Starting phenix.real_space_refine (version: dev) on Thu May 12 17:46:21 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5w3h_8756/05_2022/5w3h_8756_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5w3h_8756/05_2022/5w3h_8756.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5w3h_8756/05_2022/5w3h_8756_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5w3h_8756/05_2022/5w3h_8756_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5w3h_8756/05_2022/5w3h_8756_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5w3h_8756/05_2022/5w3h_8756.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5w3h_8756/05_2022/5w3h_8756.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5w3h_8756/05_2022/5w3h_8756_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5w3h_8756/05_2022/5w3h_8756_updated.pdb" } resolution = 4.0 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- 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= 0.048 sd= 1.119 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 53": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 54": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 59": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 84": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 104": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 109": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 162": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 186": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 211": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 263": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 283": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 285": "OE1" <-> "OE2" Residue "A PHE 352": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 405": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 409": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 419": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 433": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 31": "OD1" <-> "OD2" Residue "B PHE 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 50": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 51": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 90": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 92": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 106": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 159": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 200": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 203": "OD1" <-> "OD2" Residue "B TYR 208": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 222": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 242": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 266": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 281": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 294": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 310": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 340": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 341": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 394": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 398": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 408": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 422": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 425": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4597/modules/chem_data/mon_lib" Total number of atoms: 6876 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 3438 Number of conformers: 1 Conformer: "" Number of residues, atoms: 440, 3438 Classifications: {'peptide': 440} Link IDs: {'PTRANS': 21, 'TRANS': 418} Chain: "B" Number of atoms: 3343 Number of conformers: 1 Conformer: "" Number of residues, atoms: 427, 3343 Classifications: {'peptide': 427} Link IDs: {'PTRANS': 15, 'TRANS': 410, 'PCIS': 1} Chain: "A" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 33 Unusual residues: {'GTP': 1, ' MG': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 62 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 62 Unusual residues: {'GDP': 1, ' EP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 4.39, per 1000 atoms: 0.64 Number of scatterers: 6876 At special positions: 0 Unit cell: (71.28, 73.92, 113.52, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 41 16.00 P 5 15.00 Mg 1 11.99 O 1351 8.00 N 1167 7.00 C 4311 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: 3.01 Conformation dependent library (CDL) restraints added in 1.1 seconds 1726 Ramachandran restraints generated. 863 Oldfield, 0 Emsley, 863 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1600 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 42 helices and 5 sheets defined 49.7% alpha, 13.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.89 Creating SS restraints... Processing helix chain 'A' and resid 10 through 28 Processing helix chain 'A' and resid 47 through 50 No H-bonds generated for 'chain 'A' and resid 47 through 50' Processing helix chain 'A' and resid 58 through 60 No H-bonds generated for 'chain 'A' and resid 58 through 60' Processing helix chain 'A' and resid 73 through 80 Processing helix chain 'A' and resid 83 through 86 removed outlier: 4.018A pdb=" N ASP A 86 " --> pdb=" O PRO A 83 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 83 through 86' Processing helix chain 'A' and resid 90 through 92 No H-bonds generated for 'chain 'A' and resid 90 through 92' Processing helix chain 'A' and resid 104 through 109 Processing helix chain 'A' and resid 111 through 129 removed outlier: 4.103A pdb=" N ILE A 115 " --> pdb=" O VAL A 111 " (cutoff:3.500A) removed outlier: 4.448A pdb=" N GLY A 117 " --> pdb=" O ARG A 113 " (cutoff:3.500A) removed outlier: 5.316A pdb=" N ASP A 118 " --> pdb=" O GLU A 114 " (cutoff:3.500A) Processing helix chain 'A' and resid 146 through 161 Processing helix chain 'A' and resid 184 through 198 removed outlier: 3.908A pdb=" N THR A 194 " --> pdb=" O LEU A 190 " (cutoff:3.500A) removed outlier: 4.139A pdb=" N GLU A 197 " --> pdb=" O HIS A 193 " (cutoff:3.500A) Processing helix chain 'A' and resid 207 through 216 Processing helix chain 'A' and resid 225 through 244 removed outlier: 4.590A pdb=" N SER A 242 " --> pdb=" O SER A 238 " (cutoff:3.500A) removed outlier: 5.110A pdb=" N LEU A 243 " --> pdb=" O VAL A 239 " (cutoff:3.500A) Processing helix chain 'A' and resid 253 through 260 Processing helix chain 'A' and resid 282 through 284 No H-bonds generated for 'chain 'A' and resid 282 through 284' Processing helix chain 'A' and resid 289 through 297 removed outlier: 3.607A pdb=" N PHE A 297 " --> pdb=" O THR A 293 " (cutoff:3.500A) Processing helix chain 'A' and resid 299 through 301 No H-bonds generated for 'chain 'A' and resid 299 through 301' Processing helix chain 'A' and resid 308 through 310 No H-bonds generated for 'chain 'A' and resid 308 through 310' Processing helix chain 'A' and resid 326 through 339 Processing helix chain 'A' and resid 383 through 401 removed outlier: 3.916A pdb=" N LEU A 398 " --> pdb=" O LYS A 395 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N ALA A 401 " --> pdb=" O LEU A 398 " (cutoff:3.500A) Processing helix chain 'A' and resid 406 through 412 removed outlier: 4.137A pdb=" N GLU A 412 " --> pdb=" O TRP A 408 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 439 removed outlier: 3.502A pdb=" N ASP A 439 " --> pdb=" O GLU A 435 " (cutoff:3.500A) Processing helix chain 'B' and resid 10 through 28 Processing helix chain 'B' and resid 41 through 48 removed outlier: 4.381A pdb=" N ARG B 46 " --> pdb=" O ILE B 42 " (cutoff:3.500A) removed outlier: 5.006A pdb=" N ASN B 48 " --> pdb=" O LYS B 44 " (cutoff:3.500A) Processing helix chain 'B' and resid 55 through 57 No H-bonds generated for 'chain 'B' and resid 55 through 57' Processing helix chain 'B' and resid 70 through 78 Processing helix chain 'B' and resid 87 through 89 No H-bonds generated for 'chain 'B' and resid 87 through 89' Processing helix chain 'B' and resid 101 through 105 Processing helix chain 'B' and resid 109 through 111 No H-bonds generated for 'chain 'B' and resid 109 through 111' Processing helix chain 'B' and resid 113 through 125 Processing helix chain 'B' and resid 143 through 158 Processing helix chain 'B' and resid 181 through 195 removed outlier: 3.800A pdb=" N GLN B 191 " --> pdb=" O LEU B 187 " (cutoff:3.500A) removed outlier: 4.125A pdb=" N GLU B 194 " --> pdb=" O HIS B 190 " (cutoff:3.500A) Processing helix chain 'B' and resid 204 through 213 Processing helix chain 'B' and resid 222 through 241 removed outlier: 3.523A pdb=" N THR B 237 " --> pdb=" O MET B 233 " (cutoff:3.500A) removed outlier: 5.118A pdb=" N SER B 239 " --> pdb=" O GLY B 235 " (cutoff:3.500A) removed outlier: 5.613A pdb=" N LEU B 240 " --> pdb=" O VAL B 236 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ARG B 241 " --> pdb=" O THR B 237 " (cutoff:3.500A) Processing helix chain 'B' and resid 250 through 257 Processing helix chain 'B' and resid 278 through 281 Processing helix chain 'B' and resid 286 through 294 Processing helix chain 'B' and resid 296 through 298 No H-bonds generated for 'chain 'B' and resid 296 through 298' Processing helix chain 'B' and resid 323 through 336 Processing helix chain 'B' and resid 338 through 340 No H-bonds generated for 'chain 'B' and resid 338 through 340' Processing helix chain 'B' and resid 372 through 391 removed outlier: 4.000A pdb=" N VAL B 381 " --> pdb=" O PHE B 378 " (cutoff:3.500A) Processing helix chain 'B' and resid 395 through 401 removed outlier: 4.267A pdb=" N GLU B 401 " --> pdb=" O TRP B 397 " (cutoff:3.500A) Processing helix chain 'B' and resid 405 through 426 Processing sheet with id= A, first strand: chain 'A' and resid 93 through 95 removed outlier: 8.152A pdb=" N ILE A 94 " --> pdb=" O ALA A 66 " (cutoff:3.500A) removed outlier: 6.385A pdb=" N TYR A 68 " --> pdb=" O ILE A 94 " (cutoff:3.500A) removed outlier: 8.614A pdb=" N ILE A 67 " --> pdb=" O VAL A 4 " (cutoff:3.500A) removed outlier: 6.768A pdb=" N SER A 6 " --> pdb=" O ILE A 67 " (cutoff:3.500A) removed outlier: 7.920A pdb=" N VAL A 69 " --> pdb=" O SER A 6 " (cutoff:3.500A) removed outlier: 6.161A pdb=" N ASN A 8 " --> pdb=" O VAL A 69 " (cutoff:3.500A) removed outlier: 7.949A pdb=" N ILE A 5 " --> pdb=" O GLN A 134 " (cutoff:3.500A) removed outlier: 4.635A pdb=" N PHE A 136 " --> pdb=" O ILE A 5 " (cutoff:3.500A) removed outlier: 7.167A pdb=" N ILE A 7 " --> pdb=" O PHE A 136 " (cutoff:3.500A) removed outlier: 4.351A pdb=" N PHE A 138 " --> pdb=" O ILE A 7 " (cutoff:3.500A) removed outlier: 7.469A pdb=" N VAL A 9 " --> pdb=" O PHE A 138 " (cutoff:3.500A) removed outlier: 4.859A pdb=" N HIS A 140 " --> pdb=" O VAL A 9 " (cutoff:3.500A) removed outlier: 6.489A pdb=" N SER A 166 " --> pdb=" O PHE A 136 " (cutoff:3.500A) removed outlier: 7.800A pdb=" N PHE A 138 " --> pdb=" O SER A 166 " (cutoff:3.500A) removed outlier: 6.956A pdb=" N LEU A 168 " --> pdb=" O PHE A 138 " (cutoff:3.500A) removed outlier: 7.980A pdb=" N HIS A 140 " --> pdb=" O LEU A 168 " (cutoff:3.500A) removed outlier: 6.760A pdb=" N PHE A 170 " --> pdb=" O HIS A 140 " (cutoff:3.500A) removed outlier: 6.446A pdb=" N CYS A 201 " --> pdb=" O GLU A 169 " (cutoff:3.500A) removed outlier: 7.460A pdb=" N ALA A 171 " --> pdb=" O CYS A 201 " (cutoff:3.500A) removed outlier: 6.127A pdb=" N PHE A 203 " --> pdb=" O ALA A 171 " (cutoff:3.500A) removed outlier: 6.741A pdb=" N TYR A 173 " --> pdb=" O PHE A 203 " (cutoff:3.500A) removed outlier: 6.521A pdb=" N VAL A 205 " --> pdb=" O TYR A 173 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 270 through 273 removed outlier: 3.705A pdb=" N ALA A 315 " --> pdb=" O ASN A 381 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'B' and resid 90 through 92 removed outlier: 8.300A pdb=" N ILE B 91 " --> pdb=" O SER B 63 " (cutoff:3.500A) removed outlier: 6.356A pdb=" N ASN B 65 " --> pdb=" O ILE B 91 " (cutoff:3.500A) removed outlier: 8.517A pdb=" N ILE B 64 " --> pdb=" O ILE B 4 " (cutoff:3.500A) removed outlier: 6.765A pdb=" N HIS B 6 " --> pdb=" O ILE B 64 " (cutoff:3.500A) removed outlier: 7.818A pdb=" N VAL B 66 " --> pdb=" O HIS B 6 " (cutoff:3.500A) removed outlier: 6.118A pdb=" N SER B 8 " --> pdb=" O VAL B 66 " (cutoff:3.500A) removed outlier: 7.695A pdb=" N ILE B 5 " --> pdb=" O GLN B 131 " (cutoff:3.500A) removed outlier: 4.471A pdb=" N PHE B 133 " --> pdb=" O ILE B 5 " (cutoff:3.500A) removed outlier: 6.991A pdb=" N ILE B 7 " --> pdb=" O PHE B 133 " (cutoff:3.500A) removed outlier: 4.134A pdb=" N ILE B 135 " --> pdb=" O ILE B 7 " (cutoff:3.500A) removed outlier: 6.994A pdb=" N THR B 9 " --> pdb=" O ILE B 135 " (cutoff:3.500A) removed outlier: 4.452A pdb=" N HIS B 137 " --> pdb=" O THR B 9 " (cutoff:3.500A) removed outlier: 6.512A pdb=" N MET B 163 " --> pdb=" O PHE B 133 " (cutoff:3.500A) removed outlier: 7.581A pdb=" N ILE B 135 " --> pdb=" O MET B 163 " (cutoff:3.500A) removed outlier: 6.789A pdb=" N ALA B 165 " --> pdb=" O ILE B 135 " (cutoff:3.500A) removed outlier: 8.167A pdb=" N HIS B 137 " --> pdb=" O ALA B 165 " (cutoff:3.500A) removed outlier: 6.129A pdb=" N PHE B 167 " --> pdb=" O HIS B 137 " (cutoff:3.500A) removed outlier: 6.439A pdb=" N GLU B 198 " --> pdb=" O THR B 166 " (cutoff:3.500A) removed outlier: 7.290A pdb=" N SER B 168 " --> pdb=" O GLU B 198 " (cutoff:3.500A) removed outlier: 6.035A pdb=" N PHE B 200 " --> pdb=" O SER B 168 " (cutoff:3.500A) removed outlier: 6.815A pdb=" N LEU B 170 " --> pdb=" O PHE B 200 " (cutoff:3.500A) removed outlier: 6.642A pdb=" N ILE B 202 " --> pdb=" O LEU B 170 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 51 through 53 Processing sheet with id= E, first strand: chain 'B' and resid 267 through 271 296 hydrogen bonds defined for protein. 759 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: 1.81 Time building geometry restraints manager: 3.20 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 1230 1.32 - 1.45: 1847 1.45 - 1.57: 3887 1.57 - 1.69: 1 1.69 - 1.81: 65 Bond restraints: 7030 Sorted by residual: bond pdb=" C13 EP B 502 " pdb=" S1 EP B 502 " ideal model delta sigma weight residual 1.522 1.703 -0.181 2.00e-02 2.50e+03 8.21e+01 bond pdb=" C12 EP B 502 " pdb=" N20 EP B 502 " ideal model delta sigma weight residual 1.570 1.391 0.179 2.00e-02 2.50e+03 8.00e+01 bond pdb=" C15 EP B 502 " pdb=" S1 EP B 502 " ideal model delta sigma weight residual 1.548 1.726 -0.178 2.00e-02 2.50e+03 7.88e+01 bond pdb=" C SER A 274 " pdb=" N PRO A 275 " ideal model delta sigma weight residual 1.334 1.485 -0.151 2.34e-02 1.83e+03 4.14e+01 bond pdb=" C27 EP B 502 " pdb=" C32 EP B 502 " ideal model delta sigma weight residual 1.612 1.486 0.126 2.00e-02 2.50e+03 3.94e+01 ... (remaining 7025 not shown) Histogram of bond angle deviations from ideal: 59.56 - 75.41: 3 75.41 - 91.26: 1 91.26 - 107.11: 249 107.11 - 122.96: 8734 122.96 - 138.81: 560 Bond angle restraints: 9547 Sorted by residual: angle pdb=" C32 EP B 502 " pdb=" C27 EP B 502 " pdb=" O26 EP B 502 " ideal model delta sigma weight residual 53.02 117.09 -64.07 3.00e+00 1.11e-01 4.56e+02 angle pdb=" C21 EP B 502 " pdb=" C24 EP B 502 " pdb=" O26 EP B 502 " ideal model delta sigma weight residual 52.98 116.56 -63.58 3.00e+00 1.11e-01 4.49e+02 angle pdb=" C3 EP B 502 " pdb=" C5 EP B 502 " pdb=" C6 EP B 502 " ideal model delta sigma weight residual 67.40 115.65 -48.25 3.00e+00 1.11e-01 2.59e+02 angle pdb=" C10 EP B 502 " pdb=" C5 EP B 502 " pdb=" C3 EP B 502 " ideal model delta sigma weight residual 86.40 118.79 -32.39 3.00e+00 1.11e-01 1.17e+02 angle pdb=" C10 EP B 502 " pdb=" C5 EP B 502 " pdb=" C6 EP B 502 " ideal model delta sigma weight residual 149.08 125.55 23.53 3.00e+00 1.11e-01 6.15e+01 ... (remaining 9542 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.53: 4069 33.53 - 67.06: 81 67.06 - 100.58: 10 100.58 - 134.11: 3 134.11 - 167.64: 3 Dihedral angle restraints: 4166 sinusoidal: 1669 harmonic: 2497 Sorted by residual: dihedral pdb=" CA GLY A 39 " pdb=" C GLY A 39 " pdb=" N LEU A 40 " pdb=" CA LEU A 40 " ideal model delta harmonic sigma weight residual 180.00 142.41 37.59 0 5.00e+00 4.00e-02 5.65e+01 dihedral pdb=" C8 GTP A 500 " pdb=" C1' GTP A 500 " pdb=" N9 GTP A 500 " pdb=" O4' GTP A 500 " ideal model delta sinusoidal sigma weight residual 104.59 -63.05 167.64 1 2.00e+01 2.50e-03 4.74e+01 dihedral pdb=" O5' GTP A 500 " pdb=" O3A GTP A 500 " pdb=" PA GTP A 500 " pdb=" PB GTP A 500 " ideal model delta sinusoidal sigma weight residual -85.88 60.70 -146.58 1 2.00e+01 2.50e-03 4.40e+01 ... (remaining 4163 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.263: 1035 0.263 - 0.526: 2 0.526 - 0.789: 0 0.789 - 1.052: 0 1.052 - 1.316: 2 Chirality restraints: 1039 Sorted by residual: chirality pdb=" C27 EP B 502 " pdb=" C24 EP B 502 " pdb=" C32 EP B 502 " pdb=" O26 EP B 502 " both_signs ideal model delta sigma weight residual True 0.87 -2.19 -1.32 2.00e-01 2.50e+01 4.33e+01 chirality pdb=" C24 EP B 502 " pdb=" C21 EP B 502 " pdb=" C27 EP B 502 " pdb=" O26 EP B 502 " both_signs ideal model delta sigma weight residual True 0.87 -2.18 -1.31 2.00e-01 2.50e+01 4.30e+01 chirality pdb=" C3' GTP A 500 " pdb=" C2' GTP A 500 " pdb=" C4' GTP A 500 " pdb=" O3' GTP A 500 " both_signs ideal model delta sigma weight residual False -2.47 -2.79 0.32 2.00e-01 2.50e+01 2.52e+00 ... (remaining 1036 not shown) Planarity restraints: 1246 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C10 EP B 502 " 0.048 2.00e-02 2.50e+03 2.96e-02 1.09e+01 pdb=" C12 EP B 502 " -0.035 2.00e-02 2.50e+03 pdb=" C3 EP B 502 " -0.026 2.00e-02 2.50e+03 pdb=" C5 EP B 502 " 0.012 2.00e-02 2.50e+03 pdb=" C6 EP B 502 " 0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA B 80 " -0.012 2.00e-02 2.50e+03 2.41e-02 5.78e+00 pdb=" C ALA B 80 " 0.042 2.00e-02 2.50e+03 pdb=" O ALA B 80 " -0.016 2.00e-02 2.50e+03 pdb=" N ILE B 81 " -0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLU A 359 " 0.039 5.00e-02 4.00e+02 5.93e-02 5.62e+00 pdb=" N PRO A 360 " -0.103 5.00e-02 4.00e+02 pdb=" CA PRO A 360 " 0.031 5.00e-02 4.00e+02 pdb=" CD PRO A 360 " 0.032 5.00e-02 4.00e+02 ... (remaining 1243 not shown) Histogram of nonbonded interaction distances: 1.05 - 1.82: 1 1.82 - 2.59: 31 2.59 - 3.36: 8803 3.36 - 4.13: 16906 4.13 - 4.90: 31268 Nonbonded interactions: 57009 Sorted by model distance: nonbonded pdb=" O3G GTP A 500 " pdb="MG MG A 501 " model vdw 1.046 2.170 nonbonded pdb=" O VAL B 49 " pdb=" NH2 ARG B 62 " model vdw 2.315 2.520 nonbonded pdb=" O ARG A 2 " pdb=" OG1 THR A 52 " model vdw 2.390 2.440 nonbonded pdb=" O ASP B 40 " pdb=" N LYS B 44 " model vdw 2.400 2.520 nonbonded pdb=" OG SER A 274 " pdb=" SG CYS A 296 " model vdw 2.430 2.800 ... (remaining 57004 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== 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 Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 5 5.49 5 Mg 1 5.21 5 S 41 5.16 5 C 4311 2.51 5 N 1167 2.21 5 O 1351 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.910 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: 26.590 Check model and map are aligned: 0.100 Convert atoms to be neutral: 0.060 Process input model: 24.280 Find NCS groups from input model: 0.200 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Set scattering table: 0.010 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:2.570 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 58.740 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8463 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.007 0.181 7030 Z= 0.456 Angle : 1.455 64.072 9547 Z= 0.569 Chirality : 0.076 1.316 1039 Planarity : 0.005 0.059 1246 Dihedral : 14.890 167.640 2566 Min Nonbonded Distance : 1.046 Molprobity Statistics. All-atom Clashscore : 4.52 Ramachandran Plot: Outliers : 0.46 % Allowed : 3.82 % Favored : 95.71 % Rotamer Outliers : 0.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.24 % 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: -0.90 (0.26), residues: 863 helix: 0.08 (0.24), residues: 398 sheet: -0.28 (0.36), residues: 146 loop : -1.51 (0.31), residues: 319 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1726 Ramachandran restraints generated. 863 Oldfield, 0 Emsley, 863 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1726 Ramachandran restraints generated. 863 Oldfield, 0 Emsley, 863 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 248 residues out of total 741 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 241 time to evaluate : 0.775 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 7 outliers final: 2 residues processed: 246 average time/residue: 0.2356 time to fit residues: 72.9860 Evaluate side-chains 112 residues out of total 741 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 110 time to evaluate : 0.843 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0862 time to fit residues: 1.5183 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 72 optimal weight: 2.9990 chunk 65 optimal weight: 5.9990 chunk 36 optimal weight: 9.9990 chunk 22 optimal weight: 0.9980 chunk 43 optimal weight: 6.9990 chunk 34 optimal weight: 3.9990 chunk 67 optimal weight: 2.9990 chunk 26 optimal weight: 0.8980 chunk 40 optimal weight: 0.3980 chunk 50 optimal weight: 4.9990 chunk 78 optimal weight: 1.9990 overall best weight: 1.4584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 11 GLN A 55 HIS A 92 GLN A 230 ASN A 381 ASN B 37 HIS B 134 GLN B 212 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8534 moved from start: 0.3566 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.039 7030 Z= 0.219 Angle : 0.758 22.491 9547 Z= 0.357 Chirality : 0.044 0.166 1039 Planarity : 0.005 0.048 1246 Dihedral : 13.423 148.001 970 Min Nonbonded Distance : 2.180 Molprobity Statistics. All-atom Clashscore : 12.24 Ramachandran Plot: Outliers : 0.35 % Allowed : 3.36 % Favored : 96.29 % Rotamer Outliers : 3.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % 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: 0.26 (0.28), residues: 863 helix: 1.27 (0.27), residues: 387 sheet: 0.29 (0.38), residues: 148 loop : -1.21 (0.31), residues: 328 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1726 Ramachandran restraints generated. 863 Oldfield, 0 Emsley, 863 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1726 Ramachandran restraints generated. 863 Oldfield, 0 Emsley, 863 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 741 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 131 time to evaluate : 0.837 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 26 outliers final: 9 residues processed: 149 average time/residue: 0.1999 time to fit residues: 39.1489 Evaluate side-chains 98 residues out of total 741 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 89 time to evaluate : 0.849 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 0 residues processed: 9 average time/residue: 0.0708 time to fit residues: 2.1963 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 43 optimal weight: 0.9990 chunk 24 optimal weight: 10.0000 chunk 64 optimal weight: 0.9990 chunk 53 optimal weight: 9.9990 chunk 21 optimal weight: 7.9990 chunk 78 optimal weight: 3.9990 chunk 84 optimal weight: 0.9990 chunk 69 optimal weight: 1.9990 chunk 77 optimal weight: 4.9990 chunk 26 optimal weight: 2.9990 chunk 62 optimal weight: 2.9990 overall best weight: 1.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 207 ASN B 134 GLN B 307 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8534 moved from start: 0.4490 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.034 7030 Z= 0.203 Angle : 0.728 22.044 9547 Z= 0.338 Chirality : 0.043 0.170 1039 Planarity : 0.004 0.036 1246 Dihedral : 12.524 141.417 970 Min Nonbonded Distance : 1.935 Molprobity Statistics. All-atom Clashscore : 11.35 Ramachandran Plot: Outliers : 0.35 % Allowed : 3.71 % Favored : 95.94 % Rotamer Outliers : 1.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % 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: 0.59 (0.28), residues: 863 helix: 1.40 (0.27), residues: 389 sheet: 0.64 (0.39), residues: 148 loop : -0.95 (0.32), residues: 326 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1726 Ramachandran restraints generated. 863 Oldfield, 0 Emsley, 863 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1726 Ramachandran restraints generated. 863 Oldfield, 0 Emsley, 863 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 741 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 103 time to evaluate : 0.768 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 14 outliers final: 7 residues processed: 112 average time/residue: 0.1775 time to fit residues: 27.0558 Evaluate side-chains 92 residues out of total 741 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 85 time to evaluate : 0.785 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.0717 time to fit residues: 1.9307 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 77 optimal weight: 0.0020 chunk 58 optimal weight: 7.9990 chunk 40 optimal weight: 7.9990 chunk 8 optimal weight: 1.9990 chunk 37 optimal weight: 4.9990 chunk 52 optimal weight: 0.1980 chunk 78 optimal weight: 3.9990 chunk 83 optimal weight: 8.9990 chunk 41 optimal weight: 0.7980 chunk 74 optimal weight: 10.0000 chunk 22 optimal weight: 0.0970 overall best weight: 0.6188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 338 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 131 GLN B 134 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8492 moved from start: 0.4925 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.036 7030 Z= 0.162 Angle : 0.708 21.756 9547 Z= 0.328 Chirality : 0.042 0.153 1039 Planarity : 0.004 0.039 1246 Dihedral : 11.266 136.844 970 Min Nonbonded Distance : 2.047 Molprobity Statistics. All-atom Clashscore : 10.83 Ramachandran Plot: Outliers : 0.35 % Allowed : 3.48 % Favored : 96.18 % Rotamer Outliers : 0.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % 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: 0.65 (0.28), residues: 863 helix: 1.36 (0.26), residues: 391 sheet: 0.73 (0.40), residues: 148 loop : -0.85 (0.32), residues: 324 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1726 Ramachandran restraints generated. 863 Oldfield, 0 Emsley, 863 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1726 Ramachandran restraints generated. 863 Oldfield, 0 Emsley, 863 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 741 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 108 time to evaluate : 0.857 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 4 outliers final: 3 residues processed: 112 average time/residue: 0.2064 time to fit residues: 30.7859 Evaluate side-chains 87 residues out of total 741 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 84 time to evaluate : 0.843 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.0615 time to fit residues: 1.4708 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 69 optimal weight: 4.9990 chunk 47 optimal weight: 9.9990 chunk 1 optimal weight: 8.9990 chunk 61 optimal weight: 9.9990 chunk 34 optimal weight: 0.1980 chunk 70 optimal weight: 0.5980 chunk 57 optimal weight: 5.9990 chunk 0 optimal weight: 10.0000 chunk 42 optimal weight: 4.9990 chunk 74 optimal weight: 7.9990 chunk 20 optimal weight: 7.9990 overall best weight: 3.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 230 ASN ** A 338 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 134 GLN B 426 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8590 moved from start: 0.5432 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.043 7030 Z= 0.315 Angle : 0.765 22.003 9547 Z= 0.362 Chirality : 0.044 0.141 1039 Planarity : 0.005 0.044 1246 Dihedral : 11.231 134.208 970 Min Nonbonded Distance : 1.999 Molprobity Statistics. All-atom Clashscore : 14.09 Ramachandran Plot: Outliers : 0.35 % Allowed : 3.48 % Favored : 96.18 % Rotamer Outliers : 1.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % 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: 0.50 (0.28), residues: 863 helix: 1.23 (0.26), residues: 396 sheet: 0.70 (0.42), residues: 148 loop : -0.97 (0.33), residues: 319 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1726 Ramachandran restraints generated. 863 Oldfield, 0 Emsley, 863 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1726 Ramachandran restraints generated. 863 Oldfield, 0 Emsley, 863 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 741 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 84 time to evaluate : 0.853 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 11 outliers final: 6 residues processed: 88 average time/residue: 0.1858 time to fit residues: 22.7783 Evaluate side-chains 80 residues out of total 741 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 74 time to evaluate : 0.887 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.0850 time to fit residues: 2.0765 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 27 optimal weight: 7.9990 chunk 74 optimal weight: 3.9990 chunk 16 optimal weight: 6.9990 chunk 48 optimal weight: 6.9990 chunk 20 optimal weight: 3.9990 chunk 83 optimal weight: 0.9990 chunk 69 optimal weight: 0.9990 chunk 38 optimal weight: 2.9990 chunk 6 optimal weight: 10.0000 chunk 43 optimal weight: 1.9990 chunk 80 optimal weight: 9.9990 overall best weight: 2.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 338 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 105 HIS ** B 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 134 GLN ** B 292 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8575 moved from start: 0.5759 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.031 7030 Z= 0.227 Angle : 0.732 21.722 9547 Z= 0.340 Chirality : 0.043 0.131 1039 Planarity : 0.004 0.034 1246 Dihedral : 10.972 133.526 970 Min Nonbonded Distance : 1.778 Molprobity Statistics. All-atom Clashscore : 11.94 Ramachandran Plot: Outliers : 0.35 % Allowed : 3.71 % Favored : 95.94 % Rotamer Outliers : 1.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % 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: 0.64 (0.28), residues: 863 helix: 1.36 (0.26), residues: 384 sheet: 0.67 (0.42), residues: 148 loop : -0.77 (0.33), residues: 331 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1726 Ramachandran restraints generated. 863 Oldfield, 0 Emsley, 863 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1726 Ramachandran restraints generated. 863 Oldfield, 0 Emsley, 863 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 741 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 86 time to evaluate : 0.842 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 10 outliers final: 3 residues processed: 91 average time/residue: 0.1915 time to fit residues: 23.8777 Evaluate side-chains 80 residues out of total 741 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 77 time to evaluate : 0.843 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.0820 time to fit residues: 1.5885 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 9 optimal weight: 4.9990 chunk 47 optimal weight: 10.0000 chunk 60 optimal weight: 5.9990 chunk 70 optimal weight: 4.9990 chunk 46 optimal weight: 0.9990 chunk 82 optimal weight: 1.9990 chunk 51 optimal weight: 4.9990 chunk 50 optimal weight: 0.8980 chunk 38 optimal weight: 0.9990 chunk 33 optimal weight: 4.9990 chunk 49 optimal weight: 0.9990 overall best weight: 1.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 338 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 292 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8541 moved from start: 0.6061 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.045 7030 Z= 0.174 Angle : 0.718 21.776 9547 Z= 0.330 Chirality : 0.042 0.134 1039 Planarity : 0.004 0.035 1246 Dihedral : 10.688 132.386 970 Min Nonbonded Distance : 1.892 Molprobity Statistics. All-atom Clashscore : 11.12 Ramachandran Plot: Outliers : 0.35 % Allowed : 3.71 % Favored : 95.94 % Rotamer Outliers : 0.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % 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: 0.69 (0.28), residues: 863 helix: 1.41 (0.27), residues: 379 sheet: 0.72 (0.42), residues: 143 loop : -0.71 (0.32), residues: 341 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1726 Ramachandran restraints generated. 863 Oldfield, 0 Emsley, 863 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1726 Ramachandran restraints generated. 863 Oldfield, 0 Emsley, 863 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 741 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 92 time to evaluate : 0.856 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 3 outliers final: 1 residues processed: 94 average time/residue: 0.1702 time to fit residues: 22.4807 Evaluate side-chains 77 residues out of total 741 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 76 time to evaluate : 0.797 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0899 time to fit residues: 1.2445 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 24 optimal weight: 8.9990 chunk 16 optimal weight: 9.9990 chunk 52 optimal weight: 0.0070 chunk 56 optimal weight: 6.9990 chunk 40 optimal weight: 6.9990 chunk 7 optimal weight: 0.0040 chunk 65 optimal weight: 4.9990 chunk 75 optimal weight: 5.9990 chunk 79 optimal weight: 0.0060 chunk 72 optimal weight: 4.9990 chunk 77 optimal weight: 8.9990 overall best weight: 2.0030 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 89 HIS ** A 338 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 292 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 298 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8563 moved from start: 0.6258 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.036 7030 Z= 0.217 Angle : 0.736 21.728 9547 Z= 0.342 Chirality : 0.043 0.138 1039 Planarity : 0.004 0.042 1246 Dihedral : 10.712 133.016 970 Min Nonbonded Distance : 1.898 Molprobity Statistics. All-atom Clashscore : 12.46 Ramachandran Plot: Outliers : 0.35 % Allowed : 4.17 % Favored : 95.48 % Rotamer Outliers : 0.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % 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: 0.62 (0.28), residues: 863 helix: 1.32 (0.27), residues: 379 sheet: 0.62 (0.42), residues: 144 loop : -0.66 (0.33), residues: 340 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1726 Ramachandran restraints generated. 863 Oldfield, 0 Emsley, 863 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1726 Ramachandran restraints generated. 863 Oldfield, 0 Emsley, 863 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 741 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 84 time to evaluate : 0.842 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 4 outliers final: 2 residues processed: 87 average time/residue: 0.2013 time to fit residues: 23.6837 Evaluate side-chains 76 residues out of total 741 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 74 time to evaluate : 0.803 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0914 time to fit residues: 1.4140 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 79 optimal weight: 0.0060 chunk 46 optimal weight: 0.9980 chunk 33 optimal weight: 1.9990 chunk 60 optimal weight: 6.9990 chunk 23 optimal weight: 5.9990 chunk 69 optimal weight: 0.9980 chunk 73 optimal weight: 7.9990 chunk 76 optimal weight: 4.9990 chunk 50 optimal weight: 4.9990 chunk 81 optimal weight: 7.9990 chunk 49 optimal weight: 6.9990 overall best weight: 1.8000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 338 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 89 ASN ** B 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 292 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 298 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8546 moved from start: 0.6499 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.041 7030 Z= 0.211 Angle : 0.752 21.749 9547 Z= 0.356 Chirality : 0.043 0.145 1039 Planarity : 0.004 0.037 1246 Dihedral : 10.631 132.235 970 Min Nonbonded Distance : 1.935 Molprobity Statistics. All-atom Clashscore : 13.05 Ramachandran Plot: Outliers : 0.35 % Allowed : 4.06 % Favored : 95.60 % Rotamer Outliers : 0.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % 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: 0.45 (0.28), residues: 863 helix: 1.24 (0.27), residues: 380 sheet: 0.58 (0.42), residues: 133 loop : -0.83 (0.32), residues: 350 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1726 Ramachandran restraints generated. 863 Oldfield, 0 Emsley, 863 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1726 Ramachandran restraints generated. 863 Oldfield, 0 Emsley, 863 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 741 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 82 time to evaluate : 0.892 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 3 outliers final: 1 residues processed: 83 average time/residue: 0.1951 time to fit residues: 23.3898 Evaluate side-chains 77 residues out of total 741 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 76 time to evaluate : 0.806 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0741 time to fit residues: 1.2235 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 38 optimal weight: 2.9990 chunk 56 optimal weight: 4.9990 chunk 85 optimal weight: 5.9990 chunk 78 optimal weight: 0.9980 chunk 68 optimal weight: 1.9990 chunk 7 optimal weight: 3.9990 chunk 52 optimal weight: 10.0000 chunk 41 optimal weight: 1.9990 chunk 54 optimal weight: 9.9990 chunk 72 optimal weight: 0.1980 chunk 20 optimal weight: 3.9990 overall best weight: 1.6386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 338 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 292 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 298 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8545 moved from start: 0.6630 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.031 7030 Z= 0.202 Angle : 0.756 21.735 9547 Z= 0.353 Chirality : 0.044 0.151 1039 Planarity : 0.004 0.039 1246 Dihedral : 10.551 131.968 970 Min Nonbonded Distance : 1.966 Molprobity Statistics. All-atom Clashscore : 13.20 Ramachandran Plot: Outliers : 0.35 % Allowed : 4.17 % Favored : 95.48 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % 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: 0.44 (0.28), residues: 863 helix: 1.27 (0.27), residues: 379 sheet: 0.46 (0.42), residues: 133 loop : -0.83 (0.32), residues: 351 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1726 Ramachandran restraints generated. 863 Oldfield, 0 Emsley, 863 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1726 Ramachandran restraints generated. 863 Oldfield, 0 Emsley, 863 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 741 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 82 time to evaluate : 0.859 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 82 average time/residue: 0.1903 time to fit residues: 22.2495 Evaluate side-chains 78 residues out of total 741 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 78 time to evaluate : 0.869 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.1801 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 62 optimal weight: 5.9990 chunk 10 optimal weight: 9.9990 chunk 18 optimal weight: 0.0030 chunk 68 optimal weight: 9.9990 chunk 28 optimal weight: 5.9990 chunk 70 optimal weight: 4.9990 chunk 8 optimal weight: 5.9990 chunk 12 optimal weight: 8.9990 chunk 59 optimal weight: 1.9990 chunk 3 optimal weight: 1.9990 chunk 49 optimal weight: 6.9990 overall best weight: 2.9998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 140 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 338 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 131 GLN ** B 292 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 298 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.079474 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3184 r_free = 0.3184 target = 0.066557 restraints weight = 18791.416| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3242 r_free = 0.3242 target = 0.069153 restraints weight = 10465.521| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3282 r_free = 0.3282 target = 0.070980 restraints weight = 6869.556| |-----------------------------------------------------------------------------| r_work (final): 0.3280 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8351 moved from start: 0.6724 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.037 7030 Z= 0.290 Angle : 0.795 21.723 9547 Z= 0.376 Chirality : 0.045 0.148 1039 Planarity : 0.004 0.045 1246 Dihedral : 10.694 132.381 970 Min Nonbonded Distance : 1.932 Molprobity Statistics. All-atom Clashscore : 15.43 Ramachandran Plot: Outliers : 0.35 % Allowed : 4.40 % Favored : 95.25 % Rotamer Outliers : 0.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % 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: 0.25 (0.28), residues: 863 helix: 1.12 (0.27), residues: 384 sheet: 0.26 (0.41), residues: 135 loop : -0.93 (0.32), residues: 344 =============================================================================== Job complete usr+sys time: 1832.50 seconds wall clock time: 33 minutes 58.60 seconds (2038.60 seconds total)