Starting phenix.real_space_refine on Tue Oct 27 23:17:55 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9wpf_66141/10_2026/9wpf_66141_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/9wpf_66141/10_2026/9wpf_66141.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9wpf_66141/10_2026/9wpf_66141_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9wpf_66141/10_2026/9wpf_66141_trim.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9wpf_66141/10_2026/9wpf_66141.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9wpf_66141/10_2026/9wpf_66141.map" } resolution = 3.6 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs 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= 0.002 sd= 0.029 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: 6 Type Number sf(0) Gaussians P 6 5.49 5 S 87 5.16 5 C 8577 2.51 5 N 1992 2.21 5 O 2248 1.98 5 H 12668 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 35 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.3rc1-6221/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 25578 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 5891 Number of conformers: 1 Conformer: "" Number of residues, atoms: 366, 5891 Classifications: {'peptide': 366} Link IDs: {'PTRANS': 10, 'TRANS': 355} Chain breaks: 1 Chain: "B" Number of atoms: 6418 Number of conformers: 1 Conformer: "" Number of residues, atoms: 395, 6418 Classifications: {'peptide': 395} Link IDs: {'PTRANS': 10, 'TRANS': 384} Chain breaks: 2 Chain: "C" Number of atoms: 6462 Number of conformers: 1 Conformer: "" Number of residues, atoms: 399, 6462 Classifications: {'peptide': 399} Link IDs: {'PTRANS': 10, 'TRANS': 388} Chain breaks: 1 Chain: "D" Number of atoms: 6483 Number of conformers: 1 Conformer: "" Number of residues, atoms: 400, 6483 Classifications: {'peptide': 400} Link IDs: {'PTRANS': 10, 'TRANS': 389} Chain breaks: 1 Chain: "A" Number of atoms: 54 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 54 Unusual residues: {'PC1': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 162 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 162 Unusual residues: {'PC1': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "C" Number of atoms: 54 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 54 Unusual residues: {'PC1': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 54 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 54 Unusual residues: {'PC1': 1} Classifications: {'undetermined': 1} Time building chain proxies: 3.95, per 1000 atoms: 0.15 Number of scatterers: 25578 At special positions: 0 Unit cell: (116.44, 114.8, 118.08, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 87 16.00 P 6 15.00 O 2248 8.00 N 1992 7.00 C 8577 6.00 H 12668 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 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=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 2.49 Conformation dependent library (CDL) restraints added in 798.9 milliseconds 3084 Ramachandran restraints generated. 1542 Oldfield, 0 Emsley, 1542 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2982 Finding SS restraints... Secondary structure from input PDB file: 57 helices and 5 sheets defined 80.6% alpha, 1.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.42 Creating SS restraints... Processing helix chain 'A' and resid 6 through 13 Processing helix chain 'A' and resid 14 through 19 removed outlier: 4.243A pdb=" N LEU A 18 " --> pdb=" O GLY A 14 " (cutoff:3.500A) Processing helix chain 'A' and resid 27 through 32 Processing helix chain 'A' and resid 32 through 56 Processing helix chain 'A' and resid 59 through 86 removed outlier: 3.562A pdb=" N HIS A 86 " --> pdb=" O THR A 82 " (cutoff:3.500A) Processing helix chain 'A' and resid 86 through 95 Processing helix chain 'A' and resid 96 through 98 No H-bonds generated for 'chain 'A' and resid 96 through 98' Processing helix chain 'A' and resid 102 through 108 Processing helix chain 'A' and resid 109 through 140 Processing helix chain 'A' and resid 141 through 144 Processing helix chain 'A' and resid 146 through 150 Processing helix chain 'A' and resid 151 through 201 removed outlier: 3.573A pdb=" N LYS A 200 " --> pdb=" O SER A 196 " (cutoff:3.500A) Processing helix chain 'A' and resid 235 through 289 Proline residue: A 263 - end of helix Processing helix chain 'A' and resid 295 through 335 removed outlier: 4.287A pdb=" N ASN A 330 " --> pdb=" O ARG A 326 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N PHE A 331 " --> pdb=" O SER A 327 " (cutoff:3.500A) Processing helix chain 'A' and resid 342 through 359 Processing helix chain 'A' and resid 372 through 390 Processing helix chain 'B' and resid 4 through 9 Processing helix chain 'B' and resid 9 through 18 Processing helix chain 'B' and resid 31 through 63 Processing helix chain 'B' and resid 66 through 93 removed outlier: 4.339A pdb=" N SER B 83 " --> pdb=" O PHE B 79 " (cutoff:3.500A) Processing helix chain 'B' and resid 93 through 103 removed outlier: 3.835A pdb=" N PHE B 97 " --> pdb=" O GLY B 93 " (cutoff:3.500A) Processing helix chain 'B' and resid 110 through 112 No H-bonds generated for 'chain 'B' and resid 110 through 112' Processing helix chain 'B' and resid 113 through 152 removed outlier: 3.745A pdb=" N LEU B 131 " --> pdb=" O ARG B 127 " (cutoff:3.500A) Processing helix chain 'B' and resid 189 through 242 removed outlier: 3.660A pdb=" N VAL B 194 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 4.164A pdb=" N ASN B 236 " --> pdb=" O LYS B 232 " (cutoff:3.500A) Proline residue: B 237 - end of helix Processing helix chain 'B' and resid 302 through 333 Processing helix chain 'B' and resid 334 through 357 removed outlier: 3.653A pdb=" N LYS B 357 " --> pdb=" O TYR B 353 " (cutoff:3.500A) Processing helix chain 'B' and resid 362 through 394 removed outlier: 4.290A pdb=" N THR B 368 " --> pdb=" O PHE B 364 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N CYS B 383 " --> pdb=" O ILE B 379 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N LEU B 389 " --> pdb=" O HIS B 385 " (cutoff:3.500A) Processing helix chain 'B' and resid 396 through 400 removed outlier: 3.964A pdb=" N ALA B 399 " --> pdb=" O VAL B 396 " (cutoff:3.500A) Processing helix chain 'B' and resid 410 through 423 Processing helix chain 'B' and resid 432 through 434 No H-bonds generated for 'chain 'B' and resid 432 through 434' Processing helix chain 'B' and resid 438 through 458 removed outlier: 3.685A pdb=" N GLN B 458 " --> pdb=" O MET B 454 " (cutoff:3.500A) Processing helix chain 'C' and resid 2 through 6 Processing helix chain 'C' and resid 6 through 17 Processing helix chain 'C' and resid 28 through 60 Processing helix chain 'C' and resid 63 through 89 removed outlier: 4.230A pdb=" N SER C 80 " --> pdb=" O PHE C 76 " (cutoff:3.500A) Processing helix chain 'C' and resid 90 through 100 removed outlier: 3.995A pdb=" N PHE C 94 " --> pdb=" O GLY C 90 " (cutoff:3.500A) Processing helix chain 'C' and resid 110 through 149 removed outlier: 3.754A pdb=" N THR C 145 " --> pdb=" O ILE C 141 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N PHE C 148 " --> pdb=" O THR C 144 " (cutoff:3.500A) Processing helix chain 'C' and resid 186 through 238 removed outlier: 4.034A pdb=" N ASN C 233 " --> pdb=" O LYS C 229 " (cutoff:3.500A) Proline residue: C 234 - end of helix Processing helix chain 'C' and resid 299 through 330 Processing helix chain 'C' and resid 330 through 354 removed outlier: 3.688A pdb=" N LEU C 335 " --> pdb=" O GLY C 331 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N THR C 346 " --> pdb=" O THR C 342 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N LYS C 354 " --> pdb=" O TYR C 350 " (cutoff:3.500A) Processing helix chain 'C' and resid 359 through 392 removed outlier: 3.584A pdb=" N PHE C 363 " --> pdb=" O ASN C 359 " (cutoff:3.500A) Processing helix chain 'C' and resid 406 through 420 Processing helix chain 'C' and resid 435 through 454 removed outlier: 3.698A pdb=" N PHE C 439 " --> pdb=" O SER C 435 " (cutoff:3.500A) Processing helix chain 'D' and resid 2 through 6 Processing helix chain 'D' and resid 6 through 17 removed outlier: 3.546A pdb=" N GLY D 17 " --> pdb=" O ILE D 13 " (cutoff:3.500A) Processing helix chain 'D' and resid 28 through 61 removed outlier: 3.764A pdb=" N SER D 61 " --> pdb=" O MET D 57 " (cutoff:3.500A) Processing helix chain 'D' and resid 63 through 89 removed outlier: 4.804A pdb=" N SER D 80 " --> pdb=" O PHE D 76 " (cutoff:3.500A) Processing helix chain 'D' and resid 90 through 98 removed outlier: 3.702A pdb=" N PHE D 94 " --> pdb=" O GLY D 90 " (cutoff:3.500A) Processing helix chain 'D' and resid 107 through 109 No H-bonds generated for 'chain 'D' and resid 107 through 109' Processing helix chain 'D' and resid 110 through 149 removed outlier: 3.700A pdb=" N HIS D 114 " --> pdb=" O PHE D 110 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N THR D 140 " --> pdb=" O THR D 136 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N THR D 147 " --> pdb=" O TRP D 143 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N PHE D 148 " --> pdb=" O THR D 144 " (cutoff:3.500A) Processing helix chain 'D' and resid 186 through 239 removed outlier: 3.528A pdb=" N ILE D 190 " --> pdb=" O GLY D 186 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N ASN D 233 " --> pdb=" O LYS D 229 " (cutoff:3.500A) Proline residue: D 234 - end of helix Processing helix chain 'D' and resid 299 through 354 removed outlier: 5.123A pdb=" N SER D 332 " --> pdb=" O GLU D 328 " (cutoff:3.500A) removed outlier: 5.271A pdb=" N ALA D 333 " --> pdb=" O CYS D 329 " (cutoff:3.500A) Processing helix chain 'D' and resid 359 through 391 removed outlier: 3.897A pdb=" N LEU D 386 " --> pdb=" O HIS D 382 " (cutoff:3.500A) removed outlier: 4.355A pdb=" N SER D 391 " --> pdb=" O ILE D 387 " (cutoff:3.500A) Processing helix chain 'D' and resid 391 through 399 removed outlier: 3.909A pdb=" N GLY D 399 " --> pdb=" O GLU D 395 " (cutoff:3.500A) Processing helix chain 'D' and resid 406 through 414 removed outlier: 3.742A pdb=" N LYS D 410 " --> pdb=" O SER D 406 " (cutoff:3.500A) Processing helix chain 'D' and resid 415 through 420 Processing helix chain 'D' and resid 435 through 452 Processing sheet with id=AA1, first strand: chain 'B' and resid 159 through 160 Processing sheet with id=AA2, first strand: chain 'B' and resid 430 through 431 removed outlier: 3.893A pdb=" N PHE B 435 " --> pdb=" O GLY B 431 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 153 through 157 Processing sheet with id=AA4, first strand: chain 'C' and resid 427 through 428 removed outlier: 3.838A pdb=" N PHE C 432 " --> pdb=" O GLY C 428 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'D' and resid 153 through 157 994 hydrogen bonds defined for protein. 2967 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: 5.15 Time building geometry restraints manager: 3.27 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 12636 1.03 - 1.23: 55 1.23 - 1.42: 5610 1.42 - 1.62: 7456 1.62 - 1.81: 154 Bond restraints: 25911 Sorted by residual: bond pdb=" C31 PC1 B 503 " pdb=" O31 PC1 B 503 " ideal model delta sigma weight residual 1.330 1.401 -0.071 2.00e-02 2.50e+03 1.26e+01 bond pdb=" C31 PC1 A 501 " pdb=" O31 PC1 A 501 " ideal model delta sigma weight residual 1.330 1.399 -0.069 2.00e-02 2.50e+03 1.21e+01 bond pdb=" C31 PC1 B 502 " pdb=" O31 PC1 B 502 " ideal model delta sigma weight residual 1.330 1.399 -0.069 2.00e-02 2.50e+03 1.19e+01 bond pdb=" C21 PC1 A 501 " pdb=" O21 PC1 A 501 " ideal model delta sigma weight residual 1.331 1.399 -0.068 2.00e-02 2.50e+03 1.17e+01 bond pdb=" C21 PC1 B 502 " pdb=" O21 PC1 B 502 " ideal model delta sigma weight residual 1.331 1.399 -0.068 2.00e-02 2.50e+03 1.15e+01 ... (remaining 25906 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.86: 46210 2.86 - 5.72: 272 5.72 - 8.59: 17 8.59 - 11.45: 11 11.45 - 14.31: 6 Bond angle restraints: 46516 Sorted by residual: angle pdb=" C ILE C 202 " pdb=" CA ILE C 202 " pdb=" CB ILE C 202 " ideal model delta sigma weight residual 112.16 104.06 8.10 1.63e+00 3.76e-01 2.47e+01 angle pdb=" O12 PC1 B 502 " pdb=" P PC1 B 502 " pdb=" O14 PC1 B 502 " ideal model delta sigma weight residual 123.67 109.36 14.31 3.00e+00 1.11e-01 2.28e+01 angle pdb=" O12 PC1 A 501 " pdb=" P PC1 A 501 " pdb=" O14 PC1 A 501 " ideal model delta sigma weight residual 123.67 109.40 14.27 3.00e+00 1.11e-01 2.26e+01 angle pdb=" O12 PC1 B 501 " pdb=" P PC1 B 501 " pdb=" O14 PC1 B 501 " ideal model delta sigma weight residual 123.67 109.51 14.16 3.00e+00 1.11e-01 2.23e+01 angle pdb=" O12 PC1 D 501 " pdb=" P PC1 D 501 " pdb=" O14 PC1 D 501 " ideal model delta sigma weight residual 123.67 109.74 13.93 3.00e+00 1.11e-01 2.15e+01 ... (remaining 46511 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.74: 11371 17.74 - 35.48: 677 35.48 - 53.21: 265 53.21 - 70.95: 76 70.95 - 88.69: 9 Dihedral angle restraints: 12398 sinusoidal: 6553 harmonic: 5845 Sorted by residual: dihedral pdb=" CA TRP D 181 " pdb=" C TRP D 181 " pdb=" N ASP D 182 " pdb=" CA ASP D 182 " ideal model delta harmonic sigma weight residual -180.00 -159.25 -20.75 0 5.00e+00 4.00e-02 1.72e+01 dihedral pdb=" CA ASP D 182 " pdb=" CB ASP D 182 " pdb=" CG ASP D 182 " pdb=" OD1 ASP D 182 " ideal model delta sinusoidal sigma weight residual -30.00 -88.33 58.33 1 2.00e+01 2.50e-03 1.14e+01 dihedral pdb=" CA LEU B 456 " pdb=" C LEU B 456 " pdb=" N VAL B 457 " pdb=" CA VAL B 457 " ideal model delta harmonic sigma weight residual -180.00 -163.47 -16.53 0 5.00e+00 4.00e-02 1.09e+01 ... (remaining 12395 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.036: 1349 0.036 - 0.072: 577 0.072 - 0.109: 93 0.109 - 0.145: 18 0.145 - 0.181: 3 Chirality restraints: 2040 Sorted by residual: chirality pdb=" CA PHE B 382 " pdb=" N PHE B 382 " pdb=" C PHE B 382 " pdb=" CB PHE B 382 " both_signs ideal model delta sigma weight residual False 2.51 2.33 0.18 2.00e-01 2.50e+01 8.18e-01 chirality pdb=" CA PHE D 379 " pdb=" N PHE D 379 " pdb=" C PHE D 379 " pdb=" CB PHE D 379 " both_signs ideal model delta sigma weight residual False 2.51 2.33 0.18 2.00e-01 2.50e+01 7.86e-01 chirality pdb=" CA PHE C 379 " pdb=" N PHE C 379 " pdb=" C PHE C 379 " pdb=" CB PHE C 379 " both_signs ideal model delta sigma weight residual False 2.51 2.34 0.17 2.00e-01 2.50e+01 7.28e-01 ... (remaining 2037 not shown) Planarity restraints: 3640 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C31 PC1 B 503 " 0.046 2.00e-02 2.50e+03 2.68e-02 7.17e+00 pdb=" C32 PC1 B 503 " -0.014 2.00e-02 2.50e+03 pdb=" O31 PC1 B 503 " -0.015 2.00e-02 2.50e+03 pdb=" O32 PC1 B 503 " -0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA SER B 126 " 0.010 2.00e-02 2.50e+03 1.96e-02 3.85e+00 pdb=" C SER B 126 " -0.034 2.00e-02 2.50e+03 pdb=" O SER B 126 " 0.013 2.00e-02 2.50e+03 pdb=" N ARG B 127 " 0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PHE B 382 " -0.008 2.00e-02 2.50e+03 1.60e-02 2.55e+00 pdb=" C PHE B 382 " 0.028 2.00e-02 2.50e+03 pdb=" O PHE B 382 " -0.010 2.00e-02 2.50e+03 pdb=" N CYS B 383 " -0.009 2.00e-02 2.50e+03 ... (remaining 3637 not shown) Histogram of nonbonded interaction distances: 1.38 - 2.02: 153 2.02 - 2.67: 38393 2.67 - 3.31: 78695 3.31 - 3.96: 98581 3.96 - 4.60: 155394 Nonbonded interactions: 371216 Sorted by model distance: nonbonded pdb=" HB3 CYS A 76 " pdb=" HG CYS A 172 " model vdw 1.375 2.440 nonbonded pdb="HD12 ILE B 149 " pdb=" O32 PC1 B 503 " model vdw 1.501 2.096 nonbonded pdb="HD11 ILE B 149 " pdb=" O31 PC1 B 503 " model vdw 1.594 2.096 nonbonded pdb=" HE1 HIS B 230 " pdb=" HH TYR B 314 " model vdw 1.782 2.100 nonbonded pdb="HD13 ILE B 149 " pdb=" O32 PC1 B 503 " model vdw 1.790 2.096 ... (remaining 371211 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 Found NCS groups: ncs_group { reference = (chain 'B' and (resid 4 through 370 or (resid 371 and (name N or name CA or name \ C or name O or name CB or name CG or name CD1 or name CD2 or name CE1 or name C \ E2 or name CZ or name OH or name H or name HA or name HB2 or name HB3 or name HD \ 1 or name HD2 or name HE1 or name HE2)) or resid 372 through 459)) selection = (chain 'C' and (resid 1 through 191 or (resid 192 and (name N or name CA or name \ C or name O or name CB or name HA or name HB1 or name HB2 or name HB3)) or resi \ d 193 through 367 or (resid 368 and (name N or name CA or name C or name O or na \ me CB or name CG or name CD1 or name CD2 or name CE1 or name CE2 or name CZ or n \ ame OH or name H or name HA or name HB2 or name HB3 or name HD1 or name HD2 or n \ ame HE1 or name HE2)) or resid 369 through 397 or (resid 406 and (name N or name \ CA or name C or name O or name CB or name OG or name HA or name HB2 or name HB3 \ or name HG )) or resid 407 through 456)) selection = (chain 'D' and (resid 1 through 191 or (resid 192 and (name N or name CA or name \ C or name O or name CB or name HA or name HB1 or name HB2 or name HB3)) or resi \ d 193 through 397 or (resid 406 and (name N or name CA or name C or name O or na \ me CB or name OG or name HA or name HB2 or name HB3 or name HG )) or resid 407 t \ hrough 456)) } 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: 3.150 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.040 Extract box with map and model: 0.380 Check model and map are aligned: 0.070 Set scattering table: 0.080 Process input model: 21.740 Find NCS groups from input model: 0.320 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.360 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.190 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6296 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 : 0.007 0.071 13244 Z= 0.358 Angle : 0.832 14.311 17926 Z= 0.423 Chirality : 0.039 0.181 2040 Planarity : 0.004 0.033 2129 Dihedral : 14.318 88.689 4786 Min Nonbonded Distance : 2.315 Molprobity Statistics. All-atom Clashscore : 6.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.99 % Favored : 95.01 % Rotamer: Outliers : 3.41 % Allowed : 5.96 % Favored : 90.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.78 (0.22), residues: 1542 helix: 1.14 (0.15), residues: 1188 sheet: -0.30 (1.04), residues: 26 loop : -1.61 (0.35), residues: 328 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 318 TYR 0.015 0.002 TYR A 254 PHE 0.027 0.001 PHE B 382 TRP 0.009 0.001 TRP C 402 HIS 0.005 0.001 HIS D 227 Details of bonding type rmsd/Z covalent geometry : bond 0.00670 / 0.36 (13243) covalent geometry : angle 0.83169 / 0.42 (17926) hydrogen bonds : bond 0.11636 / 7.46 ( 994) hydrogen bonds : angle 6.11628 / 4.54 ( 2967) Misc. bond : bond 0.01056 / 0.66 ( 1) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3084 Ramachandran restraints generated. 1542 Oldfield, 0 Emsley, 1542 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3084 Ramachandran restraints generated. 1542 Oldfield, 0 Emsley, 1542 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 368 is missing expected H atoms. Skipping. Evaluate side-chains 636 residues out of total 1409 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 588 time to evaluate : 0.624 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 81 TYR cc_start: 0.6222 (t80) cc_final: 0.5991 (t80) REVERT: A 182 THR cc_start: 0.7904 (p) cc_final: 0.7661 (t) REVERT: A 190 MET cc_start: 0.5899 (tpt) cc_final: 0.5602 (tpt) REVERT: A 240 LEU cc_start: 0.8369 (tp) cc_final: 0.8039 (tp) REVERT: A 253 LYS cc_start: 0.7662 (mmmt) cc_final: 0.7212 (mmtt) REVERT: A 275 THR cc_start: 0.7756 (p) cc_final: 0.7519 (m) REVERT: A 356 ASN cc_start: 0.7034 (m-40) cc_final: 0.6608 (m-40) REVERT: B 5 LEU cc_start: 0.8597 (tp) cc_final: 0.8192 (tt) REVERT: B 9 LEU cc_start: 0.7660 (mp) cc_final: 0.7420 (mp) REVERT: B 48 ILE cc_start: 0.8160 (pt) cc_final: 0.7682 (mt) REVERT: B 83 SER cc_start: 0.7585 (m) cc_final: 0.7267 (t) REVERT: B 86 LYS cc_start: 0.7648 (mttm) cc_final: 0.7414 (mttp) REVERT: B 118 SER cc_start: 0.7751 (p) cc_final: 0.7511 (t) REVERT: B 173 VAL cc_start: 0.8426 (m) cc_final: 0.8032 (m) REVERT: B 210 SER cc_start: 0.7182 (p) cc_final: 0.6828 (t) REVERT: B 392 GLU cc_start: 0.6744 (mm-30) cc_final: 0.6450 (mm-30) REVERT: B 421 GLN cc_start: 0.7459 (mm-40) cc_final: 0.7126 (tp40) REVERT: B 444 SER cc_start: 0.7919 (m) cc_final: 0.7494 (t) REVERT: C 53 ILE cc_start: 0.7499 (mt) cc_final: 0.7288 (mt) REVERT: C 79 HIS cc_start: 0.7914 (m170) cc_final: 0.7613 (m170) REVERT: C 112 GLU cc_start: 0.7015 (tm-30) cc_final: 0.6784 (tm-30) REVERT: C 140 THR cc_start: 0.7313 (p) cc_final: 0.7078 (t) REVERT: C 146 ILE cc_start: 0.7880 (tp) cc_final: 0.7598 (tp) REVERT: C 201 PHE cc_start: 0.7490 (t80) cc_final: 0.7108 (t80) REVERT: C 223 GLU cc_start: 0.6060 (mm-30) cc_final: 0.5850 (mm-30) REVERT: C 228 LEU cc_start: 0.7276 (OUTLIER) cc_final: 0.6783 (mp) REVERT: C 236 ILE cc_start: 0.7934 (mm) cc_final: 0.7672 (mt) REVERT: C 328 GLU cc_start: 0.6396 (tp30) cc_final: 0.5912 (tp30) REVERT: C 395 GLU cc_start: 0.6750 (tt0) cc_final: 0.6542 (tt0) REVERT: D 12 LEU cc_start: 0.7366 (OUTLIER) cc_final: 0.6978 (mt) REVERT: D 45 ILE cc_start: 0.7623 (pt) cc_final: 0.7232 (pt) REVERT: D 95 TYR cc_start: 0.7245 (m-10) cc_final: 0.6822 (m-10) REVERT: D 138 PHE cc_start: 0.6801 (t80) cc_final: 0.6526 (t80) REVERT: D 197 PHE cc_start: 0.7386 (t80) cc_final: 0.7100 (t80) REVERT: D 225 LEU cc_start: 0.7563 (OUTLIER) cc_final: 0.7274 (mt) REVERT: D 350 TYR cc_start: 0.6586 (t80) cc_final: 0.6357 (t80) REVERT: D 354 LYS cc_start: 0.7512 (mmmm) cc_final: 0.7256 (mmmm) REVERT: D 441 SER cc_start: 0.6550 (m) cc_final: 0.6328 (p) REVERT: D 443 LEU cc_start: 0.8218 (tp) cc_final: 0.7839 (tt) outliers start: 48 outliers final: 25 residues processed: 615 average time/residue: 0.2459 time to fit residues: 218.6709 Evaluate side-chains 570 residues out of total 1409 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 542 time to evaluate : 0.650 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 LEU Chi-restraints excluded: chain A residue 65 ASN Chi-restraints excluded: chain A residue 90 ILE Chi-restraints excluded: chain A residue 183 MET Chi-restraints excluded: chain A residue 241 ILE Chi-restraints excluded: chain A residue 322 ILE Chi-restraints excluded: chain A residue 351 LEU Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain B residue 95 LYS Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 164 THR Chi-restraints excluded: chain B residue 193 ILE Chi-restraints excluded: chain C residue 26 ASP Chi-restraints excluded: chain C residue 62 ASN Chi-restraints excluded: chain C residue 143 TRP Chi-restraints excluded: chain C residue 202 ILE Chi-restraints excluded: chain C residue 228 LEU Chi-restraints excluded: chain C residue 318 HIS Chi-restraints excluded: chain D residue 12 LEU Chi-restraints excluded: chain D residue 20 ILE Chi-restraints excluded: chain D residue 24 TYR Chi-restraints excluded: chain D residue 60 LYS Chi-restraints excluded: chain D residue 143 TRP Chi-restraints excluded: chain D residue 156 VAL Chi-restraints excluded: chain D residue 222 CYS Chi-restraints excluded: chain D residue 225 LEU Chi-restraints excluded: chain D residue 228 LEU Chi-restraints excluded: chain D residue 403 TYR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: [98, 107, 10, 66, 130, 124, 103, 77, 122, 91, 149] chunk 98 optimal weight: 2.9990 chunk 107 optimal weight: 1.9990 chunk 10 optimal weight: 6.9990 chunk 66 optimal weight: 0.8980 chunk 130 optimal weight: 2.9990 chunk 124 optimal weight: 0.5980 chunk 103 optimal weight: 1.9990 chunk 77 optimal weight: 4.9990 chunk 122 optimal weight: 3.9990 chunk 91 optimal weight: 2.9990 chunk 149 optimal weight: 1.9990 overall best weight: 1.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 320 ASN B 106 ASN B 179 HIS ** B 211 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 230 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 436 ASN C 118 HIS C 163 ASN C 356 ASN C 382 HIS C 384 ASN ** C 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3702 r_free = 0.3702 target = 0.125483 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.106374 restraints weight = 61836.649| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3492 r_free = 0.3492 target = 0.111231 restraints weight = 21232.907| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3535 r_free = 0.3535 target = 0.114150 restraints weight = 11008.092| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3560 r_free = 0.3560 target = 0.115856 restraints weight = 7306.585| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 43)----------------| | r_work = 0.3577 r_free = 0.3577 target = 0.116918 restraints weight = 5623.112| |-----------------------------------------------------------------------------| r_work (final): 0.3582 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7178 moved from start: 0.2020 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 13244 Z= 0.263 Angle : 0.576 6.051 17926 Z= 0.335 Chirality : 0.039 0.176 2040 Planarity : 0.004 0.040 2129 Dihedral : 11.964 79.106 2016 Min Nonbonded Distance : 2.187 Molprobity Statistics. All-atom Clashscore : 10.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.09 % Favored : 95.91 % Rotamer: Outliers : 3.62 % Allowed : 15.76 % Favored : 80.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.21 (0.21), residues: 1542 helix: 1.49 (0.14), residues: 1204 sheet: -0.31 (1.02), residues: 26 loop : -1.79 (0.36), residues: 312 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 52 TYR 0.015 0.002 TYR C 95 PHE 0.025 0.001 PHE C 379 TRP 0.013 0.001 TRP D 181 HIS 0.007 0.001 HIS D 337 Details of bonding type rmsd/Z covalent geometry : bond 0.00506 / 0.26 (13243) covalent geometry : angle 0.57615 / 0.34 (17926) hydrogen bonds : bond 0.05843 / 3.96 ( 994) hydrogen bonds : angle 4.59538 / 3.38 ( 2967) Misc. bond : bond 0.00893 / 0.56 ( 1) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3084 Ramachandran restraints generated. 1542 Oldfield, 0 Emsley, 1542 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3084 Ramachandran restraints generated. 1542 Oldfield, 0 Emsley, 1542 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 368 is missing expected H atoms. Skipping. Evaluate side-chains 587 residues out of total 1409 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 536 time to evaluate : 0.622 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 52 ARG cc_start: 0.8278 (mtp180) cc_final: 0.8006 (mtp180) REVERT: A 81 TYR cc_start: 0.7884 (t80) cc_final: 0.7515 (t80) REVERT: A 190 MET cc_start: 0.7635 (tpt) cc_final: 0.7172 (tpt) REVERT: A 237 TYR cc_start: 0.8654 (t80) cc_final: 0.8212 (t80) REVERT: A 246 ASP cc_start: 0.7805 (m-30) cc_final: 0.7447 (m-30) REVERT: A 297 MET cc_start: 0.6401 (mpp) cc_final: 0.5809 (mpp) REVERT: A 343 LEU cc_start: 0.8428 (mm) cc_final: 0.8178 (tp) REVERT: A 344 LYS cc_start: 0.8394 (tttt) cc_final: 0.8100 (tttt) REVERT: A 350 LEU cc_start: 0.8697 (tp) cc_final: 0.8483 (tp) REVERT: A 354 SER cc_start: 0.7998 (p) cc_final: 0.7790 (p) REVERT: A 364 LYS cc_start: 0.8532 (ptpt) cc_final: 0.8260 (pttt) REVERT: B 83 SER cc_start: 0.7882 (m) cc_final: 0.7456 (t) REVERT: B 115 GLU cc_start: 0.7424 (tp30) cc_final: 0.6993 (tp30) REVERT: B 154 GLU cc_start: 0.6242 (pm20) cc_final: 0.6027 (pm20) REVERT: B 410 GLU cc_start: 0.7195 (tp30) cc_final: 0.6772 (tp30) REVERT: B 421 GLN cc_start: 0.8564 (mm-40) cc_final: 0.8059 (mm-40) REVERT: B 422 GLN cc_start: 0.7827 (tp40) cc_final: 0.7581 (tp40) REVERT: B 444 SER cc_start: 0.8337 (m) cc_final: 0.7984 (t) REVERT: C 49 GLN cc_start: 0.8457 (tp-100) cc_final: 0.7944 (tp40) REVERT: C 112 GLU cc_start: 0.7827 (tm-30) cc_final: 0.7466 (tm-30) REVERT: C 127 GLN cc_start: 0.7615 (tt0) cc_final: 0.7387 (tt0) REVERT: C 146 ILE cc_start: 0.8261 (tp) cc_final: 0.7825 (tt) REVERT: C 223 GLU cc_start: 0.7574 (mm-30) cc_final: 0.7339 (mm-30) REVERT: C 328 GLU cc_start: 0.7443 (tp30) cc_final: 0.6756 (tp30) REVERT: C 351 GLN cc_start: 0.7607 (mm110) cc_final: 0.7228 (mm-40) REVERT: C 355 ILE cc_start: 0.8106 (tp) cc_final: 0.7759 (mt) REVERT: C 430 LYS cc_start: 0.8648 (mppt) cc_final: 0.8346 (mppt) REVERT: D 14 GLN cc_start: 0.8424 (tt0) cc_final: 0.8010 (tt0) REVERT: D 81 MET cc_start: 0.7963 (mmm) cc_final: 0.7695 (tpt) REVERT: D 120 LYS cc_start: 0.8163 (ttpp) cc_final: 0.7628 (ttpp) REVERT: D 129 LEU cc_start: 0.8480 (tt) cc_final: 0.8263 (tp) REVERT: D 138 PHE cc_start: 0.7973 (t80) cc_final: 0.7587 (t80) REVERT: D 197 PHE cc_start: 0.8311 (t80) cc_final: 0.7983 (t80) REVERT: D 208 ASN cc_start: 0.8136 (m-40) cc_final: 0.7625 (m-40) REVERT: D 225 LEU cc_start: 0.8726 (OUTLIER) cc_final: 0.8524 (mt) REVERT: D 424 LEU cc_start: 0.8538 (mp) cc_final: 0.8287 (tp) REVERT: D 441 SER cc_start: 0.8222 (m) cc_final: 0.7690 (p) outliers start: 51 outliers final: 36 residues processed: 559 average time/residue: 0.2519 time to fit residues: 201.8544 Evaluate side-chains 553 residues out of total 1409 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 516 time to evaluate : 0.724 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 LEU Chi-restraints excluded: chain A residue 65 ASN Chi-restraints excluded: chain A residue 70 VAL Chi-restraints excluded: chain A residue 90 ILE Chi-restraints excluded: chain A residue 178 CYS Chi-restraints excluded: chain A residue 183 MET Chi-restraints excluded: chain A residue 241 ILE Chi-restraints excluded: chain A residue 299 LEU Chi-restraints excluded: chain A residue 322 ILE Chi-restraints excluded: chain A residue 351 LEU Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain B residue 88 VAL Chi-restraints excluded: chain B residue 95 LYS Chi-restraints excluded: chain B residue 124 SER Chi-restraints excluded: chain B residue 145 SER Chi-restraints excluded: chain B residue 164 THR Chi-restraints excluded: chain B residue 171 VAL Chi-restraints excluded: chain B residue 193 ILE Chi-restraints excluded: chain C residue 26 ASP Chi-restraints excluded: chain C residue 62 ASN Chi-restraints excluded: chain C residue 122 LEU Chi-restraints excluded: chain C residue 123 SER Chi-restraints excluded: chain C residue 143 TRP Chi-restraints excluded: chain C residue 318 HIS Chi-restraints excluded: chain C residue 411 THR Chi-restraints excluded: chain C residue 420 CYS Chi-restraints excluded: chain C residue 427 SER Chi-restraints excluded: chain C residue 436 LEU Chi-restraints excluded: chain D residue 20 ILE Chi-restraints excluded: chain D residue 24 TYR Chi-restraints excluded: chain D residue 60 LYS Chi-restraints excluded: chain D residue 125 MET Chi-restraints excluded: chain D residue 143 TRP Chi-restraints excluded: chain D residue 156 VAL Chi-restraints excluded: chain D residue 222 CYS Chi-restraints excluded: chain D residue 225 LEU Chi-restraints excluded: chain D residue 403 TYR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: [89, 12, 93, 118, 27, 33, 37, 54, 91, 8, 1] chunk 89 optimal weight: 0.3980 chunk 12 optimal weight: 5.9990 chunk 93 optimal weight: 2.9990 chunk 118 optimal weight: 4.9990 chunk 27 optimal weight: 3.9990 chunk 33 optimal weight: 0.5980 chunk 37 optimal weight: 0.0980 chunk 54 optimal weight: 3.9990 chunk 91 optimal weight: 2.9990 chunk 8 optimal weight: 4.9990 chunk 1 optimal weight: 9.9990 overall best weight: 1.4184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 320 ASN ** B 211 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 230 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 436 ASN ** C 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 163 ASN ** C 414 GLN ** 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 = 0.3705 r_free = 0.3705 target = 0.125551 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.106433 restraints weight = 61791.378| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.3494 r_free = 0.3494 target = 0.111293 restraints weight = 21161.478| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3537 r_free = 0.3537 target = 0.114180 restraints weight = 10994.525| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 46)----------------| | r_work = 0.3563 r_free = 0.3563 target = 0.115889 restraints weight = 7328.125| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3578 r_free = 0.3578 target = 0.116886 restraints weight = 5644.141| |-----------------------------------------------------------------------------| r_work (final): 0.3582 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7182 moved from start: 0.2492 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 13244 Z= 0.250 Angle : 0.556 5.852 17926 Z= 0.319 Chirality : 0.038 0.173 2040 Planarity : 0.003 0.028 2129 Dihedral : 11.215 75.673 2007 Min Nonbonded Distance : 2.219 Molprobity Statistics. All-atom Clashscore : 10.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.15 % Favored : 95.85 % Rotamer: Outliers : 4.05 % Allowed : 17.53 % Favored : 78.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.41 (0.21), residues: 1542 helix: 1.65 (0.14), residues: 1208 sheet: -0.27 (1.03), residues: 26 loop : -1.81 (0.36), residues: 308 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 203 TYR 0.020 0.001 TYR B 26 PHE 0.025 0.001 PHE B 382 TRP 0.016 0.001 TRP B 157 HIS 0.008 0.001 HIS D 337 Details of bonding type rmsd/Z covalent geometry : bond 0.00485 / 0.25 (13243) covalent geometry : angle 0.55568 / 0.32 (17926) hydrogen bonds : bond 0.05612 / 3.82 ( 994) hydrogen bonds : angle 4.40145 / 3.24 ( 2967) Misc. bond : bond 0.01247 / 0.78 ( 1) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3084 Ramachandran restraints generated. 1542 Oldfield, 0 Emsley, 1542 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3084 Ramachandran restraints generated. 1542 Oldfield, 0 Emsley, 1542 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 368 is missing expected H atoms. Skipping. Evaluate side-chains 576 residues out of total 1409 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 519 time to evaluate : 0.642 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 5 MET cc_start: 0.5221 (ppp) cc_final: 0.4926 (ppp) REVERT: A 52 ARG cc_start: 0.8270 (mtp180) cc_final: 0.8035 (mtp180) REVERT: A 81 TYR cc_start: 0.7909 (t80) cc_final: 0.7541 (t80) REVERT: A 190 MET cc_start: 0.7608 (tpt) cc_final: 0.7185 (tpt) REVERT: A 246 ASP cc_start: 0.7808 (m-30) cc_final: 0.7445 (m-30) REVERT: A 253 LYS cc_start: 0.8435 (mmtt) cc_final: 0.8153 (mmmt) REVERT: A 297 MET cc_start: 0.6389 (mpp) cc_final: 0.5698 (mpp) REVERT: A 321 TYR cc_start: 0.7253 (OUTLIER) cc_final: 0.6952 (t80) REVERT: A 337 ASP cc_start: 0.8038 (t0) cc_final: 0.7798 (t0) REVERT: A 343 LEU cc_start: 0.8438 (mm) cc_final: 0.8099 (tp) REVERT: A 344 LYS cc_start: 0.8370 (tttt) cc_final: 0.8071 (tttt) REVERT: A 364 LYS cc_start: 0.8566 (ptpt) cc_final: 0.8269 (pttt) REVERT: B 83 SER cc_start: 0.7915 (m) cc_final: 0.7496 (t) REVERT: B 115 GLU cc_start: 0.7524 (tp30) cc_final: 0.6965 (tp30) REVERT: B 354 GLN cc_start: 0.7864 (mm-40) cc_final: 0.7598 (mm-40) REVERT: B 388 GLU cc_start: 0.7201 (OUTLIER) cc_final: 0.6939 (tt0) REVERT: B 410 GLU cc_start: 0.7249 (tp30) cc_final: 0.7035 (tp30) REVERT: B 421 GLN cc_start: 0.8536 (mm-40) cc_final: 0.8062 (mm-40) REVERT: B 422 GLN cc_start: 0.7865 (tp40) cc_final: 0.7561 (tp40) REVERT: B 444 SER cc_start: 0.8333 (m) cc_final: 0.7991 (t) REVERT: C 49 GLN cc_start: 0.8417 (tp-100) cc_final: 0.8009 (tp40) REVERT: C 86 TYR cc_start: 0.7222 (t80) cc_final: 0.7006 (t80) REVERT: C 110 PHE cc_start: 0.7789 (m-10) cc_final: 0.7564 (m-10) REVERT: C 112 GLU cc_start: 0.7771 (tm-30) cc_final: 0.7270 (tm-30) REVERT: C 127 GLN cc_start: 0.7609 (tt0) cc_final: 0.7377 (tt0) REVERT: C 146 ILE cc_start: 0.8281 (tp) cc_final: 0.7869 (tp) REVERT: C 223 GLU cc_start: 0.7577 (mm-30) cc_final: 0.7327 (mm-30) REVERT: C 328 GLU cc_start: 0.7450 (tp30) cc_final: 0.6745 (tp30) REVERT: C 339 LEU cc_start: 0.7996 (mt) cc_final: 0.7702 (mm) REVERT: C 355 ILE cc_start: 0.8104 (tp) cc_final: 0.7780 (mt) REVERT: C 412 PHE cc_start: 0.8817 (t80) cc_final: 0.8526 (t80) REVERT: C 430 LYS cc_start: 0.8655 (mppt) cc_final: 0.8295 (mppt) REVERT: D 14 GLN cc_start: 0.8445 (tt0) cc_final: 0.8015 (tt0) REVERT: D 22 GLU cc_start: 0.7066 (mm-30) cc_final: 0.6786 (mm-30) REVERT: D 42 THR cc_start: 0.8753 (m) cc_final: 0.8387 (p) REVERT: D 81 MET cc_start: 0.8002 (mmm) cc_final: 0.7648 (mmm) REVERT: D 138 PHE cc_start: 0.8004 (t80) cc_final: 0.7645 (t80) REVERT: D 197 PHE cc_start: 0.8313 (t80) cc_final: 0.7993 (t80) REVERT: D 208 ASN cc_start: 0.8183 (m-40) cc_final: 0.7590 (m-40) REVERT: D 212 LEU cc_start: 0.8580 (tp) cc_final: 0.8211 (tp) REVERT: D 225 LEU cc_start: 0.8695 (OUTLIER) cc_final: 0.8484 (mt) REVERT: D 317 LYS cc_start: 0.8219 (mmpt) cc_final: 0.7841 (mmpt) REVERT: D 424 LEU cc_start: 0.8546 (mp) cc_final: 0.8305 (tp) REVERT: D 441 SER cc_start: 0.8215 (m) cc_final: 0.7667 (p) outliers start: 57 outliers final: 45 residues processed: 543 average time/residue: 0.2447 time to fit residues: 190.1664 Evaluate side-chains 553 residues out of total 1409 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 505 time to evaluate : 0.525 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 ASN Chi-restraints excluded: chain A residue 66 MET Chi-restraints excluded: chain A residue 90 ILE Chi-restraints excluded: chain A residue 178 CYS Chi-restraints excluded: chain A residue 183 MET Chi-restraints excluded: chain A residue 241 ILE Chi-restraints excluded: chain A residue 252 GLU Chi-restraints excluded: chain A residue 258 PHE Chi-restraints excluded: chain A residue 262 THR Chi-restraints excluded: chain A residue 299 LEU Chi-restraints excluded: chain A residue 321 TYR Chi-restraints excluded: chain A residue 322 ILE Chi-restraints excluded: chain A residue 351 LEU Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain B residue 88 VAL Chi-restraints excluded: chain B residue 95 LYS Chi-restraints excluded: chain B residue 124 SER Chi-restraints excluded: chain B residue 145 SER Chi-restraints excluded: chain B residue 146 TRP Chi-restraints excluded: chain B residue 149 ILE Chi-restraints excluded: chain B residue 171 VAL Chi-restraints excluded: chain B residue 178 LEU Chi-restraints excluded: chain B residue 193 ILE Chi-restraints excluded: chain B residue 194 VAL Chi-restraints excluded: chain B residue 388 GLU Chi-restraints excluded: chain B residue 428 ILE Chi-restraints excluded: chain C residue 22 GLU Chi-restraints excluded: chain C residue 26 ASP Chi-restraints excluded: chain C residue 55 ILE Chi-restraints excluded: chain C residue 62 ASN Chi-restraints excluded: chain C residue 97 THR Chi-restraints excluded: chain C residue 122 LEU Chi-restraints excluded: chain C residue 143 TRP Chi-restraints excluded: chain C residue 163 ASN Chi-restraints excluded: chain C residue 194 VAL Chi-restraints excluded: chain C residue 318 HIS Chi-restraints excluded: chain C residue 411 THR Chi-restraints excluded: chain C residue 427 SER Chi-restraints excluded: chain D residue 13 ILE Chi-restraints excluded: chain D residue 20 ILE Chi-restraints excluded: chain D residue 24 TYR Chi-restraints excluded: chain D residue 60 LYS Chi-restraints excluded: chain D residue 143 TRP Chi-restraints excluded: chain D residue 156 VAL Chi-restraints excluded: chain D residue 222 CYS Chi-restraints excluded: chain D residue 225 LEU Chi-restraints excluded: chain D residue 228 LEU Chi-restraints excluded: chain D residue 403 TYR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: [27, 77, 71, 11, 69, 68, 91, 50, 144, 88, 96] chunk 27 optimal weight: 3.9990 chunk 77 optimal weight: 3.9990 chunk 71 optimal weight: 1.9990 chunk 11 optimal weight: 0.8980 chunk 69 optimal weight: 2.9990 chunk 68 optimal weight: 0.5980 chunk 91 optimal weight: 0.7980 chunk 50 optimal weight: 0.6980 chunk 144 optimal weight: 1.9990 chunk 88 optimal weight: 1.9990 chunk 96 optimal weight: 1.9990 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 211 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 230 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 436 ASN ** C 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 163 ASN ** C 414 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 = 0.3714 r_free = 0.3714 target = 0.126263 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.107205 restraints weight = 61538.174| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3506 r_free = 0.3506 target = 0.112025 restraints weight = 21055.583| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3549 r_free = 0.3549 target = 0.114924 restraints weight = 10927.920| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 45)----------------| | r_work = 0.3574 r_free = 0.3574 target = 0.116630 restraints weight = 7267.370| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3590 r_free = 0.3590 target = 0.117659 restraints weight = 5597.173| |-----------------------------------------------------------------------------| r_work (final): 0.3595 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7162 moved from start: 0.2798 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 13244 Z= 0.198 Angle : 0.530 6.044 17926 Z= 0.301 Chirality : 0.036 0.165 2040 Planarity : 0.003 0.030 2129 Dihedral : 10.824 77.873 2004 Min Nonbonded Distance : 2.210 Molprobity Statistics. All-atom Clashscore : 10.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % Rotamer: Outliers : 4.40 % Allowed : 18.67 % Favored : 76.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.66 (0.22), residues: 1542 helix: 1.82 (0.15), residues: 1209 sheet: -0.18 (1.03), residues: 26 loop : -1.75 (0.36), residues: 307 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 203 TYR 0.017 0.001 TYR B 26 PHE 0.024 0.001 PHE C 379 TRP 0.016 0.001 TRP D 181 HIS 0.005 0.001 HIS D 337 Details of bonding type rmsd/Z covalent geometry : bond 0.00388 / 0.20 (13243) covalent geometry : angle 0.52964 / 0.30 (17926) hydrogen bonds : bond 0.05366 / 3.66 ( 994) hydrogen bonds : angle 4.22474 / 3.12 ( 2967) Misc. bond : bond 0.01222 / 0.76 ( 1) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3084 Ramachandran restraints generated. 1542 Oldfield, 0 Emsley, 1542 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3084 Ramachandran restraints generated. 1542 Oldfield, 0 Emsley, 1542 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 368 is missing expected H atoms. Skipping. Evaluate side-chains 574 residues out of total 1409 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 512 time to evaluate : 0.552 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 52 ARG cc_start: 0.8239 (mtp180) cc_final: 0.7895 (mtp180) REVERT: A 81 TYR cc_start: 0.7890 (t80) cc_final: 0.7525 (t80) REVERT: A 190 MET cc_start: 0.7593 (tpt) cc_final: 0.7169 (tpp) REVERT: A 246 ASP cc_start: 0.7774 (m-30) cc_final: 0.7393 (m-30) REVERT: A 308 LEU cc_start: 0.8083 (mt) cc_final: 0.7703 (tt) REVERT: A 337 ASP cc_start: 0.8032 (t0) cc_final: 0.7777 (t0) REVERT: A 343 LEU cc_start: 0.8436 (mm) cc_final: 0.8049 (tp) REVERT: A 344 LYS cc_start: 0.8357 (tttt) cc_final: 0.8019 (tttt) REVERT: A 364 LYS cc_start: 0.8576 (ptpt) cc_final: 0.8306 (pttt) REVERT: A 390 LEU cc_start: 0.7852 (OUTLIER) cc_final: 0.7630 (mt) REVERT: B 58 ILE cc_start: 0.7783 (mm) cc_final: 0.7337 (mm) REVERT: B 69 GLN cc_start: 0.8322 (mm-40) cc_final: 0.8036 (mm-40) REVERT: B 83 SER cc_start: 0.7915 (m) cc_final: 0.7481 (t) REVERT: B 115 GLU cc_start: 0.7464 (tp30) cc_final: 0.6893 (tp30) REVERT: B 388 GLU cc_start: 0.7179 (OUTLIER) cc_final: 0.6926 (tt0) REVERT: B 410 GLU cc_start: 0.7256 (tp30) cc_final: 0.6969 (tp30) REVERT: B 422 GLN cc_start: 0.7889 (tp40) cc_final: 0.7569 (tp40) REVERT: B 444 SER cc_start: 0.8324 (m) cc_final: 0.7984 (t) REVERT: C 86 TYR cc_start: 0.7190 (t80) cc_final: 0.6907 (t80) REVERT: C 112 GLU cc_start: 0.7672 (tm-30) cc_final: 0.7028 (tm-30) REVERT: C 116 ARG cc_start: 0.7849 (ttm110) cc_final: 0.7370 (ttm110) REVERT: C 127 GLN cc_start: 0.7619 (tt0) cc_final: 0.7387 (tt0) REVERT: C 146 ILE cc_start: 0.8281 (tp) cc_final: 0.7849 (tp) REVERT: C 223 GLU cc_start: 0.7535 (mm-30) cc_final: 0.7315 (mm-30) REVERT: C 328 GLU cc_start: 0.7440 (tp30) cc_final: 0.6727 (tp30) REVERT: C 339 LEU cc_start: 0.8033 (mt) cc_final: 0.7746 (mm) REVERT: C 378 MET cc_start: 0.7646 (ttm) cc_final: 0.7445 (ttp) REVERT: C 412 PHE cc_start: 0.8811 (t80) cc_final: 0.8595 (t80) REVERT: C 430 LYS cc_start: 0.8614 (mppt) cc_final: 0.8257 (mppt) REVERT: C 451 MET cc_start: 0.7436 (mmt) cc_final: 0.7163 (mmm) REVERT: D 9 ASN cc_start: 0.8189 (m-40) cc_final: 0.7957 (m-40) REVERT: D 14 GLN cc_start: 0.8443 (tt0) cc_final: 0.8001 (tt0) REVERT: D 22 GLU cc_start: 0.7065 (mm-30) cc_final: 0.6782 (mm-30) REVERT: D 81 MET cc_start: 0.7926 (mmm) cc_final: 0.7577 (mmm) REVERT: D 138 PHE cc_start: 0.8005 (t80) cc_final: 0.7659 (t80) REVERT: D 197 PHE cc_start: 0.8309 (t80) cc_final: 0.7979 (t80) REVERT: D 208 ASN cc_start: 0.8194 (m-40) cc_final: 0.7638 (m-40) REVERT: D 212 LEU cc_start: 0.8581 (tp) cc_final: 0.8128 (tp) REVERT: D 225 LEU cc_start: 0.8669 (OUTLIER) cc_final: 0.8444 (mt) REVERT: D 317 LYS cc_start: 0.8249 (mmpt) cc_final: 0.7862 (mmpt) REVERT: D 424 LEU cc_start: 0.8493 (mp) cc_final: 0.8288 (tp) REVERT: D 441 SER cc_start: 0.8180 (m) cc_final: 0.7646 (p) outliers start: 62 outliers final: 49 residues processed: 537 average time/residue: 0.2501 time to fit residues: 191.5462 Evaluate side-chains 556 residues out of total 1409 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 504 time to evaluate : 0.652 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 ASN Chi-restraints excluded: chain A residue 66 MET Chi-restraints excluded: chain A residue 116 ARG Chi-restraints excluded: chain A residue 178 CYS Chi-restraints excluded: chain A residue 183 MET Chi-restraints excluded: chain A residue 241 ILE Chi-restraints excluded: chain A residue 258 PHE Chi-restraints excluded: chain A residue 262 THR Chi-restraints excluded: chain A residue 299 LEU Chi-restraints excluded: chain A residue 322 ILE Chi-restraints excluded: chain A residue 351 LEU Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain B residue 57 VAL Chi-restraints excluded: chain B residue 88 VAL Chi-restraints excluded: chain B residue 95 LYS Chi-restraints excluded: chain B residue 124 SER Chi-restraints excluded: chain B residue 145 SER Chi-restraints excluded: chain B residue 146 TRP Chi-restraints excluded: chain B residue 149 ILE Chi-restraints excluded: chain B residue 171 VAL Chi-restraints excluded: chain B residue 178 LEU Chi-restraints excluded: chain B residue 193 ILE Chi-restraints excluded: chain B residue 194 VAL Chi-restraints excluded: chain B residue 388 GLU Chi-restraints excluded: chain B residue 428 ILE Chi-restraints excluded: chain C residue 22 GLU Chi-restraints excluded: chain C residue 26 ASP Chi-restraints excluded: chain C residue 55 ILE Chi-restraints excluded: chain C residue 97 THR Chi-restraints excluded: chain C residue 122 LEU Chi-restraints excluded: chain C residue 143 TRP Chi-restraints excluded: chain C residue 194 VAL Chi-restraints excluded: chain C residue 318 HIS Chi-restraints excluded: chain C residue 411 THR Chi-restraints excluded: chain C residue 417 CYS Chi-restraints excluded: chain C residue 420 CYS Chi-restraints excluded: chain C residue 427 SER Chi-restraints excluded: chain D residue 13 ILE Chi-restraints excluded: chain D residue 20 ILE Chi-restraints excluded: chain D residue 24 TYR Chi-restraints excluded: chain D residue 57 MET Chi-restraints excluded: chain D residue 60 LYS Chi-restraints excluded: chain D residue 98 LEU Chi-restraints excluded: chain D residue 125 MET Chi-restraints excluded: chain D residue 143 TRP Chi-restraints excluded: chain D residue 156 VAL Chi-restraints excluded: chain D residue 175 LEU Chi-restraints excluded: chain D residue 222 CYS Chi-restraints excluded: chain D residue 225 LEU Chi-restraints excluded: chain D residue 228 LEU Chi-restraints excluded: chain D residue 393 VAL Chi-restraints excluded: chain D residue 403 TYR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: [127, 63, 65, 0, 9, 132, 47, 83, 89, 21, 70] chunk 127 optimal weight: 3.9990 chunk 63 optimal weight: 2.9990 chunk 65 optimal weight: 1.9990 chunk 0 optimal weight: 10.0000 chunk 9 optimal weight: 4.9990 chunk 132 optimal weight: 0.6980 chunk 47 optimal weight: 1.9990 chunk 83 optimal weight: 1.9990 chunk 89 optimal weight: 1.9990 chunk 21 optimal weight: 2.9990 chunk 70 optimal weight: 2.9990 overall best weight: 1.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 320 ASN ** B 211 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 230 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 436 ASN ** C 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 384 ASN ** C 414 GLN ** 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 = 0.3693 r_free = 0.3693 target = 0.124895 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.105837 restraints weight = 61799.264| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3484 r_free = 0.3484 target = 0.110656 restraints weight = 21177.874| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3528 r_free = 0.3528 target = 0.113532 restraints weight = 11024.157| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3553 r_free = 0.3553 target = 0.115252 restraints weight = 7339.217| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 45)----------------| | r_work = 0.3568 r_free = 0.3568 target = 0.116273 restraints weight = 5658.115| |-----------------------------------------------------------------------------| r_work (final): 0.3572 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7192 moved from start: 0.2915 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.045 13244 Z= 0.289 Angle : 0.555 5.870 17926 Z= 0.323 Chirality : 0.038 0.173 2040 Planarity : 0.003 0.054 2129 Dihedral : 10.647 75.965 2000 Min Nonbonded Distance : 2.203 Molprobity Statistics. All-atom Clashscore : 10.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.15 % Favored : 95.85 % Rotamer: Outliers : 4.26 % Allowed : 18.88 % Favored : 76.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.59 (0.22), residues: 1542 helix: 1.77 (0.15), residues: 1210 sheet: -0.20 (1.03), residues: 26 loop : -1.78 (0.36), residues: 306 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 203 TYR 0.020 0.002 TYR B 26 PHE 0.026 0.001 PHE B 382 TRP 0.017 0.001 TRP D 181 HIS 0.005 0.001 HIS D 337 Details of bonding type rmsd/Z covalent geometry : bond 0.00556 / 0.29 (13243) covalent geometry : angle 0.55457 / 0.32 (17926) hydrogen bonds : bond 0.05461 / 3.72 ( 994) hydrogen bonds : angle 4.28052 / 3.16 ( 2967) Misc. bond : bond 0.01248 / 0.78 ( 1) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3084 Ramachandran restraints generated. 1542 Oldfield, 0 Emsley, 1542 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3084 Ramachandran restraints generated. 1542 Oldfield, 0 Emsley, 1542 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 368 is missing expected H atoms. Skipping. Evaluate side-chains 581 residues out of total 1409 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 521 time to evaluate : 0.658 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 52 ARG cc_start: 0.8270 (mtp180) cc_final: 0.7902 (mtp180) REVERT: A 81 TYR cc_start: 0.7913 (t80) cc_final: 0.7606 (t80) REVERT: A 190 MET cc_start: 0.7581 (tpt) cc_final: 0.7159 (tpp) REVERT: A 236 HIS cc_start: 0.8004 (m170) cc_final: 0.7783 (m-70) REVERT: A 246 ASP cc_start: 0.7781 (m-30) cc_final: 0.7405 (m-30) REVERT: A 297 MET cc_start: 0.6416 (mpp) cc_final: 0.5752 (mpp) REVERT: A 321 TYR cc_start: 0.7255 (OUTLIER) cc_final: 0.6912 (t80) REVERT: A 343 LEU cc_start: 0.8450 (mm) cc_final: 0.8040 (tp) REVERT: A 344 LYS cc_start: 0.8382 (tttt) cc_final: 0.8023 (tttt) REVERT: A 364 LYS cc_start: 0.8588 (ptpt) cc_final: 0.8307 (pttt) REVERT: B 58 ILE cc_start: 0.7848 (mm) cc_final: 0.7389 (mm) REVERT: B 69 GLN cc_start: 0.8275 (mm-40) cc_final: 0.7979 (mm-40) REVERT: B 83 SER cc_start: 0.7963 (m) cc_final: 0.7504 (t) REVERT: B 115 GLU cc_start: 0.7536 (tp30) cc_final: 0.6955 (tp30) REVERT: B 388 GLU cc_start: 0.7200 (mt-10) cc_final: 0.6946 (tt0) REVERT: B 410 GLU cc_start: 0.7278 (tp30) cc_final: 0.6891 (tp30) REVERT: B 422 GLN cc_start: 0.7963 (tp40) cc_final: 0.7566 (tp40) REVERT: B 444 SER cc_start: 0.8345 (m) cc_final: 0.8009 (t) REVERT: C 41 ILE cc_start: 0.8315 (mm) cc_final: 0.7964 (mm) REVERT: C 86 TYR cc_start: 0.7281 (t80) cc_final: 0.7040 (t80) REVERT: C 112 GLU cc_start: 0.7662 (tm-30) cc_final: 0.7188 (tm-30) REVERT: C 116 ARG cc_start: 0.7859 (ttm110) cc_final: 0.7418 (ttm110) REVERT: C 127 GLN cc_start: 0.7620 (tt0) cc_final: 0.7403 (tt0) REVERT: C 223 GLU cc_start: 0.7587 (mm-30) cc_final: 0.7353 (mm-30) REVERT: C 328 GLU cc_start: 0.7445 (tp30) cc_final: 0.6728 (tp30) REVERT: C 339 LEU cc_start: 0.8018 (mt) cc_final: 0.7719 (mm) REVERT: C 355 ILE cc_start: 0.8132 (tp) cc_final: 0.7798 (mt) REVERT: C 412 PHE cc_start: 0.8806 (t80) cc_final: 0.8573 (t80) REVERT: C 430 LYS cc_start: 0.8650 (mppt) cc_final: 0.8305 (mppt) REVERT: D 14 GLN cc_start: 0.8473 (tt0) cc_final: 0.8066 (tt0) REVERT: D 22 GLU cc_start: 0.7058 (mm-30) cc_final: 0.6791 (mm-30) REVERT: D 66 GLN cc_start: 0.7717 (mm-40) cc_final: 0.7490 (mt0) REVERT: D 138 PHE cc_start: 0.8015 (t80) cc_final: 0.7671 (t80) REVERT: D 197 PHE cc_start: 0.8312 (t80) cc_final: 0.7963 (t80) REVERT: D 207 SER cc_start: 0.8609 (t) cc_final: 0.8232 (p) REVERT: D 208 ASN cc_start: 0.8254 (m-40) cc_final: 0.7631 (m-40) REVERT: D 212 LEU cc_start: 0.8590 (tp) cc_final: 0.8224 (tp) REVERT: D 225 LEU cc_start: 0.8693 (OUTLIER) cc_final: 0.8471 (mt) REVERT: D 317 LYS cc_start: 0.8294 (mmpt) cc_final: 0.8026 (mmpt) REVERT: D 430 LYS cc_start: 0.7379 (mttt) cc_final: 0.7171 (mttt) REVERT: D 441 SER cc_start: 0.8218 (m) cc_final: 0.7671 (p) REVERT: D 443 LEU cc_start: 0.8544 (tp) cc_final: 0.8176 (tt) outliers start: 60 outliers final: 55 residues processed: 546 average time/residue: 0.2471 time to fit residues: 192.8045 Evaluate side-chains 570 residues out of total 1409 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 513 time to evaluate : 0.490 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 LEU Chi-restraints excluded: chain A residue 65 ASN Chi-restraints excluded: chain A residue 116 ARG Chi-restraints excluded: chain A residue 178 CYS Chi-restraints excluded: chain A residue 183 MET Chi-restraints excluded: chain A residue 241 ILE Chi-restraints excluded: chain A residue 252 GLU Chi-restraints excluded: chain A residue 262 THR Chi-restraints excluded: chain A residue 299 LEU Chi-restraints excluded: chain A residue 321 TYR Chi-restraints excluded: chain A residue 322 ILE Chi-restraints excluded: chain A residue 351 LEU Chi-restraints excluded: chain B residue 57 VAL Chi-restraints excluded: chain B residue 84 MET Chi-restraints excluded: chain B residue 88 VAL Chi-restraints excluded: chain B residue 95 LYS Chi-restraints excluded: chain B residue 124 SER Chi-restraints excluded: chain B residue 145 SER Chi-restraints excluded: chain B residue 146 TRP Chi-restraints excluded: chain B residue 149 ILE Chi-restraints excluded: chain B residue 171 VAL Chi-restraints excluded: chain B residue 178 LEU Chi-restraints excluded: chain B residue 193 ILE Chi-restraints excluded: chain B residue 194 VAL Chi-restraints excluded: chain B residue 428 ILE Chi-restraints excluded: chain C residue 22 GLU Chi-restraints excluded: chain C residue 26 ASP Chi-restraints excluded: chain C residue 55 ILE Chi-restraints excluded: chain C residue 97 THR Chi-restraints excluded: chain C residue 122 LEU Chi-restraints excluded: chain C residue 143 TRP Chi-restraints excluded: chain C residue 194 VAL Chi-restraints excluded: chain C residue 318 HIS Chi-restraints excluded: chain C residue 411 THR Chi-restraints excluded: chain C residue 417 CYS Chi-restraints excluded: chain C residue 420 CYS Chi-restraints excluded: chain C residue 427 SER Chi-restraints excluded: chain D residue 13 ILE Chi-restraints excluded: chain D residue 20 ILE Chi-restraints excluded: chain D residue 24 TYR Chi-restraints excluded: chain D residue 57 MET Chi-restraints excluded: chain D residue 58 VAL Chi-restraints excluded: chain D residue 60 LYS Chi-restraints excluded: chain D residue 98 LEU Chi-restraints excluded: chain D residue 125 MET Chi-restraints excluded: chain D residue 143 TRP Chi-restraints excluded: chain D residue 156 VAL Chi-restraints excluded: chain D residue 175 LEU Chi-restraints excluded: chain D residue 222 CYS Chi-restraints excluded: chain D residue 225 LEU Chi-restraints excluded: chain D residue 228 LEU Chi-restraints excluded: chain D residue 318 HIS Chi-restraints excluded: chain D residue 325 LEU Chi-restraints excluded: chain D residue 329 CYS Chi-restraints excluded: chain D residue 388 GLU Chi-restraints excluded: chain D residue 393 VAL Chi-restraints excluded: chain D residue 403 TYR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: [17, 114, 40, 47, 14, 61, 6, 27, 152, 153, 122] chunk 17 optimal weight: 0.8980 chunk 114 optimal weight: 3.9990 chunk 40 optimal weight: 0.5980 chunk 47 optimal weight: 1.9990 chunk 14 optimal weight: 0.9990 chunk 61 optimal weight: 0.5980 chunk 6 optimal weight: 0.9980 chunk 27 optimal weight: 1.9990 chunk 152 optimal weight: 2.9990 chunk 153 optimal weight: 2.9990 chunk 122 optimal weight: 4.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 320 ASN ** B 211 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 230 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 436 ASN ** C 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 206 HIS C 356 ASN ** C 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3720 r_free = 0.3720 target = 0.126770 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.107651 restraints weight = 61851.195| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3512 r_free = 0.3512 target = 0.112505 restraints weight = 21121.975| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3555 r_free = 0.3555 target = 0.115433 restraints weight = 10981.141| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 45)----------------| | r_work = 0.3580 r_free = 0.3580 target = 0.117156 restraints weight = 7298.996| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.3595 r_free = 0.3595 target = 0.118195 restraints weight = 5624.345| |-----------------------------------------------------------------------------| r_work (final): 0.3599 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7155 moved from start: 0.3124 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 13244 Z= 0.168 Angle : 0.507 5.225 17926 Z= 0.287 Chirality : 0.035 0.157 2040 Planarity : 0.003 0.066 2129 Dihedral : 10.306 80.761 1998 Min Nonbonded Distance : 2.295 Molprobity Statistics. All-atom Clashscore : 9.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.18 % Favored : 96.82 % Rotamer: Outliers : 4.33 % Allowed : 19.73 % Favored : 75.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.84 (0.22), residues: 1542 helix: 1.96 (0.15), residues: 1212 sheet: -0.22 (1.02), residues: 26 loop : -1.78 (0.35), residues: 304 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 203 TYR 0.021 0.001 TYR B 26 PHE 0.023 0.001 PHE C 379 TRP 0.017 0.001 TRP D 181 HIS 0.012 0.001 HIS C 206 Details of bonding type rmsd/Z covalent geometry : bond 0.00328 / 0.17 (13243) covalent geometry : angle 0.50661 / 0.29 (17926) hydrogen bonds : bond 0.05131 / 3.50 ( 994) hydrogen bonds : angle 4.06445 / 3.00 ( 2967) Misc. bond : bond 0.01210 / 0.76 ( 1) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3084 Ramachandran restraints generated. 1542 Oldfield, 0 Emsley, 1542 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3084 Ramachandran restraints generated. 1542 Oldfield, 0 Emsley, 1542 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 368 is missing expected H atoms. Skipping. Evaluate side-chains 580 residues out of total 1409 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 519 time to evaluate : 0.454 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 52 ARG cc_start: 0.8255 (mtp180) cc_final: 0.7944 (mtp180) REVERT: A 55 LEU cc_start: 0.8366 (OUTLIER) cc_final: 0.8063 (mm) REVERT: A 81 TYR cc_start: 0.7881 (t80) cc_final: 0.7535 (t80) REVERT: A 190 MET cc_start: 0.7566 (tpt) cc_final: 0.7158 (tpp) REVERT: A 246 ASP cc_start: 0.7758 (m-30) cc_final: 0.7386 (m-30) REVERT: A 297 MET cc_start: 0.6381 (mpp) cc_final: 0.5809 (mpp) REVERT: A 343 LEU cc_start: 0.8434 (mm) cc_final: 0.8032 (tp) REVERT: A 344 LYS cc_start: 0.8327 (tttt) cc_final: 0.7992 (tttt) REVERT: A 364 LYS cc_start: 0.8600 (ptpt) cc_final: 0.8323 (pttt) REVERT: B 58 ILE cc_start: 0.7783 (mm) cc_final: 0.7312 (mm) REVERT: B 83 SER cc_start: 0.7913 (m) cc_final: 0.7469 (t) REVERT: B 115 GLU cc_start: 0.7324 (tp30) cc_final: 0.6726 (tp30) REVERT: B 388 GLU cc_start: 0.7163 (OUTLIER) cc_final: 0.6924 (tt0) REVERT: B 410 GLU cc_start: 0.7249 (tp30) cc_final: 0.6869 (tp30) REVERT: B 422 GLN cc_start: 0.7874 (tp40) cc_final: 0.7359 (tp40) REVERT: B 444 SER cc_start: 0.8335 (m) cc_final: 0.7989 (t) REVERT: C 49 GLN cc_start: 0.8352 (tp-100) cc_final: 0.8108 (tp40) REVERT: C 112 GLU cc_start: 0.7629 (tm-30) cc_final: 0.7147 (tm-30) REVERT: C 116 ARG cc_start: 0.7814 (ttm110) cc_final: 0.7371 (ttm110) REVERT: C 127 GLN cc_start: 0.7576 (tt0) cc_final: 0.7352 (tt0) REVERT: C 172 ARG cc_start: 0.7769 (ttm-80) cc_final: 0.7496 (ttm-80) REVERT: C 223 GLU cc_start: 0.7540 (mm-30) cc_final: 0.7325 (mm-30) REVERT: C 328 GLU cc_start: 0.7432 (tp30) cc_final: 0.6719 (tp30) REVERT: C 412 PHE cc_start: 0.8784 (t80) cc_final: 0.8556 (t80) REVERT: C 430 LYS cc_start: 0.8573 (mppt) cc_final: 0.8205 (mppt) REVERT: C 451 MET cc_start: 0.7415 (mmt) cc_final: 0.7185 (mmm) REVERT: D 14 GLN cc_start: 0.8506 (tt0) cc_final: 0.8021 (tt0) REVERT: D 22 GLU cc_start: 0.7069 (mm-30) cc_final: 0.6802 (mm-30) REVERT: D 39 SER cc_start: 0.8108 (m) cc_final: 0.7453 (t) REVERT: D 138 PHE cc_start: 0.7998 (t80) cc_final: 0.7419 (t80) REVERT: D 197 PHE cc_start: 0.8317 (t80) cc_final: 0.7952 (t80) REVERT: D 207 SER cc_start: 0.8564 (t) cc_final: 0.8228 (p) REVERT: D 208 ASN cc_start: 0.8229 (m-40) cc_final: 0.7650 (m-40) REVERT: D 210 MET cc_start: 0.7367 (mmm) cc_final: 0.7055 (mmm) REVERT: D 223 GLU cc_start: 0.7625 (mm-30) cc_final: 0.7006 (mm-30) REVERT: D 225 LEU cc_start: 0.8646 (OUTLIER) cc_final: 0.8422 (mt) REVERT: D 315 ARG cc_start: 0.8198 (tpp80) cc_final: 0.7894 (tpp-160) REVERT: D 317 LYS cc_start: 0.8231 (OUTLIER) cc_final: 0.7988 (mmpt) REVERT: D 361 PHE cc_start: 0.8432 (t80) cc_final: 0.7733 (t80) REVERT: D 430 LYS cc_start: 0.7304 (mttt) cc_final: 0.7100 (mttt) REVERT: D 441 SER cc_start: 0.8170 (m) cc_final: 0.7636 (p) outliers start: 61 outliers final: 53 residues processed: 547 average time/residue: 0.2609 time to fit residues: 204.2811 Evaluate side-chains 572 residues out of total 1409 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 515 time to evaluate : 0.641 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 LEU Chi-restraints excluded: chain A residue 55 LEU Chi-restraints excluded: chain A residue 65 ASN Chi-restraints excluded: chain A residue 116 ARG Chi-restraints excluded: chain A residue 178 CYS Chi-restraints excluded: chain A residue 183 MET Chi-restraints excluded: chain A residue 241 ILE Chi-restraints excluded: chain A residue 252 GLU Chi-restraints excluded: chain A residue 262 THR Chi-restraints excluded: chain A residue 299 LEU Chi-restraints excluded: chain A residue 322 ILE Chi-restraints excluded: chain A residue 351 LEU Chi-restraints excluded: chain B residue 57 VAL Chi-restraints excluded: chain B residue 84 MET Chi-restraints excluded: chain B residue 88 VAL Chi-restraints excluded: chain B residue 95 LYS Chi-restraints excluded: chain B residue 124 SER Chi-restraints excluded: chain B residue 128 MET Chi-restraints excluded: chain B residue 146 TRP Chi-restraints excluded: chain B residue 149 ILE Chi-restraints excluded: chain B residue 171 VAL Chi-restraints excluded: chain B residue 178 LEU Chi-restraints excluded: chain B residue 193 ILE Chi-restraints excluded: chain B residue 194 VAL Chi-restraints excluded: chain B residue 388 GLU Chi-restraints excluded: chain B residue 428 ILE Chi-restraints excluded: chain C residue 22 GLU Chi-restraints excluded: chain C residue 26 ASP Chi-restraints excluded: chain C residue 55 ILE Chi-restraints excluded: chain C residue 122 LEU Chi-restraints excluded: chain C residue 143 TRP Chi-restraints excluded: chain C residue 194 VAL Chi-restraints excluded: chain C residue 228 LEU Chi-restraints excluded: chain C residue 318 HIS Chi-restraints excluded: chain C residue 411 THR Chi-restraints excluded: chain C residue 417 CYS Chi-restraints excluded: chain C residue 420 CYS Chi-restraints excluded: chain C residue 427 SER Chi-restraints excluded: chain D residue 13 ILE Chi-restraints excluded: chain D residue 20 ILE Chi-restraints excluded: chain D residue 24 TYR Chi-restraints excluded: chain D residue 57 MET Chi-restraints excluded: chain D residue 58 VAL Chi-restraints excluded: chain D residue 60 LYS Chi-restraints excluded: chain D residue 98 LEU Chi-restraints excluded: chain D residue 125 MET Chi-restraints excluded: chain D residue 143 TRP Chi-restraints excluded: chain D residue 156 VAL Chi-restraints excluded: chain D residue 175 LEU Chi-restraints excluded: chain D residue 222 CYS Chi-restraints excluded: chain D residue 225 LEU Chi-restraints excluded: chain D residue 228 LEU Chi-restraints excluded: chain D residue 317 LYS Chi-restraints excluded: chain D residue 325 LEU Chi-restraints excluded: chain D residue 329 CYS Chi-restraints excluded: chain D residue 388 GLU Chi-restraints excluded: chain D residue 403 TYR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: [97, 64, 50, 65, 46, 71, 85, 74, 116, 68, 88] chunk 97 optimal weight: 2.9990 chunk 64 optimal weight: 2.9990 chunk 50 optimal weight: 0.5980 chunk 65 optimal weight: 0.9990 chunk 46 optimal weight: 2.9990 chunk 71 optimal weight: 1.9990 chunk 85 optimal weight: 2.9990 chunk 74 optimal weight: 1.9990 chunk 116 optimal weight: 4.9990 chunk 68 optimal weight: 1.9990 chunk 88 optimal weight: 2.9990 overall best weight: 1.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 211 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 230 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 436 ASN ** C 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 414 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 = 0.3699 r_free = 0.3699 target = 0.125276 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.106265 restraints weight = 61949.991| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.3489 r_free = 0.3489 target = 0.111086 restraints weight = 21208.700| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3532 r_free = 0.3532 target = 0.113957 restraints weight = 11040.994| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 48)----------------| | r_work = 0.3558 r_free = 0.3558 target = 0.115661 restraints weight = 7370.412| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.3573 r_free = 0.3573 target = 0.116696 restraints weight = 5694.124| |-----------------------------------------------------------------------------| r_work (final): 0.3577 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7182 moved from start: 0.3138 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 13244 Z= 0.257 Angle : 0.541 5.530 17926 Z= 0.312 Chirality : 0.037 0.166 2040 Planarity : 0.003 0.065 2129 Dihedral : 10.278 83.801 1998 Min Nonbonded Distance : 2.199 Molprobity Statistics. All-atom Clashscore : 11.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.76 % Favored : 96.24 % Rotamer: Outliers : 4.61 % Allowed : 20.44 % Favored : 74.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.75 (0.22), residues: 1542 helix: 1.92 (0.15), residues: 1212 sheet: -0.25 (1.03), residues: 26 loop : -1.91 (0.36), residues: 304 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 203 TYR 0.020 0.002 TYR D 368 PHE 0.026 0.001 PHE B 382 TRP 0.018 0.001 TRP D 181 HIS 0.005 0.001 HIS D 337 Details of bonding type rmsd/Z covalent geometry : bond 0.00497 / 0.26 (13243) covalent geometry : angle 0.54150 / 0.31 (17926) hydrogen bonds : bond 0.05260 / 3.60 ( 994) hydrogen bonds : angle 4.15181 / 3.08 ( 2967) Misc. bond : bond 0.01235 / 0.77 ( 1) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3084 Ramachandran restraints generated. 1542 Oldfield, 0 Emsley, 1542 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3084 Ramachandran restraints generated. 1542 Oldfield, 0 Emsley, 1542 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 368 is missing expected H atoms. Skipping. Evaluate side-chains 582 residues out of total 1409 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 517 time to evaluate : 0.578 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 52 ARG cc_start: 0.8264 (mtp180) cc_final: 0.7950 (mtp180) REVERT: A 55 LEU cc_start: 0.8394 (OUTLIER) cc_final: 0.8093 (mm) REVERT: A 81 TYR cc_start: 0.7909 (t80) cc_final: 0.7569 (t80) REVERT: A 112 MET cc_start: 0.7818 (tpp) cc_final: 0.7467 (tpp) REVERT: A 190 MET cc_start: 0.7547 (tpt) cc_final: 0.7029 (tpp) REVERT: A 236 HIS cc_start: 0.7981 (m-70) cc_final: 0.7743 (m-70) REVERT: A 246 ASP cc_start: 0.7769 (m-30) cc_final: 0.7405 (m-30) REVERT: A 297 MET cc_start: 0.6412 (mpp) cc_final: 0.5866 (mpp) REVERT: A 343 LEU cc_start: 0.8447 (mm) cc_final: 0.8060 (tp) REVERT: A 344 LYS cc_start: 0.8356 (tttt) cc_final: 0.8016 (tttt) REVERT: A 391 LEU cc_start: 0.8124 (tp) cc_final: 0.7881 (tp) REVERT: B 58 ILE cc_start: 0.7816 (mm) cc_final: 0.7342 (mm) REVERT: B 83 SER cc_start: 0.7925 (m) cc_final: 0.7491 (t) REVERT: B 115 GLU cc_start: 0.7399 (tp30) cc_final: 0.6793 (tp30) REVERT: B 128 MET cc_start: 0.7480 (OUTLIER) cc_final: 0.7274 (mtm) REVERT: B 212 LEU cc_start: 0.8126 (mt) cc_final: 0.7800 (mp) REVERT: B 388 GLU cc_start: 0.7189 (mt-10) cc_final: 0.6938 (tt0) REVERT: B 410 GLU cc_start: 0.7256 (tp30) cc_final: 0.6878 (tp30) REVERT: B 422 GLN cc_start: 0.7848 (tp40) cc_final: 0.7431 (tp40) REVERT: B 444 SER cc_start: 0.8345 (m) cc_final: 0.7999 (t) REVERT: C 41 ILE cc_start: 0.8378 (mm) cc_final: 0.8031 (mm) REVERT: C 49 GLN cc_start: 0.8415 (tp-100) cc_final: 0.7992 (tp40) REVERT: C 86 TYR cc_start: 0.7295 (t80) cc_final: 0.7062 (t80) REVERT: C 112 GLU cc_start: 0.7621 (tm-30) cc_final: 0.7152 (tm-30) REVERT: C 127 GLN cc_start: 0.7584 (tt0) cc_final: 0.7370 (tt0) REVERT: C 172 ARG cc_start: 0.7810 (ttm-80) cc_final: 0.7542 (ttm-80) REVERT: C 223 GLU cc_start: 0.7563 (mm-30) cc_final: 0.7343 (mm-30) REVERT: C 325 LEU cc_start: 0.8205 (mt) cc_final: 0.8000 (mt) REVERT: C 328 GLU cc_start: 0.7422 (tp30) cc_final: 0.6721 (tp30) REVERT: C 388 GLU cc_start: 0.7572 (tp30) cc_final: 0.6942 (tp30) REVERT: C 412 PHE cc_start: 0.8793 (t80) cc_final: 0.8589 (t80) REVERT: C 451 MET cc_start: 0.7450 (mmt) cc_final: 0.7242 (mmm) REVERT: D 14 GLN cc_start: 0.8471 (tt0) cc_final: 0.8064 (tt0) REVERT: D 22 GLU cc_start: 0.7033 (mm-30) cc_final: 0.6771 (mm-30) REVERT: D 42 THR cc_start: 0.8796 (m) cc_final: 0.8579 (p) REVERT: D 138 PHE cc_start: 0.7999 (t80) cc_final: 0.7455 (t80) REVERT: D 197 PHE cc_start: 0.8325 (t80) cc_final: 0.7963 (t80) REVERT: D 207 SER cc_start: 0.8567 (t) cc_final: 0.8232 (p) REVERT: D 208 ASN cc_start: 0.8256 (m-40) cc_final: 0.7656 (m-40) REVERT: D 210 MET cc_start: 0.7397 (mmm) cc_final: 0.7073 (mmm) REVERT: D 225 LEU cc_start: 0.8668 (OUTLIER) cc_final: 0.8425 (mt) REVERT: D 317 LYS cc_start: 0.8295 (mmpt) cc_final: 0.8093 (mmpt) REVERT: D 361 PHE cc_start: 0.8434 (t80) cc_final: 0.8094 (t80) REVERT: D 441 SER cc_start: 0.8204 (m) cc_final: 0.7659 (p) REVERT: D 443 LEU cc_start: 0.8570 (tp) cc_final: 0.8198 (tt) outliers start: 65 outliers final: 56 residues processed: 547 average time/residue: 0.2638 time to fit residues: 204.6720 Evaluate side-chains 577 residues out of total 1409 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 518 time to evaluate : 0.617 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 LEU Chi-restraints excluded: chain A residue 55 LEU Chi-restraints excluded: chain A residue 65 ASN Chi-restraints excluded: chain A residue 116 ARG Chi-restraints excluded: chain A residue 178 CYS Chi-restraints excluded: chain A residue 183 MET Chi-restraints excluded: chain A residue 241 ILE Chi-restraints excluded: chain A residue 252 GLU Chi-restraints excluded: chain A residue 262 THR Chi-restraints excluded: chain A residue 299 LEU Chi-restraints excluded: chain A residue 322 ILE Chi-restraints excluded: chain A residue 351 LEU Chi-restraints excluded: chain B residue 57 VAL Chi-restraints excluded: chain B residue 84 MET Chi-restraints excluded: chain B residue 88 VAL Chi-restraints excluded: chain B residue 95 LYS Chi-restraints excluded: chain B residue 124 SER Chi-restraints excluded: chain B residue 128 MET Chi-restraints excluded: chain B residue 145 SER Chi-restraints excluded: chain B residue 146 TRP Chi-restraints excluded: chain B residue 149 ILE Chi-restraints excluded: chain B residue 164 THR Chi-restraints excluded: chain B residue 171 VAL Chi-restraints excluded: chain B residue 178 LEU Chi-restraints excluded: chain B residue 193 ILE Chi-restraints excluded: chain B residue 194 VAL Chi-restraints excluded: chain B residue 428 ILE Chi-restraints excluded: chain C residue 22 GLU Chi-restraints excluded: chain C residue 26 ASP Chi-restraints excluded: chain C residue 55 ILE Chi-restraints excluded: chain C residue 97 THR Chi-restraints excluded: chain C residue 122 LEU Chi-restraints excluded: chain C residue 143 TRP Chi-restraints excluded: chain C residue 194 VAL Chi-restraints excluded: chain C residue 228 LEU Chi-restraints excluded: chain C residue 318 HIS Chi-restraints excluded: chain C residue 411 THR Chi-restraints excluded: chain C residue 417 CYS Chi-restraints excluded: chain C residue 420 CYS Chi-restraints excluded: chain C residue 427 SER Chi-restraints excluded: chain D residue 13 ILE Chi-restraints excluded: chain D residue 20 ILE Chi-restraints excluded: chain D residue 24 TYR Chi-restraints excluded: chain D residue 57 MET Chi-restraints excluded: chain D residue 58 VAL Chi-restraints excluded: chain D residue 60 LYS Chi-restraints excluded: chain D residue 98 LEU Chi-restraints excluded: chain D residue 125 MET Chi-restraints excluded: chain D residue 143 TRP Chi-restraints excluded: chain D residue 156 VAL Chi-restraints excluded: chain D residue 175 LEU Chi-restraints excluded: chain D residue 222 CYS Chi-restraints excluded: chain D residue 225 LEU Chi-restraints excluded: chain D residue 228 LEU Chi-restraints excluded: chain D residue 318 HIS Chi-restraints excluded: chain D residue 325 LEU Chi-restraints excluded: chain D residue 329 CYS Chi-restraints excluded: chain D residue 388 GLU Chi-restraints excluded: chain D residue 403 TYR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: [28, 125, 144, 101, 151, 32, 63, 95, 27, 115, 61] chunk 28 optimal weight: 1.9990 chunk 125 optimal weight: 0.9990 chunk 144 optimal weight: 1.9990 chunk 101 optimal weight: 1.9990 chunk 151 optimal weight: 5.9990 chunk 32 optimal weight: 0.9980 chunk 63 optimal weight: 1.9990 chunk 95 optimal weight: 3.9990 chunk 27 optimal weight: 3.9990 chunk 115 optimal weight: 2.9990 chunk 61 optimal weight: 1.9990 overall best weight: 1.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 211 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 230 HIS B 436 ASN ** C 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 206 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3695 r_free = 0.3695 target = 0.125032 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.105975 restraints weight = 62322.437| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3484 r_free = 0.3484 target = 0.110796 restraints weight = 21320.473| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.113669 restraints weight = 11111.594| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3553 r_free = 0.3553 target = 0.115369 restraints weight = 7420.936| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 45)----------------| | r_work = 0.3568 r_free = 0.3568 target = 0.116395 restraints weight = 5732.132| |-----------------------------------------------------------------------------| r_work (final): 0.3575 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7186 moved from start: 0.3237 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 13244 Z= 0.266 Angle : 0.544 5.430 17926 Z= 0.316 Chirality : 0.038 0.171 2040 Planarity : 0.004 0.079 2129 Dihedral : 10.206 88.873 1998 Min Nonbonded Distance : 2.242 Molprobity Statistics. All-atom Clashscore : 11.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.70 % Favored : 96.30 % Rotamer: Outliers : 4.54 % Allowed : 20.72 % Favored : 74.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.72 (0.22), residues: 1542 helix: 1.87 (0.15), residues: 1212 sheet: -0.25 (1.03), residues: 26 loop : -1.80 (0.36), residues: 304 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG A 203 TYR 0.019 0.002 TYR B 26 PHE 0.025 0.001 PHE B 382 TRP 0.018 0.001 TRP D 181 HIS 0.011 0.001 HIS C 206 Details of bonding type rmsd/Z covalent geometry : bond 0.00512 / 0.27 (13243) covalent geometry : angle 0.54368 / 0.32 (17926) hydrogen bonds : bond 0.05280 / 3.62 ( 994) hydrogen bonds : angle 4.16174 / 3.09 ( 2967) Misc. bond : bond 0.01239 / 0.77 ( 1) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3084 Ramachandran restraints generated. 1542 Oldfield, 0 Emsley, 1542 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3084 Ramachandran restraints generated. 1542 Oldfield, 0 Emsley, 1542 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 368 is missing expected H atoms. Skipping. Evaluate side-chains 589 residues out of total 1409 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 525 time to evaluate : 0.529 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 55 LEU cc_start: 0.8395 (OUTLIER) cc_final: 0.8083 (mm) REVERT: A 81 TYR cc_start: 0.7911 (t80) cc_final: 0.7586 (t80) REVERT: A 112 MET cc_start: 0.7800 (tpp) cc_final: 0.7450 (tpp) REVERT: A 188 GLU cc_start: 0.7902 (tm-30) cc_final: 0.7070 (tm-30) REVERT: A 190 MET cc_start: 0.7489 (tpt) cc_final: 0.6951 (tpp) REVERT: A 236 HIS cc_start: 0.8007 (m-70) cc_final: 0.7776 (m-70) REVERT: A 246 ASP cc_start: 0.7768 (m-30) cc_final: 0.7374 (m-30) REVERT: A 297 MET cc_start: 0.6563 (mpp) cc_final: 0.5996 (mpp) REVERT: A 321 TYR cc_start: 0.7205 (t80) cc_final: 0.6831 (t80) REVERT: A 343 LEU cc_start: 0.8430 (mm) cc_final: 0.8059 (tp) REVERT: A 344 LYS cc_start: 0.8354 (tttt) cc_final: 0.7999 (tttt) REVERT: B 83 SER cc_start: 0.7932 (m) cc_final: 0.7496 (t) REVERT: B 115 GLU cc_start: 0.7400 (tp30) cc_final: 0.6774 (tp30) REVERT: B 128 MET cc_start: 0.7466 (OUTLIER) cc_final: 0.7164 (mtm) REVERT: B 212 LEU cc_start: 0.8127 (mt) cc_final: 0.7798 (mp) REVERT: B 410 GLU cc_start: 0.7261 (tp30) cc_final: 0.6879 (tp30) REVERT: B 422 GLN cc_start: 0.7828 (tp40) cc_final: 0.7396 (tp40) REVERT: B 425 LYS cc_start: 0.8282 (mptt) cc_final: 0.8074 (mptt) REVERT: B 444 SER cc_start: 0.8333 (m) cc_final: 0.8008 (t) REVERT: C 41 ILE cc_start: 0.8392 (mm) cc_final: 0.8053 (mm) REVERT: C 49 GLN cc_start: 0.8442 (tp-100) cc_final: 0.8138 (tp40) REVERT: C 86 TYR cc_start: 0.7307 (t80) cc_final: 0.7105 (t80) REVERT: C 112 GLU cc_start: 0.7640 (tm-30) cc_final: 0.7167 (tm-30) REVERT: C 127 GLN cc_start: 0.7584 (tt0) cc_final: 0.7372 (tt0) REVERT: C 172 ARG cc_start: 0.7839 (ttm-80) cc_final: 0.7576 (ttm-80) REVERT: C 223 GLU cc_start: 0.7569 (mm-30) cc_final: 0.7349 (mm-30) REVERT: C 328 GLU cc_start: 0.7420 (tp30) cc_final: 0.6712 (tp30) REVERT: C 388 GLU cc_start: 0.7565 (tp30) cc_final: 0.6931 (tp30) REVERT: C 451 MET cc_start: 0.7461 (mmt) cc_final: 0.7252 (mmm) REVERT: D 14 GLN cc_start: 0.8463 (tt0) cc_final: 0.8004 (tt0) REVERT: D 22 GLU cc_start: 0.7029 (mm-30) cc_final: 0.6772 (mm-30) REVERT: D 66 GLN cc_start: 0.7709 (mm-40) cc_final: 0.7431 (mt0) REVERT: D 138 PHE cc_start: 0.7995 (t80) cc_final: 0.7452 (t80) REVERT: D 197 PHE cc_start: 0.8329 (t80) cc_final: 0.7951 (t80) REVERT: D 207 SER cc_start: 0.8565 (t) cc_final: 0.8201 (p) REVERT: D 208 ASN cc_start: 0.8252 (m-40) cc_final: 0.7652 (m-40) REVERT: D 223 GLU cc_start: 0.7675 (mm-30) cc_final: 0.7141 (mm-30) REVERT: D 225 LEU cc_start: 0.8661 (OUTLIER) cc_final: 0.8431 (mt) REVERT: D 315 ARG cc_start: 0.8202 (tpp80) cc_final: 0.7911 (tpp-160) REVERT: D 361 PHE cc_start: 0.8434 (t80) cc_final: 0.8108 (t80) REVERT: D 441 SER cc_start: 0.8185 (m) cc_final: 0.7648 (p) REVERT: D 443 LEU cc_start: 0.8575 (tp) cc_final: 0.8199 (tt) outliers start: 64 outliers final: 56 residues processed: 553 average time/residue: 0.2592 time to fit residues: 204.4418 Evaluate side-chains 580 residues out of total 1409 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 521 time to evaluate : 0.669 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 LEU Chi-restraints excluded: chain A residue 55 LEU Chi-restraints excluded: chain A residue 65 ASN Chi-restraints excluded: chain A residue 116 ARG Chi-restraints excluded: chain A residue 178 CYS Chi-restraints excluded: chain A residue 183 MET Chi-restraints excluded: chain A residue 241 ILE Chi-restraints excluded: chain A residue 252 GLU Chi-restraints excluded: chain A residue 262 THR Chi-restraints excluded: chain A residue 299 LEU Chi-restraints excluded: chain A residue 322 ILE Chi-restraints excluded: chain A residue 351 LEU Chi-restraints excluded: chain B residue 9 LEU Chi-restraints excluded: chain B residue 57 VAL Chi-restraints excluded: chain B residue 84 MET Chi-restraints excluded: chain B residue 88 VAL Chi-restraints excluded: chain B residue 95 LYS Chi-restraints excluded: chain B residue 124 SER Chi-restraints excluded: chain B residue 128 MET Chi-restraints excluded: chain B residue 145 SER Chi-restraints excluded: chain B residue 146 TRP Chi-restraints excluded: chain B residue 149 ILE Chi-restraints excluded: chain B residue 164 THR Chi-restraints excluded: chain B residue 171 VAL Chi-restraints excluded: chain B residue 178 LEU Chi-restraints excluded: chain B residue 193 ILE Chi-restraints excluded: chain B residue 194 VAL Chi-restraints excluded: chain B residue 428 ILE Chi-restraints excluded: chain C residue 22 GLU Chi-restraints excluded: chain C residue 26 ASP Chi-restraints excluded: chain C residue 97 THR Chi-restraints excluded: chain C residue 122 LEU Chi-restraints excluded: chain C residue 143 TRP Chi-restraints excluded: chain C residue 194 VAL Chi-restraints excluded: chain C residue 228 LEU Chi-restraints excluded: chain C residue 318 HIS Chi-restraints excluded: chain C residue 411 THR Chi-restraints excluded: chain C residue 417 CYS Chi-restraints excluded: chain C residue 420 CYS Chi-restraints excluded: chain C residue 427 SER Chi-restraints excluded: chain D residue 13 ILE Chi-restraints excluded: chain D residue 20 ILE Chi-restraints excluded: chain D residue 24 TYR Chi-restraints excluded: chain D residue 58 VAL Chi-restraints excluded: chain D residue 60 LYS Chi-restraints excluded: chain D residue 98 LEU Chi-restraints excluded: chain D residue 125 MET Chi-restraints excluded: chain D residue 143 TRP Chi-restraints excluded: chain D residue 156 VAL Chi-restraints excluded: chain D residue 175 LEU Chi-restraints excluded: chain D residue 222 CYS Chi-restraints excluded: chain D residue 225 LEU Chi-restraints excluded: chain D residue 228 LEU Chi-restraints excluded: chain D residue 318 HIS Chi-restraints excluded: chain D residue 325 LEU Chi-restraints excluded: chain D residue 329 CYS Chi-restraints excluded: chain D residue 354 LYS Chi-restraints excluded: chain D residue 388 GLU Chi-restraints excluded: chain D residue 403 TYR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: [90, 110, 22, 92, 140, 119, 142, 124, 78, 35, 10] chunk 90 optimal weight: 0.8980 chunk 110 optimal weight: 0.9990 chunk 22 optimal weight: 0.7980 chunk 92 optimal weight: 0.2980 chunk 140 optimal weight: 0.8980 chunk 119 optimal weight: 1.9990 chunk 142 optimal weight: 1.9990 chunk 124 optimal weight: 0.6980 chunk 78 optimal weight: 0.7980 chunk 35 optimal weight: 0.9990 chunk 10 optimal weight: 2.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 211 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 236 ASN B 436 ASN ** C 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 206 HIS ** C 414 GLN ** 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 = 0.3725 r_free = 0.3725 target = 0.127073 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3444 r_free = 0.3444 target = 0.108045 restraints weight = 61815.039| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3518 r_free = 0.3518 target = 0.112891 restraints weight = 21151.997| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3561 r_free = 0.3561 target = 0.115788 restraints weight = 10987.747| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.3586 r_free = 0.3586 target = 0.117515 restraints weight = 7306.254| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3602 r_free = 0.3602 target = 0.118530 restraints weight = 5612.588| |-----------------------------------------------------------------------------| r_work (final): 0.3606 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7149 moved from start: 0.3391 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 13244 Z= 0.161 Angle : 0.522 6.975 17926 Z= 0.293 Chirality : 0.036 0.180 2040 Planarity : 0.004 0.067 2129 Dihedral : 9.966 82.096 1998 Min Nonbonded Distance : 2.291 Molprobity Statistics. All-atom Clashscore : 11.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % Rotamer: Outliers : 4.33 % Allowed : 21.72 % Favored : 73.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.95 (0.22), residues: 1542 helix: 2.00 (0.15), residues: 1223 sheet: -0.06 (1.05), residues: 26 loop : -1.70 (0.37), residues: 293 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 203 TYR 0.015 0.001 TYR A 179 PHE 0.037 0.001 PHE C 412 TRP 0.022 0.001 TRP D 181 HIS 0.009 0.001 HIS C 206 Details of bonding type rmsd/Z covalent geometry : bond 0.00317 / 0.16 (13243) covalent geometry : angle 0.52170 / 0.29 (17926) hydrogen bonds : bond 0.05044 / 3.46 ( 994) hydrogen bonds : angle 4.00420 / 2.96 ( 2967) Misc. bond : bond 0.01201 / 0.75 ( 1) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3084 Ramachandran restraints generated. 1542 Oldfield, 0 Emsley, 1542 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3084 Ramachandran restraints generated. 1542 Oldfield, 0 Emsley, 1542 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 368 is missing expected H atoms. Skipping. Evaluate side-chains 575 residues out of total 1409 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 514 time to evaluate : 0.629 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 55 LEU cc_start: 0.8369 (OUTLIER) cc_final: 0.8050 (mm) REVERT: A 81 TYR cc_start: 0.7918 (t80) cc_final: 0.7594 (t80) REVERT: A 112 MET cc_start: 0.7789 (tpp) cc_final: 0.7437 (tpp) REVERT: A 188 GLU cc_start: 0.7825 (tm-30) cc_final: 0.7241 (tm-30) REVERT: A 190 MET cc_start: 0.7509 (tpt) cc_final: 0.7001 (tpp) REVERT: A 236 HIS cc_start: 0.7989 (m-70) cc_final: 0.7724 (m-70) REVERT: A 246 ASP cc_start: 0.7756 (m-30) cc_final: 0.7360 (m-30) REVERT: A 297 MET cc_start: 0.6498 (mpp) cc_final: 0.5958 (mpp) REVERT: A 321 TYR cc_start: 0.7114 (t80) cc_final: 0.6845 (t80) REVERT: A 343 LEU cc_start: 0.8411 (mm) cc_final: 0.8034 (tp) REVERT: A 344 LYS cc_start: 0.8292 (tttt) cc_final: 0.7945 (tttt) REVERT: A 365 LEU cc_start: 0.8709 (mm) cc_final: 0.8306 (mp) REVERT: B 58 ILE cc_start: 0.7782 (mm) cc_final: 0.7326 (mm) REVERT: B 69 GLN cc_start: 0.8141 (mm-40) cc_final: 0.7902 (mm-40) REVERT: B 83 SER cc_start: 0.7897 (m) cc_final: 0.7472 (t) REVERT: B 115 GLU cc_start: 0.7253 (tp30) cc_final: 0.6671 (tp30) REVERT: B 128 MET cc_start: 0.7437 (OUTLIER) cc_final: 0.7174 (mtm) REVERT: B 212 LEU cc_start: 0.8104 (mt) cc_final: 0.7779 (mp) REVERT: B 388 GLU cc_start: 0.7199 (mt-10) cc_final: 0.6948 (tt0) REVERT: B 410 GLU cc_start: 0.7231 (tp30) cc_final: 0.6833 (tp30) REVERT: B 422 GLN cc_start: 0.7806 (tp40) cc_final: 0.7285 (tp40) REVERT: B 425 LYS cc_start: 0.8282 (mptt) cc_final: 0.8068 (mptt) REVERT: B 444 SER cc_start: 0.8318 (m) cc_final: 0.7991 (t) REVERT: C 41 ILE cc_start: 0.8353 (mm) cc_final: 0.8007 (mm) REVERT: C 49 GLN cc_start: 0.8374 (tp-100) cc_final: 0.8048 (tp40) REVERT: C 112 GLU cc_start: 0.7594 (tm-30) cc_final: 0.7107 (tm-30) REVERT: C 127 GLN cc_start: 0.7590 (tt0) cc_final: 0.7363 (tt0) REVERT: C 172 ARG cc_start: 0.7814 (ttm-80) cc_final: 0.7592 (ttm-80) REVERT: C 223 GLU cc_start: 0.7532 (mm-30) cc_final: 0.7319 (mm-30) REVERT: C 328 GLU cc_start: 0.7399 (tp30) cc_final: 0.6753 (tp30) REVERT: C 388 GLU cc_start: 0.7556 (tp30) cc_final: 0.6918 (tp30) REVERT: C 427 SER cc_start: 0.8065 (OUTLIER) cc_final: 0.7801 (p) REVERT: D 14 GLN cc_start: 0.8413 (tt0) cc_final: 0.7945 (tt0) REVERT: D 22 GLU cc_start: 0.7004 (mm-30) cc_final: 0.6707 (mm-30) REVERT: D 39 SER cc_start: 0.8113 (m) cc_final: 0.7452 (t) REVERT: D 138 PHE cc_start: 0.7987 (t80) cc_final: 0.7421 (t80) REVERT: D 197 PHE cc_start: 0.8322 (t80) cc_final: 0.7940 (t80) REVERT: D 207 SER cc_start: 0.8541 (t) cc_final: 0.8184 (p) REVERT: D 208 ASN cc_start: 0.8226 (m-40) cc_final: 0.7575 (m-40) REVERT: D 223 GLU cc_start: 0.7631 (mm-30) cc_final: 0.7081 (mm-30) REVERT: D 225 LEU cc_start: 0.8622 (OUTLIER) cc_final: 0.8396 (mt) REVERT: D 361 PHE cc_start: 0.8379 (t80) cc_final: 0.8003 (t80) REVERT: D 441 SER cc_start: 0.8162 (m) cc_final: 0.7615 (p) outliers start: 61 outliers final: 52 residues processed: 541 average time/residue: 0.2595 time to fit residues: 200.5813 Evaluate side-chains 566 residues out of total 1409 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 510 time to evaluate : 0.631 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 LEU Chi-restraints excluded: chain A residue 55 LEU Chi-restraints excluded: chain A residue 65 ASN Chi-restraints excluded: chain A residue 66 MET Chi-restraints excluded: chain A residue 116 ARG Chi-restraints excluded: chain A residue 178 CYS Chi-restraints excluded: chain A residue 241 ILE Chi-restraints excluded: chain A residue 252 GLU Chi-restraints excluded: chain A residue 262 THR Chi-restraints excluded: chain A residue 299 LEU Chi-restraints excluded: chain A residue 322 ILE Chi-restraints excluded: chain A residue 351 LEU Chi-restraints excluded: chain B residue 9 LEU Chi-restraints excluded: chain B residue 57 VAL Chi-restraints excluded: chain B residue 84 MET Chi-restraints excluded: chain B residue 88 VAL Chi-restraints excluded: chain B residue 95 LYS Chi-restraints excluded: chain B residue 124 SER Chi-restraints excluded: chain B residue 128 MET Chi-restraints excluded: chain B residue 146 TRP Chi-restraints excluded: chain B residue 149 ILE Chi-restraints excluded: chain B residue 171 VAL Chi-restraints excluded: chain B residue 178 LEU Chi-restraints excluded: chain B residue 193 ILE Chi-restraints excluded: chain B residue 194 VAL Chi-restraints excluded: chain B residue 428 ILE Chi-restraints excluded: chain C residue 22 GLU Chi-restraints excluded: chain C residue 26 ASP Chi-restraints excluded: chain C residue 97 THR Chi-restraints excluded: chain C residue 122 LEU Chi-restraints excluded: chain C residue 143 TRP Chi-restraints excluded: chain C residue 194 VAL Chi-restraints excluded: chain C residue 209 LEU Chi-restraints excluded: chain C residue 228 LEU Chi-restraints excluded: chain C residue 318 HIS Chi-restraints excluded: chain C residue 411 THR Chi-restraints excluded: chain C residue 420 CYS Chi-restraints excluded: chain C residue 427 SER Chi-restraints excluded: chain D residue 13 ILE Chi-restraints excluded: chain D residue 20 ILE Chi-restraints excluded: chain D residue 24 TYR Chi-restraints excluded: chain D residue 58 VAL Chi-restraints excluded: chain D residue 60 LYS Chi-restraints excluded: chain D residue 98 LEU Chi-restraints excluded: chain D residue 125 MET Chi-restraints excluded: chain D residue 143 TRP Chi-restraints excluded: chain D residue 156 VAL Chi-restraints excluded: chain D residue 175 LEU Chi-restraints excluded: chain D residue 222 CYS Chi-restraints excluded: chain D residue 225 LEU Chi-restraints excluded: chain D residue 228 LEU Chi-restraints excluded: chain D residue 318 HIS Chi-restraints excluded: chain D residue 329 CYS Chi-restraints excluded: chain D residue 354 LYS Chi-restraints excluded: chain D residue 388 GLU Chi-restraints excluded: chain D residue 403 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: [141, 130, 100, 90, 117, 115, 137, 148, 57, 58, 68] chunk 141 optimal weight: 4.9990 chunk 130 optimal weight: 2.9990 chunk 100 optimal weight: 2.9990 chunk 90 optimal weight: 3.9990 chunk 117 optimal weight: 2.9990 chunk 115 optimal weight: 2.9990 chunk 137 optimal weight: 0.9980 chunk 148 optimal weight: 3.9990 chunk 57 optimal weight: 1.9990 chunk 58 optimal weight: 0.7980 chunk 68 optimal weight: 0.9980 overall best weight: 1.5584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 167 GLN ** B 211 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 436 ASN ** C 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 206 HIS ** C 414 GLN ** 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 = 0.3699 r_free = 0.3699 target = 0.125243 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.106330 restraints weight = 61856.510| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3489 r_free = 0.3489 target = 0.111140 restraints weight = 21369.076| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3533 r_free = 0.3533 target = 0.114011 restraints weight = 11161.781| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3558 r_free = 0.3558 target = 0.115674 restraints weight = 7436.561| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3573 r_free = 0.3573 target = 0.116705 restraints weight = 5759.831| |-----------------------------------------------------------------------------| r_work (final): 0.3575 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7182 moved from start: 0.3436 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 13244 Z= 0.268 Angle : 0.572 7.409 17926 Z= 0.328 Chirality : 0.038 0.175 2040 Planarity : 0.004 0.062 2129 Dihedral : 9.920 75.725 1995 Min Nonbonded Distance : 2.241 Molprobity Statistics. All-atom Clashscore : 12.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.89 % Favored : 96.11 % Rotamer: Outliers : 4.12 % Allowed : 22.14 % Favored : 73.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.86 (0.22), residues: 1542 helix: 1.93 (0.15), residues: 1222 sheet: -0.04 (1.05), residues: 26 loop : -1.70 (0.38), residues: 294 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A 203 TYR 0.017 0.001 TYR B 26 PHE 0.034 0.001 PHE C 379 TRP 0.021 0.001 TRP D 181 HIS 0.010 0.001 HIS C 206 Details of bonding type rmsd/Z covalent geometry : bond 0.00519 / 0.27 (13243) covalent geometry : angle 0.57221 / 0.33 (17926) hydrogen bonds : bond 0.05216 / 3.58 ( 994) hydrogen bonds : angle 4.13719 / 3.06 ( 2967) Misc. bond : bond 0.01228 / 0.77 ( 1) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3084 Ramachandran restraints generated. 1542 Oldfield, 0 Emsley, 1542 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3084 Ramachandran restraints generated. 1542 Oldfield, 0 Emsley, 1542 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 368 is missing expected H atoms. Skipping. Evaluate side-chains 580 residues out of total 1409 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 522 time to evaluate : 0.450 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 55 LEU cc_start: 0.8392 (OUTLIER) cc_final: 0.8095 (mm) REVERT: A 81 TYR cc_start: 0.7924 (t80) cc_final: 0.7604 (t80) REVERT: A 112 MET cc_start: 0.7791 (tpp) cc_final: 0.7441 (tpp) REVERT: A 188 GLU cc_start: 0.7876 (tm-30) cc_final: 0.7224 (tm-30) REVERT: A 190 MET cc_start: 0.7491 (tpt) cc_final: 0.6959 (tpp) REVERT: A 236 HIS cc_start: 0.8020 (m-70) cc_final: 0.7799 (m-70) REVERT: A 246 ASP cc_start: 0.7765 (m-30) cc_final: 0.7419 (m-30) REVERT: A 297 MET cc_start: 0.6537 (mpp) cc_final: 0.6003 (mpp) REVERT: A 321 TYR cc_start: 0.7179 (t80) cc_final: 0.6883 (t80) REVERT: A 343 LEU cc_start: 0.8423 (mm) cc_final: 0.8063 (tp) REVERT: A 344 LYS cc_start: 0.8334 (tttt) cc_final: 0.7988 (tttt) REVERT: A 365 LEU cc_start: 0.8742 (mm) cc_final: 0.8343 (mp) REVERT: A 391 LEU cc_start: 0.8116 (tp) cc_final: 0.7650 (tt) REVERT: B 58 ILE cc_start: 0.7802 (mm) cc_final: 0.7345 (mm) REVERT: B 69 GLN cc_start: 0.8159 (mm-40) cc_final: 0.7920 (mm-40) REVERT: B 83 SER cc_start: 0.7934 (m) cc_final: 0.7505 (t) REVERT: B 115 GLU cc_start: 0.7301 (tp30) cc_final: 0.6701 (tp30) REVERT: B 128 MET cc_start: 0.7463 (OUTLIER) cc_final: 0.7198 (mtm) REVERT: B 212 LEU cc_start: 0.8109 (mt) cc_final: 0.7782 (mp) REVERT: B 388 GLU cc_start: 0.7205 (mt-10) cc_final: 0.6949 (tt0) REVERT: B 410 GLU cc_start: 0.7258 (tp30) cc_final: 0.6885 (tp30) REVERT: B 422 GLN cc_start: 0.7849 (tp40) cc_final: 0.7469 (tp40) REVERT: B 425 LYS cc_start: 0.8291 (mptt) cc_final: 0.8088 (mptt) REVERT: B 444 SER cc_start: 0.8327 (m) cc_final: 0.8006 (t) REVERT: C 41 ILE cc_start: 0.8360 (mm) cc_final: 0.8022 (mm) REVERT: C 49 GLN cc_start: 0.8442 (tp-100) cc_final: 0.8135 (tp40) REVERT: C 86 TYR cc_start: 0.7269 (t80) cc_final: 0.7044 (t80) REVERT: C 112 GLU cc_start: 0.7633 (tm-30) cc_final: 0.7154 (tm-30) REVERT: C 127 GLN cc_start: 0.7596 (tt0) cc_final: 0.7370 (tt0) REVERT: C 172 ARG cc_start: 0.7836 (ttm-80) cc_final: 0.7603 (ttm-80) REVERT: C 223 GLU cc_start: 0.7560 (mm-30) cc_final: 0.7346 (mm-30) REVERT: C 236 ILE cc_start: 0.8437 (mm) cc_final: 0.8184 (mt) REVERT: C 328 GLU cc_start: 0.7420 (tp30) cc_final: 0.6723 (tp30) REVERT: C 388 GLU cc_start: 0.7574 (tp30) cc_final: 0.6937 (tp30) REVERT: D 14 GLN cc_start: 0.8447 (tt0) cc_final: 0.7991 (tt0) REVERT: D 22 GLU cc_start: 0.7041 (mm-30) cc_final: 0.6738 (mm-30) REVERT: D 39 SER cc_start: 0.8198 (m) cc_final: 0.7533 (t) REVERT: D 66 GLN cc_start: 0.7686 (mm-40) cc_final: 0.7397 (mt0) REVERT: D 138 PHE cc_start: 0.7994 (t80) cc_final: 0.7446 (t80) REVERT: D 197 PHE cc_start: 0.8330 (t80) cc_final: 0.7940 (t80) REVERT: D 205 SER cc_start: 0.8192 (t) cc_final: 0.7478 (p) REVERT: D 207 SER cc_start: 0.8553 (t) cc_final: 0.8228 (p) REVERT: D 208 ASN cc_start: 0.8248 (m-40) cc_final: 0.7668 (m-40) REVERT: D 223 GLU cc_start: 0.7697 (mm-30) cc_final: 0.7143 (mm-30) REVERT: D 225 LEU cc_start: 0.8627 (OUTLIER) cc_final: 0.8400 (mt) REVERT: D 361 PHE cc_start: 0.8409 (t80) cc_final: 0.8055 (t80) REVERT: D 441 SER cc_start: 0.8199 (m) cc_final: 0.7637 (p) outliers start: 58 outliers final: 52 residues processed: 547 average time/residue: 0.2615 time to fit residues: 203.6059 Evaluate side-chains 575 residues out of total 1409 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 520 time to evaluate : 0.640 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 LEU Chi-restraints excluded: chain A residue 55 LEU Chi-restraints excluded: chain A residue 65 ASN Chi-restraints excluded: chain A residue 116 ARG Chi-restraints excluded: chain A residue 178 CYS Chi-restraints excluded: chain A residue 241 ILE Chi-restraints excluded: chain A residue 252 GLU Chi-restraints excluded: chain A residue 262 THR Chi-restraints excluded: chain A residue 299 LEU Chi-restraints excluded: chain A residue 322 ILE Chi-restraints excluded: chain A residue 351 LEU Chi-restraints excluded: chain B residue 9 LEU Chi-restraints excluded: chain B residue 84 MET Chi-restraints excluded: chain B residue 88 VAL Chi-restraints excluded: chain B residue 95 LYS Chi-restraints excluded: chain B residue 124 SER Chi-restraints excluded: chain B residue 128 MET Chi-restraints excluded: chain B residue 145 SER Chi-restraints excluded: chain B residue 146 TRP Chi-restraints excluded: chain B residue 149 ILE Chi-restraints excluded: chain B residue 171 VAL Chi-restraints excluded: chain B residue 178 LEU Chi-restraints excluded: chain B residue 193 ILE Chi-restraints excluded: chain B residue 194 VAL Chi-restraints excluded: chain B residue 428 ILE Chi-restraints excluded: chain C residue 22 GLU Chi-restraints excluded: chain C residue 26 ASP Chi-restraints excluded: chain C residue 97 THR Chi-restraints excluded: chain C residue 122 LEU Chi-restraints excluded: chain C residue 143 TRP Chi-restraints excluded: chain C residue 194 VAL Chi-restraints excluded: chain C residue 209 LEU Chi-restraints excluded: chain C residue 228 LEU Chi-restraints excluded: chain C residue 318 HIS Chi-restraints excluded: chain C residue 411 THR Chi-restraints excluded: chain C residue 420 CYS Chi-restraints excluded: chain C residue 427 SER Chi-restraints excluded: chain D residue 13 ILE Chi-restraints excluded: chain D residue 20 ILE Chi-restraints excluded: chain D residue 24 TYR Chi-restraints excluded: chain D residue 58 VAL Chi-restraints excluded: chain D residue 60 LYS Chi-restraints excluded: chain D residue 98 LEU Chi-restraints excluded: chain D residue 125 MET Chi-restraints excluded: chain D residue 143 TRP Chi-restraints excluded: chain D residue 156 VAL Chi-restraints excluded: chain D residue 222 CYS Chi-restraints excluded: chain D residue 225 LEU Chi-restraints excluded: chain D residue 228 LEU Chi-restraints excluded: chain D residue 318 HIS Chi-restraints excluded: chain D residue 325 LEU Chi-restraints excluded: chain D residue 329 CYS Chi-restraints excluded: chain D residue 354 LYS Chi-restraints excluded: chain D residue 388 GLU Chi-restraints excluded: chain D residue 403 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: [97, 114, 11, 42, 54, 108, 98, 69, 92, 8, 16] chunk 97 optimal weight: 2.9990 chunk 114 optimal weight: 2.9990 chunk 11 optimal weight: 0.9980 chunk 42 optimal weight: 0.7980 chunk 54 optimal weight: 0.8980 chunk 108 optimal weight: 0.7980 chunk 98 optimal weight: 0.6980 chunk 69 optimal weight: 2.9990 chunk 92 optimal weight: 0.7980 chunk 8 optimal weight: 6.9990 chunk 16 optimal weight: 0.1980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 320 ASN ** B 211 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 436 ASN ** C 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 206 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3730 r_free = 0.3730 target = 0.127258 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.108345 restraints weight = 61393.232| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3521 r_free = 0.3521 target = 0.113165 restraints weight = 21207.160| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.3564 r_free = 0.3564 target = 0.116054 restraints weight = 11049.844| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 45)----------------| | r_work = 0.3590 r_free = 0.3590 target = 0.117776 restraints weight = 7351.572| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 43)----------------| | r_work = 0.3606 r_free = 0.3606 target = 0.118833 restraints weight = 5634.925| |-----------------------------------------------------------------------------| r_work (final): 0.3609 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7140 moved from start: 0.3567 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 13244 Z= 0.158 Angle : 0.531 7.645 17926 Z= 0.296 Chirality : 0.036 0.172 2040 Planarity : 0.004 0.084 2129 Dihedral : 9.671 72.430 1995 Min Nonbonded Distance : 2.266 Molprobity Statistics. All-atom Clashscore : 12.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 4.12 % Allowed : 22.29 % Favored : 73.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.06 (0.22), residues: 1542 helix: 2.07 (0.15), residues: 1223 sheet: 0.03 (1.03), residues: 26 loop : -1.60 (0.38), residues: 293 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG A 203 TYR 0.014 0.001 TYR B 26 PHE 0.029 0.001 PHE C 379 TRP 0.022 0.001 TRP D 181 HIS 0.009 0.001 HIS C 206 Details of bonding type rmsd/Z covalent geometry : bond 0.00313 / 0.16 (13243) covalent geometry : angle 0.53123 / 0.30 (17926) hydrogen bonds : bond 0.04962 / 3.41 ( 994) hydrogen bonds : angle 3.95599 / 2.92 ( 2967) Misc. bond : bond 0.01197 / 0.75 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4983.57 seconds wall clock time: 85 minutes 45.35 seconds (5145.35 seconds total)