Starting phenix.real_space_refine on Thu Sep 26 05:07:54 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8evu_28637/09_2024/8evu_28637.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8evu_28637/09_2024/8evu_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_28637/09_2024/8evu_28637.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8evu_28637/09_2024/8evu_28637.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8evu_28637/09_2024/8evu_28637.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8evu_28637/09_2024/8evu_28637.cif" } resolution = 2.5804 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.001 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 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. Process input model Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/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: 7.94, per 1000 atoms: 0.67 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 - 3.00 Amino acid : True - 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: 3.22 Conformation dependent library (CDL) restraints added in 1.7 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... Secondary structure from input PDB file: 80 helices and 8 sheets defined 60.7% alpha, 8.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.40 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 109 through 113 Processing helix chain 'A' and resid 114 through 125 Processing helix chain 'A' and resid 126 through 131 removed outlier: 3.596A pdb=" N THR A 129 " --> pdb=" O GLY A 126 " (cutoff:3.500A) Processing helix chain 'A' and resid 162 through 170 removed outlier: 3.919A pdb=" N VAL A 166 " --> pdb=" O GLU A 162 " (cutoff:3.500A) Processing helix chain 'A' and resid 170 through 185 Processing helix chain 'A' and resid 219 through 228 Processing helix chain 'A' and resid 241 through 254 Processing helix chain 'A' and resid 282 through 287 Processing helix chain 'A' and resid 310 through 314 Processing helix chain 'A' and resid 335 through 339 Processing helix chain 'A' and resid 351 through 356 removed outlier: 3.737A pdb=" N HIS A 354 " --> pdb=" O PHE A 351 " (cutoff:3.500A) Processing helix chain 'A' and resid 378 through 384 removed outlier: 3.866A pdb=" N LYS A 382 " --> pdb=" O GLY A 378 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N VAL A 383 " --> pdb=" O ASN A 379 " (cutoff:3.500A) Processing helix chain 'A' and resid 389 through 400 Processing helix chain 'A' and resid 401 through 408 Processing helix chain 'A' and resid 409 through 413 Processing helix chain 'A' and resid 415 through 417 No H-bonds generated for 'chain 'A' and resid 415 through 417' Processing helix chain 'A' and resid 418 through 424 Processing helix chain 'A' and resid 430 through 446 removed outlier: 3.622A pdb=" N LEU A 434 " --> pdb=" O GLU A 430 " (cutoff:3.500A) Processing helix chain 'B' and resid 4 through 10 Processing helix chain 'B' and resid 10 through 15 removed outlier: 3.906A pdb=" N PHE B 14 " --> pdb=" O ILE B 10 " (cutoff:3.500A) Processing helix chain 'B' and resid 20 through 22 No H-bonds generated for 'chain 'B' and resid 20 through 22' Processing helix chain 'B' and resid 23 through 35 removed outlier: 3.694A pdb=" N LEU B 33 " --> pdb=" O ALA B 29 " (cutoff:3.500A) Processing helix chain 'B' and resid 52 through 64 removed outlier: 3.569A pdb=" N VAL B 64 " --> pdb=" O VAL B 60 " (cutoff:3.500A) Processing helix chain 'B' and resid 64 through 87 Processing helix chain 'B' and resid 89 through 99 Processing helix chain 'B' and resid 99 through 108 Processing helix chain 'B' and resid 117 through 152 Proline residue: B 131 - end of helix Processing helix chain 'B' and resid 158 through 169 Processing helix chain 'B' and resid 175 through 189 Processing helix chain 'B' and resid 191 through 195 Processing helix chain 'B' and resid 203 through 216 Processing helix chain 'B' and resid 217 through 220 Processing helix chain 'B' and resid 236 through 245 Processing helix chain 'B' and resid 246 through 249 Processing helix chain 'B' and resid 259 through 266 Processing helix chain 'B' and resid 276 through 290 Processing helix chain 'B' and resid 294 through 316 Processing helix chain 'B' and resid 320 through 325 removed outlier: 3.542A pdb=" N MET B 325 " --> pdb=" O MET B 322 " (cutoff:3.500A) Processing helix chain 'B' and resid 326 through 333 removed outlier: 3.528A pdb=" N VAL B 332 " --> pdb=" O HIS B 328 " (cutoff:3.500A) Processing helix chain 'B' and resid 335 through 343 Processing helix chain 'B' and resid 353 through 375 Processing helix chain 'B' and resid 381 through 410 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 414 Processing helix chain 'C' and resid 8 through 33 Processing helix chain 'C' and resid 33 through 54 removed outlier: 3.529A pdb=" N LYS C 45 " --> pdb=" O ALA C 41 " (cutoff:3.500A) Processing helix chain 'C' and resid 59 through 70 Processing helix chain 'C' and resid 87 through 91 Processing helix chain 'C' and resid 92 through 98 Processing helix chain 'C' and resid 99 through 101 No H-bonds generated for 'chain 'C' and resid 99 through 101' Processing helix chain 'C' and resid 177 through 181 Processing helix chain 'C' and resid 182 through 188 removed outlier: 3.777A pdb=" N GLN C 188 " --> pdb=" O ALA C 184 " (cutoff:3.500A) Processing helix chain 'C' and resid 224 through 239 Processing helix chain 'C' and resid 244 through 253 Processing helix chain 'D' and resid 9 through 17 Proline residue: D 14 - end of helix Processing helix chain 'D' and resid 27 through 34 removed outlier: 3.652A pdb=" N ALA D 31 " --> pdb=" O GLY D 27 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ALA D 33 " --> pdb=" O CYS D 29 " (cutoff:3.500A) Processing helix chain 'D' and resid 37 through 62 Processing helix chain 'D' and resid 70 through 94 Processing helix chain 'D' and resid 94 through 102 Processing helix chain 'D' and resid 103 through 109 Processing helix chain 'D' and resid 111 through 121 Processing helix chain 'D' and resid 122 through 125 removed outlier: 3.615A pdb=" N SER D 125 " --> pdb=" O ALA D 122 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 122 through 125' Processing helix chain 'D' and resid 126 through 158 Processing helix chain 'D' and resid 168 through 172 Processing helix chain 'D' and resid 178 through 182 Processing helix chain 'D' and resid 183 through 202 removed outlier: 4.233A pdb=" N ALA D 187 " --> pdb=" O LEU D 183 " (cutoff:3.500A) 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 206 Processing helix chain 'E' and resid 2 through 13 Processing helix chain 'E' and resid 24 through 31 Processing helix chain 'E' and resid 34 through 63 Proline residue: E 54 - end of helix Processing helix chain 'E' and resid 75 through 77 No H-bonds generated for 'chain 'E' and resid 75 through 77' Processing helix chain 'E' and resid 78 through 102 removed outlier: 3.575A pdb=" N GLN E 92 " --> pdb=" O ALA E 88 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N ARG E 100 " --> pdb=" O MET E 96 " (cutoff:3.500A) Processing helix chain 'E' and resid 102 through 109 Processing helix chain 'E' and resid 110 through 113 Processing helix chain 'E' and resid 119 through 133 Processing helix chain 'E' and resid 135 through 164 Processing helix chain 'E' and resid 165 through 167 No H-bonds generated for 'chain 'E' and resid 165 through 167' Processing helix chain 'E' and resid 175 through 191 Processing helix chain 'E' and resid 192 through 194 No H-bonds generated for 'chain 'E' and resid 192 through 194' Processing helix chain 'F' and resid 2 through 30 Processing sheet with id=AA1, first strand: chain 'A' and resid 2 through 3 removed outlier: 6.245A pdb=" N ILE A 2 " --> pdb=" O ASP A 212 " (cutoff:3.500A) removed outlier: 6.178A pdb=" N VAL A 189 " --> pdb=" O GLU A 207 " (cutoff:3.500A) removed outlier: 7.126A pdb=" N HIS A 209 " --> pdb=" O VAL A 189 " (cutoff:3.500A) removed outlier: 6.219A pdb=" N VAL A 191 " --> pdb=" O HIS A 209 " (cutoff:3.500A) removed outlier: 7.231A pdb=" N PHE A 211 " --> pdb=" O VAL A 191 " (cutoff:3.500A) removed outlier: 6.067A pdb=" N LYS A 193 " --> pdb=" O PHE A 211 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 17 through 22 removed outlier: 3.519A pdb=" N LEU A 274 " --> pdb=" O SER A 17 " (cutoff:3.500A) removed outlier: 5.874A pdb=" N VAL A 19 " --> pdb=" O LEU A 274 " (cutoff:3.500A) removed outlier: 7.390A pdb=" N ARG A 276 " --> pdb=" O VAL A 19 " (cutoff:3.500A) removed outlier: 7.372A pdb=" N SER A 21 " --> pdb=" O ARG A 276 " (cutoff:3.500A) removed outlier: 9.729A pdb=" N VAL A 278 " --> pdb=" O SER A 21 " (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: 5.588A pdb=" N GLN A 322 " --> pdb=" O GLY A 301 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 28 through 32 removed outlier: 6.962A pdb=" N LEU A 87 " --> pdb=" O ARG A 81 " (cutoff:3.500A) removed outlier: 6.655A pdb=" N ARG A 81 " --> pdb=" O LEU A 87 " (cutoff:3.500A) removed outlier: 6.382A pdb=" N SER A 89 " --> pdb=" O ILE A 79 " (cutoff:3.500A) removed outlier: 4.585A pdb=" N ILE A 79 " --> pdb=" O SER A 89 " (cutoff:3.500A) removed outlier: 7.030A pdb=" N VAL A 91 " --> pdb=" O VAL A 77 " (cutoff:3.500A) Processing sheet with id=AA4, 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=AA5, first strand: chain 'C' and resid 83 through 84 removed outlier: 3.959A pdb=" N LEU C 75 " --> pdb=" O VAL C 84 " (cutoff:3.500A) removed outlier: 14.780A pdb=" N VAL C 121 " --> pdb=" O VAL C 140 " (cutoff:3.500A) removed outlier: 11.628A pdb=" N VAL C 140 " --> pdb=" O VAL C 121 " (cutoff:3.500A) removed outlier: 9.161A pdb=" N VAL C 123 " --> pdb=" O LEU C 138 " (cutoff:3.500A) removed outlier: 6.193A pdb=" N LEU C 138 " --> pdb=" O VAL C 123 " (cutoff:3.500A) removed outlier: 6.403A pdb=" N TYR C 125 " --> pdb=" O VAL C 136 " (cutoff:3.500A) removed outlier: 4.497A pdb=" N VAL C 136 " --> pdb=" O TYR C 125 " (cutoff:3.500A) removed outlier: 6.719A pdb=" N VAL C 127 " --> pdb=" O SER C 134 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N LYS C 132 " --> pdb=" O ASP C 129 " (cutoff:3.500A) removed outlier: 6.474A pdb=" N MET C 148 " --> pdb=" O GLU C 169 " (cutoff:3.500A) removed outlier: 6.593A pdb=" N GLU C 169 " --> pdb=" O MET C 148 " (cutoff:3.500A) removed outlier: 7.056A pdb=" N TYR C 150 " --> pdb=" O TYR C 167 " (cutoff:3.500A) removed outlier: 4.721A pdb=" N TYR C 167 " --> pdb=" O TYR C 150 " (cutoff:3.500A) removed outlier: 6.684A pdb=" N PHE C 152 " --> pdb=" O LEU C 165 " (cutoff:3.500A) removed outlier: 4.378A pdb=" N LEU C 165 " --> pdb=" O PHE C 152 " (cutoff:3.500A) removed outlier: 6.245A pdb=" N ALA C 154 " --> pdb=" O SER C 163 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 103 through 105 Processing sheet with id=AA7, first strand: chain 'C' and resid 204 through 206 Processing sheet with id=AA8, first strand: chain 'D' and resid 159 through 160 668 hydrogen bonds defined for protein. 1890 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: 3.41 Time building geometry restraints manager: 3.65 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: 0.00 - 1.51: 16295 1.51 - 3.02: 163 3.02 - 4.54: 43 4.54 - 6.05: 15 6.05 - 7.56: 1 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: 7072 35.54 - 71.07: 30 71.07 - 106.61: 4 106.61 - 142.15: 1 142.15 - 177.68: 3 Dihedral angle restraints: 7110 sinusoidal: 2753 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 7107 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: 3125 2.80 - 3.33: 11271 3.33 - 3.85: 20185 3.85 - 4.38: 24700 4.38 - 4.90: 41563 Nonbonded interactions: 100844 Sorted by model distance: nonbonded pdb=" O GLU C 99 " pdb=" OG SER C 103 " model vdw 2.279 3.040 nonbonded pdb=" O GLU B 28 " pdb=" OG1 THR B 32 " model vdw 2.283 3.040 nonbonded pdb=" O ILE E 46 " pdb=" OG1 THR E 50 " model vdw 2.317 3.040 nonbonded pdb=" NH1 ARG B 199 " pdb=" O TYR E 166 " model vdw 2.329 3.120 nonbonded pdb=" O ASN E 57 " pdb=" ND2 ASN E 61 " model vdw 2.342 3.120 ... (remaining 100839 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 10.060 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.340 Check model and map are aligned: 0.090 Set scattering table: 0.110 Process input model: 32.760 Find NCS groups from input model: 0.150 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:12.240 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 55.810 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9045 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= 0.213 Angle : 0.444 7.562 16517 Z= 0.216 Chirality : 0.039 0.194 1899 Planarity : 0.004 0.062 2060 Dihedral : 10.101 177.684 4326 Min Nonbonded Distance : 2.279 Molprobity Statistics. All-atom Clashscore : 2.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.31 % Favored : 98.69 % Rotamer: Outliers : 0.08 % Allowed : 1.35 % Favored : 98.57 % 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 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 103 HIS 0.003 0.001 HIS B 328 PHE 0.020 0.001 PHE E 22 TYR 0.010 0.001 TYR D 141 ARG 0.003 0.000 ARG E 174 *********************** 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 : 1.382 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 43 MET cc_start: 0.9352 (mmm) cc_final: 0.9126 (tpp) REVERT: E 138 GLU cc_start: 0.8811 (mt-10) cc_final: 0.8523 (mt-10) REVERT: F 26 LYS cc_start: 0.9033 (tttt) cc_final: 0.8630 (tmmt) outliers start: 1 outliers final: 0 residues processed: 159 average time/residue: 1.6776 time to fit residues: 283.9065 Evaluate side-chains 119 residues out of total 1256 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 119 time to evaluate : 1.307 ------------------------------------------------------------------------------- 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: 0.9980 chunk 63 optimal weight: 3.9990 chunk 39 optimal weight: 0.7980 chunk 77 optimal weight: 3.9990 chunk 61 optimal weight: 0.6980 chunk 119 optimal weight: 3.9990 chunk 46 optimal weight: 10.0000 chunk 72 optimal weight: 2.9990 chunk 88 optimal weight: 2.9990 chunk 138 optimal weight: 4.9990 overall best weight: 1.6984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 91 GLN E 79 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9066 moved from start: 0.1284 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= 0.315 Angle : 0.552 7.150 16517 Z= 0.295 Chirality : 0.043 0.169 1899 Planarity : 0.004 0.039 2060 Dihedral : 9.304 173.317 1661 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 3.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 0.88 % Allowed : 6.53 % Favored : 92.60 % 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: 1.48 (0.22), residues: 1528 helix: 1.88 (0.19), residues: 789 sheet: 0.03 (0.53), residues: 88 loop : 0.08 (0.24), residues: 651 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 103 HIS 0.005 0.001 HIS B 330 PHE 0.022 0.002 PHE E 22 TYR 0.013 0.001 TYR B 360 ARG 0.005 0.001 ARG D 71 *********************** 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 127 residues out of total 1256 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 116 time to evaluate : 1.496 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 43 MET cc_start: 0.9367 (mmm) cc_final: 0.9111 (tpp) REVERT: B 13 HIS cc_start: 0.8002 (m-70) cc_final: 0.7245 (m-70) REVERT: D 9 LYS cc_start: 0.8831 (pptt) cc_final: 0.8143 (mppt) REVERT: D 96 ASP cc_start: 0.8214 (p0) cc_final: 0.7885 (p0) REVERT: E 138 GLU cc_start: 0.8797 (mt-10) cc_final: 0.8517 (mt-10) REVERT: F 26 LYS cc_start: 0.9176 (tttt) cc_final: 0.8832 (tmmt) outliers start: 11 outliers final: 4 residues processed: 122 average time/residue: 1.5431 time to fit residues: 202.3576 Evaluate side-chains 117 residues out of total 1256 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 113 time to evaluate : 1.292 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 8 GLU Chi-restraints excluded: chain C residue 123 VAL Chi-restraints excluded: chain D residue 99 LYS Chi-restraints excluded: chain E residue 1 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 76 optimal weight: 2.9990 chunk 42 optimal weight: 0.4980 chunk 114 optimal weight: 3.9990 chunk 93 optimal weight: 9.9990 chunk 38 optimal weight: 0.6980 chunk 138 optimal weight: 1.9990 chunk 149 optimal weight: 5.9990 chunk 123 optimal weight: 2.9990 chunk 137 optimal weight: 0.0470 chunk 47 optimal weight: 4.9990 chunk 110 optimal weight: 0.5980 overall best weight: 0.7680 ------------------------------------------------------------------------------- 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: 0.9039 moved from start: 0.1498 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 12170 Z= 0.177 Angle : 0.477 6.532 16517 Z= 0.254 Chirality : 0.040 0.161 1899 Planarity : 0.004 0.035 2060 Dihedral : 8.843 172.984 1661 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 3.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.96 % Favored : 98.04 % Rotamer: Outliers : 0.96 % Allowed : 7.25 % Favored : 91.80 % 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: 1.54 (0.22), residues: 1528 helix: 1.95 (0.18), residues: 797 sheet: 0.03 (0.54), residues: 89 loop : 0.05 (0.25), residues: 642 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP B 103 HIS 0.004 0.001 HIS B 330 PHE 0.016 0.001 PHE E 22 TYR 0.014 0.001 TYR B 360 ARG 0.002 0.000 ARG D 71 *********************** 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: 12 poor density : 118 time to evaluate : 1.397 Fit side-chains revert: symmetry clash REVERT: A 43 MET cc_start: 0.9379 (mmm) cc_final: 0.9127 (tpp) REVERT: B 13 HIS cc_start: 0.7662 (m-70) cc_final: 0.7191 (m-70) REVERT: B 34 PHE cc_start: 0.8998 (m-80) cc_final: 0.8670 (m-80) REVERT: D 9 LYS cc_start: 0.8766 (pptt) cc_final: 0.8158 (mppt) REVERT: D 96 ASP cc_start: 0.8256 (p0) cc_final: 0.7880 (p0) REVERT: E 138 GLU cc_start: 0.8704 (mt-10) cc_final: 0.8451 (mt-10) REVERT: F 26 LYS cc_start: 0.9190 (tttt) cc_final: 0.8819 (tmmt) outliers start: 12 outliers final: 3 residues processed: 124 average time/residue: 1.5921 time to fit residues: 212.0603 Evaluate side-chains 122 residues out of total 1256 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 119 time to evaluate : 1.406 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 406 LYS Chi-restraints excluded: chain C residue 123 VAL Chi-restraints excluded: chain E residue 1 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 136 optimal weight: 3.9990 chunk 103 optimal weight: 4.9990 chunk 71 optimal weight: 4.9990 chunk 15 optimal weight: 0.8980 chunk 65 optimal weight: 2.9990 chunk 92 optimal weight: 5.9990 chunk 138 optimal weight: 2.9990 chunk 146 optimal weight: 3.9990 chunk 72 optimal weight: 1.9990 chunk 131 optimal weight: 1.9990 chunk 39 optimal weight: 0.8980 overall best weight: 1.7586 ------------------------------------------------------------------------------- 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: 0.9066 moved from start: 0.1561 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 12170 Z= 0.317 Angle : 0.530 7.572 16517 Z= 0.281 Chirality : 0.043 0.172 1899 Planarity : 0.004 0.054 2060 Dihedral : 8.742 172.831 1661 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 3.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 0.96 % Allowed : 8.20 % Favored : 90.84 % 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: 1.90 (0.18), residues: 797 sheet: -0.26 (0.53), residues: 99 loop : 0.07 (0.25), residues: 632 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP B 103 HIS 0.007 0.001 HIS B 153 PHE 0.020 0.002 PHE E 22 TYR 0.017 0.001 TYR D 141 ARG 0.003 0.000 ARG B 151 *********************** 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 129 residues out of total 1256 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 117 time to evaluate : 1.390 Fit side-chains revert: symmetry clash REVERT: A 43 MET cc_start: 0.9380 (mmm) cc_final: 0.9103 (tpp) REVERT: B 13 HIS cc_start: 0.7841 (m-70) cc_final: 0.7355 (m-70) REVERT: B 34 PHE cc_start: 0.9017 (m-80) cc_final: 0.8692 (m-80) REVERT: D 9 LYS cc_start: 0.8798 (pptt) cc_final: 0.8176 (mppt) REVERT: D 96 ASP cc_start: 0.8306 (p0) cc_final: 0.7956 (p0) REVERT: E 138 GLU cc_start: 0.8731 (mt-10) cc_final: 0.8487 (mt-10) REVERT: F 26 LYS cc_start: 0.9220 (tttt) cc_final: 0.8849 (tmmt) outliers start: 12 outliers final: 5 residues processed: 121 average time/residue: 1.4388 time to fit residues: 187.5804 Evaluate side-chains 122 residues out of total 1256 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 117 time to evaluate : 1.480 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 384 MET Chi-restraints excluded: chain B residue 406 LYS Chi-restraints excluded: chain C residue 123 VAL Chi-restraints excluded: chain C residue 153 VAL Chi-restraints excluded: chain E residue 1 MET 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: 0.7980 chunk 2 optimal weight: 4.9990 chunk 109 optimal weight: 3.9990 chunk 60 optimal weight: 2.9990 chunk 125 optimal weight: 3.9990 chunk 101 optimal weight: 0.8980 chunk 0 optimal weight: 4.9990 chunk 75 optimal weight: 0.9990 chunk 131 optimal weight: 1.9990 chunk 37 optimal weight: 2.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- 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: 0.9064 moved from start: 0.1634 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 12170 Z= 0.282 Angle : 0.521 8.220 16517 Z= 0.275 Chirality : 0.042 0.168 1899 Planarity : 0.004 0.046 2060 Dihedral : 8.631 172.814 1661 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 3.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Rotamer: Outliers : 1.27 % Allowed : 8.12 % Favored : 90.61 % 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: 1.89 (0.18), residues: 798 sheet: -0.31 (0.52), residues: 99 loop : 0.00 (0.25), residues: 631 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP B 103 HIS 0.004 0.001 HIS B 330 PHE 0.021 0.001 PHE E 22 TYR 0.020 0.001 TYR D 141 ARG 0.003 0.000 ARG D 71 *********************** 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 134 residues out of total 1256 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 118 time to evaluate : 1.272 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 43 MET cc_start: 0.9379 (mmm) cc_final: 0.9108 (tpp) REVERT: B 13 HIS cc_start: 0.7719 (m-70) cc_final: 0.7285 (m-70) REVERT: B 34 PHE cc_start: 0.9040 (m-80) cc_final: 0.8741 (m-80) REVERT: B 68 MET cc_start: 0.9229 (ttp) cc_final: 0.8953 (ttp) REVERT: D 9 LYS cc_start: 0.8790 (pptt) cc_final: 0.8181 (mppt) REVERT: D 96 ASP cc_start: 0.8331 (p0) cc_final: 0.8039 (p0) REVERT: E 138 GLU cc_start: 0.8712 (mt-10) cc_final: 0.8471 (mt-10) REVERT: F 26 LYS cc_start: 0.9228 (tttt) cc_final: 0.8847 (tmmt) outliers start: 16 outliers final: 8 residues processed: 124 average time/residue: 1.3871 time to fit residues: 185.1716 Evaluate side-chains 124 residues out of total 1256 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 116 time to evaluate : 1.424 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain A residue 384 MET Chi-restraints excluded: chain B residue 340 MET Chi-restraints excluded: chain B residue 406 LYS Chi-restraints excluded: chain C residue 123 VAL Chi-restraints excluded: chain C residue 153 VAL Chi-restraints excluded: chain D residue 124 LYS Chi-restraints excluded: chain E residue 1 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 49 optimal weight: 1.9990 chunk 132 optimal weight: 0.5980 chunk 29 optimal weight: 0.6980 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: 3.9990 chunk 12 optimal weight: 1.9990 chunk 48 optimal weight: 0.8980 chunk 77 optimal weight: 1.9990 overall best weight: 0.9782 ------------------------------------------------------------------------------- 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: 0.9048 moved from start: 0.1745 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 12170 Z= 0.201 Angle : 0.495 7.710 16517 Z= 0.262 Chirality : 0.041 0.161 1899 Planarity : 0.004 0.040 2060 Dihedral : 8.492 173.333 1661 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 3.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer: Outliers : 1.35 % Allowed : 9.08 % Favored : 89.57 % 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: 1.48 (0.22), residues: 1528 helix: 1.97 (0.18), residues: 798 sheet: -0.26 (0.53), residues: 97 loop : -0.02 (0.24), residues: 633 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP B 103 HIS 0.004 0.001 HIS B 153 PHE 0.018 0.001 PHE E 22 TYR 0.020 0.001 TYR D 141 ARG 0.004 0.000 ARG D 71 *********************** 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 134 residues out of total 1256 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 117 time to evaluate : 1.583 Fit side-chains revert: symmetry clash REVERT: A 43 MET cc_start: 0.9390 (mmm) cc_final: 0.9126 (tpp) REVERT: B 13 HIS cc_start: 0.7609 (m-70) cc_final: 0.7200 (m-70) REVERT: B 15 GLU cc_start: 0.8556 (tp30) cc_final: 0.8050 (pp20) REVERT: B 34 PHE cc_start: 0.9017 (m-80) cc_final: 0.8730 (m-80) REVERT: D 9 LYS cc_start: 0.8791 (OUTLIER) cc_final: 0.8211 (mppt) REVERT: D 96 ASP cc_start: 0.8297 (p0) cc_final: 0.8023 (p0) REVERT: E 138 GLU cc_start: 0.8697 (mt-10) cc_final: 0.8435 (mt-10) REVERT: F 26 LYS cc_start: 0.9223 (tttt) cc_final: 0.8836 (tmmt) outliers start: 17 outliers final: 6 residues processed: 120 average time/residue: 1.5309 time to fit residues: 197.6885 Evaluate side-chains 121 residues out of total 1256 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 114 time to evaluate : 1.421 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 384 MET Chi-restraints excluded: chain B residue 107 MET Chi-restraints excluded: chain B residue 406 LYS Chi-restraints excluded: chain C residue 123 VAL Chi-restraints excluded: chain D residue 9 LYS Chi-restraints excluded: chain D residue 133 ASP Chi-restraints excluded: chain E residue 1 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 141 optimal weight: 1.9990 chunk 16 optimal weight: 3.9990 chunk 83 optimal weight: 0.6980 chunk 107 optimal weight: 0.8980 chunk 123 optimal weight: 3.9990 chunk 82 optimal weight: 2.9990 chunk 146 optimal weight: 3.9990 chunk 91 optimal weight: 5.9990 chunk 89 optimal weight: 1.9990 chunk 67 optimal weight: 3.9990 chunk 90 optimal weight: 0.9990 overall best weight: 1.3186 ------------------------------------------------------------------------------- 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: 0.9057 moved from start: 0.1762 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 12170 Z= 0.254 Angle : 0.513 8.897 16517 Z= 0.270 Chirality : 0.041 0.163 1899 Planarity : 0.004 0.039 2060 Dihedral : 8.446 173.200 1661 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 3.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % Rotamer: Outliers : 1.11 % Allowed : 9.47 % Favored : 89.41 % 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: 1.45 (0.22), residues: 1528 helix: 1.93 (0.18), residues: 804 sheet: -0.32 (0.53), residues: 99 loop : -0.03 (0.25), residues: 625 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP B 103 HIS 0.004 0.001 HIS B 153 PHE 0.020 0.001 PHE E 22 TYR 0.023 0.001 TYR D 141 ARG 0.004 0.000 ARG D 71 *********************** 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 129 residues out of total 1256 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 115 time to evaluate : 1.520 Fit side-chains revert: symmetry clash REVERT: A 43 MET cc_start: 0.9388 (mmm) cc_final: 0.9121 (tpp) REVERT: B 13 HIS cc_start: 0.7695 (m-70) cc_final: 0.7230 (m-70) REVERT: B 34 PHE cc_start: 0.9016 (m-80) cc_final: 0.8713 (m-80) REVERT: D 9 LYS cc_start: 0.8776 (OUTLIER) cc_final: 0.8229 (mppt) REVERT: D 96 ASP cc_start: 0.8352 (p0) cc_final: 0.8118 (p0) REVERT: E 138 GLU cc_start: 0.8707 (mt-10) cc_final: 0.8448 (mt-10) REVERT: F 26 LYS cc_start: 0.9239 (tttt) cc_final: 0.8831 (tmmt) outliers start: 14 outliers final: 4 residues processed: 121 average time/residue: 1.5278 time to fit residues: 198.4717 Evaluate side-chains 118 residues out of total 1256 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 113 time to evaluate : 1.460 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 384 MET Chi-restraints excluded: chain B residue 406 LYS Chi-restraints excluded: chain C residue 123 VAL Chi-restraints excluded: chain D residue 9 LYS Chi-restraints excluded: chain E residue 1 MET 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: 5.9990 chunk 44 optimal weight: 7.9990 chunk 28 optimal weight: 4.9990 chunk 93 optimal weight: 1.9990 chunk 99 optimal weight: 5.9990 chunk 72 optimal weight: 1.9990 chunk 13 optimal weight: 0.6980 chunk 115 optimal weight: 1.9990 chunk 133 optimal weight: 2.9990 chunk 140 optimal weight: 7.9990 overall best weight: 1.9388 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9075 moved from start: 0.1778 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 12170 Z= 0.347 Angle : 0.564 9.098 16517 Z= 0.296 Chirality : 0.043 0.168 1899 Planarity : 0.004 0.041 2060 Dihedral : 8.476 172.681 1661 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 3.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % Rotamer: Outliers : 0.80 % Allowed : 10.27 % Favored : 88.93 % 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: 1.34 (0.22), residues: 1528 helix: 1.84 (0.18), residues: 803 sheet: -0.30 (0.53), residues: 99 loop : -0.09 (0.25), residues: 626 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP B 103 HIS 0.005 0.001 HIS B 153 PHE 0.023 0.002 PHE E 22 TYR 0.024 0.001 TYR D 141 ARG 0.004 0.000 ARG D 71 *********************** 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 124 residues out of total 1256 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 114 time to evaluate : 1.600 Fit side-chains REVERT: A 43 MET cc_start: 0.9380 (mmm) cc_final: 0.9109 (tpp) REVERT: B 8 GLU cc_start: 0.7498 (OUTLIER) cc_final: 0.6851 (pm20) REVERT: B 13 HIS cc_start: 0.7669 (m-70) cc_final: 0.7346 (m-70) REVERT: B 15 GLU cc_start: 0.8671 (tp30) cc_final: 0.8168 (pp20) REVERT: B 34 PHE cc_start: 0.9054 (m-80) cc_final: 0.8763 (m-80) REVERT: D 9 LYS cc_start: 0.8788 (OUTLIER) cc_final: 0.8200 (mppt) REVERT: D 96 ASP cc_start: 0.8345 (p0) cc_final: 0.8137 (p0) REVERT: D 119 GLU cc_start: 0.8365 (tp30) cc_final: 0.8017 (tp30) REVERT: E 138 GLU cc_start: 0.8719 (mt-10) cc_final: 0.8489 (mt-10) REVERT: F 26 LYS cc_start: 0.9264 (tttt) cc_final: 0.8854 (tmmt) outliers start: 10 outliers final: 3 residues processed: 117 average time/residue: 1.4899 time to fit residues: 187.2166 Evaluate side-chains 119 residues out of total 1256 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 114 time to evaluate : 1.459 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 384 MET Chi-restraints excluded: chain B residue 8 GLU Chi-restraints excluded: chain B residue 406 LYS Chi-restraints excluded: chain C residue 123 VAL Chi-restraints excluded: chain D residue 9 LYS 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: 2.9990 chunk 140 optimal weight: 5.9990 chunk 82 optimal weight: 1.9990 chunk 59 optimal weight: 0.8980 chunk 107 optimal weight: 0.9990 chunk 41 optimal weight: 0.6980 chunk 123 optimal weight: 3.9990 chunk 129 optimal weight: 1.9990 chunk 89 optimal weight: 0.6980 chunk 144 optimal weight: 5.9990 overall best weight: 1.0584 ------------------------------------------------------------------------------- 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: 0.9052 moved from start: 0.1824 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 12170 Z= 0.219 Angle : 0.520 9.770 16517 Z= 0.274 Chirality : 0.041 0.161 1899 Planarity : 0.004 0.039 2060 Dihedral : 8.388 173.456 1661 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 3.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer: Outliers : 0.64 % Allowed : 10.75 % Favored : 88.61 % 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: 1.91 (0.18), residues: 804 sheet: -0.23 (0.54), residues: 97 loop : -0.09 (0.24), residues: 627 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP B 103 HIS 0.004 0.001 HIS B 153 PHE 0.019 0.001 PHE E 22 TYR 0.022 0.001 TYR D 141 ARG 0.004 0.000 ARG D 71 *********************** 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 124 residues out of total 1256 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 116 time to evaluate : 1.369 Fit side-chains revert: symmetry clash REVERT: A 43 MET cc_start: 0.9394 (mmm) cc_final: 0.9124 (tpp) REVERT: B 8 GLU cc_start: 0.7486 (OUTLIER) cc_final: 0.6839 (pm20) REVERT: B 15 GLU cc_start: 0.8715 (tp30) cc_final: 0.8100 (pp20) REVERT: B 34 PHE cc_start: 0.9015 (m-80) cc_final: 0.8719 (m-80) REVERT: D 9 LYS cc_start: 0.8755 (OUTLIER) cc_final: 0.8185 (mppt) REVERT: D 96 ASP cc_start: 0.8362 (p0) cc_final: 0.8159 (p0) REVERT: D 119 GLU cc_start: 0.8361 (tp30) cc_final: 0.8007 (tp30) REVERT: E 138 GLU cc_start: 0.8699 (mt-10) cc_final: 0.8405 (mt-10) REVERT: F 26 LYS cc_start: 0.9249 (tttt) cc_final: 0.8838 (tmmt) outliers start: 8 outliers final: 4 residues processed: 119 average time/residue: 1.5699 time to fit residues: 201.8946 Evaluate side-chains 121 residues out of total 1256 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 115 time to evaluate : 1.475 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 292 MET Chi-restraints excluded: chain A residue 384 MET Chi-restraints excluded: chain B residue 8 GLU Chi-restraints excluded: chain B residue 406 LYS Chi-restraints excluded: chain C residue 123 VAL Chi-restraints excluded: chain D residue 9 LYS 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: 1.9990 chunk 100 optimal weight: 0.8980 chunk 151 optimal weight: 4.9990 chunk 139 optimal weight: 3.9990 chunk 120 optimal weight: 0.9990 chunk 12 optimal weight: 2.9990 chunk 93 optimal weight: 5.9990 chunk 73 optimal weight: 1.9990 chunk 95 optimal weight: 0.8980 chunk 128 optimal weight: 2.9990 overall best weight: 1.3586 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9059 moved from start: 0.1846 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 12170 Z= 0.262 Angle : 0.540 9.110 16517 Z= 0.284 Chirality : 0.042 0.163 1899 Planarity : 0.004 0.038 2060 Dihedral : 8.392 173.281 1661 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 3.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.09 % Favored : 97.91 % Rotamer: Outliers : 0.72 % Allowed : 10.83 % Favored : 88.46 % 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: 1.88 (0.18), residues: 804 sheet: -0.34 (0.53), residues: 99 loop : -0.08 (0.25), residues: 625 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP B 103 HIS 0.003 0.001 HIS B 153 PHE 0.036 0.001 PHE E 22 TYR 0.024 0.001 TYR D 141 ARG 0.005 0.000 ARG D 71 ********************** 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 123 residues out of total 1256 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 114 time to evaluate : 1.419 Fit side-chains REVERT: A 43 MET cc_start: 0.9389 (mmm) cc_final: 0.9117 (tpp) REVERT: B 12 HIS cc_start: 0.8278 (p90) cc_final: 0.7781 (p90) REVERT: B 15 GLU cc_start: 0.8662 (tp30) cc_final: 0.8066 (pp20) REVERT: B 34 PHE cc_start: 0.9012 (m-80) cc_final: 0.8712 (m-80) REVERT: D 9 LYS cc_start: 0.8768 (OUTLIER) cc_final: 0.8190 (mppt) REVERT: D 119 GLU cc_start: 0.8367 (tp30) cc_final: 0.8012 (tp30) REVERT: E 138 GLU cc_start: 0.8705 (mt-10) cc_final: 0.8458 (mt-10) REVERT: F 26 LYS cc_start: 0.9246 (tttt) cc_final: 0.8836 (tmmt) outliers start: 9 outliers final: 5 residues processed: 118 average time/residue: 1.5289 time to fit residues: 193.7506 Evaluate side-chains 119 residues out of total 1256 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 113 time to evaluate : 1.416 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 292 MET Chi-restraints excluded: chain A residue 384 MET Chi-restraints excluded: chain B residue 406 LYS Chi-restraints excluded: chain C residue 123 VAL Chi-restraints excluded: chain C residue 153 VAL Chi-restraints excluded: chain D residue 9 LYS 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: 1.9990 chunk 17 optimal weight: 4.9990 chunk 33 optimal weight: 0.8980 chunk 120 optimal weight: 2.9990 chunk 50 optimal weight: 0.5980 chunk 124 optimal weight: 4.9990 chunk 15 optimal weight: 2.9990 chunk 22 optimal weight: 0.7980 chunk 106 optimal weight: 6.9990 chunk 6 optimal weight: 3.9990 overall best weight: 1.4584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.057938 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2612 r_free = 0.2612 target = 0.043657 restraints weight = 30837.037| |-----------------------------------------------------------------------------| r_work (start): 0.2602 rms_B_bonded: 2.26 r_work: 0.2491 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.2378 rms_B_bonded: 4.26 restraints_weight: 0.2500 r_work (final): 0.2378 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8945 moved from start: 0.1846 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 12170 Z= 0.276 Angle : 0.543 9.064 16517 Z= 0.285 Chirality : 0.042 0.163 1899 Planarity : 0.004 0.038 2060 Dihedral : 8.397 173.247 1661 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 3.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 0.80 % Allowed : 10.67 % Favored : 88.54 % 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: 1.36 (0.22), residues: 1528 helix: 1.86 (0.18), residues: 804 sheet: -0.34 (0.53), residues: 99 loop : -0.09 (0.24), residues: 625 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP B 103 HIS 0.003 0.001 HIS B 153 PHE 0.035 0.001 PHE E 22 TYR 0.023 0.001 TYR D 141 ARG 0.005 0.000 ARG D 71 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4146.63 seconds wall clock time: 74 minutes 50.35 seconds (4490.35 seconds total)