Starting phenix.real_space_refine on Tue Dec 31 14:33:54 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7xk7_33246/12_2024/7xk7_33246.cif Found real_map, /net/cci-nas-00/data/ceres_data/7xk7_33246/12_2024/7xk7_33246.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7xk7_33246/12_2024/7xk7_33246.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7xk7_33246/12_2024/7xk7_33246.map" model { file = "/net/cci-nas-00/data/ceres_data/7xk7_33246/12_2024/7xk7_33246.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7xk7_33246/12_2024/7xk7_33246.cif" } resolution = 2.9 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= 0.001 sd= 0.115 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: 7 Type Number sf(0) Gaussians Ca 1 9.91 5 Fe 4 7.16 5 P 7 5.49 5 S 92 5.16 5 C 9830 2.51 5 N 2451 2.21 5 O 2801 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 34 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/chem_data/mon_lib" Total number of atoms: 15186 Number of models: 1 Model: "" Number of chains: 14 Chain: "A" Number of atoms: 3421 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 446, 3416 Classifications: {'peptide': 446} Modifications used: {'COO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 21, 'TRANS': 422} Conformer: "B" Number of residues, atoms: 446, 3416 Classifications: {'peptide': 446} Modifications used: {'COO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 21, 'TRANS': 422} bond proxies already assigned to first conformer: 3474 Chain: "B" Number of atoms: 3177 Number of conformers: 1 Conformer: "" Number of residues, atoms: 412, 3177 Classifications: {'peptide': 412} Link IDs: {'PTRANS': 15, 'TRANS': 396} Chain: "C" Number of atoms: 1902 Number of conformers: 1 Conformer: "" Number of residues, atoms: 251, 1902 Classifications: {'peptide': 251} Link IDs: {'PTRANS': 7, 'TRANS': 243} Chain: "D" Number of atoms: 1580 Number of conformers: 1 Conformer: "" Number of residues, atoms: 206, 1580 Classifications: {'peptide': 206} Link IDs: {'PTRANS': 9, 'TRANS': 196} Chain: "E" Number of atoms: 1511 Number of conformers: 1 Conformer: "" Number of residues, atoms: 198, 1511 Classifications: {'peptide': 198} Link IDs: {'PTRANS': 7, 'TRANS': 190} Chain: "F" Number of atoms: 3157 Number of conformers: 1 Conformer: "" Number of residues, atoms: 408, 3157 Classifications: {'peptide': 408} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 24, 'TRANS': 383} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 8 Chain: "B" Number of atoms: 260 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 260 Unusual residues: {'FMN': 1, 'IQT': 1, 'LMT': 2, 'PEE': 2, 'RBF': 1} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 3 Chain: "C" Number of atoms: 82 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 82 Unusual residues: {' CA': 1, 'FMN': 1, 'PEE': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 3 Chain: "D" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 4 Unusual residues: {'FES': 1} Classifications: {'undetermined': 1} Chain: "F" Number of atoms: 57 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 57 Unusual residues: {'FAD': 1, 'FES': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "A" Number of atoms: 17 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 17 Classifications: {'water': 17} Link IDs: {None: 16} Chain: "B" Number of atoms: 15 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 15 Classifications: {'water': 15} Link IDs: {None: 14} Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "E" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 9324 SG CYS D 112 46.524 51.343 64.710 1.00 45.30 S ATOM 10290 SG CYS E 26 44.603 55.229 65.844 1.00 41.86 S ATOM 8685 SG CYS D 29 46.490 58.333 61.442 1.00 44.16 S ATOM 11012 SG CYS E 120 48.052 54.013 59.708 1.00 45.56 S Residues with excluded nonbonded symmetry interactions: 1 residue: pdb=" N AALA A 338 " occ=0.50 ... (8 atoms not shown) pdb=" CB BALA A 338 " occ=0.50 Time building chain proxies: 10.78, per 1000 atoms: 0.71 Number of scatterers: 15186 At special positions: 0 Unit cell: (90.64, 127.6, 153.12, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Fe 4 26.01 Ca 1 19.99 S 92 16.00 P 7 15.00 O 2801 8.00 N 2451 7.00 C 9830 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: 4.33 Conformation dependent library (CDL) restraints added in 2.6 seconds Dynamic metal coordination Iron sulfur cluster coordination pdb=" FES D 301 " pdb="FE2 FES D 301 " - pdb=" SG CYS D 29 " pdb="FE1 FES D 301 " - pdb=" SG CYS D 112 " pdb="FE2 FES D 301 " - pdb=" SG CYS E 120 " pdb="FE1 FES D 301 " - pdb=" SG CYS E 26 " pdb=" FES F 501 " pdb="FE2 FES F 501 " - pdb=" SG CYS F 111 " pdb="FE2 FES F 501 " - pdb=" SG CYS F 79 " Number of angles added : 9 3824 Ramachandran restraints generated. 1912 Oldfield, 0 Emsley, 1912 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3470 Finding SS restraints... Secondary structure from input PDB file: 87 helices and 14 sheets defined 51.8% alpha, 10.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.88 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 114 through 126 Processing helix chain 'A' and resid 127 through 131 Processing helix chain 'A' and resid 162 through 168 removed outlier: 3.949A pdb=" N VAL A 166 " --> pdb=" O GLU A 162 " (cutoff:3.500A) Processing helix chain 'A' and resid 170 through 185 removed outlier: 3.527A pdb=" N ALA A 183 " --> pdb=" O ASP A 179 " (cutoff:3.500A) 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 removed outlier: 3.849A pdb=" N VAL A 287 " --> pdb=" O LEU A 283 " (cutoff:3.500A) Processing helix chain 'A' and resid 310 through 314 removed outlier: 3.510A pdb=" N ALA A 314 " --> pdb=" O GLY A 311 " (cutoff:3.500A) Processing helix chain 'A' and resid 351 through 356 removed outlier: 3.949A pdb=" N HIS A 354 " --> pdb=" O PHE A 351 " (cutoff:3.500A) Processing helix chain 'A' and resid 378 through 384 removed outlier: 3.895A pdb=" N LYS A 382 " --> pdb=" O GLY A 378 " (cutoff:3.500A) removed outlier: 3.780A 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 409 Processing helix chain 'A' and resid 418 through 424 Processing helix chain 'A' and resid 430 through 445 removed outlier: 3.971A pdb=" N LEU A 434 " --> pdb=" O GLU A 430 " (cutoff:3.500A) Processing helix chain 'B' and resid 3 through 10 removed outlier: 3.662A pdb=" N ILE B 10 " --> pdb=" O PHE B 6 " (cutoff:3.500A) Processing helix chain 'B' and resid 11 through 14 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: 3.624A pdb=" N ALA B 29 " --> pdb=" O ALA B 25 " (cutoff:3.500A) Processing helix chain 'B' and resid 52 through 63 Processing helix chain 'B' and resid 64 through 87 Processing helix chain 'B' and resid 89 through 97 removed outlier: 3.801A pdb=" N ALA B 93 " --> pdb=" O GLY B 89 " (cutoff:3.500A) Processing helix chain 'B' and resid 99 through 108 removed outlier: 3.714A pdb=" N THR B 105 " --> pdb=" O HIS B 101 " (cutoff:3.500A) Processing helix chain 'B' and resid 117 through 151 removed outlier: 3.551A pdb=" N TYR B 128 " --> pdb=" O LEU B 124 " (cutoff:3.500A) Proline residue: B 131 - end of helix removed outlier: 3.747A pdb=" N TRP B 143 " --> pdb=" O VAL B 139 " (cutoff:3.500A) Processing helix chain 'B' and resid 158 through 168 removed outlier: 4.163A pdb=" N ILE B 164 " --> pdb=" O PHE B 160 " (cutoff:3.500A) Processing helix chain 'B' and resid 175 through 189 Processing helix chain 'B' and resid 191 through 195 Processing helix chain 'B' and resid 208 through 216 removed outlier: 3.597A pdb=" N LEU B 212 " --> pdb=" O GLY B 208 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N PHE B 214 " --> pdb=" O ALA B 210 " (cutoff:3.500A) Processing helix chain 'B' and resid 239 through 245 Processing helix chain 'B' and resid 246 through 248 No H-bonds generated for 'chain 'B' and resid 246 through 248' Processing helix chain 'B' and resid 259 through 266 removed outlier: 3.549A pdb=" N ALA B 263 " --> pdb=" O THR B 259 " (cutoff:3.500A) Processing helix chain 'B' and resid 276 through 290 removed outlier: 3.602A pdb=" N PHE B 286 " --> pdb=" O ILE B 282 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 316 Processing helix chain 'B' and resid 320 through 325 removed outlier: 3.734A pdb=" N PHE B 323 " --> pdb=" O ASN B 320 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ASN B 324 " --> pdb=" O ALA B 321 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N MET B 325 " --> pdb=" O MET B 322 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 320 through 325' Processing helix chain 'B' and resid 326 through 331 Processing helix chain 'B' and resid 335 through 343 Processing helix chain 'B' and resid 353 through 375 removed outlier: 4.022A pdb=" N TRP B 358 " --> pdb=" O ASN B 354 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N ALA B 359 " --> pdb=" O SER B 355 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N ASN B 375 " --> pdb=" O ILE B 371 " (cutoff:3.500A) Processing helix chain 'B' and resid 381 through 410 removed outlier: 3.920A pdb=" N LEU B 391 " --> pdb=" O LEU B 387 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N PHE B 392 " --> pdb=" O PHE B 388 " (cutoff:3.500A) Proline residue: B 394 - end of helix removed outlier: 3.535A pdb=" N ASP B 397 " --> pdb=" O ALA B 393 " (cutoff:3.500A) Processing helix chain 'C' and resid 7 through 33 removed outlier: 3.729A pdb=" N ILE C 25 " --> pdb=" O VAL C 21 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N LEU C 33 " --> pdb=" O ALA C 29 " (cutoff:3.500A) Processing helix chain 'C' and resid 33 through 53 removed outlier: 4.075A pdb=" N ASP C 44 " --> pdb=" O ASN C 40 " (cutoff:3.500A) removed outlier: 4.388A pdb=" N LYS C 45 " --> pdb=" O ALA C 41 " (cutoff:3.500A) Processing helix chain 'C' and resid 58 through 70 removed outlier: 4.305A pdb=" N GLN C 62 " --> pdb=" O LYS C 58 " (cutoff:3.500A) Processing helix chain 'C' and resid 92 through 97 Processing helix chain 'C' and resid 177 through 181 removed outlier: 4.026A pdb=" N VAL C 180 " --> pdb=" O GLY C 177 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N GLU C 181 " --> pdb=" O GLY C 178 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 177 through 181' Processing helix chain 'C' and resid 182 through 187 Processing helix chain 'C' and resid 227 through 239 Processing helix chain 'C' and resid 244 through 254 Processing helix chain 'D' and resid 6 through 17 removed outlier: 3.879A pdb=" N SER D 10 " --> pdb=" O GLU D 6 " (cutoff:3.500A) Proline residue: D 14 - end of helix Processing helix chain 'D' and resid 19 through 24 Processing helix chain 'D' and resid 27 through 34 removed outlier: 4.123A pdb=" N ALA D 31 " --> pdb=" O GLY D 27 " (cutoff:3.500A) Processing helix chain 'D' and resid 37 through 62 removed outlier: 3.836A pdb=" N ALA D 41 " --> pdb=" O LYS D 37 " (cutoff:3.500A) Processing helix chain 'D' and resid 70 through 94 removed outlier: 3.547A pdb=" N ALA D 92 " --> pdb=" O GLN D 88 " (cutoff:3.500A) Processing helix chain 'D' and resid 94 through 101 removed outlier: 3.584A pdb=" N SER D 98 " --> pdb=" O LEU D 94 " (cutoff:3.500A) Processing helix chain 'D' and resid 105 through 109 removed outlier: 3.526A pdb=" N ILE D 108 " --> pdb=" O VAL D 105 " (cutoff:3.500A) Processing helix chain 'D' and resid 111 through 121 removed outlier: 3.837A pdb=" N MET D 115 " --> pdb=" O ASN D 111 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N ALA D 118 " --> pdb=" O VAL D 114 " (cutoff:3.500A) Processing helix chain 'D' and resid 122 through 125 removed outlier: 3.656A 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 removed outlier: 3.669A pdb=" N VAL D 144 " --> pdb=" O GLY D 140 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N PHE D 151 " --> pdb=" O THR D 147 " (cutoff:3.500A) Processing helix chain 'D' and resid 168 through 172 Processing helix chain 'D' and resid 179 through 182 Processing helix chain 'D' and resid 183 through 202 removed outlier: 4.527A pdb=" N ALA D 187 " --> pdb=" O LEU D 183 " (cutoff:3.500A) removed outlier: 4.118A pdb=" N PHE D 188 " --> pdb=" O ALA D 184 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N PHE D 201 " --> pdb=" O ALA D 197 " (cutoff:3.500A) Processing helix chain 'D' and resid 203 through 206 removed outlier: 3.720A pdb=" N VAL D 206 " --> pdb=" O PRO D 203 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 203 through 206' Processing helix chain 'E' and resid 2 through 14 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 101 Processing helix chain 'E' and resid 102 through 110 Processing helix chain 'E' and resid 112 through 117 Processing helix chain 'E' and resid 119 through 133 removed outlier: 3.540A pdb=" N PHE E 123 " --> pdb=" O ASN E 119 " (cutoff:3.500A) 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 removed outlier: 3.657A pdb=" N PHE F 6 " --> pdb=" O SER F 2 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N LYS F 28 " --> pdb=" O PHE F 24 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N LEU F 29 " --> pdb=" O ALA F 25 " (cutoff:3.500A) Processing helix chain 'F' and resid 54 through 62 removed outlier: 3.726A pdb=" N GLY F 61 " --> pdb=" O THR F 57 " (cutoff:3.500A) removed outlier: 4.349A pdb=" N ALA F 62 " --> pdb=" O ALA F 58 " (cutoff:3.500A) Processing helix chain 'F' and resid 68 through 72 removed outlier: 3.672A pdb=" N GLY F 71 " --> pdb=" O SER F 68 " (cutoff:3.500A) Processing helix chain 'F' and resid 93 through 97 Processing helix chain 'F' and resid 99 through 104 removed outlier: 3.911A pdb=" N ARG F 104 " --> pdb=" O LYS F 100 " (cutoff:3.500A) Processing helix chain 'F' and resid 155 through 158 Processing helix chain 'F' and resid 191 through 196 removed outlier: 3.819A pdb=" N PHE F 195 " --> pdb=" O ASP F 191 " (cutoff:3.500A) Processing helix chain 'F' and resid 243 through 250 removed outlier: 3.531A pdb=" N TYR F 248 " --> pdb=" O GLN F 244 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N TRP F 250 " --> pdb=" O SER F 246 " (cutoff:3.500A) Processing helix chain 'F' and resid 284 through 297 removed outlier: 3.649A pdb=" N MET F 288 " --> pdb=" O GLY F 284 " (cutoff:3.500A) Processing helix chain 'F' and resid 313 through 317 Processing helix chain 'F' and resid 319 through 330 Processing helix chain 'F' and resid 343 through 347 removed outlier: 3.523A pdb=" N ASN F 347 " --> pdb=" O PRO F 344 " (cutoff:3.500A) Processing helix chain 'F' and resid 354 through 363 removed outlier: 3.680A pdb=" N TYR F 360 " --> pdb=" O HIS F 356 " (cutoff:3.500A) Processing helix chain 'F' and resid 369 through 373 removed outlier: 3.670A pdb=" N CYS F 373 " --> pdb=" O PRO F 370 " (cutoff:3.500A) Processing helix chain 'F' and resid 380 through 393 Processing sheet with id=AA1, first strand: chain 'A' and resid 2 through 3 removed outlier: 3.579A pdb=" N ILE A 149 " --> pdb=" O LYS A 188 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 17 through 22 removed outlier: 3.628A pdb=" N LEU A 274 " --> pdb=" O VAL A 19 " (cutoff:3.500A) removed outlier: 8.013A pdb=" N VAL A 323 " --> pdb=" O VAL A 261 " (cutoff:3.500A) removed outlier: 5.731A pdb=" N SER A 263 " --> pdb=" O VAL A 323 " (cutoff:3.500A) removed outlier: 7.293A pdb=" N VAL A 325 " --> pdb=" O SER A 263 " (cutoff:3.500A) removed outlier: 6.607A pdb=" N ALA A 265 " --> pdb=" O VAL A 325 " (cutoff:3.500A) removed outlier: 8.942A pdb=" N ARG A 327 " --> pdb=" O ALA A 265 " (cutoff:3.500A) removed outlier: 5.676A 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: 6.758A pdb=" N LEU A 87 " --> pdb=" O ARG A 81 " (cutoff:3.500A) removed outlier: 6.538A pdb=" N ARG A 81 " --> pdb=" O LEU A 87 " (cutoff:3.500A) removed outlier: 6.561A pdb=" N SER A 89 " --> pdb=" O ILE A 79 " (cutoff:3.500A) removed outlier: 4.505A pdb=" N ILE A 79 " --> pdb=" O SER A 89 " (cutoff:3.500A) removed outlier: 6.626A 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: 6.984A pdb=" N PHE A 68 " --> pdb=" O LEU A 57 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 250 through 251 Processing sheet with id=AA6, first strand: chain 'C' and resid 83 through 84 removed outlier: 3.964A pdb=" N LEU C 75 " --> pdb=" O VAL C 84 " (cutoff:3.500A) removed outlier: 14.662A pdb=" N VAL C 121 " --> pdb=" O HIS C 141 " (cutoff:3.500A) removed outlier: 12.349A pdb=" N HIS C 141 " --> pdb=" O VAL C 121 " (cutoff:3.500A) removed outlier: 7.297A pdb=" N VAL C 123 " --> pdb=" O PRO C 139 " (cutoff:3.500A) removed outlier: 6.476A pdb=" N ASP C 129 " --> pdb=" O THR C 133 " (cutoff:3.500A) removed outlier: 5.214A pdb=" N THR C 133 " --> pdb=" O ASP C 129 " (cutoff:3.500A) removed outlier: 6.593A pdb=" N MET C 148 " --> pdb=" O GLU C 169 " (cutoff:3.500A) removed outlier: 6.502A pdb=" N GLU C 169 " --> pdb=" O MET C 148 " (cutoff:3.500A) removed outlier: 6.964A pdb=" N TYR C 150 " --> pdb=" O TYR C 167 " (cutoff:3.500A) removed outlier: 4.625A pdb=" N TYR C 167 " --> pdb=" O TYR C 150 " (cutoff:3.500A) removed outlier: 6.508A pdb=" N PHE C 152 " --> pdb=" O LEU C 165 " (cutoff:3.500A) removed outlier: 4.233A pdb=" N LEU C 165 " --> pdb=" O PHE C 152 " (cutoff:3.500A) removed outlier: 6.412A pdb=" N ALA C 154 " --> pdb=" O SER C 163 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 103 through 105 Processing sheet with id=AA8, first strand: chain 'C' and resid 204 through 206 Processing sheet with id=AA9, first strand: chain 'D' and resid 159 through 160 Processing sheet with id=AB1, first strand: chain 'F' and resid 47 through 49 removed outlier: 4.013A pdb=" N THR F 49 " --> pdb=" O ILE F 35 " (cutoff:3.500A) removed outlier: 4.611A pdb=" N ILE F 35 " --> pdb=" O THR F 49 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N MET F 119 " --> pdb=" O THR F 36 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'F' and resid 80 through 82 Processing sheet with id=AB3, first strand: chain 'F' and resid 208 through 213 removed outlier: 4.365A pdb=" N GLN F 169 " --> pdb=" O GLY F 262 " (cutoff:3.500A) removed outlier: 5.349A pdb=" N GLY F 262 " --> pdb=" O GLN F 169 " (cutoff:3.500A) removed outlier: 6.475A pdb=" N GLU F 171 " --> pdb=" O ILE F 260 " (cutoff:3.500A) removed outlier: 5.768A pdb=" N ILE F 260 " --> pdb=" O GLU F 171 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N THR F 136 " --> pdb=" O ALA F 153 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'F' and resid 175 through 178 Processing sheet with id=AB5, first strand: chain 'F' and resid 351 through 352 removed outlier: 4.121A pdb=" N TYR F 351 " --> pdb=" O CYS F 337 " (cutoff:3.500A) removed outlier: 8.098A pdb=" N TRP F 308 " --> pdb=" O MET F 276 " (cutoff:3.500A) removed outlier: 6.644A pdb=" N PHE F 278 " --> pdb=" O TRP F 308 " (cutoff:3.500A) removed outlier: 7.920A pdb=" N GLY F 310 " --> pdb=" O PHE F 278 " (cutoff:3.500A) removed outlier: 7.176A pdb=" N GLY F 280 " --> pdb=" O GLY F 310 " (cutoff:3.500A) removed outlier: 6.488A pdb=" N TYR F 375 " --> pdb=" O LEU F 402 " (cutoff:3.500A) 703 hydrogen bonds defined for protein. 2016 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: 5.86 Time building geometry restraints manager: 4.79 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.15 - 1.36: 4778 1.36 - 1.57: 10546 1.57 - 1.78: 15 1.78 - 1.99: 152 1.99 - 2.20: 8 Bond restraints: 15499 Sorted by residual: bond pdb=" CA SER B 239 " pdb=" CB SER B 239 " ideal model delta sigma weight residual 1.534 1.403 0.130 1.45e-02 4.76e+03 8.09e+01 bond pdb=" C4A RBF B 502 " pdb=" N5 RBF B 502 " ideal model delta sigma weight residual 1.288 1.450 -0.162 2.00e-02 2.50e+03 6.52e+01 bond pdb=" C10 RBF B 502 " pdb=" N1 RBF B 502 " ideal model delta sigma weight residual 1.304 1.461 -0.157 2.00e-02 2.50e+03 6.18e+01 bond pdb=" C5A RBF B 502 " pdb=" N5 RBF B 502 " ideal model delta sigma weight residual 1.350 1.491 -0.141 2.00e-02 2.50e+03 4.96e+01 bond pdb=" C12 IQT B 503 " pdb=" C13 IQT B 503 " ideal model delta sigma weight residual 1.454 1.313 0.141 2.00e-02 2.50e+03 4.94e+01 ... (remaining 15494 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.79: 20829 4.79 - 9.58: 140 9.58 - 14.36: 17 14.36 - 19.15: 4 19.15 - 23.94: 1 Bond angle restraints: 20991 Sorted by residual: angle pdb=" S1 FES F 501 " pdb="FE2 FES F 501 " pdb=" S2 FES F 501 " ideal model delta sigma weight residual 104.33 91.08 13.25 1.14e+00 7.69e-01 1.35e+02 angle pdb="FE1 FES F 501 " pdb=" S2 FES F 501 " pdb="FE2 FES F 501 " ideal model delta sigma weight residual 75.66 88.85 -13.19 1.14e+00 7.69e-01 1.34e+02 angle pdb=" S1 FES D 301 " pdb="FE2 FES D 301 " pdb=" S2 FES D 301 " ideal model delta sigma weight residual 104.33 91.43 12.90 1.14e+00 7.69e-01 1.28e+02 angle pdb="FE1 FES D 301 " pdb=" S2 FES D 301 " pdb="FE2 FES D 301 " ideal model delta sigma weight residual 75.66 88.48 -12.82 1.14e+00 7.69e-01 1.26e+02 angle pdb=" S1 FES F 501 " pdb="FE1 FES F 501 " pdb=" S2 FES F 501 " ideal model delta sigma weight residual 104.33 91.13 13.20 1.20e+00 6.94e-01 1.21e+02 ... (remaining 20986 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.61: 8977 35.61 - 71.22: 216 71.22 - 106.83: 37 106.83 - 142.45: 28 142.45 - 178.06: 3 Dihedral angle restraints: 9261 sinusoidal: 3820 harmonic: 5441 Sorted by residual: dihedral pdb=" CA ILE F 39 " pdb=" C ILE F 39 " pdb=" N ASN F 40 " pdb=" CA ASN F 40 " ideal model delta harmonic sigma weight residual 180.00 -145.06 -34.94 0 5.00e+00 4.00e-02 4.88e+01 dihedral pdb=" C10 FMN B 501 " pdb=" C1' FMN B 501 " pdb=" N10 FMN B 501 " pdb=" C2' FMN B 501 " ideal model delta sinusoidal sigma weight residual 257.59 79.53 178.06 1 2.00e+01 2.50e-03 4.80e+01 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 86.97 170.62 1 2.00e+01 2.50e-03 4.77e+01 ... (remaining 9258 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.149: 2312 0.149 - 0.298: 33 0.298 - 0.446: 7 0.446 - 0.595: 2 0.595 - 0.744: 2 Chirality restraints: 2356 Sorted by residual: chirality pdb=" C16 IQT B 503 " pdb=" C15 IQT B 503 " pdb=" C17 IQT B 503 " pdb=" O4 IQT B 503 " both_signs ideal model delta sigma weight residual True 2.15 -1.41 0.74 2.00e-01 2.50e+01 1.38e+01 chirality pdb=" CA ASP F 34 " pdb=" N ASP F 34 " pdb=" C ASP F 34 " pdb=" CB ASP F 34 " both_signs ideal model delta sigma weight residual False 2.51 1.86 0.65 2.00e-01 2.50e+01 1.04e+01 chirality pdb=" C5' LMT B 505 " pdb=" C4' LMT B 505 " pdb=" C6' LMT B 505 " pdb=" O5' LMT B 505 " both_signs ideal model delta sigma weight residual False -2.51 -1.96 -0.55 2.00e-01 2.50e+01 7.53e+00 ... (remaining 2353 not shown) Planarity restraints: 2618 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C12 IQT B 503 " 0.215 2.00e-02 2.50e+03 1.96e-01 3.84e+02 pdb=" C13 IQT B 503 " -0.235 2.00e-02 2.50e+03 pdb=" C14 IQT B 503 " -0.150 2.00e-02 2.50e+03 pdb=" C15 IQT B 503 " 0.171 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C10 IQT B 503 " 0.075 2.00e-02 2.50e+03 1.63e-01 2.67e+02 pdb=" C11 IQT B 503 " -0.206 2.00e-02 2.50e+03 pdb=" C12 IQT B 503 " 0.224 2.00e-02 2.50e+03 pdb=" C13 IQT B 503 " -0.093 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' FMN C 301 " -0.069 2.00e-02 2.50e+03 2.79e-02 3.69e+01 pdb=" C10 FMN C 301 " -0.006 2.00e-02 2.50e+03 pdb=" C2 FMN C 301 " 0.023 2.00e-02 2.50e+03 pdb=" C4 FMN C 301 " -0.010 2.00e-02 2.50e+03 pdb=" C4A FMN C 301 " -0.017 2.00e-02 2.50e+03 pdb=" C5A FMN C 301 " -0.016 2.00e-02 2.50e+03 pdb=" C6 FMN C 301 " -0.015 2.00e-02 2.50e+03 pdb=" C7 FMN C 301 " 0.022 2.00e-02 2.50e+03 pdb=" C7M FMN C 301 " 0.032 2.00e-02 2.50e+03 pdb=" C8 FMN C 301 " 0.026 2.00e-02 2.50e+03 pdb=" C8M FMN C 301 " 0.017 2.00e-02 2.50e+03 pdb=" C9 FMN C 301 " -0.012 2.00e-02 2.50e+03 pdb=" C9A FMN C 301 " -0.014 2.00e-02 2.50e+03 pdb=" N1 FMN C 301 " 0.008 2.00e-02 2.50e+03 pdb=" N10 FMN C 301 " 0.002 2.00e-02 2.50e+03 pdb=" N3 FMN C 301 " 0.011 2.00e-02 2.50e+03 pdb=" N5 FMN C 301 " -0.020 2.00e-02 2.50e+03 pdb=" O2 FMN C 301 " 0.066 2.00e-02 2.50e+03 pdb=" O4 FMN C 301 " -0.029 2.00e-02 2.50e+03 ... (remaining 2615 not shown) Histogram of nonbonded interaction distances: 1.98 - 2.56: 107 2.56 - 3.15: 11679 3.15 - 3.73: 22013 3.73 - 4.32: 33677 4.32 - 4.90: 56304 Nonbonded interactions: 123780 Sorted by model distance: nonbonded pdb=" OD2 ASP B 397 " pdb=" O HOH B 601 " model vdw 1.978 3.040 nonbonded pdb=" OG SER B 113 " pdb=" OD1 ASP B 115 " model vdw 2.172 3.040 nonbonded pdb=" O4' FMN B 501 " pdb=" O5' FMN B 501 " model vdw 2.176 2.432 nonbonded pdb=" O HOH A 510 " pdb=" O HOH A 512 " model vdw 2.178 3.040 nonbonded pdb=" OE2 GLU F 275 " pdb=" OH TYR F 363 " model vdw 2.212 3.040 ... (remaining 123775 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=0.50 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: 3.210 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: 1.520 Check model and map are aligned: 0.090 Set scattering table: 0.150 Process input model: 42.820 Find NCS groups from input model: 0.340 Set up NCS constraints: 0.080 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:13.380 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 61.610 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8485 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 : 0.008 0.162 15499 Z= 0.466 Angle : 1.041 23.938 20991 Z= 0.603 Chirality : 0.059 0.744 2356 Planarity : 0.007 0.196 2618 Dihedral : 18.325 178.058 5791 Min Nonbonded Distance : 1.978 Molprobity Statistics. All-atom Clashscore : 5.02 Ramachandran Plot: Outliers : 0.10 % Allowed : 2.51 % Favored : 97.38 % Rotamer: Outliers : 0.70 % Allowed : 2.94 % Favored : 96.36 % Cbeta Deviations : 0.63 % Peptide Plane: Cis-proline : 2.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: -2.49 (0.16), residues: 1912 helix: -1.31 (0.16), residues: 853 sheet: -1.28 (0.38), residues: 149 loop : -2.00 (0.17), residues: 910 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP F 250 HIS 0.005 0.001 HIS F 291 PHE 0.024 0.002 PHE B 213 TYR 0.020 0.001 TYR D 141 ARG 0.004 0.000 ARG F 189 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3824 Ramachandran restraints generated. 1912 Oldfield, 0 Emsley, 1912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3824 Ramachandran restraints generated. 1912 Oldfield, 0 Emsley, 1912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 246 residues out of total 1568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 235 time to evaluate : 1.837 Fit side-chains REVERT: A 97 ASP cc_start: 0.8223 (p0) cc_final: 0.7870 (p0) REVERT: A 271 LYS cc_start: 0.8144 (mmtp) cc_final: 0.7809 (mtpt) REVERT: A 396 ASP cc_start: 0.7211 (m-30) cc_final: 0.6976 (m-30) REVERT: B 406 LYS cc_start: 0.8440 (mtmm) cc_final: 0.8041 (mttm) REVERT: B 412 TYR cc_start: 0.7500 (m-80) cc_final: 0.6989 (m-80) REVERT: C 116 GLN cc_start: 0.7856 (mt0) cc_final: 0.7576 (mt0) REVERT: D 202 LYS cc_start: 0.8300 (mtpp) cc_final: 0.8084 (mtpt) REVERT: F 80 ARG cc_start: 0.8397 (ptp-110) cc_final: 0.8120 (mtp180) REVERT: F 104 ARG cc_start: 0.6606 (mtm-85) cc_final: 0.6227 (mmp80) REVERT: F 169 GLN cc_start: 0.8811 (mt0) cc_final: 0.8574 (mt0) REVERT: F 199 ARG cc_start: 0.7077 (ttp-110) cc_final: 0.6833 (ttp80) outliers start: 11 outliers final: 4 residues processed: 244 average time/residue: 1.5600 time to fit residues: 413.9430 Evaluate side-chains 175 residues out of total 1568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 171 time to evaluate : 1.776 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 380 GLU Chi-restraints excluded: chain C residue 207 LYS Chi-restraints excluded: chain D residue 209 LYS Chi-restraints excluded: chain F residue 32 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 189 random chunks: chunk 159 optimal weight: 9.9990 chunk 143 optimal weight: 7.9990 chunk 79 optimal weight: 4.9990 chunk 48 optimal weight: 5.9990 chunk 96 optimal weight: 0.0670 chunk 76 optimal weight: 0.9990 chunk 148 optimal weight: 2.9990 chunk 57 optimal weight: 4.9990 chunk 90 optimal weight: 0.0170 chunk 110 optimal weight: 10.0000 chunk 171 optimal weight: 6.9990 overall best weight: 1.8162 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 88 GLN A 202 GLN B 46 HIS B 78 GLN B 178 GLN B 219 GLN B 240 GLN B 243 GLN B 313 ASN B 354 ASN C 37 GLN C 46 GLN C 216 HIS D 18 ASN D 75 GLN D 88 GLN D 100 GLN D 176 GLN D 205 GLN E 79 ASN F 97 HIS ** F 142 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 239 ASN F 362 ASN Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8512 moved from start: 0.1162 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 15499 Z= 0.271 Angle : 0.641 10.309 20991 Z= 0.324 Chirality : 0.046 0.286 2356 Planarity : 0.005 0.038 2618 Dihedral : 16.766 176.483 2430 Min Nonbonded Distance : 2.410 Molprobity Statistics. All-atom Clashscore : 4.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer: Outliers : 1.47 % Allowed : 10.09 % Favored : 88.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: -1.14 (0.18), residues: 1912 helix: -0.01 (0.17), residues: 870 sheet: -0.68 (0.38), residues: 155 loop : -1.50 (0.19), residues: 887 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP B 103 HIS 0.008 0.001 HIS F 291 PHE 0.020 0.002 PHE F 318 TYR 0.024 0.002 TYR D 141 ARG 0.004 0.000 ARG A 349 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3824 Ramachandran restraints generated. 1912 Oldfield, 0 Emsley, 1912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3824 Ramachandran restraints generated. 1912 Oldfield, 0 Emsley, 1912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 198 residues out of total 1568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 175 time to evaluate : 1.693 Fit side-chains REVERT: A 4 ILE cc_start: 0.8615 (OUTLIER) cc_final: 0.8059 (mp) REVERT: A 97 ASP cc_start: 0.8246 (p0) cc_final: 0.7864 (p0) REVERT: A 271 LYS cc_start: 0.8104 (mmtp) cc_final: 0.7770 (mtpt) REVERT: A 396 ASP cc_start: 0.7157 (m-30) cc_final: 0.6899 (m-30) REVERT: B 53 LEU cc_start: 0.8735 (OUTLIER) cc_final: 0.8341 (tp) REVERT: B 380 GLU cc_start: 0.9038 (OUTLIER) cc_final: 0.7213 (tm-30) REVERT: B 406 LYS cc_start: 0.8241 (mtmm) cc_final: 0.7918 (mttm) REVERT: C 51 GLN cc_start: 0.8292 (tm-30) cc_final: 0.8036 (tm-30) REVERT: F 34 ASP cc_start: 0.5830 (t0) cc_final: 0.5515 (m-30) REVERT: F 104 ARG cc_start: 0.6589 (mtm-85) cc_final: 0.6206 (mmp80) REVERT: F 169 GLN cc_start: 0.8756 (mt0) cc_final: 0.8501 (mt0) outliers start: 23 outliers final: 8 residues processed: 189 average time/residue: 1.6040 time to fit residues: 330.4328 Evaluate side-chains 173 residues out of total 1568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 162 time to evaluate : 1.717 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 ILE Chi-restraints excluded: chain A residue 73 SER Chi-restraints excluded: chain A residue 371 ASP Chi-restraints excluded: chain B residue 53 LEU Chi-restraints excluded: chain B residue 380 GLU Chi-restraints excluded: chain C residue 121 VAL Chi-restraints excluded: chain D residue 103 VAL Chi-restraints excluded: chain D residue 209 LYS Chi-restraints excluded: chain F residue 21 VAL Chi-restraints excluded: chain F residue 79 CYS Chi-restraints excluded: chain F residue 135 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 189 random chunks: chunk 95 optimal weight: 2.9990 chunk 53 optimal weight: 5.9990 chunk 142 optimal weight: 4.9990 chunk 116 optimal weight: 5.9990 chunk 47 optimal weight: 4.9990 chunk 171 optimal weight: 2.9990 chunk 185 optimal weight: 1.9990 chunk 153 optimal weight: 8.9990 chunk 170 optimal weight: 0.7980 chunk 58 optimal weight: 5.9990 chunk 137 optimal weight: 5.9990 overall best weight: 2.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 404 ASN C 37 GLN E 16 ASN ** F 97 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 142 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8545 moved from start: 0.1459 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.039 15499 Z= 0.377 Angle : 0.654 6.801 20991 Z= 0.333 Chirality : 0.047 0.278 2356 Planarity : 0.005 0.038 2618 Dihedral : 14.119 177.168 2425 Min Nonbonded Distance : 2.411 Molprobity Statistics. All-atom Clashscore : 4.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 2.36 % Allowed : 11.24 % Favored : 86.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.72 (0.18), residues: 1912 helix: 0.43 (0.18), residues: 870 sheet: -0.45 (0.39), residues: 157 loop : -1.38 (0.19), residues: 885 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP B 103 HIS 0.007 0.002 HIS F 97 PHE 0.027 0.002 PHE B 65 TYR 0.024 0.002 TYR D 141 ARG 0.006 0.001 ARG B 408 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3824 Ramachandran restraints generated. 1912 Oldfield, 0 Emsley, 1912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3824 Ramachandran restraints generated. 1912 Oldfield, 0 Emsley, 1912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 210 residues out of total 1568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 173 time to evaluate : 1.746 Fit side-chains REVERT: A 4 ILE cc_start: 0.8638 (OUTLIER) cc_final: 0.8044 (mp) REVERT: A 97 ASP cc_start: 0.8271 (p0) cc_final: 0.7877 (p0) REVERT: A 271 LYS cc_start: 0.8167 (mmtp) cc_final: 0.7770 (mptt) REVERT: A 332 LYS cc_start: 0.8556 (mtpt) cc_final: 0.8205 (mttm) REVERT: A 396 ASP cc_start: 0.7178 (m-30) cc_final: 0.6918 (m-30) REVERT: A 444 LYS cc_start: 0.7968 (ttmm) cc_final: 0.7329 (ttpt) REVERT: B 19 LYS cc_start: 0.6950 (mttt) cc_final: 0.6542 (mmpt) REVERT: B 22 LYS cc_start: 0.8235 (OUTLIER) cc_final: 0.7700 (mttp) REVERT: B 53 LEU cc_start: 0.8818 (OUTLIER) cc_final: 0.8382 (tp) REVERT: B 380 GLU cc_start: 0.9080 (OUTLIER) cc_final: 0.6967 (tm-30) REVERT: B 406 LYS cc_start: 0.8243 (mtmm) cc_final: 0.7933 (mttm) REVERT: C 51 GLN cc_start: 0.8373 (tm-30) cc_final: 0.8016 (tm-30) REVERT: D 88 GLN cc_start: 0.8762 (OUTLIER) cc_final: 0.6800 (mp10) REVERT: E 118 VAL cc_start: 0.8339 (t) cc_final: 0.8105 (t) REVERT: F 13 LEU cc_start: 0.8608 (mp) cc_final: 0.8315 (mm) REVERT: F 104 ARG cc_start: 0.6627 (mtm-85) cc_final: 0.6212 (mmp80) REVERT: F 169 GLN cc_start: 0.8786 (mt0) cc_final: 0.8528 (mt0) REVERT: F 315 ARG cc_start: 0.8120 (OUTLIER) cc_final: 0.6435 (ptm-80) outliers start: 37 outliers final: 14 residues processed: 195 average time/residue: 1.5123 time to fit residues: 321.0339 Evaluate side-chains 185 residues out of total 1568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 165 time to evaluate : 1.736 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 ILE Chi-restraints excluded: chain A residue 73 SER Chi-restraints excluded: chain A residue 371 ASP Chi-restraints excluded: chain B residue 22 LYS Chi-restraints excluded: chain B residue 53 LEU Chi-restraints excluded: chain B residue 333 LEU Chi-restraints excluded: chain B residue 380 GLU Chi-restraints excluded: chain C residue 80 THR Chi-restraints excluded: chain C residue 109 GLU Chi-restraints excluded: chain C residue 121 VAL Chi-restraints excluded: chain C residue 148 MET Chi-restraints excluded: chain D residue 88 GLN Chi-restraints excluded: chain D residue 103 VAL Chi-restraints excluded: chain D residue 133 ASP Chi-restraints excluded: chain F residue 21 VAL Chi-restraints excluded: chain F residue 79 CYS Chi-restraints excluded: chain F residue 99 SER Chi-restraints excluded: chain F residue 123 LEU Chi-restraints excluded: chain F residue 139 SER Chi-restraints excluded: chain F residue 315 ARG Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 189 random chunks: chunk 169 optimal weight: 6.9990 chunk 129 optimal weight: 2.9990 chunk 89 optimal weight: 1.9990 chunk 19 optimal weight: 0.6980 chunk 82 optimal weight: 2.9990 chunk 115 optimal weight: 0.7980 chunk 172 optimal weight: 3.9990 chunk 182 optimal weight: 4.9990 chunk 90 optimal weight: 2.9990 chunk 163 optimal weight: 10.0000 chunk 49 optimal weight: 3.9990 overall best weight: 1.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 37 GLN ** F 97 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 356 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8522 moved from start: 0.1588 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 15499 Z= 0.269 Angle : 0.580 8.772 20991 Z= 0.299 Chirality : 0.044 0.192 2356 Planarity : 0.004 0.038 2618 Dihedral : 12.928 176.526 2421 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 4.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 2.04 % Allowed : 12.71 % Favored : 85.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.36 (0.19), residues: 1912 helix: 0.73 (0.18), residues: 880 sheet: -0.32 (0.40), residues: 157 loop : -1.21 (0.19), residues: 875 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP B 103 HIS 0.008 0.001 HIS F 97 PHE 0.015 0.001 PHE F 318 TYR 0.021 0.001 TYR D 141 ARG 0.005 0.000 ARG F 80 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3824 Ramachandran restraints generated. 1912 Oldfield, 0 Emsley, 1912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3824 Ramachandran restraints generated. 1912 Oldfield, 0 Emsley, 1912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 201 residues out of total 1568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 169 time to evaluate : 1.780 Fit side-chains REVERT: A 4 ILE cc_start: 0.8603 (OUTLIER) cc_final: 0.8038 (mp) REVERT: A 271 LYS cc_start: 0.8084 (mmtp) cc_final: 0.7689 (mptt) REVERT: A 396 ASP cc_start: 0.7163 (m-30) cc_final: 0.6925 (m-30) REVERT: B 19 LYS cc_start: 0.6877 (mttt) cc_final: 0.6445 (mmpt) REVERT: B 22 LYS cc_start: 0.8160 (OUTLIER) cc_final: 0.7699 (mttp) REVERT: B 53 LEU cc_start: 0.8771 (OUTLIER) cc_final: 0.8299 (tp) REVERT: B 380 GLU cc_start: 0.9045 (OUTLIER) cc_final: 0.8832 (tp30) REVERT: B 406 LYS cc_start: 0.8182 (mtmm) cc_final: 0.7878 (mttm) REVERT: C 51 GLN cc_start: 0.8402 (tm-30) cc_final: 0.8004 (tm-30) REVERT: D 88 GLN cc_start: 0.8720 (OUTLIER) cc_final: 0.6752 (mp10) REVERT: F 13 LEU cc_start: 0.8588 (mp) cc_final: 0.8321 (mm) REVERT: F 104 ARG cc_start: 0.6626 (mtm-85) cc_final: 0.6207 (mmp80) REVERT: F 116 LYS cc_start: 0.7977 (mtpt) cc_final: 0.7665 (mttm) REVERT: F 169 GLN cc_start: 0.8727 (mt0) cc_final: 0.8448 (mt0) REVERT: F 315 ARG cc_start: 0.8088 (OUTLIER) cc_final: 0.6395 (ptm-80) outliers start: 32 outliers final: 7 residues processed: 191 average time/residue: 1.4835 time to fit residues: 309.7608 Evaluate side-chains 174 residues out of total 1568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 161 time to evaluate : 1.613 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 ILE Chi-restraints excluded: chain A residue 73 SER Chi-restraints excluded: chain A residue 371 ASP Chi-restraints excluded: chain B residue 22 LYS Chi-restraints excluded: chain B residue 53 LEU Chi-restraints excluded: chain B residue 333 LEU Chi-restraints excluded: chain B residue 380 GLU Chi-restraints excluded: chain C residue 95 LYS Chi-restraints excluded: chain C residue 121 VAL Chi-restraints excluded: chain D residue 88 GLN Chi-restraints excluded: chain D residue 103 VAL Chi-restraints excluded: chain D residue 133 ASP Chi-restraints excluded: chain F residue 315 ARG Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 189 random chunks: chunk 152 optimal weight: 6.9990 chunk 103 optimal weight: 5.9990 chunk 2 optimal weight: 0.0980 chunk 136 optimal weight: 3.9990 chunk 75 optimal weight: 2.9990 chunk 155 optimal weight: 10.0000 chunk 126 optimal weight: 5.9990 chunk 0 optimal weight: 6.9990 chunk 93 optimal weight: 8.9990 chunk 163 optimal weight: 9.9990 chunk 46 optimal weight: 10.0000 overall best weight: 3.8188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 37 GLN D 24 GLN ** F 97 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8570 moved from start: 0.1717 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.056 15499 Z= 0.505 Angle : 0.704 9.160 20991 Z= 0.358 Chirality : 0.049 0.262 2356 Planarity : 0.005 0.040 2618 Dihedral : 13.024 177.092 2421 Min Nonbonded Distance : 2.399 Molprobity Statistics. All-atom Clashscore : 4.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Rotamer: Outliers : 2.17 % Allowed : 13.28 % Favored : 84.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.53 (0.18), residues: 1912 helix: 0.54 (0.18), residues: 876 sheet: -0.28 (0.40), residues: 157 loop : -1.26 (0.19), residues: 879 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP B 103 HIS 0.008 0.002 HIS F 97 PHE 0.024 0.002 PHE F 318 TYR 0.025 0.002 TYR D 141 ARG 0.007 0.001 ARG B 408 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3824 Ramachandran restraints generated. 1912 Oldfield, 0 Emsley, 1912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3824 Ramachandran restraints generated. 1912 Oldfield, 0 Emsley, 1912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 201 residues out of total 1568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 167 time to evaluate : 1.684 Fit side-chains REVERT: A 4 ILE cc_start: 0.8644 (OUTLIER) cc_final: 0.8045 (mp) REVERT: A 97 ASP cc_start: 0.8351 (p0) cc_final: 0.7950 (p0) REVERT: A 271 LYS cc_start: 0.8181 (mmtp) cc_final: 0.7770 (mptt) REVERT: A 332 LYS cc_start: 0.8582 (mtpt) cc_final: 0.8189 (mttm) REVERT: A 384 MET cc_start: 0.8715 (OUTLIER) cc_final: 0.7646 (tmm) REVERT: A 396 ASP cc_start: 0.7242 (m-30) cc_final: 0.6941 (m-30) REVERT: B 19 LYS cc_start: 0.6947 (mttt) cc_final: 0.6469 (mmpt) REVERT: B 53 LEU cc_start: 0.8793 (OUTLIER) cc_final: 0.8295 (tp) REVERT: B 406 LYS cc_start: 0.8259 (mtmm) cc_final: 0.7957 (mttm) REVERT: C 51 GLN cc_start: 0.8450 (tm-30) cc_final: 0.8011 (tm-30) REVERT: F 13 LEU cc_start: 0.8562 (mp) cc_final: 0.8288 (mm) REVERT: F 104 ARG cc_start: 0.6570 (mtm-85) cc_final: 0.6189 (mmp80) REVERT: F 116 LYS cc_start: 0.8035 (mtpt) cc_final: 0.7745 (mttm) REVERT: F 169 GLN cc_start: 0.8806 (mt0) cc_final: 0.8579 (mt0) REVERT: F 315 ARG cc_start: 0.8060 (OUTLIER) cc_final: 0.6264 (ptm-80) outliers start: 34 outliers final: 14 residues processed: 189 average time/residue: 1.5089 time to fit residues: 312.2050 Evaluate side-chains 180 residues out of total 1568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 162 time to evaluate : 1.803 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 ILE Chi-restraints excluded: chain A residue 73 SER Chi-restraints excluded: chain A residue 371 ASP Chi-restraints excluded: chain A residue 384 MET Chi-restraints excluded: chain B residue 53 LEU Chi-restraints excluded: chain B residue 333 LEU Chi-restraints excluded: chain B residue 366 VAL Chi-restraints excluded: chain C residue 80 THR Chi-restraints excluded: chain C residue 109 GLU Chi-restraints excluded: chain C residue 121 VAL Chi-restraints excluded: chain D residue 103 VAL Chi-restraints excluded: chain D residue 133 ASP Chi-restraints excluded: chain F residue 21 VAL Chi-restraints excluded: chain F residue 99 SER Chi-restraints excluded: chain F residue 135 CYS Chi-restraints excluded: chain F residue 139 SER Chi-restraints excluded: chain F residue 170 ILE Chi-restraints excluded: chain F residue 315 ARG Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 189 random chunks: chunk 61 optimal weight: 0.0070 chunk 164 optimal weight: 2.9990 chunk 36 optimal weight: 0.6980 chunk 107 optimal weight: 0.9990 chunk 45 optimal weight: 4.9990 chunk 182 optimal weight: 0.9980 chunk 151 optimal weight: 8.9990 chunk 84 optimal weight: 2.9990 chunk 15 optimal weight: 1.9990 chunk 60 optimal weight: 0.8980 chunk 96 optimal weight: 1.9990 overall best weight: 0.7200 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 215 HIS D 24 GLN D 56 ASN ** F 97 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8492 moved from start: 0.1756 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 15499 Z= 0.161 Angle : 0.526 7.023 20991 Z= 0.274 Chirality : 0.042 0.157 2356 Planarity : 0.004 0.038 2618 Dihedral : 11.877 174.943 2418 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 4.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.57 % Favored : 97.43 % Rotamer: Outliers : 1.85 % Allowed : 14.43 % Favored : 83.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.01 (0.19), residues: 1912 helix: 1.06 (0.18), residues: 878 sheet: -0.27 (0.40), residues: 155 loop : -1.05 (0.20), residues: 879 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP B 103 HIS 0.006 0.001 HIS F 97 PHE 0.013 0.001 PHE D 50 TYR 0.018 0.001 TYR D 141 ARG 0.003 0.000 ARG A 349 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3824 Ramachandran restraints generated. 1912 Oldfield, 0 Emsley, 1912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3824 Ramachandran restraints generated. 1912 Oldfield, 0 Emsley, 1912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 1568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 173 time to evaluate : 1.810 Fit side-chains REVERT: A 4 ILE cc_start: 0.8580 (OUTLIER) cc_final: 0.7986 (mp) REVERT: A 271 LYS cc_start: 0.8015 (mmtp) cc_final: 0.7666 (mtpt) REVERT: A 396 ASP cc_start: 0.7168 (m-30) cc_final: 0.6882 (m-30) REVERT: B 19 LYS cc_start: 0.6833 (mttt) cc_final: 0.6341 (mmpt) REVERT: B 22 LYS cc_start: 0.7806 (OUTLIER) cc_final: 0.7338 (mmtp) REVERT: B 406 LYS cc_start: 0.8129 (mtmm) cc_final: 0.7835 (mttm) REVERT: B 412 TYR cc_start: 0.7587 (m-80) cc_final: 0.7068 (m-80) REVERT: C 51 GLN cc_start: 0.8411 (tm-30) cc_final: 0.8003 (tm-30) REVERT: D 88 GLN cc_start: 0.8736 (OUTLIER) cc_final: 0.6760 (mp10) REVERT: F 13 LEU cc_start: 0.8550 (mp) cc_final: 0.8279 (mm) REVERT: F 104 ARG cc_start: 0.6475 (mtm-85) cc_final: 0.6103 (mmp80) REVERT: F 116 LYS cc_start: 0.8016 (mtpt) cc_final: 0.7518 (mttp) REVERT: F 169 GLN cc_start: 0.8757 (mt0) cc_final: 0.8539 (mt0) REVERT: F 315 ARG cc_start: 0.8018 (OUTLIER) cc_final: 0.6296 (ptm-80) REVERT: F 382 MET cc_start: 0.6161 (ptm) cc_final: 0.5357 (tpt) outliers start: 29 outliers final: 5 residues processed: 196 average time/residue: 1.4563 time to fit residues: 312.3151 Evaluate side-chains 171 residues out of total 1568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 162 time to evaluate : 2.041 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 ILE Chi-restraints excluded: chain A residue 73 SER Chi-restraints excluded: chain B residue 22 LYS Chi-restraints excluded: chain C residue 101 SER Chi-restraints excluded: chain C residue 121 VAL Chi-restraints excluded: chain D residue 26 LEU Chi-restraints excluded: chain D residue 88 GLN Chi-restraints excluded: chain F residue 135 CYS Chi-restraints excluded: chain F residue 315 ARG Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 189 random chunks: chunk 176 optimal weight: 4.9990 chunk 20 optimal weight: 0.0870 chunk 104 optimal weight: 0.9990 chunk 133 optimal weight: 6.9990 chunk 103 optimal weight: 6.9990 chunk 153 optimal weight: 5.9990 chunk 102 optimal weight: 4.9990 chunk 182 optimal weight: 7.9990 chunk 114 optimal weight: 7.9990 chunk 111 optimal weight: 0.0970 chunk 84 optimal weight: 3.9990 overall best weight: 2.0362 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 37 GLN ** F 97 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8529 moved from start: 0.1812 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 15499 Z= 0.293 Angle : 0.582 6.567 20991 Z= 0.300 Chirality : 0.044 0.176 2356 Planarity : 0.004 0.039 2618 Dihedral : 11.746 175.271 2418 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 4.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer: Outliers : 1.79 % Allowed : 15.07 % Favored : 83.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.07 (0.19), residues: 1912 helix: 0.96 (0.18), residues: 883 sheet: -0.29 (0.41), residues: 155 loop : -1.02 (0.20), residues: 874 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP B 103 HIS 0.007 0.001 HIS F 97 PHE 0.017 0.002 PHE B 213 TYR 0.022 0.001 TYR D 141 ARG 0.005 0.000 ARG B 408 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3824 Ramachandran restraints generated. 1912 Oldfield, 0 Emsley, 1912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3824 Ramachandran restraints generated. 1912 Oldfield, 0 Emsley, 1912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 1568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 162 time to evaluate : 1.796 Fit side-chains REVERT: A 4 ILE cc_start: 0.8601 (OUTLIER) cc_final: 0.8006 (mp) REVERT: A 97 ASP cc_start: 0.8278 (p0) cc_final: 0.7896 (p0) REVERT: A 162 GLU cc_start: 0.7887 (OUTLIER) cc_final: 0.7167 (tm-30) REVERT: A 271 LYS cc_start: 0.8094 (mmtp) cc_final: 0.7692 (mptt) REVERT: A 384 MET cc_start: 0.8766 (OUTLIER) cc_final: 0.7563 (tmm) REVERT: A 396 ASP cc_start: 0.7186 (m-30) cc_final: 0.6933 (m-30) REVERT: B 19 LYS cc_start: 0.6870 (mttt) cc_final: 0.6376 (mmpt) REVERT: B 406 LYS cc_start: 0.8172 (mtmm) cc_final: 0.7882 (mttm) REVERT: B 412 TYR cc_start: 0.7659 (m-80) cc_final: 0.7181 (m-80) REVERT: C 51 GLN cc_start: 0.8436 (tm-30) cc_final: 0.8001 (tm-30) REVERT: D 88 GLN cc_start: 0.8731 (OUTLIER) cc_final: 0.6737 (mp10) REVERT: F 13 LEU cc_start: 0.8568 (mp) cc_final: 0.8302 (mm) REVERT: F 104 ARG cc_start: 0.6498 (mtm-85) cc_final: 0.6112 (mmp80) REVERT: F 116 LYS cc_start: 0.8067 (mtpt) cc_final: 0.7557 (mttp) REVERT: F 315 ARG cc_start: 0.7997 (OUTLIER) cc_final: 0.6234 (ptm-80) REVERT: F 382 MET cc_start: 0.6074 (ptm) cc_final: 0.5230 (tpt) outliers start: 28 outliers final: 13 residues processed: 183 average time/residue: 1.4634 time to fit residues: 292.9216 Evaluate side-chains 178 residues out of total 1568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 160 time to evaluate : 1.689 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 ILE Chi-restraints excluded: chain A residue 73 SER Chi-restraints excluded: chain A residue 162 GLU Chi-restraints excluded: chain A residue 371 ASP Chi-restraints excluded: chain A residue 384 MET Chi-restraints excluded: chain B residue 333 LEU Chi-restraints excluded: chain C residue 101 SER Chi-restraints excluded: chain C residue 106 LEU Chi-restraints excluded: chain C residue 109 GLU Chi-restraints excluded: chain C residue 121 VAL Chi-restraints excluded: chain D residue 88 GLN Chi-restraints excluded: chain D residue 103 VAL Chi-restraints excluded: chain D residue 133 ASP Chi-restraints excluded: chain E residue 111 ILE Chi-restraints excluded: chain F residue 99 SER Chi-restraints excluded: chain F residue 135 CYS Chi-restraints excluded: chain F residue 197 LEU Chi-restraints excluded: chain F residue 315 ARG Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 189 random chunks: chunk 112 optimal weight: 3.9990 chunk 72 optimal weight: 3.9990 chunk 108 optimal weight: 2.9990 chunk 54 optimal weight: 4.9990 chunk 35 optimal weight: 1.9990 chunk 115 optimal weight: 0.6980 chunk 124 optimal weight: 5.9990 chunk 90 optimal weight: 0.6980 chunk 16 optimal weight: 0.9990 chunk 143 optimal weight: 3.9990 chunk 165 optimal weight: 0.0870 overall best weight: 0.8962 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 97 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8482 moved from start: 0.1921 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 15499 Z= 0.165 Angle : 0.512 6.816 20991 Z= 0.268 Chirality : 0.041 0.159 2356 Planarity : 0.004 0.040 2618 Dihedral : 11.121 174.331 2418 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 4.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 1.40 % Allowed : 15.84 % Favored : 82.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.23 (0.19), residues: 1912 helix: 1.29 (0.18), residues: 873 sheet: -0.23 (0.41), residues: 156 loop : -0.92 (0.20), residues: 883 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP B 103 HIS 0.005 0.001 HIS F 97 PHE 0.012 0.001 PHE D 50 TYR 0.017 0.001 TYR D 141 ARG 0.003 0.000 ARG A 349 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3824 Ramachandran restraints generated. 1912 Oldfield, 0 Emsley, 1912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3824 Ramachandran restraints generated. 1912 Oldfield, 0 Emsley, 1912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 1568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 165 time to evaluate : 1.769 Fit side-chains REVERT: A 4 ILE cc_start: 0.8573 (OUTLIER) cc_final: 0.8002 (mp) REVERT: A 271 LYS cc_start: 0.8004 (mmtp) cc_final: 0.7656 (mtpt) REVERT: A 396 ASP cc_start: 0.7171 (m-30) cc_final: 0.6877 (m-30) REVERT: B 19 LYS cc_start: 0.6820 (mttt) cc_final: 0.6346 (mmpt) REVERT: B 22 LYS cc_start: 0.7528 (OUTLIER) cc_final: 0.7163 (mmtp) REVERT: B 53 LEU cc_start: 0.8607 (OUTLIER) cc_final: 0.8254 (tp) REVERT: B 406 LYS cc_start: 0.8106 (mtmm) cc_final: 0.7798 (mttm) REVERT: B 412 TYR cc_start: 0.7594 (m-80) cc_final: 0.7088 (m-80) REVERT: C 51 GLN cc_start: 0.8424 (tm-30) cc_final: 0.8003 (tm-30) REVERT: F 13 LEU cc_start: 0.8553 (mp) cc_final: 0.8294 (mm) REVERT: F 104 ARG cc_start: 0.6476 (mtm-85) cc_final: 0.6082 (mmp80) REVERT: F 315 ARG cc_start: 0.7996 (OUTLIER) cc_final: 0.6250 (ptm-80) REVERT: F 382 MET cc_start: 0.6064 (ptm) cc_final: 0.5294 (tpt) outliers start: 22 outliers final: 9 residues processed: 183 average time/residue: 1.4832 time to fit residues: 297.3629 Evaluate side-chains 170 residues out of total 1568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 157 time to evaluate : 1.650 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 ILE Chi-restraints excluded: chain A residue 73 SER Chi-restraints excluded: chain A residue 124 GLU Chi-restraints excluded: chain A residue 371 ASP Chi-restraints excluded: chain B residue 22 LYS Chi-restraints excluded: chain B residue 53 LEU Chi-restraints excluded: chain B residue 366 VAL Chi-restraints excluded: chain C residue 101 SER Chi-restraints excluded: chain C residue 121 VAL Chi-restraints excluded: chain D residue 103 VAL Chi-restraints excluded: chain F residue 79 CYS Chi-restraints excluded: chain F residue 135 CYS Chi-restraints excluded: chain F residue 315 ARG Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 189 random chunks: chunk 174 optimal weight: 9.9990 chunk 159 optimal weight: 10.0000 chunk 169 optimal weight: 5.9990 chunk 102 optimal weight: 4.9990 chunk 73 optimal weight: 0.9990 chunk 133 optimal weight: 5.9990 chunk 52 optimal weight: 5.9990 chunk 153 optimal weight: 20.0000 chunk 160 optimal weight: 5.9990 chunk 111 optimal weight: 2.9990 chunk 179 optimal weight: 5.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 215 HIS ** F 97 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8574 moved from start: 0.1948 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.061 15499 Z= 0.549 Angle : 0.723 8.581 20991 Z= 0.368 Chirality : 0.051 0.187 2356 Planarity : 0.005 0.040 2618 Dihedral : 11.744 176.703 2418 Min Nonbonded Distance : 2.389 Molprobity Statistics. All-atom Clashscore : 4.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.61 % Favored : 96.39 % Rotamer: Outliers : 1.98 % Allowed : 15.84 % Favored : 82.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.31 (0.19), residues: 1912 helix: 0.71 (0.17), residues: 877 sheet: -0.48 (0.40), residues: 169 loop : -1.07 (0.20), residues: 866 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP B 103 HIS 0.008 0.002 HIS B 330 PHE 0.026 0.003 PHE F 318 TYR 0.026 0.002 TYR F 217 ARG 0.008 0.001 ARG B 408 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3824 Ramachandran restraints generated. 1912 Oldfield, 0 Emsley, 1912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3824 Ramachandran restraints generated. 1912 Oldfield, 0 Emsley, 1912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 1568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 162 time to evaluate : 1.711 Fit side-chains REVERT: A 4 ILE cc_start: 0.8667 (OUTLIER) cc_final: 0.8065 (mp) REVERT: A 97 ASP cc_start: 0.8332 (p0) cc_final: 0.7922 (p0) REVERT: A 162 GLU cc_start: 0.7874 (OUTLIER) cc_final: 0.7185 (tm-30) REVERT: A 271 LYS cc_start: 0.8214 (mmtp) cc_final: 0.7793 (mptt) REVERT: A 396 ASP cc_start: 0.7220 (m-30) cc_final: 0.6948 (m-30) REVERT: B 406 LYS cc_start: 0.8254 (mtmm) cc_final: 0.7954 (mttm) REVERT: C 51 GLN cc_start: 0.8474 (tm-30) cc_final: 0.8018 (tm-30) REVERT: F 13 LEU cc_start: 0.8565 (mp) cc_final: 0.8298 (mm) REVERT: F 38 SER cc_start: 0.7491 (OUTLIER) cc_final: 0.6729 (t) REVERT: F 104 ARG cc_start: 0.6489 (mtm-85) cc_final: 0.6067 (mmp80) REVERT: F 116 LYS cc_start: 0.8115 (mtpt) cc_final: 0.7590 (mttp) REVERT: F 315 ARG cc_start: 0.8049 (OUTLIER) cc_final: 0.6261 (ptm-80) REVERT: F 382 MET cc_start: 0.6144 (ptm) cc_final: 0.5378 (tpt) outliers start: 31 outliers final: 11 residues processed: 184 average time/residue: 1.4222 time to fit residues: 286.9759 Evaluate side-chains 176 residues out of total 1568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 161 time to evaluate : 1.640 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 ILE Chi-restraints excluded: chain A residue 73 SER Chi-restraints excluded: chain A residue 162 GLU Chi-restraints excluded: chain A residue 371 ASP Chi-restraints excluded: chain B residue 366 VAL Chi-restraints excluded: chain C residue 101 SER Chi-restraints excluded: chain C residue 109 GLU Chi-restraints excluded: chain C residue 121 VAL Chi-restraints excluded: chain D residue 103 VAL Chi-restraints excluded: chain D residue 133 ASP Chi-restraints excluded: chain F residue 21 VAL Chi-restraints excluded: chain F residue 38 SER Chi-restraints excluded: chain F residue 48 VAL Chi-restraints excluded: chain F residue 79 CYS Chi-restraints excluded: chain F residue 315 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 189 random chunks: chunk 109 optimal weight: 0.9990 chunk 85 optimal weight: 6.9990 chunk 124 optimal weight: 2.9990 chunk 188 optimal weight: 0.9980 chunk 173 optimal weight: 3.9990 chunk 149 optimal weight: 2.9990 chunk 15 optimal weight: 0.7980 chunk 115 optimal weight: 0.7980 chunk 91 optimal weight: 0.9980 chunk 119 optimal weight: 1.9990 chunk 159 optimal weight: 9.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 215 HIS ** F 97 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8493 moved from start: 0.1954 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 15499 Z= 0.174 Angle : 0.533 9.979 20991 Z= 0.278 Chirality : 0.042 0.162 2356 Planarity : 0.004 0.042 2618 Dihedral : 11.001 174.021 2418 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 4.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Rotamer: Outliers : 0.96 % Allowed : 17.11 % Favored : 81.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.12 (0.19), residues: 1912 helix: 1.16 (0.18), residues: 877 sheet: -0.23 (0.41), residues: 156 loop : -0.97 (0.20), residues: 879 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP B 103 HIS 0.006 0.001 HIS F 97 PHE 0.013 0.001 PHE D 50 TYR 0.017 0.001 TYR D 141 ARG 0.002 0.000 ARG F 303 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3824 Ramachandran restraints generated. 1912 Oldfield, 0 Emsley, 1912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3824 Ramachandran restraints generated. 1912 Oldfield, 0 Emsley, 1912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 1568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 157 time to evaluate : 1.781 Fit side-chains REVERT: A 4 ILE cc_start: 0.8591 (OUTLIER) cc_final: 0.7990 (mp) REVERT: A 271 LYS cc_start: 0.8015 (mmtp) cc_final: 0.7664 (mtpt) REVERT: A 396 ASP cc_start: 0.7175 (m-30) cc_final: 0.6901 (m-30) REVERT: B 19 LYS cc_start: 0.6796 (mtpp) cc_final: 0.6179 (mmpt) REVERT: B 406 LYS cc_start: 0.8148 (mtmm) cc_final: 0.7852 (mttm) REVERT: B 412 TYR cc_start: 0.7625 (m-80) cc_final: 0.7104 (m-80) REVERT: C 51 GLN cc_start: 0.8428 (tm-30) cc_final: 0.7998 (tm-30) REVERT: F 13 LEU cc_start: 0.8545 (mp) cc_final: 0.8288 (mm) REVERT: F 104 ARG cc_start: 0.6447 (mtm-85) cc_final: 0.6039 (mmp80) REVERT: F 116 LYS cc_start: 0.8017 (mtpt) cc_final: 0.7534 (mttp) REVERT: F 315 ARG cc_start: 0.7958 (OUTLIER) cc_final: 0.6187 (ptm-80) REVERT: F 382 MET cc_start: 0.6041 (ptm) cc_final: 0.5285 (tpt) outliers start: 15 outliers final: 6 residues processed: 169 average time/residue: 1.5520 time to fit residues: 286.9697 Evaluate side-chains 165 residues out of total 1568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 157 time to evaluate : 1.828 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 ILE Chi-restraints excluded: chain A residue 73 SER Chi-restraints excluded: chain A residue 371 ASP Chi-restraints excluded: chain B residue 366 VAL Chi-restraints excluded: chain C residue 101 SER Chi-restraints excluded: chain D residue 103 VAL Chi-restraints excluded: chain F residue 79 CYS Chi-restraints excluded: chain F residue 315 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 189 random chunks: chunk 45 optimal weight: 0.0270 chunk 138 optimal weight: 6.9990 chunk 22 optimal weight: 0.6980 chunk 41 optimal weight: 0.8980 chunk 150 optimal weight: 1.9990 chunk 62 optimal weight: 5.9990 chunk 154 optimal weight: 0.6980 chunk 19 optimal weight: 3.9990 chunk 27 optimal weight: 4.9990 chunk 131 optimal weight: 2.9990 chunk 8 optimal weight: 0.9980 overall best weight: 0.6638 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 97 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3523 r_free = 0.3523 target = 0.136604 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3092 r_free = 0.3092 target = 0.100263 restraints weight = 32438.049| |-----------------------------------------------------------------------------| r_work (start): 0.3004 rms_B_bonded: 2.19 r_work: 0.2895 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.2776 rms_B_bonded: 4.14 restraints_weight: 0.2500 r_work (final): 0.2776 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2778 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2778 r_free = 0.2778 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2778 r_free = 0.2778 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2778 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8314 moved from start: 0.2108 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 15499 Z= 0.154 Angle : 0.509 9.742 20991 Z= 0.265 Chirality : 0.041 0.150 2356 Planarity : 0.004 0.041 2618 Dihedral : 10.513 174.178 2418 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 4.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % Rotamer: Outliers : 0.77 % Allowed : 17.56 % Favored : 81.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.39 (0.19), residues: 1912 helix: 1.45 (0.18), residues: 871 sheet: -0.22 (0.41), residues: 156 loop : -0.84 (0.20), residues: 885 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP B 103 HIS 0.006 0.001 HIS F 97 PHE 0.010 0.001 PHE E 28 TYR 0.016 0.001 TYR D 141 ARG 0.003 0.000 ARG F 303 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5495.47 seconds wall clock time: 99 minutes 45.79 seconds (5985.79 seconds total)