Starting phenix.real_space_refine on Tue Dec 31 10:33:20 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7onu_13002/12_2024/7onu_13002.cif Found real_map, /net/cci-nas-00/data/ceres_data/7onu_13002/12_2024/7onu_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/7onu_13002/12_2024/7onu_13002.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7onu_13002/12_2024/7onu_13002.map" model { file = "/net/cci-nas-00/data/ceres_data/7onu_13002/12_2024/7onu_13002.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7onu_13002/12_2024/7onu_13002.cif" } resolution = 3.0 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.006 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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/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: 10.23, per 1000 atoms: 0.68 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: 4.82 Conformation dependent library (CDL) restraints added in 2.0 seconds 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: 4.72 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: 5.13 Time building geometry restraints manager: 4.84 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: 2.920 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: 0.020 Extract box with map and model: 0.610 Check model and map are aligned: 0.110 Set scattering table: 0.140 Process input model: 42.730 Find NCS groups from input model: 0.400 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:13.060 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 60.070 ------------------------------------------------------------------------------- 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 15505 Z= 0.284 Angle : 0.585 7.104 21332 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.53 (0.20), 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 TRP 0.023 0.002 TRP F 101 HIS 0.004 0.001 HIS F 242 PHE 0.019 0.001 PHE F 97 TYR 0.012 0.001 TYR F 289 ARG 0.003 0.000 ARG E 541 *********************** 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 : 1.551 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: 1.6469 time to fit residues: 413.4011 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 : 1.604 ------------------------------------------------------------------------------- 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 151 optimal weight: 8.9990 chunk 135 optimal weight: 0.3980 chunk 75 optimal weight: 5.9990 chunk 46 optimal weight: 0.9990 chunk 91 optimal weight: 0.7980 chunk 72 optimal weight: 2.9990 chunk 140 optimal weight: 0.9980 chunk 54 optimal weight: 6.9990 chunk 85 optimal weight: 4.9990 chunk 104 optimal weight: 3.9990 chunk 162 optimal weight: 8.9990 overall best weight: 1.2384 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** F 147 GLN F 222 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7779 moved from start: 0.1234 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.070 15505 Z= 0.251 Angle : 0.574 10.709 21332 Z= 0.295 Chirality : 0.041 0.143 2481 Planarity : 0.005 0.052 2492 Dihedral : 15.336 153.621 3101 Min Nonbonded Distance : 2.386 Molprobity Statistics. All-atom Clashscore : 3.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.83 % Favored : 98.17 % Rotamer: Outliers : 1.94 % Allowed : 7.43 % Favored : 90.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.95 (0.20), residues: 1749 helix: 1.58 (0.17), residues: 896 sheet: -0.24 (0.36), residues: 196 loop : -0.32 (0.23), residues: 657 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP E 326 HIS 0.005 0.001 HIS E 580 PHE 0.015 0.001 PHE E 518 TYR 0.014 0.001 TYR E 484 ARG 0.007 0.001 ARG E 384 *********************** 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: 28 poor density : 149 time to evaluate : 1.686 Fit side-chains REVERT: B 48 GLU cc_start: 0.7591 (OUTLIER) cc_final: 0.7236 (mp0) REVERT: C 143 GLN cc_start: 0.7217 (OUTLIER) cc_final: 0.6610 (mm-40) REVERT: D 142 ASP cc_start: 0.6935 (t70) cc_final: 0.6269 (t70) REVERT: E 384 ARG cc_start: 0.7736 (ttm-80) cc_final: 0.7414 (ttp-170) REVERT: E 552 THR cc_start: 0.7628 (m) cc_final: 0.7341 (p) REVERT: E 580 HIS cc_start: 0.4855 (m-70) cc_final: 0.4592 (m90) REVERT: F 184 ASP cc_start: 0.7479 (OUTLIER) cc_final: 0.6975 (m-30) REVERT: F 188 ASP cc_start: 0.7439 (m-30) cc_final: 0.7098 (m-30) REVERT: F 318 GLN cc_start: 0.7755 (tm-30) cc_final: 0.7477 (tm-30) outliers start: 28 outliers final: 10 residues processed: 166 average time/residue: 1.5253 time to fit residues: 277.4349 Evaluate side-chains 149 residues out of total 1441 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 136 time to evaluate : 1.618 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 48 GLU Chi-restraints excluded: chain C residue 20 SER Chi-restraints excluded: chain C residue 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 572 VAL Chi-restraints excluded: chain F residue 97 PHE Chi-restraints excluded: chain F residue 184 ASP Chi-restraints excluded: chain F residue 311 SER Chi-restraints excluded: chain F residue 339 ASP Chi-restraints excluded: chain F residue 356 MET Chi-restraints excluded: chain F residue 382 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 179 random chunks: chunk 90 optimal weight: 1.9990 chunk 50 optimal weight: 7.9990 chunk 135 optimal weight: 0.0020 chunk 110 optimal weight: 0.7980 chunk 44 optimal weight: 2.9990 chunk 162 optimal weight: 6.9990 chunk 175 optimal weight: 6.9990 chunk 145 optimal weight: 10.0000 chunk 161 optimal weight: 0.7980 chunk 55 optimal weight: 0.9990 chunk 130 optimal weight: 0.3980 overall best weight: 0.5990 ------------------------------------------------------------------------------- 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 E 580 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7732 moved from start: 0.1656 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.052 15505 Z= 0.160 Angle : 0.496 11.652 21332 Z= 0.254 Chirality : 0.039 0.134 2481 Planarity : 0.005 0.052 2492 Dihedral : 15.033 153.583 3101 Min Nonbonded Distance : 2.343 Molprobity Statistics. All-atom Clashscore : 4.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.66 % Favored : 98.34 % Rotamer: Outliers : 1.53 % Allowed : 10.20 % Favored : 88.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.31 (0.20), residues: 1749 helix: 1.92 (0.17), residues: 898 sheet: -0.00 (0.34), residues: 220 loop : -0.28 (0.24), residues: 631 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP E 326 HIS 0.002 0.001 HIS E 504 PHE 0.010 0.001 PHE F 241 TYR 0.009 0.001 TYR F 137 ARG 0.006 0.000 ARG C 226 *********************** 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 173 residues out of total 1441 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 151 time to evaluate : 1.709 Fit side-chains revert: symmetry clash REVERT: B 107 GLN cc_start: 0.7922 (tt0) cc_final: 0.7540 (tt0) REVERT: C 143 GLN cc_start: 0.7164 (OUTLIER) cc_final: 0.6554 (mm-40) REVERT: E 531 ARG cc_start: 0.6528 (pmt170) cc_final: 0.5267 (mtm-85) REVERT: E 552 THR cc_start: 0.7615 (m) cc_final: 0.7413 (p) REVERT: E 571 GLU cc_start: 0.7091 (OUTLIER) cc_final: 0.6809 (pt0) REVERT: F 110 GLU cc_start: 0.6650 (tt0) cc_final: 0.6335 (tp30) REVERT: F 184 ASP cc_start: 0.7504 (OUTLIER) cc_final: 0.7297 (m-30) outliers start: 22 outliers final: 6 residues processed: 164 average time/residue: 1.4640 time to fit residues: 263.0594 Evaluate side-chains 149 residues out of total 1441 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 140 time to evaluate : 1.673 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 143 GLN Chi-restraints excluded: chain C residue 213 VAL Chi-restraints excluded: chain D residue 66 THR Chi-restraints excluded: chain E residue 367 CYS Chi-restraints excluded: chain E residue 372 ILE Chi-restraints excluded: chain E residue 475 ILE Chi-restraints excluded: chain E residue 571 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 160 optimal weight: 0.9990 chunk 122 optimal weight: 0.8980 chunk 84 optimal weight: 0.0470 chunk 18 optimal weight: 1.9990 chunk 77 optimal weight: 5.9990 chunk 109 optimal weight: 0.8980 chunk 163 optimal weight: 0.0570 chunk 173 optimal weight: 6.9990 chunk 85 optimal weight: 1.9990 chunk 154 optimal weight: 0.9980 chunk 46 optimal weight: 2.9990 overall best weight: 0.5796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 146 GLN D 127 ASN D 152 ASN E 437 ASN F 318 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7725 moved from start: 0.1847 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 15505 Z= 0.159 Angle : 0.492 12.282 21332 Z= 0.252 Chirality : 0.039 0.134 2481 Planarity : 0.005 0.050 2492 Dihedral : 14.858 153.612 3099 Min Nonbonded Distance : 2.153 Molprobity Statistics. All-atom Clashscore : 4.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.77 % Favored : 98.23 % Rotamer: Outliers : 1.67 % Allowed : 10.96 % Favored : 87.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.46 (0.20), residues: 1749 helix: 2.06 (0.17), residues: 898 sheet: 0.05 (0.34), residues: 220 loop : -0.25 (0.24), residues: 631 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP E 326 HIS 0.002 0.001 HIS E 580 PHE 0.017 0.001 PHE E 518 TYR 0.009 0.001 TYR E 484 ARG 0.004 0.000 ARG C 226 *********************** 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: 24 poor density : 145 time to evaluate : 1.572 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 107 GLN cc_start: 0.7917 (tt0) cc_final: 0.7492 (tt0) REVERT: C 143 GLN cc_start: 0.7142 (OUTLIER) cc_final: 0.6554 (mm-40) REVERT: E 531 ARG cc_start: 0.6445 (pmt170) cc_final: 0.5319 (mtm-85) REVERT: E 552 THR cc_start: 0.7568 (m) cc_final: 0.7306 (p) REVERT: E 571 GLU cc_start: 0.7091 (OUTLIER) cc_final: 0.6869 (pt0) REVERT: F 110 GLU cc_start: 0.6634 (tt0) cc_final: 0.6325 (tp30) outliers start: 24 outliers final: 9 residues processed: 157 average time/residue: 1.4996 time to fit residues: 257.9798 Evaluate side-chains 150 residues out of total 1441 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 139 time to evaluate : 1.733 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 257 ILE Chi-restraints excluded: chain C residue 142 ASP Chi-restraints excluded: chain C residue 143 GLN Chi-restraints excluded: chain C residue 213 VAL Chi-restraints excluded: chain E residue 367 CYS 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 571 GLU Chi-restraints excluded: chain E residue 572 VAL Chi-restraints excluded: chain F residue 311 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 179 random chunks: chunk 144 optimal weight: 4.9990 chunk 98 optimal weight: 0.9980 chunk 2 optimal weight: 3.9990 chunk 128 optimal weight: 2.9990 chunk 71 optimal weight: 0.9990 chunk 147 optimal weight: 0.8980 chunk 119 optimal weight: 1.9990 chunk 0 optimal weight: 5.9990 chunk 88 optimal weight: 4.9990 chunk 155 optimal weight: 2.9990 chunk 43 optimal weight: 0.9990 overall best weight: 1.1786 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7769 moved from start: 0.1783 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 15505 Z= 0.232 Angle : 0.530 13.215 21332 Z= 0.269 Chirality : 0.040 0.140 2481 Planarity : 0.005 0.050 2492 Dihedral : 14.875 154.546 3099 Min Nonbonded Distance : 2.332 Molprobity Statistics. All-atom Clashscore : 4.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % Rotamer: Outliers : 1.67 % Allowed : 11.94 % Favored : 86.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.31 (0.20), residues: 1749 helix: 1.94 (0.17), residues: 899 sheet: -0.02 (0.34), residues: 220 loop : -0.30 (0.24), residues: 630 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP E 326 HIS 0.003 0.001 HIS C 109 PHE 0.014 0.001 PHE E 397 TYR 0.014 0.001 TYR E 484 ARG 0.004 0.000 ARG C 226 *********************** 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 166 residues out of total 1441 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 142 time to evaluate : 1.549 Fit side-chains revert: symmetry clash REVERT: C 143 GLN cc_start: 0.7156 (OUTLIER) cc_final: 0.6590 (mm-40) REVERT: D 226 ARG cc_start: 0.8459 (OUTLIER) cc_final: 0.8003 (ptt180) REVERT: E 189 MET cc_start: 0.7839 (OUTLIER) cc_final: 0.7622 (mmt) REVERT: E 531 ARG cc_start: 0.6428 (OUTLIER) cc_final: 0.5241 (mtm-85) REVERT: E 552 THR cc_start: 0.7475 (m) cc_final: 0.7101 (p) REVERT: E 571 GLU cc_start: 0.7124 (OUTLIER) cc_final: 0.6887 (pt0) outliers start: 24 outliers final: 9 residues processed: 155 average time/residue: 1.5589 time to fit residues: 264.7499 Evaluate side-chains 150 residues out of total 1441 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 136 time to evaluate : 1.783 ------------------------------------------------------------------------------- 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 66 THR Chi-restraints excluded: chain D residue 226 ARG Chi-restraints excluded: chain E residue 189 MET Chi-restraints excluded: chain E residue 367 CYS Chi-restraints excluded: chain E residue 372 ILE Chi-restraints excluded: chain E residue 395 GLU Chi-restraints excluded: chain E residue 475 ILE Chi-restraints excluded: chain E residue 531 ARG Chi-restraints excluded: chain E residue 571 GLU Chi-restraints excluded: chain F residue 311 SER Chi-restraints excluded: chain F residue 339 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 179 random chunks: chunk 58 optimal weight: 6.9990 chunk 155 optimal weight: 2.9990 chunk 34 optimal weight: 4.9990 chunk 101 optimal weight: 3.9990 chunk 42 optimal weight: 1.9990 chunk 173 optimal weight: 6.9990 chunk 143 optimal weight: 0.7980 chunk 80 optimal weight: 4.9990 chunk 14 optimal weight: 5.9990 chunk 57 optimal weight: 0.8980 chunk 90 optimal weight: 2.9990 overall best weight: 1.9386 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7807 moved from start: 0.1763 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.089 15505 Z= 0.333 Angle : 0.587 13.979 21332 Z= 0.298 Chirality : 0.042 0.148 2481 Planarity : 0.005 0.052 2492 Dihedral : 15.014 154.910 3099 Min Nonbonded Distance : 2.323 Molprobity Statistics. All-atom Clashscore : 4.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer: Outliers : 2.29 % Allowed : 12.35 % Favored : 85.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.08 (0.20), residues: 1749 helix: 1.70 (0.17), residues: 899 sheet: -0.12 (0.33), residues: 220 loop : -0.32 (0.24), residues: 630 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP E 326 HIS 0.005 0.001 HIS C 109 PHE 0.019 0.002 PHE E 397 TYR 0.018 0.001 TYR E 484 ARG 0.007 0.001 ARG C 226 *********************** 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 179 residues out of total 1441 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 146 time to evaluate : 1.701 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 143 GLN cc_start: 0.7177 (OUTLIER) cc_final: 0.6613 (mm-40) REVERT: D 226 ARG cc_start: 0.8455 (OUTLIER) cc_final: 0.8016 (ptt180) REVERT: E 531 ARG cc_start: 0.6260 (OUTLIER) cc_final: 0.5212 (mtm-85) REVERT: E 552 THR cc_start: 0.7475 (m) cc_final: 0.7086 (p) REVERT: E 571 GLU cc_start: 0.7105 (OUTLIER) cc_final: 0.6885 (pt0) outliers start: 33 outliers final: 11 residues processed: 163 average time/residue: 1.6604 time to fit residues: 294.1448 Evaluate side-chains 147 residues out of total 1441 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 132 time to evaluate : 1.707 ------------------------------------------------------------------------------- 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 C residue 232 GLU Chi-restraints excluded: chain D residue 226 ARG 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 E residue 571 GLU Chi-restraints excluded: chain F residue 97 PHE Chi-restraints excluded: chain F residue 311 SER Chi-restraints excluded: chain F residue 339 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 179 random chunks: chunk 166 optimal weight: 6.9990 chunk 19 optimal weight: 0.6980 chunk 98 optimal weight: 0.9980 chunk 126 optimal weight: 3.9990 chunk 97 optimal weight: 1.9990 chunk 145 optimal weight: 0.9990 chunk 96 optimal weight: 0.9980 chunk 172 optimal weight: 0.0030 chunk 107 optimal weight: 0.1980 chunk 105 optimal weight: 0.5980 chunk 79 optimal weight: 6.9990 overall best weight: 0.4990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 146 GLN F 366 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7727 moved from start: 0.2037 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 15505 Z= 0.152 Angle : 0.491 12.491 21332 Z= 0.250 Chirality : 0.039 0.135 2481 Planarity : 0.005 0.050 2492 Dihedral : 14.797 153.826 3099 Min Nonbonded Distance : 2.303 Molprobity Statistics. All-atom Clashscore : 4.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.72 % Favored : 98.28 % Rotamer: Outliers : 1.25 % Allowed : 13.53 % Favored : 85.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.43 (0.20), residues: 1749 helix: 2.09 (0.17), residues: 891 sheet: -0.05 (0.34), residues: 220 loop : -0.28 (0.24), residues: 638 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP E 326 HIS 0.002 0.001 HIS C 109 PHE 0.008 0.001 PHE F 241 TYR 0.010 0.001 TYR B 168 ARG 0.007 0.000 ARG E 457 *********************** 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 162 residues out of total 1441 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 144 time to evaluate : 1.572 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: E 531 ARG cc_start: 0.6469 (pmt170) cc_final: 0.5500 (mtm-85) outliers start: 18 outliers final: 7 residues processed: 154 average time/residue: 1.5458 time to fit residues: 259.4513 Evaluate side-chains 150 residues out of total 1441 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 143 time to evaluate : 1.528 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 142 ASP Chi-restraints excluded: chain E residue 278 MET 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 F residue 311 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 179 random chunks: chunk 106 optimal weight: 2.9990 chunk 68 optimal weight: 3.9990 chunk 103 optimal weight: 6.9990 chunk 51 optimal weight: 1.9990 chunk 33 optimal weight: 4.9990 chunk 109 optimal weight: 2.9990 chunk 117 optimal weight: 0.7980 chunk 85 optimal weight: 3.9990 chunk 16 optimal weight: 4.9990 chunk 135 optimal weight: 4.9990 chunk 156 optimal weight: 5.9990 overall best weight: 2.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 143 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 146 GLN C 162 GLN D 152 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7823 moved from start: 0.1852 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.103 15505 Z= 0.416 Angle : 0.630 14.768 21332 Z= 0.319 Chirality : 0.044 0.150 2481 Planarity : 0.005 0.053 2492 Dihedral : 15.070 155.548 3099 Min Nonbonded Distance : 2.319 Molprobity Statistics. All-atom Clashscore : 3.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.57 % Favored : 97.43 % Rotamer: Outliers : 1.53 % Allowed : 13.81 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.94 (0.20), residues: 1749 helix: 1.59 (0.17), residues: 896 sheet: -0.31 (0.31), residues: 238 loop : -0.35 (0.24), residues: 615 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP E 556 HIS 0.006 0.001 HIS D 109 PHE 0.023 0.002 PHE E 397 TYR 0.020 0.002 TYR E 484 ARG 0.008 0.001 ARG C 226 *********************** 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 165 residues out of total 1441 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 143 time to evaluate : 1.593 Fit side-chains revert: symmetry clash REVERT: C 123 MET cc_start: 0.7694 (tmm) cc_final: 0.7447 (ttp) REVERT: C 143 GLN cc_start: 0.7215 (OUTLIER) cc_final: 0.6638 (mm-40) REVERT: E 457 ARG cc_start: 0.6512 (tpt90) cc_final: 0.5902 (mtp180) REVERT: E 531 ARG cc_start: 0.6370 (OUTLIER) cc_final: 0.5387 (mtm-85) outliers start: 22 outliers final: 7 residues processed: 157 average time/residue: 1.7276 time to fit residues: 294.1726 Evaluate side-chains 151 residues out of total 1441 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 142 time to evaluate : 1.493 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 142 ASP Chi-restraints excluded: chain C residue 143 GLN Chi-restraints excluded: chain C residue 213 VAL Chi-restraints excluded: chain E residue 367 CYS Chi-restraints excluded: chain E residue 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 311 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 179 random chunks: chunk 165 optimal weight: 3.9990 chunk 150 optimal weight: 0.8980 chunk 160 optimal weight: 2.9990 chunk 96 optimal weight: 0.9990 chunk 70 optimal weight: 1.9990 chunk 126 optimal weight: 0.9990 chunk 49 optimal weight: 2.9990 chunk 145 optimal weight: 0.4980 chunk 152 optimal weight: 3.9990 chunk 105 optimal weight: 0.5980 chunk 170 optimal weight: 2.9990 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 Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7761 moved from start: 0.1991 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 15505 Z= 0.187 Angle : 0.522 13.254 21332 Z= 0.265 Chirality : 0.039 0.141 2481 Planarity : 0.005 0.051 2492 Dihedral : 14.926 154.488 3099 Min Nonbonded Distance : 2.298 Molprobity Statistics. All-atom Clashscore : 4.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.94 % Favored : 98.06 % Rotamer: Outliers : 0.97 % Allowed : 14.43 % Favored : 84.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.20 (0.20), residues: 1749 helix: 1.88 (0.17), residues: 897 sheet: -0.17 (0.33), residues: 220 loop : -0.37 (0.24), residues: 632 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP E 326 HIS 0.003 0.001 HIS C 109 PHE 0.009 0.001 PHE E 397 TYR 0.011 0.001 TYR E 484 ARG 0.007 0.000 ARG C 226 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3498 Ramachandran restraints generated. 1749 Oldfield, 0 Emsley, 1749 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3498 Ramachandran restraints generated. 1749 Oldfield, 0 Emsley, 1749 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 1441 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 142 time to evaluate : 1.629 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 48 GLU cc_start: 0.7575 (pm20) cc_final: 0.7138 (pm20) REVERT: D 194 MET cc_start: 0.9062 (mmm) cc_final: 0.8815 (mmm) REVERT: E 531 ARG cc_start: 0.6403 (OUTLIER) cc_final: 0.5476 (mtm-85) outliers start: 14 outliers final: 7 residues processed: 152 average time/residue: 1.5923 time to fit residues: 263.3389 Evaluate side-chains 144 residues out of total 1441 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 136 time to evaluate : 1.538 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 213 VAL Chi-restraints excluded: chain E residue 155 ILE 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 531 ARG Chi-restraints excluded: chain F residue 311 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 179 random chunks: chunk 103 optimal weight: 6.9990 chunk 80 optimal weight: 0.0060 chunk 118 optimal weight: 0.9980 chunk 178 optimal weight: 5.9990 chunk 164 optimal weight: 4.9990 chunk 142 optimal weight: 0.8980 chunk 14 optimal weight: 5.9990 chunk 109 optimal weight: 1.9990 chunk 87 optimal weight: 0.9980 chunk 112 optimal weight: 1.9990 chunk 151 optimal weight: 0.0980 overall best weight: 0.5996 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7726 moved from start: 0.2186 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.046 15505 Z= 0.163 Angle : 0.499 13.066 21332 Z= 0.253 Chirality : 0.038 0.135 2481 Planarity : 0.005 0.051 2492 Dihedral : 14.752 153.842 3099 Min Nonbonded Distance : 2.283 Molprobity Statistics. All-atom Clashscore : 5.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.89 % Favored : 98.11 % Rotamer: Outliers : 0.56 % Allowed : 15.06 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.44 (0.20), residues: 1749 helix: 2.11 (0.17), residues: 891 sheet: -0.11 (0.33), residues: 220 loop : -0.25 (0.24), residues: 638 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP E 143 HIS 0.002 0.000 HIS E 504 PHE 0.008 0.001 PHE F 241 TYR 0.009 0.001 TYR E 484 ARG 0.007 0.000 ARG C 226 ********************** 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 157 residues out of total 1441 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 149 time to evaluate : 1.646 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 123 MET cc_start: 0.7606 (tmm) cc_final: 0.7367 (ttp) REVERT: D 194 MET cc_start: 0.9070 (mmm) cc_final: 0.8824 (mmm) REVERT: E 303 ASP cc_start: 0.7988 (t0) cc_final: 0.7601 (m-30) REVERT: E 457 ARG cc_start: 0.6405 (tpt90) cc_final: 0.5908 (mtp180) outliers start: 8 outliers final: 4 residues processed: 155 average time/residue: 1.5929 time to fit residues: 268.6178 Evaluate side-chains 143 residues out of total 1441 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 139 time to evaluate : 1.613 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 125 ASP Chi-restraints excluded: chain E residue 155 ILE Chi-restraints excluded: chain E residue 367 CYS Chi-restraints excluded: chain E residue 466 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 179 random chunks: chunk 43 optimal weight: 2.9990 chunk 130 optimal weight: 2.9990 chunk 20 optimal weight: 0.5980 chunk 39 optimal weight: 0.8980 chunk 142 optimal weight: 3.9990 chunk 59 optimal weight: 1.9990 chunk 146 optimal weight: 2.9990 chunk 18 optimal weight: 0.8980 chunk 26 optimal weight: 0.6980 chunk 124 optimal weight: 0.5980 chunk 8 optimal weight: 7.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3485 r_free = 0.3485 target = 0.127863 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3260 r_free = 0.3260 target = 0.111382 restraints weight = 20753.200| |-----------------------------------------------------------------------------| r_work (start): 0.3263 rms_B_bonded: 1.32 r_work: 0.3160 rms_B_bonded: 2.10 restraints_weight: 0.5000 r_work: 0.3042 rms_B_bonded: 3.57 restraints_weight: 0.2500 r_work (final): 0.3042 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3041 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3041 r_free = 0.3041 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.72 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3041 r_free = 0.3041 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.26 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3041 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8536 moved from start: 0.2194 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 15505 Z= 0.177 Angle : 0.503 13.267 21332 Z= 0.256 Chirality : 0.039 0.139 2481 Planarity : 0.005 0.051 2492 Dihedral : 14.741 154.366 3099 Min Nonbonded Distance : 2.282 Molprobity Statistics. All-atom Clashscore : 4.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.83 % Favored : 98.17 % Rotamer: Outliers : 0.83 % Allowed : 15.41 % Favored : 83.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.46 (0.20), residues: 1749 helix: 2.10 (0.17), residues: 891 sheet: -0.09 (0.34), residues: 220 loop : -0.22 (0.24), residues: 638 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP E 326 HIS 0.002 0.001 HIS C 109 PHE 0.019 0.001 PHE E 518 TYR 0.011 0.001 TYR E 484 ARG 0.007 0.000 ARG C 226 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5125.98 seconds wall clock time: 93 minutes 42.73 seconds (5622.73 seconds total)