Starting phenix.real_space_refine (version: dev) on Tue Apr 5 02:00:00 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7btw_30189/04_2022/7btw_30189.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7btw_30189/04_2022/7btw_30189.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7btw_30189/04_2022/7btw_30189.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7btw_30189/04_2022/7btw_30189.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7btw_30189/04_2022/7btw_30189.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7btw_30189/04_2022/7btw_30189.pdb" } resolution = 2.9 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 ------------------------------------------------------------------------------- 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= 0.020 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 Convert atoms to be neutral Process input model Symmetric amino acids flipped Residue "A PHE 241": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 285": "OD1" <-> "OD2" Residue "A PHE 413": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 172": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 230": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 241": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 285": "OD1" <-> "OD2" Residue "D PHE 413": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4553/modules/chem_data/mon_lib" Total number of atoms: 10246 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 2775 Number of conformers: 1 Conformer: "" Number of residues, atoms: 348, 2775 Classifications: {'peptide': 348} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 12, 'TRANS': 335} Chain breaks: 1 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 2410 Number of conformers: 1 Conformer: "" Number of residues, atoms: 300, 2410 Classifications: {'peptide': 300} Link IDs: {'PTRANS': 8, 'TRANS': 291} Chain breaks: 2 Chain: "C" Number of atoms: 2286 Number of conformers: 1 Conformer: "" Number of residues, atoms: 284, 2286 Classifications: {'peptide': 284} Link IDs: {'PTRANS': 6, 'TRANS': 277} Chain breaks: 2 Chain: "D" Number of atoms: 2775 Number of conformers: 1 Conformer: "" Number of residues, atoms: 348, 2775 Classifications: {'peptide': 348} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 12, 'TRANS': 335} Chain breaks: 1 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 6.16, per 1000 atoms: 0.60 Number of scatterers: 10246 At special positions: 0 Unit cell: (104.58, 103.335, 103.335, 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 45 16.00 O 1902 8.00 N 1747 7.00 C 6552 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 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: 3.79 Conformation dependent library (CDL) restraints added in 1.7 seconds 2520 Ramachandran restraints generated. 1260 Oldfield, 0 Emsley, 1260 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2394 Finding SS restraints... Secondary structure from input PDB file: 34 helices and 6 sheets defined 31.3% alpha, 39.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.59 Creating SS restraints... Processing helix chain 'A' and resid 263 through 270 removed outlier: 3.639A pdb=" N SER A 268 " --> pdb=" O GLY A 264 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N ALA A 270 " --> pdb=" O MET A 266 " (cutoff:3.500A) Processing helix chain 'A' and resid 427 through 434 removed outlier: 3.537A pdb=" N GLN A 433 " --> pdb=" O ASN A 429 " (cutoff:3.500A) Processing helix chain 'B' and resid 32 through 37 removed outlier: 3.580A pdb=" N GLU B 36 " --> pdb=" O ALA B 32 " (cutoff:3.500A) Processing helix chain 'B' and resid 80 through 95 Processing helix chain 'B' and resid 142 through 152 Processing helix chain 'B' and resid 157 through 181 removed outlier: 3.716A pdb=" N LEU B 171 " --> pdb=" O LEU B 167 " (cutoff:3.500A) removed outlier: 4.798A pdb=" N TYR B 172 " --> pdb=" O ASP B 168 " (cutoff:3.500A) Processing helix chain 'B' and resid 184 through 193 removed outlier: 3.537A pdb=" N LEU B 191 " --> pdb=" O GLN B 187 " (cutoff:3.500A) Processing helix chain 'B' and resid 203 through 216 removed outlier: 3.658A pdb=" N GLN B 213 " --> pdb=" O ASN B 209 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N LYS B 214 " --> pdb=" O SER B 210 " (cutoff:3.500A) Processing helix chain 'B' and resid 216 through 225 removed outlier: 3.615A pdb=" N LEU B 220 " --> pdb=" O SER B 216 " (cutoff:3.500A) Processing helix chain 'B' and resid 229 through 234 Processing helix chain 'B' and resid 234 through 243 removed outlier: 3.794A pdb=" N GLY B 243 " --> pdb=" O LYS B 239 " (cutoff:3.500A) Processing helix chain 'B' and resid 247 through 273 removed outlier: 3.632A pdb=" N SER B 251 " --> pdb=" O ASN B 247 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N VAL B 252 " --> pdb=" O HIS B 248 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N GLN B 267 " --> pdb=" O GLU B 263 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N LYS B 273 " --> pdb=" O LEU B 269 " (cutoff:3.500A) Processing helix chain 'B' and resid 285 through 297 removed outlier: 3.588A pdb=" N TYR B 292 " --> pdb=" O LYS B 288 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N CYS B 295 " --> pdb=" O SER B 291 " (cutoff:3.500A) Processing helix chain 'B' and resid 303 through 312 Processing helix chain 'B' and resid 313 through 323 Processing helix chain 'B' and resid 324 through 327 Processing helix chain 'C' and resid 19 through 31 Processing helix chain 'C' and resid 34 through 40 removed outlier: 3.611A pdb=" N SER C 39 " --> pdb=" O GLU C 35 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N MET C 40 " --> pdb=" O GLU C 36 " (cutoff:3.500A) Processing helix chain 'C' and resid 51 through 55 removed outlier: 3.729A pdb=" N LEU C 54 " --> pdb=" O ASN C 51 " (cutoff:3.500A) Processing helix chain 'C' and resid 73 through 84 Processing helix chain 'C' and resid 104 through 106 No H-bonds generated for 'chain 'C' and resid 104 through 106' Processing helix chain 'C' and resid 107 through 121 Processing helix chain 'C' and resid 121 through 132 removed outlier: 3.914A pdb=" N LEU C 125 " --> pdb=" O GLU C 121 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N PHE C 131 " --> pdb=" O ASP C 127 " (cutoff:3.500A) Processing helix chain 'C' and resid 133 through 140 removed outlier: 3.545A pdb=" N TYR C 140 " --> pdb=" O ASN C 136 " (cutoff:3.500A) Processing helix chain 'C' and resid 141 through 143 No H-bonds generated for 'chain 'C' and resid 141 through 143' Processing helix chain 'C' and resid 144 through 149 removed outlier: 3.506A pdb=" N LEU C 149 " --> pdb=" O PHE C 145 " (cutoff:3.500A) Processing helix chain 'C' and resid 151 through 154 removed outlier: 3.787A pdb=" N TRP C 154 " --> pdb=" O PHE C 151 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 151 through 154' Processing helix chain 'C' and resid 155 through 169 removed outlier: 3.630A pdb=" N GLN C 160 " --> pdb=" O ASN C 156 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N LEU C 161 " --> pdb=" O THR C 157 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N SER C 163 " --> pdb=" O LEU C 159 " (cutoff:3.500A) Processing helix chain 'C' and resid 210 through 244 removed outlier: 3.584A pdb=" N GLU C 215 " --> pdb=" O LYS C 211 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N LEU C 216 " --> pdb=" O GLY C 212 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N LYS C 220 " --> pdb=" O LEU C 216 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N ASP C 226 " --> pdb=" O ASN C 222 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N GLN C 230 " --> pdb=" O ASP C 226 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N LYS C 241 " --> pdb=" O LEU C 237 " (cutoff:3.500A) removed outlier: 4.688A pdb=" N LYS C 242 " --> pdb=" O ALA C 238 " (cutoff:3.500A) removed outlier: 4.318A pdb=" N LEU C 243 " --> pdb=" O ALA C 239 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N ASP C 244 " --> pdb=" O ARG C 240 " (cutoff:3.500A) Processing helix chain 'C' and resid 249 through 263 removed outlier: 3.599A pdb=" N LEU C 254 " --> pdb=" O SER C 250 " (cutoff:3.500A) Processing helix chain 'C' and resid 267 through 296 removed outlier: 4.039A pdb=" N ILE C 271 " --> pdb=" O ASP C 267 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N THR C 278 " --> pdb=" O LYS C 274 " (cutoff:3.500A) removed outlier: 7.563A pdb=" N SER C 281 " --> pdb=" O GLN C 277 " (cutoff:3.500A) removed outlier: 9.266A pdb=" N GLU C 282 " --> pdb=" O THR C 278 " (cutoff:3.500A) removed outlier: 4.351A pdb=" N LEU C 283 " --> pdb=" O PHE C 279 " (cutoff:3.500A) removed outlier: 4.142A pdb=" N LEU C 284 " --> pdb=" O GLY C 280 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N ILE C 291 " --> pdb=" O MET C 287 " (cutoff:3.500A) Processing helix chain 'C' and resid 315 through 327 removed outlier: 4.439A pdb=" N ASN C 321 " --> pdb=" O MET C 317 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N LYS C 325 " --> pdb=" O ASN C 321 " (cutoff:3.500A) Processing helix chain 'D' and resid 263 through 270 removed outlier: 3.639A pdb=" N SER D 268 " --> pdb=" O GLY D 264 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ALA D 270 " --> pdb=" O MET D 266 " (cutoff:3.500A) Processing helix chain 'D' and resid 427 through 434 removed outlier: 3.536A pdb=" N GLN D 433 " --> pdb=" O ASN D 429 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 126 through 129 removed outlier: 3.692A pdb=" N GLY A 128 " --> pdb=" O TYR A 140 " (cutoff:3.500A) removed outlier: 4.069A pdb=" N SER A 171 " --> pdb=" O LEU A 163 " (cutoff:3.500A) removed outlier: 6.496A pdb=" N GLY A 165 " --> pdb=" O HIS A 169 " (cutoff:3.500A) removed outlier: 5.188A pdb=" N HIS A 169 " --> pdb=" O GLY A 165 " (cutoff:3.500A) removed outlier: 5.859A pdb=" N ILE A 168 " --> pdb=" O ASN A 196 " (cutoff:3.500A) removed outlier: 6.298A pdb=" N ASN A 196 " --> pdb=" O ILE A 168 " (cutoff:3.500A) removed outlier: 6.534A pdb=" N SER A 184 " --> pdb=" O LEU A 180 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N GLY A 416 " --> pdb=" O TYR A 390 " (cutoff:3.500A) removed outlier: 6.538A pdb=" N THR A 440 " --> pdb=" O ILE A 463 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N THR A 442 " --> pdb=" O LEU A 461 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 126 through 129 removed outlier: 3.692A pdb=" N GLY A 128 " --> pdb=" O TYR A 140 " (cutoff:3.500A) removed outlier: 4.069A pdb=" N SER A 171 " --> pdb=" O LEU A 163 " (cutoff:3.500A) removed outlier: 6.496A pdb=" N GLY A 165 " --> pdb=" O HIS A 169 " (cutoff:3.500A) removed outlier: 5.188A pdb=" N HIS A 169 " --> pdb=" O GLY A 165 " (cutoff:3.500A) removed outlier: 5.859A pdb=" N ILE A 168 " --> pdb=" O ASN A 196 " (cutoff:3.500A) removed outlier: 6.298A pdb=" N ASN A 196 " --> pdb=" O ILE A 168 " (cutoff:3.500A) removed outlier: 6.534A pdb=" N SER A 184 " --> pdb=" O LEU A 180 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N GLY A 416 " --> pdb=" O TYR A 390 " (cutoff:3.500A) removed outlier: 6.538A pdb=" N THR A 440 " --> pdb=" O ILE A 463 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N THR A 442 " --> pdb=" O LEU A 461 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N GLN B 21 " --> pdb=" O ILE A 463 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 41 through 42 removed outlier: 3.733A pdb=" N ILE B 130 " --> pdb=" O GLY B 63 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 67 through 69 Processing sheet with id=AA5, first strand: chain 'C' and resid 44 through 47 removed outlier: 7.038A pdb=" N GLY C 4 " --> pdb=" O GLN C 45 " (cutoff:3.500A) removed outlier: 7.804A pdb=" N VAL C 47 " --> pdb=" O GLY C 4 " (cutoff:3.500A) removed outlier: 6.059A pdb=" N VAL C 6 " --> pdb=" O VAL C 47 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'D' and resid 126 through 127 removed outlier: 4.069A pdb=" N SER D 171 " --> pdb=" O LEU D 163 " (cutoff:3.500A) removed outlier: 5.859A pdb=" N ILE D 168 " --> pdb=" O ASN D 196 " (cutoff:3.500A) removed outlier: 6.297A pdb=" N ASN D 196 " --> pdb=" O ILE D 168 " (cutoff:3.500A) removed outlier: 6.533A pdb=" N SER D 184 " --> pdb=" O LEU D 180 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N GLY D 416 " --> pdb=" O TYR D 390 " (cutoff:3.500A) removed outlier: 6.539A pdb=" N THR D 440 " --> pdb=" O ILE D 463 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N THR D 442 " --> pdb=" O LEU D 461 " (cutoff:3.500A) 653 hydrogen bonds defined for protein. 1863 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: 3.20 Time building geometry restraints manager: 4.13 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.02 - 1.18: 9 1.18 - 1.34: 3201 1.34 - 1.50: 2926 1.50 - 1.65: 4261 1.65 - 1.81: 67 Bond restraints: 10464 Sorted by residual: bond pdb=" C ARG D 164 " pdb=" O ARG D 164 " ideal model delta sigma weight residual 1.234 1.023 0.211 1.28e-02 6.10e+03 2.72e+02 bond pdb=" CA ASN A 135 " pdb=" C ASN A 135 " ideal model delta sigma weight residual 1.522 1.309 0.212 1.33e-02 5.65e+03 2.55e+02 bond pdb=" C ARG A 164 " pdb=" O ARG A 164 " ideal model delta sigma weight residual 1.234 1.106 0.128 1.11e-02 8.12e+03 1.33e+02 bond pdb=" C ASN A 135 " pdb=" O ASN A 135 " ideal model delta sigma weight residual 1.238 1.032 0.206 1.83e-02 2.99e+03 1.27e+02 bond pdb=" C ASN A 133 " pdb=" O ASN A 133 " ideal model delta sigma weight residual 1.236 1.148 0.089 1.16e-02 7.43e+03 5.88e+01 ... (remaining 10459 not shown) Histogram of bond angle deviations from ideal: 95.85 - 103.96: 105 103.96 - 112.06: 4942 112.06 - 120.16: 4590 120.16 - 128.26: 4401 128.26 - 136.37: 92 Bond angle restraints: 14130 Sorted by residual: angle pdb=" N ASN A 135 " pdb=" CA ASN A 135 " pdb=" C ASN A 135 " ideal model delta sigma weight residual 113.56 95.85 17.71 1.39e+00 5.18e-01 1.62e+02 angle pdb=" O LEU D 163 " pdb=" C LEU D 163 " pdb=" N ARG D 164 " ideal model delta sigma weight residual 123.29 110.02 13.27 1.18e+00 7.18e-01 1.27e+02 angle pdb=" CA LEU D 163 " pdb=" C LEU D 163 " pdb=" N ARG D 164 " ideal model delta sigma weight residual 116.28 127.17 -10.89 1.26e+00 6.30e-01 7.47e+01 angle pdb=" C ALA D 139 " pdb=" N TYR D 140 " pdb=" CA TYR D 140 " ideal model delta sigma weight residual 122.81 108.60 14.21 1.68e+00 3.54e-01 7.15e+01 angle pdb=" C ARG D 164 " pdb=" N GLY D 165 " pdb=" CA GLY D 165 " ideal model delta sigma weight residual 120.84 136.37 -15.53 1.91e+00 2.74e-01 6.61e+01 ... (remaining 14125 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.14: 5301 17.14 - 34.29: 636 34.29 - 51.43: 200 51.43 - 68.57: 83 68.57 - 85.72: 14 Dihedral angle restraints: 6234 sinusoidal: 2526 harmonic: 3708 Sorted by residual: dihedral pdb=" CA LEU C 60 " pdb=" C LEU C 60 " pdb=" N PRO C 61 " pdb=" CA PRO C 61 " ideal model delta harmonic sigma weight residual 180.00 129.36 50.64 0 5.00e+00 4.00e-02 1.03e+02 dihedral pdb=" N ASN A 133 " pdb=" C ASN A 133 " pdb=" CA ASN A 133 " pdb=" CB ASN A 133 " ideal model delta harmonic sigma weight residual 122.80 142.10 -19.30 0 2.50e+00 1.60e-01 5.96e+01 dihedral pdb=" CA THR D 199 " pdb=" C THR D 199 " pdb=" N ASN D 200 " pdb=" CA ASN D 200 " ideal model delta harmonic sigma weight residual 180.00 142.03 37.97 0 5.00e+00 4.00e-02 5.77e+01 ... (remaining 6231 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.149: 1542 0.149 - 0.298: 27 0.298 - 0.447: 3 0.447 - 0.596: 0 0.596 - 0.745: 2 Chirality restraints: 1574 Sorted by residual: chirality pdb=" CA THR C 87 " pdb=" N THR C 87 " pdb=" C THR C 87 " pdb=" CB THR C 87 " both_signs ideal model delta sigma weight residual False 2.53 1.78 0.74 2.00e-01 2.50e+01 1.39e+01 chirality pdb=" CA ASN A 133 " pdb=" N ASN A 133 " pdb=" C ASN A 133 " pdb=" CB ASN A 133 " both_signs ideal model delta sigma weight residual False 2.51 1.82 0.69 2.00e-01 2.50e+01 1.19e+01 chirality pdb=" CA LEU B 128 " pdb=" N LEU B 128 " pdb=" C LEU B 128 " pdb=" CB LEU B 128 " both_signs ideal model delta sigma weight residual False 2.51 2.08 0.43 2.00e-01 2.50e+01 4.54e+00 ... (remaining 1571 not shown) Planarity restraints: 1790 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASN A 135 " 0.029 2.00e-02 2.50e+03 5.49e-02 3.02e+01 pdb=" C ASN A 135 " -0.095 2.00e-02 2.50e+03 pdb=" O ASN A 135 " 0.034 2.00e-02 2.50e+03 pdb=" N ASP A 136 " 0.032 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU D 163 " 0.026 2.00e-02 2.50e+03 4.62e-02 2.13e+01 pdb=" C LEU D 163 " -0.080 2.00e-02 2.50e+03 pdb=" O LEU D 163 " 0.027 2.00e-02 2.50e+03 pdb=" N ARG D 164 " 0.028 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LEU C 60 " -0.074 5.00e-02 4.00e+02 1.11e-01 1.96e+01 pdb=" N PRO C 61 " 0.191 5.00e-02 4.00e+02 pdb=" CA PRO C 61 " -0.058 5.00e-02 4.00e+02 pdb=" CD PRO C 61 " -0.059 5.00e-02 4.00e+02 ... (remaining 1787 not shown) Histogram of nonbonded interaction distances: 1.56 - 2.22: 1 2.22 - 2.89: 3711 2.89 - 3.56: 13062 3.56 - 4.23: 24478 4.23 - 4.90: 42307 Nonbonded interactions: 83559 Sorted by model distance: nonbonded pdb=" O THR D 129 " pdb=" O ALA D 137 " model vdw 1.556 3.040 nonbonded pdb=" ND2 ASN D 130 " pdb=" O GLU D 138 " model vdw 2.231 2.520 nonbonded pdb=" N ASN A 135 " pdb=" N ASP A 136 " model vdw 2.232 2.560 nonbonded pdb=" OG SER B 184 " pdb=" OE2 GLU B 301 " model vdw 2.278 2.440 nonbonded pdb=" OG SER A 344 " pdb=" O SER A 348 " model vdw 2.279 2.440 ... (remaining 83554 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 45 5.16 5 C 6552 2.51 5 N 1747 2.21 5 O 1902 1.98 5 sf(0) = scattering factor at diffraction angle 0. 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: 0.430 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: 0.020 Extract box with map and model: 2.200 Check model and map are aligned: 0.170 Convert atoms to be neutral: 0.090 Process input model: 29.530 Find NCS groups from input model: 0.460 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Set scattering table: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:12.290 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 45.250 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7588 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 : 0.008 0.212 10464 Z= 0.531 Angle : 1.122 17.707 14130 Z= 0.625 Chirality : 0.063 0.745 1574 Planarity : 0.008 0.111 1790 Dihedral : 18.161 85.718 3840 Min Nonbonded Distance : 1.556 Molprobity Statistics. All-atom Clashscore : 6.99 Ramachandran Plot: Outliers : 0.40 % Allowed : 8.02 % Favored : 91.59 % Rotamer Outliers : 9.60 % Cbeta Deviations : 0.25 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.63 % Twisted General : 0.49 % 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: -5.22 (0.18), residues: 1260 helix: -4.29 (0.11), residues: 360 sheet: -2.41 (0.24), residues: 384 loop : -3.49 (0.22), residues: 516 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2520 Ramachandran restraints generated. 1260 Oldfield, 0 Emsley, 1260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2520 Ramachandran restraints generated. 1260 Oldfield, 0 Emsley, 1260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 296 residues out of total 1148 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 110 poor density : 186 time to evaluate : 1.304 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 110 outliers final: 13 residues processed: 276 average time/residue: 1.0255 time to fit residues: 306.6863 Evaluate side-chains 131 residues out of total 1148 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 118 time to evaluate : 1.218 Switching outliers to nearest non-outliers outliers start: 13 outliers final: 11 residues processed: 2 average time/residue: 0.8455 time to fit residues: 3.5735 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 106 optimal weight: 5.9990 chunk 95 optimal weight: 3.9990 chunk 52 optimal weight: 4.9990 chunk 32 optimal weight: 3.9990 chunk 64 optimal weight: 4.9990 chunk 51 optimal weight: 0.0470 chunk 98 optimal weight: 1.9990 chunk 38 optimal weight: 0.6980 chunk 60 optimal weight: 0.6980 chunk 73 optimal weight: 6.9990 chunk 114 optimal weight: 2.9990 overall best weight: 1.2882 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 273 GLN A 422 HIS ** A 424 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 458 ASN A 476 GLN B 72 ASN ** B 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 256 GLN C 7 HIS C 82 HIS C 138 ASN C 222 ASN C 269 ASN D 175 ASN D 200 ASN D 254 GLN D 280 HIS D 303 ASN D 346 GLN D 422 HIS D 429 ASN ** D 450 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7713 moved from start: 0.2717 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.073 10464 Z= 0.251 Angle : 0.704 9.846 14130 Z= 0.377 Chirality : 0.044 0.239 1574 Planarity : 0.006 0.089 1790 Dihedral : 6.622 41.099 1365 Min Nonbonded Distance : 2.159 Molprobity Statistics. All-atom Clashscore : 10.31 Ramachandran Plot: Outliers : 0.16 % Allowed : 7.54 % Favored : 92.30 % Rotamer Outliers : 4.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.63 % Twisted General : 0.32 % 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: -3.69 (0.20), residues: 1260 helix: -1.85 (0.22), residues: 369 sheet: -1.79 (0.25), residues: 358 loop : -3.29 (0.21), residues: 533 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2520 Ramachandran restraints generated. 1260 Oldfield, 0 Emsley, 1260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2520 Ramachandran restraints generated. 1260 Oldfield, 0 Emsley, 1260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 1148 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 129 time to evaluate : 1.224 Fit side-chains outliers start: 53 outliers final: 20 residues processed: 168 average time/residue: 0.9892 time to fit residues: 181.7518 Evaluate side-chains 116 residues out of total 1148 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 96 time to evaluate : 1.212 Switching outliers to nearest non-outliers outliers start: 20 outliers final: 17 residues processed: 4 average time/residue: 0.3533 time to fit residues: 3.4494 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 63 optimal weight: 3.9990 chunk 35 optimal weight: 4.9990 chunk 95 optimal weight: 5.9990 chunk 77 optimal weight: 0.0000 chunk 31 optimal weight: 7.9990 chunk 114 optimal weight: 2.9990 chunk 123 optimal weight: 1.9990 chunk 102 optimal weight: 3.9990 chunk 113 optimal weight: 1.9990 chunk 39 optimal weight: 0.6980 chunk 91 optimal weight: 0.7980 overall best weight: 1.0988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 72 ASN ** B 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 253 ASN C 84 ASN ** C 168 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 300 ASN D 273 GLN D 303 ASN D 346 GLN D 369 GLN ** D 450 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 458 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7730 moved from start: 0.3232 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.074 10464 Z= 0.218 Angle : 0.634 9.409 14130 Z= 0.341 Chirality : 0.043 0.222 1574 Planarity : 0.006 0.085 1790 Dihedral : 6.201 40.204 1365 Min Nonbonded Distance : 2.164 Molprobity Statistics. All-atom Clashscore : 9.92 Ramachandran Plot: Outliers : 0.16 % Allowed : 7.46 % Favored : 92.38 % Rotamer Outliers : 4.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.63 % Twisted General : 0.08 % 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: -2.70 (0.22), residues: 1260 helix: -0.28 (0.26), residues: 374 sheet: -1.52 (0.24), residues: 367 loop : -3.13 (0.22), residues: 519 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2520 Ramachandran restraints generated. 1260 Oldfield, 0 Emsley, 1260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2520 Ramachandran restraints generated. 1260 Oldfield, 0 Emsley, 1260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 1148 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 124 time to evaluate : 1.204 Fit side-chains outliers start: 57 outliers final: 30 residues processed: 171 average time/residue: 0.9717 time to fit residues: 182.0283 Evaluate side-chains 135 residues out of total 1148 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 105 time to evaluate : 1.243 Switching outliers to nearest non-outliers outliers start: 30 outliers final: 26 residues processed: 4 average time/residue: 0.1104 time to fit residues: 2.4901 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 113 optimal weight: 10.0000 chunk 86 optimal weight: 3.9990 chunk 59 optimal weight: 3.9990 chunk 12 optimal weight: 0.4980 chunk 54 optimal weight: 1.9990 chunk 76 optimal weight: 0.9990 chunk 115 optimal weight: 3.9990 chunk 121 optimal weight: 7.9990 chunk 60 optimal weight: 0.9980 chunk 109 optimal weight: 3.9990 chunk 32 optimal weight: 7.9990 overall best weight: 1.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 310 HIS A 318 ASN A 347 GLN ** B 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 249 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 129 GLN D 207 GLN D 346 GLN ** D 450 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7786 moved from start: 0.3687 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.078 10464 Z= 0.295 Angle : 0.668 9.863 14130 Z= 0.358 Chirality : 0.045 0.243 1574 Planarity : 0.006 0.094 1790 Dihedral : 6.215 40.442 1365 Min Nonbonded Distance : 2.112 Molprobity Statistics. All-atom Clashscore : 10.21 Ramachandran Plot: Outliers : 0.16 % Allowed : 7.78 % Favored : 92.06 % Rotamer Outliers : 5.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.63 % Twisted General : 0.16 % 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: -2.38 (0.22), residues: 1260 helix: 0.23 (0.27), residues: 372 sheet: -1.29 (0.25), residues: 362 loop : -3.17 (0.22), residues: 526 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2520 Ramachandran restraints generated. 1260 Oldfield, 0 Emsley, 1260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2520 Ramachandran restraints generated. 1260 Oldfield, 0 Emsley, 1260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 1148 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 113 time to evaluate : 1.219 Fit side-chains outliers start: 65 outliers final: 36 residues processed: 171 average time/residue: 1.0398 time to fit residues: 193.5897 Evaluate side-chains 138 residues out of total 1148 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 102 time to evaluate : 1.274 Switching outliers to nearest non-outliers outliers start: 36 outliers final: 32 residues processed: 4 average time/residue: 0.1036 time to fit residues: 2.5406 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 101 optimal weight: 8.9990 chunk 69 optimal weight: 4.9990 chunk 1 optimal weight: 1.9990 chunk 90 optimal weight: 1.9990 chunk 50 optimal weight: 1.9990 chunk 103 optimal weight: 5.9990 chunk 84 optimal weight: 3.9990 chunk 0 optimal weight: 1.9990 chunk 62 optimal weight: 0.4980 chunk 109 optimal weight: 3.9990 chunk 30 optimal weight: 10.0000 overall best weight: 1.6988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 347 GLN ** B 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 249 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 346 GLN ** D 347 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 450 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7801 moved from start: 0.3977 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.057 10464 Z= 0.287 Angle : 0.663 10.166 14130 Z= 0.353 Chirality : 0.045 0.236 1574 Planarity : 0.006 0.092 1790 Dihedral : 6.125 40.081 1365 Min Nonbonded Distance : 2.120 Molprobity Statistics. All-atom Clashscore : 10.21 Ramachandran Plot: Outliers : 0.16 % Allowed : 8.02 % Favored : 91.83 % Rotamer Outliers : 6.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.63 % Twisted General : 0.08 % 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: -2.16 (0.22), residues: 1260 helix: 0.45 (0.27), residues: 373 sheet: -1.21 (0.25), residues: 362 loop : -3.04 (0.23), residues: 525 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2520 Ramachandran restraints generated. 1260 Oldfield, 0 Emsley, 1260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2520 Ramachandran restraints generated. 1260 Oldfield, 0 Emsley, 1260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 1148 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 112 time to evaluate : 1.309 Fit side-chains outliers start: 70 outliers final: 38 residues processed: 173 average time/residue: 0.9979 time to fit residues: 188.5857 Evaluate side-chains 141 residues out of total 1148 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 103 time to evaluate : 1.203 Switching outliers to nearest non-outliers outliers start: 38 outliers final: 36 residues processed: 2 average time/residue: 0.1067 time to fit residues: 1.9499 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 40 optimal weight: 2.9990 chunk 109 optimal weight: 4.9990 chunk 24 optimal weight: 6.9990 chunk 71 optimal weight: 2.9990 chunk 30 optimal weight: 9.9990 chunk 121 optimal weight: 9.9990 chunk 101 optimal weight: 8.9990 chunk 56 optimal weight: 6.9990 chunk 10 optimal weight: 0.9980 chunk 64 optimal weight: 0.0270 chunk 117 optimal weight: 1.9990 overall best weight: 1.8044 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 249 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 346 GLN ** D 450 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7816 moved from start: 0.4171 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.061 10464 Z= 0.302 Angle : 0.670 9.954 14130 Z= 0.357 Chirality : 0.045 0.242 1574 Planarity : 0.006 0.093 1790 Dihedral : 6.139 40.909 1365 Min Nonbonded Distance : 2.105 Molprobity Statistics. All-atom Clashscore : 10.07 Ramachandran Plot: Outliers : 0.16 % Allowed : 7.70 % Favored : 92.14 % Rotamer Outliers : 5.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.63 % Twisted General : 0.08 % 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: -1.94 (0.22), residues: 1260 helix: 0.62 (0.27), residues: 373 sheet: -1.02 (0.25), residues: 358 loop : -2.94 (0.23), residues: 529 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2520 Ramachandran restraints generated. 1260 Oldfield, 0 Emsley, 1260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2520 Ramachandran restraints generated. 1260 Oldfield, 0 Emsley, 1260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 1148 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 110 time to evaluate : 1.282 Fit side-chains outliers start: 68 outliers final: 41 residues processed: 167 average time/residue: 0.9911 time to fit residues: 181.5467 Evaluate side-chains 142 residues out of total 1148 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 101 time to evaluate : 1.366 Switching outliers to nearest non-outliers outliers start: 41 outliers final: 39 residues processed: 2 average time/residue: 0.1237 time to fit residues: 2.2799 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 13 optimal weight: 2.9990 chunk 69 optimal weight: 3.9990 chunk 89 optimal weight: 3.9990 chunk 68 optimal weight: 6.9990 chunk 102 optimal weight: 7.9990 chunk 121 optimal weight: 0.5980 chunk 76 optimal weight: 2.9990 chunk 74 optimal weight: 2.9990 chunk 56 optimal weight: 7.9990 chunk 75 optimal weight: 0.7980 chunk 48 optimal weight: 3.9990 overall best weight: 2.0786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 249 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 346 GLN ** D 450 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7835 moved from start: 0.4315 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.077 10464 Z= 0.340 Angle : 0.702 10.400 14130 Z= 0.372 Chirality : 0.046 0.250 1574 Planarity : 0.007 0.097 1790 Dihedral : 6.216 41.690 1365 Min Nonbonded Distance : 2.090 Molprobity Statistics. All-atom Clashscore : 9.97 Ramachandran Plot: Outliers : 0.08 % Allowed : 8.10 % Favored : 91.83 % Rotamer Outliers : 6.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.63 % Twisted General : 0.08 % 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: -1.92 (0.22), residues: 1260 helix: 0.64 (0.27), residues: 373 sheet: -1.03 (0.25), residues: 353 loop : -2.89 (0.23), residues: 534 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2520 Ramachandran restraints generated. 1260 Oldfield, 0 Emsley, 1260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2520 Ramachandran restraints generated. 1260 Oldfield, 0 Emsley, 1260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 1148 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 108 time to evaluate : 1.240 Fit side-chains outliers start: 69 outliers final: 41 residues processed: 167 average time/residue: 0.9472 time to fit residues: 173.9872 Evaluate side-chains 141 residues out of total 1148 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 100 time to evaluate : 1.247 Switching outliers to nearest non-outliers outliers start: 41 outliers final: 35 residues processed: 6 average time/residue: 0.1165 time to fit residues: 2.9171 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 72 optimal weight: 0.1980 chunk 36 optimal weight: 2.9990 chunk 23 optimal weight: 1.9990 chunk 77 optimal weight: 3.9990 chunk 82 optimal weight: 0.9990 chunk 60 optimal weight: 0.7980 chunk 11 optimal weight: 4.9990 chunk 95 optimal weight: 4.9990 chunk 110 optimal weight: 3.9990 chunk 116 optimal weight: 7.9990 chunk 106 optimal weight: 6.9990 overall best weight: 1.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 234 HIS ** B 249 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 346 GLN D 450 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7805 moved from start: 0.4423 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.089 10464 Z= 0.262 Angle : 0.655 10.349 14130 Z= 0.348 Chirality : 0.044 0.226 1574 Planarity : 0.006 0.104 1790 Dihedral : 5.998 40.784 1365 Min Nonbonded Distance : 2.126 Molprobity Statistics. All-atom Clashscore : 10.46 Ramachandran Plot: Outliers : 0.08 % Allowed : 7.78 % Favored : 92.14 % Rotamer Outliers : 4.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.63 % Twisted General : 0.08 % 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: -1.78 (0.23), residues: 1260 helix: 0.89 (0.27), residues: 374 sheet: -1.10 (0.26), residues: 340 loop : -2.77 (0.23), residues: 546 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2520 Ramachandran restraints generated. 1260 Oldfield, 0 Emsley, 1260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2520 Ramachandran restraints generated. 1260 Oldfield, 0 Emsley, 1260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 1148 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 108 time to evaluate : 1.207 Fit side-chains outliers start: 54 outliers final: 37 residues processed: 155 average time/residue: 1.0242 time to fit residues: 173.3217 Evaluate side-chains 147 residues out of total 1148 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 110 time to evaluate : 1.201 Switching outliers to nearest non-outliers outliers start: 37 outliers final: 33 residues processed: 4 average time/residue: 0.3614 time to fit residues: 3.5171 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 113 optimal weight: 5.9990 chunk 116 optimal weight: 9.9990 chunk 68 optimal weight: 6.9990 chunk 49 optimal weight: 2.9990 chunk 88 optimal weight: 9.9990 chunk 34 optimal weight: 0.0670 chunk 102 optimal weight: 5.9990 chunk 107 optimal weight: 1.9990 chunk 112 optimal weight: 1.9990 chunk 74 optimal weight: 3.9990 chunk 119 optimal weight: 5.9990 overall best weight: 2.2126 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 249 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 346 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7844 moved from start: 0.4491 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.105 10464 Z= 0.363 Angle : 0.716 10.578 14130 Z= 0.379 Chirality : 0.047 0.253 1574 Planarity : 0.007 0.112 1790 Dihedral : 6.200 43.130 1365 Min Nonbonded Distance : 2.075 Molprobity Statistics. All-atom Clashscore : 10.21 Ramachandran Plot: Outliers : 0.08 % Allowed : 8.81 % Favored : 91.11 % Rotamer Outliers : 4.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.63 % Twisted General : 0.08 % 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: -1.83 (0.23), residues: 1260 helix: 0.71 (0.27), residues: 375 sheet: -0.96 (0.25), residues: 357 loop : -2.88 (0.24), residues: 528 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2520 Ramachandran restraints generated. 1260 Oldfield, 0 Emsley, 1260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2520 Ramachandran restraints generated. 1260 Oldfield, 0 Emsley, 1260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 1148 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 104 time to evaluate : 1.241 Fit side-chains outliers start: 46 outliers final: 36 residues processed: 146 average time/residue: 1.0715 time to fit residues: 170.1786 Evaluate side-chains 137 residues out of total 1148 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 101 time to evaluate : 1.221 Switching outliers to nearest non-outliers outliers start: 36 outliers final: 35 residues processed: 1 average time/residue: 0.1395 time to fit residues: 1.9494 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 73 optimal weight: 0.9990 chunk 56 optimal weight: 6.9990 chunk 83 optimal weight: 1.9990 chunk 125 optimal weight: 0.8980 chunk 115 optimal weight: 1.9990 chunk 99 optimal weight: 4.9990 chunk 10 optimal weight: 3.9990 chunk 77 optimal weight: 0.7980 chunk 61 optimal weight: 6.9990 chunk 79 optimal weight: 2.9990 chunk 106 optimal weight: 6.9990 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 247 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 249 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 346 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7803 moved from start: 0.4542 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.120 10464 Z= 0.270 Angle : 0.670 10.751 14130 Z= 0.359 Chirality : 0.044 0.225 1574 Planarity : 0.007 0.120 1790 Dihedral : 5.961 40.013 1365 Min Nonbonded Distance : 2.126 Molprobity Statistics. All-atom Clashscore : 10.55 Ramachandran Plot: Outliers : 0.08 % Allowed : 7.62 % Favored : 92.30 % Rotamer Outliers : 3.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.63 % Twisted General : 0.08 % 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: -1.59 (0.23), residues: 1260 helix: 1.02 (0.28), residues: 368 sheet: -0.84 (0.25), residues: 365 loop : -2.80 (0.24), residues: 527 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2520 Ramachandran restraints generated. 1260 Oldfield, 0 Emsley, 1260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2520 Ramachandran restraints generated. 1260 Oldfield, 0 Emsley, 1260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 1148 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 105 time to evaluate : 1.286 Fit side-chains outliers start: 41 outliers final: 34 residues processed: 144 average time/residue: 1.0140 time to fit residues: 159.9271 Evaluate side-chains 130 residues out of total 1148 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 96 time to evaluate : 1.227 Switching outliers to nearest non-outliers outliers start: 34 outliers final: 33 residues processed: 2 average time/residue: 0.1407 time to fit residues: 2.1247 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 30 optimal weight: 9.9990 chunk 92 optimal weight: 7.9990 chunk 14 optimal weight: 2.9990 chunk 27 optimal weight: 5.9990 chunk 100 optimal weight: 1.9990 chunk 41 optimal weight: 0.7980 chunk 102 optimal weight: 4.9990 chunk 12 optimal weight: 0.1980 chunk 18 optimal weight: 4.9990 chunk 87 optimal weight: 10.0000 chunk 5 optimal weight: 5.9990 overall best weight: 2.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 249 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 130 ASN D 207 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3929 r_free = 0.3929 target = 0.171007 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3588 r_free = 0.3588 target = 0.138119 restraints weight = 10533.196| |-----------------------------------------------------------------------------| r_work (start): 0.3590 rms_B_bonded: 1.97 r_work: 0.3561 rms_B_bonded: 1.74 restraints_weight: 0.5000 r_work: 0.3541 rms_B_bonded: 1.79 restraints_weight: 0.2500 r_work: 0.3518 rms_B_bonded: 1.97 restraints_weight: 0.1250 r_work: 0.3488 rms_B_bonded: 2.29 restraints_weight: 0.0625 r_work: 0.3451 rms_B_bonded: 2.78 restraints_weight: 0.0312 r_work: 0.3400 rms_B_bonded: 3.52 restraints_weight: 0.0156 r_work: 0.3330 rms_B_bonded: 4.66 restraints_weight: 0.0078 r_work (final): 0.3330 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7976 moved from start: 0.4569 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.123 10464 Z= 0.368 Angle : 0.738 10.553 14130 Z= 0.392 Chirality : 0.047 0.253 1574 Planarity : 0.007 0.121 1790 Dihedral : 6.190 43.541 1365 Min Nonbonded Distance : 2.075 Molprobity Statistics. All-atom Clashscore : 11.09 Ramachandran Plot: Outliers : 0.08 % Allowed : 8.49 % Favored : 91.43 % Rotamer Outliers : 3.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.63 % Twisted General : 0.08 % 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: -1.74 (0.23), residues: 1260 helix: 0.81 (0.28), residues: 370 sheet: -0.84 (0.26), residues: 356 loop : -2.88 (0.23), residues: 534 =============================================================================== Job complete usr+sys time: 3253.73 seconds wall clock time: 59 minutes 9.21 seconds (3549.21 seconds total)