Starting phenix.real_space_refine on Tue Dec 31 04:51:03 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8dpt_27642/12_2024/8dpt_27642.cif Found real_map, /net/cci-nas-00/data/ceres_data/8dpt_27642/12_2024/8dpt_27642.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8dpt_27642/12_2024/8dpt_27642.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8dpt_27642/12_2024/8dpt_27642.map" model { file = "/net/cci-nas-00/data/ceres_data/8dpt_27642/12_2024/8dpt_27642.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8dpt_27642/12_2024/8dpt_27642.cif" } resolution = 4.0 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= 1.000 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 1420 atoms to isotropic. 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 46 5.16 5 C 8608 2.51 5 N 2330 2.21 5 O 2566 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 24 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/chem_data/mon_lib" Total number of atoms: 13550 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 3169 Number of conformers: 1 Conformer: "" Number of residues, atoms: 398, 3169 Classifications: {'peptide': 398} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PCIS': 1, 'PTRANS': 21, 'TRANS': 375} Unresolved non-hydrogen bonds: 35 Unresolved non-hydrogen angles: 43 Unresolved non-hydrogen dihedrals: 36 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'TRP:plan': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 14 Chain: "B" Number of atoms: 1262 Number of conformers: 1 Conformer: "" Number of residues, atoms: 165, 1262 Classifications: {'peptide': 165} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 150} Chain: "C" Number of atoms: 2249 Number of conformers: 1 Conformer: "" Number of residues, atoms: 294, 2249 Classifications: {'peptide': 294} Link IDs: {'PTRANS': 33, 'TRANS': 260} Chain: "I" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 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: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Restraints were copied for chains: F, H, D, E, L Time building chain proxies: 9.67, per 1000 atoms: 0.71 Number of scatterers: 13550 At special positions: 0 Unit cell: (148.03, 184.71, 137.55, 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 46 16.00 O 2566 8.00 N 2330 7.00 C 8608 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=8, symmetry=0 Simple disulfide: pdb=" SG CYS A 6 " - pdb=" SG CYS A 32 " distance=2.03 Simple disulfide: pdb=" SG CYS A 26 " - pdb=" SG CYS A 81 " distance=2.03 Simple disulfide: pdb=" SG CYS A 112 " - pdb=" SG CYS A 122 " distance=2.03 Simple disulfide: pdb=" SG CYS A 150 " - pdb=" SG CYS A 160 " distance=2.03 Simple disulfide: pdb=" SG CYS C 4 " - pdb=" SG CYS C 25 " distance=2.03 Simple disulfide: pdb=" SG CYS C 26 " - pdb=" SG CYS C 72 " distance=2.03 Simple disulfide: pdb=" SG CYS C 98 " - pdb=" SG CYS C 108 " distance=2.03 Simple disulfide: pdb=" SG CYS C 148 " - pdb=" SG CYS C 158 " distance=2.03 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 G 1 " - " NAG G 2 " " NAG H 1 " - " NAG H 2 " " NAG I 1 " - " NAG I 2 " " NAG I 2 " - " BMA I 3 " " NAG L 1 " - " NAG L 2 " " NAG L 2 " - " BMA L 3 " NAG-ASN " NAG A 601 " - " ASN A 21 " " NAG A 602 " - " ASN A 135 " " NAG D 601 " - " ASN D 21 " " NAG D 602 " - " ASN D 135 " " NAG G 1 " - " ASN A 61 " " NAG H 1 " - " ASN D 61 " " NAG I 1 " - " ASN C 172 " " NAG L 1 " - " ASN F 172 " Time building additional restraints: 3.59 Conformation dependent library (CDL) restraints added in 1.9 seconds 3404 Ramachandran restraints generated. 1702 Oldfield, 0 Emsley, 1702 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3212 Finding SS restraints... Secondary structure from input PDB file: 28 helices and 34 sheets defined 19.5% alpha, 31.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.77 Creating SS restraints... Processing helix chain 'A' and resid 29 through 37 Processing helix chain 'A' and resid 39 through 41 No H-bonds generated for 'chain 'A' and resid 39 through 41' Processing helix chain 'A' and resid 53 through 55 No H-bonds generated for 'chain 'A' and resid 53 through 55' Processing helix chain 'A' and resid 193 through 196 Processing helix chain 'A' and resid 225 through 230 Processing helix chain 'A' and resid 251 through 256 removed outlier: 3.712A pdb=" N ALA A 256 " --> pdb=" O GLU A 253 " (cutoff:3.500A) Processing helix chain 'A' and resid 333 through 338 Processing helix chain 'B' and resid 15 through 43 Processing helix chain 'B' and resid 68 through 94 removed outlier: 3.539A pdb=" N VAL B 72 " --> pdb=" O GLN B 68 " (cutoff:3.500A) Processing helix chain 'B' and resid 95 through 102 removed outlier: 4.371A pdb=" N THR B 100 " --> pdb=" O SER B 97 " (cutoff:3.500A) Processing helix chain 'B' and resid 103 through 126 removed outlier: 3.577A pdb=" N ARG B 114 " --> pdb=" O ALA B 110 " (cutoff:3.500A) Processing helix chain 'B' and resid 145 through 176 removed outlier: 3.864A pdb=" N LEU B 162 " --> pdb=" O GLY B 158 " (cutoff:3.500A) removed outlier: 4.149A pdb=" N ASP B 165 " --> pdb=" O HIS B 161 " (cutoff:3.500A) Processing helix chain 'C' and resid 63 through 67 Processing helix chain 'C' and resid 190 through 194 Processing helix chain 'D' and resid 29 through 37 Processing helix chain 'D' and resid 39 through 41 No H-bonds generated for 'chain 'D' and resid 39 through 41' Processing helix chain 'D' and resid 53 through 55 No H-bonds generated for 'chain 'D' and resid 53 through 55' Processing helix chain 'D' and resid 193 through 196 Processing helix chain 'D' and resid 225 through 230 Processing helix chain 'D' and resid 251 through 256 removed outlier: 3.712A pdb=" N ALA D 256 " --> pdb=" O GLU D 253 " (cutoff:3.500A) Processing helix chain 'D' and resid 333 through 338 Processing helix chain 'E' and resid 15 through 43 Processing helix chain 'E' and resid 68 through 94 removed outlier: 3.538A pdb=" N VAL E 72 " --> pdb=" O GLN E 68 " (cutoff:3.500A) Processing helix chain 'E' and resid 95 through 102 removed outlier: 4.371A pdb=" N THR E 100 " --> pdb=" O SER E 97 " (cutoff:3.500A) Processing helix chain 'E' and resid 103 through 126 removed outlier: 3.577A pdb=" N ARG E 114 " --> pdb=" O ALA E 110 " (cutoff:3.500A) Processing helix chain 'E' and resid 145 through 176 removed outlier: 3.864A pdb=" N LEU E 162 " --> pdb=" O GLY E 158 " (cutoff:3.500A) removed outlier: 4.150A pdb=" N ASP E 165 " --> pdb=" O HIS E 161 " (cutoff:3.500A) Processing helix chain 'F' and resid 63 through 67 Processing helix chain 'F' and resid 190 through 194 Processing sheet with id=AA1, first strand: chain 'A' and resid 8 through 10 removed outlier: 6.622A pdb=" N ALA A 64 " --> pdb=" O ILE A 60 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 15 through 17 Processing sheet with id=AA3, first strand: chain 'A' and resid 50 through 51 removed outlier: 3.626A pdb=" N LYS A 46 " --> pdb=" O THR A 80 " (cutoff:3.500A) removed outlier: 6.576A pdb=" N ILE A 83 " --> pdb=" O ASN A 92 " (cutoff:3.500A) removed outlier: 5.839A pdb=" N ASN A 92 " --> pdb=" O ILE A 83 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 159 through 161 removed outlier: 4.437A pdb=" N ASP A 125 " --> pdb=" O ASN A 109 " (cutoff:3.500A) removed outlier: 6.052A pdb=" N ASN A 109 " --> pdb=" O ASP A 125 " (cutoff:3.500A) removed outlier: 7.667A pdb=" N LYS A 199 " --> pdb=" O CYS A 112 " (cutoff:3.500A) removed outlier: 6.353A pdb=" N VAL A 114 " --> pdb=" O LYS A 199 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 145 through 146 removed outlier: 3.765A pdb=" N GLU A 173 " --> pdb=" O GLU A 141 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 150 through 151 removed outlier: 3.765A pdb=" N GLU A 173 " --> pdb=" O GLU A 141 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N PHE A 192 " --> pdb=" O ILE A 172 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 204 through 209 removed outlier: 5.514A pdb=" N ASN A 205 " --> pdb=" O THR A 223 " (cutoff:3.500A) removed outlier: 4.378A pdb=" N THR A 223 " --> pdb=" O ASN A 205 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 248 through 249 removed outlier: 3.680A pdb=" N ARG A 278 " --> pdb=" O ASN A 236 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N GLN A 238 " --> pdb=" O ARG A 276 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N ARG A 276 " --> pdb=" O GLN A 238 " (cutoff:3.500A) removed outlier: 4.242A pdb=" N ARG A 240 " --> pdb=" O VAL A 274 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N VAL A 274 " --> pdb=" O ARG A 240 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 310 through 316 removed outlier: 3.664A pdb=" N VAL A 325 " --> pdb=" O VAL A 367 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N VAL A 367 " --> pdb=" O VAL A 325 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N LEU A 327 " --> pdb=" O LEU A 365 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 356 through 360 removed outlier: 3.822A pdb=" N ASP A 343 " --> pdb=" O ARG A 381 " (cutoff:3.500A) removed outlier: 4.251A pdb=" N ALA A 376 " --> pdb=" O LEU A 392 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N LEU A 392 " --> pdb=" O ALA A 376 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N LEU A 378 " --> pdb=" O ALA A 390 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 14 through 16 removed outlier: 3.761A pdb=" N GLN C 14 " --> pdb=" O THR C 84 " (cutoff:3.500A) removed outlier: 4.150A pdb=" N GLN C 86 " --> pdb=" O GLN C 14 " (cutoff:3.500A) removed outlier: 6.297A pdb=" N LEU C 79 " --> pdb=" O THR C 74 " (cutoff:3.500A) removed outlier: 6.557A pdb=" N THR C 74 " --> pdb=" O LEU C 79 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N GLY C 81 " --> pdb=" O CYS C 72 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 22 through 25 Processing sheet with id=AB4, first strand: chain 'C' and resid 95 through 99 removed outlier: 3.798A pdb=" N CYS C 108 " --> pdb=" O CYS C 158 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 121 through 128 removed outlier: 3.625A pdb=" N ARG C 121 " --> pdb=" O VAL C 176 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 121 through 128 removed outlier: 3.625A pdb=" N ARG C 121 " --> pdb=" O VAL C 176 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 200 through 206 removed outlier: 6.305A pdb=" N GLY C 201 " --> pdb=" O THR C 219 " (cutoff:3.500A) removed outlier: 5.440A pdb=" N THR C 219 " --> pdb=" O GLY C 201 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 247 through 249 Processing sheet with id=AB9, first strand: chain 'D' and resid 8 through 10 removed outlier: 6.623A pdb=" N ALA D 64 " --> pdb=" O ILE D 60 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'D' and resid 15 through 17 Processing sheet with id=AC2, first strand: chain 'D' and resid 50 through 51 removed outlier: 3.627A pdb=" N LYS D 46 " --> pdb=" O THR D 80 " (cutoff:3.500A) removed outlier: 6.576A pdb=" N ILE D 83 " --> pdb=" O ASN D 92 " (cutoff:3.500A) removed outlier: 5.839A pdb=" N ASN D 92 " --> pdb=" O ILE D 83 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'D' and resid 159 through 161 removed outlier: 4.437A pdb=" N ASP D 125 " --> pdb=" O ASN D 109 " (cutoff:3.500A) removed outlier: 6.052A pdb=" N ASN D 109 " --> pdb=" O ASP D 125 " (cutoff:3.500A) removed outlier: 7.667A pdb=" N LYS D 199 " --> pdb=" O CYS D 112 " (cutoff:3.500A) removed outlier: 6.353A pdb=" N VAL D 114 " --> pdb=" O LYS D 199 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'D' and resid 145 through 146 removed outlier: 3.765A pdb=" N GLU D 173 " --> pdb=" O GLU D 141 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'D' and resid 150 through 151 removed outlier: 3.765A pdb=" N GLU D 173 " --> pdb=" O GLU D 141 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N PHE D 192 " --> pdb=" O ILE D 172 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'D' and resid 204 through 209 removed outlier: 5.514A pdb=" N ASN D 205 " --> pdb=" O THR D 223 " (cutoff:3.500A) removed outlier: 4.378A pdb=" N THR D 223 " --> pdb=" O ASN D 205 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'D' and resid 248 through 249 removed outlier: 3.679A pdb=" N ARG D 278 " --> pdb=" O ASN D 236 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N GLN D 238 " --> pdb=" O ARG D 276 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N ARG D 276 " --> pdb=" O GLN D 238 " (cutoff:3.500A) removed outlier: 4.243A pdb=" N ARG D 240 " --> pdb=" O VAL D 274 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N VAL D 274 " --> pdb=" O ARG D 240 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'D' and resid 310 through 316 removed outlier: 3.664A pdb=" N VAL D 325 " --> pdb=" O VAL D 367 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N VAL D 367 " --> pdb=" O VAL D 325 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N LEU D 327 " --> pdb=" O LEU D 365 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'D' and resid 356 through 360 removed outlier: 3.822A pdb=" N ASP D 343 " --> pdb=" O ARG D 381 " (cutoff:3.500A) removed outlier: 4.250A pdb=" N ALA D 376 " --> pdb=" O LEU D 392 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N LEU D 392 " --> pdb=" O ALA D 376 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N LEU D 378 " --> pdb=" O ALA D 390 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'F' and resid 14 through 16 removed outlier: 3.760A pdb=" N GLN F 14 " --> pdb=" O THR F 84 " (cutoff:3.500A) removed outlier: 4.151A pdb=" N GLN F 86 " --> pdb=" O GLN F 14 " (cutoff:3.500A) removed outlier: 6.296A pdb=" N LEU F 79 " --> pdb=" O THR F 74 " (cutoff:3.500A) removed outlier: 6.556A pdb=" N THR F 74 " --> pdb=" O LEU F 79 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N GLY F 81 " --> pdb=" O CYS F 72 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'F' and resid 22 through 25 Processing sheet with id=AD3, first strand: chain 'F' and resid 95 through 99 removed outlier: 3.797A pdb=" N CYS F 108 " --> pdb=" O CYS F 158 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'F' and resid 121 through 128 removed outlier: 3.624A pdb=" N ARG F 121 " --> pdb=" O VAL F 176 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'F' and resid 121 through 128 removed outlier: 3.624A pdb=" N ARG F 121 " --> pdb=" O VAL F 176 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'F' and resid 200 through 206 removed outlier: 6.305A pdb=" N GLY F 201 " --> pdb=" O THR F 219 " (cutoff:3.500A) removed outlier: 5.439A pdb=" N THR F 219 " --> pdb=" O GLY F 201 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'F' and resid 247 through 249 548 hydrogen bonds defined for protein. 1410 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: 4.48 Time building geometry restraints manager: 4.12 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.35: 4370 1.35 - 1.47: 3344 1.47 - 1.59: 6148 1.59 - 1.71: 0 1.71 - 1.83: 56 Bond restraints: 13918 Sorted by residual: bond pdb=" C1 NAG I 1 " pdb=" O5 NAG I 1 " ideal model delta sigma weight residual 1.406 1.448 -0.042 2.00e-02 2.50e+03 4.33e+00 bond pdb=" C1 NAG L 1 " pdb=" O5 NAG L 1 " ideal model delta sigma weight residual 1.406 1.447 -0.041 2.00e-02 2.50e+03 4.27e+00 bond pdb=" CA ASP F 151 " pdb=" C ASP F 151 " ideal model delta sigma weight residual 1.524 1.548 -0.024 1.26e-02 6.30e+03 3.67e+00 bond pdb=" CA ASP C 151 " pdb=" C ASP C 151 " ideal model delta sigma weight residual 1.524 1.546 -0.023 1.26e-02 6.30e+03 3.20e+00 bond pdb=" C1 NAG H 2 " pdb=" O5 NAG H 2 " ideal model delta sigma weight residual 1.406 1.440 -0.034 2.00e-02 2.50e+03 2.92e+00 ... (remaining 13913 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.90: 18721 3.90 - 7.80: 279 7.80 - 11.70: 30 11.70 - 15.60: 6 15.60 - 19.50: 4 Bond angle restraints: 19040 Sorted by residual: angle pdb=" CG ARG B 85 " pdb=" CD ARG B 85 " pdb=" NE ARG B 85 " ideal model delta sigma weight residual 112.00 131.50 -19.50 2.20e+00 2.07e-01 7.86e+01 angle pdb=" CG ARG E 85 " pdb=" CD ARG E 85 " pdb=" NE ARG E 85 " ideal model delta sigma weight residual 112.00 131.46 -19.46 2.20e+00 2.07e-01 7.82e+01 angle pdb=" CD ARG E 85 " pdb=" NE ARG E 85 " pdb=" CZ ARG E 85 " ideal model delta sigma weight residual 124.40 132.31 -7.91 1.40e+00 5.10e-01 3.19e+01 angle pdb=" CD ARG B 85 " pdb=" NE ARG B 85 " pdb=" CZ ARG B 85 " ideal model delta sigma weight residual 124.40 132.25 -7.85 1.40e+00 5.10e-01 3.14e+01 angle pdb=" CB ARG E 85 " pdb=" CG ARG E 85 " pdb=" CD ARG E 85 " ideal model delta sigma weight residual 111.30 123.84 -12.54 2.30e+00 1.89e-01 2.97e+01 ... (remaining 19035 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.66: 8010 21.66 - 43.32: 419 43.32 - 64.98: 65 64.98 - 86.64: 32 86.64 - 108.30: 8 Dihedral angle restraints: 8534 sinusoidal: 3556 harmonic: 4978 Sorted by residual: dihedral pdb=" C ASP F 151 " pdb=" N ASP F 151 " pdb=" CA ASP F 151 " pdb=" CB ASP F 151 " ideal model delta harmonic sigma weight residual -122.60 -137.12 14.52 0 2.50e+00 1.60e-01 3.38e+01 dihedral pdb=" C ASP C 151 " pdb=" N ASP C 151 " pdb=" CA ASP C 151 " pdb=" CB ASP C 151 " ideal model delta harmonic sigma weight residual -122.60 -137.12 14.52 0 2.50e+00 1.60e-01 3.38e+01 dihedral pdb=" CG ARG B 85 " pdb=" CD ARG B 85 " pdb=" NE ARG B 85 " pdb=" CZ ARG B 85 " ideal model delta sinusoidal sigma weight residual -90.00 -9.21 -80.79 2 1.50e+01 4.44e-03 2.08e+01 ... (remaining 8531 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.088: 1895 0.088 - 0.175: 262 0.175 - 0.263: 19 0.263 - 0.351: 4 0.351 - 0.438: 2 Chirality restraints: 2182 Sorted by residual: chirality pdb=" CA ASP C 151 " pdb=" N ASP C 151 " pdb=" C ASP C 151 " pdb=" CB ASP C 151 " both_signs ideal model delta sigma weight residual False 2.51 2.07 0.44 2.00e-01 2.50e+01 4.80e+00 chirality pdb=" CA ASP F 151 " pdb=" N ASP F 151 " pdb=" C ASP F 151 " pdb=" CB ASP F 151 " both_signs ideal model delta sigma weight residual False 2.51 2.07 0.44 2.00e-01 2.50e+01 4.79e+00 chirality pdb=" C1 NAG G 1 " pdb=" ND2 ASN A 61 " pdb=" C2 NAG G 1 " pdb=" O5 NAG G 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.08 -0.32 2.00e-01 2.50e+01 2.62e+00 ... (remaining 2179 not shown) Planarity restraints: 2440 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU B 69 " 0.060 5.00e-02 4.00e+02 8.97e-02 1.29e+01 pdb=" N PRO B 70 " -0.155 5.00e-02 4.00e+02 pdb=" CA PRO B 70 " 0.045 5.00e-02 4.00e+02 pdb=" CD PRO B 70 " 0.050 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU E 69 " -0.060 5.00e-02 4.00e+02 8.95e-02 1.28e+01 pdb=" N PRO E 70 " 0.155 5.00e-02 4.00e+02 pdb=" CA PRO E 70 " -0.045 5.00e-02 4.00e+02 pdb=" CD PRO E 70 " -0.050 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CD ARG E 85 " 0.129 9.50e-02 1.11e+02 6.27e-02 9.55e+00 pdb=" NE ARG E 85 " 0.008 2.00e-02 2.50e+03 pdb=" CZ ARG E 85 " -0.049 2.00e-02 2.50e+03 pdb=" NH1 ARG E 85 " 0.015 2.00e-02 2.50e+03 pdb=" NH2 ARG E 85 " 0.020 2.00e-02 2.50e+03 ... (remaining 2437 not shown) Histogram of nonbonded interaction distances: 2.03 - 2.60: 140 2.60 - 3.18: 11640 3.18 - 3.75: 20145 3.75 - 4.33: 26633 4.33 - 4.90: 43449 Nonbonded interactions: 102007 Sorted by model distance: nonbonded pdb=" SG CYS F 98 " pdb=" SG CYS F 108 " model vdw 2.026 3.760 nonbonded pdb=" SG CYS D 112 " pdb=" SG CYS D 122 " model vdw 2.027 3.760 nonbonded pdb=" SG CYS F 148 " pdb=" SG CYS F 158 " model vdw 2.030 3.760 nonbonded pdb=" SG CYS D 150 " pdb=" SG CYS D 160 " model vdw 2.030 3.760 nonbonded pdb=" SG CYS D 6 " pdb=" SG CYS D 32 " model vdw 2.031 3.760 ... (remaining 102002 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 'D' } ncs_group { reference = chain 'B' selection = chain 'E' } ncs_group { reference = chain 'C' selection = chain 'F' } ncs_group { reference = chain 'G' selection = chain 'H' } ncs_group { reference = chain 'I' selection = chain 'L' } 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 group one per residue 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: 1.720 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.100 Construct map_model_manager: 0.010 Extract box with map and model: 0.500 Check model and map are aligned: 0.090 Set scattering table: 0.130 Process input model: 34.520 Find NCS groups from input model: 0.330 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.760 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 40.210 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6576 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 : 0.004 0.060 13918 Z= 0.294 Angle : 1.198 19.503 19040 Z= 0.627 Chirality : 0.059 0.438 2182 Planarity : 0.007 0.090 2432 Dihedral : 14.568 108.305 5298 Min Nonbonded Distance : 2.026 Molprobity Statistics. All-atom Clashscore : 16.97 Ramachandran Plot: Outliers : 0.59 % Allowed : 5.52 % Favored : 93.89 % Rotamer: Outliers : 0.41 % Allowed : 2.39 % Favored : 97.20 % Cbeta Deviations : 0.12 % Peptide Plane: Cis-proline : 2.90 % 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: -0.83 (0.19), residues: 1702 helix: 1.25 (0.29), residues: 250 sheet: -0.06 (0.20), residues: 558 loop : -1.42 (0.19), residues: 894 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.047 0.003 TRP D 142 HIS 0.012 0.001 HIS E 86 PHE 0.039 0.003 PHE D 36 TYR 0.020 0.003 TYR A 344 ARG 0.047 0.001 ARG B 85 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3404 Ramachandran restraints generated. 1702 Oldfield, 0 Emsley, 1702 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3404 Ramachandran restraints generated. 1702 Oldfield, 0 Emsley, 1702 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 1480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 178 time to evaluate : 1.458 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 51 THR cc_start: 0.7698 (m) cc_final: 0.7137 (t) REVERT: A 220 LEU cc_start: 0.7337 (OUTLIER) cc_final: 0.7004 (mp) REVERT: B 109 GLN cc_start: 0.8246 (tm-30) cc_final: 0.7859 (tm-30) REVERT: C 157 ARG cc_start: 0.7161 (ptm-80) cc_final: 0.6855 (ttp-170) REVERT: C 282 TRP cc_start: 0.7501 (m100) cc_final: 0.6368 (m100) REVERT: D 35 TYR cc_start: 0.7123 (t80) cc_final: 0.6696 (t80) REVERT: D 57 TYR cc_start: 0.6498 (m-80) cc_final: 0.6284 (m-80) REVERT: D 220 LEU cc_start: 0.7213 (OUTLIER) cc_final: 0.6846 (mp) REVERT: F 157 ARG cc_start: 0.7134 (ptm-80) cc_final: 0.6855 (ttp-170) REVERT: F 202 LEU cc_start: 0.6647 (tp) cc_final: 0.6293 (tp) REVERT: F 282 TRP cc_start: 0.7522 (m100) cc_final: 0.6403 (m100) outliers start: 6 outliers final: 0 residues processed: 180 average time/residue: 0.2835 time to fit residues: 74.5641 Evaluate side-chains 120 residues out of total 1480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 118 time to evaluate : 1.315 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 220 LEU Chi-restraints excluded: chain D residue 220 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 141 optimal weight: 10.0000 chunk 127 optimal weight: 2.9990 chunk 70 optimal weight: 6.9990 chunk 43 optimal weight: 2.9990 chunk 85 optimal weight: 0.0060 chunk 68 optimal weight: 9.9990 chunk 131 optimal weight: 1.9990 chunk 50 optimal weight: 0.2980 chunk 80 optimal weight: 0.9980 chunk 98 optimal weight: 0.5980 chunk 152 optimal weight: 0.8980 overall best weight: 0.5596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 115 ASN D 115 ASN F 229 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6749 moved from start: 0.1807 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 13918 Z= 0.236 Angle : 0.798 9.958 19040 Z= 0.391 Chirality : 0.048 0.268 2182 Planarity : 0.006 0.057 2432 Dihedral : 8.826 68.020 2160 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 10.34 Ramachandran Plot: Outliers : 0.12 % Allowed : 2.94 % Favored : 96.94 % Rotamer: Outliers : 0.89 % Allowed : 7.45 % Favored : 91.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.90 % 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: 0.27 (0.20), residues: 1702 helix: 1.87 (0.30), residues: 252 sheet: 0.38 (0.20), residues: 546 loop : -0.39 (0.21), residues: 904 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A 124 HIS 0.006 0.001 HIS E 161 PHE 0.019 0.002 PHE C 230 TYR 0.025 0.002 TYR C 103 ARG 0.007 0.001 ARG B 85 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3404 Ramachandran restraints generated. 1702 Oldfield, 0 Emsley, 1702 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3404 Ramachandran restraints generated. 1702 Oldfield, 0 Emsley, 1702 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 1480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 153 time to evaluate : 1.470 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 123 MET cc_start: 0.5410 (mmt) cc_final: 0.5054 (mmt) REVERT: C 182 SER cc_start: 0.7762 (p) cc_final: 0.7522 (p) REVERT: F 108 CYS cc_start: 0.7784 (m) cc_final: 0.7478 (m) REVERT: F 182 SER cc_start: 0.7720 (p) cc_final: 0.7499 (p) outliers start: 13 outliers final: 5 residues processed: 162 average time/residue: 0.2359 time to fit residues: 59.0634 Evaluate side-chains 124 residues out of total 1480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 119 time to evaluate : 1.572 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 57 LEU Chi-restraints excluded: chain C residue 151 ASP Chi-restraints excluded: chain C residue 183 THR Chi-restraints excluded: chain F residue 151 ASP Chi-restraints excluded: chain F residue 230 PHE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 84 optimal weight: 1.9990 chunk 47 optimal weight: 4.9990 chunk 126 optimal weight: 0.3980 chunk 103 optimal weight: 0.5980 chunk 42 optimal weight: 1.9990 chunk 152 optimal weight: 3.9990 chunk 165 optimal weight: 0.1980 chunk 136 optimal weight: 1.9990 chunk 151 optimal weight: 0.9980 chunk 52 optimal weight: 0.9990 chunk 122 optimal weight: 20.0000 overall best weight: 0.6382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 38 GLN C 14 GLN F 14 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6817 moved from start: 0.2455 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 13918 Z= 0.215 Angle : 0.707 14.494 19040 Z= 0.345 Chirality : 0.046 0.271 2182 Planarity : 0.005 0.061 2432 Dihedral : 7.120 57.207 2156 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 9.26 Ramachandran Plot: Outliers : 0.12 % Allowed : 2.94 % Favored : 96.94 % Rotamer: Outliers : 1.50 % Allowed : 10.18 % Favored : 88.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.90 % 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: 0.40 (0.20), residues: 1702 helix: 1.58 (0.31), residues: 262 sheet: 0.42 (0.20), residues: 556 loop : -0.15 (0.22), residues: 884 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP F 166 HIS 0.012 0.001 HIS C 229 PHE 0.019 0.001 PHE D 50 TYR 0.017 0.002 TYR D 344 ARG 0.004 0.000 ARG E 118 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3404 Ramachandran restraints generated. 1702 Oldfield, 0 Emsley, 1702 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3404 Ramachandran restraints generated. 1702 Oldfield, 0 Emsley, 1702 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 1480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 129 time to evaluate : 1.450 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 89 TRP cc_start: 0.8473 (t60) cc_final: 0.8024 (t60) REVERT: B 123 MET cc_start: 0.5354 (mmt) cc_final: 0.5151 (mmt) REVERT: C 95 VAL cc_start: 0.8361 (t) cc_final: 0.7998 (m) REVERT: D 280 MET cc_start: 0.7103 (ttt) cc_final: 0.6879 (ttt) REVERT: F 108 CYS cc_start: 0.7700 (m) cc_final: 0.7330 (m) outliers start: 22 outliers final: 14 residues processed: 147 average time/residue: 0.2321 time to fit residues: 53.2132 Evaluate side-chains 120 residues out of total 1480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 106 time to evaluate : 1.530 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 SER Chi-restraints excluded: chain A residue 47 THR Chi-restraints excluded: chain A residue 160 CYS Chi-restraints excluded: chain A residue 232 ILE Chi-restraints excluded: chain B residue 18 LEU Chi-restraints excluded: chain B residue 38 GLN Chi-restraints excluded: chain B residue 57 LEU Chi-restraints excluded: chain B residue 176 THR Chi-restraints excluded: chain C residue 151 ASP Chi-restraints excluded: chain C residue 183 THR Chi-restraints excluded: chain D residue 232 ILE Chi-restraints excluded: chain F residue 151 ASP Chi-restraints excluded: chain F residue 183 THR Chi-restraints excluded: chain F residue 230 PHE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 151 optimal weight: 0.2980 chunk 114 optimal weight: 30.0000 chunk 79 optimal weight: 2.9990 chunk 16 optimal weight: 3.9990 chunk 72 optimal weight: 0.5980 chunk 102 optimal weight: 6.9990 chunk 153 optimal weight: 0.9990 chunk 162 optimal weight: 0.9980 chunk 80 optimal weight: 0.8980 chunk 145 optimal weight: 5.9990 chunk 43 optimal weight: 1.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 382 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 38 GLN ** D 382 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 229 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6888 moved from start: 0.2890 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 13918 Z= 0.214 Angle : 0.674 10.449 19040 Z= 0.329 Chirality : 0.046 0.304 2182 Planarity : 0.005 0.062 2432 Dihedral : 6.319 57.585 2156 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 9.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 2.53 % Allowed : 12.98 % Favored : 84.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.90 % 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: 1702 helix: 1.64 (0.32), residues: 252 sheet: 0.29 (0.20), residues: 564 loop : 0.09 (0.22), residues: 886 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP F 166 HIS 0.015 0.001 HIS C 229 PHE 0.012 0.002 PHE F 230 TYR 0.015 0.002 TYR A 344 ARG 0.004 0.000 ARG B 85 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3404 Ramachandran restraints generated. 1702 Oldfield, 0 Emsley, 1702 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3404 Ramachandran restraints generated. 1702 Oldfield, 0 Emsley, 1702 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 1480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 121 time to evaluate : 1.466 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 222 TRP cc_start: 0.7482 (p90) cc_final: 0.7060 (p90) REVERT: B 35 LEU cc_start: 0.7383 (OUTLIER) cc_final: 0.6974 (tt) REVERT: B 89 TRP cc_start: 0.8582 (t60) cc_final: 0.8173 (t60) REVERT: B 123 MET cc_start: 0.5416 (mmt) cc_final: 0.4997 (mmt) REVERT: C 24 LEU cc_start: 0.0936 (OUTLIER) cc_final: 0.0537 (pp) REVERT: D 222 TRP cc_start: 0.7748 (p90) cc_final: 0.7296 (p90) REVERT: F 108 CYS cc_start: 0.7658 (m) cc_final: 0.7257 (m) REVERT: F 282 TRP cc_start: 0.7764 (m100) cc_final: 0.6006 (m100) outliers start: 37 outliers final: 16 residues processed: 154 average time/residue: 0.1974 time to fit residues: 50.1708 Evaluate side-chains 128 residues out of total 1480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 110 time to evaluate : 1.517 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 SER Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain A residue 160 CYS Chi-restraints excluded: chain A residue 232 ILE Chi-restraints excluded: chain B residue 18 LEU Chi-restraints excluded: chain B residue 35 LEU Chi-restraints excluded: chain B residue 38 GLN Chi-restraints excluded: chain B residue 57 LEU Chi-restraints excluded: chain B residue 176 THR Chi-restraints excluded: chain C residue 24 LEU Chi-restraints excluded: chain C residue 183 THR Chi-restraints excluded: chain D residue 47 THR Chi-restraints excluded: chain D residue 160 CYS Chi-restraints excluded: chain D residue 232 ILE Chi-restraints excluded: chain E residue 57 LEU Chi-restraints excluded: chain E residue 176 THR Chi-restraints excluded: chain F residue 151 ASP Chi-restraints excluded: chain F residue 183 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 135 optimal weight: 7.9990 chunk 92 optimal weight: 2.9990 chunk 2 optimal weight: 0.6980 chunk 120 optimal weight: 9.9990 chunk 67 optimal weight: 0.9990 chunk 138 optimal weight: 1.9990 chunk 112 optimal weight: 4.9990 chunk 0 optimal weight: 0.5980 chunk 82 optimal weight: 0.0020 chunk 145 optimal weight: 1.9990 chunk 40 optimal weight: 0.7980 overall best weight: 0.6190 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 17 GLN ** A 382 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 38 GLN ** B 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 229 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 17 GLN D 338 ASN ** D 382 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6904 moved from start: 0.3223 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 13918 Z= 0.190 Angle : 0.648 16.160 19040 Z= 0.317 Chirality : 0.044 0.306 2182 Planarity : 0.005 0.063 2432 Dihedral : 5.963 57.114 2156 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 8.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 2.39 % Allowed : 14.00 % Favored : 83.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.90 % 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: 0.56 (0.21), residues: 1702 helix: 1.63 (0.32), residues: 252 sheet: 0.37 (0.21), residues: 546 loop : 0.12 (0.22), residues: 904 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP F 166 HIS 0.013 0.001 HIS C 229 PHE 0.020 0.001 PHE F 230 TYR 0.017 0.002 TYR D 344 ARG 0.003 0.000 ARG B 118 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3404 Ramachandran restraints generated. 1702 Oldfield, 0 Emsley, 1702 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3404 Ramachandran restraints generated. 1702 Oldfield, 0 Emsley, 1702 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 1480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 120 time to evaluate : 1.472 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 222 TRP cc_start: 0.7424 (p90) cc_final: 0.7080 (p90) REVERT: A 287 TYR cc_start: 0.5317 (m-10) cc_final: 0.4960 (m-10) REVERT: C 164 GLU cc_start: 0.8546 (OUTLIER) cc_final: 0.7551 (tp30) REVERT: D 17 GLN cc_start: 0.8358 (OUTLIER) cc_final: 0.8070 (mt0) REVERT: D 222 TRP cc_start: 0.7450 (p90) cc_final: 0.7052 (p90) REVERT: F 108 CYS cc_start: 0.7767 (m) cc_final: 0.7426 (m) REVERT: F 164 GLU cc_start: 0.8681 (OUTLIER) cc_final: 0.7683 (tp30) outliers start: 35 outliers final: 19 residues processed: 147 average time/residue: 0.2071 time to fit residues: 49.1673 Evaluate side-chains 132 residues out of total 1480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 110 time to evaluate : 1.573 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 GLN Chi-restraints excluded: chain A residue 47 THR Chi-restraints excluded: chain A residue 160 CYS Chi-restraints excluded: chain A residue 232 ILE Chi-restraints excluded: chain B residue 18 LEU Chi-restraints excluded: chain B residue 38 GLN Chi-restraints excluded: chain B residue 57 LEU Chi-restraints excluded: chain B residue 176 THR Chi-restraints excluded: chain C residue 164 GLU Chi-restraints excluded: chain C residue 183 THR Chi-restraints excluded: chain C residue 207 VAL Chi-restraints excluded: chain D residue 17 GLN Chi-restraints excluded: chain D residue 47 THR Chi-restraints excluded: chain D residue 80 THR Chi-restraints excluded: chain D residue 86 PHE Chi-restraints excluded: chain D residue 160 CYS Chi-restraints excluded: chain D residue 232 ILE Chi-restraints excluded: chain E residue 18 LEU Chi-restraints excluded: chain E residue 57 LEU Chi-restraints excluded: chain E residue 176 THR Chi-restraints excluded: chain F residue 164 GLU Chi-restraints excluded: chain F residue 183 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 54 optimal weight: 1.9990 chunk 146 optimal weight: 20.0000 chunk 32 optimal weight: 6.9990 chunk 95 optimal weight: 0.8980 chunk 40 optimal weight: 0.5980 chunk 162 optimal weight: 0.7980 chunk 134 optimal weight: 0.4980 chunk 75 optimal weight: 3.9990 chunk 13 optimal weight: 5.9990 chunk 53 optimal weight: 0.5980 chunk 85 optimal weight: 7.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 17 GLN ** B 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 229 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 382 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6928 moved from start: 0.3447 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 13918 Z= 0.198 Angle : 0.642 15.974 19040 Z= 0.314 Chirality : 0.044 0.314 2182 Planarity : 0.005 0.062 2432 Dihedral : 5.887 57.352 2156 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 8.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Rotamer: Outliers : 2.80 % Allowed : 14.75 % Favored : 82.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.90 % 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: 0.63 (0.21), residues: 1702 helix: 1.60 (0.32), residues: 252 sheet: 0.52 (0.21), residues: 522 loop : 0.12 (0.22), residues: 928 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP F 166 HIS 0.009 0.001 HIS C 229 PHE 0.017 0.002 PHE F 230 TYR 0.023 0.001 TYR F 103 ARG 0.003 0.000 ARG F 274 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3404 Ramachandran restraints generated. 1702 Oldfield, 0 Emsley, 1702 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3404 Ramachandran restraints generated. 1702 Oldfield, 0 Emsley, 1702 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 1480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 116 time to evaluate : 1.662 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 17 GLN cc_start: 0.8248 (OUTLIER) cc_final: 0.7871 (mt0) REVERT: A 222 TRP cc_start: 0.7396 (p90) cc_final: 0.7110 (p90) REVERT: C 164 GLU cc_start: 0.8666 (OUTLIER) cc_final: 0.7702 (tp30) REVERT: D 222 TRP cc_start: 0.7448 (p90) cc_final: 0.7101 (p90) REVERT: D 287 TYR cc_start: 0.5817 (m-10) cc_final: 0.5460 (m-10) REVERT: E 41 ASP cc_start: 0.8270 (t0) cc_final: 0.8011 (t0) REVERT: F 108 CYS cc_start: 0.7754 (m) cc_final: 0.7424 (m) REVERT: F 164 GLU cc_start: 0.8692 (OUTLIER) cc_final: 0.7679 (tp30) outliers start: 41 outliers final: 27 residues processed: 147 average time/residue: 0.2107 time to fit residues: 50.7805 Evaluate side-chains 133 residues out of total 1480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 103 time to evaluate : 1.346 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 SER Chi-restraints excluded: chain A residue 17 GLN Chi-restraints excluded: chain A residue 47 THR Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain A residue 160 CYS Chi-restraints excluded: chain A residue 232 ILE Chi-restraints excluded: chain B residue 18 LEU Chi-restraints excluded: chain B residue 57 LEU Chi-restraints excluded: chain B residue 73 LEU Chi-restraints excluded: chain B residue 176 THR Chi-restraints excluded: chain C residue 151 ASP Chi-restraints excluded: chain C residue 164 GLU Chi-restraints excluded: chain C residue 183 THR Chi-restraints excluded: chain C residue 207 VAL Chi-restraints excluded: chain D residue 4 ASP Chi-restraints excluded: chain D residue 47 THR Chi-restraints excluded: chain D residue 80 THR Chi-restraints excluded: chain D residue 86 PHE Chi-restraints excluded: chain D residue 160 CYS Chi-restraints excluded: chain D residue 232 ILE Chi-restraints excluded: chain D residue 338 ASN Chi-restraints excluded: chain D residue 347 THR Chi-restraints excluded: chain E residue 18 LEU Chi-restraints excluded: chain E residue 57 LEU Chi-restraints excluded: chain E residue 80 LEU Chi-restraints excluded: chain E residue 176 THR Chi-restraints excluded: chain F residue 109 THR Chi-restraints excluded: chain F residue 164 GLU Chi-restraints excluded: chain F residue 183 THR Chi-restraints excluded: chain F residue 207 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 156 optimal weight: 0.6980 chunk 18 optimal weight: 5.9990 chunk 92 optimal weight: 3.9990 chunk 118 optimal weight: 2.9990 chunk 91 optimal weight: 0.5980 chunk 136 optimal weight: 1.9990 chunk 90 optimal weight: 0.0980 chunk 161 optimal weight: 0.2980 chunk 101 optimal weight: 2.9990 chunk 98 optimal weight: 0.9980 chunk 74 optimal weight: 0.8980 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 161 HIS C 229 HIS E 161 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6921 moved from start: 0.3623 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 13918 Z= 0.170 Angle : 0.637 16.719 19040 Z= 0.312 Chirality : 0.044 0.306 2182 Planarity : 0.005 0.061 2432 Dihedral : 5.790 57.185 2156 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 8.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer: Outliers : 2.25 % Allowed : 15.57 % Favored : 82.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.90 % 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: 0.60 (0.21), residues: 1702 helix: 1.66 (0.33), residues: 252 sheet: 0.49 (0.21), residues: 554 loop : 0.07 (0.23), residues: 896 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP F 166 HIS 0.008 0.001 HIS C 229 PHE 0.016 0.001 PHE C 230 TYR 0.019 0.001 TYR A 344 ARG 0.005 0.000 ARG A 121 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3404 Ramachandran restraints generated. 1702 Oldfield, 0 Emsley, 1702 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3404 Ramachandran restraints generated. 1702 Oldfield, 0 Emsley, 1702 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 1480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 117 time to evaluate : 1.508 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 222 TRP cc_start: 0.7349 (p90) cc_final: 0.7112 (p90) REVERT: C 164 GLU cc_start: 0.8683 (OUTLIER) cc_final: 0.7700 (tp30) REVERT: D 57 TYR cc_start: 0.7042 (m-80) cc_final: 0.6769 (m-80) REVERT: D 222 TRP cc_start: 0.7508 (p90) cc_final: 0.7223 (p90) REVERT: D 280 MET cc_start: 0.6205 (ttt) cc_final: 0.5913 (ttt) REVERT: E 41 ASP cc_start: 0.8265 (t0) cc_final: 0.8011 (t0) REVERT: E 48 ASP cc_start: 0.7381 (p0) cc_final: 0.7178 (p0) REVERT: E 49 HIS cc_start: 0.7877 (p-80) cc_final: 0.7409 (p-80) REVERT: E 59 MET cc_start: 0.7436 (mtm) cc_final: 0.7178 (mtm) REVERT: F 108 CYS cc_start: 0.7694 (m) cc_final: 0.7355 (m) REVERT: F 164 GLU cc_start: 0.8719 (OUTLIER) cc_final: 0.7740 (tp30) outliers start: 33 outliers final: 23 residues processed: 142 average time/residue: 0.2086 time to fit residues: 47.8816 Evaluate side-chains 133 residues out of total 1480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 108 time to evaluate : 1.778 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 THR Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain A residue 86 PHE Chi-restraints excluded: chain A residue 160 CYS Chi-restraints excluded: chain A residue 232 ILE Chi-restraints excluded: chain A residue 347 THR Chi-restraints excluded: chain B residue 18 LEU Chi-restraints excluded: chain B residue 57 LEU Chi-restraints excluded: chain B residue 176 THR Chi-restraints excluded: chain C residue 164 GLU Chi-restraints excluded: chain C residue 183 THR Chi-restraints excluded: chain C residue 207 VAL Chi-restraints excluded: chain D residue 4 ASP Chi-restraints excluded: chain D residue 47 THR Chi-restraints excluded: chain D residue 80 THR Chi-restraints excluded: chain D residue 86 PHE Chi-restraints excluded: chain D residue 160 CYS Chi-restraints excluded: chain D residue 232 ILE Chi-restraints excluded: chain E residue 18 LEU Chi-restraints excluded: chain E residue 57 LEU Chi-restraints excluded: chain E residue 176 THR Chi-restraints excluded: chain F residue 109 THR Chi-restraints excluded: chain F residue 151 ASP Chi-restraints excluded: chain F residue 164 GLU Chi-restraints excluded: chain F residue 183 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 100 optimal weight: 0.6980 chunk 64 optimal weight: 3.9990 chunk 96 optimal weight: 0.9990 chunk 48 optimal weight: 1.9990 chunk 31 optimal weight: 2.9990 chunk 102 optimal weight: 0.8980 chunk 110 optimal weight: 5.9990 chunk 80 optimal weight: 4.9990 chunk 15 optimal weight: 1.9990 chunk 127 optimal weight: 0.0770 chunk 147 optimal weight: 0.9990 overall best weight: 0.7342 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 382 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 73 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6969 moved from start: 0.3881 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 13918 Z= 0.201 Angle : 0.654 18.530 19040 Z= 0.319 Chirality : 0.045 0.331 2182 Planarity : 0.005 0.083 2432 Dihedral : 5.759 57.592 2156 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 9.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer: Outliers : 2.39 % Allowed : 16.05 % Favored : 81.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.90 % 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: 0.53 (0.21), residues: 1702 helix: 1.61 (0.33), residues: 252 sheet: 0.49 (0.22), residues: 532 loop : 0.00 (0.22), residues: 918 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP F 166 HIS 0.011 0.001 HIS F 229 PHE 0.022 0.002 PHE C 230 TYR 0.019 0.002 TYR F 103 ARG 0.003 0.000 ARG E 118 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3404 Ramachandran restraints generated. 1702 Oldfield, 0 Emsley, 1702 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3404 Ramachandran restraints generated. 1702 Oldfield, 0 Emsley, 1702 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 1480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 118 time to evaluate : 1.424 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 232 ILE cc_start: 0.8865 (OUTLIER) cc_final: 0.8410 (mm) REVERT: C 164 GLU cc_start: 0.8746 (OUTLIER) cc_final: 0.7790 (tp30) REVERT: D 57 TYR cc_start: 0.7089 (m-80) cc_final: 0.6845 (m-80) REVERT: D 222 TRP cc_start: 0.7481 (p90) cc_final: 0.7245 (p90) REVERT: D 254 ASP cc_start: 0.8431 (t70) cc_final: 0.8212 (t0) REVERT: E 41 ASP cc_start: 0.8296 (t0) cc_final: 0.8041 (t0) REVERT: E 49 HIS cc_start: 0.8015 (p-80) cc_final: 0.7564 (p-80) REVERT: E 59 MET cc_start: 0.7728 (mtm) cc_final: 0.7469 (mtm) REVERT: F 108 CYS cc_start: 0.7658 (m) cc_final: 0.7394 (m) REVERT: F 164 GLU cc_start: 0.8673 (OUTLIER) cc_final: 0.7843 (tp30) outliers start: 35 outliers final: 24 residues processed: 148 average time/residue: 0.1986 time to fit residues: 48.4999 Evaluate side-chains 133 residues out of total 1480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 106 time to evaluate : 1.566 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 THR Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain A residue 86 PHE Chi-restraints excluded: chain A residue 160 CYS Chi-restraints excluded: chain A residue 232 ILE Chi-restraints excluded: chain A residue 347 THR Chi-restraints excluded: chain B residue 18 LEU Chi-restraints excluded: chain B residue 57 LEU Chi-restraints excluded: chain B residue 176 THR Chi-restraints excluded: chain C residue 164 GLU Chi-restraints excluded: chain C residue 183 THR Chi-restraints excluded: chain C residue 207 VAL Chi-restraints excluded: chain C residue 230 PHE Chi-restraints excluded: chain D residue 47 THR Chi-restraints excluded: chain D residue 80 THR Chi-restraints excluded: chain D residue 86 PHE Chi-restraints excluded: chain D residue 232 ILE Chi-restraints excluded: chain D residue 347 THR Chi-restraints excluded: chain E residue 18 LEU Chi-restraints excluded: chain E residue 57 LEU Chi-restraints excluded: chain E residue 80 LEU Chi-restraints excluded: chain E residue 176 THR Chi-restraints excluded: chain F residue 151 ASP Chi-restraints excluded: chain F residue 164 GLU Chi-restraints excluded: chain F residue 183 THR Chi-restraints excluded: chain F residue 204 VAL Chi-restraints excluded: chain F residue 207 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 155 optimal weight: 2.9990 chunk 141 optimal weight: 6.9990 chunk 150 optimal weight: 1.9990 chunk 90 optimal weight: 3.9990 chunk 65 optimal weight: 0.8980 chunk 118 optimal weight: 7.9990 chunk 46 optimal weight: 1.9990 chunk 136 optimal weight: 4.9990 chunk 142 optimal weight: 3.9990 chunk 99 optimal weight: 5.9990 chunk 159 optimal weight: 3.9990 overall best weight: 2.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 82 ASN A 115 ASN ** A 382 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 161 HIS ** D 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 115 ASN ** D 382 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 38 GLN E 161 HIS F 73 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7201 moved from start: 0.4589 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.078 13918 Z= 0.490 Angle : 0.877 20.085 19040 Z= 0.431 Chirality : 0.052 0.382 2182 Planarity : 0.007 0.061 2432 Dihedral : 6.627 59.802 2156 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 15.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.76 % Favored : 95.24 % Rotamer: Outliers : 2.39 % Allowed : 16.26 % Favored : 81.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.90 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: -0.27 (0.21), residues: 1702 helix: 0.21 (0.30), residues: 252 sheet: 0.09 (0.22), residues: 540 loop : -0.37 (0.22), residues: 910 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.003 TRP F 282 HIS 0.029 0.002 HIS F 229 PHE 0.032 0.003 PHE F 230 TYR 0.050 0.003 TYR C 103 ARG 0.007 0.001 ARG E 169 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3404 Ramachandran restraints generated. 1702 Oldfield, 0 Emsley, 1702 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3404 Ramachandran restraints generated. 1702 Oldfield, 0 Emsley, 1702 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 1480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 109 time to evaluate : 1.644 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 232 ILE cc_start: 0.8918 (OUTLIER) cc_final: 0.8585 (mm) REVERT: B 49 HIS cc_start: 0.8348 (p-80) cc_final: 0.8131 (p-80) REVERT: B 104 GLU cc_start: 0.8008 (mt-10) cc_final: 0.7771 (mt-10) REVERT: C 164 GLU cc_start: 0.8889 (OUTLIER) cc_final: 0.7662 (mm-30) REVERT: D 49 HIS cc_start: 0.7441 (m-70) cc_final: 0.7034 (m90) REVERT: D 232 ILE cc_start: 0.8930 (OUTLIER) cc_final: 0.8575 (mm) REVERT: D 254 ASP cc_start: 0.8510 (t70) cc_final: 0.8229 (t0) REVERT: D 280 MET cc_start: 0.7504 (ttt) cc_final: 0.7071 (ttt) REVERT: F 108 CYS cc_start: 0.7563 (m) cc_final: 0.7343 (m) REVERT: F 164 GLU cc_start: 0.8801 (OUTLIER) cc_final: 0.7532 (mm-30) outliers start: 35 outliers final: 27 residues processed: 137 average time/residue: 0.2471 time to fit residues: 54.7528 Evaluate side-chains 125 residues out of total 1480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 94 time to evaluate : 1.570 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 THR Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain A residue 160 CYS Chi-restraints excluded: chain A residue 232 ILE Chi-restraints excluded: chain A residue 347 THR Chi-restraints excluded: chain B residue 18 LEU Chi-restraints excluded: chain B residue 57 LEU Chi-restraints excluded: chain B residue 73 LEU Chi-restraints excluded: chain B residue 161 HIS Chi-restraints excluded: chain B residue 176 THR Chi-restraints excluded: chain C residue 151 ASP Chi-restraints excluded: chain C residue 164 GLU Chi-restraints excluded: chain C residue 183 THR Chi-restraints excluded: chain C residue 204 VAL Chi-restraints excluded: chain C residue 207 VAL Chi-restraints excluded: chain C residue 236 LEU Chi-restraints excluded: chain D residue 47 THR Chi-restraints excluded: chain D residue 80 THR Chi-restraints excluded: chain D residue 232 ILE Chi-restraints excluded: chain D residue 260 SER Chi-restraints excluded: chain D residue 347 THR Chi-restraints excluded: chain E residue 57 LEU Chi-restraints excluded: chain E residue 80 LEU Chi-restraints excluded: chain E residue 161 HIS Chi-restraints excluded: chain E residue 176 THR Chi-restraints excluded: chain F residue 109 THR Chi-restraints excluded: chain F residue 151 ASP Chi-restraints excluded: chain F residue 164 GLU Chi-restraints excluded: chain F residue 183 THR Chi-restraints excluded: chain F residue 204 VAL Chi-restraints excluded: chain F residue 207 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 97 optimal weight: 0.9990 chunk 75 optimal weight: 0.1980 chunk 110 optimal weight: 0.8980 chunk 167 optimal weight: 0.5980 chunk 154 optimal weight: 0.0980 chunk 133 optimal weight: 0.6980 chunk 13 optimal weight: 0.6980 chunk 102 optimal weight: 0.9990 chunk 81 optimal weight: 0.8980 chunk 105 optimal weight: 0.9980 chunk 141 optimal weight: 20.0000 overall best weight: 0.4580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 382 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7067 moved from start: 0.4513 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 13918 Z= 0.187 Angle : 0.705 18.037 19040 Z= 0.344 Chirality : 0.046 0.323 2182 Planarity : 0.006 0.077 2432 Dihedral : 6.167 57.778 2156 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 11.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Rotamer: Outliers : 1.84 % Allowed : 17.28 % Favored : 80.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.90 % 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: 0.13 (0.21), residues: 1702 helix: 1.23 (0.32), residues: 240 sheet: 0.05 (0.21), residues: 558 loop : -0.10 (0.23), residues: 904 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP A 222 HIS 0.020 0.002 HIS B 161 PHE 0.031 0.002 PHE C 230 TYR 0.036 0.002 TYR C 103 ARG 0.003 0.000 ARG B 117 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3404 Ramachandran restraints generated. 1702 Oldfield, 0 Emsley, 1702 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3404 Ramachandran restraints generated. 1702 Oldfield, 0 Emsley, 1702 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 1480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 102 time to evaluate : 3.761 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 33 MET cc_start: 0.6262 (tmm) cc_final: 0.5887 (tmm) REVERT: A 232 ILE cc_start: 0.8848 (OUTLIER) cc_final: 0.8468 (mm) REVERT: C 164 GLU cc_start: 0.8753 (OUTLIER) cc_final: 0.7594 (mm-30) REVERT: D 35 TYR cc_start: 0.7232 (t80) cc_final: 0.6890 (t80) REVERT: D 49 HIS cc_start: 0.7340 (m-70) cc_final: 0.7138 (m90) REVERT: D 57 TYR cc_start: 0.7149 (m-80) cc_final: 0.6895 (m-80) REVERT: D 232 ILE cc_start: 0.8848 (OUTLIER) cc_final: 0.8445 (mm) REVERT: D 280 MET cc_start: 0.7037 (ttt) cc_final: 0.6683 (ttt) REVERT: E 59 MET cc_start: 0.7780 (mtm) cc_final: 0.7197 (mtm) REVERT: F 164 GLU cc_start: 0.8694 (OUTLIER) cc_final: 0.7553 (mm-30) REVERT: F 255 GLU cc_start: 0.7722 (pp20) cc_final: 0.7476 (pt0) outliers start: 27 outliers final: 22 residues processed: 123 average time/residue: 0.2093 time to fit residues: 43.0808 Evaluate side-chains 120 residues out of total 1480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 94 time to evaluate : 1.488 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 THR Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain A residue 160 CYS Chi-restraints excluded: chain A residue 232 ILE Chi-restraints excluded: chain A residue 347 THR Chi-restraints excluded: chain A residue 348 LEU Chi-restraints excluded: chain B residue 57 LEU Chi-restraints excluded: chain B residue 176 THR Chi-restraints excluded: chain C residue 151 ASP Chi-restraints excluded: chain C residue 164 GLU Chi-restraints excluded: chain C residue 183 THR Chi-restraints excluded: chain C residue 207 VAL Chi-restraints excluded: chain C residue 236 LEU Chi-restraints excluded: chain D residue 47 THR Chi-restraints excluded: chain D residue 232 ILE Chi-restraints excluded: chain D residue 260 SER Chi-restraints excluded: chain D residue 338 ASN Chi-restraints excluded: chain D residue 347 THR Chi-restraints excluded: chain E residue 57 LEU Chi-restraints excluded: chain E residue 80 LEU Chi-restraints excluded: chain E residue 176 THR Chi-restraints excluded: chain F residue 151 ASP Chi-restraints excluded: chain F residue 164 GLU Chi-restraints excluded: chain F residue 183 THR Chi-restraints excluded: chain F residue 204 VAL Chi-restraints excluded: chain F residue 207 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 40 optimal weight: 0.5980 chunk 122 optimal weight: 0.0470 chunk 19 optimal weight: 0.5980 chunk 37 optimal weight: 9.9990 chunk 133 optimal weight: 1.9990 chunk 55 optimal weight: 0.7980 chunk 137 optimal weight: 0.9990 chunk 16 optimal weight: 0.9990 chunk 24 optimal weight: 5.9990 chunk 117 optimal weight: 0.0270 chunk 7 optimal weight: 3.9990 overall best weight: 0.4136 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 382 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 145 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 382 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4546 r_free = 0.4546 target = 0.215625 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.4153 r_free = 0.4153 target = 0.186849 restraints weight = 182493.377| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.4196 r_free = 0.4196 target = 0.191155 restraints weight = 110378.186| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.4166 r_free = 0.4166 target = 0.188109 restraints weight = 96067.099| |-----------------------------------------------------------------------------| r_work (final): 0.3870 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7361 moved from start: 0.4571 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 13918 Z= 0.179 Angle : 0.672 17.116 19040 Z= 0.328 Chirality : 0.045 0.305 2182 Planarity : 0.005 0.070 2432 Dihedral : 5.838 57.128 2156 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 9.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.35 % Favored : 95.65 % Rotamer: Outliers : 1.91 % Allowed : 17.55 % Favored : 80.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.90 % 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: 0.32 (0.21), residues: 1702 helix: 1.72 (0.33), residues: 240 sheet: 0.09 (0.21), residues: 558 loop : -0.01 (0.23), residues: 904 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.002 TRP D 222 HIS 0.014 0.001 HIS C 229 PHE 0.022 0.002 PHE E 43 TYR 0.023 0.002 TYR D 344 ARG 0.003 0.000 ARG B 117 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2449.68 seconds wall clock time: 47 minutes 23.83 seconds (2843.83 seconds total)