Starting phenix.real_space_refine on Mon Mar 18 18:44:52 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ttb_41604/03_2024/8ttb_41604_trim_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ttb_41604/03_2024/8ttb_41604.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.77 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ttb_41604/03_2024/8ttb_41604.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ttb_41604/03_2024/8ttb_41604.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ttb_41604/03_2024/8ttb_41604_trim_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ttb_41604/03_2024/8ttb_41604_trim_updated.pdb" } resolution = 2.77 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= 0.001 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: 8 Type Number sf(0) Gaussians Fe 1 7.16 5 Zn 1 6.06 5 P 1 5.49 5 S 63 5.16 5 C 6954 2.51 5 N 1889 2.21 5 O 2093 1.98 5 H 10903 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped None Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 21905 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: 6893 Number of conformers: 1 Conformer: "" Number of residues, atoms: 426, 6893 Classifications: {'peptide': 426} Link IDs: {'PTRANS': 14, 'TRANS': 411} Chain breaks: 3 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: 965 Number of conformers: 1 Conformer: "" Number of residues, atoms: 61, 965 Classifications: {'peptide': 61} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 55} Chain breaks: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'2RX:plan-1': 1} Unresolved non-hydrogen planarities: 1 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: 9.99, per 1000 atoms: 0.46 Number of scatterers: 21905 At special positions: 0 Unit cell: (106.683, 129.839, 114.953, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 8 Type Number sf(0) Zn 1 29.99 Fe 1 26.01 S 63 16.00 P 1 15.00 O 2093 8.00 N 1889 7.00 C 6954 6.00 H 10903 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: 16.94 Conformation dependent library (CDL) restraints added in 2.2 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN C 402 " pdb="ZN ZN C 402 " - pdb=" NE2 HIS C 59 " 2712 Ramachandran restraints generated. 1356 Oldfield, 0 Emsley, 1356 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2632 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 61 helices and 12 sheets defined 45.9% alpha, 12.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.21 Creating SS restraints... Processing helix chain 'A' and resid 11 through 21 removed outlier: 4.305A pdb=" N ARG A 21 " --> pdb=" O ILE A 17 " (cutoff:3.500A) Processing helix chain 'A' and resid 25 through 42 removed outlier: 5.299A pdb=" N SER A 36 " --> pdb=" O ILE A 32 " (cutoff:3.500A) removed outlier: 6.276A 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: 3.515A pdb=" N GLY A 74 " --> pdb=" O ALA A 70 " (cutoff:3.500A) removed outlier: 4.173A pdb=" N THR A 75 " --> pdb=" O GLU A 71 " (cutoff:3.500A) Processing helix chain 'A' and resid 83 through 98 removed outlier: 5.279A pdb=" N HIS A 87 " --> pdb=" O GLU A 84 " (cutoff:3.500A) Proline residue: A 91 - end of helix removed outlier: 3.777A 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 155 removed outlier: 4.443A pdb=" N GLY A 149 " --> pdb=" O THR A 145 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N LEU A 150 " --> pdb=" O SER A 146 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N PHE A 151 " --> pdb=" O ALA A 147 " (cutoff:3.500A) removed outlier: 5.120A pdb=" N SER A 152 " --> pdb=" O CYS A 148 " (cutoff:3.500A) removed outlier: 5.260A pdb=" N VAL A 153 " --> pdb=" O GLY A 149 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N CYS A 154 " --> pdb=" O LEU A 150 " (cutoff:3.500A) Processing helix chain 'A' and resid 160 through 175 Processing helix chain 'A' and resid 179 through 193 removed outlier: 4.318A pdb=" N GLY A 190 " --> pdb=" O ALA A 186 " (cutoff:3.500A) removed outlier: 5.036A pdb=" N GLU A 191 " --> pdb=" O SER A 187 " (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: 4.100A pdb=" N LEU A 223 " --> pdb=" O SER A 219 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N VAL A 225 " --> pdb=" O ARG A 221 " (cutoff:3.500A) removed outlier: 4.470A pdb=" N GLU A 226 " --> pdb=" O LEU A 222 " (cutoff:3.500A) Processing helix chain 'A' and resid 237 through 243 removed outlier: 3.511A pdb=" N LEU A 240 " --> pdb=" O GLN A 237 " (cutoff:3.500A) removed outlier: 4.231A pdb=" N GLU A 241 " --> pdb=" O GLU A 238 " (cutoff:3.500A) Processing helix chain 'A' and resid 245 through 252 removed outlier: 3.634A pdb=" N GLN A 250 " --> pdb=" O PRO A 246 " (cutoff:3.500A) 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: 3.720A pdb=" N LYS A 305 " --> pdb=" O ALA A 301 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N VAL A 306 " --> pdb=" O ALA A 302 " (cutoff:3.500A) removed outlier: 4.854A pdb=" N LYS A 307 " --> pdb=" O SER A 303 " (cutoff:3.500A) removed outlier: 4.858A 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 335 removed outlier: 3.635A pdb=" N GLU A 332 " --> pdb=" O PRO A 328 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N SER A 335 " --> pdb=" O LYS A 331 " (cutoff:3.500A) Processing helix chain 'A' and resid 339 through 356 removed outlier: 3.914A pdb=" N VAL A 348 " --> pdb=" O ALA A 344 " (cutoff:3.500A) removed outlier: 4.527A pdb=" N MET A 350 " --> pdb=" O ALA A 346 " (cutoff:3.500A) removed outlier: 5.872A pdb=" N GLY A 351 " --> pdb=" O SER A 347 " (cutoff:3.500A) removed outlier: 4.223A pdb=" N LEU A 352 " --> pdb=" O VAL A 348 " (cutoff:3.500A) removed outlier: 4.819A pdb=" N SER A 353 " --> pdb=" O ILE A 349 " (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 Processing helix chain 'A' and resid 389 through 394 Processing helix chain 'A' and resid 397 through 399 No H-bonds generated for 'chain 'A' and resid 397 through 399' Processing helix chain 'A' and resid 401 through 413 Proline residue: A 406 - end of helix Processing helix chain 'A' and resid 417 through 441 Proline residue: A 428 - end of helix removed outlier: 5.721A pdb=" N VAL A 436 " --> pdb=" O GLY A 432 " (cutoff:3.500A) removed outlier: 8.573A pdb=" N GLU A 437 " --> pdb=" O GLN A 433 " (cutoff:3.500A) removed outlier: 4.051A pdb=" N PHE A 438 " --> pdb=" O LEU A 434 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N GLU A 441 " --> pdb=" O GLU A 437 " (cutoff:3.500A) Processing helix chain 'A' and resid 444 through 451 removed outlier: 3.546A pdb=" N LEU A 451 " --> pdb=" O CYS A 447 " (cutoff:3.500A) Processing helix chain 'A' and resid 456 through 491 removed outlier: 3.625A pdb=" N LYS A 467 " --> pdb=" O THR A 463 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N LYS A 472 " --> pdb=" O LYS A 468 " (cutoff:3.500A) removed outlier: 6.688A pdb=" N LYS A 475 " --> pdb=" O GLU A 471 " (cutoff:3.500A) removed outlier: 8.853A pdb=" N GLU A 476 " --> pdb=" O LYS A 472 " (cutoff:3.500A) removed outlier: 4.145A pdb=" N TRP A 477 " --> pdb=" O PHE A 473 " (cutoff:3.500A) removed outlier: 4.575A pdb=" N ILE A 483 " --> pdb=" O HIS A 479 " (cutoff:3.500A) Proline residue: A 484 - end of helix removed outlier: 3.855A pdb=" N MET A 489 " --> pdb=" O LYS A 485 " (cutoff:3.500A) removed outlier: 4.306A pdb=" N SER A 490 " --> pdb=" O VAL A 486 " (cutoff:3.500A) removed outlier: 4.666A pdb=" N GLY A 491 " --> pdb=" O LEU A 487 " (cutoff:3.500A) Processing helix chain 'A' and resid 495 through 512 removed outlier: 3.545A pdb=" N THR A 501 " --> pdb=" O HIS A 497 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N LEU A 502 " --> pdb=" O ARG A 498 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N GLU A 510 " --> pdb=" O ASN A 506 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N VAL A 511 " --> pdb=" O VAL A 507 " (cutoff:3.500A) Processing helix chain 'A' and resid 514 through 517 No H-bonds generated for 'chain 'A' and resid 514 through 517' Processing helix chain 'A' and resid 521 through 530 removed outlier: 4.513A pdb=" N GLY A 530 " --> pdb=" O LEU A 526 " (cutoff:3.500A) Processing helix chain 'A' and resid 534 through 547 Processing helix chain 'A' and resid 553 through 558 Processing helix chain 'A' and resid 560 through 569 removed outlier: 3.569A 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: 4.099A pdb=" N SER B 331 " --> pdb=" O TYR B 328 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N LEU B 333 " --> pdb=" O ARG B 330 " (cutoff:3.500A) removed outlier: 5.070A 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 'C' and resid 3 through 19 Processing helix chain 'C' and resid 25 through 41 removed outlier: 4.119A 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 124 No H-bonds generated for 'chain 'C' and resid 121 through 124' Processing helix chain 'C' and resid 129 through 137 Processing helix chain 'C' and resid 141 through 152 removed outlier: 3.621A pdb=" N ASP C 151 " --> pdb=" O THR C 147 " (cutoff:3.500A) removed outlier: 4.274A pdb=" N TYR C 152 " --> pdb=" O ASP C 148 " (cutoff:3.500A) Processing helix chain 'C' and resid 177 through 182 Processing helix chain 'C' and resid 194 through 200 removed outlier: 3.830A 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 46 through 53 Processing helix chain 'D' and resid 64 through 74 Processing sheet with id= A, first strand: chain 'B' and resid 31 through 36 removed outlier: 6.232A pdb=" N GLY B 46 " --> pdb=" O SER B 32 " (cutoff:3.500A) removed outlier: 4.548A pdb=" N VAL B 34 " --> pdb=" O ALA B 44 " (cutoff:3.500A) removed outlier: 6.891A pdb=" N ALA B 44 " --> pdb=" O VAL B 34 " (cutoff:3.500A) removed outlier: 4.914A pdb=" N PHE B 36 " --> pdb=" O LEU B 42 " (cutoff:3.500A) removed outlier: 7.015A pdb=" N LEU B 42 " --> pdb=" O PHE B 36 " (cutoff:3.500A) removed outlier: 4.338A pdb=" N ARG B 51 " --> pdb=" O ASP B 47 " (cutoff:3.500A) removed outlier: 5.338A pdb=" N GLN B 56 " --> pdb=" O VAL B 73 " (cutoff:3.500A) removed outlier: 5.420A 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 Processing sheet with id= C, first strand: chain 'B' and resid 98 through 101 removed outlier: 3.643A pdb=" N LYS B 98 " --> pdb=" O THR B 114 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N ARG B 170 " --> pdb=" O LEU B 121 " (cutoff:3.500A) removed outlier: 6.453A pdb=" N LYS B 123 " --> pdb=" O PRO B 168 " (cutoff:3.500A) removed outlier: 7.475A pdb=" N SER B 125 " --> pdb=" O ALA B 166 " (cutoff:3.500A) removed outlier: 5.374A pdb=" N ALA B 166 " --> pdb=" O SER B 125 " (cutoff:3.500A) removed outlier: 6.841A pdb=" N ARG B 127 " --> pdb=" O VAL B 164 " (cutoff:3.500A) removed outlier: 5.501A 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: 6.611A pdb=" N LEU B 202 " --> pdb=" O ASN B 213 " (cutoff:3.500A) removed outlier: 5.415A 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: 3.684A 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 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: 4.368A pdb=" N HIS B 421 " --> pdb=" O ALA B 434 " (cutoff:3.500A) removed outlier: 5.898A pdb=" N GLN B 443 " --> pdb=" O PHE B 14 " (cutoff:3.500A) removed outlier: 5.369A 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: 6.944A pdb=" N THR C 156 " --> pdb=" O GLN C 46 " (cutoff:3.500A) removed outlier: 7.647A pdb=" N VAL C 48 " --> pdb=" O THR C 156 " (cutoff:3.500A) removed outlier: 6.025A pdb=" N LEU C 158 " --> pdb=" O VAL C 48 " (cutoff:3.500A) removed outlier: 6.734A pdb=" N LEU C 236 " --> pdb=" O PHE C 164 " (cutoff:3.500A) removed outlier: 8.169A pdb=" N LEU C 166 " --> pdb=" O LEU C 236 " (cutoff:3.500A) removed outlier: 6.343A 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: 6.443A pdb=" N TYR C 80 " --> pdb=" O THR C 112 " (cutoff:3.500A) removed outlier: 6.574A 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 211 430 hydrogen bonds defined for protein. 1194 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: 7.67 Time building geometry restraints manager: 17.78 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.13: 10870 1.13 - 1.41: 4596 1.41 - 1.70: 6562 1.70 - 1.99: 91 1.99 - 2.28: 1 Bond restraints: 22120 Sorted by residual: bond pdb=" C MLL C 309 " pdb=" OXT MLL C 309 " ideal model delta sigma weight residual 1.231 1.365 -0.134 2.00e-02 2.50e+03 4.51e+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 2.86e+00 bond pdb=" N ASP C 2 " pdb=" H ASP C 2 " ideal model delta sigma weight residual 0.860 0.891 -0.031 2.00e-02 2.50e+03 2.36e+00 bond pdb=" N ILE B 419 " pdb=" CA ILE B 419 " ideal model delta sigma weight residual 1.462 1.474 -0.011 1.32e-02 5.74e+03 7.55e-01 bond pdb=" CA LEU C 186 " pdb=" C LEU C 186 " ideal model delta sigma weight residual 1.531 1.523 0.008 1.12e-02 7.97e+03 5.50e-01 ... (remaining 22115 not shown) Histogram of bond angle deviations from ideal: 100.47 - 107.16: 412 107.16 - 113.86: 26580 113.86 - 120.55: 7368 120.55 - 127.25: 5507 127.25 - 133.94: 126 Bond angle restraints: 39993 Sorted by residual: angle pdb=" C LYS B 405 " pdb=" N ASP B 406 " pdb=" CA ASP B 406 " ideal model delta sigma weight residual 121.54 126.92 -5.38 1.91e+00 2.74e-01 7.93e+00 angle pdb=" CA MLL C 309 " pdb=" C MLL C 309 " pdb=" OXT MLL C 309 " ideal model delta sigma weight residual 121.00 114.12 6.88 3.00e+00 1.11e-01 5.26e+00 angle pdb=" N HIS B 326 " pdb=" CA HIS B 326 " pdb=" C HIS B 326 " ideal model delta sigma weight residual 107.32 110.90 -3.58 1.65e+00 3.67e-01 4.72e+00 angle pdb=" O43 2RX D 62 " pdb=" P40 2RX D 62 " pdb=" S41 2RX D 62 " ideal model delta sigma weight residual 106.83 100.51 6.32 3.00e+00 1.11e-01 4.44e+00 angle pdb=" CA MLL C 309 " pdb=" C MLL C 309 " pdb=" O MLL C 309 " ideal model delta sigma weight residual 121.00 127.29 -6.29 3.00e+00 1.11e-01 4.40e+00 ... (remaining 39988 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.49: 9895 15.49 - 30.98: 309 30.98 - 46.47: 115 46.47 - 61.96: 47 61.96 - 77.45: 28 Dihedral angle restraints: 10394 sinusoidal: 5685 harmonic: 4709 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 180.00 161.30 18.70 0 5.00e+00 4.00e-02 1.40e+01 dihedral pdb=" CA THR B 114 " pdb=" C THR B 114 " pdb=" N ASN B 115 " pdb=" CA ASN B 115 " ideal model delta harmonic sigma weight residual 180.00 163.59 16.41 0 5.00e+00 4.00e-02 1.08e+01 dihedral pdb=" N LEU A 196 " pdb=" CA LEU A 196 " pdb=" CB LEU A 196 " pdb=" CG LEU A 196 " ideal model delta sinusoidal sigma weight residual -60.00 -104.77 44.77 3 1.50e+01 4.44e-03 8.05e+00 ... (remaining 10391 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.027: 1080 0.027 - 0.053: 396 0.053 - 0.080: 127 0.080 - 0.106: 66 0.106 - 0.133: 39 Chirality restraints: 1708 Sorted by residual: chirality pdb=" CA ILE D 92 " pdb=" N ILE D 92 " pdb=" C ILE D 92 " pdb=" CB ILE D 92 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.42e-01 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 4.27e-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 2.57 -0.13 2.00e-01 2.50e+01 3.97e-01 ... (remaining 1705 not shown) Planarity restraints: 3273 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL A 284 " 0.017 5.00e-02 4.00e+02 2.55e-02 1.04e+00 pdb=" N PRO A 285 " -0.044 5.00e-02 4.00e+02 pdb=" CA PRO A 285 " 0.013 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 ILE A 206 " 0.016 5.00e-02 4.00e+02 2.42e-02 9.35e-01 pdb=" N PRO A 207 " -0.042 5.00e-02 4.00e+02 pdb=" CA PRO A 207 " 0.012 5.00e-02 4.00e+02 pdb=" CD PRO A 207 " 0.014 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL C 189 " -0.016 5.00e-02 4.00e+02 2.36e-02 8.91e-01 pdb=" N PRO C 190 " 0.041 5.00e-02 4.00e+02 pdb=" CA PRO C 190 " -0.012 5.00e-02 4.00e+02 pdb=" CD PRO C 190 " -0.013 5.00e-02 4.00e+02 ... (remaining 3270 not shown) Histogram of nonbonded interaction distances: 1.43 - 2.06: 363 2.06 - 2.70: 35964 2.70 - 3.33: 66793 3.33 - 3.97: 86012 3.97 - 4.60: 136827 Nonbonded interactions: 325959 Sorted by model distance: nonbonded pdb=" OXT MLL C 309 " pdb=" C10 MLL C 309 " model vdw 1.428 3.100 nonbonded pdb=" H LEU B 202 " pdb=" O PHE B 212 " model vdw 1.641 1.850 nonbonded pdb=" OD1 ASP B 9 " pdb="HH11 ARG B 375 " model vdw 1.645 1.850 nonbonded pdb="HE21 GLN C 61 " pdb=" OD2 ASP C 64 " model vdw 1.645 1.850 nonbonded pdb=" O 2RX D 62 " pdb="HD21 ASN D 66 " model vdw 1.647 1.850 ... (remaining 325954 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: 3.150 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: 0.300 Extract box with map and model: 10.190 Check model and map are aligned: 0.330 Set scattering table: 0.210 Process input model: 74.780 Find NCS groups from input model: 0.360 Set up NCS constraints: 0.050 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:13.870 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 103.250 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8712 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 0.134 11217 Z= 0.143 Angle : 0.416 6.881 15190 Z= 0.213 Chirality : 0.037 0.133 1708 Planarity : 0.002 0.025 1965 Dihedral : 7.775 72.857 4201 Min Nonbonded Distance : 1.428 Molprobity Statistics. All-atom Clashscore : 3.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.62 % Favored : 98.38 % Rotamer: Outliers : 0.00 % Allowed : 1.23 % Favored : 98.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.17 % 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: 1.83 (0.24), residues: 1356 helix: 1.97 (0.23), residues: 606 sheet: 0.87 (0.38), residues: 217 loop : 0.61 (0.28), residues: 533 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 350 HIS 0.002 0.001 HIS C 63 PHE 0.016 0.001 PHE A 538 TYR 0.007 0.001 TYR B 178 ARG 0.003 0.000 ARG B 371 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2712 Ramachandran restraints generated. 1356 Oldfield, 0 Emsley, 1356 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2712 Ramachandran restraints generated. 1356 Oldfield, 0 Emsley, 1356 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 1223 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 114 time to evaluate : 2.003 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 47 ASP cc_start: 0.7858 (m-30) cc_final: 0.7623 (m-30) outliers start: 0 outliers final: 0 residues processed: 114 average time/residue: 3.3241 time to fit residues: 404.4083 Evaluate side-chains 67 residues out of total 1223 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 67 time to evaluate : 1.900 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 114 optimal weight: 2.9990 chunk 103 optimal weight: 1.9990 chunk 57 optimal weight: 0.7980 chunk 35 optimal weight: 1.9990 chunk 69 optimal weight: 0.6980 chunk 55 optimal weight: 1.9990 chunk 106 optimal weight: 1.9990 chunk 41 optimal weight: 2.9990 chunk 64 optimal weight: 1.9990 chunk 79 optimal weight: 2.9990 chunk 123 optimal weight: 3.9990 overall best weight: 1.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 465 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8730 moved from start: 0.1398 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 11217 Z= 0.263 Angle : 0.507 5.558 15190 Z= 0.273 Chirality : 0.040 0.140 1708 Planarity : 0.004 0.054 1965 Dihedral : 4.390 63.757 1495 Min Nonbonded Distance : 1.944 Molprobity Statistics. All-atom Clashscore : 4.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Rotamer: Outliers : 0.82 % Allowed : 5.07 % Favored : 94.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.17 % 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: 1.23 (0.24), residues: 1356 helix: 1.39 (0.22), residues: 629 sheet: 0.73 (0.39), residues: 193 loop : 0.32 (0.28), residues: 534 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 203 HIS 0.006 0.001 HIS A 364 PHE 0.022 0.001 PHE A 538 TYR 0.013 0.001 TYR B 244 ARG 0.004 0.000 ARG B 142 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2712 Ramachandran restraints generated. 1356 Oldfield, 0 Emsley, 1356 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2712 Ramachandran restraints generated. 1356 Oldfield, 0 Emsley, 1356 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 78 residues out of total 1223 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 68 time to evaluate : 1.703 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 318 ARG cc_start: 0.8616 (ttp80) cc_final: 0.8395 (ttp80) outliers start: 10 outliers final: 3 residues processed: 77 average time/residue: 3.0542 time to fit residues: 253.6011 Evaluate side-chains 66 residues out of total 1223 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 63 time to evaluate : 1.674 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 GLU Chi-restraints excluded: chain C residue 4 LYS Chi-restraints excluded: chain C residue 280 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 68 optimal weight: 1.9990 chunk 38 optimal weight: 2.9990 chunk 102 optimal weight: 2.9990 chunk 84 optimal weight: 2.9990 chunk 34 optimal weight: 1.9990 chunk 123 optimal weight: 2.9990 chunk 133 optimal weight: 4.9990 chunk 110 optimal weight: 2.9990 chunk 122 optimal weight: 1.9990 chunk 42 optimal weight: 1.9990 chunk 99 optimal weight: 1.9990 overall best weight: 1.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 326 HIS C 162 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8748 moved from start: 0.1734 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 11217 Z= 0.326 Angle : 0.501 5.434 15190 Z= 0.265 Chirality : 0.040 0.135 1708 Planarity : 0.003 0.029 1965 Dihedral : 4.534 56.712 1495 Min Nonbonded Distance : 1.964 Molprobity Statistics. All-atom Clashscore : 4.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 0.49 % Allowed : 6.30 % Favored : 93.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.17 % 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: 1356 helix: 1.21 (0.22), residues: 630 sheet: 0.47 (0.39), residues: 186 loop : 0.20 (0.27), residues: 540 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 203 HIS 0.004 0.001 HIS A 304 PHE 0.024 0.001 PHE A 538 TYR 0.012 0.001 TYR B 244 ARG 0.003 0.000 ARG D 50 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2712 Ramachandran restraints generated. 1356 Oldfield, 0 Emsley, 1356 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2712 Ramachandran restraints generated. 1356 Oldfield, 0 Emsley, 1356 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 71 residues out of total 1223 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 65 time to evaluate : 1.777 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 318 ARG cc_start: 0.8643 (ttp80) cc_final: 0.8424 (ttp80) outliers start: 6 outliers final: 3 residues processed: 70 average time/residue: 3.2123 time to fit residues: 241.7108 Evaluate side-chains 63 residues out of total 1223 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 60 time to evaluate : 1.657 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 GLU Chi-restraints excluded: chain C residue 4 LYS Chi-restraints excluded: chain C residue 280 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 122 optimal weight: 2.9990 chunk 93 optimal weight: 2.9990 chunk 64 optimal weight: 2.9990 chunk 13 optimal weight: 3.9990 chunk 59 optimal weight: 1.9990 chunk 83 optimal weight: 2.9990 chunk 124 optimal weight: 2.9990 chunk 131 optimal weight: 2.9990 chunk 117 optimal weight: 0.5980 chunk 35 optimal weight: 2.9990 chunk 109 optimal weight: 1.9990 overall best weight: 2.1188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 326 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8755 moved from start: 0.1971 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 11217 Z= 0.338 Angle : 0.503 5.028 15190 Z= 0.267 Chirality : 0.040 0.136 1708 Planarity : 0.004 0.029 1965 Dihedral : 4.614 61.322 1495 Min Nonbonded Distance : 1.960 Molprobity Statistics. All-atom Clashscore : 4.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 0.57 % Allowed : 6.79 % Favored : 92.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.17 % 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: 0.84 (0.23), residues: 1356 helix: 1.16 (0.22), residues: 630 sheet: 0.24 (0.39), residues: 186 loop : 0.11 (0.27), residues: 540 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 203 HIS 0.004 0.001 HIS B 295 PHE 0.025 0.001 PHE A 538 TYR 0.013 0.001 TYR B 244 ARG 0.003 0.000 ARG D 50 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2712 Ramachandran restraints generated. 1356 Oldfield, 0 Emsley, 1356 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2712 Ramachandran restraints generated. 1356 Oldfield, 0 Emsley, 1356 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 68 residues out of total 1223 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 61 time to evaluate : 1.772 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 318 ARG cc_start: 0.8639 (ttp80) cc_final: 0.8392 (ttp80) outliers start: 7 outliers final: 4 residues processed: 68 average time/residue: 3.0661 time to fit residues: 224.9107 Evaluate side-chains 64 residues out of total 1223 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 60 time to evaluate : 1.912 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 GLU Chi-restraints excluded: chain B residue 140 ASP Chi-restraints excluded: chain C residue 4 LYS Chi-restraints excluded: chain C residue 280 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 74 optimal weight: 2.9990 chunk 1 optimal weight: 5.9990 chunk 97 optimal weight: 0.8980 chunk 54 optimal weight: 2.9990 chunk 112 optimal weight: 1.9990 chunk 90 optimal weight: 2.9990 chunk 0 optimal weight: 3.9990 chunk 67 optimal weight: 1.9990 chunk 117 optimal weight: 0.0030 chunk 33 optimal weight: 2.9990 chunk 44 optimal weight: 2.9990 overall best weight: 1.5796 ------------------------------------------------------------------------------- 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: 0.8747 moved from start: 0.2077 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 11217 Z= 0.256 Angle : 0.477 5.473 15190 Z= 0.252 Chirality : 0.039 0.135 1708 Planarity : 0.003 0.030 1965 Dihedral : 4.555 65.711 1495 Min Nonbonded Distance : 1.963 Molprobity Statistics. All-atom Clashscore : 4.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 0.41 % Allowed : 7.11 % Favored : 92.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.94 (0.24), residues: 1356 helix: 1.28 (0.22), residues: 628 sheet: 0.28 (0.39), residues: 184 loop : 0.12 (0.27), residues: 544 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 203 HIS 0.004 0.001 HIS B 295 PHE 0.023 0.001 PHE A 538 TYR 0.012 0.001 TYR B 244 ARG 0.002 0.000 ARG D 50 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2712 Ramachandran restraints generated. 1356 Oldfield, 0 Emsley, 1356 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2712 Ramachandran restraints generated. 1356 Oldfield, 0 Emsley, 1356 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 68 residues out of total 1223 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 63 time to evaluate : 1.980 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 318 ARG cc_start: 0.8642 (ttp80) cc_final: 0.8372 (ttp80) outliers start: 5 outliers final: 3 residues processed: 68 average time/residue: 3.1385 time to fit residues: 229.8952 Evaluate side-chains 62 residues out of total 1223 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 59 time to evaluate : 1.370 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 140 ASP Chi-restraints excluded: chain C residue 4 LYS Chi-restraints excluded: chain C residue 280 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 118 optimal weight: 0.7980 chunk 25 optimal weight: 1.9990 chunk 77 optimal weight: 0.9990 chunk 32 optimal weight: 0.9980 chunk 131 optimal weight: 2.9990 chunk 109 optimal weight: 1.9990 chunk 60 optimal weight: 0.6980 chunk 10 optimal weight: 3.9990 chunk 43 optimal weight: 3.9990 chunk 69 optimal weight: 2.9990 chunk 126 optimal weight: 2.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- 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: 0.8736 moved from start: 0.2140 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 11217 Z= 0.196 Angle : 0.463 5.899 15190 Z= 0.243 Chirality : 0.038 0.135 1708 Planarity : 0.003 0.031 1965 Dihedral : 4.472 68.883 1495 Min Nonbonded Distance : 1.974 Molprobity Statistics. All-atom Clashscore : 4.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.06 % Favored : 97.94 % Rotamer: Outliers : 0.25 % Allowed : 7.69 % Favored : 92.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.17 % 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: 1.04 (0.24), residues: 1356 helix: 1.39 (0.22), residues: 628 sheet: 0.30 (0.39), residues: 184 loop : 0.14 (0.27), residues: 544 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 203 HIS 0.003 0.001 HIS B 295 PHE 0.022 0.001 PHE A 538 TYR 0.011 0.001 TYR B 244 ARG 0.002 0.000 ARG D 50 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2712 Ramachandran restraints generated. 1356 Oldfield, 0 Emsley, 1356 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2712 Ramachandran restraints generated. 1356 Oldfield, 0 Emsley, 1356 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 65 residues out of total 1223 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 62 time to evaluate : 1.959 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 318 ARG cc_start: 0.8651 (ttp80) cc_final: 0.8364 (ttp80) outliers start: 3 outliers final: 2 residues processed: 65 average time/residue: 3.2217 time to fit residues: 225.7600 Evaluate side-chains 61 residues out of total 1223 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 59 time to evaluate : 1.623 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 140 ASP Chi-restraints excluded: chain C residue 4 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 14 optimal weight: 0.8980 chunk 74 optimal weight: 2.9990 chunk 96 optimal weight: 3.9990 chunk 110 optimal weight: 1.9990 chunk 73 optimal weight: 0.7980 chunk 131 optimal weight: 2.9990 chunk 82 optimal weight: 3.9990 chunk 79 optimal weight: 0.3980 chunk 60 optimal weight: 0.9980 chunk 81 optimal weight: 0.5980 chunk 52 optimal weight: 1.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- 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: 0.8724 moved from start: 0.2175 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 11217 Z= 0.156 Angle : 0.443 4.853 15190 Z= 0.232 Chirality : 0.038 0.135 1708 Planarity : 0.003 0.031 1965 Dihedral : 4.361 71.309 1495 Min Nonbonded Distance : 1.980 Molprobity Statistics. All-atom Clashscore : 4.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 0.33 % Allowed : 7.52 % Favored : 92.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.17 % 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: 1.16 (0.24), residues: 1356 helix: 1.50 (0.22), residues: 628 sheet: 0.42 (0.40), residues: 184 loop : 0.16 (0.27), residues: 544 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 203 HIS 0.002 0.001 HIS B 421 PHE 0.021 0.001 PHE A 538 TYR 0.009 0.001 TYR B 244 ARG 0.001 0.000 ARG A 418 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2712 Ramachandran restraints generated. 1356 Oldfield, 0 Emsley, 1356 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2712 Ramachandran restraints generated. 1356 Oldfield, 0 Emsley, 1356 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 65 residues out of total 1223 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 61 time to evaluate : 1.912 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 318 ARG cc_start: 0.8635 (ttp80) cc_final: 0.8329 (ttp80) REVERT: B 27 GLU cc_start: 0.7998 (OUTLIER) cc_final: 0.7642 (tt0) REVERT: C 186 LEU cc_start: 0.9048 (mt) cc_final: 0.8809 (mm) outliers start: 4 outliers final: 2 residues processed: 65 average time/residue: 3.0527 time to fit residues: 213.8746 Evaluate side-chains 62 residues out of total 1223 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 59 time to evaluate : 1.759 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 27 GLU Chi-restraints excluded: chain B residue 140 ASP Chi-restraints excluded: chain C residue 4 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 78 optimal weight: 0.3980 chunk 39 optimal weight: 3.9990 chunk 25 optimal weight: 0.9980 chunk 83 optimal weight: 3.9990 chunk 89 optimal weight: 0.8980 chunk 64 optimal weight: 2.9990 chunk 12 optimal weight: 1.9990 chunk 103 optimal weight: 0.7980 chunk 119 optimal weight: 2.9990 chunk 125 optimal weight: 1.9990 chunk 114 optimal weight: 2.9990 overall best weight: 1.0182 ------------------------------------------------------------------------------- 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: 0.8728 moved from start: 0.2228 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 11217 Z= 0.188 Angle : 0.449 5.049 15190 Z= 0.235 Chirality : 0.038 0.134 1708 Planarity : 0.003 0.031 1965 Dihedral : 4.360 73.412 1495 Min Nonbonded Distance : 1.978 Molprobity Statistics. All-atom Clashscore : 4.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 0.33 % Allowed : 7.52 % Favored : 92.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.17 % 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: 1.18 (0.24), residues: 1356 helix: 1.52 (0.22), residues: 629 sheet: 0.41 (0.40), residues: 184 loop : 0.17 (0.27), residues: 543 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 203 HIS 0.002 0.001 HIS C 167 PHE 0.022 0.001 PHE A 538 TYR 0.010 0.001 TYR B 244 ARG 0.001 0.000 ARG D 50 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2712 Ramachandran restraints generated. 1356 Oldfield, 0 Emsley, 1356 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2712 Ramachandran restraints generated. 1356 Oldfield, 0 Emsley, 1356 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 64 residues out of total 1223 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 60 time to evaluate : 1.661 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 318 ARG cc_start: 0.8642 (ttp80) cc_final: 0.8326 (ttp80) REVERT: B 27 GLU cc_start: 0.7994 (OUTLIER) cc_final: 0.7647 (tt0) REVERT: C 186 LEU cc_start: 0.9054 (mt) cc_final: 0.8815 (mm) outliers start: 4 outliers final: 2 residues processed: 64 average time/residue: 3.2942 time to fit residues: 227.6856 Evaluate side-chains 63 residues out of total 1223 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 60 time to evaluate : 1.910 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 397 ILE Chi-restraints excluded: chain B residue 27 GLU Chi-restraints excluded: chain B residue 140 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 122 optimal weight: 3.9990 chunk 125 optimal weight: 0.9980 chunk 73 optimal weight: 0.7980 chunk 53 optimal weight: 2.9990 chunk 95 optimal weight: 0.0670 chunk 37 optimal weight: 0.9990 chunk 110 optimal weight: 1.9990 chunk 115 optimal weight: 2.9990 chunk 121 optimal weight: 0.8980 chunk 80 optimal weight: 1.9990 chunk 129 optimal weight: 0.9990 overall best weight: 0.7520 ------------------------------------------------------------------------------- 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: 0.8718 moved from start: 0.2238 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 11217 Z= 0.153 Angle : 0.443 4.990 15190 Z= 0.231 Chirality : 0.038 0.134 1708 Planarity : 0.003 0.031 1965 Dihedral : 4.321 76.480 1495 Min Nonbonded Distance : 1.982 Molprobity Statistics. All-atom Clashscore : 4.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.06 % Favored : 97.94 % Rotamer: Outliers : 0.41 % Allowed : 7.60 % Favored : 91.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.17 % 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: 1.27 (0.24), residues: 1356 helix: 1.60 (0.22), residues: 629 sheet: 0.49 (0.40), residues: 184 loop : 0.19 (0.27), residues: 543 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 203 HIS 0.002 0.001 HIS C 241 PHE 0.020 0.001 PHE A 538 TYR 0.009 0.001 TYR B 244 ARG 0.001 0.000 ARG B 142 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2712 Ramachandran restraints generated. 1356 Oldfield, 0 Emsley, 1356 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2712 Ramachandran restraints generated. 1356 Oldfield, 0 Emsley, 1356 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 71 residues out of total 1223 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 66 time to evaluate : 1.886 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 318 ARG cc_start: 0.8646 (ttp80) cc_final: 0.8323 (ttp80) REVERT: C 186 LEU cc_start: 0.9045 (mt) cc_final: 0.8832 (mm) outliers start: 5 outliers final: 3 residues processed: 70 average time/residue: 3.0948 time to fit residues: 233.5649 Evaluate side-chains 65 residues out of total 1223 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 62 time to evaluate : 1.986 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 GLU Chi-restraints excluded: chain A residue 397 ILE Chi-restraints excluded: chain B residue 140 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 78 optimal weight: 1.9990 chunk 61 optimal weight: 2.9990 chunk 89 optimal weight: 0.8980 chunk 135 optimal weight: 2.9990 chunk 124 optimal weight: 0.6980 chunk 107 optimal weight: 0.6980 chunk 11 optimal weight: 3.9990 chunk 83 optimal weight: 3.9990 chunk 66 optimal weight: 0.9990 chunk 85 optimal weight: 1.9990 chunk 114 optimal weight: 1.9990 overall best weight: 1.0584 ------------------------------------------------------------------------------- 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: 0.8727 moved from start: 0.2271 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 11217 Z= 0.193 Angle : 0.454 5.916 15190 Z= 0.237 Chirality : 0.038 0.135 1708 Planarity : 0.003 0.031 1965 Dihedral : 4.371 79.137 1495 Min Nonbonded Distance : 1.977 Molprobity Statistics. All-atom Clashscore : 4.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.99 % Favored : 98.01 % Rotamer: Outliers : 0.33 % Allowed : 7.77 % Favored : 91.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.17 % 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: 1.23 (0.24), residues: 1356 helix: 1.59 (0.22), residues: 629 sheet: 0.36 (0.40), residues: 186 loop : 0.19 (0.27), residues: 541 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 203 HIS 0.002 0.001 HIS C 167 PHE 0.022 0.001 PHE A 538 TYR 0.010 0.001 TYR B 244 ARG 0.001 0.000 ARG A 418 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2712 Ramachandran restraints generated. 1356 Oldfield, 0 Emsley, 1356 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2712 Ramachandran restraints generated. 1356 Oldfield, 0 Emsley, 1356 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 66 residues out of total 1223 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 62 time to evaluate : 1.763 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 318 ARG cc_start: 0.8642 (ttp80) cc_final: 0.8323 (ttp80) REVERT: C 186 LEU cc_start: 0.9048 (mt) cc_final: 0.8822 (mm) outliers start: 4 outliers final: 3 residues processed: 66 average time/residue: 3.1122 time to fit residues: 221.3502 Evaluate side-chains 63 residues out of total 1223 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 60 time to evaluate : 1.770 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 GLU Chi-restraints excluded: chain A residue 397 ILE Chi-restraints excluded: chain B residue 140 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 33 optimal weight: 0.5980 chunk 99 optimal weight: 1.9990 chunk 15 optimal weight: 0.6980 chunk 29 optimal weight: 0.9980 chunk 108 optimal weight: 2.9990 chunk 45 optimal weight: 2.9990 chunk 110 optimal weight: 1.9990 chunk 13 optimal weight: 2.9990 chunk 19 optimal weight: 1.9990 chunk 94 optimal weight: 3.9990 chunk 6 optimal weight: 3.9990 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3292 r_free = 0.3292 target = 0.075280 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2949 r_free = 0.2949 target = 0.058709 restraints weight = 73344.537| |-----------------------------------------------------------------------------| r_work (start): 0.2928 rms_B_bonded: 2.35 r_work: 0.2809 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.2682 rms_B_bonded: 4.20 restraints_weight: 0.2500 r_work (final): 0.2682 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8825 moved from start: 0.2293 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 11217 Z= 0.218 Angle : 0.468 7.392 15190 Z= 0.243 Chirality : 0.038 0.134 1708 Planarity : 0.004 0.068 1965 Dihedral : 4.441 82.171 1495 Min Nonbonded Distance : 1.975 Molprobity Statistics. All-atom Clashscore : 4.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 0.49 % Allowed : 7.69 % Favored : 91.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.20 (0.24), residues: 1356 helix: 1.57 (0.22), residues: 629 sheet: 0.32 (0.40), residues: 186 loop : 0.17 (0.27), residues: 541 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 203 HIS 0.003 0.001 HIS B 421 PHE 0.022 0.001 PHE A 538 TYR 0.010 0.001 TYR B 244 ARG 0.012 0.000 ARG B 264 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6857.51 seconds wall clock time: 120 minutes 29.85 seconds (7229.85 seconds total)