Starting phenix.real_space_refine on Wed Sep 17 14:49:40 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9ctg_45906/09_2025/9ctg_45906.cif Found real_map, /net/cci-nas-00/data/ceres_data/9ctg_45906/09_2025/9ctg_45906.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9ctg_45906/09_2025/9ctg_45906.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9ctg_45906/09_2025/9ctg_45906.map" model { file = "/net/cci-nas-00/data/ceres_data/9ctg_45906/09_2025/9ctg_45906.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9ctg_45906/09_2025/9ctg_45906.cif" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 6 5.49 5 Mg 2 5.21 5 S 35 5.16 5 C 5896 2.51 5 N 1536 2.21 5 O 1653 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 9128 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 8955 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1157, 8955 Classifications: {'peptide': 1157} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PTRANS': 28, 'TRANS': 1128} Chain breaks: 2 Unresolved non-hydrogen bonds: 49 Unresolved non-hydrogen angles: 62 Unresolved non-hydrogen dihedrals: 43 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLU:plan': 1, 'ASP:plan': 1, 'PHE:plan': 2, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 26 Chain: "A" Number of atoms: 173 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 173 Unusual residues: {' MG': 2, 'AGS': 2, 'UPL': 9} Classifications: {'undetermined': 13} Link IDs: {None: 12} Unresolved non-hydrogen bonds: 197 Unresolved non-hydrogen angles: 206 Unresolved non-hydrogen dihedrals: 215 Unresolved non-hydrogen chiralities: 9 Time building chain proxies: 2.34, per 1000 atoms: 0.26 Number of scatterers: 9128 At special positions: 0 Unit cell: (103.584, 109.56, 129.48, 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 35 16.00 P 6 15.00 Mg 2 11.99 O 1653 8.00 N 1536 7.00 C 5896 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.94 Conformation dependent library (CDL) restraints added in 359.5 milliseconds Enol-peptide restraints added in 238.4 nanoseconds 2302 Ramachandran restraints generated. 1151 Oldfield, 0 Emsley, 1151 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2130 Finding SS restraints... Secondary structure from input PDB file: 50 helices and 4 sheets defined 70.1% alpha, 7.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.36 Creating SS restraints... Processing helix chain 'A' and resid 37 through 41 removed outlier: 3.707A pdb=" N PHE A 40 " --> pdb=" O PHE A 37 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N ARG A 41 " --> pdb=" O SER A 38 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 37 through 41' Processing helix chain 'A' and resid 44 through 63 Processing helix chain 'A' and resid 64 through 67 Processing helix chain 'A' and resid 68 through 80 removed outlier: 3.735A pdb=" N PHE A 72 " --> pdb=" O MET A 68 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N ALA A 80 " --> pdb=" O THR A 76 " (cutoff:3.500A) Processing helix chain 'A' and resid 106 through 158 removed outlier: 4.455A pdb=" N THR A 112 " --> pdb=" O GLU A 108 " (cutoff:3.500A) removed outlier: 4.336A pdb=" N ARG A 113 " --> pdb=" O GLU A 109 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N TYR A 130 " --> pdb=" O LEU A 126 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N PHE A 135 " --> pdb=" O ILE A 131 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N TRP A 136 " --> pdb=" O GLN A 132 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N GLN A 158 " --> pdb=" O ALA A 154 " (cutoff:3.500A) Processing helix chain 'A' and resid 159 through 166 Processing helix chain 'A' and resid 168 through 186 removed outlier: 3.912A pdb=" N ASN A 172 " --> pdb=" O VAL A 168 " (cutoff:3.500A) removed outlier: 4.302A pdb=" N THR A 173 " --> pdb=" O GLY A 169 " (cutoff:3.500A) removed outlier: 4.060A pdb=" N THR A 176 " --> pdb=" O ASN A 172 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N ASP A 177 " --> pdb=" O THR A 173 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N ASP A 178 " --> pdb=" O ARG A 174 " (cutoff:3.500A) removed outlier: 4.081A pdb=" N VAL A 179 " --> pdb=" O LEU A 175 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N SER A 180 " --> pdb=" O THR A 176 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N ILE A 182 " --> pdb=" O ASP A 178 " (cutoff:3.500A) Processing helix chain 'A' and resid 188 through 211 Processing helix chain 'A' and resid 212 through 220 removed outlier: 4.064A pdb=" N LEU A 216 " --> pdb=" O TRP A 212 " (cutoff:3.500A) Processing helix chain 'A' and resid 221 through 260 removed outlier: 3.707A pdb=" N LEU A 225 " --> pdb=" O ILE A 221 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N ASP A 241 " --> pdb=" O SER A 237 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N LYS A 242 " --> pdb=" O SER A 238 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N ALA A 260 " --> pdb=" O GLU A 256 " (cutoff:3.500A) Processing helix chain 'A' and resid 260 through 268 Processing helix chain 'A' and resid 269 through 318 removed outlier: 4.261A pdb=" N ASN A 280 " --> pdb=" O ARG A 276 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N LEU A 281 " --> pdb=" O TYR A 277 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N LYS A 290 " --> pdb=" O ARG A 286 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N ILE A 299 " --> pdb=" O ALA A 295 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N ALA A 302 " --> pdb=" O SER A 298 " (cutoff:3.500A) Processing helix chain 'A' and resid 319 through 324 Processing helix chain 'A' and resid 327 through 370 removed outlier: 4.367A pdb=" N ILE A 340 " --> pdb=" O PHE A 336 " (cutoff:3.500A) removed outlier: 4.545A pdb=" N GLY A 341 " --> pdb=" O SER A 337 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N ALA A 342 " --> pdb=" O VAL A 338 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N PHE A 343 " --> pdb=" O LEU A 339 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N GLY A 346 " --> pdb=" O ALA A 342 " (cutoff:3.500A) Proline residue: A 350 - end of helix removed outlier: 4.055A pdb=" N TYR A 363 " --> pdb=" O ARG A 359 " (cutoff:3.500A) removed outlier: 5.343A pdb=" N GLU A 364 " --> pdb=" O GLY A 360 " (cutoff:3.500A) removed outlier: 4.480A pdb=" N ILE A 365 " --> pdb=" O ALA A 361 " (cutoff:3.500A) Processing helix chain 'A' and resid 432 through 441 removed outlier: 3.694A pdb=" N GLN A 441 " --> pdb=" O VAL A 437 " (cutoff:3.500A) Processing helix chain 'A' and resid 462 through 469 removed outlier: 3.530A pdb=" N ILE A 469 " --> pdb=" O PHE A 465 " (cutoff:3.500A) Processing helix chain 'A' and resid 483 through 490 Processing helix chain 'A' and resid 496 through 507 Processing helix chain 'A' and resid 509 through 516 removed outlier: 3.770A pdb=" N ILE A 513 " --> pdb=" O ALA A 509 " (cutoff:3.500A) Processing helix chain 'A' and resid 525 through 529 Processing helix chain 'A' and resid 532 through 547 removed outlier: 3.810A pdb=" N LYS A 536 " --> pdb=" O SER A 532 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N GLN A 537 " --> pdb=" O GLY A 533 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N ARG A 547 " --> pdb=" O ARG A 543 " (cutoff:3.500A) Processing helix chain 'A' and resid 562 through 576 removed outlier: 3.987A pdb=" N ALA A 576 " --> pdb=" O ALA A 572 " (cutoff:3.500A) Processing helix chain 'A' and resid 589 through 594 removed outlier: 4.407A pdb=" N ASN A 594 " --> pdb=" O SER A 590 " (cutoff:3.500A) Processing helix chain 'A' and resid 611 through 618 Processing helix chain 'A' and resid 620 through 630 Processing helix chain 'A' and resid 697 through 704 Processing helix chain 'A' and resid 707 through 723 removed outlier: 3.755A pdb=" N PHE A 711 " --> pdb=" O GLU A 707 " (cutoff:3.500A) Processing helix chain 'A' and resid 726 through 740 removed outlier: 3.903A pdb=" N ILE A 730 " --> pdb=" O PRO A 726 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N PHE A 739 " --> pdb=" O ILE A 735 " (cutoff:3.500A) Processing helix chain 'A' and resid 745 through 797 removed outlier: 3.745A pdb=" N ASN A 753 " --> pdb=" O ARG A 749 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N LEU A 760 " --> pdb=" O SER A 756 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N GLY A 763 " --> pdb=" O PHE A 759 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N PHE A 771 " --> pdb=" O PHE A 767 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N GLY A 774 " --> pdb=" O PHE A 770 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N PHE A 777 " --> pdb=" O GLN A 773 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N LYS A 786 " --> pdb=" O GLU A 782 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N VAL A 792 " --> pdb=" O LEU A 788 " (cutoff:3.500A) Processing helix chain 'A' and resid 800 through 805 removed outlier: 3.819A pdb=" N PHE A 804 " --> pdb=" O ASP A 800 " (cutoff:3.500A) Processing helix chain 'A' and resid 810 through 830 removed outlier: 3.829A pdb=" N ALA A 819 " --> pdb=" O THR A 815 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N ALA A 822 " --> pdb=" O LEU A 818 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N ALA A 828 " --> pdb=" O GLN A 824 " (cutoff:3.500A) Processing helix chain 'A' and resid 831 through 853 removed outlier: 3.873A pdb=" N VAL A 835 " --> pdb=" O SER A 831 " (cutoff:3.500A) Processing helix chain 'A' and resid 857 through 863 Processing helix chain 'A' and resid 864 through 903 removed outlier: 3.694A pdb=" N LEU A 884 " --> pdb=" O SER A 880 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N LYS A 885 " --> pdb=" O GLY A 881 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N GLU A 891 " --> pdb=" O LYS A 887 " (cutoff:3.500A) removed outlier: 4.127A pdb=" N GLY A 892 " --> pdb=" O LYS A 888 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N ILE A 896 " --> pdb=" O GLY A 892 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N ALA A 897 " --> pdb=" O SER A 893 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N ASN A 903 " --> pdb=" O GLU A 899 " (cutoff:3.500A) Processing helix chain 'A' and resid 903 through 911 Processing helix chain 'A' and resid 912 through 924 Processing helix chain 'A' and resid 924 through 966 removed outlier: 3.713A pdb=" N TYR A 928 " --> pdb=" O LEU A 924 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N HIS A 936 " --> pdb=" O LEU A 932 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N MET A 949 " --> pdb=" O THR A 945 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N TYR A 950 " --> pdb=" O GLN A 946 " (cutoff:3.500A) Processing helix chain 'A' and resid 970 through 982 removed outlier: 3.851A pdb=" N VAL A 974 " --> pdb=" O SER A 970 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N LEU A 976 " --> pdb=" O GLU A 972 " (cutoff:3.500A) Processing helix chain 'A' and resid 984 through 993 Processing helix chain 'A' and resid 994 through 1014 removed outlier: 3.584A pdb=" N TYR A 998 " --> pdb=" O PHE A 994 " (cutoff:3.500A) removed outlier: 4.206A pdb=" N ILE A1003 " --> pdb=" O ALA A 999 " (cutoff:3.500A) Processing helix chain 'A' and resid 1076 through 1084 removed outlier: 4.079A pdb=" N VAL A1080 " --> pdb=" O LYS A1076 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N GLU A1084 " --> pdb=" O VAL A1080 " (cutoff:3.500A) Processing helix chain 'A' and resid 1105 through 1113 removed outlier: 3.684A pdb=" N HIS A1112 " --> pdb=" O TRP A1108 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N LEU A1113 " --> pdb=" O LEU A1109 " (cutoff:3.500A) Processing helix chain 'A' and resid 1126 through 1133 Processing helix chain 'A' and resid 1141 through 1152 Processing helix chain 'A' and resid 1154 through 1161 Processing helix chain 'A' and resid 1177 through 1192 removed outlier: 4.535A pdb=" N ARG A1192 " --> pdb=" O ARG A1188 " (cutoff:3.500A) Processing helix chain 'A' and resid 1207 through 1221 removed outlier: 3.605A pdb=" N ALA A1221 " --> pdb=" O ALA A1217 " (cutoff:3.500A) Processing helix chain 'A' and resid 1233 through 1239 removed outlier: 3.973A pdb=" N ASN A1239 " --> pdb=" O SER A1235 " (cutoff:3.500A) Processing helix chain 'A' and resid 1256 through 1263 Processing helix chain 'A' and resid 1265 through 1273 removed outlier: 3.537A pdb=" N VAL A1273 " --> pdb=" O SER A1269 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 410 through 417 removed outlier: 7.259A pdb=" N LYS A 411 " --> pdb=" O HIS A 398 " (cutoff:3.500A) removed outlier: 6.381A pdb=" N HIS A 398 " --> pdb=" O LYS A 411 " (cutoff:3.500A) removed outlier: 5.497A pdb=" N LEU A 413 " --> pdb=" O ASN A 396 " (cutoff:3.500A) removed outlier: 4.264A pdb=" N VAL A 397 " --> pdb=" O GLU A 448 " (cutoff:3.500A) removed outlier: 6.614A pdb=" N GLU A 448 " --> pdb=" O VAL A 397 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 470 through 473 removed outlier: 6.332A pdb=" N VAL A 423 " --> pdb=" O VAL A 584 " (cutoff:3.500A) removed outlier: 6.208A pdb=" N THR A 422 " --> pdb=" O VAL A 597 " (cutoff:3.500A) removed outlier: 7.592A pdb=" N ALA A 599 " --> pdb=" O THR A 422 " (cutoff:3.500A) removed outlier: 6.245A pdb=" N ALA A 424 " --> pdb=" O ALA A 599 " (cutoff:3.500A) removed outlier: 7.353A pdb=" N PHE A 601 " --> pdb=" O ALA A 424 " (cutoff:3.500A) removed outlier: 6.849A pdb=" N VAL A 426 " --> pdb=" O PHE A 601 " (cutoff:3.500A) removed outlier: 6.400A pdb=" N GLY A 600 " --> pdb=" O VAL A 607 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 1053 through 1060 removed outlier: 6.641A pdb=" N GLN A1054 " --> pdb=" O VAL A1041 " (cutoff:3.500A) removed outlier: 6.138A pdb=" N VAL A1041 " --> pdb=" O GLN A1054 " (cutoff:3.500A) removed outlier: 5.170A pdb=" N LEU A1056 " --> pdb=" O GLU A1039 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 1114 through 1116 removed outlier: 6.440A pdb=" N LEU A1197 " --> pdb=" O ILE A1228 " (cutoff:3.500A) removed outlier: 7.987A pdb=" N ILE A1230 " --> pdb=" O LEU A1197 " (cutoff:3.500A) removed outlier: 6.659A pdb=" N LEU A1199 " --> pdb=" O ILE A1230 " (cutoff:3.500A) removed outlier: 6.100A pdb=" N LEU A1066 " --> pdb=" O VAL A1229 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N GLU A1253 " --> pdb=" O VAL A1245 " (cutoff:3.500A) removed outlier: 6.575A pdb=" N GLN A1247 " --> pdb=" O VAL A1251 " (cutoff:3.500A) removed outlier: 5.028A pdb=" N VAL A1251 " --> pdb=" O GLN A1247 " (cutoff:3.500A) 573 hydrogen bonds defined for protein. 1686 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: 1.72 Time building geometry restraints manager: 1.21 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.36: 2934 1.36 - 1.51: 2465 1.51 - 1.65: 3825 1.65 - 1.80: 36 1.80 - 1.95: 25 Bond restraints: 9285 Sorted by residual: bond pdb=" CB PRO A 385 " pdb=" CG PRO A 385 " ideal model delta sigma weight residual 1.492 1.618 -0.126 5.00e-02 4.00e+02 6.40e+00 bond pdb=" N GLU A1201 " pdb=" CA GLU A1201 " ideal model delta sigma weight residual 1.462 1.488 -0.026 1.46e-02 4.69e+03 3.22e+00 bond pdb=" CA THR A 319 " pdb=" C THR A 319 " ideal model delta sigma weight residual 1.523 1.555 -0.031 1.80e-02 3.09e+03 3.06e+00 bond pdb=" C PRO A 745 " pdb=" O PRO A 745 " ideal model delta sigma weight residual 1.238 1.216 0.022 1.37e-02 5.33e+03 2.70e+00 bond pdb=" C ASP A 744 " pdb=" N PRO A 745 " ideal model delta sigma weight residual 1.337 1.354 -0.017 1.11e-02 8.12e+03 2.47e+00 ... (remaining 9280 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.65: 12243 1.65 - 3.30: 220 3.30 - 4.95: 44 4.95 - 6.61: 10 6.61 - 8.26: 4 Bond angle restraints: 12521 Sorted by residual: angle pdb=" CA PRO A 385 " pdb=" N PRO A 385 " pdb=" CD PRO A 385 " ideal model delta sigma weight residual 112.00 104.67 7.33 1.40e+00 5.10e-01 2.74e+01 angle pdb=" N ILE A1154 " pdb=" CA ILE A1154 " pdb=" C ILE A1154 " ideal model delta sigma weight residual 113.20 109.29 3.91 9.60e-01 1.09e+00 1.66e+01 angle pdb=" N PRO A 745 " pdb=" CA PRO A 745 " pdb=" C PRO A 745 " ideal model delta sigma weight residual 114.03 109.79 4.24 1.23e+00 6.61e-01 1.19e+01 angle pdb=" N PRO A 385 " pdb=" CD PRO A 385 " pdb=" CG PRO A 385 " ideal model delta sigma weight residual 103.20 98.54 4.66 1.50e+00 4.44e-01 9.65e+00 angle pdb=" N TRP A 698 " pdb=" CA TRP A 698 " pdb=" C TRP A 698 " ideal model delta sigma weight residual 112.54 108.88 3.66 1.22e+00 6.72e-01 9.00e+00 ... (remaining 12516 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 28.66: 5264 28.66 - 57.32: 270 57.32 - 85.98: 22 85.98 - 114.64: 1 114.64 - 143.29: 1 Dihedral angle restraints: 5558 sinusoidal: 2240 harmonic: 3318 Sorted by residual: dihedral pdb=" O1A AGS A1313 " pdb=" O3A AGS A1313 " pdb=" PA AGS A1313 " pdb=" PB AGS A1313 " ideal model delta sinusoidal sigma weight residual -67.73 75.56 -143.29 1 3.00e+01 1.11e-03 1.92e+01 dihedral pdb=" CA ARG A 580 " pdb=" C ARG A 580 " pdb=" N THR A 581 " pdb=" CA THR A 581 " ideal model delta harmonic sigma weight residual 180.00 161.67 18.33 0 5.00e+00 4.00e-02 1.34e+01 dihedral pdb=" CA HIS A 518 " pdb=" C HIS A 518 " pdb=" N LYS A 519 " pdb=" CA LYS A 519 " ideal model delta harmonic sigma weight residual -180.00 -162.81 -17.19 0 5.00e+00 4.00e-02 1.18e+01 ... (remaining 5555 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.027: 818 0.027 - 0.054: 404 0.054 - 0.081: 146 0.081 - 0.108: 50 0.108 - 0.135: 21 Chirality restraints: 1439 Sorted by residual: chirality pdb=" CA ILE A 585 " pdb=" N ILE A 585 " pdb=" C ILE A 585 " pdb=" CB ILE A 585 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.52e-01 chirality pdb=" CB ILE A 388 " pdb=" CA ILE A 388 " pdb=" CG1 ILE A 388 " pdb=" CG2 ILE A 388 " both_signs ideal model delta sigma weight residual False 2.64 2.51 0.13 2.00e-01 2.50e+01 4.36e-01 chirality pdb=" CA ASN A1248 " pdb=" N ASN A1248 " pdb=" C ASN A1248 " pdb=" CB ASN A1248 " both_signs ideal model delta sigma weight residual False 2.51 2.38 0.13 2.00e-01 2.50e+01 4.31e-01 ... (remaining 1436 not shown) Planarity restraints: 1562 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE A 716 " 0.013 2.00e-02 2.50e+03 1.37e-02 3.27e+00 pdb=" CG PHE A 716 " -0.032 2.00e-02 2.50e+03 pdb=" CD1 PHE A 716 " 0.005 2.00e-02 2.50e+03 pdb=" CD2 PHE A 716 " 0.009 2.00e-02 2.50e+03 pdb=" CE1 PHE A 716 " 0.002 2.00e-02 2.50e+03 pdb=" CE2 PHE A 716 " -0.001 2.00e-02 2.50e+03 pdb=" CZ PHE A 716 " 0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LYS A 384 " -0.030 5.00e-02 4.00e+02 4.36e-02 3.05e+00 pdb=" N PRO A 385 " 0.075 5.00e-02 4.00e+02 pdb=" CA PRO A 385 " -0.021 5.00e-02 4.00e+02 pdb=" CD PRO A 385 " -0.024 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLN A 725 " -0.027 5.00e-02 4.00e+02 4.14e-02 2.75e+00 pdb=" N PRO A 726 " 0.072 5.00e-02 4.00e+02 pdb=" CA PRO A 726 " -0.021 5.00e-02 4.00e+02 pdb=" CD PRO A 726 " -0.023 5.00e-02 4.00e+02 ... (remaining 1559 not shown) Histogram of nonbonded interaction distances: 1.93 - 2.52: 40 2.52 - 3.12: 6808 3.12 - 3.71: 13763 3.71 - 4.31: 18471 4.31 - 4.90: 31864 Nonbonded interactions: 70946 Sorted by model distance: nonbonded pdb="MG MG A1310 " pdb=" O1B AGS A1312 " model vdw 1.927 2.170 nonbonded pdb="MG MG A1311 " pdb=" O2G AGS A1313 " model vdw 1.989 2.170 nonbonded pdb="MG MG A1311 " pdb=" O2B AGS A1313 " model vdw 2.099 2.170 nonbonded pdb=" OE1 GLN A 475 " pdb="MG MG A1311 " model vdw 2.118 2.170 nonbonded pdb=" OG SER A 434 " pdb="MG MG A1311 " model vdw 2.136 2.170 ... (remaining 70941 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.090 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: 0.110 Check model and map are aligned: 0.020 Set scattering table: 0.010 Process input model: 10.350 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.420 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 13.060 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7729 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.126 9285 Z= 0.161 Angle : 0.598 8.258 12521 Z= 0.353 Chirality : 0.039 0.135 1439 Planarity : 0.004 0.044 1562 Dihedral : 16.152 143.295 3428 Min Nonbonded Distance : 1.927 Molprobity Statistics. All-atom Clashscore : 7.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 0.11 % Allowed : 15.78 % Favored : 84.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.52 (0.24), residues: 1151 helix: 1.08 (0.19), residues: 742 sheet: 0.45 (0.59), residues: 78 loop : -1.31 (0.31), residues: 331 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 741 TYR 0.013 0.001 TYR A 953 PHE 0.032 0.002 PHE A 716 TRP 0.009 0.001 TRP A 315 HIS 0.002 0.001 HIS A 612 Details of bonding type rmsd covalent geometry : bond 0.00354 ( 9285) covalent geometry : angle 0.59800 (12521) hydrogen bonds : bond 0.15688 ( 573) hydrogen bonds : angle 5.84475 ( 1686) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2302 Ramachandran restraints generated. 1151 Oldfield, 0 Emsley, 1151 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2302 Ramachandran restraints generated. 1151 Oldfield, 0 Emsley, 1151 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 956 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 144 time to evaluate : 0.438 Fit side-chains REVERT: A 105 MET cc_start: 0.4440 (mpp) cc_final: 0.4186 (mpp) REVERT: A 197 MET cc_start: 0.8151 (mmp) cc_final: 0.7751 (mmt) REVERT: A 227 LEU cc_start: 0.7628 (tt) cc_final: 0.7084 (mp) REVERT: A 236 LEU cc_start: 0.8134 (pp) cc_final: 0.7893 (tt) REVERT: A 405 LYS cc_start: 0.8519 (tmtt) cc_final: 0.8036 (tptt) REVERT: A 416 LYS cc_start: 0.7963 (mttt) cc_final: 0.7455 (ttpt) REVERT: A 428 ASN cc_start: 0.7807 (p0) cc_final: 0.7465 (p0) REVERT: A 454 ASP cc_start: 0.7966 (t0) cc_final: 0.7752 (m-30) REVERT: A 497 MET cc_start: 0.7764 (tpp) cc_final: 0.7306 (tpp) REVERT: A 510 TYR cc_start: 0.8540 (t80) cc_final: 0.8168 (t80) REVERT: A 514 MET cc_start: 0.8007 (mmt) cc_final: 0.7663 (mmp) REVERT: A 550 LYS cc_start: 0.7760 (mmtt) cc_final: 0.7398 (mmmt) REVERT: A 588 ARG cc_start: 0.6481 (mtp85) cc_final: 0.5930 (ttm110) REVERT: A 596 ASP cc_start: 0.7409 (m-30) cc_final: 0.7183 (m-30) REVERT: A 791 MET cc_start: 0.8579 (mtm) cc_final: 0.8328 (mtp) REVERT: A 851 PHE cc_start: 0.6997 (t80) cc_final: 0.6489 (t80) REVERT: A 876 MET cc_start: 0.8436 (tpp) cc_final: 0.8214 (mmm) REVERT: A 922 GLN cc_start: 0.8018 (tt0) cc_final: 0.7471 (tm-30) REVERT: A 968 LEU cc_start: 0.8502 (mm) cc_final: 0.8104 (mp) REVERT: A 969 MET cc_start: 0.7189 (ttm) cc_final: 0.6908 (ptm) REVERT: A 1061 LYS cc_start: 0.7655 (mmmm) cc_final: 0.7370 (mmmt) REVERT: A 1083 LEU cc_start: 0.8951 (tp) cc_final: 0.8655 (tp) outliers start: 1 outliers final: 0 residues processed: 144 average time/residue: 0.1123 time to fit residues: 22.3817 Evaluate side-chains 112 residues out of total 956 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 112 time to evaluate : 0.348 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 108 optimal weight: 10.0000 chunk 49 optimal weight: 0.8980 chunk 97 optimal weight: 3.9990 chunk 113 optimal weight: 0.6980 chunk 53 optimal weight: 5.9990 chunk 5 optimal weight: 9.9990 chunk 33 optimal weight: 0.7980 chunk 65 optimal weight: 3.9990 chunk 62 optimal weight: 8.9990 chunk 51 optimal weight: 3.9990 chunk 100 optimal weight: 6.9990 overall best weight: 2.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 143 GLN A 158 GLN A 172 ASN A 347 GLN A 391 ASN A 441 GLN A 530 GLN A 824 GLN A 842 ASN A 856 GLN ** A 914 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 990 GLN A1153 ASN A1247 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3686 r_free = 0.3686 target = 0.141010 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3363 r_free = 0.3363 target = 0.116224 restraints weight = 12333.197| |-----------------------------------------------------------------------------| r_work (start): 0.3354 rms_B_bonded: 1.76 r_work: 0.3246 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.3119 rms_B_bonded: 4.10 restraints_weight: 0.2500 r_work (final): 0.3119 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7922 moved from start: 0.1338 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 9285 Z= 0.200 Angle : 0.599 8.822 12521 Z= 0.318 Chirality : 0.042 0.138 1439 Planarity : 0.004 0.039 1562 Dihedral : 8.777 138.037 1363 Min Nonbonded Distance : 1.916 Molprobity Statistics. All-atom Clashscore : 5.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 3.50 % Allowed : 15.89 % Favored : 80.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.55 (0.24), residues: 1151 helix: 1.15 (0.19), residues: 761 sheet: 0.65 (0.63), residues: 70 loop : -1.58 (0.31), residues: 320 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A1103 TYR 0.014 0.001 TYR A 277 PHE 0.018 0.002 PHE A 72 TRP 0.010 0.001 TRP A 45 HIS 0.005 0.001 HIS A1232 Details of bonding type rmsd covalent geometry : bond 0.00472 ( 9285) covalent geometry : angle 0.59935 (12521) hydrogen bonds : bond 0.06259 ( 573) hydrogen bonds : angle 4.45900 ( 1686) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2302 Ramachandran restraints generated. 1151 Oldfield, 0 Emsley, 1151 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2302 Ramachandran restraints generated. 1151 Oldfield, 0 Emsley, 1151 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 956 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 125 time to evaluate : 0.432 Fit side-chains REVERT: A 227 LEU cc_start: 0.7745 (tt) cc_final: 0.7181 (mp) REVERT: A 405 LYS cc_start: 0.8624 (tmtt) cc_final: 0.8145 (tptt) REVERT: A 416 LYS cc_start: 0.7959 (mttt) cc_final: 0.7668 (ttpt) REVERT: A 428 ASN cc_start: 0.8034 (p0) cc_final: 0.7658 (p0) REVERT: A 476 GLU cc_start: 0.7803 (pm20) cc_final: 0.7368 (pm20) REVERT: A 497 MET cc_start: 0.7817 (tpp) cc_final: 0.7566 (tpp) REVERT: A 550 LYS cc_start: 0.8056 (mmtt) cc_final: 0.7612 (mmmt) REVERT: A 588 ARG cc_start: 0.6446 (mtp85) cc_final: 0.5928 (ttm110) REVERT: A 741 ARG cc_start: 0.6400 (ttm-80) cc_final: 0.5934 (mtt-85) REVERT: A 791 MET cc_start: 0.9050 (mtm) cc_final: 0.8813 (mtp) REVERT: A 851 PHE cc_start: 0.7246 (t80) cc_final: 0.6692 (t80) REVERT: A 861 LEU cc_start: 0.7843 (tt) cc_final: 0.7628 (tp) REVERT: A 876 MET cc_start: 0.8449 (tpp) cc_final: 0.8202 (mmm) REVERT: A 922 GLN cc_start: 0.8289 (tt0) cc_final: 0.7801 (tm-30) REVERT: A 968 LEU cc_start: 0.8575 (OUTLIER) cc_final: 0.8181 (mp) REVERT: A 1061 LYS cc_start: 0.7856 (mmmm) cc_final: 0.7629 (mmmt) REVERT: A 1113 LEU cc_start: 0.8423 (OUTLIER) cc_final: 0.7934 (pp) outliers start: 33 outliers final: 14 residues processed: 145 average time/residue: 0.1070 time to fit residues: 21.6242 Evaluate side-chains 128 residues out of total 956 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 112 time to evaluate : 0.366 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 176 THR Chi-restraints excluded: chain A residue 338 VAL Chi-restraints excluded: chain A residue 389 LYS Chi-restraints excluded: chain A residue 391 ASN Chi-restraints excluded: chain A residue 496 THR Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 571 VAL Chi-restraints excluded: chain A residue 695 VAL Chi-restraints excluded: chain A residue 848 ILE Chi-restraints excluded: chain A residue 890 LEU Chi-restraints excluded: chain A residue 898 THR Chi-restraints excluded: chain A residue 907 VAL Chi-restraints excluded: chain A residue 968 LEU Chi-restraints excluded: chain A residue 969 MET Chi-restraints excluded: chain A residue 1030 THR Chi-restraints excluded: chain A residue 1113 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 22 optimal weight: 0.9990 chunk 85 optimal weight: 6.9990 chunk 58 optimal weight: 0.6980 chunk 36 optimal weight: 10.0000 chunk 17 optimal weight: 0.9980 chunk 12 optimal weight: 2.9990 chunk 72 optimal weight: 4.9990 chunk 23 optimal weight: 0.9980 chunk 16 optimal weight: 3.9990 chunk 32 optimal weight: 7.9990 chunk 99 optimal weight: 0.0040 overall best weight: 0.7394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 166 HIS A 383 HIS A 387 ASN A 391 ASN A 856 GLN A 914 GLN A 990 GLN A1081 GLN A1247 GLN A1248 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3719 r_free = 0.3719 target = 0.143636 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.119139 restraints weight = 12248.200| |-----------------------------------------------------------------------------| r_work (start): 0.3398 rms_B_bonded: 1.78 r_work: 0.3292 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.3160 rms_B_bonded: 4.20 restraints_weight: 0.2500 r_work (final): 0.3160 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7870 moved from start: 0.1593 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 9285 Z= 0.124 Angle : 0.499 7.537 12521 Z= 0.264 Chirality : 0.039 0.146 1439 Planarity : 0.003 0.038 1562 Dihedral : 8.479 134.651 1363 Min Nonbonded Distance : 2.003 Molprobity Statistics. All-atom Clashscore : 5.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 2.44 % Allowed : 18.22 % Favored : 79.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.88 (0.25), residues: 1151 helix: 1.42 (0.19), residues: 767 sheet: 0.61 (0.64), residues: 70 loop : -1.51 (0.31), residues: 314 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 741 TYR 0.007 0.001 TYR A 853 PHE 0.016 0.001 PHE A 72 TRP 0.008 0.001 TRP A 708 HIS 0.002 0.001 HIS A 966 Details of bonding type rmsd covalent geometry : bond 0.00258 ( 9285) covalent geometry : angle 0.49908 (12521) hydrogen bonds : bond 0.05356 ( 573) hydrogen bonds : angle 4.11386 ( 1686) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2302 Ramachandran restraints generated. 1151 Oldfield, 0 Emsley, 1151 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2302 Ramachandran restraints generated. 1151 Oldfield, 0 Emsley, 1151 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 956 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 114 time to evaluate : 0.362 Fit side-chains REVERT: A 227 LEU cc_start: 0.7597 (OUTLIER) cc_final: 0.7177 (mp) REVERT: A 389 LYS cc_start: 0.6194 (OUTLIER) cc_final: 0.5790 (mttp) REVERT: A 405 LYS cc_start: 0.8563 (tmtt) cc_final: 0.8077 (tptt) REVERT: A 416 LYS cc_start: 0.7963 (mttt) cc_final: 0.7659 (ttpt) REVERT: A 428 ASN cc_start: 0.8148 (p0) cc_final: 0.7814 (p0) REVERT: A 476 GLU cc_start: 0.7811 (pm20) cc_final: 0.7358 (pm20) REVERT: A 497 MET cc_start: 0.7761 (tpp) cc_final: 0.7547 (tpp) REVERT: A 550 LYS cc_start: 0.8026 (mmtt) cc_final: 0.7609 (mmmt) REVERT: A 588 ARG cc_start: 0.6414 (mtp85) cc_final: 0.5868 (ttm110) REVERT: A 741 ARG cc_start: 0.6320 (ttm-80) cc_final: 0.5980 (mtt-85) REVERT: A 851 PHE cc_start: 0.7221 (t80) cc_final: 0.6658 (t80) REVERT: A 922 GLN cc_start: 0.8334 (tt0) cc_final: 0.7779 (tm-30) REVERT: A 968 LEU cc_start: 0.8563 (OUTLIER) cc_final: 0.8201 (mp) REVERT: A 969 MET cc_start: 0.7510 (ttm) cc_final: 0.7182 (ptm) REVERT: A 1113 LEU cc_start: 0.8352 (OUTLIER) cc_final: 0.8019 (pp) REVERT: A 1129 GLU cc_start: 0.8085 (tm-30) cc_final: 0.7809 (tt0) outliers start: 23 outliers final: 5 residues processed: 129 average time/residue: 0.1022 time to fit residues: 18.5577 Evaluate side-chains 113 residues out of total 956 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 104 time to evaluate : 0.450 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 227 LEU Chi-restraints excluded: chain A residue 389 LYS Chi-restraints excluded: chain A residue 496 THR Chi-restraints excluded: chain A residue 546 VAL Chi-restraints excluded: chain A residue 848 ILE Chi-restraints excluded: chain A residue 890 LEU Chi-restraints excluded: chain A residue 898 THR Chi-restraints excluded: chain A residue 968 LEU Chi-restraints excluded: chain A residue 1113 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 42 optimal weight: 0.2980 chunk 25 optimal weight: 0.9980 chunk 57 optimal weight: 0.0370 chunk 11 optimal weight: 5.9990 chunk 15 optimal weight: 0.0970 chunk 81 optimal weight: 4.9990 chunk 114 optimal weight: 0.0570 chunk 61 optimal weight: 4.9990 chunk 85 optimal weight: 7.9990 chunk 18 optimal weight: 5.9990 chunk 112 optimal weight: 5.9990 overall best weight: 0.2974 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 383 HIS A 438 GLN A 824 GLN A 990 GLN A1248 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3756 r_free = 0.3756 target = 0.146797 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.122442 restraints weight = 12337.893| |-----------------------------------------------------------------------------| r_work (start): 0.3442 rms_B_bonded: 1.79 r_work: 0.3339 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.3211 rms_B_bonded: 4.17 restraints_weight: 0.2500 r_work (final): 0.3211 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7823 moved from start: 0.1839 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 9285 Z= 0.111 Angle : 0.469 6.721 12521 Z= 0.248 Chirality : 0.038 0.176 1439 Planarity : 0.003 0.037 1562 Dihedral : 8.142 131.230 1363 Min Nonbonded Distance : 2.031 Molprobity Statistics. All-atom Clashscore : 6.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 2.65 % Allowed : 17.06 % Favored : 80.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.20 (0.25), residues: 1151 helix: 1.61 (0.19), residues: 771 sheet: 0.84 (0.65), residues: 70 loop : -1.30 (0.32), residues: 310 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A1110 TYR 0.007 0.001 TYR A 928 PHE 0.015 0.001 PHE A 983 TRP 0.011 0.001 TRP A 855 HIS 0.002 0.001 HIS A 612 Details of bonding type rmsd covalent geometry : bond 0.00216 ( 9285) covalent geometry : angle 0.46891 (12521) hydrogen bonds : bond 0.04634 ( 573) hydrogen bonds : angle 3.83732 ( 1686) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2302 Ramachandran restraints generated. 1151 Oldfield, 0 Emsley, 1151 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2302 Ramachandran restraints generated. 1151 Oldfield, 0 Emsley, 1151 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 956 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 118 time to evaluate : 0.324 Fit side-chains REVERT: A 227 LEU cc_start: 0.7415 (OUTLIER) cc_final: 0.7107 (mp) REVERT: A 391 ASN cc_start: 0.8721 (OUTLIER) cc_final: 0.8457 (m-40) REVERT: A 405 LYS cc_start: 0.8471 (tmtt) cc_final: 0.8004 (tptt) REVERT: A 416 LYS cc_start: 0.7965 (mttt) cc_final: 0.7677 (ttpt) REVERT: A 428 ASN cc_start: 0.8053 (p0) cc_final: 0.7730 (p0) REVERT: A 497 MET cc_start: 0.7813 (tpp) cc_final: 0.7461 (tpp) REVERT: A 550 LYS cc_start: 0.8061 (mmtt) cc_final: 0.7749 (mmmt) REVERT: A 588 ARG cc_start: 0.6441 (mtp85) cc_final: 0.5895 (ttm110) REVERT: A 630 THR cc_start: 0.4438 (OUTLIER) cc_final: 0.4190 (p) REVERT: A 741 ARG cc_start: 0.6375 (ttm-80) cc_final: 0.5880 (mtt-85) REVERT: A 765 ILE cc_start: 0.8380 (OUTLIER) cc_final: 0.8170 (mp) REVERT: A 851 PHE cc_start: 0.7217 (t80) cc_final: 0.6642 (t80) REVERT: A 922 GLN cc_start: 0.8370 (tt0) cc_final: 0.7937 (tm-30) REVERT: A 968 LEU cc_start: 0.8537 (OUTLIER) cc_final: 0.8302 (tt) REVERT: A 1113 LEU cc_start: 0.8399 (OUTLIER) cc_final: 0.8015 (pp) REVERT: A 1129 GLU cc_start: 0.7884 (tm-30) cc_final: 0.7676 (mt-10) outliers start: 25 outliers final: 7 residues processed: 135 average time/residue: 0.0982 time to fit residues: 18.5575 Evaluate side-chains 118 residues out of total 956 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 105 time to evaluate : 0.363 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 227 LEU Chi-restraints excluded: chain A residue 391 ASN Chi-restraints excluded: chain A residue 426 VAL Chi-restraints excluded: chain A residue 496 THR Chi-restraints excluded: chain A residue 546 VAL Chi-restraints excluded: chain A residue 630 THR Chi-restraints excluded: chain A residue 738 VAL Chi-restraints excluded: chain A residue 765 ILE Chi-restraints excluded: chain A residue 890 LEU Chi-restraints excluded: chain A residue 898 THR Chi-restraints excluded: chain A residue 968 LEU Chi-restraints excluded: chain A residue 1113 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 80 optimal weight: 0.0770 chunk 58 optimal weight: 6.9990 chunk 22 optimal weight: 1.9990 chunk 57 optimal weight: 4.9990 chunk 3 optimal weight: 3.9990 chunk 59 optimal weight: 0.8980 chunk 10 optimal weight: 3.9990 chunk 86 optimal weight: 4.9990 chunk 94 optimal weight: 2.9990 chunk 17 optimal weight: 0.9990 chunk 98 optimal weight: 1.9990 overall best weight: 1.1944 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 383 HIS A 824 GLN A 966 HIS ** A 990 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3707 r_free = 0.3707 target = 0.142579 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.117748 restraints weight = 12358.613| |-----------------------------------------------------------------------------| r_work (start): 0.3386 rms_B_bonded: 1.79 r_work: 0.3280 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.3149 rms_B_bonded: 4.18 restraints_weight: 0.2500 r_work (final): 0.3149 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7889 moved from start: 0.2009 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 9285 Z= 0.138 Angle : 0.497 6.702 12521 Z= 0.262 Chirality : 0.039 0.157 1439 Planarity : 0.003 0.037 1562 Dihedral : 8.218 134.543 1363 Min Nonbonded Distance : 1.953 Molprobity Statistics. All-atom Clashscore : 6.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.52 % Favored : 97.48 % Rotamer: Outliers : 3.28 % Allowed : 17.27 % Favored : 79.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.18 (0.25), residues: 1151 helix: 1.61 (0.19), residues: 768 sheet: 0.86 (0.65), residues: 70 loop : -1.32 (0.33), residues: 313 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 174 TYR 0.009 0.001 TYR A 928 PHE 0.016 0.001 PHE A 72 TRP 0.007 0.001 TRP A 315 HIS 0.003 0.001 HIS A1232 Details of bonding type rmsd covalent geometry : bond 0.00312 ( 9285) covalent geometry : angle 0.49726 (12521) hydrogen bonds : bond 0.05080 ( 573) hydrogen bonds : angle 3.84924 ( 1686) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2302 Ramachandran restraints generated. 1151 Oldfield, 0 Emsley, 1151 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2302 Ramachandran restraints generated. 1151 Oldfield, 0 Emsley, 1151 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 956 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 108 time to evaluate : 0.246 Fit side-chains REVERT: A 212 TRP cc_start: 0.7403 (t60) cc_final: 0.6493 (t-100) REVERT: A 227 LEU cc_start: 0.7579 (OUTLIER) cc_final: 0.7165 (mp) REVERT: A 236 LEU cc_start: 0.8212 (OUTLIER) cc_final: 0.7844 (tt) REVERT: A 391 ASN cc_start: 0.8709 (OUTLIER) cc_final: 0.8488 (m-40) REVERT: A 405 LYS cc_start: 0.8493 (tmtt) cc_final: 0.8022 (tptt) REVERT: A 416 LYS cc_start: 0.8028 (mttt) cc_final: 0.7733 (ttpt) REVERT: A 428 ASN cc_start: 0.8091 (p0) cc_final: 0.7781 (p0) REVERT: A 497 MET cc_start: 0.7854 (tpp) cc_final: 0.7501 (tpp) REVERT: A 550 LYS cc_start: 0.8047 (mmtt) cc_final: 0.7730 (mmmt) REVERT: A 588 ARG cc_start: 0.6448 (mtp85) cc_final: 0.5956 (ttm110) REVERT: A 630 THR cc_start: 0.4406 (OUTLIER) cc_final: 0.4177 (p) REVERT: A 741 ARG cc_start: 0.6363 (ttm-80) cc_final: 0.5899 (mtt-85) REVERT: A 765 ILE cc_start: 0.8419 (mp) cc_final: 0.8210 (mp) REVERT: A 861 LEU cc_start: 0.7692 (OUTLIER) cc_final: 0.7460 (tp) REVERT: A 922 GLN cc_start: 0.8414 (tt0) cc_final: 0.7994 (tm-30) REVERT: A 968 LEU cc_start: 0.8505 (OUTLIER) cc_final: 0.8251 (tt) REVERT: A 1052 VAL cc_start: 0.8606 (OUTLIER) cc_final: 0.8354 (m) REVERT: A 1113 LEU cc_start: 0.8328 (OUTLIER) cc_final: 0.7826 (pp) REVERT: A 1129 GLU cc_start: 0.7942 (tm-30) cc_final: 0.7724 (mt-10) outliers start: 31 outliers final: 12 residues processed: 132 average time/residue: 0.0930 time to fit residues: 17.4293 Evaluate side-chains 124 residues out of total 956 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 104 time to evaluate : 0.316 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 119 SER Chi-restraints excluded: chain A residue 144 ILE Chi-restraints excluded: chain A residue 175 LEU Chi-restraints excluded: chain A residue 227 LEU Chi-restraints excluded: chain A residue 236 LEU Chi-restraints excluded: chain A residue 338 VAL Chi-restraints excluded: chain A residue 391 ASN Chi-restraints excluded: chain A residue 496 THR Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 546 VAL Chi-restraints excluded: chain A residue 630 THR Chi-restraints excluded: chain A residue 861 LEU Chi-restraints excluded: chain A residue 890 LEU Chi-restraints excluded: chain A residue 898 THR Chi-restraints excluded: chain A residue 945 THR Chi-restraints excluded: chain A residue 968 LEU Chi-restraints excluded: chain A residue 982 VAL Chi-restraints excluded: chain A residue 1052 VAL Chi-restraints excluded: chain A residue 1113 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 56 optimal weight: 6.9990 chunk 82 optimal weight: 1.9990 chunk 30 optimal weight: 0.9990 chunk 84 optimal weight: 0.9980 chunk 20 optimal weight: 0.9980 chunk 26 optimal weight: 0.0370 chunk 109 optimal weight: 0.8980 chunk 95 optimal weight: 2.9990 chunk 107 optimal weight: 5.9990 chunk 9 optimal weight: 0.9990 chunk 0 optimal weight: 5.9990 overall best weight: 0.7860 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 383 HIS A 966 HIS A 990 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3727 r_free = 0.3727 target = 0.144274 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.118861 restraints weight = 12296.037| |-----------------------------------------------------------------------------| r_work (start): 0.3400 rms_B_bonded: 1.89 r_work: 0.3291 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.3157 rms_B_bonded: 4.40 restraints_weight: 0.2500 r_work (final): 0.3157 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7855 moved from start: 0.2134 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 9285 Z= 0.114 Angle : 0.470 6.629 12521 Z= 0.248 Chirality : 0.038 0.136 1439 Planarity : 0.003 0.037 1562 Dihedral : 8.098 132.233 1363 Min Nonbonded Distance : 2.018 Molprobity Statistics. All-atom Clashscore : 5.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 2.75 % Allowed : 17.90 % Favored : 79.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.28 (0.25), residues: 1151 helix: 1.66 (0.19), residues: 768 sheet: 1.03 (0.65), residues: 70 loop : -1.25 (0.33), residues: 313 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 174 TYR 0.008 0.001 TYR A 928 PHE 0.017 0.001 PHE A 72 TRP 0.010 0.001 TRP A 315 HIS 0.002 0.001 HIS A 145 Details of bonding type rmsd covalent geometry : bond 0.00242 ( 9285) covalent geometry : angle 0.46953 (12521) hydrogen bonds : bond 0.04718 ( 573) hydrogen bonds : angle 3.74210 ( 1686) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2302 Ramachandran restraints generated. 1151 Oldfield, 0 Emsley, 1151 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2302 Ramachandran restraints generated. 1151 Oldfield, 0 Emsley, 1151 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 956 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 103 time to evaluate : 0.347 Fit side-chains REVERT: A 212 TRP cc_start: 0.7410 (t60) cc_final: 0.6490 (t-100) REVERT: A 227 LEU cc_start: 0.7463 (OUTLIER) cc_final: 0.7121 (mp) REVERT: A 405 LYS cc_start: 0.8483 (tmtt) cc_final: 0.8003 (tptt) REVERT: A 416 LYS cc_start: 0.8056 (mttt) cc_final: 0.7719 (ttpt) REVERT: A 428 ASN cc_start: 0.8106 (p0) cc_final: 0.7479 (p0) REVERT: A 497 MET cc_start: 0.7831 (tpp) cc_final: 0.7481 (tpp) REVERT: A 550 LYS cc_start: 0.8051 (mmtt) cc_final: 0.7744 (mmmt) REVERT: A 588 ARG cc_start: 0.6484 (mtp85) cc_final: 0.6003 (ttm110) REVERT: A 630 THR cc_start: 0.4459 (OUTLIER) cc_final: 0.4223 (p) REVERT: A 741 ARG cc_start: 0.6341 (ttm-80) cc_final: 0.5885 (mtt-85) REVERT: A 765 ILE cc_start: 0.8376 (OUTLIER) cc_final: 0.8164 (mp) REVERT: A 922 GLN cc_start: 0.8435 (tt0) cc_final: 0.7985 (tm-30) REVERT: A 968 LEU cc_start: 0.8424 (OUTLIER) cc_final: 0.8169 (tt) REVERT: A 1032 GLU cc_start: 0.5272 (pp20) cc_final: 0.4918 (pp20) REVERT: A 1052 VAL cc_start: 0.8623 (OUTLIER) cc_final: 0.8414 (m) REVERT: A 1113 LEU cc_start: 0.8314 (OUTLIER) cc_final: 0.7819 (pp) REVERT: A 1129 GLU cc_start: 0.8010 (tm-30) cc_final: 0.7747 (mt-10) outliers start: 26 outliers final: 10 residues processed: 123 average time/residue: 0.0990 time to fit residues: 17.2152 Evaluate side-chains 123 residues out of total 956 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 107 time to evaluate : 0.338 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 119 SER Chi-restraints excluded: chain A residue 125 VAL Chi-restraints excluded: chain A residue 227 LEU Chi-restraints excluded: chain A residue 496 THR Chi-restraints excluded: chain A residue 546 VAL Chi-restraints excluded: chain A residue 630 THR Chi-restraints excluded: chain A residue 765 ILE Chi-restraints excluded: chain A residue 890 LEU Chi-restraints excluded: chain A residue 898 THR Chi-restraints excluded: chain A residue 945 THR Chi-restraints excluded: chain A residue 968 LEU Chi-restraints excluded: chain A residue 982 VAL Chi-restraints excluded: chain A residue 1052 VAL Chi-restraints excluded: chain A residue 1113 LEU Chi-restraints excluded: chain A residue 1167 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 90 optimal weight: 7.9990 chunk 0 optimal weight: 6.9990 chunk 74 optimal weight: 0.9990 chunk 108 optimal weight: 3.9990 chunk 114 optimal weight: 8.9990 chunk 88 optimal weight: 0.8980 chunk 97 optimal weight: 5.9990 chunk 2 optimal weight: 7.9990 chunk 105 optimal weight: 4.9990 chunk 4 optimal weight: 10.0000 chunk 12 optimal weight: 0.9990 overall best weight: 2.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 383 HIS A 966 HIS ** A 990 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3659 r_free = 0.3659 target = 0.138837 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3326 r_free = 0.3326 target = 0.112945 restraints weight = 12473.082| |-----------------------------------------------------------------------------| r_work (start): 0.3326 rms_B_bonded: 1.92 r_work: 0.3214 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.3080 rms_B_bonded: 4.40 restraints_weight: 0.2500 r_work (final): 0.3080 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7931 moved from start: 0.2278 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 9285 Z= 0.207 Angle : 0.557 7.422 12521 Z= 0.291 Chirality : 0.042 0.148 1439 Planarity : 0.004 0.037 1562 Dihedral : 8.393 137.876 1363 Min Nonbonded Distance : 1.950 Molprobity Statistics. All-atom Clashscore : 6.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.13 % Favored : 96.87 % Rotamer: Outliers : 3.71 % Allowed : 17.06 % Favored : 79.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.01 (0.25), residues: 1151 helix: 1.44 (0.18), residues: 765 sheet: 0.96 (0.65), residues: 70 loop : -1.29 (0.33), residues: 316 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 142 TYR 0.014 0.002 TYR A 277 PHE 0.022 0.002 PHE A 72 TRP 0.008 0.001 TRP A 803 HIS 0.004 0.001 HIS A 145 Details of bonding type rmsd covalent geometry : bond 0.00502 ( 9285) covalent geometry : angle 0.55742 (12521) hydrogen bonds : bond 0.05709 ( 573) hydrogen bonds : angle 3.97634 ( 1686) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2302 Ramachandran restraints generated. 1151 Oldfield, 0 Emsley, 1151 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2302 Ramachandran restraints generated. 1151 Oldfield, 0 Emsley, 1151 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 956 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 103 time to evaluate : 0.353 Fit side-chains REVERT: A 212 TRP cc_start: 0.7496 (t60) cc_final: 0.6466 (t-100) REVERT: A 227 LEU cc_start: 0.7829 (OUTLIER) cc_final: 0.7240 (mp) REVERT: A 405 LYS cc_start: 0.8542 (tmtt) cc_final: 0.8039 (tptt) REVERT: A 416 LYS cc_start: 0.8129 (mttt) cc_final: 0.7803 (ttpt) REVERT: A 428 ASN cc_start: 0.8172 (p0) cc_final: 0.7936 (p0) REVERT: A 497 MET cc_start: 0.7843 (tpp) cc_final: 0.7474 (tpp) REVERT: A 588 ARG cc_start: 0.6434 (mtp85) cc_final: 0.5957 (ttm110) REVERT: A 741 ARG cc_start: 0.6420 (ttm-80) cc_final: 0.5955 (mtt-85) REVERT: A 750 GLN cc_start: 0.6584 (mm-40) cc_final: 0.6367 (mm-40) REVERT: A 765 ILE cc_start: 0.8465 (OUTLIER) cc_final: 0.8239 (mp) REVERT: A 861 LEU cc_start: 0.7567 (OUTLIER) cc_final: 0.7326 (tp) REVERT: A 922 GLN cc_start: 0.8478 (tt0) cc_final: 0.7946 (tm-30) REVERT: A 968 LEU cc_start: 0.8449 (OUTLIER) cc_final: 0.8074 (mp) REVERT: A 1032 GLU cc_start: 0.5464 (pp20) cc_final: 0.5099 (pp20) REVERT: A 1052 VAL cc_start: 0.8634 (OUTLIER) cc_final: 0.8345 (m) REVERT: A 1113 LEU cc_start: 0.8362 (OUTLIER) cc_final: 0.7733 (pp) outliers start: 35 outliers final: 21 residues processed: 131 average time/residue: 0.0996 time to fit residues: 18.3945 Evaluate side-chains 128 residues out of total 956 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 101 time to evaluate : 0.353 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 71 VAL Chi-restraints excluded: chain A residue 119 SER Chi-restraints excluded: chain A residue 125 VAL Chi-restraints excluded: chain A residue 144 ILE Chi-restraints excluded: chain A residue 176 THR Chi-restraints excluded: chain A residue 197 MET Chi-restraints excluded: chain A residue 227 LEU Chi-restraints excluded: chain A residue 338 VAL Chi-restraints excluded: chain A residue 461 ILE Chi-restraints excluded: chain A residue 496 THR Chi-restraints excluded: chain A residue 522 THR Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 546 VAL Chi-restraints excluded: chain A residue 765 ILE Chi-restraints excluded: chain A residue 848 ILE Chi-restraints excluded: chain A residue 849 ILE Chi-restraints excluded: chain A residue 861 LEU Chi-restraints excluded: chain A residue 890 LEU Chi-restraints excluded: chain A residue 898 THR Chi-restraints excluded: chain A residue 899 GLU Chi-restraints excluded: chain A residue 945 THR Chi-restraints excluded: chain A residue 968 LEU Chi-restraints excluded: chain A residue 982 VAL Chi-restraints excluded: chain A residue 988 VAL Chi-restraints excluded: chain A residue 1052 VAL Chi-restraints excluded: chain A residue 1113 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 23 optimal weight: 2.9990 chunk 19 optimal weight: 0.7980 chunk 6 optimal weight: 7.9990 chunk 7 optimal weight: 0.9990 chunk 86 optimal weight: 2.9990 chunk 104 optimal weight: 0.9980 chunk 106 optimal weight: 0.7980 chunk 89 optimal weight: 0.9980 chunk 2 optimal weight: 4.9990 chunk 61 optimal weight: 0.5980 chunk 69 optimal weight: 1.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 383 HIS A 990 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3705 r_free = 0.3705 target = 0.142521 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.116984 restraints weight = 12311.981| |-----------------------------------------------------------------------------| r_work (start): 0.3374 rms_B_bonded: 1.90 r_work: 0.3264 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.3130 rms_B_bonded: 4.41 restraints_weight: 0.2500 r_work (final): 0.3130 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7881 moved from start: 0.2370 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 9285 Z= 0.118 Angle : 0.485 8.196 12521 Z= 0.255 Chirality : 0.039 0.129 1439 Planarity : 0.003 0.037 1562 Dihedral : 8.195 133.270 1363 Min Nonbonded Distance : 2.016 Molprobity Statistics. All-atom Clashscore : 6.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.52 % Favored : 97.48 % Rotamer: Outliers : 2.54 % Allowed : 18.96 % Favored : 78.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.25 (0.25), residues: 1151 helix: 1.60 (0.19), residues: 770 sheet: 1.05 (0.65), residues: 70 loop : -1.18 (0.34), residues: 311 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 142 TYR 0.008 0.001 TYR A1087 PHE 0.019 0.001 PHE A 72 TRP 0.010 0.001 TRP A 315 HIS 0.003 0.001 HIS A 145 Details of bonding type rmsd covalent geometry : bond 0.00251 ( 9285) covalent geometry : angle 0.48450 (12521) hydrogen bonds : bond 0.04901 ( 573) hydrogen bonds : angle 3.79123 ( 1686) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2302 Ramachandran restraints generated. 1151 Oldfield, 0 Emsley, 1151 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2302 Ramachandran restraints generated. 1151 Oldfield, 0 Emsley, 1151 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 956 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 106 time to evaluate : 0.370 Fit side-chains REVERT: A 212 TRP cc_start: 0.7482 (t60) cc_final: 0.6489 (t-100) REVERT: A 227 LEU cc_start: 0.7695 (OUTLIER) cc_final: 0.7192 (mp) REVERT: A 405 LYS cc_start: 0.8509 (tmtt) cc_final: 0.8023 (tptt) REVERT: A 416 LYS cc_start: 0.8110 (mttt) cc_final: 0.7758 (ttpt) REVERT: A 428 ASN cc_start: 0.8135 (p0) cc_final: 0.7903 (p0) REVERT: A 497 MET cc_start: 0.7779 (tpp) cc_final: 0.7428 (tpp) REVERT: A 550 LYS cc_start: 0.8051 (mmtt) cc_final: 0.7750 (mmmt) REVERT: A 588 ARG cc_start: 0.6459 (mtp85) cc_final: 0.5916 (ttm110) REVERT: A 735 ILE cc_start: 0.8877 (mt) cc_final: 0.8630 (mt) REVERT: A 741 ARG cc_start: 0.6393 (ttm-80) cc_final: 0.5968 (mtt-85) REVERT: A 765 ILE cc_start: 0.8435 (OUTLIER) cc_final: 0.8218 (mp) REVERT: A 861 LEU cc_start: 0.7607 (OUTLIER) cc_final: 0.7373 (tp) REVERT: A 922 GLN cc_start: 0.8463 (tt0) cc_final: 0.8062 (tm-30) REVERT: A 968 LEU cc_start: 0.8459 (OUTLIER) cc_final: 0.8200 (tt) REVERT: A 1032 GLU cc_start: 0.5412 (pp20) cc_final: 0.5031 (pp20) REVERT: A 1052 VAL cc_start: 0.8646 (OUTLIER) cc_final: 0.8432 (m) REVERT: A 1113 LEU cc_start: 0.8321 (OUTLIER) cc_final: 0.7802 (pp) REVERT: A 1129 GLU cc_start: 0.8137 (tm-30) cc_final: 0.7677 (tt0) outliers start: 24 outliers final: 14 residues processed: 124 average time/residue: 0.0975 time to fit residues: 17.1090 Evaluate side-chains 125 residues out of total 956 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 105 time to evaluate : 0.306 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 39 MET Chi-restraints excluded: chain A residue 119 SER Chi-restraints excluded: chain A residue 125 VAL Chi-restraints excluded: chain A residue 176 THR Chi-restraints excluded: chain A residue 227 LEU Chi-restraints excluded: chain A residue 496 THR Chi-restraints excluded: chain A residue 522 THR Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 546 VAL Chi-restraints excluded: chain A residue 738 VAL Chi-restraints excluded: chain A residue 765 ILE Chi-restraints excluded: chain A residue 849 ILE Chi-restraints excluded: chain A residue 861 LEU Chi-restraints excluded: chain A residue 890 LEU Chi-restraints excluded: chain A residue 898 THR Chi-restraints excluded: chain A residue 968 LEU Chi-restraints excluded: chain A residue 982 VAL Chi-restraints excluded: chain A residue 1052 VAL Chi-restraints excluded: chain A residue 1113 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 47 optimal weight: 1.9990 chunk 62 optimal weight: 8.9990 chunk 46 optimal weight: 1.9990 chunk 39 optimal weight: 5.9990 chunk 24 optimal weight: 5.9990 chunk 104 optimal weight: 1.9990 chunk 103 optimal weight: 2.9990 chunk 9 optimal weight: 3.9990 chunk 86 optimal weight: 0.9980 chunk 43 optimal weight: 0.9980 chunk 1 optimal weight: 2.9990 overall best weight: 1.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 383 HIS ** A 990 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1182 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3675 r_free = 0.3675 target = 0.140209 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.114666 restraints weight = 12392.996| |-----------------------------------------------------------------------------| r_work (start): 0.3340 rms_B_bonded: 1.89 r_work: 0.3228 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.3095 rms_B_bonded: 4.37 restraints_weight: 0.2500 r_work (final): 0.3095 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7917 moved from start: 0.2490 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 9285 Z= 0.158 Angle : 0.520 8.564 12521 Z= 0.273 Chirality : 0.040 0.129 1439 Planarity : 0.003 0.037 1562 Dihedral : 8.314 135.709 1363 Min Nonbonded Distance : 1.985 Molprobity Statistics. All-atom Clashscore : 6.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 3.07 % Allowed : 18.22 % Favored : 78.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.13 (0.25), residues: 1151 helix: 1.49 (0.19), residues: 772 sheet: 1.00 (0.65), residues: 70 loop : -1.18 (0.34), residues: 309 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 142 TYR 0.010 0.001 TYR A 277 PHE 0.022 0.002 PHE A 72 TRP 0.009 0.001 TRP A 315 HIS 0.003 0.001 HIS A 145 Details of bonding type rmsd covalent geometry : bond 0.00370 ( 9285) covalent geometry : angle 0.52030 (12521) hydrogen bonds : bond 0.05354 ( 573) hydrogen bonds : angle 3.88335 ( 1686) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2302 Ramachandran restraints generated. 1151 Oldfield, 0 Emsley, 1151 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2302 Ramachandran restraints generated. 1151 Oldfield, 0 Emsley, 1151 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 956 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 105 time to evaluate : 0.351 Fit side-chains REVERT: A 212 TRP cc_start: 0.7556 (t60) cc_final: 0.6477 (t-100) REVERT: A 227 LEU cc_start: 0.7800 (OUTLIER) cc_final: 0.7232 (mp) REVERT: A 405 LYS cc_start: 0.8534 (tmtt) cc_final: 0.8031 (tptt) REVERT: A 416 LYS cc_start: 0.8162 (mttt) cc_final: 0.7836 (ttpt) REVERT: A 497 MET cc_start: 0.7806 (tpp) cc_final: 0.7453 (tpp) REVERT: A 588 ARG cc_start: 0.6421 (mtp85) cc_final: 0.5995 (ttp-170) REVERT: A 735 ILE cc_start: 0.8893 (mt) cc_final: 0.8648 (mt) REVERT: A 741 ARG cc_start: 0.6417 (ttm-80) cc_final: 0.5988 (mtt-85) REVERT: A 765 ILE cc_start: 0.8455 (OUTLIER) cc_final: 0.8221 (mp) REVERT: A 861 LEU cc_start: 0.7582 (OUTLIER) cc_final: 0.7337 (tp) REVERT: A 885 LYS cc_start: 0.7342 (ttpt) cc_final: 0.6898 (mmtm) REVERT: A 922 GLN cc_start: 0.8519 (tt0) cc_final: 0.7975 (tm-30) REVERT: A 968 LEU cc_start: 0.8437 (OUTLIER) cc_final: 0.8163 (tt) REVERT: A 1052 VAL cc_start: 0.8644 (OUTLIER) cc_final: 0.8370 (m) REVERT: A 1113 LEU cc_start: 0.8317 (OUTLIER) cc_final: 0.7716 (pp) REVERT: A 1129 GLU cc_start: 0.8181 (tm-30) cc_final: 0.7669 (tt0) outliers start: 29 outliers final: 19 residues processed: 127 average time/residue: 0.1034 time to fit residues: 18.4220 Evaluate side-chains 127 residues out of total 956 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 102 time to evaluate : 0.344 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 39 MET Chi-restraints excluded: chain A residue 71 VAL Chi-restraints excluded: chain A residue 119 SER Chi-restraints excluded: chain A residue 125 VAL Chi-restraints excluded: chain A residue 144 ILE Chi-restraints excluded: chain A residue 176 THR Chi-restraints excluded: chain A residue 227 LEU Chi-restraints excluded: chain A residue 338 VAL Chi-restraints excluded: chain A residue 496 THR Chi-restraints excluded: chain A residue 522 THR Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 546 VAL Chi-restraints excluded: chain A residue 738 VAL Chi-restraints excluded: chain A residue 765 ILE Chi-restraints excluded: chain A residue 849 ILE Chi-restraints excluded: chain A residue 861 LEU Chi-restraints excluded: chain A residue 890 LEU Chi-restraints excluded: chain A residue 898 THR Chi-restraints excluded: chain A residue 899 GLU Chi-restraints excluded: chain A residue 945 THR Chi-restraints excluded: chain A residue 968 LEU Chi-restraints excluded: chain A residue 982 VAL Chi-restraints excluded: chain A residue 1052 VAL Chi-restraints excluded: chain A residue 1113 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 0 optimal weight: 6.9990 chunk 31 optimal weight: 3.9990 chunk 4 optimal weight: 9.9990 chunk 59 optimal weight: 0.9980 chunk 24 optimal weight: 4.9990 chunk 80 optimal weight: 2.9990 chunk 49 optimal weight: 2.9990 chunk 86 optimal weight: 0.9980 chunk 78 optimal weight: 0.0000 chunk 111 optimal weight: 0.9990 chunk 6 optimal weight: 7.9990 overall best weight: 1.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 383 HIS A 824 GLN ** A 990 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3691 r_free = 0.3691 target = 0.141503 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.115962 restraints weight = 12415.940| |-----------------------------------------------------------------------------| r_work (start): 0.3357 rms_B_bonded: 1.90 r_work: 0.3246 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.3110 rms_B_bonded: 4.43 restraints_weight: 0.2500 r_work (final): 0.3110 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7898 moved from start: 0.2562 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 9285 Z= 0.132 Angle : 0.496 8.979 12521 Z= 0.260 Chirality : 0.039 0.130 1439 Planarity : 0.003 0.038 1562 Dihedral : 8.245 133.761 1363 Min Nonbonded Distance : 2.007 Molprobity Statistics. All-atom Clashscore : 6.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.52 % Favored : 97.48 % Rotamer: Outliers : 2.75 % Allowed : 18.54 % Favored : 78.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.21 (0.25), residues: 1151 helix: 1.56 (0.18), residues: 778 sheet: 0.70 (0.61), residues: 78 loop : -1.19 (0.35), residues: 295 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 142 TYR 0.009 0.001 TYR A1087 PHE 0.020 0.001 PHE A 72 TRP 0.006 0.001 TRP A 315 HIS 0.002 0.001 HIS A 145 Details of bonding type rmsd covalent geometry : bond 0.00299 ( 9285) covalent geometry : angle 0.49586 (12521) hydrogen bonds : bond 0.05028 ( 573) hydrogen bonds : angle 3.80561 ( 1686) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2302 Ramachandran restraints generated. 1151 Oldfield, 0 Emsley, 1151 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2302 Ramachandran restraints generated. 1151 Oldfield, 0 Emsley, 1151 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 956 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 106 time to evaluate : 0.419 Fit side-chains REVERT: A 212 TRP cc_start: 0.7543 (t60) cc_final: 0.6449 (t-100) REVERT: A 227 LEU cc_start: 0.7733 (OUTLIER) cc_final: 0.7222 (mp) REVERT: A 405 LYS cc_start: 0.8512 (tmtt) cc_final: 0.8015 (tptt) REVERT: A 416 LYS cc_start: 0.8171 (mttt) cc_final: 0.7843 (ttpt) REVERT: A 497 MET cc_start: 0.7794 (tpp) cc_final: 0.7436 (tpp) REVERT: A 550 LYS cc_start: 0.8116 (mmtt) cc_final: 0.7839 (mmmt) REVERT: A 588 ARG cc_start: 0.6405 (mtp85) cc_final: 0.5974 (ttp-170) REVERT: A 735 ILE cc_start: 0.8867 (mt) cc_final: 0.8610 (mt) REVERT: A 741 ARG cc_start: 0.6333 (ttm-80) cc_final: 0.6009 (mtt-85) REVERT: A 765 ILE cc_start: 0.8452 (OUTLIER) cc_final: 0.8220 (mp) REVERT: A 861 LEU cc_start: 0.7616 (OUTLIER) cc_final: 0.7395 (tp) REVERT: A 885 LYS cc_start: 0.7397 (ttpt) cc_final: 0.6999 (mmtm) REVERT: A 922 GLN cc_start: 0.8526 (tt0) cc_final: 0.7977 (tm-30) REVERT: A 968 LEU cc_start: 0.8431 (OUTLIER) cc_final: 0.8166 (tt) REVERT: A 1032 GLU cc_start: 0.5367 (pp20) cc_final: 0.4891 (pp20) REVERT: A 1052 VAL cc_start: 0.8676 (OUTLIER) cc_final: 0.8411 (m) REVERT: A 1113 LEU cc_start: 0.8310 (OUTLIER) cc_final: 0.7766 (pp) REVERT: A 1129 GLU cc_start: 0.8126 (tm-30) cc_final: 0.7632 (tt0) outliers start: 26 outliers final: 19 residues processed: 126 average time/residue: 0.1060 time to fit residues: 18.6407 Evaluate side-chains 129 residues out of total 956 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 104 time to evaluate : 0.339 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 39 MET Chi-restraints excluded: chain A residue 71 VAL Chi-restraints excluded: chain A residue 119 SER Chi-restraints excluded: chain A residue 125 VAL Chi-restraints excluded: chain A residue 144 ILE Chi-restraints excluded: chain A residue 176 THR Chi-restraints excluded: chain A residue 227 LEU Chi-restraints excluded: chain A residue 338 VAL Chi-restraints excluded: chain A residue 496 THR Chi-restraints excluded: chain A residue 522 THR Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 546 VAL Chi-restraints excluded: chain A residue 738 VAL Chi-restraints excluded: chain A residue 765 ILE Chi-restraints excluded: chain A residue 849 ILE Chi-restraints excluded: chain A residue 861 LEU Chi-restraints excluded: chain A residue 890 LEU Chi-restraints excluded: chain A residue 898 THR Chi-restraints excluded: chain A residue 899 GLU Chi-restraints excluded: chain A residue 945 THR Chi-restraints excluded: chain A residue 968 LEU Chi-restraints excluded: chain A residue 982 VAL Chi-restraints excluded: chain A residue 1052 VAL Chi-restraints excluded: chain A residue 1113 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 95 optimal weight: 0.5980 chunk 27 optimal weight: 6.9990 chunk 89 optimal weight: 0.7980 chunk 56 optimal weight: 4.9990 chunk 54 optimal weight: 0.9980 chunk 114 optimal weight: 6.9990 chunk 29 optimal weight: 0.1980 chunk 30 optimal weight: 2.9990 chunk 59 optimal weight: 0.8980 chunk 61 optimal weight: 0.7980 chunk 52 optimal weight: 6.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 383 HIS A 990 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3722 r_free = 0.3722 target = 0.144112 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.118857 restraints weight = 12202.073| |-----------------------------------------------------------------------------| r_work (start): 0.3396 rms_B_bonded: 1.88 r_work: 0.3287 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.3151 rms_B_bonded: 4.43 restraints_weight: 0.2500 r_work (final): 0.3151 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7855 moved from start: 0.2650 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 9285 Z= 0.110 Angle : 0.468 8.064 12521 Z= 0.246 Chirality : 0.038 0.130 1439 Planarity : 0.003 0.038 1562 Dihedral : 8.041 130.258 1363 Min Nonbonded Distance : 2.029 Molprobity Statistics. All-atom Clashscore : 6.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 2.54 % Allowed : 19.28 % Favored : 78.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.39 (0.25), residues: 1151 helix: 1.69 (0.19), residues: 778 sheet: 0.81 (0.61), residues: 78 loop : -1.13 (0.35), residues: 295 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A1110 TYR 0.008 0.001 TYR A 928 PHE 0.021 0.001 PHE A 767 TRP 0.007 0.001 TRP A 708 HIS 0.002 0.000 HIS A 612 Details of bonding type rmsd covalent geometry : bond 0.00230 ( 9285) covalent geometry : angle 0.46816 (12521) hydrogen bonds : bond 0.04528 ( 573) hydrogen bonds : angle 3.66961 ( 1686) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2425.93 seconds wall clock time: 42 minutes 21.54 seconds (2541.54 seconds total)