Starting phenix.real_space_refine on Tue Mar 3 20:50:20 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7tad_25771/03_2026/7tad_25771.cif Found real_map, /net/cci-nas-00/data/ceres_data/7tad_25771/03_2026/7tad_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_25771/03_2026/7tad_25771.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7tad_25771/03_2026/7tad_25771.map" model { file = "/net/cci-nas-00/data/ceres_data/7tad_25771/03_2026/7tad_25771.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7tad_25771/03_2026/7tad_25771.cif" } resolution = 3.6 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 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, 'ASP:plan': 3, 'ASN:plan1': 1, 'ARG:plan': 1} 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: {'GLU:plan': 8, 'ASP:plan': 1, 'GLN:plan1': 1, 'ARG:plan': 2} 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: {'ARG:plan': 1, 'GLN:plan1': 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: {'ARG:plan': 1, 'GLN:plan1': 2, '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: 1.95, per 1000 atoms: 0.23 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: 0.62 Conformation dependent library (CDL) restraints added in 383.3 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: 0.24 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: 1.61 Time building geometry restraints manager: 0.86 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 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 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: 5.580 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: 0.090 Check model and map are aligned: 0.020 Set scattering table: 0.010 Process input model: 9.890 Find NCS groups from input model: 0.140 Set up NCS constraints: 0.010 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:1.410 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.160 ------------------------------------------------------------------------------- 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.68 (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 ARG 0.010 0.001 ARG C 274 TYR 0.028 0.002 TYR D 365 PHE 0.014 0.002 PHE A 91 TRP 0.025 0.003 TRP C 235 HIS 0.017 0.001 HIS A 157 Details of bonding type rmsd covalent geometry : bond 0.00289 ( 8674) covalent geometry : angle 0.69678 (11736) hydrogen bonds : bond 0.12035 ( 636) hydrogen bonds : angle 4.69620 ( 1872) metal coordination : bond 0.02937 ( 8) metal coordination : angle 5.40160 ( 6) *********************** 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 : 0.330 Fit side-chains REVERT: B 245 LEU cc_start: 0.8744 (tp) cc_final: 0.8531 (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: 0.0879 time to fit residues: 15.6951 Evaluate side-chains 99 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 99 time to evaluate : 0.305 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 108 optimal weight: 0.6980 chunk 49 optimal weight: 0.5980 chunk 97 optimal weight: 0.0370 chunk 53 optimal weight: 3.9990 chunk 5 optimal weight: 0.5980 chunk 33 optimal weight: 2.9990 chunk 65 optimal weight: 8.9990 chunk 62 optimal weight: 0.9980 chunk 51 optimal weight: 0.8980 chunk 100 optimal weight: 0.6980 chunk 106 optimal weight: 0.5980 overall best weight: 0.5058 ------------------------------------------------------------------------------- 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 = 0.4487 r_free = 0.4487 target = 0.208842 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4129 r_free = 0.4129 target = 0.171050 restraints weight = 10633.977| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.4150 r_free = 0.4150 target = 0.173612 restraints weight = 7490.720| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.4160 r_free = 0.4160 target = 0.174654 restraints weight = 5170.584| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.4167 r_free = 0.4167 target = 0.175453 restraints weight = 4498.236| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.4170 r_free = 0.4170 target = 0.175786 restraints weight = 4395.875| |-----------------------------------------------------------------------------| r_work (final): 0.4171 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6357 moved from start: 0.1542 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 8682 Z= 0.146 Angle : 0.586 7.765 11742 Z= 0.293 Chirality : 0.038 0.188 1398 Planarity : 0.005 0.073 1498 Dihedral : 5.022 53.841 1208 Min Nonbonded Distance : 2.405 Molprobity Statistics. All-atom Clashscore : 7.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.37 % Favored : 98.63 % Rotamer: Outliers : 1.01 % Allowed : 7.49 % Favored : 91.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.00 (0.25), residues: 1093 helix: 1.90 (0.18), residues: 828 sheet: 0.30 (0.95), residues: 32 loop : -0.55 (0.40), residues: 233 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 81 TYR 0.025 0.002 TYR A 186 PHE 0.018 0.002 PHE C 366 TRP 0.016 0.002 TRP D 376 HIS 0.004 0.001 HIS B 80 Details of bonding type rmsd covalent geometry : bond 0.00335 ( 8674) covalent geometry : angle 0.58394 (11736) hydrogen bonds : bond 0.03949 ( 636) hydrogen bonds : angle 3.77517 ( 1872) metal coordination : bond 0.02002 ( 8) metal coordination : angle 2.22487 ( 6) *********************** 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: 9 poor density : 124 time to evaluate : 0.335 Fit side-chains REVERT: A 330 TYR cc_start: 0.6830 (m-80) cc_final: 0.6308 (m-10) REVERT: B 283 LYS cc_start: 0.8719 (pptt) cc_final: 0.8452 (pptt) REVERT: C 234 MET cc_start: 0.5699 (ppp) cc_final: 0.5418 (ppp) REVERT: D 331 PHE cc_start: 0.7258 (m-80) cc_final: 0.7024 (m-80) outliers start: 9 outliers final: 7 residues processed: 126 average time/residue: 0.0834 time to fit residues: 15.0364 Evaluate side-chains 112 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 105 time to evaluate : 0.221 ------------------------------------------------------------------------------- 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 175 THR 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 40 optimal weight: 1.9990 chunk 82 optimal weight: 1.9990 chunk 101 optimal weight: 0.5980 chunk 49 optimal weight: 0.7980 chunk 15 optimal weight: 0.5980 chunk 65 optimal weight: 1.9990 chunk 41 optimal weight: 0.9990 chunk 6 optimal weight: 1.9990 chunk 9 optimal weight: 0.3980 chunk 37 optimal weight: 0.9990 chunk 38 optimal weight: 0.5980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 271 HIS C 345 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4451 r_free = 0.4451 target = 0.204765 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.4058 r_free = 0.4058 target = 0.164381 restraints weight = 10486.955| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.4091 r_free = 0.4091 target = 0.167537 restraints weight = 7236.710| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.4113 r_free = 0.4113 target = 0.169732 restraints weight = 5513.444| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.4129 r_free = 0.4129 target = 0.171254 restraints weight = 4547.392| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.4136 r_free = 0.4136 target = 0.171965 restraints weight = 3969.244| |-----------------------------------------------------------------------------| r_work (final): 0.4136 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6427 moved from start: 0.2272 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 8682 Z= 0.155 Angle : 0.578 11.049 11742 Z= 0.287 Chirality : 0.038 0.156 1398 Planarity : 0.004 0.059 1498 Dihedral : 5.005 54.295 1208 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 7.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.83 % Favored : 98.17 % Rotamer: Outliers : 2.35 % Allowed : 8.94 % Favored : 88.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.30 (0.26), residues: 1093 helix: 2.06 (0.18), residues: 831 sheet: 0.23 (0.95), residues: 30 loop : -0.17 (0.42), residues: 232 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 236 TYR 0.026 0.002 TYR B 186 PHE 0.016 0.002 PHE C 366 TRP 0.024 0.003 TRP D 376 HIS 0.005 0.001 HIS B 80 Details of bonding type rmsd covalent geometry : bond 0.00363 ( 8674) covalent geometry : angle 0.57535 (11736) hydrogen bonds : bond 0.03994 ( 636) hydrogen bonds : angle 3.74977 ( 1872) metal coordination : bond 0.01782 ( 8) metal coordination : angle 2.47464 ( 6) *********************** 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 148 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 127 time to evaluate : 0.313 Fit side-chains REVERT: A 330 TYR cc_start: 0.6911 (m-80) cc_final: 0.6380 (m-10) REVERT: A 339 ARG cc_start: 0.7493 (mmt180) cc_final: 0.7288 (mmt180) REVERT: B 75 ARG cc_start: 0.6911 (ttm110) cc_final: 0.6542 (mtm180) REVERT: B 149 GLU cc_start: 0.6653 (mt-10) cc_final: 0.6426 (mt-10) REVERT: B 283 LYS cc_start: 0.9014 (pptt) cc_final: 0.8770 (pptt) REVERT: D 172 MET cc_start: 0.4416 (mpp) cc_final: 0.3646 (mtt) REVERT: D 331 PHE cc_start: 0.7109 (m-80) cc_final: 0.6857 (m-80) outliers start: 21 outliers final: 14 residues processed: 138 average time/residue: 0.0903 time to fit residues: 17.1105 Evaluate side-chains 126 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 112 time to evaluate : 0.307 ------------------------------------------------------------------------------- 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 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 316 LYS Chi-restraints excluded: chain C residue 175 THR 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 55 optimal weight: 9.9990 chunk 4 optimal weight: 0.7980 chunk 103 optimal weight: 0.7980 chunk 108 optimal weight: 0.6980 chunk 14 optimal weight: 0.3980 chunk 57 optimal weight: 4.9990 chunk 89 optimal weight: 0.9980 chunk 90 optimal weight: 0.5980 chunk 76 optimal weight: 0.0040 chunk 63 optimal weight: 1.9990 chunk 80 optimal weight: 2.9990 overall best weight: 0.4992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 154 ASN D 295 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4420 r_free = 0.4420 target = 0.202564 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.4036 r_free = 0.4036 target = 0.162934 restraints weight = 10385.280| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.4067 r_free = 0.4067 target = 0.166043 restraints weight = 7032.232| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.4089 r_free = 0.4089 target = 0.168247 restraints weight = 5321.975| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.4105 r_free = 0.4105 target = 0.169767 restraints weight = 4359.903| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.4113 r_free = 0.4113 target = 0.170646 restraints weight = 3786.708| |-----------------------------------------------------------------------------| r_work (final): 0.4110 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6437 moved from start: 0.2525 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 8682 Z= 0.138 Angle : 0.556 10.957 11742 Z= 0.274 Chirality : 0.037 0.137 1398 Planarity : 0.004 0.052 1498 Dihedral : 5.284 59.531 1208 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 7.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Rotamer: Outliers : 2.46 % Allowed : 12.29 % Favored : 85.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.49 (0.26), residues: 1093 helix: 2.21 (0.18), residues: 829 sheet: 0.15 (0.93), residues: 30 loop : -0.18 (0.42), residues: 234 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 236 TYR 0.029 0.002 TYR A 186 PHE 0.017 0.002 PHE B 90 TRP 0.023 0.002 TRP C 245 HIS 0.004 0.001 HIS B 80 Details of bonding type rmsd covalent geometry : bond 0.00322 ( 8674) covalent geometry : angle 0.55293 (11736) hydrogen bonds : bond 0.03705 ( 636) hydrogen bonds : angle 3.62414 ( 1872) metal coordination : bond 0.01793 ( 8) metal coordination : angle 2.46189 ( 6) *********************** 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 142 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 120 time to evaluate : 0.298 Fit side-chains REVERT: A 330 TYR cc_start: 0.6908 (m-80) cc_final: 0.6315 (m-10) REVERT: C 231 MET cc_start: 0.6917 (mpp) cc_final: 0.6457 (mpp) REVERT: D 172 MET cc_start: 0.4345 (mpp) cc_final: 0.3803 (mtt) REVERT: D 331 PHE cc_start: 0.7087 (m-80) cc_final: 0.6863 (m-80) outliers start: 22 outliers final: 15 residues processed: 133 average time/residue: 0.0926 time to fit residues: 17.0129 Evaluate side-chains 127 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 112 time to evaluate : 0.324 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 B residue 316 LYS Chi-restraints excluded: chain C 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 50 optimal weight: 0.9990 chunk 40 optimal weight: 0.0570 chunk 12 optimal weight: 1.9990 chunk 6 optimal weight: 1.9990 chunk 5 optimal weight: 0.7980 chunk 7 optimal weight: 0.0980 chunk 59 optimal weight: 1.9990 chunk 34 optimal weight: 0.3980 chunk 49 optimal weight: 0.9980 chunk 97 optimal weight: 0.0980 chunk 89 optimal weight: 0.6980 overall best weight: 0.2698 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 210 ASN C 278 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4445 r_free = 0.4445 target = 0.205618 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.4060 r_free = 0.4060 target = 0.165590 restraints weight = 10430.890| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.4092 r_free = 0.4092 target = 0.168746 restraints weight = 7163.062| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.4115 r_free = 0.4115 target = 0.170962 restraints weight = 5437.135| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.4127 r_free = 0.4127 target = 0.172273 restraints weight = 4453.327| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.4134 r_free = 0.4134 target = 0.172929 restraints weight = 3900.376| |-----------------------------------------------------------------------------| r_work (final): 0.4129 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6393 moved from start: 0.2641 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 8682 Z= 0.108 Angle : 0.521 11.143 11742 Z= 0.255 Chirality : 0.035 0.124 1398 Planarity : 0.004 0.047 1498 Dihedral : 5.012 57.567 1208 Min Nonbonded Distance : 2.421 Molprobity Statistics. All-atom Clashscore : 6.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Rotamer: Outliers : 1.79 % Allowed : 13.63 % Favored : 84.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.85 (0.26), residues: 1093 helix: 2.48 (0.18), residues: 829 sheet: 0.32 (0.95), residues: 30 loop : -0.09 (0.41), residues: 234 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 236 TYR 0.023 0.002 TYR A 186 PHE 0.023 0.001 PHE B 90 TRP 0.024 0.002 TRP C 245 HIS 0.003 0.001 HIS B 80 Details of bonding type rmsd covalent geometry : bond 0.00240 ( 8674) covalent geometry : angle 0.51852 (11736) hydrogen bonds : bond 0.03251 ( 636) hydrogen bonds : angle 3.45833 ( 1872) metal coordination : bond 0.01326 ( 8) metal coordination : angle 2.16669 ( 6) *********************** 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 137 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 121 time to evaluate : 0.289 Fit side-chains REVERT: B 47 GLN cc_start: 0.7269 (mm-40) cc_final: 0.6617 (tm-30) REVERT: B 283 LYS cc_start: 0.8761 (pptt) cc_final: 0.8353 (pptt) REVERT: B 367 MET cc_start: 0.8382 (mpp) cc_final: 0.8083 (ptp) REVERT: C 231 MET cc_start: 0.7038 (mpp) cc_final: 0.6229 (mpp) REVERT: D 172 MET cc_start: 0.4197 (mpp) cc_final: 0.3751 (mtt) outliers start: 16 outliers final: 12 residues processed: 130 average time/residue: 0.0934 time to fit residues: 16.6346 Evaluate side-chains 122 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 110 time to evaluate : 0.300 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 135 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 123 VAL Chi-restraints excluded: chain B residue 201 ASP 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 71 optimal weight: 0.6980 chunk 26 optimal weight: 0.9980 chunk 44 optimal weight: 0.9990 chunk 4 optimal weight: 0.5980 chunk 8 optimal weight: 0.9980 chunk 53 optimal weight: 0.3980 chunk 48 optimal weight: 0.9990 chunk 12 optimal weight: 0.6980 chunk 57 optimal weight: 0.9990 chunk 104 optimal weight: 0.8980 chunk 35 optimal weight: 0.7980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 354 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4396 r_free = 0.4396 target = 0.199983 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.3998 r_free = 0.3998 target = 0.159621 restraints weight = 10448.228| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.4030 r_free = 0.4030 target = 0.162595 restraints weight = 7293.652| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.4049 r_free = 0.4049 target = 0.164540 restraints weight = 5633.373| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.4066 r_free = 0.4066 target = 0.166114 restraints weight = 4663.094| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 20)----------------| | r_work = 0.4073 r_free = 0.4073 target = 0.166745 restraints weight = 4083.908| |-----------------------------------------------------------------------------| r_work (final): 0.4071 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6509 moved from start: 0.2990 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 8682 Z= 0.158 Angle : 0.586 10.950 11742 Z= 0.288 Chirality : 0.037 0.201 1398 Planarity : 0.004 0.046 1498 Dihedral : 5.221 59.760 1208 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 8.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Rotamer: Outliers : 2.68 % Allowed : 14.19 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.55 (0.26), residues: 1093 helix: 2.30 (0.18), residues: 827 sheet: -0.57 (1.03), residues: 20 loop : -0.22 (0.40), residues: 246 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 236 TYR 0.024 0.002 TYR B 186 PHE 0.029 0.002 PHE B 90 TRP 0.026 0.002 TRP C 245 HIS 0.005 0.001 HIS B 80 Details of bonding type rmsd covalent geometry : bond 0.00375 ( 8674) covalent geometry : angle 0.58314 (11736) hydrogen bonds : bond 0.03911 ( 636) hydrogen bonds : angle 3.67541 ( 1872) metal coordination : bond 0.01888 ( 8) metal coordination : angle 2.58433 ( 6) *********************** 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 143 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 119 time to evaluate : 0.222 Fit side-chains REVERT: A 330 TYR cc_start: 0.7046 (m-80) cc_final: 0.6459 (m-10) REVERT: B 283 LYS cc_start: 0.8815 (pptt) cc_final: 0.8505 (pptt) REVERT: B 367 MET cc_start: 0.8304 (mpp) cc_final: 0.8049 (ptp) REVERT: C 231 MET cc_start: 0.7159 (mpp) cc_final: 0.6775 (mpp) REVERT: D 172 MET cc_start: 0.4390 (mpp) cc_final: 0.3985 (mtt) outliers start: 24 outliers final: 19 residues processed: 133 average time/residue: 0.0931 time to fit residues: 17.2890 Evaluate side-chains 129 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 110 time to evaluate : 0.338 ------------------------------------------------------------------------------- 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 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 201 ASP Chi-restraints excluded: chain B residue 227 ILE Chi-restraints excluded: chain B residue 316 LYS Chi-restraints excluded: chain C residue 175 THR 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 80 optimal weight: 0.8980 chunk 107 optimal weight: 0.6980 chunk 98 optimal weight: 0.0020 chunk 95 optimal weight: 0.9980 chunk 41 optimal weight: 0.1980 chunk 1 optimal weight: 0.5980 chunk 56 optimal weight: 0.9980 chunk 44 optimal weight: 8.9990 chunk 54 optimal weight: 1.9990 chunk 61 optimal weight: 9.9990 chunk 37 optimal weight: 0.8980 overall best weight: 0.4788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4412 r_free = 0.4412 target = 0.202039 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.4014 r_free = 0.4014 target = 0.161105 restraints weight = 10467.724| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.4047 r_free = 0.4047 target = 0.164278 restraints weight = 7187.825| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 56)----------------| | r_work = 0.4071 r_free = 0.4071 target = 0.166543 restraints weight = 5465.347| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.4083 r_free = 0.4083 target = 0.167848 restraints weight = 4475.608| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 43)----------------| | r_work = 0.4096 r_free = 0.4096 target = 0.169045 restraints weight = 3912.344| |-----------------------------------------------------------------------------| r_work (final): 0.4099 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6461 moved from start: 0.3113 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= 0.133 Angle : 0.561 10.942 11742 Z= 0.276 Chirality : 0.037 0.158 1398 Planarity : 0.004 0.046 1498 Dihedral : 5.061 59.800 1208 Min Nonbonded Distance : 2.398 Molprobity Statistics. All-atom Clashscore : 7.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer: Outliers : 2.68 % Allowed : 15.08 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.63 (0.26), residues: 1093 helix: 2.35 (0.18), residues: 829 sheet: -0.68 (1.01), residues: 20 loop : -0.17 (0.40), residues: 244 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 236 TYR 0.022 0.002 TYR B 186 PHE 0.032 0.002 PHE B 90 TRP 0.028 0.002 TRP C 245 HIS 0.004 0.001 HIS B 80 Details of bonding type rmsd covalent geometry : bond 0.00314 ( 8674) covalent geometry : angle 0.55907 (11736) hydrogen bonds : bond 0.03550 ( 636) hydrogen bonds : angle 3.57331 ( 1872) metal coordination : bond 0.01445 ( 8) metal coordination : angle 2.26475 ( 6) *********************** 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 137 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 113 time to evaluate : 0.300 Fit side-chains revert: symmetry clash REVERT: A 330 TYR cc_start: 0.6947 (m-80) cc_final: 0.6442 (m-10) REVERT: B 283 LYS cc_start: 0.8804 (pptt) cc_final: 0.8549 (pptt) REVERT: B 367 MET cc_start: 0.8325 (mpp) cc_final: 0.8050 (ptp) REVERT: C 231 MET cc_start: 0.7109 (mpp) cc_final: 0.6485 (mpp) REVERT: C 234 MET cc_start: 0.6330 (ppp) cc_final: 0.5937 (ppp) REVERT: D 172 MET cc_start: 0.4368 (mpp) cc_final: 0.3769 (mtt) outliers start: 24 outliers final: 20 residues processed: 129 average time/residue: 0.0827 time to fit residues: 15.3584 Evaluate side-chains 128 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 108 time to evaluate : 0.301 ------------------------------------------------------------------------------- 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 193 VAL Chi-restraints excluded: chain A residue 211 ILE Chi-restraints excluded: chain A residue 232 VAL 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 201 ASP Chi-restraints excluded: chain B residue 227 ILE Chi-restraints excluded: chain B residue 316 LYS Chi-restraints excluded: chain C residue 175 THR 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 28 optimal weight: 0.8980 chunk 82 optimal weight: 0.3980 chunk 32 optimal weight: 0.0870 chunk 58 optimal weight: 0.8980 chunk 36 optimal weight: 0.1980 chunk 106 optimal weight: 0.0970 chunk 64 optimal weight: 5.9990 chunk 17 optimal weight: 0.9990 chunk 25 optimal weight: 0.9990 chunk 29 optimal weight: 0.3980 chunk 72 optimal weight: 0.9990 overall best weight: 0.2356 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4434 r_free = 0.4434 target = 0.204778 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4088 r_free = 0.4088 target = 0.168250 restraints weight = 10168.981| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.4091 r_free = 0.4091 target = 0.168929 restraints weight = 7017.642| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.4101 r_free = 0.4101 target = 0.170040 restraints weight = 6119.445| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.4110 r_free = 0.4110 target = 0.171048 restraints weight = 4861.537| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.4113 r_free = 0.4113 target = 0.171315 restraints weight = 4502.604| |-----------------------------------------------------------------------------| r_work (final): 0.4116 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6422 moved from start: 0.3106 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 8682 Z= 0.105 Angle : 0.526 10.996 11742 Z= 0.256 Chirality : 0.036 0.206 1398 Planarity : 0.004 0.045 1498 Dihedral : 4.621 48.800 1208 Min Nonbonded Distance : 2.402 Molprobity Statistics. All-atom Clashscore : 7.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer: Outliers : 1.68 % Allowed : 16.09 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.91 (0.26), residues: 1093 helix: 2.55 (0.18), residues: 830 sheet: -0.61 (0.99), residues: 20 loop : -0.04 (0.40), residues: 243 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 236 TYR 0.020 0.001 TYR B 186 PHE 0.037 0.001 PHE B 90 TRP 0.029 0.002 TRP C 245 HIS 0.003 0.001 HIS B 80 Details of bonding type rmsd covalent geometry : bond 0.00233 ( 8674) covalent geometry : angle 0.52414 (11736) hydrogen bonds : bond 0.03128 ( 636) hydrogen bonds : angle 3.41133 ( 1872) metal coordination : bond 0.00939 ( 8) metal coordination : angle 1.94870 ( 6) *********************** 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 134 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 119 time to evaluate : 0.302 Fit side-chains revert: symmetry clash REVERT: B 47 GLN cc_start: 0.7252 (mm-40) cc_final: 0.6599 (tm-30) REVERT: B 138 SER cc_start: 0.8309 (m) cc_final: 0.8107 (p) REVERT: C 231 MET cc_start: 0.6977 (mpp) cc_final: 0.6307 (mpp) REVERT: D 172 MET cc_start: 0.4339 (mpp) cc_final: 0.3792 (mtt) outliers start: 15 outliers final: 12 residues processed: 130 average time/residue: 0.0830 time to fit residues: 15.4815 Evaluate side-chains 125 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 113 time to evaluate : 0.320 ------------------------------------------------------------------------------- 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 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 201 ASP 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 98 optimal weight: 0.8980 chunk 45 optimal weight: 0.0470 chunk 34 optimal weight: 0.6980 chunk 24 optimal weight: 2.9990 chunk 38 optimal weight: 0.9990 chunk 57 optimal weight: 0.5980 chunk 9 optimal weight: 0.4980 chunk 106 optimal weight: 1.9990 chunk 17 optimal weight: 0.7980 chunk 60 optimal weight: 4.9990 chunk 77 optimal weight: 0.5980 overall best weight: 0.4878 ------------------------------------------------------------------------------- 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 = 0.4409 r_free = 0.4409 target = 0.201709 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.4084 r_free = 0.4084 target = 0.167847 restraints weight = 10098.005| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.4069 r_free = 0.4069 target = 0.166957 restraints weight = 7487.381| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.4067 r_free = 0.4067 target = 0.166879 restraints weight = 6967.762| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.4071 r_free = 0.4071 target = 0.167286 restraints weight = 5995.890| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.4081 r_free = 0.4081 target = 0.168446 restraints weight = 5373.808| |-----------------------------------------------------------------------------| r_work (final): 0.4083 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6498 moved from start: 0.3261 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= 0.137 Angle : 0.579 10.989 11742 Z= 0.282 Chirality : 0.037 0.198 1398 Planarity : 0.004 0.045 1498 Dihedral : 4.799 49.730 1208 Min Nonbonded Distance : 2.404 Molprobity Statistics. All-atom Clashscore : 7.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer: Outliers : 1.79 % Allowed : 15.87 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.64 (0.26), residues: 1093 helix: 2.32 (0.18), residues: 836 sheet: -0.81 (0.97), residues: 20 loop : -0.08 (0.40), residues: 237 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 339 TYR 0.026 0.002 TYR B 186 PHE 0.012 0.002 PHE C 331 TRP 0.030 0.002 TRP C 245 HIS 0.004 0.001 HIS B 80 Details of bonding type rmsd covalent geometry : bond 0.00324 ( 8674) covalent geometry : angle 0.57663 (11736) hydrogen bonds : bond 0.03556 ( 636) hydrogen bonds : angle 3.57213 ( 1872) metal coordination : bond 0.01374 ( 8) metal coordination : angle 2.22311 ( 6) *********************** 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 128 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 112 time to evaluate : 0.262 Fit side-chains REVERT: A 330 TYR cc_start: 0.6782 (m-80) cc_final: 0.6345 (m-10) REVERT: C 231 MET cc_start: 0.7009 (mpp) cc_final: 0.6589 (mpp) REVERT: D 172 MET cc_start: 0.4377 (mpp) cc_final: 0.4076 (mtt) outliers start: 16 outliers final: 14 residues processed: 123 average time/residue: 0.0782 time to fit residues: 14.1817 Evaluate side-chains 124 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 110 time to evaluate : 0.319 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 95 LEU 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 232 VAL 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 201 ASP 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 82 optimal weight: 0.0060 chunk 61 optimal weight: 8.9990 chunk 12 optimal weight: 0.9980 chunk 29 optimal weight: 0.7980 chunk 13 optimal weight: 0.7980 chunk 36 optimal weight: 0.5980 chunk 43 optimal weight: 0.4980 chunk 46 optimal weight: 0.9980 chunk 34 optimal weight: 0.6980 chunk 77 optimal weight: 0.2980 chunk 55 optimal weight: 8.9990 overall best weight: 0.4196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4418 r_free = 0.4418 target = 0.202817 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4067 r_free = 0.4067 target = 0.166934 restraints weight = 10173.528| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.4079 r_free = 0.4079 target = 0.168485 restraints weight = 7540.526| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4085 r_free = 0.4085 target = 0.169142 restraints weight = 5399.448| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.4088 r_free = 0.4088 target = 0.169520 restraints weight = 5015.603| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.4091 r_free = 0.4091 target = 0.169806 restraints weight = 4716.968| |-----------------------------------------------------------------------------| r_work (final): 0.4091 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6488 moved from start: 0.3331 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 : 0.588 10.892 11742 Z= 0.284 Chirality : 0.037 0.190 1398 Planarity : 0.004 0.045 1498 Dihedral : 4.746 43.574 1208 Min Nonbonded Distance : 2.407 Molprobity Statistics. All-atom Clashscore : 7.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Rotamer: Outliers : 1.79 % Allowed : 16.54 % Favored : 81.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.66 (0.26), residues: 1093 helix: 2.32 (0.18), residues: 836 sheet: -0.66 (0.98), residues: 20 loop : -0.01 (0.40), residues: 237 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 339 TYR 0.023 0.002 TYR B 186 PHE 0.043 0.002 PHE B 90 TRP 0.033 0.002 TRP C 245 HIS 0.004 0.001 HIS B 80 Details of bonding type rmsd covalent geometry : bond 0.00303 ( 8674) covalent geometry : angle 0.58611 (11736) hydrogen bonds : bond 0.03446 ( 636) hydrogen bonds : angle 3.57285 ( 1872) metal coordination : bond 0.01259 ( 8) metal coordination : angle 2.21356 ( 6) ********************** 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 131 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 115 time to evaluate : 0.292 Fit side-chains REVERT: A 330 TYR cc_start: 0.6783 (m-80) cc_final: 0.6357 (m-10) REVERT: B 367 MET cc_start: 0.8198 (mpp) cc_final: 0.7897 (ptp) REVERT: C 231 MET cc_start: 0.7065 (mpp) cc_final: 0.6621 (mpp) REVERT: D 172 MET cc_start: 0.4398 (mpp) cc_final: 0.4101 (mtt) outliers start: 16 outliers final: 15 residues processed: 127 average time/residue: 0.0842 time to fit residues: 15.0891 Evaluate side-chains 128 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 113 time to evaluate : 0.294 ------------------------------------------------------------------------------- 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 135 VAL Chi-restraints excluded: chain A residue 156 CYS Chi-restraints excluded: chain A residue 193 VAL Chi-restraints excluded: chain A residue 232 VAL 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 201 ASP 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 108 optimal weight: 0.8980 chunk 39 optimal weight: 0.5980 chunk 65 optimal weight: 0.7980 chunk 76 optimal weight: 0.7980 chunk 33 optimal weight: 0.4980 chunk 23 optimal weight: 0.6980 chunk 4 optimal weight: 0.6980 chunk 9 optimal weight: 0.5980 chunk 51 optimal weight: 0.0570 chunk 11 optimal weight: 1.9990 chunk 56 optimal weight: 7.9990 overall best weight: 0.4898 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4410 r_free = 0.4410 target = 0.201823 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.4080 r_free = 0.4080 target = 0.167336 restraints weight = 10113.895| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.4058 r_free = 0.4058 target = 0.165988 restraints weight = 7620.258| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.4065 r_free = 0.4065 target = 0.166700 restraints weight = 6871.309| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.4068 r_free = 0.4068 target = 0.167044 restraints weight = 5646.029| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.4086 r_free = 0.4086 target = 0.168918 restraints weight = 5213.610| |-----------------------------------------------------------------------------| r_work (final): 0.4085 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6497 moved from start: 0.3437 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 8682 Z= 0.139 Angle : 0.606 10.986 11742 Z= 0.292 Chirality : 0.038 0.195 1398 Planarity : 0.004 0.046 1498 Dihedral : 4.819 45.799 1208 Min Nonbonded Distance : 2.409 Molprobity Statistics. All-atom Clashscore : 7.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer: Outliers : 2.12 % Allowed : 16.76 % Favored : 81.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.63 (0.26), residues: 1093 helix: 2.29 (0.18), residues: 836 sheet: -0.66 (1.00), residues: 20 loop : 0.02 (0.41), residues: 237 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 222 TYR 0.023 0.002 TYR B 186 PHE 0.039 0.002 PHE B 90 TRP 0.036 0.002 TRP C 245 HIS 0.004 0.001 HIS B 80 Details of bonding type rmsd covalent geometry : bond 0.00330 ( 8674) covalent geometry : angle 0.60369 (11736) hydrogen bonds : bond 0.03574 ( 636) hydrogen bonds : angle 3.63877 ( 1872) metal coordination : bond 0.01343 ( 8) metal coordination : angle 2.44721 ( 6) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1823.04 seconds wall clock time: 31 minutes 55.89 seconds (1915.89 seconds total)