Starting phenix.real_space_refine on Sat Sep 12 11:04:06 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7onu_13002/09_2026/7onu_13002.cif Found real_map, /net/cci-nas-00/data/ceres_data/7onu_13002/09_2026/7onu_13002.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7onu_13002/09_2026/7onu_13002.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7onu_13002/09_2026/7onu_13002.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/7onu_13002/09_2026/7onu_13002.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7onu_13002/09_2026/7onu_13002.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7onu_13002/09_2026/7onu_13002.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7onu_13002/09_2026/7onu_13002.map" } resolution = 3.0 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= 0.006 sd= 1.101 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 Zn 1 6.06 5 P 74 5.49 5 Mg 1 5.21 5 S 68 5.16 5 C 9272 2.51 5 N 2644 2.21 5 O 3023 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 15083 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 1848 Number of conformers: 1 Conformer: "" Number of residues, atoms: 255, 1848 Classifications: {'peptide': 255} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 241} Chain: "B" Number of atoms: 1848 Number of conformers: 1 Conformer: "" Number of residues, atoms: 255, 1848 Classifications: {'peptide': 255} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 241} Chain: "C" Number of atoms: 1848 Number of conformers: 1 Conformer: "" Number of residues, atoms: 255, 1848 Classifications: {'peptide': 255} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 241} Chain: "D" Number of atoms: 1848 Number of conformers: 1 Conformer: "" Number of residues, atoms: 255, 1848 Classifications: {'peptide': 255} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 241} Chain: "E" Number of atoms: 3810 Number of conformers: 1 Conformer: "" Number of residues, atoms: 467, 3810 Classifications: {'peptide': 467} Link IDs: {'PTRANS': 16, 'TRANS': 450} Chain: "F" Number of atoms: 2287 Number of conformers: 1 Conformer: "" Number of residues, atoms: 276, 2287 Classifications: {'peptide': 276} Link IDs: {'PTRANS': 8, 'TRANS': 267} Chain breaks: 1 Chain: "T" Number of atoms: 1416 Number of conformers: 1 Conformer: "" Number of residues, atoms: 66, 1416 Classifications: {'RNAv2': 66} Modifications used: {'rna2p_pur': 10, 'rna2p_pyr': 5, 'rna3p_pur': 29, 'rna3p_pyr': 22} Link IDs: {'rna2p': 14, 'rna3p': 51} Chain breaks: 1 Chain: "A" Number of atoms: 44 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 44 Unusual residues: {'NAD': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 44 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 44 Unusual residues: {'NAD': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 44 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 44 Unusual residues: {'NAD': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 44 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 44 Unusual residues: {'NAD': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MG': 1, ' ZN': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 9296 SG CYS E 348 49.966 77.669 20.738 1.00112.31 S ATOM 9312 SG CYS E 351 47.988 79.278 18.153 1.00115.74 S ATOM 11175 SG CYS E 578 47.198 75.487 18.852 1.00107.57 S Time building chain proxies: 3.18, per 1000 atoms: 0.21 Number of scatterers: 15083 At special positions: 0 Unit cell: (93.4081, 109.254, 167.634, 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) Zn 1 29.99 S 68 16.00 P 74 15.00 Mg 1 11.99 O 3023 8.00 N 2644 7.00 C 9272 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=0, symmetry=0 Time building additional restraints: 1.13 Conformation dependent library (CDL) restraints added in 502.8 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN E 601 " pdb="ZN ZN E 601 " - pdb=" NE2 HIS E 557 " pdb="ZN ZN E 601 " - pdb=" SG CYS E 351 " pdb="ZN ZN E 601 " - pdb=" SG CYS E 348 " pdb="ZN ZN E 601 " - pdb=" SG CYS E 578 " Number of angles added : 3 3498 Ramachandran restraints generated. 1749 Oldfield, 0 Emsley, 1749 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3210 Finding SS restraints... Secondary structure from input PDB file: 73 helices and 12 sheets defined 54.9% alpha, 10.6% beta 18 base pairs and 35 stacking pairs defined. Time for finding SS restraints: 1.82 Creating SS restraints... Processing helix chain 'A' and resid 20 through 33 Processing helix chain 'A' and resid 46 through 55 removed outlier: 3.561A pdb=" N GLY A 55 " --> pdb=" O ALA A 51 " (cutoff:3.500A) Processing helix chain 'A' and resid 67 through 83 Processing helix chain 'A' and resid 110 through 138 removed outlier: 3.775A pdb=" N GLY A 124 " --> pdb=" O VAL A 120 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N THR A 125 " --> pdb=" O ASN A 121 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N GLY A 134 " --> pdb=" O ARG A 130 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N GLU A 135 " --> pdb=" O LEU A 131 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N GLN A 138 " --> pdb=" O GLY A 134 " (cutoff:3.500A) Processing helix chain 'A' and resid 155 through 159 Processing helix chain 'A' and resid 165 through 187 removed outlier: 4.554A pdb=" N LEU A 180 " --> pdb=" O VAL A 176 " (cutoff:3.500A) Proline residue: A 181 - end of helix Processing helix chain 'A' and resid 203 through 208 removed outlier: 4.044A pdb=" N SER A 208 " --> pdb=" O LEU A 205 " (cutoff:3.500A) Processing helix chain 'A' and resid 210 through 220 Processing helix chain 'A' and resid 229 through 243 removed outlier: 3.504A pdb=" N TYR A 233 " --> pdb=" O ASP A 229 " (cutoff:3.500A) Processing helix chain 'B' and resid 20 through 33 removed outlier: 3.529A pdb=" N LEU B 24 " --> pdb=" O SER B 20 " (cutoff:3.500A) Processing helix chain 'B' and resid 42 through 45 Processing helix chain 'B' and resid 46 through 55 removed outlier: 4.007A pdb=" N GLN B 50 " --> pdb=" O GLY B 46 " (cutoff:3.500A) Processing helix chain 'B' and resid 67 through 83 Processing helix chain 'B' and resid 110 through 137 removed outlier: 3.885A pdb=" N GLY B 124 " --> pdb=" O VAL B 120 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N THR B 125 " --> pdb=" O ASN B 121 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N GLY B 134 " --> pdb=" O ARG B 130 " (cutoff:3.500A) Processing helix chain 'B' and resid 155 through 159 Processing helix chain 'B' and resid 165 through 187 removed outlier: 4.616A pdb=" N LEU B 180 " --> pdb=" O VAL B 176 " (cutoff:3.500A) Proline residue: B 181 - end of helix Processing helix chain 'B' and resid 203 through 209 removed outlier: 4.366A pdb=" N LEU B 209 " --> pdb=" O LEU B 205 " (cutoff:3.500A) Processing helix chain 'B' and resid 210 through 220 Processing helix chain 'B' and resid 229 through 242 Processing helix chain 'C' and resid 20 through 33 Processing helix chain 'C' and resid 46 through 54 Processing helix chain 'C' and resid 67 through 83 Processing helix chain 'C' and resid 110 through 137 removed outlier: 3.594A pdb=" N MET C 123 " --> pdb=" O ASP C 119 " (cutoff:3.500A) Processing helix chain 'C' and resid 155 through 159 Processing helix chain 'C' and resid 165 through 187 removed outlier: 4.639A pdb=" N LEU C 180 " --> pdb=" O VAL C 176 " (cutoff:3.500A) Proline residue: C 181 - end of helix Processing helix chain 'C' and resid 203 through 208 removed outlier: 3.820A pdb=" N SER C 208 " --> pdb=" O PRO C 204 " (cutoff:3.500A) Processing helix chain 'C' and resid 210 through 221 removed outlier: 3.501A pdb=" N VAL C 221 " --> pdb=" O LEU C 217 " (cutoff:3.500A) Processing helix chain 'C' and resid 229 through 243 removed outlier: 3.503A pdb=" N TYR C 233 " --> pdb=" O ASP C 229 " (cutoff:3.500A) Processing helix chain 'D' and resid 21 through 34 Processing helix chain 'D' and resid 46 through 55 removed outlier: 3.892A pdb=" N GLN D 50 " --> pdb=" O GLY D 46 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N GLY D 55 " --> pdb=" O ALA D 51 " (cutoff:3.500A) Processing helix chain 'D' and resid 67 through 83 Processing helix chain 'D' and resid 110 through 122 Processing helix chain 'D' and resid 122 through 137 Processing helix chain 'D' and resid 155 through 159 Processing helix chain 'D' and resid 165 through 186 removed outlier: 4.629A pdb=" N LEU D 180 " --> pdb=" O VAL D 176 " (cutoff:3.500A) Proline residue: D 181 - end of helix Processing helix chain 'D' and resid 203 through 208 Processing helix chain 'D' and resid 210 through 221 Processing helix chain 'D' and resid 229 through 243 Processing helix chain 'E' and resid 120 through 136 removed outlier: 4.880A pdb=" N GLU E 133 " --> pdb=" O GLU E 129 " (cutoff:3.500A) removed outlier: 4.962A pdb=" N ASN E 134 " --> pdb=" O ASP E 130 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N GLY E 136 " --> pdb=" O LYS E 132 " (cutoff:3.500A) Processing helix chain 'E' and resid 139 through 152 Processing helix chain 'E' and resid 154 through 169 removed outlier: 3.538A pdb=" N ALA E 158 " --> pdb=" O SER E 154 " (cutoff:3.500A) Processing helix chain 'E' and resid 174 through 188 Processing helix chain 'E' and resid 190 through 205 Processing helix chain 'E' and resid 209 through 221 Processing helix chain 'E' and resid 226 through 237 removed outlier: 4.181A pdb=" N LEU E 230 " --> pdb=" O TRP E 226 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N LEU E 231 " --> pdb=" O ARG E 227 " (cutoff:3.500A) Processing helix chain 'E' and resid 243 through 257 removed outlier: 3.611A pdb=" N TYR E 247 " --> pdb=" O SER E 243 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N HIS E 257 " --> pdb=" O GLY E 253 " (cutoff:3.500A) Processing helix chain 'E' and resid 259 through 273 removed outlier: 3.655A pdb=" N ALA E 263 " --> pdb=" O ASP E 259 " (cutoff:3.500A) Processing helix chain 'E' and resid 278 through 290 removed outlier: 3.861A pdb=" N LEU E 282 " --> pdb=" O MET E 278 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N LYS E 290 " --> pdb=" O PHE E 286 " (cutoff:3.500A) Processing helix chain 'E' and resid 294 through 312 Processing helix chain 'E' and resid 316 through 329 Processing helix chain 'E' and resid 361 through 377 removed outlier: 3.637A pdb=" N ASP E 375 " --> pdb=" O LYS E 371 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N ILE E 377 " --> pdb=" O MET E 373 " (cutoff:3.500A) Processing helix chain 'E' and resid 387 through 401 Processing helix chain 'E' and resid 410 through 415 Processing helix chain 'E' and resid 421 through 435 Processing helix chain 'E' and resid 447 through 449 No H-bonds generated for 'chain 'E' and resid 447 through 449' Processing helix chain 'E' and resid 456 through 467 Processing helix chain 'E' and resid 478 through 490 Processing helix chain 'E' and resid 501 through 507 Processing helix chain 'E' and resid 510 through 524 Processing helix chain 'F' and resid 93 through 104 removed outlier: 3.567A pdb=" N GLU F 99 " --> pdb=" O ARG F 95 " (cutoff:3.500A) Processing helix chain 'F' and resid 113 through 122 Processing helix chain 'F' and resid 125 through 156 Processing helix chain 'F' and resid 182 through 202 Processing helix chain 'F' and resid 210 through 215 removed outlier: 4.448A pdb=" N ASN F 213 " --> pdb=" O ALA F 210 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N MET F 215 " --> pdb=" O GLU F 212 " (cutoff:3.500A) Processing helix chain 'F' and resid 216 through 236 Processing helix chain 'F' and resid 252 through 262 Processing helix chain 'F' and resid 263 through 269 removed outlier: 3.570A pdb=" N TRP F 266 " --> pdb=" O GLN F 263 " (cutoff:3.500A) removed outlier: 4.332A pdb=" N ASP F 267 " --> pdb=" O GLU F 264 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N LEU F 269 " --> pdb=" O TRP F 266 " (cutoff:3.500A) Processing helix chain 'F' and resid 277 through 282 removed outlier: 3.537A pdb=" N PHE F 282 " --> pdb=" O HIS F 278 " (cutoff:3.500A) Processing helix chain 'F' and resid 320 through 329 Processing helix chain 'F' and resid 337 through 341 Processing helix chain 'F' and resid 352 through 365 Processing helix chain 'F' and resid 368 through 373 Processing helix chain 'F' and resid 374 through 376 No H-bonds generated for 'chain 'F' and resid 374 through 376' Processing sheet with id=AA1, first strand: chain 'A' and resid 58 through 62 removed outlier: 6.489A pdb=" N ALA A 37 " --> pdb=" O VAL A 59 " (cutoff:3.500A) removed outlier: 7.504A pdb=" N ALA A 61 " --> pdb=" O ALA A 37 " (cutoff:3.500A) removed outlier: 6.233A pdb=" N LEU A 39 " --> pdb=" O ALA A 61 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 101 through 102 Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 62 removed outlier: 6.379A pdb=" N VAL B 12 " --> pdb=" O VAL B 87 " (cutoff:3.500A) removed outlier: 7.726A pdb=" N VAL B 89 " --> pdb=" O VAL B 12 " (cutoff:3.500A) removed outlier: 6.426A pdb=" N VAL B 14 " --> pdb=" O VAL B 89 " (cutoff:3.500A) removed outlier: 6.581A pdb=" N ALA B 88 " --> pdb=" O ILE B 151 " (cutoff:3.500A) removed outlier: 7.729A pdb=" N THR B 153 " --> pdb=" O ALA B 88 " (cutoff:3.500A) removed outlier: 7.385A pdb=" N ASN B 90 " --> pdb=" O THR B 153 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 101 through 102 Processing sheet with id=AA5, first strand: chain 'C' and resid 58 through 62 removed outlier: 6.589A pdb=" N ALA C 88 " --> pdb=" O ILE C 151 " (cutoff:3.500A) removed outlier: 8.007A pdb=" N THR C 153 " --> pdb=" O ALA C 88 " (cutoff:3.500A) removed outlier: 7.361A pdb=" N ASN C 90 " --> pdb=" O THR C 153 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 101 through 102 Processing sheet with id=AA7, first strand: chain 'D' and resid 58 through 62 removed outlier: 6.491A pdb=" N VAL D 12 " --> pdb=" O VAL D 87 " (cutoff:3.500A) removed outlier: 8.067A pdb=" N VAL D 89 " --> pdb=" O VAL D 12 " (cutoff:3.500A) removed outlier: 6.607A pdb=" N VAL D 14 " --> pdb=" O VAL D 89 " (cutoff:3.500A) removed outlier: 6.518A pdb=" N ALA D 88 " --> pdb=" O ILE D 151 " (cutoff:3.500A) removed outlier: 7.838A pdb=" N THR D 153 " --> pdb=" O ALA D 88 " (cutoff:3.500A) removed outlier: 7.247A pdb=" N ASN D 90 " --> pdb=" O THR D 153 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 101 through 102 Processing sheet with id=AA9, first strand: chain 'E' and resid 347 through 348 removed outlier: 3.633A pdb=" N GLN E 347 " --> pdb=" O ARG E 343 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'E' and resid 469 through 472 removed outlier: 6.311A pdb=" N VAL E 442 " --> pdb=" O PHE E 470 " (cutoff:3.500A) removed outlier: 7.539A pdb=" N ALA E 472 " --> pdb=" O VAL E 442 " (cutoff:3.500A) removed outlier: 6.969A pdb=" N GLY E 444 " --> pdb=" O ALA E 472 " (cutoff:3.500A) removed outlier: 7.747A pdb=" N LEU E 443 " --> pdb=" O VAL E 406 " (cutoff:3.500A) removed outlier: 6.624A pdb=" N ILE E 408 " --> pdb=" O LEU E 443 " (cutoff:3.500A) removed outlier: 8.995A pdb=" N ARG E 445 " --> pdb=" O ILE E 408 " (cutoff:3.500A) removed outlier: 6.898A pdb=" N VAL E 407 " --> pdb=" O ILE E 496 " (cutoff:3.500A) removed outlier: 6.213A pdb=" N PHE E 495 " --> pdb=" O LEU E 526 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'F' and resid 272 through 273 removed outlier: 6.419A pdb=" N ILE F 243 " --> pdb=" O THR F 272 " (cutoff:3.500A) removed outlier: 6.481A pdb=" N LEU F 205 " --> pdb=" O TYR F 244 " (cutoff:3.500A) removed outlier: 7.216A pdb=" N CYS F 246 " --> pdb=" O LEU F 205 " (cutoff:3.500A) removed outlier: 6.113A pdb=" N PHE F 207 " --> pdb=" O CYS F 246 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N TYR F 307 " --> pdb=" O PRO F 204 " (cutoff:3.500A) removed outlier: 4.657A pdb=" N GLY F 310 " --> pdb=" O LEU F 290 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N ALA F 332 " --> pdb=" O ILE F 287 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'F' and resid 342 through 344 removed outlier: 6.673A pdb=" N GLN F 343 " --> pdb=" O THR F 382 " (cutoff:3.500A) 734 hydrogen bonds defined for protein. 2136 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 42 hydrogen bonds 72 hydrogen bond angles 0 basepair planarities 18 basepair parallelities 35 stacking parallelities Total time for adding SS restraints: 2.25 Time building geometry restraints manager: 1.44 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 2497 1.32 - 1.44: 4153 1.44 - 1.56: 8601 1.56 - 1.69: 146 1.69 - 1.81: 108 Bond restraints: 15505 Sorted by residual: bond pdb=" C3N NAD B 301 " pdb=" C4N NAD B 301 " ideal model delta sigma weight residual 1.390 1.486 -0.096 2.00e-02 2.50e+03 2.33e+01 bond pdb=" C3N NAD D 301 " pdb=" C4N NAD D 301 " ideal model delta sigma weight residual 1.390 1.486 -0.096 2.00e-02 2.50e+03 2.30e+01 bond pdb=" C3N NAD A 301 " pdb=" C4N NAD A 301 " ideal model delta sigma weight residual 1.390 1.486 -0.096 2.00e-02 2.50e+03 2.29e+01 bond pdb=" C3N NAD C 301 " pdb=" C4N NAD C 301 " ideal model delta sigma weight residual 1.390 1.486 -0.096 2.00e-02 2.50e+03 2.28e+01 bond pdb=" C4N NAD C 301 " pdb=" C5N NAD C 301 " ideal model delta sigma weight residual 1.384 1.471 -0.087 2.00e-02 2.50e+03 1.90e+01 ... (remaining 15500 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.42: 20466 1.42 - 2.84: 607 2.84 - 4.26: 207 4.26 - 5.68: 46 5.68 - 7.10: 6 Bond angle restraints: 21332 Sorted by residual: angle pdb=" N PHE F 97 " pdb=" CA PHE F 97 " pdb=" C PHE F 97 " ideal model delta sigma weight residual 111.07 105.72 5.35 1.07e+00 8.73e-01 2.50e+01 angle pdb=" CA PHE F 97 " pdb=" CB PHE F 97 " pdb=" CG PHE F 97 " ideal model delta sigma weight residual 113.80 117.89 -4.09 1.00e+00 1.00e+00 1.68e+01 angle pdb=" N TRP F 101 " pdb=" CA TRP F 101 " pdb=" C TRP F 101 " ideal model delta sigma weight residual 111.36 106.97 4.39 1.09e+00 8.42e-01 1.62e+01 angle pdb=" CA TRP F 101 " pdb=" C TRP F 101 " pdb=" O TRP F 101 " ideal model delta sigma weight residual 120.42 116.16 4.26 1.06e+00 8.90e-01 1.61e+01 angle pdb=" CA PHE F 97 " pdb=" C PHE F 97 " pdb=" O PHE F 97 " ideal model delta sigma weight residual 120.82 117.39 3.43 1.05e+00 9.07e-01 1.07e+01 ... (remaining 21327 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.99: 8128 17.99 - 35.98: 729 35.98 - 53.97: 134 53.97 - 71.96: 96 71.96 - 89.95: 22 Dihedral angle restraints: 9109 sinusoidal: 4106 harmonic: 5003 Sorted by residual: dihedral pdb=" C4' G T 9 " pdb=" C3' G T 9 " pdb=" C2' G T 9 " pdb=" C1' G T 9 " ideal model delta sinusoidal sigma weight residual 36.34 -38.04 74.38 1 3.10e+00 1.04e-01 7.30e+02 dihedral pdb=" C4' A T 34 " pdb=" C3' A T 34 " pdb=" C2' A T 34 " pdb=" C1' A T 34 " ideal model delta sinusoidal sigma weight residual 36.34 -36.75 73.10 1 3.10e+00 1.04e-01 7.09e+02 dihedral pdb=" C4' G T 41 " pdb=" C3' G T 41 " pdb=" C2' G T 41 " pdb=" C1' G T 41 " ideal model delta sinusoidal sigma weight residual 36.35 -36.43 72.78 1 3.10e+00 1.04e-01 7.03e+02 ... (remaining 9106 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.063: 2086 0.063 - 0.125: 279 0.125 - 0.188: 15 0.188 - 0.251: 86 0.251 - 0.313: 15 Chirality restraints: 2481 Sorted by residual: chirality pdb=" C2' G T 9 " pdb=" C3' G T 9 " pdb=" O2' G T 9 " pdb=" C1' G T 9 " both_signs ideal model delta sigma weight residual False -2.79 -2.48 -0.31 2.00e-01 2.50e+01 2.46e+00 chirality pdb=" C2' A T 33 " pdb=" C3' A T 33 " pdb=" O2' A T 33 " pdb=" C1' A T 33 " both_signs ideal model delta sigma weight residual False -2.79 -2.50 -0.29 2.00e-01 2.50e+01 2.07e+00 chirality pdb=" C2' G T 30 " pdb=" C3' G T 30 " pdb=" O2' G T 30 " pdb=" C1' G T 30 " both_signs ideal model delta sigma weight residual False -2.79 -2.51 -0.28 2.00e-01 2.50e+01 2.02e+00 ... (remaining 2478 not shown) Planarity restraints: 2492 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1D NAD A 301 " 0.046 2.00e-02 2.50e+03 4.57e-02 4.18e+01 pdb=" C2N NAD A 301 " -0.101 2.00e-02 2.50e+03 pdb=" C3N NAD A 301 " -0.013 2.00e-02 2.50e+03 pdb=" C4N NAD A 301 " -0.007 2.00e-02 2.50e+03 pdb=" C5N NAD A 301 " 0.004 2.00e-02 2.50e+03 pdb=" C6N NAD A 301 " 0.017 2.00e-02 2.50e+03 pdb=" C7N NAD A 301 " 0.062 2.00e-02 2.50e+03 pdb=" N1N NAD A 301 " -0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1D NAD C 301 " -0.055 2.00e-02 2.50e+03 4.03e-02 3.25e+01 pdb=" C2N NAD C 301 " 0.089 2.00e-02 2.50e+03 pdb=" C3N NAD C 301 " 0.005 2.00e-02 2.50e+03 pdb=" C4N NAD C 301 " -0.025 2.00e-02 2.50e+03 pdb=" C5N NAD C 301 " 0.002 2.00e-02 2.50e+03 pdb=" C6N NAD C 301 " 0.012 2.00e-02 2.50e+03 pdb=" C7N NAD C 301 " -0.036 2.00e-02 2.50e+03 pdb=" N1N NAD C 301 " 0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1D NAD B 301 " -0.028 2.00e-02 2.50e+03 2.75e-02 1.52e+01 pdb=" C2N NAD B 301 " 0.063 2.00e-02 2.50e+03 pdb=" C3N NAD B 301 " 0.005 2.00e-02 2.50e+03 pdb=" C4N NAD B 301 " 0.000 2.00e-02 2.50e+03 pdb=" C5N NAD B 301 " 0.002 2.00e-02 2.50e+03 pdb=" C6N NAD B 301 " -0.010 2.00e-02 2.50e+03 pdb=" C7N NAD B 301 " -0.035 2.00e-02 2.50e+03 pdb=" N1N NAD B 301 " 0.002 2.00e-02 2.50e+03 ... (remaining 2489 not shown) Histogram of nonbonded interaction distances: 1.89 - 2.49: 54 2.49 - 3.09: 10672 3.09 - 3.70: 23138 3.70 - 4.30: 36261 4.30 - 4.90: 58682 Nonbonded interactions: 128807 Sorted by model distance: nonbonded pdb=" OD2 ASP A 41 " pdb=" O3B NAD A 301 " model vdw 1.890 3.040 nonbonded pdb=" OH TYR B 168 " pdb=" O2D NAD B 301 " model vdw 1.968 3.040 nonbonded pdb=" OH TYR F 211 " pdb=" OH TYR F 289 " model vdw 2.005 3.040 nonbonded pdb=" OD2 ASP C 41 " pdb=" O3B NAD C 301 " model vdw 2.067 3.040 nonbonded pdb=" OD2 ASP A 64 " pdb=" OG1 THR A 66 " model vdw 2.083 3.040 ... (remaining 128802 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 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' } 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=0.72 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: 5.040 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.300 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 15.960 Find NCS groups from input model: 0.150 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:6.200 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.770 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8056 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 : 0.005 0.096 15509 Z= 0.218 Angle : 0.673 8.558 21335 Z= 0.323 Chirality : 0.062 0.313 2481 Planarity : 0.005 0.056 2492 Dihedral : 15.619 89.955 5899 Min Nonbonded Distance : 1.890 Molprobity Statistics. All-atom Clashscore : 4.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 0.07 % Allowed : 0.14 % Favored : 99.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % 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: 0.53 (0.20), residues: 1749 helix: 1.26 (0.17), residues: 893 sheet: -0.49 (0.35), residues: 198 loop : -0.54 (0.23), residues: 658 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 541 TYR 0.012 0.001 TYR F 289 PHE 0.019 0.001 PHE F 97 TRP 0.023 0.002 TRP F 101 HIS 0.004 0.001 HIS F 242 Details of bonding type rmsd/Z covalent geometry : bond 0.00461 / 0.22 (15505) covalent geometry : angle 0.66805 / 0.32 (21332) hydrogen bonds : bond 0.14149 / 9.58 ( 776) hydrogen bonds : angle 6.10299 / 4.22 ( 2208) metal coordination : bond 0.01507 / 0.75 ( 4) metal coordination : angle 6.57466 / 3.45 ( 3) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3498 Ramachandran restraints generated. 1749 Oldfield, 0 Emsley, 1749 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3498 Ramachandran restraints generated. 1749 Oldfield, 0 Emsley, 1749 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 232 residues out of total 1441 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 231 time to evaluate : 0.383 Fit side-chains REVERT: A 116 ARG cc_start: 0.8610 (ttp80) cc_final: 0.8389 (ttm170) REVERT: B 212 LYS cc_start: 0.5080 (tttt) cc_final: 0.4435 (mmpt) REVERT: D 142 ASP cc_start: 0.6980 (t70) cc_final: 0.6691 (p0) REVERT: E 552 THR cc_start: 0.7539 (m) cc_final: 0.7240 (p) outliers start: 1 outliers final: 1 residues processed: 232 average time/residue: 0.7131 time to fit residues: 179.1636 Evaluate side-chains 143 residues out of total 1441 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 142 time to evaluate : 0.413 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 97 PHE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 179 random chunks: chunk 98 optimal weight: 2.9990 chunk 107 optimal weight: 1.9990 chunk 10 optimal weight: 0.8980 chunk 66 optimal weight: 0.7980 chunk 130 optimal weight: 0.5980 chunk 124 optimal weight: 4.9990 chunk 103 optimal weight: 0.6980 chunk 77 optimal weight: 4.9990 chunk 122 optimal weight: 0.8980 chunk 91 optimal weight: 0.7980 chunk 149 optimal weight: 5.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 115 GLN B 146 GLN B 220 GLN C 260 GLN D 220 GLN E 222 HIS E 530 ASN E 540 GLN ** E 580 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 147 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3484 r_free = 0.3484 target = 0.127972 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3262 r_free = 0.3262 target = 0.111408 restraints weight = 20703.303| |-----------------------------------------------------------------------------| r_work (start): 0.3265 rms_B_bonded: 1.32 r_work: 0.3159 rms_B_bonded: 2.14 restraints_weight: 0.5000 r_work: 0.3040 rms_B_bonded: 3.61 restraints_weight: 0.2500 r_work (final): 0.3040 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3043 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3043 r_free = 0.3043 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.72 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3043 r_free = 0.3043 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.17 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (8 function evaluations) r_final: 0.3043 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8784 moved from start: 0.1360 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 15509 Z= 0.145 Angle : 0.761 16.072 21335 Z= 0.344 Chirality : 0.064 1.124 2481 Planarity : 0.005 0.052 2492 Dihedral : 13.603 163.181 2685 Min Nonbonded Distance : 2.365 Molprobity Statistics. All-atom Clashscore : 4.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.94 % Favored : 98.06 % Rotamer: Outliers : 1.67 % Allowed : 7.43 % Favored : 90.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % 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: 1.05 (0.20), residues: 1749 helix: 1.69 (0.17), residues: 897 sheet: -0.22 (0.36), residues: 196 loop : -0.33 (0.23), residues: 656 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG F 181 TYR 0.012 0.001 TYR E 484 PHE 0.015 0.001 PHE E 518 TRP 0.018 0.001 TRP E 326 HIS 0.005 0.001 HIS E 580 Details of bonding type rmsd/Z covalent geometry : bond 0.00325 / 0.14 (15505) covalent geometry : angle 0.75954 / 0.34 (21332) hydrogen bonds : bond 0.04550 / 3.10 ( 776) hydrogen bonds : angle 4.68344 / 3.30 ( 2208) metal coordination : bond 0.00606 / 0.31 ( 4) metal coordination : angle 4.36189 / 2.34 ( 3) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3498 Ramachandran restraints generated. 1749 Oldfield, 0 Emsley, 1749 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3498 Ramachandran restraints generated. 1749 Oldfield, 0 Emsley, 1749 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 1441 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 149 time to evaluate : 0.426 Fit side-chains REVERT: B 53 LYS cc_start: 0.8317 (mtpp) cc_final: 0.7947 (tttp) REVERT: C 143 GLN cc_start: 0.7653 (OUTLIER) cc_final: 0.7149 (mm-40) REVERT: F 184 ASP cc_start: 0.8360 (OUTLIER) cc_final: 0.7737 (m-30) REVERT: F 188 ASP cc_start: 0.8182 (m-30) cc_final: 0.7871 (m-30) outliers start: 24 outliers final: 8 residues processed: 163 average time/residue: 0.6230 time to fit residues: 111.5362 Evaluate side-chains 140 residues out of total 1441 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 130 time to evaluate : 0.486 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 20 SER Chi-restraints excluded: chain C residue 143 GLN Chi-restraints excluded: chain C residue 213 VAL Chi-restraints excluded: chain E residue 372 ILE Chi-restraints excluded: chain E residue 391 LEU Chi-restraints excluded: chain E residue 531 ARG Chi-restraints excluded: chain E residue 572 VAL Chi-restraints excluded: chain F residue 97 PHE Chi-restraints excluded: chain F residue 184 ASP Chi-restraints excluded: chain F residue 356 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 179 random chunks: chunk 67 optimal weight: 6.9990 chunk 145 optimal weight: 0.3980 chunk 141 optimal weight: 3.9990 chunk 82 optimal weight: 5.9990 chunk 31 optimal weight: 0.5980 chunk 144 optimal weight: 0.9980 chunk 137 optimal weight: 0.9980 chunk 61 optimal weight: 0.9980 chunk 25 optimal weight: 6.9990 chunk 119 optimal weight: 2.9990 chunk 162 optimal weight: 8.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 146 GLN C 50 GLN E 273 HIS E 540 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.128915 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3264 r_free = 0.3264 target = 0.111472 restraints weight = 20900.331| |-----------------------------------------------------------------------------| r_work (start): 0.3263 rms_B_bonded: 1.43 r_work: 0.3153 rms_B_bonded: 2.27 restraints_weight: 0.5000 r_work: 0.3030 rms_B_bonded: 3.83 restraints_weight: 0.2500 r_work (final): 0.3030 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3036 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3036 r_free = 0.3036 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.17 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3036 r_free = 0.3036 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3036 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8764 moved from start: 0.1734 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 15509 Z= 0.130 Angle : 0.641 13.316 21335 Z= 0.298 Chirality : 0.053 0.631 2481 Planarity : 0.005 0.051 2492 Dihedral : 13.730 173.289 2685 Min Nonbonded Distance : 2.329 Molprobity Statistics. All-atom Clashscore : 4.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.72 % Favored : 98.28 % Rotamer: Outliers : 2.15 % Allowed : 9.58 % Favored : 88.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % 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: 1.27 (0.20), residues: 1749 helix: 1.88 (0.17), residues: 898 sheet: -0.03 (0.34), residues: 220 loop : -0.28 (0.24), residues: 631 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 226 TYR 0.011 0.001 TYR E 484 PHE 0.010 0.001 PHE E 198 TRP 0.016 0.001 TRP E 326 HIS 0.003 0.001 HIS E 273 Details of bonding type rmsd/Z covalent geometry : bond 0.00298 / 0.13 (15505) covalent geometry : angle 0.63962 / 0.30 (21332) hydrogen bonds : bond 0.04031 / 2.76 ( 776) hydrogen bonds : angle 4.39915 / 3.11 ( 2208) metal coordination : bond 0.00612 / 0.31 ( 4) metal coordination : angle 2.95412 / 1.54 ( 3) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3498 Ramachandran restraints generated. 1749 Oldfield, 0 Emsley, 1749 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3498 Ramachandran restraints generated. 1749 Oldfield, 0 Emsley, 1749 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 1441 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 149 time to evaluate : 0.547 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 52 LYS cc_start: 0.8372 (tptp) cc_final: 0.8124 (tmtp) REVERT: B 48 GLU cc_start: 0.7768 (OUTLIER) cc_final: 0.7366 (mp0) REVERT: C 143 GLN cc_start: 0.7551 (OUTLIER) cc_final: 0.7052 (mm-40) REVERT: D 142 ASP cc_start: 0.7288 (t70) cc_final: 0.6953 (t0) REVERT: F 184 ASP cc_start: 0.8389 (OUTLIER) cc_final: 0.8090 (m-30) REVERT: F 188 ASP cc_start: 0.8366 (m-30) cc_final: 0.8074 (t70) REVERT: F 239 ASP cc_start: 0.8223 (t70) cc_final: 0.7996 (t70) outliers start: 31 outliers final: 13 residues processed: 164 average time/residue: 0.6200 time to fit residues: 111.7571 Evaluate side-chains 148 residues out of total 1441 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 132 time to evaluate : 0.524 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 48 GLU Chi-restraints excluded: chain C residue 20 SER Chi-restraints excluded: chain C residue 142 ASP Chi-restraints excluded: chain C residue 143 GLN Chi-restraints excluded: chain C residue 213 VAL Chi-restraints excluded: chain E residue 125 ASP Chi-restraints excluded: chain E residue 367 CYS Chi-restraints excluded: chain E residue 372 ILE Chi-restraints excluded: chain E residue 391 LEU Chi-restraints excluded: chain E residue 466 GLN Chi-restraints excluded: chain E residue 572 VAL Chi-restraints excluded: chain F residue 121 MET Chi-restraints excluded: chain F residue 184 ASP Chi-restraints excluded: chain F residue 311 SER Chi-restraints excluded: chain F residue 339 ASP Chi-restraints excluded: chain F residue 356 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 179 random chunks: chunk 96 optimal weight: 1.9990 chunk 51 optimal weight: 3.9990 chunk 145 optimal weight: 0.0170 chunk 75 optimal weight: 5.9990 chunk 70 optimal weight: 2.9990 chunk 115 optimal weight: 0.6980 chunk 114 optimal weight: 2.9990 chunk 12 optimal weight: 0.8980 chunk 125 optimal weight: 0.7980 chunk 3 optimal weight: 0.9990 chunk 72 optimal weight: 6.9990 overall best weight: 0.6820 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 146 GLN E 437 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.130085 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3283 r_free = 0.3283 target = 0.112806 restraints weight = 20817.374| |-----------------------------------------------------------------------------| r_work (start): 0.3290 rms_B_bonded: 1.40 r_work: 0.3178 rms_B_bonded: 2.27 restraints_weight: 0.5000 r_work: 0.3055 rms_B_bonded: 3.84 restraints_weight: 0.2500 r_work (final): 0.3055 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3053 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3053 r_free = 0.3053 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3053 r_free = 0.3053 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3053 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8763 moved from start: 0.2008 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 15509 Z= 0.119 Angle : 0.614 12.085 21335 Z= 0.286 Chirality : 0.051 0.571 2481 Planarity : 0.005 0.050 2492 Dihedral : 13.563 172.967 2683 Min Nonbonded Distance : 2.183 Molprobity Statistics. All-atom Clashscore : 4.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.77 % Favored : 98.23 % Rotamer: Outliers : 1.87 % Allowed : 11.10 % Favored : 87.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % 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: 1.40 (0.20), residues: 1749 helix: 2.02 (0.17), residues: 899 sheet: 0.01 (0.34), residues: 220 loop : -0.29 (0.24), residues: 630 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 226 TYR 0.009 0.001 TYR E 484 PHE 0.016 0.001 PHE E 518 TRP 0.014 0.001 TRP E 326 HIS 0.002 0.001 HIS E 504 Details of bonding type rmsd/Z covalent geometry : bond 0.00271 / 0.12 (15505) covalent geometry : angle 0.61311 / 0.29 (21332) hydrogen bonds : bond 0.03704 / 2.53 ( 776) hydrogen bonds : angle 4.24717 / 3.01 ( 2208) metal coordination : bond 0.00730 / 0.37 ( 4) metal coordination : angle 2.37097 / 1.24 ( 3) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3498 Ramachandran restraints generated. 1749 Oldfield, 0 Emsley, 1749 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3498 Ramachandran restraints generated. 1749 Oldfield, 0 Emsley, 1749 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 1441 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 142 time to evaluate : 0.411 Fit side-chains REVERT: C 143 GLN cc_start: 0.7504 (OUTLIER) cc_final: 0.7041 (mm-40) REVERT: E 531 ARG cc_start: 0.7323 (pmt170) cc_final: 0.6308 (mtm-85) REVERT: F 184 ASP cc_start: 0.8425 (OUTLIER) cc_final: 0.8133 (m-30) REVERT: F 188 ASP cc_start: 0.8446 (m-30) cc_final: 0.8169 (t70) outliers start: 27 outliers final: 9 residues processed: 155 average time/residue: 0.6154 time to fit residues: 104.5919 Evaluate side-chains 146 residues out of total 1441 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 135 time to evaluate : 0.545 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 257 ILE Chi-restraints excluded: chain C residue 142 ASP Chi-restraints excluded: chain C residue 143 GLN Chi-restraints excluded: chain C residue 213 VAL Chi-restraints excluded: chain D residue 66 THR Chi-restraints excluded: chain E residue 125 ASP Chi-restraints excluded: chain E residue 367 CYS Chi-restraints excluded: chain E residue 395 GLU Chi-restraints excluded: chain E residue 475 ILE Chi-restraints excluded: chain F residue 184 ASP Chi-restraints excluded: chain F residue 311 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 179 random chunks: chunk 115 optimal weight: 0.6980 chunk 166 optimal weight: 0.0980 chunk 99 optimal weight: 0.2980 chunk 7 optimal weight: 4.9990 chunk 95 optimal weight: 0.0070 chunk 159 optimal weight: 0.0770 chunk 49 optimal weight: 5.9990 chunk 136 optimal weight: 1.9990 chunk 69 optimal weight: 1.9990 chunk 5 optimal weight: 5.9990 chunk 74 optimal weight: 0.5980 overall best weight: 0.2156 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 146 GLN F 318 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.134058 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3339 r_free = 0.3339 target = 0.116727 restraints weight = 20739.300| |-----------------------------------------------------------------------------| r_work (start): 0.3346 rms_B_bonded: 1.41 r_work: 0.3234 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.3115 rms_B_bonded: 3.88 restraints_weight: 0.2500 r_work (final): 0.3115 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3114 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3114 r_free = 0.3114 target_work(ls_wunit_k1) = 0.101 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3114 r_free = 0.3114 target_work(ls_wunit_k1) = 0.101 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3114 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8700 moved from start: 0.2348 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 15509 Z= 0.098 Angle : 0.577 11.872 21335 Z= 0.267 Chirality : 0.049 0.425 2481 Planarity : 0.005 0.050 2492 Dihedral : 13.377 177.507 2683 Min Nonbonded Distance : 2.334 Molprobity Statistics. All-atom Clashscore : 4.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.60 % Favored : 98.40 % Rotamer: Outliers : 1.25 % Allowed : 12.14 % Favored : 86.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % 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: 1.63 (0.20), residues: 1749 helix: 2.29 (0.17), residues: 891 sheet: 0.08 (0.35), residues: 220 loop : -0.26 (0.24), residues: 638 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 226 TYR 0.009 0.001 TYR B 168 PHE 0.011 0.001 PHE E 518 TRP 0.011 0.001 TRP E 326 HIS 0.002 0.000 HIS E 321 Details of bonding type rmsd/Z covalent geometry : bond 0.00211 / 0.10 (15505) covalent geometry : angle 0.57695 / 0.27 (21332) hydrogen bonds : bond 0.03145 / 2.13 ( 776) hydrogen bonds : angle 4.06628 / 2.89 ( 2208) metal coordination : bond 0.00721 / 0.36 ( 4) metal coordination : angle 1.84000 / 0.97 ( 3) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3498 Ramachandran restraints generated. 1749 Oldfield, 0 Emsley, 1749 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3498 Ramachandran restraints generated. 1749 Oldfield, 0 Emsley, 1749 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 1441 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 160 time to evaluate : 0.614 Fit side-chains REVERT: B 69 LYS cc_start: 0.8744 (mtmm) cc_final: 0.8513 (mttt) REVERT: C 123 MET cc_start: 0.8282 (tmm) cc_final: 0.8060 (ttp) REVERT: D 226 ARG cc_start: 0.8562 (OUTLIER) cc_final: 0.8059 (ptt180) REVERT: E 531 ARG cc_start: 0.7253 (pmt170) cc_final: 0.6302 (mtm-85) REVERT: F 184 ASP cc_start: 0.8358 (OUTLIER) cc_final: 0.8071 (m-30) REVERT: F 188 ASP cc_start: 0.8449 (m-30) cc_final: 0.8138 (t70) outliers start: 18 outliers final: 6 residues processed: 170 average time/residue: 0.7141 time to fit residues: 132.4622 Evaluate side-chains 144 residues out of total 1441 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 136 time to evaluate : 0.554 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 142 ASP Chi-restraints excluded: chain D residue 226 ARG Chi-restraints excluded: chain E residue 278 MET Chi-restraints excluded: chain E residue 367 CYS Chi-restraints excluded: chain E residue 372 ILE Chi-restraints excluded: chain F residue 184 ASP Chi-restraints excluded: chain F residue 311 SER Chi-restraints excluded: chain F residue 339 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 179 random chunks: chunk 66 optimal weight: 4.9990 chunk 152 optimal weight: 3.9990 chunk 46 optimal weight: 0.0170 chunk 105 optimal weight: 0.5980 chunk 82 optimal weight: 3.9990 chunk 39 optimal weight: 1.9990 chunk 100 optimal weight: 0.0770 chunk 27 optimal weight: 4.9990 chunk 65 optimal weight: 0.7980 chunk 97 optimal weight: 3.9990 chunk 102 optimal weight: 0.0470 overall best weight: 0.3074 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 146 GLN D 127 ASN D 152 ASN F 147 GLN F 318 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3575 r_free = 0.3575 target = 0.135031 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.118295 restraints weight = 20583.326| |-----------------------------------------------------------------------------| r_work (start): 0.3357 rms_B_bonded: 1.31 r_work: 0.3251 rms_B_bonded: 2.16 restraints_weight: 0.5000 r_work: 0.3133 rms_B_bonded: 3.68 restraints_weight: 0.2500 r_work (final): 0.3133 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3135 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3135 r_free = 0.3135 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3135 r_free = 0.3135 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3135 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8689 moved from start: 0.2512 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 15509 Z= 0.100 Angle : 0.580 12.046 21335 Z= 0.268 Chirality : 0.048 0.409 2481 Planarity : 0.005 0.050 2492 Dihedral : 13.206 177.975 2683 Min Nonbonded Distance : 2.351 Molprobity Statistics. All-atom Clashscore : 5.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer: Outliers : 1.25 % Allowed : 13.25 % Favored : 85.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % 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: 1.70 (0.20), residues: 1749 helix: 2.33 (0.17), residues: 892 sheet: 0.14 (0.35), residues: 220 loop : -0.23 (0.24), residues: 637 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 226 TYR 0.007 0.001 TYR B 168 PHE 0.009 0.001 PHE F 241 TRP 0.010 0.001 TRP E 143 HIS 0.002 0.000 HIS C 109 Details of bonding type rmsd/Z covalent geometry : bond 0.00221 / 0.10 (15505) covalent geometry : angle 0.58016 / 0.27 (21332) hydrogen bonds : bond 0.03193 / 2.18 ( 776) hydrogen bonds : angle 4.02003 / 2.86 ( 2208) metal coordination : bond 0.00703 / 0.35 ( 4) metal coordination : angle 1.72804 / 0.91 ( 3) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3498 Ramachandran restraints generated. 1749 Oldfield, 0 Emsley, 1749 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3498 Ramachandran restraints generated. 1749 Oldfield, 0 Emsley, 1749 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 1441 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 140 time to evaluate : 0.559 Fit side-chains REVERT: A 116 ARG cc_start: 0.8902 (ttp-170) cc_final: 0.8588 (ttm170) REVERT: A 143 GLN cc_start: 0.6539 (OUTLIER) cc_final: 0.6314 (pt0) REVERT: B 53 LYS cc_start: 0.8282 (mtpp) cc_final: 0.7979 (ttmm) REVERT: B 69 LYS cc_start: 0.8730 (mtmm) cc_final: 0.8502 (mttt) REVERT: B 107 GLN cc_start: 0.8538 (tt0) cc_final: 0.8292 (tt0) REVERT: B 185 ASP cc_start: 0.8561 (m-30) cc_final: 0.8351 (m-30) REVERT: C 123 MET cc_start: 0.8235 (tmm) cc_final: 0.8021 (ttp) REVERT: D 79 LYS cc_start: 0.8293 (OUTLIER) cc_final: 0.7806 (mtpt) REVERT: D 226 ARG cc_start: 0.8555 (OUTLIER) cc_final: 0.8042 (ptt180) REVERT: E 148 MET cc_start: 0.7803 (mtm) cc_final: 0.7512 (mtp) REVERT: E 531 ARG cc_start: 0.7105 (pmt170) cc_final: 0.6323 (mtm-85) REVERT: F 184 ASP cc_start: 0.8340 (OUTLIER) cc_final: 0.8030 (m-30) REVERT: F 188 ASP cc_start: 0.8393 (m-30) cc_final: 0.8108 (t70) REVERT: F 343 GLN cc_start: 0.8761 (mm-40) cc_final: 0.8556 (tp40) outliers start: 18 outliers final: 7 residues processed: 150 average time/residue: 0.6878 time to fit residues: 112.9414 Evaluate side-chains 144 residues out of total 1441 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 133 time to evaluate : 0.448 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 143 GLN Chi-restraints excluded: chain C residue 142 ASP Chi-restraints excluded: chain C residue 213 VAL Chi-restraints excluded: chain D residue 79 LYS Chi-restraints excluded: chain D residue 226 ARG Chi-restraints excluded: chain E residue 278 MET Chi-restraints excluded: chain E residue 367 CYS Chi-restraints excluded: chain E residue 372 ILE Chi-restraints excluded: chain E residue 395 GLU Chi-restraints excluded: chain F residue 184 ASP Chi-restraints excluded: chain F residue 311 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 179 random chunks: chunk 86 optimal weight: 6.9990 chunk 73 optimal weight: 1.9990 chunk 112 optimal weight: 3.9990 chunk 72 optimal weight: 2.9990 chunk 103 optimal weight: 5.9990 chunk 11 optimal weight: 3.9990 chunk 64 optimal weight: 4.9990 chunk 96 optimal weight: 0.9980 chunk 135 optimal weight: 3.9990 chunk 157 optimal weight: 0.6980 chunk 147 optimal weight: 0.0870 overall best weight: 1.3562 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 146 GLN D 152 ASN F 147 GLN F 318 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3482 r_free = 0.3482 target = 0.127682 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3242 r_free = 0.3242 target = 0.109980 restraints weight = 20682.997| |-----------------------------------------------------------------------------| r_work (start): 0.3245 rms_B_bonded: 1.43 r_work: 0.3133 rms_B_bonded: 2.26 restraints_weight: 0.5000 r_work: 0.3012 rms_B_bonded: 3.81 restraints_weight: 0.2500 r_work (final): 0.3012 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3018 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3018 r_free = 0.3018 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3018 r_free = 0.3018 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3018 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8785 moved from start: 0.2170 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.068 15509 Z= 0.167 Angle : 0.663 13.472 21335 Z= 0.308 Chirality : 0.052 0.616 2481 Planarity : 0.005 0.050 2492 Dihedral : 13.309 171.854 2683 Min Nonbonded Distance : 2.372 Molprobity Statistics. All-atom Clashscore : 4.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.06 % Favored : 97.94 % Rotamer: Outliers : 1.60 % Allowed : 13.12 % Favored : 85.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % 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: 1.37 (0.20), residues: 1749 helix: 1.97 (0.17), residues: 900 sheet: 0.03 (0.34), residues: 220 loop : -0.27 (0.24), residues: 629 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 226 TYR 0.014 0.001 TYR E 484 PHE 0.016 0.001 PHE E 397 TRP 0.013 0.001 TRP E 143 HIS 0.004 0.001 HIS F 242 Details of bonding type rmsd/Z covalent geometry : bond 0.00399 / 0.17 (15505) covalent geometry : angle 0.66231 / 0.31 (21332) hydrogen bonds : bond 0.04391 / 3.01 ( 776) hydrogen bonds : angle 4.30176 / 3.05 ( 2208) metal coordination : bond 0.00698 / 0.35 ( 4) metal coordination : angle 2.54057 / 1.33 ( 3) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3498 Ramachandran restraints generated. 1749 Oldfield, 0 Emsley, 1749 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3498 Ramachandran restraints generated. 1749 Oldfield, 0 Emsley, 1749 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 1441 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 150 time to evaluate : 0.570 Fit side-chains REVERT: A 44 ASN cc_start: 0.7558 (m-40) cc_final: 0.7228 (t0) REVERT: B 69 LYS cc_start: 0.8735 (mtmm) cc_final: 0.8490 (mttt) REVERT: B 107 GLN cc_start: 0.8586 (tt0) cc_final: 0.8304 (tt0) REVERT: C 143 GLN cc_start: 0.7677 (OUTLIER) cc_final: 0.7295 (mm-40) REVERT: D 79 LYS cc_start: 0.8264 (OUTLIER) cc_final: 0.8054 (mtpp) REVERT: D 226 ARG cc_start: 0.8605 (OUTLIER) cc_final: 0.8156 (ptt180) REVERT: E 531 ARG cc_start: 0.7430 (pmt170) cc_final: 0.6459 (mtm-85) REVERT: F 184 ASP cc_start: 0.8446 (OUTLIER) cc_final: 0.8129 (m-30) REVERT: F 188 ASP cc_start: 0.8377 (m-30) cc_final: 0.8075 (t70) outliers start: 23 outliers final: 7 residues processed: 164 average time/residue: 0.7112 time to fit residues: 126.9708 Evaluate side-chains 140 residues out of total 1441 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 129 time to evaluate : 0.492 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 142 ASP Chi-restraints excluded: chain C residue 143 GLN Chi-restraints excluded: chain C residue 213 VAL Chi-restraints excluded: chain D residue 79 LYS Chi-restraints excluded: chain D residue 226 ARG Chi-restraints excluded: chain E residue 367 CYS Chi-restraints excluded: chain E residue 395 GLU Chi-restraints excluded: chain E residue 420 VAL Chi-restraints excluded: chain F residue 184 ASP Chi-restraints excluded: chain F residue 311 SER Chi-restraints excluded: chain F residue 339 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 179 random chunks: chunk 167 optimal weight: 7.9990 chunk 21 optimal weight: 0.7980 chunk 169 optimal weight: 5.9990 chunk 18 optimal weight: 0.9990 chunk 157 optimal weight: 0.6980 chunk 60 optimal weight: 0.8980 chunk 132 optimal weight: 2.9990 chunk 16 optimal weight: 3.9990 chunk 70 optimal weight: 2.9990 chunk 175 optimal weight: 5.9990 chunk 73 optimal weight: 1.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 146 GLN C 162 GLN F 147 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3496 r_free = 0.3496 target = 0.128992 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3270 r_free = 0.3270 target = 0.112189 restraints weight = 20849.290| |-----------------------------------------------------------------------------| r_work (start): 0.3268 rms_B_bonded: 1.31 r_work: 0.3161 rms_B_bonded: 2.14 restraints_weight: 0.5000 r_work: 0.3043 rms_B_bonded: 3.62 restraints_weight: 0.2500 r_work (final): 0.3043 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3045 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3045 r_free = 0.3045 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3045 r_free = 0.3045 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3045 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8781 moved from start: 0.2212 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 15509 Z= 0.147 Angle : 0.646 12.948 21335 Z= 0.300 Chirality : 0.051 0.603 2481 Planarity : 0.005 0.050 2492 Dihedral : 13.305 173.624 2683 Min Nonbonded Distance : 2.343 Molprobity Statistics. All-atom Clashscore : 4.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.94 % Favored : 98.06 % Rotamer: Outliers : 1.67 % Allowed : 13.95 % Favored : 84.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % 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: 1.36 (0.20), residues: 1749 helix: 1.96 (0.17), residues: 900 sheet: -0.01 (0.33), residues: 220 loop : -0.27 (0.24), residues: 629 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 226 TYR 0.012 0.001 TYR E 484 PHE 0.012 0.001 PHE E 397 TRP 0.012 0.001 TRP E 326 HIS 0.003 0.001 HIS C 109 Details of bonding type rmsd/Z covalent geometry : bond 0.00345 / 0.15 (15505) covalent geometry : angle 0.64518 / 0.30 (21332) hydrogen bonds : bond 0.04097 / 2.80 ( 776) hydrogen bonds : angle 4.26753 / 3.02 ( 2208) metal coordination : bond 0.00750 / 0.38 ( 4) metal coordination : angle 2.29021 / 1.20 ( 3) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3498 Ramachandran restraints generated. 1749 Oldfield, 0 Emsley, 1749 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3498 Ramachandran restraints generated. 1749 Oldfield, 0 Emsley, 1749 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 1441 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 134 time to evaluate : 0.510 Fit side-chains REVERT: A 44 ASN cc_start: 0.7561 (m-40) cc_final: 0.7267 (t0) REVERT: B 69 LYS cc_start: 0.8779 (mtmm) cc_final: 0.8551 (mttt) REVERT: B 107 GLN cc_start: 0.8606 (tt0) cc_final: 0.8280 (tt0) REVERT: E 148 MET cc_start: 0.7874 (mtm) cc_final: 0.7539 (mtp) REVERT: E 531 ARG cc_start: 0.7353 (pmt170) cc_final: 0.6494 (mtm-85) REVERT: F 184 ASP cc_start: 0.8453 (OUTLIER) cc_final: 0.8147 (m-30) REVERT: F 188 ASP cc_start: 0.8395 (m-30) cc_final: 0.8086 (t70) outliers start: 24 outliers final: 8 residues processed: 148 average time/residue: 0.6512 time to fit residues: 105.3747 Evaluate side-chains 141 residues out of total 1441 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 132 time to evaluate : 0.563 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 213 VAL Chi-restraints excluded: chain E residue 367 CYS Chi-restraints excluded: chain E residue 372 ILE Chi-restraints excluded: chain E residue 395 GLU Chi-restraints excluded: chain E residue 420 VAL Chi-restraints excluded: chain E residue 475 ILE Chi-restraints excluded: chain F residue 184 ASP Chi-restraints excluded: chain F residue 311 SER Chi-restraints excluded: chain F residue 339 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 179 random chunks: chunk 51 optimal weight: 2.9990 chunk 2 optimal weight: 2.9990 chunk 95 optimal weight: 0.7980 chunk 151 optimal weight: 6.9990 chunk 112 optimal weight: 0.7980 chunk 18 optimal weight: 1.9990 chunk 154 optimal weight: 0.9990 chunk 48 optimal weight: 0.6980 chunk 131 optimal weight: 1.9990 chunk 74 optimal weight: 4.9990 chunk 173 optimal weight: 5.9990 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 146 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3497 r_free = 0.3497 target = 0.129025 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3266 r_free = 0.3266 target = 0.111816 restraints weight = 20817.726| |-----------------------------------------------------------------------------| r_work (start): 0.3264 rms_B_bonded: 1.38 r_work: 0.3150 rms_B_bonded: 2.26 restraints_weight: 0.5000 r_work: 0.3028 rms_B_bonded: 3.83 restraints_weight: 0.2500 r_work (final): 0.3028 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3028 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3028 r_free = 0.3028 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3028 r_free = 0.3028 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3028 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8790 moved from start: 0.2241 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 15509 Z= 0.144 Angle : 0.639 13.306 21335 Z= 0.297 Chirality : 0.051 0.603 2481 Planarity : 0.005 0.050 2492 Dihedral : 13.304 173.877 2683 Min Nonbonded Distance : 2.326 Molprobity Statistics. All-atom Clashscore : 4.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.06 % Favored : 97.94 % Rotamer: Outliers : 1.11 % Allowed : 14.78 % Favored : 84.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % 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: 1.35 (0.20), residues: 1749 helix: 1.96 (0.17), residues: 900 sheet: 0.01 (0.34), residues: 220 loop : -0.26 (0.24), residues: 629 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 226 TYR 0.012 0.001 TYR E 484 PHE 0.014 0.001 PHE E 397 TRP 0.013 0.001 TRP E 143 HIS 0.003 0.001 HIS C 109 Details of bonding type rmsd/Z covalent geometry : bond 0.00339 / 0.14 (15505) covalent geometry : angle 0.63883 / 0.30 (21332) hydrogen bonds : bond 0.04083 / 2.79 ( 776) hydrogen bonds : angle 4.26542 / 3.02 ( 2208) metal coordination : bond 0.00805 / 0.40 ( 4) metal coordination : angle 2.31706 / 1.22 ( 3) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3498 Ramachandran restraints generated. 1749 Oldfield, 0 Emsley, 1749 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3498 Ramachandran restraints generated. 1749 Oldfield, 0 Emsley, 1749 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 1441 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 140 time to evaluate : 0.601 Fit side-chains REVERT: A 44 ASN cc_start: 0.7605 (m-40) cc_final: 0.7304 (t0) REVERT: A 48 GLU cc_start: 0.7871 (pm20) cc_final: 0.7665 (tp30) REVERT: B 69 LYS cc_start: 0.8776 (mtmm) cc_final: 0.8543 (mttt) REVERT: B 107 GLN cc_start: 0.8624 (tt0) cc_final: 0.8304 (tt0) REVERT: E 531 ARG cc_start: 0.7250 (pmt170) cc_final: 0.6393 (mtm-85) REVERT: F 184 ASP cc_start: 0.8468 (OUTLIER) cc_final: 0.8173 (m-30) REVERT: F 188 ASP cc_start: 0.8434 (m-30) cc_final: 0.8121 (t70) outliers start: 16 outliers final: 8 residues processed: 152 average time/residue: 0.6790 time to fit residues: 112.9120 Evaluate side-chains 141 residues out of total 1441 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 132 time to evaluate : 0.507 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 142 ASP Chi-restraints excluded: chain C residue 213 VAL Chi-restraints excluded: chain E residue 367 CYS Chi-restraints excluded: chain E residue 372 ILE Chi-restraints excluded: chain E residue 395 GLU Chi-restraints excluded: chain E residue 420 VAL Chi-restraints excluded: chain F residue 184 ASP Chi-restraints excluded: chain F residue 311 SER Chi-restraints excluded: chain F residue 339 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 179 random chunks: chunk 107 optimal weight: 0.1980 chunk 59 optimal weight: 2.9990 chunk 21 optimal weight: 0.6980 chunk 52 optimal weight: 4.9990 chunk 24 optimal weight: 5.9990 chunk 44 optimal weight: 0.5980 chunk 175 optimal weight: 4.9990 chunk 73 optimal weight: 0.9980 chunk 141 optimal weight: 0.6980 chunk 101 optimal weight: 3.9990 chunk 18 optimal weight: 1.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 146 GLN F 318 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3526 r_free = 0.3526 target = 0.130867 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3301 r_free = 0.3301 target = 0.113936 restraints weight = 20585.316| |-----------------------------------------------------------------------------| r_work (start): 0.3305 rms_B_bonded: 1.32 r_work: 0.3198 rms_B_bonded: 2.17 restraints_weight: 0.5000 r_work: 0.3078 rms_B_bonded: 3.67 restraints_weight: 0.2500 r_work (final): 0.3078 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3081 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3081 r_free = 0.3081 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3081 r_free = 0.3081 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3081 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8745 moved from start: 0.2398 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 15509 Z= 0.116 Angle : 0.608 12.701 21335 Z= 0.282 Chirality : 0.050 0.530 2481 Planarity : 0.005 0.049 2492 Dihedral : 13.228 176.921 2683 Min Nonbonded Distance : 2.321 Molprobity Statistics. All-atom Clashscore : 5.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.89 % Favored : 98.11 % Rotamer: Outliers : 0.90 % Allowed : 15.06 % Favored : 84.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % 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: 1.53 (0.20), residues: 1749 helix: 2.13 (0.17), residues: 894 sheet: 0.05 (0.34), residues: 220 loop : -0.19 (0.24), residues: 635 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 226 TYR 0.009 0.001 TYR E 484 PHE 0.011 0.001 PHE E 397 TRP 0.013 0.001 TRP E 143 HIS 0.002 0.001 HIS C 109 Details of bonding type rmsd/Z covalent geometry : bond 0.00265 / 0.12 (15505) covalent geometry : angle 0.60803 / 0.28 (21332) hydrogen bonds : bond 0.03618 / 2.47 ( 776) hydrogen bonds : angle 4.16095 / 2.96 ( 2208) metal coordination : bond 0.00787 / 0.40 ( 4) metal coordination : angle 1.96520 / 1.03 ( 3) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3498 Ramachandran restraints generated. 1749 Oldfield, 0 Emsley, 1749 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3498 Ramachandran restraints generated. 1749 Oldfield, 0 Emsley, 1749 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 1441 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 143 time to evaluate : 0.543 Fit side-chains REVERT: A 44 ASN cc_start: 0.7608 (m-40) cc_final: 0.7327 (t0) REVERT: B 69 LYS cc_start: 0.8737 (mtmm) cc_final: 0.8494 (mttt) REVERT: B 107 GLN cc_start: 0.8614 (tt0) cc_final: 0.8234 (tt0) REVERT: C 143 GLN cc_start: 0.7474 (OUTLIER) cc_final: 0.7087 (mm-40) REVERT: E 148 MET cc_start: 0.7925 (mtm) cc_final: 0.7549 (mtp) REVERT: E 531 ARG cc_start: 0.7150 (pmt170) cc_final: 0.6443 (mtm-85) REVERT: F 184 ASP cc_start: 0.8302 (OUTLIER) cc_final: 0.8004 (m-30) REVERT: F 188 ASP cc_start: 0.8417 (m-30) cc_final: 0.8115 (t70) outliers start: 13 outliers final: 7 residues processed: 151 average time/residue: 0.6454 time to fit residues: 106.6304 Evaluate side-chains 142 residues out of total 1441 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 133 time to evaluate : 0.434 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 142 ASP Chi-restraints excluded: chain C residue 143 GLN Chi-restraints excluded: chain C residue 213 VAL Chi-restraints excluded: chain E residue 367 CYS Chi-restraints excluded: chain E residue 372 ILE Chi-restraints excluded: chain E residue 395 GLU Chi-restraints excluded: chain E residue 420 VAL Chi-restraints excluded: chain F residue 184 ASP Chi-restraints excluded: chain F residue 311 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 179 random chunks: chunk 106 optimal weight: 0.9980 chunk 33 optimal weight: 1.9990 chunk 74 optimal weight: 5.9990 chunk 83 optimal weight: 1.9990 chunk 0 optimal weight: 6.9990 chunk 168 optimal weight: 0.9980 chunk 36 optimal weight: 0.6980 chunk 39 optimal weight: 3.9990 chunk 65 optimal weight: 0.2980 chunk 140 optimal weight: 1.9990 chunk 90 optimal weight: 0.9980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 146 GLN D 152 ASN E 580 HIS F 147 GLN F 318 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3519 r_free = 0.3519 target = 0.130619 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3297 r_free = 0.3297 target = 0.113904 restraints weight = 20603.810| |-----------------------------------------------------------------------------| r_work (start): 0.3296 rms_B_bonded: 1.30 r_work: 0.3188 rms_B_bonded: 2.14 restraints_weight: 0.5000 r_work: 0.3069 rms_B_bonded: 3.63 restraints_weight: 0.2500 r_work (final): 0.3069 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3071 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3071 r_free = 0.3071 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3071 r_free = 0.3071 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3071 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8756 moved from start: 0.2388 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 15509 Z= 0.126 Angle : 0.618 13.115 21335 Z= 0.286 Chirality : 0.050 0.538 2481 Planarity : 0.005 0.049 2492 Dihedral : 13.221 175.991 2683 Min Nonbonded Distance : 2.323 Molprobity Statistics. All-atom Clashscore : 4.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer: Outliers : 1.11 % Allowed : 15.06 % Favored : 83.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % 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: 1.50 (0.20), residues: 1749 helix: 2.09 (0.17), residues: 895 sheet: 0.03 (0.34), residues: 220 loop : -0.18 (0.24), residues: 634 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 226 TYR 0.010 0.001 TYR E 484 PHE 0.018 0.001 PHE E 518 TRP 0.012 0.001 TRP E 143 HIS 0.002 0.001 HIS C 109 Details of bonding type rmsd/Z covalent geometry : bond 0.00293 / 0.13 (15505) covalent geometry : angle 0.61761 / 0.29 (21332) hydrogen bonds : bond 0.03793 / 2.59 ( 776) hydrogen bonds : angle 4.18810 / 2.98 ( 2208) metal coordination : bond 0.00733 / 0.37 ( 4) metal coordination : angle 2.09883 / 1.10 ( 3) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4903.09 seconds wall clock time: 84 minutes 29.12 seconds (5069.12 seconds total)