Starting phenix.real_space_refine on Sat Aug 23 17:24:57 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8tp2_41464/08_2025/8tp2_41464.cif Found real_map, /net/cci-nas-00/data/ceres_data/8tp2_41464/08_2025/8tp2_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 { model { file = "/net/cci-nas-00/data/ceres_data/8tp2_41464/08_2025/8tp2_41464.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8tp2_41464/08_2025/8tp2_41464.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8tp2_41464/08_2025/8tp2_41464.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8tp2_41464/08_2025/8tp2_41464.map" } 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-2.0-5787/lib/python3.9/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 dihedrals: 9 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 dihedrals: 9 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 dihedrals: 9 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 dihedrals: 12 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 dihedrals: 9 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 dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Time building chain proxies: 3.45, per 1000 atoms: 0.26 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: 1.16 Conformation dependent library (CDL) restraints added in 568.8 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 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: 0.67 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: 2.80 Time building geometry restraints manager: 1.55 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: 8172 18.08 - 36.16: 220 36.16 - 54.24: 37 54.24 - 72.32: 32 72.32 - 90.40: 18 Dihedral angle restraints: 8479 sinusoidal: 3681 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 8476 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: 3.380 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: 0.190 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 14.450 Find NCS groups from input model: 0.270 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:1.330 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.740 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8226 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 : 10.562 90.404 5359 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 aren 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 covalent geometry : bond 0.02072 (13788) covalent geometry : angle 1.69412 (18675) SS BOND : bond 0.01174 ( 20) SS BOND : angle 2.98721 ( 40) hydrogen bonds : bond 0.13596 ( 543) hydrogen bonds : angle 7.00594 ( 1533) link_BETA1-4 : bond 0.06935 ( 3) link_BETA1-4 : angle 4.99765 ( 9) link_BETA1-6 : bond 0.05584 ( 3) link_BETA1-6 : angle 2.55582 ( 9) link_NAG-ASN : bond 0.06937 ( 13) link_NAG-ASN : angle 2.83322 ( 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 : 0.561 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: 0.8217 (t70) outliers start: 0 outliers final: 0 residues processed: 349 average time/residue: 0.1599 time to fit residues: 75.7415 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 : 0.498 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: 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 = 0.125401 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3237 r_free = 0.3237 target = 0.104641 restraints weight = 18436.892| |-----------------------------------------------------------------------------| r_work (start): 0.3234 rms_B_bonded: 1.82 r_work: 0.3112 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: 0.8352 moved from start: 0.2564 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 13827 Z= 0.153 Angle : 0.617 6.739 18772 Z= 0.339 Chirality : 0.043 0.224 2062 Planarity : 0.004 0.065 2399 Dihedral : 5.523 49.392 2187 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 4.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 1.37 % Allowed : 6.14 % Favored : 92.49 % 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 aren not related in a simple way. whole: 0.80 (0.20), residues: 1662 helix: 2.34 (0.28), residues: 332 sheet: 0.79 (0.26), residues: 380 loop : -0.20 (0.19), residues: 950 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 262a TYR 0.018 0.002 TYR B 17 PHE 0.021 0.002 PHE B 118 TRP 0.015 0.002 TRP L 96 HIS 0.012 0.001 HIS C 355 Details of bonding type rmsd covalent geometry : bond 0.00341 (13788) covalent geometry : angle 0.60974 (18675) SS BOND : bond 0.00323 ( 20) SS BOND : angle 0.96270 ( 40) hydrogen bonds : bond 0.05349 ( 543) hydrogen bonds : angle 5.54546 ( 1533) link_BETA1-4 : bond 0.00356 ( 3) link_BETA1-4 : angle 2.23521 ( 9) link_BETA1-6 : bond 0.00853 ( 3) link_BETA1-6 : angle 0.91436 ( 9) link_NAG-ASN : bond 0.00364 ( 13) link_NAG-ASN : angle 1.64968 ( 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 221 residues out of total 1465 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 201 time to evaluate : 0.597 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: L 54 ARG cc_start: 0.8058 (mtm110) cc_final: 0.7806 (mmm-85) REVERT: L 92 ASN cc_start: 0.8743 (t0) cc_final: 0.8358 (t0) REVERT: C 160 ASN cc_start: 0.8555 (m110) cc_final: 0.8281 (t0) REVERT: C 435 ARG cc_start: 0.7948 (mmm160) cc_final: 0.7555 (mmp-170) REVERT: C 445 LYS cc_start: 0.8692 (tptp) cc_final: 0.8229 (ttmm) REVERT: A 24 GLU cc_start: 0.7850 (mm-30) cc_final: 0.7499 (mt-10) REVERT: A 50 LYS cc_start: 0.7926 (mttt) cc_final: 0.7547 (mtpt) REVERT: A 129 GLN cc_start: 0.7687 (mt0) cc_final: 0.7386 (mm110) REVERT: A 487 ASP cc_start: 0.7754 (t0) cc_final: 0.7169 (t70) REVERT: B 27 ASP cc_start: 0.8031 (m-30) cc_final: 0.7808 (m-30) REVERT: B 239 MET cc_start: 0.8115 (OUTLIER) cc_final: 0.7824 (mtm) REVERT: B 275 GLU cc_start: 0.7799 (mm-30) cc_final: 0.7090 (mp0) REVERT: B 401 ASN cc_start: 0.8666 (m-40) cc_final: 0.8277 (p0) outliers start: 20 outliers final: 11 residues processed: 214 average time/residue: 0.1359 time to fit residues: 41.4409 Evaluate side-chains 172 residues out of total 1465 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 160 time to evaluate : 0.564 ------------------------------------------------------------------------------- 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: 6.9990 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: 3.9990 chunk 47 optimal weight: 1.9990 chunk 74 optimal weight: 0.9990 chunk 55 optimal weight: 3.9990 chunk 146 optimal weight: 4.9990 chunk 155 optimal weight: 4.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3352 r_free = 0.3352 target = 0.113177 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3043 r_free = 0.3043 target = 0.092167 restraints weight = 18973.944| |-----------------------------------------------------------------------------| r_work (start): 0.3044 rms_B_bonded: 1.84 r_work: 0.2919 rms_B_bonded: 2.26 restraints_weight: 0.5000 r_work: 0.2787 rms_B_bonded: 3.74 restraints_weight: 0.2500 r_work (final): 0.2787 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8499 moved from start: 0.3303 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.108 13827 Z= 0.363 Angle : 0.743 7.424 18772 Z= 0.392 Chirality : 0.050 0.266 2062 Planarity : 0.005 0.067 2399 Dihedral : 5.911 59.885 2187 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 5.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 1.98 % Allowed : 8.87 % Favored : 89.15 % 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 aren not related in a simple way. whole: 0.18 (0.19), residues: 1662 helix: 1.74 (0.27), residues: 333 sheet: 0.52 (0.25), residues: 398 loop : -0.67 (0.18), residues: 931 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 405 TYR 0.020 0.003 TYR B 17 PHE 0.054 0.004 PHE A 118 TRP 0.015 0.003 TRP A 84 HIS 0.009 0.002 HIS B 183 Details of bonding type rmsd covalent geometry : bond 0.00888 (13788) covalent geometry : angle 0.73707 (18675) SS BOND : bond 0.00632 ( 20) SS BOND : angle 1.19424 ( 40) hydrogen bonds : bond 0.05594 ( 543) hydrogen bonds : angle 5.55193 ( 1533) link_BETA1-4 : bond 0.00346 ( 3) link_BETA1-4 : angle 1.79855 ( 9) link_BETA1-6 : bond 0.00939 ( 3) link_BETA1-6 : angle 0.88311 ( 9) link_NAG-ASN : bond 0.00831 ( 13) link_NAG-ASN : angle 1.84521 ( 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 204 residues out of total 1465 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 175 time to evaluate : 0.549 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: H 5 GLN cc_start: 0.8093 (tp40) cc_final: 0.7885 (tp-100) REVERT: L 90 GLN cc_start: 0.8812 (tm-30) cc_final: 0.8558 (tm-30) REVERT: L 92 ASN cc_start: 0.8877 (t0) cc_final: 0.8467 (t0) REVERT: C 160 ASN cc_start: 0.8607 (m110) cc_final: 0.8260 (t0) REVERT: C 188 GLU cc_start: 0.8306 (mm-30) cc_final: 0.7892 (mt-10) REVERT: C 348 ASP cc_start: 0.6509 (m-30) cc_final: 0.6188 (m-30) REVERT: C 435 ARG cc_start: 0.8136 (mmm160) cc_final: 0.7553 (mmp-170) REVERT: C 445 LYS cc_start: 0.8645 (tptp) cc_final: 0.8108 (ttmm) REVERT: C 478 MET cc_start: 0.7721 (mmt) cc_final: 0.7119 (mmt) REVERT: A 24 GLU cc_start: 0.7873 (mm-30) cc_final: 0.7421 (mt-10) REVERT: A 160 ASN cc_start: 0.6921 (t0) cc_final: 0.6640 (t0) REVERT: A 313 LYS cc_start: 0.8400 (pttt) cc_final: 0.8188 (ptmt) REVERT: A 367 LYS cc_start: 0.8301 (mttp) cc_final: 0.8051 (mptt) REVERT: A 487 ASP cc_start: 0.7841 (t0) cc_final: 0.7320 (t70) REVERT: B 27 ASP cc_start: 0.8301 (m-30) cc_final: 0.8064 (m-30) REVERT: B 239 MET cc_start: 0.8280 (OUTLIER) cc_final: 0.7997 (mtm) REVERT: B 275 GLU cc_start: 0.7921 (mm-30) cc_final: 0.7186 (mp0) REVERT: B 435 ARG cc_start: 0.8444 (mtp180) cc_final: 0.8077 (mtt180) outliers start: 29 outliers final: 22 residues processed: 199 average time/residue: 0.1456 time to fit residues: 40.6624 Evaluate side-chains 185 residues out of total 1465 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 162 time to evaluate : 0.561 ------------------------------------------------------------------------------- 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 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 273 THR Chi-restraints excluded: chain C residue 291 THR Chi-restraints excluded: chain C residue 369 SER 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 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 72 optimal weight: 1.9990 chunk 63 optimal weight: 0.6980 chunk 98 optimal weight: 0.7980 chunk 142 optimal weight: 0.0070 chunk 124 optimal weight: 0.5980 chunk 113 optimal weight: 0.8980 chunk 2 optimal weight: 0.8980 chunk 77 optimal weight: 0.5980 chunk 153 optimal weight: 1.9990 chunk 71 optimal weight: 0.9990 chunk 126 optimal weight: 0.0980 overall best weight: 0.3998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.122941 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3206 r_free = 0.3206 target = 0.102383 restraints weight = 18439.145| |-----------------------------------------------------------------------------| r_work (start): 0.3199 rms_B_bonded: 1.76 r_work: 0.3088 rms_B_bonded: 2.12 restraints_weight: 0.5000 r_work: 0.2960 rms_B_bonded: 3.58 restraints_weight: 0.2500 r_work (final): 0.2960 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8400 moved from start: 0.3509 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 13827 Z= 0.115 Angle : 0.539 11.655 18772 Z= 0.286 Chirality : 0.041 0.235 2062 Planarity : 0.004 0.041 2399 Dihedral : 5.339 59.570 2187 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 4.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 1.30 % Allowed : 10.03 % 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 aren not related in a simple way. whole: 0.38 (0.20), residues: 1662 helix: 2.30 (0.27), residues: 333 sheet: 0.47 (0.25), residues: 415 loop : -0.63 (0.19), residues: 914 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG L 61 TYR 0.018 0.001 TYR L 49 PHE 0.019 0.001 PHE A 118 TRP 0.015 0.001 TRP C 84 HIS 0.003 0.001 HIS C 471 Details of bonding type rmsd covalent geometry : bond 0.00244 (13788) covalent geometry : angle 0.53034 (18675) SS BOND : bond 0.00182 ( 20) SS BOND : angle 0.63810 ( 40) hydrogen bonds : bond 0.04370 ( 543) hydrogen bonds : angle 5.17798 ( 1533) link_BETA1-4 : bond 0.00215 ( 3) link_BETA1-4 : angle 1.33585 ( 9) link_BETA1-6 : bond 0.00688 ( 3) link_BETA1-6 : angle 1.17283 ( 9) link_NAG-ASN : bond 0.00176 ( 13) link_NAG-ASN : angle 2.04243 ( 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 201 residues out of total 1465 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 182 time to evaluate : 0.558 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: L 49 TYR cc_start: 0.8525 (p90) cc_final: 0.8318 (p90) REVERT: L 90 GLN cc_start: 0.8707 (tm-30) cc_final: 0.8407 (pp30) REVERT: L 92 ASN cc_start: 0.8769 (t0) cc_final: 0.8386 (t0) REVERT: L 93 ASN cc_start: 0.8951 (t0) cc_final: 0.8645 (t0) REVERT: C 160 ASN cc_start: 0.8500 (m110) cc_final: 0.8260 (t0) REVERT: C 188 GLU cc_start: 0.8338 (mm-30) cc_final: 0.7940 (mt-10) REVERT: C 348 ASP cc_start: 0.6502 (m-30) cc_final: 0.6259 (m-30) REVERT: C 442 SER cc_start: 0.8929 (t) cc_final: 0.8664 (m) REVERT: C 445 LYS cc_start: 0.8642 (tptp) cc_final: 0.8141 (mttp) REVERT: A 24 GLU cc_start: 0.7700 (mm-30) cc_final: 0.7385 (mt-10) REVERT: A 129 GLN cc_start: 0.7662 (mt0) cc_final: 0.7380 (mm110) REVERT: A 160 ASN cc_start: 0.6558 (t0) cc_final: 0.6358 (t0) REVERT: A 174 GLU cc_start: 0.7287 (tp30) cc_final: 0.6817 (tt0) REVERT: A 367 LYS cc_start: 0.8127 (mttp) cc_final: 0.7889 (mmtm) REVERT: A 401 ASN cc_start: 0.8757 (p0) cc_final: 0.8505 (p0) REVERT: A 487 ASP cc_start: 0.7618 (t0) cc_final: 0.7138 (t70) REVERT: B 27 ASP cc_start: 0.8215 (m-30) cc_final: 0.7970 (m-30) REVERT: B 59 LEU cc_start: 0.8816 (OUTLIER) cc_final: 0.8506 (tp) REVERT: B 435 ARG cc_start: 0.8333 (mtp180) cc_final: 0.7944 (mtt180) REVERT: B 445 LYS cc_start: 0.8305 (tttm) cc_final: 0.8096 (ttmm) outliers start: 19 outliers final: 10 residues processed: 195 average time/residue: 0.1534 time to fit residues: 41.4610 Evaluate side-chains 173 residues out of total 1465 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 162 time to evaluate : 0.531 ------------------------------------------------------------------------------- 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 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 B residue 59 LEU Chi-restraints excluded: chain B residue 323 VAL 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: 1.9990 chunk 17 optimal weight: 10.0000 chunk 43 optimal weight: 0.9990 chunk 158 optimal weight: 1.9990 chunk 75 optimal weight: 3.9990 chunk 66 optimal weight: 0.9980 chunk 76 optimal weight: 0.7980 chunk 134 optimal weight: 3.9990 chunk 153 optimal weight: 5.9990 chunk 116 optimal weight: 0.7980 chunk 47 optimal weight: 3.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 5 GLN ** L 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 483 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.116756 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3100 r_free = 0.3100 target = 0.095983 restraints weight = 18718.909| |-----------------------------------------------------------------------------| r_work (start): 0.3093 rms_B_bonded: 1.82 r_work: 0.2972 rms_B_bonded: 2.23 restraints_weight: 0.5000 r_work: 0.2838 rms_B_bonded: 3.75 restraints_weight: 0.2500 r_work (final): 0.2838 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8448 moved from start: 0.3634 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 13827 Z= 0.160 Angle : 0.570 15.276 18772 Z= 0.297 Chirality : 0.042 0.228 2062 Planarity : 0.004 0.042 2399 Dihedral : 5.185 55.684 2187 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 4.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.01 % Favored : 96.99 % Rotamer: Outliers : 1.57 % Allowed : 10.51 % Favored : 87.92 % 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 aren not related in a simple way. whole: 0.34 (0.20), residues: 1662 helix: 2.34 (0.27), residues: 333 sheet: 0.47 (0.27), residues: 395 loop : -0.68 (0.19), residues: 934 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 262a TYR 0.014 0.002 TYR L 49 PHE 0.029 0.002 PHE A 118 TRP 0.010 0.001 TRP C 84 HIS 0.007 0.001 HIS B 355 Details of bonding type rmsd covalent geometry : bond 0.00377 (13788) covalent geometry : angle 0.54616 (18675) SS BOND : bond 0.00390 ( 20) SS BOND : angle 1.00155 ( 40) hydrogen bonds : bond 0.04477 ( 543) hydrogen bonds : angle 5.20420 ( 1533) link_BETA1-4 : bond 0.00276 ( 3) link_BETA1-4 : angle 1.47378 ( 9) link_BETA1-6 : bond 0.00615 ( 3) link_BETA1-6 : angle 0.97966 ( 9) link_NAG-ASN : bond 0.00262 ( 13) link_NAG-ASN : angle 3.47436 ( 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 195 residues out of total 1465 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 172 time to evaluate : 0.563 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: L 90 GLN cc_start: 0.8771 (tm-30) cc_final: 0.8525 (pp30) REVERT: L 92 ASN cc_start: 0.8756 (t0) cc_final: 0.8376 (t0) REVERT: L 93 ASN cc_start: 0.9095 (t0) cc_final: 0.8807 (t0) REVERT: C 188 GLU cc_start: 0.8313 (mm-30) cc_final: 0.7914 (mt-10) REVERT: C 304 GLU cc_start: 0.7089 (mt-10) cc_final: 0.6868 (mt-10) REVERT: C 348 ASP cc_start: 0.6559 (m-30) cc_final: 0.6261 (m-30) REVERT: C 435 ARG cc_start: 0.8162 (mtp85) cc_final: 0.7607 (mtt90) REVERT: C 445 LYS cc_start: 0.8561 (tptp) cc_final: 0.7960 (ttmm) REVERT: A 24 GLU cc_start: 0.7841 (mm-30) cc_final: 0.7433 (mt-10) REVERT: A 129 GLN cc_start: 0.7819 (mt0) cc_final: 0.7441 (mm110) REVERT: A 174 GLU cc_start: 0.7319 (tp30) cc_final: 0.6870 (tt0) REVERT: A 367 LYS cc_start: 0.8227 (mttp) cc_final: 0.8011 (mmtm) REVERT: A 401 ASN cc_start: 0.8691 (p0) cc_final: 0.8439 (p0) REVERT: A 487 ASP cc_start: 0.7652 (t0) cc_final: 0.7204 (t70) REVERT: B 27 ASP cc_start: 0.8342 (m-30) cc_final: 0.8101 (m-30) REVERT: B 435 ARG cc_start: 0.8377 (mtp180) cc_final: 0.8095 (mtm180) REVERT: B 445 LYS cc_start: 0.8425 (tttm) cc_final: 0.8178 (ttmm) outliers start: 23 outliers final: 18 residues processed: 191 average time/residue: 0.1475 time to fit residues: 39.3269 Evaluate side-chains 180 residues out of total 1465 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 162 time to evaluate : 0.568 ------------------------------------------------------------------------------- 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 12 SER 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 291 THR 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 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: 5.9990 chunk 99 optimal weight: 1.9990 chunk 165 optimal weight: 0.5980 chunk 83 optimal weight: 0.0870 chunk 60 optimal weight: 3.9990 chunk 44 optimal weight: 0.7980 chunk 144 optimal weight: 0.2980 chunk 47 optimal weight: 2.9990 chunk 153 optimal weight: 6.9990 chunk 33 optimal weight: 2.9990 chunk 49 optimal weight: 1.9990 overall best weight: 0.7560 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 160 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.118145 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3120 r_free = 0.3120 target = 0.097299 restraints weight = 18523.876| |-----------------------------------------------------------------------------| r_work (start): 0.3112 rms_B_bonded: 1.83 r_work: 0.2990 rms_B_bonded: 2.26 restraints_weight: 0.5000 r_work: 0.2857 rms_B_bonded: 3.77 restraints_weight: 0.2500 r_work (final): 0.2857 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8429 moved from start: 0.3777 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 13827 Z= 0.124 Angle : 0.528 12.939 18772 Z= 0.277 Chirality : 0.041 0.220 2062 Planarity : 0.004 0.035 2399 Dihedral : 5.050 57.739 2187 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 4.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 1.57 % Allowed : 10.99 % Favored : 87.44 % 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 aren not related in a simple way. whole: 0.46 (0.20), residues: 1662 helix: 2.52 (0.27), residues: 333 sheet: 0.52 (0.27), residues: 395 loop : -0.62 (0.19), residues: 934 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG L 54 TYR 0.008 0.001 TYR A 17 PHE 0.023 0.002 PHE A 118 TRP 0.011 0.001 TRP C 84 HIS 0.007 0.001 HIS B 355 Details of bonding type rmsd covalent geometry : bond 0.00283 (13788) covalent geometry : angle 0.50753 (18675) SS BOND : bond 0.00195 ( 20) SS BOND : angle 0.90200 ( 40) hydrogen bonds : bond 0.04218 ( 543) hydrogen bonds : angle 5.07610 ( 1533) link_BETA1-4 : bond 0.00290 ( 3) link_BETA1-4 : angle 1.33934 ( 9) link_BETA1-6 : bond 0.00558 ( 3) link_BETA1-6 : angle 1.09884 ( 9) link_NAG-ASN : bond 0.00150 ( 13) link_NAG-ASN : angle 3.07576 ( 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 198 residues out of total 1465 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 175 time to evaluate : 0.573 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: L 54 ARG cc_start: 0.8037 (mtm110) cc_final: 0.7689 (mmm-85) REVERT: L 92 ASN cc_start: 0.8734 (t0) cc_final: 0.8398 (t0) REVERT: L 93 ASN cc_start: 0.9046 (t0) cc_final: 0.8808 (t0) REVERT: C 188 GLU cc_start: 0.8318 (mm-30) cc_final: 0.7909 (mt-10) REVERT: C 280 LYS cc_start: 0.7695 (tptt) cc_final: 0.7460 (ttmm) REVERT: C 348 ASP cc_start: 0.6607 (m-30) cc_final: 0.6300 (m-30) REVERT: C 435 ARG cc_start: 0.8127 (mtp85) cc_final: 0.7559 (mtt90) REVERT: C 445 LYS cc_start: 0.8607 (tptp) cc_final: 0.8042 (mttp) REVERT: C 485 THR cc_start: 0.8547 (t) cc_final: 0.8316 (p) REVERT: A 24 GLU cc_start: 0.7815 (mm-30) cc_final: 0.7451 (mt-10) REVERT: A 129 GLN cc_start: 0.7772 (mt0) cc_final: 0.7415 (mm110) REVERT: A 174 GLU cc_start: 0.7429 (tp30) cc_final: 0.6980 (tt0) REVERT: A 367 LYS cc_start: 0.8191 (mttp) cc_final: 0.7990 (mptt) REVERT: A 401 ASN cc_start: 0.8667 (p0) cc_final: 0.8428 (p0) REVERT: A 487 ASP cc_start: 0.7643 (t0) cc_final: 0.7195 (t70) REVERT: B 27 ASP cc_start: 0.8332 (m-30) cc_final: 0.8066 (m-30) REVERT: B 348 ASP cc_start: 0.7028 (t0) cc_final: 0.6772 (t0) REVERT: B 435 ARG cc_start: 0.8419 (mtp180) cc_final: 0.8128 (mtm180) REVERT: B 445 LYS cc_start: 0.8344 (tttm) cc_final: 0.8104 (ttmm) REVERT: B 478 MET cc_start: 0.6748 (mtt) cc_final: 0.6515 (mmm) outliers start: 23 outliers final: 17 residues processed: 194 average time/residue: 0.1451 time to fit residues: 39.4507 Evaluate side-chains 178 residues out of total 1465 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 161 time to evaluate : 0.553 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 7 SER 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 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 291 THR 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 323 VAL Chi-restraints excluded: chain B residue 335 ILE 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: 2.9990 chunk 3 optimal weight: 2.9990 chunk 148 optimal weight: 3.9990 chunk 122 optimal weight: 0.9980 chunk 29 optimal weight: 0.6980 chunk 81 optimal weight: 0.7980 chunk 39 optimal weight: 3.9990 chunk 67 optimal weight: 4.9990 overall best weight: 1.6984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 210 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 = 0.3405 r_free = 0.3405 target = 0.116438 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3104 r_free = 0.3104 target = 0.095732 restraints weight = 18750.821| |-----------------------------------------------------------------------------| r_work (start): 0.3105 rms_B_bonded: 1.80 r_work: 0.2979 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.2846 rms_B_bonded: 3.74 restraints_weight: 0.2500 r_work (final): 0.2846 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8483 moved from start: 0.3878 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.073 13827 Z= 0.212 Angle : 0.604 14.586 18772 Z= 0.313 Chirality : 0.044 0.233 2062 Planarity : 0.004 0.044 2399 Dihedral : 5.271 56.313 2187 Min Nonbonded Distance : 2.414 Molprobity Statistics. All-atom Clashscore : 4.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 2.39 % Allowed : 10.58 % 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 aren not related in a simple way. whole: 0.32 (0.20), residues: 1662 helix: 2.33 (0.27), residues: 333 sheet: 0.44 (0.27), residues: 395 loop : -0.69 (0.19), residues: 934 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 262a TYR 0.020 0.002 TYR L 49 PHE 0.037 0.003 PHE A 118 TRP 0.009 0.002 TRP A 84 HIS 0.006 0.001 HIS B 183 Details of bonding type rmsd covalent geometry : bond 0.00513 (13788) covalent geometry : angle 0.58249 (18675) SS BOND : bond 0.00271 ( 20) SS BOND : angle 0.89988 ( 40) hydrogen bonds : bond 0.04675 ( 543) hydrogen bonds : angle 5.22846 ( 1533) link_BETA1-4 : bond 0.00210 ( 3) link_BETA1-4 : angle 1.41241 ( 9) link_BETA1-6 : bond 0.00696 ( 3) link_BETA1-6 : angle 0.99376 ( 9) link_NAG-ASN : bond 0.00346 ( 13) link_NAG-ASN : angle 3.44238 ( 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 190 residues out of total 1465 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 155 time to evaluate : 0.555 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: L 92 ASN cc_start: 0.8796 (t0) cc_final: 0.8439 (t0) REVERT: L 93 ASN cc_start: 0.8970 (t0) cc_final: 0.8743 (t0) REVERT: C 188 GLU cc_start: 0.8370 (mm-30) cc_final: 0.7966 (mt-10) REVERT: C 348 ASP cc_start: 0.6725 (m-30) cc_final: 0.6330 (m-30) REVERT: C 435 ARG cc_start: 0.8127 (mtp85) cc_final: 0.7616 (mmp-170) REVERT: C 445 LYS cc_start: 0.8610 (tptp) cc_final: 0.8079 (ttmm) REVERT: A 24 GLU cc_start: 0.7789 (mm-30) cc_final: 0.7399 (mt-10) REVERT: A 137 ARG cc_start: 0.7168 (OUTLIER) cc_final: 0.6898 (ptp90) REVERT: A 160 ASN cc_start: 0.6585 (t0) cc_final: 0.6326 (t0) REVERT: A 174 GLU cc_start: 0.7396 (tp30) cc_final: 0.6883 (tt0) REVERT: A 367 LYS cc_start: 0.8250 (mttp) cc_final: 0.8001 (mmtm) REVERT: A 401 ASN cc_start: 0.8716 (p0) cc_final: 0.8470 (p0) REVERT: A 487 ASP cc_start: 0.7786 (t0) cc_final: 0.7327 (t70) REVERT: B 27 ASP cc_start: 0.8309 (m-30) cc_final: 0.8052 (m-30) REVERT: B 348 ASP cc_start: 0.7198 (t0) cc_final: 0.6973 (t0) REVERT: B 435 ARG cc_start: 0.8445 (mtp180) cc_final: 0.8092 (mtt180) REVERT: B 445 LYS cc_start: 0.8407 (tttm) cc_final: 0.8178 (ttmm) outliers start: 35 outliers final: 27 residues processed: 185 average time/residue: 0.1520 time to fit residues: 38.8494 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 : 0.546 ------------------------------------------------------------------------------- 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 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 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 A residue 118 PHE Chi-restraints excluded: chain A residue 137 ARG Chi-restraints excluded: chain A residue 210 ASN 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 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 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: 0.9980 chunk 37 optimal weight: 2.9990 chunk 32 optimal weight: 0.5980 chunk 84 optimal weight: 1.9990 chunk 85 optimal weight: 0.3980 chunk 11 optimal weight: 2.9990 chunk 63 optimal weight: 3.9990 chunk 74 optimal weight: 0.6980 chunk 51 optimal weight: 3.9990 chunk 138 optimal weight: 0.6980 chunk 8 optimal weight: 6.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 454 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.118543 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3137 r_free = 0.3137 target = 0.097966 restraints weight = 18381.424| |-----------------------------------------------------------------------------| r_work (start): 0.3132 rms_B_bonded: 1.79 r_work: 0.3010 rms_B_bonded: 2.22 restraints_weight: 0.5000 r_work: 0.2877 rms_B_bonded: 3.73 restraints_weight: 0.2500 r_work (final): 0.2877 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8447 moved from start: 0.3962 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 13827 Z= 0.121 Angle : 0.541 17.476 18772 Z= 0.281 Chirality : 0.041 0.235 2062 Planarity : 0.004 0.033 2399 Dihedral : 5.069 55.352 2187 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 5.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Rotamer: Outliers : 1.50 % Allowed : 11.67 % Favored : 86.83 % 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 aren not related in a simple way. whole: 0.45 (0.20), residues: 1662 helix: 2.52 (0.27), residues: 333 sheet: 0.53 (0.27), residues: 405 loop : -0.65 (0.19), residues: 924 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG L 54 TYR 0.008 0.001 TYR A 17 PHE 0.022 0.002 PHE A 118 TRP 0.012 0.001 TRP A 84 HIS 0.007 0.001 HIS B 355 Details of bonding type rmsd covalent geometry : bond 0.00276 (13788) covalent geometry : angle 0.51586 (18675) SS BOND : bond 0.00201 ( 20) SS BOND : angle 0.80418 ( 40) hydrogen bonds : bond 0.04219 ( 543) hydrogen bonds : angle 5.06921 ( 1533) link_BETA1-4 : bond 0.00279 ( 3) link_BETA1-4 : angle 1.26335 ( 9) link_BETA1-6 : bond 0.00500 ( 3) link_BETA1-6 : angle 1.09981 ( 9) link_NAG-ASN : bond 0.00225 ( 13) link_NAG-ASN : angle 3.52059 ( 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: 22 poor density : 169 time to evaluate : 0.564 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 45 LEU cc_start: 0.7940 (mm) cc_final: 0.7697 (mt) REVERT: L 54 ARG cc_start: 0.7983 (mtm110) cc_final: 0.7688 (mmm-85) REVERT: L 92 ASN cc_start: 0.8679 (t0) cc_final: 0.8363 (t0) REVERT: L 93 ASN cc_start: 0.8922 (t0) cc_final: 0.8699 (t0) REVERT: C 188 GLU cc_start: 0.8387 (mm-30) cc_final: 0.7988 (mt-10) REVERT: C 348 ASP cc_start: 0.6735 (m-30) cc_final: 0.6365 (m-30) REVERT: C 435 ARG cc_start: 0.8075 (mtp85) cc_final: 0.7562 (mmp-170) REVERT: C 445 LYS cc_start: 0.8573 (tptp) cc_final: 0.8055 (mttp) REVERT: A 24 GLU cc_start: 0.7773 (mm-30) cc_final: 0.7407 (mt-10) REVERT: A 129 GLN cc_start: 0.7759 (mt0) cc_final: 0.7420 (mm110) REVERT: A 160 ASN cc_start: 0.6579 (t0) cc_final: 0.6324 (t0) REVERT: A 174 GLU cc_start: 0.7308 (tp30) cc_final: 0.6834 (tt0) REVERT: A 401 ASN cc_start: 0.8690 (p0) cc_final: 0.8450 (p0) REVERT: A 487 ASP cc_start: 0.7653 (t0) cc_final: 0.7226 (t70) REVERT: B 27 ASP cc_start: 0.8295 (m-30) cc_final: 0.8036 (m-30) REVERT: B 435 ARG cc_start: 0.8399 (mtp180) cc_final: 0.8038 (mtt180) REVERT: B 445 LYS cc_start: 0.8328 (tttm) cc_final: 0.8111 (ttmm) outliers start: 22 outliers final: 22 residues processed: 186 average time/residue: 0.1493 time to fit residues: 38.7212 Evaluate side-chains 179 residues out of total 1465 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 157 time to evaluate : 0.541 ------------------------------------------------------------------------------- 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 38 GLN 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 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 483 ASN 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 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: 3.9990 chunk 56 optimal weight: 6.9990 chunk 65 optimal weight: 1.9990 chunk 108 optimal weight: 0.0370 chunk 27 optimal weight: 3.9990 chunk 144 optimal weight: 5.9990 chunk 87 optimal weight: 0.9980 chunk 1 optimal weight: 0.9990 chunk 36 optimal weight: 2.9990 chunk 85 optimal weight: 0.7980 overall best weight: 0.9662 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 210 ASN B 401 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3428 r_free = 0.3428 target = 0.118153 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3128 r_free = 0.3128 target = 0.097364 restraints weight = 18647.605| |-----------------------------------------------------------------------------| r_work (start): 0.3130 rms_B_bonded: 1.81 r_work: 0.3006 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.2871 rms_B_bonded: 3.77 restraints_weight: 0.2500 r_work (final): 0.2871 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8456 moved from start: 0.4012 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 13827 Z= 0.140 Angle : 0.540 14.241 18772 Z= 0.282 Chirality : 0.042 0.248 2062 Planarity : 0.004 0.037 2399 Dihedral : 4.956 51.954 2187 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 4.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.01 % Favored : 96.99 % Rotamer: Outliers : 1.91 % Allowed : 11.67 % Favored : 86.42 % 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 aren not related in a simple way. whole: 0.50 (0.20), residues: 1662 helix: 2.53 (0.27), residues: 333 sheet: 0.63 (0.27), residues: 398 loop : -0.64 (0.19), residues: 931 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG L 54 TYR 0.010 0.001 TYR A 17 PHE 0.026 0.002 PHE A 118 TRP 0.010 0.001 TRP A 84 HIS 0.004 0.001 HIS B 183 Details of bonding type rmsd covalent geometry : bond 0.00330 (13788) covalent geometry : angle 0.51906 (18675) SS BOND : bond 0.00238 ( 20) SS BOND : angle 0.86720 ( 40) hydrogen bonds : bond 0.04265 ( 543) hydrogen bonds : angle 5.05850 ( 1533) link_BETA1-4 : bond 0.00272 ( 3) link_BETA1-4 : angle 1.28535 ( 9) link_BETA1-6 : bond 0.00538 ( 3) link_BETA1-6 : angle 1.05836 ( 9) link_NAG-ASN : bond 0.00191 ( 13) link_NAG-ASN : angle 3.14544 ( 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 194 residues out of total 1465 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 166 time to evaluate : 0.468 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 45 LEU cc_start: 0.8025 (mm) cc_final: 0.7782 (mt) REVERT: L 54 ARG cc_start: 0.8029 (mtm110) cc_final: 0.7743 (mmm-85) REVERT: L 92 ASN cc_start: 0.8696 (t0) cc_final: 0.8437 (t0) REVERT: L 93 ASN cc_start: 0.8916 (t0) cc_final: 0.8707 (t0) REVERT: C 188 GLU cc_start: 0.8402 (mm-30) cc_final: 0.8007 (mt-10) REVERT: C 348 ASP cc_start: 0.6770 (m-30) cc_final: 0.6387 (m-30) REVERT: C 435 ARG cc_start: 0.8087 (mtp85) cc_final: 0.7566 (mtt90) REVERT: C 445 LYS cc_start: 0.8627 (tptp) cc_final: 0.8074 (mttp) REVERT: C 490 LYS cc_start: 0.8542 (mtpp) cc_final: 0.8259 (ttmt) REVERT: A 24 GLU cc_start: 0.7794 (mm-30) cc_final: 0.7415 (mt-10) REVERT: A 129 GLN cc_start: 0.7763 (mt0) cc_final: 0.7409 (mm110) REVERT: A 160 ASN cc_start: 0.6551 (t0) cc_final: 0.6319 (t0) REVERT: A 174 GLU cc_start: 0.7338 (tp30) cc_final: 0.6801 (tt0) REVERT: A 401 ASN cc_start: 0.8703 (p0) cc_final: 0.8444 (p0) REVERT: A 487 ASP cc_start: 0.7654 (t0) cc_final: 0.7223 (t70) REVERT: B 27 ASP cc_start: 0.8284 (m-30) cc_final: 0.8041 (m-30) REVERT: B 435 ARG cc_start: 0.8407 (mtp180) cc_final: 0.8106 (mtm180) REVERT: B 445 LYS cc_start: 0.8310 (tttm) cc_final: 0.8097 (ttmm) outliers start: 28 outliers final: 24 residues processed: 187 average time/residue: 0.1411 time to fit residues: 37.1246 Evaluate side-chains 183 residues out of total 1465 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 159 time to evaluate : 0.579 ------------------------------------------------------------------------------- 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 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 442 SER 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 21 optimal weight: 0.4980 chunk 20 optimal weight: 0.9990 chunk 125 optimal weight: 1.9990 chunk 133 optimal weight: 1.9990 chunk 12 optimal weight: 4.9990 chunk 136 optimal weight: 3.9990 chunk 72 optimal weight: 3.9990 chunk 140 optimal weight: 0.6980 chunk 68 optimal weight: 0.6980 chunk 75 optimal weight: 2.9990 chunk 102 optimal weight: 3.9990 overall best weight: 0.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 354 HIS A 210 ASN B 401 ASN B 483 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3430 r_free = 0.3430 target = 0.118267 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3126 r_free = 0.3126 target = 0.097145 restraints weight = 18480.969| |-----------------------------------------------------------------------------| r_work (start): 0.3128 rms_B_bonded: 1.86 r_work: 0.3004 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work: 0.2870 rms_B_bonded: 3.76 restraints_weight: 0.2500 r_work (final): 0.2870 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8427 moved from start: 0.4071 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= 0.140 Angle : 0.536 11.845 18772 Z= 0.282 Chirality : 0.042 0.245 2062 Planarity : 0.004 0.033 2399 Dihedral : 5.018 59.865 2187 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 5.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.71 % Favored : 97.29 % Rotamer: Outliers : 1.77 % Allowed : 12.22 % 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 aren not related in a simple way. whole: 0.51 (0.20), residues: 1662 helix: 2.56 (0.27), residues: 333 sheet: 0.63 (0.27), residues: 398 loop : -0.63 (0.19), residues: 931 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG L 54 TYR 0.022 0.001 TYR L 49 PHE 0.025 0.002 PHE A 118 TRP 0.011 0.001 TRP A 84 HIS 0.004 0.001 HIS B 183 Details of bonding type rmsd covalent geometry : bond 0.00331 (13788) covalent geometry : angle 0.52067 (18675) SS BOND : bond 0.00264 ( 20) SS BOND : angle 0.86674 ( 40) hydrogen bonds : bond 0.04236 ( 543) hydrogen bonds : angle 5.04315 ( 1533) link_BETA1-4 : bond 0.00250 ( 3) link_BETA1-4 : angle 1.22867 ( 9) link_BETA1-6 : bond 0.00540 ( 3) link_BETA1-6 : angle 1.07246 ( 9) link_NAG-ASN : bond 0.00188 ( 13) link_NAG-ASN : angle 2.68416 ( 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 193 residues out of total 1465 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 167 time to evaluate : 0.606 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 45 LEU cc_start: 0.7941 (mm) cc_final: 0.7637 (mt) REVERT: L 38 GLN cc_start: 0.8326 (OUTLIER) cc_final: 0.7833 (mt0) REVERT: L 54 ARG cc_start: 0.8126 (mtm110) cc_final: 0.7784 (mmm-85) REVERT: L 92 ASN cc_start: 0.8742 (t0) cc_final: 0.8502 (t0) REVERT: L 93 ASN cc_start: 0.8935 (t0) cc_final: 0.8733 (t0) REVERT: C 188 GLU cc_start: 0.8425 (mm-30) cc_final: 0.8024 (mt-10) REVERT: C 280 LYS cc_start: 0.7606 (tptt) cc_final: 0.7286 (ttmm) REVERT: C 435 ARG cc_start: 0.8051 (mtp85) cc_final: 0.7485 (mtt90) REVERT: C 445 LYS cc_start: 0.8602 (tptp) cc_final: 0.7983 (mttp) REVERT: C 490 LYS cc_start: 0.8517 (mtpp) cc_final: 0.8242 (ttmt) REVERT: A 24 GLU cc_start: 0.7789 (mm-30) cc_final: 0.7375 (mt-10) REVERT: A 129 GLN cc_start: 0.7765 (mt0) cc_final: 0.7367 (mm110) REVERT: A 160 ASN cc_start: 0.6487 (t0) cc_final: 0.6260 (t0) REVERT: A 174 GLU cc_start: 0.7474 (tp30) cc_final: 0.6917 (tt0) REVERT: A 401 ASN cc_start: 0.8682 (p0) cc_final: 0.8420 (p0) REVERT: A 487 ASP cc_start: 0.7669 (t0) cc_final: 0.7206 (t70) REVERT: B 27 ASP cc_start: 0.8309 (m-30) cc_final: 0.8076 (m-30) REVERT: B 435 ARG cc_start: 0.8425 (mtp180) cc_final: 0.8101 (mtm180) REVERT: B 445 LYS cc_start: 0.8269 (tttm) cc_final: 0.8036 (ttmm) outliers start: 26 outliers final: 23 residues processed: 186 average time/residue: 0.1492 time to fit residues: 38.8011 Evaluate side-chains 184 residues out of total 1465 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 160 time to evaluate : 0.532 ------------------------------------------------------------------------------- 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 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 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 210 ASN 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 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: 2.9990 chunk 52 optimal weight: 0.9990 chunk 81 optimal weight: 0.9980 chunk 45 optimal weight: 3.9990 chunk 113 optimal weight: 1.9990 chunk 108 optimal weight: 3.9990 chunk 163 optimal weight: 0.5980 chunk 34 optimal weight: 1.9990 chunk 17 optimal weight: 6.9990 chunk 150 optimal weight: 0.2980 overall best weight: 0.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 210 ASN B 401 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.118218 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3130 r_free = 0.3130 target = 0.097482 restraints weight = 18632.786| |-----------------------------------------------------------------------------| r_work (start): 0.3129 rms_B_bonded: 1.80 r_work: 0.3004 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.2872 rms_B_bonded: 3.76 restraints_weight: 0.2500 r_work (final): 0.2872 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8455 moved from start: 0.4113 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 13827 Z= 0.141 Angle : 0.540 11.100 18772 Z= 0.285 Chirality : 0.042 0.223 2062 Planarity : 0.004 0.036 2399 Dihedral : 4.985 55.266 2187 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 5.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 1.64 % Allowed : 12.35 % 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 aren not related in a simple way. whole: 0.51 (0.20), residues: 1662 helix: 2.57 (0.27), residues: 333 sheet: 0.66 (0.27), residues: 396 loop : -0.65 (0.19), residues: 933 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG L 54 TYR 0.010 0.001 TYR A 17 PHE 0.025 0.002 PHE A 118 TRP 0.010 0.001 TRP A 84 HIS 0.004 0.001 HIS B 117 Details of bonding type rmsd covalent geometry : bond 0.00334 (13788) covalent geometry : angle 0.52453 (18675) SS BOND : bond 0.00275 ( 20) SS BOND : angle 1.12621 ( 40) hydrogen bonds : bond 0.04223 ( 543) hydrogen bonds : angle 5.04103 ( 1533) link_BETA1-4 : bond 0.00250 ( 3) link_BETA1-4 : angle 1.22785 ( 9) link_BETA1-6 : bond 0.00512 ( 3) link_BETA1-6 : angle 1.06831 ( 9) link_NAG-ASN : bond 0.00187 ( 13) link_NAG-ASN : angle 2.55169 ( 39) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3827.03 seconds wall clock time: 66 minutes 36.03 seconds (3996.03 seconds total)