Starting phenix.real_space_refine on Mon Jul 28 19:36:31 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9mip_48300/07_2025/9mip_48300.cif Found real_map, /net/cci-nas-00/data/ceres_data/9mip_48300/07_2025/9mip_48300.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9mip_48300/07_2025/9mip_48300.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9mip_48300/07_2025/9mip_48300.map" model { file = "/net/cci-nas-00/data/ceres_data/9mip_48300/07_2025/9mip_48300.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9mip_48300/07_2025/9mip_48300.cif" } resolution = 3.4 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= 0.017 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians Mn 2 7.51 5 S 58 5.16 5 C 6766 2.51 5 N 1763 2.21 5 O 1960 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 37 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib" Total number of atoms: 10549 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 4543 Number of conformers: 1 Conformer: "" Number of residues, atoms: 583, 4543 Classifications: {'peptide': 583} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 26, 'TRANS': 556} Chain: "B" Number of atoms: 3573 Number of conformers: 1 Conformer: "" Number of residues, atoms: 429, 3573 Classifications: {'peptide': 429} Link IDs: {'PTRANS': 27, 'TRANS': 401} Chain: "C" Number of atoms: 2431 Number of conformers: 1 Conformer: "" Number of residues, atoms: 300, 2431 Classifications: {'peptide': 300} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 12, 'TRANS': 287} Chain breaks: 1 Chain: "C" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 6.20, per 1000 atoms: 0.59 Number of scatterers: 10549 At special positions: 0 Unit cell: (109.824, 116.16, 115.104, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Mn 2 24.99 S 58 16.00 O 1960 8.00 N 1763 7.00 C 6766 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.50 Conformation dependent library (CDL) restraints added in 1.1 seconds 2608 Ramachandran restraints generated. 1304 Oldfield, 0 Emsley, 1304 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2528 Finding SS restraints... Secondary structure from input PDB file: 74 helices and 2 sheets defined 75.7% alpha, 2.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.99 Creating SS restraints... Processing helix chain 'A' and resid 9 through 22 removed outlier: 3.511A pdb=" N ILE A 13 " --> pdb=" O SER A 9 " (cutoff:3.500A) Processing helix chain 'A' and resid 24 through 34 removed outlier: 3.586A pdb=" N ARG A 28 " --> pdb=" O ASP A 24 " (cutoff:3.500A) Processing helix chain 'A' and resid 34 through 59 removed outlier: 3.880A pdb=" N ILE A 38 " --> pdb=" O LYS A 34 " (cutoff:3.500A) removed outlier: 6.031A pdb=" N VAL A 44 " --> pdb=" O LEU A 40 " (cutoff:3.500A) removed outlier: 7.811A pdb=" N GLU A 45 " --> pdb=" O ALA A 41 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N ARG A 46 " --> pdb=" O LEU A 42 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N ARG A 48 " --> pdb=" O VAL A 44 " (cutoff:3.500A) removed outlier: 4.212A pdb=" N SER A 49 " --> pdb=" O GLU A 45 " (cutoff:3.500A) Proline residue: A 53 - end of helix Processing helix chain 'A' and resid 62 through 75 Processing helix chain 'A' and resid 82 through 87 removed outlier: 4.345A pdb=" N HIS A 87 " --> pdb=" O PRO A 83 " (cutoff:3.500A) Processing helix chain 'A' and resid 89 through 98 Processing helix chain 'A' and resid 101 through 117 removed outlier: 4.051A pdb=" N HIS A 117 " --> pdb=" O ARG A 113 " (cutoff:3.500A) Processing helix chain 'A' and resid 120 through 127 Processing helix chain 'A' and resid 127 through 137 Processing helix chain 'A' and resid 140 through 149 removed outlier: 3.924A pdb=" N GLY A 149 " --> pdb=" O THR A 145 " (cutoff:3.500A) Processing helix chain 'A' and resid 150 through 155 removed outlier: 3.742A pdb=" N CYS A 154 " --> pdb=" O LEU A 150 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N TYR A 155 " --> pdb=" O PHE A 151 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 150 through 155' Processing helix chain 'A' and resid 156 through 158 No H-bonds generated for 'chain 'A' and resid 156 through 158' Processing helix chain 'A' and resid 159 through 175 Processing helix chain 'A' and resid 178 through 196 removed outlier: 4.421A pdb=" N GLY A 190 " --> pdb=" O ALA A 186 " (cutoff:3.500A) removed outlier: 4.869A pdb=" N GLU A 191 " --> pdb=" O SER A 187 " (cutoff:3.500A) Processing helix chain 'A' and resid 197 through 214 removed outlier: 4.637A pdb=" N ILE A 206 " --> pdb=" O LYS A 202 " (cutoff:3.500A) Proline residue: A 207 - end of helix Processing helix chain 'A' and resid 217 through 235 removed outlier: 4.497A pdb=" N VAL A 229 " --> pdb=" O VAL A 225 " (cutoff:3.500A) removed outlier: 5.157A pdb=" N ASN A 230 " --> pdb=" O GLU A 226 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N ILE A 231 " --> pdb=" O ALA A 227 " (cutoff:3.500A) Processing helix chain 'A' and resid 236 through 244 removed outlier: 3.912A pdb=" N GLU A 241 " --> pdb=" O GLN A 237 " (cutoff:3.500A) removed outlier: 4.814A pdb=" N ALA A 242 " --> pdb=" O GLU A 238 " (cutoff:3.500A) Processing helix chain 'A' and resid 244 through 253 Processing helix chain 'A' and resid 256 through 266 Processing helix chain 'A' and resid 266 through 275 Processing helix chain 'A' and resid 275 through 292 removed outlier: 3.637A pdb=" N VAL A 284 " --> pdb=" O LYS A 280 " (cutoff:3.500A) Proline residue: A 285 - end of helix Processing helix chain 'A' and resid 295 through 312 removed outlier: 3.541A pdb=" N ARG A 299 " --> pdb=" O GLU A 295 " (cutoff:3.500A) removed outlier: 4.639A pdb=" N LYS A 307 " --> pdb=" O SER A 303 " (cutoff:3.500A) removed outlier: 4.916A pdb=" N GLU A 308 " --> pdb=" O HIS A 304 " (cutoff:3.500A) Processing helix chain 'A' and resid 317 through 335 removed outlier: 4.605A pdb=" N LEU A 327 " --> pdb=" O MET A 323 " (cutoff:3.500A) Proline residue: A 328 - end of helix removed outlier: 3.996A pdb=" N SER A 335 " --> pdb=" O LYS A 331 " (cutoff:3.500A) Processing helix chain 'A' and resid 338 through 350 removed outlier: 3.596A pdb=" N LYS A 342 " --> pdb=" O ASN A 338 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N MET A 350 " --> pdb=" O ALA A 346 " (cutoff:3.500A) Processing helix chain 'A' and resid 351 through 356 removed outlier: 4.649A pdb=" N ILE A 355 " --> pdb=" O GLY A 351 " (cutoff:3.500A) Processing helix chain 'A' and resid 357 through 375 removed outlier: 3.894A pdb=" N ILE A 362 " --> pdb=" O LYS A 358 " (cutoff:3.500A) removed outlier: 4.454A pdb=" N LEU A 366 " --> pdb=" O ILE A 362 " (cutoff:3.500A) Proline residue: A 367 - end of helix Processing helix chain 'A' and resid 377 through 387 removed outlier: 4.013A pdb=" N ARG A 381 " --> pdb=" O CYS A 377 " (cutoff:3.500A) Processing helix chain 'A' and resid 390 through 395 removed outlier: 4.178A pdb=" N VAL A 394 " --> pdb=" O CYS A 390 " (cutoff:3.500A) Processing helix chain 'A' and resid 396 through 412 Proline residue: A 406 - end of helix Processing helix chain 'A' and resid 416 through 435 Proline residue: A 428 - end of helix Processing helix chain 'A' and resid 435 through 443 Processing helix chain 'A' and resid 443 through 452 Processing helix chain 'A' and resid 455 through 474 removed outlier: 4.144A pdb=" N LYS A 472 " --> pdb=" O LYS A 468 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N GLY A 474 " --> pdb=" O VAL A 470 " (cutoff:3.500A) Processing helix chain 'A' and resid 474 through 482 removed outlier: 3.639A pdb=" N ALA A 478 " --> pdb=" O GLY A 474 " (cutoff:3.500A) Processing helix chain 'A' and resid 482 through 489 removed outlier: 3.591A pdb=" N ALA A 488 " --> pdb=" O PRO A 484 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N MET A 489 " --> pdb=" O LYS A 485 " (cutoff:3.500A) Processing helix chain 'A' and resid 490 through 492 No H-bonds generated for 'chain 'A' and resid 490 through 492' Processing helix chain 'A' and resid 494 through 529 removed outlier: 4.262A pdb=" N GLU A 510 " --> pdb=" O ASN A 506 " (cutoff:3.500A) removed outlier: 4.664A pdb=" N VAL A 511 " --> pdb=" O VAL A 507 " (cutoff:3.500A) removed outlier: 6.237A pdb=" N GLN A 514 " --> pdb=" O GLU A 510 " (cutoff:3.500A) removed outlier: 8.766A pdb=" N ASP A 515 " --> pdb=" O VAL A 511 " (cutoff:3.500A) removed outlier: 4.361A pdb=" N ILE A 516 " --> pdb=" O CYS A 512 " (cutoff:3.500A) removed outlier: 4.492A pdb=" N LEU A 522 " --> pdb=" O THR A 518 " (cutoff:3.500A) Proline residue: A 523 - end of helix Processing helix chain 'A' and resid 533 through 548 Processing helix chain 'A' and resid 552 through 559 Processing helix chain 'A' and resid 559 through 569 removed outlier: 3.657A pdb=" N ILE A 563 " --> pdb=" O GLU A 559 " (cutoff:3.500A) Processing helix chain 'A' and resid 572 through 587 Processing helix chain 'B' and resid 37 through 49 Processing helix chain 'B' and resid 62 through 80 Processing helix chain 'B' and resid 90 through 104 removed outlier: 4.344A pdb=" N GLU B 94 " --> pdb=" O PRO B 90 " (cutoff:3.500A) Processing helix chain 'B' and resid 130 through 147 Processing helix chain 'B' and resid 151 through 157 removed outlier: 4.086A pdb=" N LYS B 157 " --> pdb=" O ASN B 153 " (cutoff:3.500A) Processing helix chain 'B' and resid 160 through 170 Processing helix chain 'B' and resid 171 through 173 No H-bonds generated for 'chain 'B' and resid 171 through 173' Processing helix chain 'B' and resid 175 through 193 Processing helix chain 'B' and resid 196 through 214 Processing helix chain 'B' and resid 220 through 234 Processing helix chain 'B' and resid 240 through 250 Processing helix chain 'B' and resid 251 through 257 Processing helix chain 'B' and resid 259 through 278 removed outlier: 4.068A pdb=" N TYR B 263 " --> pdb=" O SER B 259 " (cutoff:3.500A) Proline residue: B 265 - end of helix Processing helix chain 'B' and resid 281 through 292 removed outlier: 3.552A pdb=" N VAL B 285 " --> pdb=" O LEU B 281 " (cutoff:3.500A) Processing helix chain 'B' and resid 297 through 315 removed outlier: 3.640A pdb=" N GLU B 301 " --> pdb=" O HIS B 297 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N VAL B 314 " --> pdb=" O GLU B 310 " (cutoff:3.500A) Processing helix chain 'B' and resid 316 through 336 removed outlier: 3.579A pdb=" N LYS B 322 " --> pdb=" O SER B 318 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N ILE B 323 " --> pdb=" O GLU B 319 " (cutoff:3.500A) removed outlier: 4.926A pdb=" N GLU B 325 " --> pdb=" O VAL B 321 " (cutoff:3.500A) Proline residue: B 326 - end of helix Processing helix chain 'B' and resid 339 through 348 Processing helix chain 'B' and resid 349 through 351 No H-bonds generated for 'chain 'B' and resid 349 through 351' Processing helix chain 'B' and resid 352 through 377 removed outlier: 6.386A pdb=" N ALA B 364 " --> pdb=" O SER B 360 " (cutoff:3.500A) removed outlier: 6.879A pdb=" N LYS B 365 " --> pdb=" O ASP B 361 " (cutoff:3.500A) Proline residue: B 368 - end of helix Proline residue: B 372 - end of helix Processing helix chain 'B' and resid 383 through 401 Processing helix chain 'B' and resid 401 through 435 removed outlier: 3.607A pdb=" N PHE B 405 " --> pdb=" O ASN B 401 " (cutoff:3.500A) removed outlier: 5.068A pdb=" N LYS B 420 " --> pdb=" O LYS B 416 " (cutoff:3.500A) removed outlier: 4.368A pdb=" N LEU B 421 " --> pdb=" O LEU B 417 " (cutoff:3.500A) Processing helix chain 'C' and resid 3 through 19 Processing helix chain 'C' and resid 24 through 40 Processing helix chain 'C' and resid 61 through 72 Processing helix chain 'C' and resid 92 through 106 Processing helix chain 'C' and resid 116 through 119 removed outlier: 3.602A pdb=" N GLU C 119 " --> pdb=" O GLY C 116 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 116 through 119' Processing helix chain 'C' and resid 120 through 127 Processing helix chain 'C' and resid 129 through 138 Processing helix chain 'C' and resid 140 through 152 Processing helix chain 'C' and resid 176 through 183 removed outlier: 3.682A pdb=" N ILE C 180 " --> pdb=" O THR C 176 " (cutoff:3.500A) Processing helix chain 'C' and resid 193 through 199 Processing helix chain 'C' and resid 221 through 233 Processing helix chain 'C' and resid 264 through 268 Processing sheet with id=AA1, first strand: chain 'C' and resid 47 through 48 removed outlier: 6.351A pdb=" N VAL C 237 " --> pdb=" O VAL C 257 " (cutoff:3.500A) removed outlier: 7.669A pdb=" N ILE C 259 " --> pdb=" O VAL C 237 " (cutoff:3.500A) removed outlier: 6.237A pdb=" N ARG C 239 " --> pdb=" O ILE C 259 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N THR C 258 " --> pdb=" O ASN C 249 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 111 through 114 removed outlier: 6.446A pdb=" N TYR C 80 " --> pdb=" O THR C 112 " (cutoff:3.500A) removed outlier: 7.990A pdb=" N LEU C 114 " --> pdb=" O TYR C 80 " (cutoff:3.500A) removed outlier: 7.207A pdb=" N PHE C 82 " --> pdb=" O LEU C 114 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N ALA C 273 " --> pdb=" O PHE C 289 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N PHE C 289 " --> pdb=" O ALA C 273 " (cutoff:3.500A) 624 hydrogen bonds defined for protein. 1851 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.89 Time building geometry restraints manager: 2.97 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 2050 1.33 - 1.45: 2475 1.45 - 1.57: 6167 1.57 - 1.69: 0 1.69 - 1.82: 87 Bond restraints: 10779 Sorted by residual: bond pdb=" N LEU A 52 " pdb=" CA LEU A 52 " ideal model delta sigma weight residual 1.462 1.492 -0.030 7.70e-03 1.69e+04 1.50e+01 bond pdb=" N ASN B 440 " pdb=" CA ASN B 440 " ideal model delta sigma weight residual 1.463 1.489 -0.026 6.90e-03 2.10e+04 1.39e+01 bond pdb=" C GLU A 379 " pdb=" N VAL A 380 " ideal model delta sigma weight residual 1.334 1.290 0.044 1.25e-02 6.40e+03 1.24e+01 bond pdb=" N VAL C 256 " pdb=" CA VAL C 256 " ideal model delta sigma weight residual 1.456 1.496 -0.039 1.14e-02 7.69e+03 1.18e+01 bond pdb=" C LEU A 382 " pdb=" N ASN A 383 " ideal model delta sigma weight residual 1.334 1.291 0.043 1.27e-02 6.20e+03 1.17e+01 ... (remaining 10774 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.42: 11585 1.42 - 2.85: 2525 2.85 - 4.27: 469 4.27 - 5.70: 38 5.70 - 7.12: 6 Bond angle restraints: 14623 Sorted by residual: angle pdb=" CA GLY A 43 " pdb=" C GLY A 43 " pdb=" O GLY A 43 " ideal model delta sigma weight residual 122.29 117.92 4.37 8.10e-01 1.52e+00 2.91e+01 angle pdb=" C ILE C 113 " pdb=" N LEU C 114 " pdb=" CA LEU C 114 " ideal model delta sigma weight residual 122.81 116.82 5.99 1.57e+00 4.06e-01 1.46e+01 angle pdb=" CA LEU B 107 " pdb=" C LEU B 107 " pdb=" N PRO B 108 " ideal model delta sigma weight residual 118.23 121.73 -3.50 9.20e-01 1.18e+00 1.45e+01 angle pdb=" N PRO A 156 " pdb=" CA PRO A 156 " pdb=" C PRO A 156 " ideal model delta sigma weight residual 113.84 118.71 -4.87 1.30e+00 5.92e-01 1.40e+01 angle pdb=" CA GLU A 379 " pdb=" C GLU A 379 " pdb=" N VAL A 380 " ideal model delta sigma weight residual 117.07 121.34 -4.27 1.14e+00 7.69e-01 1.40e+01 ... (remaining 14618 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.22: 5808 16.22 - 32.44: 569 32.44 - 48.66: 147 48.66 - 64.88: 32 64.88 - 81.10: 8 Dihedral angle restraints: 6564 sinusoidal: 2684 harmonic: 3880 Sorted by residual: dihedral pdb=" C PHE A 578 " pdb=" N PHE A 578 " pdb=" CA PHE A 578 " pdb=" CB PHE A 578 " ideal model delta harmonic sigma weight residual -122.60 -131.63 9.03 0 2.50e+00 1.60e-01 1.31e+01 dihedral pdb=" C THR A 281 " pdb=" N THR A 281 " pdb=" CA THR A 281 " pdb=" CB THR A 281 " ideal model delta harmonic sigma weight residual -122.00 -130.66 8.66 0 2.50e+00 1.60e-01 1.20e+01 dihedral pdb=" C PHE B 104 " pdb=" N PHE B 104 " pdb=" CA PHE B 104 " pdb=" CB PHE B 104 " ideal model delta harmonic sigma weight residual -122.60 -130.60 8.00 0 2.50e+00 1.60e-01 1.02e+01 ... (remaining 6561 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.053: 963 0.053 - 0.106: 375 0.106 - 0.159: 209 0.159 - 0.212: 97 0.212 - 0.264: 15 Chirality restraints: 1659 Sorted by residual: chirality pdb=" CA GLN C 61 " pdb=" N GLN C 61 " pdb=" C GLN C 61 " pdb=" CB GLN C 61 " both_signs ideal model delta sigma weight residual False 2.51 2.77 -0.26 2.00e-01 2.50e+01 1.75e+00 chirality pdb=" CA GLU B 316 " pdb=" N GLU B 316 " pdb=" C GLU B 316 " pdb=" CB GLU B 316 " both_signs ideal model delta sigma weight residual False 2.51 2.76 -0.25 2.00e-01 2.50e+01 1.53e+00 chirality pdb=" CA THR A 281 " pdb=" N THR A 281 " pdb=" C THR A 281 " pdb=" CB THR A 281 " both_signs ideal model delta sigma weight residual False 2.53 2.28 0.24 2.00e-01 2.50e+01 1.49e+00 ... (remaining 1656 not shown) Planarity restraints: 1877 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ILE C 163 " 0.017 2.00e-02 2.50e+03 3.56e-02 1.27e+01 pdb=" C ILE C 163 " -0.062 2.00e-02 2.50e+03 pdb=" O ILE C 163 " 0.023 2.00e-02 2.50e+03 pdb=" N PHE C 164 " 0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLY C 208 " 0.014 2.00e-02 2.50e+03 2.78e-02 7.72e+00 pdb=" C GLY C 208 " -0.048 2.00e-02 2.50e+03 pdb=" O GLY C 208 " 0.018 2.00e-02 2.50e+03 pdb=" N TRP C 209 " 0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU A 356 " -0.013 2.00e-02 2.50e+03 2.69e-02 7.26e+00 pdb=" C LEU A 356 " 0.047 2.00e-02 2.50e+03 pdb=" O LEU A 356 " -0.017 2.00e-02 2.50e+03 pdb=" N GLY A 357 " -0.016 2.00e-02 2.50e+03 ... (remaining 1874 not shown) Histogram of nonbonded interaction distances: 1.85 - 2.46: 12 2.46 - 3.07: 7209 3.07 - 3.68: 16868 3.68 - 4.29: 24223 4.29 - 4.90: 39602 Nonbonded interactions: 87914 Sorted by model distance: nonbonded pdb=" OD1 ASN C 117 " pdb="MN MN C 401 " model vdw 1.847 2.320 nonbonded pdb=" OD2 ASP C 85 " pdb="MN MN C 401 " model vdw 2.070 2.320 nonbonded pdb=" ND1 HIS C 241 " pdb="MN MN C 401 " model vdw 2.252 2.400 nonbonded pdb=" OG SER A 152 " pdb=" OE2 GLU A 191 " model vdw 2.253 3.040 nonbonded pdb=" O LEU B 305 " pdb=" OH TYR B 349 " model vdw 2.348 3.040 ... (remaining 87909 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== 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: 0.930 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.400 Check model and map are aligned: 0.070 Set scattering table: 0.090 Process input model: 24.740 Find NCS groups from input model: 0.080 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.490 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.850 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8335 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 : 0.010 0.047 10779 Z= 0.750 Angle : 1.190 7.122 14623 Z= 0.927 Chirality : 0.079 0.264 1659 Planarity : 0.005 0.059 1877 Dihedral : 14.147 81.099 4036 Min Nonbonded Distance : 1.847 Molprobity Statistics. All-atom Clashscore : 4.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Rotamer: Outliers : 0.00 % Allowed : 13.37 % Favored : 86.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.60 (0.24), residues: 1304 helix: 0.86 (0.18), residues: 893 sheet: -0.72 (0.78), residues: 41 loop : -0.38 (0.33), residues: 370 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP A 450 HIS 0.005 0.001 HIS C 241 PHE 0.029 0.001 PHE A 54 TYR 0.017 0.001 TYR A 261 ARG 0.005 0.000 ARG A 183 Details of bonding type rmsd hydrogen bonds : bond 0.18801 ( 624) hydrogen bonds : angle 6.14429 ( 1851) covalent geometry : bond 0.00974 (10779) covalent geometry : angle 1.19049 (14623) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2608 Ramachandran restraints generated. 1304 Oldfield, 0 Emsley, 1304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2608 Ramachandran restraints generated. 1304 Oldfield, 0 Emsley, 1304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 1174 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 159 time to evaluate : 1.147 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: A 76 PHE cc_start: 0.7516 (m-10) cc_final: 0.7246 (m-80) REVERT: A 106 ASP cc_start: 0.9325 (m-30) cc_final: 0.9065 (m-30) REVERT: A 245 MET cc_start: 0.9087 (mmp) cc_final: 0.8619 (mmp) REVERT: A 323 MET cc_start: 0.9202 (mtm) cc_final: 0.8926 (mmm) REVERT: A 356 LEU cc_start: 0.9494 (mt) cc_final: 0.9138 (mt) REVERT: A 379 GLU cc_start: 0.8899 (mp0) cc_final: 0.8518 (mp0) REVERT: B 65 TRP cc_start: 0.8147 (m-10) cc_final: 0.7933 (m-10) REVERT: B 356 MET cc_start: 0.8772 (mmm) cc_final: 0.8330 (mmm) REVERT: B 391 TYR cc_start: 0.7420 (m-10) cc_final: 0.7080 (m-80) REVERT: B 398 MET cc_start: 0.9241 (ptm) cc_final: 0.9012 (ppp) REVERT: B 399 GLU cc_start: 0.9599 (tt0) cc_final: 0.9157 (mt-10) REVERT: B 423 MET cc_start: 0.9438 (mmt) cc_final: 0.9213 (ptt) REVERT: C 195 MET cc_start: 0.8763 (mtm) cc_final: 0.8435 (ttm) REVERT: C 196 CYS cc_start: 0.8131 (t) cc_final: 0.7625 (t) REVERT: C 275 ILE cc_start: 0.8552 (mt) cc_final: 0.8198 (mm) REVERT: C 277 GLU cc_start: 0.9086 (mm-30) cc_final: 0.8556 (mm-30) REVERT: C 284 TYR cc_start: 0.8697 (p90) cc_final: 0.8237 (p90) outliers start: 0 outliers final: 0 residues processed: 159 average time/residue: 0.2287 time to fit residues: 51.1419 Evaluate side-chains 102 residues out of total 1174 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 102 time to evaluate : 1.139 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 109 optimal weight: 0.9990 chunk 98 optimal weight: 20.0000 chunk 54 optimal weight: 4.9990 chunk 33 optimal weight: 1.9990 chunk 66 optimal weight: 0.7980 chunk 52 optimal weight: 0.8980 chunk 101 optimal weight: 1.9990 chunk 39 optimal weight: 2.9990 chunk 61 optimal weight: 6.9990 chunk 75 optimal weight: 0.9980 chunk 118 optimal weight: 4.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 360 ASN B 297 HIS B 442 GLN C 59 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3547 r_free = 0.3547 target = 0.069020 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3136 r_free = 0.3136 target = 0.052290 restraints weight = 48444.029| |-----------------------------------------------------------------------------| r_work (start): 0.3113 rms_B_bonded: 5.17 r_work (final): 0.3113 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8445 moved from start: 0.1820 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 10779 Z= 0.138 Angle : 0.603 8.054 14623 Z= 0.303 Chirality : 0.041 0.149 1659 Planarity : 0.004 0.043 1877 Dihedral : 3.969 32.730 1415 Min Nonbonded Distance : 2.028 Molprobity Statistics. All-atom Clashscore : 8.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.46 % Favored : 98.54 % Rotamer: Outliers : 1.70 % Allowed : 14.65 % Favored : 83.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.69 (0.24), residues: 1304 helix: 1.66 (0.18), residues: 899 sheet: -0.94 (0.72), residues: 48 loop : 0.18 (0.33), residues: 357 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 450 HIS 0.005 0.001 HIS B 297 PHE 0.023 0.001 PHE A 54 TYR 0.018 0.001 TYR A 456 ARG 0.005 0.000 ARG A 398 Details of bonding type rmsd hydrogen bonds : bond 0.04465 ( 624) hydrogen bonds : angle 4.52788 ( 1851) covalent geometry : bond 0.00301 (10779) covalent geometry : angle 0.60288 (14623) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2608 Ramachandran restraints generated. 1304 Oldfield, 0 Emsley, 1304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2608 Ramachandran restraints generated. 1304 Oldfield, 0 Emsley, 1304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 1174 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 106 time to evaluate : 1.162 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 356 LEU cc_start: 0.9462 (mt) cc_final: 0.9202 (tp) REVERT: A 424 ILE cc_start: 0.9589 (mt) cc_final: 0.9276 (tt) REVERT: A 427 MET cc_start: 0.9421 (tpt) cc_final: 0.8942 (tpp) REVERT: A 521 MET cc_start: 0.8123 (ptt) cc_final: 0.7907 (ptt) REVERT: B 65 TRP cc_start: 0.8381 (m-10) cc_final: 0.8127 (m-10) REVERT: B 76 MET cc_start: 0.9399 (mmm) cc_final: 0.9175 (mpp) REVERT: B 94 GLU cc_start: 0.8964 (mp0) cc_final: 0.8569 (mp0) REVERT: B 103 MET cc_start: 0.8950 (mmt) cc_final: 0.8714 (mmt) REVERT: B 105 ARG cc_start: 0.8238 (pmt-80) cc_final: 0.7864 (pmt-80) REVERT: B 356 MET cc_start: 0.8714 (mmm) cc_final: 0.8251 (mmm) REVERT: B 391 TYR cc_start: 0.7450 (m-10) cc_final: 0.6972 (m-80) REVERT: B 398 MET cc_start: 0.9355 (ptm) cc_final: 0.9017 (tmm) REVERT: B 399 GLU cc_start: 0.9652 (tt0) cc_final: 0.9328 (pt0) REVERT: C 87 VAL cc_start: 0.8830 (m) cc_final: 0.8277 (p) REVERT: C 165 CYS cc_start: 0.8485 (OUTLIER) cc_final: 0.7578 (t) REVERT: C 195 MET cc_start: 0.8783 (mtm) cc_final: 0.8534 (ttm) REVERT: C 196 CYS cc_start: 0.8056 (t) cc_final: 0.7749 (t) REVERT: C 277 GLU cc_start: 0.9118 (mm-30) cc_final: 0.8643 (mm-30) outliers start: 20 outliers final: 8 residues processed: 119 average time/residue: 0.2414 time to fit residues: 40.9842 Evaluate side-chains 96 residues out of total 1174 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 87 time to evaluate : 1.150 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 LEU Chi-restraints excluded: chain A residue 60 TYR Chi-restraints excluded: chain A residue 150 LEU Chi-restraints excluded: chain B residue 31 ARG Chi-restraints excluded: chain B residue 217 HIS Chi-restraints excluded: chain C residue 113 ILE Chi-restraints excluded: chain C residue 120 SER Chi-restraints excluded: chain C residue 135 ARG Chi-restraints excluded: chain C residue 165 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 112 optimal weight: 4.9990 chunk 70 optimal weight: 5.9990 chunk 33 optimal weight: 5.9990 chunk 62 optimal weight: 0.0170 chunk 45 optimal weight: 4.9990 chunk 80 optimal weight: 0.9990 chunk 129 optimal weight: 0.0770 chunk 85 optimal weight: 6.9990 chunk 53 optimal weight: 1.9990 chunk 72 optimal weight: 0.7980 chunk 71 optimal weight: 5.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 288 GLN B 203 GLN C 59 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3552 r_free = 0.3552 target = 0.069015 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3146 r_free = 0.3146 target = 0.052430 restraints weight = 49152.995| |-----------------------------------------------------------------------------| r_work (start): 0.3106 rms_B_bonded: 5.25 r_work (final): 0.3106 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8477 moved from start: 0.2240 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 10779 Z= 0.116 Angle : 0.582 10.233 14623 Z= 0.285 Chirality : 0.040 0.137 1659 Planarity : 0.004 0.040 1877 Dihedral : 3.876 27.273 1415 Min Nonbonded Distance : 2.072 Molprobity Statistics. All-atom Clashscore : 7.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.61 % Favored : 98.39 % Rotamer: Outliers : 2.21 % Allowed : 14.65 % Favored : 83.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.90 (0.24), residues: 1304 helix: 1.80 (0.18), residues: 906 sheet: -0.79 (0.65), residues: 58 loop : 0.33 (0.34), residues: 340 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 131 HIS 0.003 0.001 HIS A 520 PHE 0.027 0.001 PHE A 54 TYR 0.016 0.001 TYR A 261 ARG 0.005 0.000 ARG A 398 Details of bonding type rmsd hydrogen bonds : bond 0.03700 ( 624) hydrogen bonds : angle 4.18524 ( 1851) covalent geometry : bond 0.00248 (10779) covalent geometry : angle 0.58233 (14623) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2608 Ramachandran restraints generated. 1304 Oldfield, 0 Emsley, 1304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2608 Ramachandran restraints generated. 1304 Oldfield, 0 Emsley, 1304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 1174 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 100 time to evaluate : 1.165 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 269 GLU cc_start: 0.9124 (mp0) cc_final: 0.8723 (mp0) REVERT: A 356 LEU cc_start: 0.9408 (mt) cc_final: 0.9136 (tp) REVERT: A 427 MET cc_start: 0.9407 (tpt) cc_final: 0.8984 (tpp) REVERT: B 65 TRP cc_start: 0.8325 (m-10) cc_final: 0.7875 (m-10) REVERT: B 76 MET cc_start: 0.9341 (mmm) cc_final: 0.9070 (mmm) REVERT: B 94 GLU cc_start: 0.8936 (mp0) cc_final: 0.8500 (mp0) REVERT: B 105 ARG cc_start: 0.8396 (pmt-80) cc_final: 0.8192 (pmt-80) REVERT: B 274 PHE cc_start: 0.8888 (OUTLIER) cc_final: 0.8023 (t80) REVERT: B 356 MET cc_start: 0.8655 (mmm) cc_final: 0.8212 (mmm) REVERT: B 398 MET cc_start: 0.9313 (ptm) cc_final: 0.9077 (tmm) REVERT: B 399 GLU cc_start: 0.9601 (tt0) cc_final: 0.9384 (pt0) REVERT: C 83 MET cc_start: 0.6348 (ptt) cc_final: 0.5816 (ptt) REVERT: C 85 ASP cc_start: 0.8258 (OUTLIER) cc_final: 0.7808 (m-30) REVERT: C 87 VAL cc_start: 0.8880 (m) cc_final: 0.8426 (p) REVERT: C 195 MET cc_start: 0.8826 (mtm) cc_final: 0.8570 (ttm) REVERT: C 196 CYS cc_start: 0.8107 (t) cc_final: 0.7801 (t) REVERT: C 277 GLU cc_start: 0.8983 (mm-30) cc_final: 0.8714 (mm-30) outliers start: 26 outliers final: 10 residues processed: 118 average time/residue: 0.2127 time to fit residues: 36.8909 Evaluate side-chains 103 residues out of total 1174 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 91 time to evaluate : 1.264 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 TYR Chi-restraints excluded: chain A residue 75 THR Chi-restraints excluded: chain A residue 150 LEU Chi-restraints excluded: chain A residue 404 LEU Chi-restraints excluded: chain A residue 465 ASN Chi-restraints excluded: chain A residue 507 VAL Chi-restraints excluded: chain B residue 31 ARG Chi-restraints excluded: chain B residue 274 PHE Chi-restraints excluded: chain B residue 375 TYR Chi-restraints excluded: chain C residue 85 ASP Chi-restraints excluded: chain C residue 120 SER Chi-restraints excluded: chain C residue 135 ARG Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 36 optimal weight: 7.9990 chunk 96 optimal weight: 10.0000 chunk 53 optimal weight: 4.9990 chunk 89 optimal weight: 5.9990 chunk 37 optimal weight: 0.9990 chunk 122 optimal weight: 5.9990 chunk 72 optimal weight: 0.9980 chunk 31 optimal weight: 5.9990 chunk 2 optimal weight: 10.0000 chunk 113 optimal weight: 2.9990 chunk 22 optimal weight: 4.9990 overall best weight: 2.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 237 GLN A 360 ASN B 151 GLN ** C 59 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3420 r_free = 0.3420 target = 0.064094 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2969 r_free = 0.2969 target = 0.047013 restraints weight = 49524.362| |-----------------------------------------------------------------------------| r_work (start): 0.2951 rms_B_bonded: 5.06 r_work (final): 0.2951 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8608 moved from start: 0.2968 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.060 10779 Z= 0.248 Angle : 0.682 8.672 14623 Z= 0.341 Chirality : 0.043 0.156 1659 Planarity : 0.004 0.039 1877 Dihedral : 4.248 23.046 1415 Min Nonbonded Distance : 1.901 Molprobity Statistics. All-atom Clashscore : 10.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.99 % Favored : 98.01 % Rotamer: Outliers : 3.41 % Allowed : 14.74 % Favored : 81.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1304 helix: 1.69 (0.18), residues: 903 sheet: -1.03 (0.63), residues: 58 loop : 0.16 (0.34), residues: 343 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 250 HIS 0.007 0.002 HIS A 520 PHE 0.024 0.002 PHE A 76 TYR 0.023 0.002 TYR B 391 ARG 0.007 0.001 ARG A 398 Details of bonding type rmsd hydrogen bonds : bond 0.04364 ( 624) hydrogen bonds : angle 4.47892 ( 1851) covalent geometry : bond 0.00552 (10779) covalent geometry : angle 0.68188 (14623) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2608 Ramachandran restraints generated. 1304 Oldfield, 0 Emsley, 1304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2608 Ramachandran restraints generated. 1304 Oldfield, 0 Emsley, 1304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 1174 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 89 time to evaluate : 1.340 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 269 GLU cc_start: 0.9085 (mp0) cc_final: 0.8694 (mp0) REVERT: A 356 LEU cc_start: 0.9529 (mt) cc_final: 0.9147 (tp) REVERT: A 427 MET cc_start: 0.9400 (tpt) cc_final: 0.9003 (tpp) REVERT: B 65 TRP cc_start: 0.8266 (m-10) cc_final: 0.7769 (m-10) REVERT: B 76 MET cc_start: 0.9425 (mmm) cc_final: 0.9158 (mmt) REVERT: B 94 GLU cc_start: 0.9033 (mp0) cc_final: 0.8677 (mp0) REVERT: B 303 MET cc_start: 0.9385 (mtm) cc_final: 0.9170 (mtm) REVERT: B 356 MET cc_start: 0.8743 (mmm) cc_final: 0.8272 (mmm) REVERT: B 398 MET cc_start: 0.9320 (ptm) cc_final: 0.9058 (tmm) REVERT: B 399 GLU cc_start: 0.9688 (tt0) cc_final: 0.9478 (pt0) REVERT: C 85 ASP cc_start: 0.8580 (OUTLIER) cc_final: 0.7982 (m-30) REVERT: C 87 VAL cc_start: 0.9223 (m) cc_final: 0.8769 (p) REVERT: C 191 HIS cc_start: 0.9118 (m-70) cc_final: 0.8857 (m-70) REVERT: C 196 CYS cc_start: 0.8123 (t) cc_final: 0.7860 (t) REVERT: C 277 GLU cc_start: 0.8910 (mm-30) cc_final: 0.8618 (mm-30) outliers start: 40 outliers final: 22 residues processed: 121 average time/residue: 0.2120 time to fit residues: 37.8078 Evaluate side-chains 102 residues out of total 1174 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 79 time to evaluate : 1.271 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 LEU Chi-restraints excluded: chain A residue 51 LEU Chi-restraints excluded: chain A residue 60 TYR Chi-restraints excluded: chain A residue 99 VAL Chi-restraints excluded: chain A residue 150 LEU Chi-restraints excluded: chain A residue 195 VAL Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 424 ILE Chi-restraints excluded: chain A residue 429 LEU Chi-restraints excluded: chain A residue 465 ASN Chi-restraints excluded: chain A residue 483 ILE Chi-restraints excluded: chain A residue 507 VAL Chi-restraints excluded: chain A residue 538 PHE Chi-restraints excluded: chain A residue 540 VAL Chi-restraints excluded: chain B residue 31 ARG Chi-restraints excluded: chain B residue 233 ASN Chi-restraints excluded: chain B residue 274 PHE Chi-restraints excluded: chain B residue 334 CYS Chi-restraints excluded: chain C residue 31 LEU Chi-restraints excluded: chain C residue 85 ASP Chi-restraints excluded: chain C residue 120 SER Chi-restraints excluded: chain C residue 256 VAL Chi-restraints excluded: chain C residue 266 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 71 optimal weight: 0.7980 chunk 4 optimal weight: 0.8980 chunk 61 optimal weight: 6.9990 chunk 14 optimal weight: 0.7980 chunk 126 optimal weight: 0.8980 chunk 52 optimal weight: 0.9990 chunk 32 optimal weight: 2.9990 chunk 116 optimal weight: 1.9990 chunk 53 optimal weight: 0.8980 chunk 57 optimal weight: 0.9990 chunk 97 optimal weight: 9.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 59 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3478 r_free = 0.3478 target = 0.066194 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3047 r_free = 0.3047 target = 0.049229 restraints weight = 49056.905| |-----------------------------------------------------------------------------| r_work (start): 0.3016 rms_B_bonded: 5.17 r_work (final): 0.3016 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8542 moved from start: 0.3067 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 10779 Z= 0.112 Angle : 0.600 11.817 14623 Z= 0.291 Chirality : 0.040 0.181 1659 Planarity : 0.004 0.039 1877 Dihedral : 4.044 18.078 1415 Min Nonbonded Distance : 2.074 Molprobity Statistics. All-atom Clashscore : 8.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.76 % Favored : 98.24 % Rotamer: Outliers : 1.70 % Allowed : 16.27 % Favored : 82.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.81 (0.24), residues: 1304 helix: 1.77 (0.18), residues: 905 sheet: -0.88 (0.64), residues: 58 loop : 0.21 (0.34), residues: 341 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 250 HIS 0.004 0.001 HIS A 364 PHE 0.020 0.001 PHE A 54 TYR 0.041 0.001 TYR B 391 ARG 0.007 0.000 ARG A 398 Details of bonding type rmsd hydrogen bonds : bond 0.03517 ( 624) hydrogen bonds : angle 4.16385 ( 1851) covalent geometry : bond 0.00246 (10779) covalent geometry : angle 0.59963 (14623) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2608 Ramachandran restraints generated. 1304 Oldfield, 0 Emsley, 1304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2608 Ramachandran restraints generated. 1304 Oldfield, 0 Emsley, 1304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 1174 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 88 time to evaluate : 1.179 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 269 GLU cc_start: 0.9079 (mp0) cc_final: 0.8691 (mp0) REVERT: A 427 MET cc_start: 0.9434 (tpt) cc_final: 0.9200 (tpp) REVERT: A 521 MET cc_start: 0.8003 (ptt) cc_final: 0.7478 (ptt) REVERT: B 65 TRP cc_start: 0.8178 (m-10) cc_final: 0.7681 (m-10) REVERT: B 76 MET cc_start: 0.9397 (mmm) cc_final: 0.9139 (mmt) REVERT: B 94 GLU cc_start: 0.8852 (mp0) cc_final: 0.8516 (mp0) REVERT: B 103 MET cc_start: 0.8620 (mmt) cc_final: 0.8332 (mtt) REVERT: B 274 PHE cc_start: 0.8992 (OUTLIER) cc_final: 0.8409 (t80) REVERT: B 356 MET cc_start: 0.8766 (mmm) cc_final: 0.8239 (mmm) REVERT: B 375 TYR cc_start: 0.8803 (OUTLIER) cc_final: 0.8254 (m-80) REVERT: B 398 MET cc_start: 0.9314 (ptm) cc_final: 0.8967 (tmm) REVERT: B 399 GLU cc_start: 0.9670 (tt0) cc_final: 0.9428 (pt0) REVERT: C 85 ASP cc_start: 0.8499 (OUTLIER) cc_final: 0.7961 (m-30) REVERT: C 87 VAL cc_start: 0.9171 (m) cc_final: 0.8766 (p) REVERT: C 191 HIS cc_start: 0.9130 (m-70) cc_final: 0.8877 (m-70) REVERT: C 196 CYS cc_start: 0.8167 (t) cc_final: 0.7791 (t) REVERT: C 277 GLU cc_start: 0.8880 (mm-30) cc_final: 0.8581 (mm-30) outliers start: 20 outliers final: 11 residues processed: 104 average time/residue: 0.2056 time to fit residues: 31.9056 Evaluate side-chains 102 residues out of total 1174 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 88 time to evaluate : 1.164 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 TYR Chi-restraints excluded: chain A residue 99 VAL Chi-restraints excluded: chain A residue 150 LEU Chi-restraints excluded: chain A residue 452 VAL Chi-restraints excluded: chain A residue 465 ASN Chi-restraints excluded: chain A residue 483 ILE Chi-restraints excluded: chain A residue 540 VAL Chi-restraints excluded: chain B residue 31 ARG Chi-restraints excluded: chain B residue 274 PHE Chi-restraints excluded: chain B residue 375 TYR Chi-restraints excluded: chain C residue 75 SER Chi-restraints excluded: chain C residue 85 ASP Chi-restraints excluded: chain C residue 111 ILE Chi-restraints excluded: chain C residue 266 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 62 optimal weight: 5.9990 chunk 100 optimal weight: 6.9990 chunk 65 optimal weight: 1.9990 chunk 12 optimal weight: 0.9980 chunk 112 optimal weight: 5.9990 chunk 19 optimal weight: 0.9990 chunk 54 optimal weight: 8.9990 chunk 1 optimal weight: 3.9990 chunk 64 optimal weight: 5.9990 chunk 94 optimal weight: 5.9990 chunk 107 optimal weight: 3.9990 overall best weight: 2.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 364 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.063923 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2970 r_free = 0.2970 target = 0.046909 restraints weight = 50048.923| |-----------------------------------------------------------------------------| r_work (start): 0.2948 rms_B_bonded: 5.05 r_work (final): 0.2948 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8604 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 : 0.004 0.048 10779 Z= 0.200 Angle : 0.643 11.191 14623 Z= 0.316 Chirality : 0.041 0.167 1659 Planarity : 0.004 0.040 1877 Dihedral : 4.142 19.050 1415 Min Nonbonded Distance : 1.983 Molprobity Statistics. All-atom Clashscore : 10.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Rotamer: Outliers : 2.56 % Allowed : 15.93 % Favored : 81.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.73 (0.24), residues: 1304 helix: 1.71 (0.18), residues: 903 sheet: -0.87 (0.66), residues: 53 loop : 0.11 (0.34), residues: 348 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 250 HIS 0.004 0.001 HIS A 87 PHE 0.014 0.001 PHE B 274 TYR 0.042 0.001 TYR B 391 ARG 0.008 0.000 ARG A 398 Details of bonding type rmsd hydrogen bonds : bond 0.03878 ( 624) hydrogen bonds : angle 4.34219 ( 1851) covalent geometry : bond 0.00449 (10779) covalent geometry : angle 0.64340 (14623) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2608 Ramachandran restraints generated. 1304 Oldfield, 0 Emsley, 1304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2608 Ramachandran restraints generated. 1304 Oldfield, 0 Emsley, 1304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 1174 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 86 time to evaluate : 1.157 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 269 GLU cc_start: 0.9044 (mp0) cc_final: 0.8667 (mp0) REVERT: A 427 MET cc_start: 0.9414 (tpt) cc_final: 0.9176 (tpp) REVERT: B 65 TRP cc_start: 0.8252 (m-10) cc_final: 0.7738 (m-10) REVERT: B 76 MET cc_start: 0.9422 (mmm) cc_final: 0.9131 (mmt) REVERT: B 94 GLU cc_start: 0.8889 (mp0) cc_final: 0.8575 (mp0) REVERT: B 274 PHE cc_start: 0.9046 (OUTLIER) cc_final: 0.8485 (t80) REVERT: B 303 MET cc_start: 0.9370 (mtm) cc_final: 0.9144 (mtm) REVERT: B 324 MET cc_start: 0.8715 (pmm) cc_final: 0.8457 (pmm) REVERT: B 356 MET cc_start: 0.8849 (mmm) cc_final: 0.8273 (mmm) REVERT: B 375 TYR cc_start: 0.8869 (OUTLIER) cc_final: 0.8330 (m-80) REVERT: B 398 MET cc_start: 0.9363 (ptm) cc_final: 0.9076 (tmm) REVERT: B 399 GLU cc_start: 0.9671 (tt0) cc_final: 0.9416 (pt0) REVERT: C 85 ASP cc_start: 0.8414 (OUTLIER) cc_final: 0.7733 (m-30) REVERT: C 191 HIS cc_start: 0.9089 (m-70) cc_final: 0.8860 (m-70) REVERT: C 196 CYS cc_start: 0.8139 (t) cc_final: 0.7865 (t) REVERT: C 275 ILE cc_start: 0.8407 (OUTLIER) cc_final: 0.8109 (mm) REVERT: C 277 GLU cc_start: 0.8824 (mm-30) cc_final: 0.8447 (mm-30) outliers start: 30 outliers final: 20 residues processed: 106 average time/residue: 0.1839 time to fit residues: 30.4215 Evaluate side-chains 105 residues out of total 1174 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 81 time to evaluate : 1.253 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 LEU Chi-restraints excluded: chain A residue 60 TYR Chi-restraints excluded: chain A residue 75 THR Chi-restraints excluded: chain A residue 96 LEU Chi-restraints excluded: chain A residue 99 VAL Chi-restraints excluded: chain A residue 150 LEU Chi-restraints excluded: chain A residue 452 VAL Chi-restraints excluded: chain A residue 465 ASN Chi-restraints excluded: chain A residue 483 ILE Chi-restraints excluded: chain A residue 538 PHE Chi-restraints excluded: chain A residue 540 VAL Chi-restraints excluded: chain B residue 274 PHE Chi-restraints excluded: chain B residue 334 CYS Chi-restraints excluded: chain B residue 375 TYR Chi-restraints excluded: chain C residue 28 VAL Chi-restraints excluded: chain C residue 75 SER Chi-restraints excluded: chain C residue 85 ASP Chi-restraints excluded: chain C residue 107 TYR Chi-restraints excluded: chain C residue 111 ILE Chi-restraints excluded: chain C residue 120 SER Chi-restraints excluded: chain C residue 166 LEU Chi-restraints excluded: chain C residue 256 VAL Chi-restraints excluded: chain C residue 266 CYS Chi-restraints excluded: chain C residue 275 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 74 optimal weight: 2.9990 chunk 108 optimal weight: 3.9990 chunk 16 optimal weight: 3.9990 chunk 78 optimal weight: 0.9990 chunk 50 optimal weight: 1.9990 chunk 119 optimal weight: 2.9990 chunk 11 optimal weight: 5.9990 chunk 92 optimal weight: 0.9980 chunk 3 optimal weight: 7.9990 chunk 1 optimal weight: 4.9990 chunk 104 optimal weight: 4.9990 overall best weight: 1.9988 ------------------------------------------------------------------------------- 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 = 0.3427 r_free = 0.3427 target = 0.064163 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2985 r_free = 0.2985 target = 0.047221 restraints weight = 50330.897| |-----------------------------------------------------------------------------| r_work (start): 0.2952 rms_B_bonded: 5.09 r_work (final): 0.2952 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8594 moved from start: 0.3571 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 10779 Z= 0.167 Angle : 0.626 12.511 14623 Z= 0.307 Chirality : 0.041 0.176 1659 Planarity : 0.004 0.038 1877 Dihedral : 4.139 19.591 1415 Min Nonbonded Distance : 2.048 Molprobity Statistics. All-atom Clashscore : 9.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Rotamer: Outliers : 2.56 % Allowed : 16.01 % Favored : 81.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.75 (0.24), residues: 1304 helix: 1.73 (0.18), residues: 905 sheet: -0.94 (0.66), residues: 53 loop : 0.11 (0.34), residues: 346 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 450 HIS 0.004 0.001 HIS A 520 PHE 0.015 0.001 PHE B 274 TYR 0.043 0.001 TYR B 391 ARG 0.007 0.000 ARG A 398 Details of bonding type rmsd hydrogen bonds : bond 0.03659 ( 624) hydrogen bonds : angle 4.31447 ( 1851) covalent geometry : bond 0.00379 (10779) covalent geometry : angle 0.62642 (14623) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2608 Ramachandran restraints generated. 1304 Oldfield, 0 Emsley, 1304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2608 Ramachandran restraints generated. 1304 Oldfield, 0 Emsley, 1304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 1174 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 85 time to evaluate : 1.279 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 63 ASP cc_start: 0.8859 (m-30) cc_final: 0.8509 (p0) REVERT: A 269 GLU cc_start: 0.9040 (mp0) cc_final: 0.8665 (mp0) REVERT: A 427 MET cc_start: 0.9437 (tpt) cc_final: 0.9205 (tpp) REVERT: B 65 TRP cc_start: 0.8221 (m-10) cc_final: 0.7719 (m-10) REVERT: B 94 GLU cc_start: 0.8874 (mp0) cc_final: 0.8549 (mp0) REVERT: B 274 PHE cc_start: 0.9072 (OUTLIER) cc_final: 0.8562 (t80) REVERT: B 324 MET cc_start: 0.8738 (pmm) cc_final: 0.8425 (pmm) REVERT: B 356 MET cc_start: 0.8878 (mmm) cc_final: 0.8279 (mmm) REVERT: B 370 MET cc_start: 0.9079 (mmm) cc_final: 0.8635 (mmp) REVERT: B 375 TYR cc_start: 0.8896 (OUTLIER) cc_final: 0.8283 (m-80) REVERT: B 398 MET cc_start: 0.9357 (ptm) cc_final: 0.9010 (tmm) REVERT: B 413 LYS cc_start: 0.9661 (pttm) cc_final: 0.9418 (mmtt) REVERT: C 85 ASP cc_start: 0.8355 (OUTLIER) cc_final: 0.7748 (m-30) REVERT: C 191 HIS cc_start: 0.9101 (m-70) cc_final: 0.8884 (m-70) REVERT: C 196 CYS cc_start: 0.8333 (t) cc_final: 0.7968 (t) REVERT: C 254 ARG cc_start: 0.8751 (OUTLIER) cc_final: 0.8356 (mmt90) REVERT: C 275 ILE cc_start: 0.8400 (OUTLIER) cc_final: 0.8068 (mm) REVERT: C 277 GLU cc_start: 0.8849 (mm-30) cc_final: 0.8443 (mm-30) outliers start: 30 outliers final: 21 residues processed: 108 average time/residue: 0.2003 time to fit residues: 32.8846 Evaluate side-chains 106 residues out of total 1174 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 80 time to evaluate : 1.310 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 TYR Chi-restraints excluded: chain A residue 75 THR Chi-restraints excluded: chain A residue 96 LEU Chi-restraints excluded: chain A residue 99 VAL Chi-restraints excluded: chain A residue 150 LEU Chi-restraints excluded: chain A residue 195 VAL Chi-restraints excluded: chain A residue 429 LEU Chi-restraints excluded: chain A residue 452 VAL Chi-restraints excluded: chain A residue 465 ASN Chi-restraints excluded: chain A residue 483 ILE Chi-restraints excluded: chain A residue 538 PHE Chi-restraints excluded: chain A residue 540 VAL Chi-restraints excluded: chain B residue 252 LEU Chi-restraints excluded: chain B residue 274 PHE Chi-restraints excluded: chain B residue 334 CYS Chi-restraints excluded: chain B residue 375 TYR Chi-restraints excluded: chain C residue 28 VAL Chi-restraints excluded: chain C residue 75 SER Chi-restraints excluded: chain C residue 85 ASP Chi-restraints excluded: chain C residue 107 TYR Chi-restraints excluded: chain C residue 111 ILE Chi-restraints excluded: chain C residue 120 SER Chi-restraints excluded: chain C residue 254 ARG Chi-restraints excluded: chain C residue 256 VAL Chi-restraints excluded: chain C residue 266 CYS Chi-restraints excluded: chain C residue 275 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 21 optimal weight: 0.5980 chunk 99 optimal weight: 9.9990 chunk 45 optimal weight: 4.9990 chunk 121 optimal weight: 5.9990 chunk 20 optimal weight: 0.8980 chunk 95 optimal weight: 0.9980 chunk 111 optimal weight: 0.9990 chunk 3 optimal weight: 9.9990 chunk 2 optimal weight: 5.9990 chunk 34 optimal weight: 0.8980 chunk 56 optimal weight: 0.6980 overall best weight: 0.8180 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.065487 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3030 r_free = 0.3030 target = 0.048643 restraints weight = 48840.869| |-----------------------------------------------------------------------------| r_work (start): 0.2996 rms_B_bonded: 5.08 r_work (final): 0.2996 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8557 moved from start: 0.3623 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 10779 Z= 0.111 Angle : 0.611 10.885 14623 Z= 0.296 Chirality : 0.040 0.186 1659 Planarity : 0.004 0.042 1877 Dihedral : 4.070 21.742 1415 Min Nonbonded Distance : 2.113 Molprobity Statistics. All-atom Clashscore : 7.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer: Outliers : 1.79 % Allowed : 17.12 % Favored : 81.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.75 (0.24), residues: 1304 helix: 1.73 (0.18), residues: 912 sheet: -0.81 (0.67), residues: 53 loop : 0.07 (0.35), residues: 339 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 450 HIS 0.003 0.001 HIS C 167 PHE 0.016 0.001 PHE A 538 TYR 0.044 0.001 TYR B 391 ARG 0.007 0.000 ARG A 398 Details of bonding type rmsd hydrogen bonds : bond 0.03282 ( 624) hydrogen bonds : angle 4.17755 ( 1851) covalent geometry : bond 0.00247 (10779) covalent geometry : angle 0.61127 (14623) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2608 Ramachandran restraints generated. 1304 Oldfield, 0 Emsley, 1304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2608 Ramachandran restraints generated. 1304 Oldfield, 0 Emsley, 1304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 1174 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 90 time to evaluate : 1.245 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 63 ASP cc_start: 0.8674 (m-30) cc_final: 0.8258 (p0) REVERT: A 269 GLU cc_start: 0.9037 (mp0) cc_final: 0.8515 (mp0) REVERT: A 366 LEU cc_start: 0.9701 (OUTLIER) cc_final: 0.9300 (mm) REVERT: A 427 MET cc_start: 0.9423 (tpt) cc_final: 0.9155 (tpp) REVERT: A 489 MET cc_start: 0.9228 (ptm) cc_final: 0.8952 (tmm) REVERT: A 499 MET cc_start: 0.8739 (mmp) cc_final: 0.8405 (mmp) REVERT: A 521 MET cc_start: 0.8073 (ptt) cc_final: 0.7552 (ptt) REVERT: B 65 TRP cc_start: 0.8133 (m-10) cc_final: 0.7614 (m-10) REVERT: B 76 MET cc_start: 0.9584 (mmt) cc_final: 0.9188 (mmm) REVERT: B 94 GLU cc_start: 0.8840 (mp0) cc_final: 0.8500 (mp0) REVERT: B 274 PHE cc_start: 0.9019 (OUTLIER) cc_final: 0.8465 (t80) REVERT: B 324 MET cc_start: 0.8729 (pmm) cc_final: 0.8393 (pmm) REVERT: B 356 MET cc_start: 0.8889 (mmm) cc_final: 0.8302 (mmm) REVERT: B 375 TYR cc_start: 0.8896 (OUTLIER) cc_final: 0.8323 (m-80) REVERT: B 398 MET cc_start: 0.9363 (ptm) cc_final: 0.9006 (tmm) REVERT: C 85 ASP cc_start: 0.8354 (OUTLIER) cc_final: 0.7759 (m-30) REVERT: C 191 HIS cc_start: 0.9122 (m-70) cc_final: 0.8917 (m-70) REVERT: C 196 CYS cc_start: 0.8155 (t) cc_final: 0.7796 (t) REVERT: C 254 ARG cc_start: 0.8710 (OUTLIER) cc_final: 0.8304 (mmt90) REVERT: C 277 GLU cc_start: 0.8868 (mm-30) cc_final: 0.8552 (mm-30) outliers start: 21 outliers final: 13 residues processed: 106 average time/residue: 0.1945 time to fit residues: 31.5734 Evaluate side-chains 103 residues out of total 1174 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 85 time to evaluate : 1.238 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 TYR Chi-restraints excluded: chain A residue 75 THR Chi-restraints excluded: chain A residue 96 LEU Chi-restraints excluded: chain A residue 99 VAL Chi-restraints excluded: chain A residue 150 LEU Chi-restraints excluded: chain A residue 366 LEU Chi-restraints excluded: chain A residue 429 LEU Chi-restraints excluded: chain A residue 452 VAL Chi-restraints excluded: chain A residue 483 ILE Chi-restraints excluded: chain A residue 540 VAL Chi-restraints excluded: chain B residue 252 LEU Chi-restraints excluded: chain B residue 274 PHE Chi-restraints excluded: chain B residue 375 TYR Chi-restraints excluded: chain C residue 75 SER Chi-restraints excluded: chain C residue 85 ASP Chi-restraints excluded: chain C residue 111 ILE Chi-restraints excluded: chain C residue 254 ARG Chi-restraints excluded: chain C residue 266 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 57 optimal weight: 7.9990 chunk 106 optimal weight: 5.9990 chunk 61 optimal weight: 6.9990 chunk 1 optimal weight: 0.6980 chunk 120 optimal weight: 0.7980 chunk 12 optimal weight: 0.9990 chunk 115 optimal weight: 6.9990 chunk 113 optimal weight: 0.8980 chunk 59 optimal weight: 0.8980 chunk 75 optimal weight: 0.9980 chunk 9 optimal weight: 0.7980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 360 ASN ** A 465 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 187 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3455 r_free = 0.3455 target = 0.065471 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3020 r_free = 0.3020 target = 0.048519 restraints weight = 49810.051| |-----------------------------------------------------------------------------| r_work (start): 0.3003 rms_B_bonded: 5.13 r_work (final): 0.3003 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8529 moved from start: 0.3691 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 10779 Z= 0.114 Angle : 0.643 20.265 14623 Z= 0.306 Chirality : 0.040 0.169 1659 Planarity : 0.004 0.043 1877 Dihedral : 4.012 20.703 1415 Min Nonbonded Distance : 2.086 Molprobity Statistics. All-atom Clashscore : 8.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.99 % Favored : 98.01 % Rotamer: Outliers : 1.53 % Allowed : 17.80 % Favored : 80.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.72 (0.24), residues: 1304 helix: 1.71 (0.18), residues: 911 sheet: -0.70 (0.66), residues: 53 loop : 0.05 (0.34), residues: 340 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP A 450 HIS 0.003 0.001 HIS C 167 PHE 0.015 0.001 PHE A 538 TYR 0.042 0.001 TYR B 391 ARG 0.008 0.000 ARG A 398 Details of bonding type rmsd hydrogen bonds : bond 0.03276 ( 624) hydrogen bonds : angle 4.15193 ( 1851) covalent geometry : bond 0.00256 (10779) covalent geometry : angle 0.64312 (14623) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2608 Ramachandran restraints generated. 1304 Oldfield, 0 Emsley, 1304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2608 Ramachandran restraints generated. 1304 Oldfield, 0 Emsley, 1304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 1174 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 86 time to evaluate : 1.186 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 245 MET cc_start: 0.8976 (mmp) cc_final: 0.8677 (mmp) REVERT: A 269 GLU cc_start: 0.9072 (mp0) cc_final: 0.8550 (mp0) REVERT: A 366 LEU cc_start: 0.9691 (OUTLIER) cc_final: 0.9293 (mm) REVERT: A 427 MET cc_start: 0.9428 (tpt) cc_final: 0.9206 (tpp) REVERT: A 499 MET cc_start: 0.8754 (mmp) cc_final: 0.8448 (mmp) REVERT: A 521 MET cc_start: 0.8104 (ptt) cc_final: 0.7783 (ptt) REVERT: B 65 TRP cc_start: 0.8150 (m-10) cc_final: 0.7640 (m-10) REVERT: B 76 MET cc_start: 0.9585 (mmt) cc_final: 0.9201 (mmm) REVERT: B 94 GLU cc_start: 0.8855 (mp0) cc_final: 0.8506 (mp0) REVERT: B 274 PHE cc_start: 0.9004 (OUTLIER) cc_final: 0.8465 (t80) REVERT: B 324 MET cc_start: 0.8710 (pmm) cc_final: 0.8376 (pmm) REVERT: B 341 GLN cc_start: 0.9194 (mt0) cc_final: 0.8912 (mt0) REVERT: B 356 MET cc_start: 0.8928 (mmm) cc_final: 0.8340 (mmm) REVERT: B 370 MET cc_start: 0.9008 (mmm) cc_final: 0.8585 (mmp) REVERT: B 375 TYR cc_start: 0.8945 (OUTLIER) cc_final: 0.8364 (m-80) REVERT: B 398 MET cc_start: 0.9370 (ptm) cc_final: 0.9022 (tmm) REVERT: C 85 ASP cc_start: 0.8246 (OUTLIER) cc_final: 0.7614 (m-30) REVERT: C 191 HIS cc_start: 0.9194 (m-70) cc_final: 0.8988 (m-70) REVERT: C 196 CYS cc_start: 0.8064 (t) cc_final: 0.7622 (t) REVERT: C 277 GLU cc_start: 0.8881 (mm-30) cc_final: 0.8614 (mm-30) outliers start: 18 outliers final: 14 residues processed: 101 average time/residue: 0.2018 time to fit residues: 31.2390 Evaluate side-chains 101 residues out of total 1174 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 83 time to evaluate : 1.261 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 TYR Chi-restraints excluded: chain A residue 96 LEU Chi-restraints excluded: chain A residue 99 VAL Chi-restraints excluded: chain A residue 150 LEU Chi-restraints excluded: chain A residue 366 LEU Chi-restraints excluded: chain A residue 429 LEU Chi-restraints excluded: chain A residue 452 VAL Chi-restraints excluded: chain A residue 483 ILE Chi-restraints excluded: chain A residue 540 VAL Chi-restraints excluded: chain B residue 252 LEU Chi-restraints excluded: chain B residue 274 PHE Chi-restraints excluded: chain B residue 375 TYR Chi-restraints excluded: chain C residue 75 SER Chi-restraints excluded: chain C residue 85 ASP Chi-restraints excluded: chain C residue 111 ILE Chi-restraints excluded: chain C residue 120 SER Chi-restraints excluded: chain C residue 254 ARG Chi-restraints excluded: chain C residue 266 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 27 optimal weight: 0.9980 chunk 99 optimal weight: 10.0000 chunk 31 optimal weight: 1.9990 chunk 78 optimal weight: 4.9990 chunk 76 optimal weight: 0.7980 chunk 84 optimal weight: 3.9990 chunk 81 optimal weight: 0.6980 chunk 19 optimal weight: 1.9990 chunk 57 optimal weight: 7.9990 chunk 90 optimal weight: 4.9990 chunk 16 optimal weight: 0.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 465 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 187 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.065417 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3039 r_free = 0.3039 target = 0.048798 restraints weight = 48684.148| |-----------------------------------------------------------------------------| r_work (start): 0.3005 rms_B_bonded: 5.02 r_work (final): 0.3005 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8550 moved from start: 0.3757 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 10779 Z= 0.124 Angle : 0.667 19.427 14623 Z= 0.316 Chirality : 0.040 0.169 1659 Planarity : 0.004 0.048 1877 Dihedral : 4.009 20.490 1415 Min Nonbonded Distance : 1.981 Molprobity Statistics. All-atom Clashscore : 8.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Rotamer: Outliers : 1.70 % Allowed : 17.97 % Favored : 80.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.71 (0.24), residues: 1304 helix: 1.71 (0.18), residues: 911 sheet: -0.71 (0.66), residues: 58 loop : 0.03 (0.34), residues: 335 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 450 HIS 0.003 0.001 HIS C 167 PHE 0.014 0.001 PHE A 538 TYR 0.045 0.001 TYR B 391 ARG 0.008 0.000 ARG A 398 Details of bonding type rmsd hydrogen bonds : bond 0.03316 ( 624) hydrogen bonds : angle 4.18136 ( 1851) covalent geometry : bond 0.00281 (10779) covalent geometry : angle 0.66710 (14623) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2608 Ramachandran restraints generated. 1304 Oldfield, 0 Emsley, 1304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2608 Ramachandran restraints generated. 1304 Oldfield, 0 Emsley, 1304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 1174 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 83 time to evaluate : 1.160 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 245 MET cc_start: 0.8899 (mmp) cc_final: 0.8479 (mmp) REVERT: A 269 GLU cc_start: 0.9046 (mp0) cc_final: 0.8520 (mp0) REVERT: A 366 LEU cc_start: 0.9696 (OUTLIER) cc_final: 0.9298 (mm) REVERT: A 427 MET cc_start: 0.9424 (tpt) cc_final: 0.9197 (tpp) REVERT: A 489 MET cc_start: 0.9242 (ptm) cc_final: 0.8979 (tmm) REVERT: A 499 MET cc_start: 0.8744 (mmp) cc_final: 0.8441 (mmp) REVERT: A 521 MET cc_start: 0.8099 (ptt) cc_final: 0.7779 (ptt) REVERT: B 65 TRP cc_start: 0.8149 (m-10) cc_final: 0.7607 (m-10) REVERT: B 76 MET cc_start: 0.9587 (mmt) cc_final: 0.9215 (mmm) REVERT: B 94 GLU cc_start: 0.8867 (mp0) cc_final: 0.8515 (mp0) REVERT: B 274 PHE cc_start: 0.9018 (OUTLIER) cc_final: 0.8461 (t80) REVERT: B 324 MET cc_start: 0.8737 (pmm) cc_final: 0.8386 (pmm) REVERT: B 341 GLN cc_start: 0.9196 (mt0) cc_final: 0.8917 (mt0) REVERT: B 356 MET cc_start: 0.8906 (mmm) cc_final: 0.8308 (mmm) REVERT: B 375 TYR cc_start: 0.8926 (OUTLIER) cc_final: 0.8353 (m-80) REVERT: B 398 MET cc_start: 0.9377 (ptm) cc_final: 0.9030 (tmm) REVERT: C 85 ASP cc_start: 0.8219 (OUTLIER) cc_final: 0.7599 (m-30) REVERT: C 191 HIS cc_start: 0.9140 (m-70) cc_final: 0.8934 (m-70) REVERT: C 196 CYS cc_start: 0.7959 (t) cc_final: 0.7518 (t) REVERT: C 277 GLU cc_start: 0.8835 (mm-30) cc_final: 0.8568 (mm-30) outliers start: 20 outliers final: 15 residues processed: 101 average time/residue: 0.1839 time to fit residues: 28.6840 Evaluate side-chains 101 residues out of total 1174 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 82 time to evaluate : 1.147 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 TYR Chi-restraints excluded: chain A residue 96 LEU Chi-restraints excluded: chain A residue 99 VAL Chi-restraints excluded: chain A residue 150 LEU Chi-restraints excluded: chain A residue 366 LEU Chi-restraints excluded: chain A residue 429 LEU Chi-restraints excluded: chain A residue 452 VAL Chi-restraints excluded: chain A residue 465 ASN Chi-restraints excluded: chain A residue 483 ILE Chi-restraints excluded: chain A residue 540 VAL Chi-restraints excluded: chain B residue 252 LEU Chi-restraints excluded: chain B residue 274 PHE Chi-restraints excluded: chain B residue 375 TYR Chi-restraints excluded: chain C residue 75 SER Chi-restraints excluded: chain C residue 85 ASP Chi-restraints excluded: chain C residue 111 ILE Chi-restraints excluded: chain C residue 120 SER Chi-restraints excluded: chain C residue 254 ARG Chi-restraints excluded: chain C residue 266 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 68 optimal weight: 1.9990 chunk 123 optimal weight: 0.9990 chunk 97 optimal weight: 4.9990 chunk 117 optimal weight: 0.9990 chunk 36 optimal weight: 0.8980 chunk 20 optimal weight: 0.9990 chunk 71 optimal weight: 0.9990 chunk 12 optimal weight: 0.0170 chunk 34 optimal weight: 1.9990 chunk 69 optimal weight: 0.9980 chunk 41 optimal weight: 0.7980 overall best weight: 0.7420 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 465 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.065821 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3032 r_free = 0.3032 target = 0.048923 restraints weight = 49002.544| |-----------------------------------------------------------------------------| r_work (start): 0.3017 rms_B_bonded: 5.16 r_work (final): 0.3017 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8549 moved from start: 0.3793 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 10779 Z= 0.112 Angle : 0.655 20.157 14623 Z= 0.310 Chirality : 0.040 0.166 1659 Planarity : 0.004 0.053 1877 Dihedral : 4.007 20.518 1415 Min Nonbonded Distance : 1.914 Molprobity Statistics. All-atom Clashscore : 8.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.99 % Favored : 98.01 % Rotamer: Outliers : 1.79 % Allowed : 17.72 % Favored : 80.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.65 (0.24), residues: 1304 helix: 1.67 (0.18), residues: 917 sheet: -0.73 (0.66), residues: 58 loop : -0.05 (0.35), residues: 329 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 450 HIS 0.003 0.001 HIS C 167 PHE 0.015 0.001 PHE A 538 TYR 0.046 0.001 TYR B 391 ARG 0.008 0.000 ARG A 398 Details of bonding type rmsd hydrogen bonds : bond 0.03238 ( 624) hydrogen bonds : angle 4.13537 ( 1851) covalent geometry : bond 0.00248 (10779) covalent geometry : angle 0.65525 (14623) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3988.38 seconds wall clock time: 69 minutes 36.23 seconds (4176.23 seconds total)