded: chain C residue 273 THR Chi-restraints excluded: chain C residue 277 CYS Chi-restraints excluded: chain C residue 291 THR Chi-restraints excluded: chain C residue 323 VAL Chi-restraints excluded: chain C residue 442 SER Chi-restraints excluded: chain A residue 118 PHE Chi-restraints excluded: chain A residue 277 CYS Chi-restraints excluded: chain A residue 291 THR Chi-restraints excluded: chain A residue 442 SER Chi-restraints excluded: chain B residue 118 PHE Chi-restraints excluded: chain B residue 155 THR Chi-restraints excluded: chain B residue 277 CYS Chi-restraints excluded: chain B residue 323 VAL Chi-restraints excluded: chain B residue 335 ILE Chi-restraints excluded: chain B residue 346 MET Chi-restraints excluded: chain B residue 477 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 80 optimal weight: 2.9990 chunk 10 optimal weight: 0.3980 chunk 52 optimal weight: 1.9990 chunk 81 optimal weight: 1.9990 chunk 45 optimal weight: 2.9990 chunk 113 optimal weight: 2.9990 chunk 108 optimal weight: 2.9990 chunk 163 optimal weight: 0.8980 chunk 34 optimal weight: 2.9990 chunk 17 optimal weight: 10.0000 chunk 150 optimal weight: 0.1980 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 401 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.119466 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3151 r_free = 0.3151 target = 0.098717 restraints weight = 18687.059| |-----------------------------------------------------------------------------| r_work (start): 0.3140 rms_B_bonded: 1.80 r_work: 0.3023 rms_B_bonded: 2.16 restraints_weight: 0.5000 r_work: 0.2891 rms_B_bonded: 3.65 restraints_weight: 0.2500 r_work (final): 0.2891 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8664 moved from start: 0.4173 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 13827 Z= 0.151 Angle : 0.538 7.966 18772 Z= 0.284 Chirality : 0.042 0.208 2062 Planarity : 0.004 0.035 2399 Dihedral : 4.418 17.823 1800 Min Nonbonded Distance : 2.384 Molprobity Statistics. All-atom Clashscore : 5.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Rotamer: Outliers : 2.05 % Allowed : 12.49 % Favored : 85.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % 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 are not related in a simple way. whole: 0.50 (0.21), residues: 1662 helix: 2.53 (0.27), residues: 333 sheet: 0.60 (0.27), residues: 398 loop : -0.62 (0.20), residues: 931 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG L 61 TYR 0.026 0.001 TYR L 49 PHE 0.026 0.002 PHE A 118 TRP 0.011 0.001 TRP A 84 HIS 0.004 0.001 HIS A 295 Details of bonding type rmsd/Z covalent geometry : bond 0.00357 / 0.15 (13788) covalent geometry : angle 0.52642 / 0.28 (18675) SS BOND : bond 0.00222 / 0.15 ( 20) SS BOND : angle 0.83173 / 0.67 ( 40) hydrogen bonds : bond 0.04293 / 2.94 ( 543) hydrogen bonds : angle 5.09674 / 3.54 ( 1533) link_BETA1-4 : bond 0.00276 / 0.14 ( 3) link_BETA1-4 : angle 1.05749 / 0.67 ( 9) link_BETA1-6 : bond 0.00596 / 0.29 ( 3) link_BETA1-6 : angle 0.98567 / 0.63 ( 9) link_NAG-ASN : bond 0.00167 / 0.11 ( 13) link_NAG-ASN : angle 2.36672 / 1.65 ( 39) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3622.86 seconds wall clock time: 63 minutes 0.06 seconds (3780.06 seconds total)