Starting phenix.real_space_refine on Thu Jul 31 15:49:38 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8tp2_41464/07_2025/8tp2_41464.cif Found real_map, /net/cci-nas-00/data/ceres_data/8tp2_41464/07_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8tp2_41464/07_2025/8tp2_41464.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8tp2_41464/07_2025/8tp2_41464.map" model { file = "/net/cci-nas-00/data/ceres_data/8tp2_41464/07_2025/8tp2_41464.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8tp2_41464/07_2025/8tp2_41464.cif" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 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): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/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: 8.34, per 1000 atoms: 0.62 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: 3.08 Conformation dependent library (CDL) restraints added in 1.6 seconds 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: 1.84 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: 4.73 Time building geometry restraints manager: 3.72 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 495 or resid 501 throu \ gh 503)) selection = (chain 'C' and (resid 11 through 324 or resid 335 through 495 or resid 501 throu \ gh 503)) } ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'F' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.320 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: 0.480 Check model and map are aligned: 0.090 Set scattering table: 0.120 Process input model: 32.480 Find NCS groups from input model: 0.550 Set up NCS constraints: 0.050 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: 0.010 Load rotamer database and sin/cos tables:2.720 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 38.830 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.79 (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 TRP 0.052 0.007 TRP A 84 HIS 0.012 0.003 HIS C 183 PHE 0.048 0.006 PHE B 118 TYR 0.064 0.008 TYR A 486 ARG 0.007 0.001 ARG C 93 Details of bonding type rmsd link_NAG-ASN : bond 0.06937 ( 13) link_NAG-ASN : angle 2.83322 ( 39) link_BETA1-4 : bond 0.06935 ( 3) link_BETA1-4 : angle 4.99765 ( 9) hydrogen bonds : bond 0.13596 ( 543) hydrogen bonds : angle 7.00594 ( 1533) link_BETA1-6 : bond 0.05584 ( 3) link_BETA1-6 : angle 2.55582 ( 9) SS BOND : bond 0.01174 ( 20) SS BOND : angle 2.98721 ( 40) covalent geometry : bond 0.02072 (13788) covalent geometry : angle 1.69412 (18675) *********************** 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 : 1.437 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: H 47 TYR cc_start: 0.8848 (t80) cc_final: 0.8641 (t80) REVERT: L 83 PHE cc_start: 0.7366 (m-80) cc_final: 0.7152 (m-80) REVERT: L 90 GLN cc_start: 0.8395 (tm130) cc_final: 0.8070 (tm-30) REVERT: C 435 ARG cc_start: 0.7909 (mmm160) cc_final: 0.7684 (mmp-170) REVERT: C 441 ASP cc_start: 0.8129 (m-30) cc_final: 0.7924 (m-30) REVERT: C 445 LYS cc_start: 0.8499 (tptp) cc_final: 0.8231 (ttmm) REVERT: C 450 LYS cc_start: 0.8961 (tttt) cc_final: 0.8625 (ttpp) REVERT: A 132 THR cc_start: 0.8426 (p) cc_final: 0.8213 (p) REVERT: A 160 ASN cc_start: 0.7250 (m-40) cc_final: 0.6810 (t0) REVERT: A 335 ILE cc_start: 0.6682 (pt) cc_final: 0.6120 (tt) REVERT: A 402 LEU cc_start: 0.9146 (mt) cc_final: 0.8922 (mt) REVERT: B 27 ASP cc_start: 0.7654 (m-30) cc_final: 0.7424 (m-30) REVERT: B 190 GLU cc_start: 0.6994 (tt0) cc_final: 0.6606 (tt0) REVERT: B 275 GLU cc_start: 0.7523 (mm-30) cc_final: 0.7233 (mp0) REVERT: B 366 ASP cc_start: 0.8447 (t0) cc_final: 0.8218 (t70) outliers start: 0 outliers final: 0 residues processed: 349 average time/residue: 0.3212 time to fit residues: 151.9039 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 : 1.423 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 140 optimal weight: 0.9980 chunk 125 optimal weight: 0.9980 chunk 69 optimal weight: 1.9990 chunk 42 optimal weight: 3.9990 chunk 84 optimal weight: 0.7980 chunk 67 optimal weight: 0.8980 chunk 130 optimal weight: 0.4980 chunk 50 optimal weight: 0.8980 chunk 79 optimal weight: 0.8980 chunk 96 optimal weight: 2.9990 chunk 150 optimal weight: 1.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- 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 A 354 HIS B 12 GLN B 130 HIS B 175 GLN B 183 HIS Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.124696 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3226 r_free = 0.3226 target = 0.103890 restraints weight = 18469.813| |-----------------------------------------------------------------------------| r_work (start): 0.3223 rms_B_bonded: 1.82 r_work: 0.3100 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.2969 rms_B_bonded: 3.84 restraints_weight: 0.2500 r_work (final): 0.2969 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8365 moved from start: 0.2476 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 13827 Z= 0.172 Angle : 0.642 6.602 18772 Z= 0.355 Chirality : 0.043 0.181 2062 Planarity : 0.005 0.066 2399 Dihedral : 5.522 47.953 2187 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 4.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 1.37 % Allowed : 6.28 % Favored : 92.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.77 (0.20), residues: 1662 helix: 2.27 (0.28), residues: 332 sheet: 0.80 (0.26), residues: 380 loop : -0.21 (0.19), residues: 950 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP L 96 HIS 0.011 0.001 HIS C 355 PHE 0.025 0.002 PHE C 118 TYR 0.016 0.002 TYR H 98 ARG 0.004 0.001 ARG L 61 Details of bonding type rmsd link_NAG-ASN : bond 0.00273 ( 13) link_NAG-ASN : angle 1.69640 ( 39) link_BETA1-4 : bond 0.00316 ( 3) link_BETA1-4 : angle 2.44630 ( 9) hydrogen bonds : bond 0.05614 ( 543) hydrogen bonds : angle 5.59863 ( 1533) link_BETA1-6 : bond 0.01069 ( 3) link_BETA1-6 : angle 0.89207 ( 9) SS BOND : bond 0.00328 ( 20) SS BOND : angle 1.02676 ( 40) covalent geometry : bond 0.00388 (13788) covalent geometry : angle 0.63499 (18675) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3324 Ramachandran restraints generated. 1662 Oldfield, 0 Emsley, 1662 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3324 Ramachandran restraints generated. 1662 Oldfield, 0 Emsley, 1662 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 217 residues out of total 1465 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 197 time to evaluate : 1.438 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: L 54 ARG cc_start: 0.8087 (mtm110) cc_final: 0.7809 (mmm-85) REVERT: L 92 ASN cc_start: 0.8750 (t0) cc_final: 0.8344 (t0) REVERT: C 160 ASN cc_start: 0.8557 (m110) cc_final: 0.8254 (t0) REVERT: C 435 ARG cc_start: 0.7989 (mmm160) cc_final: 0.7596 (mmp-170) REVERT: C 445 LYS cc_start: 0.8696 (tptp) cc_final: 0.8228 (ttmm) REVERT: A 24 GLU cc_start: 0.7811 (mm-30) cc_final: 0.7461 (mt-10) REVERT: A 50 LYS cc_start: 0.7870 (mttt) cc_final: 0.7475 (mtpt) REVERT: A 129 GLN cc_start: 0.7691 (mt0) cc_final: 0.7382 (mm110) REVERT: A 174 GLU cc_start: 0.7245 (tp30) cc_final: 0.6777 (tt0) REVERT: A 487 ASP cc_start: 0.7773 (t0) cc_final: 0.7191 (t70) REVERT: B 27 ASP cc_start: 0.8029 (m-30) cc_final: 0.7823 (m-30) REVERT: B 239 MET cc_start: 0.8170 (OUTLIER) cc_final: 0.7866 (mtm) REVERT: B 275 GLU cc_start: 0.7810 (mm-30) cc_final: 0.7087 (mp0) REVERT: B 401 ASN cc_start: 0.8676 (m-40) cc_final: 0.8294 (p0) outliers start: 20 outliers final: 11 residues processed: 210 average time/residue: 0.2683 time to fit residues: 80.4319 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 : 1.429 ------------------------------------------------------------------------------- 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 9 optimal weight: 5.9990 chunk 118 optimal weight: 0.9990 chunk 39 optimal weight: 3.9990 chunk 64 optimal weight: 1.9990 chunk 153 optimal weight: 6.9990 chunk 59 optimal weight: 3.9990 chunk 91 optimal weight: 0.9980 chunk 114 optimal weight: 2.9990 chunk 129 optimal weight: 0.9980 chunk 88 optimal weight: 0.9980 chunk 8 optimal weight: 4.9990 overall best weight: 1.1984 ------------------------------------------------------------------------------- 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 B 117 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.121192 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3169 r_free = 0.3169 target = 0.100065 restraints weight = 18564.536| |-----------------------------------------------------------------------------| r_work (start): 0.3165 rms_B_bonded: 1.83 r_work: 0.3041 rms_B_bonded: 2.27 restraints_weight: 0.5000 r_work: 0.2910 rms_B_bonded: 3.78 restraints_weight: 0.2500 r_work (final): 0.2910 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8427 moved from start: 0.3094 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 13827 Z= 0.173 Angle : 0.571 4.943 18772 Z= 0.309 Chirality : 0.043 0.240 2062 Planarity : 0.004 0.059 2399 Dihedral : 5.282 57.535 2187 Min Nonbonded Distance : 2.588 Molprobity Statistics. All-atom Clashscore : 4.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 1.37 % Allowed : 8.67 % Favored : 89.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.58 (0.20), residues: 1662 helix: 2.29 (0.27), residues: 333 sheet: 0.63 (0.25), residues: 407 loop : -0.43 (0.19), residues: 922 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A 84 HIS 0.005 0.001 HIS C 18 PHE 0.033 0.002 PHE C 118 TYR 0.015 0.002 TYR B 17 ARG 0.005 0.001 ARG A 229 Details of bonding type rmsd link_NAG-ASN : bond 0.00330 ( 13) link_NAG-ASN : angle 1.53764 ( 39) link_BETA1-4 : bond 0.00558 ( 3) link_BETA1-4 : angle 1.68276 ( 9) hydrogen bonds : bond 0.04794 ( 543) hydrogen bonds : angle 5.23689 ( 1533) link_BETA1-6 : bond 0.00605 ( 3) link_BETA1-6 : angle 0.84100 ( 9) SS BOND : bond 0.00588 ( 20) SS BOND : angle 0.82263 ( 40) covalent geometry : bond 0.00405 (13788) covalent geometry : angle 0.56585 (18675) *********************** 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 199 residues out of total 1465 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 179 time to evaluate : 1.461 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: L 92 ASN cc_start: 0.8759 (t0) cc_final: 0.8352 (t0) REVERT: C 112 LEU cc_start: 0.8054 (mt) cc_final: 0.7804 (mt) REVERT: C 160 ASN cc_start: 0.8488 (m110) cc_final: 0.8282 (t0) REVERT: C 435 ARG cc_start: 0.7964 (mmm160) cc_final: 0.7517 (mmp-170) REVERT: C 445 LYS cc_start: 0.8655 (tptp) cc_final: 0.8136 (ttmm) REVERT: A 24 GLU cc_start: 0.7813 (mm-30) cc_final: 0.7439 (mt-10) REVERT: A 50 LYS cc_start: 0.8052 (mttt) cc_final: 0.7733 (mtpt) REVERT: A 129 GLN cc_start: 0.7761 (mt0) cc_final: 0.7435 (mm110) REVERT: A 160 ASN cc_start: 0.6490 (t0) cc_final: 0.6230 (t0) REVERT: A 367 LYS cc_start: 0.8200 (mttp) cc_final: 0.7970 (mptt) REVERT: A 487 ASP cc_start: 0.7809 (t0) cc_final: 0.7344 (t70) REVERT: B 27 ASP cc_start: 0.8265 (m-30) cc_final: 0.8045 (m-30) REVERT: B 239 MET cc_start: 0.8120 (OUTLIER) cc_final: 0.7887 (mtm) REVERT: B 275 GLU cc_start: 0.7734 (mm-30) cc_final: 0.6964 (mp0) REVERT: B 401 ASN cc_start: 0.8804 (m-40) cc_final: 0.8291 (p0) REVERT: B 435 ARG cc_start: 0.8352 (mtp180) cc_final: 0.8088 (mtt180) outliers start: 20 outliers final: 17 residues processed: 191 average time/residue: 0.3054 time to fit residues: 81.0320 Evaluate side-chains 181 residues out of total 1465 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 163 time to evaluate : 1.612 ------------------------------------------------------------------------------- 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 11 ASP Chi-restraints excluded: chain C residue 82 VAL Chi-restraints excluded: chain C residue 125 ASP Chi-restraints excluded: chain C residue 291 THR Chi-restraints excluded: chain A residue 210 ASN Chi-restraints excluded: chain A residue 291 THR Chi-restraints excluded: chain A residue 335 ILE Chi-restraints excluded: chain B residue 118 PHE Chi-restraints excluded: chain B residue 155 THR Chi-restraints excluded: chain B residue 239 MET Chi-restraints excluded: chain B residue 457 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 90 optimal weight: 3.9990 chunk 104 optimal weight: 6.9990 chunk 33 optimal weight: 0.7980 chunk 4 optimal weight: 0.0050 chunk 86 optimal weight: 1.9990 chunk 103 optimal weight: 2.9990 chunk 132 optimal weight: 1.9990 chunk 102 optimal weight: 2.9990 chunk 123 optimal weight: 3.9990 chunk 131 optimal weight: 0.5980 chunk 154 optimal weight: 5.9990 overall best weight: 1.0798 ------------------------------------------------------------------------------- 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 196 GLN B 483 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3497 r_free = 0.3497 target = 0.122515 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3200 r_free = 0.3200 target = 0.101969 restraints weight = 18500.627| |-----------------------------------------------------------------------------| r_work (start): 0.3195 rms_B_bonded: 1.77 r_work: 0.3072 rms_B_bonded: 2.22 restraints_weight: 0.5000 r_work: 0.2942 rms_B_bonded: 3.75 restraints_weight: 0.2500 r_work (final): 0.2942 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8434 moved from start: 0.3357 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 13827 Z= 0.155 Angle : 0.565 14.801 18772 Z= 0.296 Chirality : 0.042 0.226 2062 Planarity : 0.004 0.044 2399 Dihedral : 5.072 47.783 2187 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 4.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Rotamer: Outliers : 1.77 % Allowed : 9.22 % Favored : 89.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.51 (0.20), residues: 1662 helix: 2.36 (0.27), residues: 333 sheet: 0.60 (0.26), residues: 400 loop : -0.52 (0.19), residues: 929 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 84 HIS 0.004 0.001 HIS B 117 PHE 0.028 0.002 PHE C 118 TYR 0.017 0.002 TYR L 49 ARG 0.006 0.000 ARG L 61 Details of bonding type rmsd link_NAG-ASN : bond 0.00394 ( 13) link_NAG-ASN : angle 3.15194 ( 39) link_BETA1-4 : bond 0.00196 ( 3) link_BETA1-4 : angle 1.53231 ( 9) hydrogen bonds : bond 0.04573 ( 543) hydrogen bonds : angle 5.16847 ( 1533) link_BETA1-6 : bond 0.00579 ( 3) link_BETA1-6 : angle 0.92858 ( 9) SS BOND : bond 0.00234 ( 20) SS BOND : angle 0.64154 ( 40) covalent geometry : bond 0.00364 (13788) covalent geometry : angle 0.54517 (18675) *********************** 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 195 residues out of total 1465 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 169 time to evaluate : 1.560 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: L 54 ARG cc_start: 0.7964 (mtm110) cc_final: 0.7643 (mmm-85) REVERT: L 92 ASN cc_start: 0.8787 (t0) cc_final: 0.8484 (t0) REVERT: C 112 LEU cc_start: 0.7971 (mt) cc_final: 0.7687 (mt) REVERT: C 445 LYS cc_start: 0.8603 (tptp) cc_final: 0.8064 (ttmm) REVERT: A 24 GLU cc_start: 0.7828 (mm-30) cc_final: 0.7471 (mt-10) REVERT: A 50 LYS cc_start: 0.8092 (mttt) cc_final: 0.7742 (mtpt) REVERT: A 129 GLN cc_start: 0.7757 (mt0) cc_final: 0.7418 (mm110) REVERT: A 160 ASN cc_start: 0.6634 (t0) cc_final: 0.6342 (t0) REVERT: A 367 LYS cc_start: 0.8238 (mttp) cc_final: 0.7991 (mmtm) REVERT: A 401 ASN cc_start: 0.8784 (p0) cc_final: 0.8529 (p0) REVERT: A 487 ASP cc_start: 0.7705 (t0) cc_final: 0.7304 (t70) REVERT: B 27 ASP cc_start: 0.8247 (m-30) cc_final: 0.8027 (m-30) REVERT: B 275 GLU cc_start: 0.7738 (mm-30) cc_final: 0.6960 (mp0) REVERT: B 368 GLU cc_start: 0.8429 (tt0) cc_final: 0.8200 (pt0) REVERT: B 435 ARG cc_start: 0.8339 (mtp180) cc_final: 0.8098 (mtt180) outliers start: 26 outliers final: 19 residues processed: 188 average time/residue: 0.3034 time to fit residues: 79.2510 Evaluate side-chains 179 residues out of total 1465 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 160 time to evaluate : 1.439 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 7 SER Chi-restraints excluded: chain H residue 20 LEU Chi-restraints excluded: chain H residue 82 THR Chi-restraints excluded: chain 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 291 THR Chi-restraints excluded: chain C residue 442 SER 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 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 68 optimal weight: 5.9990 chunk 38 optimal weight: 5.9990 chunk 49 optimal weight: 0.9990 chunk 95 optimal weight: 0.9990 chunk 105 optimal weight: 8.9990 chunk 154 optimal weight: 5.9990 chunk 82 optimal weight: 0.0770 chunk 80 optimal weight: 0.0980 chunk 123 optimal weight: 3.9990 chunk 59 optimal weight: 0.6980 chunk 138 optimal weight: 2.9990 overall best weight: 0.5742 ------------------------------------------------------------------------------- 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** A 210 ASN B 483 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3489 r_free = 0.3489 target = 0.122467 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3196 r_free = 0.3196 target = 0.101684 restraints weight = 18594.001| |-----------------------------------------------------------------------------| r_work (start): 0.3193 rms_B_bonded: 1.81 r_work: 0.3074 rms_B_bonded: 2.20 restraints_weight: 0.5000 r_work: 0.2943 rms_B_bonded: 3.70 restraints_weight: 0.2500 r_work (final): 0.2943 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8388 moved from start: 0.3549 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 13827 Z= 0.111 Angle : 0.526 15.959 18772 Z= 0.274 Chirality : 0.040 0.213 2062 Planarity : 0.004 0.047 2399 Dihedral : 4.852 54.568 2187 Min Nonbonded Distance : 2.333 Molprobity Statistics. All-atom Clashscore : 4.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.47 % Favored : 97.53 % Rotamer: Outliers : 1.50 % Allowed : 9.56 % Favored : 88.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.58 (0.20), residues: 1662 helix: 2.57 (0.27), residues: 333 sheet: 0.56 (0.26), residues: 412 loop : -0.52 (0.19), residues: 917 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 84 HIS 0.008 0.001 HIS B 355 PHE 0.020 0.002 PHE C 118 TYR 0.012 0.001 TYR H 98 ARG 0.005 0.000 ARG L 61 Details of bonding type rmsd link_NAG-ASN : bond 0.00187 ( 13) link_NAG-ASN : angle 3.69045 ( 39) link_BETA1-4 : bond 0.00284 ( 3) link_BETA1-4 : angle 1.38974 ( 9) hydrogen bonds : bond 0.04189 ( 543) hydrogen bonds : angle 5.02873 ( 1533) link_BETA1-6 : bond 0.00537 ( 3) link_BETA1-6 : angle 1.06003 ( 9) SS BOND : bond 0.00189 ( 20) SS BOND : angle 0.49321 ( 40) covalent geometry : bond 0.00244 (13788) covalent geometry : angle 0.49746 (18675) *********************** 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 204 residues out of total 1465 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 182 time to evaluate : 1.583 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 54 ARG cc_start: 0.8021 (mtm110) cc_final: 0.7644 (mmm-85) REVERT: L 82 ASP cc_start: 0.7725 (m-30) cc_final: 0.7460 (m-30) REVERT: L 92 ASN cc_start: 0.8713 (t0) cc_final: 0.8485 (t0) REVERT: C 112 LEU cc_start: 0.7899 (mt) cc_final: 0.7574 (mt) REVERT: C 188 GLU cc_start: 0.8357 (mm-30) cc_final: 0.7957 (mt-10) REVERT: C 435 ARG cc_start: 0.8010 (mtp85) cc_final: 0.7714 (mtt90) REVERT: C 445 LYS cc_start: 0.8605 (tptp) cc_final: 0.8027 (mttp) REVERT: A 24 GLU cc_start: 0.7781 (mm-30) cc_final: 0.7441 (mt-10) REVERT: A 50 LYS cc_start: 0.8034 (mttt) cc_final: 0.7713 (mtpt) REVERT: A 129 GLN cc_start: 0.7706 (mt0) cc_final: 0.7368 (mm110) REVERT: A 174 GLU cc_start: 0.7253 (tp30) cc_final: 0.6840 (tt0) REVERT: A 367 LYS cc_start: 0.8189 (mttp) cc_final: 0.7986 (mmtm) REVERT: A 401 ASN cc_start: 0.8640 (p0) cc_final: 0.8387 (p0) REVERT: A 487 ASP cc_start: 0.7558 (t0) cc_final: 0.7129 (t70) REVERT: B 27 ASP cc_start: 0.8299 (m-30) cc_final: 0.8079 (m-30) outliers start: 22 outliers final: 16 residues processed: 199 average time/residue: 0.3026 time to fit residues: 83.8899 Evaluate side-chains 176 residues out of total 1465 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 160 time to evaluate : 1.580 ------------------------------------------------------------------------------- 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 125 ASP Chi-restraints excluded: chain C residue 291 THR Chi-restraints excluded: chain A residue 277 CYS Chi-restraints excluded: chain A residue 291 THR Chi-restraints excluded: chain A residue 335 ILE Chi-restraints excluded: chain A residue 442 SER Chi-restraints excluded: chain B residue 118 PHE Chi-restraints excluded: chain B residue 323 VAL Chi-restraints excluded: chain B residue 335 ILE Chi-restraints excluded: chain B residue 477 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 22 optimal weight: 3.9990 chunk 10 optimal weight: 5.9990 chunk 141 optimal weight: 2.9990 chunk 35 optimal weight: 0.4980 chunk 160 optimal weight: 3.9990 chunk 7 optimal weight: 7.9990 chunk 101 optimal weight: 3.9990 chunk 103 optimal weight: 4.9990 chunk 80 optimal weight: 1.9990 chunk 70 optimal weight: 0.7980 chunk 149 optimal weight: 2.9990 overall best weight: 1.8586 ------------------------------------------------------------------------------- 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 A 160 ASN A 210 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 = 0.3382 r_free = 0.3382 target = 0.115026 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3072 r_free = 0.3072 target = 0.094018 restraints weight = 18935.763| |-----------------------------------------------------------------------------| r_work (start): 0.3068 rms_B_bonded: 1.86 r_work: 0.2943 rms_B_bonded: 2.27 restraints_weight: 0.5000 r_work: 0.2809 rms_B_bonded: 3.78 restraints_weight: 0.2500 r_work (final): 0.2809 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8470 moved from start: 0.3738 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.074 13827 Z= 0.228 Angle : 0.641 22.653 18772 Z= 0.327 Chirality : 0.045 0.230 2062 Planarity : 0.004 0.046 2399 Dihedral : 5.308 59.566 2187 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 5.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.01 % Favored : 96.99 % Rotamer: Outliers : 1.98 % Allowed : 10.10 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.35 (0.20), residues: 1662 helix: 2.34 (0.27), residues: 333 sheet: 0.38 (0.26), residues: 409 loop : -0.63 (0.19), residues: 920 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP A 84 HIS 0.007 0.002 HIS B 117 PHE 0.043 0.003 PHE A 118 TYR 0.019 0.002 TYR L 49 ARG 0.009 0.001 ARG A 435 Details of bonding type rmsd link_NAG-ASN : bond 0.00418 ( 13) link_NAG-ASN : angle 4.79465 ( 39) link_BETA1-4 : bond 0.00360 ( 3) link_BETA1-4 : angle 1.53195 ( 9) hydrogen bonds : bond 0.04812 ( 543) hydrogen bonds : angle 5.21381 ( 1533) link_BETA1-6 : bond 0.01142 ( 3) link_BETA1-6 : angle 0.94540 ( 9) SS BOND : bond 0.00297 ( 20) SS BOND : angle 0.73123 ( 40) covalent geometry : bond 0.00551 (13788) covalent geometry : angle 0.60154 (18675) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3324 Ramachandran restraints generated. 1662 Oldfield, 0 Emsley, 1662 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3324 Ramachandran restraints generated. 1662 Oldfield, 0 Emsley, 1662 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 1465 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 164 time to evaluate : 1.512 Fit side-chains revert: symmetry clash REVERT: L 92 ASN cc_start: 0.8803 (t0) cc_final: 0.8546 (t0) REVERT: C 112 LEU cc_start: 0.8222 (mt) cc_final: 0.7941 (mt) REVERT: C 188 GLU cc_start: 0.8330 (mm-30) cc_final: 0.7929 (mt-10) REVERT: C 280 LYS cc_start: 0.7801 (tptt) cc_final: 0.7561 (ttmm) REVERT: C 445 LYS cc_start: 0.8643 (tptp) cc_final: 0.8066 (ttmm) REVERT: A 24 GLU cc_start: 0.7835 (mm-30) cc_final: 0.7423 (mt-10) REVERT: A 160 ASN cc_start: 0.6455 (t0) cc_final: 0.6185 (t0) REVERT: A 174 GLU cc_start: 0.7420 (tp30) cc_final: 0.6852 (tt0) REVERT: A 186 ASN cc_start: 0.7315 (t0) cc_final: 0.7001 (t0) REVERT: A 367 LYS cc_start: 0.8249 (mttp) cc_final: 0.8036 (mmtm) REVERT: A 401 ASN cc_start: 0.8692 (p0) cc_final: 0.8436 (p0) REVERT: A 487 ASP cc_start: 0.7704 (t0) cc_final: 0.7244 (t70) REVERT: B 27 ASP cc_start: 0.8378 (m-30) cc_final: 0.8129 (m-30) REVERT: B 478 MET cc_start: 0.6842 (mtt) cc_final: 0.6542 (mmm) outliers start: 29 outliers final: 23 residues processed: 187 average time/residue: 0.2997 time to fit residues: 78.0810 Evaluate side-chains 176 residues out of total 1465 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 153 time to evaluate : 1.390 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 7 SER Chi-restraints excluded: chain H residue 20 LEU Chi-restraints excluded: chain H residue 82 THR Chi-restraints excluded: chain H residue 110 ILE 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 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 291 THR Chi-restraints excluded: chain C residue 389 ASN Chi-restraints excluded: chain C residue 442 SER 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 16 optimal weight: 4.9990 chunk 23 optimal weight: 0.9980 chunk 45 optimal weight: 2.9990 chunk 36 optimal weight: 0.9990 chunk 43 optimal weight: 0.2980 chunk 157 optimal weight: 2.9990 chunk 1 optimal weight: 0.8980 chunk 2 optimal weight: 1.9990 chunk 109 optimal weight: 1.9990 chunk 119 optimal weight: 4.9990 chunk 120 optimal weight: 0.6980 overall best weight: 0.7782 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.118755 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3139 r_free = 0.3139 target = 0.098109 restraints weight = 18655.233| |-----------------------------------------------------------------------------| r_work (start): 0.3139 rms_B_bonded: 1.81 r_work: 0.3014 rms_B_bonded: 2.26 restraints_weight: 0.5000 r_work: 0.2879 rms_B_bonded: 3.80 restraints_weight: 0.2500 r_work (final): 0.2879 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8446 moved from start: 0.3867 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 13827 Z= 0.125 Angle : 0.541 18.749 18772 Z= 0.281 Chirality : 0.041 0.218 2062 Planarity : 0.004 0.036 2399 Dihedral : 4.962 57.716 2187 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 5.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 1.50 % Allowed : 10.92 % Favored : 87.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.50 (0.20), residues: 1662 helix: 2.55 (0.27), residues: 333 sheet: 0.54 (0.27), residues: 405 loop : -0.59 (0.19), residues: 924 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 84 HIS 0.007 0.001 HIS B 355 PHE 0.023 0.002 PHE A 118 TYR 0.009 0.001 TYR A 17 ARG 0.005 0.000 ARG A 262a Details of bonding type rmsd link_NAG-ASN : bond 0.00148 ( 13) link_NAG-ASN : angle 4.06524 ( 39) link_BETA1-4 : bond 0.00272 ( 3) link_BETA1-4 : angle 1.26600 ( 9) hydrogen bonds : bond 0.04274 ( 543) hydrogen bonds : angle 5.07042 ( 1533) link_BETA1-6 : bond 0.00525 ( 3) link_BETA1-6 : angle 1.06790 ( 9) SS BOND : bond 0.00194 ( 20) SS BOND : angle 1.08442 ( 40) covalent geometry : bond 0.00290 (13788) covalent geometry : angle 0.50613 (18675) *********************** 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 187 residues out of total 1465 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 165 time to evaluate : 1.647 Fit side-chains revert: symmetry clash REVERT: L 54 ARG cc_start: 0.8045 (mtm110) cc_final: 0.7685 (mmm-85) REVERT: C 112 LEU cc_start: 0.8099 (mt) cc_final: 0.7801 (mt) REVERT: C 188 GLU cc_start: 0.8340 (mm-30) cc_final: 0.7941 (mt-10) REVERT: C 445 LYS cc_start: 0.8615 (tptp) cc_final: 0.8102 (mttp) REVERT: A 24 GLU cc_start: 0.7820 (mm-30) cc_final: 0.7446 (mt-10) REVERT: A 129 GLN cc_start: 0.7799 (mt0) cc_final: 0.7415 (mm110) REVERT: A 160 ASN cc_start: 0.6423 (t0) cc_final: 0.6156 (t0) REVERT: A 174 GLU cc_start: 0.7385 (tp30) cc_final: 0.6942 (tt0) REVERT: A 186 ASN cc_start: 0.7316 (t0) cc_final: 0.7003 (t0) REVERT: A 401 ASN cc_start: 0.8681 (p0) cc_final: 0.8424 (p0) REVERT: A 487 ASP cc_start: 0.7620 (t0) cc_final: 0.7147 (t70) REVERT: B 27 ASP cc_start: 0.8259 (m-30) cc_final: 0.8004 (m-30) REVERT: B 276 ASN cc_start: 0.7695 (t0) cc_final: 0.7476 (t0) REVERT: B 348 ASP cc_start: 0.7089 (t0) cc_final: 0.6777 (t0) REVERT: B 478 MET cc_start: 0.6796 (mtt) cc_final: 0.6541 (mmm) outliers start: 22 outliers final: 19 residues processed: 182 average time/residue: 0.3101 time to fit residues: 79.4865 Evaluate side-chains 173 residues out of total 1465 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 154 time to evaluate : 1.546 ------------------------------------------------------------------------------- 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 125 ASP Chi-restraints excluded: chain C residue 291 THR Chi-restraints excluded: chain A residue 277 CYS Chi-restraints excluded: chain A residue 291 THR Chi-restraints excluded: chain A residue 434 GLU Chi-restraints excluded: chain A residue 453 MET Chi-restraints excluded: chain B residue 118 PHE Chi-restraints excluded: chain B residue 155 THR Chi-restraints excluded: chain B residue 323 VAL Chi-restraints excluded: chain B residue 335 ILE Chi-restraints excluded: chain B residue 457 ASP Chi-restraints excluded: chain B residue 477 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 29 optimal weight: 1.9990 chunk 95 optimal weight: 4.9990 chunk 36 optimal weight: 3.9990 chunk 73 optimal weight: 0.8980 chunk 99 optimal weight: 2.9990 chunk 56 optimal weight: 0.4980 chunk 69 optimal weight: 0.8980 chunk 94 optimal weight: 8.9990 chunk 165 optimal weight: 0.9990 chunk 30 optimal weight: 0.9980 chunk 157 optimal weight: 2.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 92 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 = 0.3489 r_free = 0.3489 target = 0.122006 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3194 r_free = 0.3194 target = 0.101524 restraints weight = 18772.844| |-----------------------------------------------------------------------------| r_work (start): 0.3183 rms_B_bonded: 1.78 r_work: 0.3070 rms_B_bonded: 2.14 restraints_weight: 0.5000 r_work: 0.2944 rms_B_bonded: 3.61 restraints_weight: 0.2500 r_work (final): 0.2944 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8422 moved from start: 0.3950 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= 0.132 Angle : 0.538 17.181 18772 Z= 0.280 Chirality : 0.041 0.271 2062 Planarity : 0.004 0.035 2399 Dihedral : 4.804 50.444 2187 Min Nonbonded Distance : 2.412 Molprobity Statistics. All-atom Clashscore : 5.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 1.64 % Allowed : 10.85 % Favored : 87.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.58 (0.20), residues: 1662 helix: 2.60 (0.27), residues: 333 sheet: 0.66 (0.27), residues: 398 loop : -0.57 (0.19), residues: 931 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 84 HIS 0.007 0.001 HIS B 355 PHE 0.025 0.002 PHE A 118 TYR 0.020 0.001 TYR L 49 ARG 0.005 0.000 ARG A 262a Details of bonding type rmsd link_NAG-ASN : bond 0.00155 ( 13) link_NAG-ASN : angle 3.79382 ( 39) link_BETA1-4 : bond 0.00248 ( 3) link_BETA1-4 : angle 1.30393 ( 9) hydrogen bonds : bond 0.04234 ( 543) hydrogen bonds : angle 5.03605 ( 1533) link_BETA1-6 : bond 0.00511 ( 3) link_BETA1-6 : angle 1.05139 ( 9) SS BOND : bond 0.00199 ( 20) SS BOND : angle 0.91690 ( 40) covalent geometry : bond 0.00308 (13788) covalent geometry : angle 0.50802 (18675) *********************** 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 183 residues out of total 1465 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 159 time to evaluate : 1.678 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: L 54 ARG cc_start: 0.8091 (mtm110) cc_final: 0.7764 (mmm-85) REVERT: C 112 LEU cc_start: 0.8011 (mt) cc_final: 0.7715 (mt) REVERT: C 188 GLU cc_start: 0.8444 (mm-30) cc_final: 0.8047 (mt-10) REVERT: C 445 LYS cc_start: 0.8616 (tptp) cc_final: 0.8068 (mttp) REVERT: A 24 GLU cc_start: 0.7763 (mm-30) cc_final: 0.7398 (mt-10) REVERT: A 129 GLN cc_start: 0.7704 (mt0) cc_final: 0.7360 (mm110) REVERT: A 160 ASN cc_start: 0.6569 (t0) cc_final: 0.6309 (t0) REVERT: A 174 GLU cc_start: 0.7245 (tp30) cc_final: 0.6877 (tt0) REVERT: A 186 ASN cc_start: 0.7334 (t0) cc_final: 0.7034 (t0) REVERT: A 401 ASN cc_start: 0.8734 (p0) cc_final: 0.8463 (p0) REVERT: A 487 ASP cc_start: 0.7583 (t0) cc_final: 0.7164 (t70) REVERT: B 27 ASP cc_start: 0.8224 (m-30) cc_final: 0.7977 (m-30) REVERT: B 348 ASP cc_start: 0.7107 (t0) cc_final: 0.6856 (t0) REVERT: B 478 MET cc_start: 0.6774 (mtt) cc_final: 0.6548 (mmm) outliers start: 24 outliers final: 22 residues processed: 178 average time/residue: 0.2998 time to fit residues: 75.2901 Evaluate side-chains 174 residues out of total 1465 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 152 time to evaluate : 1.494 ------------------------------------------------------------------------------- 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 125 ASP 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 434 GLU Chi-restraints excluded: chain A residue 453 MET 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 13 optimal weight: 9.9990 chunk 160 optimal weight: 4.9990 chunk 8 optimal weight: 0.6980 chunk 91 optimal weight: 3.9990 chunk 139 optimal weight: 0.9990 chunk 72 optimal weight: 3.9990 chunk 78 optimal weight: 1.9990 chunk 131 optimal weight: 8.9990 chunk 143 optimal weight: 3.9990 chunk 12 optimal weight: 3.9990 chunk 104 optimal weight: 5.9990 overall best weight: 2.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3382 r_free = 0.3382 target = 0.114741 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3076 r_free = 0.3076 target = 0.093902 restraints weight = 18728.756| |-----------------------------------------------------------------------------| r_work (start): 0.3081 rms_B_bonded: 1.83 r_work: 0.2958 rms_B_bonded: 2.21 restraints_weight: 0.5000 r_work: 0.2823 rms_B_bonded: 3.70 restraints_weight: 0.2500 r_work (final): 0.2823 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8472 moved from start: 0.4001 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.092 13827 Z= 0.274 Angle : 0.657 16.702 18772 Z= 0.341 Chirality : 0.046 0.268 2062 Planarity : 0.005 0.053 2399 Dihedral : 5.233 41.984 2187 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 5.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 1.77 % Allowed : 11.13 % Favored : 87.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.23 (0.20), residues: 1662 helix: 2.20 (0.27), residues: 333 sheet: 0.42 (0.27), residues: 393 loop : -0.73 (0.19), residues: 936 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP C 343 HIS 0.008 0.002 HIS B 183 PHE 0.046 0.003 PHE A 118 TYR 0.014 0.002 TYR A 17 ARG 0.005 0.001 ARG C 229 Details of bonding type rmsd link_NAG-ASN : bond 0.00349 ( 13) link_NAG-ASN : angle 3.77317 ( 39) link_BETA1-4 : bond 0.00176 ( 3) link_BETA1-4 : angle 1.42007 ( 9) hydrogen bonds : bond 0.04923 ( 543) hydrogen bonds : angle 5.32035 ( 1533) link_BETA1-6 : bond 0.00803 ( 3) link_BETA1-6 : angle 0.99075 ( 9) SS BOND : bond 0.00363 ( 20) SS BOND : angle 1.13298 ( 40) covalent geometry : bond 0.00668 (13788) covalent geometry : angle 0.63286 (18675) *********************** 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 180 residues out of total 1465 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 154 time to evaluate : 1.613 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: L 38 GLN cc_start: 0.8234 (OUTLIER) cc_final: 0.8014 (mt0) REVERT: L 54 ARG cc_start: 0.8171 (mtm110) cc_final: 0.7711 (mmm-85) REVERT: C 112 LEU cc_start: 0.8403 (mt) cc_final: 0.8140 (mt) REVERT: C 188 GLU cc_start: 0.8370 (mm-30) cc_final: 0.7987 (mt-10) REVERT: C 445 LYS cc_start: 0.8618 (tptp) cc_final: 0.8016 (ttmm) REVERT: A 24 GLU cc_start: 0.7769 (mm-30) cc_final: 0.7317 (mt-10) REVERT: A 160 ASN cc_start: 0.6637 (t0) cc_final: 0.6395 (t0) REVERT: A 174 GLU cc_start: 0.7475 (tp30) cc_final: 0.6832 (tt0) REVERT: A 186 ASN cc_start: 0.7393 (t0) cc_final: 0.7135 (t0) REVERT: A 487 ASP cc_start: 0.7807 (t0) cc_final: 0.7257 (t70) REVERT: B 27 ASP cc_start: 0.8347 (m-30) cc_final: 0.8106 (m-30) REVERT: B 348 ASP cc_start: 0.7422 (t0) cc_final: 0.7199 (t0) outliers start: 26 outliers final: 25 residues processed: 176 average time/residue: 0.3015 time to fit residues: 75.2124 Evaluate side-chains 177 residues out of total 1465 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 151 time to evaluate : 1.438 ------------------------------------------------------------------------------- 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 38 GLN Chi-restraints excluded: chain L residue 85 VAL Chi-restraints excluded: chain C residue 46 THR Chi-restraints excluded: chain C residue 63 ASP Chi-restraints excluded: chain C residue 118 PHE Chi-restraints excluded: chain C residue 125 ASP 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 277 CYS Chi-restraints excluded: chain A residue 291 THR Chi-restraints excluded: chain A residue 335 ILE Chi-restraints excluded: chain A residue 434 GLU 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 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 117 optimal weight: 1.9990 chunk 7 optimal weight: 6.9990 chunk 15 optimal weight: 0.6980 chunk 126 optimal weight: 0.9990 chunk 35 optimal weight: 0.0980 chunk 144 optimal weight: 0.6980 chunk 56 optimal weight: 0.8980 chunk 38 optimal weight: 4.9990 chunk 40 optimal weight: 0.4980 chunk 75 optimal weight: 0.8980 chunk 45 optimal weight: 1.9990 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 197 ASN C 354 HIS A 210 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3428 r_free = 0.3428 target = 0.118100 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3136 r_free = 0.3136 target = 0.097854 restraints weight = 18579.685| |-----------------------------------------------------------------------------| r_work (start): 0.3138 rms_B_bonded: 1.77 r_work: 0.3015 rms_B_bonded: 2.22 restraints_weight: 0.5000 r_work: 0.2883 rms_B_bonded: 3.72 restraints_weight: 0.2500 r_work (final): 0.2883 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8444 moved from start: 0.4093 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= 0.116 Angle : 0.531 15.550 18772 Z= 0.279 Chirality : 0.041 0.217 2062 Planarity : 0.003 0.034 2399 Dihedral : 4.835 41.361 2187 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 5.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer: Outliers : 1.30 % Allowed : 11.95 % Favored : 86.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.48 (0.20), residues: 1662 helix: 2.54 (0.27), residues: 333 sheet: 0.55 (0.27), residues: 403 loop : -0.63 (0.20), residues: 926 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 84 HIS 0.003 0.001 HIS B 117 PHE 0.021 0.002 PHE A 118 TYR 0.008 0.001 TYR H 91 ARG 0.004 0.000 ARG A 262a Details of bonding type rmsd link_NAG-ASN : bond 0.00153 ( 13) link_NAG-ASN : angle 3.37599 ( 39) link_BETA1-4 : bond 0.00268 ( 3) link_BETA1-4 : angle 1.17688 ( 9) hydrogen bonds : bond 0.04179 ( 543) hydrogen bonds : angle 5.06410 ( 1533) link_BETA1-6 : bond 0.00446 ( 3) link_BETA1-6 : angle 1.12206 ( 9) SS BOND : bond 0.00242 ( 20) SS BOND : angle 0.93012 ( 40) covalent geometry : bond 0.00262 (13788) covalent geometry : angle 0.50597 (18675) ********************** 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 177 residues out of total 1465 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 158 time to evaluate : 1.625 Fit side-chains revert: symmetry clash REVERT: L 54 ARG cc_start: 0.8124 (mtm110) cc_final: 0.7746 (mmm-85) REVERT: C 112 LEU cc_start: 0.8091 (mt) cc_final: 0.7791 (mt) REVERT: C 188 GLU cc_start: 0.8380 (mm-30) cc_final: 0.7989 (mt-10) REVERT: C 280 LYS cc_start: 0.7752 (tptt) cc_final: 0.7552 (ttmm) REVERT: C 445 LYS cc_start: 0.8579 (tptp) cc_final: 0.8041 (mttp) REVERT: C 490 LYS cc_start: 0.8540 (mtpp) cc_final: 0.8257 (ttmt) REVERT: A 24 GLU cc_start: 0.7763 (mm-30) cc_final: 0.7380 (mt-10) REVERT: A 129 GLN cc_start: 0.7754 (mt0) cc_final: 0.7398 (mm110) REVERT: A 160 ASN cc_start: 0.6539 (t0) cc_final: 0.6305 (t0) REVERT: A 174 GLU cc_start: 0.7294 (tp30) cc_final: 0.6825 (tt0) REVERT: A 186 ASN cc_start: 0.7419 (t0) cc_final: 0.7176 (t0) REVERT: A 487 ASP cc_start: 0.7731 (t0) cc_final: 0.7211 (t70) REVERT: B 27 ASP cc_start: 0.8269 (m-30) cc_final: 0.8038 (m-30) outliers start: 19 outliers final: 17 residues processed: 174 average time/residue: 0.2993 time to fit residues: 73.6640 Evaluate side-chains 168 residues out of total 1465 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 151 time to evaluate : 1.540 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 20 LEU Chi-restraints excluded: chain H residue 82 THR Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 12 SER 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 C residue 323 VAL Chi-restraints excluded: chain A residue 277 CYS Chi-restraints excluded: chain A residue 291 THR Chi-restraints excluded: chain A residue 434 GLU 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 72 optimal weight: 4.9990 chunk 116 optimal weight: 2.9990 chunk 98 optimal weight: 5.9990 chunk 134 optimal weight: 1.9990 chunk 115 optimal weight: 5.9990 chunk 62 optimal weight: 0.7980 chunk 16 optimal weight: 2.9990 chunk 158 optimal weight: 0.6980 chunk 159 optimal weight: 3.9990 chunk 32 optimal weight: 1.9990 chunk 28 optimal weight: 2.9990 overall best weight: 1.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 210 ASN B 401 ASN B 483 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.116503 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3104 r_free = 0.3104 target = 0.095768 restraints weight = 18729.491| |-----------------------------------------------------------------------------| r_work (start): 0.3102 rms_B_bonded: 1.81 r_work: 0.2977 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.2846 rms_B_bonded: 3.73 restraints_weight: 0.2500 r_work (final): 0.2846 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8481 moved from start: 0.4109 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.070 13827 Z= 0.210 Angle : 0.606 15.512 18772 Z= 0.315 Chirality : 0.044 0.228 2062 Planarity : 0.004 0.040 2399 Dihedral : 5.035 37.753 2187 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 5.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 1.77 % Allowed : 11.60 % Favored : 86.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.36 (0.20), residues: 1662 helix: 2.39 (0.27), residues: 333 sheet: 0.57 (0.28), residues: 379 loop : -0.71 (0.19), residues: 950 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP C 343 HIS 0.006 0.001 HIS B 117 PHE 0.036 0.002 PHE A 118 TYR 0.022 0.002 TYR L 49 ARG 0.004 0.000 ARG A 262a Details of bonding type rmsd link_NAG-ASN : bond 0.00236 ( 13) link_NAG-ASN : angle 3.42545 ( 39) link_BETA1-4 : bond 0.00214 ( 3) link_BETA1-4 : angle 1.27592 ( 9) hydrogen bonds : bond 0.04580 ( 543) hydrogen bonds : angle 5.26617 ( 1533) link_BETA1-6 : bond 0.00616 ( 3) link_BETA1-6 : angle 1.00825 ( 9) SS BOND : bond 0.00289 ( 20) SS BOND : angle 1.60723 ( 40) covalent geometry : bond 0.00508 (13788) covalent geometry : angle 0.58075 (18675) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7734.95 seconds wall clock time: 133 minutes 6.61 seconds (7986.61 seconds total)