Starting phenix.real_space_refine on Tue May 7 05:45:31 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8uo1_42424/05_2024/8uo1_42424_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8uo1_42424/05_2024/8uo1_42424.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8uo1_42424/05_2024/8uo1_42424.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8uo1_42424/05_2024/8uo1_42424.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8uo1_42424/05_2024/8uo1_42424_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8uo1_42424/05_2024/8uo1_42424_updated.pdb" } resolution = 3.6 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.020 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 Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 3 5.49 5 Mg 1 5.21 5 S 36 5.16 5 C 4405 2.51 5 N 1222 2.21 5 O 1248 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 61": "NH1" <-> "NH2" Residue "A GLU 327": "OE1" <-> "OE2" Residue "B GLU 138": "OE1" <-> "OE2" Residue "R GLU 122": "OE1" <-> "OE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5322/modules/chem_data/mon_lib" Total number of atoms: 6915 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 2242 Number of conformers: 1 Conformer: "" Number of residues, atoms: 334, 2242 Classifications: {'peptide': 334} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 146} Link IDs: {'PTRANS': 10, 'TRANS': 323} Chain breaks: 4 Unresolved chain link angles: 4 Unresolved non-hydrogen bonds: 551 Unresolved non-hydrogen angles: 689 Unresolved non-hydrogen dihedrals: 448 Unresolved non-hydrogen chiralities: 29 Planarities with less than four sites: {'GLN:plan1': 10, 'HIS:plan': 1, 'TYR:plan': 4, 'ASN:plan1': 10, 'TRP:plan': 1, 'ASP:plan': 18, 'PHE:plan': 5, 'GLU:plan': 25, 'ARG:plan': 13} Unresolved non-hydrogen planarities: 361 Chain: "B" Number of atoms: 2405 Number of conformers: 1 Conformer: "" Number of residues, atoms: 335, 2405 Classifications: {'peptide': 335} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 45} Link IDs: {'PTRANS': 5, 'TRANS': 329} Chain breaks: 1 Unresolved non-hydrogen bonds: 167 Unresolved non-hydrogen angles: 207 Unresolved non-hydrogen dihedrals: 127 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLN:plan1': 7, 'GLU:plan': 6, 'ARG:plan': 7, 'ASN:plan1': 3, 'ASP:plan': 13} Unresolved non-hydrogen planarities: 135 Chain: "G" Number of atoms: 344 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 344 Classifications: {'peptide': 55} Incomplete info: {'truncation_to_alanine': 23} Link IDs: {'PTRANS': 4, 'TRANS': 50} Unresolved non-hydrogen bonds: 80 Unresolved non-hydrogen angles: 95 Unresolved non-hydrogen dihedrals: 65 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 5, 'ARG:plan': 2, 'ASN:plan1': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 43 Chain: "R" Number of atoms: 1876 Number of conformers: 1 Conformer: "" Number of residues, atoms: 282, 1876 Classifications: {'peptide': 282} Incomplete info: {'truncation_to_alanine': 117} Link IDs: {'PTRANS': 7, 'TRANS': 274} Chain breaks: 1 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 407 Unresolved non-hydrogen angles: 517 Unresolved non-hydrogen dihedrals: 325 Unresolved non-hydrogen chiralities: 46 Planarities with less than four sites: {'GLN:plan1': 8, 'HIS:plan': 2, 'TYR:plan': 2, 'ASN:plan1': 5, 'TRP:plan': 1, 'ASP:plan': 6, 'PHE:plan': 5, 'GLU:plan': 10, 'ARG:plan': 9} Unresolved non-hydrogen planarities: 213 Chain: "A" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 33 Unusual residues: {' MG': 1, 'GTP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "R" Number of atoms: 15 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 15 Unusual residues: {'G1I': 1} Classifications: {'undetermined': 1} Time building chain proxies: 4.59, per 1000 atoms: 0.66 Number of scatterers: 6915 At special positions: 0 Unit cell: (84.1669, 134.493, 99.7855, 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 36 16.00 P 3 15.00 Mg 1 11.99 O 1248 8.00 N 1222 7.00 C 4405 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS R 106 " - pdb=" SG CYS R 191 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 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: 2.96 Conformation dependent library (CDL) restraints added in 1.6 seconds 1972 Ramachandran restraints generated. 986 Oldfield, 0 Emsley, 986 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1914 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 29 helices and 9 sheets defined 44.4% alpha, 12.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.48 Creating SS restraints... Processing helix chain 'A' and resid 11 through 39 removed outlier: 3.802A pdb=" N GLN A 19 " --> pdb=" O GLU A 15 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N GLN A 35 " --> pdb=" O GLN A 31 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N VAL A 36 " --> pdb=" O LYS A 32 " (cutoff:3.500A) Processing helix chain 'A' and resid 53 through 62 Processing helix chain 'A' and resid 90 through 111 removed outlier: 3.756A pdb=" N ASP A 94 " --> pdb=" O THR A 90 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N LYS A 96 " --> pdb=" O VAL A 92 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N ASN A 97 " --> pdb=" O GLN A 93 " (cutoff:3.500A) removed outlier: 4.163A pdb=" N SER A 111 " --> pdb=" O VAL A 107 " (cutoff:3.500A) Processing helix chain 'A' and resid 125 through 133 Processing helix chain 'A' and resid 144 through 154 removed outlier: 3.664A pdb=" N LYS A 151 " --> pdb=" O TYR A 147 " (cutoff:3.500A) Processing helix chain 'A' and resid 173 through 179 removed outlier: 3.688A pdb=" N GLN A 176 " --> pdb=" O ASP A 173 " (cutoff:3.500A) Processing helix chain 'A' and resid 196 through 199 No H-bonds generated for 'chain 'A' and resid 196 through 199' Processing helix chain 'A' and resid 234 through 236 No H-bonds generated for 'chain 'A' and resid 234 through 236' Processing helix chain 'A' and resid 265 through 277 Processing helix chain 'A' and resid 294 through 302 removed outlier: 3.547A pdb=" N GLU A 299 " --> pdb=" O ASP A 295 " (cutoff:3.500A) Processing helix chain 'A' and resid 308 through 311 No H-bonds generated for 'chain 'A' and resid 308 through 311' Processing helix chain 'A' and resid 313 through 315 No H-bonds generated for 'chain 'A' and resid 313 through 315' Processing helix chain 'A' and resid 334 through 351 removed outlier: 3.591A pdb=" N PHE A 340 " --> pdb=" O ARG A 336 " (cutoff:3.500A) removed outlier: 4.324A pdb=" N ILE A 348 " --> pdb=" O GLU A 344 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N SER A 349 " --> pdb=" O PHE A 345 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N ALA A 351 " --> pdb=" O ARG A 347 " (cutoff:3.500A) Processing helix chain 'A' and resid 372 through 390 removed outlier: 3.825A pdb=" N ASP A 381 " --> pdb=" O ASN A 377 " (cutoff:3.500A) Processing helix chain 'B' and resid 5 through 23 removed outlier: 3.734A pdb=" N GLN B 9 " --> pdb=" O ASP B 5 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N GLU B 10 " --> pdb=" O GLN B 6 " (cutoff:3.500A) Processing helix chain 'B' and resid 30 through 36 removed outlier: 5.031A pdb=" N ASN B 36 " --> pdb=" O GLN B 32 " (cutoff:3.500A) Processing helix chain 'G' and resid 9 through 23 removed outlier: 3.605A pdb=" N LEU G 19 " --> pdb=" O LEU G 15 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N LYS G 20 " --> pdb=" O VAL G 16 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N MET G 21 " --> pdb=" O GLU G 17 " (cutoff:3.500A) Processing helix chain 'G' and resid 30 through 44 Processing helix chain 'G' and resid 56 through 58 No H-bonds generated for 'chain 'G' and resid 56 through 58' Processing helix chain 'R' and resid 32 through 60 removed outlier: 3.521A pdb=" N ILE R 38 " --> pdb=" O VAL R 34 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N ILE R 43 " --> pdb=" O VAL R 39 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N VAL R 54 " --> pdb=" O GLY R 50 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ALA R 59 " --> pdb=" O ILE R 55 " (cutoff:3.500A) Processing helix chain 'R' and resid 69 through 95 removed outlier: 4.226A pdb=" N VAL R 87 " --> pdb=" O GLY R 83 " (cutoff:3.500A) Proline residue: R 88 - end of helix Processing helix chain 'R' and resid 103 through 136 removed outlier: 3.668A pdb=" N ILE R 121 " --> pdb=" O VAL R 117 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N GLU R 122 " --> pdb=" O THR R 118 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N THR R 123 " --> pdb=" O ALA R 119 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N LEU R 124 " --> pdb=" O SER R 120 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N CYS R 125 " --> pdb=" O ILE R 121 " (cutoff:3.500A) Processing helix chain 'R' and resid 141 through 144 No H-bonds generated for 'chain 'R' and resid 141 through 144' Processing helix chain 'R' and resid 147 through 170 removed outlier: 3.865A pdb=" N LEU R 167 " --> pdb=" O LEU R 163 " (cutoff:3.500A) Proline residue: R 168 - end of helix Processing helix chain 'R' and resid 179 through 186 Processing helix chain 'R' and resid 197 through 237 removed outlier: 4.916A pdb=" N VAL R 210 " --> pdb=" O VAL R 206 " (cutoff:3.500A) Proline residue: R 211 - end of helix removed outlier: 3.702A pdb=" N ILE R 214 " --> pdb=" O VAL R 210 " (cutoff:3.500A) Processing helix chain 'R' and resid 269 through 298 removed outlier: 3.966A pdb=" N PHE R 282 " --> pdb=" O ILE R 278 " (cutoff:3.500A) Proline residue: R 288 - end of helix removed outlier: 4.210A pdb=" N ILE R 294 " --> pdb=" O PHE R 290 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N VAL R 295 " --> pdb=" O ILE R 291 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N VAL R 297 " --> pdb=" O ASN R 293 " (cutoff:3.500A) Processing helix chain 'R' and resid 305 through 325 removed outlier: 3.760A pdb=" N VAL R 317 " --> pdb=" O TRP R 313 " (cutoff:3.500A) removed outlier: 4.435A pdb=" N ASN R 318 " --> pdb=" O ILE R 314 " (cutoff:3.500A) removed outlier: 4.942A pdb=" N SER R 319 " --> pdb=" O GLY R 315 " (cutoff:3.500A) removed outlier: 4.403A pdb=" N GLY R 320 " --> pdb=" O TYR R 316 " (cutoff:3.500A) Proline residue: R 323 - end of helix Processing helix chain 'R' and resid 330 through 338 Processing sheet with id= A, first strand: chain 'A' and resid 40 through 44 removed outlier: 6.845A pdb=" N ASN A 218 " --> pdb=" O HIS A 41 " (cutoff:3.500A) removed outlier: 8.106A pdb=" N LEU A 43 " --> pdb=" O ASN A 218 " (cutoff:3.500A) removed outlier: 6.609A pdb=" N HIS A 220 " --> pdb=" O LEU A 43 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 243 through 249 removed outlier: 7.011A pdb=" N SER A 286 " --> pdb=" O ILE A 244 " (cutoff:3.500A) removed outlier: 7.580A pdb=" N PHE A 246 " --> pdb=" O SER A 286 " (cutoff:3.500A) removed outlier: 6.283A pdb=" N ILE A 288 " --> pdb=" O PHE A 246 " (cutoff:3.500A) removed outlier: 7.779A pdb=" N VAL A 248 " --> pdb=" O ILE A 288 " (cutoff:3.500A) removed outlier: 6.734A pdb=" N PHE A 290 " --> pdb=" O VAL A 248 " (cutoff:3.500A) No H-bonds generated for sheet with id= B Processing sheet with id= C, first strand: chain 'B' and resid 91 through 94 removed outlier: 3.826A pdb=" N HIS B 91 " --> pdb=" O ILE B 81 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ILE B 93 " --> pdb=" O LEU B 79 " (cutoff:3.500A) removed outlier: 4.643A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N SER B 74 " --> pdb=" O LYS B 78 " (cutoff:3.500A) removed outlier: 4.067A pdb=" N LEU B 70 " --> pdb=" O TRP B 82 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N ALA B 73 " --> pdb=" O ALA B 60 " (cutoff:3.500A) removed outlier: 4.252A pdb=" N ALA B 60 " --> pdb=" O ALA B 73 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 111 through 114 removed outlier: 3.589A pdb=" N VAL B 112 " --> pdb=" O TYR B 124 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N ARG B 137 " --> pdb=" O ILE B 123 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 7.034A pdb=" N VAL B 135 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 178 through 181 removed outlier: 3.676A pdb=" N THR B 178 " --> pdb=" O LEU B 168 " (cutoff:3.500A) removed outlier: 4.728A pdb=" N THR B 165 " --> pdb=" O SER B 161 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N SER B 161 " --> pdb=" O THR B 165 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N CYS B 148 " --> pdb=" O SER B 160 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 220 through 222 removed outlier: 3.942A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N LYS B 209 " --> pdb=" O SER B 201 " (cutoff:3.500A) removed outlier: 4.040A pdb=" N PHE B 199 " --> pdb=" O TRP B 211 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N VAL B 200 " --> pdb=" O SER B 191 " (cutoff:3.500A) removed outlier: 4.244A pdb=" N SER B 191 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N SER B 189 " --> pdb=" O GLY B 202 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'B' and resid 229 through 232 removed outlier: 3.508A pdb=" N ASN B 230 " --> pdb=" O GLY B 244 " (cutoff:3.500A) removed outlier: 7.356A pdb=" N GLY B 244 " --> pdb=" O ASN B 230 " (cutoff:3.500A) removed outlier: 4.683A pdb=" N ILE B 232 " --> pdb=" O ALA B 242 " (cutoff:3.500A) removed outlier: 6.828A pdb=" N ALA B 242 " --> pdb=" O ILE B 232 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N PHE B 241 " --> pdb=" O PHE B 253 " (cutoff:3.500A) removed outlier: 4.679A pdb=" N THR B 249 " --> pdb=" O SER B 245 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N MET B 262 " --> pdb=" O LEU B 252 " (cutoff:3.500A) removed outlier: 6.980A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 6.288A pdb=" N GLU B 260 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'B' and resid 284 through 287 removed outlier: 3.504A pdb=" N LEU B 285 " --> pdb=" O TRP B 297 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'B' and resid 47 through 51 removed outlier: 6.894A pdb=" N ILE B 338 " --> pdb=" O ARG B 48 " (cutoff:3.500A) removed outlier: 4.962A pdb=" N THR B 50 " --> pdb=" O LEU B 336 " (cutoff:3.500A) removed outlier: 6.870A pdb=" N LEU B 336 " --> pdb=" O THR B 50 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N CYS B 317 " --> pdb=" O GLY B 330 " (cutoff:3.500A) 331 hydrogen bonds defined for protein. 966 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.34 Time building geometry restraints manager: 3.17 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: 1211 1.32 - 1.45: 1893 1.45 - 1.57: 3893 1.57 - 1.69: 6 1.69 - 1.82: 49 Bond restraints: 7052 Sorted by residual: bond pdb=" C ILE A 207 " pdb=" N PHE A 208 " ideal model delta sigma weight residual 1.330 1.442 -0.112 1.46e-02 4.69e+03 5.91e+01 bond pdb=" CA LYS A 338 " pdb=" C LYS A 338 " ideal model delta sigma weight residual 1.523 1.438 0.085 1.30e-02 5.92e+03 4.31e+01 bond pdb=" CA VAL A 334 " pdb=" C VAL A 334 " ideal model delta sigma weight residual 1.523 1.459 0.064 1.27e-02 6.20e+03 2.55e+01 bond pdb=" CA ASP A 331 " pdb=" C ASP A 331 " ideal model delta sigma weight residual 1.527 1.480 0.047 1.02e-02 9.61e+03 2.12e+01 bond pdb=" CA ALA A 337 " pdb=" C ALA A 337 " ideal model delta sigma weight residual 1.523 1.463 0.060 1.30e-02 5.92e+03 2.12e+01 ... (remaining 7047 not shown) Histogram of bond angle deviations from ideal: 100.47 - 107.18: 189 107.18 - 113.90: 4002 113.90 - 120.62: 2904 120.62 - 127.33: 2503 127.33 - 134.05: 79 Bond angle restraints: 9677 Sorted by residual: angle pdb=" N PRO A 143 " pdb=" CA PRO A 143 " pdb=" C PRO A 143 " ideal model delta sigma weight residual 110.70 124.54 -13.84 1.22e+00 6.72e-01 1.29e+02 angle pdb=" N GLU A 344 " pdb=" CA GLU A 344 " pdb=" C GLU A 344 " ideal model delta sigma weight residual 111.28 102.95 8.33 1.09e+00 8.42e-01 5.84e+01 angle pdb=" C PRO A 143 " pdb=" CA PRO A 143 " pdb=" CB PRO A 143 " ideal model delta sigma weight residual 110.92 103.19 7.73 1.22e+00 6.72e-01 4.02e+01 angle pdb=" N VAL A 334 " pdb=" CA VAL A 334 " pdb=" C VAL A 334 " ideal model delta sigma weight residual 110.62 104.23 6.39 1.02e+00 9.61e-01 3.92e+01 angle pdb=" N ILE A 341 " pdb=" CA ILE A 341 " pdb=" C ILE A 341 " ideal model delta sigma weight residual 110.62 104.57 6.05 1.02e+00 9.61e-01 3.52e+01 ... (remaining 9672 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 30.04: 3971 30.04 - 60.09: 89 60.09 - 90.13: 8 90.13 - 120.17: 1 120.17 - 150.21: 2 Dihedral angle restraints: 4071 sinusoidal: 1134 harmonic: 2937 Sorted by residual: dihedral pdb=" CB CYS R 106 " pdb=" SG CYS R 106 " pdb=" SG CYS R 191 " pdb=" CB CYS R 191 " ideal model delta sinusoidal sigma weight residual 93.00 -179.65 -87.35 1 1.00e+01 1.00e-02 9.16e+01 dihedral pdb=" C5' GTP A 401 " pdb=" O5' GTP A 401 " pdb=" PA GTP A 401 " pdb=" O3A GTP A 401 " ideal model delta sinusoidal sigma weight residual 69.27 -140.52 -150.21 1 2.00e+01 2.50e-03 4.48e+01 dihedral pdb=" C8 GTP A 401 " pdb=" C1' GTP A 401 " pdb=" N9 GTP A 401 " pdb=" O4' GTP A 401 " ideal model delta sinusoidal sigma weight residual 104.59 -27.42 132.01 1 2.00e+01 2.50e-03 4.01e+01 ... (remaining 4068 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.071: 988 0.071 - 0.142: 154 0.142 - 0.214: 30 0.214 - 0.285: 2 0.285 - 0.356: 1 Chirality restraints: 1175 Sorted by residual: chirality pdb=" CA TYR A 339 " pdb=" N TYR A 339 " pdb=" C TYR A 339 " pdb=" CB TYR A 339 " both_signs ideal model delta sigma weight residual False 2.51 2.15 0.36 2.00e-01 2.50e+01 3.17e+00 chirality pdb=" CA LEU A 63 " pdb=" N LEU A 63 " pdb=" C LEU A 63 " pdb=" CB LEU A 63 " both_signs ideal model delta sigma weight residual False 2.51 2.73 -0.22 2.00e-01 2.50e+01 1.20e+00 chirality pdb=" CA ILE A 95 " pdb=" N ILE A 95 " pdb=" C ILE A 95 " pdb=" CB ILE A 95 " both_signs ideal model delta sigma weight residual False 2.43 2.65 -0.21 2.00e-01 2.50e+01 1.15e+00 ... (remaining 1172 not shown) Planarity restraints: 1233 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA PRO A 138 " -0.013 2.00e-02 2.50e+03 2.61e-02 6.81e+00 pdb=" C PRO A 138 " 0.045 2.00e-02 2.50e+03 pdb=" O PRO A 138 " -0.017 2.00e-02 2.50e+03 pdb=" N ASP A 139 " -0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL A 256 " -0.012 2.00e-02 2.50e+03 2.49e-02 6.18e+00 pdb=" C VAL A 256 " 0.043 2.00e-02 2.50e+03 pdb=" O VAL A 256 " -0.017 2.00e-02 2.50e+03 pdb=" N ILE A 257 " -0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLN A 262 " -0.012 2.00e-02 2.50e+03 2.44e-02 5.98e+00 pdb=" C GLN A 262 " 0.042 2.00e-02 2.50e+03 pdb=" O GLN A 262 " -0.016 2.00e-02 2.50e+03 pdb=" N THR A 263 " -0.015 2.00e-02 2.50e+03 ... (remaining 1230 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.77: 1213 2.77 - 3.30: 6689 3.30 - 3.83: 10710 3.83 - 4.37: 11539 4.37 - 4.90: 20720 Nonbonded interactions: 50871 Sorted by model distance: nonbonded pdb=" O LEU R 64 " pdb=" ND2 ASN R 69 " model vdw 2.233 2.520 nonbonded pdb=" O GLN A 59 " pdb=" CG2 ILE A 62 " model vdw 2.236 3.460 nonbonded pdb=" NE2 HIS B 142 " pdb=" OG SER B 161 " model vdw 2.288 2.520 nonbonded pdb=" O ILE B 58 " pdb=" OG SER B 316 " model vdw 2.310 2.440 nonbonded pdb=" N GLU A 370 " pdb=" OE1 GLU A 370 " model vdw 2.332 2.520 ... (remaining 50866 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 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: 2.020 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 7.630 Check model and map are aligned: 0.050 Set scattering table: 0.070 Process input model: 24.450 Find NCS groups from input model: 0.220 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.750 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 37.240 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8028 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 : 0.006 0.112 7052 Z= 0.453 Angle : 0.917 13.842 9677 Z= 0.632 Chirality : 0.056 0.356 1175 Planarity : 0.004 0.031 1233 Dihedral : 13.475 150.214 2154 Min Nonbonded Distance : 2.233 Molprobity Statistics. All-atom Clashscore : 5.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer: Outliers : 0.18 % Allowed : 0.55 % Favored : 99.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.78 (0.26), residues: 986 helix: 1.97 (0.24), residues: 439 sheet: -0.49 (0.43), residues: 154 loop : -0.71 (0.28), residues: 393 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP R 105 HIS 0.006 0.001 HIS A 64 PHE 0.012 0.001 PHE B 234 TYR 0.020 0.001 TYR A 339 ARG 0.002 0.000 ARG A 232 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1972 Ramachandran restraints generated. 986 Oldfield, 0 Emsley, 986 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1972 Ramachandran restraints generated. 986 Oldfield, 0 Emsley, 986 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 874 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 122 time to evaluate : 0.775 Fit side-chains REVERT: A 208 PHE cc_start: 0.7817 (m-80) cc_final: 0.7460 (m-80) REVERT: A 264 ASN cc_start: 0.8027 (m-40) cc_final: 0.7805 (t0) REVERT: B 59 TYR cc_start: 0.8716 (m-80) cc_final: 0.8415 (m-80) outliers start: 1 outliers final: 0 residues processed: 123 average time/residue: 0.1465 time to fit residues: 25.7372 Evaluate side-chains 94 residues out of total 874 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 94 time to evaluate : 0.755 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 83 optimal weight: 3.9990 chunk 75 optimal weight: 0.8980 chunk 41 optimal weight: 3.9990 chunk 25 optimal weight: 0.6980 chunk 50 optimal weight: 6.9990 chunk 40 optimal weight: 2.9990 chunk 77 optimal weight: 4.9990 chunk 30 optimal weight: 1.9990 chunk 47 optimal weight: 0.9980 chunk 57 optimal weight: 1.9990 chunk 89 optimal weight: 5.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 213 GLN A 294 GLN G 44 HIS R 93 HIS R 312 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8087 moved from start: 0.1486 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 7052 Z= 0.226 Angle : 0.505 6.616 9677 Z= 0.277 Chirality : 0.042 0.127 1175 Planarity : 0.003 0.034 1233 Dihedral : 7.406 145.483 1085 Min Nonbonded Distance : 2.190 Molprobity Statistics. All-atom Clashscore : 4.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 2.76 % Allowed : 10.50 % Favored : 86.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.81 (0.27), residues: 986 helix: 2.20 (0.24), residues: 440 sheet: -0.84 (0.41), residues: 166 loop : -0.78 (0.29), residues: 380 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 339 HIS 0.004 0.001 HIS B 62 PHE 0.013 0.001 PHE A 340 TYR 0.016 0.001 TYR A 253 ARG 0.004 0.000 ARG G 27 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1972 Ramachandran restraints generated. 986 Oldfield, 0 Emsley, 986 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1972 Ramachandran restraints generated. 986 Oldfield, 0 Emsley, 986 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 874 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 96 time to evaluate : 0.841 Fit side-chains revert: symmetry clash outliers start: 15 outliers final: 15 residues processed: 100 average time/residue: 0.1385 time to fit residues: 20.4819 Evaluate side-chains 105 residues out of total 874 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 90 time to evaluate : 0.782 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 HIS Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 364 THR Chi-restraints excluded: chain B residue 103 CYS Chi-restraints excluded: chain R residue 116 CYS Chi-restraints excluded: chain R residue 136 THR Chi-restraints excluded: chain R residue 166 PHE Chi-restraints excluded: chain R residue 189 THR Chi-restraints excluded: chain R residue 206 VAL Chi-restraints excluded: chain R residue 207 SER Chi-restraints excluded: chain R residue 296 HIS Chi-restraints excluded: chain R residue 309 ILE Chi-restraints excluded: chain R residue 312 ASN Chi-restraints excluded: chain R residue 314 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 49 optimal weight: 0.9990 chunk 27 optimal weight: 3.9990 chunk 74 optimal weight: 8.9990 chunk 61 optimal weight: 0.0770 chunk 24 optimal weight: 4.9990 chunk 90 optimal weight: 0.9980 chunk 97 optimal weight: 2.9990 chunk 80 optimal weight: 0.9980 chunk 89 optimal weight: 0.8980 chunk 30 optimal weight: 3.9990 chunk 72 optimal weight: 0.6980 overall best weight: 0.7338 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 294 GLN B 75 GLN G 44 HIS ** R 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 312 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8064 moved from start: 0.1760 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.020 7052 Z= 0.146 Angle : 0.448 6.256 9677 Z= 0.245 Chirality : 0.040 0.125 1175 Planarity : 0.003 0.032 1233 Dihedral : 7.202 150.129 1085 Min Nonbonded Distance : 2.167 Molprobity Statistics. All-atom Clashscore : 3.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.93 % Favored : 98.07 % Rotamer: Outliers : 3.68 % Allowed : 13.08 % Favored : 83.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.94 (0.27), residues: 986 helix: 2.37 (0.25), residues: 439 sheet: -0.77 (0.40), residues: 172 loop : -0.79 (0.29), residues: 375 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 82 HIS 0.002 0.000 HIS R 296 PHE 0.008 0.001 PHE R 193 TYR 0.019 0.001 TYR A 253 ARG 0.002 0.000 ARG G 27 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1972 Ramachandran restraints generated. 986 Oldfield, 0 Emsley, 986 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1972 Ramachandran restraints generated. 986 Oldfield, 0 Emsley, 986 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 874 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 95 time to evaluate : 0.809 Fit side-chains revert: symmetry clash outliers start: 20 outliers final: 17 residues processed: 104 average time/residue: 0.1430 time to fit residues: 22.3560 Evaluate side-chains 101 residues out of total 874 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 84 time to evaluate : 0.833 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 SER Chi-restraints excluded: chain A residue 64 HIS Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 250 SER Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 364 THR Chi-restraints excluded: chain A residue 393 LEU Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 300 LEU Chi-restraints excluded: chain R residue 106 CYS Chi-restraints excluded: chain R residue 116 CYS Chi-restraints excluded: chain R residue 166 PHE Chi-restraints excluded: chain R residue 206 VAL Chi-restraints excluded: chain R residue 230 LEU Chi-restraints excluded: chain R residue 296 HIS Chi-restraints excluded: chain R residue 309 ILE Chi-restraints excluded: chain R residue 321 PHE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 88 optimal weight: 0.9990 chunk 67 optimal weight: 3.9990 chunk 46 optimal weight: 0.8980 chunk 9 optimal weight: 4.9990 chunk 42 optimal weight: 5.9990 chunk 60 optimal weight: 1.9990 chunk 90 optimal weight: 0.8980 chunk 95 optimal weight: 0.9990 chunk 47 optimal weight: 3.9990 chunk 85 optimal weight: 7.9990 chunk 25 optimal weight: 0.4980 overall best weight: 0.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 44 HIS ** R 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8075 moved from start: 0.2010 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 7052 Z= 0.158 Angle : 0.451 8.935 9677 Z= 0.242 Chirality : 0.040 0.123 1175 Planarity : 0.003 0.034 1233 Dihedral : 7.092 154.195 1085 Min Nonbonded Distance : 2.156 Molprobity Statistics. All-atom Clashscore : 4.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.03 % Favored : 97.97 % Rotamer: Outliers : 3.87 % Allowed : 14.18 % Favored : 81.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.09 (0.27), residues: 986 helix: 2.43 (0.25), residues: 442 sheet: -0.53 (0.42), residues: 168 loop : -0.76 (0.29), residues: 376 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP R 99 HIS 0.003 0.001 HIS B 62 PHE 0.009 0.001 PHE B 241 TYR 0.016 0.001 TYR A 253 ARG 0.004 0.000 ARG G 27 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1972 Ramachandran restraints generated. 986 Oldfield, 0 Emsley, 986 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1972 Ramachandran restraints generated. 986 Oldfield, 0 Emsley, 986 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 874 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 87 time to evaluate : 0.802 Fit side-chains revert: symmetry clash REVERT: A 378 ASP cc_start: 0.8700 (m-30) cc_final: 0.8236 (m-30) REVERT: B 258 ASP cc_start: 0.7975 (t0) cc_final: 0.7714 (t0) outliers start: 21 outliers final: 20 residues processed: 97 average time/residue: 0.1389 time to fit residues: 20.0678 Evaluate side-chains 104 residues out of total 874 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 84 time to evaluate : 0.853 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 SER Chi-restraints excluded: chain A residue 64 HIS Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 250 SER Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 364 THR Chi-restraints excluded: chain A residue 393 LEU Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 300 LEU Chi-restraints excluded: chain B residue 329 THR Chi-restraints excluded: chain R residue 106 CYS Chi-restraints excluded: chain R residue 116 CYS Chi-restraints excluded: chain R residue 166 PHE Chi-restraints excluded: chain R residue 189 THR Chi-restraints excluded: chain R residue 206 VAL Chi-restraints excluded: chain R residue 230 LEU Chi-restraints excluded: chain R residue 296 HIS Chi-restraints excluded: chain R residue 309 ILE Chi-restraints excluded: chain R residue 314 ILE Chi-restraints excluded: chain R residue 321 PHE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 79 optimal weight: 1.9990 chunk 54 optimal weight: 0.2980 chunk 1 optimal weight: 2.9990 chunk 71 optimal weight: 8.9990 chunk 39 optimal weight: 0.9980 chunk 81 optimal weight: 0.8980 chunk 66 optimal weight: 30.0000 chunk 0 optimal weight: 9.9990 chunk 48 optimal weight: 0.8980 chunk 85 optimal weight: 7.9990 chunk 24 optimal weight: 8.9990 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 75 GLN G 44 HIS ** R 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 312 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8091 moved from start: 0.2144 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 7052 Z= 0.175 Angle : 0.455 6.731 9677 Z= 0.244 Chirality : 0.040 0.122 1175 Planarity : 0.003 0.054 1233 Dihedral : 7.096 156.171 1085 Min Nonbonded Distance : 2.157 Molprobity Statistics. All-atom Clashscore : 4.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.03 % Favored : 97.97 % Rotamer: Outliers : 5.16 % Allowed : 14.73 % Favored : 80.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.15 (0.27), residues: 986 helix: 2.50 (0.25), residues: 441 sheet: -0.42 (0.43), residues: 156 loop : -0.79 (0.29), residues: 389 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 82 HIS 0.002 0.001 HIS R 296 PHE 0.010 0.001 PHE B 241 TYR 0.009 0.001 TYR R 308 ARG 0.006 0.000 ARG G 27 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1972 Ramachandran restraints generated. 986 Oldfield, 0 Emsley, 986 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1972 Ramachandran restraints generated. 986 Oldfield, 0 Emsley, 986 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 874 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 86 time to evaluate : 0.786 Fit side-chains revert: symmetry clash REVERT: B 258 ASP cc_start: 0.8006 (t0) cc_final: 0.7772 (t0) outliers start: 28 outliers final: 24 residues processed: 100 average time/residue: 0.1340 time to fit residues: 19.9455 Evaluate side-chains 106 residues out of total 874 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 82 time to evaluate : 0.794 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 SER Chi-restraints excluded: chain A residue 64 HIS Chi-restraints excluded: chain A residue 207 ILE Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 250 SER Chi-restraints excluded: chain A residue 264 ASN Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 364 THR Chi-restraints excluded: chain A residue 393 LEU Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 300 LEU Chi-restraints excluded: chain B residue 329 THR Chi-restraints excluded: chain G residue 19 LEU Chi-restraints excluded: chain R residue 106 CYS Chi-restraints excluded: chain R residue 116 CYS Chi-restraints excluded: chain R residue 166 PHE Chi-restraints excluded: chain R residue 189 THR Chi-restraints excluded: chain R residue 206 VAL Chi-restraints excluded: chain R residue 207 SER Chi-restraints excluded: chain R residue 230 LEU Chi-restraints excluded: chain R residue 309 ILE Chi-restraints excluded: chain R residue 312 ASN Chi-restraints excluded: chain R residue 314 ILE Chi-restraints excluded: chain R residue 321 PHE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 32 optimal weight: 0.6980 chunk 86 optimal weight: 4.9990 chunk 18 optimal weight: 2.9990 chunk 56 optimal weight: 4.9990 chunk 23 optimal weight: 0.9980 chunk 95 optimal weight: 0.6980 chunk 79 optimal weight: 3.9990 chunk 44 optimal weight: 0.6980 chunk 7 optimal weight: 5.9990 chunk 31 optimal weight: 0.8980 chunk 50 optimal weight: 2.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 75 GLN G 44 HIS ** R 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 93 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8078 moved from start: 0.2227 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 7052 Z= 0.147 Angle : 0.446 6.577 9677 Z= 0.238 Chirality : 0.040 0.122 1175 Planarity : 0.003 0.031 1233 Dihedral : 7.045 157.255 1085 Min Nonbonded Distance : 2.172 Molprobity Statistics. All-atom Clashscore : 4.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.03 % Favored : 97.97 % Rotamer: Outliers : 4.24 % Allowed : 16.76 % Favored : 79.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.21 (0.27), residues: 986 helix: 2.55 (0.25), residues: 442 sheet: -0.37 (0.43), residues: 156 loop : -0.77 (0.29), residues: 388 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP R 313 HIS 0.005 0.001 HIS R 93 PHE 0.008 0.001 PHE B 241 TYR 0.009 0.001 TYR R 308 ARG 0.003 0.000 ARG G 27 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1972 Ramachandran restraints generated. 986 Oldfield, 0 Emsley, 986 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1972 Ramachandran restraints generated. 986 Oldfield, 0 Emsley, 986 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 874 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 87 time to evaluate : 0.867 Fit side-chains revert: symmetry clash REVERT: B 258 ASP cc_start: 0.8030 (t0) cc_final: 0.7804 (t0) outliers start: 23 outliers final: 21 residues processed: 97 average time/residue: 0.1388 time to fit residues: 19.9310 Evaluate side-chains 104 residues out of total 874 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 83 time to evaluate : 0.841 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 SER Chi-restraints excluded: chain A residue 64 HIS Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 250 SER Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 364 THR Chi-restraints excluded: chain A residue 393 LEU Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 300 LEU Chi-restraints excluded: chain G residue 19 LEU Chi-restraints excluded: chain R residue 106 CYS Chi-restraints excluded: chain R residue 116 CYS Chi-restraints excluded: chain R residue 166 PHE Chi-restraints excluded: chain R residue 189 THR Chi-restraints excluded: chain R residue 206 VAL Chi-restraints excluded: chain R residue 207 SER Chi-restraints excluded: chain R residue 230 LEU Chi-restraints excluded: chain R residue 296 HIS Chi-restraints excluded: chain R residue 309 ILE Chi-restraints excluded: chain R residue 314 ILE Chi-restraints excluded: chain R residue 321 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 92 optimal weight: 1.9990 chunk 10 optimal weight: 1.9990 chunk 54 optimal weight: 1.9990 chunk 69 optimal weight: 0.9990 chunk 80 optimal weight: 0.8980 chunk 53 optimal weight: 0.9990 chunk 95 optimal weight: 0.1980 chunk 59 optimal weight: 0.0870 chunk 58 optimal weight: 0.3980 chunk 44 optimal weight: 2.9990 chunk 38 optimal weight: 5.9990 overall best weight: 0.5160 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 44 HIS ** R 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8048 moved from start: 0.2326 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 7052 Z= 0.119 Angle : 0.435 6.663 9677 Z= 0.230 Chirality : 0.039 0.122 1175 Planarity : 0.003 0.031 1233 Dihedral : 6.944 158.975 1085 Min Nonbonded Distance : 2.168 Molprobity Statistics. All-atom Clashscore : 3.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.42 % Favored : 98.58 % Rotamer: Outliers : 3.31 % Allowed : 17.50 % Favored : 79.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.29 (0.27), residues: 986 helix: 2.55 (0.25), residues: 444 sheet: -0.26 (0.44), residues: 155 loop : -0.70 (0.29), residues: 387 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP R 99 HIS 0.002 0.000 HIS R 296 PHE 0.007 0.001 PHE R 193 TYR 0.009 0.001 TYR R 132 ARG 0.004 0.000 ARG G 27 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1972 Ramachandran restraints generated. 986 Oldfield, 0 Emsley, 986 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1972 Ramachandran restraints generated. 986 Oldfield, 0 Emsley, 986 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 874 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 86 time to evaluate : 0.783 Fit side-chains revert: symmetry clash REVERT: A 378 ASP cc_start: 0.8595 (m-30) cc_final: 0.8118 (m-30) outliers start: 18 outliers final: 16 residues processed: 95 average time/residue: 0.1339 time to fit residues: 18.8551 Evaluate side-chains 97 residues out of total 874 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 81 time to evaluate : 0.790 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 SER Chi-restraints excluded: chain A residue 64 HIS Chi-restraints excluded: chain A residue 250 SER Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 393 LEU Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain G residue 19 LEU Chi-restraints excluded: chain R residue 106 CYS Chi-restraints excluded: chain R residue 166 PHE Chi-restraints excluded: chain R residue 189 THR Chi-restraints excluded: chain R residue 206 VAL Chi-restraints excluded: chain R residue 207 SER Chi-restraints excluded: chain R residue 230 LEU Chi-restraints excluded: chain R residue 296 HIS Chi-restraints excluded: chain R residue 309 ILE Chi-restraints excluded: chain R residue 321 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 56 optimal weight: 0.6980 chunk 28 optimal weight: 0.7980 chunk 18 optimal weight: 2.9990 chunk 60 optimal weight: 0.8980 chunk 65 optimal weight: 7.9990 chunk 47 optimal weight: 0.0060 chunk 8 optimal weight: 9.9990 chunk 75 optimal weight: 0.7980 chunk 86 optimal weight: 6.9990 chunk 91 optimal weight: 0.7980 chunk 83 optimal weight: 2.9990 overall best weight: 0.6196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 259 GLN G 44 HIS ** R 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8054 moved from start: 0.2377 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 7052 Z= 0.132 Angle : 0.445 7.342 9677 Z= 0.235 Chirality : 0.039 0.128 1175 Planarity : 0.003 0.031 1233 Dihedral : 6.923 159.062 1085 Min Nonbonded Distance : 2.181 Molprobity Statistics. All-atom Clashscore : 3.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.83 % Favored : 98.17 % Rotamer: Outliers : 3.50 % Allowed : 17.68 % Favored : 78.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.33 (0.27), residues: 986 helix: 2.59 (0.25), residues: 445 sheet: -0.14 (0.44), residues: 151 loop : -0.73 (0.29), residues: 390 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP R 99 HIS 0.002 0.000 HIS R 296 PHE 0.008 0.001 PHE B 241 TYR 0.008 0.001 TYR R 132 ARG 0.001 0.000 ARG G 27 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1972 Ramachandran restraints generated. 986 Oldfield, 0 Emsley, 986 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1972 Ramachandran restraints generated. 986 Oldfield, 0 Emsley, 986 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 874 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 83 time to evaluate : 0.877 Fit side-chains REVERT: A 378 ASP cc_start: 0.8578 (m-30) cc_final: 0.8131 (m-30) outliers start: 19 outliers final: 18 residues processed: 93 average time/residue: 0.1452 time to fit residues: 19.8993 Evaluate side-chains 100 residues out of total 874 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 82 time to evaluate : 0.846 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 SER Chi-restraints excluded: chain A residue 64 HIS Chi-restraints excluded: chain A residue 250 SER Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 364 THR Chi-restraints excluded: chain A residue 393 LEU Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain G residue 19 LEU Chi-restraints excluded: chain R residue 106 CYS Chi-restraints excluded: chain R residue 116 CYS Chi-restraints excluded: chain R residue 166 PHE Chi-restraints excluded: chain R residue 189 THR Chi-restraints excluded: chain R residue 206 VAL Chi-restraints excluded: chain R residue 207 SER Chi-restraints excluded: chain R residue 230 LEU Chi-restraints excluded: chain R residue 296 HIS Chi-restraints excluded: chain R residue 309 ILE Chi-restraints excluded: chain R residue 321 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 88 optimal weight: 0.9990 chunk 91 optimal weight: 0.9990 chunk 53 optimal weight: 5.9990 chunk 38 optimal weight: 4.9990 chunk 69 optimal weight: 0.7980 chunk 27 optimal weight: 1.9990 chunk 80 optimal weight: 0.9990 chunk 84 optimal weight: 0.6980 chunk 58 optimal weight: 3.9990 chunk 94 optimal weight: 0.7980 chunk 57 optimal weight: 1.9990 overall best weight: 0.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 44 HIS ** R 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8072 moved from start: 0.2395 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 7052 Z= 0.156 Angle : 0.459 7.915 9677 Z= 0.242 Chirality : 0.040 0.122 1175 Planarity : 0.003 0.031 1233 Dihedral : 6.937 158.803 1085 Min Nonbonded Distance : 2.177 Molprobity Statistics. All-atom Clashscore : 4.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.03 % Favored : 97.97 % Rotamer: Outliers : 3.87 % Allowed : 17.50 % Favored : 78.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.33 (0.27), residues: 986 helix: 2.61 (0.25), residues: 445 sheet: -0.17 (0.44), residues: 151 loop : -0.76 (0.29), residues: 390 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP R 99 HIS 0.003 0.001 HIS B 142 PHE 0.009 0.001 PHE B 241 TYR 0.009 0.001 TYR R 132 ARG 0.001 0.000 ARG B 137 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1972 Ramachandran restraints generated. 986 Oldfield, 0 Emsley, 986 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1972 Ramachandran restraints generated. 986 Oldfield, 0 Emsley, 986 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 874 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 82 time to evaluate : 0.812 Fit side-chains REVERT: B 59 TYR cc_start: 0.8750 (m-80) cc_final: 0.8477 (m-80) outliers start: 21 outliers final: 20 residues processed: 93 average time/residue: 0.1386 time to fit residues: 19.0733 Evaluate side-chains 101 residues out of total 874 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 81 time to evaluate : 0.820 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 SER Chi-restraints excluded: chain A residue 64 HIS Chi-restraints excluded: chain A residue 250 SER Chi-restraints excluded: chain A residue 264 ASN Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 364 THR Chi-restraints excluded: chain A residue 393 LEU Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 300 LEU Chi-restraints excluded: chain G residue 19 LEU Chi-restraints excluded: chain R residue 106 CYS Chi-restraints excluded: chain R residue 116 CYS Chi-restraints excluded: chain R residue 166 PHE Chi-restraints excluded: chain R residue 189 THR Chi-restraints excluded: chain R residue 206 VAL Chi-restraints excluded: chain R residue 207 SER Chi-restraints excluded: chain R residue 230 LEU Chi-restraints excluded: chain R residue 296 HIS Chi-restraints excluded: chain R residue 309 ILE Chi-restraints excluded: chain R residue 321 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 44 optimal weight: 2.9990 chunk 65 optimal weight: 6.9990 chunk 98 optimal weight: 0.9990 chunk 90 optimal weight: 0.8980 chunk 78 optimal weight: 3.9990 chunk 8 optimal weight: 10.0000 chunk 60 optimal weight: 2.9990 chunk 48 optimal weight: 3.9990 chunk 62 optimal weight: 3.9990 chunk 83 optimal weight: 0.5980 chunk 24 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: B 156 GLN G 44 HIS ** R 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8132 moved from start: 0.2470 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 7052 Z= 0.257 Angle : 0.510 7.995 9677 Z= 0.273 Chirality : 0.041 0.125 1175 Planarity : 0.003 0.032 1233 Dihedral : 7.148 156.810 1085 Min Nonbonded Distance : 2.167 Molprobity Statistics. All-atom Clashscore : 5.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.35 % Favored : 96.65 % Rotamer: Outliers : 3.68 % Allowed : 18.05 % Favored : 78.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.09 (0.27), residues: 986 helix: 2.51 (0.25), residues: 439 sheet: -0.38 (0.43), residues: 156 loop : -0.91 (0.29), residues: 391 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 339 HIS 0.003 0.001 HIS B 311 PHE 0.012 0.001 PHE B 241 TYR 0.013 0.002 TYR R 199 ARG 0.003 0.000 ARG B 137 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1972 Ramachandran restraints generated. 986 Oldfield, 0 Emsley, 986 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1972 Ramachandran restraints generated. 986 Oldfield, 0 Emsley, 986 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 874 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 82 time to evaluate : 0.753 Fit side-chains REVERT: A 378 ASP cc_start: 0.8740 (m-30) cc_final: 0.8285 (m-30) outliers start: 20 outliers final: 17 residues processed: 92 average time/residue: 0.1371 time to fit residues: 18.8197 Evaluate side-chains 98 residues out of total 874 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 81 time to evaluate : 0.814 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 SER Chi-restraints excluded: chain A residue 64 HIS Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 250 SER Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 364 THR Chi-restraints excluded: chain B residue 300 LEU Chi-restraints excluded: chain R residue 106 CYS Chi-restraints excluded: chain R residue 116 CYS Chi-restraints excluded: chain R residue 166 PHE Chi-restraints excluded: chain R residue 189 THR Chi-restraints excluded: chain R residue 206 VAL Chi-restraints excluded: chain R residue 207 SER Chi-restraints excluded: chain R residue 230 LEU Chi-restraints excluded: chain R residue 296 HIS Chi-restraints excluded: chain R residue 309 ILE Chi-restraints excluded: chain R residue 321 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 72 optimal weight: 7.9990 chunk 11 optimal weight: 0.0770 chunk 21 optimal weight: 0.2980 chunk 78 optimal weight: 3.9990 chunk 32 optimal weight: 0.8980 chunk 80 optimal weight: 0.9980 chunk 9 optimal weight: 1.9990 chunk 14 optimal weight: 4.9990 chunk 69 optimal weight: 0.7980 chunk 4 optimal weight: 0.7980 chunk 56 optimal weight: 1.9990 overall best weight: 0.5738 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 44 HIS R 51 ASN ** R 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3639 r_free = 0.3639 target = 0.127435 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3286 r_free = 0.3286 target = 0.101918 restraints weight = 12966.578| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3326 r_free = 0.3326 target = 0.104666 restraints weight = 7314.743| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.106355 restraints weight = 5130.824| |-----------------------------------------------------------------------------| r_work (final): 0.3345 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8026 moved from start: 0.2516 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 7052 Z= 0.131 Angle : 0.458 8.475 9677 Z= 0.242 Chirality : 0.040 0.122 1175 Planarity : 0.003 0.032 1233 Dihedral : 7.033 158.956 1085 Min Nonbonded Distance : 2.178 Molprobity Statistics. All-atom Clashscore : 4.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.62 % Favored : 98.38 % Rotamer: Outliers : 3.13 % Allowed : 18.78 % Favored : 78.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.12 (0.27), residues: 986 helix: 2.45 (0.25), residues: 447 sheet: -0.32 (0.44), residues: 151 loop : -0.87 (0.29), residues: 388 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP R 105 HIS 0.002 0.000 HIS R 296 PHE 0.008 0.001 PHE B 241 TYR 0.009 0.001 TYR R 132 ARG 0.005 0.000 ARG G 27 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1562.22 seconds wall clock time: 29 minutes 5.80 seconds (1745.80 seconds total)