Starting phenix.real_space_refine on Wed Mar 4 19:45:47 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7xk7_33246/03_2026/7xk7_33246.cif Found real_map, /net/cci-nas-00/data/ceres_data/7xk7_33246/03_2026/7xk7_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_33246/03_2026/7xk7_33246.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7xk7_33246/03_2026/7xk7_33246.map" model { file = "/net/cci-nas-00/data/ceres_data/7xk7_33246/03_2026/7xk7_33246.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7xk7_33246/03_2026/7xk7_33246.cif" } resolution = 2.9 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/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 Unresolved non-hydrogen dihedrals: 1 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 Unresolved non-hydrogen dihedrals: 1 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: 3.55, per 1000 atoms: 0.23 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: 1.25 Conformation dependent library (CDL) restraints added in 718.2 milliseconds 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: 0.48 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: 2.37 Time building geometry restraints manager: 1.59 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: 20828 4.79 - 9.58: 141 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 - 29.21: 8845 29.21 - 58.41: 338 58.41 - 87.62: 29 87.62 - 116.82: 34 116.82 - 146.03: 17 Dihedral angle restraints: 9263 sinusoidal: 3822 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=" C ASP F 34 " pdb=" N ASP F 34 " pdb=" CA ASP F 34 " pdb=" CB ASP F 34 " ideal model delta harmonic sigma weight residual -122.60 -138.96 16.36 0 2.50e+00 1.60e-01 4.28e+01 dihedral pdb=" N ASP F 34 " pdb=" C ASP F 34 " pdb=" CA ASP F 34 " pdb=" CB ASP F 34 " ideal model delta harmonic sigma weight residual 122.80 138.49 -15.69 0 2.50e+00 1.60e-01 3.94e+01 ... (remaining 9260 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: 2620 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 " -0.062 2.00e-02 2.50e+03 2.74e-02 3.39e+01 pdb=" C10 FMN C 301 " -0.007 2.00e-02 2.50e+03 pdb=" C2 FMN C 301 " 0.020 2.00e-02 2.50e+03 pdb=" C4 FMN C 301 " -0.019 2.00e-02 2.50e+03 pdb=" C4A FMN C 301 " -0.022 2.00e-02 2.50e+03 pdb=" C5A FMN C 301 " -0.019 2.00e-02 2.50e+03 pdb=" C6 FMN C 301 " -0.020 2.00e-02 2.50e+03 pdb=" C7 FMN C 301 " 0.019 2.00e-02 2.50e+03 pdb=" C7M FMN C 301 " 0.028 2.00e-02 2.50e+03 pdb=" C8 FMN C 301 " 0.028 2.00e-02 2.50e+03 pdb=" C8M FMN C 301 " 0.022 2.00e-02 2.50e+03 pdb=" C9 FMN C 301 " -0.008 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 " 0.004 2.00e-02 2.50e+03 pdb=" N3 FMN C 301 " 0.004 2.00e-02 2.50e+03 pdb=" N5 FMN C 301 " -0.027 2.00e-02 2.50e+03 pdb=" O2 FMN C 301 " 0.064 2.00e-02 2.50e+03 ... (remaining 2617 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: 2.030 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: 0.260 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 15.110 Find NCS groups from input model: 0.090 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.810 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.400 ------------------------------------------------------------------------------- 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 : 0.015 0.753 15507 Z= 0.553 Angle : 1.140 38.421 21000 Z= 0.605 Chirality : 0.059 0.744 2356 Planarity : 0.007 0.196 2620 Dihedral : 17.940 146.028 5793 Min Nonbonded Distance : 1.978 Molprobity Statistics. All-atom Clashscore : 4.96 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. 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 ARG 0.004 0.000 ARG F 189 TYR 0.020 0.001 TYR D 141 PHE 0.024 0.002 PHE B 213 TRP 0.024 0.002 TRP F 250 HIS 0.005 0.001 HIS F 291 Details of bonding type rmsd covalent geometry : bond 0.00768 (15499) covalent geometry : angle 1.04185 (20991) hydrogen bonds : bond 0.18496 ( 703) hydrogen bonds : angle 6.84736 ( 2016) metal coordination : bond 0.67104 ( 6) metal coordination : angle 22.34970 ( 9) Misc. bond : bond 0.04403 ( 2) *********************** 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 : 0.558 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: 0.6714 time to fit residues: 178.2915 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 : 0.597 ------------------------------------------------------------------------------- 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 98 optimal weight: 3.9990 chunk 107 optimal weight: 1.9990 chunk 10 optimal weight: 0.3980 chunk 66 optimal weight: 0.9980 chunk 130 optimal weight: 8.9990 chunk 124 optimal weight: 5.9990 chunk 103 optimal weight: 7.9990 chunk 77 optimal weight: 0.6980 chunk 122 optimal weight: 0.9990 chunk 91 optimal weight: 4.9990 chunk 149 optimal weight: 0.6980 overall best weight: 0.7582 ------------------------------------------------------------------------------- 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 A 215 HIS 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 56 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 Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3554 r_free = 0.3554 target = 0.136549 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3148 r_free = 0.3148 target = 0.102059 restraints weight = 33966.561| |-----------------------------------------------------------------------------| r_work (start): 0.3093 rms_B_bonded: 2.08 r_work: 0.2976 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.2860 rms_B_bonded: 3.99 restraints_weight: 0.2500 r_work (final): 0.2860 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2864 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2864 r_free = 0.2864 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2864 r_free = 0.2864 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2864 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8538 moved from start: 0.1197 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 15507 Z= 0.119 Angle : 0.611 17.922 21000 Z= 0.300 Chirality : 0.044 0.289 2356 Planarity : 0.004 0.037 2620 Dihedral : 15.840 130.880 2432 Min Nonbonded Distance : 2.400 Molprobity Statistics. All-atom Clashscore : 4.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % Rotamer: Outliers : 1.40 % Allowed : 9.64 % Favored : 88.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.02 (0.18), residues: 1912 helix: 0.12 (0.17), residues: 873 sheet: -0.69 (0.38), residues: 153 loop : -1.46 (0.19), residues: 886 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 349 TYR 0.021 0.001 TYR D 141 PHE 0.015 0.001 PHE F 318 TRP 0.023 0.001 TRP B 103 HIS 0.008 0.001 HIS F 291 Details of bonding type rmsd covalent geometry : bond 0.00256 (15499) covalent geometry : angle 0.59247 (20991) hydrogen bonds : bond 0.04544 ( 703) hydrogen bonds : angle 4.87873 ( 2016) metal coordination : bond 0.02104 ( 6) metal coordination : angle 7.24701 ( 9) Misc. bond : bond 0.00060 ( 2) *********************** 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 202 residues out of total 1568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 180 time to evaluate : 0.583 Fit side-chains REVERT: A 4 ILE cc_start: 0.8654 (OUTLIER) cc_final: 0.8111 (mp) REVERT: A 97 ASP cc_start: 0.8592 (p0) cc_final: 0.8263 (p0) REVERT: A 271 LYS cc_start: 0.8324 (mmtp) cc_final: 0.7710 (mtpt) REVERT: B 21 GLU cc_start: 0.6781 (tt0) cc_final: 0.6400 (tt0) REVERT: B 22 LYS cc_start: 0.8066 (OUTLIER) cc_final: 0.7304 (mttt) REVERT: B 243 GLN cc_start: 0.8952 (mt0) cc_final: 0.8675 (mt0) REVERT: B 380 GLU cc_start: 0.9075 (OUTLIER) cc_final: 0.7397 (tm-30) REVERT: B 406 LYS cc_start: 0.8160 (mtmm) cc_final: 0.7681 (mttm) REVERT: B 412 TYR cc_start: 0.8088 (m-80) cc_final: 0.7649 (m-80) REVERT: C 51 GLN cc_start: 0.8323 (tm-30) cc_final: 0.8060 (tm-30) REVERT: F 80 ARG cc_start: 0.8413 (ptp-110) cc_final: 0.8103 (mtp180) REVERT: F 104 ARG cc_start: 0.6424 (mtm-85) cc_final: 0.5927 (mmp80) REVERT: F 169 GLN cc_start: 0.8659 (mt0) cc_final: 0.8397 (mt0) REVERT: F 186 GLU cc_start: 0.7618 (pm20) cc_final: 0.7414 (pm20) REVERT: F 206 GLU cc_start: 0.7715 (pp20) cc_final: 0.7514 (pp20) REVERT: F 329 GLU cc_start: 0.7322 (mm-30) cc_final: 0.7048 (tt0) outliers start: 22 outliers final: 7 residues processed: 193 average time/residue: 0.7231 time to fit residues: 151.8574 Evaluate side-chains 171 residues out of total 1568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 161 time to evaluate : 0.562 ------------------------------------------------------------------------------- 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 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 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 68 optimal weight: 5.9990 chunk 141 optimal weight: 0.7980 chunk 48 optimal weight: 5.9990 chunk 14 optimal weight: 2.9990 chunk 74 optimal weight: 3.9990 chunk 11 optimal weight: 3.9990 chunk 151 optimal weight: 4.9990 chunk 179 optimal weight: 7.9990 chunk 69 optimal weight: 4.9990 chunk 180 optimal weight: 2.9990 chunk 174 optimal weight: 10.0000 overall best weight: 2.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 404 ASN E 16 ASN ** F 97 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 362 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.131139 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3035 r_free = 0.3035 target = 0.095424 restraints weight = 35400.001| |-----------------------------------------------------------------------------| r_work (start): 0.2979 rms_B_bonded: 2.26 r_work: 0.2861 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.2744 rms_B_bonded: 4.16 restraints_weight: 0.2500 r_work (final): 0.2744 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2719 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2719 r_free = 0.2719 target_work(ls_wunit_k1) = 0.075 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2719 r_free = 0.2719 target_work(ls_wunit_k1) = 0.075 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2719 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8509 moved from start: 0.1478 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.045 15507 Z= 0.248 Angle : 0.683 16.223 21000 Z= 0.341 Chirality : 0.047 0.278 2356 Planarity : 0.005 0.038 2620 Dihedral : 12.957 136.294 2427 Min Nonbonded Distance : 2.405 Molprobity Statistics. All-atom Clashscore : 4.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer: Outliers : 2.30 % Allowed : 11.24 % Favored : 86.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.64 (0.18), residues: 1912 helix: 0.46 (0.18), residues: 876 sheet: -0.43 (0.39), residues: 157 loop : -1.31 (0.19), residues: 879 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 408 TYR 0.025 0.002 TYR D 141 PHE 0.030 0.002 PHE B 65 TRP 0.025 0.002 TRP B 103 HIS 0.008 0.002 HIS B 330 Details of bonding type rmsd covalent geometry : bond 0.00614 (15499) covalent geometry : angle 0.66939 (20991) hydrogen bonds : bond 0.06028 ( 703) hydrogen bonds : angle 4.84503 ( 2016) metal coordination : bond 0.01045 ( 6) metal coordination : angle 6.51167 ( 9) Misc. bond : bond 0.00233 ( 2) *********************** 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 215 residues out of total 1568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 179 time to evaluate : 0.574 Fit side-chains REVERT: A 4 ILE cc_start: 0.8657 (OUTLIER) cc_final: 0.8030 (mp) REVERT: A 97 ASP cc_start: 0.8643 (p0) cc_final: 0.8330 (p0) REVERT: A 271 LYS cc_start: 0.8340 (mmtp) cc_final: 0.7782 (mptt) REVERT: A 332 LYS cc_start: 0.8446 (mtpt) cc_final: 0.7910 (mttm) REVERT: A 444 LYS cc_start: 0.7543 (ttmm) cc_final: 0.6704 (ttpt) REVERT: B 19 LYS cc_start: 0.6677 (mttt) cc_final: 0.6147 (mmpt) REVERT: B 21 GLU cc_start: 0.7101 (tt0) cc_final: 0.6379 (tt0) REVERT: B 22 LYS cc_start: 0.8123 (OUTLIER) cc_final: 0.7451 (mttp) REVERT: B 380 GLU cc_start: 0.9271 (OUTLIER) cc_final: 0.7008 (tm-30) REVERT: B 406 LYS cc_start: 0.8066 (mtmm) cc_final: 0.7585 (mttm) REVERT: C 51 GLN cc_start: 0.8280 (tm-30) cc_final: 0.7902 (tm-30) REVERT: D 88 GLN cc_start: 0.8513 (OUTLIER) cc_final: 0.6605 (mp10) REVERT: D 99 LYS cc_start: 0.8356 (tptm) cc_final: 0.7920 (ttmm) REVERT: F 80 ARG cc_start: 0.8349 (ptp-110) cc_final: 0.7970 (mtp180) REVERT: F 104 ARG cc_start: 0.6421 (mtm-85) cc_final: 0.5909 (mmp80) REVERT: F 169 GLN cc_start: 0.8578 (mt0) cc_final: 0.8324 (mt0) REVERT: F 206 GLU cc_start: 0.7641 (pp20) cc_final: 0.7401 (pp20) REVERT: F 315 ARG cc_start: 0.7846 (OUTLIER) cc_final: 0.6189 (ptm-80) REVERT: F 329 GLU cc_start: 0.7315 (mm-30) cc_final: 0.7021 (tt0) outliers start: 36 outliers final: 10 residues processed: 201 average time/residue: 0.7166 time to fit residues: 156.8642 Evaluate side-chains 185 residues out of total 1568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 170 time to evaluate : 0.506 ------------------------------------------------------------------------------- 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 330 ARG Chi-restraints excluded: chain A residue 371 ASP Chi-restraints excluded: chain B residue 22 LYS Chi-restraints excluded: chain B residue 380 GLU Chi-restraints excluded: chain C residue 101 SER 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 21 VAL Chi-restraints excluded: chain F residue 79 CYS Chi-restraints excluded: chain F residue 123 LEU 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 129 optimal weight: 2.9990 chunk 153 optimal weight: 9.9990 chunk 43 optimal weight: 1.9990 chunk 2 optimal weight: 0.9990 chunk 96 optimal weight: 0.0020 chunk 107 optimal weight: 5.9990 chunk 55 optimal weight: 7.9990 chunk 49 optimal weight: 3.9990 chunk 41 optimal weight: 1.9990 chunk 175 optimal weight: 5.9990 chunk 179 optimal weight: 6.9990 overall best weight: 1.5996 ------------------------------------------------------------------------------- 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** F 356 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3490 r_free = 0.3490 target = 0.133176 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3059 r_free = 0.3059 target = 0.097178 restraints weight = 37566.112| |-----------------------------------------------------------------------------| r_work (start): 0.2994 rms_B_bonded: 2.34 r_work: 0.2875 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.2756 rms_B_bonded: 4.31 restraints_weight: 0.2500 r_work (final): 0.2756 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2731 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2731 r_free = 0.2731 target_work(ls_wunit_k1) = 0.076 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2731 r_free = 0.2731 target_work(ls_wunit_k1) = 0.076 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2731 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8467 moved from start: 0.1565 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 15507 Z= 0.152 Angle : 0.573 14.097 21000 Z= 0.290 Chirality : 0.043 0.196 2356 Planarity : 0.004 0.037 2620 Dihedral : 11.769 132.927 2423 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 4.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Rotamer: Outliers : 2.04 % Allowed : 12.77 % Favored : 85.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.29 (0.19), residues: 1912 helix: 0.77 (0.18), residues: 884 sheet: -0.35 (0.40), residues: 155 loop : -1.13 (0.20), residues: 873 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 349 TYR 0.021 0.001 TYR D 141 PHE 0.015 0.001 PHE B 213 TRP 0.022 0.001 TRP B 103 HIS 0.007 0.001 HIS F 97 Details of bonding type rmsd covalent geometry : bond 0.00361 (15499) covalent geometry : angle 0.56135 (20991) hydrogen bonds : bond 0.04782 ( 703) hydrogen bonds : angle 4.61971 ( 2016) metal coordination : bond 0.00864 ( 6) metal coordination : angle 5.57156 ( 9) Misc. bond : bond 0.00133 ( 2) *********************** 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 202 residues out of total 1568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 170 time to evaluate : 0.690 Fit side-chains REVERT: A 4 ILE cc_start: 0.8630 (OUTLIER) cc_final: 0.8035 (mp) REVERT: A 271 LYS cc_start: 0.8248 (mmtp) cc_final: 0.7541 (mtpt) REVERT: A 384 MET cc_start: 0.8939 (OUTLIER) cc_final: 0.7746 (tmm) REVERT: B 19 LYS cc_start: 0.6639 (mttt) cc_final: 0.6122 (mmpt) REVERT: B 21 GLU cc_start: 0.7147 (tt0) cc_final: 0.6414 (tt0) REVERT: B 22 LYS cc_start: 0.8102 (OUTLIER) cc_final: 0.7491 (mttt) REVERT: B 380 GLU cc_start: 0.9214 (OUTLIER) cc_final: 0.8928 (tp30) REVERT: B 406 LYS cc_start: 0.7933 (mtmm) cc_final: 0.7499 (mttm) REVERT: B 412 TYR cc_start: 0.8153 (m-80) cc_final: 0.7714 (m-80) REVERT: C 51 GLN cc_start: 0.8299 (tm-30) cc_final: 0.7876 (tm-30) REVERT: D 88 GLN cc_start: 0.8444 (OUTLIER) cc_final: 0.6438 (mp10) REVERT: D 99 LYS cc_start: 0.8384 (tptm) cc_final: 0.7969 (ttmm) REVERT: F 13 LEU cc_start: 0.7962 (mp) cc_final: 0.7705 (mm) REVERT: F 80 ARG cc_start: 0.8352 (ptp-110) cc_final: 0.8098 (mtp-110) REVERT: F 104 ARG cc_start: 0.6402 (mtm-85) cc_final: 0.5882 (mmp80) REVERT: F 116 LYS cc_start: 0.8006 (mtpt) cc_final: 0.7691 (mttm) REVERT: F 169 GLN cc_start: 0.8503 (mt0) cc_final: 0.8195 (mt0) REVERT: F 206 GLU cc_start: 0.7718 (pp20) cc_final: 0.7439 (pp20) REVERT: F 315 ARG cc_start: 0.7794 (OUTLIER) cc_final: 0.6146 (ptm-80) REVERT: F 329 GLU cc_start: 0.7325 (mm-30) cc_final: 0.6991 (tt0) outliers start: 32 outliers final: 9 residues processed: 192 average time/residue: 0.7064 time to fit residues: 147.7438 Evaluate side-chains 181 residues out of total 1568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 166 time to evaluate : 0.551 ------------------------------------------------------------------------------- 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 22 LYS Chi-restraints excluded: chain B residue 380 GLU 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 26 LEU 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 99 SER 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 17 optimal weight: 2.9990 chunk 165 optimal weight: 0.0470 chunk 23 optimal weight: 4.9990 chunk 115 optimal weight: 0.7980 chunk 9 optimal weight: 0.6980 chunk 38 optimal weight: 3.9990 chunk 89 optimal weight: 0.5980 chunk 178 optimal weight: 5.9990 chunk 40 optimal weight: 3.9990 chunk 86 optimal weight: 7.9990 chunk 172 optimal weight: 0.8980 overall best weight: 0.6078 ------------------------------------------------------------------------------- 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 = 0.3534 r_free = 0.3534 target = 0.137042 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3086 r_free = 0.3086 target = 0.100271 restraints weight = 27453.263| |-----------------------------------------------------------------------------| r_work (start): 0.3042 rms_B_bonded: 2.10 r_work: 0.2940 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.2823 rms_B_bonded: 4.14 restraints_weight: 0.2500 r_work (final): 0.2823 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2811 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2811 r_free = 0.2811 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2811 r_free = 0.2811 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2811 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8597 moved from start: 0.1693 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 15507 Z= 0.103 Angle : 0.518 12.189 21000 Z= 0.265 Chirality : 0.042 0.229 2356 Planarity : 0.004 0.039 2620 Dihedral : 10.762 129.973 2423 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 4.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Rotamer: Outliers : 1.40 % Allowed : 13.47 % Favored : 85.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.11 (0.19), residues: 1912 helix: 1.18 (0.18), residues: 872 sheet: -0.22 (0.40), residues: 156 loop : -1.00 (0.20), residues: 884 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 349 TYR 0.018 0.001 TYR D 141 PHE 0.011 0.001 PHE D 50 TRP 0.021 0.001 TRP B 103 HIS 0.006 0.001 HIS F 97 Details of bonding type rmsd covalent geometry : bond 0.00224 (15499) covalent geometry : angle 0.50958 (20991) hydrogen bonds : bond 0.03967 ( 703) hydrogen bonds : angle 4.43718 ( 2016) metal coordination : bond 0.00584 ( 6) metal coordination : angle 4.54935 ( 9) Misc. bond : bond 0.00051 ( 2) *********************** 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 196 residues out of total 1568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 174 time to evaluate : 0.594 Fit side-chains REVERT: A 4 ILE cc_start: 0.8801 (OUTLIER) cc_final: 0.8185 (mp) REVERT: A 97 ASP cc_start: 0.8606 (p0) cc_final: 0.8320 (p0) REVERT: A 271 LYS cc_start: 0.8285 (mmtp) cc_final: 0.7679 (mtpt) REVERT: B 19 LYS cc_start: 0.6683 (mttt) cc_final: 0.6167 (mmpt) REVERT: B 21 GLU cc_start: 0.7133 (tt0) cc_final: 0.6515 (tt0) REVERT: B 22 LYS cc_start: 0.8133 (OUTLIER) cc_final: 0.7556 (mttp) REVERT: B 406 LYS cc_start: 0.8136 (mtmm) cc_final: 0.7735 (mttm) REVERT: B 412 TYR cc_start: 0.8108 (m-80) cc_final: 0.7614 (m-80) REVERT: C 51 GLN cc_start: 0.8434 (tm-30) cc_final: 0.8013 (tm-30) REVERT: D 88 GLN cc_start: 0.8660 (OUTLIER) cc_final: 0.6764 (mp10) REVERT: D 99 LYS cc_start: 0.8511 (tptm) cc_final: 0.8102 (ttmm) REVERT: E 15 GLU cc_start: 0.8609 (mt-10) cc_final: 0.8388 (mt-10) REVERT: E 70 VAL cc_start: 0.8546 (t) cc_final: 0.8254 (m) REVERT: F 13 LEU cc_start: 0.8253 (mp) cc_final: 0.7954 (mm) REVERT: F 104 ARG cc_start: 0.6490 (mtm-85) cc_final: 0.5945 (mmp80) REVERT: F 116 LYS cc_start: 0.8057 (mtpt) cc_final: 0.7768 (mttm) REVERT: F 169 GLN cc_start: 0.8715 (mt0) cc_final: 0.8407 (mt0) REVERT: F 206 GLU cc_start: 0.7672 (pp20) cc_final: 0.7468 (pp20) REVERT: F 315 ARG cc_start: 0.7921 (OUTLIER) cc_final: 0.6246 (ptm-80) REVERT: F 329 GLU cc_start: 0.7375 (mm-30) cc_final: 0.7056 (tt0) outliers start: 22 outliers final: 5 residues processed: 191 average time/residue: 0.6958 time to fit residues: 145.0502 Evaluate side-chains 176 residues out of total 1568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 167 time to evaluate : 0.591 ------------------------------------------------------------------------------- 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 C residue 121 VAL Chi-restraints excluded: chain D residue 88 GLN 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 189 random chunks: chunk 91 optimal weight: 7.9990 chunk 34 optimal weight: 0.9980 chunk 182 optimal weight: 0.0030 chunk 10 optimal weight: 0.0970 chunk 62 optimal weight: 5.9990 chunk 98 optimal weight: 7.9990 chunk 95 optimal weight: 7.9990 chunk 116 optimal weight: 0.9990 chunk 55 optimal weight: 9.9990 chunk 136 optimal weight: 0.0030 chunk 187 optimal weight: 3.9990 overall best weight: 0.4200 ------------------------------------------------------------------------------- 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 = 0.3571 r_free = 0.3571 target = 0.137839 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3146 r_free = 0.3146 target = 0.102794 restraints weight = 22480.549| |-----------------------------------------------------------------------------| r_work (start): 0.3120 rms_B_bonded: 1.70 r_work: 0.3036 rms_B_bonded: 2.06 restraints_weight: 0.5000 r_work: 0.2927 rms_B_bonded: 3.42 restraints_weight: 0.2500 r_work (final): 0.2927 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2926 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2926 r_free = 0.2926 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2926 r_free = 0.2926 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2926 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8466 moved from start: 0.1914 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 15507 Z= 0.093 Angle : 0.491 10.326 21000 Z= 0.252 Chirality : 0.041 0.152 2356 Planarity : 0.004 0.038 2620 Dihedral : 9.920 117.333 2420 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 4.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 1.60 % Allowed : 13.98 % Favored : 84.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.41 (0.19), residues: 1912 helix: 1.46 (0.18), residues: 872 sheet: -0.15 (0.40), residues: 156 loop : -0.86 (0.20), residues: 884 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG F 80 TYR 0.017 0.001 TYR D 141 PHE 0.010 0.001 PHE E 28 TRP 0.020 0.001 TRP B 103 HIS 0.006 0.001 HIS B 330 Details of bonding type rmsd covalent geometry : bond 0.00197 (15499) covalent geometry : angle 0.48437 (20991) hydrogen bonds : bond 0.03565 ( 703) hydrogen bonds : angle 4.28780 ( 2016) metal coordination : bond 0.00330 ( 6) metal coordination : angle 3.82734 ( 9) Misc. bond : bond 0.00038 ( 2) *********************** 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 206 residues out of total 1568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 181 time to evaluate : 0.562 Fit side-chains REVERT: A 4 ILE cc_start: 0.8597 (OUTLIER) cc_final: 0.8029 (mp) REVERT: A 97 ASP cc_start: 0.8480 (p0) cc_final: 0.8192 (p0) REVERT: A 271 LYS cc_start: 0.8147 (mmtp) cc_final: 0.7524 (mtpt) REVERT: B 19 LYS cc_start: 0.6637 (mttt) cc_final: 0.6125 (mmpt) REVERT: B 21 GLU cc_start: 0.7084 (tt0) cc_final: 0.6314 (tt0) REVERT: B 22 LYS cc_start: 0.8111 (OUTLIER) cc_final: 0.7535 (mttt) REVERT: B 406 LYS cc_start: 0.7903 (mtmm) cc_final: 0.7499 (mttm) REVERT: B 412 TYR cc_start: 0.8018 (m-80) cc_final: 0.7563 (m-80) REVERT: C 51 GLN cc_start: 0.8352 (tm-30) cc_final: 0.7912 (tm-30) REVERT: D 99 LYS cc_start: 0.8384 (tptm) cc_final: 0.8024 (ttmm) REVERT: E 15 GLU cc_start: 0.8628 (mt-10) cc_final: 0.8339 (mt-10) REVERT: E 70 VAL cc_start: 0.8499 (t) cc_final: 0.8220 (m) REVERT: F 13 LEU cc_start: 0.8098 (mp) cc_final: 0.7825 (mm) REVERT: F 104 ARG cc_start: 0.6463 (mtm-85) cc_final: 0.5926 (mmp80) REVERT: F 206 GLU cc_start: 0.7613 (pp20) cc_final: 0.7377 (pp20) REVERT: F 315 ARG cc_start: 0.7838 (OUTLIER) cc_final: 0.6189 (ptm-80) REVERT: F 329 GLU cc_start: 0.7351 (mm-30) cc_final: 0.7035 (tt0) REVERT: F 382 MET cc_start: 0.6581 (ptm) cc_final: 0.5167 (tpt) outliers start: 25 outliers final: 9 residues processed: 197 average time/residue: 0.6503 time to fit residues: 140.6202 Evaluate side-chains 179 residues out of total 1568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 167 time to evaluate : 0.594 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 ILE Chi-restraints excluded: chain A residue 371 ASP Chi-restraints excluded: chain B residue 22 LYS Chi-restraints excluded: chain B residue 122 MET 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 103 VAL Chi-restraints excluded: chain D residue 133 ASP Chi-restraints excluded: chain F residue 79 CYS Chi-restraints excluded: chain F residue 197 LEU 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 9 optimal weight: 4.9990 chunk 132 optimal weight: 0.0370 chunk 150 optimal weight: 4.9990 chunk 73 optimal weight: 2.9990 chunk 178 optimal weight: 3.9990 chunk 14 optimal weight: 2.9990 chunk 45 optimal weight: 6.9990 chunk 131 optimal weight: 3.9990 chunk 147 optimal weight: 0.0020 chunk 72 optimal weight: 0.6980 chunk 144 optimal weight: 7.9990 overall best weight: 1.3470 ------------------------------------------------------------------------------- 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 = 0.3542 r_free = 0.3542 target = 0.135389 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3133 r_free = 0.3133 target = 0.100843 restraints weight = 33135.455| |-----------------------------------------------------------------------------| r_work (start): 0.3085 rms_B_bonded: 2.06 r_work: 0.2962 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.2845 rms_B_bonded: 3.98 restraints_weight: 0.2500 r_work (final): 0.2845 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2847 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2847 r_free = 0.2847 target_work(ls_wunit_k1) = 0.082 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2847 r_free = 0.2847 target_work(ls_wunit_k1) = 0.082 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2847 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8526 moved from start: 0.1880 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 15507 Z= 0.136 Angle : 0.531 11.168 21000 Z= 0.272 Chirality : 0.042 0.158 2356 Planarity : 0.004 0.040 2620 Dihedral : 9.708 96.075 2420 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 4.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 1.53 % Allowed : 14.94 % Favored : 83.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.39 (0.19), residues: 1912 helix: 1.36 (0.18), residues: 878 sheet: -0.10 (0.40), residues: 155 loop : -0.80 (0.20), residues: 879 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG F 80 TYR 0.020 0.001 TYR D 141 PHE 0.014 0.001 PHE B 213 TRP 0.024 0.001 TRP B 103 HIS 0.006 0.001 HIS F 97 Details of bonding type rmsd covalent geometry : bond 0.00325 (15499) covalent geometry : angle 0.52342 (20991) hydrogen bonds : bond 0.04272 ( 703) hydrogen bonds : angle 4.36377 ( 2016) metal coordination : bond 0.00789 ( 6) metal coordination : angle 4.41385 ( 9) Misc. bond : bond 0.00090 ( 2) *********************** 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 193 residues out of total 1568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 169 time to evaluate : 0.598 Fit side-chains REVERT: A 4 ILE cc_start: 0.8654 (OUTLIER) cc_final: 0.8054 (mp) REVERT: A 97 ASP cc_start: 0.8545 (p0) cc_final: 0.8263 (p0) REVERT: A 271 LYS cc_start: 0.8251 (mmtp) cc_final: 0.7610 (mtpt) REVERT: B 19 LYS cc_start: 0.6641 (mttt) cc_final: 0.6112 (mmpt) REVERT: B 21 GLU cc_start: 0.7192 (tt0) cc_final: 0.6463 (tt0) REVERT: B 22 LYS cc_start: 0.8127 (OUTLIER) cc_final: 0.7567 (mttt) REVERT: B 406 LYS cc_start: 0.7993 (mtmm) cc_final: 0.7581 (mttm) REVERT: B 412 TYR cc_start: 0.8089 (m-80) cc_final: 0.7643 (m-80) REVERT: C 51 GLN cc_start: 0.8402 (tm-30) cc_final: 0.7958 (tm-30) REVERT: D 99 LYS cc_start: 0.8391 (tptm) cc_final: 0.8013 (ttmm) REVERT: E 15 GLU cc_start: 0.8645 (mt-10) cc_final: 0.8410 (mt-10) REVERT: E 70 VAL cc_start: 0.8474 (t) cc_final: 0.8163 (m) REVERT: F 13 LEU cc_start: 0.8102 (mp) cc_final: 0.7823 (mm) REVERT: F 104 ARG cc_start: 0.6363 (mtm-85) cc_final: 0.5893 (mmp80) REVERT: F 315 ARG cc_start: 0.7787 (OUTLIER) cc_final: 0.6100 (ptm-80) REVERT: F 329 GLU cc_start: 0.7428 (mm-30) cc_final: 0.7033 (tt0) REVERT: F 382 MET cc_start: 0.6655 (ptm) cc_final: 0.5258 (tpt) outliers start: 24 outliers final: 10 residues processed: 187 average time/residue: 0.6652 time to fit residues: 136.1039 Evaluate side-chains 178 residues out of total 1568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 165 time to evaluate : 0.555 ------------------------------------------------------------------------------- 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 122 MET 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 D residue 133 ASP Chi-restraints excluded: chain F residue 79 CYS 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 73 optimal weight: 0.5980 chunk 161 optimal weight: 1.9990 chunk 134 optimal weight: 1.9990 chunk 76 optimal weight: 3.9990 chunk 120 optimal weight: 3.9990 chunk 89 optimal weight: 1.9990 chunk 88 optimal weight: 3.9990 chunk 20 optimal weight: 3.9990 chunk 16 optimal weight: 0.9990 chunk 177 optimal weight: 5.9990 chunk 64 optimal weight: 1.9990 overall best weight: 1.5188 ------------------------------------------------------------------------------- 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 = 0.3534 r_free = 0.3534 target = 0.134721 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3116 r_free = 0.3116 target = 0.100018 restraints weight = 27685.630| |-----------------------------------------------------------------------------| r_work (start): 0.3076 rms_B_bonded: 1.85 r_work: 0.2972 rms_B_bonded: 2.17 restraints_weight: 0.5000 r_work: 0.2861 rms_B_bonded: 3.57 restraints_weight: 0.2500 r_work (final): 0.2861 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2861 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2861 r_free = 0.2861 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2861 r_free = 0.2861 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2861 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8552 moved from start: 0.1887 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 15507 Z= 0.145 Angle : 0.541 10.926 21000 Z= 0.277 Chirality : 0.043 0.164 2356 Planarity : 0.004 0.040 2620 Dihedral : 9.518 81.510 2420 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 4.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 1.53 % Allowed : 15.39 % Favored : 83.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.34 (0.19), residues: 1912 helix: 1.29 (0.18), residues: 885 sheet: -0.10 (0.40), residues: 156 loop : -0.81 (0.20), residues: 871 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 408 TYR 0.020 0.001 TYR D 141 PHE 0.014 0.001 PHE B 213 TRP 0.023 0.001 TRP B 103 HIS 0.007 0.001 HIS B 330 Details of bonding type rmsd covalent geometry : bond 0.00348 (15499) covalent geometry : angle 0.53280 (20991) hydrogen bonds : bond 0.04457 ( 703) hydrogen bonds : angle 4.40181 ( 2016) metal coordination : bond 0.00759 ( 6) metal coordination : angle 4.49199 ( 9) Misc. bond : bond 0.00098 ( 2) *********************** 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 192 residues out of total 1568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 168 time to evaluate : 0.572 Fit side-chains REVERT: A 4 ILE cc_start: 0.8666 (OUTLIER) cc_final: 0.8070 (mp) REVERT: A 97 ASP cc_start: 0.8527 (p0) cc_final: 0.8226 (p0) REVERT: A 162 GLU cc_start: 0.8076 (OUTLIER) cc_final: 0.7134 (tm-30) REVERT: A 271 LYS cc_start: 0.8268 (mmtp) cc_final: 0.7660 (mtpt) REVERT: A 384 MET cc_start: 0.8993 (OUTLIER) cc_final: 0.7605 (tmm) REVERT: B 19 LYS cc_start: 0.6734 (mttt) cc_final: 0.6134 (mmpt) REVERT: B 21 GLU cc_start: 0.7196 (tt0) cc_final: 0.6461 (tt0) REVERT: B 22 LYS cc_start: 0.8182 (OUTLIER) cc_final: 0.7605 (mttt) REVERT: B 406 LYS cc_start: 0.8066 (mtmm) cc_final: 0.7676 (mttm) REVERT: B 412 TYR cc_start: 0.8093 (m-80) cc_final: 0.7638 (m-80) REVERT: C 51 GLN cc_start: 0.8450 (tm-30) cc_final: 0.7998 (tm-30) REVERT: D 99 LYS cc_start: 0.8392 (tptm) cc_final: 0.8040 (ttmm) REVERT: F 13 LEU cc_start: 0.8141 (mp) cc_final: 0.7858 (mm) REVERT: F 104 ARG cc_start: 0.6330 (mtm-85) cc_final: 0.5876 (mmp80) REVERT: F 315 ARG cc_start: 0.7808 (OUTLIER) cc_final: 0.6136 (ptm-80) REVERT: F 329 GLU cc_start: 0.7455 (mm-30) cc_final: 0.7081 (tt0) REVERT: F 382 MET cc_start: 0.6655 (ptm) cc_final: 0.5298 (tpt) outliers start: 24 outliers final: 10 residues processed: 182 average time/residue: 0.6683 time to fit residues: 133.0906 Evaluate side-chains 181 residues out of total 1568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 166 time to evaluate : 0.533 ------------------------------------------------------------------------------- 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 101 THR 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 22 LYS Chi-restraints excluded: chain B residue 122 MET 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 D residue 133 ASP Chi-restraints excluded: chain F residue 79 CYS Chi-restraints excluded: chain F residue 197 LEU 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 154 optimal weight: 3.9990 chunk 170 optimal weight: 8.9990 chunk 85 optimal weight: 7.9990 chunk 90 optimal weight: 0.8980 chunk 47 optimal weight: 5.9990 chunk 101 optimal weight: 5.9990 chunk 94 optimal weight: 6.9990 chunk 25 optimal weight: 0.0060 chunk 23 optimal weight: 4.9990 chunk 76 optimal weight: 3.9990 chunk 35 optimal weight: 2.9990 overall best weight: 2.3802 ------------------------------------------------------------------------------- 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 = 0.3509 r_free = 0.3509 target = 0.132512 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3090 r_free = 0.3090 target = 0.097825 restraints weight = 29954.918| |-----------------------------------------------------------------------------| r_work (start): 0.3043 rms_B_bonded: 1.88 r_work: 0.2933 rms_B_bonded: 2.22 restraints_weight: 0.5000 r_work: 0.2823 rms_B_bonded: 3.64 restraints_weight: 0.2500 r_work (final): 0.2823 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2827 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2827 r_free = 0.2827 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2827 r_free = 0.2827 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2827 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8609 moved from start: 0.1869 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 15507 Z= 0.204 Angle : 0.603 12.335 21000 Z= 0.306 Chirality : 0.045 0.168 2356 Planarity : 0.004 0.040 2620 Dihedral : 9.686 81.688 2420 Min Nonbonded Distance : 2.411 Molprobity Statistics. All-atom Clashscore : 4.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer: Outliers : 1.40 % Allowed : 15.45 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.19 (0.19), residues: 1912 helix: 1.15 (0.18), residues: 882 sheet: -0.12 (0.41), residues: 155 loop : -0.86 (0.20), residues: 875 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 408 TYR 0.023 0.002 TYR D 141 PHE 0.019 0.002 PHE F 11 TRP 0.025 0.001 TRP B 103 HIS 0.006 0.001 HIS F 97 Details of bonding type rmsd covalent geometry : bond 0.00503 (15499) covalent geometry : angle 0.59315 (20991) hydrogen bonds : bond 0.05206 ( 703) hydrogen bonds : angle 4.55787 ( 2016) metal coordination : bond 0.00896 ( 6) metal coordination : angle 5.27870 ( 9) Misc. bond : bond 0.00134 ( 2) *********************** 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 190 residues out of total 1568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 168 time to evaluate : 0.535 Fit side-chains revert: symmetry clash REVERT: A 4 ILE cc_start: 0.8726 (OUTLIER) cc_final: 0.8100 (mp) REVERT: A 97 ASP cc_start: 0.8571 (p0) cc_final: 0.8240 (p0) REVERT: A 162 GLU cc_start: 0.8117 (OUTLIER) cc_final: 0.7269 (tm-30) REVERT: A 271 LYS cc_start: 0.8356 (mmtp) cc_final: 0.7729 (mtpt) REVERT: B 19 LYS cc_start: 0.6815 (mttt) cc_final: 0.6232 (mmpt) REVERT: B 22 LYS cc_start: 0.8274 (ptmm) cc_final: 0.7614 (mttt) REVERT: B 406 LYS cc_start: 0.8188 (mtmm) cc_final: 0.7783 (mttm) REVERT: B 412 TYR cc_start: 0.8135 (m-80) cc_final: 0.7663 (m-80) REVERT: C 51 GLN cc_start: 0.8505 (tm-30) cc_final: 0.8049 (tm-30) REVERT: D 99 LYS cc_start: 0.8400 (tptm) cc_final: 0.8048 (ttmm) REVERT: E 15 GLU cc_start: 0.8710 (mt-10) cc_final: 0.8477 (mt-10) REVERT: F 13 LEU cc_start: 0.8221 (mp) cc_final: 0.7952 (mm) REVERT: F 104 ARG cc_start: 0.6357 (mtm-85) cc_final: 0.5866 (mmp80) REVERT: F 116 LYS cc_start: 0.8138 (mtpt) cc_final: 0.7424 (mttp) REVERT: F 315 ARG cc_start: 0.7838 (OUTLIER) cc_final: 0.6133 (ptm-80) REVERT: F 329 GLU cc_start: 0.7476 (mm-30) cc_final: 0.7093 (tt0) REVERT: F 382 MET cc_start: 0.6750 (ptm) cc_final: 0.5422 (tpt) outliers start: 22 outliers final: 11 residues processed: 183 average time/residue: 0.6785 time to fit residues: 135.8874 Evaluate side-chains 179 residues out of total 1568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 165 time to evaluate : 0.565 ------------------------------------------------------------------------------- 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 101 THR Chi-restraints excluded: chain A residue 162 GLU Chi-restraints excluded: chain A residue 371 ASP Chi-restraints excluded: chain B residue 333 LEU 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 E residue 111 ILE 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 67 optimal weight: 2.9990 chunk 27 optimal weight: 4.9990 chunk 62 optimal weight: 3.9990 chunk 186 optimal weight: 0.9980 chunk 54 optimal weight: 4.9990 chunk 128 optimal weight: 0.7980 chunk 153 optimal weight: 0.9980 chunk 81 optimal weight: 0.9980 chunk 14 optimal weight: 3.9990 chunk 127 optimal weight: 0.0010 chunk 51 optimal weight: 5.9990 overall best weight: 0.7586 ------------------------------------------------------------------------------- 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 = 0.3550 r_free = 0.3550 target = 0.135922 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3138 r_free = 0.3138 target = 0.101082 restraints weight = 31498.099| |-----------------------------------------------------------------------------| r_work (start): 0.3089 rms_B_bonded: 2.00 r_work: 0.2977 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.2863 rms_B_bonded: 3.83 restraints_weight: 0.2500 r_work (final): 0.2863 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2865 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2865 r_free = 0.2865 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2865 r_free = 0.2865 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2865 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8513 moved from start: 0.1967 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 15507 Z= 0.109 Angle : 0.518 10.235 21000 Z= 0.266 Chirality : 0.041 0.159 2356 Planarity : 0.004 0.042 2620 Dihedral : 9.157 83.698 2420 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 4.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.57 % Favored : 97.43 % Rotamer: Outliers : 1.15 % Allowed : 15.96 % Favored : 82.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.42 (0.19), residues: 1912 helix: 1.40 (0.18), residues: 881 sheet: -0.09 (0.40), residues: 156 loop : -0.79 (0.20), residues: 875 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG F 80 TYR 0.016 0.001 TYR D 141 PHE 0.010 0.001 PHE E 28 TRP 0.019 0.001 TRP B 103 HIS 0.007 0.001 HIS F 97 Details of bonding type rmsd covalent geometry : bond 0.00249 (15499) covalent geometry : angle 0.51029 (20991) hydrogen bonds : bond 0.03954 ( 703) hydrogen bonds : angle 4.35577 ( 2016) metal coordination : bond 0.00408 ( 6) metal coordination : angle 4.30651 ( 9) Misc. bond : bond 0.00062 ( 2) ********************** 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 186 residues out of total 1568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 168 time to evaluate : 0.456 Fit side-chains revert: symmetry clash REVERT: A 4 ILE cc_start: 0.8657 (OUTLIER) cc_final: 0.8057 (mp) REVERT: A 271 LYS cc_start: 0.8211 (mmtp) cc_final: 0.7583 (mtpt) REVERT: B 19 LYS cc_start: 0.6746 (mttt) cc_final: 0.6169 (mmpt) REVERT: B 22 LYS cc_start: 0.8170 (ptmm) cc_final: 0.7534 (mttt) REVERT: B 406 LYS cc_start: 0.7987 (mtmm) cc_final: 0.7578 (mttm) REVERT: B 412 TYR cc_start: 0.8082 (m-80) cc_final: 0.7630 (m-80) REVERT: C 51 GLN cc_start: 0.8429 (tm-30) cc_final: 0.7979 (tm-30) REVERT: D 99 LYS cc_start: 0.8327 (tptm) cc_final: 0.7957 (ttmm) REVERT: E 15 GLU cc_start: 0.8630 (mt-10) cc_final: 0.8423 (mt-10) REVERT: F 13 LEU cc_start: 0.8111 (mp) cc_final: 0.7841 (mm) REVERT: F 104 ARG cc_start: 0.6342 (mtm-85) cc_final: 0.5865 (mmp80) REVERT: F 315 ARG cc_start: 0.7777 (OUTLIER) cc_final: 0.6122 (ptm-80) REVERT: F 329 GLU cc_start: 0.7441 (mm-30) cc_final: 0.7017 (tt0) REVERT: F 382 MET cc_start: 0.6670 (ptm) cc_final: 0.5310 (tpt) outliers start: 18 outliers final: 9 residues processed: 181 average time/residue: 0.6653 time to fit residues: 131.7197 Evaluate side-chains 179 residues out of total 1568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 168 time to evaluate : 0.560 ------------------------------------------------------------------------------- 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 C residue 101 SER 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 E residue 25 MET Chi-restraints excluded: chain E residue 111 ILE 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 107 optimal weight: 6.9990 chunk 146 optimal weight: 3.9990 chunk 82 optimal weight: 5.9990 chunk 26 optimal weight: 0.6980 chunk 4 optimal weight: 5.9990 chunk 138 optimal weight: 0.9980 chunk 94 optimal weight: 4.9990 chunk 118 optimal weight: 4.9990 chunk 108 optimal weight: 4.9990 chunk 53 optimal weight: 4.9990 chunk 46 optimal weight: 6.9990 overall best weight: 3.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 24 GLN ** F 97 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3496 r_free = 0.3496 target = 0.131369 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3077 r_free = 0.3077 target = 0.096769 restraints weight = 28908.524| |-----------------------------------------------------------------------------| r_work (start): 0.3031 rms_B_bonded: 1.84 r_work: 0.2922 rms_B_bonded: 2.18 restraints_weight: 0.5000 r_work: 0.2810 rms_B_bonded: 3.59 restraints_weight: 0.2500 r_work (final): 0.2810 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2811 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2811 r_free = 0.2811 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2811 r_free = 0.2811 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2811 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8614 moved from start: 0.1926 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.044 15507 Z= 0.255 Angle : 0.656 12.859 21000 Z= 0.331 Chirality : 0.047 0.194 2356 Planarity : 0.004 0.040 2620 Dihedral : 9.712 82.522 2420 Min Nonbonded Distance : 2.395 Molprobity Statistics. All-atom Clashscore : 4.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.09 % Favored : 96.91 % Rotamer: Outliers : 1.09 % Allowed : 16.54 % Favored : 82.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.07 (0.19), residues: 1912 helix: 1.02 (0.18), residues: 879 sheet: -0.20 (0.41), residues: 155 loop : -0.89 (0.20), residues: 878 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 408 TYR 0.025 0.002 TYR D 141 PHE 0.022 0.002 PHE F 11 TRP 0.027 0.002 TRP B 103 HIS 0.007 0.002 HIS F 97 Details of bonding type rmsd covalent geometry : bond 0.00634 (15499) covalent geometry : angle 0.64588 (20991) hydrogen bonds : bond 0.05695 ( 703) hydrogen bonds : angle 4.63995 ( 2016) metal coordination : bond 0.01176 ( 6) metal coordination : angle 5.66961 ( 9) Misc. bond : bond 0.00167 ( 2) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5821.83 seconds wall clock time: 99 minutes 38.90 seconds (5978.90 seconds total)