Starting phenix.real_space_refine on Wed Feb 4 04:26:44 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9wxm_66350/02_2026/9wxm_66350.cif Found real_map, /net/cci-nas-00/data/ceres_data/9wxm_66350/02_2026/9wxm_66350.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9wxm_66350/02_2026/9wxm_66350.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9wxm_66350/02_2026/9wxm_66350.map" model { file = "/net/cci-nas-00/data/ceres_data/9wxm_66350/02_2026/9wxm_66350.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9wxm_66350/02_2026/9wxm_66350.cif" } resolution = 3.3 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= 0.011 sd= 0.077 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 63 5.16 5 C 5537 2.51 5 N 1468 2.21 5 O 1575 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 4 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 8643 Number of models: 1 Model: "" Number of chains: 6 Chain: "L" Number of atoms: 105 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 105 Classifications: {'peptide': 14} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 3, 'TRANS': 10} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "R" Number of atoms: 2233 Number of conformers: 1 Conformer: "" Number of residues, atoms: 287, 2233 Classifications: {'peptide': 287} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PTRANS': 12, 'TRANS': 274} Unresolved non-hydrogen bonds: 48 Unresolved non-hydrogen angles: 64 Unresolved non-hydrogen dihedrals: 40 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLU:plan': 2, 'ASP:plan': 1, 'TYR:plan': 2, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 30 Chain: "A" Number of atoms: 1699 Number of conformers: 1 Conformer: "" Number of residues, atoms: 220, 1699 Classifications: {'peptide': 220} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 28} Link IDs: {'PTRANS': 2, 'TRANS': 217} Chain breaks: 2 Unresolved non-hydrogen bonds: 83 Unresolved non-hydrogen angles: 103 Unresolved non-hydrogen dihedrals: 63 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'ASP:plan': 6, 'GLU:plan': 5, 'GLN:plan1': 1, 'ARG:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 50 Chain: "B" Number of atoms: 2496 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 2496 Classifications: {'peptide': 338} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 27} Link IDs: {'PTRANS': 5, 'TRANS': 332} Unresolved non-hydrogen bonds: 105 Unresolved non-hydrogen angles: 128 Unresolved non-hydrogen dihedrals: 82 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLU:plan': 5, 'ASP:plan': 4, 'GLN:plan1': 4, 'ARG:plan': 5, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 76 Chain: "C" Number of atoms: 357 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 357 Classifications: {'peptide': 54} Incomplete info: {'truncation_to_alanine': 16} Link IDs: {'PTRANS': 4, 'TRANS': 49} Unresolved non-hydrogen bonds: 62 Unresolved non-hydrogen angles: 72 Unresolved non-hydrogen dihedrals: 52 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 2, 'ARG:plan': 2, 'GLU:plan': 2, 'ASN:plan1': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 35 Chain: "D" Number of atoms: 1753 Number of conformers: 1 Conformer: "" Number of residues, atoms: 234, 1753 Classifications: {'peptide': 234} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PTRANS': 10, 'TRANS': 223} Chain breaks: 1 Unresolved non-hydrogen bonds: 48 Unresolved non-hydrogen angles: 60 Unresolved non-hydrogen dihedrals: 39 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 5, 'ASP:plan': 2, 'ARG:plan': 1, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 42 Time building chain proxies: 1.73, per 1000 atoms: 0.20 Number of scatterers: 8643 At special positions: 0 Unit cell: (92.106, 117.81, 128.52, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 63 16.00 O 1575 8.00 N 1468 7.00 C 5537 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS R 106 " - pdb=" SG CYS R 183 " distance=2.03 Simple disulfide: pdb=" SG CYS D 22 " - pdb=" SG CYS D 96 " distance=2.03 Simple disulfide: pdb=" SG CYS D 147 " - pdb=" SG CYS D 217 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.41 Conformation dependent library (CDL) restraints added in 245.4 milliseconds 2258 Ramachandran restraints generated. 1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2150 Finding SS restraints... Secondary structure from input PDB file: 28 helices and 15 sheets defined 36.8% alpha, 18.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.23 Creating SS restraints... Processing helix chain 'L' and resid 44 through 48 Processing helix chain 'R' and resid 34 through 60 removed outlier: 3.591A pdb=" N VAL R 38 " --> pdb=" O VAL R 34 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N PHE R 60 " --> pdb=" O GLY R 56 " (cutoff:3.500A) Processing helix chain 'R' and resid 66 through 81 removed outlier: 4.232A pdb=" N ILE R 70 " --> pdb=" O ARG R 66 " (cutoff:3.500A) removed outlier: 4.040A pdb=" N PHE R 71 " --> pdb=" O LEU R 67 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N ILE R 81 " --> pdb=" O ALA R 77 " (cutoff:3.500A) Processing helix chain 'R' and resid 85 through 89 Processing helix chain 'R' and resid 104 through 136 removed outlier: 3.638A pdb=" N GLY R 108 " --> pdb=" O PHE R 104 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N VAL R 121 " --> pdb=" O MET R 117 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N LEU R 122 " --> pdb=" O HIS R 118 " (cutoff:3.500A) Processing helix chain 'R' and resid 140 through 145 removed outlier: 3.895A pdb=" N PHE R 144 " --> pdb=" O VAL R 140 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N ARG R 145 " --> pdb=" O SER R 141 " (cutoff:3.500A) No H-bonds generated for 'chain 'R' and resid 140 through 145' Processing helix chain 'R' and resid 146 through 165 Processing helix chain 'R' and resid 165 through 172 removed outlier: 3.533A pdb=" N LEU R 169 " --> pdb=" O GLY R 165 " (cutoff:3.500A) Processing helix chain 'R' and resid 189 through 204 Processing helix chain 'R' and resid 204 through 228 removed outlier: 4.026A pdb=" N GLN R 228 " --> pdb=" O ALA R 224 " (cutoff:3.500A) Processing helix chain 'R' and resid 232 through 235 Processing helix chain 'R' and resid 236 through 271 removed outlier: 3.628A pdb=" N ILE R 240 " --> pdb=" O LEU R 236 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N LEU R 255 " --> pdb=" O LEU R 251 " (cutoff:3.500A) Proline residue: R 256 - end of helix removed outlier: 3.741A pdb=" N GLN R 271 " --> pdb=" O SER R 267 " (cutoff:3.500A) Processing helix chain 'R' and resid 278 through 305 Proline residue: R 289 - end of helix removed outlier: 3.545A pdb=" N PHE R 292 " --> pdb=" O GLY R 288 " (cutoff:3.500A) Proline residue: R 299 - end of helix Processing helix chain 'R' and resid 308 through 318 removed outlier: 3.583A pdb=" N VAL R 314 " --> pdb=" O ARG R 310 " (cutoff:3.500A) Processing helix chain 'A' and resid 6 through 33 removed outlier: 3.556A pdb=" N ALA A 11 " --> pdb=" O ALA A 7 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N GLU A 14 " --> pdb=" O LYS A 10 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N LYS A 32 " --> pdb=" O GLU A 28 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N GLU A 33 " --> pdb=" O LYS A 29 " (cutoff:3.500A) Processing helix chain 'A' and resid 46 through 53 removed outlier: 4.529A pdb=" N VAL A 50 " --> pdb=" O LYS A 46 " (cutoff:3.500A) Processing helix chain 'A' and resid 207 through 216 removed outlier: 3.557A pdb=" N TRP A 211 " --> pdb=" O ARG A 208 " (cutoff:3.500A) removed outlier: 4.701A pdb=" N ILE A 212 " --> pdb=" O LYS A 209 " (cutoff:3.500A) removed outlier: 5.125A pdb=" N HIS A 213 " --> pdb=" O LYS A 210 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N CYS A 214 " --> pdb=" O TRP A 211 " (cutoff:3.500A) Processing helix chain 'A' and resid 241 through 255 removed outlier: 3.716A pdb=" N ASN A 255 " --> pdb=" O ASP A 251 " (cutoff:3.500A) Processing helix chain 'A' and resid 270 through 279 removed outlier: 4.247A pdb=" N LYS A 279 " --> pdb=" O GLU A 275 " (cutoff:3.500A) Processing helix chain 'A' and resid 282 through 286 removed outlier: 3.706A pdb=" N ILE A 285 " --> pdb=" O PRO A 282 " (cutoff:3.500A) Processing helix chain 'A' and resid 296 through 309 Processing helix chain 'A' and resid 327 through 352 removed outlier: 3.566A pdb=" N ASN A 331 " --> pdb=" O THR A 327 " (cutoff:3.500A) removed outlier: 4.431A pdb=" N PHE A 334 " --> pdb=" O LYS A 330 " (cutoff:3.500A) removed outlier: 4.118A pdb=" N VAL A 335 " --> pdb=" O ASN A 331 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N ILE A 344 " --> pdb=" O THR A 340 " (cutoff:3.500A) Processing helix chain 'B' and resid 4 through 24 Processing helix chain 'B' and resid 29 through 34 removed outlier: 3.585A pdb=" N ILE B 33 " --> pdb=" O THR B 29 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N THR B 34 " --> pdb=" O LEU B 30 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 29 through 34' Processing helix chain 'C' and resid 11 through 25 removed outlier: 3.715A pdb=" N ILE C 25 " --> pdb=" O MET C 21 " (cutoff:3.500A) Processing helix chain 'C' and resid 29 through 44 removed outlier: 4.059A pdb=" N ALA C 33 " --> pdb=" O LYS C 29 " (cutoff:3.500A) Processing helix chain 'D' and resid 53 through 56 removed outlier: 3.848A pdb=" N GLY D 56 " --> pdb=" O SER D 53 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 53 through 56' Processing helix chain 'D' and resid 62 through 65 removed outlier: 3.562A pdb=" N LYS D 65 " --> pdb=" O ASP D 62 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 62 through 65' Processing sheet with id=AA1, first strand: chain 'A' and resid 185 through 191 removed outlier: 3.677A pdb=" N PHE A 189 " --> pdb=" O PHE A 196 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N LEU A 194 " --> pdb=" O PHE A 191 " (cutoff:3.500A) removed outlier: 6.784A pdb=" N LYS A 35 " --> pdb=" O ALA A 220 " (cutoff:3.500A) removed outlier: 7.771A pdb=" N ILE A 222 " --> pdb=" O LYS A 35 " (cutoff:3.500A) removed outlier: 6.086A pdb=" N LEU A 37 " --> pdb=" O ILE A 222 " (cutoff:3.500A) removed outlier: 7.337A pdb=" N CYS A 224 " --> pdb=" O LEU A 37 " (cutoff:3.500A) removed outlier: 6.839A pdb=" N LEU A 39 " --> pdb=" O CYS A 224 " (cutoff:3.500A) removed outlier: 8.817A pdb=" N ALA A 226 " --> pdb=" O LEU A 39 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 47 through 51 removed outlier: 6.718A pdb=" N ILE B 338 " --> pdb=" O ARG B 48 " (cutoff:3.500A) removed outlier: 4.453A pdb=" N THR B 50 " --> pdb=" O LEU B 336 " (cutoff:3.500A) removed outlier: 6.546A pdb=" N LEU B 336 " --> pdb=" O THR B 50 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63 removed outlier: 3.955A pdb=" N ALA B 60 " --> pdb=" O ALA B 73 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N ILE B 80 " --> pdb=" O SER B 72 " (cutoff:3.500A) removed outlier: 4.130A pdb=" N SER B 74 " --> pdb=" O LYS B 78 " (cutoff:3.500A) removed outlier: 4.478A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N HIS B 91 " --> pdb=" O ILE B 81 " (cutoff:3.500A) removed outlier: 6.733A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 6.125A pdb=" N LYS B 89 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 103 through 105 removed outlier: 7.899A pdb=" N ILE B 123 " --> pdb=" O SER B 136 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N ARG B 134 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 146 through 151 removed outlier: 3.550A pdb=" N CYS B 148 " --> pdb=" O SER B 160 " (cutoff:3.500A) removed outlier: 4.238A pdb=" N THR B 165 " --> pdb=" O SER B 161 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N THR B 178 " --> pdb=" O LEU B 168 " (cutoff:3.500A) removed outlier: 7.120A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 6.707A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 187 through 192 removed outlier: 6.822A pdb=" N GLY B 202 " --> pdb=" O MET B 188 " (cutoff:3.500A) removed outlier: 4.676A pdb=" N LEU B 190 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 6.917A pdb=" N VAL B 200 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 5.354A pdb=" N LEU B 192 " --> pdb=" O LEU B 198 " (cutoff:3.500A) removed outlier: 7.578A pdb=" N LEU B 198 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 4.323A pdb=" N SER B 207 " --> pdb=" O ALA B 203 " (cutoff:3.500A) removed outlier: 6.686A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.405A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.402A pdb=" N GLY B 244 " --> pdb=" O ASN B 230 " (cutoff:3.500A) removed outlier: 4.244A pdb=" N ILE B 232 " --> pdb=" O ALA B 242 " (cutoff:3.500A) removed outlier: 6.716A pdb=" N ALA B 242 " --> pdb=" O ILE B 232 " (cutoff:3.500A) removed outlier: 4.905A pdb=" N PHE B 234 " --> pdb=" O ALA B 240 " (cutoff:3.500A) removed outlier: 7.053A pdb=" N ALA B 240 " --> pdb=" O PHE B 234 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N LEU B 252 " --> pdb=" O MET B 262 " (cutoff:3.500A) removed outlier: 4.667A pdb=" N MET B 262 " --> pdb=" O LEU B 252 " (cutoff:3.500A) removed outlier: 7.454A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 6.686A pdb=" N GLU B 260 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 273 through 276 removed outlier: 6.626A pdb=" N GLY B 288 " --> pdb=" O THR B 274 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N TYR B 289 " --> pdb=" O ASN B 293 " (cutoff:3.500A) removed outlier: 4.766A pdb=" N ASN B 293 " --> pdb=" O TYR B 289 " (cutoff:3.500A) removed outlier: 4.311A pdb=" N GLY B 306 " --> pdb=" O VAL B 296 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'D' and resid 3 through 4 removed outlier: 3.593A pdb=" N SER D 25 " --> pdb=" O GLN D 3 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 10 through 12 removed outlier: 5.471A pdb=" N GLY D 10 " --> pdb=" O THR D 118 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N LEU D 117 " --> pdb=" O ALA D 92 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 58 through 60 removed outlier: 4.452A pdb=" N PHE D 110 " --> pdb=" O ARG D 98 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 71 through 73 Processing sheet with id=AB4, first strand: chain 'D' and resid 128 through 130 removed outlier: 3.751A pdb=" N PHE D 200 " --> pdb=" O CYS D 147 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 134 through 136 removed outlier: 6.711A pdb=" N VAL D 135 " --> pdb=" O GLU D 234 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB5 Processing sheet with id=AB6, first strand: chain 'D' and resid 182 through 183 removed outlier: 5.592A pdb=" N LEU D 175 " --> pdb=" O LEU D 166 " (cutoff:3.500A) removed outlier: 6.110A pdb=" N LEU D 166 " --> pdb=" O LEU D 175 " (cutoff:3.500A) removed outlier: 4.100A pdb=" N ILE D 177 " --> pdb=" O TRP D 164 " (cutoff:3.500A) 387 hydrogen bonds defined for protein. 1086 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.31 Time building geometry restraints manager: 0.59 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.35: 2755 1.35 - 1.46: 2196 1.46 - 1.58: 3794 1.58 - 1.70: 0 1.70 - 1.82: 85 Bond restraints: 8830 Sorted by residual: bond pdb=" CG ARG D 148 " pdb=" CD ARG D 148 " ideal model delta sigma weight residual 1.520 1.553 -0.033 3.00e-02 1.11e+03 1.18e+00 bond pdb=" CB GLU D 89 " pdb=" CG GLU D 89 " ideal model delta sigma weight residual 1.520 1.548 -0.028 3.00e-02 1.11e+03 9.01e-01 bond pdb=" CG1 ILE R 265 " pdb=" CD1 ILE R 265 " ideal model delta sigma weight residual 1.513 1.476 0.037 3.90e-02 6.57e+02 8.92e-01 bond pdb=" CG GLU D 89 " pdb=" CD GLU D 89 " ideal model delta sigma weight residual 1.516 1.537 -0.021 2.50e-02 1.60e+03 7.08e-01 bond pdb=" CA GLY B 202 " pdb=" C GLY B 202 " ideal model delta sigma weight residual 1.520 1.514 0.006 7.30e-03 1.88e+04 7.02e-01 ... (remaining 8825 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.43: 11748 1.43 - 2.87: 195 2.87 - 4.30: 36 4.30 - 5.74: 18 5.74 - 7.17: 3 Bond angle restraints: 12000 Sorted by residual: angle pdb=" C ALA L 53 " pdb=" CA ALA L 53 " pdb=" CB ALA L 53 " ideal model delta sigma weight residual 110.42 115.74 -5.32 1.99e+00 2.53e-01 7.16e+00 angle pdb=" C ASP B 163 " pdb=" N THR B 164 " pdb=" CA THR B 164 " ideal model delta sigma weight residual 121.54 126.15 -4.61 1.91e+00 2.74e-01 5.82e+00 angle pdb=" CG ARG D 148 " pdb=" CD ARG D 148 " pdb=" NE ARG D 148 " ideal model delta sigma weight residual 112.00 117.17 -5.17 2.20e+00 2.07e-01 5.51e+00 angle pdb=" CB GLU D 89 " pdb=" CG GLU D 89 " pdb=" CD GLU D 89 " ideal model delta sigma weight residual 112.60 116.56 -3.96 1.70e+00 3.46e-01 5.43e+00 angle pdb=" C PHE A 191 " pdb=" CA PHE A 191 " pdb=" CB PHE A 191 " ideal model delta sigma weight residual 112.43 108.02 4.41 1.91e+00 2.74e-01 5.33e+00 ... (remaining 11995 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.24: 4703 17.24 - 34.48: 405 34.48 - 51.72: 79 51.72 - 68.96: 10 68.96 - 86.20: 7 Dihedral angle restraints: 5204 sinusoidal: 1877 harmonic: 3327 Sorted by residual: dihedral pdb=" CB CYS D 147 " pdb=" SG CYS D 147 " pdb=" SG CYS D 217 " pdb=" CB CYS D 217 " ideal model delta sinusoidal sigma weight residual 93.00 148.17 -55.17 1 1.00e+01 1.00e-02 4.12e+01 dihedral pdb=" CB CYS R 106 " pdb=" SG CYS R 106 " pdb=" SG CYS R 183 " pdb=" CB CYS R 183 " ideal model delta sinusoidal sigma weight residual -86.00 -121.18 35.18 1 1.00e+01 1.00e-02 1.75e+01 dihedral pdb=" CA ALA R 188 " pdb=" C ALA R 188 " pdb=" N THR R 189 " pdb=" CA THR R 189 " ideal model delta harmonic sigma weight residual 180.00 161.82 18.18 0 5.00e+00 4.00e-02 1.32e+01 ... (remaining 5201 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.025: 828 0.025 - 0.051: 355 0.051 - 0.076: 108 0.076 - 0.102: 69 0.102 - 0.127: 37 Chirality restraints: 1397 Sorted by residual: chirality pdb=" CA ILE B 81 " pdb=" N ILE B 81 " pdb=" C ILE B 81 " pdb=" CB ILE B 81 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.05e-01 chirality pdb=" CA ILE D 204 " pdb=" N ILE D 204 " pdb=" C ILE D 204 " pdb=" CB ILE D 204 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 3.91e-01 chirality pdb=" CA ILE B 37 " pdb=" N ILE B 37 " pdb=" C ILE B 37 " pdb=" CB ILE B 37 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.12 2.00e-01 2.50e+01 3.73e-01 ... (remaining 1394 not shown) Planarity restraints: 1505 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR D 138 " 0.049 5.00e-02 4.00e+02 7.45e-02 8.89e+00 pdb=" N PRO D 139 " -0.129 5.00e-02 4.00e+02 pdb=" CA PRO D 139 " 0.039 5.00e-02 4.00e+02 pdb=" CD PRO D 139 " 0.041 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY R 288 " -0.036 5.00e-02 4.00e+02 5.42e-02 4.70e+00 pdb=" N PRO R 289 " 0.094 5.00e-02 4.00e+02 pdb=" CA PRO R 289 " -0.028 5.00e-02 4.00e+02 pdb=" CD PRO R 289 " -0.030 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR R 189 " 0.029 5.00e-02 4.00e+02 4.47e-02 3.19e+00 pdb=" N PRO R 190 " -0.077 5.00e-02 4.00e+02 pdb=" CA PRO R 190 " 0.023 5.00e-02 4.00e+02 pdb=" CD PRO R 190 " 0.025 5.00e-02 4.00e+02 ... (remaining 1502 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.77: 1488 2.77 - 3.30: 8136 3.30 - 3.83: 14377 3.83 - 4.37: 15922 4.37 - 4.90: 28572 Nonbonded interactions: 68495 Sorted by model distance: nonbonded pdb=" OG SER D 17 " pdb=" OE1 GLN D 82 " model vdw 2.237 3.040 nonbonded pdb=" O ASP C 48 " pdb=" OG1 THR C 52 " model vdw 2.245 3.040 nonbonded pdb=" OG SER B 74 " pdb=" OD1 ASP B 76 " model vdw 2.255 3.040 nonbonded pdb=" N GLU B 172 " pdb=" OE1 GLU B 172 " model vdw 2.262 3.120 nonbonded pdb=" OG SER B 161 " pdb=" OD1 ASP B 163 " model vdw 2.279 3.040 ... (remaining 68490 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 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.090 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: 0.000 Extract box with map and model: 0.130 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 7.280 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.010 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:0.960 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 9.540 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6838 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 : 0.002 0.041 8833 Z= 0.096 Angle : 0.504 7.170 12006 Z= 0.267 Chirality : 0.039 0.127 1397 Planarity : 0.004 0.075 1505 Dihedral : 13.578 86.202 3045 Min Nonbonded Distance : 2.237 Molprobity Statistics. All-atom Clashscore : 7.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.16 % Favored : 95.84 % Rotamer: Outliers : 0.11 % Allowed : 0.22 % Favored : 99.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.42 (0.26), residues: 1129 helix: 1.57 (0.28), residues: 382 sheet: 0.97 (0.36), residues: 242 loop : -1.12 (0.27), residues: 505 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG D 148 TYR 0.013 0.001 TYR B 124 PHE 0.017 0.001 PHE A 191 TRP 0.005 0.001 TRP B 63 HIS 0.006 0.001 HIS B 62 Details of bonding type rmsd covalent geometry : bond 0.00205 ( 8830) covalent geometry : angle 0.50415 (12000) SS BOND : bond 0.00059 ( 3) SS BOND : angle 0.93209 ( 6) hydrogen bonds : bond 0.19207 ( 387) hydrogen bonds : angle 6.48349 ( 1086) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2258 Ramachandran restraints generated. 1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2258 Ramachandran restraints generated. 1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 989 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 144 time to evaluate : 0.300 Fit side-chains REVERT: C 48 ASP cc_start: 0.6579 (t0) cc_final: 0.6353 (t0) outliers start: 1 outliers final: 0 residues processed: 145 average time/residue: 0.0780 time to fit residues: 15.7149 Evaluate side-chains 116 residues out of total 989 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 116 time to evaluate : 0.216 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 108 optimal weight: 6.9990 chunk 49 optimal weight: 1.9990 chunk 97 optimal weight: 1.9990 chunk 53 optimal weight: 0.0170 chunk 5 optimal weight: 1.9990 chunk 33 optimal weight: 3.9990 chunk 65 optimal weight: 4.9990 chunk 62 optimal weight: 0.9990 chunk 51 optimal weight: 7.9990 chunk 100 optimal weight: 5.9990 chunk 106 optimal weight: 0.9990 overall best weight: 1.2026 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 56 GLN R 281 GLN B 88 ASN B 91 HIS D 39 GLN D 167 GLN D 220 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3963 r_free = 0.3963 target = 0.106650 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3681 r_free = 0.3681 target = 0.089590 restraints weight = 21581.311| |-----------------------------------------------------------------------------| r_work (start): 0.3671 rms_B_bonded: 2.71 r_work: 0.3495 rms_B_bonded: 3.40 restraints_weight: 0.5000 r_work (final): 0.3495 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7493 moved from start: 0.2054 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 8833 Z= 0.172 Angle : 0.588 8.175 12006 Z= 0.305 Chirality : 0.043 0.151 1397 Planarity : 0.004 0.059 1505 Dihedral : 3.715 16.952 1228 Min Nonbonded Distance : 2.579 Molprobity Statistics. All-atom Clashscore : 8.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.52 % Favored : 95.48 % Rotamer: Outliers : 1.34 % Allowed : 8.39 % Favored : 90.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.33 (0.26), residues: 1129 helix: 1.42 (0.27), residues: 386 sheet: 0.66 (0.34), residues: 261 loop : -1.02 (0.28), residues: 482 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 49 TYR 0.018 0.002 TYR A 320 PHE 0.019 0.002 PHE B 292 TRP 0.019 0.001 TRP B 211 HIS 0.007 0.002 HIS B 183 Details of bonding type rmsd covalent geometry : bond 0.00400 ( 8830) covalent geometry : angle 0.58763 (12000) SS BOND : bond 0.00306 ( 3) SS BOND : angle 1.36062 ( 6) hydrogen bonds : bond 0.03946 ( 387) hydrogen bonds : angle 4.38573 ( 1086) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2258 Ramachandran restraints generated. 1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2258 Ramachandran restraints generated. 1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 989 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 128 time to evaluate : 0.323 Fit side-chains REVERT: R 89 TRP cc_start: 0.6542 (t-100) cc_final: 0.6246 (t-100) REVERT: R 113 ILE cc_start: 0.8391 (OUTLIER) cc_final: 0.7882 (mp) REVERT: R 187 LYS cc_start: 0.4900 (ptmm) cc_final: 0.4548 (ptmt) REVERT: C 48 ASP cc_start: 0.7230 (t0) cc_final: 0.6848 (t0) outliers start: 12 outliers final: 7 residues processed: 136 average time/residue: 0.0764 time to fit residues: 14.3859 Evaluate side-chains 128 residues out of total 989 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 120 time to evaluate : 0.244 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 38 VAL Chi-restraints excluded: chain R residue 113 ILE Chi-restraints excluded: chain R residue 128 SER Chi-restraints excluded: chain R residue 213 THR Chi-restraints excluded: chain R residue 217 CYS Chi-restraints excluded: chain A residue 224 CYS Chi-restraints excluded: chain B residue 181 THR Chi-restraints excluded: chain B residue 187 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 102 optimal weight: 0.0070 chunk 107 optimal weight: 2.9990 chunk 59 optimal weight: 2.9990 chunk 92 optimal weight: 3.9990 chunk 61 optimal weight: 2.9990 chunk 79 optimal weight: 0.8980 chunk 95 optimal weight: 4.9990 chunk 73 optimal weight: 3.9990 chunk 53 optimal weight: 0.0980 chunk 27 optimal weight: 1.9990 chunk 26 optimal weight: 5.9990 overall best weight: 1.2002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 56 GLN B 125 ASN B 142 HIS B 293 ASN D 182 ASN D 220 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3917 r_free = 0.3917 target = 0.104424 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3631 r_free = 0.3631 target = 0.087245 restraints weight = 21316.122| |-----------------------------------------------------------------------------| r_work (start): 0.3621 rms_B_bonded: 2.69 r_work: 0.3436 rms_B_bonded: 3.40 restraints_weight: 0.5000 r_work (final): 0.3436 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7556 moved from start: 0.2684 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 8833 Z= 0.162 Angle : 0.569 9.055 12006 Z= 0.292 Chirality : 0.042 0.162 1397 Planarity : 0.004 0.061 1505 Dihedral : 3.832 16.265 1228 Min Nonbonded Distance : 2.584 Molprobity Statistics. All-atom Clashscore : 8.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.05 % Favored : 94.95 % Rotamer: Outliers : 2.68 % Allowed : 12.30 % Favored : 85.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.24 (0.26), residues: 1129 helix: 1.51 (0.28), residues: 378 sheet: 0.51 (0.34), residues: 245 loop : -1.08 (0.27), residues: 506 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG D 148 TYR 0.013 0.002 TYR A 320 PHE 0.016 0.002 PHE B 292 TRP 0.011 0.001 TRP B 211 HIS 0.006 0.002 HIS R 225 Details of bonding type rmsd covalent geometry : bond 0.00380 ( 8830) covalent geometry : angle 0.56854 (12000) SS BOND : bond 0.00125 ( 3) SS BOND : angle 1.05087 ( 6) hydrogen bonds : bond 0.03760 ( 387) hydrogen bonds : angle 4.19935 ( 1086) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2258 Ramachandran restraints generated. 1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2258 Ramachandran restraints generated. 1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 989 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 126 time to evaluate : 0.343 Fit side-chains REVERT: R 113 ILE cc_start: 0.8308 (OUTLIER) cc_final: 0.7704 (mp) REVERT: B 222 PHE cc_start: 0.8464 (m-80) cc_final: 0.8227 (m-80) REVERT: B 325 MET cc_start: 0.8054 (OUTLIER) cc_final: 0.7820 (ttp) REVERT: C 48 ASP cc_start: 0.7383 (t0) cc_final: 0.6941 (t0) outliers start: 24 outliers final: 14 residues processed: 139 average time/residue: 0.0865 time to fit residues: 16.6097 Evaluate side-chains 137 residues out of total 989 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 121 time to evaluate : 0.313 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 38 VAL Chi-restraints excluded: chain R residue 55 MET Chi-restraints excluded: chain R residue 113 ILE Chi-restraints excluded: chain R residue 128 SER Chi-restraints excluded: chain R residue 213 THR Chi-restraints excluded: chain R residue 217 CYS Chi-restraints excluded: chain R residue 252 VAL Chi-restraints excluded: chain A residue 213 HIS Chi-restraints excluded: chain A residue 224 CYS Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain B residue 159 THR Chi-restraints excluded: chain B residue 181 THR Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 325 MET Chi-restraints excluded: chain D residue 2 VAL Chi-restraints excluded: chain D residue 218 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 23 optimal weight: 2.9990 chunk 10 optimal weight: 0.8980 chunk 81 optimal weight: 3.9990 chunk 7 optimal weight: 8.9990 chunk 16 optimal weight: 0.9980 chunk 76 optimal weight: 0.9980 chunk 18 optimal weight: 0.1980 chunk 37 optimal weight: 1.9990 chunk 29 optimal weight: 5.9990 chunk 69 optimal weight: 0.8980 chunk 98 optimal weight: 3.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 220 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3922 r_free = 0.3922 target = 0.104851 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3640 r_free = 0.3640 target = 0.087816 restraints weight = 21653.310| |-----------------------------------------------------------------------------| r_work (start): 0.3628 rms_B_bonded: 2.68 r_work: 0.3448 rms_B_bonded: 3.32 restraints_weight: 0.5000 r_work (final): 0.3448 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7537 moved from start: 0.2847 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 8833 Z= 0.127 Angle : 0.546 12.060 12006 Z= 0.277 Chirality : 0.041 0.142 1397 Planarity : 0.004 0.061 1505 Dihedral : 3.724 17.274 1228 Min Nonbonded Distance : 2.596 Molprobity Statistics. All-atom Clashscore : 7.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.43 % Favored : 95.57 % Rotamer: Outliers : 2.46 % Allowed : 15.10 % Favored : 82.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.26 (0.26), residues: 1129 helix: 1.44 (0.28), residues: 385 sheet: 0.45 (0.34), residues: 245 loop : -0.97 (0.28), residues: 499 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG D 148 TYR 0.015 0.001 TYR A 296 PHE 0.013 0.001 PHE B 292 TRP 0.013 0.001 TRP B 211 HIS 0.005 0.001 HIS R 225 Details of bonding type rmsd covalent geometry : bond 0.00298 ( 8830) covalent geometry : angle 0.54567 (12000) SS BOND : bond 0.00160 ( 3) SS BOND : angle 0.99885 ( 6) hydrogen bonds : bond 0.03292 ( 387) hydrogen bonds : angle 4.07470 ( 1086) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2258 Ramachandran restraints generated. 1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2258 Ramachandran restraints generated. 1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 989 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 124 time to evaluate : 0.283 Fit side-chains REVERT: R 113 ILE cc_start: 0.8301 (OUTLIER) cc_final: 0.7783 (mp) REVERT: R 316 CYS cc_start: 0.5536 (t) cc_final: 0.5146 (p) REVERT: B 325 MET cc_start: 0.8026 (OUTLIER) cc_final: 0.7765 (ttp) REVERT: C 48 ASP cc_start: 0.7360 (t0) cc_final: 0.6933 (t0) outliers start: 22 outliers final: 11 residues processed: 137 average time/residue: 0.0897 time to fit residues: 16.9764 Evaluate side-chains 129 residues out of total 989 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 116 time to evaluate : 0.338 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 38 VAL Chi-restraints excluded: chain R residue 55 MET Chi-restraints excluded: chain R residue 113 ILE Chi-restraints excluded: chain R residue 213 THR Chi-restraints excluded: chain R residue 217 CYS Chi-restraints excluded: chain R residue 252 VAL Chi-restraints excluded: chain A residue 213 HIS Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 181 THR Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 325 MET Chi-restraints excluded: chain D residue 2 VAL Chi-restraints excluded: chain D residue 218 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 107 optimal weight: 2.9990 chunk 24 optimal weight: 0.9980 chunk 90 optimal weight: 7.9990 chunk 38 optimal weight: 3.9990 chunk 81 optimal weight: 6.9990 chunk 60 optimal weight: 1.9990 chunk 108 optimal weight: 5.9990 chunk 53 optimal weight: 3.9990 chunk 78 optimal weight: 0.9990 chunk 83 optimal weight: 7.9990 chunk 4 optimal weight: 0.9980 overall best weight: 1.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 56 GLN ** B 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 220 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3873 r_free = 0.3873 target = 0.102241 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3577 r_free = 0.3577 target = 0.084854 restraints weight = 21619.799| |-----------------------------------------------------------------------------| r_work (start): 0.3566 rms_B_bonded: 2.80 r_work: 0.3380 rms_B_bonded: 3.35 restraints_weight: 0.5000 r_work (final): 0.3380 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7620 moved from start: 0.3420 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 8833 Z= 0.204 Angle : 0.621 12.028 12006 Z= 0.317 Chirality : 0.043 0.180 1397 Planarity : 0.005 0.063 1505 Dihedral : 4.144 18.164 1228 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 9.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.85 % Favored : 94.15 % Rotamer: Outliers : 4.03 % Allowed : 16.11 % Favored : 79.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.06 (0.26), residues: 1129 helix: 1.19 (0.28), residues: 380 sheet: 0.33 (0.35), residues: 233 loop : -0.96 (0.27), residues: 516 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG D 148 TYR 0.016 0.002 TYR R 132 PHE 0.023 0.002 PHE B 292 TRP 0.009 0.001 TRP D 47 HIS 0.007 0.002 HIS R 225 Details of bonding type rmsd covalent geometry : bond 0.00486 ( 8830) covalent geometry : angle 0.62091 (12000) SS BOND : bond 0.00282 ( 3) SS BOND : angle 1.13009 ( 6) hydrogen bonds : bond 0.03985 ( 387) hydrogen bonds : angle 4.24105 ( 1086) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2258 Ramachandran restraints generated. 1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2258 Ramachandran restraints generated. 1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 989 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 116 time to evaluate : 0.346 Fit side-chains REVERT: R 113 ILE cc_start: 0.8248 (OUTLIER) cc_final: 0.7687 (mp) REVERT: R 272 GLU cc_start: 0.5092 (OUTLIER) cc_final: 0.4858 (tt0) REVERT: B 262 MET cc_start: 0.7315 (pmm) cc_final: 0.6970 (ptp) REVERT: B 266 HIS cc_start: 0.7980 (t-170) cc_final: 0.7702 (t-170) REVERT: B 325 MET cc_start: 0.8170 (OUTLIER) cc_final: 0.7968 (ttp) REVERT: C 48 ASP cc_start: 0.7429 (t0) cc_final: 0.7097 (t0) REVERT: D 19 LYS cc_start: 0.8303 (tptm) cc_final: 0.8073 (mmmm) outliers start: 36 outliers final: 20 residues processed: 141 average time/residue: 0.0745 time to fit residues: 14.8337 Evaluate side-chains 136 residues out of total 989 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 113 time to evaluate : 0.336 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 38 VAL Chi-restraints excluded: chain R residue 55 MET Chi-restraints excluded: chain R residue 113 ILE Chi-restraints excluded: chain R residue 128 SER Chi-restraints excluded: chain R residue 139 VAL Chi-restraints excluded: chain R residue 213 THR Chi-restraints excluded: chain R residue 217 CYS Chi-restraints excluded: chain R residue 222 LEU Chi-restraints excluded: chain R residue 252 VAL Chi-restraints excluded: chain R residue 272 GLU Chi-restraints excluded: chain R residue 296 CYS Chi-restraints excluded: chain A residue 213 HIS Chi-restraints excluded: chain A residue 214 CYS Chi-restraints excluded: chain A residue 224 CYS Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 159 THR Chi-restraints excluded: chain B residue 181 THR Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 209 LYS Chi-restraints excluded: chain B residue 325 MET Chi-restraints excluded: chain D residue 2 VAL Chi-restraints excluded: chain D residue 5 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 98 optimal weight: 0.6980 chunk 105 optimal weight: 2.9990 chunk 94 optimal weight: 2.9990 chunk 78 optimal weight: 0.9990 chunk 36 optimal weight: 0.7980 chunk 111 optimal weight: 1.9990 chunk 32 optimal weight: 0.9980 chunk 56 optimal weight: 0.0470 chunk 43 optimal weight: 1.9990 chunk 47 optimal weight: 1.9990 chunk 29 optimal weight: 4.9990 overall best weight: 0.7080 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 56 GLN D 220 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3905 r_free = 0.3905 target = 0.104062 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3618 r_free = 0.3618 target = 0.086937 restraints weight = 21521.254| |-----------------------------------------------------------------------------| r_work (start): 0.3608 rms_B_bonded: 2.70 r_work: 0.3427 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work (final): 0.3427 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7567 moved from start: 0.3365 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 8833 Z= 0.125 Angle : 0.565 11.460 12006 Z= 0.285 Chirality : 0.041 0.138 1397 Planarity : 0.004 0.062 1505 Dihedral : 3.853 18.278 1228 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 7.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.69 % Favored : 95.31 % Rotamer: Outliers : 3.36 % Allowed : 17.67 % Favored : 78.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.10 (0.26), residues: 1129 helix: 1.27 (0.28), residues: 384 sheet: 0.30 (0.34), residues: 237 loop : -0.98 (0.28), residues: 508 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG D 148 TYR 0.010 0.001 TYR D 178 PHE 0.014 0.001 PHE R 204 TRP 0.014 0.001 TRP B 211 HIS 0.004 0.001 HIS R 225 Details of bonding type rmsd covalent geometry : bond 0.00294 ( 8830) covalent geometry : angle 0.56471 (12000) SS BOND : bond 0.00167 ( 3) SS BOND : angle 0.94095 ( 6) hydrogen bonds : bond 0.03277 ( 387) hydrogen bonds : angle 4.05267 ( 1086) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2258 Ramachandran restraints generated. 1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2258 Ramachandran restraints generated. 1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 989 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 119 time to evaluate : 0.322 Fit side-chains REVERT: R 113 ILE cc_start: 0.8223 (OUTLIER) cc_final: 0.7711 (mp) REVERT: B 209 LYS cc_start: 0.7961 (OUTLIER) cc_final: 0.7577 (mtmm) REVERT: B 262 MET cc_start: 0.7266 (pmm) cc_final: 0.6858 (ptp) REVERT: B 266 HIS cc_start: 0.7985 (t-170) cc_final: 0.7700 (t-170) REVERT: C 48 ASP cc_start: 0.7455 (t0) cc_final: 0.7136 (t0) outliers start: 30 outliers final: 20 residues processed: 137 average time/residue: 0.1013 time to fit residues: 19.0467 Evaluate side-chains 130 residues out of total 989 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 108 time to evaluate : 0.337 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 55 MET Chi-restraints excluded: chain R residue 113 ILE Chi-restraints excluded: chain R residue 128 SER Chi-restraints excluded: chain R residue 139 VAL Chi-restraints excluded: chain R residue 213 THR Chi-restraints excluded: chain R residue 217 CYS Chi-restraints excluded: chain R residue 252 VAL Chi-restraints excluded: chain R residue 282 LEU Chi-restraints excluded: chain R residue 296 CYS Chi-restraints excluded: chain A residue 213 HIS Chi-restraints excluded: chain A residue 214 CYS Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 93 ILE Chi-restraints excluded: chain B residue 138 GLU Chi-restraints excluded: chain B residue 159 THR Chi-restraints excluded: chain B residue 181 THR Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 209 LYS Chi-restraints excluded: chain D residue 2 VAL Chi-restraints excluded: chain D residue 11 LEU Chi-restraints excluded: chain D residue 218 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 40 optimal weight: 0.6980 chunk 59 optimal weight: 0.9990 chunk 111 optimal weight: 0.0970 chunk 99 optimal weight: 0.1980 chunk 21 optimal weight: 0.7980 chunk 26 optimal weight: 9.9990 chunk 38 optimal weight: 2.9990 chunk 77 optimal weight: 1.9990 chunk 17 optimal weight: 2.9990 chunk 43 optimal weight: 0.9990 chunk 3 optimal weight: 0.8980 overall best weight: 0.5378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 56 GLN D 220 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3917 r_free = 0.3917 target = 0.104869 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3636 r_free = 0.3636 target = 0.087843 restraints weight = 21571.271| |-----------------------------------------------------------------------------| r_work (start): 0.3622 rms_B_bonded: 2.68 r_work: 0.3440 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work (final): 0.3440 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7551 moved from start: 0.3347 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 8833 Z= 0.114 Angle : 0.562 11.222 12006 Z= 0.282 Chirality : 0.040 0.134 1397 Planarity : 0.004 0.062 1505 Dihedral : 3.737 18.172 1228 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 7.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.14 % Favored : 94.86 % Rotamer: Outliers : 3.58 % Allowed : 18.23 % Favored : 78.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.18 (0.26), residues: 1129 helix: 1.41 (0.28), residues: 381 sheet: 0.33 (0.34), residues: 237 loop : -0.98 (0.28), residues: 511 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 148 TYR 0.011 0.001 TYR D 178 PHE 0.020 0.001 PHE R 39 TRP 0.014 0.001 TRP B 211 HIS 0.003 0.001 HIS R 225 Details of bonding type rmsd covalent geometry : bond 0.00264 ( 8830) covalent geometry : angle 0.56168 (12000) SS BOND : bond 0.00179 ( 3) SS BOND : angle 0.93090 ( 6) hydrogen bonds : bond 0.03078 ( 387) hydrogen bonds : angle 3.96335 ( 1086) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2258 Ramachandran restraints generated. 1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2258 Ramachandran restraints generated. 1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 989 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 116 time to evaluate : 0.344 Fit side-chains REVERT: R 113 ILE cc_start: 0.8148 (OUTLIER) cc_final: 0.7581 (mp) REVERT: B 262 MET cc_start: 0.7211 (pmm) cc_final: 0.6810 (ptp) REVERT: B 266 HIS cc_start: 0.7941 (t-170) cc_final: 0.7664 (t-170) REVERT: C 48 ASP cc_start: 0.7428 (t0) cc_final: 0.7152 (t0) outliers start: 32 outliers final: 24 residues processed: 134 average time/residue: 0.0950 time to fit residues: 17.6035 Evaluate side-chains 137 residues out of total 989 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 112 time to evaluate : 0.441 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 55 MET Chi-restraints excluded: chain R residue 113 ILE Chi-restraints excluded: chain R residue 119 CYS Chi-restraints excluded: chain R residue 127 MET Chi-restraints excluded: chain R residue 128 SER Chi-restraints excluded: chain R residue 139 VAL Chi-restraints excluded: chain R residue 156 SER Chi-restraints excluded: chain R residue 213 THR Chi-restraints excluded: chain R residue 217 CYS Chi-restraints excluded: chain R residue 252 VAL Chi-restraints excluded: chain R residue 282 LEU Chi-restraints excluded: chain R residue 296 CYS Chi-restraints excluded: chain A residue 213 HIS Chi-restraints excluded: chain A residue 214 CYS Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 93 ILE Chi-restraints excluded: chain B residue 138 GLU Chi-restraints excluded: chain B residue 159 THR Chi-restraints excluded: chain B residue 181 THR Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain C residue 51 LEU Chi-restraints excluded: chain D residue 2 VAL Chi-restraints excluded: chain D residue 5 VAL Chi-restraints excluded: chain D residue 218 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 75 optimal weight: 5.9990 chunk 42 optimal weight: 0.7980 chunk 23 optimal weight: 2.9990 chunk 14 optimal weight: 3.9990 chunk 103 optimal weight: 7.9990 chunk 28 optimal weight: 0.5980 chunk 44 optimal weight: 10.0000 chunk 71 optimal weight: 1.9990 chunk 3 optimal weight: 2.9990 chunk 6 optimal weight: 0.8980 chunk 4 optimal weight: 1.9990 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 56 GLN D 220 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3883 r_free = 0.3883 target = 0.102799 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3596 r_free = 0.3596 target = 0.085675 restraints weight = 21465.311| |-----------------------------------------------------------------------------| r_work (start): 0.3583 rms_B_bonded: 2.75 r_work: 0.3400 rms_B_bonded: 3.31 restraints_weight: 0.5000 r_work (final): 0.3400 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7597 moved from start: 0.3597 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.067 8833 Z= 0.171 Angle : 0.612 12.357 12006 Z= 0.312 Chirality : 0.043 0.163 1397 Planarity : 0.004 0.063 1505 Dihedral : 3.941 18.732 1228 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 9.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.11 % Favored : 93.89 % Rotamer: Outliers : 3.69 % Allowed : 18.46 % Favored : 77.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.03 (0.26), residues: 1129 helix: 1.29 (0.28), residues: 376 sheet: 0.20 (0.34), residues: 237 loop : -1.00 (0.27), residues: 516 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 148 TYR 0.013 0.002 TYR B 59 PHE 0.017 0.002 PHE B 292 TRP 0.012 0.001 TRP D 47 HIS 0.007 0.001 HIS B 183 Details of bonding type rmsd covalent geometry : bond 0.00413 ( 8830) covalent geometry : angle 0.61149 (12000) SS BOND : bond 0.00244 ( 3) SS BOND : angle 0.93389 ( 6) hydrogen bonds : bond 0.03588 ( 387) hydrogen bonds : angle 4.07899 ( 1086) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2258 Ramachandran restraints generated. 1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2258 Ramachandran restraints generated. 1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 989 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 111 time to evaluate : 0.352 Fit side-chains REVERT: R 113 ILE cc_start: 0.8261 (OUTLIER) cc_final: 0.7714 (mp) REVERT: B 262 MET cc_start: 0.7305 (pmm) cc_final: 0.6997 (ptp) REVERT: B 266 HIS cc_start: 0.8026 (t-170) cc_final: 0.7764 (t-170) REVERT: C 48 ASP cc_start: 0.7421 (t0) cc_final: 0.7104 (t0) outliers start: 33 outliers final: 27 residues processed: 129 average time/residue: 0.0943 time to fit residues: 16.9220 Evaluate side-chains 137 residues out of total 989 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 109 time to evaluate : 0.337 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 57 VAL Chi-restraints excluded: chain R residue 55 MET Chi-restraints excluded: chain R residue 113 ILE Chi-restraints excluded: chain R residue 119 CYS Chi-restraints excluded: chain R residue 127 MET Chi-restraints excluded: chain R residue 128 SER Chi-restraints excluded: chain R residue 139 VAL Chi-restraints excluded: chain R residue 156 SER Chi-restraints excluded: chain R residue 213 THR Chi-restraints excluded: chain R residue 217 CYS Chi-restraints excluded: chain R residue 252 VAL Chi-restraints excluded: chain R residue 279 ILE Chi-restraints excluded: chain R residue 282 LEU Chi-restraints excluded: chain R residue 296 CYS Chi-restraints excluded: chain A residue 213 HIS Chi-restraints excluded: chain A residue 214 CYS Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 93 ILE Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 159 THR Chi-restraints excluded: chain B residue 181 THR Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain C residue 51 LEU Chi-restraints excluded: chain D residue 2 VAL Chi-restraints excluded: chain D residue 5 VAL Chi-restraints excluded: chain D residue 218 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 49 optimal weight: 1.9990 chunk 72 optimal weight: 0.0670 chunk 69 optimal weight: 3.9990 chunk 80 optimal weight: 0.9980 chunk 53 optimal weight: 8.9990 chunk 61 optimal weight: 1.9990 chunk 45 optimal weight: 0.9980 chunk 68 optimal weight: 0.5980 chunk 74 optimal weight: 0.5980 chunk 37 optimal weight: 2.9990 chunk 67 optimal weight: 0.7980 overall best weight: 0.6118 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 56 GLN D 220 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3907 r_free = 0.3907 target = 0.104106 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3624 r_free = 0.3624 target = 0.087000 restraints weight = 21277.585| |-----------------------------------------------------------------------------| r_work (start): 0.3612 rms_B_bonded: 2.68 r_work: 0.3426 rms_B_bonded: 3.43 restraints_weight: 0.5000 r_work (final): 0.3426 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7568 moved from start: 0.3526 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.070 8833 Z= 0.123 Angle : 0.600 12.288 12006 Z= 0.305 Chirality : 0.042 0.211 1397 Planarity : 0.004 0.062 1505 Dihedral : 3.797 19.078 1228 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 8.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.14 % Favored : 94.86 % Rotamer: Outliers : 3.24 % Allowed : 19.35 % Favored : 77.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.11 (0.26), residues: 1129 helix: 1.32 (0.28), residues: 384 sheet: 0.30 (0.34), residues: 242 loop : -1.02 (0.28), residues: 503 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 148 TYR 0.010 0.001 TYR D 178 PHE 0.015 0.001 PHE R 204 TRP 0.014 0.001 TRP B 211 HIS 0.005 0.001 HIS B 183 Details of bonding type rmsd covalent geometry : bond 0.00290 ( 8830) covalent geometry : angle 0.59986 (12000) SS BOND : bond 0.00191 ( 3) SS BOND : angle 0.91396 ( 6) hydrogen bonds : bond 0.03183 ( 387) hydrogen bonds : angle 4.05276 ( 1086) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2258 Ramachandran restraints generated. 1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2258 Ramachandran restraints generated. 1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 989 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 113 time to evaluate : 0.354 Fit side-chains REVERT: R 113 ILE cc_start: 0.8160 (OUTLIER) cc_final: 0.7635 (mp) REVERT: B 262 MET cc_start: 0.7245 (pmm) cc_final: 0.6899 (ptp) REVERT: B 266 HIS cc_start: 0.8003 (t-170) cc_final: 0.7748 (t-170) REVERT: C 48 ASP cc_start: 0.7439 (t0) cc_final: 0.7185 (t0) outliers start: 29 outliers final: 25 residues processed: 129 average time/residue: 0.0962 time to fit residues: 17.2587 Evaluate side-chains 133 residues out of total 989 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 107 time to evaluate : 0.345 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 57 VAL Chi-restraints excluded: chain R residue 55 MET Chi-restraints excluded: chain R residue 113 ILE Chi-restraints excluded: chain R residue 119 CYS Chi-restraints excluded: chain R residue 127 MET Chi-restraints excluded: chain R residue 139 VAL Chi-restraints excluded: chain R residue 156 SER Chi-restraints excluded: chain R residue 213 THR Chi-restraints excluded: chain R residue 217 CYS Chi-restraints excluded: chain R residue 252 VAL Chi-restraints excluded: chain R residue 296 CYS Chi-restraints excluded: chain A residue 213 HIS Chi-restraints excluded: chain A residue 214 CYS Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 93 ILE Chi-restraints excluded: chain B residue 138 GLU Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 159 THR Chi-restraints excluded: chain B residue 181 THR Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain C residue 51 LEU Chi-restraints excluded: chain D residue 2 VAL Chi-restraints excluded: chain D residue 5 VAL Chi-restraints excluded: chain D residue 11 LEU Chi-restraints excluded: chain D residue 218 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 81 optimal weight: 5.9990 chunk 12 optimal weight: 3.9990 chunk 17 optimal weight: 0.8980 chunk 47 optimal weight: 4.9990 chunk 94 optimal weight: 0.7980 chunk 24 optimal weight: 0.3980 chunk 106 optimal weight: 1.9990 chunk 83 optimal weight: 1.9990 chunk 77 optimal weight: 7.9990 chunk 59 optimal weight: 2.9990 chunk 67 optimal weight: 4.9990 overall best weight: 1.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 220 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3880 r_free = 0.3880 target = 0.102705 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3593 r_free = 0.3593 target = 0.085699 restraints weight = 21562.927| |-----------------------------------------------------------------------------| r_work (start): 0.3581 rms_B_bonded: 2.60 r_work: 0.3401 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work (final): 0.3401 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7595 moved from start: 0.3718 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 8833 Z= 0.172 Angle : 0.634 13.012 12006 Z= 0.326 Chirality : 0.043 0.220 1397 Planarity : 0.004 0.062 1505 Dihedral : 3.969 19.231 1228 Min Nonbonded Distance : 2.377 Molprobity Statistics. All-atom Clashscore : 8.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.02 % Favored : 93.98 % Rotamer: Outliers : 3.24 % Allowed : 19.13 % Favored : 77.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.00 (0.26), residues: 1129 helix: 1.25 (0.28), residues: 378 sheet: 0.14 (0.33), residues: 248 loop : -1.03 (0.27), residues: 503 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG D 148 TYR 0.017 0.002 TYR A 287 PHE 0.017 0.002 PHE R 39 TRP 0.012 0.001 TRP D 47 HIS 0.006 0.001 HIS R 225 Details of bonding type rmsd covalent geometry : bond 0.00414 ( 8830) covalent geometry : angle 0.63355 (12000) SS BOND : bond 0.00256 ( 3) SS BOND : angle 0.95827 ( 6) hydrogen bonds : bond 0.03590 ( 387) hydrogen bonds : angle 4.17869 ( 1086) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2258 Ramachandran restraints generated. 1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2258 Ramachandran restraints generated. 1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 989 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 108 time to evaluate : 0.358 Fit side-chains REVERT: R 113 ILE cc_start: 0.8160 (OUTLIER) cc_final: 0.7630 (mp) REVERT: A 18 MET cc_start: 0.7790 (mmt) cc_final: 0.7415 (mmt) REVERT: B 262 MET cc_start: 0.7304 (pmm) cc_final: 0.7031 (ptp) REVERT: B 266 HIS cc_start: 0.8013 (t-170) cc_final: 0.7771 (t-170) REVERT: C 48 ASP cc_start: 0.7448 (t0) cc_final: 0.7169 (t0) outliers start: 29 outliers final: 27 residues processed: 126 average time/residue: 0.0993 time to fit residues: 17.3164 Evaluate side-chains 134 residues out of total 989 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 106 time to evaluate : 0.274 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 57 VAL Chi-restraints excluded: chain R residue 55 MET Chi-restraints excluded: chain R residue 113 ILE Chi-restraints excluded: chain R residue 119 CYS Chi-restraints excluded: chain R residue 127 MET Chi-restraints excluded: chain R residue 139 VAL Chi-restraints excluded: chain R residue 156 SER Chi-restraints excluded: chain R residue 213 THR Chi-restraints excluded: chain R residue 217 CYS Chi-restraints excluded: chain R residue 252 VAL Chi-restraints excluded: chain R residue 279 ILE Chi-restraints excluded: chain R residue 296 CYS Chi-restraints excluded: chain A residue 213 HIS Chi-restraints excluded: chain A residue 214 CYS Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 93 ILE Chi-restraints excluded: chain B residue 138 GLU Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 159 THR Chi-restraints excluded: chain B residue 181 THR Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain C residue 51 LEU Chi-restraints excluded: chain D residue 2 VAL Chi-restraints excluded: chain D residue 5 VAL Chi-restraints excluded: chain D residue 11 LEU Chi-restraints excluded: chain D residue 218 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 58 optimal weight: 0.9990 chunk 24 optimal weight: 0.9980 chunk 50 optimal weight: 0.5980 chunk 94 optimal weight: 0.7980 chunk 6 optimal weight: 0.5980 chunk 88 optimal weight: 0.0370 chunk 8 optimal weight: 3.9990 chunk 31 optimal weight: 1.9990 chunk 87 optimal weight: 4.9990 chunk 38 optimal weight: 2.9990 chunk 28 optimal weight: 0.5980 overall best weight: 0.5258 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 56 GLN D 220 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3906 r_free = 0.3906 target = 0.104159 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3626 r_free = 0.3626 target = 0.087188 restraints weight = 21401.244| |-----------------------------------------------------------------------------| r_work (start): 0.3616 rms_B_bonded: 2.69 r_work: 0.3428 rms_B_bonded: 3.46 restraints_weight: 0.5000 r_work (final): 0.3428 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7564 moved from start: 0.3612 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 8833 Z= 0.123 Angle : 0.614 12.274 12006 Z= 0.317 Chirality : 0.042 0.255 1397 Planarity : 0.004 0.062 1505 Dihedral : 3.809 19.507 1228 Min Nonbonded Distance : 2.380 Molprobity Statistics. All-atom Clashscore : 7.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.14 % Favored : 94.86 % Rotamer: Outliers : 3.24 % Allowed : 19.46 % Favored : 77.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.09 (0.26), residues: 1129 helix: 1.34 (0.28), residues: 378 sheet: 0.31 (0.33), residues: 249 loop : -1.07 (0.27), residues: 502 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG D 148 TYR 0.016 0.001 TYR A 287 PHE 0.019 0.001 PHE R 39 TRP 0.014 0.001 TRP B 211 HIS 0.004 0.001 HIS B 183 Details of bonding type rmsd covalent geometry : bond 0.00284 ( 8830) covalent geometry : angle 0.61384 (12000) SS BOND : bond 0.00201 ( 3) SS BOND : angle 0.93052 ( 6) hydrogen bonds : bond 0.03227 ( 387) hydrogen bonds : angle 4.05730 ( 1086) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2011.99 seconds wall clock time: 35 minutes 26.76 seconds (2126.76 seconds total)