Starting phenix.real_space_refine on Tue Feb 11 17:41:51 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8unm_42409/02_2025/8unm_42409.cif Found real_map, /net/cci-nas-00/data/ceres_data/8unm_42409/02_2025/8unm_42409.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8unm_42409/02_2025/8unm_42409.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8unm_42409/02_2025/8unm_42409.map" model { file = "/net/cci-nas-00/data/ceres_data/8unm_42409/02_2025/8unm_42409.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8unm_42409/02_2025/8unm_42409.cif" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.022 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 3 5.49 5 S 38 5.16 5 C 4128 2.51 5 N 1110 2.21 5 O 1136 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib" Total number of atoms: 6415 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1641 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 224, 1629 Classifications: {'peptide': 224} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 66} Link IDs: {'PTRANS': 5, 'TRANS': 218} Chain breaks: 4 Unresolved non-hydrogen bonds: 242 Unresolved non-hydrogen angles: 292 Unresolved non-hydrogen dihedrals: 194 Unresolved non-hydrogen chiralities: 10 Planarities with less than four sites: {'GLN:plan1': 1, 'ASN:plan1': 1, 'ASP:plan': 10, 'PHE:plan': 1, 'GLU:plan': 16, 'ARG:plan': 10} Unresolved non-hydrogen planarities: 157 Conformer: "B" Number of residues, atoms: 224, 1629 Classifications: {'peptide': 224} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 66} Link IDs: {'PTRANS': 5, 'TRANS': 218} Chain breaks: 4 Unresolved non-hydrogen bonds: 242 Unresolved non-hydrogen angles: 292 Unresolved non-hydrogen dihedrals: 194 Unresolved non-hydrogen chiralities: 10 Planarities with less than four sites: {'GLN:plan1': 1, 'ASN:plan1': 1, 'ASP:plan': 10, 'PHE:plan': 1, 'GLU:plan': 16, 'ARG:plan': 10} Unresolved non-hydrogen planarities: 157 bond proxies already assigned to first conformer: 1647 Chain: "B" Number of atoms: 2359 Number of conformers: 1 Conformer: "" Number of residues, atoms: 329, 2359 Classifications: {'peptide': 329} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 47} Link IDs: {'PTRANS': 5, 'TRANS': 323} Chain breaks: 1 Unresolved non-hydrogen bonds: 168 Unresolved non-hydrogen angles: 206 Unresolved non-hydrogen dihedrals: 130 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 6, 'GLU:plan': 5, 'ARG:plan': 8, 'ASN:plan1': 2, 'ASP:plan': 14} Unresolved non-hydrogen planarities: 132 Chain: "G" Number of atoms: 312 Number of conformers: 1 Conformer: "" Number of residues, atoms: 51, 312 Classifications: {'peptide': 51} Incomplete info: {'truncation_to_alanine': 25} Link IDs: {'PTRANS': 4, 'TRANS': 46} Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 86 Unresolved non-hydrogen angles: 103 Unresolved non-hydrogen dihedrals: 71 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLU:plan': 5, 'ARG:plan': 2, 'ASN:plan1': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 39 Chain: "R" Number of atoms: 2056 Number of conformers: 1 Conformer: "" Number of residues, atoms: 285, 2056 Classifications: {'peptide': 285} Incomplete info: {'truncation_to_alanine': 66} Link IDs: {'PTRANS': 7, 'TRANS': 277} Chain breaks: 1 Unresolved non-hydrogen bonds: 247 Unresolved non-hydrogen angles: 307 Unresolved non-hydrogen dihedrals: 201 Unresolved non-hydrogen chiralities: 18 Planarities with less than four sites: {'GLN:plan1': 6, 'HIS:plan': 2, 'TYR:plan': 1, 'ASN:plan1': 2, 'TRP:plan': 1, 'ASP:plan': 5, 'GLU:plan': 11, 'ARG:plan': 6} Unresolved non-hydrogen planarities: 145 Chain: "A" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 32 Unusual residues: {'GTP': 1} Classifications: {'undetermined': 1} Chain: "R" Number of atoms: 15 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 15 Unusual residues: {'G1I': 1} Classifications: {'undetermined': 1} Residues with excluded nonbonded symmetry interactions: 1 residue: pdb=" N ATYR A 360 " occ=0.51 ... (22 atoms not shown) pdb=" OH BTYR A 360 " occ=0.49 Time building chain proxies: 5.64, per 1000 atoms: 0.88 Number of scatterers: 6415 At special positions: 0 Unit cell: (81.5638, 131.89, 97.1824, 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 38 16.00 P 3 15.00 O 1136 8.00 N 1110 7.00 C 4128 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS R 106 " - pdb=" SG CYS R 191 " 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: 1.54 Conformation dependent library (CDL) restraints added in 1.1 seconds 1744 Ramachandran restraints generated. 872 Oldfield, 0 Emsley, 872 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1688 Finding SS restraints... Secondary structure from input PDB file: 30 helices and 8 sheets defined 48.0% alpha, 17.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.75 Creating SS restraints... Processing helix chain 'A' and resid 13 through 40 removed outlier: 4.020A pdb=" N LYS A 17 " --> pdb=" O ARG A 13 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N GLN A 35 " --> pdb=" O GLN A 31 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N VAL A 36 " --> pdb=" O LYS A 32 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N THR A 40 " --> pdb=" O VAL A 36 " (cutoff:3.500A) Processing helix chain 'A' and resid 52 through 59 Processing helix chain 'A' and resid 233 through 239 removed outlier: 4.016A pdb=" N GLN A 236 " --> pdb=" O LYS A 233 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N ASN A 239 " --> pdb=" O GLN A 236 " (cutoff:3.500A) Processing helix chain 'A' and resid 265 through 278 Processing helix chain 'A' and resid 293 through 304 removed outlier: 3.730A pdb=" N GLY A 304 " --> pdb=" O LYS A 300 " (cutoff:3.500A) Processing helix chain 'A' and resid 307 through 312 removed outlier: 3.837A pdb=" N TYR A 311 " --> pdb=" O LYS A 307 " (cutoff:3.500A) Processing helix chain 'A' and resid 313 through 317 Processing helix chain 'A' and resid 333 through 350 removed outlier: 3.981A pdb=" N ILE A 348 " --> pdb=" O GLU A 344 " (cutoff:3.500A) Processing helix chain 'A' and resid 370 through 391 Processing helix chain 'B' and resid 9 through 26 removed outlier: 3.767A pdb=" N GLN B 13 " --> pdb=" O GLN B 9 " (cutoff:3.500A) Processing helix chain 'B' and resid 29 through 34 removed outlier: 3.575A pdb=" N ILE B 33 " --> pdb=" O THR B 29 " (cutoff:3.500A) Processing helix chain 'B' and resid 35 through 37 No H-bonds generated for 'chain 'B' and resid 35 through 37' Processing helix chain 'G' and resid 13 through 24 removed outlier: 3.520A pdb=" N GLN G 18 " --> pdb=" O LYS G 14 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N ASN G 24 " --> pdb=" O LYS G 20 " (cutoff:3.500A) Processing helix chain 'G' and resid 29 through 44 removed outlier: 3.582A pdb=" N ALA G 33 " --> pdb=" O LYS G 29 " (cutoff:3.500A) Processing helix chain 'G' and resid 45 through 47 No H-bonds generated for 'chain 'G' and resid 45 through 47' Processing helix chain 'R' and resid 31 through 61 removed outlier: 3.555A pdb=" N ILE R 38 " --> pdb=" O VAL R 34 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N ASN R 51 " --> pdb=" O ILE R 47 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N PHE R 61 " --> pdb=" O ALA R 57 " (cutoff:3.500A) Processing helix chain 'R' and resid 67 through 97 removed outlier: 4.309A pdb=" N PHE R 71 " --> pdb=" O VAL R 67 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N ILE R 72 " --> pdb=" O THR R 68 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N VAL R 87 " --> pdb=" O GLY R 83 " (cutoff:3.500A) Proline residue: R 88 - end of helix Processing helix chain 'R' and resid 102 through 137 removed outlier: 4.066A pdb=" N ILE R 121 " --> pdb=" O VAL R 117 " (cutoff:3.500A) removed outlier: 4.367A pdb=" N GLU R 122 " --> pdb=" O THR R 118 " (cutoff:3.500A) removed outlier: 4.069A pdb=" N THR R 123 " --> pdb=" O ALA R 119 " (cutoff:3.500A) removed outlier: 4.609A pdb=" N LEU R 124 " --> pdb=" O SER R 120 " (cutoff:3.500A) Processing helix chain 'R' and resid 140 through 145 Processing helix chain 'R' and resid 146 through 164 removed outlier: 3.899A pdb=" N ARG R 151 " --> pdb=" O LYS R 147 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N VAL R 152 " --> pdb=" O ASN R 148 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N THR R 164 " --> pdb=" O VAL R 160 " (cutoff:3.500A) Processing helix chain 'R' and resid 165 through 171 removed outlier: 3.580A pdb=" N ILE R 169 " --> pdb=" O SER R 165 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N MET R 171 " --> pdb=" O LEU R 167 " (cutoff:3.500A) Processing helix chain 'R' and resid 178 through 187 Processing helix chain 'R' and resid 196 through 208 removed outlier: 3.613A pdb=" N ALA R 200 " --> pdb=" O ASN R 196 " (cutoff:3.500A) Processing helix chain 'R' and resid 209 through 238 removed outlier: 3.843A pdb=" N VAL R 213 " --> pdb=" O TYR R 209 " (cutoff:3.500A) removed outlier: 4.040A pdb=" N ILE R 214 " --> pdb=" O VAL R 210 " (cutoff:3.500A) removed outlier: 4.144A pdb=" N MET R 215 " --> pdb=" O PRO R 211 " (cutoff:3.500A) Processing helix chain 'R' and resid 269 through 287 removed outlier: 3.893A pdb=" N PHE R 282 " --> pdb=" O ILE R 278 " (cutoff:3.500A) Processing helix chain 'R' and resid 288 through 299 removed outlier: 4.392A pdb=" N ILE R 294 " --> pdb=" O PHE R 290 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N VAL R 297 " --> pdb=" O ASN R 293 " (cutoff:3.500A) Processing helix chain 'R' and resid 304 through 317 removed outlier: 3.617A pdb=" N VAL R 317 " --> pdb=" O TRP R 313 " (cutoff:3.500A) Processing helix chain 'R' and resid 318 through 321 Processing helix chain 'R' and resid 322 through 327 removed outlier: 3.600A pdb=" N CYS R 327 " --> pdb=" O PRO R 323 " (cutoff:3.500A) Processing helix chain 'R' and resid 329 through 339 Processing sheet with id=AA1, first strand: chain 'A' and resid 207 through 213 removed outlier: 3.582A pdb=" N PHE A 212 " --> pdb=" O PHE A 219 " (cutoff:3.500A) removed outlier: 4.311A pdb=" N VAL A 224 " --> pdb=" O LEU A 45 " (cutoff:3.500A) removed outlier: 7.242A pdb=" N GLY A 47 " --> pdb=" O VAL A 224 " (cutoff:3.500A) removed outlier: 7.307A pdb=" N ARG A 42 " --> pdb=" O ALA A 243 " (cutoff:3.500A) removed outlier: 8.202A pdb=" N ILE A 245 " --> pdb=" O ARG A 42 " (cutoff:3.500A) removed outlier: 6.578A pdb=" N LEU A 44 " --> pdb=" O ILE A 245 " (cutoff:3.500A) removed outlier: 7.674A pdb=" N VAL A 247 " --> pdb=" O LEU A 44 " (cutoff:3.500A) removed outlier: 7.163A pdb=" N LEU A 46 " --> pdb=" O VAL A 247 " (cutoff:3.500A) removed outlier: 9.388A pdb=" N ALA A 249 " --> pdb=" O LEU A 46 " (cutoff:3.500A) removed outlier: 7.533A pdb=" N VAL A 287 " --> pdb=" O ATYR A 360 " (cutoff:3.500A) removed outlier: 7.991A pdb=" N HIS A 362 " --> pdb=" O VAL A 287 " (cutoff:3.500A) removed outlier: 6.495A pdb=" N LEU A 289 " --> pdb=" O HIS A 362 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 47 through 51 removed outlier: 6.716A pdb=" N ILE B 338 " --> pdb=" O ARG B 48 " (cutoff:3.500A) removed outlier: 4.634A pdb=" N THR B 50 " --> pdb=" O LEU B 336 " (cutoff:3.500A) removed outlier: 6.786A 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: 7.048A pdb=" N ALA B 73 " --> pdb=" O TYR B 59 " (cutoff:3.500A) removed outlier: 4.303A pdb=" N MET B 61 " --> pdb=" O VAL B 71 " (cutoff:3.500A) removed outlier: 6.752A pdb=" N VAL B 71 " --> pdb=" O MET B 61 " (cutoff:3.500A) removed outlier: 5.190A pdb=" N TRP B 63 " --> pdb=" O LEU B 69 " (cutoff:3.500A) removed outlier: 7.195A pdb=" N LEU B 69 " --> pdb=" O TRP B 63 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N LEU B 70 " --> pdb=" O TRP B 82 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N SER B 74 " --> pdb=" O LYS B 78 " (cutoff:3.500A) removed outlier: 4.164A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N HIS B 91 " --> pdb=" O ILE B 81 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 100 through 105 removed outlier: 7.070A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.604A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.734A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 5.094A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 7.260A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 4.168A pdb=" N GLY B 116 " --> pdb=" O ILE B 120 " (cutoff:3.500A) removed outlier: 5.202A pdb=" N ILE B 120 " --> pdb=" O GLY B 116 " (cutoff:3.500A) removed outlier: 6.468A pdb=" N CYS B 121 " --> pdb=" O GLU B 138 " (cutoff:3.500A) removed outlier: 4.619A pdb=" N GLU B 138 " --> pdb=" O CYS B 121 " (cutoff:3.500A) removed outlier: 6.943A pdb=" N ILE B 123 " --> pdb=" O SER B 136 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 146 through 151 removed outlier: 7.150A pdb=" N SER B 160 " --> pdb=" O SER B 147 " (cutoff:3.500A) removed outlier: 4.728A pdb=" N CYS B 149 " --> pdb=" O VAL B 158 " (cutoff:3.500A) removed outlier: 7.022A pdb=" N VAL B 158 " --> pdb=" O CYS B 149 " (cutoff:3.500A) removed outlier: 5.663A pdb=" N PHE B 151 " --> pdb=" O GLN B 156 " (cutoff:3.500A) removed outlier: 7.693A pdb=" N GLN B 156 " --> pdb=" O PHE B 151 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N ILE B 157 " --> pdb=" O TRP B 169 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N THR B 178 " --> pdb=" O LEU B 168 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 187 through 192 removed outlier: 6.830A pdb=" N GLY B 202 " --> pdb=" O MET B 188 " (cutoff:3.500A) removed outlier: 4.564A pdb=" N LEU B 190 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 6.783A pdb=" N VAL B 200 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 5.032A pdb=" N LEU B 192 " --> pdb=" O LEU B 198 " (cutoff:3.500A) removed outlier: 7.115A pdb=" N LEU B 198 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N PHE B 199 " --> pdb=" O TRP B 211 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.700A pdb=" N GLY B 244 " --> pdb=" O ASN B 230 " (cutoff:3.500A) removed outlier: 4.514A pdb=" N ILE B 232 " --> pdb=" O ALA B 242 " (cutoff:3.500A) removed outlier: 6.833A pdb=" N ALA B 242 " --> pdb=" O ILE B 232 " (cutoff:3.500A) removed outlier: 4.770A pdb=" N PHE B 234 " --> pdb=" O ALA B 240 " (cutoff:3.500A) removed outlier: 7.096A pdb=" N ALA B 240 " --> pdb=" O PHE B 234 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N PHE B 241 " --> pdb=" O PHE B 253 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ARG B 251 " --> pdb=" O THR B 243 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N MET B 262 " --> pdb=" O LEU B 252 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 273 through 278 removed outlier: 3.836A pdb=" N SER B 275 " --> pdb=" O GLY B 288 " (cutoff:3.500A) removed outlier: 4.590A pdb=" N ASN B 293 " --> pdb=" O TYR B 289 " (cutoff:3.500A) removed outlier: 6.791A pdb=" N CYS B 294 " --> pdb=" O VAL B 307 " (cutoff:3.500A) removed outlier: 4.919A pdb=" N VAL B 307 " --> pdb=" O CYS B 294 " (cutoff:3.500A) removed outlier: 6.526A pdb=" N VAL B 296 " --> pdb=" O ALA B 305 " (cutoff:3.500A) 338 hydrogen bonds defined for protein. 984 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: 1.75 Time building geometry restraints manager: 1.80 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 1281 1.33 - 1.45: 1654 1.45 - 1.57: 3567 1.57 - 1.69: 5 1.69 - 1.81: 50 Bond restraints: 6557 Sorted by residual: bond pdb=" C5 GTP A 401 " pdb=" C6 GTP A 401 " ideal model delta sigma weight residual 1.390 1.479 -0.089 2.00e-02 2.50e+03 1.97e+01 bond pdb=" C4 GTP A 401 " pdb=" C5 GTP A 401 " ideal model delta sigma weight residual 1.390 1.463 -0.073 2.00e-02 2.50e+03 1.34e+01 bond pdb=" N ASP A 310 " pdb=" CA ASP A 310 " ideal model delta sigma weight residual 1.459 1.423 0.036 1.20e-02 6.94e+03 9.01e+00 bond pdb=" CA ILE A 308 " pdb=" C ILE A 308 " ideal model delta sigma weight residual 1.522 1.478 0.044 1.50e-02 4.44e+03 8.73e+00 bond pdb=" CA GLU A 309 " pdb=" C GLU A 309 " ideal model delta sigma weight residual 1.523 1.487 0.037 1.30e-02 5.92e+03 7.88e+00 ... (remaining 6552 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.11: 8843 2.11 - 4.22: 111 4.22 - 6.33: 24 6.33 - 8.43: 3 8.43 - 10.54: 3 Bond angle restraints: 8984 Sorted by residual: angle pdb=" N ASP A 323 " pdb=" CA ASP A 323 " pdb=" C ASP A 323 " ideal model delta sigma weight residual 111.36 117.97 -6.61 1.09e+00 8.42e-01 3.67e+01 angle pdb=" N ALA A 324 " pdb=" CA ALA A 324 " pdb=" C ALA A 324 " ideal model delta sigma weight residual 110.23 116.88 -6.65 1.45e+00 4.76e-01 2.10e+01 angle pdb=" C VAL R 34 " pdb=" CA VAL R 34 " pdb=" CB VAL R 34 " ideal model delta sigma weight residual 111.97 106.54 5.43 1.28e+00 6.10e-01 1.80e+01 angle pdb=" N MET A 60 " pdb=" CA MET A 60 " pdb=" C MET A 60 " ideal model delta sigma weight residual 111.28 107.13 4.15 1.09e+00 8.42e-01 1.45e+01 angle pdb=" N LYS A 58 " pdb=" CA LYS A 58 " pdb=" C LYS A 58 " ideal model delta sigma weight residual 111.36 115.47 -4.11 1.09e+00 8.42e-01 1.42e+01 ... (remaining 8979 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 31.43: 3692 31.43 - 62.85: 64 62.85 - 94.28: 3 94.28 - 125.71: 2 125.71 - 157.13: 4 Dihedral angle restraints: 3765 sinusoidal: 1168 harmonic: 2597 Sorted by residual: dihedral pdb=" C4' GTP A 401 " pdb=" C5' GTP A 401 " pdb=" O5' GTP A 401 " pdb=" PA GTP A 401 " ideal model delta sinusoidal sigma weight residual 260.87 103.74 157.13 1 2.00e+01 2.50e-03 4.61e+01 dihedral pdb=" O3B GTP A 401 " pdb=" O3A GTP A 401 " pdb=" PB GTP A 401 " pdb=" PA GTP A 401 " ideal model delta sinusoidal sigma weight residual 291.08 143.91 147.17 1 2.00e+01 2.50e-03 4.42e+01 dihedral pdb=" O5' GTP A 401 " pdb=" O3A GTP A 401 " pdb=" PA GTP A 401 " pdb=" PB GTP A 401 " ideal model delta sinusoidal sigma weight residual -85.88 56.92 -142.80 1 2.00e+01 2.50e-03 4.31e+01 ... (remaining 3762 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.038: 754 0.038 - 0.075: 223 0.075 - 0.113: 85 0.113 - 0.150: 14 0.150 - 0.188: 4 Chirality restraints: 1080 Sorted by residual: chirality pdb=" CA TYR A 311 " pdb=" N TYR A 311 " pdb=" C TYR A 311 " pdb=" CB TYR A 311 " both_signs ideal model delta sigma weight residual False 2.51 2.32 0.19 2.00e-01 2.50e+01 8.83e-01 chirality pdb=" CAJ G1I R 501 " pdb=" CAF G1I R 501 " pdb=" CAI G1I R 501 " pdb=" OAM G1I R 501 " both_signs ideal model delta sigma weight residual False 2.40 2.57 -0.17 2.00e-01 2.50e+01 7.18e-01 chirality pdb=" CA ALA A 324 " pdb=" N ALA A 324 " pdb=" C ALA A 324 " pdb=" CB ALA A 324 " both_signs ideal model delta sigma weight residual False 2.48 2.32 0.17 2.00e-01 2.50e+01 6.90e-01 ... (remaining 1077 not shown) Planarity restraints: 1125 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR A 325 " -0.046 5.00e-02 4.00e+02 6.98e-02 7.80e+00 pdb=" N PRO A 326 " 0.121 5.00e-02 4.00e+02 pdb=" CA PRO A 326 " -0.035 5.00e-02 4.00e+02 pdb=" CD PRO A 326 " -0.039 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER R 329 " -0.039 5.00e-02 4.00e+02 5.94e-02 5.65e+00 pdb=" N PRO R 330 " 0.103 5.00e-02 4.00e+02 pdb=" CA PRO R 330 " -0.031 5.00e-02 4.00e+02 pdb=" CD PRO R 330 " -0.033 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL R 210 " 0.030 5.00e-02 4.00e+02 4.56e-02 3.33e+00 pdb=" N PRO R 211 " -0.079 5.00e-02 4.00e+02 pdb=" CA PRO R 211 " 0.023 5.00e-02 4.00e+02 pdb=" CD PRO R 211 " 0.026 5.00e-02 4.00e+02 ... (remaining 1122 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 733 2.75 - 3.28: 6015 3.28 - 3.82: 10014 3.82 - 4.36: 10783 4.36 - 4.90: 20309 Nonbonded interactions: 47854 Sorted by model distance: nonbonded pdb=" O THR A 325 " pdb=" OH TYR A 339 " model vdw 2.208 3.040 nonbonded pdb=" OD2 ASP R 113 " pdb=" OAM G1I R 501 " model vdw 2.257 3.040 nonbonded pdb=" O GLN A 267 " pdb=" OD1 ASN A 271 " model vdw 2.304 3.040 nonbonded pdb=" OG1 THR B 86 " pdb=" OD1 ASN B 88 " model vdw 2.365 3.040 nonbonded pdb=" NE2 HIS A 220 " pdb=" CZ PHE A 222 " model vdw 2.410 3.420 ... (remaining 47849 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=0.49 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: 1.470 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: 0.230 Check model and map are aligned: 0.040 Set scattering table: 0.060 Process input model: 19.990 Find NCS groups from input model: 0.080 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.730 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.620 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8330 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 : 0.005 0.089 6557 Z= 0.307 Angle : 0.639 10.542 8984 Z= 0.369 Chirality : 0.042 0.188 1080 Planarity : 0.004 0.070 1125 Dihedral : 13.954 157.134 2074 Min Nonbonded Distance : 2.208 Molprobity Statistics. All-atom Clashscore : 3.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 0.00 % Allowed : 0.35 % Favored : 99.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.00 (0.29), residues: 872 helix: 2.26 (0.27), residues: 378 sheet: 0.16 (0.41), residues: 172 loop : -1.01 (0.31), residues: 322 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP R 99 HIS 0.012 0.001 HIS A 220 PHE 0.013 0.001 PHE B 235 TYR 0.026 0.001 TYR B 59 ARG 0.005 0.000 ARG A 356 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1744 Ramachandran restraints generated. 872 Oldfield, 0 Emsley, 872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1744 Ramachandran restraints generated. 872 Oldfield, 0 Emsley, 872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 768 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 96 time to evaluate : 0.741 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 96 average time/residue: 0.1592 time to fit residues: 21.0570 Evaluate side-chains 68 residues out of total 768 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 68 time to evaluate : 0.709 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 73 optimal weight: 3.9990 chunk 65 optimal weight: 1.9990 chunk 36 optimal weight: 0.1980 chunk 22 optimal weight: 1.9990 chunk 44 optimal weight: 0.9990 chunk 35 optimal weight: 3.9990 chunk 68 optimal weight: 1.9990 chunk 26 optimal weight: 7.9990 chunk 41 optimal weight: 7.9990 chunk 50 optimal weight: 4.9990 chunk 79 optimal weight: 5.9990 overall best weight: 1.4388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 292 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.116309 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3081 r_free = 0.3081 target = 0.089214 restraints weight = 36780.159| |-----------------------------------------------------------------------------| r_work (start): 0.3101 rms_B_bonded: 4.91 r_work (final): 0.3101 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3101 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3101 r_free = 0.3101 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3101 r_free = 0.3101 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3101 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8333 moved from start: 0.0901 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 6557 Z= 0.250 Angle : 0.508 6.663 8984 Z= 0.278 Chirality : 0.042 0.152 1080 Planarity : 0.004 0.052 1125 Dihedral : 10.343 152.371 969 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 3.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % Rotamer: Outliers : 0.53 % Allowed : 8.48 % Favored : 90.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.04 (0.29), residues: 872 helix: 2.16 (0.27), residues: 392 sheet: 0.09 (0.40), residues: 174 loop : -0.89 (0.31), residues: 306 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 297 HIS 0.016 0.001 HIS A 220 PHE 0.010 0.001 PHE B 199 TYR 0.029 0.001 TYR B 59 ARG 0.003 0.000 ARG A 356 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1744 Ramachandran restraints generated. 872 Oldfield, 0 Emsley, 872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1744 Ramachandran restraints generated. 872 Oldfield, 0 Emsley, 872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 768 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 76 time to evaluate : 0.785 Fit side-chains revert: symmetry clash outliers start: 3 outliers final: 3 residues processed: 78 average time/residue: 0.1615 time to fit residues: 17.8032 Evaluate side-chains 74 residues out of total 768 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 71 time to evaluate : 0.724 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 189 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 64 optimal weight: 2.9990 chunk 44 optimal weight: 0.1980 chunk 22 optimal weight: 0.8980 chunk 27 optimal weight: 0.7980 chunk 45 optimal weight: 0.9980 chunk 18 optimal weight: 0.4980 chunk 23 optimal weight: 6.9990 chunk 21 optimal weight: 0.5980 chunk 74 optimal weight: 5.9990 chunk 34 optimal weight: 3.9990 chunk 32 optimal weight: 0.9980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 292 ASN R 51 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3497 r_free = 0.3497 target = 0.119339 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3146 r_free = 0.3146 target = 0.092935 restraints weight = 37031.299| |-----------------------------------------------------------------------------| r_work (start): 0.3155 rms_B_bonded: 5.10 r_work (final): 0.3155 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3153 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3153 r_free = 0.3153 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3153 r_free = 0.3153 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3153 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8252 moved from start: 0.1202 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 6557 Z= 0.142 Angle : 0.453 7.430 8984 Z= 0.243 Chirality : 0.041 0.154 1080 Planarity : 0.004 0.048 1125 Dihedral : 9.674 152.381 969 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 2.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.73 % Favored : 98.27 % Rotamer: Outliers : 0.71 % Allowed : 10.60 % Favored : 88.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.32 (0.29), residues: 872 helix: 2.38 (0.27), residues: 389 sheet: 0.36 (0.40), residues: 173 loop : -0.79 (0.31), residues: 310 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 297 HIS 0.011 0.001 HIS A 220 PHE 0.010 0.001 PHE R 61 TYR 0.010 0.001 TYR B 59 ARG 0.003 0.000 ARG A 356 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1744 Ramachandran restraints generated. 872 Oldfield, 0 Emsley, 872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1744 Ramachandran restraints generated. 872 Oldfield, 0 Emsley, 872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 768 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 81 time to evaluate : 0.737 Fit side-chains revert: symmetry clash outliers start: 4 outliers final: 1 residues processed: 82 average time/residue: 0.1698 time to fit residues: 19.7083 Evaluate side-chains 73 residues out of total 768 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 72 time to evaluate : 0.752 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 128 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 0 optimal weight: 20.0000 chunk 18 optimal weight: 0.8980 chunk 79 optimal weight: 0.9980 chunk 7 optimal weight: 0.4980 chunk 40 optimal weight: 2.9990 chunk 83 optimal weight: 0.9980 chunk 56 optimal weight: 6.9990 chunk 9 optimal weight: 0.0020 chunk 49 optimal weight: 3.9990 chunk 37 optimal weight: 0.3980 chunk 63 optimal weight: 0.9990 overall best weight: 0.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3509 r_free = 0.3509 target = 0.120025 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3156 r_free = 0.3156 target = 0.093421 restraints weight = 37965.628| |-----------------------------------------------------------------------------| r_work (start): 0.3159 rms_B_bonded: 5.09 r_work (final): 0.3159 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3160 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3160 r_free = 0.3160 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3160 r_free = 0.3160 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3160 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8244 moved from start: 0.1432 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 6557 Z= 0.136 Angle : 0.443 7.277 8984 Z= 0.234 Chirality : 0.040 0.166 1080 Planarity : 0.003 0.044 1125 Dihedral : 9.210 154.145 969 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 2.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.73 % Favored : 98.27 % Rotamer: Outliers : 1.77 % Allowed : 11.84 % Favored : 86.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.42 (0.29), residues: 872 helix: 2.59 (0.27), residues: 383 sheet: 0.38 (0.40), residues: 173 loop : -0.85 (0.31), residues: 316 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 297 HIS 0.009 0.001 HIS A 220 PHE 0.008 0.001 PHE A 376 TYR 0.010 0.001 TYR B 59 ARG 0.004 0.000 ARG A 342 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1744 Ramachandran restraints generated. 872 Oldfield, 0 Emsley, 872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1744 Ramachandran restraints generated. 872 Oldfield, 0 Emsley, 872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 768 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 87 time to evaluate : 0.747 Fit side-chains revert: symmetry clash REVERT: B 234 PHE cc_start: 0.9177 (OUTLIER) cc_final: 0.8013 (m-80) outliers start: 10 outliers final: 6 residues processed: 92 average time/residue: 0.1576 time to fit residues: 20.5213 Evaluate side-chains 86 residues out of total 768 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 79 time to evaluate : 0.742 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 THR Chi-restraints excluded: chain A residue 247 VAL Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain R residue 77 CYS Chi-restraints excluded: chain R residue 307 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 51 optimal weight: 0.2980 chunk 56 optimal weight: 3.9990 chunk 10 optimal weight: 0.9990 chunk 14 optimal weight: 0.0270 chunk 18 optimal weight: 5.9990 chunk 7 optimal weight: 0.9990 chunk 62 optimal weight: 10.0000 chunk 65 optimal weight: 4.9990 chunk 39 optimal weight: 0.9980 chunk 8 optimal weight: 1.9990 chunk 20 optimal weight: 2.9990 overall best weight: 0.6642 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3508 r_free = 0.3508 target = 0.119565 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3143 r_free = 0.3143 target = 0.093206 restraints weight = 33764.629| |-----------------------------------------------------------------------------| r_work (start): 0.3162 rms_B_bonded: 4.94 r_work (final): 0.3162 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3162 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3162 r_free = 0.3162 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3162 r_free = 0.3162 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3162 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8247 moved from start: 0.1563 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.020 6557 Z= 0.142 Angle : 0.447 7.258 8984 Z= 0.234 Chirality : 0.040 0.166 1080 Planarity : 0.003 0.042 1125 Dihedral : 8.882 153.591 969 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 2.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.96 % Favored : 98.04 % Rotamer: Outliers : 2.12 % Allowed : 11.48 % Favored : 86.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.48 (0.29), residues: 872 helix: 2.66 (0.27), residues: 383 sheet: 0.38 (0.40), residues: 174 loop : -0.81 (0.31), residues: 315 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 297 HIS 0.010 0.001 HIS A 220 PHE 0.014 0.001 PHE A 222 TYR 0.008 0.001 TYR A 339 ARG 0.004 0.000 ARG A 342 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1744 Ramachandran restraints generated. 872 Oldfield, 0 Emsley, 872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1744 Ramachandran restraints generated. 872 Oldfield, 0 Emsley, 872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 768 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 86 time to evaluate : 0.730 Fit side-chains revert: symmetry clash REVERT: B 143 THR cc_start: 0.9425 (OUTLIER) cc_final: 0.9120 (p) REVERT: B 234 PHE cc_start: 0.9209 (OUTLIER) cc_final: 0.8066 (m-80) outliers start: 12 outliers final: 10 residues processed: 93 average time/residue: 0.1724 time to fit residues: 22.5722 Evaluate side-chains 92 residues out of total 768 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 80 time to evaluate : 0.735 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 55 THR Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain G residue 41 CYS Chi-restraints excluded: chain R residue 77 CYS Chi-restraints excluded: chain R residue 296 HIS Chi-restraints excluded: chain R residue 307 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 49 optimal weight: 3.9990 chunk 78 optimal weight: 2.9990 chunk 62 optimal weight: 9.9990 chunk 19 optimal weight: 1.9990 chunk 67 optimal weight: 2.9990 chunk 81 optimal weight: 0.8980 chunk 55 optimal weight: 7.9990 chunk 71 optimal weight: 3.9990 chunk 22 optimal weight: 0.8980 chunk 66 optimal weight: 0.9980 chunk 80 optimal weight: 0.9980 overall best weight: 1.1582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3477 r_free = 0.3477 target = 0.117588 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3118 r_free = 0.3118 target = 0.090946 restraints weight = 39452.524| |-----------------------------------------------------------------------------| r_work (start): 0.3123 rms_B_bonded: 5.16 r_work (final): 0.3123 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3122 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3122 r_free = 0.3122 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3122 r_free = 0.3122 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3122 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8296 moved from start: 0.1544 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 6557 Z= 0.208 Angle : 0.478 8.370 8984 Z= 0.252 Chirality : 0.041 0.169 1080 Planarity : 0.004 0.047 1125 Dihedral : 8.696 148.432 969 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 2.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % Rotamer: Outliers : 2.65 % Allowed : 12.37 % Favored : 84.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.38 (0.29), residues: 872 helix: 2.62 (0.27), residues: 383 sheet: 0.28 (0.40), residues: 174 loop : -0.91 (0.31), residues: 315 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 297 HIS 0.014 0.001 HIS A 220 PHE 0.017 0.001 PHE A 222 TYR 0.012 0.001 TYR B 59 ARG 0.004 0.000 ARG A 342 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1744 Ramachandran restraints generated. 872 Oldfield, 0 Emsley, 872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1744 Ramachandran restraints generated. 872 Oldfield, 0 Emsley, 872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 768 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 82 time to evaluate : 0.684 Fit side-chains revert: symmetry clash REVERT: B 143 THR cc_start: 0.9432 (OUTLIER) cc_final: 0.9097 (p) REVERT: B 234 PHE cc_start: 0.9237 (OUTLIER) cc_final: 0.8125 (m-80) REVERT: B 259 GLN cc_start: 0.8647 (pm20) cc_final: 0.7647 (pm20) outliers start: 15 outliers final: 11 residues processed: 91 average time/residue: 0.1495 time to fit residues: 19.2094 Evaluate side-chains 92 residues out of total 768 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 79 time to evaluate : 0.743 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 THR Chi-restraints excluded: chain A residue 247 VAL Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain G residue 41 CYS Chi-restraints excluded: chain R residue 77 CYS Chi-restraints excluded: chain R residue 296 HIS Chi-restraints excluded: chain R residue 307 VAL Chi-restraints excluded: chain R residue 317 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 70 optimal weight: 2.9990 chunk 4 optimal weight: 1.9990 chunk 34 optimal weight: 0.4980 chunk 18 optimal weight: 5.9990 chunk 16 optimal weight: 0.9980 chunk 26 optimal weight: 0.5980 chunk 59 optimal weight: 7.9990 chunk 12 optimal weight: 4.9990 chunk 79 optimal weight: 0.8980 chunk 21 optimal weight: 0.6980 chunk 76 optimal weight: 1.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 294 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3493 r_free = 0.3493 target = 0.118922 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3125 r_free = 0.3125 target = 0.091734 restraints weight = 43354.999| |-----------------------------------------------------------------------------| r_work (start): 0.3133 rms_B_bonded: 5.58 r_work (final): 0.3133 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3136 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3136 r_free = 0.3136 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3136 r_free = 0.3136 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3136 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8266 moved from start: 0.1636 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 6557 Z= 0.152 Angle : 0.454 7.927 8984 Z= 0.238 Chirality : 0.041 0.166 1080 Planarity : 0.004 0.054 1125 Dihedral : 8.646 146.935 969 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 2.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer: Outliers : 2.83 % Allowed : 12.72 % Favored : 84.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.45 (0.29), residues: 872 helix: 2.64 (0.27), residues: 383 sheet: 0.38 (0.40), residues: 173 loop : -0.86 (0.31), residues: 316 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 297 HIS 0.012 0.001 HIS A 220 PHE 0.015 0.001 PHE R 61 TYR 0.008 0.001 TYR A 339 ARG 0.004 0.000 ARG A 342 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1744 Ramachandran restraints generated. 872 Oldfield, 0 Emsley, 872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1744 Ramachandran restraints generated. 872 Oldfield, 0 Emsley, 872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 768 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 83 time to evaluate : 0.730 Fit side-chains revert: symmetry clash REVERT: B 143 THR cc_start: 0.9411 (OUTLIER) cc_final: 0.9070 (p) REVERT: B 234 PHE cc_start: 0.9229 (OUTLIER) cc_final: 0.8071 (m-80) REVERT: B 259 GLN cc_start: 0.8628 (pm20) cc_final: 0.7980 (pm20) outliers start: 16 outliers final: 13 residues processed: 93 average time/residue: 0.1531 time to fit residues: 20.2903 Evaluate side-chains 96 residues out of total 768 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 81 time to evaluate : 0.736 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 55 THR Chi-restraints excluded: chain A residue 247 VAL Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain G residue 41 CYS Chi-restraints excluded: chain R residue 77 CYS Chi-restraints excluded: chain R residue 146 THR Chi-restraints excluded: chain R residue 296 HIS Chi-restraints excluded: chain R residue 307 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 1 optimal weight: 0.6980 chunk 25 optimal weight: 4.9990 chunk 12 optimal weight: 0.8980 chunk 30 optimal weight: 1.9990 chunk 61 optimal weight: 0.9990 chunk 5 optimal weight: 0.0770 chunk 56 optimal weight: 3.9990 chunk 7 optimal weight: 2.9990 chunk 33 optimal weight: 0.0570 chunk 73 optimal weight: 4.9990 chunk 52 optimal weight: 2.9990 overall best weight: 0.5458 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 294 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3513 r_free = 0.3513 target = 0.120015 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3148 r_free = 0.3148 target = 0.093721 restraints weight = 25388.677| |-----------------------------------------------------------------------------| r_work (start): 0.3168 rms_B_bonded: 4.20 r_work: 0.3032 rms_B_bonded: 4.62 restraints_weight: 0.5000 r_work (final): 0.3032 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3021 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3021 r_free = 0.3021 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3021 r_free = 0.3021 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3021 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8337 moved from start: 0.1781 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 6557 Z= 0.132 Angle : 0.445 9.324 8984 Z= 0.232 Chirality : 0.040 0.182 1080 Planarity : 0.004 0.058 1125 Dihedral : 8.647 145.678 969 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 2.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.84 % Favored : 98.16 % Rotamer: Outliers : 2.65 % Allowed : 13.78 % Favored : 83.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.48 (0.29), residues: 872 helix: 2.66 (0.27), residues: 384 sheet: 0.40 (0.40), residues: 173 loop : -0.84 (0.31), residues: 315 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 297 HIS 0.012 0.001 HIS A 220 PHE 0.017 0.001 PHE A 222 TYR 0.008 0.001 TYR R 219 ARG 0.004 0.000 ARG A 342 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1744 Ramachandran restraints generated. 872 Oldfield, 0 Emsley, 872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1744 Ramachandran restraints generated. 872 Oldfield, 0 Emsley, 872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 768 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 90 time to evaluate : 0.581 Fit side-chains revert: symmetry clash REVERT: B 143 THR cc_start: 0.9424 (OUTLIER) cc_final: 0.9089 (p) REVERT: B 234 PHE cc_start: 0.9258 (OUTLIER) cc_final: 0.8109 (m-80) REVERT: B 259 GLN cc_start: 0.8918 (pm20) cc_final: 0.8294 (pm20) outliers start: 15 outliers final: 13 residues processed: 98 average time/residue: 0.1808 time to fit residues: 23.8504 Evaluate side-chains 102 residues out of total 768 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 87 time to evaluate : 0.714 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 55 THR Chi-restraints excluded: chain A residue 247 VAL Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain G residue 41 CYS Chi-restraints excluded: chain R residue 77 CYS Chi-restraints excluded: chain R residue 146 THR Chi-restraints excluded: chain R residue 296 HIS Chi-restraints excluded: chain R residue 307 VAL Chi-restraints excluded: chain R residue 317 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 28 optimal weight: 1.9990 chunk 62 optimal weight: 6.9990 chunk 30 optimal weight: 1.9990 chunk 3 optimal weight: 5.9990 chunk 53 optimal weight: 4.9990 chunk 43 optimal weight: 2.9990 chunk 72 optimal weight: 0.0060 chunk 81 optimal weight: 0.6980 chunk 41 optimal weight: 0.8980 chunk 6 optimal weight: 2.9990 chunk 68 optimal weight: 0.6980 overall best weight: 0.8598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3493 r_free = 0.3493 target = 0.118654 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3125 r_free = 0.3125 target = 0.091775 restraints weight = 42080.798| |-----------------------------------------------------------------------------| r_work (start): 0.3139 rms_B_bonded: 5.45 r_work (final): 0.3139 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3138 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3138 r_free = 0.3138 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3138 r_free = 0.3138 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3138 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8268 moved from start: 0.1775 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 6557 Z= 0.167 Angle : 0.464 8.740 8984 Z= 0.241 Chirality : 0.041 0.180 1080 Planarity : 0.004 0.057 1125 Dihedral : 8.789 158.286 969 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 2.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer: Outliers : 2.83 % Allowed : 13.96 % Favored : 83.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.44 (0.29), residues: 872 helix: 2.67 (0.27), residues: 383 sheet: 0.34 (0.40), residues: 174 loop : -0.88 (0.31), residues: 315 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 297 HIS 0.011 0.001 HIS A 220 PHE 0.014 0.001 PHE R 61 TYR 0.010 0.001 TYR B 59 ARG 0.004 0.000 ARG A 342 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1744 Ramachandran restraints generated. 872 Oldfield, 0 Emsley, 872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1744 Ramachandran restraints generated. 872 Oldfield, 0 Emsley, 872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 768 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 88 time to evaluate : 0.688 Fit side-chains revert: symmetry clash REVERT: B 143 THR cc_start: 0.9393 (OUTLIER) cc_final: 0.9036 (p) REVERT: B 234 PHE cc_start: 0.9228 (OUTLIER) cc_final: 0.8122 (m-80) REVERT: B 259 GLN cc_start: 0.8674 (pm20) cc_final: 0.8020 (pm20) outliers start: 16 outliers final: 13 residues processed: 97 average time/residue: 0.1820 time to fit residues: 24.3351 Evaluate side-chains 101 residues out of total 768 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 86 time to evaluate : 0.699 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 55 THR Chi-restraints excluded: chain A residue 247 VAL Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain G residue 41 CYS Chi-restraints excluded: chain R residue 77 CYS Chi-restraints excluded: chain R residue 146 THR Chi-restraints excluded: chain R residue 296 HIS Chi-restraints excluded: chain R residue 307 VAL Chi-restraints excluded: chain R residue 317 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 66 optimal weight: 1.9990 chunk 16 optimal weight: 0.9980 chunk 0 optimal weight: 20.0000 chunk 33 optimal weight: 0.0270 chunk 25 optimal weight: 1.9990 chunk 80 optimal weight: 5.9990 chunk 21 optimal weight: 0.8980 chunk 37 optimal weight: 6.9990 chunk 7 optimal weight: 0.9990 chunk 22 optimal weight: 1.9990 chunk 26 optimal weight: 3.9990 overall best weight: 0.9842 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3485 r_free = 0.3485 target = 0.118053 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3111 r_free = 0.3111 target = 0.091073 restraints weight = 37115.227| |-----------------------------------------------------------------------------| r_work (start): 0.3125 rms_B_bonded: 5.14 r_work (final): 0.3125 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3124 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3124 r_free = 0.3124 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3124 r_free = 0.3124 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3124 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8290 moved from start: 0.1757 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 6557 Z= 0.182 Angle : 0.468 8.715 8984 Z= 0.245 Chirality : 0.041 0.180 1080 Planarity : 0.004 0.055 1125 Dihedral : 9.049 177.496 969 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 2.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer: Outliers : 2.65 % Allowed : 14.49 % Favored : 82.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.41 (0.29), residues: 872 helix: 2.65 (0.27), residues: 383 sheet: 0.36 (0.40), residues: 172 loop : -0.93 (0.31), residues: 317 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 297 HIS 0.012 0.001 HIS A 220 PHE 0.015 0.001 PHE R 61 TYR 0.011 0.001 TYR B 59 ARG 0.004 0.000 ARG A 342 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1744 Ramachandran restraints generated. 872 Oldfield, 0 Emsley, 872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1744 Ramachandran restraints generated. 872 Oldfield, 0 Emsley, 872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 768 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 83 time to evaluate : 0.670 Fit side-chains revert: symmetry clash REVERT: B 234 PHE cc_start: 0.9253 (OUTLIER) cc_final: 0.8193 (m-80) REVERT: B 259 GLN cc_start: 0.8646 (pm20) cc_final: 0.8003 (pm20) outliers start: 15 outliers final: 14 residues processed: 91 average time/residue: 0.1646 time to fit residues: 20.8469 Evaluate side-chains 97 residues out of total 768 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 82 time to evaluate : 0.702 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 55 THR Chi-restraints excluded: chain A residue 247 VAL Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain G residue 41 CYS Chi-restraints excluded: chain R residue 77 CYS Chi-restraints excluded: chain R residue 146 THR Chi-restraints excluded: chain R residue 296 HIS Chi-restraints excluded: chain R residue 307 VAL Chi-restraints excluded: chain R residue 317 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 86 optimal weight: 1.9990 chunk 70 optimal weight: 3.9990 chunk 28 optimal weight: 0.0980 chunk 64 optimal weight: 3.9990 chunk 40 optimal weight: 0.5980 chunk 85 optimal weight: 0.5980 chunk 34 optimal weight: 5.9990 chunk 74 optimal weight: 4.9990 chunk 81 optimal weight: 1.9990 chunk 21 optimal weight: 0.6980 chunk 60 optimal weight: 0.9990 overall best weight: 0.5982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3509 r_free = 0.3509 target = 0.119845 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3135 r_free = 0.3135 target = 0.092891 restraints weight = 40098.997| |-----------------------------------------------------------------------------| r_work (start): 0.3150 rms_B_bonded: 5.44 r_work: 0.2981 rms_B_bonded: 5.43 restraints_weight: 2.0000 r_work (final): 0.2981 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2989 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2989 r_free = 0.2989 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2989 r_free = 0.2989 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2989 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8371 moved from start: 0.1888 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 6557 Z= 0.139 Angle : 0.451 8.650 8984 Z= 0.234 Chirality : 0.040 0.187 1080 Planarity : 0.004 0.057 1125 Dihedral : 8.694 168.312 969 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 2.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.96 % Favored : 98.04 % Rotamer: Outliers : 2.30 % Allowed : 14.84 % Favored : 82.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.53 (0.29), residues: 872 helix: 2.70 (0.27), residues: 383 sheet: 0.63 (0.41), residues: 166 loop : -0.90 (0.30), residues: 323 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 297 HIS 0.011 0.001 HIS A 220 PHE 0.019 0.001 PHE R 61 TYR 0.007 0.001 TYR B 59 ARG 0.004 0.000 ARG A 342 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2890.54 seconds wall clock time: 52 minutes 10.46 seconds (3130.46 seconds total)