Starting phenix.real_space_refine on Thu Jun 4 20:51:04 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8zyr_60577/06_2026/8zyr_60577.cif Found real_map, /net/cci-nas-00/data/ceres_data/8zyr_60577/06_2026/8zyr_60577.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.07 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8zyr_60577/06_2026/8zyr_60577.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8zyr_60577/06_2026/8zyr_60577.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8zyr_60577/06_2026/8zyr_60577.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8zyr_60577/06_2026/8zyr_60577.map" } resolution = 4.07 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.021 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 2 5.49 5 S 80 5.16 5 C 9823 2.51 5 N 2694 2.21 5 O 2890 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 2 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6079/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 15489 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 3920 Number of conformers: 1 Conformer: "" Number of residues, atoms: 493, 3920 Classifications: {'peptide': 493} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PCIS': 3, 'PTRANS': 27, 'TRANS': 462} Unresolved non-hydrogen bonds: 29 Unresolved non-hydrogen angles: 38 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'TYR:plan': 1, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 16 Chain: "B" Number of atoms: 3833 Number of conformers: 1 Conformer: "" Number of residues, atoms: 484, 3833 Classifications: {'peptide': 484} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PCIS': 3, 'PTRANS': 21, 'TRANS': 458} Chain: "C" Number of atoms: 3820 Number of conformers: 1 Conformer: "" Number of residues, atoms: 483, 3820 Classifications: {'peptide': 483} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 3, 'PTRANS': 23, 'TRANS': 456} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Chain: "D" Number of atoms: 3901 Number of conformers: 1 Conformer: "" Number of residues, atoms: 492, 3901 Classifications: {'peptide': 492} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PCIS': 3, 'PTRANS': 27, 'TRANS': 461} Unresolved non-hydrogen bonds: 41 Unresolved non-hydrogen angles: 51 Unresolved non-hydrogen dihedrals: 41 Planarities with less than four sites: {'TYR:plan': 1, 'TRP:plan': 1, 'ARG:plan': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 25 Chain: "B" Number of atoms: 15 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 15 Unusual residues: {'H6P': 1} Classifications: {'undetermined': 1} Time building chain proxies: 3.69, per 1000 atoms: 0.24 Number of scatterers: 15489 At special positions: 0 Unit cell: (111.1, 190.3, 267.3, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 80 16.00 P 2 15.00 O 2890 8.00 N 2694 7.00 C 9823 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=10, symmetry=0 Simple disulfide: pdb=" SG CYS A 23 " - pdb=" SG CYS A 97 " distance=2.03 Simple disulfide: pdb=" SG CYS A 137 " - pdb=" SG CYS A 191 " distance=2.03 Simple disulfide: pdb=" SG CYS A 219 " - pdb=" SG CYS D 219 " distance=2.03 Simple disulfide: pdb=" SG CYS A 237 " - pdb=" SG CYS D 237 " distance=2.03 Simple disulfide: pdb=" SG CYS B 23 " - pdb=" SG CYS B 97 " distance=2.03 Simple disulfide: pdb=" SG CYS B 137 " - pdb=" SG CYS B 191 " distance=2.03 Simple disulfide: pdb=" SG CYS C 23 " - pdb=" SG CYS C 97 " distance=2.04 Simple disulfide: pdb=" SG CYS C 137 " - pdb=" SG CYS C 191 " distance=2.03 Simple disulfide: pdb=" SG CYS D 23 " - pdb=" SG CYS D 97 " distance=2.03 Simple disulfide: pdb=" SG CYS D 137 " - pdb=" SG CYS D 191 " distance=2.04 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 Time building additional restraints: 1.31 Conformation dependent library (CDL) restraints added in 476.1 milliseconds 3888 Ramachandran restraints generated. 1944 Oldfield, 0 Emsley, 1944 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3628 Finding SS restraints... Secondary structure from input PDB file: 21 helices and 28 sheets defined 18.6% alpha, 30.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.58 Creating SS restraints... Processing helix chain 'A' and resid 61 through 65 Processing helix chain 'A' and resid 88 through 92 removed outlier: 3.933A pdb=" N ASN A 92 " --> pdb=" O ALA A 89 " (cutoff:3.500A) Processing helix chain 'A' and resid 217 through 221 removed outlier: 3.627A pdb=" N ALA A 220 " --> pdb=" O SER A 217 " (cutoff:3.500A) Processing helix chain 'A' and resid 222 through 260 removed outlier: 3.793A pdb=" N ILE A 226 " --> pdb=" O ALA A 222 " (cutoff:3.500A) Proline residue: A 233 - end of helix removed outlier: 3.549A pdb=" N GLU A 256 " --> pdb=" O SER A 252 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N PHE A 257 " --> pdb=" O GLY A 253 " (cutoff:3.500A) Processing helix chain 'A' and resid 262 through 292 Processing helix chain 'A' and resid 429 through 431 No H-bonds generated for 'chain 'A' and resid 429 through 431' Processing helix chain 'B' and resid 74 through 77 Processing helix chain 'B' and resid 88 through 92 Processing helix chain 'B' and resid 209 through 215 removed outlier: 4.208A pdb=" N PHE B 213 " --> pdb=" O ALA B 209 " (cutoff:3.500A) Processing helix chain 'B' and resid 226 through 292 Processing helix chain 'B' and resid 299 through 308 Processing helix chain 'C' and resid 61 through 65 removed outlier: 3.541A pdb=" N ARG C 65 " --> pdb=" O ALA C 62 " (cutoff:3.500A) Processing helix chain 'C' and resid 74 through 78 Processing helix chain 'C' and resid 88 through 92 Processing helix chain 'C' and resid 220 through 226 removed outlier: 3.747A pdb=" N ALA C 224 " --> pdb=" O ILE C 220 " (cutoff:3.500A) Processing helix chain 'C' and resid 226 through 293 Processing helix chain 'C' and resid 299 through 308 removed outlier: 3.849A pdb=" N LYS C 304 " --> pdb=" O TYR C 300 " (cutoff:3.500A) removed outlier: 5.517A pdb=" N MET C 305 " --> pdb=" O HIS C 301 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N ALA C 306 " --> pdb=" O GLU C 302 " (cutoff:3.500A) Processing helix chain 'C' and resid 316 through 320 Processing helix chain 'D' and resid 88 through 92 Processing helix chain 'D' and resid 221 through 253 removed outlier: 3.791A pdb=" N ILE D 225 " --> pdb=" O VAL D 221 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N ILE D 232 " --> pdb=" O VAL D 228 " (cutoff:3.500A) Proline residue: D 233 - end of helix removed outlier: 4.583A pdb=" N LYS D 243 " --> pdb=" O TYR D 239 " (cutoff:3.500A) removed outlier: 4.244A pdb=" N LEU D 244 " --> pdb=" O TRP D 240 " (cutoff:3.500A) Processing helix chain 'D' and resid 254 through 293 Processing sheet with id=AA1, first strand: chain 'A' and resid 11 through 12 removed outlier: 6.506A pdb=" N ILE A 11 " --> pdb=" O VAL A 113 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 19 through 23 removed outlier: 3.587A pdb=" N THR A 19 " --> pdb=" O ILE A 84 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 122 through 123 Processing sheet with id=AA4, first strand: chain 'A' and resid 127 through 129 removed outlier: 4.254A pdb=" N GLY A 127 " --> pdb=" O ARG A 134 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 157 through 158 removed outlier: 3.974A pdb=" N TRP A 150 " --> pdb=" O ALA A 158 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N MET A 189 " --> pdb=" O ILE A 206 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 298 through 299 removed outlier: 4.390A pdb=" N LEU D 297 " --> pdb=" O ALA A 299 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 313 through 315 removed outlier: 3.874A pdb=" N VAL A 322 " --> pdb=" O ILE A 469 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N ILE A 469 " --> pdb=" O VAL A 322 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N PHE A 470 " --> pdb=" O GLU A 363 " (cutoff:3.500A) removed outlier: 4.538A pdb=" N SER A 434 " --> pdb=" O PHE A 425 " (cutoff:3.500A) removed outlier: 6.599A pdb=" N PHE A 435 " --> pdb=" O ILE A 444 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 346 through 348 removed outlier: 4.392A pdb=" N TRP A 370 " --> pdb=" O MET A 398 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 3 through 5 Processing sheet with id=AB1, first strand: chain 'B' and resid 11 through 14 removed outlier: 5.774A pdb=" N ILE B 11 " --> pdb=" O LYS B 113 " (cutoff:3.500A) removed outlier: 7.011A pdb=" N ALA B 115 " --> pdb=" O ILE B 11 " (cutoff:3.500A) removed outlier: 6.076A pdb=" N ALA B 13 " --> pdb=" O ALA B 115 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N LEU B 112 " --> pdb=" O GLY B 93 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N GLY B 93 " --> pdb=" O LEU B 112 " (cutoff:3.500A) removed outlier: 4.512A pdb=" N VAL B 49 " --> pdb=" O VAL B 56 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 161 through 167 removed outlier: 4.625A pdb=" N ALA B 176 " --> pdb=" O ALA B 163 " (cutoff:3.500A) removed outlier: 4.784A pdb=" N VAL B 165 " --> pdb=" O ALA B 174 " (cutoff:3.500A) removed outlier: 6.045A pdb=" N ALA B 174 " --> pdb=" O VAL B 165 " (cutoff:3.500A) removed outlier: 6.723A pdb=" N GLY B 132 " --> pdb=" O TYR B 128 " (cutoff:3.500A) removed outlier: 4.652A pdb=" N TYR B 128 " --> pdb=" O GLY B 132 " (cutoff:3.500A) removed outlier: 6.601A pdb=" N HIS B 134 " --> pdb=" O LYS B 126 " (cutoff:3.500A) removed outlier: 4.115A pdb=" N TRP C 150 " --> pdb=" O ILE C 158 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 157 through 158 removed outlier: 4.127A pdb=" N TRP B 150 " --> pdb=" O ILE B 158 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N VAL B 189 " --> pdb=" O ILE B 206 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N ILE B 206 " --> pdb=" O VAL B 189 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N ALA B 204 " --> pdb=" O CYS B 191 " (cutoff:3.500A) removed outlier: 8.587A pdb=" N ILE C 123 " --> pdb=" O THR B 203 " (cutoff:3.500A) removed outlier: 6.301A pdb=" N SER B 205 " --> pdb=" O ILE C 123 " (cutoff:3.500A) removed outlier: 7.577A pdb=" N VAL C 125 " --> pdb=" O SER B 205 " (cutoff:3.500A) removed outlier: 6.152A pdb=" N SER B 207 " --> pdb=" O VAL C 125 " (cutoff:3.500A) removed outlier: 7.788A pdb=" N GLY C 127 " --> pdb=" O SER B 207 " (cutoff:3.500A) removed outlier: 6.491A pdb=" N HIS C 134 " --> pdb=" O LYS C 126 " (cutoff:3.500A) removed outlier: 4.204A pdb=" N TYR C 128 " --> pdb=" O GLY C 132 " (cutoff:3.500A) removed outlier: 6.123A pdb=" N GLY C 132 " --> pdb=" O TYR C 128 " (cutoff:3.500A) removed outlier: 5.567A pdb=" N HIS C 134 " --> pdb=" O MET C 181 " (cutoff:3.500A) removed outlier: 6.689A pdb=" N MET C 181 " --> pdb=" O HIS C 134 " (cutoff:3.500A) removed outlier: 5.317A pdb=" N GLU C 136 " --> pdb=" O VAL C 179 " (cutoff:3.500A) removed outlier: 7.266A pdb=" N VAL C 179 " --> pdb=" O GLU C 136 " (cutoff:3.500A) removed outlier: 5.497A pdb=" N ARG C 138 " --> pdb=" O ALA C 177 " (cutoff:3.500A) removed outlier: 7.286A pdb=" N ALA C 177 " --> pdb=" O ARG C 138 " (cutoff:3.500A) removed outlier: 5.370A pdb=" N THR C 140 " --> pdb=" O VAL C 175 " (cutoff:3.500A) removed outlier: 6.326A pdb=" N VAL C 175 " --> pdb=" O THR C 140 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 157 through 158 removed outlier: 4.127A pdb=" N TRP B 150 " --> pdb=" O ILE B 158 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N VAL B 189 " --> pdb=" O ILE B 206 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N ILE B 206 " --> pdb=" O VAL B 189 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N ALA B 204 " --> pdb=" O CYS B 191 " (cutoff:3.500A) removed outlier: 8.587A pdb=" N ILE C 123 " --> pdb=" O THR B 203 " (cutoff:3.500A) removed outlier: 6.301A pdb=" N SER B 205 " --> pdb=" O ILE C 123 " (cutoff:3.500A) removed outlier: 7.577A pdb=" N VAL C 125 " --> pdb=" O SER B 205 " (cutoff:3.500A) removed outlier: 6.152A pdb=" N SER B 207 " --> pdb=" O VAL C 125 " (cutoff:3.500A) removed outlier: 7.788A pdb=" N GLY C 127 " --> pdb=" O SER B 207 " (cutoff:3.500A) removed outlier: 6.491A pdb=" N HIS C 134 " --> pdb=" O LYS C 126 " (cutoff:3.500A) removed outlier: 4.204A pdb=" N TYR C 128 " --> pdb=" O GLY C 132 " (cutoff:3.500A) removed outlier: 6.123A pdb=" N GLY C 132 " --> pdb=" O TYR C 128 " (cutoff:3.500A) removed outlier: 5.567A pdb=" N HIS C 134 " --> pdb=" O MET C 181 " (cutoff:3.500A) removed outlier: 6.689A pdb=" N MET C 181 " --> pdb=" O HIS C 134 " (cutoff:3.500A) removed outlier: 5.317A pdb=" N GLU C 136 " --> pdb=" O VAL C 179 " (cutoff:3.500A) removed outlier: 7.266A pdb=" N VAL C 179 " --> pdb=" O GLU C 136 " (cutoff:3.500A) removed outlier: 5.497A pdb=" N ARG C 138 " --> pdb=" O ALA C 177 " (cutoff:3.500A) removed outlier: 7.286A pdb=" N ALA C 177 " --> pdb=" O ARG C 138 " (cutoff:3.500A) removed outlier: 5.370A pdb=" N THR C 140 " --> pdb=" O VAL C 175 " (cutoff:3.500A) removed outlier: 6.326A pdb=" N VAL C 175 " --> pdb=" O THR C 140 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N VAL C 166 " --> pdb=" O ALA C 174 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 309 through 310 removed outlier: 3.578A pdb=" N LYS B 309 " --> pdb=" O ARG B 365 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N TYR B 367 " --> pdb=" O LYS B 309 " (cutoff:3.500A) removed outlier: 5.828A pdb=" N ASN B 446 " --> pdb=" O HIS B 452 " (cutoff:3.500A) removed outlier: 5.613A pdb=" N HIS B 452 " --> pdb=" O ASN B 446 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 324 through 326 Processing sheet with id=AB7, first strand: chain 'B' and resid 354 through 355 removed outlier: 3.561A pdb=" N THR B 414 " --> pdb=" O THR B 420 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N THR B 420 " --> pdb=" O THR B 414 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 3 through 5 Processing sheet with id=AB9, first strand: chain 'C' and resid 11 through 14 removed outlier: 6.101A pdb=" N ILE C 11 " --> pdb=" O LYS C 113 " (cutoff:3.500A) removed outlier: 7.433A pdb=" N ALA C 115 " --> pdb=" O ILE C 11 " (cutoff:3.500A) removed outlier: 6.535A pdb=" N ALA C 13 " --> pdb=" O ALA C 115 " (cutoff:3.500A) removed outlier: 6.593A pdb=" N SER C 40 " --> pdb=" O VAL C 46 " (cutoff:3.500A) removed outlier: 6.610A pdb=" N VAL C 46 " --> pdb=" O SER C 40 " (cutoff:3.500A) removed outlier: 4.743A pdb=" N ALA C 51 " --> pdb=" O LYS C 54 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N LYS C 54 " --> pdb=" O ALA C 51 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 324 through 326 Processing sheet with id=AC2, first strand: chain 'C' and resid 354 through 355 removed outlier: 3.758A pdb=" N PHE C 470 " --> pdb=" O VAL C 355 " (cutoff:3.500A) removed outlier: 4.250A pdb=" N TYR C 413 " --> pdb=" O LEU C 423 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N LEU C 423 " --> pdb=" O TYR C 413 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 452 through 456 removed outlier: 6.125A pdb=" N HIS C 453 " --> pdb=" O ASN C 447 " (cutoff:3.500A) removed outlier: 5.933A pdb=" N ASN C 447 " --> pdb=" O HIS C 453 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N THR C 481 " --> pdb=" O GLU C 371 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'D' and resid 3 through 5 removed outlier: 4.293A pdb=" N VAL D 5 " --> pdb=" O HIS D 24 " (cutoff:3.500A) removed outlier: 4.898A pdb=" N HIS D 24 " --> pdb=" O VAL D 5 " (cutoff:3.500A) removed outlier: 4.234A pdb=" N THR D 19 " --> pdb=" O ILE D 84 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N ILE D 84 " --> pdb=" O THR D 19 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N CYS D 23 " --> pdb=" O VAL D 80 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N VAL D 80 " --> pdb=" O CYS D 23 " (cutoff:3.500A) removed outlier: 4.172A pdb=" N ASP D 74 " --> pdb=" O SER D 79 " (cutoff:3.500A) removed outlier: 8.359A pdb=" N ALA D 81 " --> pdb=" O SER D 72 " (cutoff:3.500A) removed outlier: 5.856A pdb=" N SER D 72 " --> pdb=" O ALA D 81 " (cutoff:3.500A) removed outlier: 7.141A pdb=" N VAL D 83 " --> pdb=" O PHE D 70 " (cutoff:3.500A) removed outlier: 5.496A pdb=" N PHE D 70 " --> pdb=" O VAL D 83 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'D' and resid 11 through 13 removed outlier: 4.581A pdb=" N ILE D 11 " --> pdb=" O HIS D 111 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N VAL D 113 " --> pdb=" O ILE D 11 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N LEU D 112 " --> pdb=" O GLY D 93 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N GLY D 93 " --> pdb=" O LEU D 112 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N PHE D 48 " --> pdb=" O TRP D 38 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'D' and resid 122 through 129 removed outlier: 3.547A pdb=" N ARG D 126 " --> pdb=" O ARG D 134 " (cutoff:3.500A) removed outlier: 6.215A pdb=" N ARG D 134 " --> pdb=" O ARG D 126 " (cutoff:3.500A) removed outlier: 4.135A pdb=" N HIS D 128 " --> pdb=" O GLY D 132 " (cutoff:3.500A) removed outlier: 6.009A pdb=" N GLY D 132 " --> pdb=" O HIS D 128 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N VAL D 175 " --> pdb=" O SER D 139 " (cutoff:3.500A) removed outlier: 4.170A pdb=" N GLY D 141 " --> pdb=" O PHE D 173 " (cutoff:3.500A) removed outlier: 6.201A pdb=" N PHE D 173 " --> pdb=" O GLY D 141 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'D' and resid 122 through 129 removed outlier: 3.547A pdb=" N ARG D 126 " --> pdb=" O ARG D 134 " (cutoff:3.500A) removed outlier: 6.215A pdb=" N ARG D 134 " --> pdb=" O ARG D 126 " (cutoff:3.500A) removed outlier: 4.135A pdb=" N HIS D 128 " --> pdb=" O GLY D 132 " (cutoff:3.500A) removed outlier: 6.009A pdb=" N GLY D 132 " --> pdb=" O HIS D 128 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'D' and resid 157 through 158 removed outlier: 3.875A pdb=" N TRP D 150 " --> pdb=" O ALA D 158 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'D' and resid 313 through 315 removed outlier: 3.807A pdb=" N VAL D 322 " --> pdb=" O ILE D 469 " (cutoff:3.500A) removed outlier: 5.291A pdb=" N ASN D 437 " --> pdb=" O HIS D 443 " (cutoff:3.500A) removed outlier: 6.273A pdb=" N HIS D 443 " --> pdb=" O ASN D 437 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'D' and resid 346 through 348 removed outlier: 4.113A pdb=" N TRP D 370 " --> pdb=" O MET D 398 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N HIS D 399 " --> pdb=" O GLN D 402 " (cutoff:3.500A) 645 hydrogen bonds defined for protein. 1728 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.66 Time building geometry restraints manager: 1.75 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.94 - 1.12: 1 1.12 - 1.29: 2591 1.29 - 1.47: 6244 1.47 - 1.65: 6895 1.65 - 1.82: 119 Bond restraints: 15850 Sorted by residual: bond pdb=" CG PRO C 419 " pdb=" CD PRO C 419 " ideal model delta sigma weight residual 1.512 0.943 0.569 2.70e-02 1.37e+03 4.45e+02 bond pdb=" N PRO C 419 " pdb=" CD PRO C 419 " ideal model delta sigma weight residual 1.474 1.611 -0.137 1.40e-02 5.10e+03 9.63e+01 bond pdb=" C27 H6P B 501 " pdb=" C30 H6P B 501 " ideal model delta sigma weight residual 1.334 1.524 -0.190 2.00e-02 2.50e+03 9.04e+01 bond pdb=" N PRO C 419 " pdb=" CA PRO C 419 " ideal model delta sigma weight residual 1.468 1.362 0.106 1.70e-02 3.46e+03 3.90e+01 bond pdb=" CB PRO C 419 " pdb=" CG PRO C 419 " ideal model delta sigma weight residual 1.506 1.736 -0.230 3.90e-02 6.57e+02 3.48e+01 ... (remaining 15845 not shown) Histogram of bond angle deviations from ideal: 0.00 - 5.02: 21442 5.02 - 10.04: 30 10.04 - 15.06: 8 15.06 - 20.08: 4 20.08 - 25.10: 1 Bond angle restraints: 21485 Sorted by residual: angle pdb=" N PRO C 419 " pdb=" CD PRO C 419 " pdb=" CG PRO C 419 " ideal model delta sigma weight residual 103.80 78.70 25.10 1.20e+00 6.94e-01 4.38e+02 angle pdb=" CA PRO C 419 " pdb=" N PRO C 419 " pdb=" CD PRO C 419 " ideal model delta sigma weight residual 111.50 95.68 15.82 1.40e+00 5.10e-01 1.28e+02 angle pdb=" N PRO C 339 " pdb=" CD PRO C 339 " pdb=" CG PRO C 339 " ideal model delta sigma weight residual 103.20 88.57 14.63 1.50e+00 4.44e-01 9.51e+01 angle pdb=" C ARG B 218 " pdb=" N TRP B 219 " pdb=" CA TRP B 219 " ideal model delta sigma weight residual 121.70 136.98 -15.28 1.80e+00 3.09e-01 7.20e+01 angle pdb=" CA PRO C 339 " pdb=" N PRO C 339 " pdb=" CD PRO C 339 " ideal model delta sigma weight residual 112.00 101.49 10.51 1.40e+00 5.10e-01 5.64e+01 ... (remaining 21480 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 28.15: 9243 28.15 - 56.31: 340 56.31 - 84.46: 11 84.46 - 112.61: 3 112.61 - 140.77: 2 Dihedral angle restraints: 9599 sinusoidal: 3962 harmonic: 5637 Sorted by residual: dihedral pdb=" CA ARG A 293 " pdb=" C ARG A 293 " pdb=" N ARG A 294 " pdb=" CA ARG A 294 " ideal model delta harmonic sigma weight residual -180.00 -132.80 -47.20 0 5.00e+00 4.00e-02 8.91e+01 dihedral pdb=" CA ARG A 294 " pdb=" C ARG A 294 " pdb=" N THR A 295 " pdb=" CA THR A 295 " ideal model delta harmonic sigma weight residual 180.00 151.58 28.42 0 5.00e+00 4.00e-02 3.23e+01 dihedral pdb=" CA SER A 407 " pdb=" C SER A 407 " pdb=" N SER A 408 " pdb=" CA SER A 408 " ideal model delta harmonic sigma weight residual 180.00 155.96 24.04 0 5.00e+00 4.00e-02 2.31e+01 ... (remaining 9596 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.058: 1901 0.058 - 0.115: 402 0.115 - 0.173: 36 0.173 - 0.230: 0 0.230 - 0.288: 1 Chirality restraints: 2340 Sorted by residual: chirality pdb=" CA PRO C 419 " pdb=" N PRO C 419 " pdb=" C PRO C 419 " pdb=" CB PRO C 419 " both_signs ideal model delta sigma weight residual False 2.72 2.43 0.29 2.00e-01 2.50e+01 2.07e+00 chirality pdb=" CA VAL B 370 " pdb=" N VAL B 370 " pdb=" C VAL B 370 " pdb=" CB VAL B 370 " both_signs ideal model delta sigma weight residual False 2.44 2.60 -0.15 2.00e-01 2.50e+01 5.92e-01 chirality pdb=" CA GLU A 278 " pdb=" N GLU A 278 " pdb=" C GLU A 278 " pdb=" CB GLU A 278 " both_signs ideal model delta sigma weight residual False 2.51 2.36 0.15 2.00e-01 2.50e+01 5.56e-01 ... (remaining 2337 not shown) Planarity restraints: 2789 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C21 H6P B 501 " 0.017 2.00e-02 2.50e+03 3.05e-01 1.17e+03 pdb=" C27 H6P B 501 " -0.542 2.00e-02 2.50e+03 pdb=" C28 H6P B 501 " 0.258 2.00e-02 2.50e+03 pdb=" C30 H6P B 501 " 0.321 2.00e-02 2.50e+03 pdb=" C31 H6P B 501 " -0.054 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLU C 418 " -0.068 5.00e-02 4.00e+02 9.33e-02 1.39e+01 pdb=" N PRO C 419 " 0.161 5.00e-02 4.00e+02 pdb=" CA PRO C 419 " -0.053 5.00e-02 4.00e+02 pdb=" CD PRO C 419 " -0.040 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLU C 338 " -0.061 5.00e-02 4.00e+02 8.62e-02 1.19e+01 pdb=" N PRO C 339 " 0.149 5.00e-02 4.00e+02 pdb=" CA PRO C 339 " -0.041 5.00e-02 4.00e+02 pdb=" CD PRO C 339 " -0.047 5.00e-02 4.00e+02 ... (remaining 2786 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.74: 1431 2.74 - 3.28: 15021 3.28 - 3.82: 25346 3.82 - 4.36: 28158 4.36 - 4.90: 48588 Nonbonded interactions: 118544 Sorted by model distance: nonbonded pdb=" OG SER B 327 " pdb=" OE1 GLU B 328 " model vdw 2.205 3.040 nonbonded pdb=" OD2 ASP B 120 " pdb=" OG1 THR C 203 " model vdw 2.225 3.040 nonbonded pdb=" O LEU A 387 " pdb=" OG SER A 407 " model vdw 2.232 3.040 nonbonded pdb=" O ARG D 151 " pdb=" OG SER D 190 " model vdw 2.233 3.040 nonbonded pdb=" NH2 ARG A 187 " pdb=" OE1 GLU A 210 " model vdw 2.235 3.120 ... (remaining 118539 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 1 through 144 or (resid 145 and (name N or name CA or name \ C or name O or name CB )) or resid 146 through 323 or (resid 324 and (name N or \ name CA or name C or name O or name CB )) or resid 325 through 396 or (resid 39 \ 7 and (name N or name CA or name C or name O or name CB )) or resid 398 through \ 492)) selection = (chain 'D' and (resid 1 through 370 or (resid 371 and (name N or name CA or name \ C or name O or name CB )) or resid 372 through 492)) } ncs_group { reference = (chain 'B' and (resid 1 through 36 or resid 38 through 91 or (resid 92 and (name \ N or name CA or name C or name O or name CB )) or resid 93 through 122 or resid \ 125 through 128 or resid 130 through 148 or resid 150 through 151 or resid 154 \ through 159 or resid 161 through 186 or resid 188 through 191 or resid 193 throu \ gh 194 or resid 196 through 217 or resid 219 through 228 or resid 231 through 23 \ 4 or resid 236 through 237 or resid 239 through 242 or resid 244 through 245 or \ resid 247 through 248 or resid 253 or resid 257 through 258 or resid 260 or resi \ d 263 through 264 or resid 271 through 272 or resid 274 or resid 276 or resid 27 \ 8 through 279 or resid 281 through 283 or resid 285 through 286 or resid 288 thr \ ough 290 or resid 293 through 295 or resid 299 through 300 or resid 302 through \ 304 or resid 306 through 317 or resid 319 through 321 or resid 323 through 336 o \ r resid 338 through 339 or resid 341 through 349 or resid 351 or resid 353 throu \ gh 359 or resid 361 or resid 363 through 387 or resid 389 through 400 or resid 4 \ 02 through 413 or resid 415 through 425 or resid 428 or resid 430 through 432 or \ resid 434 through 440 or resid 442 through 447 or resid 449 through 453 or resi \ d 455 through 456 or resid 460 through 463 or resid 465 through 482)) selection = (chain 'C' and (resid 1 through 36 or resid 38 through 122 or resid 125 through \ 128 or resid 130 through 148 or resid 150 through 151 or resid 154 through 159 o \ r resid 161 through 186 or resid 188 through 191 or resid 193 through 194 or res \ id 196 through 217 or resid 219 through 228 or resid 231 through 234 or resid 23 \ 6 through 237 or resid 239 through 242 or resid 244 through 245 or resid 247 thr \ ough 248 or resid 253 or resid 257 through 258 or resid 260 or resid 263 through \ 264 or resid 271 through 272 or resid 274 or resid 276 or resid 278 through 279 \ or resid 281 through 283 or resid 285 through 286 or resid 288 through 290 or r \ esid 293 through 295 or resid 299 through 300 or resid 302 through 304 or resid \ 306 through 317 or resid 319 through 321 or resid 323 through 336 or resid 338 t \ hrough 339 or resid 341 through 349 or resid 351 or resid 353 through 359 or res \ id 361 or resid 363 through 387 or resid 389 through 390 or resid 392 through 40 \ 1 or resid 403 through 414 or resid 416 through 426 or resid 429 or resid 431 th \ rough 433 or resid 435 through 441 or resid 443 through 448 or resid 450 through \ 454 or resid 456 through 457 or resid 461 through 464 or resid 466 through 483) \ ) } 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: 22.040 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.300 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 14.620 Find NCS groups from input model: 0.280 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.850 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.010 Total: 39.220 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5053 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 : 0.007 0.569 15860 Z= 0.286 Angle : 0.836 25.101 21505 Z= 0.493 Chirality : 0.046 0.288 2340 Planarity : 0.008 0.305 2789 Dihedral : 13.440 140.766 5941 Min Nonbonded Distance : 2.205 Molprobity Statistics. All-atom Clashscore : 14.45 Ramachandran Plot: Outliers : 0.10 % Allowed : 6.12 % Favored : 93.78 % Rotamer: Outliers : 0.12 % Allowed : 3.10 % Favored : 96.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.91 % Cis-general : 0.05 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: -0.67 (0.19), residues: 1944 helix: 2.82 (0.29), residues: 299 sheet: -0.50 (0.22), residues: 585 loop : -1.42 (0.19), residues: 1060 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 22 TYR 0.018 0.001 TYR A 359 PHE 0.023 0.001 PHE C 99 TRP 0.029 0.002 TRP C 242 HIS 0.006 0.001 HIS A 298 Details of bonding type rmsd/Z covalent geometry : bond 0.00658 / 0.29 (15850) covalent geometry : angle 0.83612 / 0.49 (21485) SS BOND : bond 0.00467 / 0.25 ( 10) SS BOND : angle 0.86320 / 0.54 ( 20) hydrogen bonds : bond 0.15245 / 10.00 ( 622) hydrogen bonds : angle 7.21514 / 4.93 ( 1728) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3888 Ramachandran restraints generated. 1944 Oldfield, 0 Emsley, 1944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3888 Ramachandran restraints generated. 1944 Oldfield, 0 Emsley, 1944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 64 residues out of total 1693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 62 time to evaluate : 0.683 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 2 outliers final: 0 residues processed: 64 average time/residue: 0.1498 time to fit residues: 14.5413 Evaluate side-chains 47 residues out of total 1693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 47 time to evaluate : 0.547 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 194 random chunks: chunk 98 optimal weight: 0.0870 chunk 107 optimal weight: 4.9990 chunk 10 optimal weight: 8.9990 chunk 66 optimal weight: 10.0000 chunk 130 optimal weight: 20.0000 chunk 124 optimal weight: 5.9990 chunk 103 optimal weight: 10.0000 chunk 77 optimal weight: 2.9990 chunk 122 optimal weight: 0.9980 chunk 91 optimal weight: 0.6980 chunk 149 optimal weight: 0.0980 overall best weight: 0.9760 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 100 GLN ** B 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 289 GLN D 60 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3985 r_free = 0.3985 target = 0.058162 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3220 r_free = 0.3220 target = 0.037152 restraints weight = 181529.610| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3154 r_free = 0.3154 target = 0.035900 restraints weight = 145942.247| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3156 r_free = 0.3156 target = 0.035994 restraints weight = 130763.663| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3153 r_free = 0.3153 target = 0.035938 restraints weight = 137019.155| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3159 r_free = 0.3159 target = 0.036018 restraints weight = 107588.248| |-----------------------------------------------------------------------------| r_work (final): 0.3079 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7823 moved from start: 0.1301 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 15860 Z= 0.130 Angle : 0.584 8.286 21505 Z= 0.309 Chirality : 0.044 0.151 2340 Planarity : 0.005 0.054 2789 Dihedral : 6.556 144.808 2160 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 12.60 Ramachandran Plot: Outliers : 0.15 % Allowed : 5.09 % Favored : 94.75 % Rotamer: Outliers : 0.06 % Allowed : 3.45 % Favored : 96.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.91 % Cis-general : 0.05 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: -0.67 (0.19), residues: 1944 helix: 2.81 (0.29), residues: 300 sheet: -0.60 (0.21), residues: 627 loop : -1.37 (0.19), residues: 1017 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 67 TYR 0.016 0.001 TYR A 98 PHE 0.016 0.001 PHE C 457 TRP 0.042 0.001 TRP C 303 HIS 0.006 0.001 HIS C 379 Details of bonding type rmsd/Z covalent geometry : bond 0.00286 / 0.13 (15850) covalent geometry : angle 0.58367 / 0.31 (21485) SS BOND : bond 0.00398 / 0.20 ( 10) SS BOND : angle 0.83580 / 0.51 ( 20) hydrogen bonds : bond 0.04256 / 2.72 ( 622) hydrogen bonds : angle 6.08297 / 4.17 ( 1728) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3888 Ramachandran restraints generated. 1944 Oldfield, 0 Emsley, 1944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3888 Ramachandran restraints generated. 1944 Oldfield, 0 Emsley, 1944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 52 residues out of total 1693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 51 time to evaluate : 0.646 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 213 MET cc_start: 0.6739 (mpp) cc_final: 0.6039 (mpp) REVERT: C 34 MET cc_start: 0.3846 (mmp) cc_final: 0.0980 (tmm) REVERT: D 125 MET cc_start: 0.8996 (tpt) cc_final: 0.8687 (tpp) outliers start: 1 outliers final: 0 residues processed: 52 average time/residue: 0.1194 time to fit residues: 10.0268 Evaluate side-chains 47 residues out of total 1693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 47 time to evaluate : 0.640 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 194 random chunks: chunk 106 optimal weight: 5.9990 chunk 38 optimal weight: 0.6980 chunk 158 optimal weight: 5.9990 chunk 181 optimal weight: 0.9980 chunk 30 optimal weight: 2.9990 chunk 147 optimal weight: 0.4980 chunk 113 optimal weight: 5.9990 chunk 90 optimal weight: 3.9990 chunk 138 optimal weight: 20.0000 chunk 189 optimal weight: 4.9990 chunk 140 optimal weight: 20.0000 overall best weight: 1.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 85 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 122 HIS B 157 ASN C 24 HIS D 60 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3746 r_free = 0.3746 target = 0.048833 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3251 r_free = 0.3251 target = 0.038697 restraints weight = 260656.972| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3267 r_free = 0.3267 target = 0.038895 restraints weight = 167767.686| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3262 r_free = 0.3262 target = 0.038814 restraints weight = 121616.806| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3267 r_free = 0.3267 target = 0.038895 restraints weight = 127767.123| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3270 r_free = 0.3270 target = 0.038934 restraints weight = 108679.374| |-----------------------------------------------------------------------------| r_work (final): 0.3186 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7484 moved from start: 0.2136 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.076 15860 Z= 0.187 Angle : 0.616 7.115 21505 Z= 0.323 Chirality : 0.044 0.158 2340 Planarity : 0.005 0.056 2789 Dihedral : 6.766 146.078 2160 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 15.43 Ramachandran Plot: Outliers : 0.15 % Allowed : 5.25 % Favored : 94.60 % Rotamer: Outliers : 0.00 % Allowed : 3.87 % Favored : 96.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.91 % Cis-general : 0.05 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.79 (0.19), residues: 1944 helix: 2.36 (0.28), residues: 308 sheet: -0.59 (0.21), residues: 605 loop : -1.41 (0.19), residues: 1031 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 420 TYR 0.023 0.002 TYR D 359 PHE 0.017 0.002 PHE D 425 TRP 0.047 0.002 TRP C 242 HIS 0.006 0.001 HIS D 491 Details of bonding type rmsd/Z covalent geometry : bond 0.00411 / 0.19 (15850) covalent geometry : angle 0.61602 / 0.32 (21485) SS BOND : bond 0.00315 / 0.15 ( 10) SS BOND : angle 0.78467 / 0.50 ( 20) hydrogen bonds : bond 0.04493 / 2.85 ( 622) hydrogen bonds : angle 6.05503 / 4.18 ( 1728) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3888 Ramachandran restraints generated. 1944 Oldfield, 0 Emsley, 1944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3888 Ramachandran restraints generated. 1944 Oldfield, 0 Emsley, 1944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 50 residues out of total 1693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 50 time to evaluate : 0.653 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 189 MET cc_start: 0.7267 (tpt) cc_final: 0.6788 (tpt) REVERT: B 14 MET cc_start: 0.7865 (tpt) cc_final: 0.7623 (tpt) REVERT: C 291 MET cc_start: 0.9375 (tpp) cc_final: 0.9093 (tpp) REVERT: C 301 HIS cc_start: 0.9074 (m-70) cc_final: 0.8873 (m-70) REVERT: C 396 MET cc_start: 0.6787 (tpt) cc_final: 0.6338 (tpt) REVERT: D 125 MET cc_start: 0.8568 (tpt) cc_final: 0.8338 (tpp) outliers start: 0 outliers final: 0 residues processed: 50 average time/residue: 0.1237 time to fit residues: 9.7850 Evaluate side-chains 46 residues out of total 1693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 46 time to evaluate : 0.565 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 194 random chunks: chunk 135 optimal weight: 9.9990 chunk 107 optimal weight: 6.9990 chunk 157 optimal weight: 0.0670 chunk 117 optimal weight: 9.9990 chunk 43 optimal weight: 2.9990 chunk 153 optimal weight: 6.9990 chunk 63 optimal weight: 0.9990 chunk 28 optimal weight: 4.9990 chunk 184 optimal weight: 3.9990 chunk 94 optimal weight: 0.8980 chunk 173 optimal weight: 0.9990 overall best weight: 1.1924 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 85 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 60 GLN ** 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 = 0.3756 r_free = 0.3756 target = 0.048864 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.3253 r_free = 0.3253 target = 0.038235 restraints weight = 261125.998| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 53)----------------| | r_work = 0.3281 r_free = 0.3281 target = 0.038830 restraints weight = 151475.422| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3298 r_free = 0.3298 target = 0.039207 restraints weight = 107926.818| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3308 r_free = 0.3308 target = 0.039393 restraints weight = 87441.132| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3308 r_free = 0.3308 target = 0.039393 restraints weight = 77597.175| |-----------------------------------------------------------------------------| r_work (final): 0.3221 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7426 moved from start: 0.2386 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 15860 Z= 0.136 Angle : 0.560 7.439 21505 Z= 0.293 Chirality : 0.043 0.156 2340 Planarity : 0.005 0.134 2789 Dihedral : 6.497 140.726 2160 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 12.89 Ramachandran Plot: Outliers : 0.15 % Allowed : 4.68 % Favored : 95.16 % Rotamer: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.91 % Cis-general : 0.05 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: -0.62 (0.19), residues: 1944 helix: 2.86 (0.28), residues: 296 sheet: -0.56 (0.21), residues: 603 loop : -1.31 (0.19), residues: 1045 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 44 TYR 0.015 0.001 TYR D 359 PHE 0.014 0.001 PHE A 425 TRP 0.042 0.001 TRP C 303 HIS 0.004 0.001 HIS C 379 Details of bonding type rmsd/Z covalent geometry : bond 0.00302 / 0.14 (15850) covalent geometry : angle 0.55928 / 0.29 (21485) SS BOND : bond 0.00325 / 0.16 ( 10) SS BOND : angle 0.87787 / 0.58 ( 20) hydrogen bonds : bond 0.04022 / 2.59 ( 622) hydrogen bonds : angle 5.85123 / 4.02 ( 1728) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3888 Ramachandran restraints generated. 1944 Oldfield, 0 Emsley, 1944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3888 Ramachandran restraints generated. 1944 Oldfield, 0 Emsley, 1944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 50 residues out of total 1693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 50 time to evaluate : 0.636 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 189 MET cc_start: 0.7014 (tpt) cc_final: 0.6473 (tpt) REVERT: C 291 MET cc_start: 0.9301 (tpp) cc_final: 0.9059 (tpp) REVERT: C 301 HIS cc_start: 0.9002 (m-70) cc_final: 0.8769 (m-70) REVERT: C 396 MET cc_start: 0.7022 (tpt) cc_final: 0.6629 (tpt) outliers start: 0 outliers final: 0 residues processed: 50 average time/residue: 0.1176 time to fit residues: 9.4705 Evaluate side-chains 45 residues out of total 1693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 45 time to evaluate : 0.590 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 194 random chunks: chunk 193 optimal weight: 6.9990 chunk 102 optimal weight: 0.0370 chunk 92 optimal weight: 5.9990 chunk 64 optimal weight: 7.9990 chunk 130 optimal weight: 20.0000 chunk 172 optimal weight: 1.9990 chunk 145 optimal weight: 9.9990 chunk 114 optimal weight: 0.8980 chunk 4 optimal weight: 5.9990 chunk 148 optimal weight: 9.9990 chunk 112 optimal weight: 0.6980 overall best weight: 1.9262 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 85 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 366 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3724 r_free = 0.3724 target = 0.048231 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3248 r_free = 0.3248 target = 0.038513 restraints weight = 260477.528| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3240 r_free = 0.3240 target = 0.038254 restraints weight = 186699.903| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3241 r_free = 0.3241 target = 0.038272 restraints weight = 148923.440| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3242 r_free = 0.3242 target = 0.038299 restraints weight = 134323.005| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3249 r_free = 0.3249 target = 0.038370 restraints weight = 123403.241| |-----------------------------------------------------------------------------| r_work (final): 0.3163 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7533 moved from start: 0.3088 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.079 15860 Z= 0.196 Angle : 0.619 6.976 21505 Z= 0.322 Chirality : 0.044 0.179 2340 Planarity : 0.005 0.056 2789 Dihedral : 6.762 142.501 2160 Min Nonbonded Distance : 2.572 Molprobity Statistics. All-atom Clashscore : 16.60 Ramachandran Plot: Outliers : 0.15 % Allowed : 5.92 % Favored : 93.93 % Rotamer: Outliers : 0.06 % Allowed : 2.62 % Favored : 97.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.91 % Cis-general : 0.05 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: -0.81 (0.19), residues: 1944 helix: 2.44 (0.28), residues: 302 sheet: -0.78 (0.21), residues: 597 loop : -1.30 (0.19), residues: 1045 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG C 44 TYR 0.024 0.002 TYR D 359 PHE 0.017 0.002 PHE D 425 TRP 0.056 0.002 TRP C 242 HIS 0.008 0.002 HIS B 297 Details of bonding type rmsd/Z covalent geometry : bond 0.00433 / 0.20 (15850) covalent geometry : angle 0.61856 / 0.32 (21485) SS BOND : bond 0.00253 / 0.12 ( 10) SS BOND : angle 0.90069 / 0.66 ( 20) hydrogen bonds : bond 0.04358 / 2.79 ( 622) hydrogen bonds : angle 5.99108 / 4.14 ( 1728) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3888 Ramachandran restraints generated. 1944 Oldfield, 0 Emsley, 1944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3888 Ramachandran restraints generated. 1944 Oldfield, 0 Emsley, 1944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 54 residues out of total 1693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 53 time to evaluate : 0.626 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 189 MET cc_start: 0.7675 (tpt) cc_final: 0.7061 (tpt) REVERT: A 213 MET cc_start: 0.5139 (mpp) cc_final: 0.4613 (mpp) REVERT: B 14 MET cc_start: 0.7916 (tpt) cc_final: 0.7613 (tpt) REVERT: C 291 MET cc_start: 0.9425 (tpp) cc_final: 0.9152 (tpp) REVERT: C 349 PHE cc_start: 0.7250 (m-80) cc_final: 0.7028 (m-80) REVERT: C 396 MET cc_start: 0.7271 (tpt) cc_final: 0.6901 (tpt) REVERT: C 430 ARG cc_start: 0.9721 (tpt90) cc_final: 0.9380 (tpt90) REVERT: D 125 MET cc_start: 0.8645 (tpt) cc_final: 0.8367 (tpp) outliers start: 1 outliers final: 0 residues processed: 54 average time/residue: 0.1304 time to fit residues: 11.1330 Evaluate side-chains 46 residues out of total 1693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 46 time to evaluate : 0.532 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 194 random chunks: chunk 183 optimal weight: 4.9990 chunk 74 optimal weight: 5.9990 chunk 193 optimal weight: 4.9990 chunk 178 optimal weight: 2.9990 chunk 133 optimal weight: 20.0000 chunk 15 optimal weight: 4.9990 chunk 89 optimal weight: 0.6980 chunk 109 optimal weight: 10.0000 chunk 138 optimal weight: 10.0000 chunk 168 optimal weight: 6.9990 chunk 45 optimal weight: 1.9990 overall best weight: 3.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 85 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 134 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 329 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3904 r_free = 0.3904 target = 0.056152 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3105 r_free = 0.3105 target = 0.034706 restraints weight = 186564.496| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3090 r_free = 0.3090 target = 0.034400 restraints weight = 145752.596| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3083 r_free = 0.3083 target = 0.034225 restraints weight = 131425.561| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3087 r_free = 0.3087 target = 0.034333 restraints weight = 124996.448| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3095 r_free = 0.3095 target = 0.034353 restraints weight = 107705.247| |-----------------------------------------------------------------------------| r_work (final): 0.3056 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7952 moved from start: 0.4079 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.097 15860 Z= 0.289 Angle : 0.727 10.649 21505 Z= 0.379 Chirality : 0.046 0.181 2340 Planarity : 0.006 0.129 2789 Dihedral : 7.130 138.385 2160 Min Nonbonded Distance : 2.395 Molprobity Statistics. All-atom Clashscore : 23.12 Ramachandran Plot: Outliers : 0.21 % Allowed : 7.00 % Favored : 92.80 % Rotamer: Outliers : 0.00 % Allowed : 3.99 % Favored : 96.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.91 % Cis-general : 0.05 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: -1.14 (0.19), residues: 1944 helix: 1.90 (0.28), residues: 304 sheet: -0.95 (0.21), residues: 569 loop : -1.46 (0.18), residues: 1071 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 44 TYR 0.033 0.002 TYR D 359 PHE 0.023 0.002 PHE D 425 TRP 0.019 0.002 TRP C 303 HIS 0.012 0.002 HIS B 297 Details of bonding type rmsd/Z covalent geometry : bond 0.00633 / 0.29 (15850) covalent geometry : angle 0.72711 / 0.38 (21485) SS BOND : bond 0.00529 / 0.27 ( 10) SS BOND : angle 0.95056 / 0.66 ( 20) hydrogen bonds : bond 0.05046 / 3.21 ( 622) hydrogen bonds : angle 6.50333 / 4.49 ( 1728) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3888 Ramachandran restraints generated. 1944 Oldfield, 0 Emsley, 1944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3888 Ramachandran restraints generated. 1944 Oldfield, 0 Emsley, 1944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 54 residues out of total 1693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 54 time to evaluate : 0.530 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 166 MET cc_start: 0.9013 (tmm) cc_final: 0.8803 (tmm) REVERT: A 213 MET cc_start: 0.7958 (mpp) cc_final: 0.7596 (mpp) REVERT: A 398 MET cc_start: 0.8126 (mmm) cc_final: 0.7672 (mmm) REVERT: D 79 SER cc_start: 0.9139 (t) cc_final: 0.8913 (p) REVERT: D 125 MET cc_start: 0.9425 (tpt) cc_final: 0.9178 (tpp) outliers start: 0 outliers final: 0 residues processed: 54 average time/residue: 0.1083 time to fit residues: 9.6954 Evaluate side-chains 45 residues out of total 1693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 45 time to evaluate : 0.618 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 194 random chunks: chunk 140 optimal weight: 20.0000 chunk 25 optimal weight: 2.9990 chunk 96 optimal weight: 1.9990 chunk 60 optimal weight: 5.9990 chunk 15 optimal weight: 2.9990 chunk 20 optimal weight: 4.9990 chunk 10 optimal weight: 3.9990 chunk 155 optimal weight: 6.9990 chunk 143 optimal weight: 20.0000 chunk 171 optimal weight: 5.9990 chunk 2 optimal weight: 0.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 85 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 134 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 298 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 = 0.3702 r_free = 0.3702 target = 0.047522 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3240 r_free = 0.3240 target = 0.038121 restraints weight = 260602.805| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3227 r_free = 0.3227 target = 0.037760 restraints weight = 187286.674| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3225 r_free = 0.3225 target = 0.037744 restraints weight = 150580.600| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3228 r_free = 0.3228 target = 0.037781 restraints weight = 139552.914| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3231 r_free = 0.3231 target = 0.037823 restraints weight = 126500.807| |-----------------------------------------------------------------------------| r_work (final): 0.3140 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7597 moved from start: 0.4407 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.081 15860 Z= 0.239 Angle : 0.689 10.457 21505 Z= 0.355 Chirality : 0.046 0.218 2340 Planarity : 0.006 0.096 2789 Dihedral : 7.106 139.662 2160 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 20.36 Ramachandran Plot: Outliers : 0.21 % Allowed : 6.22 % Favored : 93.57 % Rotamer: Outliers : 0.00 % Allowed : 1.37 % Favored : 98.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.91 % Cis-general : 0.05 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: -1.21 (0.19), residues: 1944 helix: 1.94 (0.28), residues: 304 sheet: -1.07 (0.21), residues: 579 loop : -1.48 (0.19), residues: 1061 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 54 TYR 0.024 0.002 TYR D 436 PHE 0.018 0.002 PHE D 425 TRP 0.051 0.002 TRP C 303 HIS 0.019 0.002 HIS A 298 Details of bonding type rmsd/Z covalent geometry : bond 0.00527 / 0.24 (15850) covalent geometry : angle 0.68928 / 0.36 (21485) SS BOND : bond 0.00342 / 0.16 ( 10) SS BOND : angle 0.78224 / 0.55 ( 20) hydrogen bonds : bond 0.04663 / 2.98 ( 622) hydrogen bonds : angle 6.40470 / 4.42 ( 1728) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3888 Ramachandran restraints generated. 1944 Oldfield, 0 Emsley, 1944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3888 Ramachandran restraints generated. 1944 Oldfield, 0 Emsley, 1944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 50 residues out of total 1693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 50 time to evaluate : 0.622 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 174 MET cc_start: 0.8476 (ptm) cc_final: 0.7958 (tmm) REVERT: A 398 MET cc_start: 0.8294 (mmm) cc_final: 0.7952 (mmp) REVERT: C 291 MET cc_start: 0.9460 (tpp) cc_final: 0.9203 (tpp) REVERT: C 349 PHE cc_start: 0.7376 (m-80) cc_final: 0.7135 (m-80) REVERT: C 396 MET cc_start: 0.7445 (tpt) cc_final: 0.6847 (tpt) REVERT: D 61 MET cc_start: 0.1686 (pmm) cc_final: 0.1347 (pmm) REVERT: D 125 MET cc_start: 0.9085 (tpt) cc_final: 0.8766 (tpp) outliers start: 0 outliers final: 0 residues processed: 50 average time/residue: 0.1169 time to fit residues: 9.5812 Evaluate side-chains 46 residues out of total 1693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 46 time to evaluate : 0.475 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 194 random chunks: chunk 87 optimal weight: 0.9980 chunk 161 optimal weight: 0.9990 chunk 174 optimal weight: 0.8980 chunk 61 optimal weight: 3.9990 chunk 186 optimal weight: 0.9980 chunk 141 optimal weight: 20.0000 chunk 1 optimal weight: 0.9990 chunk 47 optimal weight: 0.6980 chunk 5 optimal weight: 2.9990 chunk 98 optimal weight: 7.9990 chunk 126 optimal weight: 3.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 85 HIS ** B 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 157 ASN B 297 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3723 r_free = 0.3723 target = 0.048532 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3228 r_free = 0.3228 target = 0.036752 restraints weight = 231204.540| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3255 r_free = 0.3255 target = 0.037182 restraints weight = 153275.661| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3236 r_free = 0.3236 target = 0.036674 restraints weight = 123998.995| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3241 r_free = 0.3241 target = 0.036753 restraints weight = 119613.039| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3244 r_free = 0.3244 target = 0.036772 restraints weight = 104548.137| |-----------------------------------------------------------------------------| r_work (final): 0.3127 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7746 moved from start: 0.4371 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.066 15860 Z= 0.126 Angle : 0.586 7.732 21505 Z= 0.304 Chirality : 0.045 0.155 2340 Planarity : 0.005 0.070 2789 Dihedral : 6.586 131.190 2160 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 14.35 Ramachandran Plot: Outliers : 0.15 % Allowed : 4.89 % Favored : 94.96 % Rotamer: Outliers : 0.00 % Allowed : 1.31 % Favored : 98.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.91 % Cis-general : 0.05 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: -0.97 (0.19), residues: 1944 helix: 2.33 (0.28), residues: 302 sheet: -0.99 (0.21), residues: 617 loop : -1.34 (0.19), residues: 1025 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 56 TYR 0.012 0.001 TYR A 98 PHE 0.018 0.001 PHE A 425 TRP 0.048 0.001 TRP C 303 HIS 0.006 0.001 HIS A 24 Details of bonding type rmsd/Z covalent geometry : bond 0.00281 / 0.13 (15850) covalent geometry : angle 0.58625 / 0.30 (21485) SS BOND : bond 0.00284 / 0.14 ( 10) SS BOND : angle 0.67544 / 0.46 ( 20) hydrogen bonds : bond 0.03981 / 2.56 ( 622) hydrogen bonds : angle 5.99621 / 4.15 ( 1728) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3888 Ramachandran restraints generated. 1944 Oldfield, 0 Emsley, 1944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3888 Ramachandran restraints generated. 1944 Oldfield, 0 Emsley, 1944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 48 residues out of total 1693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 48 time to evaluate : 0.431 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 174 MET cc_start: 0.8492 (ptm) cc_final: 0.8054 (tmm) REVERT: A 189 MET cc_start: 0.7990 (mmm) cc_final: 0.7687 (tpt) REVERT: C 396 MET cc_start: 0.9290 (tpt) cc_final: 0.9002 (tpt) REVERT: D 61 MET cc_start: 0.2366 (pmm) cc_final: 0.2066 (pmm) REVERT: D 213 MET cc_start: 0.4575 (mmp) cc_final: 0.4245 (tpt) outliers start: 0 outliers final: 0 residues processed: 48 average time/residue: 0.1269 time to fit residues: 9.7092 Evaluate side-chains 43 residues out of total 1693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 43 time to evaluate : 0.676 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 194 random chunks: chunk 6 optimal weight: 1.9990 chunk 10 optimal weight: 5.9990 chunk 27 optimal weight: 4.9990 chunk 184 optimal weight: 4.9990 chunk 17 optimal weight: 0.9990 chunk 167 optimal weight: 0.0670 chunk 87 optimal weight: 0.7980 chunk 31 optimal weight: 0.7980 chunk 53 optimal weight: 9.9990 chunk 74 optimal weight: 7.9990 chunk 170 optimal weight: 6.9990 overall best weight: 0.9322 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 157 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3724 r_free = 0.3724 target = 0.047797 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3259 r_free = 0.3259 target = 0.038271 restraints weight = 261841.064| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3261 r_free = 0.3261 target = 0.038171 restraints weight = 173815.524| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3252 r_free = 0.3252 target = 0.038075 restraints weight = 143279.494| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3256 r_free = 0.3256 target = 0.038151 restraints weight = 156588.569| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3263 r_free = 0.3263 target = 0.038236 restraints weight = 126235.467| |-----------------------------------------------------------------------------| r_work (final): 0.3181 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7495 moved from start: 0.4457 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 15860 Z= 0.126 Angle : 0.576 7.662 21505 Z= 0.300 Chirality : 0.044 0.152 2340 Planarity : 0.005 0.057 2789 Dihedral : 6.442 131.651 2160 Min Nonbonded Distance : 2.356 Molprobity Statistics. All-atom Clashscore : 13.64 Ramachandran Plot: Outliers : 0.15 % Allowed : 4.99 % Favored : 94.86 % Rotamer: Outliers : 0.00 % Allowed : 0.18 % Favored : 99.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.91 % Cis-general : 0.05 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: -0.81 (0.19), residues: 1944 helix: 2.40 (0.28), residues: 301 sheet: -0.91 (0.21), residues: 622 loop : -1.19 (0.19), residues: 1021 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 182 TYR 0.012 0.001 TYR D 359 PHE 0.017 0.001 PHE C 445 TRP 0.043 0.001 TRP C 303 HIS 0.005 0.001 HIS B 366 Details of bonding type rmsd/Z covalent geometry : bond 0.00278 / 0.13 (15850) covalent geometry : angle 0.57545 / 0.30 (21485) SS BOND : bond 0.00211 / 0.11 ( 10) SS BOND : angle 0.71179 / 0.48 ( 20) hydrogen bonds : bond 0.03940 / 2.54 ( 622) hydrogen bonds : angle 5.83361 / 4.02 ( 1728) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3888 Ramachandran restraints generated. 1944 Oldfield, 0 Emsley, 1944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3888 Ramachandran restraints generated. 1944 Oldfield, 0 Emsley, 1944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 48 residues out of total 1693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 48 time to evaluate : 0.725 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 174 MET cc_start: 0.8483 (ptm) cc_final: 0.8078 (tmm) REVERT: C 349 PHE cc_start: 0.7354 (m-80) cc_final: 0.7132 (m-80) REVERT: C 396 MET cc_start: 0.6661 (tpt) cc_final: 0.6180 (tpt) REVERT: D 61 MET cc_start: 0.1440 (pmm) cc_final: 0.1172 (pmm) REVERT: D 125 MET cc_start: 0.8847 (tpt) cc_final: 0.8514 (tpp) REVERT: D 213 MET cc_start: 0.4127 (mmp) cc_final: 0.3864 (tpt) outliers start: 0 outliers final: 0 residues processed: 48 average time/residue: 0.1273 time to fit residues: 9.8649 Evaluate side-chains 43 residues out of total 1693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 43 time to evaluate : 0.606 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 194 random chunks: chunk 48 optimal weight: 1.9990 chunk 171 optimal weight: 0.9990 chunk 150 optimal weight: 5.9990 chunk 14 optimal weight: 2.9990 chunk 102 optimal weight: 6.9990 chunk 132 optimal weight: 20.0000 chunk 157 optimal weight: 8.9990 chunk 54 optimal weight: 7.9990 chunk 126 optimal weight: 0.9990 chunk 156 optimal weight: 9.9990 chunk 72 optimal weight: 20.0000 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 134 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 297 HIS ** C 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 298 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 = 0.3902 r_free = 0.3902 target = 0.055791 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3171 r_free = 0.3171 target = 0.035412 restraints weight = 187084.608| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3152 r_free = 0.3152 target = 0.035027 restraints weight = 141904.512| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3131 r_free = 0.3131 target = 0.034634 restraints weight = 128119.387| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3137 r_free = 0.3137 target = 0.034709 restraints weight = 116832.283| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3142 r_free = 0.3142 target = 0.034785 restraints weight = 102639.327| |-----------------------------------------------------------------------------| r_work (final): 0.3095 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7908 moved from start: 0.4939 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.074 15860 Z= 0.249 Angle : 0.688 8.230 21505 Z= 0.357 Chirality : 0.045 0.196 2340 Planarity : 0.006 0.072 2789 Dihedral : 7.085 142.468 2160 Min Nonbonded Distance : 2.371 Molprobity Statistics. All-atom Clashscore : 20.10 Ramachandran Plot: Outliers : 0.15 % Allowed : 6.89 % Favored : 92.95 % Rotamer: Outliers : 0.00 % Allowed : 0.18 % Favored : 99.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.91 % Cis-general : 0.05 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: -1.02 (0.19), residues: 1944 helix: 2.11 (0.28), residues: 303 sheet: -1.04 (0.21), residues: 609 loop : -1.29 (0.19), residues: 1032 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 182 TYR 0.021 0.002 TYR D 436 PHE 0.018 0.002 PHE D 425 TRP 0.037 0.002 TRP C 303 HIS 0.009 0.002 HIS A 298 Details of bonding type rmsd/Z covalent geometry : bond 0.00545 / 0.25 (15850) covalent geometry : angle 0.68743 / 0.36 (21485) SS BOND : bond 0.00260 / 0.12 ( 10) SS BOND : angle 0.90794 / 0.63 ( 20) hydrogen bonds : bond 0.04591 / 2.94 ( 622) hydrogen bonds : angle 6.21422 / 4.29 ( 1728) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3888 Ramachandran restraints generated. 1944 Oldfield, 0 Emsley, 1944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3888 Ramachandran restraints generated. 1944 Oldfield, 0 Emsley, 1944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 46 residues out of total 1693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 46 time to evaluate : 0.666 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 174 MET cc_start: 0.9014 (ptm) cc_final: 0.8478 (tmm) REVERT: A 213 MET cc_start: 0.7631 (mpp) cc_final: 0.7283 (mpp) REVERT: A 398 MET cc_start: 0.7687 (mmm) cc_final: 0.7469 (mmp) outliers start: 0 outliers final: 0 residues processed: 46 average time/residue: 0.1175 time to fit residues: 8.6534 Evaluate side-chains 43 residues out of total 1693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 43 time to evaluate : 0.612 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 194 random chunks: chunk 49 optimal weight: 2.9990 chunk 69 optimal weight: 6.9990 chunk 15 optimal weight: 0.7980 chunk 65 optimal weight: 20.0000 chunk 5 optimal weight: 1.9990 chunk 35 optimal weight: 0.9990 chunk 144 optimal weight: 20.0000 chunk 60 optimal weight: 5.9990 chunk 158 optimal weight: 0.7980 chunk 95 optimal weight: 0.9990 chunk 68 optimal weight: 0.1980 overall best weight: 0.7584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 297 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3723 r_free = 0.3723 target = 0.047583 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3239 r_free = 0.3239 target = 0.037806 restraints weight = 261807.307| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3265 r_free = 0.3265 target = 0.038286 restraints weight = 167275.987| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3268 r_free = 0.3268 target = 0.038273 restraints weight = 115183.194| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3271 r_free = 0.3271 target = 0.038323 restraints weight = 126245.458| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3275 r_free = 0.3275 target = 0.038397 restraints weight = 107592.767| |-----------------------------------------------------------------------------| r_work (final): 0.3179 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7511 moved from start: 0.4868 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 15860 Z= 0.116 Angle : 0.586 7.915 21505 Z= 0.304 Chirality : 0.044 0.154 2340 Planarity : 0.005 0.056 2789 Dihedral : 6.459 129.604 2160 Min Nonbonded Distance : 2.398 Molprobity Statistics. All-atom Clashscore : 13.19 Ramachandran Plot: Outliers : 0.15 % Allowed : 4.84 % Favored : 95.01 % Rotamer: Outliers : 0.00 % Allowed : 0.12 % Favored : 99.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.91 % Cis-general : 0.05 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: -0.89 (0.19), residues: 1944 helix: 2.26 (0.29), residues: 303 sheet: -0.89 (0.20), residues: 632 loop : -1.27 (0.19), residues: 1009 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG C 243 TYR 0.013 0.001 TYR D 359 PHE 0.016 0.001 PHE A 425 TRP 0.059 0.002 TRP C 242 HIS 0.004 0.001 HIS B 366 Details of bonding type rmsd/Z covalent geometry : bond 0.00257 / 0.12 (15850) covalent geometry : angle 0.58625 / 0.30 (21485) SS BOND : bond 0.00292 / 0.13 ( 10) SS BOND : angle 0.64898 / 0.44 ( 20) hydrogen bonds : bond 0.03885 / 2.53 ( 622) hydrogen bonds : angle 5.83562 / 4.02 ( 1728) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3797.99 seconds wall clock time: 66 minutes 10.24 seconds (3970.24 seconds total)