Starting phenix.real_space_refine on Sun Dec 29 11:52:10 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7plv_13503/12_2024/7plv_13503.cif Found real_map, /net/cci-nas-00/data/ceres_data/7plv_13503/12_2024/7plv_13503.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7plv_13503/12_2024/7plv_13503.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7plv_13503/12_2024/7plv_13503.map" model { file = "/net/cci-nas-00/data/ceres_data/7plv_13503/12_2024/7plv_13503.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7plv_13503/12_2024/7plv_13503.cif" } resolution = 3.5 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.001 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 2 5.49 5 Mg 1 5.21 5 S 63 5.16 5 C 6462 2.51 5 N 1722 2.21 5 O 1889 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 43 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/chem_data/mon_lib" Total number of atoms: 10139 Number of models: 1 Model: "" Number of chains: 6 Chain: "B" Number of atoms: 1059 Number of conformers: 1 Conformer: "" Number of residues, atoms: 139, 1059 Classifications: {'peptide': 139} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PTRANS': 3, 'TRANS': 135} Chain breaks: 2 Unresolved non-hydrogen bonds: 45 Unresolved non-hydrogen angles: 53 Unresolved non-hydrogen dihedrals: 37 Planarities with less than four sites: {'GLU:plan': 3, 'ARG:plan': 2, 'ASN:plan1': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 31 Chain: "A" Number of atoms: 6097 Number of conformers: 1 Conformer: "" Number of residues, atoms: 747, 6097 Classifications: {'peptide': 747} Link IDs: {'PTRANS': 27, 'TRANS': 719} Chain breaks: 4 Chain: "C" Number of atoms: 2900 Number of conformers: 1 Conformer: "" Number of residues, atoms: 371, 2900 Classifications: {'peptide': 371} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 351} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'HIC:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "H" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 29 Classifications: {'peptide': 3} Link IDs: {'TRANS': 2} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'EEP:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "H" Number of atoms: 26 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 26 Classifications: {'peptide': 4} Modifications used: {'DTH_chir_02_both': 1, 'PEPT-D': 1} Link IDs: {'TRANS': 3} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'HYP:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "C" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 6.62, per 1000 atoms: 0.65 Number of scatterers: 10139 At special positions: 0 Unit cell: (103.88, 131.44, 152.64, 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 63 16.00 P 2 15.00 Mg 1 11.99 O 1889 8.00 N 1722 7.00 C 6462 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied TRANS " TRP H 1 " - " ALA H 7 " " DTH H 4 " - " ALA H 3 " Time building additional restraints: 2.81 Conformation dependent library (CDL) restraints added in 1.4 seconds 2472 Ramachandran restraints generated. 1236 Oldfield, 0 Emsley, 1236 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Skipped Input residue name is d-peptide pdb=" CB DTH H 4 " Number of C-beta restraints generated: 2378 Finding SS restraints... Secondary structure from input PDB file: 60 helices and 14 sheets defined 55.2% alpha, 12.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.14 Creating SS restraints... Processing helix chain 'B' and resid 5 through 19 Processing helix chain 'B' and resid 29 through 39 removed outlier: 4.200A pdb=" N GLY B 33 " --> pdb=" O TYR B 29 " (cutoff:3.500A) removed outlier: 4.457A pdb=" N ASP B 34 " --> pdb=" O SER B 30 " (cutoff:3.500A) Processing helix chain 'B' and resid 44 through 53 Processing helix chain 'B' and resid 56 through 63 Processing helix chain 'B' and resid 67 through 79 Proline residue: B 72 - end of helix Processing helix chain 'B' and resid 87 through 95 Processing helix chain 'B' and resid 105 through 116 Processing helix chain 'B' and resid 121 through 130 Processing helix chain 'B' and resid 140 through 150 Processing helix chain 'A' and resid 81 through 95 Processing helix chain 'A' and resid 120 through 128 Processing helix chain 'A' and resid 138 through 153 Processing helix chain 'A' and resid 164 through 167 Processing helix chain 'A' and resid 168 through 185 Processing helix chain 'A' and resid 191 through 207 removed outlier: 3.645A pdb=" N LYS A 195 " --> pdb=" O ASN A 191 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N ASN A 200 " --> pdb=" O VAL A 196 " (cutoff:3.500A) Proline residue: A 201 - end of helix Processing helix chain 'A' and resid 245 through 250 removed outlier: 3.544A pdb=" N ARG A 248 " --> pdb=" O GLU A 245 " (cutoff:3.500A) Processing helix chain 'A' and resid 259 through 268 removed outlier: 4.251A pdb=" N TYR A 263 " --> pdb=" O TYR A 259 " (cutoff:3.500A) Processing helix chain 'A' and resid 271 through 278 removed outlier: 4.276A pdb=" N THR A 276 " --> pdb=" O GLU A 273 " (cutoff:3.500A) Processing helix chain 'A' and resid 285 through 290 removed outlier: 3.967A pdb=" N GLN A 290 " --> pdb=" O HIS A 286 " (cutoff:3.500A) Processing helix chain 'A' and resid 300 through 316 removed outlier: 3.855A pdb=" N VAL A 306 " --> pdb=" O ALA A 302 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N ALA A 311 " --> pdb=" O ASN A 307 " (cutoff:3.500A) Processing helix chain 'A' and resid 318 through 337 removed outlier: 3.531A pdb=" N ASN A 337 " --> pdb=" O LEU A 333 " (cutoff:3.500A) Processing helix chain 'A' and resid 354 through 365 Processing helix chain 'A' and resid 367 through 375 removed outlier: 3.857A pdb=" N HIS A 373 " --> pdb=" O GLU A 369 " (cutoff:3.500A) Processing helix chain 'A' and resid 392 through 424 Processing helix chain 'A' and resid 448 through 479 removed outlier: 3.552A pdb=" N GLN A 464 " --> pdb=" O LYS A 460 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N TYR A 477 " --> pdb=" O GLU A 473 " (cutoff:3.500A) Processing helix chain 'A' and resid 483 through 487 Processing helix chain 'A' and resid 492 through 501 removed outlier: 3.612A pdb=" N LEU A 498 " --> pdb=" O PRO A 494 " (cutoff:3.500A) Processing helix chain 'A' and resid 506 through 515 removed outlier: 3.666A pdb=" N LYS A 514 " --> pdb=" O ASP A 510 " (cutoff:3.500A) Processing helix chain 'A' and resid 519 through 532 removed outlier: 3.598A pdb=" N ALA A 524 " --> pdb=" O ASP A 520 " (cutoff:3.500A) Processing helix chain 'A' and resid 563 through 569 removed outlier: 3.649A pdb=" N ASN A 568 " --> pdb=" O PHE A 564 " (cutoff:3.500A) Processing helix chain 'A' and resid 573 through 582 removed outlier: 3.743A pdb=" N ILE A 577 " --> pdb=" O TYR A 573 " (cutoff:3.500A) Processing helix chain 'A' and resid 587 through 593 removed outlier: 3.537A pdb=" N GLU A 591 " --> pdb=" O LYS A 587 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N PHE A 593 " --> pdb=" O LEU A 589 " (cutoff:3.500A) Processing helix chain 'A' and resid 630 through 634 Processing helix chain 'A' and resid 635 through 652 Processing helix chain 'A' and resid 674 through 685 removed outlier: 3.837A pdb=" N GLN A 680 " --> pdb=" O LYS A 676 " (cutoff:3.500A) Processing helix chain 'A' and resid 686 through 695 Processing helix chain 'A' and resid 704 through 712 Processing helix chain 'A' and resid 713 through 715 No H-bonds generated for 'chain 'A' and resid 713 through 715' Processing helix chain 'A' and resid 723 through 736 removed outlier: 3.766A pdb=" N GLU A 733 " --> pdb=" O LYS A 729 " (cutoff:3.500A) Processing helix chain 'A' and resid 738 through 740 No H-bonds generated for 'chain 'A' and resid 738 through 740' Processing helix chain 'A' and resid 754 through 792 Processing helix chain 'C' and resid 55 through 61 Processing helix chain 'C' and resid 78 through 92 removed outlier: 4.353A pdb=" N LYS C 84 " --> pdb=" O ASP C 80 " (cutoff:3.500A) Processing helix chain 'C' and resid 112 through 126 removed outlier: 4.183A pdb=" N ARG C 116 " --> pdb=" O PRO C 112 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N GLU C 117 " --> pdb=" O LYS C 113 " (cutoff:3.500A) Processing helix chain 'C' and resid 137 through 146 removed outlier: 4.077A pdb=" N LEU C 142 " --> pdb=" O ALA C 138 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N TYR C 143 " --> pdb=" O VAL C 139 " (cutoff:3.500A) Processing helix chain 'C' and resid 172 through 175 Processing helix chain 'C' and resid 181 through 196 removed outlier: 3.548A pdb=" N LYS C 191 " --> pdb=" O ASP C 187 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N GLU C 195 " --> pdb=" O LYS C 191 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N ARG C 196 " --> pdb=" O ILE C 192 " (cutoff:3.500A) Processing helix chain 'C' and resid 202 through 217 removed outlier: 4.276A pdb=" N ILE C 208 " --> pdb=" O ALA C 204 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N ASP C 211 " --> pdb=" O GLU C 207 " (cutoff:3.500A) Processing helix chain 'C' and resid 222 through 233 removed outlier: 3.798A pdb=" N GLU C 226 " --> pdb=" O ASP C 222 " (cutoff:3.500A) Processing helix chain 'C' and resid 234 through 237 Processing helix chain 'C' and resid 251 through 260 removed outlier: 4.262A pdb=" N PHE C 255 " --> pdb=" O GLY C 251 " (cutoff:3.500A) Proline residue: C 258 - end of helix Processing helix chain 'C' and resid 273 through 285 removed outlier: 3.600A pdb=" N CYS C 285 " --> pdb=" O SER C 281 " (cutoff:3.500A) Processing helix chain 'C' and resid 286 through 296 removed outlier: 3.698A pdb=" N ARG C 290 " --> pdb=" O ASP C 286 " (cutoff:3.500A) removed outlier: 4.430A pdb=" N LYS C 291 " --> pdb=" O ILE C 287 " (cutoff:3.500A) removed outlier: 5.305A pdb=" N ASP C 292 " --> pdb=" O ASP C 288 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N ALA C 295 " --> pdb=" O LYS C 291 " (cutoff:3.500A) Processing helix chain 'C' and resid 301 through 306 removed outlier: 4.361A pdb=" N TYR C 306 " --> pdb=" O THR C 303 " (cutoff:3.500A) Processing helix chain 'C' and resid 308 through 319 Processing helix chain 'C' and resid 332 through 336 removed outlier: 4.602A pdb=" N LYS C 336 " --> pdb=" O PRO C 333 " (cutoff:3.500A) Processing helix chain 'C' and resid 337 through 349 Processing helix chain 'C' and resid 350 through 355 removed outlier: 3.762A pdb=" N GLN C 354 " --> pdb=" O THR C 351 " (cutoff:3.500A) Processing helix chain 'C' and resid 359 through 366 Processing helix chain 'C' and resid 368 through 374 removed outlier: 3.789A pdb=" N ARG C 372 " --> pdb=" O SER C 368 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 26 through 28 Processing sheet with id=AA2, first strand: chain 'A' and resid 12 through 16 removed outlier: 4.661A pdb=" N LEU A 42 " --> pdb=" O LYS A 46 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N LYS A 46 " --> pdb=" O LEU A 42 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 100 through 102 removed outlier: 3.884A pdb=" N GLN A 157 " --> pdb=" O PHE A 432 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N GLY A 163 " --> pdb=" O ILE A 438 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N GLY A 236 " --> pdb=" O GLY A 227 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 208 through 209 Processing sheet with id=AA5, first strand: chain 'A' and resid 341 through 344 removed outlier: 6.235A pdb=" N SER A 347 " --> pdb=" O ARG A 343 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 377 through 382 Processing sheet with id=AA7, first strand: chain 'A' and resid 538 through 539 Processing sheet with id=AA8, first strand: chain 'A' and resid 700 through 703 removed outlier: 3.553A pdb=" N SER A 700 " --> pdb=" O PHE A 751 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 29 through 32 removed outlier: 6.706A pdb=" N LEU C 8 " --> pdb=" O LEU C 104 " (cutoff:3.500A) removed outlier: 8.528A pdb=" N THR C 106 " --> pdb=" O LEU C 8 " (cutoff:3.500A) removed outlier: 8.410A pdb=" N CYS C 10 " --> pdb=" O THR C 106 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 53 through 54 Processing sheet with id=AB2, first strand: chain 'C' and resid 71 through 72 Processing sheet with id=AB3, first strand: chain 'C' and resid 169 through 170 Processing sheet with id=AB4, first strand: chain 'C' and resid 169 through 170 removed outlier: 6.470A pdb=" N ILE C 151 " --> pdb=" O VAL C 298 " (cutoff:3.500A) removed outlier: 7.525A pdb=" N SER C 300 " --> pdb=" O ILE C 151 " (cutoff:3.500A) removed outlier: 5.917A pdb=" N LEU C 153 " --> pdb=" O SER C 300 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 238 through 241 524 hydrogen bonds defined for protein. 1470 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: 3.27 Time building geometry restraints manager: 3.09 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 1691 1.32 - 1.44: 2733 1.44 - 1.56: 5825 1.56 - 1.69: 3 1.69 - 1.81: 102 Bond restraints: 10354 Sorted by residual: bond pdb=" CA EEP H 2 " pdb=" C EEP H 2 " ideal model delta sigma weight residual 1.572 1.453 0.119 2.00e-02 2.50e+03 3.55e+01 bond pdb=" C HYP H 6 " pdb=" N ALA H 7 " ideal model delta sigma weight residual 1.329 1.374 -0.045 1.40e-02 5.10e+03 1.03e+01 bond pdb=" C EEP H 2 " pdb=" O EEP H 2 " ideal model delta sigma weight residual 1.263 1.200 0.063 2.00e-02 2.50e+03 9.91e+00 bond pdb=" CA TRP H 1 " pdb=" C TRP H 1 " ideal model delta sigma weight residual 1.525 1.468 0.057 2.10e-02 2.27e+03 7.45e+00 bond pdb=" CE1 HIC C 73 " pdb=" NE2 HIC C 73 " ideal model delta sigma weight residual 1.347 1.400 -0.053 2.00e-02 2.50e+03 7.15e+00 ... (remaining 10349 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.49: 13739 2.49 - 4.98: 216 4.98 - 7.47: 20 7.47 - 9.96: 5 9.96 - 12.45: 2 Bond angle restraints: 13982 Sorted by residual: angle pdb=" C HYP H 6 " pdb=" N ALA H 7 " pdb=" CA ALA H 7 " ideal model delta sigma weight residual 121.70 111.07 10.63 1.80e+00 3.09e-01 3.49e+01 angle pdb=" N HYP H 6 " pdb=" CA HYP H 6 " pdb=" CB HYP H 6 " ideal model delta sigma weight residual 103.00 108.87 -5.87 1.10e+00 8.26e-01 2.85e+01 angle pdb=" CA EEP H 2 " pdb=" CB EEP H 2 " pdb=" CG EEP H 2 " ideal model delta sigma weight residual 115.99 103.54 12.45 3.00e+00 1.11e-01 1.72e+01 angle pdb=" CD2 TRP H 1 " pdb=" CE2 TRP H 1 " pdb=" CZ2 TRP H 1 " ideal model delta sigma weight residual 122.40 118.25 4.15 1.00e+00 1.00e+00 1.72e+01 angle pdb=" CA DTH H 4 " pdb=" C DTH H 4 " pdb=" N CYS H 5 " ideal model delta sigma weight residual 116.20 123.69 -7.49 2.00e+00 2.50e-01 1.40e+01 ... (remaining 13977 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 31.86: 6093 31.86 - 63.72: 120 63.72 - 95.58: 38 95.58 - 127.44: 1 127.44 - 159.30: 2 Dihedral angle restraints: 6254 sinusoidal: 2564 harmonic: 3690 Sorted by residual: dihedral pdb=" O1B ADP C 401 " pdb=" O3A ADP C 401 " pdb=" PB ADP C 401 " pdb=" PA ADP C 401 " ideal model delta sinusoidal sigma weight residual -60.00 99.30 -159.30 1 2.00e+01 2.50e-03 4.65e+01 dihedral pdb=" O2A ADP C 401 " pdb=" O3A ADP C 401 " pdb=" PA ADP C 401 " pdb=" PB ADP C 401 " ideal model delta sinusoidal sigma weight residual -60.00 85.37 -145.37 1 2.00e+01 2.50e-03 4.37e+01 dihedral pdb=" C5' ADP C 401 " pdb=" O5' ADP C 401 " pdb=" PA ADP C 401 " pdb=" O2A ADP C 401 " ideal model delta sinusoidal sigma weight residual 300.00 177.96 122.04 1 2.00e+01 2.50e-03 3.67e+01 ... (remaining 6251 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.041: 1003 0.041 - 0.081: 378 0.081 - 0.122: 114 0.122 - 0.162: 29 0.162 - 0.203: 4 Chirality restraints: 1528 Sorted by residual: chirality pdb=" CA CYS H 5 " pdb=" N CYS H 5 " pdb=" C CYS H 5 " pdb=" CB CYS H 5 " both_signs ideal model delta sigma weight residual False 2.51 2.71 -0.20 2.00e-01 2.50e+01 1.03e+00 chirality pdb=" CA GLU A 512 " pdb=" N GLU A 512 " pdb=" C GLU A 512 " pdb=" CB GLU A 512 " both_signs ideal model delta sigma weight residual False 2.51 2.31 0.20 2.00e-01 2.50e+01 9.81e-01 chirality pdb=" CA PHE C 255 " pdb=" N PHE C 255 " pdb=" C PHE C 255 " pdb=" CB PHE C 255 " both_signs ideal model delta sigma weight residual False 2.51 2.34 0.17 2.00e-01 2.50e+01 7.56e-01 ... (remaining 1525 not shown) Planarity restraints: 1791 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG A 213 " -0.174 9.50e-02 1.11e+02 9.87e-02 4.98e+01 pdb=" NE ARG A 213 " 0.050 2.00e-02 2.50e+03 pdb=" CZ ARG A 213 " -0.116 2.00e-02 2.50e+03 pdb=" NH1 ARG A 213 " 0.041 2.00e-02 2.50e+03 pdb=" NH2 ARG A 213 " 0.032 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 677 " 0.164 9.50e-02 1.11e+02 9.42e-02 4.69e+01 pdb=" NE ARG A 677 " -0.048 2.00e-02 2.50e+03 pdb=" CZ ARG A 677 " 0.112 2.00e-02 2.50e+03 pdb=" NH1 ARG A 677 " -0.040 2.00e-02 2.50e+03 pdb=" NH2 ARG A 677 " -0.031 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG C 196 " 0.125 9.50e-02 1.11e+02 7.29e-02 2.90e+01 pdb=" NE ARG C 196 " -0.038 2.00e-02 2.50e+03 pdb=" CZ ARG C 196 " 0.089 2.00e-02 2.50e+03 pdb=" NH1 ARG C 196 " -0.031 2.00e-02 2.50e+03 pdb=" NH2 ARG C 196 " -0.025 2.00e-02 2.50e+03 ... (remaining 1788 not shown) Histogram of nonbonded interaction distances: 1.73 - 2.37: 13 2.37 - 3.00: 5420 3.00 - 3.63: 14892 3.63 - 4.27: 22403 4.27 - 4.90: 37983 Nonbonded interactions: 80711 Sorted by model distance: nonbonded pdb=" CD1 TRP H 1 " pdb=" SG CYS H 5 " model vdw 1.732 3.620 nonbonded pdb=" OH TYR C 218 " pdb=" OE2 GLU C 226 " model vdw 2.167 3.040 nonbonded pdb=" NH2 ARG B 37 " pdb=" O PRO B 43 " model vdw 2.173 3.120 nonbonded pdb=" OD1 ASN C 128 " pdb=" NZ LYS C 359 " model vdw 2.214 3.120 nonbonded pdb=" O ASN C 92 " pdb=" NH1 ARG C 95 " model vdw 2.218 3.120 ... (remaining 80706 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.350 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.350 Check model and map are aligned: 0.070 Set scattering table: 0.090 Process input model: 25.580 Find NCS groups from input model: 0.090 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.900 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.480 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8289 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 : 0.005 0.119 10354 Z= 0.297 Angle : 0.808 12.450 13982 Z= 0.481 Chirality : 0.048 0.203 1528 Planarity : 0.008 0.124 1789 Dihedral : 15.024 159.301 3870 Min Nonbonded Distance : 1.732 Molprobity Statistics. All-atom Clashscore : 4.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.40 % Favored : 99.60 % Rotamer: Outliers : 0.00 % Allowed : 0.18 % Favored : 99.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.54 (0.21), residues: 1236 helix: -1.60 (0.17), residues: 611 sheet: 0.34 (0.36), residues: 162 loop : -0.39 (0.27), residues: 463 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.003 TRP A 374 HIS 0.010 0.002 HIS A 418 PHE 0.034 0.002 PHE C 255 TYR 0.040 0.006 TYR C 306 ARG 0.118 0.012 ARG A 213 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2472 Ramachandran restraints generated. 1236 Oldfield, 0 Emsley, 1236 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2472 Ramachandran restraints generated. 1236 Oldfield, 0 Emsley, 1236 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 1093 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 147 time to evaluate : 1.197 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 12 PHE cc_start: 0.9310 (m-10) cc_final: 0.8758 (m-10) REVERT: B 66 ASP cc_start: 0.8944 (p0) cc_final: 0.8367 (p0) REVERT: C 44 MET cc_start: 0.7946 (mtp) cc_final: 0.7737 (ttt) outliers start: 0 outliers final: 0 residues processed: 147 average time/residue: 0.2671 time to fit residues: 53.3445 Evaluate side-chains 85 residues out of total 1093 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 85 time to evaluate : 1.330 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 104 optimal weight: 0.5980 chunk 93 optimal weight: 2.9990 chunk 52 optimal weight: 0.7980 chunk 32 optimal weight: 0.7980 chunk 63 optimal weight: 0.9980 chunk 50 optimal weight: 0.4980 chunk 97 optimal weight: 0.7980 chunk 37 optimal weight: 0.8980 chunk 59 optimal weight: 2.9990 chunk 72 optimal weight: 1.9990 chunk 112 optimal weight: 0.3980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 75 GLN A 81 HIS A 264 GLN A 283 ASN A 463 GLN A 464 GLN ** A 468 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 497 ASN ** A 681 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 59 GLN C 280 ASN C 296 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8313 moved from start: 0.2197 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 10354 Z= 0.183 Angle : 0.615 7.853 13982 Z= 0.322 Chirality : 0.042 0.229 1528 Planarity : 0.004 0.052 1789 Dihedral : 9.254 158.460 1396 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 5.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.08 % Favored : 99.92 % Rotamer: Outliers : 1.11 % Allowed : 5.18 % Favored : 93.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.66 (0.23), residues: 1236 helix: 0.47 (0.20), residues: 610 sheet: 0.85 (0.39), residues: 158 loop : 0.51 (0.29), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 484 HIS 0.009 0.001 HIS A 418 PHE 0.026 0.002 PHE C 255 TYR 0.018 0.001 TYR A 787 ARG 0.004 0.000 ARG C 372 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2472 Ramachandran restraints generated. 1236 Oldfield, 0 Emsley, 1236 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2472 Ramachandran restraints generated. 1236 Oldfield, 0 Emsley, 1236 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 1093 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 91 time to evaluate : 1.258 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 50 LYS cc_start: 0.9384 (ttpp) cc_final: 0.9109 (ptmm) REVERT: B 66 ASP cc_start: 0.8828 (p0) cc_final: 0.8269 (p0) REVERT: B 93 PHE cc_start: 0.9114 (OUTLIER) cc_final: 0.8782 (t80) REVERT: B 140 ASN cc_start: 0.8920 (t0) cc_final: 0.8715 (t0) REVERT: A 682 LEU cc_start: 0.9329 (OUTLIER) cc_final: 0.9027 (mm) outliers start: 12 outliers final: 3 residues processed: 99 average time/residue: 0.2397 time to fit residues: 34.3330 Evaluate side-chains 78 residues out of total 1093 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 73 time to evaluate : 1.223 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 93 PHE Chi-restraints excluded: chain B residue 139 ILE Chi-restraints excluded: chain A residue 535 CYS Chi-restraints excluded: chain A residue 682 LEU Chi-restraints excluded: chain C residue 211 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 62 optimal weight: 1.9990 chunk 34 optimal weight: 1.9990 chunk 93 optimal weight: 2.9990 chunk 76 optimal weight: 0.7980 chunk 31 optimal weight: 0.5980 chunk 112 optimal weight: 0.9980 chunk 121 optimal weight: 2.9990 chunk 100 optimal weight: 0.5980 chunk 111 optimal weight: 2.9990 chunk 38 optimal weight: 0.8980 chunk 90 optimal weight: 0.0670 overall best weight: 0.5918 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 468 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 681 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 705 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8319 moved from start: 0.2706 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 10354 Z= 0.165 Angle : 0.554 7.643 13982 Z= 0.284 Chirality : 0.040 0.172 1528 Planarity : 0.004 0.054 1789 Dihedral : 8.644 158.123 1396 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 6.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.24 % Favored : 99.76 % Rotamer: Outliers : 0.83 % Allowed : 6.10 % Favored : 93.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.15 (0.23), residues: 1236 helix: 1.03 (0.21), residues: 622 sheet: 0.80 (0.39), residues: 160 loop : 0.60 (0.29), residues: 454 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 484 HIS 0.007 0.001 HIS A 418 PHE 0.022 0.001 PHE C 255 TYR 0.015 0.001 TYR A 50 ARG 0.003 0.000 ARG A 779 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2472 Ramachandran restraints generated. 1236 Oldfield, 0 Emsley, 1236 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2472 Ramachandran restraints generated. 1236 Oldfield, 0 Emsley, 1236 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 1093 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 80 time to evaluate : 1.261 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 50 LYS cc_start: 0.9370 (ttpp) cc_final: 0.9134 (ptmm) REVERT: B 93 PHE cc_start: 0.9072 (OUTLIER) cc_final: 0.8740 (t80) REVERT: B 140 ASN cc_start: 0.8812 (t0) cc_final: 0.8513 (t0) REVERT: A 682 LEU cc_start: 0.9305 (OUTLIER) cc_final: 0.8956 (mm) REVERT: C 236 LEU cc_start: 0.8350 (mp) cc_final: 0.8041 (mt) outliers start: 9 outliers final: 4 residues processed: 87 average time/residue: 0.2242 time to fit residues: 29.0839 Evaluate side-chains 71 residues out of total 1093 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 65 time to evaluate : 1.151 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 44 THR Chi-restraints excluded: chain B residue 93 PHE Chi-restraints excluded: chain A residue 682 LEU Chi-restraints excluded: chain A residue 735 LEU Chi-restraints excluded: chain C residue 211 ASP Chi-restraints excluded: chain C residue 250 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 111 optimal weight: 0.7980 chunk 84 optimal weight: 2.9990 chunk 58 optimal weight: 1.9990 chunk 12 optimal weight: 20.0000 chunk 53 optimal weight: 0.5980 chunk 75 optimal weight: 2.9990 chunk 113 optimal weight: 2.9990 chunk 119 optimal weight: 0.5980 chunk 59 optimal weight: 2.9990 chunk 107 optimal weight: 4.9990 chunk 32 optimal weight: 1.9990 overall best weight: 1.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 410 ASN ** A 468 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 775 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8363 moved from start: 0.3007 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 10354 Z= 0.245 Angle : 0.585 9.004 13982 Z= 0.294 Chirality : 0.041 0.184 1528 Planarity : 0.004 0.058 1789 Dihedral : 8.446 157.300 1396 Min Nonbonded Distance : 2.196 Molprobity Statistics. All-atom Clashscore : 6.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.57 % Favored : 99.43 % Rotamer: Outliers : 1.29 % Allowed : 6.75 % Favored : 91.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.35 (0.24), residues: 1236 helix: 1.28 (0.21), residues: 622 sheet: 0.84 (0.39), residues: 160 loop : 0.58 (0.29), residues: 454 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 484 HIS 0.007 0.001 HIS A 418 PHE 0.021 0.001 PHE C 255 TYR 0.015 0.001 TYR A 259 ARG 0.002 0.000 ARG C 335 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2472 Ramachandran restraints generated. 1236 Oldfield, 0 Emsley, 1236 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2472 Ramachandran restraints generated. 1236 Oldfield, 0 Emsley, 1236 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 1093 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 69 time to evaluate : 1.204 Fit side-chains revert: symmetry clash REVERT: B 66 ASP cc_start: 0.8591 (p0) cc_final: 0.8363 (p0) REVERT: B 93 PHE cc_start: 0.9059 (OUTLIER) cc_final: 0.8747 (t80) REVERT: B 140 ASN cc_start: 0.8878 (t0) cc_final: 0.8548 (t0) REVERT: A 682 LEU cc_start: 0.9367 (OUTLIER) cc_final: 0.8965 (mm) REVERT: C 236 LEU cc_start: 0.8385 (mp) cc_final: 0.8086 (mt) outliers start: 14 outliers final: 6 residues processed: 81 average time/residue: 0.2172 time to fit residues: 26.4135 Evaluate side-chains 72 residues out of total 1093 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 64 time to evaluate : 1.203 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 44 THR Chi-restraints excluded: chain B residue 93 PHE Chi-restraints excluded: chain B residue 139 ILE Chi-restraints excluded: chain A residue 682 LEU Chi-restraints excluded: chain A residue 735 LEU Chi-restraints excluded: chain C residue 101 HIS Chi-restraints excluded: chain C residue 211 ASP Chi-restraints excluded: chain C residue 250 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 99 optimal weight: 0.6980 chunk 68 optimal weight: 2.9990 chunk 1 optimal weight: 6.9990 chunk 89 optimal weight: 2.9990 chunk 49 optimal weight: 4.9990 chunk 102 optimal weight: 3.9990 chunk 82 optimal weight: 0.0980 chunk 0 optimal weight: 2.9990 chunk 61 optimal weight: 0.9990 chunk 107 optimal weight: 0.4980 chunk 30 optimal weight: 0.0970 overall best weight: 0.4780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 468 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 775 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 225 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8323 moved from start: 0.3302 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 10354 Z= 0.149 Angle : 0.548 8.673 13982 Z= 0.273 Chirality : 0.040 0.186 1528 Planarity : 0.003 0.055 1789 Dihedral : 8.204 155.436 1396 Min Nonbonded Distance : 2.078 Molprobity Statistics. All-atom Clashscore : 5.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.57 % Favored : 99.43 % Rotamer: Outliers : 0.92 % Allowed : 7.86 % Favored : 91.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.50 (0.24), residues: 1236 helix: 1.43 (0.21), residues: 628 sheet: 0.87 (0.39), residues: 158 loop : 0.61 (0.30), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 484 HIS 0.005 0.001 HIS A 418 PHE 0.017 0.001 PHE C 255 TYR 0.012 0.001 TYR A 50 ARG 0.003 0.000 ARG C 372 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2472 Ramachandran restraints generated. 1236 Oldfield, 0 Emsley, 1236 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2472 Ramachandran restraints generated. 1236 Oldfield, 0 Emsley, 1236 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 1093 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 73 time to evaluate : 1.231 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 12 PHE cc_start: 0.9162 (m-10) cc_final: 0.8661 (m-10) REVERT: B 66 ASP cc_start: 0.8804 (p0) cc_final: 0.8538 (p0) REVERT: B 93 PHE cc_start: 0.9038 (OUTLIER) cc_final: 0.8731 (t80) REVERT: B 140 ASN cc_start: 0.8928 (t0) cc_final: 0.8597 (t0) REVERT: A 682 LEU cc_start: 0.9276 (OUTLIER) cc_final: 0.8906 (mm) REVERT: C 47 MET cc_start: 0.7322 (tpp) cc_final: 0.6547 (tpp) REVERT: C 236 LEU cc_start: 0.8385 (mp) cc_final: 0.8109 (mt) REVERT: C 305 MET cc_start: 0.8179 (mmm) cc_final: 0.7959 (mmm) outliers start: 10 outliers final: 2 residues processed: 81 average time/residue: 0.2161 time to fit residues: 26.1198 Evaluate side-chains 68 residues out of total 1093 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 64 time to evaluate : 1.205 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 93 PHE Chi-restraints excluded: chain B residue 139 ILE Chi-restraints excluded: chain A residue 682 LEU Chi-restraints excluded: chain C residue 101 HIS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 40 optimal weight: 3.9990 chunk 107 optimal weight: 0.2980 chunk 23 optimal weight: 5.9990 chunk 70 optimal weight: 3.9990 chunk 29 optimal weight: 0.8980 chunk 119 optimal weight: 0.0470 chunk 99 optimal weight: 1.9990 chunk 55 optimal weight: 0.0020 chunk 9 optimal weight: 8.9990 chunk 39 optimal weight: 2.9990 chunk 62 optimal weight: 0.7980 overall best weight: 0.4086 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 468 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 775 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8315 moved from start: 0.3510 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 10354 Z= 0.143 Angle : 0.553 10.004 13982 Z= 0.270 Chirality : 0.041 0.205 1528 Planarity : 0.003 0.055 1789 Dihedral : 8.035 153.218 1396 Min Nonbonded Distance : 2.015 Molprobity Statistics. All-atom Clashscore : 5.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.57 % Favored : 99.43 % Rotamer: Outliers : 0.74 % Allowed : 8.69 % Favored : 90.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.56 (0.24), residues: 1236 helix: 1.51 (0.21), residues: 628 sheet: 0.85 (0.38), residues: 158 loop : 0.61 (0.30), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 484 HIS 0.005 0.001 HIS A 418 PHE 0.016 0.001 PHE C 255 TYR 0.010 0.001 TYR A 50 ARG 0.002 0.000 ARG C 372 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2472 Ramachandran restraints generated. 1236 Oldfield, 0 Emsley, 1236 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2472 Ramachandran restraints generated. 1236 Oldfield, 0 Emsley, 1236 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 1093 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 73 time to evaluate : 1.232 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 12 PHE cc_start: 0.9302 (m-10) cc_final: 0.9041 (m-10) REVERT: B 66 ASP cc_start: 0.8889 (p0) cc_final: 0.8631 (p0) REVERT: B 93 PHE cc_start: 0.9051 (OUTLIER) cc_final: 0.8771 (t80) REVERT: B 140 ASN cc_start: 0.8959 (t0) cc_final: 0.8639 (t0) REVERT: A 564 PHE cc_start: 0.9083 (OUTLIER) cc_final: 0.8742 (t80) REVERT: A 682 LEU cc_start: 0.9270 (OUTLIER) cc_final: 0.8895 (mm) REVERT: C 47 MET cc_start: 0.6993 (tpp) cc_final: 0.6514 (tpp) REVERT: C 236 LEU cc_start: 0.8381 (mp) cc_final: 0.8114 (mt) outliers start: 8 outliers final: 2 residues processed: 80 average time/residue: 0.2352 time to fit residues: 27.8998 Evaluate side-chains 72 residues out of total 1093 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 67 time to evaluate : 1.098 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 44 THR Chi-restraints excluded: chain B residue 93 PHE Chi-restraints excluded: chain B residue 139 ILE Chi-restraints excluded: chain A residue 564 PHE Chi-restraints excluded: chain A residue 682 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 115 optimal weight: 0.9990 chunk 13 optimal weight: 4.9990 chunk 68 optimal weight: 3.9990 chunk 87 optimal weight: 2.9990 chunk 67 optimal weight: 0.0020 chunk 100 optimal weight: 1.9990 chunk 66 optimal weight: 3.9990 chunk 119 optimal weight: 0.6980 chunk 74 optimal weight: 1.9990 chunk 72 optimal weight: 0.9980 chunk 55 optimal weight: 0.9980 overall best weight: 0.7390 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 81 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 468 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 681 GLN ** A 775 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8333 moved from start: 0.3644 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 10354 Z= 0.175 Angle : 0.562 10.789 13982 Z= 0.277 Chirality : 0.040 0.183 1528 Planarity : 0.003 0.056 1789 Dihedral : 7.970 150.119 1396 Min Nonbonded Distance : 1.977 Molprobity Statistics. All-atom Clashscore : 6.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.57 % Favored : 99.43 % Rotamer: Outliers : 1.02 % Allowed : 8.50 % Favored : 90.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.65 (0.24), residues: 1236 helix: 1.64 (0.21), residues: 622 sheet: 0.84 (0.39), residues: 158 loop : 0.58 (0.30), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.042 0.002 TRP C 79 HIS 0.005 0.001 HIS A 418 PHE 0.016 0.001 PHE C 255 TYR 0.012 0.001 TYR A 259 ARG 0.002 0.000 ARG C 372 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2472 Ramachandran restraints generated. 1236 Oldfield, 0 Emsley, 1236 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2472 Ramachandran restraints generated. 1236 Oldfield, 0 Emsley, 1236 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 1093 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 69 time to evaluate : 1.230 Fit side-chains revert: symmetry clash REVERT: B 19 PHE cc_start: 0.7758 (m-80) cc_final: 0.7351 (m-80) REVERT: B 66 ASP cc_start: 0.8863 (p0) cc_final: 0.8608 (p0) REVERT: B 93 PHE cc_start: 0.9060 (OUTLIER) cc_final: 0.8805 (t80) REVERT: B 140 ASN cc_start: 0.8992 (t0) cc_final: 0.8690 (t0) REVERT: A 564 PHE cc_start: 0.9107 (OUTLIER) cc_final: 0.8770 (t80) REVERT: C 47 MET cc_start: 0.7017 (tpp) cc_final: 0.6561 (tpp) REVERT: C 236 LEU cc_start: 0.8395 (mp) cc_final: 0.8129 (mt) outliers start: 11 outliers final: 5 residues processed: 79 average time/residue: 0.2174 time to fit residues: 26.1429 Evaluate side-chains 68 residues out of total 1093 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 61 time to evaluate : 1.295 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 44 THR Chi-restraints excluded: chain B residue 93 PHE Chi-restraints excluded: chain B residue 139 ILE Chi-restraints excluded: chain A residue 81 HIS Chi-restraints excluded: chain A residue 564 PHE Chi-restraints excluded: chain C residue 101 HIS Chi-restraints excluded: chain C residue 250 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 73 optimal weight: 0.0170 chunk 47 optimal weight: 1.9990 chunk 71 optimal weight: 2.9990 chunk 36 optimal weight: 0.0270 chunk 23 optimal weight: 10.0000 chunk 75 optimal weight: 3.9990 chunk 81 optimal weight: 3.9990 chunk 59 optimal weight: 2.9990 chunk 11 optimal weight: 5.9990 chunk 93 optimal weight: 0.9980 chunk 108 optimal weight: 5.9990 overall best weight: 1.2080 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 81 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 468 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 638 HIS ** A 775 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8368 moved from start: 0.3693 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 10354 Z= 0.242 Angle : 0.604 12.265 13982 Z= 0.297 Chirality : 0.042 0.191 1528 Planarity : 0.004 0.056 1789 Dihedral : 7.989 145.231 1396 Min Nonbonded Distance : 1.944 Molprobity Statistics. All-atom Clashscore : 6.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.73 % Favored : 99.27 % Rotamer: Outliers : 1.02 % Allowed : 9.06 % Favored : 89.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.61 (0.24), residues: 1236 helix: 1.64 (0.21), residues: 624 sheet: 0.83 (0.40), residues: 155 loop : 0.51 (0.29), residues: 457 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 484 HIS 0.005 0.001 HIS A 418 PHE 0.017 0.001 PHE C 255 TYR 0.016 0.001 TYR A 259 ARG 0.002 0.000 ARG C 335 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2472 Ramachandran restraints generated. 1236 Oldfield, 0 Emsley, 1236 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2472 Ramachandran restraints generated. 1236 Oldfield, 0 Emsley, 1236 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 75 residues out of total 1093 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 64 time to evaluate : 1.175 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 19 PHE cc_start: 0.7817 (m-80) cc_final: 0.7403 (m-80) REVERT: B 66 ASP cc_start: 0.8950 (p0) cc_final: 0.8686 (p0) REVERT: B 93 PHE cc_start: 0.9040 (OUTLIER) cc_final: 0.8800 (t80) REVERT: B 140 ASN cc_start: 0.9022 (t0) cc_final: 0.8723 (t0) REVERT: A 564 PHE cc_start: 0.9169 (OUTLIER) cc_final: 0.8809 (t80) REVERT: C 236 LEU cc_start: 0.8392 (mp) cc_final: 0.8119 (mt) outliers start: 11 outliers final: 7 residues processed: 74 average time/residue: 0.2271 time to fit residues: 25.2612 Evaluate side-chains 71 residues out of total 1093 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 62 time to evaluate : 1.257 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 93 PHE Chi-restraints excluded: chain B residue 119 LYS Chi-restraints excluded: chain B residue 139 ILE Chi-restraints excluded: chain A residue 81 HIS Chi-restraints excluded: chain A residue 211 THR Chi-restraints excluded: chain A residue 564 PHE Chi-restraints excluded: chain A residue 782 LEU Chi-restraints excluded: chain C residue 101 HIS Chi-restraints excluded: chain C residue 250 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 114 optimal weight: 0.9990 chunk 104 optimal weight: 0.9980 chunk 111 optimal weight: 1.9990 chunk 67 optimal weight: 0.2980 chunk 48 optimal weight: 2.9990 chunk 87 optimal weight: 0.8980 chunk 34 optimal weight: 3.9990 chunk 100 optimal weight: 1.9990 chunk 105 optimal weight: 0.6980 chunk 110 optimal weight: 0.8980 chunk 73 optimal weight: 1.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 81 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 468 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 775 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8349 moved from start: 0.3796 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 10354 Z= 0.179 Angle : 0.577 12.873 13982 Z= 0.284 Chirality : 0.041 0.182 1528 Planarity : 0.003 0.055 1789 Dihedral : 7.899 139.816 1396 Min Nonbonded Distance : 1.988 Molprobity Statistics. All-atom Clashscore : 5.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.73 % Favored : 99.27 % Rotamer: Outliers : 1.02 % Allowed : 8.96 % Favored : 90.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.63 (0.24), residues: 1236 helix: 1.69 (0.21), residues: 624 sheet: 0.80 (0.39), residues: 155 loop : 0.46 (0.29), residues: 457 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 484 HIS 0.005 0.001 HIS A 418 PHE 0.023 0.001 PHE B 12 TYR 0.012 0.001 TYR A 259 ARG 0.002 0.000 ARG B 64 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2472 Ramachandran restraints generated. 1236 Oldfield, 0 Emsley, 1236 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2472 Ramachandran restraints generated. 1236 Oldfield, 0 Emsley, 1236 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 1093 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 66 time to evaluate : 1.129 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 19 PHE cc_start: 0.7767 (m-80) cc_final: 0.7554 (m-80) REVERT: B 66 ASP cc_start: 0.8956 (p0) cc_final: 0.8706 (p0) REVERT: B 93 PHE cc_start: 0.9010 (m-80) cc_final: 0.8786 (t80) REVERT: B 140 ASN cc_start: 0.9000 (t0) cc_final: 0.8695 (t0) REVERT: A 564 PHE cc_start: 0.9158 (OUTLIER) cc_final: 0.8781 (t80) REVERT: C 47 MET cc_start: 0.7047 (tpp) cc_final: 0.6366 (tpp) REVERT: C 236 LEU cc_start: 0.8386 (mp) cc_final: 0.8112 (mt) outliers start: 11 outliers final: 9 residues processed: 76 average time/residue: 0.2356 time to fit residues: 26.6956 Evaluate side-chains 72 residues out of total 1093 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 62 time to evaluate : 1.254 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 119 LYS Chi-restraints excluded: chain B residue 139 ILE Chi-restraints excluded: chain A residue 81 HIS Chi-restraints excluded: chain A residue 211 THR Chi-restraints excluded: chain A residue 564 PHE Chi-restraints excluded: chain A residue 735 LEU Chi-restraints excluded: chain A residue 782 LEU Chi-restraints excluded: chain C residue 101 HIS Chi-restraints excluded: chain C residue 250 ILE Chi-restraints excluded: chain C residue 269 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 117 optimal weight: 0.9980 chunk 71 optimal weight: 0.8980 chunk 55 optimal weight: 0.8980 chunk 81 optimal weight: 0.4980 chunk 123 optimal weight: 0.9980 chunk 113 optimal weight: 0.0980 chunk 98 optimal weight: 0.9980 chunk 10 optimal weight: 5.9990 chunk 75 optimal weight: 0.7980 chunk 60 optimal weight: 0.0870 chunk 78 optimal weight: 0.5980 overall best weight: 0.4158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 81 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 468 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 775 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8322 moved from start: 0.3957 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 10354 Z= 0.147 Angle : 0.595 13.021 13982 Z= 0.283 Chirality : 0.040 0.176 1528 Planarity : 0.003 0.055 1789 Dihedral : 7.720 131.808 1396 Min Nonbonded Distance : 2.028 Molprobity Statistics. All-atom Clashscore : 5.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.97 % Favored : 99.03 % Rotamer: Outliers : 0.65 % Allowed : 9.61 % Favored : 89.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.66 (0.24), residues: 1236 helix: 1.76 (0.21), residues: 623 sheet: 0.80 (0.39), residues: 155 loop : 0.42 (0.29), residues: 458 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRP C 86 HIS 0.005 0.001 HIS A 418 PHE 0.020 0.001 PHE B 12 TYR 0.010 0.001 TYR A 102 ARG 0.002 0.000 ARG B 64 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2472 Ramachandran restraints generated. 1236 Oldfield, 0 Emsley, 1236 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2472 Ramachandran restraints generated. 1236 Oldfield, 0 Emsley, 1236 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 1093 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 72 time to evaluate : 1.375 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 19 PHE cc_start: 0.7730 (m-80) cc_final: 0.7517 (m-80) REVERT: B 66 ASP cc_start: 0.8977 (p0) cc_final: 0.8735 (p0) REVERT: B 140 ASN cc_start: 0.8957 (t0) cc_final: 0.8670 (t0) REVERT: A 564 PHE cc_start: 0.9101 (OUTLIER) cc_final: 0.8664 (t80) REVERT: C 47 MET cc_start: 0.7022 (tpp) cc_final: 0.6347 (tpp) REVERT: C 236 LEU cc_start: 0.8392 (mp) cc_final: 0.8120 (mt) REVERT: C 355 MET cc_start: 0.8278 (mmm) cc_final: 0.7903 (mmp) outliers start: 7 outliers final: 3 residues processed: 79 average time/residue: 0.2257 time to fit residues: 27.1409 Evaluate side-chains 70 residues out of total 1093 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 66 time to evaluate : 1.192 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 139 ILE Chi-restraints excluded: chain A residue 564 PHE Chi-restraints excluded: chain A residue 782 LEU Chi-restraints excluded: chain C residue 101 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 104 optimal weight: 2.9990 chunk 30 optimal weight: 1.9990 chunk 90 optimal weight: 0.2980 chunk 14 optimal weight: 0.5980 chunk 27 optimal weight: 3.9990 chunk 98 optimal weight: 0.0870 chunk 41 optimal weight: 0.2980 chunk 101 optimal weight: 4.9990 chunk 12 optimal weight: 9.9990 chunk 18 optimal weight: 0.0470 chunk 86 optimal weight: 6.9990 overall best weight: 0.2656 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 81 HIS ** A 468 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 775 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 = 0.3331 r_free = 0.3331 target = 0.059503 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2888 r_free = 0.2888 target = 0.043801 restraints weight = 45021.010| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2934 r_free = 0.2934 target = 0.045437 restraints weight = 21628.739| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.2966 r_free = 0.2966 target = 0.046542 restraints weight = 13324.061| |-----------------------------------------------------------------------------| r_work (final): 0.2954 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8489 moved from start: 0.4140 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 10354 Z= 0.138 Angle : 0.598 13.317 13982 Z= 0.284 Chirality : 0.040 0.180 1528 Planarity : 0.003 0.054 1789 Dihedral : 7.550 122.066 1396 Min Nonbonded Distance : 2.070 Molprobity Statistics. All-atom Clashscore : 6.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.89 % Favored : 99.11 % Rotamer: Outliers : 0.65 % Allowed : 10.17 % Favored : 89.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.72 (0.24), residues: 1236 helix: 1.85 (0.21), residues: 620 sheet: 0.91 (0.39), residues: 155 loop : 0.36 (0.29), residues: 461 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP C 86 HIS 0.004 0.001 HIS A 418 PHE 0.018 0.001 PHE B 12 TYR 0.011 0.001 TYR A 787 ARG 0.002 0.000 ARG B 64 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1990.42 seconds wall clock time: 37 minutes 53.72 seconds (2273.72 seconds total)