Starting phenix.real_space_refine on Fri Jul 3 15:31:07 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8dpt_27642/07_2026/8dpt_27642.cif Found real_map, /net/cci-nas-00/data/ceres_data/8dpt_27642/07_2026/8dpt_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 { restraint_files = "/net/cci-nas-00/data/ceres_data/8dpt_27642/07_2026/8dpt_27642.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8dpt_27642/07_2026/8dpt_27642.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8dpt_27642/07_2026/8dpt_27642.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8dpt_27642/07_2026/8dpt_27642.map" model { file = "/net/cci-nas-00/data/ceres_data/8dpt_27642/07_2026/8dpt_27642.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8dpt_27642/07_2026/8dpt_27642.cif" } resolution = 4.0 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 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: 6 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: D, E, F, L, H Time building chain proxies: 3.37, per 1000 atoms: 0.25 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=16, 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 Simple disulfide: pdb=" SG CYS D 6 " - pdb=" SG CYS D 32 " distance=2.03 Simple disulfide: pdb=" SG CYS D 26 " - pdb=" SG CYS D 81 " distance=2.03 Simple disulfide: pdb=" SG CYS D 112 " - pdb=" SG CYS D 122 " distance=2.03 Simple disulfide: pdb=" SG CYS D 150 " - pdb=" SG CYS D 160 " distance=2.03 Simple disulfide: pdb=" SG CYS F 4 " - pdb=" SG CYS F 25 " distance=2.03 Simple disulfide: pdb=" SG CYS F 26 " - pdb=" SG CYS F 72 " distance=2.03 Simple disulfide: pdb=" SG CYS F 98 " - pdb=" SG CYS F 108 " distance=2.03 Simple disulfide: pdb=" SG CYS F 148 " - pdb=" SG CYS F 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: 0.83 Conformation dependent library (CDL) restraints added in 434.1 milliseconds 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: 0.42 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: 1.60 Time building geometry restraints manager: 1.10 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 - 17.07: 7741 17.07 - 34.14: 607 34.14 - 51.21: 122 51.21 - 68.28: 32 68.28 - 85.35: 18 Dihedral angle restraints: 8520 sinusoidal: 3542 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 8517 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: 2.09 - 2.65: 254 2.65 - 3.22: 12538 3.22 - 3.78: 20119 3.78 - 4.34: 26435 4.34 - 4.90: 42637 Nonbonded interactions: 101983 Sorted by model distance: nonbonded pdb=" OG SER D 261 " pdb=" OG SER F 247 " model vdw 2.093 3.040 nonbonded pdb=" OG SER A 261 " pdb=" OG SER C 247 " model vdw 2.100 3.040 nonbonded pdb=" NE2 GLN B 38 " pdb=" OE1 GLU B 104 " model vdw 2.135 3.120 nonbonded pdb=" NE2 GLN E 38 " pdb=" OE1 GLU E 104 " model vdw 2.136 3.120 nonbonded pdb=" OG1 THR A 347 " pdb=" OG1 THR A 377 " model vdw 2.150 3.040 ... (remaining 101978 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.02 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'D' } ncs_group { reference = chain 'B' selection = chain 'E' } ncs_group { reference = chain 'C' selection = chain 'F' } ncs_group { reference = chain 'I' selection = chain 'L' } ncs_group { reference = chain 'G' selection = chain 'H' } 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: 1.460 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.030 Construct map_model_manager: 0.010 Extract box with map and model: 0.230 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 11.200 Find NCS groups from input model: 0.070 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.090 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.190 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6818 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 13948 Z= 0.203 Angle : 1.211 19.503 19114 Z= 0.630 Chirality : 0.059 0.438 2182 Planarity : 0.007 0.090 2432 Dihedral : 13.488 85.355 5260 Min Nonbonded Distance : 2.093 Molprobity Statistics. All-atom Clashscore : 17.05 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.83 (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 ARG 0.047 0.001 ARG B 85 TYR 0.020 0.003 TYR A 344 PHE 0.039 0.003 PHE D 36 TRP 0.047 0.003 TRP D 142 HIS 0.012 0.001 HIS E 86 Details of bonding type rmsd/Z covalent geometry : bond 0.00445 / 0.20 (13918) covalent geometry : angle 1.19847 / 0.63 (19040) SS BOND : bond 0.00269 / 0.13 ( 16) SS BOND : angle 2.64312 / 1.59 ( 32) hydrogen bonds : bond 0.25308 / 16.61 ( 520) hydrogen bonds : angle 8.79719 / 5.93 ( 1410) link_BETA1-4 : bond 0.00723 / 0.41 ( 6) link_BETA1-4 : angle 3.51647 / 1.57 ( 18) link_NAG-ASN : bond 0.00927 / 0.48 ( 8) link_NAG-ASN : angle 3.18960 / 1.86 ( 24) *********************** 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 : 0.424 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: 0.7860 (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: 0.6285 (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: 0.6856 (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: 0.1066 time to fit residues: 28.2577 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 : 0.337 ------------------------------------------------------------------------------- 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 98 optimal weight: 0.8980 chunk 107 optimal weight: 0.8980 chunk 10 optimal weight: 2.9990 chunk 66 optimal weight: 20.0000 chunk 130 optimal weight: 0.5980 chunk 124 optimal weight: 1.9990 chunk 103 optimal weight: 0.7980 chunk 77 optimal weight: 0.8980 chunk 122 optimal weight: 8.9990 chunk 91 optimal weight: 0.8980 chunk 149 optimal weight: 0.8980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 92 ASN B 38 GLN D 92 ASN D 115 ASN F 229 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4570 r_free = 0.4570 target = 0.219577 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 92)----------------| | r_work = 0.4228 r_free = 0.4228 target = 0.192155 restraints weight = 17425.243| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.4221 r_free = 0.4221 target = 0.190759 restraints weight = 18131.575| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.4219 r_free = 0.4219 target = 0.190396 restraints weight = 19117.339| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.4222 r_free = 0.4222 target = 0.190603 restraints weight = 17265.486| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.4222 r_free = 0.4222 target = 0.190585 restraints weight = 16297.809| |-----------------------------------------------------------------------------| r_work (final): 0.4214 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7190 moved from start: 0.1846 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.078 13948 Z= 0.177 Angle : 0.819 10.396 19114 Z= 0.402 Chirality : 0.048 0.297 2182 Planarity : 0.006 0.057 2432 Dihedral : 7.034 58.346 2122 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 10.57 Ramachandran Plot: Outliers : 0.12 % Allowed : 3.00 % Favored : 96.89 % Rotamer: Outliers : 1.09 % Allowed : 7.86 % Favored : 91.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.90 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.24 (0.20), residues: 1702 helix: 1.90 (0.30), residues: 252 sheet: 0.30 (0.19), residues: 546 loop : -0.38 (0.21), residues: 904 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG B 85 TYR 0.023 0.002 TYR C 103 PHE 0.018 0.002 PHE C 230 TRP 0.018 0.002 TRP A 124 HIS 0.006 0.001 HIS E 161 Details of bonding type rmsd/Z covalent geometry : bond 0.00405 / 0.18 (13918) covalent geometry : angle 0.80920 / 0.40 (19040) SS BOND : bond 0.00326 / 0.18 ( 16) SS BOND : angle 2.34906 / 1.23 ( 32) hydrogen bonds : bond 0.05383 / 3.57 ( 520) hydrogen bonds : angle 6.05031 / 4.08 ( 1410) link_BETA1-4 : bond 0.00758 / 0.42 ( 6) link_BETA1-4 : angle 2.51996 / 1.17 ( 18) link_NAG-ASN : bond 0.00432 / 0.23 ( 8) link_NAG-ASN : angle 1.65854 / 0.87 ( 24) *********************** 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 163 residues out of total 1480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 147 time to evaluate : 0.496 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 123 MET cc_start: 0.4675 (mmt) cc_final: 0.4355 (mmt) REVERT: C 182 SER cc_start: 0.7224 (p) cc_final: 0.6969 (p) REVERT: C 229 HIS cc_start: 0.4766 (m170) cc_final: 0.4447 (m170) REVERT: E 89 TRP cc_start: 0.8525 (t60) cc_final: 0.8321 (t60) REVERT: F 182 SER cc_start: 0.7177 (p) cc_final: 0.6936 (p) REVERT: F 288 GLU cc_start: 0.6914 (mm-30) cc_final: 0.6547 (mm-30) outliers start: 16 outliers final: 7 residues processed: 158 average time/residue: 0.0847 time to fit residues: 21.0384 Evaluate side-chains 122 residues out of total 1480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 115 time to evaluate : 0.365 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 38 GLN 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 183 THR 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 43 optimal weight: 1.9990 chunk 149 optimal weight: 2.9990 chunk 164 optimal weight: 4.9990 chunk 151 optimal weight: 1.9990 chunk 21 optimal weight: 1.9990 chunk 24 optimal weight: 7.9990 chunk 19 optimal weight: 0.5980 chunk 165 optimal weight: 0.7980 chunk 143 optimal weight: 1.9990 chunk 17 optimal weight: 0.8980 chunk 147 optimal weight: 5.9990 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 382 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 38 GLN ** C 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 229 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 382 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4474 r_free = 0.4474 target = 0.208036 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.4352 r_free = 0.4352 target = 0.195318 restraints weight = 17482.689| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.4171 r_free = 0.4171 target = 0.183607 restraints weight = 33536.407| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.4125 r_free = 0.4125 target = 0.178724 restraints weight = 26447.669| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.4122 r_free = 0.4122 target = 0.178359 restraints weight = 24102.530| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.4123 r_free = 0.4123 target = 0.178551 restraints weight = 21605.596| |-----------------------------------------------------------------------------| r_work (final): 0.4125 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7291 moved from start: 0.2784 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.062 13948 Z= 0.202 Angle : 0.772 14.281 19114 Z= 0.380 Chirality : 0.048 0.305 2182 Planarity : 0.005 0.060 2432 Dihedral : 6.468 57.702 2118 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 11.05 Ramachandran Plot: Outliers : 0.12 % Allowed : 3.88 % Favored : 96.00 % Rotamer: Outliers : 2.19 % Allowed : 10.93 % Favored : 86.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.90 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.10 (0.20), residues: 1702 helix: 0.95 (0.31), residues: 276 sheet: 0.28 (0.20), residues: 538 loop : -0.27 (0.21), residues: 888 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG F 235 TYR 0.018 0.002 TYR A 344 PHE 0.022 0.002 PHE D 50 TRP 0.016 0.002 TRP B 89 HIS 0.007 0.001 HIS F 229 Details of bonding type rmsd/Z covalent geometry : bond 0.00471 / 0.20 (13918) covalent geometry : angle 0.76231 / 0.38 (19040) SS BOND : bond 0.00435 / 0.25 ( 16) SS BOND : angle 1.92094 / 1.11 ( 32) hydrogen bonds : bond 0.04629 / 3.05 ( 520) hydrogen bonds : angle 5.55326 / 3.77 ( 1410) link_BETA1-4 : bond 0.00586 / 0.31 ( 6) link_BETA1-4 : angle 2.61855 / 1.19 ( 18) link_NAG-ASN : bond 0.00335 / 0.18 ( 8) link_NAG-ASN : angle 1.77427 / 0.98 ( 24) *********************** 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 158 residues out of total 1480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 126 time to evaluate : 0.509 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 35 LEU cc_start: 0.7866 (OUTLIER) cc_final: 0.7406 (tt) REVERT: C 282 TRP cc_start: 0.7459 (m-10) cc_final: 0.6560 (m-10) outliers start: 32 outliers final: 17 residues processed: 151 average time/residue: 0.0995 time to fit residues: 23.4125 Evaluate side-chains 119 residues out of total 1480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 101 time to evaluate : 0.512 ------------------------------------------------------------------------------- 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 B residue 35 LEU Chi-restraints excluded: chain B residue 57 LEU Chi-restraints excluded: chain B residue 176 THR Chi-restraints excluded: chain C residue 183 THR Chi-restraints excluded: chain C residue 281 THR Chi-restraints excluded: chain D residue 25 VAL Chi-restraints excluded: chain D residue 47 THR Chi-restraints excluded: chain D residue 80 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 F residue 151 ASP Chi-restraints excluded: chain F residue 183 THR Chi-restraints excluded: chain F residue 281 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 110 optimal weight: 5.9990 chunk 32 optimal weight: 20.0000 chunk 53 optimal weight: 0.8980 chunk 149 optimal weight: 0.7980 chunk 68 optimal weight: 4.9990 chunk 117 optimal weight: 0.8980 chunk 108 optimal weight: 5.9990 chunk 107 optimal weight: 0.6980 chunk 75 optimal weight: 3.9990 chunk 130 optimal weight: 0.8980 chunk 126 optimal weight: 0.2980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 382 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 14 GLN ** D 382 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 14 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4492 r_free = 0.4492 target = 0.209814 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4368 r_free = 0.4368 target = 0.196985 restraints weight = 17722.674| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.4135 r_free = 0.4135 target = 0.182426 restraints weight = 41882.698| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.4110 r_free = 0.4110 target = 0.178328 restraints weight = 31720.072| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.4109 r_free = 0.4109 target = 0.178151 restraints weight = 27687.679| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.4116 r_free = 0.4116 target = 0.178759 restraints weight = 21057.067| |-----------------------------------------------------------------------------| r_work (final): 0.4123 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7324 moved from start: 0.3100 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 13948 Z= 0.140 Angle : 0.678 9.620 19114 Z= 0.330 Chirality : 0.045 0.302 2182 Planarity : 0.005 0.062 2432 Dihedral : 6.257 57.335 2118 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 8.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer: Outliers : 1.84 % Allowed : 13.52 % Favored : 84.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.90 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.32 (0.20), residues: 1702 helix: 1.26 (0.31), residues: 264 sheet: 0.22 (0.20), residues: 548 loop : -0.00 (0.22), residues: 890 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 121 TYR 0.019 0.002 TYR F 103 PHE 0.025 0.002 PHE F 230 TRP 0.014 0.001 TRP F 166 HIS 0.009 0.001 HIS F 229 Details of bonding type rmsd/Z covalent geometry : bond 0.00316 / 0.14 (13918) covalent geometry : angle 0.66714 / 0.33 (19040) SS BOND : bond 0.00748 / 0.42 ( 16) SS BOND : angle 2.07568 / 1.15 ( 32) hydrogen bonds : bond 0.03857 / 2.53 ( 520) hydrogen bonds : angle 5.21431 / 3.55 ( 1410) link_BETA1-4 : bond 0.00585 / 0.32 ( 6) link_BETA1-4 : angle 2.44537 / 1.09 ( 18) link_NAG-ASN : bond 0.00346 / 0.19 ( 8) link_NAG-ASN : angle 1.65638 / 0.93 ( 24) *********************** 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 151 residues out of total 1480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 124 time to evaluate : 0.507 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 17 GLN cc_start: 0.8035 (mp10) cc_final: 0.7785 (mt0) REVERT: D 17 GLN cc_start: 0.8083 (mp10) cc_final: 0.7842 (mt0) REVERT: F 282 TRP cc_start: 0.7455 (m-10) cc_final: 0.6888 (m-10) outliers start: 27 outliers final: 13 residues processed: 148 average time/residue: 0.0917 time to fit residues: 22.1456 Evaluate side-chains 121 residues out of total 1480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 108 time to evaluate : 0.489 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 160 CYS 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 4 ASP Chi-restraints excluded: chain D residue 47 THR Chi-restraints excluded: chain D residue 160 CYS 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 183 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 45 optimal weight: 1.9990 chunk 49 optimal weight: 0.5980 chunk 3 optimal weight: 0.9980 chunk 165 optimal weight: 0.9990 chunk 66 optimal weight: 0.3980 chunk 65 optimal weight: 0.6980 chunk 47 optimal weight: 4.9990 chunk 17 optimal weight: 1.9990 chunk 71 optimal weight: 2.9990 chunk 70 optimal weight: 8.9990 chunk 6 optimal weight: 5.9990 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 382 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 161 HIS C 229 HIS ** D 382 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 38 GLN E 161 HIS F 229 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4490 r_free = 0.4490 target = 0.210348 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4407 r_free = 0.4407 target = 0.201425 restraints weight = 17511.906| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.4328 r_free = 0.4328 target = 0.194238 restraints weight = 24920.245| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.4287 r_free = 0.4287 target = 0.190836 restraints weight = 46800.405| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.4275 r_free = 0.4275 target = 0.190094 restraints weight = 36809.934| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.4258 r_free = 0.4258 target = 0.188581 restraints weight = 31157.003| |-----------------------------------------------------------------------------| r_work (final): 0.4257 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7071 moved from start: 0.3462 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 13948 Z= 0.139 Angle : 0.672 9.624 19114 Z= 0.328 Chirality : 0.045 0.326 2182 Planarity : 0.005 0.063 2432 Dihedral : 6.037 57.325 2118 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 8.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer: Outliers : 2.94 % Allowed : 14.41 % Favored : 82.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.90 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.34 (0.20), residues: 1702 helix: 1.48 (0.32), residues: 252 sheet: 0.23 (0.21), residues: 528 loop : -0.03 (0.22), residues: 922 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 117 TYR 0.044 0.002 TYR C 103 PHE 0.021 0.001 PHE C 230 TRP 0.016 0.002 TRP F 166 HIS 0.013 0.001 HIS C 229 Details of bonding type rmsd/Z covalent geometry : bond 0.00319 / 0.14 (13918) covalent geometry : angle 0.66005 / 0.32 (19040) SS BOND : bond 0.00414 / 0.24 ( 16) SS BOND : angle 2.28180 / 1.19 ( 32) hydrogen bonds : bond 0.03600 / 2.36 ( 520) hydrogen bonds : angle 4.96843 / 3.39 ( 1410) link_BETA1-4 : bond 0.00522 / 0.28 ( 6) link_BETA1-4 : angle 2.46363 / 1.10 ( 18) link_NAG-ASN : bond 0.00312 / 0.17 ( 8) link_NAG-ASN : angle 1.73523 / 0.98 ( 24) *********************** 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 169 residues out of total 1480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 126 time to evaluate : 0.495 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 17 GLN cc_start: 0.8033 (mp10) cc_final: 0.7821 (mt0) REVERT: C 151 ASP cc_start: 0.3907 (OUTLIER) cc_final: 0.3696 (p0) REVERT: C 164 GLU cc_start: 0.8763 (OUTLIER) cc_final: 0.7975 (tp30) REVERT: C 257 VAL cc_start: 0.5643 (OUTLIER) cc_final: 0.5341 (m) REVERT: D 17 GLN cc_start: 0.8041 (mp10) cc_final: 0.7823 (mt0) REVERT: D 287 TYR cc_start: 0.5149 (m-10) cc_final: 0.4917 (m-10) REVERT: D 291 TRP cc_start: 0.8024 (m100) cc_final: 0.7738 (m100) REVERT: E 59 MET cc_start: 0.7969 (mtm) cc_final: 0.7706 (mtm) REVERT: F 164 GLU cc_start: 0.8717 (OUTLIER) cc_final: 0.7971 (tp30) REVERT: F 257 VAL cc_start: 0.5547 (OUTLIER) cc_final: 0.5248 (m) outliers start: 43 outliers final: 20 residues processed: 161 average time/residue: 0.0825 time to fit residues: 21.6118 Evaluate side-chains 130 residues out of total 1480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 105 time to evaluate : 0.377 ------------------------------------------------------------------------------- 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 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 204 VAL Chi-restraints excluded: chain C residue 257 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 160 CYS 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 58 VAL 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 257 VAL Chi-restraints excluded: chain F residue 281 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 49 optimal weight: 0.9990 chunk 129 optimal weight: 1.9990 chunk 83 optimal weight: 0.4980 chunk 46 optimal weight: 1.9990 chunk 166 optimal weight: 0.8980 chunk 95 optimal weight: 0.9980 chunk 84 optimal weight: 0.3980 chunk 151 optimal weight: 0.8980 chunk 60 optimal weight: 3.9990 chunk 53 optimal weight: 1.9990 chunk 115 optimal weight: 20.0000 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 338 ASN ** A 382 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 73 GLN ** C 229 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 382 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 73 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4582 r_free = 0.4582 target = 0.218445 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.4166 r_free = 0.4166 target = 0.186813 restraints weight = 180148.649| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.4181 r_free = 0.4181 target = 0.188652 restraints weight = 109411.739| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.4185 r_free = 0.4185 target = 0.188627 restraints weight = 93347.515| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.4179 r_free = 0.4179 target = 0.187804 restraints weight = 102341.475| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.4181 r_free = 0.4181 target = 0.187792 restraints weight = 93437.746| |-----------------------------------------------------------------------------| r_work (final): 0.3980 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7529 moved from start: 0.3734 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 13948 Z= 0.136 Angle : 0.678 12.285 19114 Z= 0.329 Chirality : 0.045 0.303 2182 Planarity : 0.005 0.061 2432 Dihedral : 5.924 57.511 2118 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 9.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 2.60 % Allowed : 15.30 % Favored : 82.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.90 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.33 (0.21), residues: 1702 helix: 1.50 (0.32), residues: 252 sheet: 0.22 (0.21), residues: 542 loop : -0.06 (0.22), residues: 908 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG F 274 TYR 0.046 0.002 TYR F 103 PHE 0.027 0.002 PHE F 230 TRP 0.023 0.002 TRP D 222 HIS 0.010 0.001 HIS C 229 Details of bonding type rmsd/Z covalent geometry : bond 0.00309 / 0.14 (13918) covalent geometry : angle 0.66246 / 0.32 (19040) SS BOND : bond 0.00709 / 0.40 ( 16) SS BOND : angle 2.77661 / 1.50 ( 32) hydrogen bonds : bond 0.03503 / 2.30 ( 520) hydrogen bonds : angle 4.91322 / 3.35 ( 1410) link_BETA1-4 : bond 0.00501 / 0.27 ( 6) link_BETA1-4 : angle 2.43805 / 1.09 ( 18) link_NAG-ASN : bond 0.00287 / 0.16 ( 8) link_NAG-ASN : angle 1.72314 / 1.00 ( 24) *********************** 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 163 residues out of total 1480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 125 time to evaluate : 0.474 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 232 ILE cc_start: 0.8823 (OUTLIER) cc_final: 0.8583 (mm) REVERT: B 49 HIS cc_start: 0.7846 (p-80) cc_final: 0.7528 (p-80) REVERT: C 164 GLU cc_start: 0.8704 (OUTLIER) cc_final: 0.7922 (tp30) REVERT: C 257 VAL cc_start: 0.5553 (OUTLIER) cc_final: 0.5264 (m) REVERT: D 291 TRP cc_start: 0.7992 (m100) cc_final: 0.7708 (m100) REVERT: F 164 GLU cc_start: 0.8598 (OUTLIER) cc_final: 0.7746 (tp30) REVERT: F 257 VAL cc_start: 0.5838 (OUTLIER) cc_final: 0.5527 (m) outliers start: 38 outliers final: 21 residues processed: 156 average time/residue: 0.0898 time to fit residues: 22.6106 Evaluate side-chains 124 residues out of total 1480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 98 time to evaluate : 0.510 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 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 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 164 GLU Chi-restraints excluded: chain C residue 171 ILE 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 257 VAL Chi-restraints excluded: chain D residue 4 ASP Chi-restraints excluded: chain D residue 47 THR Chi-restraints excluded: chain D residue 160 CYS 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 171 ILE Chi-restraints excluded: chain F residue 183 THR Chi-restraints excluded: chain F residue 204 VAL Chi-restraints excluded: chain F residue 257 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 153 optimal weight: 0.2980 chunk 128 optimal weight: 8.9990 chunk 61 optimal weight: 9.9990 chunk 152 optimal weight: 0.5980 chunk 151 optimal weight: 2.9990 chunk 154 optimal weight: 0.8980 chunk 90 optimal weight: 0.9980 chunk 92 optimal weight: 1.9990 chunk 119 optimal weight: 20.0000 chunk 123 optimal weight: 0.5980 chunk 127 optimal weight: 0.2980 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 382 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 229 HIS ** E 49 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4586 r_free = 0.4586 target = 0.218859 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.4186 r_free = 0.4186 target = 0.189700 restraints weight = 182011.109| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.4226 r_free = 0.4226 target = 0.193534 restraints weight = 109235.726| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.4200 r_free = 0.4200 target = 0.190691 restraints weight = 93358.270| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.4204 r_free = 0.4204 target = 0.190684 restraints weight = 102100.285| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.4201 r_free = 0.4201 target = 0.190228 restraints weight = 93781.297| |-----------------------------------------------------------------------------| r_work (final): 0.4006 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7503 moved from start: 0.3902 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 13948 Z= 0.120 Angle : 0.674 15.994 19114 Z= 0.327 Chirality : 0.045 0.299 2182 Planarity : 0.005 0.060 2432 Dihedral : 5.809 57.282 2118 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 9.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer: Outliers : 2.39 % Allowed : 16.12 % Favored : 81.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.90 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.42 (0.21), residues: 1702 helix: 1.63 (0.32), residues: 252 sheet: 0.32 (0.22), residues: 532 loop : -0.04 (0.22), residues: 918 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 117 TYR 0.030 0.001 TYR F 103 PHE 0.015 0.001 PHE C 230 TRP 0.016 0.001 TRP C 166 HIS 0.013 0.001 HIS F 229 Details of bonding type rmsd/Z covalent geometry : bond 0.00271 / 0.12 (13918) covalent geometry : angle 0.65712 / 0.32 (19040) SS BOND : bond 0.00458 / 0.26 ( 16) SS BOND : angle 2.98621 / 1.57 ( 32) hydrogen bonds : bond 0.03351 / 2.20 ( 520) hydrogen bonds : angle 4.84269 / 3.30 ( 1410) link_BETA1-4 : bond 0.00452 / 0.25 ( 6) link_BETA1-4 : angle 2.40821 / 1.07 ( 18) link_NAG-ASN : bond 0.00308 / 0.18 ( 8) link_NAG-ASN : angle 1.70081 / 0.99 ( 24) *********************** 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 153 residues out of total 1480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 118 time to evaluate : 0.513 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 33 MET cc_start: 0.6064 (tmm) cc_final: 0.5760 (tmm) REVERT: B 49 HIS cc_start: 0.7686 (p-80) cc_final: 0.7463 (p-80) REVERT: C 164 GLU cc_start: 0.8631 (OUTLIER) cc_final: 0.7841 (tp30) REVERT: F 164 GLU cc_start: 0.8617 (OUTLIER) cc_final: 0.7837 (tp30) REVERT: F 257 VAL cc_start: 0.5717 (OUTLIER) cc_final: 0.5385 (m) outliers start: 35 outliers final: 26 residues processed: 148 average time/residue: 0.0874 time to fit residues: 21.3280 Evaluate side-chains 142 residues out of total 1480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 113 time to evaluate : 0.493 ------------------------------------------------------------------------------- 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 185 VAL Chi-restraints excluded: chain A residue 348 LEU Chi-restraints excluded: chain B residue 57 LEU Chi-restraints excluded: chain B residue 73 LEU Chi-restraints excluded: chain B residue 163 THR 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 204 VAL 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 160 CYS Chi-restraints excluded: chain D residue 185 VAL Chi-restraints excluded: chain D residue 347 THR Chi-restraints excluded: chain E residue 18 LEU Chi-restraints excluded: chain E residue 80 LEU Chi-restraints excluded: chain E residue 176 THR Chi-restraints excluded: chain F residue 58 VAL 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 257 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 132 optimal weight: 0.8980 chunk 11 optimal weight: 0.6980 chunk 141 optimal weight: 20.0000 chunk 57 optimal weight: 20.0000 chunk 146 optimal weight: 3.9990 chunk 80 optimal weight: 0.9980 chunk 96 optimal weight: 3.9990 chunk 164 optimal weight: 0.9990 chunk 76 optimal weight: 0.5980 chunk 127 optimal weight: 0.2980 chunk 89 optimal weight: 0.0870 overall best weight: 0.5158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 382 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 49 HIS ** 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 = 0.4579 r_free = 0.4579 target = 0.218522 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.4192 r_free = 0.4192 target = 0.189773 restraints weight = 182458.853| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.4211 r_free = 0.4211 target = 0.192034 restraints weight = 111520.212| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.4208 r_free = 0.4208 target = 0.190859 restraints weight = 95077.535| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.4208 r_free = 0.4208 target = 0.191004 restraints weight = 103289.076| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.4208 r_free = 0.4208 target = 0.190777 restraints weight = 93071.546| |-----------------------------------------------------------------------------| r_work (final): 0.4018 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7481 moved from start: 0.4044 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 13948 Z= 0.122 Angle : 0.689 17.459 19114 Z= 0.335 Chirality : 0.044 0.298 2182 Planarity : 0.005 0.059 2432 Dihedral : 5.738 57.335 2118 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 9.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer: Outliers : 2.80 % Allowed : 17.08 % Favored : 80.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.90 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.47 (0.21), residues: 1702 helix: 1.71 (0.32), residues: 252 sheet: 0.31 (0.22), residues: 534 loop : 0.02 (0.23), residues: 916 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG E 118 TYR 0.013 0.001 TYR D 57 PHE 0.021 0.001 PHE F 230 TRP 0.016 0.001 TRP F 166 HIS 0.011 0.001 HIS F 229 Details of bonding type rmsd/Z covalent geometry : bond 0.00277 / 0.12 (13918) covalent geometry : angle 0.67023 / 0.33 (19040) SS BOND : bond 0.00537 / 0.30 ( 16) SS BOND : angle 3.23968 / 1.70 ( 32) hydrogen bonds : bond 0.03340 / 2.19 ( 520) hydrogen bonds : angle 4.81723 / 3.28 ( 1410) link_BETA1-4 : bond 0.00480 / 0.27 ( 6) link_BETA1-4 : angle 2.39274 / 1.06 ( 18) link_NAG-ASN : bond 0.00311 / 0.18 ( 8) link_NAG-ASN : angle 1.77518 / 1.03 ( 24) *********************** 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 163 residues out of total 1480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 122 time to evaluate : 0.314 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 49 HIS cc_start: 0.7823 (p-80) cc_final: 0.7552 (p-80) REVERT: B 59 MET cc_start: 0.7750 (mtm) cc_final: 0.7349 (mtm) REVERT: C 164 GLU cc_start: 0.8780 (OUTLIER) cc_final: 0.7987 (tp30) REVERT: D 33 MET cc_start: 0.6188 (tmm) cc_final: 0.5968 (tmm) REVERT: F 164 GLU cc_start: 0.8693 (OUTLIER) cc_final: 0.7936 (tp30) REVERT: F 257 VAL cc_start: 0.5727 (OUTLIER) cc_final: 0.5392 (m) outliers start: 41 outliers final: 31 residues processed: 158 average time/residue: 0.0831 time to fit residues: 21.3781 Evaluate side-chains 155 residues out of total 1480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 121 time to evaluate : 0.511 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 ASP 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 185 VAL Chi-restraints excluded: chain A residue 348 LEU Chi-restraints excluded: chain B residue 57 LEU Chi-restraints excluded: chain B residue 80 LEU Chi-restraints excluded: chain B residue 163 THR Chi-restraints excluded: chain B residue 176 THR Chi-restraints excluded: chain C residue 109 THR Chi-restraints excluded: chain C residue 164 GLU Chi-restraints excluded: chain C residue 171 ILE 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 230 PHE 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 185 VAL Chi-restraints excluded: chain D residue 347 THR Chi-restraints excluded: chain E residue 18 LEU Chi-restraints excluded: chain E residue 73 LEU Chi-restraints excluded: chain E residue 80 LEU Chi-restraints excluded: chain E residue 176 THR Chi-restraints excluded: chain F residue 58 VAL 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 257 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 144 optimal weight: 7.9990 chunk 14 optimal weight: 2.9990 chunk 87 optimal weight: 1.9990 chunk 106 optimal weight: 0.8980 chunk 37 optimal weight: 10.0000 chunk 154 optimal weight: 9.9990 chunk 118 optimal weight: 5.9990 chunk 6 optimal weight: 2.9990 chunk 93 optimal weight: 2.9990 chunk 3 optimal weight: 0.6980 chunk 134 optimal weight: 0.0370 overall best weight: 1.3262 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 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 = 0.4523 r_free = 0.4523 target = 0.212388 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.4098 r_free = 0.4098 target = 0.182049 restraints weight = 183032.749| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.4131 r_free = 0.4131 target = 0.185408 restraints weight = 112002.374| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.4117 r_free = 0.4117 target = 0.183449 restraints weight = 99834.394| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.4114 r_free = 0.4114 target = 0.182923 restraints weight = 105645.704| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.4115 r_free = 0.4115 target = 0.182800 restraints weight = 97923.097| |-----------------------------------------------------------------------------| r_work (final): 0.3807 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7640 moved from start: 0.4305 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 13948 Z= 0.189 Angle : 0.753 18.342 19114 Z= 0.368 Chirality : 0.046 0.317 2182 Planarity : 0.005 0.058 2432 Dihedral : 5.947 58.387 2118 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 11.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.17 % Favored : 95.83 % Rotamer: Outliers : 2.60 % Allowed : 17.35 % Favored : 80.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.90 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.21 (0.21), residues: 1702 helix: 1.24 (0.32), residues: 252 sheet: 0.10 (0.22), residues: 548 loop : -0.04 (0.23), residues: 902 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG E 117 TYR 0.029 0.002 TYR C 103 PHE 0.038 0.002 PHE F 230 TRP 0.017 0.002 TRP F 166 HIS 0.017 0.001 HIS F 229 Details of bonding type rmsd/Z covalent geometry : bond 0.00445 / 0.19 (13918) covalent geometry : angle 0.73359 / 0.36 (19040) SS BOND : bond 0.00813 / 0.46 ( 16) SS BOND : angle 3.51522 / 1.87 ( 32) hydrogen bonds : bond 0.03834 / 2.52 ( 520) hydrogen bonds : angle 5.06272 / 3.47 ( 1410) link_BETA1-4 : bond 0.00486 / 0.26 ( 6) link_BETA1-4 : angle 2.52726 / 1.13 ( 18) link_NAG-ASN : bond 0.00251 / 0.13 ( 8) link_NAG-ASN : angle 1.88168 / 1.10 ( 24) *********************** 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 154 residues out of total 1480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 116 time to evaluate : 0.522 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 33 MET cc_start: 0.6254 (tmm) cc_final: 0.5842 (tmm) REVERT: A 232 ILE cc_start: 0.8817 (OUTLIER) cc_final: 0.8596 (mm) REVERT: A 291 TRP cc_start: 0.8074 (m100) cc_final: 0.7776 (m100) REVERT: C 103 TYR cc_start: 0.8316 (p90) cc_final: 0.8095 (p90) REVERT: C 164 GLU cc_start: 0.8876 (OUTLIER) cc_final: 0.8170 (tp30) REVERT: C 230 PHE cc_start: 0.7916 (OUTLIER) cc_final: 0.7696 (p90) REVERT: F 164 GLU cc_start: 0.8701 (OUTLIER) cc_final: 0.8034 (tp30) REVERT: F 257 VAL cc_start: 0.5634 (OUTLIER) cc_final: 0.5377 (m) outliers start: 38 outliers final: 28 residues processed: 147 average time/residue: 0.0817 time to fit residues: 20.1853 Evaluate side-chains 134 residues out of total 1480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 101 time to evaluate : 0.494 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 ASP 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 185 VAL Chi-restraints excluded: chain A residue 232 ILE Chi-restraints excluded: chain A residue 348 LEU Chi-restraints excluded: chain B residue 57 LEU Chi-restraints excluded: chain B residue 73 LEU Chi-restraints excluded: chain B residue 163 THR Chi-restraints excluded: chain B residue 176 THR Chi-restraints excluded: chain C residue 109 THR Chi-restraints excluded: chain C residue 164 GLU Chi-restraints excluded: chain C residue 171 ILE 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 230 PHE 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 160 CYS Chi-restraints excluded: chain D residue 185 VAL Chi-restraints excluded: chain D residue 347 THR Chi-restraints excluded: chain E residue 18 LEU Chi-restraints excluded: chain E residue 73 LEU Chi-restraints excluded: chain E residue 80 LEU Chi-restraints excluded: chain E residue 176 THR Chi-restraints excluded: chain F residue 164 GLU Chi-restraints excluded: chain F residue 171 ILE Chi-restraints excluded: chain F residue 183 THR Chi-restraints excluded: chain F residue 204 VAL Chi-restraints excluded: chain F residue 257 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 47 optimal weight: 0.9980 chunk 51 optimal weight: 6.9990 chunk 157 optimal weight: 0.9980 chunk 13 optimal weight: 5.9990 chunk 99 optimal weight: 7.9990 chunk 56 optimal weight: 20.0000 chunk 17 optimal weight: 2.9990 chunk 63 optimal weight: 0.9980 chunk 137 optimal weight: 1.9990 chunk 77 optimal weight: 0.7980 chunk 11 optimal weight: 0.8980 overall best weight: 0.9380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 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 = 0.4528 r_free = 0.4528 target = 0.213013 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.4125 r_free = 0.4125 target = 0.183755 restraints weight = 182715.003| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.4142 r_free = 0.4142 target = 0.185724 restraints weight = 111148.941| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4132 r_free = 0.4132 target = 0.184024 restraints weight = 93953.459| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.4134 r_free = 0.4134 target = 0.184218 restraints weight = 104993.733| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.4136 r_free = 0.4136 target = 0.184222 restraints weight = 94015.067| |-----------------------------------------------------------------------------| r_work (final): 0.3853 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7590 moved from start: 0.4433 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 13948 Z= 0.151 Angle : 0.720 17.686 19114 Z= 0.351 Chirality : 0.045 0.308 2182 Planarity : 0.005 0.057 2432 Dihedral : 5.921 57.785 2118 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 10.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.41 % Favored : 96.59 % Rotamer: Outliers : 2.19 % Allowed : 17.90 % Favored : 79.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.90 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.36 (0.21), residues: 1702 helix: 1.73 (0.32), residues: 240 sheet: 0.09 (0.22), residues: 548 loop : 0.04 (0.23), residues: 914 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 118 TYR 0.027 0.001 TYR F 103 PHE 0.023 0.001 PHE F 230 TRP 0.020 0.002 TRP D 222 HIS 0.014 0.002 HIS C 229 Details of bonding type rmsd/Z covalent geometry : bond 0.00353 / 0.15 (13918) covalent geometry : angle 0.70045 / 0.34 (19040) SS BOND : bond 0.00476 / 0.28 ( 16) SS BOND : angle 3.39042 / 1.83 ( 32) hydrogen bonds : bond 0.03557 / 2.35 ( 520) hydrogen bonds : angle 4.98776 / 3.40 ( 1410) link_BETA1-4 : bond 0.00463 / 0.25 ( 6) link_BETA1-4 : angle 2.45662 / 1.09 ( 18) link_NAG-ASN : bond 0.00253 / 0.15 ( 8) link_NAG-ASN : angle 1.83723 / 1.08 ( 24) ********************** 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 146 residues out of total 1480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 114 time to evaluate : 0.488 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 33 MET cc_start: 0.6065 (tmm) cc_final: 0.5664 (tmm) REVERT: C 164 GLU cc_start: 0.8694 (OUTLIER) cc_final: 0.7988 (tp30) REVERT: C 230 PHE cc_start: 0.7840 (OUTLIER) cc_final: 0.7600 (p90) REVERT: D 33 MET cc_start: 0.6418 (tmm) cc_final: 0.6163 (tmm) REVERT: D 35 TYR cc_start: 0.7747 (t80) cc_final: 0.7195 (t80) REVERT: F 164 GLU cc_start: 0.8672 (OUTLIER) cc_final: 0.8164 (tp30) REVERT: F 257 VAL cc_start: 0.5890 (OUTLIER) cc_final: 0.5467 (m) outliers start: 32 outliers final: 27 residues processed: 139 average time/residue: 0.0830 time to fit residues: 19.2027 Evaluate side-chains 140 residues out of total 1480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 109 time to evaluate : 0.442 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 ASP 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 185 VAL Chi-restraints excluded: chain A residue 348 LEU Chi-restraints excluded: chain B residue 57 LEU Chi-restraints excluded: chain B residue 163 THR Chi-restraints excluded: chain B residue 176 THR Chi-restraints excluded: chain C residue 109 THR Chi-restraints excluded: chain C residue 164 GLU Chi-restraints excluded: chain C residue 171 ILE 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 230 PHE 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 160 CYS Chi-restraints excluded: chain D residue 185 VAL Chi-restraints excluded: chain D residue 347 THR Chi-restraints excluded: chain E residue 57 LEU Chi-restraints excluded: chain E residue 73 LEU Chi-restraints excluded: chain E residue 80 LEU Chi-restraints excluded: chain E residue 176 THR Chi-restraints excluded: chain F residue 164 GLU Chi-restraints excluded: chain F residue 171 ILE Chi-restraints excluded: chain F residue 183 THR Chi-restraints excluded: chain F residue 204 VAL Chi-restraints excluded: chain F residue 257 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 20 optimal weight: 6.9990 chunk 162 optimal weight: 0.9980 chunk 113 optimal weight: 5.9990 chunk 56 optimal weight: 3.9990 chunk 41 optimal weight: 2.9990 chunk 15 optimal weight: 0.9990 chunk 165 optimal weight: 0.8980 chunk 94 optimal weight: 0.4980 chunk 99 optimal weight: 10.0000 chunk 122 optimal weight: 0.0270 chunk 24 optimal weight: 3.9990 overall best weight: 0.6840 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 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 = 0.4539 r_free = 0.4539 target = 0.214192 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.4138 r_free = 0.4138 target = 0.185039 restraints weight = 186010.926| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.4182 r_free = 0.4182 target = 0.189441 restraints weight = 112575.494| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.4150 r_free = 0.4150 target = 0.185864 restraints weight = 98002.841| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.4153 r_free = 0.4153 target = 0.185916 restraints weight = 105015.227| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.4151 r_free = 0.4151 target = 0.185515 restraints weight = 99183.355| |-----------------------------------------------------------------------------| r_work (final): 0.3952 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7577 moved from start: 0.4507 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 13948 Z= 0.133 Angle : 0.703 17.911 19114 Z= 0.343 Chirality : 0.045 0.304 2182 Planarity : 0.005 0.057 2432 Dihedral : 5.805 57.527 2118 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 10.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.82 % Favored : 96.18 % Rotamer: Outliers : 2.32 % Allowed : 17.96 % Favored : 79.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.90 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.44 (0.21), residues: 1702 helix: 1.88 (0.33), residues: 240 sheet: 0.13 (0.22), residues: 548 loop : 0.06 (0.23), residues: 914 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 117 TYR 0.026 0.002 TYR F 103 PHE 0.023 0.002 PHE F 230 TRP 0.019 0.002 TRP F 166 HIS 0.014 0.001 HIS C 229 Details of bonding type rmsd/Z covalent geometry : bond 0.00308 / 0.13 (13918) covalent geometry : angle 0.68374 / 0.34 (19040) SS BOND : bond 0.00515 / 0.31 ( 16) SS BOND : angle 3.37540 / 1.73 ( 32) hydrogen bonds : bond 0.03422 / 2.24 ( 520) hydrogen bonds : angle 4.89910 / 3.34 ( 1410) link_BETA1-4 : bond 0.00435 / 0.24 ( 6) link_BETA1-4 : angle 2.45106 / 1.09 ( 18) link_NAG-ASN : bond 0.00285 / 0.17 ( 8) link_NAG-ASN : angle 1.81551 / 1.07 ( 24) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1972.65 seconds wall clock time: 35 minutes 0.53 seconds (2100.53 seconds total)