Starting phenix.real_space_refine on Sat Jun 7 10:08:57 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7tad_25771/06_2025/7tad_25771.cif Found real_map, /net/cci-nas-00/data/ceres_data/7tad_25771/06_2025/7tad_25771.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7tad_25771/06_2025/7tad_25771.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7tad_25771/06_2025/7tad_25771.map" model { file = "/net/cci-nas-00/data/ceres_data/7tad_25771/06_2025/7tad_25771.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7tad_25771/06_2025/7tad_25771.cif" } resolution = 3.6 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 1.095 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: 5 Type Number sf(0) Gaussians Zn 2 6.06 5 S 49 5.16 5 C 5431 2.51 5 N 1471 2.21 5 O 1597 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 8 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 8550 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 2620 Number of conformers: 1 Conformer: "" Number of residues, atoms: 348, 2620 Classifications: {'peptide': 348} Incomplete info: {'truncation_to_alanine': 25} Link IDs: {'PTRANS': 10, 'TRANS': 337} Chain breaks: 2 Unresolved non-hydrogen bonds: 94 Unresolved non-hydrogen angles: 109 Unresolved non-hydrogen dihedrals: 79 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 8, 'ASN:plan1': 1, 'ARG:plan': 1, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 48 Chain: "B" Number of atoms: 2595 Number of conformers: 1 Conformer: "" Number of residues, atoms: 348, 2595 Classifications: {'peptide': 348} Incomplete info: {'truncation_to_alanine': 32} Link IDs: {'PTRANS': 10, 'TRANS': 337} Chain breaks: 2 Unresolved non-hydrogen bonds: 119 Unresolved non-hydrogen angles: 137 Unresolved non-hydrogen dihedrals: 101 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 8, 'ARG:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 49 Chain: "C" Number of atoms: 1666 Number of conformers: 1 Conformer: "" Number of residues, atoms: 210, 1666 Classifications: {'peptide': 210} Link IDs: {'PCIS': 1, 'PTRANS': 3, 'TRANS': 205} Chain breaks: 1 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'GLN:plan1': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 6 Chain: "D" Number of atoms: 1631 Number of conformers: 1 Conformer: "" Number of residues, atoms: 207, 1631 Classifications: {'peptide': 207} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PCIS': 1, 'PTRANS': 3, 'TRANS': 202} Chain breaks: 1 Unresolved non-hydrogen bonds: 25 Unresolved non-hydrogen angles: 29 Unresolved non-hydrogen dihedrals: 21 Planarities with less than four sites: {'GLN:plan1': 2, 'ARG:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 14 Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 18 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 18 Unusual residues: {'PLM': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 18 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 18 Unusual residues: {'PLM': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 759 SG CYS A 150 41.718 93.268 99.306 1.00 37.67 S ATOM 791 SG CYS A 155 38.621 94.313 101.290 1.00 47.37 S ATOM 825 SG CYS A 160 39.156 90.552 99.705 1.00 34.45 S ATOM 3396 SG CYS B 150 22.251 34.411 136.649 1.00 98.60 S ATOM 3428 SG CYS B 155 21.179 37.413 138.560 1.00101.80 S ATOM 3462 SG CYS B 160 24.512 37.614 136.784 1.00 76.62 S Time building chain proxies: 6.03, per 1000 atoms: 0.71 Number of scatterers: 8550 At special positions: 0 Unit cell: (68.224, 118.326, 178.022, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Zn 2 29.99 S 49 16.00 O 1597 8.00 N 1471 7.00 C 5431 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: 2.32 Conformation dependent library (CDL) restraints added in 952.6 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A 701 " pdb="ZN ZN A 701 " - pdb=" ND1 HIS A 157 " pdb="ZN ZN A 701 " - pdb=" SG CYS A 150 " pdb="ZN ZN A 701 " - pdb=" SG CYS A 155 " pdb="ZN ZN A 701 " - pdb=" SG CYS A 160 " pdb=" ZN B 701 " pdb="ZN ZN B 701 " - pdb=" ND1 HIS B 157 " pdb="ZN ZN B 701 " - pdb=" SG CYS B 150 " pdb="ZN ZN B 701 " - pdb=" SG CYS B 155 " pdb="ZN ZN B 701 " - pdb=" SG CYS B 160 " Number of angles added : 6 2186 Ramachandran restraints generated. 1093 Oldfield, 0 Emsley, 1093 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2152 Finding SS restraints... Secondary structure from input PDB file: 62 helices and 2 sheets defined 80.4% alpha, 1.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.84 Creating SS restraints... Processing helix chain 'A' and resid 42 through 59 removed outlier: 3.611A pdb=" N LEU A 46 " --> pdb=" O ASP A 42 " (cutoff:3.500A) Processing helix chain 'A' and resid 60 through 64 removed outlier: 4.002A pdb=" N TYR A 64 " --> pdb=" O ASP A 61 " (cutoff:3.500A) Processing helix chain 'A' and resid 80 through 88 removed outlier: 3.627A pdb=" N LEU A 84 " --> pdb=" O HIS A 80 " (cutoff:3.500A) Processing helix chain 'A' and resid 88 through 99 Processing helix chain 'A' and resid 114 through 118 Processing helix chain 'A' and resid 124 through 138 removed outlier: 3.926A pdb=" N VAL A 128 " --> pdb=" O GLY A 124 " (cutoff:3.500A) Processing helix chain 'A' and resid 160 through 177 Processing helix chain 'A' and resid 179 through 195 removed outlier: 4.486A pdb=" N ASP A 195 " --> pdb=" O LEU A 191 " (cutoff:3.500A) Processing helix chain 'A' and resid 198 through 212 removed outlier: 3.836A pdb=" N VAL A 204 " --> pdb=" O GLU A 200 " (cutoff:3.500A) Processing helix chain 'A' and resid 216 through 229 Processing helix chain 'A' and resid 233 through 241 Processing helix chain 'A' and resid 242 through 256 Processing helix chain 'A' and resid 264 through 276 Processing helix chain 'A' and resid 278 through 289 Processing helix chain 'A' and resid 292 through 297 Processing helix chain 'A' and resid 297 through 305 Processing helix chain 'A' and resid 307 through 316 Processing helix chain 'A' and resid 331 through 340 Processing helix chain 'A' and resid 341 through 352 Processing helix chain 'A' and resid 364 through 373 removed outlier: 3.640A pdb=" N THR A 373 " --> pdb=" O ALA A 369 " (cutoff:3.500A) Processing helix chain 'A' and resid 374 through 379 removed outlier: 3.907A pdb=" N ASN A 379 " --> pdb=" O VAL A 376 " (cutoff:3.500A) Processing helix chain 'A' and resid 389 through 404 removed outlier: 3.554A pdb=" N LYS A 403 " --> pdb=" O GLU A 399 " (cutoff:3.500A) Processing helix chain 'B' and resid 42 through 59 removed outlier: 3.627A pdb=" N LEU B 46 " --> pdb=" O ASP B 42 " (cutoff:3.500A) Processing helix chain 'B' and resid 60 through 64 removed outlier: 3.861A pdb=" N TYR B 64 " --> pdb=" O ASP B 61 " (cutoff:3.500A) Processing helix chain 'B' and resid 80 through 88 removed outlier: 3.615A pdb=" N LEU B 84 " --> pdb=" O HIS B 80 " (cutoff:3.500A) Processing helix chain 'B' and resid 88 through 99 Processing helix chain 'B' and resid 114 through 118 Processing helix chain 'B' and resid 124 through 138 removed outlier: 3.883A pdb=" N VAL B 128 " --> pdb=" O GLY B 124 " (cutoff:3.500A) Processing helix chain 'B' and resid 160 through 177 Processing helix chain 'B' and resid 179 through 195 removed outlier: 4.669A pdb=" N ASP B 195 " --> pdb=" O LEU B 191 " (cutoff:3.500A) Processing helix chain 'B' and resid 198 through 212 removed outlier: 3.955A pdb=" N VAL B 204 " --> pdb=" O GLU B 200 " (cutoff:3.500A) Processing helix chain 'B' and resid 213 through 215 No H-bonds generated for 'chain 'B' and resid 213 through 215' Processing helix chain 'B' and resid 216 through 230 Processing helix chain 'B' and resid 233 through 241 removed outlier: 3.793A pdb=" N LEU B 237 " --> pdb=" O ASP B 233 " (cutoff:3.500A) Processing helix chain 'B' and resid 242 through 256 Processing helix chain 'B' and resid 264 through 276 Processing helix chain 'B' and resid 278 through 287 Processing helix chain 'B' and resid 292 through 297 Processing helix chain 'B' and resid 297 through 306 Processing helix chain 'B' and resid 307 through 317 Processing helix chain 'B' and resid 331 through 340 Processing helix chain 'B' and resid 341 through 351 Processing helix chain 'B' and resid 364 through 373 Processing helix chain 'B' and resid 374 through 379 removed outlier: 3.563A pdb=" N ASN B 379 " --> pdb=" O VAL B 376 " (cutoff:3.500A) Processing helix chain 'B' and resid 389 through 403 Processing helix chain 'C' and resid 165 through 194 Processing helix chain 'C' and resid 197 through 226 Processing helix chain 'C' and resid 226 through 233 removed outlier: 3.500A pdb=" N LEU C 230 " --> pdb=" O ASP C 226 " (cutoff:3.500A) Processing helix chain 'C' and resid 239 through 244 removed outlier: 3.568A pdb=" N GLN C 244 " --> pdb=" O ARG C 241 " (cutoff:3.500A) Processing helix chain 'C' and resid 250 through 259 Processing helix chain 'C' and resid 260 through 262 No H-bonds generated for 'chain 'C' and resid 260 through 262' Processing helix chain 'C' and resid 266 through 306 removed outlier: 3.760A pdb=" N ILE C 304 " --> pdb=" O GLU C 300 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N GLN C 305 " --> pdb=" O SER C 301 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N ILE C 306 " --> pdb=" O ILE C 302 " (cutoff:3.500A) Processing helix chain 'C' and resid 316 through 350 Processing helix chain 'C' and resid 351 through 377 Processing helix chain 'D' and resid 165 through 194 Processing helix chain 'D' and resid 197 through 226 removed outlier: 3.600A pdb=" N ALA D 225 " --> pdb=" O ASP D 221 " (cutoff:3.500A) Processing helix chain 'D' and resid 226 through 233 removed outlier: 3.700A pdb=" N GLY D 233 " --> pdb=" O PHE D 229 " (cutoff:3.500A) Processing helix chain 'D' and resid 239 through 243 Processing helix chain 'D' and resid 250 through 263 Proline residue: D 260 - end of helix removed outlier: 4.025A pdb=" N GLU D 263 " --> pdb=" O MET D 259 " (cutoff:3.500A) Processing helix chain 'D' and resid 266 through 307 Processing helix chain 'D' and resid 317 through 350 removed outlier: 3.509A pdb=" N ASP D 336 " --> pdb=" O VAL D 332 " (cutoff:3.500A) Processing helix chain 'D' and resid 351 through 378 Processing sheet with id=AA1, first strand: chain 'A' and resid 76 through 79 Processing sheet with id=AA2, first strand: chain 'B' and resid 76 through 79 removed outlier: 6.551A pdb=" N LYS B 68 " --> pdb=" O LEU B 112 " (cutoff:3.500A) 636 hydrogen bonds defined for protein. 1872 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.69 Time building geometry restraints manager: 2.71 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.35: 2859 1.35 - 1.47: 1825 1.47 - 1.59: 3918 1.59 - 1.71: 0 1.71 - 1.83: 72 Bond restraints: 8674 Sorted by residual: bond pdb=" CG LEU D 298 " pdb=" CD1 LEU D 298 " ideal model delta sigma weight residual 1.521 1.485 0.036 3.30e-02 9.18e+02 1.19e+00 bond pdb=" CG PRO C 264 " pdb=" CD PRO C 264 " ideal model delta sigma weight residual 1.512 1.483 0.029 2.70e-02 1.37e+03 1.15e+00 bond pdb=" CG PRO D 264 " pdb=" CD PRO D 264 " ideal model delta sigma weight residual 1.512 1.487 0.025 2.70e-02 1.37e+03 8.59e-01 bond pdb=" CG LEU A 191 " pdb=" CD1 LEU A 191 " ideal model delta sigma weight residual 1.521 1.491 0.030 3.30e-02 9.18e+02 8.39e-01 bond pdb=" C1 PLM C 501 " pdb=" C2 PLM C 501 " ideal model delta sigma weight residual 1.542 1.524 0.018 2.00e-02 2.50e+03 8.32e-01 ... (remaining 8669 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.12: 11485 2.12 - 4.25: 206 4.25 - 6.37: 37 6.37 - 8.50: 5 8.50 - 10.62: 3 Bond angle restraints: 11736 Sorted by residual: angle pdb=" CB MET D 172 " pdb=" CG MET D 172 " pdb=" SD MET D 172 " ideal model delta sigma weight residual 112.70 123.32 -10.62 3.00e+00 1.11e-01 1.25e+01 angle pdb=" CA ARG D 236 " pdb=" CB ARG D 236 " pdb=" CG ARG D 236 " ideal model delta sigma weight residual 114.10 120.53 -6.43 2.00e+00 2.50e-01 1.03e+01 angle pdb=" CA GLU C 263 " pdb=" CB GLU C 263 " pdb=" CG GLU C 263 " ideal model delta sigma weight residual 114.10 119.79 -5.69 2.00e+00 2.50e-01 8.10e+00 angle pdb=" CA LEU A 191 " pdb=" CB LEU A 191 " pdb=" CG LEU A 191 " ideal model delta sigma weight residual 116.30 125.83 -9.53 3.50e+00 8.16e-02 7.42e+00 angle pdb=" CB MET D 346 " pdb=" CG MET D 346 " pdb=" SD MET D 346 " ideal model delta sigma weight residual 112.70 120.72 -8.02 3.00e+00 1.11e-01 7.15e+00 ... (remaining 11731 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.97: 4813 17.97 - 35.93: 398 35.93 - 53.90: 80 53.90 - 71.86: 14 71.86 - 89.83: 9 Dihedral angle restraints: 5314 sinusoidal: 2035 harmonic: 3279 Sorted by residual: dihedral pdb=" CB GLU B 76 " pdb=" CG GLU B 76 " pdb=" CD GLU B 76 " pdb=" OE1 GLU B 76 " ideal model delta sinusoidal sigma weight residual 0.00 89.83 -89.83 1 3.00e+01 1.11e-03 1.06e+01 dihedral pdb=" N LYS B 370 " pdb=" CA LYS B 370 " pdb=" CB LYS B 370 " pdb=" CG LYS B 370 " ideal model delta sinusoidal sigma weight residual -180.00 -122.95 -57.05 3 1.50e+01 4.44e-03 9.42e+00 dihedral pdb=" CB GLU D 240 " pdb=" CG GLU D 240 " pdb=" CD GLU D 240 " pdb=" OE1 GLU D 240 " ideal model delta sinusoidal sigma weight residual 0.00 82.58 -82.58 1 3.00e+01 1.11e-03 9.29e+00 ... (remaining 5311 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.040: 1041 0.040 - 0.080: 268 0.080 - 0.120: 65 0.120 - 0.160: 20 0.160 - 0.200: 4 Chirality restraints: 1398 Sorted by residual: chirality pdb=" CA TYR A 186 " pdb=" N TYR A 186 " pdb=" C TYR A 186 " pdb=" CB TYR A 186 " both_signs ideal model delta sigma weight residual False 2.51 2.31 0.20 2.00e-01 2.50e+01 9.97e-01 chirality pdb=" CA TYR B 186 " pdb=" N TYR B 186 " pdb=" C TYR B 186 " pdb=" CB TYR B 186 " both_signs ideal model delta sigma weight residual False 2.51 2.32 0.19 2.00e-01 2.50e+01 8.71e-01 chirality pdb=" CA HIS A 157 " pdb=" N HIS A 157 " pdb=" C HIS A 157 " pdb=" CB HIS A 157 " both_signs ideal model delta sigma weight residual False 2.51 2.34 0.17 2.00e-01 2.50e+01 7.64e-01 ... (remaining 1395 not shown) Planarity restraints: 1498 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C MET C 259 " 0.079 5.00e-02 4.00e+02 1.19e-01 2.25e+01 pdb=" N PRO C 260 " -0.205 5.00e-02 4.00e+02 pdb=" CA PRO C 260 " 0.062 5.00e-02 4.00e+02 pdb=" CD PRO C 260 " 0.064 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ARG D 250 " 0.065 5.00e-02 4.00e+02 9.96e-02 1.59e+01 pdb=" N PRO D 251 " -0.172 5.00e-02 4.00e+02 pdb=" CA PRO D 251 " 0.053 5.00e-02 4.00e+02 pdb=" CD PRO D 251 " 0.054 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLU A 341 " -0.063 5.00e-02 4.00e+02 9.48e-02 1.44e+01 pdb=" N PRO A 342 " 0.164 5.00e-02 4.00e+02 pdb=" CA PRO A 342 " -0.050 5.00e-02 4.00e+02 pdb=" CD PRO A 342 " -0.052 5.00e-02 4.00e+02 ... (remaining 1495 not shown) Histogram of nonbonded interaction distances: 2.13 - 2.68: 98 2.68 - 3.24: 8585 3.24 - 3.79: 13616 3.79 - 4.35: 17170 4.35 - 4.90: 28482 Nonbonded interactions: 67951 Sorted by model distance: nonbonded pdb=" OD1 ASP A 277 " pdb=" OG1 THR A 310 " model vdw 2.126 3.040 nonbonded pdb=" OG1 THR D 237 " pdb=" OE2 GLU D 240 " model vdw 2.244 3.040 nonbonded pdb=" OD1 ASP A 120 " pdb=" OH TYR A 172 " model vdw 2.245 3.040 nonbonded pdb=" NH2 ARG A 325 " pdb=" OE1 GLU A 357 " model vdw 2.248 3.120 nonbonded pdb=" NZ LYS A 239 " pdb=" OD2 ASP A 275 " model vdw 2.259 3.120 ... (remaining 67946 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' and (resid 41 through 67 or (resid 68 and (name N or name CA or name \ C or name O or name CB )) or resid 69 through 166 or (resid 167 and (name N or n \ ame CA or name C or name O or name CB or name CG )) or resid 168 through 216 or \ (resid 217 and (name N or name CA or name C or name O or name CB )) or resid 218 \ through 228 or (resid 229 and (name N or name CA or name C or name O or name CB \ )) or resid 230 through 257 or (resid 258 through 260 and (name N or name CA or \ name C or name O or name CB )) or resid 261 or (resid 262 through 265 and (name \ N or name CA or name C or name O or name CB )) or resid 266 through 287 or (res \ id 288 through 289 and (name N or name CA or name C or name O or name CB )) or r \ esid 290 through 337 or (resid 338 and (name N or name CA or name C or name O or \ name CB )) or resid 339 through 349 or (resid 350 through 351 and (name N or na \ me CA or name C or name O or name CB )) or resid 352 through 365 or (resid 366 a \ nd (name N or name CA or name C or name O or name CB )) or resid 367 through 370 \ or (resid 371 through 372 and (name N or name CA or name C or name O or name CB \ )) or resid 373 through 379 or (resid 388 and (name N or name CA or name C or n \ ame O or name CB )) or resid 389 through 391 or (resid 392 and (name N or name C \ A or name C or name O or name CB )) or resid 393 through 395 or (resid 396 and ( \ name N or name CA or name C or name O or name CB )) or resid 397 or (resid 398 t \ hrough 399 and (name N or name CA or name C or name O or name CB )) or resid 400 \ or (resid 401 through 404 and (name N or name CA or name C or name O or name CB \ )) or resid 701)) selection = (chain 'B' and (resid 41 through 43 or (resid 44 through 45 and (name N or name \ CA or name C or name O or name CB )) or resid 46 through 58 or (resid 59 and (na \ me N or name CA or name C or name O or name CB )) or resid 60 through 114 or (re \ sid 115 and (name N or name CA or name C or name O or name CB or name CG )) or r \ esid 116 through 118 or (resid 119 and (name N or name CA or name C or name O or \ name CB )) or resid 120 through 121 or (resid 122 and (name N or name CA or nam \ e C or name O or name CB or name CG )) or resid 123 through 137 or (resid 138 an \ d (name N or name CA or name C or name O or name CB )) or resid 139 through 144 \ or (resid 145 and (name N or name CA or name C or name O or name CB )) or resid \ 146 through 148 or (resid 149 and (name N or name CA or name C or name O or name \ CB )) or resid 150 through 195 or (resid 196 and (name N or name CA or name C o \ r name O or name CB )) or resid 197 through 242 or (resid 243 and (name N or nam \ e CA or name C or name O or name CB )) or resid 244 through 250 or (resid 251 an \ d (name N or name CA or name C or name O or name CB )) or resid 252 through 253 \ or (resid 254 through 256 and (name N or name CA or name C or name O or name CB \ )) or (resid 257 through 260 and (name N or name CA or name C or name O or name \ CB )) or resid 261 through 317 or (resid 318 and (name N or name CA or name C or \ name O or name CB )) or resid 319 through 378 or (resid 379 through 388 and (na \ me N or name CA or name C or name O or name CB )) or resid 389 through 401 or (r \ esid 402 through 404 and (name N or name CA or name C or name O or name CB )) or \ resid 701)) } ncs_group { reference = (chain 'C' and (resid 164 through 306 or (resid 307 and (name N or name CA or na \ me C or name O or name CB )) or resid 316 through 321 or (resid 322 and (name N \ or name CA or name C or name O or name CB )) or resid 323 through 325 or (resid \ 326 through 327 and (name N or name CA or name C or name O or name CB )) or resi \ d 328 through 332 or (resid 333 and (name N or name CA or name C or name O or na \ me CB )) or resid 334 through 343 or (resid 344 and (name N or name CA or name C \ or name O or name CB )) or resid 345 through 347 or (resid 348 and (name N or n \ ame CA or name C or name O or name CB )) or resid 349 through 378 or resid 501)) \ selection = (chain 'D' and (resid 164 through 258 or (resid 259 and (name N or name CA or na \ me C or name O or name CB or name CG )) or resid 260 through 378 or resid 501)) } 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=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue 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: 4.330 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.300 Check model and map are aligned: 0.060 Set scattering table: 0.080 Process input model: 25.390 Find NCS groups from input model: 0.370 Set up NCS constraints: 0.040 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:3.290 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.870 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6167 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 : 0.003 0.064 8682 Z= 0.139 Angle : 0.707 10.621 11742 Z= 0.356 Chirality : 0.041 0.200 1398 Planarity : 0.007 0.119 1498 Dihedral : 14.284 89.830 3162 Min Nonbonded Distance : 2.126 Molprobity Statistics. All-atom Clashscore : 10.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 0.00 % Allowed : 1.12 % Favored : 98.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % 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: 0.68 (0.24), residues: 1093 helix: 0.94 (0.17), residues: 825 sheet: 0.03 (0.95), residues: 32 loop : -1.00 (0.36), residues: 236 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.003 TRP C 235 HIS 0.017 0.001 HIS A 157 PHE 0.014 0.002 PHE A 91 TYR 0.028 0.002 TYR D 365 ARG 0.010 0.001 ARG C 274 Details of bonding type rmsd hydrogen bonds : bond 0.12035 ( 636) hydrogen bonds : angle 4.69620 ( 1872) metal coordination : bond 0.02937 ( 8) metal coordination : angle 5.40160 ( 6) covalent geometry : bond 0.00289 ( 8674) covalent geometry : angle 0.69678 (11736) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2186 Ramachandran restraints generated. 1093 Oldfield, 0 Emsley, 1093 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2186 Ramachandran restraints generated. 1093 Oldfield, 0 Emsley, 1093 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 125 time to evaluate : 1.044 Fit side-chains REVERT: B 245 LEU cc_start: 0.8744 (tp) cc_final: 0.8532 (tp) REVERT: C 346 MET cc_start: 0.8742 (tpt) cc_final: 0.8480 (tpt) outliers start: 0 outliers final: 0 residues processed: 125 average time/residue: 0.2272 time to fit residues: 40.0736 Evaluate side-chains 100 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 100 time to evaluate : 1.117 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 92 optimal weight: 1.9990 chunk 82 optimal weight: 0.9990 chunk 45 optimal weight: 0.6980 chunk 28 optimal weight: 0.7980 chunk 55 optimal weight: 0.7980 chunk 44 optimal weight: 0.0470 chunk 85 optimal weight: 0.9980 chunk 33 optimal weight: 2.9990 chunk 51 optimal weight: 0.1980 chunk 63 optimal weight: 0.9990 chunk 98 optimal weight: 0.0980 overall best weight: 0.3678 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 307 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4511 r_free = 0.4511 target = 0.211483 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4163 r_free = 0.4163 target = 0.174470 restraints weight = 10483.667| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4191 r_free = 0.4191 target = 0.177863 restraints weight = 7335.125| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4194 r_free = 0.4194 target = 0.178224 restraints weight = 4898.612| |-----------------------------------------------------------------------------| r_work (final): 0.4196 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6305 moved from start: 0.1400 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 8682 Z= 0.127 Angle : 0.557 7.954 11742 Z= 0.278 Chirality : 0.037 0.174 1398 Planarity : 0.005 0.072 1498 Dihedral : 4.799 53.244 1208 Min Nonbonded Distance : 2.419 Molprobity Statistics. All-atom Clashscore : 6.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.28 % Favored : 98.72 % Rotamer: Outliers : 0.78 % Allowed : 7.49 % Favored : 91.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % 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: 2.14 (0.25), residues: 1093 helix: 2.00 (0.18), residues: 828 sheet: 0.42 (0.98), residues: 32 loop : -0.50 (0.40), residues: 233 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP D 376 HIS 0.003 0.001 HIS B 80 PHE 0.014 0.002 PHE C 366 TYR 0.024 0.002 TYR A 186 ARG 0.003 0.000 ARG A 81 Details of bonding type rmsd hydrogen bonds : bond 0.03733 ( 636) hydrogen bonds : angle 3.69935 ( 1872) metal coordination : bond 0.01899 ( 8) metal coordination : angle 2.11528 ( 6) covalent geometry : bond 0.00283 ( 8674) covalent geometry : angle 0.55528 (11736) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2186 Ramachandran restraints generated. 1093 Oldfield, 0 Emsley, 1093 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2186 Ramachandran restraints generated. 1093 Oldfield, 0 Emsley, 1093 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 126 time to evaluate : 0.964 Fit side-chains REVERT: A 330 TYR cc_start: 0.6719 (m-80) cc_final: 0.6303 (m-10) REVERT: C 234 MET cc_start: 0.5620 (ppp) cc_final: 0.5266 (ppp) REVERT: D 331 PHE cc_start: 0.7245 (m-80) cc_final: 0.7013 (m-80) outliers start: 7 outliers final: 6 residues processed: 128 average time/residue: 0.2222 time to fit residues: 40.1043 Evaluate side-chains 112 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 106 time to evaluate : 2.072 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 211 ILE Chi-restraints excluded: chain A residue 285 LEU Chi-restraints excluded: chain A residue 299 LEU Chi-restraints excluded: chain B residue 123 VAL Chi-restraints excluded: chain B residue 227 ILE Chi-restraints excluded: chain D residue 193 GLN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 91 optimal weight: 0.8980 chunk 106 optimal weight: 0.9980 chunk 73 optimal weight: 0.4980 chunk 14 optimal weight: 0.8980 chunk 103 optimal weight: 0.0970 chunk 96 optimal weight: 1.9990 chunk 81 optimal weight: 0.7980 chunk 55 optimal weight: 0.4980 chunk 62 optimal weight: 0.9980 chunk 9 optimal weight: 2.9990 chunk 42 optimal weight: 0.9990 overall best weight: 0.5578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 271 HIS C 176 HIS ** C 214 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 345 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4465 r_free = 0.4465 target = 0.206467 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.4074 r_free = 0.4074 target = 0.165857 restraints weight = 10634.847| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.4106 r_free = 0.4106 target = 0.168975 restraints weight = 7279.882| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.4130 r_free = 0.4130 target = 0.171219 restraints weight = 5524.346| |-----------------------------------------------------------------------------| r_work (final): 0.4132 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6427 moved from start: 0.2098 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 8682 Z= 0.149 Angle : 0.566 10.903 11742 Z= 0.281 Chirality : 0.037 0.225 1398 Planarity : 0.004 0.059 1498 Dihedral : 4.910 51.859 1208 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 8.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.65 % Favored : 98.35 % Rotamer: Outliers : 2.01 % Allowed : 9.05 % Favored : 88.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % 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: 2.40 (0.26), residues: 1093 helix: 2.12 (0.18), residues: 830 sheet: 0.46 (0.97), residues: 30 loop : -0.13 (0.42), residues: 233 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.003 TRP D 376 HIS 0.004 0.001 HIS B 80 PHE 0.017 0.002 PHE C 366 TYR 0.025 0.002 TYR B 186 ARG 0.003 0.000 ARG C 236 Details of bonding type rmsd hydrogen bonds : bond 0.03882 ( 636) hydrogen bonds : angle 3.70068 ( 1872) metal coordination : bond 0.01650 ( 8) metal coordination : angle 2.40038 ( 6) covalent geometry : bond 0.00348 ( 8674) covalent geometry : angle 0.56344 (11736) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2186 Ramachandran restraints generated. 1093 Oldfield, 0 Emsley, 1093 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2186 Ramachandran restraints generated. 1093 Oldfield, 0 Emsley, 1093 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 117 time to evaluate : 0.874 Fit side-chains REVERT: A 330 TYR cc_start: 0.6878 (m-80) cc_final: 0.6361 (m-10) REVERT: A 390 LYS cc_start: 0.7714 (ttmm) cc_final: 0.7332 (mmtp) REVERT: B 149 GLU cc_start: 0.6810 (mt-10) cc_final: 0.6590 (mt-10) REVERT: B 283 LYS cc_start: 0.8762 (pptt) cc_final: 0.8348 (pptt) REVERT: B 367 MET cc_start: 0.8475 (mpp) cc_final: 0.8054 (ptp) REVERT: D 172 MET cc_start: 0.4516 (mpp) cc_final: 0.3649 (mtt) REVERT: D 331 PHE cc_start: 0.7074 (m-80) cc_final: 0.6849 (m-80) outliers start: 18 outliers final: 12 residues processed: 127 average time/residue: 0.2013 time to fit residues: 35.9477 Evaluate side-chains 120 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 108 time to evaluate : 0.999 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 156 CYS Chi-restraints excluded: chain A residue 211 ILE Chi-restraints excluded: chain A residue 285 LEU Chi-restraints excluded: chain A residue 299 LEU Chi-restraints excluded: chain A residue 396 GLU Chi-restraints excluded: chain B residue 123 VAL Chi-restraints excluded: chain B residue 227 ILE Chi-restraints excluded: chain B residue 281 LEU Chi-restraints excluded: chain B residue 316 LYS Chi-restraints excluded: chain D residue 193 GLN Chi-restraints excluded: chain D residue 337 HIS Chi-restraints excluded: chain D residue 342 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 6 optimal weight: 2.9990 chunk 101 optimal weight: 0.5980 chunk 42 optimal weight: 0.9980 chunk 76 optimal weight: 0.0370 chunk 18 optimal weight: 1.9990 chunk 63 optimal weight: 3.9990 chunk 60 optimal weight: 3.9990 chunk 68 optimal weight: 0.6980 chunk 55 optimal weight: 7.9990 chunk 53 optimal weight: 0.5980 chunk 62 optimal weight: 0.9990 overall best weight: 0.5858 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 154 ASN ** C 214 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 295 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4413 r_free = 0.4413 target = 0.202006 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.4054 r_free = 0.4054 target = 0.164894 restraints weight = 10233.239| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4075 r_free = 0.4075 target = 0.167201 restraints weight = 7039.270| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4081 r_free = 0.4081 target = 0.167857 restraints weight = 5095.545| |-----------------------------------------------------------------------------| r_work (final): 0.4078 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6491 moved from start: 0.2513 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 8682 Z= 0.150 Angle : 0.561 11.350 11742 Z= 0.279 Chirality : 0.037 0.177 1398 Planarity : 0.004 0.053 1498 Dihedral : 5.057 55.166 1208 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 7.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.10 % Favored : 97.90 % Rotamer: Outliers : 2.46 % Allowed : 10.84 % Favored : 86.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % 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: 2.45 (0.26), residues: 1093 helix: 2.16 (0.18), residues: 829 sheet: 0.19 (0.94), residues: 30 loop : -0.12 (0.42), residues: 234 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.003 TRP D 376 HIS 0.005 0.001 HIS B 80 PHE 0.020 0.002 PHE B 90 TYR 0.026 0.002 TYR A 186 ARG 0.004 0.000 ARG C 236 Details of bonding type rmsd hydrogen bonds : bond 0.03836 ( 636) hydrogen bonds : angle 3.67803 ( 1872) metal coordination : bond 0.01748 ( 8) metal coordination : angle 2.40623 ( 6) covalent geometry : bond 0.00355 ( 8674) covalent geometry : angle 0.55890 (11736) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2186 Ramachandran restraints generated. 1093 Oldfield, 0 Emsley, 1093 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2186 Ramachandran restraints generated. 1093 Oldfield, 0 Emsley, 1093 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 123 time to evaluate : 0.981 Fit side-chains revert: symmetry clash REVERT: B 75 ARG cc_start: 0.6994 (ttm110) cc_final: 0.6650 (mtm180) REVERT: D 172 MET cc_start: 0.4511 (mpp) cc_final: 0.4031 (mtt) outliers start: 22 outliers final: 15 residues processed: 135 average time/residue: 0.2138 time to fit residues: 39.9224 Evaluate side-chains 126 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 111 time to evaluate : 1.055 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 135 VAL Chi-restraints excluded: chain A residue 156 CYS Chi-restraints excluded: chain A residue 193 VAL Chi-restraints excluded: chain A residue 211 ILE Chi-restraints excluded: chain A residue 285 LEU Chi-restraints excluded: chain A residue 299 LEU Chi-restraints excluded: chain A residue 396 GLU Chi-restraints excluded: chain B residue 227 ILE Chi-restraints excluded: chain B residue 281 LEU Chi-restraints excluded: chain B residue 316 LYS Chi-restraints excluded: chain D residue 175 THR Chi-restraints excluded: chain D residue 193 GLN Chi-restraints excluded: chain D residue 203 MET Chi-restraints excluded: chain D residue 337 HIS Chi-restraints excluded: chain D residue 342 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 18 optimal weight: 0.8980 chunk 49 optimal weight: 0.6980 chunk 64 optimal weight: 9.9990 chunk 11 optimal weight: 1.9990 chunk 98 optimal weight: 0.0060 chunk 50 optimal weight: 0.5980 chunk 39 optimal weight: 0.9990 chunk 17 optimal weight: 0.5980 chunk 13 optimal weight: 0.9980 chunk 41 optimal weight: 0.9980 chunk 60 optimal weight: 0.9990 overall best weight: 0.5596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 278 GLN C 354 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4407 r_free = 0.4407 target = 0.201746 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.4022 r_free = 0.4022 target = 0.161754 restraints weight = 10167.737| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.4052 r_free = 0.4052 target = 0.164833 restraints weight = 6960.378| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.4075 r_free = 0.4075 target = 0.166994 restraints weight = 5267.965| |-----------------------------------------------------------------------------| r_work (final): 0.4074 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6499 moved from start: 0.2761 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 8682 Z= 0.146 Angle : 0.556 10.689 11742 Z= 0.277 Chirality : 0.037 0.147 1398 Planarity : 0.004 0.048 1498 Dihedral : 5.175 58.465 1208 Min Nonbonded Distance : 2.398 Molprobity Statistics. All-atom Clashscore : 7.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Rotamer: Outliers : 2.46 % Allowed : 12.18 % Favored : 85.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % 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: 2.48 (0.26), residues: 1093 helix: 2.22 (0.18), residues: 829 sheet: -0.37 (1.03), residues: 20 loop : -0.19 (0.40), residues: 244 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP C 245 HIS 0.005 0.001 HIS B 80 PHE 0.026 0.002 PHE B 90 TYR 0.024 0.002 TYR B 186 ARG 0.004 0.000 ARG B 222 Details of bonding type rmsd hydrogen bonds : bond 0.03752 ( 636) hydrogen bonds : angle 3.67657 ( 1872) metal coordination : bond 0.01838 ( 8) metal coordination : angle 2.52313 ( 6) covalent geometry : bond 0.00346 ( 8674) covalent geometry : angle 0.55352 (11736) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2186 Ramachandran restraints generated. 1093 Oldfield, 0 Emsley, 1093 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2186 Ramachandran restraints generated. 1093 Oldfield, 0 Emsley, 1093 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 123 time to evaluate : 0.896 Fit side-chains REVERT: A 186 TYR cc_start: 0.7362 (OUTLIER) cc_final: 0.7161 (m-10) REVERT: A 330 TYR cc_start: 0.7104 (m-80) cc_final: 0.6541 (m-10) REVERT: B 75 ARG cc_start: 0.7023 (ttm110) cc_final: 0.6673 (mtm180) REVERT: B 283 LYS cc_start: 0.8697 (pptt) cc_final: 0.8440 (pptt) REVERT: B 367 MET cc_start: 0.8281 (mpp) cc_final: 0.7871 (ptp) REVERT: D 172 MET cc_start: 0.4401 (mpp) cc_final: 0.3923 (mtt) outliers start: 22 outliers final: 16 residues processed: 136 average time/residue: 0.2080 time to fit residues: 39.0115 Evaluate side-chains 131 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 114 time to evaluate : 0.879 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 135 VAL Chi-restraints excluded: chain A residue 156 CYS Chi-restraints excluded: chain A residue 186 TYR Chi-restraints excluded: chain A residue 193 VAL Chi-restraints excluded: chain A residue 211 ILE Chi-restraints excluded: chain A residue 285 LEU Chi-restraints excluded: chain A residue 299 LEU Chi-restraints excluded: chain A residue 331 THR Chi-restraints excluded: chain A residue 396 GLU Chi-restraints excluded: chain B residue 129 VAL Chi-restraints excluded: chain B residue 227 ILE Chi-restraints excluded: chain B residue 281 LEU Chi-restraints excluded: chain B residue 316 LYS Chi-restraints excluded: chain D residue 175 THR Chi-restraints excluded: chain D residue 193 GLN Chi-restraints excluded: chain D residue 337 HIS Chi-restraints excluded: chain D residue 342 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 0 optimal weight: 1.9990 chunk 104 optimal weight: 0.9980 chunk 68 optimal weight: 0.0980 chunk 5 optimal weight: 0.9980 chunk 33 optimal weight: 1.9990 chunk 82 optimal weight: 0.0170 chunk 14 optimal weight: 0.8980 chunk 15 optimal weight: 0.8980 chunk 105 optimal weight: 0.9980 chunk 71 optimal weight: 0.6980 chunk 81 optimal weight: 0.9980 overall best weight: 0.5218 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 210 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4404 r_free = 0.4404 target = 0.201378 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4068 r_free = 0.4068 target = 0.166520 restraints weight = 10244.489| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.4049 r_free = 0.4049 target = 0.164869 restraints weight = 6764.092| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.4059 r_free = 0.4059 target = 0.165934 restraints weight = 6095.494| |-----------------------------------------------------------------------------| r_work (final): 0.4053 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6516 moved from start: 0.2938 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 8682 Z= 0.141 Angle : 0.558 11.027 11742 Z= 0.276 Chirality : 0.037 0.151 1398 Planarity : 0.004 0.047 1498 Dihedral : 5.214 59.388 1208 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 7.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.47 % Favored : 97.53 % Rotamer: Outliers : 2.35 % Allowed : 13.85 % Favored : 83.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % 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: 2.54 (0.26), residues: 1093 helix: 2.29 (0.18), residues: 829 sheet: -0.66 (1.03), residues: 20 loop : -0.20 (0.40), residues: 244 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP C 245 HIS 0.004 0.001 HIS B 80 PHE 0.031 0.002 PHE B 90 TYR 0.023 0.002 TYR B 186 ARG 0.003 0.000 ARG B 222 Details of bonding type rmsd hydrogen bonds : bond 0.03670 ( 636) hydrogen bonds : angle 3.63439 ( 1872) metal coordination : bond 0.01506 ( 8) metal coordination : angle 2.44579 ( 6) covalent geometry : bond 0.00333 ( 8674) covalent geometry : angle 0.55512 (11736) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2186 Ramachandran restraints generated. 1093 Oldfield, 0 Emsley, 1093 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2186 Ramachandran restraints generated. 1093 Oldfield, 0 Emsley, 1093 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 121 time to evaluate : 0.940 Fit side-chains revert: symmetry clash REVERT: A 186 TYR cc_start: 0.7320 (OUTLIER) cc_final: 0.7108 (m-10) REVERT: A 330 TYR cc_start: 0.6982 (m-80) cc_final: 0.6477 (m-10) REVERT: B 75 ARG cc_start: 0.7056 (ttm110) cc_final: 0.6704 (mtm180) REVERT: B 283 LYS cc_start: 0.8583 (pptt) cc_final: 0.8291 (pptt) REVERT: B 367 MET cc_start: 0.8239 (mpp) cc_final: 0.7953 (ptp) REVERT: C 234 MET cc_start: 0.6355 (ppp) cc_final: 0.5960 (ppp) REVERT: C 236 ARG cc_start: 0.6748 (mmm160) cc_final: 0.6399 (mmm160) REVERT: D 172 MET cc_start: 0.4355 (mpp) cc_final: 0.3981 (mtt) outliers start: 21 outliers final: 16 residues processed: 135 average time/residue: 0.1999 time to fit residues: 37.6493 Evaluate side-chains 129 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 112 time to evaluate : 0.940 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 CYS Chi-restraints excluded: chain A residue 135 VAL Chi-restraints excluded: chain A residue 156 CYS Chi-restraints excluded: chain A residue 186 TYR Chi-restraints excluded: chain A residue 211 ILE Chi-restraints excluded: chain A residue 285 LEU Chi-restraints excluded: chain A residue 299 LEU Chi-restraints excluded: chain A residue 322 VAL Chi-restraints excluded: chain A residue 331 THR Chi-restraints excluded: chain A residue 396 GLU Chi-restraints excluded: chain B residue 129 VAL Chi-restraints excluded: chain B residue 227 ILE Chi-restraints excluded: chain B residue 316 LYS Chi-restraints excluded: chain D residue 175 THR Chi-restraints excluded: chain D residue 193 GLN Chi-restraints excluded: chain D residue 337 HIS Chi-restraints excluded: chain D residue 342 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 17 optimal weight: 0.5980 chunk 51 optimal weight: 0.5980 chunk 105 optimal weight: 3.9990 chunk 92 optimal weight: 3.9990 chunk 35 optimal weight: 0.9980 chunk 91 optimal weight: 0.3980 chunk 1 optimal weight: 0.5980 chunk 31 optimal weight: 0.9990 chunk 10 optimal weight: 0.9990 chunk 71 optimal weight: 0.0070 chunk 36 optimal weight: 0.7980 overall best weight: 0.4398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 214 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4410 r_free = 0.4410 target = 0.202308 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.4075 r_free = 0.4075 target = 0.166904 restraints weight = 10349.973| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.4061 r_free = 0.4061 target = 0.165749 restraints weight = 7177.346| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4071 r_free = 0.4071 target = 0.166748 restraints weight = 6234.032| |-----------------------------------------------------------------------------| r_work (final): 0.4066 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6494 moved from start: 0.3046 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 8682 Z= 0.129 Angle : 0.548 10.469 11742 Z= 0.271 Chirality : 0.036 0.154 1398 Planarity : 0.004 0.046 1498 Dihedral : 5.140 57.757 1208 Min Nonbonded Distance : 2.400 Molprobity Statistics. All-atom Clashscore : 7.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Rotamer: Outliers : 2.46 % Allowed : 14.41 % Favored : 83.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % 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: 2.66 (0.26), residues: 1093 helix: 2.35 (0.18), residues: 829 sheet: -0.70 (1.03), residues: 20 loop : -0.06 (0.40), residues: 244 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP C 245 HIS 0.004 0.001 HIS B 80 PHE 0.022 0.002 PHE B 90 TYR 0.022 0.002 TYR B 186 ARG 0.002 0.000 ARG B 222 Details of bonding type rmsd hydrogen bonds : bond 0.03522 ( 636) hydrogen bonds : angle 3.57164 ( 1872) metal coordination : bond 0.01315 ( 8) metal coordination : angle 2.13333 ( 6) covalent geometry : bond 0.00303 ( 8674) covalent geometry : angle 0.54558 (11736) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2186 Ramachandran restraints generated. 1093 Oldfield, 0 Emsley, 1093 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2186 Ramachandran restraints generated. 1093 Oldfield, 0 Emsley, 1093 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 120 time to evaluate : 0.873 Fit side-chains REVERT: A 186 TYR cc_start: 0.7283 (OUTLIER) cc_final: 0.7012 (m-10) REVERT: A 330 TYR cc_start: 0.6963 (m-80) cc_final: 0.6474 (m-10) REVERT: B 283 LYS cc_start: 0.8534 (pptt) cc_final: 0.8329 (pptt) REVERT: B 367 MET cc_start: 0.7988 (mpp) cc_final: 0.7725 (ptp) REVERT: C 234 MET cc_start: 0.6442 (ppp) cc_final: 0.6157 (ppp) REVERT: C 236 ARG cc_start: 0.6754 (mmm160) cc_final: 0.6469 (mmm160) REVERT: D 172 MET cc_start: 0.4319 (mpp) cc_final: 0.3986 (mtt) outliers start: 22 outliers final: 17 residues processed: 135 average time/residue: 0.1914 time to fit residues: 36.3012 Evaluate side-chains 130 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 112 time to evaluate : 0.939 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 CYS Chi-restraints excluded: chain A residue 156 CYS Chi-restraints excluded: chain A residue 186 TYR Chi-restraints excluded: chain A residue 193 VAL Chi-restraints excluded: chain A residue 211 ILE Chi-restraints excluded: chain A residue 285 LEU Chi-restraints excluded: chain A residue 299 LEU Chi-restraints excluded: chain A residue 322 VAL Chi-restraints excluded: chain A residue 331 THR Chi-restraints excluded: chain A residue 396 GLU Chi-restraints excluded: chain B residue 129 VAL Chi-restraints excluded: chain B residue 201 ASP Chi-restraints excluded: chain B residue 316 LYS Chi-restraints excluded: chain C residue 196 ILE Chi-restraints excluded: chain D residue 175 THR Chi-restraints excluded: chain D residue 193 GLN Chi-restraints excluded: chain D residue 337 HIS Chi-restraints excluded: chain D residue 342 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 88 optimal weight: 0.9980 chunk 14 optimal weight: 0.9990 chunk 86 optimal weight: 0.4980 chunk 21 optimal weight: 0.6980 chunk 7 optimal weight: 0.9990 chunk 10 optimal weight: 0.9980 chunk 3 optimal weight: 0.0370 chunk 28 optimal weight: 0.0980 chunk 106 optimal weight: 1.9990 chunk 40 optimal weight: 1.9990 chunk 83 optimal weight: 0.5980 overall best weight: 0.3858 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 214 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4416 r_free = 0.4416 target = 0.202813 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.4029 r_free = 0.4029 target = 0.162759 restraints weight = 10423.392| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.4061 r_free = 0.4061 target = 0.165817 restraints weight = 7159.020| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.4084 r_free = 0.4084 target = 0.168062 restraints weight = 5465.551| |-----------------------------------------------------------------------------| r_work (final): 0.4086 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6476 moved from start: 0.3154 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 8682 Z= 0.123 Angle : 0.549 11.046 11742 Z= 0.268 Chirality : 0.037 0.213 1398 Planarity : 0.004 0.046 1498 Dihedral : 5.044 56.763 1208 Min Nonbonded Distance : 2.393 Molprobity Statistics. All-atom Clashscore : 7.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Rotamer: Outliers : 1.90 % Allowed : 15.87 % Favored : 82.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % 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: 2.75 (0.26), residues: 1093 helix: 2.41 (0.18), residues: 830 sheet: -0.74 (1.01), residues: 20 loop : -0.00 (0.40), residues: 243 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP C 245 HIS 0.004 0.001 HIS B 80 PHE 0.021 0.001 PHE B 90 TYR 0.022 0.001 TYR B 186 ARG 0.002 0.000 ARG D 339 Details of bonding type rmsd hydrogen bonds : bond 0.03409 ( 636) hydrogen bonds : angle 3.53984 ( 1872) metal coordination : bond 0.01250 ( 8) metal coordination : angle 2.00751 ( 6) covalent geometry : bond 0.00286 ( 8674) covalent geometry : angle 0.54682 (11736) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2186 Ramachandran restraints generated. 1093 Oldfield, 0 Emsley, 1093 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2186 Ramachandran restraints generated. 1093 Oldfield, 0 Emsley, 1093 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 116 time to evaluate : 0.959 Fit side-chains revert: symmetry clash REVERT: A 186 TYR cc_start: 0.7253 (OUTLIER) cc_final: 0.6990 (m-10) REVERT: A 330 TYR cc_start: 0.6922 (m-80) cc_final: 0.6456 (m-10) REVERT: C 234 MET cc_start: 0.6415 (ppp) cc_final: 0.6191 (ppp) REVERT: D 172 MET cc_start: 0.4287 (mpp) cc_final: 0.3964 (mtt) outliers start: 17 outliers final: 14 residues processed: 126 average time/residue: 0.2074 time to fit residues: 36.6107 Evaluate side-chains 126 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 111 time to evaluate : 0.915 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 156 CYS Chi-restraints excluded: chain A residue 186 TYR Chi-restraints excluded: chain A residue 193 VAL Chi-restraints excluded: chain A residue 211 ILE Chi-restraints excluded: chain A residue 299 LEU Chi-restraints excluded: chain A residue 319 LEU Chi-restraints excluded: chain A residue 322 VAL Chi-restraints excluded: chain A residue 331 THR Chi-restraints excluded: chain A residue 396 GLU Chi-restraints excluded: chain B residue 201 ASP Chi-restraints excluded: chain B residue 227 ILE Chi-restraints excluded: chain C residue 196 ILE Chi-restraints excluded: chain D residue 193 GLN Chi-restraints excluded: chain D residue 337 HIS Chi-restraints excluded: chain D residue 342 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 102 optimal weight: 0.6980 chunk 90 optimal weight: 1.9990 chunk 27 optimal weight: 0.8980 chunk 8 optimal weight: 0.4980 chunk 69 optimal weight: 0.0770 chunk 12 optimal weight: 0.5980 chunk 29 optimal weight: 0.6980 chunk 13 optimal weight: 0.5980 chunk 65 optimal weight: 0.4980 chunk 17 optimal weight: 0.6980 chunk 36 optimal weight: 0.3980 overall best weight: 0.4138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 214 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4414 r_free = 0.4414 target = 0.202272 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4066 r_free = 0.4066 target = 0.166261 restraints weight = 10409.445| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.4059 r_free = 0.4059 target = 0.166068 restraints weight = 7370.106| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.4058 r_free = 0.4058 target = 0.165937 restraints weight = 6731.153| |-----------------------------------------------------------------------------| r_work (final): 0.4062 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6515 moved from start: 0.3239 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 8682 Z= 0.129 Angle : 0.561 10.862 11742 Z= 0.275 Chirality : 0.037 0.187 1398 Planarity : 0.004 0.045 1498 Dihedral : 5.003 53.562 1208 Min Nonbonded Distance : 2.400 Molprobity Statistics. All-atom Clashscore : 7.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Rotamer: Outliers : 2.12 % Allowed : 15.53 % Favored : 82.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % 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: 2.76 (0.26), residues: 1093 helix: 2.41 (0.18), residues: 830 sheet: -0.94 (0.99), residues: 20 loop : 0.05 (0.40), residues: 243 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP C 245 HIS 0.004 0.001 HIS B 80 PHE 0.014 0.002 PHE C 331 TYR 0.021 0.002 TYR B 186 ARG 0.004 0.000 ARG D 236 Details of bonding type rmsd hydrogen bonds : bond 0.03469 ( 636) hydrogen bonds : angle 3.56162 ( 1872) metal coordination : bond 0.01270 ( 8) metal coordination : angle 2.06702 ( 6) covalent geometry : bond 0.00303 ( 8674) covalent geometry : angle 0.55949 (11736) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2186 Ramachandran restraints generated. 1093 Oldfield, 0 Emsley, 1093 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2186 Ramachandran restraints generated. 1093 Oldfield, 0 Emsley, 1093 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 111 time to evaluate : 0.947 Fit side-chains revert: symmetry clash REVERT: A 186 TYR cc_start: 0.7259 (OUTLIER) cc_final: 0.7004 (m-10) REVERT: A 330 TYR cc_start: 0.6889 (m-80) cc_final: 0.6436 (m-10) REVERT: B 195 ASP cc_start: 0.6857 (p0) cc_final: 0.6615 (t0) REVERT: C 231 MET cc_start: 0.7068 (mpp) cc_final: 0.6468 (mpp) REVERT: D 172 MET cc_start: 0.4374 (mpp) cc_final: 0.4101 (mtt) outliers start: 19 outliers final: 16 residues processed: 124 average time/residue: 0.1817 time to fit residues: 33.0669 Evaluate side-chains 126 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 109 time to evaluate : 0.869 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 CYS Chi-restraints excluded: chain A residue 95 LEU Chi-restraints excluded: chain A residue 156 CYS Chi-restraints excluded: chain A residue 186 TYR Chi-restraints excluded: chain A residue 193 VAL Chi-restraints excluded: chain A residue 211 ILE Chi-restraints excluded: chain A residue 299 LEU Chi-restraints excluded: chain A residue 319 LEU Chi-restraints excluded: chain A residue 331 THR Chi-restraints excluded: chain A residue 396 GLU Chi-restraints excluded: chain B residue 129 VAL Chi-restraints excluded: chain B residue 201 ASP Chi-restraints excluded: chain B residue 227 ILE Chi-restraints excluded: chain C residue 196 ILE Chi-restraints excluded: chain D residue 193 GLN Chi-restraints excluded: chain D residue 337 HIS Chi-restraints excluded: chain D residue 342 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 64 optimal weight: 5.9990 chunk 43 optimal weight: 0.6980 chunk 62 optimal weight: 8.9990 chunk 37 optimal weight: 0.5980 chunk 44 optimal weight: 2.9990 chunk 108 optimal weight: 0.9980 chunk 59 optimal weight: 3.9990 chunk 105 optimal weight: 0.5980 chunk 58 optimal weight: 10.0000 chunk 52 optimal weight: 1.9990 chunk 3 optimal weight: 0.5980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 278 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4382 r_free = 0.4382 target = 0.198778 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.4061 r_free = 0.4061 target = 0.164724 restraints weight = 10173.133| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.4046 r_free = 0.4046 target = 0.163944 restraints weight = 9244.479| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.4069 r_free = 0.4069 target = 0.166451 restraints weight = 7283.480| |-----------------------------------------------------------------------------| r_work (final): 0.4069 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6535 moved from start: 0.3482 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 8682 Z= 0.172 Angle : 0.618 10.933 11742 Z= 0.305 Chirality : 0.039 0.208 1398 Planarity : 0.004 0.045 1498 Dihedral : 5.284 54.642 1208 Min Nonbonded Distance : 2.395 Molprobity Statistics. All-atom Clashscore : 8.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Rotamer: Outliers : 2.35 % Allowed : 15.64 % Favored : 82.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % 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: 2.37 (0.26), residues: 1093 helix: 2.13 (0.18), residues: 833 sheet: -1.10 (1.00), residues: 20 loop : -0.13 (0.40), residues: 240 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.003 TRP C 245 HIS 0.005 0.001 HIS A 300 PHE 0.023 0.002 PHE B 90 TYR 0.024 0.002 TYR B 186 ARG 0.005 0.000 ARG D 339 Details of bonding type rmsd hydrogen bonds : bond 0.04014 ( 636) hydrogen bonds : angle 3.79579 ( 1872) metal coordination : bond 0.01714 ( 8) metal coordination : angle 2.51372 ( 6) covalent geometry : bond 0.00418 ( 8674) covalent geometry : angle 0.61572 (11736) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2186 Ramachandran restraints generated. 1093 Oldfield, 0 Emsley, 1093 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2186 Ramachandran restraints generated. 1093 Oldfield, 0 Emsley, 1093 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 115 time to evaluate : 0.948 Fit side-chains revert: symmetry clash REVERT: A 330 TYR cc_start: 0.7084 (m-80) cc_final: 0.6604 (m-10) REVERT: D 172 MET cc_start: 0.4483 (mpp) cc_final: 0.4157 (mtt) outliers start: 21 outliers final: 17 residues processed: 130 average time/residue: 0.2276 time to fit residues: 42.4492 Evaluate side-chains 128 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 111 time to evaluate : 1.017 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 CYS Chi-restraints excluded: chain A residue 95 LEU Chi-restraints excluded: chain A residue 156 CYS Chi-restraints excluded: chain A residue 193 VAL Chi-restraints excluded: chain A residue 211 ILE Chi-restraints excluded: chain A residue 232 VAL Chi-restraints excluded: chain A residue 299 LEU Chi-restraints excluded: chain A residue 331 THR Chi-restraints excluded: chain A residue 396 GLU Chi-restraints excluded: chain B residue 129 VAL Chi-restraints excluded: chain B residue 201 ASP Chi-restraints excluded: chain B residue 227 ILE Chi-restraints excluded: chain C residue 196 ILE Chi-restraints excluded: chain D residue 175 THR Chi-restraints excluded: chain D residue 193 GLN Chi-restraints excluded: chain D residue 337 HIS Chi-restraints excluded: chain D residue 342 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 45 optimal weight: 0.7980 chunk 15 optimal weight: 0.5980 chunk 30 optimal weight: 2.9990 chunk 68 optimal weight: 0.0870 chunk 17 optimal weight: 0.7980 chunk 7 optimal weight: 0.9990 chunk 31 optimal weight: 0.0030 chunk 52 optimal weight: 0.7980 chunk 80 optimal weight: 0.5980 chunk 85 optimal weight: 0.5980 chunk 98 optimal weight: 0.9980 overall best weight: 0.3768 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 210 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 214 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4402 r_free = 0.4402 target = 0.204264 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.4075 r_free = 0.4075 target = 0.169266 restraints weight = 9983.888| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.4057 r_free = 0.4057 target = 0.167695 restraints weight = 7838.489| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4076 r_free = 0.4076 target = 0.169733 restraints weight = 6397.912| |-----------------------------------------------------------------------------| r_work (final): 0.4075 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6422 moved from start: 0.3439 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 8682 Z= 0.128 Angle : 0.590 11.038 11742 Z= 0.288 Chirality : 0.038 0.184 1398 Planarity : 0.004 0.046 1498 Dihedral : 5.135 59.984 1208 Min Nonbonded Distance : 2.404 Molprobity Statistics. All-atom Clashscore : 8.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer: Outliers : 2.23 % Allowed : 15.53 % Favored : 82.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % 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: 2.60 (0.26), residues: 1093 helix: 2.27 (0.18), residues: 836 sheet: -1.09 (0.98), residues: 20 loop : 0.02 (0.40), residues: 237 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.002 TRP C 245 HIS 0.005 0.001 HIS A 300 PHE 0.020 0.002 PHE B 90 TYR 0.022 0.001 TYR B 186 ARG 0.004 0.000 ARG B 222 Details of bonding type rmsd hydrogen bonds : bond 0.03536 ( 636) hydrogen bonds : angle 3.65693 ( 1872) metal coordination : bond 0.01234 ( 8) metal coordination : angle 2.12418 ( 6) covalent geometry : bond 0.00300 ( 8674) covalent geometry : angle 0.58785 (11736) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4227.51 seconds wall clock time: 75 minutes 23.46 seconds (4523.46 seconds total)