Starting phenix.real_space_refine on Fri Feb 14 17:46:50 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7plv_13503/02_2025/7plv_13503.cif Found real_map, /net/cci-nas-00/data/ceres_data/7plv_13503/02_2025/7plv_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_13503/02_2025/7plv_13503.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7plv_13503/02_2025/7plv_13503.map" model { file = "/net/cci-nas-00/data/ceres_data/7plv_13503/02_2025/7plv_13503.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7plv_13503/02_2025/7plv_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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/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: 6.38, per 1000 atoms: 0.63 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: 2.58 Conformation dependent library (CDL) restraints added in 1.2 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: 1.19 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: 3.26 Time building geometry restraints manager: 2.90 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: 1.830 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: 0.500 Check model and map are aligned: 0.080 Set scattering table: 0.090 Process input model: 24.830 Find NCS groups from input model: 0.080 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.710 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.170 ------------------------------------------------------------------------------- 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 : 1.172 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: 0.2631 time to fit residues: 52.4908 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 : 1.095 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3312 r_free = 0.3312 target = 0.058865 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2854 r_free = 0.2854 target = 0.043049 restraints weight = 45707.031| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.2901 r_free = 0.2901 target = 0.044672 restraints weight = 21899.813| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.2935 r_free = 0.2935 target = 0.045795 restraints weight = 13512.274| |-----------------------------------------------------------------------------| r_work (final): 0.2925 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8478 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 : 1.122 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 50 LYS cc_start: 0.9495 (ttpp) cc_final: 0.9232 (ptmm) REVERT: B 66 ASP cc_start: 0.8853 (p0) cc_final: 0.8376 (p0) REVERT: B 93 PHE cc_start: 0.9368 (OUTLIER) cc_final: 0.8980 (t80) REVERT: A 503 MET cc_start: 0.8621 (mmt) cc_final: 0.8237 (mmt) REVERT: A 682 LEU cc_start: 0.9380 (OUTLIER) cc_final: 0.9013 (mm) REVERT: C 44 MET cc_start: 0.8765 (mtp) cc_final: 0.8425 (ttt) outliers start: 12 outliers final: 3 residues processed: 99 average time/residue: 0.2326 time to fit residues: 33.0744 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 : 1.129 ------------------------------------------------------------------------------- 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 99 optimal weight: 0.7980 chunk 88 optimal weight: 3.9990 chunk 38 optimal weight: 0.8980 chunk 117 optimal weight: 0.9980 chunk 75 optimal weight: 1.9990 chunk 6 optimal weight: 9.9990 chunk 34 optimal weight: 1.9990 chunk 61 optimal weight: 2.9990 chunk 5 optimal weight: 7.9990 chunk 111 optimal weight: 2.9990 chunk 52 optimal weight: 1.9990 overall best weight: 1.3384 ------------------------------------------------------------------------------- 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 705 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3281 r_free = 0.3281 target = 0.057697 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2810 r_free = 0.2810 target = 0.041606 restraints weight = 46583.221| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.2857 r_free = 0.2857 target = 0.043205 restraints weight = 22375.016| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.2890 r_free = 0.2890 target = 0.044283 restraints weight = 13884.402| |-----------------------------------------------------------------------------| r_work (final): 0.2883 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8538 moved from start: 0.2673 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 10354 Z= 0.263 Angle : 0.587 7.538 13982 Z= 0.303 Chirality : 0.042 0.155 1528 Planarity : 0.004 0.058 1789 Dihedral : 8.724 158.548 1396 Min Nonbonded Distance : 2.313 Molprobity Statistics. All-atom Clashscore : 6.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.16 % Favored : 99.84 % Rotamer: Outliers : 1.29 % Allowed : 6.01 % Favored : 92.70 % 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: 1.06 (0.23), residues: 1236 helix: 0.97 (0.21), residues: 620 sheet: 0.81 (0.39), residues: 158 loop : 0.52 (0.29), residues: 458 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 484 HIS 0.008 0.001 HIS A 418 PHE 0.024 0.001 PHE C 255 TYR 0.016 0.001 TYR A 259 ARG 0.003 0.000 ARG C 290 *********************** 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 90 residues out of total 1093 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 76 time to evaluate : 1.178 Fit side-chains revert: symmetry clash REVERT: B 93 PHE cc_start: 0.9351 (OUTLIER) cc_final: 0.8971 (t80) REVERT: A 445 GLU cc_start: 0.7964 (pm20) cc_final: 0.7709 (pm20) REVERT: A 478 MET cc_start: 0.9476 (tpp) cc_final: 0.9009 (tpp) REVERT: A 503 MET cc_start: 0.8621 (mmt) cc_final: 0.8253 (mmt) REVERT: A 682 LEU cc_start: 0.9392 (OUTLIER) cc_final: 0.8945 (mm) REVERT: C 44 MET cc_start: 0.8885 (mtp) cc_final: 0.8625 (tpp) REVERT: C 125 GLU cc_start: 0.8060 (OUTLIER) cc_final: 0.7791 (mp0) REVERT: C 171 LEU cc_start: 0.9455 (mt) cc_final: 0.9249 (mp) REVERT: C 305 MET cc_start: 0.8828 (mmm) cc_final: 0.8488 (mmm) outliers start: 14 outliers final: 7 residues processed: 88 average time/residue: 0.2019 time to fit residues: 27.0645 Evaluate side-chains 75 residues out of total 1093 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 65 time to evaluate : 1.178 ------------------------------------------------------------------------------- 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 565 LEU Chi-restraints excluded: chain A residue 682 LEU Chi-restraints excluded: chain A residue 735 LEU Chi-restraints excluded: chain C residue 125 GLU Chi-restraints excluded: chain C residue 193 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 88 optimal weight: 0.6980 chunk 52 optimal weight: 1.9990 chunk 21 optimal weight: 3.9990 chunk 25 optimal weight: 0.8980 chunk 31 optimal weight: 1.9990 chunk 23 optimal weight: 0.6980 chunk 14 optimal weight: 0.9990 chunk 12 optimal weight: 20.0000 chunk 105 optimal weight: 1.9990 chunk 56 optimal weight: 0.8980 chunk 38 optimal weight: 0.5980 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 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3298 r_free = 0.3298 target = 0.058242 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2839 r_free = 0.2839 target = 0.042278 restraints weight = 45664.907| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2886 r_free = 0.2886 target = 0.043905 restraints weight = 21734.790| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.2919 r_free = 0.2919 target = 0.045003 restraints weight = 13383.737| |-----------------------------------------------------------------------------| r_work (final): 0.2909 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8511 moved from start: 0.3022 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 10354 Z= 0.177 Angle : 0.545 9.080 13982 Z= 0.276 Chirality : 0.041 0.170 1528 Planarity : 0.004 0.056 1789 Dihedral : 8.374 157.982 1396 Min Nonbonded Distance : 2.115 Molprobity Statistics. All-atom Clashscore : 6.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.73 % Favored : 99.27 % Rotamer: Outliers : 1.02 % Allowed : 7.76 % 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: 1.36 (0.24), residues: 1236 helix: 1.31 (0.21), residues: 620 sheet: 0.78 (0.39), residues: 160 loop : 0.58 (0.29), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 484 HIS 0.006 0.001 HIS A 418 PHE 0.019 0.001 PHE C 255 TYR 0.014 0.001 TYR A 50 ARG 0.002 0.000 ARG A 542 *********************** 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 85 residues out of total 1093 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 74 time to evaluate : 1.107 Fit side-chains revert: symmetry clash REVERT: B 66 ASP cc_start: 0.8748 (p0) cc_final: 0.8548 (p0) REVERT: B 93 PHE cc_start: 0.9326 (OUTLIER) cc_final: 0.8947 (t80) REVERT: A 132 MET cc_start: 0.8055 (ttm) cc_final: 0.7711 (tpp) REVERT: A 177 MET cc_start: 0.8377 (ptt) cc_final: 0.8124 (ppp) REVERT: A 305 MET cc_start: 0.8750 (tpp) cc_final: 0.8380 (tpp) REVERT: A 445 GLU cc_start: 0.8014 (pm20) cc_final: 0.7786 (pm20) REVERT: A 478 MET cc_start: 0.9435 (tpp) cc_final: 0.8942 (tpp) REVERT: A 503 MET cc_start: 0.8578 (mmt) cc_final: 0.8239 (mmt) REVERT: C 123 MET cc_start: 0.9358 (tpp) cc_final: 0.9132 (mmm) REVERT: C 125 GLU cc_start: 0.8063 (OUTLIER) cc_final: 0.7806 (mp0) REVERT: C 167 GLU cc_start: 0.8769 (OUTLIER) cc_final: 0.8463 (mp0) REVERT: C 305 MET cc_start: 0.8785 (mmm) cc_final: 0.8430 (mmm) outliers start: 11 outliers final: 3 residues processed: 83 average time/residue: 0.2148 time to fit residues: 26.3759 Evaluate side-chains 73 residues out of total 1093 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 67 time to evaluate : 1.104 ------------------------------------------------------------------------------- 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 C residue 101 HIS Chi-restraints excluded: chain C residue 125 GLU Chi-restraints excluded: chain C residue 167 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 40 optimal weight: 3.9990 chunk 22 optimal weight: 0.8980 chunk 120 optimal weight: 1.9990 chunk 17 optimal weight: 6.9990 chunk 106 optimal weight: 1.9990 chunk 31 optimal weight: 0.6980 chunk 71 optimal weight: 5.9990 chunk 19 optimal weight: 0.5980 chunk 86 optimal weight: 1.9990 chunk 18 optimal weight: 2.9990 chunk 58 optimal weight: 0.8980 overall best weight: 1.0182 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3288 r_free = 0.3288 target = 0.057858 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2836 r_free = 0.2836 target = 0.042171 restraints weight = 45510.805| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.2882 r_free = 0.2882 target = 0.043755 restraints weight = 21815.363| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.2915 r_free = 0.2915 target = 0.044822 restraints weight = 13455.066| |-----------------------------------------------------------------------------| r_work (final): 0.2900 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8529 moved from start: 0.3207 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 10354 Z= 0.215 Angle : 0.554 8.914 13982 Z= 0.279 Chirality : 0.041 0.190 1528 Planarity : 0.004 0.057 1789 Dihedral : 8.312 157.652 1396 Min Nonbonded Distance : 1.987 Molprobity Statistics. All-atom Clashscore : 6.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.73 % Favored : 99.27 % Rotamer: Outliers : 1.20 % Allowed : 8.13 % Favored : 90.67 % 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: 1.49 (0.24), residues: 1236 helix: 1.45 (0.21), residues: 626 sheet: 0.86 (0.39), residues: 158 loop : 0.56 (0.30), residues: 452 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 484 HIS 0.006 0.001 HIS A 418 PHE 0.019 0.001 PHE C 255 TYR 0.014 0.001 TYR A 259 ARG 0.002 0.000 ARG B 64 *********************** 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 82 residues out of total 1093 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 69 time to evaluate : 1.216 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 12 PHE cc_start: 0.9333 (m-10) cc_final: 0.8850 (m-10) REVERT: B 93 PHE cc_start: 0.9286 (OUTLIER) cc_final: 0.8937 (t80) REVERT: A 132 MET cc_start: 0.8028 (ttm) cc_final: 0.7711 (tpt) REVERT: A 478 MET cc_start: 0.9400 (tpp) cc_final: 0.9035 (tpp) REVERT: A 503 MET cc_start: 0.8603 (mmt) cc_final: 0.8286 (mmt) REVERT: A 564 PHE cc_start: 0.9235 (OUTLIER) cc_final: 0.8762 (t80) REVERT: C 123 MET cc_start: 0.9333 (tpp) cc_final: 0.8918 (mmm) REVERT: C 125 GLU cc_start: 0.7969 (OUTLIER) cc_final: 0.7750 (mp0) REVERT: C 167 GLU cc_start: 0.8810 (OUTLIER) cc_final: 0.8534 (mp0) REVERT: C 305 MET cc_start: 0.8792 (mmm) cc_final: 0.8444 (mmm) REVERT: H 1 TRP cc_start: 0.8656 (m100) cc_final: 0.8111 (m100) outliers start: 13 outliers final: 3 residues processed: 81 average time/residue: 0.2042 time to fit residues: 25.6400 Evaluate side-chains 74 residues out of total 1093 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 67 time to evaluate : 1.276 ------------------------------------------------------------------------------- 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 564 PHE Chi-restraints excluded: chain C residue 101 HIS Chi-restraints excluded: chain C residue 125 GLU Chi-restraints excluded: chain C residue 167 GLU Chi-restraints excluded: chain C residue 250 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 31 optimal weight: 0.8980 chunk 8 optimal weight: 8.9990 chunk 120 optimal weight: 2.9990 chunk 20 optimal weight: 0.3980 chunk 11 optimal weight: 5.9990 chunk 1 optimal weight: 8.9990 chunk 87 optimal weight: 2.9990 chunk 84 optimal weight: 1.9990 chunk 113 optimal weight: 0.9990 chunk 77 optimal weight: 0.9990 chunk 109 optimal weight: 1.9990 overall best weight: 1.0586 ------------------------------------------------------------------------------- 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 638 HIS ** A 775 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 225 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3283 r_free = 0.3283 target = 0.057548 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.2827 r_free = 0.2827 target = 0.041825 restraints weight = 45817.569| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.2872 r_free = 0.2872 target = 0.043397 restraints weight = 22009.553| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.2905 r_free = 0.2905 target = 0.044466 restraints weight = 13624.205| |-----------------------------------------------------------------------------| r_work (final): 0.2892 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8540 moved from start: 0.3361 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 10354 Z= 0.217 Angle : 0.552 9.676 13982 Z= 0.278 Chirality : 0.041 0.187 1528 Planarity : 0.004 0.057 1789 Dihedral : 8.253 157.667 1396 Min Nonbonded Distance : 1.976 Molprobity Statistics. All-atom Clashscore : 5.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.81 % Favored : 99.19 % Rotamer: Outliers : 1.29 % Allowed : 8.04 % Favored : 90.67 % 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: 1.55 (0.24), residues: 1236 helix: 1.53 (0.21), residues: 623 sheet: 0.86 (0.39), residues: 158 loop : 0.56 (0.30), residues: 455 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 79 HIS 0.006 0.001 HIS A 418 PHE 0.018 0.001 PHE C 255 TYR 0.014 0.001 TYR A 259 ARG 0.002 0.000 ARG B 64 *********************** 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 86 residues out of total 1093 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 72 time to evaluate : 1.258 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 12 PHE cc_start: 0.9502 (m-10) cc_final: 0.9156 (m-10) REVERT: B 19 PHE cc_start: 0.7891 (m-80) cc_final: 0.7562 (m-80) REVERT: B 93 PHE cc_start: 0.9275 (OUTLIER) cc_final: 0.8964 (t80) REVERT: A 132 MET cc_start: 0.8052 (ttm) cc_final: 0.7721 (tpt) REVERT: A 478 MET cc_start: 0.9416 (tpp) cc_final: 0.8905 (tpp) REVERT: A 503 MET cc_start: 0.8604 (mmt) cc_final: 0.8303 (mmt) REVERT: A 564 PHE cc_start: 0.9282 (OUTLIER) cc_final: 0.8782 (t80) REVERT: C 123 MET cc_start: 0.9336 (tpp) cc_final: 0.8932 (mmm) REVERT: C 125 GLU cc_start: 0.7958 (OUTLIER) cc_final: 0.7738 (mp0) REVERT: C 167 GLU cc_start: 0.8833 (OUTLIER) cc_final: 0.8555 (mp0) REVERT: C 227 MET cc_start: 0.9016 (tpt) cc_final: 0.8776 (tpt) REVERT: C 305 MET cc_start: 0.8765 (mmm) cc_final: 0.8396 (mmm) outliers start: 14 outliers final: 5 residues processed: 83 average time/residue: 0.2073 time to fit residues: 26.1933 Evaluate side-chains 75 residues out of total 1093 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 66 time to evaluate : 1.244 ------------------------------------------------------------------------------- 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 564 PHE Chi-restraints excluded: chain C residue 101 HIS Chi-restraints excluded: chain C residue 125 GLU Chi-restraints excluded: chain C residue 167 GLU Chi-restraints excluded: chain C residue 211 ASP Chi-restraints excluded: chain C residue 250 ILE Chi-restraints excluded: chain C residue 269 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 54 optimal weight: 0.0870 chunk 44 optimal weight: 2.9990 chunk 34 optimal weight: 0.9990 chunk 76 optimal weight: 0.5980 chunk 10 optimal weight: 8.9990 chunk 64 optimal weight: 2.9990 chunk 98 optimal weight: 0.9990 chunk 47 optimal weight: 0.9990 chunk 65 optimal weight: 0.0570 chunk 36 optimal weight: 2.9990 chunk 66 optimal weight: 1.9990 overall best weight: 0.5480 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.058344 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2853 r_free = 0.2853 target = 0.042656 restraints weight = 45590.526| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.2899 r_free = 0.2899 target = 0.044275 restraints weight = 21707.337| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.2931 r_free = 0.2931 target = 0.045350 restraints weight = 13344.747| |-----------------------------------------------------------------------------| r_work (final): 0.2920 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8514 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 : 0.002 0.033 10354 Z= 0.152 Angle : 0.538 11.337 13982 Z= 0.268 Chirality : 0.040 0.186 1528 Planarity : 0.003 0.054 1789 Dihedral : 8.135 155.453 1396 Min Nonbonded Distance : 2.017 Molprobity Statistics. All-atom Clashscore : 5.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.73 % Favored : 99.27 % Rotamer: Outliers : 0.92 % Allowed : 8.78 % Favored : 90.30 % 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: 1.68 (0.24), residues: 1236 helix: 1.67 (0.21), residues: 623 sheet: 0.86 (0.38), residues: 158 loop : 0.59 (0.30), residues: 455 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 484 HIS 0.005 0.001 HIS A 418 PHE 0.022 0.001 PHE B 12 TYR 0.010 0.001 TYR A 50 ARG 0.001 0.000 ARG A 542 *********************** 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 79 residues out of total 1093 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 69 time to evaluate : 1.160 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 19 PHE cc_start: 0.7940 (m-80) cc_final: 0.7574 (m-80) REVERT: B 93 PHE cc_start: 0.9252 (OUTLIER) cc_final: 0.8969 (t80) REVERT: A 132 MET cc_start: 0.8049 (ttm) cc_final: 0.7761 (tpt) REVERT: A 177 MET cc_start: 0.8429 (tmm) cc_final: 0.8201 (ppp) REVERT: A 478 MET cc_start: 0.9344 (tpp) cc_final: 0.9063 (tpp) REVERT: A 503 MET cc_start: 0.8583 (mmt) cc_final: 0.8300 (mmt) REVERT: A 564 PHE cc_start: 0.9219 (OUTLIER) cc_final: 0.8536 (t80) REVERT: C 123 MET cc_start: 0.9256 (tpp) cc_final: 0.8915 (mmm) REVERT: C 125 GLU cc_start: 0.7926 (OUTLIER) cc_final: 0.7719 (mp0) REVERT: C 167 GLU cc_start: 0.8823 (OUTLIER) cc_final: 0.8370 (mp0) REVERT: C 227 MET cc_start: 0.8932 (tpt) cc_final: 0.8680 (tpt) REVERT: C 305 MET cc_start: 0.8785 (mmm) cc_final: 0.8428 (mmm) outliers start: 10 outliers final: 2 residues processed: 77 average time/residue: 0.2137 time to fit residues: 24.9174 Evaluate side-chains 70 residues out of total 1093 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 64 time to evaluate : 1.346 ------------------------------------------------------------------------------- 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 564 PHE Chi-restraints excluded: chain C residue 101 HIS Chi-restraints excluded: chain C residue 125 GLU Chi-restraints excluded: chain C residue 167 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 69 optimal weight: 0.5980 chunk 0 optimal weight: 10.0000 chunk 32 optimal weight: 1.9990 chunk 43 optimal weight: 0.9980 chunk 23 optimal weight: 9.9990 chunk 26 optimal weight: 0.7980 chunk 120 optimal weight: 0.5980 chunk 96 optimal weight: 1.9990 chunk 105 optimal weight: 0.6980 chunk 59 optimal weight: 2.9990 chunk 118 optimal weight: 0.0070 overall best weight: 0.5398 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.058616 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2846 r_free = 0.2846 target = 0.042470 restraints weight = 46281.374| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.2893 r_free = 0.2893 target = 0.044128 restraints weight = 22041.528| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.2926 r_free = 0.2926 target = 0.045240 restraints weight = 13590.854| |-----------------------------------------------------------------------------| r_work (final): 0.2918 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8516 moved from start: 0.3691 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 10354 Z= 0.152 Angle : 0.540 11.816 13982 Z= 0.268 Chirality : 0.040 0.182 1528 Planarity : 0.003 0.056 1789 Dihedral : 8.022 152.382 1396 Min Nonbonded Distance : 1.992 Molprobity Statistics. All-atom Clashscore : 5.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.89 % Favored : 99.11 % Rotamer: Outliers : 0.83 % Allowed : 9.33 % Favored : 89.83 % 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: 1.74 (0.24), residues: 1236 helix: 1.76 (0.21), residues: 623 sheet: 0.79 (0.39), residues: 155 loop : 0.58 (0.30), residues: 458 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP A 484 HIS 0.005 0.001 HIS A 418 PHE 0.023 0.001 PHE B 12 TYR 0.010 0.001 TYR A 259 ARG 0.002 0.000 ARG B 64 *********************** 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 81 residues out of total 1093 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 72 time to evaluate : 1.273 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 93 PHE cc_start: 0.9252 (OUTLIER) cc_final: 0.8996 (t80) REVERT: A 132 MET cc_start: 0.8071 (ttm) cc_final: 0.7763 (tpp) REVERT: A 177 MET cc_start: 0.8450 (tmm) cc_final: 0.8195 (ppp) REVERT: A 478 MET cc_start: 0.9284 (tpp) cc_final: 0.8894 (tpp) REVERT: A 503 MET cc_start: 0.8598 (mmt) cc_final: 0.8311 (mmt) REVERT: A 564 PHE cc_start: 0.9191 (OUTLIER) cc_final: 0.8474 (t80) REVERT: C 47 MET cc_start: 0.8342 (tpp) cc_final: 0.8099 (tpp) REVERT: C 123 MET cc_start: 0.9254 (tpp) cc_final: 0.8915 (mmm) REVERT: C 125 GLU cc_start: 0.7933 (OUTLIER) cc_final: 0.7715 (mp0) REVERT: C 167 GLU cc_start: 0.8836 (OUTLIER) cc_final: 0.8395 (mp0) REVERT: C 305 MET cc_start: 0.8785 (mmm) cc_final: 0.8406 (mmm) outliers start: 9 outliers final: 3 residues processed: 80 average time/residue: 0.2389 time to fit residues: 27.9091 Evaluate side-chains 73 residues out of total 1093 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 66 time to evaluate : 1.098 ------------------------------------------------------------------------------- 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 564 PHE Chi-restraints excluded: chain C residue 101 HIS Chi-restraints excluded: chain C residue 125 GLU Chi-restraints excluded: chain C residue 167 GLU 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 57 optimal weight: 0.9990 chunk 72 optimal weight: 1.9990 chunk 14 optimal weight: 0.9980 chunk 75 optimal weight: 0.9990 chunk 69 optimal weight: 0.7980 chunk 53 optimal weight: 0.8980 chunk 120 optimal weight: 1.9990 chunk 19 optimal weight: 0.9990 chunk 30 optimal weight: 5.9990 chunk 74 optimal weight: 0.6980 chunk 79 optimal weight: 1.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- 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 = 0.3297 r_free = 0.3297 target = 0.058191 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2829 r_free = 0.2829 target = 0.041974 restraints weight = 46252.009| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.2877 r_free = 0.2877 target = 0.043619 restraints weight = 22169.457| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.2911 r_free = 0.2911 target = 0.044734 restraints weight = 13699.670| |-----------------------------------------------------------------------------| r_work (final): 0.2902 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8534 moved from start: 0.3761 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 10354 Z= 0.194 Angle : 0.562 12.631 13982 Z= 0.278 Chirality : 0.041 0.179 1528 Planarity : 0.003 0.056 1789 Dihedral : 7.989 148.007 1396 Min Nonbonded Distance : 1.959 Molprobity Statistics. All-atom Clashscore : 5.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.81 % Favored : 99.19 % Rotamer: Outliers : 0.74 % Allowed : 9.61 % Favored : 89.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.70 (0.24), residues: 1236 helix: 1.76 (0.21), residues: 627 sheet: 0.81 (0.39), residues: 155 loop : 0.48 (0.29), residues: 454 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.002 TRP A 484 HIS 0.005 0.001 HIS A 418 PHE 0.023 0.001 PHE B 12 TYR 0.013 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 80 residues out of total 1093 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 72 time to evaluate : 1.195 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 73 MET cc_start: 0.8124 (pmm) cc_final: 0.7870 (pmm) REVERT: B 93 PHE cc_start: 0.9248 (m-80) cc_final: 0.9004 (t80) REVERT: A 132 MET cc_start: 0.8080 (ttm) cc_final: 0.7775 (tpp) REVERT: A 177 MET cc_start: 0.8489 (tmm) cc_final: 0.8158 (tmm) REVERT: A 503 MET cc_start: 0.8628 (mmt) cc_final: 0.8311 (mmt) REVERT: A 564 PHE cc_start: 0.9229 (OUTLIER) cc_final: 0.8579 (t80) REVERT: C 47 MET cc_start: 0.8360 (tpp) cc_final: 0.8119 (tpp) REVERT: C 123 MET cc_start: 0.9258 (tpp) cc_final: 0.8898 (mmm) REVERT: C 125 GLU cc_start: 0.7973 (OUTLIER) cc_final: 0.7762 (mp0) REVERT: C 167 GLU cc_start: 0.8836 (OUTLIER) cc_final: 0.8397 (mp0) REVERT: C 305 MET cc_start: 0.8793 (mmm) cc_final: 0.8429 (mmm) outliers start: 8 outliers final: 4 residues processed: 80 average time/residue: 0.2324 time to fit residues: 27.4012 Evaluate side-chains 74 residues out of total 1093 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 67 time to evaluate : 1.156 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 A residue 782 LEU Chi-restraints excluded: chain C residue 101 HIS Chi-restraints excluded: chain C residue 125 GLU Chi-restraints excluded: chain C residue 167 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 73 optimal weight: 2.9990 chunk 95 optimal weight: 2.9990 chunk 87 optimal weight: 1.9990 chunk 57 optimal weight: 1.9990 chunk 20 optimal weight: 0.7980 chunk 86 optimal weight: 6.9990 chunk 83 optimal weight: 0.9990 chunk 72 optimal weight: 0.5980 chunk 52 optimal weight: 0.9980 chunk 43 optimal weight: 2.9990 chunk 68 optimal weight: 0.7980 overall best weight: 0.8382 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3295 r_free = 0.3295 target = 0.058128 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2830 r_free = 0.2830 target = 0.041923 restraints weight = 46189.395| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.2877 r_free = 0.2877 target = 0.043556 restraints weight = 22007.237| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.2910 r_free = 0.2910 target = 0.044652 restraints weight = 13581.025| |-----------------------------------------------------------------------------| r_work (final): 0.2902 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8532 moved from start: 0.3833 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 10354 Z= 0.192 Angle : 0.589 13.163 13982 Z= 0.286 Chirality : 0.041 0.178 1528 Planarity : 0.003 0.056 1789 Dihedral : 7.984 144.807 1396 Min Nonbonded Distance : 1.970 Molprobity Statistics. All-atom Clashscore : 6.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.89 % Favored : 99.11 % Rotamer: Outliers : 0.65 % Allowed : 10.07 % Favored : 89.28 % 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: 1.80 (0.21), residues: 626 sheet: 0.82 (0.39), residues: 155 loop : 0.47 (0.29), residues: 455 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.002 TRP A 484 HIS 0.005 0.001 HIS A 418 PHE 0.021 0.001 PHE B 12 TYR 0.013 0.001 TYR A 259 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 76 residues out of total 1093 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 69 time to evaluate : 1.221 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 93 PHE cc_start: 0.9232 (m-80) cc_final: 0.9000 (t80) REVERT: A 132 MET cc_start: 0.8043 (ttm) cc_final: 0.7789 (tpp) REVERT: A 177 MET cc_start: 0.8476 (tmm) cc_final: 0.8139 (tmm) REVERT: A 503 MET cc_start: 0.8625 (mmt) cc_final: 0.8309 (mmt) REVERT: A 564 PHE cc_start: 0.9225 (OUTLIER) cc_final: 0.8578 (t80) REVERT: C 47 MET cc_start: 0.8327 (tpp) cc_final: 0.8095 (tpp) REVERT: C 123 MET cc_start: 0.9257 (tpp) cc_final: 0.8898 (mmm) REVERT: C 125 GLU cc_start: 0.7966 (OUTLIER) cc_final: 0.7757 (mp0) REVERT: C 167 GLU cc_start: 0.8839 (OUTLIER) cc_final: 0.8411 (mp0) REVERT: C 305 MET cc_start: 0.8791 (mmm) cc_final: 0.8427 (mmm) outliers start: 7 outliers final: 4 residues processed: 76 average time/residue: 0.2364 time to fit residues: 26.7468 Evaluate side-chains 73 residues out of total 1093 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 66 time to evaluate : 1.245 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 A residue 782 LEU Chi-restraints excluded: chain C residue 101 HIS Chi-restraints excluded: chain C residue 125 GLU Chi-restraints excluded: chain C residue 167 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 103 optimal weight: 0.0970 chunk 5 optimal weight: 7.9990 chunk 88 optimal weight: 3.9990 chunk 60 optimal weight: 0.9990 chunk 17 optimal weight: 0.8980 chunk 57 optimal weight: 1.9990 chunk 72 optimal weight: 0.9980 chunk 110 optimal weight: 0.9990 chunk 11 optimal weight: 3.9990 chunk 14 optimal weight: 0.6980 chunk 45 optimal weight: 3.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- 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 = 0.3300 r_free = 0.3300 target = 0.058270 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2836 r_free = 0.2836 target = 0.042151 restraints weight = 45987.185| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.2883 r_free = 0.2883 target = 0.043770 restraints weight = 21993.723| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.2916 r_free = 0.2916 target = 0.044885 restraints weight = 13592.235| |-----------------------------------------------------------------------------| r_work (final): 0.2907 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8528 moved from start: 0.3929 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= 0.180 Angle : 0.600 13.107 13982 Z= 0.288 Chirality : 0.041 0.175 1528 Planarity : 0.003 0.055 1789 Dihedral : 7.905 137.719 1396 Min Nonbonded Distance : 1.984 Molprobity Statistics. All-atom Clashscore : 6.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.89 % Favored : 99.11 % Rotamer: Outliers : 0.92 % Allowed : 9.89 % 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: 1.77 (0.24), residues: 1236 helix: 1.86 (0.21), residues: 625 sheet: 0.84 (0.38), residues: 155 loop : 0.46 (0.29), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRP A 484 HIS 0.005 0.001 HIS A 418 PHE 0.019 0.001 PHE B 12 TYR 0.012 0.001 TYR A 259 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: 3151.57 seconds wall clock time: 57 minutes 33.38 seconds (3453.38 seconds total)