Starting phenix.real_space_refine on Mon Jun 16 18:00:37 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8swn_40821/06_2025/8swn_40821_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/8swn_40821/06_2025/8swn_40821.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8swn_40821/06_2025/8swn_40821.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8swn_40821/06_2025/8swn_40821.map" model { file = "/net/cci-nas-00/data/ceres_data/8swn_40821/06_2025/8swn_40821_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8swn_40821/06_2025/8swn_40821_trim.cif" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.003 sd= 0.075 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: 7 Type Number sf(0) Gaussians P 7 5.49 5 Mg 2 5.21 5 S 36 5.16 5 C 5934 2.51 5 N 1529 2.21 5 O 1645 1.98 5 H 9269 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 58 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 18422 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 18308 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1135, 18308 Classifications: {'peptide': 1135} Link IDs: {'PCIS': 1, 'PTRANS': 33, 'TRANS': 1100} Chain breaks: 4 Chain: "A" Number of atoms: 114 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 114 Unusual residues: {' MG': 2, 'ATP': 2, 'PTY': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Time building chain proxies: 9.39, per 1000 atoms: 0.51 Number of scatterers: 18422 At special positions: 0 Unit cell: (72.558, 90.906, 147.618, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) S 36 16.00 P 7 15.00 Mg 2 11.99 O 1645 8.00 N 1529 7.00 C 5934 6.00 H 9269 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 5.09 Conformation dependent library (CDL) restraints added in 1.3 seconds 2250 Ramachandran restraints generated. 1125 Oldfield, 0 Emsley, 1125 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2144 Finding SS restraints... Secondary structure from input PDB file: 49 helices and 5 sheets defined 72.3% alpha, 8.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.70 Creating SS restraints... Processing helix chain 'A' and resid 48 through 52 Processing helix chain 'A' and resid 57 through 75 removed outlier: 3.596A pdb=" N GLU A 72 " --> pdb=" O VAL A 68 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N LYS A 73 " --> pdb=" O LEU A 69 " (cutoff:3.500A) Processing helix chain 'A' and resid 79 through 93 removed outlier: 5.817A pdb=" N LYS A 90 " --> pdb=" O LYS A 86 " (cutoff:3.500A) removed outlier: 5.910A pdb=" N SER A 91 " --> pdb=" O CYS A 87 " (cutoff:3.500A) Processing helix chain 'A' and resid 95 through 121 removed outlier: 3.643A pdb=" N THR A 99 " --> pdb=" O LEU A 95 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N VAL A 107 " --> pdb=" O GLU A 103 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N VAL A 108 " --> pdb=" O SER A 104 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N GLN A 109 " --> pdb=" O THR A 105 " (cutoff:3.500A) Proline residue: A 110 - end of helix removed outlier: 3.526A pdb=" N LYS A 115 " --> pdb=" O ILE A 111 " (cutoff:3.500A) Processing helix chain 'A' and resid 127 through 181 removed outlier: 3.503A pdb=" N HIS A 153 " --> pdb=" O ALA A 149 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N HIS A 158 " --> pdb=" O LEU A 154 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N GLN A 160 " --> pdb=" O PHE A 156 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N ARG A 180 " --> pdb=" O ARG A 176 " (cutoff:3.500A) Processing helix chain 'A' and resid 184 through 189 Processing helix chain 'A' and resid 190 through 200 Processing helix chain 'A' and resid 201 through 203 No H-bonds generated for 'chain 'A' and resid 201 through 203' Processing helix chain 'A' and resid 204 through 212 removed outlier: 4.254A pdb=" N THR A 209 " --> pdb=" O PHE A 205 " (cutoff:3.500A) removed outlier: 4.729A pdb=" N ILE A 210 " --> pdb=" O ASP A 206 " (cutoff:3.500A) removed outlier: 4.141A pdb=" N PHE A 211 " --> pdb=" O GLN A 207 " (cutoff:3.500A) Processing helix chain 'A' and resid 213 through 234 Proline residue: A 219 - end of helix removed outlier: 3.774A pdb=" N MET A 231 " --> pdb=" O ALA A 227 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N GLU A 232 " --> pdb=" O LEU A 228 " (cutoff:3.500A) Processing helix chain 'A' and resid 237 through 254 removed outlier: 3.910A pdb=" N VAL A 243 " --> pdb=" O ALA A 239 " (cutoff:3.500A) removed outlier: 4.094A pdb=" N ILE A 246 " --> pdb=" O ALA A 242 " (cutoff:3.500A) Proline residue: A 249 - end of helix Processing helix chain 'A' and resid 254 through 290 removed outlier: 3.538A pdb=" N PHE A 258 " --> pdb=" O ILE A 254 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N PHE A 268 " --> pdb=" O LYS A 264 " (cutoff:3.500A) removed outlier: 5.928A pdb=" N ARG A 284 " --> pdb=" O ILE A 280 " (cutoff:3.500A) removed outlier: 6.401A pdb=" N ILE A 285 " --> pdb=" O THR A 281 " (cutoff:3.500A) Processing helix chain 'A' and resid 291 through 342 removed outlier: 3.561A pdb=" N PHE A 295 " --> pdb=" O TRP A 291 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N LYS A 309 " --> pdb=" O LYS A 305 " (cutoff:3.500A) removed outlier: 5.305A pdb=" N SER A 328 " --> pdb=" O PHE A 324 " (cutoff:3.500A) removed outlier: 4.773A pdb=" N LYS A 329 " --> pdb=" O PHE A 325 " (cutoff:3.500A) Processing helix chain 'A' and resid 347 through 367 removed outlier: 4.820A pdb=" N LEU A 363 " --> pdb=" O GLY A 359 " (cutoff:3.500A) removed outlier: 5.695A pdb=" N THR A 364 " --> pdb=" O ALA A 360 " (cutoff:3.500A) Processing helix chain 'A' and resid 367 through 391 removed outlier: 3.998A pdb=" N VAL A 381 " --> pdb=" O SER A 377 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N SER A 382 " --> pdb=" O GLU A 378 " (cutoff:3.500A) Processing helix chain 'A' and resid 450 through 459 Processing helix chain 'A' and resid 489 through 495 Processing helix chain 'A' and resid 500 through 511 Processing helix chain 'A' and resid 513 through 520 Processing helix chain 'A' and resid 522 through 525 Processing helix chain 'A' and resid 536 through 551 removed outlier: 3.750A pdb=" N ALA A 548 " --> pdb=" O ASN A 544 " (cutoff:3.500A) Processing helix chain 'A' and resid 566 through 577 Processing helix chain 'A' and resid 593 through 600 removed outlier: 4.825A pdb=" N LYS A 598 " --> pdb=" O GLN A 595 " (cutoff:3.500A) Processing helix chain 'A' and resid 697 through 707 removed outlier: 3.755A pdb=" N TYR A 701 " --> pdb=" O GLY A 697 " (cutoff:3.500A) Processing helix chain 'A' and resid 710 through 745 removed outlier: 3.653A pdb=" N ASP A 732 " --> pdb=" O TYR A 728 " (cutoff:3.500A) Processing helix chain 'A' and resid 760 through 807 removed outlier: 3.747A pdb=" N PHE A 787 " --> pdb=" O SER A 783 " (cutoff:3.500A) Processing helix chain 'A' and resid 809 through 816 removed outlier: 3.870A pdb=" N PHE A 813 " --> pdb=" O PRO A 809 " (cutoff:3.500A) Processing helix chain 'A' and resid 817 through 834 removed outlier: 3.904A pdb=" N ARG A 824 " --> pdb=" O ARG A 820 " (cutoff:3.500A) removed outlier: 4.988A pdb=" N ILE A 829 " --> pdb=" O PHE A 825 " (cutoff:3.500A) Processing helix chain 'A' and resid 834 through 861 removed outlier: 4.372A pdb=" N LEU A 838 " --> pdb=" O ASP A 834 " (cutoff:3.500A) Processing helix chain 'A' and resid 864 through 882 removed outlier: 3.502A pdb=" N VAL A 869 " --> pdb=" O ALA A 865 " (cutoff:3.500A) Proline residue: A 870 - end of helix Processing helix chain 'A' and resid 900 through 910 Processing helix chain 'A' and resid 910 through 917 Processing helix chain 'A' and resid 919 through 970 removed outlier: 3.755A pdb=" N ARG A 951 " --> pdb=" O TRP A 947 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N ALA A 954 " --> pdb=" O VAL A 950 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N LEU A 968 " --> pdb=" O ALA A 964 " (cutoff:3.500A) Processing helix chain 'A' and resid 971 through 974 Processing helix chain 'A' and resid 975 through 1018 removed outlier: 4.370A pdb=" N MET A 990 " --> pdb=" O ALA A 986 " (cutoff:3.500A) removed outlier: 5.130A pdb=" N GLY A 991 " --> pdb=" O LEU A 987 " (cutoff:3.500A) removed outlier: 4.116A pdb=" N ILE A1008 " --> pdb=" O GLU A1004 " (cutoff:3.500A) removed outlier: 4.374A pdb=" N SER A1009 " --> pdb=" O ASN A1005 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N VAL A1010 " --> pdb=" O MET A1006 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N TYR A1016 " --> pdb=" O ARG A1012 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N ASP A1018 " --> pdb=" O ILE A1014 " (cutoff:3.500A) Processing helix chain 'A' and resid 1080 through 1089 removed outlier: 3.845A pdb=" N ILE A1085 " --> pdb=" O LYS A1081 " (cutoff:3.500A) Processing helix chain 'A' and resid 1106 through 1108 No H-bonds generated for 'chain 'A' and resid 1106 through 1108' Processing helix chain 'A' and resid 1109 through 1115 Processing helix chain 'A' and resid 1130 through 1136 Processing helix chain 'A' and resid 1142 through 1153 Processing helix chain 'A' and resid 1155 through 1161 Processing helix chain 'A' and resid 1164 through 1168 Processing helix chain 'A' and resid 1171 through 1175 Processing helix chain 'A' and resid 1178 through 1193 Processing helix chain 'A' and resid 1208 through 1223 removed outlier: 3.929A pdb=" N LEU A1214 " --> pdb=" O ARG A1210 " (cutoff:3.500A) Processing helix chain 'A' and resid 1234 through 1238 Processing helix chain 'A' and resid 1257 through 1264 removed outlier: 3.508A pdb=" N ASN A1264 " --> pdb=" O VAL A1260 " (cutoff:3.500A) Processing helix chain 'A' and resid 1267 through 1276 removed outlier: 3.563A pdb=" N LYS A1271 " --> pdb=" O SER A1267 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N LEU A1276 " --> pdb=" O MET A1272 " (cutoff:3.500A) Processing helix chain 'A' and resid 1277 through 1297 Processing sheet with id=AA1, first strand: chain 'A' and resid 428 through 435 removed outlier: 6.698A pdb=" N GLN A 429 " --> pdb=" O THR A 416 " (cutoff:3.500A) removed outlier: 6.271A pdb=" N THR A 416 " --> pdb=" O GLN A 429 " (cutoff:3.500A) removed outlier: 5.224A pdb=" N LEU A 431 " --> pdb=" O ASP A 414 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N ILE A 409 " --> pdb=" O HIS A 472 " (cutoff:3.500A) removed outlier: 4.284A pdb=" N PHE A 415 " --> pdb=" O GLN A 466 " (cutoff:3.500A) removed outlier: 6.715A pdb=" N GLN A 466 " --> pdb=" O PHE A 415 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 475 through 478 removed outlier: 6.473A pdb=" N ALA A 476 " --> pdb=" O LEU A 557 " (cutoff:3.500A) removed outlier: 7.400A pdb=" N ASP A 559 " --> pdb=" O ALA A 476 " (cutoff:3.500A) removed outlier: 6.860A pdb=" N VAL A 478 " --> pdb=" O ASP A 559 " (cutoff:3.500A) removed outlier: 6.548A pdb=" N LEU A 441 " --> pdb=" O LEU A 589 " (cutoff:3.500A) removed outlier: 6.416A pdb=" N LEU A 440 " --> pdb=" O GLN A 602 " (cutoff:3.500A) removed outlier: 7.881A pdb=" N LEU A 604 " --> pdb=" O LEU A 440 " (cutoff:3.500A) removed outlier: 6.440A pdb=" N ALA A 442 " --> pdb=" O LEU A 604 " (cutoff:3.500A) removed outlier: 7.502A pdb=" N LEU A 606 " --> pdb=" O ALA A 442 " (cutoff:3.500A) removed outlier: 6.488A pdb=" N VAL A 444 " --> pdb=" O LEU A 606 " (cutoff:3.500A) removed outlier: 6.634A pdb=" N ILE A 603 " --> pdb=" O LYS A 614 " (cutoff:3.500A) removed outlier: 4.471A pdb=" N LYS A 614 " --> pdb=" O ILE A 603 " (cutoff:3.500A) removed outlier: 6.973A pdb=" N ILE A 605 " --> pdb=" O VAL A 612 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 487 through 488 Processing sheet with id=AA4, first strand: chain 'A' and resid 1058 through 1065 removed outlier: 6.774A pdb=" N LYS A1059 " --> pdb=" O ASN A1047 " (cutoff:3.500A) removed outlier: 6.414A pdb=" N ASN A1047 " --> pdb=" O LYS A1059 " (cutoff:3.500A) removed outlier: 5.174A pdb=" N LEU A1061 " --> pdb=" O ASN A1045 " (cutoff:3.500A) removed outlier: 5.574A pdb=" N PHE A1043 " --> pdb=" O TRP A1099 " (cutoff:3.500A) removed outlier: 7.154A pdb=" N TRP A1099 " --> pdb=" O PHE A1043 " (cutoff:3.500A) removed outlier: 5.128A pdb=" N ASN A1045 " --> pdb=" O LYS A1097 " (cutoff:3.500A) removed outlier: 5.003A pdb=" N LYS A1097 " --> pdb=" O ASN A1045 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 1117 through 1120 removed outlier: 6.605A pdb=" N LYS A1070 " --> pdb=" O LYS A1243 " (cutoff:3.500A) removed outlier: 7.917A pdb=" N MET A1245 " --> pdb=" O LYS A1070 " (cutoff:3.500A) removed outlier: 6.446A pdb=" N GLY A1072 " --> pdb=" O MET A1245 " (cutoff:3.500A) removed outlier: 7.704A pdb=" N LEU A1247 " --> pdb=" O GLY A1072 " (cutoff:3.500A) removed outlier: 6.702A pdb=" N VAL A1074 " --> pdb=" O LEU A1247 " (cutoff:3.500A) removed outlier: 6.019A pdb=" N ILE A1244 " --> pdb=" O TYR A1255 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N TYR A1255 " --> pdb=" O ILE A1244 " (cutoff:3.500A) removed outlier: 6.807A pdb=" N VAL A1246 " --> pdb=" O LYS A1253 " (cutoff:3.500A) 607 hydrogen bonds defined for protein. 1761 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: 7.98 Time building geometry restraints manager: 6.12 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 8227 1.03 - 1.23: 1128 1.23 - 1.43: 4018 1.43 - 1.62: 5182 1.62 - 1.82: 59 Bond restraints: 18614 Sorted by residual: bond pdb=" ND1 HIS A 158 " pdb=" CE1 HIS A 158 " ideal model delta sigma weight residual 1.321 1.235 0.086 1.00e-02 1.00e+04 7.42e+01 bond pdb=" N TYR A 358 " pdb=" H TYR A 358 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.73e+01 bond pdb=" CE1 HIS A 158 " pdb=" HE1 HIS A 158 " ideal model delta sigma weight residual 0.930 1.081 -0.151 2.00e-02 2.50e+03 5.72e+01 bond pdb=" N ILE A 233 " pdb=" H ILE A 233 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.71e+01 bond pdb=" CE1 PHE A 211 " pdb=" HE1 PHE A 211 " ideal model delta sigma weight residual 0.930 1.081 -0.151 2.00e-02 2.50e+03 5.71e+01 ... (remaining 18609 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.78: 32674 4.78 - 9.56: 969 9.56 - 14.34: 21 14.34 - 19.13: 0 19.13 - 23.91: 4 Bond angle restraints: 33668 Sorted by residual: angle pdb=" PB ATP A1404 " pdb=" O3B ATP A1404 " pdb=" PG ATP A1404 " ideal model delta sigma weight residual 139.87 115.96 23.91 1.00e+00 1.00e+00 5.72e+02 angle pdb=" PB ATP A1405 " pdb=" O3B ATP A1405 " pdb=" PG ATP A1405 " ideal model delta sigma weight residual 139.87 116.17 23.70 1.00e+00 1.00e+00 5.62e+02 angle pdb=" PA ATP A1404 " pdb=" O3A ATP A1404 " pdb=" PB ATP A1404 " ideal model delta sigma weight residual 136.83 113.83 23.00 1.00e+00 1.00e+00 5.29e+02 angle pdb=" PA ATP A1405 " pdb=" O3A ATP A1405 " pdb=" PB ATP A1405 " ideal model delta sigma weight residual 136.83 115.96 20.87 1.00e+00 1.00e+00 4.36e+02 angle pdb=" C5' ATP A1404 " pdb=" O5' ATP A1404 " pdb=" PA ATP A1404 " ideal model delta sigma weight residual 121.27 109.68 11.59 1.00e+00 1.00e+00 1.34e+02 ... (remaining 33663 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.63: 8142 21.63 - 43.25: 311 43.25 - 64.88: 223 64.88 - 86.50: 46 86.50 - 108.13: 2 Dihedral angle restraints: 8724 sinusoidal: 4769 harmonic: 3955 Sorted by residual: dihedral pdb=" CA ARG A 76 " pdb=" C ARG A 76 " pdb=" N GLU A 77 " pdb=" CA GLU A 77 " ideal model delta harmonic sigma weight residual 180.00 149.08 30.92 0 5.00e+00 4.00e-02 3.82e+01 dihedral pdb=" C PHE A 156 " pdb=" N PHE A 156 " pdb=" CA PHE A 156 " pdb=" CB PHE A 156 " ideal model delta harmonic sigma weight residual -122.60 -137.50 14.90 0 2.50e+00 1.60e-01 3.55e+01 dihedral pdb=" CA HIS A 55 " pdb=" C HIS A 55 " pdb=" N LEU A 56 " pdb=" CA LEU A 56 " ideal model delta harmonic sigma weight residual 180.00 151.39 28.61 0 5.00e+00 4.00e-02 3.27e+01 ... (remaining 8721 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.149: 1280 0.149 - 0.298: 17 0.298 - 0.447: 11 0.447 - 0.596: 92 0.596 - 0.745: 64 Chirality restraints: 1464 Sorted by residual: chirality pdb=" CA PHE A 156 " pdb=" N PHE A 156 " pdb=" C PHE A 156 " pdb=" CB PHE A 156 " both_signs ideal model delta sigma weight residual False 2.51 1.77 0.74 2.00e-01 2.50e+01 1.39e+01 chirality pdb=" CB VAL A 208 " pdb=" CA VAL A 208 " pdb=" CG1 VAL A 208 " pdb=" CG2 VAL A 208 " both_signs ideal model delta sigma weight residual False -2.63 -1.91 -0.72 2.00e-01 2.50e+01 1.29e+01 chirality pdb=" CB ILE A 84 " pdb=" CA ILE A 84 " pdb=" CG1 ILE A 84 " pdb=" CG2 ILE A 84 " both_signs ideal model delta sigma weight residual False 2.64 1.93 0.71 2.00e-01 2.50e+01 1.27e+01 ... (remaining 1461 not shown) Planarity restraints: 2656 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP A 216 " -0.020 2.00e-02 2.50e+03 6.63e-02 1.76e+02 pdb=" CG TRP A 216 " 0.060 2.00e-02 2.50e+03 pdb=" CD1 TRP A 216 " 0.061 2.00e-02 2.50e+03 pdb=" CD2 TRP A 216 " 0.052 2.00e-02 2.50e+03 pdb=" NE1 TRP A 216 " 0.023 2.00e-02 2.50e+03 pdb=" CE2 TRP A 216 " 0.063 2.00e-02 2.50e+03 pdb=" CE3 TRP A 216 " -0.011 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 216 " 0.046 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 216 " -0.010 2.00e-02 2.50e+03 pdb=" CH2 TRP A 216 " 0.027 2.00e-02 2.50e+03 pdb=" HD1 TRP A 216 " 0.010 2.00e-02 2.50e+03 pdb=" HE1 TRP A 216 " -0.210 2.00e-02 2.50e+03 pdb=" HE3 TRP A 216 " -0.071 2.00e-02 2.50e+03 pdb=" HZ2 TRP A 216 " 0.018 2.00e-02 2.50e+03 pdb=" HZ3 TRP A 216 " -0.051 2.00e-02 2.50e+03 pdb=" HH2 TRP A 216 " 0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 92 " 0.159 2.00e-02 2.50e+03 6.66e-02 1.33e+02 pdb=" CG TYR A 92 " -0.027 2.00e-02 2.50e+03 pdb=" CD1 TYR A 92 " -0.055 2.00e-02 2.50e+03 pdb=" CD2 TYR A 92 " -0.046 2.00e-02 2.50e+03 pdb=" CE1 TYR A 92 " -0.041 2.00e-02 2.50e+03 pdb=" CE2 TYR A 92 " -0.036 2.00e-02 2.50e+03 pdb=" CZ TYR A 92 " -0.003 2.00e-02 2.50e+03 pdb=" OH TYR A 92 " 0.130 2.00e-02 2.50e+03 pdb=" HD1 TYR A 92 " -0.031 2.00e-02 2.50e+03 pdb=" HD2 TYR A 92 " -0.031 2.00e-02 2.50e+03 pdb=" HE1 TYR A 92 " -0.005 2.00e-02 2.50e+03 pdb=" HE2 TYR A 92 " -0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A1295 " -0.112 9.50e-02 1.11e+02 5.80e-02 4.57e+01 pdb=" NE ARG A1295 " 0.023 2.00e-02 2.50e+03 pdb=" CZ ARG A1295 " -0.030 2.00e-02 2.50e+03 pdb=" NH1 ARG A1295 " -0.065 2.00e-02 2.50e+03 pdb=" NH2 ARG A1295 " 0.055 2.00e-02 2.50e+03 pdb="HH11 ARG A1295 " -0.000 2.00e-02 2.50e+03 pdb="HH12 ARG A1295 " 0.075 2.00e-02 2.50e+03 pdb="HH21 ARG A1295 " 0.005 2.00e-02 2.50e+03 pdb="HH22 ARG A1295 " -0.058 2.00e-02 2.50e+03 ... (remaining 2653 not shown) Histogram of nonbonded interaction distances: 1.53 - 2.15: 607 2.15 - 2.76: 34262 2.76 - 3.37: 52584 3.37 - 3.99: 66979 3.99 - 4.60: 106283 Nonbonded interactions: 260715 Sorted by model distance: nonbonded pdb=" OD2 ASP A 270 " pdb="HH22 ARG A 385 " model vdw 1.534 2.450 nonbonded pdb="HD21 ASN A 196 " pdb=" OD1 ASP A 270 " model vdw 1.597 2.450 nonbonded pdb=" OE1 GLU A 121 " pdb=" HG SER A 349 " model vdw 1.611 2.450 nonbonded pdb=" HG SER A 259 " pdb=" O13 PTY A1403 " model vdw 1.623 2.450 nonbonded pdb=" O ARG A 362 " pdb=" HG1 THR A 366 " model vdw 1.637 2.450 ... (remaining 260710 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=0.00 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: 1.860 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: 0.320 Extract box with map and model: 0.800 Check model and map are aligned: 0.140 Set scattering table: 0.180 Process input model: 43.700 Find NCS groups from input model: 0.150 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.930 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 50.140 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8370 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 : 0.020 0.147 9345 Z= 1.015 Angle : 1.665 23.907 12669 Z= 1.142 Chirality : 0.202 0.745 1464 Planarity : 0.009 0.100 1559 Dihedral : 13.416 108.130 3463 Min Nonbonded Distance : 1.789 Molprobity Statistics. All-atom Clashscore : 0.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.24 % Favored : 98.76 % Rotamer: Outliers : 0.00 % Allowed : 1.53 % Favored : 98.47 % Cbeta Deviations : 7.93 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.67 (0.23), residues: 1125 helix: -0.66 (0.16), residues: 753 sheet: 0.41 (0.52), residues: 84 loop : 0.53 (0.36), residues: 288 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.006 TRP A 216 HIS 0.013 0.002 HIS A1233 PHE 0.034 0.004 PHE A 156 TYR 0.142 0.008 TYR A 92 ARG 0.026 0.002 ARG A1295 Details of bonding type rmsd hydrogen bonds : bond 0.20152 ( 607) hydrogen bonds : angle 7.66150 ( 1761) covalent geometry : bond 0.02008 ( 9345) covalent geometry : angle 1.66503 (12669) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2250 Ramachandran restraints generated. 1125 Oldfield, 0 Emsley, 1125 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2250 Ramachandran restraints generated. 1125 Oldfield, 0 Emsley, 1125 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 193 time to evaluate : 1.449 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 241 MET cc_start: 0.7562 (tpp) cc_final: 0.7004 (tpt) REVERT: A 293 LYS cc_start: 0.8339 (mttm) cc_final: 0.7942 (ttpt) REVERT: A 1018 ASP cc_start: 0.8257 (m-30) cc_final: 0.8055 (t0) REVERT: A 1131 MET cc_start: 0.8564 (tpt) cc_final: 0.8243 (tpt) outliers start: 0 outliers final: 0 residues processed: 193 average time/residue: 0.7615 time to fit residues: 186.4888 Evaluate side-chains 104 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 104 time to evaluate : 1.403 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 95 optimal weight: 0.8980 chunk 85 optimal weight: 2.9990 chunk 47 optimal weight: 0.8980 chunk 29 optimal weight: 0.6980 chunk 57 optimal weight: 2.9990 chunk 45 optimal weight: 2.9990 chunk 88 optimal weight: 2.9990 chunk 34 optimal weight: 0.6980 chunk 53 optimal weight: 0.9980 chunk 65 optimal weight: 0.9980 chunk 102 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 731 GLN A 742 GLN A 994 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3495 r_free = 0.3495 target = 0.124976 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3176 r_free = 0.3176 target = 0.100356 restraints weight = 34393.668| |-----------------------------------------------------------------------------| r_work (start): 0.3135 rms_B_bonded: 2.12 r_work: 0.3031 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.2908 rms_B_bonded: 4.03 restraints_weight: 0.2500 r_work (final): 0.2908 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8289 moved from start: 0.2470 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 9345 Z= 0.160 Angle : 0.579 5.603 12669 Z= 0.331 Chirality : 0.040 0.152 1464 Planarity : 0.005 0.044 1559 Dihedral : 9.943 100.108 1335 Min Nonbonded Distance : 1.949 Molprobity Statistics. All-atom Clashscore : 1.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.53 % Favored : 99.47 % Rotamer: Outliers : 0.51 % Allowed : 4.48 % Favored : 95.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.90 (0.24), residues: 1125 helix: 0.78 (0.18), residues: 766 sheet: 0.05 (0.56), residues: 78 loop : 0.65 (0.36), residues: 281 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 711 HIS 0.002 0.001 HIS A1060 PHE 0.013 0.001 PHE A 993 TYR 0.014 0.001 TYR A 339 ARG 0.006 0.001 ARG A1012 Details of bonding type rmsd hydrogen bonds : bond 0.07161 ( 607) hydrogen bonds : angle 5.33734 ( 1761) covalent geometry : bond 0.00314 ( 9345) covalent geometry : angle 0.57890 (12669) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2250 Ramachandran restraints generated. 1125 Oldfield, 0 Emsley, 1125 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2250 Ramachandran restraints generated. 1125 Oldfield, 0 Emsley, 1125 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 116 time to evaluate : 1.506 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 595 GLN cc_start: 0.7800 (mp10) cc_final: 0.7552 (pm20) REVERT: A 1002 GLU cc_start: 0.8023 (mm-30) cc_final: 0.7756 (mm-30) REVERT: A 1018 ASP cc_start: 0.8461 (m-30) cc_final: 0.8186 (t0) REVERT: A 1133 LYS cc_start: 0.8068 (mmtt) cc_final: 0.7472 (tttt) outliers start: 5 outliers final: 2 residues processed: 117 average time/residue: 0.6465 time to fit residues: 99.2614 Evaluate side-chains 93 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 91 time to evaluate : 1.521 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 104 SER Chi-restraints excluded: chain A residue 815 ARG Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 87 optimal weight: 2.9990 chunk 5 optimal weight: 2.9990 chunk 20 optimal weight: 1.9990 chunk 53 optimal weight: 0.5980 chunk 72 optimal weight: 1.9990 chunk 34 optimal weight: 1.9990 chunk 17 optimal weight: 0.7980 chunk 18 optimal weight: 1.9990 chunk 39 optimal weight: 0.8980 chunk 54 optimal weight: 0.9990 chunk 104 optimal weight: 0.7980 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3503 r_free = 0.3503 target = 0.123599 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3201 r_free = 0.3201 target = 0.100726 restraints weight = 35782.786| |-----------------------------------------------------------------------------| r_work (start): 0.3200 rms_B_bonded: 1.93 r_work: 0.3102 rms_B_bonded: 2.17 restraints_weight: 0.5000 r_work: 0.2987 rms_B_bonded: 3.67 restraints_weight: 0.2500 r_work (final): 0.2987 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8397 moved from start: 0.3312 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 9345 Z= 0.133 Angle : 0.501 5.348 12669 Z= 0.280 Chirality : 0.038 0.145 1464 Planarity : 0.004 0.051 1559 Dihedral : 8.711 83.079 1335 Min Nonbonded Distance : 1.895 Molprobity Statistics. All-atom Clashscore : 1.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.98 % Favored : 99.02 % Rotamer: Outliers : 0.81 % Allowed : 5.70 % Favored : 93.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.63 (0.25), residues: 1125 helix: 1.49 (0.19), residues: 772 sheet: -0.33 (0.54), residues: 79 loop : 0.61 (0.37), residues: 274 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A 711 HIS 0.003 0.001 HIS A 710 PHE 0.012 0.001 PHE A 993 TYR 0.012 0.001 TYR A 737 ARG 0.008 0.001 ARG A 350 Details of bonding type rmsd hydrogen bonds : bond 0.05681 ( 607) hydrogen bonds : angle 4.74292 ( 1761) covalent geometry : bond 0.00277 ( 9345) covalent geometry : angle 0.50109 (12669) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2250 Ramachandran restraints generated. 1125 Oldfield, 0 Emsley, 1125 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2250 Ramachandran restraints generated. 1125 Oldfield, 0 Emsley, 1125 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 98 time to evaluate : 1.409 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 509 LYS cc_start: 0.8642 (ptmt) cc_final: 0.8298 (ttpt) REVERT: A 823 ASN cc_start: 0.7925 (m-40) cc_final: 0.7588 (m-40) outliers start: 8 outliers final: 4 residues processed: 104 average time/residue: 0.5626 time to fit residues: 80.1667 Evaluate side-chains 84 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 80 time to evaluate : 1.451 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 104 SER Chi-restraints excluded: chain A residue 292 GLU Chi-restraints excluded: chain A residue 958 VAL Chi-restraints excluded: chain A residue 962 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 49 optimal weight: 1.9990 chunk 89 optimal weight: 3.9990 chunk 4 optimal weight: 0.9980 chunk 81 optimal weight: 2.9990 chunk 24 optimal weight: 1.9990 chunk 29 optimal weight: 2.9990 chunk 112 optimal weight: 5.9990 chunk 15 optimal weight: 0.9980 chunk 64 optimal weight: 2.9990 chunk 43 optimal weight: 1.9990 chunk 48 optimal weight: 0.8980 overall best weight: 1.3784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3482 r_free = 0.3482 target = 0.121555 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3167 r_free = 0.3167 target = 0.098260 restraints weight = 36650.422| |-----------------------------------------------------------------------------| r_work (start): 0.3149 rms_B_bonded: 2.01 r_work: 0.3050 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work: 0.2939 rms_B_bonded: 3.74 restraints_weight: 0.2500 r_work (final): 0.2939 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8429 moved from start: 0.3677 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 9345 Z= 0.156 Angle : 0.499 6.529 12669 Z= 0.279 Chirality : 0.038 0.145 1464 Planarity : 0.004 0.039 1559 Dihedral : 8.308 87.362 1335 Min Nonbonded Distance : 1.839 Molprobity Statistics. All-atom Clashscore : 2.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.07 % Favored : 98.93 % Rotamer: Outliers : 1.12 % Allowed : 6.10 % Favored : 92.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.85 (0.25), residues: 1125 helix: 1.72 (0.19), residues: 760 sheet: -0.36 (0.54), residues: 79 loop : 0.56 (0.36), residues: 286 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 711 HIS 0.003 0.001 HIS A 592 PHE 0.010 0.001 PHE A 214 TYR 0.012 0.001 TYR A 737 ARG 0.005 0.001 ARG A 180 Details of bonding type rmsd hydrogen bonds : bond 0.05598 ( 607) hydrogen bonds : angle 4.63536 ( 1761) covalent geometry : bond 0.00352 ( 9345) covalent geometry : angle 0.49882 (12669) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2250 Ramachandran restraints generated. 1125 Oldfield, 0 Emsley, 1125 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2250 Ramachandran restraints generated. 1125 Oldfield, 0 Emsley, 1125 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 82 time to evaluate : 1.425 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 509 LYS cc_start: 0.8635 (OUTLIER) cc_final: 0.8402 (ttpt) REVERT: A 602 GLN cc_start: 0.7419 (mt0) cc_final: 0.7178 (pt0) REVERT: A 823 ASN cc_start: 0.7896 (m-40) cc_final: 0.7569 (m-40) REVERT: A 994 GLN cc_start: 0.8439 (mt0) cc_final: 0.8188 (mt0) REVERT: A 1133 LYS cc_start: 0.8178 (OUTLIER) cc_final: 0.7388 (tttt) outliers start: 11 outliers final: 7 residues processed: 91 average time/residue: 0.5492 time to fit residues: 68.8313 Evaluate side-chains 87 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 78 time to evaluate : 1.377 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 104 SER Chi-restraints excluded: chain A residue 292 GLU Chi-restraints excluded: chain A residue 361 VAL Chi-restraints excluded: chain A residue 509 LYS Chi-restraints excluded: chain A residue 608 ASP Chi-restraints excluded: chain A residue 736 SER Chi-restraints excluded: chain A residue 958 VAL Chi-restraints excluded: chain A residue 962 VAL Chi-restraints excluded: chain A residue 1133 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 12 optimal weight: 2.9990 chunk 76 optimal weight: 0.8980 chunk 84 optimal weight: 0.6980 chunk 87 optimal weight: 0.8980 chunk 23 optimal weight: 0.9990 chunk 1 optimal weight: 0.5980 chunk 78 optimal weight: 3.9990 chunk 86 optimal weight: 0.7980 chunk 72 optimal weight: 0.8980 chunk 108 optimal weight: 3.9990 chunk 88 optimal weight: 2.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 994 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3513 r_free = 0.3513 target = 0.123548 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3203 r_free = 0.3203 target = 0.100731 restraints weight = 36557.040| |-----------------------------------------------------------------------------| r_work (start): 0.3178 rms_B_bonded: 1.98 r_work: 0.3081 rms_B_bonded: 2.23 restraints_weight: 0.5000 r_work: 0.2967 rms_B_bonded: 3.75 restraints_weight: 0.2500 r_work (final): 0.2967 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8399 moved from start: 0.3946 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 9345 Z= 0.117 Angle : 0.455 4.842 12669 Z= 0.254 Chirality : 0.037 0.142 1464 Planarity : 0.004 0.058 1559 Dihedral : 7.593 76.986 1335 Min Nonbonded Distance : 1.877 Molprobity Statistics. All-atom Clashscore : 2.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.89 % Favored : 99.11 % Rotamer: Outliers : 0.81 % Allowed : 6.61 % Favored : 92.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.30 (0.25), residues: 1125 helix: 2.07 (0.19), residues: 753 sheet: -0.36 (0.55), residues: 79 loop : 0.79 (0.37), residues: 293 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP A 711 HIS 0.003 0.001 HIS A 798 PHE 0.007 0.001 PHE A 574 TYR 0.010 0.001 TYR A 737 ARG 0.008 0.000 ARG A 350 Details of bonding type rmsd hydrogen bonds : bond 0.04970 ( 607) hydrogen bonds : angle 4.40384 ( 1761) covalent geometry : bond 0.00248 ( 9345) covalent geometry : angle 0.45514 (12669) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2250 Ramachandran restraints generated. 1125 Oldfield, 0 Emsley, 1125 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2250 Ramachandran restraints generated. 1125 Oldfield, 0 Emsley, 1125 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 87 time to evaluate : 1.517 Fit side-chains revert: symmetry clash REVERT: A 509 LYS cc_start: 0.8595 (OUTLIER) cc_final: 0.8363 (ttpt) REVERT: A 602 GLN cc_start: 0.7411 (mt0) cc_final: 0.7175 (pt0) REVERT: A 823 ASN cc_start: 0.7856 (m-40) cc_final: 0.7559 (m-40) REVERT: A 994 GLN cc_start: 0.8326 (mt0) cc_final: 0.8024 (mt0) REVERT: A 1133 LYS cc_start: 0.8141 (OUTLIER) cc_final: 0.7318 (tttt) outliers start: 8 outliers final: 6 residues processed: 92 average time/residue: 0.5521 time to fit residues: 71.5887 Evaluate side-chains 92 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 84 time to evaluate : 1.557 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 104 SER Chi-restraints excluded: chain A residue 292 GLU Chi-restraints excluded: chain A residue 361 VAL Chi-restraints excluded: chain A residue 509 LYS Chi-restraints excluded: chain A residue 958 VAL Chi-restraints excluded: chain A residue 962 VAL Chi-restraints excluded: chain A residue 1133 LYS Chi-restraints excluded: chain A residue 1263 GLN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 11 optimal weight: 0.9980 chunk 91 optimal weight: 2.9990 chunk 85 optimal weight: 2.9990 chunk 87 optimal weight: 0.7980 chunk 78 optimal weight: 0.9990 chunk 38 optimal weight: 2.9990 chunk 25 optimal weight: 1.9990 chunk 68 optimal weight: 1.9990 chunk 86 optimal weight: 0.8980 chunk 63 optimal weight: 2.9990 chunk 61 optimal weight: 4.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1216 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3489 r_free = 0.3489 target = 0.121765 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3174 r_free = 0.3174 target = 0.098680 restraints weight = 36843.190| |-----------------------------------------------------------------------------| r_work (start): 0.3177 rms_B_bonded: 1.99 r_work: 0.3076 rms_B_bonded: 2.22 restraints_weight: 0.5000 r_work: 0.2963 rms_B_bonded: 3.73 restraints_weight: 0.2500 r_work (final): 0.2963 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8442 moved from start: 0.4064 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 9345 Z= 0.136 Angle : 0.462 5.347 12669 Z= 0.259 Chirality : 0.037 0.142 1464 Planarity : 0.004 0.042 1559 Dihedral : 7.591 76.947 1335 Min Nonbonded Distance : 1.815 Molprobity Statistics. All-atom Clashscore : 2.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.24 % Favored : 98.76 % Rotamer: Outliers : 1.02 % Allowed : 6.92 % Favored : 92.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.29 (0.25), residues: 1125 helix: 2.07 (0.19), residues: 753 sheet: -0.30 (0.56), residues: 79 loop : 0.76 (0.37), residues: 293 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 711 HIS 0.002 0.001 HIS A1233 PHE 0.009 0.001 PHE A 214 TYR 0.011 0.001 TYR A 339 ARG 0.007 0.000 ARG A 180 Details of bonding type rmsd hydrogen bonds : bond 0.05081 ( 607) hydrogen bonds : angle 4.38518 ( 1761) covalent geometry : bond 0.00301 ( 9345) covalent geometry : angle 0.46170 (12669) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2250 Ramachandran restraints generated. 1125 Oldfield, 0 Emsley, 1125 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2250 Ramachandran restraints generated. 1125 Oldfield, 0 Emsley, 1125 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 83 time to evaluate : 1.596 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 509 LYS cc_start: 0.8615 (OUTLIER) cc_final: 0.8370 (ttpt) REVERT: A 602 GLN cc_start: 0.7446 (mt0) cc_final: 0.7136 (pt0) REVERT: A 823 ASN cc_start: 0.7897 (m-40) cc_final: 0.7583 (m-40) REVERT: A 994 GLN cc_start: 0.8329 (mt0) cc_final: 0.8045 (mt0) REVERT: A 1133 LYS cc_start: 0.8189 (OUTLIER) cc_final: 0.7404 (tttt) outliers start: 10 outliers final: 6 residues processed: 91 average time/residue: 0.5493 time to fit residues: 67.9696 Evaluate side-chains 87 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 79 time to evaluate : 1.366 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 104 SER Chi-restraints excluded: chain A residue 292 GLU Chi-restraints excluded: chain A residue 361 VAL Chi-restraints excluded: chain A residue 509 LYS Chi-restraints excluded: chain A residue 736 SER Chi-restraints excluded: chain A residue 958 VAL Chi-restraints excluded: chain A residue 962 VAL Chi-restraints excluded: chain A residue 1133 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 83 optimal weight: 0.5980 chunk 105 optimal weight: 2.9990 chunk 94 optimal weight: 2.9990 chunk 15 optimal weight: 1.9990 chunk 24 optimal weight: 1.9990 chunk 44 optimal weight: 2.9990 chunk 36 optimal weight: 4.9990 chunk 10 optimal weight: 2.9990 chunk 66 optimal weight: 0.6980 chunk 31 optimal weight: 1.9990 chunk 56 optimal weight: 3.9990 overall best weight: 1.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3477 r_free = 0.3477 target = 0.120758 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3162 r_free = 0.3162 target = 0.097879 restraints weight = 36890.733| |-----------------------------------------------------------------------------| r_work (start): 0.3140 rms_B_bonded: 1.96 r_work: 0.3043 rms_B_bonded: 2.20 restraints_weight: 0.5000 r_work: 0.2932 rms_B_bonded: 3.70 restraints_weight: 0.2500 r_work (final): 0.2932 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8444 moved from start: 0.4176 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 9345 Z= 0.157 Angle : 0.480 6.310 12669 Z= 0.269 Chirality : 0.038 0.143 1464 Planarity : 0.004 0.048 1559 Dihedral : 7.762 79.313 1335 Min Nonbonded Distance : 1.799 Molprobity Statistics. All-atom Clashscore : 2.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.33 % Favored : 98.67 % Rotamer: Outliers : 0.92 % Allowed : 7.63 % Favored : 91.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.18 (0.25), residues: 1125 helix: 1.97 (0.19), residues: 754 sheet: 0.19 (0.59), residues: 67 loop : 0.53 (0.36), residues: 304 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.001 TRP A 711 HIS 0.003 0.001 HIS A 798 PHE 0.010 0.001 PHE A 214 TYR 0.012 0.001 TYR A 339 ARG 0.007 0.000 ARG A 180 Details of bonding type rmsd hydrogen bonds : bond 0.05221 ( 607) hydrogen bonds : angle 4.42699 ( 1761) covalent geometry : bond 0.00357 ( 9345) covalent geometry : angle 0.47974 (12669) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2250 Ramachandran restraints generated. 1125 Oldfield, 0 Emsley, 1125 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2250 Ramachandran restraints generated. 1125 Oldfield, 0 Emsley, 1125 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 81 time to evaluate : 1.421 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 509 LYS cc_start: 0.8579 (OUTLIER) cc_final: 0.8339 (ttpt) REVERT: A 823 ASN cc_start: 0.7873 (m-40) cc_final: 0.7562 (m-40) REVERT: A 994 GLN cc_start: 0.8328 (mt0) cc_final: 0.8010 (mt0) outliers start: 9 outliers final: 8 residues processed: 87 average time/residue: 0.5380 time to fit residues: 64.8041 Evaluate side-chains 89 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 80 time to evaluate : 1.656 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 104 SER Chi-restraints excluded: chain A residue 223 ILE Chi-restraints excluded: chain A residue 292 GLU Chi-restraints excluded: chain A residue 361 VAL Chi-restraints excluded: chain A residue 509 LYS Chi-restraints excluded: chain A residue 736 SER Chi-restraints excluded: chain A residue 958 VAL Chi-restraints excluded: chain A residue 962 VAL Chi-restraints excluded: chain A residue 1263 GLN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 38 optimal weight: 2.9990 chunk 40 optimal weight: 2.9990 chunk 9 optimal weight: 3.9990 chunk 96 optimal weight: 2.9990 chunk 3 optimal weight: 0.6980 chunk 2 optimal weight: 0.5980 chunk 43 optimal weight: 0.9980 chunk 108 optimal weight: 2.9990 chunk 98 optimal weight: 0.7980 chunk 48 optimal weight: 0.9980 chunk 18 optimal weight: 0.0980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3511 r_free = 0.3511 target = 0.123394 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3201 r_free = 0.3201 target = 0.100535 restraints weight = 36636.557| |-----------------------------------------------------------------------------| r_work (start): 0.3185 rms_B_bonded: 1.97 r_work: 0.3089 rms_B_bonded: 2.21 restraints_weight: 0.5000 r_work: 0.2975 rms_B_bonded: 3.73 restraints_weight: 0.2500 r_work (final): 0.2975 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8404 moved from start: 0.4303 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 9345 Z= 0.106 Angle : 0.437 5.024 12669 Z= 0.243 Chirality : 0.036 0.146 1464 Planarity : 0.004 0.051 1559 Dihedral : 7.235 74.246 1335 Min Nonbonded Distance : 1.848 Molprobity Statistics. All-atom Clashscore : 2.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.07 % Favored : 98.93 % Rotamer: Outliers : 1.02 % Allowed : 7.93 % Favored : 91.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.46 (0.25), residues: 1125 helix: 2.24 (0.19), residues: 755 sheet: 0.22 (0.58), residues: 67 loop : 0.51 (0.37), residues: 303 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRP A 711 HIS 0.003 0.001 HIS A 798 PHE 0.009 0.001 PHE A 875 TYR 0.008 0.001 TYR A 339 ARG 0.006 0.000 ARG A 180 Details of bonding type rmsd hydrogen bonds : bond 0.04697 ( 607) hydrogen bonds : angle 4.24037 ( 1761) covalent geometry : bond 0.00216 ( 9345) covalent geometry : angle 0.43692 (12669) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2250 Ramachandran restraints generated. 1125 Oldfield, 0 Emsley, 1125 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2250 Ramachandran restraints generated. 1125 Oldfield, 0 Emsley, 1125 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 89 time to evaluate : 1.438 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 509 LYS cc_start: 0.8545 (OUTLIER) cc_final: 0.8309 (ttpt) REVERT: A 823 ASN cc_start: 0.7785 (m-40) cc_final: 0.7520 (m-40) REVERT: A 994 GLN cc_start: 0.8248 (mt0) cc_final: 0.7965 (mt0) outliers start: 10 outliers final: 9 residues processed: 95 average time/residue: 0.6335 time to fit residues: 82.2690 Evaluate side-chains 92 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 82 time to evaluate : 1.428 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 104 SER Chi-restraints excluded: chain A residue 223 ILE Chi-restraints excluded: chain A residue 292 GLU Chi-restraints excluded: chain A residue 361 VAL Chi-restraints excluded: chain A residue 509 LYS Chi-restraints excluded: chain A residue 736 SER Chi-restraints excluded: chain A residue 761 LEU Chi-restraints excluded: chain A residue 958 VAL Chi-restraints excluded: chain A residue 962 VAL Chi-restraints excluded: chain A residue 1263 GLN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 24 optimal weight: 1.9990 chunk 61 optimal weight: 2.9990 chunk 26 optimal weight: 1.9990 chunk 112 optimal weight: 7.9990 chunk 48 optimal weight: 1.9990 chunk 111 optimal weight: 0.9990 chunk 87 optimal weight: 2.9990 chunk 33 optimal weight: 1.9990 chunk 52 optimal weight: 3.9990 chunk 69 optimal weight: 0.7980 chunk 36 optimal weight: 3.9990 overall best weight: 1.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1216 GLN A1263 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3479 r_free = 0.3479 target = 0.120835 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3162 r_free = 0.3162 target = 0.097859 restraints weight = 37215.188| |-----------------------------------------------------------------------------| r_work (start): 0.3156 rms_B_bonded: 1.98 r_work: 0.3047 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.2930 rms_B_bonded: 3.80 restraints_weight: 0.2500 r_work (final): 0.2930 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8453 moved from start: 0.4336 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 9345 Z= 0.165 Angle : 0.482 5.767 12669 Z= 0.270 Chirality : 0.038 0.197 1464 Planarity : 0.004 0.047 1559 Dihedral : 7.593 72.197 1335 Min Nonbonded Distance : 1.790 Molprobity Statistics. All-atom Clashscore : 2.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.78 % Favored : 98.22 % Rotamer: Outliers : 1.12 % Allowed : 7.93 % Favored : 90.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.20 (0.25), residues: 1125 helix: 2.05 (0.19), residues: 754 sheet: 0.25 (0.59), residues: 67 loop : 0.36 (0.36), residues: 304 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.001 TRP A 711 HIS 0.003 0.001 HIS A 798 PHE 0.011 0.001 PHE A 214 TYR 0.012 0.001 TYR A 339 ARG 0.006 0.000 ARG A 180 Details of bonding type rmsd hydrogen bonds : bond 0.05185 ( 607) hydrogen bonds : angle 4.39048 ( 1761) covalent geometry : bond 0.00380 ( 9345) covalent geometry : angle 0.48168 (12669) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2250 Ramachandran restraints generated. 1125 Oldfield, 0 Emsley, 1125 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2250 Ramachandran restraints generated. 1125 Oldfield, 0 Emsley, 1125 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 79 time to evaluate : 1.527 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 509 LYS cc_start: 0.8563 (OUTLIER) cc_final: 0.8279 (ttpt) REVERT: A 823 ASN cc_start: 0.7889 (m-40) cc_final: 0.7566 (m-40) REVERT: A 994 GLN cc_start: 0.8331 (mt0) cc_final: 0.8051 (mt0) REVERT: A 1236 ASN cc_start: 0.8457 (OUTLIER) cc_final: 0.7953 (p0) outliers start: 11 outliers final: 9 residues processed: 87 average time/residue: 0.5885 time to fit residues: 72.0795 Evaluate side-chains 89 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 78 time to evaluate : 1.457 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 104 SER Chi-restraints excluded: chain A residue 223 ILE Chi-restraints excluded: chain A residue 292 GLU Chi-restraints excluded: chain A residue 361 VAL Chi-restraints excluded: chain A residue 509 LYS Chi-restraints excluded: chain A residue 736 SER Chi-restraints excluded: chain A residue 761 LEU Chi-restraints excluded: chain A residue 958 VAL Chi-restraints excluded: chain A residue 962 VAL Chi-restraints excluded: chain A residue 1236 ASN Chi-restraints excluded: chain A residue 1263 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 38 optimal weight: 2.9990 chunk 90 optimal weight: 3.9990 chunk 75 optimal weight: 2.9990 chunk 13 optimal weight: 1.9990 chunk 62 optimal weight: 2.9990 chunk 5 optimal weight: 2.9990 chunk 29 optimal weight: 0.9990 chunk 78 optimal weight: 1.9990 chunk 102 optimal weight: 2.9990 chunk 105 optimal weight: 0.9980 chunk 20 optimal weight: 0.9980 overall best weight: 1.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.120333 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3152 r_free = 0.3152 target = 0.097264 restraints weight = 37174.831| |-----------------------------------------------------------------------------| r_work (start): 0.3156 rms_B_bonded: 1.99 r_work: 0.3047 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.2930 rms_B_bonded: 3.82 restraints_weight: 0.2500 r_work (final): 0.2930 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8444 moved from start: 0.4369 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 9345 Z= 0.154 Angle : 0.477 5.586 12669 Z= 0.267 Chirality : 0.038 0.167 1464 Planarity : 0.004 0.048 1559 Dihedral : 7.580 71.559 1335 Min Nonbonded Distance : 1.799 Molprobity Statistics. All-atom Clashscore : 2.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.60 % Favored : 98.40 % Rotamer: Outliers : 1.12 % Allowed : 7.93 % Favored : 90.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.16 (0.25), residues: 1125 helix: 2.01 (0.19), residues: 754 sheet: 0.53 (0.64), residues: 57 loop : 0.30 (0.35), residues: 314 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.001 TRP A 711 HIS 0.003 0.001 HIS A 798 PHE 0.010 0.001 PHE A 214 TYR 0.034 0.001 TYR A1259 ARG 0.007 0.000 ARG A 180 Details of bonding type rmsd hydrogen bonds : bond 0.05129 ( 607) hydrogen bonds : angle 4.38431 ( 1761) covalent geometry : bond 0.00349 ( 9345) covalent geometry : angle 0.47718 (12669) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2250 Ramachandran restraints generated. 1125 Oldfield, 0 Emsley, 1125 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2250 Ramachandran restraints generated. 1125 Oldfield, 0 Emsley, 1125 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 77 time to evaluate : 1.402 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 509 LYS cc_start: 0.8559 (OUTLIER) cc_final: 0.8278 (ttpt) REVERT: A 823 ASN cc_start: 0.7824 (m-40) cc_final: 0.7526 (m-40) REVERT: A 994 GLN cc_start: 0.8322 (mt0) cc_final: 0.8042 (mt0) REVERT: A 1236 ASN cc_start: 0.8458 (OUTLIER) cc_final: 0.7953 (p0) outliers start: 11 outliers final: 9 residues processed: 85 average time/residue: 0.5278 time to fit residues: 61.9564 Evaluate side-chains 88 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 77 time to evaluate : 1.585 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 104 SER Chi-restraints excluded: chain A residue 223 ILE Chi-restraints excluded: chain A residue 292 GLU Chi-restraints excluded: chain A residue 361 VAL Chi-restraints excluded: chain A residue 509 LYS Chi-restraints excluded: chain A residue 736 SER Chi-restraints excluded: chain A residue 761 LEU Chi-restraints excluded: chain A residue 958 VAL Chi-restraints excluded: chain A residue 962 VAL Chi-restraints excluded: chain A residue 1236 ASN Chi-restraints excluded: chain A residue 1263 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 42 optimal weight: 1.9990 chunk 94 optimal weight: 2.9990 chunk 59 optimal weight: 2.9990 chunk 111 optimal weight: 1.9990 chunk 19 optimal weight: 3.9990 chunk 28 optimal weight: 0.9990 chunk 92 optimal weight: 1.9990 chunk 91 optimal weight: 1.9990 chunk 105 optimal weight: 2.9990 chunk 52 optimal weight: 3.9990 chunk 35 optimal weight: 3.9990 overall best weight: 1.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1263 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.119043 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3132 r_free = 0.3132 target = 0.095888 restraints weight = 37334.755| |-----------------------------------------------------------------------------| r_work (start): 0.3125 rms_B_bonded: 1.99 r_work: 0.3026 rms_B_bonded: 2.23 restraints_weight: 0.5000 r_work: 0.2913 rms_B_bonded: 3.75 restraints_weight: 0.2500 r_work (final): 0.2913 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8469 moved from start: 0.4391 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 9345 Z= 0.184 Angle : 0.499 5.679 12669 Z= 0.281 Chirality : 0.039 0.152 1464 Planarity : 0.004 0.048 1559 Dihedral : 7.834 75.941 1335 Min Nonbonded Distance : 1.787 Molprobity Statistics. All-atom Clashscore : 2.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.69 % Favored : 98.31 % Rotamer: Outliers : 1.22 % Allowed : 7.83 % Favored : 90.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.97 (0.25), residues: 1125 helix: 1.85 (0.19), residues: 754 sheet: 0.52 (0.65), residues: 57 loop : 0.23 (0.35), residues: 314 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.001 TRP A 711 HIS 0.004 0.001 HIS A 798 PHE 0.011 0.001 PHE A 214 TYR 0.013 0.001 TYR A 339 ARG 0.007 0.000 ARG A 180 Details of bonding type rmsd hydrogen bonds : bond 0.05450 ( 607) hydrogen bonds : angle 4.49806 ( 1761) covalent geometry : bond 0.00429 ( 9345) covalent geometry : angle 0.49892 (12669) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9556.19 seconds wall clock time: 165 minutes 20.35 seconds (9920.35 seconds total)