Starting phenix.real_space_refine (version: dev) on Mon Dec 12 20:13:35 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8evu_28637/12_2022/8evu_28637_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8evu_28637/12_2022/8evu_28637.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.5804 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8evu_28637/12_2022/8evu_28637.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8evu_28637/12_2022/8evu_28637.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8evu_28637/12_2022/8evu_28637_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8evu_28637/12_2022/8evu_28637_updated.pdb" } resolution = 2.5804 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 65.958 42.181 63.643 1.00 79.57 S ATOM 10247 SG CYS E 26 64.578 45.018 65.377 1.00 65.74 S ATOM 8651 SG CYS D 29 62.336 42.626 69.152 1.00 69.87 S ATOM 10969 SG CYS E 120 64.405 39.385 68.240 1.00 75.41 S Time building chain proxies: 7.21, per 1000 atoms: 0.61 Number of scatterers: 11902 At special positions: 0 Unit cell: (99.324, 110.004, 133.5, 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: 6.08 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: 72 helices and 8 sheets defined 53.4% alpha, 7.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.20 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 110 through 112 No H-bonds generated for 'chain 'A' and resid 110 through 112' 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 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: 3.691A 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: 4.840A 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: 4.637A pdb=" N HIS B 12 " --> pdb=" O GLU B 8 " (cutoff:3.500A) removed outlier: 5.178A pdb=" N HIS B 13 " --> pdb=" O ASP B 9 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N PHE B 14 " --> pdb=" O ILE B 10 " (cutoff:3.500A) Processing helix chain 'B' and resid 21 through 34 removed outlier: 4.721A pdb=" N ALA B 25 " --> pdb=" O LYS B 22 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N GLU B 28 " --> pdb=" O ALA B 25 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N ALA B 31 " --> pdb=" O GLU B 28 " (cutoff:3.500A) removed outlier: 4.704A 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: 8.667A pdb=" N ALA B 246 " --> pdb=" O ALA B 242 " (cutoff:3.500A) removed outlier: 8.802A pdb=" N GLY B 247 " --> pdb=" O GLN B 243 " (cutoff:3.500A) removed outlier: 3.810A 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: 3.528A 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: 3.585A pdb=" N LEU B 391 " --> pdb=" O LEU B 387 " (cutoff:3.500A) removed outlier: 3.770A 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: 3.529A pdb=" N LYS C 45 " --> pdb=" O ALA C 41 " (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 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: 3.777A pdb=" N GLN C 188 " --> pdb=" O ALA C 184 " (cutoff:3.500A) removed outlier: 4.180A 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: 3.506A pdb=" N ALA D 33 " --> pdb=" O CYS D 29 " (cutoff:3.500A) removed outlier: 4.104A pdb=" N THR D 35 " --> pdb=" O ALA D 31 " (cutoff:3.500A) removed outlier: 5.378A 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: 6.352A pdb=" N VAL D 103 " --> pdb=" O LYS D 99 " (cutoff:3.500A) removed outlier: 6.901A pdb=" N PHE D 104 " --> pdb=" O GLN D 100 " (cutoff:3.500A) removed outlier: 4.289A pdb=" N VAL D 105 " --> pdb=" O LEU D 101 " (cutoff:3.500A) removed outlier: 5.007A pdb=" N GLY D 106 " --> pdb=" O SER D 102 " (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: 3.638A 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: 3.823A pdb=" N SER E 32 " --> pdb=" O PHE E 28 " (cutoff:3.500A) removed outlier: 5.437A 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: 4.553A pdb=" N PHE E 80 " --> pdb=" O PHE E 77 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N ILE E 81 " --> pdb=" O LEU E 78 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N PHE E 83 " --> pdb=" O PHE E 80 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N ILE E 84 " --> pdb=" O ILE E 81 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N ALA E 88 " --> pdb=" O GLY E 85 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N VAL E 91 " --> pdb=" O ALA E 88 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N LEU E 98 " --> pdb=" O GLU E 95 " (cutoff:3.500A) removed outlier: 4.366A pdb=" N ASP E 99 " --> pdb=" O MET E 96 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N PHE E 101 " --> pdb=" O LEU E 98 " (cutoff:3.500A) Processing helix chain 'E' and resid 103 through 108 Processing helix chain 'E' and resid 110 through 116 Proline residue: E 114 - end of helix No H-bonds generated for 'chain 'E' and resid 110 through 116' Processing helix chain 'E' and resid 120 through 132 Processing helix chain 'E' and resid 136 through 166 removed outlier: 3.805A pdb=" N LYS E 165 " --> pdb=" O ARG E 161 " (cutoff:3.500A) removed outlier: 5.291A pdb=" N TYR E 166 " --> pdb=" O GLU E 162 " (cutoff:3.500A) Processing helix chain 'E' and resid 176 through 193 removed outlier: 4.129A pdb=" N SER E 192 " --> pdb=" O LEU E 188 " (cutoff:3.500A) removed outlier: 4.989A pdb=" N PHE E 193 " --> pdb=" O GLY E 189 " (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: 3.751A pdb=" N GLU A 78 " --> pdb=" O VAL A 91 " (cutoff:3.500A) removed outlier: 6.428A pdb=" N GLU A 93 " --> pdb=" O VAL A 76 " (cutoff:3.500A) removed outlier: 5.808A 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: 7.130A 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: 6.790A pdb=" N LYS A 188 " --> pdb=" O ILE A 149 " (cutoff:3.500A) removed outlier: 7.993A pdb=" N VAL A 151 " --> pdb=" O LYS A 188 " (cutoff:3.500A) removed outlier: 6.515A 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: 5.588A pdb=" N GLN A 322 " --> pdb=" O GLY A 301 " (cutoff:3.500A) removed outlier: 7.991A pdb=" N VAL A 323 " --> pdb=" O VAL A 261 " (cutoff:3.500A) removed outlier: 6.190A pdb=" N SER A 263 " --> pdb=" O VAL A 323 " (cutoff:3.500A) removed outlier: 7.481A pdb=" N VAL A 325 " --> pdb=" O SER A 263 " (cutoff:3.500A) removed outlier: 6.749A pdb=" N ALA A 265 " --> pdb=" O VAL A 325 " (cutoff:3.500A) removed outlier: 8.935A pdb=" N ARG A 327 " --> pdb=" O ALA A 265 " (cutoff:3.500A) removed outlier: 7.708A pdb=" N SER A 17 " --> pdb=" O LEU A 274 " (cutoff:3.500A) removed outlier: 9.957A pdb=" N ARG A 276 " --> pdb=" O SER A 17 " (cutoff:3.500A) removed outlier: 12.656A pdb=" N VAL A 19 " --> pdb=" O ARG A 276 " (cutoff:3.500A) removed outlier: 14.286A pdb=" N VAL A 278 " --> pdb=" O VAL A 19 " (cutoff:3.500A) removed outlier: 13.993A 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: 14.252A pdb=" N VAL C 121 " --> pdb=" O HIS C 141 " (cutoff:3.500A) removed outlier: 12.402A pdb=" N HIS C 141 " --> pdb=" O VAL C 121 " (cutoff:3.500A) removed outlier: 7.080A pdb=" N VAL C 123 " --> pdb=" O PRO C 139 " (cutoff:3.500A) removed outlier: 5.962A pdb=" N ASP C 129 " --> pdb=" O THR C 133 " (cutoff:3.500A) removed outlier: 6.031A pdb=" N THR C 133 " --> pdb=" O ASP C 129 " (cutoff:3.500A) removed outlier: 6.821A pdb=" N PHE C 152 " --> pdb=" O TYR C 167 " (cutoff:3.500A) removed outlier: 5.271A pdb=" N TYR C 167 " --> pdb=" O PHE C 152 " (cutoff:3.500A) removed outlier: 6.975A pdb=" N ALA C 154 " --> pdb=" O LEU C 165 " (cutoff:3.500A) removed outlier: 5.819A 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 206 561 hydrogen bonds defined for protein. 1581 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: 3.24 Time building geometry restraints manager: 6.43 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: 5002 1.42 - 1.61: 7044 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 1.425 -0.086 2.00e-02 2.50e+03 1.84e+01 bond pdb=" C1 UQ1 B 602 " pdb=" C2 UQ1 B 602 " ideal model delta sigma weight residual 1.485 1.408 0.077 2.00e-02 2.50e+03 1.47e+01 bond pdb=" C4 RBF B 601 " pdb=" C4A RBF B 601 " ideal model delta sigma weight residual 1.481 1.406 0.075 2.00e-02 2.50e+03 1.40e+01 bond pdb=" C1 UQ1 B 602 " pdb=" C6 UQ1 B 602 " ideal model delta sigma weight residual 1.485 1.411 0.074 2.00e-02 2.50e+03 1.38e+01 bond pdb=" C4A FMN B 600 " pdb=" N5 FMN B 600 " ideal model delta sigma weight residual 1.380 1.307 0.073 2.00e-02 2.50e+03 1.33e+01 ... (remaining 12165 not shown) Histogram of bond angle deviations from ideal: 75.57 - 87.27: 2 87.27 - 98.96: 0 98.96 - 110.65: 3986 110.65 - 122.35: 11103 122.35 - 134.04: 1426 Bond angle restraints: 16517 Sorted by residual: angle pdb=" C3 UQ1 B 602 " pdb=" C2 UQ1 B 602 " pdb=" O2 UQ1 B 602 " ideal model delta sigma weight residual 122.52 130.08 -7.56 3.00e+00 1.11e-01 6.35e+00 angle pdb=" N VAL A 287 " pdb=" CA VAL A 287 " pdb=" CB VAL A 287 " ideal model delta sigma weight residual 111.81 107.07 4.74 2.24e+00 1.99e-01 4.47e+00 angle pdb=" C ILE C 115 " pdb=" N GLN C 116 " pdb=" CA GLN C 116 " ideal model delta sigma weight residual 121.54 125.54 -4.00 1.91e+00 2.74e-01 4.39e+00 angle pdb=" C1 UQ1 B 602 " pdb=" C2 UQ1 B 602 " pdb=" O2 UQ1 B 602 " ideal model delta sigma weight residual 117.10 111.14 5.96 3.00e+00 1.11e-01 3.95e+00 angle pdb=" CA TRP B 103 " pdb=" CB TRP B 103 " pdb=" CG TRP B 103 " ideal model delta sigma weight residual 113.60 117.23 -3.63 1.90e+00 2.77e-01 3.66e+00 ... (remaining 16512 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.54: 7057 35.54 - 71.07: 30 71.07 - 106.61: 4 106.61 - 142.15: 1 142.15 - 177.68: 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 79.91 177.68 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 -113.98 -170.76 1 2.00e+01 2.50e-03 4.77e+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 89.21 168.38 1 2.00e+01 2.50e-03 4.75e+01 ... (remaining 7092 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.039: 1366 0.039 - 0.078: 409 0.078 - 0.116: 110 0.116 - 0.155: 13 0.155 - 0.194: 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 -2.47 0.19 2.00e-01 2.50e+01 9.41e-01 chirality pdb=" CA ILE C 205 " pdb=" N ILE C 205 " pdb=" C ILE C 205 " pdb=" CB ILE C 205 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 3.93e-01 chirality pdb=" CA ILE A 92 " pdb=" N ILE A 92 " pdb=" C ILE A 92 " pdb=" CB ILE A 92 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.12 2.00e-01 2.50e+01 3.87e-01 ... (remaining 1896 not shown) Planarity restraints: 2060 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1 UQ1 B 602 " 0.028 2.00e-02 2.50e+03 6.15e-02 1.14e+02 pdb=" C2 UQ1 B 602 " 0.011 2.00e-02 2.50e+03 pdb=" C3 UQ1 B 602 " 0.012 2.00e-02 2.50e+03 pdb=" C4 UQ1 B 602 " 0.056 2.00e-02 2.50e+03 pdb=" C5 UQ1 B 602 " 0.004 2.00e-02 2.50e+03 pdb=" C6 UQ1 B 602 " -0.001 2.00e-02 2.50e+03 pdb=" C7 UQ1 B 602 " -0.070 2.00e-02 2.50e+03 pdb=" CM5 UQ1 B 602 " -0.064 2.00e-02 2.50e+03 pdb=" O1 UQ1 B 602 " 0.074 2.00e-02 2.50e+03 pdb=" O2 UQ1 B 602 " -0.031 2.00e-02 2.50e+03 pdb=" O3 UQ1 B 602 " -0.124 2.00e-02 2.50e+03 pdb=" O4 UQ1 B 602 " 0.103 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C10 UQ1 B 602 " 0.007 2.00e-02 2.50e+03 4.18e-02 2.18e+01 pdb=" C11 UQ1 B 602 " -0.042 2.00e-02 2.50e+03 pdb=" C7 UQ1 B 602 " -0.050 2.00e-02 2.50e+03 pdb=" C8 UQ1 B 602 " 0.062 2.00e-02 2.50e+03 pdb=" C9 UQ1 B 602 " 0.024 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' FMN C 301 " 0.013 2.00e-02 2.50e+03 7.11e-03 2.40e+00 pdb=" C10 FMN C 301 " 0.004 2.00e-02 2.50e+03 pdb=" C2 FMN C 301 " -0.007 2.00e-02 2.50e+03 pdb=" C4 FMN C 301 " 0.002 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 " -0.004 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 " 0.003 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 " 0.006 2.00e-02 2.50e+03 pdb=" N3 FMN C 301 " -0.004 2.00e-02 2.50e+03 pdb=" N5 FMN C 301 " 0.008 2.00e-02 2.50e+03 pdb=" O2 FMN C 301 " -0.019 2.00e-02 2.50e+03 pdb=" O4 FMN C 301 " 0.003 2.00e-02 2.50e+03 ... (remaining 2057 not shown) Histogram of nonbonded interaction distances: 2.28 - 2.80: 3132 2.80 - 3.33: 11359 3.33 - 3.85: 20267 3.85 - 4.38: 24929 4.38 - 4.90: 41585 Nonbonded interactions: 101272 Sorted by model distance: nonbonded pdb=" O GLU C 99 " pdb=" OG SER C 103 " model vdw 2.279 2.440 nonbonded pdb=" O GLU B 28 " pdb=" OG1 THR B 32 " model vdw 2.283 2.440 nonbonded pdb=" O ILE E 46 " pdb=" OG1 THR E 50 " model vdw 2.317 2.440 nonbonded pdb=" NH1 ARG B 199 " pdb=" O TYR E 166 " model vdw 2.329 2.520 nonbonded pdb=" O ASN E 57 " pdb=" ND2 ASN E 61 " model vdw 2.342 2.520 ... (remaining 101267 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: 2.400 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: 11.400 Check model and map are aligned: 0.190 Convert atoms to be neutral: 0.110 Process input model: 38.260 Find NCS groups from input model: 0.280 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:13.500 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 66.210 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9164 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 0.086 12170 Z= 0.226 Angle : 0.444 7.562 16517 Z= 0.216 Chirality : 0.039 0.194 1899 Planarity : 0.004 0.062 2060 Dihedral : 10.092 177.684 4311 Min Nonbonded Distance : 2.279 Molprobity Statistics. All-atom Clashscore : 2.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.31 % Favored : 98.69 % Rotamer Outliers : 0.08 % 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: 1.17 (0.21), residues: 1528 helix: 1.47 (0.18), residues: 786 sheet: 0.62 (0.58), residues: 74 loop : 0.05 (0.24), residues: 668 *********************** 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 159 residues out of total 1256 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 158 time to evaluate : 3.649 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 159 average time/residue: 1.6284 time to fit residues: 276.9297 Evaluate side-chains 118 residues out of total 1256 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 118 time to evaluate : 1.366 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.8195 ------------------------------------------------------------------------------- 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: 0.8980 chunk 63 optimal weight: 3.9990 chunk 39 optimal weight: 1.9990 chunk 77 optimal weight: 3.9990 chunk 61 optimal weight: 1.9990 chunk 119 optimal weight: 4.9990 chunk 46 optimal weight: 8.9990 chunk 72 optimal weight: 2.9990 chunk 88 optimal weight: 3.9990 chunk 138 optimal weight: 3.9990 overall best weight: 2.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 12 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 91 GLN E 79 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9194 moved from start: 0.1225 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.035 12170 Z= 0.412 Angle : 0.565 6.795 16517 Z= 0.297 Chirality : 0.044 0.142 1899 Planarity : 0.004 0.041 2060 Dihedral : 9.247 178.874 1646 Min Nonbonded Distance : 2.204 Molprobity Statistics. All-atom Clashscore : 4.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.03 % Favored : 97.97 % 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: 1.35 (0.22), residues: 1528 helix: 1.76 (0.19), residues: 784 sheet: -0.06 (0.52), residues: 88 loop : 0.06 (0.25), residues: 656 *********************** 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 131 residues out of total 1256 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 117 time to evaluate : 1.448 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 14 outliers final: 5 residues processed: 123 average time/residue: 1.3925 time to fit residues: 185.0824 Evaluate side-chains 119 residues out of total 1256 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 114 time to evaluate : 1.175 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 3 residues processed: 2 average time/residue: 1.0279 time to fit residues: 3.9499 ------------------------------------------------------------------------------- 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: 0.6980 chunk 42 optimal weight: 4.9990 chunk 114 optimal weight: 2.9990 chunk 93 optimal weight: 7.9990 chunk 38 optimal weight: 0.6980 chunk 138 optimal weight: 0.9990 chunk 149 optimal weight: 4.9990 chunk 123 optimal weight: 2.9990 chunk 137 optimal weight: 2.9990 chunk 47 optimal weight: 3.9990 chunk 110 optimal weight: 2.9990 overall best weight: 1.6786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 12 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 91 GLN E 56 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9185 moved from start: 0.1373 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.030 12170 Z= 0.298 Angle : 0.502 5.940 16517 Z= 0.265 Chirality : 0.042 0.135 1899 Planarity : 0.004 0.039 2060 Dihedral : 8.716 176.861 1646 Min Nonbonded Distance : 2.176 Molprobity Statistics. All-atom Clashscore : 4.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.90 % Favored : 98.10 % Rotamer Outliers : 1.04 % 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: 1.31 (0.22), residues: 1528 helix: 1.77 (0.19), residues: 797 sheet: -0.21 (0.53), residues: 87 loop : -0.03 (0.25), residues: 644 *********************** 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 127 residues out of total 1256 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 114 time to evaluate : 1.377 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 13 outliers final: 2 residues processed: 120 average time/residue: 1.4614 time to fit residues: 189.4675 Evaluate side-chains 111 residues out of total 1256 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 109 time to evaluate : 1.398 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 2 residues processed: 0 time to fit residues: 1.9066 ------------------------------------------------------------------------------- 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: 1.9990 chunk 103 optimal weight: 3.9990 chunk 71 optimal weight: 4.9990 chunk 15 optimal weight: 3.9990 chunk 65 optimal weight: 2.9990 chunk 92 optimal weight: 6.9990 chunk 138 optimal weight: 1.9990 chunk 146 optimal weight: 1.9990 chunk 72 optimal weight: 1.9990 chunk 131 optimal weight: 0.8980 chunk 39 optimal weight: 0.6980 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 91 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9183 moved from start: 0.1464 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.030 12170 Z= 0.278 Angle : 0.501 6.928 16517 Z= 0.262 Chirality : 0.041 0.137 1899 Planarity : 0.004 0.038 2060 Dihedral : 8.590 176.035 1646 Min Nonbonded Distance : 2.181 Molprobity Statistics. All-atom Clashscore : 4.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % Rotamer Outliers : 1.04 % 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: 1.77 (0.19), residues: 799 sheet: -0.29 (0.53), residues: 87 loop : -0.01 (0.25), residues: 642 *********************** 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 126 residues out of total 1256 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 113 time to evaluate : 1.431 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 13 outliers final: 3 residues processed: 120 average time/residue: 1.4350 time to fit residues: 185.9944 Evaluate side-chains 115 residues out of total 1256 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 112 time to evaluate : 1.515 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 2 residues processed: 1 average time/residue: 1.2632 time to fit residues: 3.3113 ------------------------------------------------------------------------------- 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: 2.9990 chunk 83 optimal weight: 3.9990 chunk 2 optimal weight: 0.0470 chunk 109 optimal weight: 5.9990 chunk 60 optimal weight: 0.9980 chunk 125 optimal weight: 6.9990 chunk 101 optimal weight: 2.9990 chunk 0 optimal weight: 4.9990 chunk 75 optimal weight: 0.2980 chunk 131 optimal weight: 0.7980 chunk 37 optimal weight: 3.9990 overall best weight: 1.0280 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 91 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9170 moved from start: 0.1525 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.030 12170 Z= 0.201 Angle : 0.468 7.041 16517 Z= 0.245 Chirality : 0.040 0.132 1899 Planarity : 0.003 0.037 2060 Dihedral : 8.427 175.319 1646 Min Nonbonded Distance : 2.186 Molprobity Statistics. All-atom Clashscore : 4.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Rotamer Outliers : 0.96 % 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: 1.92 (0.19), residues: 791 sheet: -0.25 (0.54), residues: 85 loop : -0.03 (0.24), residues: 652 *********************** 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 127 residues out of total 1256 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 115 time to evaluate : 1.461 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 12 outliers final: 4 residues processed: 120 average time/residue: 1.3684 time to fit residues: 178.1586 Evaluate side-chains 117 residues out of total 1256 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 113 time to evaluate : 1.440 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 2 residues processed: 2 average time/residue: 1.2087 time to fit residues: 4.5309 ------------------------------------------------------------------------------- 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: 0.3980 chunk 29 optimal weight: 3.9990 chunk 86 optimal weight: 4.9990 chunk 36 optimal weight: 3.9990 chunk 147 optimal weight: 0.6980 chunk 122 optimal weight: 3.9990 chunk 68 optimal weight: 4.9990 chunk 12 optimal weight: 3.9990 chunk 48 optimal weight: 0.5980 chunk 77 optimal weight: 2.9990 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 91 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9170 moved from start: 0.1585 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.033 12170 Z= 0.213 Angle : 0.478 8.054 16517 Z= 0.249 Chirality : 0.040 0.133 1899 Planarity : 0.003 0.037 2060 Dihedral : 8.356 175.144 1646 Min Nonbonded Distance : 2.187 Molprobity Statistics. All-atom Clashscore : 4.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer Outliers : 0.80 % 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: 1.46 (0.22), residues: 1528 helix: 1.94 (0.19), residues: 792 sheet: -0.13 (0.56), residues: 83 loop : -0.02 (0.24), residues: 653 *********************** 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 128 residues out of total 1256 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 118 time to evaluate : 1.327 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 10 outliers final: 5 residues processed: 122 average time/residue: 1.3494 time to fit residues: 178.1319 Evaluate side-chains 121 residues out of total 1256 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 116 time to evaluate : 1.444 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 2 residues processed: 3 average time/residue: 0.9479 time to fit residues: 4.9557 ------------------------------------------------------------------------------- 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: 6.9990 chunk 16 optimal weight: 2.9990 chunk 83 optimal weight: 3.9990 chunk 107 optimal weight: 3.9990 chunk 123 optimal weight: 3.9990 chunk 82 optimal weight: 2.9990 chunk 146 optimal weight: 1.9990 chunk 91 optimal weight: 2.9990 chunk 89 optimal weight: 0.7980 chunk 67 optimal weight: 3.9990 chunk 90 optimal weight: 0.0060 overall best weight: 1.7602 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 91 GLN E 92 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9187 moved from start: 0.1617 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.033 12170 Z= 0.316 Angle : 0.520 8.538 16517 Z= 0.269 Chirality : 0.042 0.136 1899 Planarity : 0.004 0.038 2060 Dihedral : 8.376 175.014 1646 Min Nonbonded Distance : 2.168 Molprobity Statistics. All-atom Clashscore : 4.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % 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: 1.40 (0.22), residues: 1528 helix: 1.87 (0.19), residues: 798 sheet: -0.30 (0.54), residues: 87 loop : -0.04 (0.25), residues: 643 *********************** 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 124 residues out of total 1256 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 116 time to evaluate : 1.511 Fit side-chains revert: symmetry clash outliers start: 8 outliers final: 3 residues processed: 119 average time/residue: 1.4436 time to fit residues: 185.6839 Evaluate side-chains 117 residues out of total 1256 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 114 time to evaluate : 1.460 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 2 residues processed: 1 average time/residue: 1.1918 time to fit residues: 3.1510 ------------------------------------------------------------------------------- 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: 0.8980 chunk 87 optimal weight: 5.9990 chunk 44 optimal weight: 10.0000 chunk 28 optimal weight: 2.9990 chunk 93 optimal weight: 8.9990 chunk 99 optimal weight: 3.9990 chunk 72 optimal weight: 1.9990 chunk 13 optimal weight: 0.9990 chunk 115 optimal weight: 0.9990 chunk 133 optimal weight: 2.9990 chunk 140 optimal weight: 6.9990 overall best weight: 1.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 91 GLN E 92 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9183 moved from start: 0.1637 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.035 12170 Z= 0.286 Angle : 0.512 9.135 16517 Z= 0.265 Chirality : 0.041 0.135 1899 Planarity : 0.004 0.038 2060 Dihedral : 8.348 175.037 1646 Min Nonbonded Distance : 2.169 Molprobity Statistics. All-atom Clashscore : 4.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % 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: 1.38 (0.22), residues: 1528 helix: 1.86 (0.19), residues: 798 sheet: -0.30 (0.54), residues: 87 loop : -0.04 (0.25), residues: 643 *********************** 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 123 residues out of total 1256 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 114 time to evaluate : 1.384 Fit side-chains revert: symmetry clash outliers start: 9 outliers final: 3 residues processed: 120 average time/residue: 1.3477 time to fit residues: 175.3375 Evaluate side-chains 118 residues out of total 1256 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 115 time to evaluate : 1.438 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 2 residues processed: 1 average time/residue: 1.0944 time to fit residues: 3.0735 ------------------------------------------------------------------------------- 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: 2.9990 chunk 136 optimal weight: 0.4980 chunk 140 optimal weight: 0.0170 chunk 82 optimal weight: 2.9990 chunk 59 optimal weight: 0.7980 chunk 107 optimal weight: 2.9990 chunk 41 optimal weight: 4.9990 chunk 123 optimal weight: 2.9990 chunk 129 optimal weight: 3.9990 chunk 89 optimal weight: 0.2980 chunk 144 optimal weight: 5.9990 overall best weight: 0.9220 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 91 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9166 moved from start: 0.1682 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.035 12170 Z= 0.191 Angle : 0.480 8.703 16517 Z= 0.249 Chirality : 0.040 0.130 1899 Planarity : 0.003 0.037 2060 Dihedral : 8.297 175.841 1646 Min Nonbonded Distance : 2.187 Molprobity Statistics. All-atom Clashscore : 4.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % Rotamer Outliers : 0.32 % 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: 1.49 (0.22), residues: 1528 helix: 1.98 (0.19), residues: 792 sheet: -0.13 (0.56), residues: 83 loop : -0.03 (0.24), residues: 653 *********************** 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 122 residues out of total 1256 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 118 time to evaluate : 1.665 Fit side-chains revert: symmetry clash outliers start: 4 outliers final: 3 residues processed: 120 average time/residue: 1.4182 time to fit residues: 185.0034 Evaluate side-chains 117 residues out of total 1256 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 114 time to evaluate : 1.397 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 2 residues processed: 1 average time/residue: 0.2627 time to fit residues: 2.1907 ------------------------------------------------------------------------------- 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: 3.9990 chunk 68 optimal weight: 0.6980 chunk 100 optimal weight: 5.9990 chunk 151 optimal weight: 0.9980 chunk 139 optimal weight: 2.9990 chunk 120 optimal weight: 3.9990 chunk 12 optimal weight: 2.9990 chunk 93 optimal weight: 1.9990 chunk 73 optimal weight: 2.9990 chunk 95 optimal weight: 5.9990 chunk 128 optimal weight: 3.9990 overall best weight: 1.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 91 GLN C 198 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9191 moved from start: 0.1689 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.037 12170 Z= 0.345 Angle : 0.548 10.277 16517 Z= 0.281 Chirality : 0.042 0.139 1899 Planarity : 0.004 0.037 2060 Dihedral : 8.359 175.410 1646 Min Nonbonded Distance : 2.161 Molprobity Statistics. All-atom Clashscore : 4.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer Outliers : 0.56 % 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: 1.38 (0.22), residues: 1528 helix: 1.84 (0.19), residues: 798 sheet: -0.29 (0.54), residues: 89 loop : -0.01 (0.25), residues: 641 ********************** 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 122 residues out of total 1256 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 115 time to evaluate : 1.415 Fit side-chains revert: symmetry clash outliers start: 7 outliers final: 3 residues processed: 119 average time/residue: 1.4070 time to fit residues: 181.0271 Evaluate side-chains 119 residues out of total 1256 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 116 time to evaluate : 1.387 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 2 residues processed: 1 average time/residue: 0.1509 time to fit residues: 2.2186 ------------------------------------------------------------------------------- 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: 3.9990 chunk 111 optimal weight: 2.9990 chunk 17 optimal weight: 3.9990 chunk 33 optimal weight: 1.9990 chunk 120 optimal weight: 2.9990 chunk 50 optimal weight: 0.8980 chunk 124 optimal weight: 0.7980 chunk 15 optimal weight: 1.9990 chunk 22 optimal weight: 0.7980 chunk 106 optimal weight: 7.9990 chunk 6 optimal weight: 2.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 91 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2971 r_free = 0.2971 target = 0.058007 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2613 r_free = 0.2613 target = 0.043731 restraints weight = 30715.693| |-----------------------------------------------------------------------------| r_work (start): 0.2602 rms_B_bonded: 2.24 r_work: 0.2491 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.2379 rms_B_bonded: 4.23 restraints_weight: 0.2500 r_work (final): 0.2379 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9080 moved from start: 0.1700 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.036 12170 Z= 0.246 Angle : 0.512 9.594 16517 Z= 0.263 Chirality : 0.041 0.132 1899 Planarity : 0.004 0.037 2060 Dihedral : 8.322 175.495 1646 Min Nonbonded Distance : 2.170 Molprobity Statistics. All-atom Clashscore : 4.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer Outliers : 0.56 % 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: 1.91 (0.19), residues: 792 sheet: -0.35 (0.53), residues: 97 loop : 0.01 (0.25), residues: 639 =============================================================================== Job complete usr+sys time: 3831.70 seconds wall clock time: 69 minutes 11.00 seconds (4151.00 seconds total)