Starting phenix.real_space_refine on Mon Mar 18 15:40:23 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8so0_40644/03_2024/8so0_40644_trim_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8so0_40644/03_2024/8so0_40644.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.79961 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8so0_40644/03_2024/8so0_40644.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8so0_40644/03_2024/8so0_40644.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8so0_40644/03_2024/8so0_40644_trim_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8so0_40644/03_2024/8so0_40644_trim_updated.pdb" } resolution = 2.79961 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.000 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians Fe 1 7.16 5 Zn 1 6.06 5 S 62 5.16 5 C 6794 2.51 5 N 1850 2.21 5 O 2048 1.98 5 H 10646 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B PHE 84": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B TYR 244": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 21402 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 9162 Number of conformers: 1 Conformer: "" Number of residues, atoms: 581, 9162 Classifications: {'peptide': 581} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 26, 'TRANS': 554} Chain: "B" Number of atoms: 6849 Number of conformers: 1 Conformer: "" Number of residues, atoms: 423, 6849 Classifications: {'peptide': 423} Link IDs: {'PTRANS': 14, 'TRANS': 408} Chain breaks: 4 Chain: "C" Number of atoms: 4883 Number of conformers: 1 Conformer: "" Number of residues, atoms: 308, 4883 Classifications: {'peptide': 308} Modifications used: {'COO': 1} Link IDs: {'PCIS': 3, 'PTRANS': 10, 'TRANS': 294} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Planarities with less than four sites: {'MLL%COO:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "D" Number of atoms: 506 Number of conformers: 1 Conformer: "" Number of residues, atoms: 31, 506 Classifications: {'peptide': 31} Link IDs: {'TRANS': 30} Chain: "C" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' FE': 1, ' ZN': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 8.87, per 1000 atoms: 0.41 Number of scatterers: 21402 At special positions: 0 Unit cell: (101.994, 127.626, 106.8, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 1 29.99 Fe 1 26.01 S 62 16.00 O 2048 8.00 N 1850 7.00 C 6794 6.00 H 10646 1.00 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: 15.91 Conformation dependent library (CDL) restraints added in 2.1 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN C 402 " pdb="ZN ZN C 402 " - pdb=" NE2 HIS C 59 " 2652 Ramachandran restraints generated. 1326 Oldfield, 0 Emsley, 1326 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2576 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 67 helices and 12 sheets defined 47.6% alpha, 13.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.57 Creating SS restraints... Processing helix chain 'A' and resid 11 through 21 removed outlier: 4.366A pdb=" N ARG A 21 " --> pdb=" O ILE A 17 " (cutoff:3.500A) Processing helix chain 'A' and resid 25 through 42 removed outlier: 5.236A pdb=" N SER A 36 " --> pdb=" O ILE A 32 " (cutoff:3.500A) removed outlier: 6.231A pdb=" N THR A 37 " --> pdb=" O LYS A 33 " (cutoff:3.500A) Processing helix chain 'A' and resid 44 through 49 Processing helix chain 'A' and resid 51 through 55 Processing helix chain 'A' and resid 63 through 75 removed outlier: 3.985A pdb=" N THR A 75 " --> pdb=" O GLU A 71 " (cutoff:3.500A) Processing helix chain 'A' and resid 83 through 98 removed outlier: 5.430A pdb=" N HIS A 87 " --> pdb=" O GLU A 84 " (cutoff:3.500A) Proline residue: A 91 - end of helix removed outlier: 3.681A pdb=" N SER A 95 " --> pdb=" O PRO A 92 " (cutoff:3.500A) Processing helix chain 'A' and resid 102 through 116 Processing helix chain 'A' and resid 121 through 126 Processing helix chain 'A' and resid 128 through 136 Processing helix chain 'A' and resid 141 through 149 removed outlier: 3.575A pdb=" N CYS A 148 " --> pdb=" O ARG A 144 " (cutoff:3.500A) removed outlier: 4.450A pdb=" N GLY A 149 " --> pdb=" O THR A 145 " (cutoff:3.500A) Processing helix chain 'A' and resid 151 through 157 Proline residue: A 156 - end of helix Processing helix chain 'A' and resid 160 through 175 Processing helix chain 'A' and resid 179 through 195 removed outlier: 4.426A pdb=" N GLY A 190 " --> pdb=" O ALA A 186 " (cutoff:3.500A) removed outlier: 5.082A pdb=" N GLU A 191 " --> pdb=" O SER A 187 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N VAL A 195 " --> pdb=" O GLU A 191 " (cutoff:3.500A) Processing helix chain 'A' and resid 198 through 203 Processing helix chain 'A' and resid 205 through 214 Processing helix chain 'A' and resid 218 through 234 removed outlier: 4.031A pdb=" N LEU A 223 " --> pdb=" O SER A 219 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N ALA A 224 " --> pdb=" O VAL A 220 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N VAL A 225 " --> pdb=" O ARG A 221 " (cutoff:3.500A) removed outlier: 4.409A pdb=" N GLU A 226 " --> pdb=" O LEU A 222 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N LEU A 234 " --> pdb=" O ASN A 230 " (cutoff:3.500A) Processing helix chain 'A' and resid 237 through 243 removed outlier: 4.119A pdb=" N GLU A 241 " --> pdb=" O GLU A 238 " (cutoff:3.500A) Processing helix chain 'A' and resid 245 through 252 Processing helix chain 'A' and resid 257 through 265 Processing helix chain 'A' and resid 267 through 274 Processing helix chain 'A' and resid 276 through 281 Processing helix chain 'A' and resid 283 through 291 Processing helix chain 'A' and resid 296 through 312 removed outlier: 3.796A pdb=" N LYS A 305 " --> pdb=" O ALA A 301 " (cutoff:3.500A) removed outlier: 4.813A pdb=" N LYS A 307 " --> pdb=" O SER A 303 " (cutoff:3.500A) removed outlier: 4.897A pdb=" N GLU A 308 " --> pdb=" O HIS A 304 " (cutoff:3.500A) Processing helix chain 'A' and resid 318 through 324 Processing helix chain 'A' and resid 326 through 334 removed outlier: 3.612A pdb=" N GLU A 332 " --> pdb=" O PRO A 328 " (cutoff:3.500A) Processing helix chain 'A' and resid 339 through 346 Processing helix chain 'A' and resid 349 through 356 removed outlier: 3.562A pdb=" N SER A 353 " --> pdb=" O MET A 350 " (cutoff:3.500A) Proline residue: A 354 - end of helix Processing helix chain 'A' and resid 358 through 363 Processing helix chain 'A' and resid 365 through 373 Processing helix chain 'A' and resid 378 through 387 removed outlier: 3.513A pdb=" N ASN A 387 " --> pdb=" O ASN A 383 " (cutoff:3.500A) Processing helix chain 'A' and resid 389 through 395 removed outlier: 3.845A pdb=" N GLU A 393 " --> pdb=" O ASP A 389 " (cutoff:3.500A) removed outlier: 4.701A pdb=" N VAL A 394 " --> pdb=" O CYS A 390 " (cutoff:3.500A) Processing helix chain 'A' and resid 398 through 412 removed outlier: 4.175A pdb=" N GLN A 402 " --> pdb=" O ARG A 398 " (cutoff:3.500A) removed outlier: 4.819A pdb=" N SER A 403 " --> pdb=" O GLN A 399 " (cutoff:3.500A) Proline residue: A 406 - end of helix Processing helix chain 'A' and resid 417 through 425 Processing helix chain 'A' and resid 427 through 434 Processing helix chain 'A' and resid 436 through 442 Processing helix chain 'A' and resid 444 through 452 removed outlier: 3.586A pdb=" N LEU A 451 " --> pdb=" O CYS A 447 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N VAL A 452 " --> pdb=" O MET A 448 " (cutoff:3.500A) Processing helix chain 'A' and resid 456 through 473 removed outlier: 3.792A pdb=" N LYS A 467 " --> pdb=" O THR A 463 " (cutoff:3.500A) Processing helix chain 'A' and resid 475 through 481 Processing helix chain 'A' and resid 483 through 491 removed outlier: 3.708A pdb=" N ALA A 488 " --> pdb=" O PRO A 484 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N MET A 489 " --> pdb=" O LYS A 485 " (cutoff:3.500A) removed outlier: 4.230A pdb=" N SER A 490 " --> pdb=" O VAL A 486 " (cutoff:3.500A) removed outlier: 4.761A pdb=" N GLY A 491 " --> pdb=" O LEU A 487 " (cutoff:3.500A) Processing helix chain 'A' and resid 495 through 512 removed outlier: 3.539A pdb=" N THR A 501 " --> pdb=" O HIS A 497 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N LEU A 502 " --> pdb=" O ARG A 498 " (cutoff:3.500A) removed outlier: 4.090A pdb=" N GLU A 510 " --> pdb=" O ASN A 506 " (cutoff:3.500A) removed outlier: 4.078A pdb=" N VAL A 511 " --> pdb=" O VAL A 507 " (cutoff:3.500A) Processing helix chain 'A' and resid 514 through 519 Processing helix chain 'A' and resid 522 through 530 removed outlier: 4.612A pdb=" N GLY A 530 " --> pdb=" O LEU A 526 " (cutoff:3.500A) Processing helix chain 'A' and resid 534 through 548 Processing helix chain 'A' and resid 553 through 558 Processing helix chain 'A' and resid 560 through 569 removed outlier: 3.683A pdb=" N GLN A 569 " --> pdb=" O GLU A 565 " (cutoff:3.500A) Processing helix chain 'A' and resid 573 through 586 Processing helix chain 'B' and resid 27 through 29 No H-bonds generated for 'chain 'B' and resid 27 through 29' Processing helix chain 'B' and resid 146 through 148 No H-bonds generated for 'chain 'B' and resid 146 through 148' Processing helix chain 'B' and resid 222 through 224 No H-bonds generated for 'chain 'B' and resid 222 through 224' Processing helix chain 'B' and resid 282 through 285 No H-bonds generated for 'chain 'B' and resid 282 through 285' Processing helix chain 'B' and resid 327 through 339 removed outlier: 3.943A pdb=" N SER B 331 " --> pdb=" O TYR B 328 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N LEU B 333 " --> pdb=" O ARG B 330 " (cutoff:3.500A) removed outlier: 4.926A pdb=" N CYS B 334 " --> pdb=" O SER B 331 " (cutoff:3.500A) Processing helix chain 'B' and resid 341 through 343 No H-bonds generated for 'chain 'B' and resid 341 through 343' Processing helix chain 'B' and resid 383 through 385 No H-bonds generated for 'chain 'B' and resid 383 through 385' Processing helix chain 'B' and resid 410 through 412 No H-bonds generated for 'chain 'B' and resid 410 through 412' Processing helix chain 'C' and resid 3 through 18 Processing helix chain 'C' and resid 25 through 41 removed outlier: 3.590A pdb=" N GLU C 37 " --> pdb=" O GLU C 33 " (cutoff:3.500A) removed outlier: 4.106A pdb=" N LYS C 41 " --> pdb=" O GLU C 37 " (cutoff:3.500A) Processing helix chain 'C' and resid 62 through 72 Processing helix chain 'C' and resid 93 through 106 Processing helix chain 'C' and resid 121 through 127 Processing helix chain 'C' and resid 129 through 137 Processing helix chain 'C' and resid 141 through 152 removed outlier: 3.827A pdb=" N ASP C 151 " --> pdb=" O THR C 147 " (cutoff:3.500A) removed outlier: 4.325A pdb=" N TYR C 152 " --> pdb=" O ASP C 148 " (cutoff:3.500A) Processing helix chain 'C' and resid 177 through 181 Processing helix chain 'C' and resid 194 through 200 removed outlier: 3.554A pdb=" N LEU C 199 " --> pdb=" O MET C 195 " (cutoff:3.500A) Processing helix chain 'C' and resid 222 through 232 Processing helix chain 'C' and resid 265 through 267 No H-bonds generated for 'chain 'C' and resid 265 through 267' Processing helix chain 'D' and resid 84 through 93 Processing helix chain 'D' and resid 98 through 110 Processing sheet with id= A, first strand: chain 'B' and resid 31 through 36 removed outlier: 6.216A pdb=" N GLY B 46 " --> pdb=" O SER B 32 " (cutoff:3.500A) removed outlier: 4.400A pdb=" N VAL B 34 " --> pdb=" O ALA B 44 " (cutoff:3.500A) removed outlier: 6.854A pdb=" N ALA B 44 " --> pdb=" O VAL B 34 " (cutoff:3.500A) removed outlier: 4.707A pdb=" N PHE B 36 " --> pdb=" O LEU B 42 " (cutoff:3.500A) removed outlier: 7.145A pdb=" N LEU B 42 " --> pdb=" O PHE B 36 " (cutoff:3.500A) removed outlier: 4.353A pdb=" N ARG B 51 " --> pdb=" O ASP B 47 " (cutoff:3.500A) removed outlier: 5.429A pdb=" N GLN B 56 " --> pdb=" O VAL B 73 " (cutoff:3.500A) removed outlier: 5.549A pdb=" N VAL B 73 " --> pdb=" O GLN B 56 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'B' and resid 83 through 85 removed outlier: 3.520A pdb=" N GLU B 83 " --> pdb=" O ILE B 92 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'B' and resid 98 through 101 removed outlier: 3.681A pdb=" N LYS B 98 " --> pdb=" O THR B 114 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N ARG B 170 " --> pdb=" O LEU B 121 " (cutoff:3.500A) removed outlier: 6.571A pdb=" N LYS B 123 " --> pdb=" O PRO B 168 " (cutoff:3.500A) removed outlier: 7.480A pdb=" N SER B 125 " --> pdb=" O ALA B 166 " (cutoff:3.500A) removed outlier: 5.369A pdb=" N ALA B 166 " --> pdb=" O SER B 125 " (cutoff:3.500A) removed outlier: 6.949A pdb=" N ARG B 127 " --> pdb=" O VAL B 164 " (cutoff:3.500A) removed outlier: 5.446A pdb=" N VAL B 164 " --> pdb=" O ARG B 127 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 129 through 132 Processing sheet with id= E, first strand: chain 'B' and resid 182 through 185 removed outlier: 6.614A pdb=" N LEU B 202 " --> pdb=" O ASN B 213 " (cutoff:3.500A) removed outlier: 5.459A pdb=" N ASN B 213 " --> pdb=" O LEU B 202 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 267 through 269 removed outlier: 3.837A pdb=" N ALA B 231 " --> pdb=" O SER B 245 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'B' and resid 290 through 293 removed outlier: 3.502A pdb=" N ASP B 290 " --> pdb=" O ARG B 303 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'B' and resid 348 through 350 Processing sheet with id= I, first strand: chain 'B' and resid 421 through 424 removed outlier: 4.490A pdb=" N HIS B 421 " --> pdb=" O ALA B 434 " (cutoff:3.500A) removed outlier: 5.870A pdb=" N GLN B 443 " --> pdb=" O PHE B 14 " (cutoff:3.500A) removed outlier: 5.405A pdb=" N PHE B 14 " --> pdb=" O GLN B 443 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'C' and resid 45 through 48 removed outlier: 7.083A pdb=" N THR C 156 " --> pdb=" O GLN C 46 " (cutoff:3.500A) removed outlier: 7.646A pdb=" N VAL C 48 " --> pdb=" O THR C 156 " (cutoff:3.500A) removed outlier: 5.986A pdb=" N LEU C 158 " --> pdb=" O VAL C 48 " (cutoff:3.500A) removed outlier: 6.607A pdb=" N LEU C 236 " --> pdb=" O PHE C 164 " (cutoff:3.500A) removed outlier: 8.063A pdb=" N LEU C 166 " --> pdb=" O LEU C 236 " (cutoff:3.500A) removed outlier: 6.217A pdb=" N SER C 238 " --> pdb=" O LEU C 166 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'C' and resid 111 through 113 removed outlier: 6.490A pdb=" N TYR C 80 " --> pdb=" O THR C 112 " (cutoff:3.500A) removed outlier: 6.541A pdb=" N THR C 53 " --> pdb=" O LEU C 81 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'C' and resid 209 through 211 428 hydrogen bonds defined for protein. 1191 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: 7.40 Time building geometry restraints manager: 16.72 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 10613 1.03 - 1.23: 33 1.23 - 1.42: 4565 1.42 - 1.61: 6308 1.61 - 1.81: 91 Bond restraints: 21610 Sorted by residual: bond pdb=" C MLL C 309 " pdb=" OXT MLL C 309 " ideal model delta sigma weight residual 1.231 1.366 -0.135 2.00e-02 2.50e+03 4.53e+01 bond pdb=" N ASP C 2 " pdb=" CA ASP C 2 " ideal model delta sigma weight residual 1.458 1.490 -0.032 1.90e-02 2.77e+03 2.87e+00 bond pdb=" N ASP C 2 " pdb=" H ASP C 2 " ideal model delta sigma weight residual 0.860 0.889 -0.029 2.00e-02 2.50e+03 2.14e+00 bond pdb=" CA ILE B 419 " pdb=" CB ILE B 419 " ideal model delta sigma weight residual 1.528 1.539 -0.011 1.34e-02 5.57e+03 7.28e-01 bond pdb=" CA LEU C 186 " pdb=" CB LEU C 186 " ideal model delta sigma weight residual 1.523 1.532 -0.009 1.21e-02 6.83e+03 5.36e-01 ... (remaining 21605 not shown) Histogram of bond angle deviations from ideal: 100.47 - 107.17: 404 107.17 - 113.87: 25883 113.87 - 120.57: 7263 120.57 - 127.27: 5375 127.27 - 133.97: 123 Bond angle restraints: 39048 Sorted by residual: angle pdb=" N VAL C 58 " pdb=" CA VAL C 58 " pdb=" C VAL C 58 " ideal model delta sigma weight residual 112.12 109.04 3.08 8.40e-01 1.42e+00 1.34e+01 angle pdb=" CA MLL C 309 " pdb=" C MLL C 309 " pdb=" OXT MLL C 309 " ideal model delta sigma weight residual 121.00 114.28 6.72 3.00e+00 1.11e-01 5.02e+00 angle pdb=" N ASP D 95 " pdb=" CA ASP D 95 " pdb=" C ASP D 95 " ideal model delta sigma weight residual 111.24 114.06 -2.82 1.29e+00 6.01e-01 4.76e+00 angle pdb=" N MLL C 309 " pdb=" CA MLL C 309 " pdb=" CB MLL C 309 " ideal model delta sigma weight residual 110.50 114.07 -3.57 1.70e+00 3.46e-01 4.41e+00 angle pdb=" CA MLL C 309 " pdb=" C MLL C 309 " pdb=" O MLL C 309 " ideal model delta sigma weight residual 121.00 127.12 -6.12 3.00e+00 1.11e-01 4.17e+00 ... (remaining 39043 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.94: 9647 15.94 - 31.87: 311 31.87 - 47.81: 121 47.81 - 63.74: 47 63.74 - 79.68: 27 Dihedral angle restraints: 10153 sinusoidal: 5548 harmonic: 4605 Sorted by residual: dihedral pdb=" CA TYR C 127 " pdb=" C TYR C 127 " pdb=" N GLY C 128 " pdb=" CA GLY C 128 " ideal model delta harmonic sigma weight residual 180.00 160.43 19.57 0 5.00e+00 4.00e-02 1.53e+01 dihedral pdb=" CA ASP D 95 " pdb=" C ASP D 95 " pdb=" N LEU D 96 " pdb=" CA LEU D 96 " ideal model delta harmonic sigma weight residual -180.00 -164.62 -15.38 0 5.00e+00 4.00e-02 9.46e+00 dihedral pdb=" CA ARG C 239 " pdb=" CB ARG C 239 " pdb=" CG ARG C 239 " pdb=" CD ARG C 239 " ideal model delta sinusoidal sigma weight residual -60.00 -113.65 53.65 3 1.50e+01 4.44e-03 9.22e+00 ... (remaining 10150 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.025: 1050 0.025 - 0.050: 391 0.050 - 0.076: 130 0.076 - 0.101: 49 0.101 - 0.126: 56 Chirality restraints: 1676 Sorted by residual: chirality pdb=" CA ILE B 430 " pdb=" N ILE B 430 " pdb=" C ILE B 430 " pdb=" CB ILE B 430 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 3.96e-01 chirality pdb=" CA VAL B 34 " pdb=" N VAL B 34 " pdb=" C VAL B 34 " pdb=" CB VAL B 34 " both_signs ideal model delta sigma weight residual False 2.44 2.56 -0.12 2.00e-01 2.50e+01 3.76e-01 chirality pdb=" CA ILE B 171 " pdb=" N ILE B 171 " pdb=" C ILE B 171 " pdb=" CB ILE B 171 " both_signs ideal model delta sigma weight residual False 2.43 2.55 -0.12 2.00e-01 2.50e+01 3.68e-01 ... (remaining 1673 not shown) Planarity restraints: 3201 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE A 538 " -0.010 2.00e-02 2.50e+03 6.35e-03 1.21e+00 pdb=" CG PHE A 538 " 0.019 2.00e-02 2.50e+03 pdb=" CD1 PHE A 538 " -0.004 2.00e-02 2.50e+03 pdb=" CD2 PHE A 538 " -0.000 2.00e-02 2.50e+03 pdb=" CE1 PHE A 538 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 PHE A 538 " -0.004 2.00e-02 2.50e+03 pdb=" CZ PHE A 538 " -0.001 2.00e-02 2.50e+03 pdb=" HD1 PHE A 538 " -0.000 2.00e-02 2.50e+03 pdb=" HD2 PHE A 538 " 0.001 2.00e-02 2.50e+03 pdb=" HE1 PHE A 538 " -0.001 2.00e-02 2.50e+03 pdb=" HE2 PHE A 538 " -0.001 2.00e-02 2.50e+03 pdb=" HZ PHE A 538 " -0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C VAL A 284 " 0.016 5.00e-02 4.00e+02 2.39e-02 9.15e-01 pdb=" N PRO A 285 " -0.041 5.00e-02 4.00e+02 pdb=" CA PRO A 285 " 0.012 5.00e-02 4.00e+02 pdb=" CD PRO A 285 " 0.014 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU A 366 " 0.015 5.00e-02 4.00e+02 2.23e-02 7.94e-01 pdb=" N PRO A 367 " -0.039 5.00e-02 4.00e+02 pdb=" CA PRO A 367 " 0.011 5.00e-02 4.00e+02 pdb=" CD PRO A 367 " 0.013 5.00e-02 4.00e+02 ... (remaining 3198 not shown) Histogram of nonbonded interaction distances: 1.43 - 2.06: 358 2.06 - 2.70: 34303 2.70 - 3.33: 64217 3.33 - 3.97: 82793 3.97 - 4.60: 131025 Nonbonded interactions: 312696 Sorted by model distance: nonbonded pdb=" OXT MLL C 309 " pdb=" C10 MLL C 309 " model vdw 1.427 3.100 nonbonded pdb=" OD1 ASP B 196 " pdb=" H ARG B 199 " model vdw 1.557 1.850 nonbonded pdb=" OE1 GLU A 379 " pdb=" H GLU A 379 " model vdw 1.622 1.850 nonbonded pdb=" O HIS C 252 " pdb="HD21 ASN C 255 " model vdw 1.629 1.850 nonbonded pdb=" HH TYR B 86 " pdb=" OD2 ASP C 131 " model vdw 1.632 1.850 ... (remaining 312691 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 9.660 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: 0.290 Extract box with map and model: 33.280 Check model and map are aligned: 0.380 Set scattering table: 0.190 Process input model: 73.230 Find NCS groups from input model: 0.370 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:12.360 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 129.830 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8581 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 : 0.002 0.135 10964 Z= 0.151 Angle : 0.411 6.720 14848 Z= 0.220 Chirality : 0.037 0.126 1676 Planarity : 0.003 0.024 1920 Dihedral : 8.085 76.670 4099 Min Nonbonded Distance : 1.427 Molprobity Statistics. All-atom Clashscore : 1.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.89 % Favored : 98.11 % Rotamer: Outliers : 0.08 % Allowed : 0.83 % Favored : 99.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.66 % 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: 1.96 (0.24), residues: 1326 helix: 2.00 (0.22), residues: 629 sheet: 0.87 (0.37), residues: 212 loop : 0.73 (0.29), residues: 485 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 350 HIS 0.003 0.001 HIS C 118 PHE 0.019 0.001 PHE A 538 TYR 0.008 0.001 TYR C 265 ARG 0.002 0.000 ARG B 371 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2652 Ramachandran restraints generated. 1326 Oldfield, 0 Emsley, 1326 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2652 Ramachandran restraints generated. 1326 Oldfield, 0 Emsley, 1326 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 208 residues out of total 1200 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 207 time to evaluate : 1.782 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 262 MET cc_start: 0.9073 (mmm) cc_final: 0.8778 (mmm) REVERT: B 161 ASP cc_start: 0.7857 (m-30) cc_final: 0.7549 (p0) REVERT: B 315 MET cc_start: 0.8072 (mtt) cc_final: 0.7821 (ttt) outliers start: 1 outliers final: 2 residues processed: 208 average time/residue: 3.2329 time to fit residues: 715.2709 Evaluate side-chains 90 residues out of total 1200 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 88 time to evaluate : 1.760 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 ILE Chi-restraints excluded: chain B residue 326 HIS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 112 optimal weight: 4.9990 chunk 100 optimal weight: 5.9990 chunk 55 optimal weight: 5.9990 chunk 34 optimal weight: 0.3980 chunk 67 optimal weight: 1.9990 chunk 53 optimal weight: 3.9990 chunk 104 optimal weight: 0.4980 chunk 40 optimal weight: 4.9990 chunk 63 optimal weight: 0.9990 chunk 77 optimal weight: 3.9990 chunk 120 optimal weight: 0.7980 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 364 HIS A 569 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8597 moved from start: 0.2223 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 10964 Z= 0.180 Angle : 0.502 7.127 14848 Z= 0.269 Chirality : 0.038 0.147 1676 Planarity : 0.003 0.043 1920 Dihedral : 4.262 42.090 1462 Min Nonbonded Distance : 1.896 Molprobity Statistics. All-atom Clashscore : 4.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.43 % Favored : 98.57 % Rotamer: Outliers : 1.42 % Allowed : 8.75 % Favored : 89.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.66 % 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: 1.70 (0.24), residues: 1326 helix: 1.80 (0.22), residues: 625 sheet: 0.87 (0.38), residues: 198 loop : 0.53 (0.28), residues: 503 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 203 HIS 0.004 0.001 HIS A 364 PHE 0.024 0.001 PHE A 538 TYR 0.009 0.001 TYR B 244 ARG 0.009 0.000 ARG C 89 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2652 Ramachandran restraints generated. 1326 Oldfield, 0 Emsley, 1326 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2652 Ramachandran restraints generated. 1326 Oldfield, 0 Emsley, 1326 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 1200 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 91 time to evaluate : 1.582 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 161 ASP cc_start: 0.7842 (m-30) cc_final: 0.7525 (p0) REVERT: B 324 GLN cc_start: 0.9007 (mm-40) cc_final: 0.8356 (mm-40) REVERT: B 393 LYS cc_start: 0.8580 (mmmt) cc_final: 0.7912 (mmtm) REVERT: C 8 LYS cc_start: 0.8699 (mmtp) cc_final: 0.8424 (mppt) REVERT: C 191 HIS cc_start: 0.7263 (m90) cc_final: 0.6559 (m170) REVERT: D 94 MET cc_start: 0.5996 (OUTLIER) cc_final: 0.5765 (mtm) outliers start: 17 outliers final: 11 residues processed: 102 average time/residue: 3.2732 time to fit residues: 356.4113 Evaluate side-chains 92 residues out of total 1200 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 80 time to evaluate : 1.592 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 266 LYS Chi-restraints excluded: chain A residue 308 GLU Chi-restraints excluded: chain A residue 327 LEU Chi-restraints excluded: chain A residue 366 LEU Chi-restraints excluded: chain B residue 90 LEU Chi-restraints excluded: chain B residue 280 PHE Chi-restraints excluded: chain B residue 304 ASP Chi-restraints excluded: chain B residue 326 HIS Chi-restraints excluded: chain B residue 390 THR Chi-restraints excluded: chain C residue 175 ASP Chi-restraints excluded: chain C residue 202 ASP Chi-restraints excluded: chain D residue 94 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 67 optimal weight: 2.9990 chunk 37 optimal weight: 3.9990 chunk 100 optimal weight: 4.9990 chunk 82 optimal weight: 5.9990 chunk 33 optimal weight: 1.9990 chunk 120 optimal weight: 4.9990 chunk 130 optimal weight: 0.9980 chunk 107 optimal weight: 0.7980 chunk 119 optimal weight: 4.9990 chunk 41 optimal weight: 0.9990 chunk 97 optimal weight: 2.9990 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 8 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8620 moved from start: 0.2673 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 10964 Z= 0.222 Angle : 0.488 5.646 14848 Z= 0.259 Chirality : 0.038 0.146 1676 Planarity : 0.004 0.056 1920 Dihedral : 4.384 39.976 1460 Min Nonbonded Distance : 1.855 Molprobity Statistics. All-atom Clashscore : 3.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Rotamer: Outliers : 1.58 % Allowed : 8.83 % Favored : 89.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.66 % 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: 1.39 (0.24), residues: 1326 helix: 1.61 (0.22), residues: 626 sheet: 0.60 (0.38), residues: 198 loop : 0.31 (0.28), residues: 502 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 203 HIS 0.004 0.001 HIS C 63 PHE 0.040 0.002 PHE B 280 TYR 0.012 0.001 TYR B 178 ARG 0.006 0.001 ARG C 295 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2652 Ramachandran restraints generated. 1326 Oldfield, 0 Emsley, 1326 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2652 Ramachandran restraints generated. 1326 Oldfield, 0 Emsley, 1326 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 1200 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 87 time to evaluate : 1.872 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 353 SER cc_start: 0.9514 (m) cc_final: 0.9230 (p) REVERT: A 425 GLU cc_start: 0.8751 (OUTLIER) cc_final: 0.8035 (mp0) REVERT: B 280 PHE cc_start: 0.8288 (t80) cc_final: 0.7523 (t80) REVERT: B 393 LYS cc_start: 0.8591 (mmmt) cc_final: 0.8005 (mptp) REVERT: C 191 HIS cc_start: 0.7463 (m90) cc_final: 0.6791 (m170) outliers start: 19 outliers final: 12 residues processed: 103 average time/residue: 3.1101 time to fit residues: 344.1532 Evaluate side-chains 91 residues out of total 1200 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 78 time to evaluate : 1.940 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 160 SER Chi-restraints excluded: chain A residue 266 LYS Chi-restraints excluded: chain A residue 327 LEU Chi-restraints excluded: chain A residue 366 LEU Chi-restraints excluded: chain A residue 410 GLU Chi-restraints excluded: chain A residue 425 GLU Chi-restraints excluded: chain B residue 90 LEU Chi-restraints excluded: chain B residue 304 ASP Chi-restraints excluded: chain B residue 326 HIS Chi-restraints excluded: chain B residue 390 THR Chi-restraints excluded: chain C residue 175 ASP Chi-restraints excluded: chain C residue 202 ASP Chi-restraints excluded: chain C residue 282 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 119 optimal weight: 5.9990 chunk 90 optimal weight: 3.9990 chunk 62 optimal weight: 0.9990 chunk 13 optimal weight: 2.9990 chunk 57 optimal weight: 5.9990 chunk 81 optimal weight: 2.9990 chunk 121 optimal weight: 3.9990 chunk 128 optimal weight: 2.9990 chunk 63 optimal weight: 0.6980 chunk 115 optimal weight: 2.9990 chunk 34 optimal weight: 1.9990 overall best weight: 1.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8633 moved from start: 0.2974 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 10964 Z= 0.260 Angle : 0.495 6.067 14848 Z= 0.264 Chirality : 0.039 0.149 1676 Planarity : 0.003 0.030 1920 Dihedral : 4.446 41.481 1460 Min Nonbonded Distance : 1.816 Molprobity Statistics. All-atom Clashscore : 4.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % Rotamer: Outliers : 2.00 % Allowed : 9.67 % Favored : 88.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.66 % 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: 1.19 (0.23), residues: 1326 helix: 1.54 (0.22), residues: 618 sheet: 0.36 (0.37), residues: 198 loop : 0.16 (0.27), residues: 510 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 203 HIS 0.007 0.001 HIS C 299 PHE 0.027 0.002 PHE A 538 TYR 0.013 0.001 TYR B 178 ARG 0.005 0.001 ARG A 527 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2652 Ramachandran restraints generated. 1326 Oldfield, 0 Emsley, 1326 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2652 Ramachandran restraints generated. 1326 Oldfield, 0 Emsley, 1326 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 1200 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 81 time to evaluate : 1.658 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 353 SER cc_start: 0.9516 (m) cc_final: 0.9232 (p) REVERT: A 399 GLN cc_start: 0.8272 (OUTLIER) cc_final: 0.7632 (mt0) REVERT: A 425 GLU cc_start: 0.8732 (OUTLIER) cc_final: 0.7973 (mp0) REVERT: B 324 GLN cc_start: 0.9080 (mm-40) cc_final: 0.8867 (mm-40) REVERT: B 393 LYS cc_start: 0.8602 (mmmt) cc_final: 0.8015 (mptp) REVERT: B 398 CYS cc_start: 0.8052 (t) cc_final: 0.7183 (p) REVERT: C 191 HIS cc_start: 0.7506 (m90) cc_final: 0.6960 (m170) outliers start: 24 outliers final: 16 residues processed: 103 average time/residue: 3.0208 time to fit residues: 334.9291 Evaluate side-chains 98 residues out of total 1200 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 80 time to evaluate : 1.890 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 PHE Chi-restraints excluded: chain A residue 160 SER Chi-restraints excluded: chain A residue 266 LYS Chi-restraints excluded: chain A residue 308 GLU Chi-restraints excluded: chain A residue 327 LEU Chi-restraints excluded: chain A residue 366 LEU Chi-restraints excluded: chain A residue 399 GLN Chi-restraints excluded: chain A residue 410 GLU Chi-restraints excluded: chain A residue 425 GLU Chi-restraints excluded: chain B residue 8 ASN Chi-restraints excluded: chain B residue 90 LEU Chi-restraints excluded: chain B residue 304 ASP Chi-restraints excluded: chain B residue 326 HIS Chi-restraints excluded: chain B residue 390 THR Chi-restraints excluded: chain C residue 57 ASP Chi-restraints excluded: chain C residue 175 ASP Chi-restraints excluded: chain C residue 202 ASP Chi-restraints excluded: chain C residue 282 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 107 optimal weight: 0.8980 chunk 72 optimal weight: 0.2980 chunk 1 optimal weight: 6.9990 chunk 95 optimal weight: 3.9990 chunk 53 optimal weight: 3.9990 chunk 109 optimal weight: 3.9990 chunk 88 optimal weight: 2.9990 chunk 0 optimal weight: 3.9990 chunk 65 optimal weight: 2.9990 chunk 115 optimal weight: 3.9990 chunk 32 optimal weight: 2.9990 overall best weight: 2.0386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8638 moved from start: 0.3197 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 10964 Z= 0.273 Angle : 0.504 5.760 14848 Z= 0.270 Chirality : 0.039 0.149 1676 Planarity : 0.004 0.032 1920 Dihedral : 4.522 41.815 1460 Min Nonbonded Distance : 1.819 Molprobity Statistics. All-atom Clashscore : 4.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer: Outliers : 1.83 % Allowed : 10.17 % Favored : 88.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.66 % 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: 0.99 (0.23), residues: 1326 helix: 1.48 (0.22), residues: 618 sheet: 0.11 (0.36), residues: 211 loop : -0.03 (0.27), residues: 497 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 203 HIS 0.006 0.001 HIS C 299 PHE 0.053 0.002 PHE A 76 TYR 0.013 0.001 TYR B 178 ARG 0.004 0.000 ARG B 389 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2652 Ramachandran restraints generated. 1326 Oldfield, 0 Emsley, 1326 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2652 Ramachandran restraints generated. 1326 Oldfield, 0 Emsley, 1326 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 1200 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 87 time to evaluate : 1.605 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 353 SER cc_start: 0.9507 (m) cc_final: 0.9238 (p) REVERT: A 425 GLU cc_start: 0.8752 (OUTLIER) cc_final: 0.7985 (mp0) REVERT: B 324 GLN cc_start: 0.9095 (mm-40) cc_final: 0.8894 (mm-40) REVERT: B 393 LYS cc_start: 0.8610 (mmmt) cc_final: 0.8024 (mptp) REVERT: B 398 CYS cc_start: 0.8094 (t) cc_final: 0.7315 (p) outliers start: 22 outliers final: 15 residues processed: 107 average time/residue: 3.0697 time to fit residues: 352.4986 Evaluate side-chains 98 residues out of total 1200 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 82 time to evaluate : 1.657 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 160 SER Chi-restraints excluded: chain A residue 266 LYS Chi-restraints excluded: chain A residue 308 GLU Chi-restraints excluded: chain A residue 327 LEU Chi-restraints excluded: chain A residue 366 LEU Chi-restraints excluded: chain A residue 410 GLU Chi-restraints excluded: chain A residue 425 GLU Chi-restraints excluded: chain B residue 8 ASN Chi-restraints excluded: chain B residue 90 LEU Chi-restraints excluded: chain B residue 304 ASP Chi-restraints excluded: chain B residue 326 HIS Chi-restraints excluded: chain B residue 390 THR Chi-restraints excluded: chain C residue 134 LEU Chi-restraints excluded: chain C residue 175 ASP Chi-restraints excluded: chain C residue 202 ASP Chi-restraints excluded: chain C residue 282 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 43 optimal weight: 2.9990 chunk 115 optimal weight: 3.9990 chunk 25 optimal weight: 2.9990 chunk 75 optimal weight: 2.9990 chunk 31 optimal weight: 3.9990 chunk 128 optimal weight: 2.9990 chunk 106 optimal weight: 2.9990 chunk 59 optimal weight: 2.9990 chunk 10 optimal weight: 2.9990 chunk 42 optimal weight: 0.9990 chunk 67 optimal weight: 1.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8650 moved from start: 0.3378 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 10964 Z= 0.315 Angle : 0.517 5.714 14848 Z= 0.277 Chirality : 0.040 0.150 1676 Planarity : 0.004 0.063 1920 Dihedral : 4.604 42.578 1460 Min Nonbonded Distance : 1.804 Molprobity Statistics. All-atom Clashscore : 4.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % Rotamer: Outliers : 2.00 % Allowed : 10.17 % Favored : 87.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.66 % 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: 0.76 (0.23), residues: 1326 helix: 1.31 (0.22), residues: 623 sheet: 0.02 (0.36), residues: 211 loop : -0.19 (0.27), residues: 492 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 203 HIS 0.008 0.001 HIS C 299 PHE 0.028 0.002 PHE A 538 TYR 0.014 0.002 TYR B 178 ARG 0.007 0.000 ARG A 527 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2652 Ramachandran restraints generated. 1326 Oldfield, 0 Emsley, 1326 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2652 Ramachandran restraints generated. 1326 Oldfield, 0 Emsley, 1326 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 1200 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 84 time to evaluate : 1.842 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 353 SER cc_start: 0.9507 (m) cc_final: 0.9251 (p) REVERT: A 399 GLN cc_start: 0.8266 (OUTLIER) cc_final: 0.7538 (mt0) REVERT: A 425 GLU cc_start: 0.8761 (OUTLIER) cc_final: 0.7984 (mp0) REVERT: B 393 LYS cc_start: 0.8634 (mmmt) cc_final: 0.7992 (mmtm) REVERT: B 398 CYS cc_start: 0.8120 (t) cc_final: 0.7441 (p) REVERT: C 191 HIS cc_start: 0.7527 (m90) cc_final: 0.7068 (m170) outliers start: 24 outliers final: 17 residues processed: 106 average time/residue: 3.1579 time to fit residues: 360.2187 Evaluate side-chains 100 residues out of total 1200 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 81 time to evaluate : 1.722 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 160 SER Chi-restraints excluded: chain A residue 266 LYS Chi-restraints excluded: chain A residue 308 GLU Chi-restraints excluded: chain A residue 327 LEU Chi-restraints excluded: chain A residue 366 LEU Chi-restraints excluded: chain A residue 399 GLN Chi-restraints excluded: chain A residue 410 GLU Chi-restraints excluded: chain A residue 425 GLU Chi-restraints excluded: chain B residue 8 ASN Chi-restraints excluded: chain B residue 90 LEU Chi-restraints excluded: chain B residue 326 HIS Chi-restraints excluded: chain B residue 390 THR Chi-restraints excluded: chain C residue 57 ASP Chi-restraints excluded: chain C residue 131 ASP Chi-restraints excluded: chain C residue 134 LEU Chi-restraints excluded: chain C residue 175 ASP Chi-restraints excluded: chain C residue 202 ASP Chi-restraints excluded: chain C residue 280 ASP Chi-restraints excluded: chain C residue 282 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 124 optimal weight: 4.9990 chunk 14 optimal weight: 4.9990 chunk 73 optimal weight: 2.9990 chunk 93 optimal weight: 1.9990 chunk 72 optimal weight: 0.9980 chunk 108 optimal weight: 3.9990 chunk 71 optimal weight: 4.9990 chunk 128 optimal weight: 0.0970 chunk 80 optimal weight: 2.9990 chunk 78 optimal weight: 0.9990 chunk 59 optimal weight: 2.9990 overall best weight: 1.4184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 8 ASN B 324 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8635 moved from start: 0.3428 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 10964 Z= 0.207 Angle : 0.478 6.493 14848 Z= 0.253 Chirality : 0.038 0.148 1676 Planarity : 0.004 0.055 1920 Dihedral : 4.461 42.431 1460 Min Nonbonded Distance : 1.830 Molprobity Statistics. All-atom Clashscore : 4.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % Rotamer: Outliers : 1.58 % Allowed : 10.75 % Favored : 87.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.66 % 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: 0.90 (0.23), residues: 1326 helix: 1.45 (0.22), residues: 622 sheet: 0.16 (0.37), residues: 201 loop : -0.19 (0.27), residues: 503 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 203 HIS 0.004 0.001 HIS C 299 PHE 0.026 0.001 PHE A 538 TYR 0.012 0.001 TYR B 244 ARG 0.007 0.000 ARG A 527 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2652 Ramachandran restraints generated. 1326 Oldfield, 0 Emsley, 1326 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2652 Ramachandran restraints generated. 1326 Oldfield, 0 Emsley, 1326 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 1200 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 84 time to evaluate : 1.769 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 353 SER cc_start: 0.9506 (m) cc_final: 0.9247 (p) REVERT: A 425 GLU cc_start: 0.8738 (OUTLIER) cc_final: 0.7968 (mp0) REVERT: B 393 LYS cc_start: 0.8628 (mmmt) cc_final: 0.7995 (mmtm) REVERT: B 398 CYS cc_start: 0.8116 (t) cc_final: 0.7510 (p) REVERT: C 191 HIS cc_start: 0.7530 (m90) cc_final: 0.7065 (m170) outliers start: 19 outliers final: 15 residues processed: 101 average time/residue: 2.9956 time to fit residues: 325.3497 Evaluate side-chains 98 residues out of total 1200 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 82 time to evaluate : 1.741 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 160 SER Chi-restraints excluded: chain A residue 266 LYS Chi-restraints excluded: chain A residue 308 GLU Chi-restraints excluded: chain A residue 327 LEU Chi-restraints excluded: chain A residue 366 LEU Chi-restraints excluded: chain A residue 410 GLU Chi-restraints excluded: chain A residue 425 GLU Chi-restraints excluded: chain B residue 8 ASN Chi-restraints excluded: chain B residue 90 LEU Chi-restraints excluded: chain B residue 304 ASP Chi-restraints excluded: chain B residue 326 HIS Chi-restraints excluded: chain C residue 57 ASP Chi-restraints excluded: chain C residue 131 ASP Chi-restraints excluded: chain C residue 175 ASP Chi-restraints excluded: chain C residue 202 ASP Chi-restraints excluded: chain C residue 282 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 79 optimal weight: 1.9990 chunk 51 optimal weight: 3.9990 chunk 76 optimal weight: 2.9990 chunk 38 optimal weight: 0.7980 chunk 25 optimal weight: 3.9990 chunk 24 optimal weight: 1.9990 chunk 81 optimal weight: 0.8980 chunk 87 optimal weight: 0.6980 chunk 63 optimal weight: 4.9990 chunk 11 optimal weight: 3.9990 chunk 100 optimal weight: 6.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 90 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8630 moved from start: 0.3461 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 10964 Z= 0.192 Angle : 0.472 6.389 14848 Z= 0.249 Chirality : 0.038 0.146 1676 Planarity : 0.004 0.058 1920 Dihedral : 4.435 42.143 1460 Min Nonbonded Distance : 1.830 Molprobity Statistics. All-atom Clashscore : 4.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % Rotamer: Outliers : 1.58 % Allowed : 10.75 % Favored : 87.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.66 % 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: 0.93 (0.23), residues: 1326 helix: 1.47 (0.22), residues: 624 sheet: 0.19 (0.37), residues: 201 loop : -0.18 (0.27), residues: 501 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 203 HIS 0.004 0.001 HIS C 299 PHE 0.025 0.001 PHE A 538 TYR 0.012 0.001 TYR B 244 ARG 0.008 0.000 ARG A 527 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2652 Ramachandran restraints generated. 1326 Oldfield, 0 Emsley, 1326 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2652 Ramachandran restraints generated. 1326 Oldfield, 0 Emsley, 1326 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 1200 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 85 time to evaluate : 1.813 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 353 SER cc_start: 0.9501 (m) cc_final: 0.9244 (p) REVERT: A 399 GLN cc_start: 0.8234 (OUTLIER) cc_final: 0.7557 (mt0) REVERT: A 425 GLU cc_start: 0.8744 (OUTLIER) cc_final: 0.7960 (mp0) REVERT: B 393 LYS cc_start: 0.8633 (mmmt) cc_final: 0.8005 (mmtm) REVERT: B 398 CYS cc_start: 0.8123 (t) cc_final: 0.7517 (p) REVERT: C 191 HIS cc_start: 0.7532 (m90) cc_final: 0.7070 (m170) outliers start: 19 outliers final: 13 residues processed: 101 average time/residue: 2.9911 time to fit residues: 324.6505 Evaluate side-chains 99 residues out of total 1200 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 84 time to evaluate : 1.680 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 160 SER Chi-restraints excluded: chain A residue 266 LYS Chi-restraints excluded: chain A residue 327 LEU Chi-restraints excluded: chain A residue 366 LEU Chi-restraints excluded: chain A residue 399 GLN Chi-restraints excluded: chain A residue 410 GLU Chi-restraints excluded: chain A residue 425 GLU Chi-restraints excluded: chain B residue 90 LEU Chi-restraints excluded: chain B residue 304 ASP Chi-restraints excluded: chain B residue 326 HIS Chi-restraints excluded: chain C residue 57 ASP Chi-restraints excluded: chain C residue 175 ASP Chi-restraints excluded: chain C residue 202 ASP Chi-restraints excluded: chain C residue 280 ASP Chi-restraints excluded: chain C residue 282 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 116 optimal weight: 2.9990 chunk 122 optimal weight: 4.9990 chunk 112 optimal weight: 3.9990 chunk 119 optimal weight: 3.9990 chunk 71 optimal weight: 5.9990 chunk 52 optimal weight: 2.9990 chunk 93 optimal weight: 2.9990 chunk 36 optimal weight: 3.9990 chunk 107 optimal weight: 0.7980 chunk 78 optimal weight: 0.3980 chunk 126 optimal weight: 3.9990 overall best weight: 2.0386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8643 moved from start: 0.3523 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 10964 Z= 0.267 Angle : 0.495 6.109 14848 Z= 0.264 Chirality : 0.039 0.148 1676 Planarity : 0.004 0.060 1920 Dihedral : 4.497 42.126 1460 Min Nonbonded Distance : 1.815 Molprobity Statistics. All-atom Clashscore : 4.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % Rotamer: Outliers : 1.33 % Allowed : 11.25 % Favored : 87.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.66 % 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: 0.80 (0.23), residues: 1326 helix: 1.36 (0.22), residues: 625 sheet: -0.01 (0.36), residues: 211 loop : -0.17 (0.27), residues: 490 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 203 HIS 0.006 0.001 HIS C 299 PHE 0.026 0.002 PHE A 538 TYR 0.013 0.001 TYR B 178 ARG 0.009 0.000 ARG A 527 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2652 Ramachandran restraints generated. 1326 Oldfield, 0 Emsley, 1326 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2652 Ramachandran restraints generated. 1326 Oldfield, 0 Emsley, 1326 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 1200 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 81 time to evaluate : 1.736 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 353 SER cc_start: 0.9501 (m) cc_final: 0.9251 (p) REVERT: A 399 GLN cc_start: 0.8238 (OUTLIER) cc_final: 0.7568 (mt0) REVERT: A 425 GLU cc_start: 0.8748 (OUTLIER) cc_final: 0.7977 (mp0) REVERT: B 393 LYS cc_start: 0.8633 (mmmt) cc_final: 0.8005 (mmtm) REVERT: B 398 CYS cc_start: 0.8146 (t) cc_final: 0.7553 (p) REVERT: C 191 HIS cc_start: 0.7555 (m90) cc_final: 0.7139 (m-70) outliers start: 16 outliers final: 14 residues processed: 96 average time/residue: 3.0784 time to fit residues: 317.0481 Evaluate side-chains 97 residues out of total 1200 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 81 time to evaluate : 1.742 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 160 SER Chi-restraints excluded: chain A residue 266 LYS Chi-restraints excluded: chain A residue 327 LEU Chi-restraints excluded: chain A residue 366 LEU Chi-restraints excluded: chain A residue 399 GLN Chi-restraints excluded: chain A residue 410 GLU Chi-restraints excluded: chain A residue 425 GLU Chi-restraints excluded: chain B residue 90 LEU Chi-restraints excluded: chain B residue 304 ASP Chi-restraints excluded: chain B residue 326 HIS Chi-restraints excluded: chain C residue 57 ASP Chi-restraints excluded: chain C residue 175 ASP Chi-restraints excluded: chain C residue 202 ASP Chi-restraints excluded: chain C residue 280 ASP Chi-restraints excluded: chain C residue 282 LEU Chi-restraints excluded: chain D residue 83 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 77 optimal weight: 1.9990 chunk 59 optimal weight: 2.9990 chunk 87 optimal weight: 0.5980 chunk 132 optimal weight: 7.9990 chunk 121 optimal weight: 3.9990 chunk 105 optimal weight: 0.9990 chunk 10 optimal weight: 2.9990 chunk 81 optimal weight: 3.9990 chunk 64 optimal weight: 2.9990 chunk 83 optimal weight: 0.6980 chunk 112 optimal weight: 0.7980 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 90 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8625 moved from start: 0.3538 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 10964 Z= 0.165 Angle : 0.462 6.081 14848 Z= 0.244 Chirality : 0.037 0.146 1676 Planarity : 0.004 0.062 1920 Dihedral : 4.349 41.926 1460 Min Nonbonded Distance : 1.837 Molprobity Statistics. All-atom Clashscore : 4.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % Rotamer: Outliers : 1.42 % Allowed : 11.33 % Favored : 87.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.66 % 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: 0.98 (0.24), residues: 1326 helix: 1.52 (0.22), residues: 625 sheet: 0.23 (0.37), residues: 201 loop : -0.17 (0.27), residues: 500 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 203 HIS 0.004 0.001 HIS C 299 PHE 0.025 0.001 PHE A 538 TYR 0.012 0.001 TYR B 244 ARG 0.009 0.000 ARG A 527 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2652 Ramachandran restraints generated. 1326 Oldfield, 0 Emsley, 1326 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2652 Ramachandran restraints generated. 1326 Oldfield, 0 Emsley, 1326 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 1200 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 82 time to evaluate : 1.916 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 353 SER cc_start: 0.9499 (m) cc_final: 0.9257 (p) REVERT: A 399 GLN cc_start: 0.8244 (OUTLIER) cc_final: 0.7547 (mt0) REVERT: A 425 GLU cc_start: 0.8740 (OUTLIER) cc_final: 0.8038 (mp0) REVERT: B 393 LYS cc_start: 0.8633 (mmmt) cc_final: 0.8012 (mmtm) REVERT: B 398 CYS cc_start: 0.8150 (t) cc_final: 0.7569 (p) REVERT: C 8 LYS cc_start: 0.8679 (mmtp) cc_final: 0.8450 (mmmt) REVERT: C 191 HIS cc_start: 0.7498 (m90) cc_final: 0.7055 (m170) outliers start: 17 outliers final: 11 residues processed: 97 average time/residue: 3.0378 time to fit residues: 317.2064 Evaluate side-chains 92 residues out of total 1200 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 79 time to evaluate : 1.733 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 266 LYS Chi-restraints excluded: chain A residue 327 LEU Chi-restraints excluded: chain A residue 399 GLN Chi-restraints excluded: chain A residue 410 GLU Chi-restraints excluded: chain A residue 425 GLU Chi-restraints excluded: chain B residue 90 LEU Chi-restraints excluded: chain B residue 304 ASP Chi-restraints excluded: chain B residue 326 HIS Chi-restraints excluded: chain C residue 57 ASP Chi-restraints excluded: chain C residue 175 ASP Chi-restraints excluded: chain C residue 202 ASP Chi-restraints excluded: chain C residue 280 ASP Chi-restraints excluded: chain C residue 282 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 32 optimal weight: 0.0370 chunk 97 optimal weight: 0.9980 chunk 15 optimal weight: 1.9990 chunk 29 optimal weight: 1.9990 chunk 105 optimal weight: 0.7980 chunk 44 optimal weight: 2.9990 chunk 108 optimal weight: 3.9990 chunk 13 optimal weight: 2.9990 chunk 19 optimal weight: 0.1980 chunk 92 optimal weight: 0.9980 chunk 6 optimal weight: 4.9990 overall best weight: 0.6058 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.090353 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2951 r_free = 0.2951 target = 0.067378 restraints weight = 58143.188| |-----------------------------------------------------------------------------| r_work (start): 0.2937 rms_B_bonded: 2.31 r_work: 0.2815 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.2689 rms_B_bonded: 4.18 restraints_weight: 0.2500 r_work (final): 0.2689 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8690 moved from start: 0.3583 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 10964 Z= 0.132 Angle : 0.448 6.048 14848 Z= 0.234 Chirality : 0.037 0.167 1676 Planarity : 0.003 0.063 1920 Dihedral : 4.175 40.951 1460 Min Nonbonded Distance : 1.860 Molprobity Statistics. All-atom Clashscore : 4.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.96 % Favored : 98.04 % Rotamer: Outliers : 1.25 % Allowed : 11.42 % Favored : 87.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.66 % 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: 1.19 (0.24), residues: 1326 helix: 1.71 (0.22), residues: 623 sheet: 0.30 (0.37), residues: 201 loop : -0.06 (0.27), residues: 502 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 203 HIS 0.002 0.001 HIS C 63 PHE 0.023 0.001 PHE A 538 TYR 0.010 0.001 TYR B 244 ARG 0.009 0.000 ARG A 527 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8728.92 seconds wall clock time: 153 minutes 19.37 seconds (9199.37 seconds total)