Starting phenix.real_space_refine on Sun Aug 24 09:52:56 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8swn_40821/08_2025/8swn_40821_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/8swn_40821/08_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 { model { file = "/net/cci-nas-00/data/ceres_data/8swn_40821/08_2025/8swn_40821_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8swn_40821/08_2025/8swn_40821_trim.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8swn_40821/08_2025/8swn_40821.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8swn_40821/08_2025/8swn_40821.map" } resolution = 3.1 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= 0.003 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/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: 3.56, per 1000 atoms: 0.19 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: 1.72 Conformation dependent library (CDL) restraints added in 647.7 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 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: 0.65 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: 4.49 Time building geometry restraints manager: 2.36 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: 1.760 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: 0.110 Extract box with map and model: 0.270 Check model and map are aligned: 0.060 Set scattering table: 0.050 Process input model: 19.330 Find NCS groups from input model: 0.060 Set up NCS constraints: 0.030 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:1.470 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.140 ------------------------------------------------------------------------------- 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 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: -0.67 (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 ARG 0.026 0.002 ARG A1295 TYR 0.142 0.008 TYR A 92 PHE 0.034 0.004 PHE A 156 TRP 0.040 0.006 TRP A 216 HIS 0.013 0.002 HIS A1233 Details of bonding type rmsd covalent geometry : bond 0.02008 ( 9345) covalent geometry : angle 1.66503 (12669) hydrogen bonds : bond 0.20152 ( 607) hydrogen bonds : angle 7.66150 ( 1761) *********************** 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 : 0.407 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: 0.7003 (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: 0.8056 (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: 0.3632 time to fit residues: 87.5427 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 : 0.578 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 108 optimal weight: 3.9990 chunk 49 optimal weight: 1.9990 chunk 97 optimal weight: 0.0570 chunk 53 optimal weight: 2.9990 chunk 5 optimal weight: 0.9980 chunk 33 optimal weight: 0.7980 chunk 65 optimal weight: 2.9990 chunk 62 optimal weight: 0.5980 chunk 51 optimal weight: 1.9990 chunk 100 optimal weight: 0.9980 chunk 106 optimal weight: 3.9990 overall best weight: 0.6898 ------------------------------------------------------------------------------- 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 = 0.3490 r_free = 0.3490 target = 0.124592 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3172 r_free = 0.3172 target = 0.099979 restraints weight = 34518.996| |-----------------------------------------------------------------------------| r_work (start): 0.3128 rms_B_bonded: 2.12 r_work: 0.3022 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.2898 rms_B_bonded: 4.05 restraints_weight: 0.2500 r_work (final): 0.2898 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8267 moved from start: 0.2468 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 9345 Z= 0.157 Angle : 0.588 5.684 12669 Z= 0.337 Chirality : 0.040 0.158 1464 Planarity : 0.005 0.046 1559 Dihedral : 9.804 97.331 1335 Min Nonbonded Distance : 1.946 Molprobity Statistics. All-atom Clashscore : 1.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.53 % Favored : 99.47 % Rotamer: Outliers : 0.41 % Allowed : 4.58 % 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 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: 0.98 (0.24), residues: 1125 helix: 0.83 (0.18), residues: 766 sheet: 0.09 (0.56), residues: 78 loop : 0.69 (0.37), residues: 281 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 180 TYR 0.014 0.001 TYR A 339 PHE 0.013 0.001 PHE A 993 TRP 0.019 0.001 TRP A 711 HIS 0.005 0.001 HIS A 158 Details of bonding type rmsd covalent geometry : bond 0.00311 ( 9345) covalent geometry : angle 0.58751 (12669) hydrogen bonds : bond 0.07140 ( 607) hydrogen bonds : angle 5.31910 ( 1761) *********************** 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 122 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 118 time to evaluate : 0.427 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 972 LYS cc_start: 0.8780 (ptmt) cc_final: 0.8559 (mmtt) REVERT: A 1002 GLU cc_start: 0.7986 (mm-30) cc_final: 0.7689 (mm-30) REVERT: A 1018 ASP cc_start: 0.8455 (m-30) cc_final: 0.8171 (t0) REVERT: A 1131 MET cc_start: 0.8081 (tpt) cc_final: 0.7709 (tpt) REVERT: A 1133 LYS cc_start: 0.8039 (mmtt) cc_final: 0.7438 (tttt) outliers start: 4 outliers final: 2 residues processed: 119 average time/residue: 0.2868 time to fit residues: 44.3226 Evaluate side-chains 94 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 92 time to evaluate : 0.497 ------------------------------------------------------------------------------- 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 9 optimal weight: 5.9990 chunk 32 optimal weight: 1.9990 chunk 35 optimal weight: 3.9990 chunk 24 optimal weight: 1.9990 chunk 58 optimal weight: 0.6980 chunk 74 optimal weight: 3.9990 chunk 17 optimal weight: 0.8980 chunk 1 optimal weight: 1.9990 chunk 72 optimal weight: 0.9990 chunk 101 optimal weight: 2.9990 chunk 61 optimal weight: 0.5980 overall best weight: 1.0384 ------------------------------------------------------------------------------- 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 = 0.3496 r_free = 0.3496 target = 0.122965 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3191 r_free = 0.3191 target = 0.100006 restraints weight = 36326.195| |-----------------------------------------------------------------------------| r_work (start): 0.3199 rms_B_bonded: 1.95 r_work: 0.3089 rms_B_bonded: 2.27 restraints_weight: 0.5000 r_work: 0.2966 rms_B_bonded: 3.83 restraints_weight: 0.2500 r_work (final): 0.2966 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8409 moved from start: 0.3346 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 9345 Z= 0.139 Angle : 0.501 5.321 12669 Z= 0.281 Chirality : 0.038 0.143 1464 Planarity : 0.004 0.039 1559 Dihedral : 8.467 78.154 1335 Min Nonbonded Distance : 1.864 Molprobity Statistics. All-atom Clashscore : 1.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.80 % Favored : 99.20 % Rotamer: Outliers : 1.02 % Allowed : 5.49 % 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 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: 1.63 (0.25), residues: 1125 helix: 1.53 (0.19), residues: 766 sheet: -0.32 (0.54), residues: 79 loop : 0.50 (0.36), residues: 280 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 180 TYR 0.012 0.001 TYR A 737 PHE 0.013 0.001 PHE A 705 TRP 0.023 0.001 TRP A 711 HIS 0.004 0.001 HIS A 710 Details of bonding type rmsd covalent geometry : bond 0.00297 ( 9345) covalent geometry : angle 0.50054 (12669) hydrogen bonds : bond 0.05747 ( 607) hydrogen bonds : angle 4.72624 ( 1761) *********************** 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 108 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 98 time to evaluate : 0.308 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 509 LYS cc_start: 0.8636 (OUTLIER) cc_final: 0.8294 (ttpt) REVERT: A 972 LYS cc_start: 0.8725 (ptmt) cc_final: 0.8525 (mmtt) REVERT: A 975 ASP cc_start: 0.7626 (t0) cc_final: 0.7320 (t0) REVERT: A 1259 TYR cc_start: 0.7027 (t80) cc_final: 0.6826 (t80) outliers start: 10 outliers final: 5 residues processed: 106 average time/residue: 0.2149 time to fit residues: 31.1549 Evaluate side-chains 86 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 80 time to evaluate : 0.570 ------------------------------------------------------------------------------- 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 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 Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 85 optimal weight: 2.9990 chunk 2 optimal weight: 0.7980 chunk 72 optimal weight: 6.9990 chunk 47 optimal weight: 2.9990 chunk 58 optimal weight: 2.9990 chunk 17 optimal weight: 0.9980 chunk 67 optimal weight: 1.9990 chunk 38 optimal weight: 2.9990 chunk 108 optimal weight: 3.9990 chunk 36 optimal weight: 1.9990 chunk 100 optimal weight: 3.9990 overall best weight: 1.7586 ------------------------------------------------------------------------------- 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 = 0.3459 r_free = 0.3459 target = 0.119669 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3144 r_free = 0.3144 target = 0.096692 restraints weight = 37069.618| |-----------------------------------------------------------------------------| r_work (start): 0.3137 rms_B_bonded: 1.99 r_work: 0.3038 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.2927 rms_B_bonded: 3.75 restraints_weight: 0.2500 r_work (final): 0.2927 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8450 moved from start: 0.3684 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 9345 Z= 0.182 Angle : 0.518 6.233 12669 Z= 0.291 Chirality : 0.039 0.145 1464 Planarity : 0.004 0.038 1559 Dihedral : 8.286 80.824 1335 Min Nonbonded Distance : 1.816 Molprobity Statistics. All-atom Clashscore : 2.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.24 % Favored : 98.76 % Rotamer: Outliers : 1.22 % Allowed : 6.10 % Favored : 92.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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: 1.68 (0.24), residues: 1125 helix: 1.60 (0.19), residues: 759 sheet: -0.35 (0.55), residues: 79 loop : 0.45 (0.35), residues: 287 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 180 TYR 0.014 0.001 TYR A1255 PHE 0.011 0.001 PHE A 214 TRP 0.013 0.001 TRP A 711 HIS 0.003 0.001 HIS A 592 Details of bonding type rmsd covalent geometry : bond 0.00421 ( 9345) covalent geometry : angle 0.51758 (12669) hydrogen bonds : bond 0.05852 ( 607) hydrogen bonds : angle 4.71493 ( 1761) *********************** 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 92 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 80 time to evaluate : 0.438 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 509 LYS cc_start: 0.8616 (OUTLIER) cc_final: 0.8270 (ttpt) REVERT: A 975 ASP cc_start: 0.7625 (t0) cc_final: 0.7286 (t0) REVERT: A 1133 LYS cc_start: 0.8194 (OUTLIER) cc_final: 0.7396 (tttt) REVERT: A 1243 LYS cc_start: 0.7807 (mtpt) cc_final: 0.7585 (mttp) outliers start: 12 outliers final: 8 residues processed: 89 average time/residue: 0.2366 time to fit residues: 28.6423 Evaluate side-chains 88 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 78 time to evaluate : 0.390 ------------------------------------------------------------------------------- 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 Chi-restraints excluded: chain A residue 1263 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 17 optimal weight: 0.8980 chunk 37 optimal weight: 1.9990 chunk 73 optimal weight: 3.9990 chunk 48 optimal weight: 1.9990 chunk 33 optimal weight: 2.9990 chunk 91 optimal weight: 1.9990 chunk 49 optimal weight: 1.9990 chunk 47 optimal weight: 0.9990 chunk 55 optimal weight: 6.9990 chunk 56 optimal weight: 3.9990 chunk 21 optimal weight: 1.9990 overall best weight: 1.5788 ------------------------------------------------------------------------------- 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 = 0.3465 r_free = 0.3465 target = 0.119995 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3150 r_free = 0.3150 target = 0.096973 restraints weight = 37035.841| |-----------------------------------------------------------------------------| r_work (start): 0.3133 rms_B_bonded: 1.99 r_work: 0.3034 rms_B_bonded: 2.23 restraints_weight: 0.5000 r_work: 0.2923 rms_B_bonded: 3.73 restraints_weight: 0.2500 r_work (final): 0.2923 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8452 moved from start: 0.3915 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 9345 Z= 0.167 Angle : 0.493 5.201 12669 Z= 0.276 Chirality : 0.038 0.144 1464 Planarity : 0.004 0.043 1559 Dihedral : 8.009 79.426 1335 Min Nonbonded Distance : 1.810 Molprobity Statistics. All-atom Clashscore : 2.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.33 % Favored : 98.67 % 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 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: 1.88 (0.25), residues: 1125 helix: 1.75 (0.19), residues: 753 sheet: 0.02 (0.58), residues: 67 loop : 0.46 (0.36), residues: 305 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 180 TYR 0.012 0.001 TYR A 339 PHE 0.009 0.001 PHE A 214 TRP 0.024 0.001 TRP A 711 HIS 0.003 0.001 HIS A 798 Details of bonding type rmsd covalent geometry : bond 0.00383 ( 9345) covalent geometry : angle 0.49272 (12669) hydrogen bonds : bond 0.05517 ( 607) hydrogen bonds : angle 4.60045 ( 1761) *********************** 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 93 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 83 time to evaluate : 0.511 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 509 LYS cc_start: 0.8628 (OUTLIER) cc_final: 0.8297 (ttpt) REVERT: A 1133 LYS cc_start: 0.8136 (OUTLIER) cc_final: 0.7335 (tttt) REVERT: A 1243 LYS cc_start: 0.7866 (mtpt) cc_final: 0.7613 (mttp) outliers start: 10 outliers final: 8 residues processed: 91 average time/residue: 0.2693 time to fit residues: 33.5818 Evaluate side-chains 90 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 80 time to evaluate : 0.523 ------------------------------------------------------------------------------- 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 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 55 optimal weight: 4.9990 chunk 108 optimal weight: 3.9990 chunk 112 optimal weight: 9.9990 chunk 62 optimal weight: 2.9990 chunk 67 optimal weight: 1.9990 chunk 23 optimal weight: 0.9990 chunk 53 optimal weight: 4.9990 chunk 0 optimal weight: 3.9990 chunk 74 optimal weight: 3.9990 chunk 94 optimal weight: 2.9990 chunk 21 optimal weight: 1.9990 overall best weight: 2.1990 ------------------------------------------------------------------------------- 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 = 0.3432 r_free = 0.3432 target = 0.117517 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3114 r_free = 0.3114 target = 0.094598 restraints weight = 37250.098| |-----------------------------------------------------------------------------| r_work (start): 0.3101 rms_B_bonded: 1.98 r_work: 0.3004 rms_B_bonded: 2.21 restraints_weight: 0.5000 r_work: 0.2894 rms_B_bonded: 3.70 restraints_weight: 0.2500 r_work (final): 0.2894 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8487 moved from start: 0.4047 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 9345 Z= 0.217 Angle : 0.528 5.705 12669 Z= 0.298 Chirality : 0.040 0.144 1464 Planarity : 0.004 0.054 1559 Dihedral : 8.447 88.428 1335 Min Nonbonded Distance : 1.777 Molprobity Statistics. All-atom Clashscore : 2.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.60 % Favored : 98.40 % Rotamer: Outliers : 1.12 % Allowed : 7.32 % Favored : 91.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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: 1.60 (0.24), residues: 1125 helix: 1.53 (0.18), residues: 754 sheet: 0.04 (0.58), residues: 67 loop : 0.30 (0.35), residues: 304 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 180 TYR 0.014 0.001 TYR A 339 PHE 0.012 0.002 PHE A 214 TRP 0.023 0.001 TRP A 711 HIS 0.003 0.001 HIS A 592 Details of bonding type rmsd covalent geometry : bond 0.00514 ( 9345) covalent geometry : angle 0.52815 (12669) hydrogen bonds : bond 0.05923 ( 607) hydrogen bonds : angle 4.71304 ( 1761) *********************** 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: 11 poor density : 82 time to evaluate : 0.556 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 509 LYS cc_start: 0.8629 (OUTLIER) cc_final: 0.8300 (ttpt) REVERT: A 1133 LYS cc_start: 0.8180 (OUTLIER) cc_final: 0.7391 (tttt) REVERT: A 1243 LYS cc_start: 0.7941 (mtpt) cc_final: 0.7657 (mttp) outliers start: 11 outliers final: 8 residues processed: 91 average time/residue: 0.2288 time to fit residues: 28.0795 Evaluate side-chains 89 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 79 time to evaluate : 0.586 ------------------------------------------------------------------------------- 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 Chi-restraints excluded: chain A residue 1263 GLN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 85 optimal weight: 1.9990 chunk 74 optimal weight: 3.9990 chunk 108 optimal weight: 3.9990 chunk 54 optimal weight: 1.9990 chunk 56 optimal weight: 3.9990 chunk 7 optimal weight: 3.9990 chunk 101 optimal weight: 1.9990 chunk 90 optimal weight: 2.9990 chunk 41 optimal weight: 2.9990 chunk 9 optimal weight: 3.9990 chunk 99 optimal weight: 2.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- 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 = 0.3429 r_free = 0.3429 target = 0.117236 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3110 r_free = 0.3110 target = 0.094331 restraints weight = 37837.521| |-----------------------------------------------------------------------------| r_work (start): 0.3101 rms_B_bonded: 1.99 r_work: 0.2992 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.2874 rms_B_bonded: 3.81 restraints_weight: 0.2500 r_work (final): 0.2874 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8503 moved from start: 0.4198 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.038 9345 Z= 0.231 Angle : 0.537 6.412 12669 Z= 0.302 Chirality : 0.040 0.149 1464 Planarity : 0.004 0.059 1559 Dihedral : 8.479 87.299 1335 Min Nonbonded Distance : 1.791 Molprobity Statistics. All-atom Clashscore : 2.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.69 % Favored : 98.31 % Rotamer: Outliers : 1.42 % Allowed : 7.53 % 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 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: 1.42 (0.24), residues: 1125 helix: 1.40 (0.18), residues: 752 sheet: 0.33 (0.63), residues: 57 loop : 0.12 (0.34), residues: 316 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 180 TYR 0.014 0.001 TYR A 339 PHE 0.013 0.002 PHE A 352 TRP 0.029 0.001 TRP A 711 HIS 0.003 0.001 HIS A 592 Details of bonding type rmsd covalent geometry : bond 0.00550 ( 9345) covalent geometry : angle 0.53679 (12669) hydrogen bonds : bond 0.05984 ( 607) hydrogen bonds : angle 4.75675 ( 1761) *********************** 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 97 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 83 time to evaluate : 0.514 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 509 LYS cc_start: 0.8597 (OUTLIER) cc_final: 0.8393 (ttpt) REVERT: A 1133 LYS cc_start: 0.8161 (OUTLIER) cc_final: 0.7367 (tttt) REVERT: A 1243 LYS cc_start: 0.7954 (mtpt) cc_final: 0.7642 (mttp) outliers start: 14 outliers final: 12 residues processed: 93 average time/residue: 0.2620 time to fit residues: 32.4424 Evaluate side-chains 96 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 82 time to evaluate : 0.444 ------------------------------------------------------------------------------- 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 328 SER 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 761 LEU Chi-restraints excluded: chain A residue 803 GLU 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 1210 ARG 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 62 optimal weight: 1.9990 chunk 69 optimal weight: 0.7980 chunk 11 optimal weight: 2.9990 chunk 25 optimal weight: 0.9990 chunk 77 optimal weight: 2.9990 chunk 21 optimal weight: 1.9990 chunk 31 optimal weight: 0.0770 chunk 94 optimal weight: 2.9990 chunk 109 optimal weight: 4.9990 chunk 1 optimal weight: 0.9990 chunk 15 optimal weight: 1.9990 overall best weight: 0.9744 ------------------------------------------------------------------------------- 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 = 0.3446 r_free = 0.3446 target = 0.120577 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3121 r_free = 0.3121 target = 0.096241 restraints weight = 35728.422| |-----------------------------------------------------------------------------| r_work (start): 0.3091 rms_B_bonded: 2.12 r_work: 0.2986 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.2867 rms_B_bonded: 4.02 restraints_weight: 0.2500 r_work (final): 0.2867 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8347 moved from start: 0.4314 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= 0.126 Angle : 0.468 5.251 12669 Z= 0.261 Chirality : 0.037 0.152 1464 Planarity : 0.005 0.123 1559 Dihedral : 7.887 79.672 1335 Min Nonbonded Distance : 1.820 Molprobity Statistics. All-atom Clashscore : 2.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.42 % Favored : 98.58 % Rotamer: Outliers : 0.92 % Allowed : 8.34 % Favored : 90.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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: 1.95 (0.25), residues: 1125 helix: 1.82 (0.19), residues: 754 sheet: 0.38 (0.62), residues: 57 loop : 0.29 (0.35), residues: 314 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG A1012 TYR 0.010 0.001 TYR A 339 PHE 0.008 0.001 PHE A 993 TRP 0.030 0.001 TRP A 711 HIS 0.003 0.001 HIS A 798 Details of bonding type rmsd covalent geometry : bond 0.00270 ( 9345) covalent geometry : angle 0.46818 (12669) hydrogen bonds : bond 0.05135 ( 607) hydrogen bonds : angle 4.48122 ( 1761) *********************** 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 96 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 87 time to evaluate : 0.377 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 509 LYS cc_start: 0.8430 (OUTLIER) cc_final: 0.8210 (ttpt) REVERT: A 1210 ARG cc_start: 0.7255 (OUTLIER) cc_final: 0.6855 (mtt-85) outliers start: 9 outliers final: 7 residues processed: 92 average time/residue: 0.2572 time to fit residues: 31.8445 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 : 0.518 ------------------------------------------------------------------------------- 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 953 ASP Chi-restraints excluded: chain A residue 958 VAL Chi-restraints excluded: chain A residue 962 VAL Chi-restraints excluded: chain A residue 1210 ARG 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 6 optimal weight: 2.9990 chunk 30 optimal weight: 1.9990 chunk 111 optimal weight: 10.0000 chunk 106 optimal weight: 1.9990 chunk 87 optimal weight: 1.9990 chunk 78 optimal weight: 2.9990 chunk 64 optimal weight: 2.9990 chunk 19 optimal weight: 3.9990 chunk 2 optimal weight: 2.9990 chunk 15 optimal weight: 0.6980 chunk 42 optimal weight: 2.9990 overall best weight: 1.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 994 GLN A1216 GLN A1263 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.117902 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3084 r_free = 0.3084 target = 0.093733 restraints weight = 36366.471| |-----------------------------------------------------------------------------| r_work (start): 0.3083 rms_B_bonded: 2.10 r_work: 0.2979 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.2858 rms_B_bonded: 4.02 restraints_weight: 0.2500 r_work (final): 0.2858 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8392 moved from start: 0.4333 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.033 9345 Z= 0.194 Angle : 0.498 5.676 12669 Z= 0.280 Chirality : 0.039 0.145 1464 Planarity : 0.004 0.059 1559 Dihedral : 8.025 76.432 1335 Min Nonbonded Distance : 1.786 Molprobity Statistics. All-atom Clashscore : 3.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.78 % Favored : 98.22 % Rotamer: Outliers : 1.22 % Allowed : 8.04 % Favored : 90.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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: 1.77 (0.25), residues: 1125 helix: 1.70 (0.19), residues: 754 sheet: 0.44 (0.62), residues: 57 loop : 0.19 (0.35), residues: 314 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 180 TYR 0.012 0.001 TYR A 339 PHE 0.011 0.001 PHE A 214 TRP 0.029 0.001 TRP A 711 HIS 0.002 0.001 HIS A 152 Details of bonding type rmsd covalent geometry : bond 0.00454 ( 9345) covalent geometry : angle 0.49823 (12669) hydrogen bonds : bond 0.05537 ( 607) hydrogen bonds : angle 4.57526 ( 1761) *********************** 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 92 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 80 time to evaluate : 0.582 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 408 MET cc_start: 0.7574 (OUTLIER) cc_final: 0.7327 (mtt) REVERT: A 509 LYS cc_start: 0.8455 (OUTLIER) cc_final: 0.8247 (ttpt) REVERT: A 1133 LYS cc_start: 0.7997 (OUTLIER) cc_final: 0.7117 (tttt) REVERT: A 1210 ARG cc_start: 0.7266 (OUTLIER) cc_final: 0.6778 (mtt-85) outliers start: 12 outliers final: 8 residues processed: 87 average time/residue: 0.2576 time to fit residues: 30.4785 Evaluate side-chains 91 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 79 time to evaluate : 0.503 ------------------------------------------------------------------------------- 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 408 MET Chi-restraints excluded: chain A residue 509 LYS Chi-restraints excluded: chain A residue 761 LEU Chi-restraints excluded: chain A residue 953 ASP 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 1210 ARG 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 24 optimal weight: 1.9990 chunk 19 optimal weight: 3.9990 chunk 21 optimal weight: 1.9990 chunk 94 optimal weight: 0.9990 chunk 98 optimal weight: 0.5980 chunk 106 optimal weight: 2.9990 chunk 50 optimal weight: 0.0270 chunk 71 optimal weight: 0.8980 chunk 3 optimal weight: 0.0970 chunk 12 optimal weight: 1.9990 chunk 80 optimal weight: 0.9980 overall best weight: 0.5236 ------------------------------------------------------------------------------- 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 = 0.3445 r_free = 0.3445 target = 0.120476 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3117 r_free = 0.3117 target = 0.095900 restraints weight = 36073.988| |-----------------------------------------------------------------------------| r_work (start): 0.3098 rms_B_bonded: 2.15 r_work: 0.2994 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.2874 rms_B_bonded: 4.07 restraints_weight: 0.2500 r_work (final): 0.2874 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8327 moved from start: 0.4416 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 9345 Z= 0.109 Angle : 0.458 5.178 12669 Z= 0.255 Chirality : 0.037 0.150 1464 Planarity : 0.004 0.062 1559 Dihedral : 7.707 81.495 1335 Min Nonbonded Distance : 1.830 Molprobity Statistics. All-atom Clashscore : 3.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.33 % Favored : 98.67 % Rotamer: Outliers : 1.42 % Allowed : 7.93 % Favored : 90.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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: 2.12 (0.25), residues: 1125 helix: 1.99 (0.19), residues: 753 sheet: 0.50 (0.63), residues: 57 loop : 0.28 (0.35), residues: 315 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A1012 TYR 0.029 0.001 TYR A1259 PHE 0.008 0.001 PHE A 813 TRP 0.033 0.001 TRP A 711 HIS 0.003 0.001 HIS A 798 Details of bonding type rmsd covalent geometry : bond 0.00218 ( 9345) covalent geometry : angle 0.45843 (12669) hydrogen bonds : bond 0.04904 ( 607) hydrogen bonds : angle 4.39773 ( 1761) ********************** 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 97 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 83 time to evaluate : 0.453 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 408 MET cc_start: 0.7411 (OUTLIER) cc_final: 0.7171 (mtt) REVERT: A 509 LYS cc_start: 0.8410 (OUTLIER) cc_final: 0.8202 (ttpt) REVERT: A 1133 LYS cc_start: 0.7917 (OUTLIER) cc_final: 0.7023 (tttt) REVERT: A 1210 ARG cc_start: 0.7235 (OUTLIER) cc_final: 0.6736 (mtt-85) REVERT: A 1236 ASN cc_start: 0.8483 (OUTLIER) cc_final: 0.7965 (p0) outliers start: 14 outliers final: 7 residues processed: 92 average time/residue: 0.2646 time to fit residues: 32.7457 Evaluate side-chains 91 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 79 time to evaluate : 0.460 ------------------------------------------------------------------------------- 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 408 MET Chi-restraints excluded: chain A residue 509 LYS 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 1133 LYS Chi-restraints excluded: chain A residue 1210 ARG 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 73 optimal weight: 0.9980 chunk 28 optimal weight: 0.4980 chunk 19 optimal weight: 2.9990 chunk 102 optimal weight: 1.9990 chunk 34 optimal weight: 0.9980 chunk 104 optimal weight: 0.0270 chunk 105 optimal weight: 0.8980 chunk 59 optimal weight: 1.9990 chunk 17 optimal weight: 1.9990 chunk 61 optimal weight: 0.7980 chunk 94 optimal weight: 2.9990 overall best weight: 0.6438 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 994 GLN A1263 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3477 r_free = 0.3477 target = 0.122907 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3159 r_free = 0.3159 target = 0.098726 restraints weight = 35563.579| |-----------------------------------------------------------------------------| r_work (start): 0.3117 rms_B_bonded: 2.11 r_work: 0.3013 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.2892 rms_B_bonded: 4.02 restraints_weight: 0.2500 r_work (final): 0.2892 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8330 moved from start: 0.4499 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= 0.109 Angle : 0.449 5.852 12669 Z= 0.249 Chirality : 0.037 0.197 1464 Planarity : 0.004 0.056 1559 Dihedral : 7.543 89.011 1335 Min Nonbonded Distance : 1.827 Molprobity Statistics. All-atom Clashscore : 3.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.78 % Favored : 98.22 % Rotamer: Outliers : 1.53 % Allowed : 8.04 % Favored : 90.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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: 2.32 (0.25), residues: 1125 helix: 2.14 (0.19), residues: 753 sheet: 0.55 (0.64), residues: 57 loop : 0.35 (0.36), residues: 315 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A1012 TYR 0.011 0.001 TYR A1259 PHE 0.008 0.001 PHE A 120 TRP 0.033 0.001 TRP A 711 HIS 0.003 0.000 HIS A 798 Details of bonding type rmsd covalent geometry : bond 0.00224 ( 9345) covalent geometry : angle 0.44894 (12669) hydrogen bonds : bond 0.04721 ( 607) hydrogen bonds : angle 4.30909 ( 1761) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4327.87 seconds wall clock time: 74 minutes 0.66 seconds (4440.66 seconds total)