Starting phenix.real_space_refine (version: dev) on Mon Dec 12 20:11:13 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ew3_28641/12_2022/8ew3_28641_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ew3_28641/12_2022/8ew3_28641.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.65159 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ew3_28641/12_2022/8ew3_28641.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ew3_28641/12_2022/8ew3_28641.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ew3_28641/12_2022/8ew3_28641_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ew3_28641/12_2022/8ew3_28641_updated.pdb" } resolution = 2.65159 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.001 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 None Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/chem_data/mon_lib" Total number of atoms: 11902 Number of models: 1 Model: "" Number of chains: 9 Chain: "A" Number of atoms: 3416 Number of conformers: 1 Conformer: "" Number of residues, atoms: 446, 3416 Classifications: {'peptide': 446} Modifications used: {'COO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 21, 'TRANS': 422} Chain: "B" Number of atoms: 3182 Number of conformers: 1 Conformer: "" Number of residues, atoms: 412, 3182 Classifications: {'peptide': 412} Link IDs: {'PTRANS': 15, 'TRANS': 396} Chain: "C" Number of atoms: 1894 Number of conformers: 1 Conformer: "" Number of residues, atoms: 250, 1894 Classifications: {'peptide': 250} Link IDs: {'PTRANS': 7, 'TRANS': 242} Chain: "D" Number of atoms: 1545 Number of conformers: 1 Conformer: "" Number of residues, atoms: 202, 1545 Classifications: {'peptide': 202} Link IDs: {'PTRANS': 9, 'TRANS': 192} Chain: "E" Number of atoms: 1512 Number of conformers: 1 Conformer: "" Number of residues, atoms: 198, 1512 Classifications: {'peptide': 198} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 190} Chain: "F" Number of atoms: 244 Number of conformers: 1 Conformer: "" Number of residues, atoms: 32, 244 Classifications: {'peptide': 32} Link IDs: {'PTRANS': 1, 'TRANS': 30} Chain: "B" Number of atoms: 75 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 75 Unusual residues: {'FMN': 1, 'RBF': 1, 'UQ1': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 3 Chain: "C" Number of atoms: 30 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 30 Unusual residues: {'FMN': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 3 Chain: "E" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 4 Unusual residues: {'FES': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 9290 SG CYS D 112 66.314 41.140 63.217 1.00 95.11 S ATOM 10247 SG CYS E 26 64.807 44.084 64.882 1.00 82.26 S ATOM 8651 SG CYS D 29 62.941 41.588 68.946 1.00104.84 S ATOM 10969 SG CYS E 120 64.555 38.368 67.743 1.00 78.16 S Time building chain proxies: 7.15, per 1000 atoms: 0.60 Number of scatterers: 11902 At special positions: 0 Unit cell: (99.324, 108.936, 132.432, 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) Fe 2 26.01 S 68 16.00 P 2 15.00 O 2135 8.00 N 1949 7.00 C 7746 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=2, symmetry=0 Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 5.14 Conformation dependent library (CDL) restraints added in 2.0 seconds Dynamic metal coordination Iron sulfur cluster coordination pdb=" FES E 301 " pdb=" FE1 FES E 301 " - pdb=" SG CYS D 112 " pdb=" FE1 FES E 301 " - pdb=" SG CYS E 26 " pdb=" FE2 FES E 301 " - pdb=" SG CYS D 29 " pdb=" FE2 FES E 301 " - pdb=" SG CYS E 120 " Number of angles added : 6 3056 Ramachandran restraints generated. 1528 Oldfield, 0 Emsley, 1528 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2784 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 70 helices and 8 sheets defined 53.2% alpha, 7.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.15 Creating SS restraints... Processing helix chain 'A' and resid 83 through 85 No H-bonds generated for 'chain 'A' and resid 83 through 85' Processing helix chain 'A' and resid 115 through 125 Processing helix chain 'A' and resid 127 through 130 Processing helix chain 'A' and resid 163 through 169 removed outlier: 3.531A pdb=" N GLU A 169 " --> pdb=" O VAL A 165 " (cutoff:3.500A) Processing helix chain 'A' and resid 171 through 184 Processing helix chain 'A' and resid 220 through 227 Processing helix chain 'A' and resid 241 through 253 Processing helix chain 'A' and resid 283 through 286 No H-bonds generated for 'chain 'A' and resid 283 through 286' Processing helix chain 'A' and resid 311 through 313 No H-bonds generated for 'chain 'A' and resid 311 through 313' Processing helix chain 'A' and resid 336 through 338 No H-bonds generated for 'chain 'A' and resid 336 through 338' Processing helix chain 'A' and resid 352 through 355 Processing helix chain 'A' and resid 379 through 383 removed outlier: 3.678A pdb=" N VAL A 383 " --> pdb=" O ASN A 379 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 379 through 383' Processing helix chain 'A' and resid 390 through 399 Processing helix chain 'A' and resid 402 through 407 Processing helix chain 'A' and resid 410 through 412 No H-bonds generated for 'chain 'A' and resid 410 through 412' Processing helix chain 'A' and resid 416 through 423 removed outlier: 4.842A pdb=" N LEU A 420 " --> pdb=" O ASP A 417 " (cutoff:3.500A) Processing helix chain 'A' and resid 431 through 445 Processing helix chain 'B' and resid 4 through 14 removed outlier: 4.634A pdb=" N HIS B 12 " --> pdb=" O GLU B 8 " (cutoff:3.500A) removed outlier: 5.187A pdb=" N HIS B 13 " --> pdb=" O ASP B 9 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N PHE B 14 " --> pdb=" O ILE B 10 " (cutoff:3.500A) Processing helix chain 'B' and resid 21 through 34 removed outlier: 4.730A pdb=" N ALA B 25 " --> pdb=" O LYS B 22 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N GLU B 28 " --> pdb=" O ALA B 25 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N ALA B 31 " --> pdb=" O GLU B 28 " (cutoff:3.500A) removed outlier: 4.719A pdb=" N THR B 32 " --> pdb=" O ALA B 29 " (cutoff:3.500A) Processing helix chain 'B' and resid 53 through 63 Processing helix chain 'B' and resid 65 through 86 Processing helix chain 'B' and resid 90 through 98 Processing helix chain 'B' and resid 100 through 107 Processing helix chain 'B' and resid 118 through 151 Proline residue: B 131 - end of helix Processing helix chain 'B' and resid 159 through 169 Processing helix chain 'B' and resid 176 through 188 Processing helix chain 'B' and resid 192 through 194 No H-bonds generated for 'chain 'B' and resid 192 through 194' Processing helix chain 'B' and resid 204 through 215 Processing helix chain 'B' and resid 217 through 219 No H-bonds generated for 'chain 'B' and resid 217 through 219' Processing helix chain 'B' and resid 237 through 248 removed outlier: 8.658A pdb=" N ALA B 246 " --> pdb=" O ALA B 242 " (cutoff:3.500A) removed outlier: 8.801A pdb=" N GLY B 247 " --> pdb=" O GLN B 243 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N ALA B 248 " --> pdb=" O GLY B 244 " (cutoff:3.500A) Processing helix chain 'B' and resid 260 through 265 Processing helix chain 'B' and resid 277 through 289 Processing helix chain 'B' and resid 295 through 315 Processing helix chain 'B' and resid 321 through 324 Processing helix chain 'B' and resid 327 through 332 removed outlier: 3.581A pdb=" N VAL B 332 " --> pdb=" O HIS B 328 " (cutoff:3.500A) Processing helix chain 'B' and resid 336 through 342 Processing helix chain 'B' and resid 354 through 374 Processing helix chain 'B' and resid 382 through 409 removed outlier: 3.624A pdb=" N LEU B 391 " --> pdb=" O LEU B 387 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N PHE B 392 " --> pdb=" O PHE B 388 " (cutoff:3.500A) Proline residue: B 394 - end of helix Processing helix chain 'B' and resid 411 through 413 No H-bonds generated for 'chain 'B' and resid 411 through 413' Processing helix chain 'C' and resid 8 through 32 Processing helix chain 'C' and resid 34 through 53 removed outlier: 3.526A pdb=" N LYS C 45 " --> pdb=" O ALA C 41 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N LYS C 48 " --> pdb=" O ASP C 44 " (cutoff:3.500A) Processing helix chain 'C' and resid 60 through 70 Processing helix chain 'C' and resid 88 through 90 No H-bonds generated for 'chain 'C' and resid 88 through 90' Processing helix chain 'C' and resid 93 through 98 removed outlier: 3.510A pdb=" N LYS C 98 " --> pdb=" O ARG C 94 " (cutoff:3.500A) Processing helix chain 'C' and resid 100 through 102 No H-bonds generated for 'chain 'C' and resid 100 through 102' Processing helix chain 'C' and resid 178 through 181 Processing helix chain 'C' and resid 183 through 189 removed outlier: 3.758A pdb=" N GLN C 188 " --> pdb=" O ALA C 184 " (cutoff:3.500A) removed outlier: 4.196A pdb=" N TRP C 189 " --> pdb=" O TRP C 185 " (cutoff:3.500A) Processing helix chain 'C' and resid 225 through 238 Processing helix chain 'C' and resid 245 through 252 Processing helix chain 'D' and resid 9 through 16 Proline residue: D 14 - end of helix Processing helix chain 'D' and resid 28 through 36 removed outlier: 3.545A pdb=" N ALA D 33 " --> pdb=" O CYS D 29 " (cutoff:3.500A) removed outlier: 4.185A pdb=" N THR D 35 " --> pdb=" O ALA D 31 " (cutoff:3.500A) removed outlier: 5.482A pdb=" N THR D 36 " --> pdb=" O LEU D 32 " (cutoff:3.500A) Processing helix chain 'D' and resid 38 through 61 Processing helix chain 'D' and resid 71 through 93 Processing helix chain 'D' and resid 95 through 108 removed outlier: 6.330A pdb=" N VAL D 103 " --> pdb=" O LYS D 99 " (cutoff:3.500A) removed outlier: 6.906A pdb=" N PHE D 104 " --> pdb=" O GLN D 100 " (cutoff:3.500A) removed outlier: 4.335A pdb=" N VAL D 105 " --> pdb=" O LEU D 101 " (cutoff:3.500A) removed outlier: 5.108A pdb=" N GLY D 106 " --> pdb=" O SER D 102 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ILE D 108 " --> pdb=" O PHE D 104 " (cutoff:3.500A) Processing helix chain 'D' and resid 112 through 120 Processing helix chain 'D' and resid 122 through 124 No H-bonds generated for 'chain 'D' and resid 122 through 124' Processing helix chain 'D' and resid 127 through 157 Processing helix chain 'D' and resid 169 through 171 No H-bonds generated for 'chain 'D' and resid 169 through 171' Processing helix chain 'D' and resid 179 through 182 Processing helix chain 'D' and resid 184 through 201 removed outlier: 3.780A pdb=" N PHE D 188 " --> pdb=" O ALA D 184 " (cutoff:3.500A) Processing helix chain 'D' and resid 203 through 205 No H-bonds generated for 'chain 'D' and resid 203 through 205' Processing helix chain 'E' and resid 2 through 12 Processing helix chain 'E' and resid 25 through 33 removed outlier: 3.518A pdb=" N ALA E 30 " --> pdb=" O CYS E 26 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N SER E 32 " --> pdb=" O PHE E 28 " (cutoff:3.500A) removed outlier: 5.398A pdb=" N LYS E 33 " --> pdb=" O LEU E 29 " (cutoff:3.500A) Processing helix chain 'E' and resid 35 through 62 Proline residue: E 54 - end of helix Processing helix chain 'E' and resid 76 through 101 removed outlier: 4.633A pdb=" N PHE E 80 " --> pdb=" O PHE E 77 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N ILE E 81 " --> pdb=" O LEU E 78 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N PHE E 83 " --> pdb=" O PHE E 80 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N LEU E 90 " --> pdb=" O ILE E 87 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N LEU E 98 " --> pdb=" O GLU E 95 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N ASP E 99 " --> pdb=" O MET E 96 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N ARG E 100 " --> pdb=" O ILE E 97 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N PHE E 101 " --> pdb=" O LEU E 98 " (cutoff:3.500A) Processing helix chain 'E' and resid 103 through 116 removed outlier: 4.657A pdb=" N ILE E 111 " --> pdb=" O ASN E 107 " (cutoff:3.500A) removed outlier: 5.810A pdb=" N PHE E 112 " --> pdb=" O ALA E 108 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N LEU E 113 " --> pdb=" O LEU E 109 " (cutoff:3.500A) Proline residue: E 114 - end of helix Processing helix chain 'E' and resid 120 through 132 Processing helix chain 'E' and resid 136 through 166 removed outlier: 3.817A pdb=" N LYS E 165 " --> pdb=" O ARG E 161 " (cutoff:3.500A) removed outlier: 5.252A pdb=" N TYR E 166 " --> pdb=" O GLU E 162 " (cutoff:3.500A) Processing helix chain 'E' and resid 176 through 192 removed outlier: 3.513A pdb=" N ILE E 181 " --> pdb=" O GLY E 177 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N GLY E 189 " --> pdb=" O LEU E 185 " (cutoff:3.500A) removed outlier: 4.592A pdb=" N SER E 192 " --> pdb=" O LEU E 188 " (cutoff:3.500A) Processing helix chain 'F' and resid 2 through 29 Processing sheet with id= A, first strand: chain 'A' and resid 2 through 4 Processing sheet with id= B, first strand: chain 'A' and resid 28 through 32 removed outlier: 3.754A pdb=" N GLU A 78 " --> pdb=" O VAL A 91 " (cutoff:3.500A) removed outlier: 6.424A pdb=" N GLU A 93 " --> pdb=" O VAL A 76 " (cutoff:3.500A) removed outlier: 5.791A pdb=" N VAL A 76 " --> pdb=" O GLU A 93 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 41 through 43 removed outlier: 7.088A pdb=" N PHE A 68 " --> pdb=" O LEU A 57 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 132 through 134 removed outlier: 6.793A pdb=" N LYS A 188 " --> pdb=" O ILE A 149 " (cutoff:3.500A) removed outlier: 7.996A pdb=" N VAL A 151 " --> pdb=" O LYS A 188 " (cutoff:3.500A) removed outlier: 6.510A pdb=" N TYR A 190 " --> pdb=" O VAL A 151 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'A' and resid 306 through 308 removed outlier: 5.606A pdb=" N GLN A 322 " --> pdb=" O GLY A 301 " (cutoff:3.500A) removed outlier: 8.039A pdb=" N VAL A 323 " --> pdb=" O VAL A 261 " (cutoff:3.500A) removed outlier: 6.223A pdb=" N SER A 263 " --> pdb=" O VAL A 323 " (cutoff:3.500A) removed outlier: 7.518A pdb=" N VAL A 325 " --> pdb=" O SER A 263 " (cutoff:3.500A) removed outlier: 6.796A pdb=" N ALA A 265 " --> pdb=" O VAL A 325 " (cutoff:3.500A) removed outlier: 8.963A pdb=" N ARG A 327 " --> pdb=" O ALA A 265 " (cutoff:3.500A) removed outlier: 7.685A pdb=" N SER A 17 " --> pdb=" O LEU A 274 " (cutoff:3.500A) removed outlier: 9.934A pdb=" N ARG A 276 " --> pdb=" O SER A 17 " (cutoff:3.500A) removed outlier: 12.654A pdb=" N VAL A 19 " --> pdb=" O ARG A 276 " (cutoff:3.500A) removed outlier: 14.300A pdb=" N VAL A 278 " --> pdb=" O VAL A 19 " (cutoff:3.500A) removed outlier: 14.013A pdb=" N SER A 21 " --> pdb=" O VAL A 278 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'C' and resid 71 through 77 removed outlier: 14.213A pdb=" N VAL C 121 " --> pdb=" O HIS C 141 " (cutoff:3.500A) removed outlier: 12.378A pdb=" N HIS C 141 " --> pdb=" O VAL C 121 " (cutoff:3.500A) removed outlier: 7.070A pdb=" N VAL C 123 " --> pdb=" O PRO C 139 " (cutoff:3.500A) removed outlier: 5.984A pdb=" N ASP C 129 " --> pdb=" O THR C 133 " (cutoff:3.500A) removed outlier: 6.019A pdb=" N THR C 133 " --> pdb=" O ASP C 129 " (cutoff:3.500A) removed outlier: 6.852A pdb=" N PHE C 152 " --> pdb=" O TYR C 167 " (cutoff:3.500A) removed outlier: 5.309A pdb=" N TYR C 167 " --> pdb=" O PHE C 152 " (cutoff:3.500A) removed outlier: 7.000A pdb=" N ALA C 154 " --> pdb=" O LEU C 165 " (cutoff:3.500A) removed outlier: 5.856A pdb=" N LEU C 165 " --> pdb=" O ALA C 154 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'C' and resid 103 through 105 Processing sheet with id= H, first strand: chain 'C' and resid 204 through 206 557 hydrogen bonds defined for protein. 1566 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.49 Time building geometry restraints manager: 5.35 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.42: 5004 1.42 - 1.61: 7042 1.61 - 1.81: 120 1.81 - 2.01: 0 2.01 - 2.20: 4 Bond restraints: 12170 Sorted by residual: bond pdb=" C2 UQ1 B 602 " pdb=" C3 UQ1 B 602 " ideal model delta sigma weight residual 1.339 1.421 -0.082 2.00e-02 2.50e+03 1.69e+01 bond pdb=" C4 RBF B 601 " pdb=" C4A RBF B 601 " ideal model delta sigma weight residual 1.481 1.405 0.076 2.00e-02 2.50e+03 1.43e+01 bond pdb=" C4A FMN B 600 " pdb=" N5 FMN B 600 " ideal model delta sigma weight residual 1.380 1.306 0.074 2.00e-02 2.50e+03 1.36e+01 bond pdb=" C4A FMN C 301 " pdb=" N5 FMN C 301 " ideal model delta sigma weight residual 1.380 1.307 0.073 2.00e-02 2.50e+03 1.34e+01 bond pdb=" C1 UQ1 B 602 " pdb=" C2 UQ1 B 602 " ideal model delta sigma weight residual 1.485 1.412 0.073 2.00e-02 2.50e+03 1.33e+01 ... (remaining 12165 not shown) Histogram of bond angle deviations from ideal: 75.60 - 87.28: 2 87.28 - 98.96: 0 98.96 - 110.64: 3974 110.64 - 122.32: 11099 122.32 - 134.01: 1442 Bond angle restraints: 16517 Sorted by residual: angle pdb=" C ILE C 115 " pdb=" N GLN C 116 " pdb=" CA GLN C 116 " ideal model delta sigma weight residual 121.54 126.49 -4.95 1.91e+00 2.74e-01 6.73e+00 angle pdb=" C3 UQ1 B 602 " pdb=" C2 UQ1 B 602 " pdb=" O2 UQ1 B 602 " ideal model delta sigma weight residual 122.52 130.03 -7.51 3.00e+00 1.11e-01 6.26e+00 angle pdb=" C1 UQ1 B 602 " pdb=" C2 UQ1 B 602 " pdb=" O2 UQ1 B 602 " ideal model delta sigma weight residual 117.10 110.63 6.47 3.00e+00 1.11e-01 4.65e+00 angle pdb=" N VAL A 287 " pdb=" CA VAL A 287 " pdb=" CB VAL A 287 " ideal model delta sigma weight residual 111.81 107.29 4.52 2.24e+00 1.99e-01 4.07e+00 angle pdb=" CA TRP B 103 " pdb=" CB TRP B 103 " pdb=" CG TRP B 103 " ideal model delta sigma weight residual 113.60 116.95 -3.35 1.90e+00 2.77e-01 3.11e+00 ... (remaining 16512 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.58: 7058 35.58 - 71.16: 29 71.16 - 106.75: 4 106.75 - 142.33: 1 142.33 - 177.91: 3 Dihedral angle restraints: 7095 sinusoidal: 2738 harmonic: 4357 Sorted by residual: dihedral pdb=" C10 FMN C 301 " pdb=" C1' FMN C 301 " pdb=" N10 FMN C 301 " pdb=" C2' FMN C 301 " ideal model delta sinusoidal sigma weight residual 257.59 79.68 177.91 1 2.00e+01 2.50e-03 4.80e+01 dihedral pdb=" C5' FMN C 301 " pdb=" O5' FMN C 301 " pdb=" P FMN C 301 " pdb=" O1P FMN C 301 " ideal model delta sinusoidal sigma weight residual 75.26 -115.18 -169.57 1 2.00e+01 2.50e-03 4.76e+01 dihedral pdb=" C10 FMN B 600 " pdb=" C1' FMN B 600 " pdb=" N10 FMN B 600 " pdb=" C2' FMN B 600 " ideal model delta sinusoidal sigma weight residual 257.59 89.23 168.37 1 2.00e+01 2.50e-03 4.75e+01 ... (remaining 7092 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.036: 1330 0.036 - 0.072: 427 0.072 - 0.108: 117 0.108 - 0.144: 24 0.144 - 0.180: 1 Chirality restraints: 1899 Sorted by residual: chirality pdb=" C4' RBF B 601 " pdb=" C3' RBF B 601 " pdb=" C5' RBF B 601 " pdb=" O4' RBF B 601 " both_signs ideal model delta sigma weight residual False -2.27 -2.45 0.18 2.00e-01 2.50e+01 8.10e-01 chirality pdb=" CA VAL A 139 " pdb=" N VAL A 139 " pdb=" C VAL A 139 " pdb=" CB VAL A 139 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.12 2.00e-01 2.50e+01 3.88e-01 chirality pdb=" CA VAL A 90 " pdb=" N VAL A 90 " pdb=" C VAL A 90 " pdb=" CB VAL A 90 " both_signs ideal model delta sigma weight residual False 2.44 2.56 -0.12 2.00e-01 2.50e+01 3.75e-01 ... (remaining 1896 not shown) Planarity restraints: 2060 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1 UQ1 B 602 " 0.081 2.00e-02 2.50e+03 1.21e-01 4.42e+02 pdb=" C2 UQ1 B 602 " -0.017 2.00e-02 2.50e+03 pdb=" C3 UQ1 B 602 " -0.030 2.00e-02 2.50e+03 pdb=" C4 UQ1 B 602 " 0.093 2.00e-02 2.50e+03 pdb=" C5 UQ1 B 602 " -0.005 2.00e-02 2.50e+03 pdb=" C6 UQ1 B 602 " -0.032 2.00e-02 2.50e+03 pdb=" C7 UQ1 B 602 " -0.157 2.00e-02 2.50e+03 pdb=" CM5 UQ1 B 602 " -0.085 2.00e-02 2.50e+03 pdb=" O1 UQ1 B 602 " 0.202 2.00e-02 2.50e+03 pdb=" O2 UQ1 B 602 " -0.073 2.00e-02 2.50e+03 pdb=" O3 UQ1 B 602 " -0.190 2.00e-02 2.50e+03 pdb=" O4 UQ1 B 602 " 0.213 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C10 UQ1 B 602 " 0.005 2.00e-02 2.50e+03 2.18e-02 5.92e+00 pdb=" C11 UQ1 B 602 " -0.019 2.00e-02 2.50e+03 pdb=" C7 UQ1 B 602 " -0.026 2.00e-02 2.50e+03 pdb=" C8 UQ1 B 602 " 0.036 2.00e-02 2.50e+03 pdb=" C9 UQ1 B 602 " 0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' FMN C 301 " 0.012 2.00e-02 2.50e+03 7.40e-03 2.60e+00 pdb=" C10 FMN C 301 " 0.006 2.00e-02 2.50e+03 pdb=" C2 FMN C 301 " -0.007 2.00e-02 2.50e+03 pdb=" C4 FMN C 301 " 0.003 2.00e-02 2.50e+03 pdb=" C4A FMN C 301 " 0.006 2.00e-02 2.50e+03 pdb=" C5A FMN C 301 " 0.004 2.00e-02 2.50e+03 pdb=" C6 FMN C 301 " 0.002 2.00e-02 2.50e+03 pdb=" C7 FMN C 301 " -0.005 2.00e-02 2.50e+03 pdb=" C7M FMN C 301 " -0.007 2.00e-02 2.50e+03 pdb=" C8 FMN C 301 " -0.006 2.00e-02 2.50e+03 pdb=" C8M FMN C 301 " -0.009 2.00e-02 2.50e+03 pdb=" C9 FMN C 301 " 0.002 2.00e-02 2.50e+03 pdb=" C9A FMN C 301 " 0.003 2.00e-02 2.50e+03 pdb=" N1 FMN C 301 " 0.002 2.00e-02 2.50e+03 pdb=" N10 FMN C 301 " 0.008 2.00e-02 2.50e+03 pdb=" N3 FMN C 301 " -0.005 2.00e-02 2.50e+03 pdb=" N5 FMN C 301 " 0.009 2.00e-02 2.50e+03 pdb=" O2 FMN C 301 " -0.019 2.00e-02 2.50e+03 pdb=" O4 FMN C 301 " 0.002 2.00e-02 2.50e+03 ... (remaining 2057 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.79: 2791 2.79 - 3.32: 11331 3.32 - 3.84: 20144 3.84 - 4.37: 24935 4.37 - 4.90: 41667 Nonbonded interactions: 100868 Sorted by model distance: nonbonded pdb=" O GLU C 99 " pdb=" OG SER C 103 " model vdw 2.260 2.440 nonbonded pdb=" O ALA B 377 " pdb=" O2' FMN C 301 " model vdw 2.293 2.440 nonbonded pdb=" O GLU B 28 " pdb=" OG1 THR B 32 " model vdw 2.295 2.440 nonbonded pdb=" NH1 ARG C 118 " pdb=" O MET C 242 " model vdw 2.327 2.520 nonbonded pdb=" NH1 ARG B 199 " pdb=" O TYR E 166 " model vdw 2.335 2.520 ... (remaining 100863 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 Fe 2 7.16 5 P 2 5.49 5 S 68 5.16 5 C 7746 2.51 5 N 1949 2.21 5 O 2135 1.98 5 sf(0) = scattering factor at diffraction angle 0. Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.460 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: 10.990 Check model and map are aligned: 0.200 Convert atoms to be neutral: 0.110 Process input model: 35.510 Find NCS groups from input model: 0.330 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Set scattering table: 0.020 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:12.100 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 61.770 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9039 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 : 0.003 0.082 12170 Z= 0.214 Angle : 0.446 7.509 16517 Z= 0.217 Chirality : 0.039 0.180 1899 Planarity : 0.004 0.121 2060 Dihedral : 10.089 177.911 4311 Min Nonbonded Distance : 2.260 Molprobity Statistics. All-atom Clashscore : 3.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.70 % Favored : 98.30 % Rotamer Outliers : 0.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % 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 (0.21), residues: 1528 helix: 1.44 (0.18), residues: 772 sheet: 0.54 (0.58), residues: 76 loop : 0.05 (0.24), residues: 680 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3056 Ramachandran restraints generated. 1528 Oldfield, 0 Emsley, 1528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3056 Ramachandran restraints generated. 1528 Oldfield, 0 Emsley, 1528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 1256 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 168 time to evaluate : 1.492 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 2 outliers final: 0 residues processed: 170 average time/residue: 1.4470 time to fit residues: 264.6976 Evaluate side-chains 113 residues out of total 1256 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 113 time to evaluate : 1.434 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.7026 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 128 optimal weight: 4.9990 chunk 115 optimal weight: 3.9990 chunk 63 optimal weight: 3.9990 chunk 39 optimal weight: 3.9990 chunk 77 optimal weight: 1.9990 chunk 61 optimal weight: 1.9990 chunk 119 optimal weight: 4.9990 chunk 46 optimal weight: 2.9990 chunk 72 optimal weight: 3.9990 chunk 88 optimal weight: 5.9990 chunk 138 optimal weight: 1.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 79 ASN E 119 ASN E 197 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9087 moved from start: 0.1458 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.007 0.035 12170 Z= 0.428 Angle : 0.589 8.865 16517 Z= 0.307 Chirality : 0.044 0.141 1899 Planarity : 0.004 0.058 2060 Dihedral : 9.207 177.573 1646 Min Nonbonded Distance : 2.174 Molprobity Statistics. All-atom Clashscore : 5.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.03 % Favored : 97.97 % Rotamer Outliers : 1.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.41 (0.22), residues: 1528 helix: 1.76 (0.19), residues: 785 sheet: -0.13 (0.52), residues: 90 loop : 0.17 (0.25), residues: 653 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3056 Ramachandran restraints generated. 1528 Oldfield, 0 Emsley, 1528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3056 Ramachandran restraints generated. 1528 Oldfield, 0 Emsley, 1528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 1256 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 117 time to evaluate : 1.499 Fit side-chains revert: symmetry clash outliers start: 18 outliers final: 3 residues processed: 123 average time/residue: 1.3966 time to fit residues: 185.7523 Evaluate side-chains 115 residues out of total 1256 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 112 time to evaluate : 1.436 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 1 residues processed: 2 average time/residue: 0.1978 time to fit residues: 2.5785 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 76 optimal weight: 1.9990 chunk 42 optimal weight: 0.8980 chunk 114 optimal weight: 3.9990 chunk 93 optimal weight: 0.3980 chunk 38 optimal weight: 2.9990 chunk 138 optimal weight: 0.9990 chunk 149 optimal weight: 5.9990 chunk 123 optimal weight: 0.7980 chunk 137 optimal weight: 0.9980 chunk 47 optimal weight: 3.9990 chunk 110 optimal weight: 4.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 110 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9055 moved from start: 0.1670 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.023 12170 Z= 0.175 Angle : 0.480 8.906 16517 Z= 0.250 Chirality : 0.040 0.127 1899 Planarity : 0.004 0.035 2060 Dihedral : 8.779 176.766 1646 Min Nonbonded Distance : 2.183 Molprobity Statistics. All-atom Clashscore : 5.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.83 % Favored : 98.17 % Rotamer Outliers : 1.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % 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: 1.52 (0.22), residues: 1528 helix: 1.87 (0.19), residues: 786 sheet: 0.27 (0.56), residues: 76 loop : 0.13 (0.24), residues: 666 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3056 Ramachandran restraints generated. 1528 Oldfield, 0 Emsley, 1528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3056 Ramachandran restraints generated. 1528 Oldfield, 0 Emsley, 1528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 1256 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 116 time to evaluate : 1.416 Fit side-chains revert: symmetry clash outliers start: 14 outliers final: 4 residues processed: 121 average time/residue: 1.3870 time to fit residues: 181.4410 Evaluate side-chains 116 residues out of total 1256 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 112 time to evaluate : 1.412 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 1 residues processed: 3 average time/residue: 1.1758 time to fit residues: 5.6642 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 136 optimal weight: 2.9990 chunk 103 optimal weight: 5.9990 chunk 71 optimal weight: 3.9990 chunk 15 optimal weight: 0.9980 chunk 65 optimal weight: 2.9990 chunk 92 optimal weight: 6.9990 chunk 138 optimal weight: 0.7980 chunk 146 optimal weight: 0.6980 chunk 72 optimal weight: 2.9990 chunk 131 optimal weight: 4.9990 chunk 39 optimal weight: 1.9990 overall best weight: 1.4984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9074 moved from start: 0.1856 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.024 12170 Z= 0.263 Angle : 0.516 8.640 16517 Z= 0.265 Chirality : 0.041 0.130 1899 Planarity : 0.004 0.037 2060 Dihedral : 8.597 175.365 1646 Min Nonbonded Distance : 2.178 Molprobity Statistics. All-atom Clashscore : 5.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer Outliers : 1.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % 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: 1.47 (0.22), residues: 1528 helix: 1.85 (0.19), residues: 789 sheet: 0.13 (0.57), residues: 76 loop : 0.09 (0.24), residues: 663 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3056 Ramachandran restraints generated. 1528 Oldfield, 0 Emsley, 1528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3056 Ramachandran restraints generated. 1528 Oldfield, 0 Emsley, 1528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 1256 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 115 time to evaluate : 1.496 Fit side-chains revert: symmetry clash outliers start: 21 outliers final: 7 residues processed: 124 average time/residue: 1.4803 time to fit residues: 197.6186 Evaluate side-chains 117 residues out of total 1256 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 110 time to evaluate : 1.361 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 3 residues processed: 4 average time/residue: 0.9740 time to fit residues: 6.1143 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 122 optimal weight: 3.9990 chunk 83 optimal weight: 3.9990 chunk 2 optimal weight: 5.9990 chunk 109 optimal weight: 4.9990 chunk 60 optimal weight: 0.9980 chunk 125 optimal weight: 2.9990 chunk 101 optimal weight: 3.9990 chunk 0 optimal weight: 4.9990 chunk 75 optimal weight: 4.9990 chunk 131 optimal weight: 3.9990 chunk 37 optimal weight: 4.9990 overall best weight: 3.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 116 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9114 moved from start: 0.2102 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.008 0.042 12170 Z= 0.507 Angle : 0.630 10.808 16517 Z= 0.322 Chirality : 0.046 0.152 1899 Planarity : 0.004 0.041 2060 Dihedral : 8.760 172.647 1646 Min Nonbonded Distance : 2.159 Molprobity Statistics. All-atom Clashscore : 6.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % Rotamer Outliers : 1.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % 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: 1.18 (0.21), residues: 1528 helix: 1.62 (0.18), residues: 786 sheet: -0.30 (0.54), residues: 88 loop : 0.00 (0.24), residues: 654 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3056 Ramachandran restraints generated. 1528 Oldfield, 0 Emsley, 1528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3056 Ramachandran restraints generated. 1528 Oldfield, 0 Emsley, 1528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 1256 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 109 time to evaluate : 1.370 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 22 outliers final: 12 residues processed: 119 average time/residue: 1.3911 time to fit residues: 179.0165 Evaluate side-chains 121 residues out of total 1256 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 109 time to evaluate : 1.425 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 5 residues processed: 7 average time/residue: 0.9825 time to fit residues: 9.4888 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 49 optimal weight: 0.6980 chunk 132 optimal weight: 0.9980 chunk 29 optimal weight: 1.9990 chunk 86 optimal weight: 1.9990 chunk 36 optimal weight: 0.8980 chunk 147 optimal weight: 0.6980 chunk 122 optimal weight: 0.9980 chunk 68 optimal weight: 1.9990 chunk 12 optimal weight: 0.6980 chunk 48 optimal weight: 0.9990 chunk 77 optimal weight: 0.5980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9066 moved from start: 0.2155 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.032 12170 Z= 0.166 Angle : 0.495 9.911 16517 Z= 0.255 Chirality : 0.040 0.129 1899 Planarity : 0.003 0.034 2060 Dihedral : 8.507 174.176 1646 Min Nonbonded Distance : 2.194 Molprobity Statistics. All-atom Clashscore : 5.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.09 % Favored : 97.91 % Rotamer Outliers : 1.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % 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: 1.43 (0.22), residues: 1528 helix: 1.85 (0.19), residues: 787 sheet: 0.28 (0.59), residues: 74 loop : 0.01 (0.24), residues: 667 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3056 Ramachandran restraints generated. 1528 Oldfield, 0 Emsley, 1528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3056 Ramachandran restraints generated. 1528 Oldfield, 0 Emsley, 1528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 1256 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 113 time to evaluate : 1.458 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 14 outliers final: 6 residues processed: 121 average time/residue: 1.3386 time to fit residues: 175.1968 Evaluate side-chains 115 residues out of total 1256 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 109 time to evaluate : 1.283 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 5 residues processed: 1 average time/residue: 0.2799 time to fit residues: 2.0310 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 141 optimal weight: 5.9990 chunk 16 optimal weight: 4.9990 chunk 83 optimal weight: 1.9990 chunk 107 optimal weight: 1.9990 chunk 123 optimal weight: 4.9990 chunk 82 optimal weight: 2.9990 chunk 146 optimal weight: 2.9990 chunk 91 optimal weight: 2.9990 chunk 89 optimal weight: 0.9990 chunk 67 optimal weight: 0.9980 chunk 90 optimal weight: 0.8980 overall best weight: 1.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9080 moved from start: 0.2188 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.032 12170 Z= 0.245 Angle : 0.527 10.174 16517 Z= 0.267 Chirality : 0.041 0.138 1899 Planarity : 0.004 0.034 2060 Dihedral : 8.468 174.156 1646 Min Nonbonded Distance : 2.192 Molprobity Statistics. All-atom Clashscore : 5.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Rotamer Outliers : 1.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.44 (0.22), residues: 1528 helix: 1.86 (0.19), residues: 787 sheet: 0.17 (0.59), residues: 76 loop : 0.01 (0.24), residues: 665 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3056 Ramachandran restraints generated. 1528 Oldfield, 0 Emsley, 1528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3056 Ramachandran restraints generated. 1528 Oldfield, 0 Emsley, 1528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 1256 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 111 time to evaluate : 1.401 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 14 outliers final: 8 residues processed: 118 average time/residue: 1.3643 time to fit residues: 174.2279 Evaluate side-chains 116 residues out of total 1256 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 108 time to evaluate : 1.401 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 6 residues processed: 2 average time/residue: 0.7297 time to fit residues: 3.5115 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 58 optimal weight: 2.9990 chunk 87 optimal weight: 6.9990 chunk 44 optimal weight: 9.9990 chunk 28 optimal weight: 1.9990 chunk 93 optimal weight: 8.9990 chunk 99 optimal weight: 4.9990 chunk 72 optimal weight: 2.9990 chunk 13 optimal weight: 0.4980 chunk 115 optimal weight: 0.9990 chunk 133 optimal weight: 4.9990 chunk 140 optimal weight: 0.0970 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9077 moved from start: 0.2243 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.034 12170 Z= 0.237 Angle : 0.528 10.869 16517 Z= 0.268 Chirality : 0.041 0.131 1899 Planarity : 0.003 0.034 2060 Dihedral : 8.376 174.240 1646 Min Nonbonded Distance : 2.194 Molprobity Statistics. All-atom Clashscore : 6.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer Outliers : 1.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.44 (0.22), residues: 1528 helix: 1.87 (0.19), residues: 787 sheet: 0.17 (0.59), residues: 76 loop : 0.01 (0.24), residues: 665 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3056 Ramachandran restraints generated. 1528 Oldfield, 0 Emsley, 1528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3056 Ramachandran restraints generated. 1528 Oldfield, 0 Emsley, 1528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 1256 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 112 time to evaluate : 1.486 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 14 outliers final: 7 residues processed: 119 average time/residue: 1.3983 time to fit residues: 179.7918 Evaluate side-chains 117 residues out of total 1256 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 110 time to evaluate : 1.388 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 5 residues processed: 2 average time/residue: 0.6661 time to fit residues: 3.3485 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 128 optimal weight: 1.9990 chunk 136 optimal weight: 1.9990 chunk 140 optimal weight: 6.9990 chunk 82 optimal weight: 2.9990 chunk 59 optimal weight: 3.9990 chunk 107 optimal weight: 4.9990 chunk 41 optimal weight: 0.5980 chunk 123 optimal weight: 0.9980 chunk 129 optimal weight: 2.9990 chunk 89 optimal weight: 3.9990 chunk 144 optimal weight: 6.9990 overall best weight: 1.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9088 moved from start: 0.2270 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.040 12170 Z= 0.294 Angle : 0.556 12.691 16517 Z= 0.280 Chirality : 0.042 0.133 1899 Planarity : 0.004 0.035 2060 Dihedral : 8.329 174.765 1646 Min Nonbonded Distance : 2.183 Molprobity Statistics. All-atom Clashscore : 6.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer Outliers : 0.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % 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 (0.22), residues: 1528 helix: 1.78 (0.19), residues: 790 sheet: -0.25 (0.56), residues: 86 loop : 0.01 (0.24), residues: 652 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3056 Ramachandran restraints generated. 1528 Oldfield, 0 Emsley, 1528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3056 Ramachandran restraints generated. 1528 Oldfield, 0 Emsley, 1528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 1256 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 110 time to evaluate : 1.480 Fit side-chains revert: symmetry clash outliers start: 9 outliers final: 6 residues processed: 115 average time/residue: 1.4223 time to fit residues: 177.2681 Evaluate side-chains 115 residues out of total 1256 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 109 time to evaluate : 1.306 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 4 residues processed: 2 average time/residue: 0.7130 time to fit residues: 3.4609 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 88 optimal weight: 4.9990 chunk 68 optimal weight: 0.6980 chunk 100 optimal weight: 4.9990 chunk 151 optimal weight: 5.9990 chunk 139 optimal weight: 0.9990 chunk 120 optimal weight: 3.9990 chunk 12 optimal weight: 2.9990 chunk 93 optimal weight: 9.9990 chunk 73 optimal weight: 2.9990 chunk 95 optimal weight: 0.9990 chunk 128 optimal weight: 3.9990 overall best weight: 1.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9087 moved from start: 0.2348 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.046 12170 Z= 0.298 Angle : 0.573 12.691 16517 Z= 0.287 Chirality : 0.042 0.140 1899 Planarity : 0.004 0.034 2060 Dihedral : 8.282 175.441 1646 Min Nonbonded Distance : 2.182 Molprobity Statistics. All-atom Clashscore : 6.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % Rotamer Outliers : 0.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % 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: 1.30 (0.22), residues: 1528 helix: 1.77 (0.19), residues: 789 sheet: -0.29 (0.56), residues: 86 loop : -0.02 (0.24), residues: 653 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3056 Ramachandran restraints generated. 1528 Oldfield, 0 Emsley, 1528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3056 Ramachandran restraints generated. 1528 Oldfield, 0 Emsley, 1528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 1256 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 112 time to evaluate : 1.331 Fit side-chains revert: symmetry clash outliers start: 8 outliers final: 5 residues processed: 117 average time/residue: 1.3920 time to fit residues: 176.7518 Evaluate side-chains 114 residues out of total 1256 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 109 time to evaluate : 1.422 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 4 residues processed: 1 average time/residue: 0.2651 time to fit residues: 2.2442 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 36 optimal weight: 4.9990 chunk 111 optimal weight: 0.8980 chunk 17 optimal weight: 4.9990 chunk 33 optimal weight: 0.9990 chunk 120 optimal weight: 0.8980 chunk 50 optimal weight: 0.0770 chunk 124 optimal weight: 2.9990 chunk 15 optimal weight: 2.9990 chunk 22 optimal weight: 3.9990 chunk 106 optimal weight: 7.9990 chunk 6 optimal weight: 4.9990 overall best weight: 1.1742 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3125 r_free = 0.3125 target = 0.063582 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2733 r_free = 0.2733 target = 0.047264 restraints weight = 31195.426| |-----------------------------------------------------------------------------| r_work (start): 0.2717 rms_B_bonded: 2.43 r_work: 0.2606 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.2491 rms_B_bonded: 4.57 restraints_weight: 0.2500 r_work (final): 0.2491 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8962 moved from start: 0.2366 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.041 12170 Z= 0.220 Angle : 0.532 12.467 16517 Z= 0.269 Chirality : 0.041 0.134 1899 Planarity : 0.004 0.033 2060 Dihedral : 8.192 176.501 1646 Min Nonbonded Distance : 2.188 Molprobity Statistics. All-atom Clashscore : 6.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % Rotamer Outliers : 0.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % 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 (0.22), residues: 1528 helix: 1.79 (0.19), residues: 789 sheet: -0.29 (0.56), residues: 86 loop : 0.00 (0.24), residues: 653 =============================================================================== Job complete usr+sys time: 3832.17 seconds wall clock time: 69 minutes 20.73 seconds (4160.73 seconds total)