Starting phenix.real_space_refine (version: 1.21rc1) on Tue Jul 4 19:30:19 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tad_25771/07_2023/7tad_25771_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tad_25771/07_2023/7tad_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tad_25771/07_2023/7tad_25771.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tad_25771/07_2023/7tad_25771.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tad_25771/07_2023/7tad_25771_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tad_25771/07_2023/7tad_25771_updated.pdb" } 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 ------------------------------------------------------------------------------- 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 Residue "A TYR 64": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 288": "OE1" <-> "OE2" Residue "A GLU 399": "OE1" <-> "OE2" Residue "B GLU 113": "OE1" <-> "OE2" Residue "B GLU 149": "OE1" <-> "OE2" Residue "C GLU 173": "OE1" <-> "OE2" Residue "C GLU 285": "OE1" <-> "OE2" Residue "D TYR 365": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5013/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: 4.65, per 1000 atoms: 0.54 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 - 3.50 Amino acid : False - 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: 3.24 Conformation dependent library (CDL) restraints added in 1.4 seconds 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... running ksdssp... Secondary structure from input PDB file: 59 helices and 2 sheets defined 71.0% alpha, 1.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.71 Creating SS restraints... Processing helix chain 'A' and resid 43 through 58 Processing helix chain 'A' and resid 60 through 63 Processing helix chain 'A' and resid 81 through 87 Processing helix chain 'A' and resid 89 through 98 Processing helix chain 'A' and resid 114 through 117 No H-bonds generated for 'chain 'A' and resid 114 through 117' Processing helix chain 'A' and resid 125 through 137 Processing helix chain 'A' and resid 161 through 176 Processing helix chain 'A' and resid 180 through 194 Processing helix chain 'A' and resid 199 through 211 removed outlier: 3.836A pdb=" N VAL A 204 " --> pdb=" O GLU A 200 " (cutoff:3.500A) Processing helix chain 'A' and resid 217 through 228 Processing helix chain 'A' and resid 234 through 240 Processing helix chain 'A' and resid 243 through 255 Processing helix chain 'A' and resid 265 through 275 Processing helix chain 'A' and resid 279 through 288 Processing helix chain 'A' and resid 293 through 296 No H-bonds generated for 'chain 'A' and resid 293 through 296' Processing helix chain 'A' and resid 298 through 304 Processing helix chain 'A' and resid 308 through 317 removed outlier: 3.602A pdb=" N LEU A 317 " --> pdb=" O ASP A 313 " (cutoff:3.500A) Processing helix chain 'A' and resid 332 through 339 Processing helix chain 'A' and resid 342 through 351 Processing helix chain 'A' and resid 365 through 372 Processing helix chain 'A' and resid 375 through 378 Processing helix chain 'A' and resid 390 through 403 removed outlier: 3.554A pdb=" N LYS A 403 " --> pdb=" O GLU A 399 " (cutoff:3.500A) Processing helix chain 'B' and resid 43 through 63 Proline residue: B 60 - end of helix removed outlier: 3.695A pdb=" N PHE B 63 " --> pdb=" O SER B 59 " (cutoff:3.500A) Processing helix chain 'B' and resid 81 through 87 Processing helix chain 'B' and resid 89 through 98 Processing helix chain 'B' and resid 114 through 117 No H-bonds generated for 'chain 'B' and resid 114 through 117' Processing helix chain 'B' and resid 125 through 137 Processing helix chain 'B' and resid 161 through 176 Processing helix chain 'B' and resid 180 through 196 removed outlier: 4.669A pdb=" N ASP B 195 " --> pdb=" O LEU B 191 " (cutoff:3.500A) removed outlier: 5.495A pdb=" N LYS B 196 " --> pdb=" O ASP B 192 " (cutoff:3.500A) Processing helix chain 'B' and resid 199 through 211 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 229 removed outlier: 3.713A pdb=" N CYS B 216 " --> pdb=" O GLY B 213 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N MET B 217 " --> pdb=" O LYS B 214 " (cutoff:3.500A) removed outlier: 6.059A pdb=" N LYS B 218 " --> pdb=" O ALA B 215 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N LEU B 219 " --> pdb=" O CYS B 216 " (cutoff:3.500A) Processing helix chain 'B' and resid 234 through 240 Processing helix chain 'B' and resid 243 through 255 Processing helix chain 'B' and resid 265 through 275 Processing helix chain 'B' and resid 279 through 288 removed outlier: 3.787A pdb=" N GLU B 288 " --> pdb=" O LEU B 284 " (cutoff:3.500A) Processing helix chain 'B' and resid 293 through 296 No H-bonds generated for 'chain 'B' and resid 293 through 296' Processing helix chain 'B' and resid 298 through 305 Processing helix chain 'B' and resid 308 through 316 Processing helix chain 'B' and resid 332 through 339 Processing helix chain 'B' and resid 342 through 351 Processing helix chain 'B' and resid 365 through 372 Processing helix chain 'B' and resid 375 through 378 Processing helix chain 'B' and resid 390 through 402 Processing helix chain 'C' and resid 165 through 193 Processing helix chain 'C' and resid 198 through 225 Processing helix chain 'C' and resid 227 through 232 Processing helix chain 'C' and resid 240 through 243 Processing helix chain 'C' and resid 251 through 259 Processing helix chain 'C' and resid 267 through 305 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) Processing helix chain 'C' and resid 316 through 349 Processing helix chain 'C' and resid 352 through 376 Processing helix chain 'D' and resid 165 through 193 Processing helix chain 'D' and resid 198 through 225 removed outlier: 3.600A pdb=" N ALA D 225 " --> pdb=" O ASP D 221 " (cutoff:3.500A) Processing helix chain 'D' and resid 227 through 232 Processing helix chain 'D' and resid 240 through 242 No H-bonds generated for 'chain 'D' and resid 240 through 242' Processing helix chain 'D' and resid 251 through 262 Proline residue: D 260 - end of helix Processing helix chain 'D' and resid 267 through 306 Processing helix chain 'D' and resid 317 through 349 removed outlier: 3.509A pdb=" N ASP D 336 " --> pdb=" O VAL D 332 " (cutoff:3.500A) Processing helix chain 'D' and resid 352 through 377 Processing sheet with id= A, first strand: chain 'A' and resid 76 through 79 Processing sheet with id= B, first strand: chain 'B' and resid 76 through 79 550 hydrogen bonds defined for protein. 1602 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: 2.26 Time building geometry restraints manager: 3.48 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: 99.27 - 106.22: 157 106.22 - 113.17: 4878 113.17 - 120.12: 3095 120.12 - 127.07: 3539 127.07 - 134.02: 67 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: 99 2.68 - 3.24: 8659 3.24 - 3.79: 13685 3.79 - 4.35: 17344 4.35 - 4.90: 28508 Nonbonded interactions: 68295 Sorted by model distance: nonbonded pdb=" OD1 ASP A 277 " pdb=" OG1 THR A 310 " model vdw 2.126 2.440 nonbonded pdb=" OG1 THR D 237 " pdb=" OE2 GLU D 240 " model vdw 2.244 2.440 nonbonded pdb=" OD1 ASP A 120 " pdb=" OH TYR A 172 " model vdw 2.245 2.440 nonbonded pdb=" NH2 ARG A 325 " pdb=" OE1 GLU A 357 " model vdw 2.248 2.520 nonbonded pdb=" NZ LYS A 239 " pdb=" OD2 ASP A 275 " model vdw 2.259 2.520 ... (remaining 68290 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model 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: 2.960 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: 12.540 Check model and map are aligned: 0.140 Set scattering table: 0.080 Process input model: 25.720 Find NCS groups from input model: 0.470 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:2.640 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 44.600 ------------------------------------------------------------------------------- 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 0.036 8674 Z= 0.185 Angle : 0.697 10.621 11736 Z= 0.355 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 % 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 *********************** 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 fitting. rotamer outliers: 0 poor density : 125 time to evaluate : 0.981 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 125 average time/residue: 0.2027 time to fit residues: 35.4590 Evaluate side-chains 100 residues out of total 966 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 100 time to evaluate : 0.983 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.2914 ------------------------------------------------------------------------------- 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: 0.5980 chunk 28 optimal weight: 0.8980 chunk 55 optimal weight: 0.0170 chunk 44 optimal weight: 6.9990 chunk 85 optimal weight: 0.9990 chunk 33 optimal weight: 1.9990 chunk 51 optimal weight: 0.9990 chunk 63 optimal weight: 5.9990 chunk 98 optimal weight: 0.9990 overall best weight: 0.7022 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6449 moved from start: 0.1753 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.035 8674 Z= 0.267 Angle : 0.603 7.519 11736 Z= 0.302 Chirality : 0.038 0.164 1398 Planarity : 0.005 0.074 1498 Dihedral : 5.518 57.912 1208 Min Nonbonded Distance : 2.158 Molprobity Statistics. All-atom Clashscore : 10.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.19 % Favored : 98.81 % Rotamer Outliers : 0.89 % 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: 1.54 (0.25), residues: 1093 helix: 1.63 (0.18), residues: 817 sheet: 0.11 (0.92), residues: 32 loop : -0.84 (0.37), residues: 244 *********************** 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 135 residues out of total 966 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 127 time to evaluate : 0.887 Fit side-chains outliers start: 8 outliers final: 8 residues processed: 129 average time/residue: 0.1974 time to fit residues: 35.9081 Evaluate side-chains 114 residues out of total 966 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 106 time to evaluate : 0.994 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.0893 time to fit residues: 2.6356 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 55 optimal weight: 8.9990 chunk 30 optimal weight: 1.9990 chunk 82 optimal weight: 0.4980 chunk 67 optimal weight: 3.9990 chunk 27 optimal weight: 0.5980 chunk 99 optimal weight: 0.9980 chunk 107 optimal weight: 0.7980 chunk 88 optimal weight: 0.5980 chunk 98 optimal weight: 1.9990 chunk 33 optimal weight: 3.9990 chunk 79 optimal weight: 0.5980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 51 ASN C 176 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6484 moved from start: 0.2332 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.032 8674 Z= 0.237 Angle : 0.564 10.543 11736 Z= 0.279 Chirality : 0.038 0.211 1398 Planarity : 0.004 0.060 1498 Dihedral : 5.212 56.561 1208 Min Nonbonded Distance : 2.187 Molprobity Statistics. All-atom Clashscore : 9.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.56 % Favored : 98.44 % Rotamer Outliers : 0.89 % 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: 1.75 (0.25), residues: 1093 helix: 1.74 (0.18), residues: 824 sheet: -0.05 (0.86), residues: 32 loop : -0.63 (0.39), residues: 237 *********************** 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 139 residues out of total 966 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 131 time to evaluate : 0.979 Fit side-chains outliers start: 8 outliers final: 7 residues processed: 136 average time/residue: 0.1994 time to fit residues: 38.0135 Evaluate side-chains 125 residues out of total 966 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 118 time to evaluate : 1.168 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.0852 time to fit residues: 2.5547 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 97 optimal weight: 0.0170 chunk 74 optimal weight: 0.0070 chunk 51 optimal weight: 0.7980 chunk 10 optimal weight: 1.9990 chunk 47 optimal weight: 0.5980 chunk 66 optimal weight: 9.9990 chunk 99 optimal weight: 0.7980 chunk 105 optimal weight: 3.9990 chunk 94 optimal weight: 0.8980 chunk 28 optimal weight: 0.8980 chunk 87 optimal weight: 0.5980 overall best weight: 0.4036 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 271 HIS D 295 GLN D 324 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6451 moved from start: 0.2565 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.029 8674 Z= 0.181 Angle : 0.534 11.203 11736 Z= 0.259 Chirality : 0.036 0.174 1398 Planarity : 0.004 0.052 1498 Dihedral : 5.375 58.994 1208 Min Nonbonded Distance : 2.197 Molprobity Statistics. All-atom Clashscore : 9.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Rotamer Outliers : 1.01 % 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: 2.13 (0.26), residues: 1093 helix: 2.01 (0.18), residues: 820 sheet: -0.14 (0.90), residues: 30 loop : -0.43 (0.38), residues: 243 *********************** 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 127 residues out of total 966 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 118 time to evaluate : 0.905 Fit side-chains outliers start: 9 outliers final: 5 residues processed: 122 average time/residue: 0.2095 time to fit residues: 35.5978 Evaluate side-chains 112 residues out of total 966 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 107 time to evaluate : 0.992 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.0795 time to fit residues: 2.1075 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 59 optimal weight: 8.9990 chunk 1 optimal weight: 0.6980 chunk 78 optimal weight: 0.9980 chunk 43 optimal weight: 0.0980 chunk 89 optimal weight: 0.9990 chunk 72 optimal weight: 0.7980 chunk 0 optimal weight: 0.9990 chunk 53 optimal weight: 0.1980 chunk 94 optimal weight: 0.5980 chunk 26 optimal weight: 0.2980 chunk 35 optimal weight: 0.6980 overall best weight: 0.3780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6445 moved from start: 0.2726 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.035 8674 Z= 0.180 Angle : 0.524 11.129 11736 Z= 0.257 Chirality : 0.036 0.248 1398 Planarity : 0.004 0.048 1498 Dihedral : 5.009 57.640 1208 Min Nonbonded Distance : 2.129 Molprobity Statistics. All-atom Clashscore : 8.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.10 % Favored : 97.90 % Rotamer Outliers : 0.67 % 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: 2.29 (0.26), residues: 1093 helix: 2.15 (0.18), residues: 820 sheet: -0.21 (0.89), residues: 30 loop : -0.42 (0.38), residues: 243 *********************** 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 126 residues out of total 966 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 120 time to evaluate : 0.941 Fit side-chains revert: symmetry clash outliers start: 6 outliers final: 1 residues processed: 123 average time/residue: 0.1969 time to fit residues: 34.0746 Evaluate side-chains 112 residues out of total 966 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 111 time to evaluate : 0.909 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0770 time to fit residues: 1.4367 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 94 optimal weight: 0.6980 chunk 20 optimal weight: 0.7980 chunk 61 optimal weight: 9.9990 chunk 26 optimal weight: 0.7980 chunk 105 optimal weight: 0.6980 chunk 87 optimal weight: 0.0980 chunk 48 optimal weight: 0.5980 chunk 8 optimal weight: 0.0980 chunk 34 optimal weight: 0.8980 chunk 55 optimal weight: 10.0000 chunk 101 optimal weight: 0.6980 overall best weight: 0.4380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 324 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6466 moved from start: 0.2908 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.033 8674 Z= 0.194 Angle : 0.535 10.843 11736 Z= 0.261 Chirality : 0.036 0.136 1398 Planarity : 0.004 0.049 1498 Dihedral : 5.037 51.995 1208 Min Nonbonded Distance : 2.218 Molprobity Statistics. All-atom Clashscore : 8.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer Outliers : 1.23 % 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: 2.17 (0.26), residues: 1093 helix: 2.06 (0.18), residues: 828 sheet: -0.83 (0.93), residues: 20 loop : -0.48 (0.37), residues: 245 *********************** 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 128 residues out of total 966 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 117 time to evaluate : 1.004 Fit side-chains revert: symmetry clash outliers start: 11 outliers final: 8 residues processed: 122 average time/residue: 0.1896 time to fit residues: 33.2406 Evaluate side-chains 116 residues out of total 966 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 108 time to evaluate : 0.947 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.0811 time to fit residues: 2.6644 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 11 optimal weight: 0.9990 chunk 60 optimal weight: 2.9990 chunk 77 optimal weight: 0.3980 chunk 59 optimal weight: 5.9990 chunk 88 optimal weight: 0.4980 chunk 58 optimal weight: 8.9990 chunk 105 optimal weight: 2.9990 chunk 65 optimal weight: 0.7980 chunk 64 optimal weight: 0.0770 chunk 48 optimal weight: 0.6980 chunk 41 optimal weight: 0.9980 overall best weight: 0.4938 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 210 ASN ** B 210 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6488 moved from start: 0.3116 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.037 8674 Z= 0.212 Angle : 0.550 10.887 11736 Z= 0.269 Chirality : 0.036 0.141 1398 Planarity : 0.004 0.050 1498 Dihedral : 5.060 55.838 1208 Min Nonbonded Distance : 2.200 Molprobity Statistics. All-atom Clashscore : 9.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.47 % Favored : 97.53 % Rotamer Outliers : 0.89 % 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: 2.12 (0.26), residues: 1093 helix: 2.01 (0.18), residues: 829 sheet: -1.04 (0.94), residues: 20 loop : -0.44 (0.37), residues: 244 *********************** 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 124 residues out of total 966 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 116 time to evaluate : 0.947 Fit side-chains revert: symmetry clash outliers start: 8 outliers final: 3 residues processed: 122 average time/residue: 0.2057 time to fit residues: 35.3086 Evaluate side-chains 114 residues out of total 966 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 111 time to evaluate : 0.946 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.0871 time to fit residues: 1.7628 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 62 optimal weight: 4.9990 chunk 31 optimal weight: 0.9980 chunk 20 optimal weight: 0.0970 chunk 66 optimal weight: 8.9990 chunk 71 optimal weight: 0.8980 chunk 51 optimal weight: 0.8980 chunk 9 optimal weight: 0.0980 chunk 82 optimal weight: 0.5980 chunk 95 optimal weight: 0.9980 chunk 100 optimal weight: 0.8980 chunk 91 optimal weight: 0.9980 overall best weight: 0.5178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 343 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6500 moved from start: 0.3246 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.038 8674 Z= 0.219 Angle : 0.567 10.843 11736 Z= 0.276 Chirality : 0.037 0.175 1398 Planarity : 0.004 0.050 1498 Dihedral : 5.165 59.593 1208 Min Nonbonded Distance : 2.196 Molprobity Statistics. All-atom Clashscore : 9.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.47 % Favored : 97.53 % Rotamer Outliers : 1.01 % 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: 2.08 (0.26), residues: 1093 helix: 1.95 (0.18), residues: 830 sheet: -1.28 (0.90), residues: 20 loop : -0.30 (0.38), residues: 243 *********************** 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 125 residues out of total 966 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 116 time to evaluate : 1.030 Fit side-chains revert: symmetry clash outliers start: 9 outliers final: 6 residues processed: 120 average time/residue: 0.2054 time to fit residues: 34.6706 Evaluate side-chains 118 residues out of total 966 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 112 time to evaluate : 0.961 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.0826 time to fit residues: 2.2896 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 97 optimal weight: 0.4980 chunk 100 optimal weight: 0.5980 chunk 58 optimal weight: 9.9990 chunk 42 optimal weight: 0.1980 chunk 76 optimal weight: 0.9990 chunk 30 optimal weight: 1.9990 chunk 88 optimal weight: 0.9990 chunk 92 optimal weight: 0.7980 chunk 64 optimal weight: 0.9980 chunk 103 optimal weight: 0.5980 chunk 63 optimal weight: 0.9990 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 210 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6509 moved from start: 0.3369 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.037 8674 Z= 0.226 Angle : 0.579 11.047 11736 Z= 0.281 Chirality : 0.037 0.171 1398 Planarity : 0.004 0.050 1498 Dihedral : 5.035 55.025 1208 Min Nonbonded Distance : 2.182 Molprobity Statistics. All-atom Clashscore : 9.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer Outliers : 0.45 % 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: 2.01 (0.26), residues: 1093 helix: 1.90 (0.18), residues: 829 sheet: -1.33 (0.89), residues: 20 loop : -0.32 (0.38), residues: 244 *********************** 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 116 residues out of total 966 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 112 time to evaluate : 1.134 Fit side-chains revert: symmetry clash outliers start: 4 outliers final: 2 residues processed: 115 average time/residue: 0.1919 time to fit residues: 31.9539 Evaluate side-chains 112 residues out of total 966 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 110 time to evaluate : 0.947 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0864 time to fit residues: 1.6122 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 49 optimal weight: 0.6980 chunk 71 optimal weight: 1.9990 chunk 108 optimal weight: 0.5980 chunk 99 optimal weight: 0.0270 chunk 86 optimal weight: 0.5980 chunk 8 optimal weight: 0.6980 chunk 66 optimal weight: 5.9990 chunk 53 optimal weight: 1.9990 chunk 68 optimal weight: 0.0970 chunk 92 optimal weight: 0.9990 chunk 26 optimal weight: 0.0570 overall best weight: 0.2754 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6439 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 0.031 8674 Z= 0.165 Angle : 0.556 10.974 11736 Z= 0.267 Chirality : 0.036 0.220 1398 Planarity : 0.004 0.049 1498 Dihedral : 4.592 41.908 1208 Min Nonbonded Distance : 2.171 Molprobity Statistics. All-atom Clashscore : 8.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % Rotamer Outliers : 0.22 % 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: 2.36 (0.26), residues: 1093 helix: 2.16 (0.18), residues: 825 sheet: -1.12 (0.92), residues: 20 loop : -0.18 (0.38), residues: 248 ********************** 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 123 residues out of total 966 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 121 time to evaluate : 1.008 Fit side-chains revert: symmetry clash outliers start: 2 outliers final: 2 residues processed: 121 average time/residue: 0.2111 time to fit residues: 35.8964 Evaluate side-chains 117 residues out of total 966 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 115 time to evaluate : 1.035 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0860 time to fit residues: 1.8146 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 79 optimal weight: 0.4980 chunk 12 optimal weight: 0.7980 chunk 24 optimal weight: 1.9990 chunk 86 optimal weight: 0.7980 chunk 36 optimal weight: 0.9980 chunk 88 optimal weight: 0.9980 chunk 10 optimal weight: 0.9990 chunk 15 optimal weight: 0.7980 chunk 76 optimal weight: 0.0670 chunk 4 optimal weight: 0.6980 chunk 62 optimal weight: 5.9990 overall best weight: 0.5718 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 189 HIS B 210 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4395 r_free = 0.4395 target = 0.202941 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4054 r_free = 0.4054 target = 0.166835 restraints weight = 9905.216| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.4035 r_free = 0.4035 target = 0.165481 restraints weight = 8042.464| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.4054 r_free = 0.4054 target = 0.167514 restraints weight = 7080.941| |-----------------------------------------------------------------------------| r_work (final): 0.4054 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6490 moved from start: 0.3487 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.038 8674 Z= 0.235 Angle : 0.596 10.824 11736 Z= 0.288 Chirality : 0.037 0.216 1398 Planarity : 0.004 0.050 1498 Dihedral : 5.006 46.866 1208 Min Nonbonded Distance : 2.196 Molprobity Statistics. All-atom Clashscore : 9.80 Ramachandran Plot: Outliers : 0.09 % Allowed : 2.65 % Favored : 97.26 % Rotamer Outliers : 0.34 % 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: 2.07 (0.26), residues: 1093 helix: 1.95 (0.18), residues: 828 sheet: -1.31 (0.92), residues: 20 loop : -0.32 (0.37), residues: 245 =============================================================================== Job complete usr+sys time: 1879.98 seconds wall clock time: 34 minutes 52.79 seconds (2092.79 seconds total)