Starting phenix.real_space_refine on Tue Jul 29 00:25:49 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9n0y_48798/07_2025/9n0y_48798.cif Found real_map, /net/cci-nas-00/data/ceres_data/9n0y_48798/07_2025/9n0y_48798.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.71 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9n0y_48798/07_2025/9n0y_48798.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9n0y_48798/07_2025/9n0y_48798.map" model { file = "/net/cci-nas-00/data/ceres_data/9n0y_48798/07_2025/9n0y_48798.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9n0y_48798/07_2025/9n0y_48798.cif" } resolution = 3.71 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= 0.001 sd= 0.019 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: 4 Type Number sf(0) Gaussians S 62 5.16 5 C 6824 2.51 5 N 1846 2.21 5 O 2060 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 24 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: 10792 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 4521 Number of conformers: 1 Conformer: "" Number of residues, atoms: 580, 4521 Classifications: {'peptide': 580} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 26, 'TRANS': 553} Chain: "B" Number of atoms: 3594 Number of conformers: 1 Conformer: "" Number of residues, atoms: 439, 3594 Classifications: {'peptide': 439} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 15, 'TRANS': 423} Chain: "C" Number of atoms: 2504 Number of conformers: 1 Conformer: "" Number of residues, atoms: 309, 2504 Classifications: {'peptide': 309} Link IDs: {'PCIS': 2, 'PTRANS': 11, 'TRANS': 295} Chain: "D" Number of atoms: 173 Number of conformers: 1 Conformer: "" Number of residues, atoms: 22, 173 Classifications: {'peptide': 22} Link IDs: {'PTRANS': 2, 'TRANS': 19} Time building chain proxies: 6.70, per 1000 atoms: 0.62 Number of scatterers: 10792 At special positions: 0 Unit cell: (107.73, 106.02, 124.83, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 62 16.00 O 2060 8.00 N 1846 7.00 C 6824 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: 2.71 Conformation dependent library (CDL) restraints added in 1.7 seconds 2684 Ramachandran restraints generated. 1342 Oldfield, 0 Emsley, 1342 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2590 Finding SS restraints... Secondary structure from input PDB file: 58 helices and 14 sheets defined 49.3% alpha, 7.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.37 Creating SS restraints... Processing helix chain 'A' and resid 10 through 21 removed outlier: 3.743A pdb=" N ASP A 18 " --> pdb=" O ALA A 14 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N GLU A 19 " --> pdb=" O VAL A 15 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N LEU A 20 " --> pdb=" O LEU A 16 " (cutoff:3.500A) removed outlier: 4.278A pdb=" N ARG A 21 " --> pdb=" O ILE A 17 " (cutoff:3.500A) Processing helix chain 'A' and resid 24 through 33 Processing helix chain 'A' and resid 34 through 43 removed outlier: 3.511A pdb=" N ILE A 38 " --> pdb=" O LYS A 34 " (cutoff:3.500A) Processing helix chain 'A' and resid 43 through 51 Processing helix chain 'A' and resid 51 through 57 removed outlier: 4.392A pdb=" N ASP A 57 " --> pdb=" O PRO A 53 " (cutoff:3.500A) Processing helix chain 'A' and resid 62 through 75 removed outlier: 3.846A pdb=" N GLU A 71 " --> pdb=" O LEU A 67 " (cutoff:3.500A) Processing helix chain 'A' and resid 85 through 88 Processing helix chain 'A' and resid 89 through 97 removed outlier: 3.519A pdb=" N LEU A 93 " --> pdb=" O LEU A 89 " (cutoff:3.500A) Processing helix chain 'A' and resid 101 through 117 removed outlier: 3.993A pdb=" N HIS A 117 " --> pdb=" O ARG A 113 " (cutoff:3.500A) Processing helix chain 'A' and resid 120 through 136 removed outlier: 4.955A pdb=" N VAL A 129 " --> pdb=" O GLU A 125 " (cutoff:3.500A) Proline residue: A 130 - end of helix Processing helix chain 'A' and resid 140 through 148 removed outlier: 3.787A pdb=" N ARG A 144 " --> pdb=" O TRP A 140 " (cutoff:3.500A) Processing helix chain 'A' and resid 150 through 155 removed outlier: 3.584A pdb=" N CYS A 154 " --> pdb=" O LEU A 150 " (cutoff:3.500A) Processing helix chain 'A' and resid 159 through 174 Processing helix chain 'A' and resid 178 through 196 removed outlier: 3.889A pdb=" N ARG A 182 " --> pdb=" O THR A 178 " (cutoff:3.500A) removed outlier: 4.063A pdb=" N LYS A 188 " --> pdb=" O ALA A 184 " (cutoff:3.500A) removed outlier: 4.676A pdb=" N GLY A 190 " --> pdb=" O ALA A 186 " (cutoff:3.500A) removed outlier: 4.995A pdb=" N GLU A 191 " --> pdb=" O SER A 187 " (cutoff:3.500A) removed outlier: 4.234A pdb=" N VAL A 195 " --> pdb=" O GLU A 191 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N LEU A 196 " --> pdb=" O PHE A 192 " (cutoff:3.500A) Processing helix chain 'A' and resid 197 through 214 removed outlier: 4.642A 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 220 through 233 removed outlier: 4.026A pdb=" N ALA A 224 " --> pdb=" O VAL A 220 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N VAL A 225 " --> pdb=" O ARG A 221 " (cutoff:3.500A) removed outlier: 5.240A pdb=" N GLU A 226 " --> pdb=" O LEU A 222 " (cutoff:3.500A) Processing helix chain 'A' and resid 244 through 252 Processing helix chain 'A' and resid 256 through 265 removed outlier: 3.805A pdb=" N ARG A 260 " --> pdb=" O SER A 256 " (cutoff:3.500A) Processing helix chain 'A' and resid 266 through 292 Proline residue: A 276 - end of helix removed outlier: 5.401A 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 305 removed outlier: 4.070A pdb=" N ARG A 299 " --> pdb=" O GLU A 295 " (cutoff:3.500A) Processing helix chain 'A' and resid 305 through 311 Processing helix chain 'A' and resid 317 through 334 removed outlier: 4.933A pdb=" N LEU A 327 " --> pdb=" O MET A 323 " (cutoff:3.500A) Proline residue: A 328 - end of helix Processing helix chain 'A' and resid 338 through 347 removed outlier: 3.685A pdb=" N LYS A 342 " --> pdb=" O ASN A 338 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N SER A 347 " --> pdb=" O SER A 343 " (cutoff:3.500A) Processing helix chain 'A' and resid 348 through 351 removed outlier: 3.570A pdb=" N GLY A 351 " --> pdb=" O VAL A 348 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 348 through 351' Processing helix chain 'A' and resid 352 through 373 removed outlier: 7.187A pdb=" N LYS A 358 " --> pdb=" O PRO A 354 " (cutoff:3.500A) removed outlier: 9.154A pdb=" N ASP A 359 " --> pdb=" O ILE A 355 " (cutoff:3.500A) removed outlier: 4.475A pdb=" N ASN A 360 " --> pdb=" O LEU A 356 " (cutoff:3.500A) removed outlier: 4.787A 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: 3.906A pdb=" N ARG A 381 " --> pdb=" O CYS A 377 " (cutoff:3.500A) Processing helix chain 'A' and resid 388 through 396 removed outlier: 3.779A pdb=" N VAL A 394 " --> pdb=" O CYS A 390 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N GLY A 396 " --> pdb=" O ASN A 392 " (cutoff:3.500A) Processing helix chain 'A' and resid 397 through 412 removed outlier: 4.475A pdb=" N SER A 403 " --> pdb=" O GLN A 399 " (cutoff:3.500A) removed outlier: 4.354A pdb=" N LEU A 405 " --> pdb=" O SER A 401 " (cutoff:3.500A) Proline residue: A 406 - end of helix Processing helix chain 'A' and resid 416 through 435 removed outlier: 4.038A pdb=" N ARG A 420 " --> pdb=" O LYS A 416 " (cutoff:3.500A) 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 removed outlier: 4.102A pdb=" N CYS A 447 " --> pdb=" O LEU A 443 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N MET A 448 " --> pdb=" O ASN A 444 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N VAL A 452 " --> pdb=" O MET A 448 " (cutoff:3.500A) Processing helix chain 'A' and resid 455 through 474 removed outlier: 3.516A pdb=" N LYS A 467 " --> pdb=" O THR A 463 " (cutoff:3.500A) Processing helix chain 'A' and resid 474 through 482 Processing helix chain 'A' and resid 482 through 490 removed outlier: 4.359A pdb=" N VAL A 486 " --> pdb=" O ILE A 482 " (cutoff:3.500A) Processing helix chain 'A' and resid 494 through 510 removed outlier: 3.839A pdb=" N ARG A 498 " --> pdb=" O ASN A 494 " (cutoff:3.500A) removed outlier: 4.438A pdb=" N GLU A 510 " --> pdb=" O ASN A 506 " (cutoff:3.500A) Processing helix chain 'A' and resid 513 through 529 removed outlier: 4.677A 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 removed outlier: 3.755A pdb=" N ARG A 537 " --> pdb=" O VAL A 533 " (cutoff:3.500A) Processing helix chain 'A' and resid 549 through 551 No H-bonds generated for 'chain 'A' and resid 549 through 551' Processing helix chain 'A' and resid 552 through 559 Processing helix chain 'A' and resid 559 through 568 removed outlier: 3.581A pdb=" N ILE A 563 " --> pdb=" O GLU A 559 " (cutoff:3.500A) Processing helix chain 'A' and resid 573 through 586 Processing helix chain 'B' and resid 26 through 30 removed outlier: 3.690A pdb=" N ASP B 29 " --> pdb=" O ALA B 26 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ILE B 30 " --> pdb=" O GLU B 27 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 26 through 30' Processing helix chain 'B' and resid 281 through 286 Processing helix chain 'B' and resid 326 through 330 Processing helix chain 'B' and resid 332 through 338 Processing helix chain 'B' and resid 411 through 413 No H-bonds generated for 'chain 'B' and resid 411 through 413' Processing helix chain 'C' and resid 2 through 18 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 107 Processing helix chain 'C' and resid 120 through 127 Processing helix chain 'C' and resid 128 through 138 Processing helix chain 'C' and resid 140 through 151 removed outlier: 3.798A pdb=" N ASP C 151 " --> pdb=" O THR C 147 " (cutoff:3.500A) Processing helix chain 'C' and resid 176 through 183 removed outlier: 3.782A pdb=" N ILE C 180 " --> pdb=" O THR C 176 " (cutoff:3.500A) Processing helix chain 'C' and resid 193 through 201 Processing helix chain 'C' and resid 221 through 232 Processing helix chain 'C' and resid 264 through 268 Processing helix chain 'D' and resid 77 through 81 Processing sheet with id=AA1, first strand: chain 'B' and resid 12 through 13 removed outlier: 3.612A pdb=" N GLN B 443 " --> pdb=" O CYS B 13 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 34 through 36 removed outlier: 3.606A pdb=" N GLU B 35 " --> pdb=" O ALA B 44 " (cutoff:3.500A) removed outlier: 7.255A pdb=" N VAL B 52 " --> pdb=" O THR B 76 " (cutoff:3.500A) removed outlier: 4.790A pdb=" N THR B 76 " --> pdb=" O VAL B 52 " (cutoff:3.500A) removed outlier: 6.878A pdb=" N ILE B 54 " --> pdb=" O TYR B 74 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 111 through 114 removed outlier: 3.860A pdb=" N LEU B 111 " --> pdb=" O TRP B 122 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N SER B 113 " --> pdb=" O LYS B 120 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N ILE B 119 " --> pdb=" O PHE B 172 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N ARG B 170 " --> pdb=" O LEU B 121 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 124 through 132 removed outlier: 3.519A pdb=" N SER B 125 " --> pdb=" O GLU B 165 " (cutoff:3.500A) removed outlier: 5.307A pdb=" N LYS B 129 " --> pdb=" O ASP B 161 " (cutoff:3.500A) removed outlier: 7.895A pdb=" N ASP B 161 " --> pdb=" O LYS B 129 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 183 through 185 removed outlier: 3.633A pdb=" N SER B 184 " --> pdb=" O LEU B 193 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N TYR B 192 " --> pdb=" O TRP B 203 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N SER B 194 " --> pdb=" O ASN B 201 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N VAL B 215 " --> pdb=" O ILE B 200 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 210 through 211 Processing sheet with id=AA7, first strand: chain 'B' and resid 251 through 252 removed outlier: 3.554A pdb=" N PHE B 269 " --> pdb=" O ILE B 251 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 291 through 293 Processing sheet with id=AA9, first strand: chain 'B' and resid 348 through 349 removed outlier: 3.568A pdb=" N CYS B 349 " --> pdb=" O MET B 358 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N MET B 358 " --> pdb=" O CYS B 349 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N MET B 368 " --> pdb=" O ILE B 377 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N ILE B 377 " --> pdb=" O MET B 368 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 397 through 398 removed outlier: 3.617A pdb=" N CYS B 398 " --> pdb=" O ILE B 408 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'C' and resid 52 through 53 Processing sheet with id=AB3, first strand: chain 'C' and resid 80 through 82 removed outlier: 6.368A pdb=" N TYR C 80 " --> pdb=" O THR C 112 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB3 Processing sheet with id=AB4, first strand: chain 'C' and resid 157 through 159 removed outlier: 6.063A pdb=" N PHE C 164 " --> pdb=" O SER C 238 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 210 through 211 402 hydrogen bonds defined for protein. 1164 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: 2.81 Time building geometry restraints manager: 3.18 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 3587 1.34 - 1.46: 2187 1.46 - 1.58: 5146 1.58 - 1.70: 0 1.70 - 1.82: 91 Bond restraints: 11011 Sorted by residual: bond pdb=" N ILE A 482 " pdb=" CA ILE A 482 " ideal model delta sigma weight residual 1.459 1.503 -0.044 1.25e-02 6.40e+03 1.26e+01 bond pdb=" N ILE A 483 " pdb=" CA ILE A 483 " ideal model delta sigma weight residual 1.461 1.501 -0.040 1.23e-02 6.61e+03 1.07e+01 bond pdb=" N TYR D 67 " pdb=" CA TYR D 67 " ideal model delta sigma weight residual 1.458 1.491 -0.034 1.22e-02 6.72e+03 7.63e+00 bond pdb=" N ASP D 66 " pdb=" CA ASP D 66 " ideal model delta sigma weight residual 1.455 1.489 -0.035 1.27e-02 6.20e+03 7.44e+00 bond pdb=" N TYR D 72 " pdb=" CA TYR D 72 " ideal model delta sigma weight residual 1.455 1.488 -0.033 1.27e-02 6.20e+03 6.72e+00 ... (remaining 11006 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.60: 14856 3.60 - 7.20: 65 7.20 - 10.81: 2 10.81 - 14.41: 1 14.41 - 18.01: 1 Bond angle restraints: 14925 Sorted by residual: angle pdb=" N PHE B 442 " pdb=" CA PHE B 442 " pdb=" C PHE B 442 " ideal model delta sigma weight residual 109.96 91.95 18.01 1.49e+00 4.50e-01 1.46e+02 angle pdb=" C PHE B 442 " pdb=" CA PHE B 442 " pdb=" CB PHE B 442 " ideal model delta sigma weight residual 110.16 121.00 -10.84 1.44e+00 4.82e-01 5.67e+01 angle pdb=" C SER B 89 " pdb=" N LEU B 90 " pdb=" CA LEU B 90 " ideal model delta sigma weight residual 121.90 115.20 6.70 1.26e+00 6.30e-01 2.83e+01 angle pdb=" N PRO D 84 " pdb=" CA PRO D 84 " pdb=" C PRO D 84 " ideal model delta sigma weight residual 112.47 120.50 -8.03 2.06e+00 2.36e-01 1.52e+01 angle pdb=" CA MET D 71 " pdb=" C MET D 71 " pdb=" O MET D 71 " ideal model delta sigma weight residual 121.67 118.18 3.49 9.30e-01 1.16e+00 1.41e+01 ... (remaining 14920 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.99: 6039 17.99 - 35.98: 543 35.98 - 53.98: 93 53.98 - 71.97: 18 71.97 - 89.96: 12 Dihedral angle restraints: 6705 sinusoidal: 2724 harmonic: 3981 Sorted by residual: dihedral pdb=" CA VAL D 83 " pdb=" C VAL D 83 " pdb=" N PRO D 84 " pdb=" CA PRO D 84 " ideal model delta harmonic sigma weight residual -180.00 -155.36 -24.64 0 5.00e+00 4.00e-02 2.43e+01 dihedral pdb=" CA ILE B 185 " pdb=" C ILE B 185 " pdb=" N ASN B 186 " pdb=" CA ASN B 186 " ideal model delta harmonic sigma weight residual -180.00 -156.15 -23.85 0 5.00e+00 4.00e-02 2.28e+01 dihedral pdb=" CA PHE B 242 " pdb=" C PHE B 242 " pdb=" N VAL B 243 " pdb=" CA VAL B 243 " ideal model delta harmonic sigma weight residual -180.00 -157.12 -22.88 0 5.00e+00 4.00e-02 2.09e+01 ... (remaining 6702 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.034: 1037 0.034 - 0.068: 428 0.068 - 0.102: 155 0.102 - 0.136: 50 0.136 - 0.170: 14 Chirality restraints: 1684 Sorted by residual: chirality pdb=" CA PRO D 84 " pdb=" N PRO D 84 " pdb=" C PRO D 84 " pdb=" CB PRO D 84 " both_signs ideal model delta sigma weight residual False 2.72 2.55 0.17 2.00e-01 2.50e+01 7.20e-01 chirality pdb=" CB VAL A 452 " pdb=" CA VAL A 452 " pdb=" CG1 VAL A 452 " pdb=" CG2 VAL A 452 " both_signs ideal model delta sigma weight residual False -2.63 -2.46 -0.17 2.00e-01 2.50e+01 7.15e-01 chirality pdb=" CB ILE B 441 " pdb=" CA ILE B 441 " pdb=" CG1 ILE B 441 " pdb=" CG2 ILE B 441 " both_signs ideal model delta sigma weight residual False 2.64 2.81 -0.17 2.00e-01 2.50e+01 7.04e-01 ... (remaining 1681 not shown) Planarity restraints: 1932 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LYS B 387 " 0.027 5.00e-02 4.00e+02 4.02e-02 2.59e+00 pdb=" N PRO B 388 " -0.070 5.00e-02 4.00e+02 pdb=" CA PRO B 388 " 0.020 5.00e-02 4.00e+02 pdb=" CD PRO B 388 " 0.022 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU A 366 " 0.026 5.00e-02 4.00e+02 3.93e-02 2.47e+00 pdb=" N PRO A 367 " -0.068 5.00e-02 4.00e+02 pdb=" CA PRO A 367 " 0.020 5.00e-02 4.00e+02 pdb=" CD PRO A 367 " 0.022 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB PHE B 234 " -0.011 2.00e-02 2.50e+03 1.18e-02 2.42e+00 pdb=" CG PHE B 234 " 0.026 2.00e-02 2.50e+03 pdb=" CD1 PHE B 234 " -0.008 2.00e-02 2.50e+03 pdb=" CD2 PHE B 234 " -0.001 2.00e-02 2.50e+03 pdb=" CE1 PHE B 234 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 PHE B 234 " -0.008 2.00e-02 2.50e+03 pdb=" CZ PHE B 234 " 0.003 2.00e-02 2.50e+03 ... (remaining 1929 not shown) Histogram of nonbonded interaction distances: 1.88 - 2.49: 73 2.49 - 3.09: 8049 3.09 - 3.69: 15676 3.69 - 4.30: 22437 4.30 - 4.90: 37146 Nonbonded interactions: 83381 Sorted by model distance: nonbonded pdb=" OD1 ASN C 117 " pdb=" NE2 HIS C 167 " model vdw 1.884 3.120 nonbonded pdb=" O ILE A 397 " pdb=" OG SER A 401 " model vdw 2.235 3.040 nonbonded pdb=" O GLY A 357 " pdb=" OG1 THR A 361 " model vdw 2.238 3.040 nonbonded pdb=" O LYS B 393 " pdb=" NH1 ARG B 395 " model vdw 2.247 3.120 nonbonded pdb=" ND2 ASN B 135 " pdb=" O ARG B 153 " model vdw 2.295 3.120 ... (remaining 83376 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.160 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: 0.420 Check model and map are aligned: 0.070 Set scattering table: 0.100 Process input model: 27.050 Find NCS groups from input model: 0.090 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:3.000 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.940 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8235 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 : 0.004 0.044 11011 Z= 0.209 Angle : 0.705 18.008 14925 Z= 0.411 Chirality : 0.045 0.170 1684 Planarity : 0.004 0.040 1932 Dihedral : 14.462 89.959 4115 Min Nonbonded Distance : 1.884 Molprobity Statistics. All-atom Clashscore : 8.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.99 % Favored : 90.01 % Rotamer: Outliers : 0.00 % Allowed : 7.21 % Favored : 92.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % 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: -3.71 (0.22), residues: 1342 helix: -1.21 (0.21), residues: 576 sheet: -4.24 (0.32), residues: 189 loop : -3.08 (0.24), residues: 577 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP C 143 HIS 0.004 0.001 HIS C 230 PHE 0.026 0.002 PHE B 234 TYR 0.013 0.001 TYR B 244 ARG 0.002 0.000 ARG C 181 Details of bonding type rmsd hydrogen bonds : bond 0.15702 ( 402) hydrogen bonds : angle 6.60221 ( 1164) covalent geometry : bond 0.00423 (11011) covalent geometry : angle 0.70539 (14925) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2684 Ramachandran restraints generated. 1342 Oldfield, 0 Emsley, 1342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2684 Ramachandran restraints generated. 1342 Oldfield, 0 Emsley, 1342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 1207 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 190 time to evaluate : 1.249 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 394 VAL cc_start: 0.9060 (t) cc_final: 0.8785 (p) REVERT: B 395 ARG cc_start: 0.8613 (mmt-90) cc_final: 0.7995 (mpt180) REVERT: C 9 GLU cc_start: 0.7065 (tp30) cc_final: 0.6718 (tp30) REVERT: C 92 TYR cc_start: 0.8110 (m-80) cc_final: 0.7806 (m-80) REVERT: C 195 MET cc_start: 0.7304 (pmm) cc_final: 0.6993 (pmm) REVERT: C 245 MET cc_start: 0.8117 (tpp) cc_final: 0.7722 (tpp) REVERT: C 260 PHE cc_start: 0.8698 (t80) cc_final: 0.7803 (t80) outliers start: 0 outliers final: 0 residues processed: 190 average time/residue: 0.2876 time to fit residues: 75.1396 Evaluate side-chains 112 residues out of total 1207 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 112 time to evaluate : 1.195 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 112 optimal weight: 0.3980 chunk 100 optimal weight: 0.8980 chunk 55 optimal weight: 3.9990 chunk 34 optimal weight: 5.9990 chunk 67 optimal weight: 0.6980 chunk 53 optimal weight: 0.9990 chunk 104 optimal weight: 7.9990 chunk 40 optimal weight: 2.9990 chunk 63 optimal weight: 4.9990 chunk 77 optimal weight: 0.0770 chunk 120 optimal weight: 0.1980 overall best weight: 0.4538 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 109 GLN B 240 ASN B 277 ASN ** B 363 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 255 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3921 r_free = 0.3921 target = 0.145794 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.099556 restraints weight = 16693.335| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3316 r_free = 0.3316 target = 0.100397 restraints weight = 13112.861| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3322 r_free = 0.3322 target = 0.100811 restraints weight = 10385.567| |-----------------------------------------------------------------------------| r_work (final): 0.3254 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8240 moved from start: 0.1637 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 11011 Z= 0.118 Angle : 0.607 8.966 14925 Z= 0.316 Chirality : 0.044 0.144 1684 Planarity : 0.004 0.046 1932 Dihedral : 4.989 25.793 1468 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 6.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.11 % Favored : 93.89 % Rotamer: Outliers : 1.08 % Allowed : 13.59 % Favored : 85.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.49 (0.23), residues: 1342 helix: -0.09 (0.22), residues: 580 sheet: -3.86 (0.36), residues: 158 loop : -2.61 (0.25), residues: 604 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 143 HIS 0.008 0.001 HIS C 241 PHE 0.032 0.001 PHE A 538 TYR 0.014 0.001 TYR B 86 ARG 0.008 0.000 ARG B 318 Details of bonding type rmsd hydrogen bonds : bond 0.03598 ( 402) hydrogen bonds : angle 5.08295 ( 1164) covalent geometry : bond 0.00254 (11011) covalent geometry : angle 0.60662 (14925) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2684 Ramachandran restraints generated. 1342 Oldfield, 0 Emsley, 1342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2684 Ramachandran restraints generated. 1342 Oldfield, 0 Emsley, 1342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 1207 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 132 time to evaluate : 1.274 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 426 TYR cc_start: 0.8888 (m-80) cc_final: 0.8678 (m-80) REVERT: A 489 MET cc_start: 0.7705 (tmm) cc_final: 0.7365 (tmm) REVERT: B 395 ARG cc_start: 0.8362 (mmt-90) cc_final: 0.8101 (mpt180) REVERT: C 89 ARG cc_start: 0.8184 (mtm180) cc_final: 0.7944 (mtm180) REVERT: C 245 MET cc_start: 0.7908 (tpp) cc_final: 0.7695 (tpp) REVERT: C 260 PHE cc_start: 0.8511 (t80) cc_final: 0.7854 (t80) outliers start: 13 outliers final: 5 residues processed: 140 average time/residue: 0.2110 time to fit residues: 43.7765 Evaluate side-chains 109 residues out of total 1207 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 104 time to evaluate : 1.276 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 VAL Chi-restraints excluded: chain A residue 388 LEU Chi-restraints excluded: chain A residue 540 VAL Chi-restraints excluded: chain B residue 291 VAL Chi-restraints excluded: chain B residue 313 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 11 optimal weight: 1.9990 chunk 114 optimal weight: 4.9990 chunk 12 optimal weight: 2.9990 chunk 129 optimal weight: 1.9990 chunk 71 optimal weight: 7.9990 chunk 2 optimal weight: 0.9990 chunk 9 optimal weight: 1.9990 chunk 132 optimal weight: 6.9990 chunk 7 optimal weight: 6.9990 chunk 84 optimal weight: 3.9990 chunk 4 optimal weight: 5.9990 overall best weight: 1.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 237 GLN B 201 ASN ** B 363 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 288 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3867 r_free = 0.3867 target = 0.141568 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3241 r_free = 0.3241 target = 0.095874 restraints weight = 17143.012| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3258 r_free = 0.3258 target = 0.096780 restraints weight = 12858.206| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3258 r_free = 0.3258 target = 0.096927 restraints weight = 10219.084| |-----------------------------------------------------------------------------| r_work (final): 0.3176 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8318 moved from start: 0.1835 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 11011 Z= 0.206 Angle : 0.629 7.250 14925 Z= 0.329 Chirality : 0.045 0.171 1684 Planarity : 0.004 0.047 1932 Dihedral : 5.124 24.110 1468 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 7.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.12 % Favored : 91.88 % Rotamer: Outliers : 2.49 % Allowed : 15.49 % Favored : 82.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.32 (0.23), residues: 1342 helix: 0.18 (0.22), residues: 578 sheet: -4.10 (0.32), residues: 181 loop : -2.43 (0.26), residues: 583 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 424 HIS 0.006 0.001 HIS C 241 PHE 0.027 0.002 PHE A 538 TYR 0.019 0.001 TYR B 74 ARG 0.004 0.000 ARG B 318 Details of bonding type rmsd hydrogen bonds : bond 0.04010 ( 402) hydrogen bonds : angle 5.11161 ( 1164) covalent geometry : bond 0.00491 (11011) covalent geometry : angle 0.62880 (14925) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2684 Ramachandran restraints generated. 1342 Oldfield, 0 Emsley, 1342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2684 Ramachandran restraints generated. 1342 Oldfield, 0 Emsley, 1342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 1207 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 112 time to evaluate : 1.699 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 341 CYS cc_start: 0.8150 (m) cc_final: 0.7895 (m) REVERT: B 395 ARG cc_start: 0.8459 (mmt-90) cc_final: 0.8182 (mpt180) REVERT: B 439 LEU cc_start: 0.8784 (OUTLIER) cc_final: 0.8394 (tt) REVERT: C 260 PHE cc_start: 0.8501 (t80) cc_final: 0.7884 (t80) REVERT: D 72 TYR cc_start: 0.4641 (OUTLIER) cc_final: 0.4010 (p90) outliers start: 30 outliers final: 18 residues processed: 127 average time/residue: 0.2188 time to fit residues: 42.7391 Evaluate side-chains 124 residues out of total 1207 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 104 time to evaluate : 1.305 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 VAL Chi-restraints excluded: chain A residue 239 ASP Chi-restraints excluded: chain A residue 263 VAL Chi-restraints excluded: chain A residue 388 LEU Chi-restraints excluded: chain A residue 522 LEU Chi-restraints excluded: chain A residue 540 VAL Chi-restraints excluded: chain B residue 45 THR Chi-restraints excluded: chain B residue 160 MET Chi-restraints excluded: chain B residue 182 SER Chi-restraints excluded: chain B residue 215 VAL Chi-restraints excluded: chain B residue 250 THR Chi-restraints excluded: chain B residue 291 VAL Chi-restraints excluded: chain B residue 313 LEU Chi-restraints excluded: chain B residue 359 THR Chi-restraints excluded: chain B residue 431 ILE Chi-restraints excluded: chain B residue 439 LEU Chi-restraints excluded: chain C residue 78 THR Chi-restraints excluded: chain C residue 105 VAL Chi-restraints excluded: chain C residue 159 VAL Chi-restraints excluded: chain D residue 72 TYR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 77 optimal weight: 0.5980 chunk 69 optimal weight: 0.8980 chunk 25 optimal weight: 1.9990 chunk 93 optimal weight: 0.9980 chunk 12 optimal weight: 0.0770 chunk 17 optimal weight: 0.8980 chunk 113 optimal weight: 6.9990 chunk 115 optimal weight: 5.9990 chunk 13 optimal weight: 0.7980 chunk 56 optimal weight: 3.9990 chunk 92 optimal weight: 3.9990 overall best weight: 0.6538 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 363 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 = 0.3910 r_free = 0.3910 target = 0.145114 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3275 r_free = 0.3275 target = 0.097559 restraints weight = 16842.538| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3300 r_free = 0.3300 target = 0.099546 restraints weight = 12491.505| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.099913 restraints weight = 9421.132| |-----------------------------------------------------------------------------| r_work (final): 0.3264 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8268 moved from start: 0.2128 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 11011 Z= 0.110 Angle : 0.559 8.185 14925 Z= 0.291 Chirality : 0.043 0.148 1684 Planarity : 0.004 0.045 1932 Dihedral : 4.864 22.861 1468 Min Nonbonded Distance : 2.567 Molprobity Statistics. All-atom Clashscore : 6.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.81 % Favored : 94.19 % Rotamer: Outliers : 1.33 % Allowed : 17.32 % Favored : 81.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % 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: 1342 helix: 0.51 (0.23), residues: 573 sheet: -4.01 (0.33), residues: 164 loop : -2.21 (0.25), residues: 605 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 143 HIS 0.006 0.001 HIS A 479 PHE 0.025 0.001 PHE A 538 TYR 0.018 0.001 TYR B 86 ARG 0.002 0.000 ARG B 257 Details of bonding type rmsd hydrogen bonds : bond 0.03240 ( 402) hydrogen bonds : angle 4.79914 ( 1164) covalent geometry : bond 0.00245 (11011) covalent geometry : angle 0.55881 (14925) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2684 Ramachandran restraints generated. 1342 Oldfield, 0 Emsley, 1342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2684 Ramachandran restraints generated. 1342 Oldfield, 0 Emsley, 1342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 1207 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 120 time to evaluate : 2.532 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 528 MET cc_start: 0.8589 (mmt) cc_final: 0.8349 (mmt) REVERT: B 341 CYS cc_start: 0.7973 (m) cc_final: 0.7668 (m) REVERT: B 395 ARG cc_start: 0.8368 (mmt-90) cc_final: 0.8122 (mpt180) REVERT: C 260 PHE cc_start: 0.8454 (t80) cc_final: 0.7749 (t80) REVERT: D 72 TYR cc_start: 0.4461 (OUTLIER) cc_final: 0.3960 (p90) outliers start: 16 outliers final: 7 residues processed: 131 average time/residue: 0.2574 time to fit residues: 52.1884 Evaluate side-chains 118 residues out of total 1207 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 110 time to evaluate : 1.377 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 388 LEU Chi-restraints excluded: chain B residue 45 THR Chi-restraints excluded: chain B residue 160 MET Chi-restraints excluded: chain B residue 291 VAL Chi-restraints excluded: chain B residue 313 LEU Chi-restraints excluded: chain B residue 431 ILE Chi-restraints excluded: chain C residue 275 ILE Chi-restraints excluded: chain D residue 72 TYR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 109 optimal weight: 3.9990 chunk 72 optimal weight: 5.9990 chunk 94 optimal weight: 3.9990 chunk 61 optimal weight: 2.9990 chunk 2 optimal weight: 4.9990 chunk 119 optimal weight: 0.6980 chunk 5 optimal weight: 2.9990 chunk 27 optimal weight: 0.0670 chunk 86 optimal weight: 2.9990 chunk 121 optimal weight: 10.0000 chunk 117 optimal weight: 10.0000 overall best weight: 1.9524 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 363 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 288 GLN ** 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 = 0.3866 r_free = 0.3866 target = 0.141600 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3216 r_free = 0.3216 target = 0.094158 restraints weight = 17156.396| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3235 r_free = 0.3235 target = 0.095577 restraints weight = 13187.981| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3237 r_free = 0.3237 target = 0.095711 restraints weight = 10268.895| |-----------------------------------------------------------------------------| r_work (final): 0.3175 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8356 moved from start: 0.2225 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 11011 Z= 0.202 Angle : 0.614 7.165 14925 Z= 0.319 Chirality : 0.045 0.170 1684 Planarity : 0.004 0.042 1932 Dihedral : 5.001 23.550 1468 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 7.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.05 % Favored : 91.95 % Rotamer: Outliers : 2.24 % Allowed : 18.06 % Favored : 79.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % 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: 1342 helix: 0.47 (0.23), residues: 576 sheet: -4.02 (0.32), residues: 177 loop : -2.10 (0.26), residues: 589 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 143 HIS 0.005 0.001 HIS A 479 PHE 0.022 0.002 PHE A 538 TYR 0.020 0.001 TYR B 74 ARG 0.002 0.000 ARG B 210 Details of bonding type rmsd hydrogen bonds : bond 0.03710 ( 402) hydrogen bonds : angle 4.96533 ( 1164) covalent geometry : bond 0.00486 (11011) covalent geometry : angle 0.61446 (14925) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2684 Ramachandran restraints generated. 1342 Oldfield, 0 Emsley, 1342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2684 Ramachandran restraints generated. 1342 Oldfield, 0 Emsley, 1342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 1207 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 109 time to evaluate : 1.495 Fit side-chains revert: symmetry clash REVERT: B 341 CYS cc_start: 0.7948 (m) cc_final: 0.7600 (m) REVERT: B 395 ARG cc_start: 0.8475 (mmt-90) cc_final: 0.8174 (mpt180) REVERT: B 439 LEU cc_start: 0.8783 (OUTLIER) cc_final: 0.8410 (tt) REVERT: C 195 MET cc_start: 0.7435 (pmm) cc_final: 0.7113 (pmm) REVERT: C 250 TRP cc_start: 0.7477 (m100) cc_final: 0.7252 (m-10) REVERT: C 260 PHE cc_start: 0.8557 (t80) cc_final: 0.7944 (t80) REVERT: D 72 TYR cc_start: 0.4536 (OUTLIER) cc_final: 0.4055 (p90) outliers start: 27 outliers final: 21 residues processed: 129 average time/residue: 0.2533 time to fit residues: 49.8331 Evaluate side-chains 131 residues out of total 1207 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 108 time to evaluate : 1.446 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 VAL Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain A residue 263 VAL Chi-restraints excluded: chain A residue 293 ASP Chi-restraints excluded: chain A residue 388 LEU Chi-restraints excluded: chain A residue 502 LEU Chi-restraints excluded: chain A residue 522 LEU Chi-restraints excluded: chain A residue 540 VAL Chi-restraints excluded: chain B residue 45 THR Chi-restraints excluded: chain B residue 160 MET Chi-restraints excluded: chain B residue 215 VAL Chi-restraints excluded: chain B residue 250 THR Chi-restraints excluded: chain B residue 291 VAL Chi-restraints excluded: chain B residue 313 LEU Chi-restraints excluded: chain B residue 354 ASP Chi-restraints excluded: chain B residue 359 THR Chi-restraints excluded: chain B residue 368 MET Chi-restraints excluded: chain B residue 422 THR Chi-restraints excluded: chain B residue 431 ILE Chi-restraints excluded: chain B residue 439 LEU Chi-restraints excluded: chain C residue 256 VAL Chi-restraints excluded: chain C residue 301 THR Chi-restraints excluded: chain D residue 72 TYR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 43 optimal weight: 0.9980 chunk 101 optimal weight: 0.0070 chunk 66 optimal weight: 0.0050 chunk 110 optimal weight: 4.9990 chunk 17 optimal weight: 0.3980 chunk 22 optimal weight: 0.1980 chunk 64 optimal weight: 1.9990 chunk 25 optimal weight: 0.8980 chunk 19 optimal weight: 0.9980 chunk 30 optimal weight: 0.7980 chunk 88 optimal weight: 0.8980 overall best weight: 0.2812 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 363 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 241 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3924 r_free = 0.3924 target = 0.146368 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3298 r_free = 0.3298 target = 0.099883 restraints weight = 17050.147| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3332 r_free = 0.3332 target = 0.102159 restraints weight = 12037.284| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3325 r_free = 0.3325 target = 0.101745 restraints weight = 9135.898| |-----------------------------------------------------------------------------| r_work (final): 0.3261 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8237 moved from start: 0.2537 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 11011 Z= 0.101 Angle : 0.554 8.447 14925 Z= 0.286 Chirality : 0.042 0.141 1684 Planarity : 0.004 0.042 1932 Dihedral : 4.652 21.701 1468 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 6.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.47 % Favored : 95.53 % Rotamer: Outliers : 1.33 % Allowed : 19.06 % Favored : 79.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % 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: -1.60 (0.24), residues: 1342 helix: 0.66 (0.23), residues: 579 sheet: -3.68 (0.33), residues: 180 loop : -1.94 (0.25), residues: 583 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 143 HIS 0.005 0.001 HIS A 479 PHE 0.019 0.001 PHE A 538 TYR 0.016 0.001 TYR A 577 ARG 0.002 0.000 ARG A 171 Details of bonding type rmsd hydrogen bonds : bond 0.02880 ( 402) hydrogen bonds : angle 4.65929 ( 1164) covalent geometry : bond 0.00215 (11011) covalent geometry : angle 0.55370 (14925) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2684 Ramachandran restraints generated. 1342 Oldfield, 0 Emsley, 1342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2684 Ramachandran restraints generated. 1342 Oldfield, 0 Emsley, 1342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 1207 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 117 time to evaluate : 2.248 Fit side-chains revert: symmetry clash REVERT: B 341 CYS cc_start: 0.7952 (m) cc_final: 0.7601 (m) REVERT: B 395 ARG cc_start: 0.8381 (mmt-90) cc_final: 0.8148 (mpt180) REVERT: B 439 LEU cc_start: 0.8638 (OUTLIER) cc_final: 0.8392 (tt) REVERT: C 83 MET cc_start: 0.8595 (mmm) cc_final: 0.7894 (mmt) REVERT: C 143 TRP cc_start: 0.8022 (t60) cc_final: 0.7548 (t60) REVERT: C 195 MET cc_start: 0.7391 (pmm) cc_final: 0.7140 (pmm) REVERT: C 218 TYR cc_start: 0.8177 (m-80) cc_final: 0.7969 (m-80) REVERT: C 260 PHE cc_start: 0.8496 (t80) cc_final: 0.7738 (t80) REVERT: D 72 TYR cc_start: 0.4301 (OUTLIER) cc_final: 0.3809 (p90) outliers start: 16 outliers final: 9 residues processed: 131 average time/residue: 0.2812 time to fit residues: 57.6636 Evaluate side-chains 119 residues out of total 1207 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 108 time to evaluate : 1.729 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 VAL Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain B residue 45 THR Chi-restraints excluded: chain B residue 291 VAL Chi-restraints excluded: chain B residue 313 LEU Chi-restraints excluded: chain B residue 357 VAL Chi-restraints excluded: chain B residue 359 THR Chi-restraints excluded: chain B residue 439 LEU Chi-restraints excluded: chain C residue 256 VAL Chi-restraints excluded: chain C residue 275 ILE Chi-restraints excluded: chain D residue 72 TYR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 124 optimal weight: 0.8980 chunk 88 optimal weight: 2.9990 chunk 96 optimal weight: 4.9990 chunk 105 optimal weight: 6.9990 chunk 59 optimal weight: 3.9990 chunk 0 optimal weight: 10.0000 chunk 9 optimal weight: 3.9990 chunk 108 optimal weight: 4.9990 chunk 92 optimal weight: 4.9990 chunk 122 optimal weight: 6.9990 chunk 48 optimal weight: 0.2980 overall best weight: 2.4386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 240 ASN ** B 363 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 241 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 288 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3857 r_free = 0.3857 target = 0.140719 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3215 r_free = 0.3215 target = 0.094480 restraints weight = 17380.024| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3240 r_free = 0.3240 target = 0.095835 restraints weight = 13366.455| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3239 r_free = 0.3239 target = 0.095758 restraints weight = 10252.496| |-----------------------------------------------------------------------------| r_work (final): 0.3179 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8332 moved from start: 0.2512 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.049 11011 Z= 0.244 Angle : 0.651 7.441 14925 Z= 0.338 Chirality : 0.045 0.183 1684 Planarity : 0.004 0.040 1932 Dihedral : 4.990 23.771 1468 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 8.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.42 % Favored : 91.58 % Rotamer: Outliers : 1.91 % Allowed : 19.47 % Favored : 78.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % 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: 1342 helix: 0.58 (0.23), residues: 580 sheet: -3.73 (0.35), residues: 177 loop : -1.99 (0.26), residues: 585 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP C 250 HIS 0.005 0.001 HIS B 425 PHE 0.019 0.002 PHE A 538 TYR 0.023 0.002 TYR B 74 ARG 0.003 0.000 ARG A 260 Details of bonding type rmsd hydrogen bonds : bond 0.03781 ( 402) hydrogen bonds : angle 4.93362 ( 1164) covalent geometry : bond 0.00580 (11011) covalent geometry : angle 0.65102 (14925) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2684 Ramachandran restraints generated. 1342 Oldfield, 0 Emsley, 1342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2684 Ramachandran restraints generated. 1342 Oldfield, 0 Emsley, 1342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 1207 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 109 time to evaluate : 1.529 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 291 MET cc_start: 0.8844 (OUTLIER) cc_final: 0.8580 (ttp) REVERT: B 341 CYS cc_start: 0.7921 (m) cc_final: 0.7591 (m) REVERT: B 395 ARG cc_start: 0.8463 (mmt-90) cc_final: 0.8188 (mpt180) REVERT: B 439 LEU cc_start: 0.8832 (OUTLIER) cc_final: 0.8484 (tt) REVERT: C 195 MET cc_start: 0.7474 (pmm) cc_final: 0.7249 (pmm) REVERT: C 260 PHE cc_start: 0.8488 (t80) cc_final: 0.7958 (t80) REVERT: D 72 TYR cc_start: 0.4628 (OUTLIER) cc_final: 0.4122 (p90) outliers start: 23 outliers final: 14 residues processed: 128 average time/residue: 0.2948 time to fit residues: 56.7483 Evaluate side-chains 117 residues out of total 1207 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 100 time to evaluate : 1.397 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 VAL Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain A residue 239 ASP Chi-restraints excluded: chain A residue 291 MET Chi-restraints excluded: chain A residue 388 LEU Chi-restraints excluded: chain A residue 400 LEU Chi-restraints excluded: chain A residue 502 LEU Chi-restraints excluded: chain A residue 522 LEU Chi-restraints excluded: chain B residue 45 THR Chi-restraints excluded: chain B residue 291 VAL Chi-restraints excluded: chain B residue 313 LEU Chi-restraints excluded: chain B residue 359 THR Chi-restraints excluded: chain B residue 422 THR Chi-restraints excluded: chain B residue 431 ILE Chi-restraints excluded: chain B residue 439 LEU Chi-restraints excluded: chain C residue 301 THR Chi-restraints excluded: chain D residue 72 TYR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 132 optimal weight: 6.9990 chunk 88 optimal weight: 0.9990 chunk 108 optimal weight: 0.9980 chunk 86 optimal weight: 0.7980 chunk 83 optimal weight: 5.9990 chunk 95 optimal weight: 3.9990 chunk 115 optimal weight: 7.9990 chunk 103 optimal weight: 3.9990 chunk 69 optimal weight: 0.6980 chunk 110 optimal weight: 2.9990 chunk 40 optimal weight: 0.6980 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 363 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 429 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3897 r_free = 0.3897 target = 0.143918 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3276 r_free = 0.3276 target = 0.098111 restraints weight = 17105.424| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3275 r_free = 0.3275 target = 0.098028 restraints weight = 12424.996| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3274 r_free = 0.3274 target = 0.098316 restraints weight = 10615.096| |-----------------------------------------------------------------------------| r_work (final): 0.3226 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8294 moved from start: 0.2684 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 11011 Z= 0.120 Angle : 0.588 9.426 14925 Z= 0.301 Chirality : 0.043 0.148 1684 Planarity : 0.004 0.038 1932 Dihedral : 4.806 23.015 1468 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 7.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.29 % Favored : 94.71 % Rotamer: Outliers : 1.82 % Allowed : 19.97 % Favored : 78.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % 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: -1.51 (0.24), residues: 1342 helix: 0.71 (0.23), residues: 578 sheet: -3.59 (0.34), residues: 180 loop : -1.87 (0.26), residues: 584 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 143 HIS 0.005 0.001 HIS A 479 PHE 0.017 0.001 PHE A 538 TYR 0.018 0.001 TYR A 577 ARG 0.002 0.000 ARG B 318 Details of bonding type rmsd hydrogen bonds : bond 0.03066 ( 402) hydrogen bonds : angle 4.72942 ( 1164) covalent geometry : bond 0.00276 (11011) covalent geometry : angle 0.58808 (14925) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2684 Ramachandran restraints generated. 1342 Oldfield, 0 Emsley, 1342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2684 Ramachandran restraints generated. 1342 Oldfield, 0 Emsley, 1342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 1207 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 110 time to evaluate : 1.458 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 426 TYR cc_start: 0.8798 (m-80) cc_final: 0.8565 (m-80) REVERT: B 341 CYS cc_start: 0.7955 (m) cc_final: 0.7586 (m) REVERT: B 395 ARG cc_start: 0.8433 (mmt-90) cc_final: 0.8154 (mpt180) REVERT: B 439 LEU cc_start: 0.8746 (OUTLIER) cc_final: 0.8463 (tt) REVERT: C 83 MET cc_start: 0.8824 (mmm) cc_final: 0.8597 (mmt) REVERT: C 143 TRP cc_start: 0.8018 (t60) cc_final: 0.7554 (t60) REVERT: C 195 MET cc_start: 0.7543 (pmm) cc_final: 0.7321 (pmm) REVERT: C 218 TYR cc_start: 0.7982 (m-80) cc_final: 0.7758 (m-80) REVERT: C 260 PHE cc_start: 0.8525 (t80) cc_final: 0.7773 (t80) REVERT: D 72 TYR cc_start: 0.4429 (OUTLIER) cc_final: 0.3982 (p90) outliers start: 22 outliers final: 17 residues processed: 125 average time/residue: 0.2473 time to fit residues: 46.7219 Evaluate side-chains 127 residues out of total 1207 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 108 time to evaluate : 1.737 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 VAL Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain A residue 86 VAL Chi-restraints excluded: chain A residue 291 MET Chi-restraints excluded: chain A residue 388 LEU Chi-restraints excluded: chain A residue 540 VAL Chi-restraints excluded: chain B residue 45 THR Chi-restraints excluded: chain B residue 250 THR Chi-restraints excluded: chain B residue 291 VAL Chi-restraints excluded: chain B residue 313 LEU Chi-restraints excluded: chain B residue 357 VAL Chi-restraints excluded: chain B residue 359 THR Chi-restraints excluded: chain B residue 368 MET Chi-restraints excluded: chain B residue 431 ILE Chi-restraints excluded: chain B residue 439 LEU Chi-restraints excluded: chain C residue 256 VAL Chi-restraints excluded: chain C residue 275 ILE Chi-restraints excluded: chain C residue 301 THR Chi-restraints excluded: chain D residue 72 TYR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 109 optimal weight: 2.9990 chunk 95 optimal weight: 0.6980 chunk 87 optimal weight: 0.8980 chunk 31 optimal weight: 4.9990 chunk 75 optimal weight: 2.9990 chunk 15 optimal weight: 1.9990 chunk 64 optimal weight: 1.9990 chunk 22 optimal weight: 0.9980 chunk 112 optimal weight: 1.9990 chunk 30 optimal weight: 0.9990 chunk 73 optimal weight: 0.9980 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 363 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 = 0.3896 r_free = 0.3896 target = 0.143787 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3246 r_free = 0.3246 target = 0.095606 restraints weight = 17320.573| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3264 r_free = 0.3264 target = 0.097004 restraints weight = 14478.739| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3275 r_free = 0.3275 target = 0.097855 restraints weight = 10578.894| |-----------------------------------------------------------------------------| r_work (final): 0.3183 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8285 moved from start: 0.2773 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 11011 Z= 0.125 Angle : 0.583 8.843 14925 Z= 0.297 Chirality : 0.042 0.144 1684 Planarity : 0.004 0.038 1932 Dihedral : 4.719 22.541 1468 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 7.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.18 % Favored : 93.82 % Rotamer: Outliers : 1.82 % Allowed : 20.13 % Favored : 78.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % 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: -1.40 (0.24), residues: 1342 helix: 0.77 (0.23), residues: 581 sheet: -3.44 (0.35), residues: 180 loop : -1.82 (0.26), residues: 581 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 143 HIS 0.005 0.001 HIS A 479 PHE 0.017 0.001 PHE A 538 TYR 0.018 0.001 TYR B 86 ARG 0.002 0.000 ARG B 318 Details of bonding type rmsd hydrogen bonds : bond 0.03087 ( 402) hydrogen bonds : angle 4.64106 ( 1164) covalent geometry : bond 0.00293 (11011) covalent geometry : angle 0.58283 (14925) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2684 Ramachandran restraints generated. 1342 Oldfield, 0 Emsley, 1342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2684 Ramachandran restraints generated. 1342 Oldfield, 0 Emsley, 1342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 1207 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 107 time to evaluate : 1.588 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 426 TYR cc_start: 0.8782 (m-80) cc_final: 0.8555 (m-80) REVERT: B 341 CYS cc_start: 0.7954 (m) cc_final: 0.7575 (m) REVERT: B 395 ARG cc_start: 0.8448 (mmt-90) cc_final: 0.8149 (mpt180) REVERT: B 439 LEU cc_start: 0.8756 (OUTLIER) cc_final: 0.8340 (tt) REVERT: C 143 TRP cc_start: 0.7996 (t60) cc_final: 0.7561 (t60) REVERT: C 195 MET cc_start: 0.7549 (pmm) cc_final: 0.7345 (pmm) REVERT: C 218 TYR cc_start: 0.7851 (m-80) cc_final: 0.7642 (m-80) REVERT: C 260 PHE cc_start: 0.8492 (t80) cc_final: 0.7807 (t80) REVERT: D 72 TYR cc_start: 0.4494 (OUTLIER) cc_final: 0.4008 (p90) outliers start: 22 outliers final: 18 residues processed: 124 average time/residue: 0.2699 time to fit residues: 49.7336 Evaluate side-chains 125 residues out of total 1207 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 105 time to evaluate : 1.563 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 VAL Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain A residue 86 VAL Chi-restraints excluded: chain A residue 180 MET Chi-restraints excluded: chain A residue 263 VAL Chi-restraints excluded: chain A residue 388 LEU Chi-restraints excluded: chain A residue 502 LEU Chi-restraints excluded: chain B residue 45 THR Chi-restraints excluded: chain B residue 215 VAL Chi-restraints excluded: chain B residue 291 VAL Chi-restraints excluded: chain B residue 313 LEU Chi-restraints excluded: chain B residue 357 VAL Chi-restraints excluded: chain B residue 359 THR Chi-restraints excluded: chain B residue 368 MET Chi-restraints excluded: chain B residue 422 THR Chi-restraints excluded: chain B residue 431 ILE Chi-restraints excluded: chain B residue 439 LEU Chi-restraints excluded: chain C residue 275 ILE Chi-restraints excluded: chain C residue 301 THR Chi-restraints excluded: chain D residue 72 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 82 optimal weight: 0.0030 chunk 15 optimal weight: 2.9990 chunk 22 optimal weight: 0.8980 chunk 75 optimal weight: 0.9990 chunk 48 optimal weight: 2.9990 chunk 62 optimal weight: 0.9980 chunk 80 optimal weight: 0.6980 chunk 99 optimal weight: 3.9990 chunk 129 optimal weight: 2.9990 chunk 63 optimal weight: 0.9980 chunk 35 optimal weight: 1.9990 overall best weight: 0.7190 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 363 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 = 0.3915 r_free = 0.3915 target = 0.145305 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3306 r_free = 0.3306 target = 0.100096 restraints weight = 17088.928| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3325 r_free = 0.3325 target = 0.101270 restraints weight = 12426.279| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.100872 restraints weight = 9712.136| |-----------------------------------------------------------------------------| r_work (final): 0.3290 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8236 moved from start: 0.2930 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 11011 Z= 0.111 Angle : 0.582 10.035 14925 Z= 0.293 Chirality : 0.042 0.142 1684 Planarity : 0.004 0.038 1932 Dihedral : 4.597 21.743 1468 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 7.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.29 % Favored : 94.71 % Rotamer: Outliers : 1.74 % Allowed : 20.22 % Favored : 78.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.19 (0.24), residues: 1342 helix: 0.93 (0.23), residues: 577 sheet: -3.21 (0.37), residues: 169 loop : -1.78 (0.26), residues: 596 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 143 HIS 0.005 0.001 HIS A 479 PHE 0.016 0.001 PHE A 538 TYR 0.017 0.001 TYR B 86 ARG 0.002 0.000 ARG A 249 Details of bonding type rmsd hydrogen bonds : bond 0.02923 ( 402) hydrogen bonds : angle 4.52400 ( 1164) covalent geometry : bond 0.00257 (11011) covalent geometry : angle 0.58184 (14925) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2684 Ramachandran restraints generated. 1342 Oldfield, 0 Emsley, 1342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2684 Ramachandran restraints generated. 1342 Oldfield, 0 Emsley, 1342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 1207 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 111 time to evaluate : 3.902 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 291 MET cc_start: 0.8809 (OUTLIER) cc_final: 0.8418 (ttp) REVERT: A 426 TYR cc_start: 0.8755 (m-80) cc_final: 0.8523 (m-80) REVERT: B 341 CYS cc_start: 0.7906 (m) cc_final: 0.7523 (m) REVERT: B 395 ARG cc_start: 0.8442 (mmt-90) cc_final: 0.8153 (mpt180) REVERT: B 439 LEU cc_start: 0.8696 (OUTLIER) cc_final: 0.8434 (tt) REVERT: C 143 TRP cc_start: 0.7962 (t60) cc_final: 0.7548 (t60) REVERT: C 195 MET cc_start: 0.7541 (pmm) cc_final: 0.7340 (pmm) REVERT: C 260 PHE cc_start: 0.8451 (t80) cc_final: 0.7705 (t80) REVERT: D 72 TYR cc_start: 0.4515 (OUTLIER) cc_final: 0.4091 (p90) outliers start: 21 outliers final: 16 residues processed: 125 average time/residue: 0.3122 time to fit residues: 60.2405 Evaluate side-chains 126 residues out of total 1207 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 107 time to evaluate : 2.383 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 VAL Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain A residue 86 VAL Chi-restraints excluded: chain A residue 180 MET Chi-restraints excluded: chain A residue 291 MET Chi-restraints excluded: chain A residue 388 LEU Chi-restraints excluded: chain A residue 502 LEU Chi-restraints excluded: chain A residue 540 VAL Chi-restraints excluded: chain B residue 45 THR Chi-restraints excluded: chain B residue 291 VAL Chi-restraints excluded: chain B residue 313 LEU Chi-restraints excluded: chain B residue 357 VAL Chi-restraints excluded: chain B residue 359 THR Chi-restraints excluded: chain B residue 422 THR Chi-restraints excluded: chain B residue 431 ILE Chi-restraints excluded: chain B residue 439 LEU Chi-restraints excluded: chain C residue 256 VAL Chi-restraints excluded: chain C residue 275 ILE Chi-restraints excluded: chain D residue 72 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 11 optimal weight: 2.9990 chunk 80 optimal weight: 0.9980 chunk 4 optimal weight: 3.9990 chunk 116 optimal weight: 0.9990 chunk 35 optimal weight: 1.9990 chunk 48 optimal weight: 0.7980 chunk 109 optimal weight: 1.9990 chunk 117 optimal weight: 1.9990 chunk 40 optimal weight: 2.9990 chunk 121 optimal weight: 8.9990 chunk 37 optimal weight: 1.9990 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 363 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 288 GLN ** 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 = 0.3890 r_free = 0.3890 target = 0.143308 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3231 r_free = 0.3231 target = 0.095229 restraints weight = 17204.532| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3260 r_free = 0.3260 target = 0.096805 restraints weight = 12940.513| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3267 r_free = 0.3267 target = 0.097454 restraints weight = 10103.166| |-----------------------------------------------------------------------------| r_work (final): 0.3210 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8303 moved from start: 0.2920 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 11011 Z= 0.154 Angle : 0.608 9.853 14925 Z= 0.307 Chirality : 0.043 0.154 1684 Planarity : 0.004 0.038 1932 Dihedral : 4.684 22.831 1468 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 7.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.56 % Favored : 93.44 % Rotamer: Outliers : 2.07 % Allowed : 19.80 % Favored : 78.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % 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: -1.21 (0.24), residues: 1342 helix: 0.96 (0.23), residues: 573 sheet: -3.12 (0.37), residues: 179 loop : -1.81 (0.26), residues: 590 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 143 HIS 0.005 0.001 HIS A 479 PHE 0.017 0.001 PHE A 369 TYR 0.023 0.001 TYR B 86 ARG 0.004 0.000 ARG C 89 Details of bonding type rmsd hydrogen bonds : bond 0.03163 ( 402) hydrogen bonds : angle 4.61251 ( 1164) covalent geometry : bond 0.00368 (11011) covalent geometry : angle 0.60777 (14925) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4056.63 seconds wall clock time: 76 minutes 27.67 seconds (4587.67 seconds total)