Starting phenix.real_space_refine on Mon Jun 9 01:46:27 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8bjf_16088/06_2025/8bjf_16088.cif Found real_map, /net/cci-nas-00/data/ceres_data/8bjf_16088/06_2025/8bjf_16088.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8bjf_16088/06_2025/8bjf_16088.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8bjf_16088/06_2025/8bjf_16088.map" model { file = "/net/cci-nas-00/data/ceres_data/8bjf_16088/06_2025/8bjf_16088.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8bjf_16088/06_2025/8bjf_16088.cif" } resolution = 3.0 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= -0.001 sd= 0.082 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: 4 Type Number sf(0) Gaussians S 43 5.16 5 C 6379 2.51 5 N 1602 2.21 5 O 1717 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 9741 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 9545 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1195, 9545 Classifications: {'peptide': 1195} Link IDs: {'PTRANS': 37, 'TRANS': 1157} Chain breaks: 3 Chain: "A" Number of atoms: 196 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 196 Unusual residues: {'CLR': 2, 'Y01': 4} Classifications: {'undetermined': 6} Link IDs: {None: 5} Time building chain proxies: 7.49, per 1000 atoms: 0.77 Number of scatterers: 9741 At special positions: 0 Unit cell: (75.712, 103.168, 145.6, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 43 16.00 O 1717 8.00 N 1602 7.00 C 6379 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.63 Conformation dependent library (CDL) restraints added in 1.4 seconds 2374 Ramachandran restraints generated. 1187 Oldfield, 0 Emsley, 1187 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2266 Finding SS restraints... Secondary structure from input PDB file: 58 helices and 6 sheets defined 72.2% alpha, 7.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.24 Creating SS restraints... Processing helix chain 'A' and resid 11 through 16 removed outlier: 3.596A pdb=" N ALA A 16 " --> pdb=" O LEU A 13 " (cutoff:3.500A) Processing helix chain 'A' and resid 17 through 23 Processing helix chain 'A' and resid 24 through 26 No H-bonds generated for 'chain 'A' and resid 24 through 26' Processing helix chain 'A' and resid 27 through 37 removed outlier: 3.617A pdb=" N PHE A 31 " --> pdb=" O LEU A 27 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N LYS A 36 " --> pdb=" O LYS A 32 " (cutoff:3.500A) Processing helix chain 'A' and resid 40 through 44 Processing helix chain 'A' and resid 48 through 51 Processing helix chain 'A' and resid 52 through 74 removed outlier: 3.513A pdb=" N PHE A 63 " --> pdb=" O GLU A 59 " (cutoff:3.500A) Processing helix chain 'A' and resid 79 through 93 removed outlier: 5.361A pdb=" N LYS A 90 " --> pdb=" O LYS A 86 " (cutoff:3.500A) removed outlier: 5.429A pdb=" N SER A 91 " --> pdb=" O CYS A 87 " (cutoff:3.500A) Processing helix chain 'A' and resid 94 through 122 removed outlier: 4.122A pdb=" N PHE A 98 " --> pdb=" O VAL A 94 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N VAL A 107 " --> pdb=" O GLU A 103 " (cutoff:3.500A) Proline residue: A 110 - end of helix removed outlier: 3.755A pdb=" N PHE A 120 " --> pdb=" O ILE A 116 " (cutoff:3.500A) Processing helix chain 'A' and resid 127 through 150 Processing helix chain 'A' and resid 150 through 181 removed outlier: 4.243A pdb=" N LEU A 154 " --> pdb=" O ILE A 150 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N GLY A 163 " --> pdb=" O VAL A 159 " (cutoff:3.500A) removed outlier: 3.727A 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 removed outlier: 3.628A pdb=" N LEU A 198 " --> pdb=" O ILE A 194 " (cutoff:3.500A) 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: 4.157A pdb=" N THR A 209 " --> pdb=" O PHE A 205 " (cutoff:3.500A) removed outlier: 4.431A pdb=" N VAL A 210 " --> pdb=" O ASP A 206 " (cutoff:3.500A) removed outlier: 4.179A 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 Processing helix chain 'A' and resid 236 through 282 removed outlier: 4.039A pdb=" N GLY A 240 " --> pdb=" O SER A 236 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N VAL A 243 " --> pdb=" O ALA A 239 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N LEU A 248 " --> pdb=" O LEU A 244 " (cutoff:3.500A) Proline residue: A 249 - end of helix removed outlier: 3.717A pdb=" N THR A 267 " --> pdb=" O SER A 263 " (cutoff:3.500A) removed outlier: 4.159A pdb=" N PHE A 268 " --> pdb=" O LYS A 264 " (cutoff:3.500A) Processing helix chain 'A' and resid 282 through 290 Processing helix chain 'A' and resid 291 through 342 removed outlier: 3.828A pdb=" N LEU A 316 " --> pdb=" O ARG A 312 " (cutoff:3.500A) removed outlier: 4.762A pdb=" N SER A 328 " --> pdb=" O PHE A 324 " (cutoff:3.500A) removed outlier: 4.975A pdb=" N LYS A 329 " --> pdb=" O PHE A 325 " (cutoff:3.500A) Processing helix chain 'A' and resid 347 through 367 removed outlier: 3.981A pdb=" N LEU A 363 " --> pdb=" O GLY A 359 " (cutoff:3.500A) removed outlier: 4.144A pdb=" N THR A 364 " --> pdb=" O ALA A 360 " (cutoff:3.500A) Processing helix chain 'A' and resid 367 through 391 removed outlier: 3.620A pdb=" N PHE A 389 " --> pdb=" O ARG A 385 " (cutoff:3.500A) Processing helix chain 'A' and resid 452 through 459 Processing helix chain 'A' and resid 489 through 495 Processing helix chain 'A' and resid 500 through 510 Processing helix chain 'A' and resid 512 through 517 Processing helix chain 'A' and resid 536 through 552 Processing helix chain 'A' and resid 566 through 576 Processing helix chain 'A' and resid 593 through 600 Processing helix chain 'A' and resid 616 through 620 Processing helix chain 'A' and resid 697 through 706 removed outlier: 3.536A pdb=" N TYR A 701 " --> pdb=" O GLY A 697 " (cutoff:3.500A) Processing helix chain 'A' and resid 710 through 744 removed outlier: 3.754A pdb=" N ASP A 732 " --> pdb=" O TYR A 728 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N LEU A 735 " --> pdb=" O GLN A 731 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N MET A 744 " --> pdb=" O ASN A 740 " (cutoff:3.500A) Processing helix chain 'A' and resid 760 through 807 Processing helix chain 'A' and resid 809 through 816 removed outlier: 3.672A pdb=" N PHE A 813 " --> pdb=" O PRO A 809 " (cutoff:3.500A) Processing helix chain 'A' and resid 817 through 827 removed outlier: 3.899A pdb=" N ARG A 824 " --> pdb=" O ARG A 820 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N PHE A 825 " --> pdb=" O ILE A 821 " (cutoff:3.500A) Processing helix chain 'A' and resid 827 through 835 Processing helix chain 'A' and resid 835 through 861 removed outlier: 3.603A pdb=" N ALA A 857 " --> pdb=" O VAL A 853 " (cutoff:3.500A) Processing helix chain 'A' and resid 862 through 866 removed outlier: 3.503A pdb=" N ALA A 865 " --> pdb=" O PRO A 862 " (cutoff:3.500A) Processing helix chain 'A' and resid 867 through 910 removed outlier: 3.771A pdb=" N LEU A 871 " --> pdb=" O PRO A 867 " (cutoff:3.500A) removed outlier: 4.127A pdb=" N THR A 885 " --> pdb=" O TYR A 881 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N ASP A 888 " --> pdb=" O GLU A 884 " (cutoff:3.500A) removed outlier: 4.273A pdb=" N SER A 898 " --> pdb=" O SER A 894 " (cutoff:3.500A) Proline residue: A 899 - end of helix removed outlier: 3.516A pdb=" N LEU A 904 " --> pdb=" O VAL A 900 " (cutoff:3.500A) Processing helix chain 'A' and resid 910 through 917 Processing helix chain 'A' and resid 919 through 970 removed outlier: 3.553A pdb=" N ARG A 951 " --> pdb=" O TRP A 947 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N CYS A 956 " --> pdb=" O LEU A 952 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N LEU A 968 " --> pdb=" O ALA A 964 " (cutoff:3.500A) Processing helix chain 'A' and resid 975 through 987 Processing helix chain 'A' and resid 988 through 998 removed outlier: 3.705A pdb=" N MET A 992 " --> pdb=" O THR A 988 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N GLN A 994 " --> pdb=" O MET A 990 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N TRP A 995 " --> pdb=" O GLY A 991 " (cutoff:3.500A) Processing helix chain 'A' and resid 1000 through 1016 removed outlier: 4.876A pdb=" N SER A1009 " --> pdb=" O ASN A1005 " (cutoff:3.500A) Processing helix chain 'A' and resid 1080 through 1089 removed outlier: 3.882A pdb=" N ILE A1085 " --> pdb=" O LYS A1081 " (cutoff:3.500A) Processing helix chain 'A' and resid 1109 through 1115 Processing helix chain 'A' and resid 1131 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 1167 Processing helix chain 'A' and resid 1171 through 1175 Processing helix chain 'A' and resid 1178 through 1194 Processing helix chain 'A' and resid 1203 through 1207 Processing helix chain 'A' and resid 1208 through 1223 Processing helix chain 'A' and resid 1234 through 1238 Processing helix chain 'A' and resid 1257 through 1264 removed outlier: 3.614A pdb=" N ASN A1264 " --> pdb=" O VAL A1260 " (cutoff:3.500A) Processing helix chain 'A' and resid 1267 through 1275 Processing helix chain 'A' and resid 1276 through 1278 No H-bonds generated for 'chain 'A' and resid 1276 through 1278' Processing helix chain 'A' and resid 1279 through 1292 removed outlier: 3.688A pdb=" N ALA A1283 " --> pdb=" O ALA A1279 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N VAL A1291 " --> pdb=" O THR A1287 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N TYR A1292 " --> pdb=" O ALA A1288 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 428 through 435 removed outlier: 3.597A pdb=" N LEU A 428 " --> pdb=" O ALA A 417 " (cutoff:3.500A) removed outlier: 4.519A pdb=" N PHE A 415 " --> pdb=" O GLY A 430 " (cutoff:3.500A) removed outlier: 6.163A pdb=" N SER A 432 " --> pdb=" O GLN A 413 " (cutoff:3.500A) removed outlier: 6.459A pdb=" N GLN A 413 " --> pdb=" O SER A 432 " (cutoff:3.500A) removed outlier: 6.814A pdb=" N THR A 434 " --> pdb=" O HIS A 411 " (cutoff:3.500A) removed outlier: 7.188A pdb=" N HIS A 411 " --> pdb=" O THR A 434 " (cutoff:3.500A) removed outlier: 4.367A pdb=" N PHE A 415 " --> pdb=" O HIS A 466 " (cutoff:3.500A) removed outlier: 6.765A pdb=" N HIS 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: 6.208A pdb=" N ALA A 476 " --> pdb=" O LEU A 557 " (cutoff:3.500A) removed outlier: 6.221A pdb=" N LEU A 441 " --> pdb=" O LEU A 589 " (cutoff:3.500A) removed outlier: 6.465A pdb=" N LEU A 440 " --> pdb=" O GLN A 602 " (cutoff:3.500A) removed outlier: 7.620A pdb=" N LEU A 604 " --> pdb=" O LEU A 440 " (cutoff:3.500A) removed outlier: 6.291A pdb=" N ALA A 442 " --> pdb=" O LEU A 604 " (cutoff:3.500A) removed outlier: 7.615A pdb=" N LEU A 606 " --> pdb=" O ALA A 442 " (cutoff:3.500A) removed outlier: 6.116A pdb=" N VAL A 444 " --> pdb=" O LEU A 606 " (cutoff:3.500A) removed outlier: 6.467A pdb=" N LYS A 607 " --> pdb=" O MET A 611 " (cutoff:3.500A) removed outlier: 5.305A pdb=" N MET A 611 " --> pdb=" O LYS A 607 " (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: 6.954A pdb=" N LYS A1059 " --> pdb=" O ASN A1047 " (cutoff:3.500A) removed outlier: 6.562A pdb=" N ASN A1047 " --> pdb=" O LYS A1059 " (cutoff:3.500A) removed outlier: 5.156A pdb=" N LEU A1061 " --> pdb=" O ASN A1045 " (cutoff:3.500A) removed outlier: 5.151A pdb=" N PHE A1043 " --> pdb=" O TRP A1099 " (cutoff:3.500A) removed outlier: 7.010A pdb=" N TRP A1099 " --> pdb=" O PHE A1043 " (cutoff:3.500A) removed outlier: 5.122A pdb=" N ASN A1045 " --> pdb=" O LYS A1097 " (cutoff:3.500A) removed outlier: 4.778A pdb=" N LYS A1097 " --> pdb=" O ASN A1045 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 1118 through 1120 removed outlier: 6.565A pdb=" N LEU A1198 " --> pdb=" O LEU A1229 " (cutoff:3.500A) removed outlier: 7.800A pdb=" N ILE A1231 " --> pdb=" O LEU A1198 " (cutoff:3.500A) removed outlier: 6.285A pdb=" N ILE A1200 " --> pdb=" O ILE A1231 " (cutoff:3.500A) removed outlier: 6.092A pdb=" N LYS A1070 " --> pdb=" O LYS A1243 " (cutoff:3.500A) removed outlier: 7.208A pdb=" N MET A1245 " --> pdb=" O LYS A1070 " (cutoff:3.500A) removed outlier: 6.051A pdb=" N GLY A1072 " --> pdb=" O MET A1245 " (cutoff:3.500A) removed outlier: 7.162A pdb=" N LEU A1247 " --> pdb=" O GLY A1072 " (cutoff:3.500A) removed outlier: 6.174A pdb=" N VAL A1074 " --> pdb=" O LEU A1247 " (cutoff:3.500A) removed outlier: 6.896A pdb=" N ASP A1248 " --> pdb=" O LEU A1252 " (cutoff:3.500A) removed outlier: 5.314A pdb=" N LEU A1252 " --> pdb=" O ASP A1248 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 1129 through 1130 removed outlier: 4.146A pdb=" N GLY A1129 " --> pdb=" O LEU A1170 " (cutoff:3.500A) 618 hydrogen bonds defined for protein. 1782 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: 4.01 Time building geometry restraints manager: 3.12 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 3035 1.34 - 1.46: 1831 1.46 - 1.58: 5020 1.58 - 1.69: 7 1.69 - 1.81: 70 Bond restraints: 9963 Sorted by residual: bond pdb=" CAI Y01 A1404 " pdb=" CAK Y01 A1404 " ideal model delta sigma weight residual 1.492 1.404 0.088 2.00e-02 2.50e+03 1.95e+01 bond pdb=" CAI Y01 A1406 " pdb=" CAK Y01 A1406 " ideal model delta sigma weight residual 1.492 1.405 0.087 2.00e-02 2.50e+03 1.91e+01 bond pdb=" CAI Y01 A1402 " pdb=" CAK Y01 A1402 " ideal model delta sigma weight residual 1.492 1.406 0.086 2.00e-02 2.50e+03 1.85e+01 bond pdb=" CAI Y01 A1403 " pdb=" CAK Y01 A1403 " ideal model delta sigma weight residual 1.492 1.407 0.085 2.00e-02 2.50e+03 1.82e+01 bond pdb=" C23 CLR A1405 " pdb=" C24 CLR A1405 " ideal model delta sigma weight residual 1.525 1.578 -0.053 2.00e-02 2.50e+03 7.12e+00 ... (remaining 9958 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.42: 13324 2.42 - 4.84: 172 4.84 - 7.25: 23 7.25 - 9.67: 10 9.67 - 12.09: 8 Bond angle restraints: 13537 Sorted by residual: angle pdb=" OAG Y01 A1404 " pdb=" CAY Y01 A1404 " pdb=" OAW Y01 A1404 " ideal model delta sigma weight residual 123.38 111.29 12.09 3.00e+00 1.11e-01 1.62e+01 angle pdb=" CAM Y01 A1404 " pdb=" CAY Y01 A1404 " pdb=" OAW Y01 A1404 " ideal model delta sigma weight residual 111.19 123.23 -12.04 3.00e+00 1.11e-01 1.61e+01 angle pdb=" CAM Y01 A1403 " pdb=" CAY Y01 A1403 " pdb=" OAW Y01 A1403 " ideal model delta sigma weight residual 111.19 123.00 -11.81 3.00e+00 1.11e-01 1.55e+01 angle pdb=" OAG Y01 A1403 " pdb=" CAY Y01 A1403 " pdb=" OAW Y01 A1403 " ideal model delta sigma weight residual 123.38 111.72 11.66 3.00e+00 1.11e-01 1.51e+01 angle pdb=" OAG Y01 A1402 " pdb=" CAY Y01 A1402 " pdb=" OAW Y01 A1402 " ideal model delta sigma weight residual 123.38 111.99 11.39 3.00e+00 1.11e-01 1.44e+01 ... (remaining 13532 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.21: 5965 24.21 - 48.42: 223 48.42 - 72.62: 30 72.62 - 96.83: 16 96.83 - 121.04: 2 Dihedral angle restraints: 6236 sinusoidal: 2742 harmonic: 3494 Sorted by residual: dihedral pdb=" CA MET A 409 " pdb=" C MET A 409 " pdb=" N VAL A 410 " pdb=" CA VAL A 410 " ideal model delta harmonic sigma weight residual 180.00 153.73 26.27 0 5.00e+00 4.00e-02 2.76e+01 dihedral pdb=" CA SER A 396 " pdb=" C SER A 396 " pdb=" N GLN A 397 " pdb=" CA GLN A 397 " ideal model delta harmonic sigma weight residual -180.00 -153.91 -26.09 0 5.00e+00 4.00e-02 2.72e+01 dihedral pdb=" CA ARG A 37 " pdb=" C ARG A 37 " pdb=" N ARG A 38 " pdb=" CA ARG A 38 " ideal model delta harmonic sigma weight residual 180.00 154.46 25.54 0 5.00e+00 4.00e-02 2.61e+01 ... (remaining 6233 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.076: 1432 0.076 - 0.152: 135 0.152 - 0.229: 8 0.229 - 0.305: 6 0.305 - 0.381: 4 Chirality restraints: 1585 Sorted by residual: chirality pdb=" C17 CLR A1401 " pdb=" C13 CLR A1401 " pdb=" C16 CLR A1401 " pdb=" C20 CLR A1401 " both_signs ideal model delta sigma weight residual False 2.55 2.93 -0.38 2.00e-01 2.50e+01 3.63e+00 chirality pdb=" C20 CLR A1405 " pdb=" C17 CLR A1405 " pdb=" C21 CLR A1405 " pdb=" C22 CLR A1405 " both_signs ideal model delta sigma weight residual False 2.59 2.92 -0.33 2.00e-01 2.50e+01 2.72e+00 chirality pdb=" C13 CLR A1405 " pdb=" C12 CLR A1405 " pdb=" C14 CLR A1405 " pdb=" C17 CLR A1405 " both_signs ideal model delta sigma weight residual False -2.93 -3.24 0.31 2.00e-01 2.50e+01 2.45e+00 ... (remaining 1582 not shown) Planarity restraints: 1648 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR A1292 " -0.010 2.00e-02 2.50e+03 2.06e-02 8.51e+00 pdb=" CG TYR A1292 " 0.012 2.00e-02 2.50e+03 pdb=" CD1 TYR A1292 " -0.026 2.00e-02 2.50e+03 pdb=" CD2 TYR A1292 " 0.000 2.00e-02 2.50e+03 pdb=" CE1 TYR A1292 " 0.027 2.00e-02 2.50e+03 pdb=" CE2 TYR A1292 " 0.001 2.00e-02 2.50e+03 pdb=" CZ TYR A1292 " 0.027 2.00e-02 2.50e+03 pdb=" OH TYR A1292 " -0.032 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 891 " -0.211 9.50e-02 1.11e+02 9.51e-02 6.67e+00 pdb=" NE ARG A 891 " 0.019 2.00e-02 2.50e+03 pdb=" CZ ARG A 891 " -0.016 2.00e-02 2.50e+03 pdb=" NH1 ARG A 891 " 0.008 2.00e-02 2.50e+03 pdb=" NH2 ARG A 891 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A1030 " -0.196 9.50e-02 1.11e+02 8.84e-02 6.27e+00 pdb=" NE ARG A1030 " 0.019 2.00e-02 2.50e+03 pdb=" CZ ARG A1030 " -0.019 2.00e-02 2.50e+03 pdb=" NH1 ARG A1030 " 0.009 2.00e-02 2.50e+03 pdb=" NH2 ARG A1030 " 0.000 2.00e-02 2.50e+03 ... (remaining 1645 not shown) Histogram of nonbonded interaction distances: 2.27 - 2.80: 2312 2.80 - 3.32: 9793 3.32 - 3.85: 16125 3.85 - 4.37: 20135 4.37 - 4.90: 33265 Nonbonded interactions: 81630 Sorted by model distance: nonbonded pdb=" NZ LYS A1070 " pdb=" O CYS A1226 " model vdw 2.273 3.120 nonbonded pdb=" NZ LYS A1081 " pdb=" OE2 GLU A1202 " model vdw 2.279 3.120 nonbonded pdb=" OG1 THR A 269 " pdb=" OE2 GLU A 306 " model vdw 2.296 3.040 nonbonded pdb=" ND1 HIS A 35 " pdb=" OE1 GLU A 884 " model vdw 2.308 3.120 nonbonded pdb=" OH TYR A 92 " pdb=" O THR A 209 " model vdw 2.308 3.040 ... (remaining 81625 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: 64.540 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.450 Check model and map are aligned: 0.080 Set scattering table: 0.100 Process input model: 28.840 Find NCS groups from input model: 0.120 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:13.310 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 107.500 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8095 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.088 9963 Z= 0.223 Angle : 0.756 12.091 13537 Z= 0.352 Chirality : 0.051 0.381 1585 Planarity : 0.008 0.095 1648 Dihedral : 13.711 121.039 3970 Min Nonbonded Distance : 2.273 Molprobity Statistics. All-atom Clashscore : 3.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 0.38 % Allowed : 3.17 % Favored : 96.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -1.24 (0.22), residues: 1187 helix: -1.01 (0.15), residues: 768 sheet: 0.27 (0.70), residues: 57 loop : -0.08 (0.34), residues: 362 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP A 419 HIS 0.006 0.001 HIS A 153 PHE 0.026 0.002 PHE A 336 TYR 0.032 0.004 TYR A1292 ARG 0.022 0.003 ARG A1030 Details of bonding type rmsd hydrogen bonds : bond 0.20184 ( 618) hydrogen bonds : angle 7.61028 ( 1782) covalent geometry : bond 0.00485 ( 9963) covalent geometry : angle 0.75622 (13537) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2374 Ramachandran restraints generated. 1187 Oldfield, 0 Emsley, 1187 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2374 Ramachandran restraints generated. 1187 Oldfield, 0 Emsley, 1187 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 1042 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 117 time to evaluate : 1.276 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 36 LYS cc_start: 0.8283 (OUTLIER) cc_final: 0.8081 (mtpt) REVERT: A 52 ARG cc_start: 0.7724 (mtt180) cc_final: 0.7432 (mmt180) REVERT: A 126 MET cc_start: 0.7639 (mmm) cc_final: 0.7402 (mpt) REVERT: A 611 MET cc_start: 0.6782 (ttp) cc_final: 0.6222 (tmt) REVERT: A 803 GLU cc_start: 0.7768 (tp30) cc_final: 0.7553 (tp30) REVERT: A 887 ARG cc_start: 0.7279 (mtm110) cc_final: 0.6759 (mtt90) REVERT: A 909 GLN cc_start: 0.7928 (tt0) cc_final: 0.7598 (tt0) REVERT: A 998 ARG cc_start: 0.6981 (mtm-85) cc_final: 0.6606 (mpt90) REVERT: A 1004 GLU cc_start: 0.7690 (mt-10) cc_final: 0.7362 (mt-10) REVERT: A 1042 ILE cc_start: 0.7287 (mt) cc_final: 0.7041 (pt) REVERT: A 1044 ASP cc_start: 0.6924 (t0) cc_final: 0.5902 (p0) REVERT: A 1097 LYS cc_start: 0.7350 (mttt) cc_final: 0.6822 (mttp) REVERT: A 1098 ILE cc_start: 0.7046 (mt) cc_final: 0.6790 (mt) REVERT: A 1166 MET cc_start: 0.5909 (mmm) cc_final: 0.5569 (mmm) REVERT: A 1243 LYS cc_start: 0.5774 (mttt) cc_final: 0.5456 (mtmt) outliers start: 4 outliers final: 1 residues processed: 121 average time/residue: 1.3397 time to fit residues: 173.8370 Evaluate side-chains 87 residues out of total 1042 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 85 time to evaluate : 1.025 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 LYS Chi-restraints excluded: chain A residue 1103 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 100 optimal weight: 3.9990 chunk 90 optimal weight: 0.8980 chunk 50 optimal weight: 1.9990 chunk 30 optimal weight: 0.9990 chunk 60 optimal weight: 2.9990 chunk 48 optimal weight: 4.9990 chunk 93 optimal weight: 0.6980 chunk 36 optimal weight: 0.9980 chunk 56 optimal weight: 0.0040 chunk 69 optimal weight: 0.1980 chunk 108 optimal weight: 0.7980 overall best weight: 0.5192 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 251 GLN A 397 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4117 r_free = 0.4117 target = 0.197664 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.119519 restraints weight = 9807.501| |-----------------------------------------------------------------------------| r_work (start): 0.3241 rms_B_bonded: 2.43 r_work: 0.3045 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.2891 rms_B_bonded: 4.25 restraints_weight: 0.2500 r_work (final): 0.2891 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7377 moved from start: 0.1677 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 9963 Z= 0.145 Angle : 0.582 8.677 13537 Z= 0.298 Chirality : 0.042 0.189 1585 Planarity : 0.004 0.052 1648 Dihedral : 6.660 57.807 1707 Min Nonbonded Distance : 2.612 Molprobity Statistics. All-atom Clashscore : 5.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.18 % Favored : 98.82 % Rotamer: Outliers : 1.44 % Allowed : 7.01 % Favored : 91.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.50 (0.24), residues: 1187 helix: 0.59 (0.17), residues: 794 sheet: -0.15 (0.65), residues: 59 loop : 0.12 (0.36), residues: 334 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 733 HIS 0.007 0.001 HIS A 934 PHE 0.022 0.002 PHE A 336 TYR 0.015 0.002 TYR A 119 ARG 0.006 0.000 ARG A 547 Details of bonding type rmsd hydrogen bonds : bond 0.04712 ( 618) hydrogen bonds : angle 4.76207 ( 1782) covalent geometry : bond 0.00328 ( 9963) covalent geometry : angle 0.58152 (13537) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2374 Ramachandran restraints generated. 1187 Oldfield, 0 Emsley, 1187 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2374 Ramachandran restraints generated. 1187 Oldfield, 0 Emsley, 1187 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 1042 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 107 time to evaluate : 1.091 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 36 LYS cc_start: 0.7874 (OUTLIER) cc_final: 0.7652 (mtmt) REVERT: A 52 ARG cc_start: 0.7284 (mtt180) cc_final: 0.6409 (mmt180) REVERT: A 74 ASP cc_start: 0.6841 (t0) cc_final: 0.6425 (t0) REVERT: A 126 MET cc_start: 0.7403 (mmm) cc_final: 0.6882 (mpt) REVERT: A 207 GLN cc_start: 0.7578 (mt0) cc_final: 0.7051 (mt0) REVERT: A 528 ILE cc_start: 0.5870 (OUTLIER) cc_final: 0.5529 (mm) REVERT: A 558 LEU cc_start: 0.7446 (mm) cc_final: 0.7150 (mm) REVERT: A 611 MET cc_start: 0.6948 (ttp) cc_final: 0.6141 (tmt) REVERT: A 803 GLU cc_start: 0.7520 (tp30) cc_final: 0.6910 (tp30) REVERT: A 887 ARG cc_start: 0.6311 (mtm110) cc_final: 0.5588 (mtt90) REVERT: A 909 GLN cc_start: 0.7588 (tt0) cc_final: 0.7098 (tt0) REVERT: A 998 ARG cc_start: 0.7117 (mtm-85) cc_final: 0.6143 (mpt90) REVERT: A 1011 GLU cc_start: 0.6789 (pt0) cc_final: 0.6201 (tp30) REVERT: A 1042 ILE cc_start: 0.6725 (mt) cc_final: 0.6496 (pt) REVERT: A 1044 ASP cc_start: 0.6579 (t0) cc_final: 0.5593 (p0) REVERT: A 1093 GLU cc_start: 0.8783 (mm-30) cc_final: 0.8415 (mp0) REVERT: A 1097 LYS cc_start: 0.6863 (mttt) cc_final: 0.6486 (mttp) REVERT: A 1166 MET cc_start: 0.4774 (mmm) cc_final: 0.4522 (mmm) REVERT: A 1253 LYS cc_start: 0.7122 (mmtt) cc_final: 0.6289 (mtpp) outliers start: 15 outliers final: 4 residues processed: 116 average time/residue: 1.2940 time to fit residues: 161.6930 Evaluate side-chains 92 residues out of total 1042 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 86 time to evaluate : 1.143 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 LYS Chi-restraints excluded: chain A residue 50 GLU Chi-restraints excluded: chain A residue 344 SER Chi-restraints excluded: chain A residue 528 ILE Chi-restraints excluded: chain A residue 826 SER Chi-restraints excluded: chain A residue 1057 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 19 optimal weight: 0.0070 chunk 76 optimal weight: 0.0870 chunk 87 optimal weight: 0.9980 chunk 5 optimal weight: 1.9990 chunk 44 optimal weight: 0.7980 chunk 99 optimal weight: 4.9990 chunk 116 optimal weight: 7.9990 chunk 1 optimal weight: 0.0050 chunk 13 optimal weight: 0.9990 chunk 4 optimal weight: 0.7980 chunk 6 optimal weight: 3.9990 overall best weight: 0.3390 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 153 HIS A1148 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4175 r_free = 0.4175 target = 0.202738 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3517 r_free = 0.3517 target = 0.133409 restraints weight = 9963.723| |-----------------------------------------------------------------------------| r_work (start): 0.3358 rms_B_bonded: 2.11 r_work: 0.3096 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.2948 rms_B_bonded: 4.02 restraints_weight: 0.2500 r_work (final): 0.2948 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7544 moved from start: 0.2193 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 9963 Z= 0.117 Angle : 0.512 8.792 13537 Z= 0.259 Chirality : 0.039 0.183 1585 Planarity : 0.004 0.054 1648 Dihedral : 6.202 59.972 1705 Min Nonbonded Distance : 2.623 Molprobity Statistics. All-atom Clashscore : 5.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.85 % Favored : 98.15 % Rotamer: Outliers : 1.54 % Allowed : 8.54 % Favored : 89.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.22 (0.24), residues: 1187 helix: 1.19 (0.18), residues: 785 sheet: -0.07 (0.59), residues: 69 loop : 0.32 (0.36), residues: 333 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 733 HIS 0.005 0.001 HIS A 153 PHE 0.024 0.001 PHE A 336 TYR 0.011 0.001 TYR A 119 ARG 0.007 0.000 ARG A 815 Details of bonding type rmsd hydrogen bonds : bond 0.04242 ( 618) hydrogen bonds : angle 4.38981 ( 1782) covalent geometry : bond 0.00255 ( 9963) covalent geometry : angle 0.51180 (13537) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2374 Ramachandran restraints generated. 1187 Oldfield, 0 Emsley, 1187 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2374 Ramachandran restraints generated. 1187 Oldfield, 0 Emsley, 1187 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 1042 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 100 time to evaluate : 1.039 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 36 LYS cc_start: 0.8071 (OUTLIER) cc_final: 0.7860 (mtmt) REVERT: A 52 ARG cc_start: 0.7478 (mtt180) cc_final: 0.6695 (mmt180) REVERT: A 74 ASP cc_start: 0.7131 (t0) cc_final: 0.6560 (t0) REVERT: A 126 MET cc_start: 0.7510 (mmm) cc_final: 0.7020 (mpt) REVERT: A 207 GLN cc_start: 0.7756 (mt0) cc_final: 0.7227 (mt0) REVERT: A 611 MET cc_start: 0.6853 (ttp) cc_final: 0.6082 (tmt) REVERT: A 803 GLU cc_start: 0.7705 (tp30) cc_final: 0.7179 (tp30) REVERT: A 909 GLN cc_start: 0.7740 (tt0) cc_final: 0.7283 (tt0) REVERT: A 998 ARG cc_start: 0.7458 (mtm-85) cc_final: 0.6469 (mpt90) REVERT: A 1011 GLU cc_start: 0.7137 (pt0) cc_final: 0.6471 (tp30) REVERT: A 1042 ILE cc_start: 0.6971 (mt) cc_final: 0.6701 (pt) REVERT: A 1044 ASP cc_start: 0.6598 (t0) cc_final: 0.5774 (p0) REVERT: A 1093 GLU cc_start: 0.8732 (mm-30) cc_final: 0.8333 (mp0) REVERT: A 1097 LYS cc_start: 0.7031 (mttt) cc_final: 0.6659 (mttp) REVERT: A 1166 MET cc_start: 0.5045 (mmm) cc_final: 0.4833 (mmm) REVERT: A 1169 GLU cc_start: 0.6772 (mt-10) cc_final: 0.6161 (tm-30) outliers start: 16 outliers final: 6 residues processed: 110 average time/residue: 1.4376 time to fit residues: 169.7164 Evaluate side-chains 91 residues out of total 1042 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 84 time to evaluate : 1.655 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 LYS Chi-restraints excluded: chain A residue 44 MET Chi-restraints excluded: chain A residue 344 SER Chi-restraints excluded: chain A residue 395 ILE Chi-restraints excluded: chain A residue 409 MET Chi-restraints excluded: chain A residue 984 SER Chi-restraints excluded: chain A residue 1057 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 80 optimal weight: 0.2980 chunk 58 optimal weight: 9.9990 chunk 77 optimal weight: 0.5980 chunk 84 optimal weight: 0.9980 chunk 81 optimal weight: 1.9990 chunk 3 optimal weight: 0.6980 chunk 92 optimal weight: 0.0170 chunk 100 optimal weight: 0.8980 chunk 15 optimal weight: 0.3980 chunk 20 optimal weight: 0.8980 chunk 16 optimal weight: 0.5980 overall best weight: 0.3818 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 831 HIS A1148 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4290 r_free = 0.4290 target = 0.210020 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3785 r_free = 0.3785 target = 0.151592 restraints weight = 9786.827| |-----------------------------------------------------------------------------| r_work (start): 0.3571 rms_B_bonded: 2.48 r_work: 0.3216 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.3071 rms_B_bonded: 3.96 restraints_weight: 0.2500 r_work (final): 0.3071 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7749 moved from start: 0.2456 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 9963 Z= 0.119 Angle : 0.497 7.316 13537 Z= 0.252 Chirality : 0.039 0.182 1585 Planarity : 0.004 0.052 1648 Dihedral : 6.052 57.998 1705 Min Nonbonded Distance : 2.624 Molprobity Statistics. All-atom Clashscore : 5.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.68 % Favored : 98.32 % Rotamer: Outliers : 1.34 % Allowed : 10.46 % Favored : 88.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.49 (0.24), residues: 1187 helix: 1.40 (0.18), residues: 790 sheet: 0.12 (0.61), residues: 69 loop : 0.39 (0.37), residues: 328 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 733 HIS 0.005 0.001 HIS A 153 PHE 0.022 0.001 PHE A 336 TYR 0.011 0.001 TYR A 556 ARG 0.005 0.000 ARG A 815 Details of bonding type rmsd hydrogen bonds : bond 0.04065 ( 618) hydrogen bonds : angle 4.23921 ( 1782) covalent geometry : bond 0.00265 ( 9963) covalent geometry : angle 0.49709 (13537) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2374 Ramachandran restraints generated. 1187 Oldfield, 0 Emsley, 1187 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2374 Ramachandran restraints generated. 1187 Oldfield, 0 Emsley, 1187 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 1042 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 93 time to evaluate : 1.182 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 52 ARG cc_start: 0.7643 (mtt180) cc_final: 0.6913 (mmt180) REVERT: A 74 ASP cc_start: 0.7349 (t0) cc_final: 0.6706 (t0) REVERT: A 126 MET cc_start: 0.7549 (mmm) cc_final: 0.7098 (mpt) REVERT: A 207 GLN cc_start: 0.7987 (mt0) cc_final: 0.7527 (mt0) REVERT: A 611 MET cc_start: 0.6761 (ttp) cc_final: 0.6042 (tmt) REVERT: A 803 GLU cc_start: 0.7864 (tp30) cc_final: 0.7310 (tp30) REVERT: A 909 GLN cc_start: 0.7853 (tt0) cc_final: 0.7392 (tt0) REVERT: A 998 ARG cc_start: 0.7682 (mtm-85) cc_final: 0.6735 (mpt90) REVERT: A 1011 GLU cc_start: 0.7335 (pt0) cc_final: 0.6640 (tp30) REVERT: A 1044 ASP cc_start: 0.6638 (t0) cc_final: 0.6057 (p0) REVERT: A 1093 GLU cc_start: 0.8663 (mm-30) cc_final: 0.8245 (mp0) REVERT: A 1097 LYS cc_start: 0.7160 (mttt) cc_final: 0.6787 (mttp) REVERT: A 1166 MET cc_start: 0.5154 (mmm) cc_final: 0.4923 (mmm) REVERT: A 1169 GLU cc_start: 0.6949 (mt-10) cc_final: 0.6468 (tm-30) REVERT: A 1243 LYS cc_start: 0.5306 (mttt) cc_final: 0.4919 (mptt) outliers start: 14 outliers final: 7 residues processed: 101 average time/residue: 1.6517 time to fit residues: 180.1459 Evaluate side-chains 93 residues out of total 1042 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 86 time to evaluate : 2.167 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 MET Chi-restraints excluded: chain A residue 344 SER Chi-restraints excluded: chain A residue 395 ILE Chi-restraints excluded: chain A residue 806 LEU Chi-restraints excluded: chain A residue 984 SER Chi-restraints excluded: chain A residue 1057 VAL Chi-restraints excluded: chain A residue 1061 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 96 optimal weight: 10.0000 chunk 64 optimal weight: 0.8980 chunk 102 optimal weight: 0.0370 chunk 29 optimal weight: 3.9990 chunk 17 optimal weight: 0.5980 chunk 82 optimal weight: 1.9990 chunk 117 optimal weight: 6.9990 chunk 7 optimal weight: 0.3980 chunk 68 optimal weight: 1.9990 chunk 113 optimal weight: 6.9990 chunk 74 optimal weight: 0.9980 overall best weight: 0.5858 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1148 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4056 r_free = 0.4056 target = 0.192460 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3512 r_free = 0.3512 target = 0.135745 restraints weight = 9837.350| |-----------------------------------------------------------------------------| r_work (start): 0.3453 rms_B_bonded: 3.09 r_work: 0.2997 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.2853 rms_B_bonded: 4.43 restraints_weight: 0.2500 r_work (final): 0.2853 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8082 moved from start: 0.2506 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 9963 Z= 0.137 Angle : 0.506 7.020 13537 Z= 0.257 Chirality : 0.040 0.186 1585 Planarity : 0.004 0.050 1648 Dihedral : 6.076 57.856 1701 Min Nonbonded Distance : 2.622 Molprobity Statistics. All-atom Clashscore : 5.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.43 % Favored : 98.57 % Rotamer: Outliers : 1.63 % Allowed : 11.04 % Favored : 87.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.53 (0.24), residues: 1187 helix: 1.42 (0.18), residues: 786 sheet: 0.12 (0.61), residues: 69 loop : 0.45 (0.37), residues: 332 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 733 HIS 0.006 0.001 HIS A 934 PHE 0.023 0.002 PHE A 336 TYR 0.010 0.001 TYR A 339 ARG 0.007 0.000 ARG A 815 Details of bonding type rmsd hydrogen bonds : bond 0.04201 ( 618) hydrogen bonds : angle 4.26546 ( 1782) covalent geometry : bond 0.00318 ( 9963) covalent geometry : angle 0.50589 (13537) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2374 Ramachandran restraints generated. 1187 Oldfield, 0 Emsley, 1187 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2374 Ramachandran restraints generated. 1187 Oldfield, 0 Emsley, 1187 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 1042 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 89 time to evaluate : 1.165 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 52 ARG cc_start: 0.7982 (mtt180) cc_final: 0.7362 (mmt180) REVERT: A 74 ASP cc_start: 0.7548 (t0) cc_final: 0.6880 (t0) REVERT: A 126 MET cc_start: 0.7722 (mmm) cc_final: 0.7313 (mpt) REVERT: A 611 MET cc_start: 0.6628 (ttp) cc_final: 0.5957 (tmt) REVERT: A 803 GLU cc_start: 0.8172 (tp30) cc_final: 0.7689 (tp30) REVERT: A 909 GLN cc_start: 0.8101 (tt0) cc_final: 0.7605 (tt0) REVERT: A 998 ARG cc_start: 0.7994 (mtm-85) cc_final: 0.7111 (mpt90) REVERT: A 1011 GLU cc_start: 0.7696 (pt0) cc_final: 0.7131 (tp30) REVERT: A 1044 ASP cc_start: 0.6587 (t0) cc_final: 0.6144 (p0) REVERT: A 1093 GLU cc_start: 0.8798 (mm-30) cc_final: 0.8396 (mp0) REVERT: A 1097 LYS cc_start: 0.7446 (mttt) cc_final: 0.7113 (mttp) REVERT: A 1166 MET cc_start: 0.5428 (mmm) cc_final: 0.5208 (mmm) REVERT: A 1243 LYS cc_start: 0.5537 (mttt) cc_final: 0.5103 (mptt) outliers start: 17 outliers final: 9 residues processed: 101 average time/residue: 1.3202 time to fit residues: 143.8025 Evaluate side-chains 93 residues out of total 1042 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 84 time to evaluate : 1.193 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 MET Chi-restraints excluded: chain A residue 50 GLU Chi-restraints excluded: chain A residue 344 SER Chi-restraints excluded: chain A residue 395 ILE Chi-restraints excluded: chain A residue 826 SER Chi-restraints excluded: chain A residue 944 THR Chi-restraints excluded: chain A residue 984 SER Chi-restraints excluded: chain A residue 1057 VAL Chi-restraints excluded: chain A residue 1061 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 67 optimal weight: 0.9990 chunk 39 optimal weight: 0.0270 chunk 53 optimal weight: 8.9990 chunk 4 optimal weight: 2.9990 chunk 85 optimal weight: 0.5980 chunk 99 optimal weight: 2.9990 chunk 62 optimal weight: 0.7980 chunk 108 optimal weight: 0.9990 chunk 54 optimal weight: 0.8980 chunk 56 optimal weight: 9.9990 chunk 110 optimal weight: 0.7980 overall best weight: 0.6238 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 492 ASN A1148 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4365 r_free = 0.4365 target = 0.214714 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3849 r_free = 0.3849 target = 0.156641 restraints weight = 10023.274| |-----------------------------------------------------------------------------| r_work (start): 0.3811 rms_B_bonded: 3.46 r_work: 0.3399 rms_B_bonded: 3.42 restraints_weight: 0.5000 r_work (final): 0.3399 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8164 moved from start: 0.2618 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 9963 Z= 0.141 Angle : 0.515 9.203 13537 Z= 0.259 Chirality : 0.040 0.188 1585 Planarity : 0.004 0.049 1648 Dihedral : 6.124 58.004 1701 Min Nonbonded Distance : 2.619 Molprobity Statistics. All-atom Clashscore : 5.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.68 % Favored : 98.32 % Rotamer: Outliers : 1.73 % Allowed : 11.32 % Favored : 86.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.48 (0.24), residues: 1187 helix: 1.40 (0.18), residues: 786 sheet: 0.08 (0.61), residues: 69 loop : 0.41 (0.36), residues: 332 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 733 HIS 0.006 0.001 HIS A 934 PHE 0.023 0.002 PHE A 336 TYR 0.010 0.001 TYR A 881 ARG 0.007 0.000 ARG A 815 Details of bonding type rmsd hydrogen bonds : bond 0.04239 ( 618) hydrogen bonds : angle 4.26791 ( 1782) covalent geometry : bond 0.00332 ( 9963) covalent geometry : angle 0.51521 (13537) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2374 Ramachandran restraints generated. 1187 Oldfield, 0 Emsley, 1187 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2374 Ramachandran restraints generated. 1187 Oldfield, 0 Emsley, 1187 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 1042 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 84 time to evaluate : 1.124 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 52 ARG cc_start: 0.8102 (mtt180) cc_final: 0.7616 (mmt180) REVERT: A 74 ASP cc_start: 0.7676 (t0) cc_final: 0.7003 (t0) REVERT: A 126 MET cc_start: 0.7724 (mmm) cc_final: 0.7433 (mpt) REVERT: A 288 MET cc_start: 0.8406 (OUTLIER) cc_final: 0.8183 (mtp) REVERT: A 611 MET cc_start: 0.6593 (ttp) cc_final: 0.5863 (tmt) REVERT: A 803 GLU cc_start: 0.8100 (tp30) cc_final: 0.7773 (tp30) REVERT: A 909 GLN cc_start: 0.8011 (tt0) cc_final: 0.7580 (tt0) REVERT: A 998 ARG cc_start: 0.7839 (mtm-85) cc_final: 0.7231 (mpt90) REVERT: A 1011 GLU cc_start: 0.7631 (pt0) cc_final: 0.7343 (tp30) REVERT: A 1044 ASP cc_start: 0.6687 (t0) cc_final: 0.6295 (p0) REVERT: A 1093 GLU cc_start: 0.8639 (mm-30) cc_final: 0.8291 (mp0) REVERT: A 1097 LYS cc_start: 0.7581 (mttt) cc_final: 0.7263 (mttp) REVERT: A 1166 MET cc_start: 0.5583 (mmm) cc_final: 0.5349 (mmm) REVERT: A 1243 LYS cc_start: 0.5621 (mttt) cc_final: 0.5144 (mptt) outliers start: 18 outliers final: 8 residues processed: 97 average time/residue: 1.2363 time to fit residues: 129.7774 Evaluate side-chains 91 residues out of total 1042 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 82 time to evaluate : 1.047 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 LYS Chi-restraints excluded: chain A residue 50 GLU Chi-restraints excluded: chain A residue 288 MET Chi-restraints excluded: chain A residue 344 SER Chi-restraints excluded: chain A residue 395 ILE Chi-restraints excluded: chain A residue 826 SER Chi-restraints excluded: chain A residue 944 THR Chi-restraints excluded: chain A residue 1057 VAL Chi-restraints excluded: chain A residue 1061 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 79 optimal weight: 0.9980 chunk 81 optimal weight: 1.9990 chunk 33 optimal weight: 0.5980 chunk 41 optimal weight: 1.9990 chunk 34 optimal weight: 0.5980 chunk 23 optimal weight: 0.6980 chunk 85 optimal weight: 0.5980 chunk 68 optimal weight: 1.9990 chunk 10 optimal weight: 0.8980 chunk 83 optimal weight: 0.5980 chunk 112 optimal weight: 0.7980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1148 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4131 r_free = 0.4131 target = 0.198255 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3568 r_free = 0.3568 target = 0.140916 restraints weight = 9880.892| |-----------------------------------------------------------------------------| r_work (start): 0.3423 rms_B_bonded: 3.86 r_work: 0.2993 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.2836 rms_B_bonded: 4.48 restraints_weight: 0.2500 r_work (final): 0.2836 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7866 moved from start: 0.2699 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 9963 Z= 0.140 Angle : 0.513 8.782 13537 Z= 0.257 Chirality : 0.040 0.189 1585 Planarity : 0.004 0.047 1648 Dihedral : 6.083 58.242 1701 Min Nonbonded Distance : 2.621 Molprobity Statistics. All-atom Clashscore : 5.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.85 % Favored : 98.15 % Rotamer: Outliers : 1.34 % Allowed : 12.28 % Favored : 86.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.57 (0.24), residues: 1187 helix: 1.47 (0.18), residues: 781 sheet: -0.04 (0.55), residues: 80 loop : 0.49 (0.38), residues: 326 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 733 HIS 0.006 0.001 HIS A 934 PHE 0.023 0.002 PHE A 336 TYR 0.011 0.001 TYR A 881 ARG 0.006 0.000 ARG A 815 Details of bonding type rmsd hydrogen bonds : bond 0.04213 ( 618) hydrogen bonds : angle 4.24802 ( 1782) covalent geometry : bond 0.00330 ( 9963) covalent geometry : angle 0.51261 (13537) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2374 Ramachandran restraints generated. 1187 Oldfield, 0 Emsley, 1187 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2374 Ramachandran restraints generated. 1187 Oldfield, 0 Emsley, 1187 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 1042 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 83 time to evaluate : 1.095 Fit side-chains revert: symmetry clash REVERT: A 52 ARG cc_start: 0.7715 (mtt180) cc_final: 0.6955 (mmt180) REVERT: A 74 ASP cc_start: 0.7384 (t0) cc_final: 0.6691 (t0) REVERT: A 126 MET cc_start: 0.7647 (mmm) cc_final: 0.7162 (mpt) REVERT: A 196 ASN cc_start: 0.6828 (m-40) cc_final: 0.6526 (t0) REVERT: A 611 MET cc_start: 0.6715 (ttp) cc_final: 0.5937 (tmt) REVERT: A 803 GLU cc_start: 0.8000 (tp30) cc_final: 0.7439 (tp30) REVERT: A 909 GLN cc_start: 0.7948 (tt0) cc_final: 0.7436 (tt0) REVERT: A 998 ARG cc_start: 0.7807 (mtm-85) cc_final: 0.6802 (mpt90) REVERT: A 1011 GLU cc_start: 0.7452 (pt0) cc_final: 0.6829 (tp30) REVERT: A 1044 ASP cc_start: 0.6450 (t0) cc_final: 0.5915 (p0) REVERT: A 1093 GLU cc_start: 0.8811 (mm-30) cc_final: 0.8360 (mp0) REVERT: A 1097 LYS cc_start: 0.7229 (mttt) cc_final: 0.6884 (mttp) REVERT: A 1166 MET cc_start: 0.5069 (mmm) cc_final: 0.4863 (mmm) REVERT: A 1243 LYS cc_start: 0.5355 (mttt) cc_final: 0.4940 (mptt) outliers start: 14 outliers final: 8 residues processed: 93 average time/residue: 1.2824 time to fit residues: 128.6238 Evaluate side-chains 88 residues out of total 1042 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 80 time to evaluate : 1.012 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 GLU Chi-restraints excluded: chain A residue 344 SER Chi-restraints excluded: chain A residue 395 ILE Chi-restraints excluded: chain A residue 454 LEU Chi-restraints excluded: chain A residue 826 SER Chi-restraints excluded: chain A residue 944 THR Chi-restraints excluded: chain A residue 1057 VAL Chi-restraints excluded: chain A residue 1061 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 106 optimal weight: 0.0030 chunk 55 optimal weight: 0.0270 chunk 33 optimal weight: 0.0870 chunk 40 optimal weight: 10.0000 chunk 99 optimal weight: 4.9990 chunk 11 optimal weight: 0.5980 chunk 87 optimal weight: 0.9980 chunk 49 optimal weight: 5.9990 chunk 82 optimal weight: 0.9990 chunk 32 optimal weight: 0.5980 chunk 44 optimal weight: 2.9990 overall best weight: 0.2626 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1148 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4149 r_free = 0.4149 target = 0.201293 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.125552 restraints weight = 9946.508| |-----------------------------------------------------------------------------| r_work (start): 0.3321 rms_B_bonded: 2.84 r_work: 0.3120 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.2963 rms_B_bonded: 4.44 restraints_weight: 0.2500 r_work (final): 0.2963 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7530 moved from start: 0.2971 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 9963 Z= 0.105 Angle : 0.479 8.348 13537 Z= 0.240 Chirality : 0.039 0.184 1585 Planarity : 0.004 0.046 1648 Dihedral : 5.877 59.133 1701 Min Nonbonded Distance : 2.621 Molprobity Statistics. All-atom Clashscore : 5.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.85 % Favored : 98.15 % Rotamer: Outliers : 0.77 % Allowed : 13.34 % Favored : 85.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.84 (0.24), residues: 1187 helix: 1.71 (0.18), residues: 784 sheet: 0.02 (0.56), residues: 80 loop : 0.52 (0.38), residues: 323 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 733 HIS 0.005 0.001 HIS A 153 PHE 0.018 0.001 PHE A 336 TYR 0.009 0.001 TYR A 881 ARG 0.007 0.000 ARG A 815 Details of bonding type rmsd hydrogen bonds : bond 0.03805 ( 618) hydrogen bonds : angle 4.07535 ( 1782) covalent geometry : bond 0.00230 ( 9963) covalent geometry : angle 0.47874 (13537) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2374 Ramachandran restraints generated. 1187 Oldfield, 0 Emsley, 1187 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2374 Ramachandran restraints generated. 1187 Oldfield, 0 Emsley, 1187 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 1042 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 90 time to evaluate : 1.015 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 52 ARG cc_start: 0.7348 (mtt180) cc_final: 0.6523 (tpt170) REVERT: A 74 ASP cc_start: 0.7206 (t0) cc_final: 0.6650 (t0) REVERT: A 126 MET cc_start: 0.7529 (mmm) cc_final: 0.7034 (mpt) REVERT: A 611 MET cc_start: 0.6734 (ttp) cc_final: 0.5938 (tmt) REVERT: A 803 GLU cc_start: 0.7639 (tp30) cc_final: 0.7021 (tp30) REVERT: A 909 GLN cc_start: 0.7758 (tt0) cc_final: 0.7236 (tt0) REVERT: A 998 ARG cc_start: 0.7620 (mtm-85) cc_final: 0.6499 (mpt90) REVERT: A 1011 GLU cc_start: 0.7085 (pt0) cc_final: 0.6360 (tp30) REVERT: A 1044 ASP cc_start: 0.6321 (t0) cc_final: 0.5886 (p0) REVERT: A 1093 GLU cc_start: 0.8737 (mm-30) cc_final: 0.8285 (mp0) REVERT: A 1097 LYS cc_start: 0.7087 (mttt) cc_final: 0.6780 (mttp) REVERT: A 1169 GLU cc_start: 0.6915 (mt-10) cc_final: 0.6454 (tm-30) REVERT: A 1243 LYS cc_start: 0.5223 (mttt) cc_final: 0.4859 (mptt) outliers start: 8 outliers final: 6 residues processed: 95 average time/residue: 1.2901 time to fit residues: 131.7936 Evaluate side-chains 87 residues out of total 1042 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 81 time to evaluate : 1.014 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 GLU Chi-restraints excluded: chain A residue 344 SER Chi-restraints excluded: chain A residue 395 ILE Chi-restraints excluded: chain A residue 454 LEU Chi-restraints excluded: chain A residue 1057 VAL Chi-restraints excluded: chain A residue 1061 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 19 optimal weight: 0.8980 chunk 62 optimal weight: 0.8980 chunk 92 optimal weight: 0.6980 chunk 16 optimal weight: 0.6980 chunk 40 optimal weight: 0.4980 chunk 6 optimal weight: 0.8980 chunk 23 optimal weight: 1.9990 chunk 4 optimal weight: 0.6980 chunk 61 optimal weight: 0.3980 chunk 82 optimal weight: 0.9990 chunk 77 optimal weight: 0.6980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1148 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4108 r_free = 0.4108 target = 0.196723 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3540 r_free = 0.3540 target = 0.138080 restraints weight = 9981.382| |-----------------------------------------------------------------------------| r_work (start): 0.3442 rms_B_bonded: 3.74 r_work: 0.2962 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work: 0.2804 rms_B_bonded: 4.97 restraints_weight: 0.2500 r_work (final): 0.2804 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7874 moved from start: 0.2893 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 9963 Z= 0.139 Angle : 0.525 10.305 13537 Z= 0.261 Chirality : 0.040 0.186 1585 Planarity : 0.004 0.046 1648 Dihedral : 6.020 58.729 1701 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 5.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.94 % Favored : 98.06 % Rotamer: Outliers : 0.96 % Allowed : 13.72 % Favored : 85.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.73 (0.24), residues: 1187 helix: 1.61 (0.18), residues: 781 sheet: -0.02 (0.56), residues: 80 loop : 0.54 (0.38), residues: 326 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 733 HIS 0.005 0.001 HIS A 934 PHE 0.028 0.002 PHE A1048 TYR 0.011 0.001 TYR A 881 ARG 0.007 0.000 ARG A 815 Details of bonding type rmsd hydrogen bonds : bond 0.04146 ( 618) hydrogen bonds : angle 4.20189 ( 1782) covalent geometry : bond 0.00326 ( 9963) covalent geometry : angle 0.52536 (13537) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2374 Ramachandran restraints generated. 1187 Oldfield, 0 Emsley, 1187 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2374 Ramachandran restraints generated. 1187 Oldfield, 0 Emsley, 1187 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 1042 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 87 time to evaluate : 0.987 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 52 ARG cc_start: 0.7738 (mtt180) cc_final: 0.6948 (mmt180) REVERT: A 74 ASP cc_start: 0.7362 (t0) cc_final: 0.6786 (t0) REVERT: A 126 MET cc_start: 0.7642 (mmm) cc_final: 0.7162 (mpt) REVERT: A 611 MET cc_start: 0.6659 (ttp) cc_final: 0.5885 (tmt) REVERT: A 803 GLU cc_start: 0.7994 (tp30) cc_final: 0.7447 (tp30) REVERT: A 909 GLN cc_start: 0.7972 (tt0) cc_final: 0.7481 (tt0) REVERT: A 998 ARG cc_start: 0.7868 (mtm-85) cc_final: 0.6827 (mpt90) REVERT: A 1011 GLU cc_start: 0.7496 (pt0) cc_final: 0.6835 (tp30) REVERT: A 1044 ASP cc_start: 0.6338 (t0) cc_final: 0.5943 (p0) REVERT: A 1093 GLU cc_start: 0.8800 (mm-30) cc_final: 0.8352 (mp0) REVERT: A 1097 LYS cc_start: 0.7269 (mttt) cc_final: 0.7005 (mttp) REVERT: A 1169 GLU cc_start: 0.6920 (mt-10) cc_final: 0.6483 (tm-30) REVERT: A 1243 LYS cc_start: 0.5405 (mttt) cc_final: 0.4985 (mptt) outliers start: 10 outliers final: 8 residues processed: 93 average time/residue: 1.3905 time to fit residues: 138.6267 Evaluate side-chains 92 residues out of total 1042 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 84 time to evaluate : 1.070 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 LYS Chi-restraints excluded: chain A residue 50 GLU Chi-restraints excluded: chain A residue 344 SER Chi-restraints excluded: chain A residue 395 ILE Chi-restraints excluded: chain A residue 454 LEU Chi-restraints excluded: chain A residue 984 SER Chi-restraints excluded: chain A residue 1057 VAL Chi-restraints excluded: chain A residue 1061 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 98 optimal weight: 5.9990 chunk 114 optimal weight: 2.9990 chunk 30 optimal weight: 0.7980 chunk 38 optimal weight: 0.7980 chunk 69 optimal weight: 0.6980 chunk 101 optimal weight: 0.0020 chunk 87 optimal weight: 0.8980 chunk 66 optimal weight: 1.9990 chunk 71 optimal weight: 0.1980 chunk 77 optimal weight: 0.8980 chunk 9 optimal weight: 0.6980 overall best weight: 0.4788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1148 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4095 r_free = 0.4095 target = 0.196031 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3575 r_free = 0.3575 target = 0.141138 restraints weight = 9917.304| |-----------------------------------------------------------------------------| r_work (start): 0.3502 rms_B_bonded: 4.05 r_work: 0.2997 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work: 0.2841 rms_B_bonded: 4.83 restraints_weight: 0.2500 r_work (final): 0.2841 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7874 moved from start: 0.2961 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 9963 Z= 0.126 Angle : 0.511 10.261 13537 Z= 0.254 Chirality : 0.040 0.187 1585 Planarity : 0.004 0.045 1648 Dihedral : 5.964 58.803 1701 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 5.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.94 % Favored : 98.06 % Rotamer: Outliers : 0.67 % Allowed : 14.01 % Favored : 85.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.75 (0.24), residues: 1187 helix: 1.63 (0.18), residues: 785 sheet: 0.00 (0.55), residues: 80 loop : 0.49 (0.37), residues: 322 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 733 HIS 0.005 0.001 HIS A 934 PHE 0.021 0.001 PHE A 336 TYR 0.011 0.001 TYR A 917 ARG 0.003 0.000 ARG A 317 Details of bonding type rmsd hydrogen bonds : bond 0.04055 ( 618) hydrogen bonds : angle 4.15324 ( 1782) covalent geometry : bond 0.00289 ( 9963) covalent geometry : angle 0.51144 (13537) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2374 Ramachandran restraints generated. 1187 Oldfield, 0 Emsley, 1187 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2374 Ramachandran restraints generated. 1187 Oldfield, 0 Emsley, 1187 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 1042 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 87 time to evaluate : 1.056 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 52 ARG cc_start: 0.7754 (mtt180) cc_final: 0.6974 (mmt180) REVERT: A 74 ASP cc_start: 0.7372 (t0) cc_final: 0.6789 (t0) REVERT: A 126 MET cc_start: 0.7628 (mmm) cc_final: 0.7157 (mpt) REVERT: A 611 MET cc_start: 0.6601 (ttp) cc_final: 0.5851 (tmt) REVERT: A 803 GLU cc_start: 0.7987 (tp30) cc_final: 0.7405 (tp30) REVERT: A 909 GLN cc_start: 0.7951 (tt0) cc_final: 0.7452 (tt0) REVERT: A 998 ARG cc_start: 0.7840 (mtm-85) cc_final: 0.6812 (mpt90) REVERT: A 1011 GLU cc_start: 0.7486 (pt0) cc_final: 0.6828 (tp30) REVERT: A 1044 ASP cc_start: 0.6353 (t0) cc_final: 0.5991 (p0) REVERT: A 1093 GLU cc_start: 0.8797 (mm-30) cc_final: 0.8341 (mp0) REVERT: A 1097 LYS cc_start: 0.7313 (mttt) cc_final: 0.7059 (mttp) REVERT: A 1169 GLU cc_start: 0.6900 (mt-10) cc_final: 0.6491 (tm-30) REVERT: A 1243 LYS cc_start: 0.5502 (mttt) cc_final: 0.5083 (mptt) outliers start: 7 outliers final: 6 residues processed: 92 average time/residue: 1.4551 time to fit residues: 144.0139 Evaluate side-chains 90 residues out of total 1042 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 84 time to evaluate : 1.020 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 GLU Chi-restraints excluded: chain A residue 344 SER Chi-restraints excluded: chain A residue 395 ILE Chi-restraints excluded: chain A residue 454 LEU Chi-restraints excluded: chain A residue 1057 VAL Chi-restraints excluded: chain A residue 1061 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 34 optimal weight: 0.5980 chunk 45 optimal weight: 4.9990 chunk 98 optimal weight: 2.9990 chunk 1 optimal weight: 0.6980 chunk 112 optimal weight: 9.9990 chunk 76 optimal weight: 2.9990 chunk 101 optimal weight: 3.9990 chunk 55 optimal weight: 9.9990 chunk 46 optimal weight: 1.9990 chunk 81 optimal weight: 0.6980 chunk 96 optimal weight: 0.9990 overall best weight: 0.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1148 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4114 r_free = 0.4114 target = 0.196098 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3589 r_free = 0.3589 target = 0.141117 restraints weight = 9828.669| |-----------------------------------------------------------------------------| r_work (start): 0.3430 rms_B_bonded: 3.71 r_work: 0.2929 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.2777 rms_B_bonded: 4.50 restraints_weight: 0.2500 r_work (final): 0.2777 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7946 moved from start: 0.2786 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 9963 Z= 0.191 Angle : 0.580 10.256 13537 Z= 0.287 Chirality : 0.042 0.195 1585 Planarity : 0.004 0.046 1648 Dihedral : 6.294 59.939 1701 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 5.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.02 % Favored : 97.98 % Rotamer: Outliers : 1.06 % Allowed : 13.34 % Favored : 85.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.39 (0.24), residues: 1187 helix: 1.37 (0.18), residues: 781 sheet: -0.15 (0.55), residues: 80 loop : 0.35 (0.37), residues: 326 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 733 HIS 0.006 0.001 HIS A 934 PHE 0.030 0.002 PHE A1048 TYR 0.013 0.002 TYR A 881 ARG 0.004 0.000 ARG A 317 Details of bonding type rmsd hydrogen bonds : bond 0.04608 ( 618) hydrogen bonds : angle 4.39842 ( 1782) covalent geometry : bond 0.00463 ( 9963) covalent geometry : angle 0.57964 (13537) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8367.81 seconds wall clock time: 147 minutes 25.38 seconds (8845.38 seconds total)