Starting phenix.real_space_refine on Wed Mar 4 18:16:10 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7onu_13002/03_2026/7onu_13002.cif Found real_map, /net/cci-nas-00/data/ceres_data/7onu_13002/03_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_13002/03_2026/7onu_13002.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7onu_13002/03_2026/7onu_13002.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7onu_13002/03_2026/7onu_13002.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7onu_13002/03_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): 0.01s 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: 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: {'RNA': 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: 3.43, per 1000 atoms: 0.23 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: 1.68 Conformation dependent library (CDL) restraints added in 659.0 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: 1.60 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: 2.49 Time building geometry restraints manager: 2.09 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: 20729 1.42 - 2.84: 435 2.84 - 4.26: 131 4.26 - 5.68: 31 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 - 30.90: 9138 30.90 - 61.80: 307 61.80 - 92.71: 79 92.71 - 123.61: 0 123.61 - 154.51: 1 Dihedral angle restraints: 9525 sinusoidal: 4522 harmonic: 5003 Sorted by residual: dihedral pdb=" O4' U T 50 " pdb=" C1' U T 50 " pdb=" N1 U T 50 " pdb=" C2 U T 50 " ideal model delta sinusoidal sigma weight residual 200.00 45.49 154.51 1 1.50e+01 4.44e-03 8.12e+01 dihedral pdb=" CA GLU C 232 " pdb=" C GLU C 232 " pdb=" N TYR C 233 " pdb=" CA TYR C 233 " ideal model delta harmonic sigma weight residual 180.00 160.23 19.77 0 5.00e+00 4.00e-02 1.56e+01 dihedral pdb=" CA LEU F 182 " pdb=" C LEU F 182 " pdb=" N TRP F 183 " pdb=" CA TRP F 183 " ideal model delta harmonic sigma weight residual -180.00 -162.43 -17.57 0 5.00e+00 4.00e-02 1.23e+01 ... (remaining 9522 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.044: 2008 0.044 - 0.088: 330 0.088 - 0.132: 134 0.132 - 0.176: 4 0.176 - 0.219: 5 Chirality restraints: 2481 Sorted by residual: chirality pdb=" CA PHE F 97 " pdb=" N PHE F 97 " pdb=" C PHE F 97 " pdb=" CB PHE F 97 " both_signs ideal model delta sigma weight residual False 2.51 2.73 -0.22 2.00e-01 2.50e+01 1.20e+00 chirality pdb=" C1D NAD D 301 " pdb=" C2D NAD D 301 " pdb=" N1N NAD D 301 " pdb=" O4D NAD D 301 " both_signs ideal model delta sigma weight residual False 2.41 2.63 -0.22 2.00e-01 2.50e+01 1.18e+00 chirality pdb=" C1D NAD C 301 " pdb=" C2D NAD C 301 " pdb=" N1N NAD C 301 " pdb=" O4D NAD C 301 " both_signs ideal model delta sigma weight residual False 2.41 2.63 -0.22 2.00e-01 2.50e+01 1.16e+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: 5.020 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: 0.240 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 16.700 Find NCS groups from input model: 0.170 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: 0.010 Load rotamer database and sin/cos tables:6.050 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.270 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7770 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= 0.214 Angle : 0.590 8.558 21335 Z= 0.298 Chirality : 0.040 0.219 2481 Planarity : 0.005 0.056 2492 Dihedral : 16.016 154.509 6315 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 covalent geometry : bond 0.00453 (15505) covalent geometry : angle 0.58487 (21332) hydrogen bonds : bond 0.14149 ( 776) hydrogen bonds : angle 6.10299 ( 2208) metal coordination : bond 0.01507 ( 4) metal coordination : angle 6.57466 ( 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 : 0.579 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: 0.7337 time to fit residues: 183.8511 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 : 0.569 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: B 115 GLN B 146 GLN B 220 GLN C 260 GLN D 220 GLN E 222 HIS E 273 HIS E 530 ASN E 540 GLN E 580 HIS F 147 GLN F 222 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3476 r_free = 0.3476 target = 0.127471 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3245 r_free = 0.3245 target = 0.110406 restraints weight = 20756.737| |-----------------------------------------------------------------------------| r_work (start): 0.3246 rms_B_bonded: 1.43 r_work: 0.3139 rms_B_bonded: 2.23 restraints_weight: 0.5000 r_work: 0.3017 rms_B_bonded: 3.76 restraints_weight: 0.2500 r_work (final): 0.3017 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3024 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3024 r_free = 0.3024 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.72 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3024 r_free = 0.3024 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.29 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3024 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8537 moved from start: 0.1350 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.066 15509 Z= 0.127 Angle : 0.548 10.589 21335 Z= 0.281 Chirality : 0.040 0.141 2481 Planarity : 0.005 0.053 2492 Dihedral : 15.253 153.348 3101 Min Nonbonded Distance : 2.393 Molprobity Statistics. All-atom Clashscore : 4.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.83 % Favored : 98.17 % Rotamer: Outliers : 1.80 % Allowed : 7.22 % Favored : 90.98 % 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: 1.07 (0.20), residues: 1749 helix: 1.69 (0.17), residues: 897 sheet: -0.13 (0.34), residues: 220 loop : -0.32 (0.24), residues: 632 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 384 TYR 0.011 0.001 TYR E 484 PHE 0.014 0.001 PHE E 518 TRP 0.017 0.001 TRP E 326 HIS 0.004 0.001 HIS E 580 Details of bonding type rmsd covalent geometry : bond 0.00293 (15505) covalent geometry : angle 0.54599 (21332) hydrogen bonds : bond 0.04269 ( 776) hydrogen bonds : angle 4.58489 ( 2208) metal coordination : bond 0.00628 ( 4) metal coordination : angle 4.31653 ( 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 177 residues out of total 1441 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 151 time to evaluate : 0.439 Fit side-chains REVERT: C 143 GLN cc_start: 0.7660 (OUTLIER) cc_final: 0.7166 (mm-40) REVERT: E 531 ARG cc_start: 0.7423 (OUTLIER) cc_final: 0.7203 (pmt170) REVERT: F 184 ASP cc_start: 0.8319 (OUTLIER) cc_final: 0.7629 (m-30) REVERT: F 188 ASP cc_start: 0.8140 (m-30) cc_final: 0.7793 (m-30) REVERT: F 239 ASP cc_start: 0.8186 (t70) cc_final: 0.7954 (t70) REVERT: F 318 GLN cc_start: 0.8009 (tm-30) cc_final: 0.7563 (tm-30) outliers start: 26 outliers final: 7 residues processed: 167 average time/residue: 0.6771 time to fit residues: 123.3882 Evaluate side-chains 136 residues out of total 1441 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 126 time to evaluate : 0.531 ------------------------------------------------------------------------------- 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 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: 0.7980 chunk 141 optimal weight: 0.1980 chunk 82 optimal weight: 4.9990 chunk 31 optimal weight: 0.6980 chunk 144 optimal weight: 0.9990 chunk 137 optimal weight: 3.9990 chunk 61 optimal weight: 0.9980 chunk 25 optimal weight: 6.9990 chunk 119 optimal weight: 0.5980 chunk 162 optimal weight: 0.0370 overall best weight: 0.4658 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 146 GLN C 50 GLN E 540 GLN F 278 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3506 r_free = 0.3506 target = 0.129555 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3286 r_free = 0.3286 target = 0.113140 restraints weight = 20977.715| |-----------------------------------------------------------------------------| r_work (start): 0.3292 rms_B_bonded: 1.33 r_work: 0.3186 rms_B_bonded: 2.14 restraints_weight: 0.5000 r_work: 0.3068 rms_B_bonded: 3.62 restraints_weight: 0.2500 r_work (final): 0.3068 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3070 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3070 r_free = 0.3070 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.29 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3070 r_free = 0.3070 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.3070 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8513 moved from start: 0.1766 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.052 15509 Z= 0.102 Angle : 0.486 11.923 21335 Z= 0.249 Chirality : 0.039 0.133 2481 Planarity : 0.005 0.052 2492 Dihedral : 15.012 153.362 3101 Min Nonbonded Distance : 2.349 Molprobity Statistics. All-atom Clashscore : 4.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.60 % Favored : 98.40 % Rotamer: Outliers : 1.67 % Allowed : 10.34 % Favored : 87.99 % 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: 2.01 (0.17), residues: 898 sheet: 0.05 (0.34), residues: 220 loop : -0.27 (0.24), residues: 631 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 226 TYR 0.009 0.001 TYR F 137 PHE 0.009 0.001 PHE E 198 TRP 0.014 0.001 TRP E 326 HIS 0.002 0.001 HIS E 504 Details of bonding type rmsd covalent geometry : bond 0.00227 (15505) covalent geometry : angle 0.48547 (21332) hydrogen bonds : bond 0.03590 ( 776) hydrogen bonds : angle 4.27550 ( 2208) metal coordination : bond 0.00789 ( 4) metal coordination : angle 2.71318 ( 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 172 residues out of total 1441 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 148 time to evaluate : 0.414 Fit side-chains revert: symmetry clash REVERT: A 52 LYS cc_start: 0.8434 (tptp) cc_final: 0.8193 (tmtp) REVERT: B 104 LYS cc_start: 0.8377 (mptt) cc_final: 0.7983 (mtpt) REVERT: D 142 ASP cc_start: 0.7155 (t70) cc_final: 0.6849 (t0) REVERT: D 226 ARG cc_start: 0.8625 (ptt90) cc_final: 0.8269 (ptm160) REVERT: F 110 GLU cc_start: 0.7207 (tt0) cc_final: 0.6867 (tp30) REVERT: F 184 ASP cc_start: 0.8398 (OUTLIER) cc_final: 0.8102 (m-30) REVERT: F 188 ASP cc_start: 0.8269 (m-30) cc_final: 0.8058 (t70) REVERT: F 239 ASP cc_start: 0.8172 (t70) cc_final: 0.7968 (t70) outliers start: 24 outliers final: 5 residues processed: 163 average time/residue: 0.6445 time to fit residues: 114.7187 Evaluate side-chains 138 residues out of total 1441 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 132 time to evaluate : 0.422 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 257 ILE Chi-restraints excluded: chain C residue 213 VAL Chi-restraints excluded: chain E residue 367 CYS 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 179 random chunks: chunk 96 optimal weight: 0.6980 chunk 51 optimal weight: 0.9980 chunk 145 optimal weight: 0.6980 chunk 75 optimal weight: 5.9990 chunk 70 optimal weight: 2.9990 chunk 115 optimal weight: 0.5980 chunk 114 optimal weight: 2.9990 chunk 12 optimal weight: 0.9990 chunk 125 optimal weight: 0.6980 chunk 3 optimal weight: 0.9990 chunk 72 optimal weight: 0.6980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 146 GLN D 152 ASN E 437 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3489 r_free = 0.3489 target = 0.128177 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3266 r_free = 0.3266 target = 0.111735 restraints weight = 20934.728| |-----------------------------------------------------------------------------| r_work (start): 0.3272 rms_B_bonded: 1.33 r_work: 0.3168 rms_B_bonded: 2.12 restraints_weight: 0.5000 r_work: 0.3049 rms_B_bonded: 3.59 restraints_weight: 0.2500 r_work (final): 0.3049 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3056 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3056 r_free = 0.3056 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 = 0.3056 r_free = 0.3056 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.3056 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8527 moved from start: 0.1868 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= 0.112 Angle : 0.494 12.613 21335 Z= 0.252 Chirality : 0.039 0.134 2481 Planarity : 0.005 0.050 2492 Dihedral : 14.884 153.651 3099 Min Nonbonded Distance : 2.160 Molprobity Statistics. All-atom Clashscore : 4.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.77 % Favored : 98.23 % Rotamer: Outliers : 1.60 % Allowed : 11.38 % 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: 1.47 (0.20), residues: 1749 helix: 2.08 (0.17), residues: 898 sheet: 0.07 (0.34), residues: 220 loop : -0.25 (0.24), residues: 631 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 226 TYR 0.010 0.001 TYR E 484 PHE 0.020 0.001 PHE E 518 TRP 0.012 0.001 TRP E 326 HIS 0.002 0.001 HIS C 109 Details of bonding type rmsd covalent geometry : bond 0.00258 (15505) covalent geometry : angle 0.49373 (21332) hydrogen bonds : bond 0.03654 ( 776) hydrogen bonds : angle 4.22484 ( 2208) metal coordination : bond 0.00704 ( 4) metal coordination : angle 2.24970 ( 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: 23 poor density : 146 time to evaluate : 0.506 Fit side-chains revert: symmetry clash REVERT: B 104 LYS cc_start: 0.8400 (mptt) cc_final: 0.8014 (mtpt) REVERT: B 107 GLN cc_start: 0.8256 (tt0) cc_final: 0.7814 (tt0) REVERT: B 116 ARG cc_start: 0.8171 (ttp80) cc_final: 0.7933 (ttp-170) REVERT: D 79 LYS cc_start: 0.8332 (OUTLIER) cc_final: 0.7837 (mtpt) REVERT: D 142 ASP cc_start: 0.7227 (t70) cc_final: 0.6856 (t0) REVERT: E 531 ARG cc_start: 0.7333 (OUTLIER) cc_final: 0.6109 (mtm-85) REVERT: F 110 GLU cc_start: 0.7216 (tt0) cc_final: 0.6876 (tp30) REVERT: F 184 ASP cc_start: 0.8430 (OUTLIER) cc_final: 0.8138 (m-30) REVERT: F 188 ASP cc_start: 0.8384 (m-30) cc_final: 0.8147 (t70) outliers start: 23 outliers final: 11 residues processed: 160 average time/residue: 0.6850 time to fit residues: 119.3803 Evaluate side-chains 143 residues out of total 1441 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 129 time to evaluate : 0.448 ------------------------------------------------------------------------------- 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 213 VAL Chi-restraints excluded: chain D residue 79 LYS 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 395 GLU Chi-restraints excluded: chain E residue 475 ILE Chi-restraints excluded: chain E residue 531 ARG Chi-restraints excluded: chain E residue 572 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 179 random chunks: chunk 115 optimal weight: 0.6980 chunk 166 optimal weight: 3.9990 chunk 99 optimal weight: 5.9990 chunk 7 optimal weight: 3.9990 chunk 95 optimal weight: 0.9980 chunk 159 optimal weight: 0.9990 chunk 49 optimal weight: 5.9990 chunk 136 optimal weight: 0.9990 chunk 69 optimal weight: 0.0060 chunk 5 optimal weight: 4.9990 chunk 74 optimal weight: 0.0030 overall best weight: 0.5408 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 146 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3499 r_free = 0.3499 target = 0.128955 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3277 r_free = 0.3277 target = 0.112490 restraints weight = 21035.491| |-----------------------------------------------------------------------------| r_work (start): 0.3290 rms_B_bonded: 1.33 r_work: 0.3184 rms_B_bonded: 2.14 restraints_weight: 0.5000 r_work: 0.3066 rms_B_bonded: 3.63 restraints_weight: 0.2500 r_work (final): 0.3066 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3066 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3066 r_free = 0.3066 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 = 0.3066 r_free = 0.3066 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.3066 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8512 moved from start: 0.2010 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= 0.102 Angle : 0.479 12.332 21335 Z= 0.242 Chirality : 0.038 0.133 2481 Planarity : 0.005 0.049 2492 Dihedral : 14.768 153.582 3099 Min Nonbonded Distance : 2.323 Molprobity Statistics. All-atom Clashscore : 4.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.66 % Favored : 98.34 % Rotamer: Outliers : 1.60 % Allowed : 11.80 % 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: 1.57 (0.20), residues: 1749 helix: 2.21 (0.17), residues: 893 sheet: 0.06 (0.34), residues: 220 loop : -0.25 (0.24), residues: 636 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 226 TYR 0.009 0.001 TYR E 484 PHE 0.012 0.001 PHE E 518 TRP 0.012 0.001 TRP E 326 HIS 0.002 0.001 HIS E 504 Details of bonding type rmsd covalent geometry : bond 0.00231 (15505) covalent geometry : angle 0.47819 (21332) hydrogen bonds : bond 0.03417 ( 776) hydrogen bonds : angle 4.14234 ( 2208) metal coordination : bond 0.00732 ( 4) metal coordination : angle 2.06072 ( 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 165 residues out of total 1441 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 142 time to evaluate : 0.447 Fit side-chains REVERT: B 69 LYS cc_start: 0.8771 (mtmm) cc_final: 0.8551 (mttt) REVERT: B 107 GLN cc_start: 0.8258 (tt0) cc_final: 0.7913 (tt0) REVERT: C 123 MET cc_start: 0.8239 (tmm) cc_final: 0.8013 (ttp) REVERT: C 143 GLN cc_start: 0.7458 (OUTLIER) cc_final: 0.7100 (mm-40) REVERT: D 79 LYS cc_start: 0.8302 (OUTLIER) cc_final: 0.8097 (mtpp) REVERT: D 142 ASP cc_start: 0.7347 (t70) cc_final: 0.7077 (t0) REVERT: D 226 ARG cc_start: 0.8581 (OUTLIER) cc_final: 0.8121 (ptt180) REVERT: E 531 ARG cc_start: 0.7320 (OUTLIER) cc_final: 0.6187 (mtm-85) REVERT: F 110 GLU cc_start: 0.7216 (tt0) cc_final: 0.6874 (tp30) REVERT: F 184 ASP cc_start: 0.8427 (OUTLIER) cc_final: 0.8139 (m-30) REVERT: F 188 ASP cc_start: 0.8401 (m-30) cc_final: 0.8121 (t70) outliers start: 23 outliers final: 7 residues processed: 156 average time/residue: 0.6809 time to fit residues: 115.5051 Evaluate side-chains 145 residues out of total 1441 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 133 time to evaluate : 0.598 ------------------------------------------------------------------------------- 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 372 ILE Chi-restraints excluded: chain E residue 395 GLU Chi-restraints excluded: chain E residue 475 ILE Chi-restraints excluded: chain E residue 531 ARG Chi-restraints excluded: chain F residue 184 ASP Chi-restraints excluded: chain F residue 311 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 179 random chunks: chunk 66 optimal weight: 0.7980 chunk 152 optimal weight: 0.9990 chunk 46 optimal weight: 3.9990 chunk 105 optimal weight: 0.1980 chunk 82 optimal weight: 0.9980 chunk 39 optimal weight: 4.9990 chunk 100 optimal weight: 0.0050 chunk 27 optimal weight: 4.9990 chunk 65 optimal weight: 0.6980 chunk 97 optimal weight: 0.9980 chunk 102 optimal weight: 0.0060 overall best weight: 0.3410 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 146 GLN C 162 GLN D 127 ASN D 152 ASN F 318 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3529 r_free = 0.3529 target = 0.131201 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.114330 restraints weight = 20860.473| |-----------------------------------------------------------------------------| r_work (start): 0.3310 rms_B_bonded: 1.40 r_work: 0.3201 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work: 0.3080 rms_B_bonded: 3.82 restraints_weight: 0.2500 r_work (final): 0.3080 ------------------------------------------------------------------------------- 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 | |-----------------------------------------------------------------------------| r_final: 0.3081 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8493 moved from start: 0.2223 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 15509 Z= 0.093 Angle : 0.468 12.100 21335 Z= 0.237 Chirality : 0.038 0.131 2481 Planarity : 0.005 0.050 2492 Dihedral : 14.622 153.156 3099 Min Nonbonded Distance : 2.308 Molprobity Statistics. All-atom Clashscore : 4.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.94 % Favored : 98.06 % Rotamer: Outliers : 1.18 % Allowed : 12.77 % Favored : 86.05 % 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: 1.69 (0.20), residues: 1749 helix: 2.34 (0.17), residues: 891 sheet: 0.10 (0.35), residues: 220 loop : -0.23 (0.24), residues: 638 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 226 TYR 0.008 0.001 TYR B 168 PHE 0.009 0.001 PHE E 518 TRP 0.011 0.001 TRP E 326 HIS 0.002 0.000 HIS E 504 Details of bonding type rmsd covalent geometry : bond 0.00207 (15505) covalent geometry : angle 0.46730 (21332) hydrogen bonds : bond 0.03136 ( 776) hydrogen bonds : angle 4.04700 ( 2208) metal coordination : bond 0.00680 ( 4) metal coordination : angle 1.78672 ( 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: 17 poor density : 141 time to evaluate : 0.572 Fit side-chains revert: symmetry clash REVERT: B 69 LYS cc_start: 0.8733 (mtmm) cc_final: 0.8505 (mttt) REVERT: B 107 GLN cc_start: 0.8267 (tt0) cc_final: 0.7927 (tt0) REVERT: C 123 MET cc_start: 0.8257 (tmm) cc_final: 0.8030 (ttp) REVERT: C 138 GLN cc_start: 0.7810 (mm110) cc_final: 0.7402 (mt0) REVERT: C 143 GLN cc_start: 0.7442 (OUTLIER) cc_final: 0.7106 (mm-40) REVERT: D 79 LYS cc_start: 0.8265 (OUTLIER) cc_final: 0.8061 (mtpp) REVERT: D 226 ARG cc_start: 0.8577 (OUTLIER) cc_final: 0.8062 (ptt180) REVERT: E 148 MET cc_start: 0.7846 (mtm) cc_final: 0.7531 (mtp) REVERT: E 531 ARG cc_start: 0.7234 (OUTLIER) cc_final: 0.6150 (mtm-85) REVERT: F 110 GLU cc_start: 0.7235 (tt0) cc_final: 0.6893 (tp30) REVERT: F 184 ASP cc_start: 0.8448 (OUTLIER) cc_final: 0.8170 (m-30) REVERT: F 188 ASP cc_start: 0.8408 (m-30) cc_final: 0.8138 (t70) outliers start: 17 outliers final: 6 residues processed: 151 average time/residue: 0.6906 time to fit residues: 113.5169 Evaluate side-chains 145 residues out of total 1441 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 134 time to evaluate : 0.354 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 142 ASP Chi-restraints excluded: chain C residue 143 GLN 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 372 ILE Chi-restraints excluded: chain E residue 395 GLU Chi-restraints excluded: chain E residue 475 ILE Chi-restraints excluded: chain E residue 531 ARG 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: 0.8980 chunk 73 optimal weight: 2.9990 chunk 112 optimal weight: 3.9990 chunk 72 optimal weight: 0.9990 chunk 103 optimal weight: 6.9990 chunk 11 optimal weight: 3.9990 chunk 64 optimal weight: 3.9990 chunk 96 optimal weight: 0.9990 chunk 135 optimal weight: 4.9990 chunk 157 optimal weight: 0.6980 chunk 147 optimal weight: 2.9990 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 146 GLN D 152 ASN F 318 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.126190 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3227 r_free = 0.3227 target = 0.109073 restraints weight = 20862.242| |-----------------------------------------------------------------------------| r_work (start): 0.3227 rms_B_bonded: 1.41 r_work: 0.3117 rms_B_bonded: 2.23 restraints_weight: 0.5000 r_work: 0.2996 rms_B_bonded: 3.76 restraints_weight: 0.2500 r_work (final): 0.2996 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3003 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3003 r_free = 0.3003 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3003 r_free = 0.3003 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.3003 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8579 moved from start: 0.1962 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 15509 Z= 0.155 Angle : 0.539 13.350 21335 Z= 0.270 Chirality : 0.040 0.138 2481 Planarity : 0.005 0.049 2492 Dihedral : 14.767 154.663 3099 Min Nonbonded Distance : 2.324 Molprobity Statistics. All-atom Clashscore : 4.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer: Outliers : 1.60 % Allowed : 12.91 % 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: 1.43 (0.20), residues: 1749 helix: 2.02 (0.17), residues: 900 sheet: 0.00 (0.34), residues: 220 loop : -0.22 (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 0.014 0.001 PHE E 397 TRP 0.011 0.001 TRP E 326 HIS 0.004 0.001 HIS F 242 Details of bonding type rmsd covalent geometry : bond 0.00370 (15505) covalent geometry : angle 0.53821 (21332) hydrogen bonds : bond 0.04211 ( 776) hydrogen bonds : angle 4.28337 ( 2208) metal coordination : bond 0.00748 ( 4) metal coordination : angle 2.53315 ( 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 170 residues out of total 1441 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 147 time to evaluate : 0.474 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 44 ASN cc_start: 0.7576 (m-40) cc_final: 0.7289 (t0) REVERT: B 69 LYS cc_start: 0.8790 (mtmm) cc_final: 0.8558 (mttt) REVERT: B 107 GLN cc_start: 0.8279 (tt0) cc_final: 0.8073 (tt0) REVERT: C 143 GLN cc_start: 0.7504 (OUTLIER) cc_final: 0.7099 (mm-40) REVERT: D 79 LYS cc_start: 0.8340 (OUTLIER) cc_final: 0.7857 (mtpt) REVERT: D 142 ASP cc_start: 0.6977 (t0) cc_final: 0.6665 (t0) REVERT: D 226 ARG cc_start: 0.8622 (OUTLIER) cc_final: 0.8171 (ptt180) REVERT: E 531 ARG cc_start: 0.7267 (OUTLIER) cc_final: 0.6066 (mtm-85) REVERT: F 184 ASP cc_start: 0.8486 (OUTLIER) cc_final: 0.8181 (m-30) REVERT: F 188 ASP cc_start: 0.8407 (m-30) cc_final: 0.8109 (t70) outliers start: 23 outliers final: 9 residues processed: 158 average time/residue: 0.7517 time to fit residues: 128.2069 Evaluate side-chains 151 residues out of total 1441 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 137 time to evaluate : 0.550 ------------------------------------------------------------------------------- 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 E residue 466 GLN Chi-restraints excluded: chain E residue 475 ILE Chi-restraints excluded: chain E residue 531 ARG 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: 0.9980 chunk 21 optimal weight: 0.8980 chunk 169 optimal weight: 5.9990 chunk 18 optimal weight: 2.9990 chunk 157 optimal weight: 0.6980 chunk 60 optimal weight: 3.9990 chunk 132 optimal weight: 2.9990 chunk 16 optimal weight: 3.9990 chunk 70 optimal weight: 2.9990 chunk 175 optimal weight: 6.9990 chunk 73 optimal weight: 1.9990 overall best weight: 1.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 146 GLN C 102 ASN F 318 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3450 r_free = 0.3450 target = 0.125674 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3219 r_free = 0.3219 target = 0.108988 restraints weight = 21085.382| |-----------------------------------------------------------------------------| r_work (start): 0.3216 rms_B_bonded: 1.34 r_work: 0.3109 rms_B_bonded: 2.13 restraints_weight: 0.5000 r_work: 0.2991 rms_B_bonded: 3.58 restraints_weight: 0.2500 r_work (final): 0.2991 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2990 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2990 r_free = 0.2990 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2990 r_free = 0.2990 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.2990 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8587 moved from start: 0.1916 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 15509 Z= 0.175 Angle : 0.563 13.379 21335 Z= 0.283 Chirality : 0.041 0.144 2481 Planarity : 0.005 0.050 2492 Dihedral : 14.873 154.640 3099 Min Nonbonded Distance : 2.317 Molprobity Statistics. All-atom Clashscore : 4.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 1.87 % Allowed : 13.12 % Favored : 85.01 % 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: 1.25 (0.20), residues: 1749 helix: 1.88 (0.17), residues: 900 sheet: -0.12 (0.33), residues: 222 loop : -0.29 (0.24), residues: 627 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 226 TYR 0.015 0.001 TYR E 484 PHE 0.016 0.001 PHE E 397 TRP 0.011 0.001 TRP E 326 HIS 0.004 0.001 HIS C 109 Details of bonding type rmsd covalent geometry : bond 0.00419 (15505) covalent geometry : angle 0.56237 (21332) hydrogen bonds : bond 0.04458 ( 776) hydrogen bonds : angle 4.38143 ( 2208) metal coordination : bond 0.00766 ( 4) metal coordination : angle 2.67351 ( 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 172 residues out of total 1441 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 145 time to evaluate : 0.544 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 44 ASN cc_start: 0.7574 (m-40) cc_final: 0.7281 (t0) REVERT: B 69 LYS cc_start: 0.8790 (mtmm) cc_final: 0.8553 (mttt) REVERT: B 107 GLN cc_start: 0.8333 (tt0) cc_final: 0.8127 (tt0) REVERT: C 140 GLU cc_start: 0.8595 (OUTLIER) cc_final: 0.8143 (mp0) REVERT: C 143 GLN cc_start: 0.7479 (OUTLIER) cc_final: 0.7061 (mm-40) REVERT: D 142 ASP cc_start: 0.7173 (t0) cc_final: 0.6913 (t0) REVERT: D 194 MET cc_start: 0.9187 (mmm) cc_final: 0.8963 (mmm) REVERT: E 501 MET cc_start: 0.8943 (mtp) cc_final: 0.8731 (mtp) REVERT: E 531 ARG cc_start: 0.7311 (OUTLIER) cc_final: 0.6110 (mtm-85) REVERT: F 184 ASP cc_start: 0.8497 (OUTLIER) cc_final: 0.8178 (m-30) REVERT: F 188 ASP cc_start: 0.8362 (m-30) cc_final: 0.8071 (t70) outliers start: 27 outliers final: 9 residues processed: 159 average time/residue: 0.7165 time to fit residues: 123.8094 Evaluate side-chains 150 residues out of total 1441 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 137 time to evaluate : 0.473 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 140 GLU 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 387 THR Chi-restraints excluded: chain E residue 395 GLU Chi-restraints excluded: chain E residue 466 GLN Chi-restraints excluded: chain E residue 475 ILE Chi-restraints excluded: chain E residue 531 ARG 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: 0.0870 chunk 151 optimal weight: 0.0870 chunk 112 optimal weight: 0.8980 chunk 18 optimal weight: 2.9990 chunk 154 optimal weight: 2.9990 chunk 48 optimal weight: 0.7980 chunk 131 optimal weight: 0.9990 chunk 74 optimal weight: 3.9990 chunk 173 optimal weight: 6.9990 overall best weight: 0.5738 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3493 r_free = 0.3493 target = 0.128442 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3261 r_free = 0.3261 target = 0.111339 restraints weight = 20848.171| |-----------------------------------------------------------------------------| r_work (start): 0.3266 rms_B_bonded: 1.43 r_work: 0.3155 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.3033 rms_B_bonded: 3.78 restraints_weight: 0.2500 r_work (final): 0.3033 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3038 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3038 r_free = 0.3038 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 = 0.3038 r_free = 0.3038 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.3038 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8525 moved from start: 0.2115 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 15509 Z= 0.107 Angle : 0.503 12.311 21335 Z= 0.253 Chirality : 0.039 0.136 2481 Planarity : 0.005 0.050 2492 Dihedral : 14.744 153.931 3099 Min Nonbonded Distance : 2.307 Molprobity Statistics. All-atom Clashscore : 4.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.83 % Favored : 98.17 % Rotamer: Outliers : 1.11 % Allowed : 14.23 % Favored : 84.66 % 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: 1.52 (0.20), residues: 1749 helix: 2.16 (0.17), residues: 891 sheet: -0.04 (0.34), residues: 220 loop : -0.21 (0.24), residues: 638 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 0.008 0.001 PHE F 241 TRP 0.013 0.001 TRP E 326 HIS 0.002 0.001 HIS E 504 Details of bonding type rmsd covalent geometry : bond 0.00243 (15505) covalent geometry : angle 0.50256 (21332) hydrogen bonds : bond 0.03530 ( 776) hydrogen bonds : angle 4.18567 ( 2208) metal coordination : bond 0.00794 ( 4) metal coordination : angle 2.11161 ( 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 164 residues out of total 1441 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 148 time to evaluate : 0.459 Fit side-chains revert: symmetry clash REVERT: A 44 ASN cc_start: 0.7585 (m-40) cc_final: 0.7270 (t0) REVERT: B 69 LYS cc_start: 0.8716 (mtmm) cc_final: 0.8468 (mttt) REVERT: C 112 GLU cc_start: 0.7988 (mp0) cc_final: 0.7606 (tm-30) REVERT: C 143 GLN cc_start: 0.7433 (OUTLIER) cc_final: 0.7084 (mm-40) REVERT: D 142 ASP cc_start: 0.7119 (t0) cc_final: 0.6815 (t0) REVERT: E 148 MET cc_start: 0.7984 (mtm) cc_final: 0.7623 (mtp) REVERT: E 531 ARG cc_start: 0.7327 (OUTLIER) cc_final: 0.6222 (mtm-85) REVERT: F 184 ASP cc_start: 0.8456 (OUTLIER) cc_final: 0.8157 (m-30) REVERT: F 188 ASP cc_start: 0.8374 (m-30) cc_final: 0.8070 (t70) outliers start: 16 outliers final: 7 residues processed: 156 average time/residue: 0.7190 time to fit residues: 121.5835 Evaluate side-chains 153 residues out of total 1441 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 143 time to evaluate : 0.564 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 142 ASP Chi-restraints excluded: chain C residue 143 GLN Chi-restraints excluded: chain E residue 367 CYS Chi-restraints excluded: chain E residue 387 THR Chi-restraints excluded: chain E residue 395 GLU Chi-restraints excluded: chain E residue 475 ILE Chi-restraints excluded: chain E residue 531 ARG 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: 0.9980 chunk 59 optimal weight: 4.9990 chunk 21 optimal weight: 0.3980 chunk 52 optimal weight: 5.9990 chunk 24 optimal weight: 4.9990 chunk 44 optimal weight: 0.9980 chunk 175 optimal weight: 6.9990 chunk 73 optimal weight: 0.9990 chunk 141 optimal weight: 0.0010 chunk 101 optimal weight: 1.9990 chunk 18 optimal weight: 0.7980 overall best weight: 0.6386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 146 GLN D 152 ASN F 318 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3494 r_free = 0.3494 target = 0.128533 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3265 r_free = 0.3265 target = 0.111592 restraints weight = 20770.390| |-----------------------------------------------------------------------------| r_work (start): 0.3271 rms_B_bonded: 1.39 r_work: 0.3160 rms_B_bonded: 2.23 restraints_weight: 0.5000 r_work: 0.3039 rms_B_bonded: 3.77 restraints_weight: 0.2500 r_work (final): 0.3039 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3044 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3044 r_free = 0.3044 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 = 0.3044 r_free = 0.3044 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.3044 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8538 moved from start: 0.2202 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 15509 Z= 0.109 Angle : 0.502 12.690 21335 Z= 0.253 Chirality : 0.038 0.135 2481 Planarity : 0.005 0.049 2492 Dihedral : 14.683 154.042 3099 Min Nonbonded Distance : 2.302 Molprobity Statistics. All-atom Clashscore : 4.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.89 % Favored : 98.11 % Rotamer: Outliers : 0.97 % Allowed : 14.57 % Favored : 84.46 % 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: 1.55 (0.20), residues: 1749 helix: 2.18 (0.17), residues: 892 sheet: -0.03 (0.34), residues: 220 loop : -0.18 (0.24), residues: 637 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 0.009 0.001 PHE E 397 TRP 0.012 0.001 TRP E 143 HIS 0.002 0.001 HIS E 504 Details of bonding type rmsd covalent geometry : bond 0.00252 (15505) covalent geometry : angle 0.50184 (21332) hydrogen bonds : bond 0.03527 ( 776) hydrogen bonds : angle 4.16026 ( 2208) metal coordination : bond 0.00815 ( 4) metal coordination : angle 2.07440 ( 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 158 residues out of total 1441 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 144 time to evaluate : 0.352 Fit side-chains revert: symmetry clash REVERT: A 44 ASN cc_start: 0.7606 (m-40) cc_final: 0.7302 (t0) REVERT: A 48 GLU cc_start: 0.7845 (pm20) cc_final: 0.7528 (tp30) REVERT: B 69 LYS cc_start: 0.8767 (mtmm) cc_final: 0.8525 (mttt) REVERT: C 138 GLN cc_start: 0.7894 (mm110) cc_final: 0.7416 (mt0) REVERT: C 143 GLN cc_start: 0.7472 (OUTLIER) cc_final: 0.7101 (mm-40) REVERT: D 142 ASP cc_start: 0.7162 (t0) cc_final: 0.6894 (t0) REVERT: E 148 MET cc_start: 0.7904 (mtm) cc_final: 0.7579 (mtp) REVERT: E 531 ARG cc_start: 0.7275 (OUTLIER) cc_final: 0.6217 (mtm-85) REVERT: F 184 ASP cc_start: 0.8489 (OUTLIER) cc_final: 0.8201 (m-30) REVERT: F 188 ASP cc_start: 0.8449 (m-30) cc_final: 0.8149 (t70) outliers start: 14 outliers final: 9 residues processed: 154 average time/residue: 0.6942 time to fit residues: 115.9430 Evaluate side-chains 153 residues out of total 1441 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 141 time to evaluate : 0.529 ------------------------------------------------------------------------------- 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 137 LYS Chi-restraints excluded: chain E residue 367 CYS Chi-restraints excluded: chain E residue 387 THR Chi-restraints excluded: chain E residue 395 GLU Chi-restraints excluded: chain E residue 475 ILE Chi-restraints excluded: chain E residue 531 ARG 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 106 optimal weight: 1.9990 chunk 33 optimal weight: 2.9990 chunk 74 optimal weight: 4.9990 chunk 83 optimal weight: 6.9990 chunk 0 optimal weight: 6.9990 chunk 168 optimal weight: 2.9990 chunk 36 optimal weight: 0.7980 chunk 39 optimal weight: 0.9990 chunk 65 optimal weight: 0.4980 chunk 140 optimal weight: 0.6980 chunk 90 optimal weight: 0.9990 overall best weight: 0.7984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3488 r_free = 0.3488 target = 0.128068 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3257 r_free = 0.3257 target = 0.111058 restraints weight = 20778.830| |-----------------------------------------------------------------------------| r_work (start): 0.3259 rms_B_bonded: 1.40 r_work: 0.3147 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.3027 rms_B_bonded: 3.77 restraints_weight: 0.2500 r_work (final): 0.3027 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3035 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3035 r_free = 0.3035 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 = 0.3035 r_free = 0.3035 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.3035 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8547 moved from start: 0.2193 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= 0.118 Angle : 0.511 12.747 21335 Z= 0.257 Chirality : 0.039 0.136 2481 Planarity : 0.005 0.050 2492 Dihedral : 14.682 154.410 3099 Min Nonbonded Distance : 2.303 Molprobity Statistics. All-atom Clashscore : 4.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.77 % Favored : 98.23 % Rotamer: Outliers : 1.04 % Allowed : 14.57 % 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: 1.52 (0.20), residues: 1749 helix: 2.14 (0.17), residues: 892 sheet: -0.07 (0.34), residues: 222 loop : -0.18 (0.24), residues: 635 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 0.010 0.001 PHE E 397 TRP 0.012 0.001 TRP E 326 HIS 0.002 0.001 HIS E 504 Details of bonding type rmsd covalent geometry : bond 0.00277 (15505) covalent geometry : angle 0.51022 (21332) hydrogen bonds : bond 0.03646 ( 776) hydrogen bonds : angle 4.17934 ( 2208) metal coordination : bond 0.00804 ( 4) metal coordination : angle 2.14191 ( 3) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4826.74 seconds wall clock time: 82 minutes 57.15 seconds (4977.15 seconds total)