Starting phenix.real_space_refine on Fri Feb 14 11:38:39 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8bjf_16088/02_2025/8bjf_16088.cif Found real_map, /net/cci-nas-00/data/ceres_data/8bjf_16088/02_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_16088/02_2025/8bjf_16088.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8bjf_16088/02_2025/8bjf_16088.map" model { file = "/net/cci-nas-00/data/ceres_data/8bjf_16088/02_2025/8bjf_16088.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8bjf_16088/02_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-5592/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: 7.07, per 1000 atoms: 0.73 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: 2.36 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: 1.31 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: 3.87 Time building geometry restraints manager: 2.74 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: 3.580 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: 0.430 Check model and map are aligned: 0.080 Set scattering table: 0.100 Process input model: 26.690 Find NCS groups from input model: 0.110 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:13.510 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 44.550 ------------------------------------------------------------------------------- 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= 0.331 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 *********************** 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 : 1.074 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: 1.3528 time to fit residues: 175.9527 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 : 1.049 ------------------------------------------------------------------------------- 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 = 0.119522 restraints weight = 9807.499| |-----------------------------------------------------------------------------| r_work (start): 0.3230 rms_B_bonded: 2.43 r_work: 0.3033 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.2880 rms_B_bonded: 4.25 restraints_weight: 0.2500 r_work (final): 0.2880 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7429 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= 0.205 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 *********************** 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 : 1.133 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 36 LYS cc_start: 0.7918 (OUTLIER) cc_final: 0.7696 (mtmt) REVERT: A 52 ARG cc_start: 0.7340 (mtt180) cc_final: 0.6472 (mmt180) REVERT: A 74 ASP cc_start: 0.6874 (t0) cc_final: 0.6456 (t0) REVERT: A 126 MET cc_start: 0.7415 (mmm) cc_final: 0.6896 (mpt) REVERT: A 207 GLN cc_start: 0.7629 (mt0) cc_final: 0.7107 (mt0) REVERT: A 528 ILE cc_start: 0.5912 (OUTLIER) cc_final: 0.5564 (mm) REVERT: A 558 LEU cc_start: 0.7491 (mm) cc_final: 0.7194 (mm) REVERT: A 611 MET cc_start: 0.6946 (ttp) cc_final: 0.6140 (tmt) REVERT: A 803 GLU cc_start: 0.7560 (tp30) cc_final: 0.6952 (tp30) REVERT: A 807 LYS cc_start: 0.7498 (mttt) cc_final: 0.7295 (mttt) REVERT: A 887 ARG cc_start: 0.6371 (mtm110) cc_final: 0.5645 (mtt90) REVERT: A 909 GLN cc_start: 0.7612 (tt0) cc_final: 0.7123 (tt0) REVERT: A 998 ARG cc_start: 0.7156 (mtm-85) cc_final: 0.6188 (mpt90) REVERT: A 1011 GLU cc_start: 0.6843 (pt0) cc_final: 0.6254 (tp30) REVERT: A 1042 ILE cc_start: 0.6766 (mt) cc_final: 0.6533 (pt) REVERT: A 1044 ASP cc_start: 0.6604 (t0) cc_final: 0.5617 (p0) REVERT: A 1093 GLU cc_start: 0.8788 (mm-30) cc_final: 0.8419 (mp0) REVERT: A 1097 LYS cc_start: 0.6903 (mttt) cc_final: 0.6522 (mttp) REVERT: A 1166 MET cc_start: 0.4834 (mmm) cc_final: 0.4577 (mmm) REVERT: A 1253 LYS cc_start: 0.7143 (mmtt) cc_final: 0.6305 (mtpp) outliers start: 15 outliers final: 4 residues processed: 116 average time/residue: 1.3060 time to fit residues: 163.0297 Evaluate side-chains 93 residues out of total 1042 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 87 time to evaluate : 0.975 ------------------------------------------------------------------------------- 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: 0.3980 chunk 76 optimal weight: 0.0980 chunk 87 optimal weight: 1.9990 chunk 5 optimal weight: 1.9990 chunk 44 optimal weight: 0.7980 chunk 99 optimal weight: 4.9990 chunk 116 optimal weight: 6.9990 chunk 1 optimal weight: 0.0040 chunk 13 optimal weight: 0.9980 chunk 4 optimal weight: 0.6980 chunk 6 optimal weight: 3.9990 overall best weight: 0.3992 ------------------------------------------------------------------------------- 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 = 0.4185 r_free = 0.4185 target = 0.203311 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3552 r_free = 0.3552 target = 0.135119 restraints weight = 9941.944| |-----------------------------------------------------------------------------| r_work (start): 0.3357 rms_B_bonded: 2.33 r_work: 0.3078 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.2926 rms_B_bonded: 4.35 restraints_weight: 0.2500 r_work (final): 0.2926 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7540 moved from start: 0.2194 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= 0.168 Angle : 0.515 8.803 13537 Z= 0.261 Chirality : 0.040 0.183 1585 Planarity : 0.004 0.053 1648 Dihedral : 6.211 59.821 1705 Min Nonbonded Distance : 2.623 Molprobity Statistics. All-atom Clashscore : 4.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.85 % Favored : 98.15 % Rotamer: Outliers : 1.54 % Allowed : 8.64 % Favored : 89.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.20 (0.24), residues: 1187 helix: 1.18 (0.18), residues: 785 sheet: -0.05 (0.59), residues: 69 loop : 0.31 (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 0.025 0.001 PHE A 336 TYR 0.011 0.001 TYR A 119 ARG 0.006 0.000 ARG A 815 *********************** 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 118 residues out of total 1042 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 102 time to evaluate : 1.012 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 36 LYS cc_start: 0.8035 (OUTLIER) cc_final: 0.7819 (mtmt) REVERT: A 52 ARG cc_start: 0.7440 (mtt180) cc_final: 0.6632 (mmt180) REVERT: A 74 ASP cc_start: 0.7086 (t0) cc_final: 0.6529 (t0) REVERT: A 126 MET cc_start: 0.7495 (mmm) cc_final: 0.6998 (mpt) REVERT: A 207 GLN cc_start: 0.7742 (mt0) cc_final: 0.7204 (mt0) REVERT: A 611 MET cc_start: 0.6881 (ttp) cc_final: 0.6104 (tmt) REVERT: A 803 GLU cc_start: 0.7673 (tp30) cc_final: 0.7342 (mm-30) REVERT: A 909 GLN cc_start: 0.7753 (tt0) cc_final: 0.7293 (tt0) REVERT: A 998 ARG cc_start: 0.7516 (mtm-85) cc_final: 0.6487 (mpt90) REVERT: A 1011 GLU cc_start: 0.7159 (pt0) cc_final: 0.6476 (tp30) REVERT: A 1042 ILE cc_start: 0.6920 (mt) cc_final: 0.6662 (pt) REVERT: A 1044 ASP cc_start: 0.6514 (t0) cc_final: 0.5686 (p0) REVERT: A 1093 GLU cc_start: 0.8719 (mm-30) cc_final: 0.8328 (mp0) REVERT: A 1097 LYS cc_start: 0.6984 (mttt) cc_final: 0.6590 (mttp) REVERT: A 1166 MET cc_start: 0.4960 (mmm) cc_final: 0.4750 (mmm) REVERT: A 1169 GLU cc_start: 0.6834 (mt-10) cc_final: 0.6213 (tm-30) outliers start: 16 outliers final: 6 residues processed: 112 average time/residue: 1.4221 time to fit residues: 170.6868 Evaluate side-chains 92 residues out of total 1042 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 85 time to evaluate : 1.099 ------------------------------------------------------------------------------- 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: 0.7980 chunk 58 optimal weight: 9.9990 chunk 77 optimal weight: 0.9990 chunk 84 optimal weight: 0.9990 chunk 81 optimal weight: 1.9990 chunk 3 optimal weight: 0.9990 chunk 92 optimal weight: 0.9990 chunk 100 optimal weight: 0.9990 chunk 15 optimal weight: 0.5980 chunk 20 optimal weight: 0.5980 chunk 16 optimal weight: 0.8980 overall best weight: 0.7782 ------------------------------------------------------------------------------- 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 = 0.4143 r_free = 0.4143 target = 0.199148 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.125932 restraints weight = 9788.547| |-----------------------------------------------------------------------------| r_work (start): 0.3279 rms_B_bonded: 2.59 r_work: 0.2993 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.2838 rms_B_bonded: 4.37 restraints_weight: 0.2500 r_work (final): 0.2838 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7574 moved from start: 0.2271 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 9963 Z= 0.241 Angle : 0.542 7.538 13537 Z= 0.274 Chirality : 0.041 0.191 1585 Planarity : 0.004 0.053 1648 Dihedral : 6.305 59.275 1705 Min Nonbonded Distance : 2.618 Molprobity Statistics. All-atom Clashscore : 5.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.52 % Favored : 98.48 % Rotamer: Outliers : 1.54 % Allowed : 10.08 % Favored : 88.39 % 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: 1.23 (0.24), residues: 1187 helix: 1.18 (0.18), residues: 786 sheet: 0.14 (0.61), residues: 69 loop : 0.35 (0.36), residues: 332 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 733 HIS 0.007 0.001 HIS A 153 PHE 0.027 0.002 PHE A 336 TYR 0.012 0.001 TYR A 881 ARG 0.005 0.000 ARG A 815 *********************** 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 109 residues out of total 1042 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 93 time to evaluate : 1.178 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 36 LYS cc_start: 0.7944 (OUTLIER) cc_final: 0.7707 (mtmt) REVERT: A 52 ARG cc_start: 0.7400 (mtt180) cc_final: 0.6565 (mmt180) REVERT: A 74 ASP cc_start: 0.7198 (t0) cc_final: 0.6590 (t0) REVERT: A 126 MET cc_start: 0.7511 (mmm) cc_final: 0.7008 (mpt) REVERT: A 284 ARG cc_start: 0.7246 (OUTLIER) cc_final: 0.6984 (mtt90) REVERT: A 611 MET cc_start: 0.6840 (ttp) cc_final: 0.6073 (tmt) REVERT: A 803 GLU cc_start: 0.7636 (tp30) cc_final: 0.7407 (mm-30) REVERT: A 909 GLN cc_start: 0.7746 (tt0) cc_final: 0.7212 (tt0) REVERT: A 998 ARG cc_start: 0.7609 (mtm-85) cc_final: 0.6501 (mpt90) REVERT: A 1011 GLU cc_start: 0.7076 (pt0) cc_final: 0.6382 (tp30) REVERT: A 1044 ASP cc_start: 0.6508 (t0) cc_final: 0.5760 (p0) REVERT: A 1093 GLU cc_start: 0.8774 (mm-30) cc_final: 0.8363 (mp0) REVERT: A 1097 LYS cc_start: 0.7065 (mttt) cc_final: 0.6716 (mttp) REVERT: A 1166 MET cc_start: 0.4912 (mmm) cc_final: 0.4704 (mmm) REVERT: A 1243 LYS cc_start: 0.5138 (mttt) cc_final: 0.4779 (mptt) REVERT: A 1253 LYS cc_start: 0.7190 (mmtt) cc_final: 0.6840 (mmpt) outliers start: 16 outliers final: 6 residues processed: 104 average time/residue: 1.3344 time to fit residues: 149.6906 Evaluate side-chains 96 residues out of total 1042 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 88 time to evaluate : 1.026 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 LYS Chi-restraints excluded: chain A residue 284 ARG 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 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: 8.9990 chunk 64 optimal weight: 0.9990 chunk 102 optimal weight: 0.0070 chunk 29 optimal weight: 3.9990 chunk 17 optimal weight: 0.5980 chunk 82 optimal weight: 0.9980 chunk 117 optimal weight: 9.9990 chunk 7 optimal weight: 0.5980 chunk 68 optimal weight: 1.9990 chunk 113 optimal weight: 5.9990 chunk 74 optimal weight: 0.9980 overall best weight: 0.6398 ------------------------------------------------------------------------------- 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 = 0.4168 r_free = 0.4168 target = 0.201327 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3337 r_free = 0.3337 target = 0.120140 restraints weight = 9703.281| |-----------------------------------------------------------------------------| r_work (start): 0.3223 rms_B_bonded: 1.95 r_work: 0.3075 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.2925 rms_B_bonded: 3.99 restraints_weight: 0.2500 r_work (final): 0.2925 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7546 moved from start: 0.2465 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 9963 Z= 0.210 Angle : 0.516 7.869 13537 Z= 0.261 Chirality : 0.040 0.189 1585 Planarity : 0.004 0.050 1648 Dihedral : 6.213 57.353 1705 Min Nonbonded Distance : 2.618 Molprobity Statistics. All-atom Clashscore : 5.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.52 % Favored : 98.48 % Rotamer: Outliers : 1.44 % Allowed : 10.84 % Favored : 87.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.36 (0.24), residues: 1187 helix: 1.28 (0.18), residues: 786 sheet: 0.11 (0.59), residues: 69 loop : 0.41 (0.36), residues: 332 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 733 HIS 0.007 0.001 HIS A 153 PHE 0.024 0.002 PHE A 336 TYR 0.011 0.001 TYR A 881 ARG 0.006 0.000 ARG A 815 *********************** 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 107 residues out of total 1042 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 92 time to evaluate : 1.144 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 36 LYS cc_start: 0.7954 (OUTLIER) cc_final: 0.7729 (mtmt) REVERT: A 52 ARG cc_start: 0.7354 (mtt180) cc_final: 0.6547 (mmt180) REVERT: A 74 ASP cc_start: 0.7218 (t0) cc_final: 0.6586 (t0) REVERT: A 126 MET cc_start: 0.7540 (mmm) cc_final: 0.7047 (mpt) REVERT: A 611 MET cc_start: 0.6706 (ttp) cc_final: 0.5997 (tmt) REVERT: A 803 GLU cc_start: 0.7578 (tp30) cc_final: 0.7325 (mm-30) REVERT: A 909 GLN cc_start: 0.7719 (tt0) cc_final: 0.7194 (tt0) REVERT: A 998 ARG cc_start: 0.7590 (mtm-85) cc_final: 0.6493 (mpt90) REVERT: A 1011 GLU cc_start: 0.7110 (pt0) cc_final: 0.6445 (tp30) REVERT: A 1044 ASP cc_start: 0.6395 (t0) cc_final: 0.5785 (p0) REVERT: A 1093 GLU cc_start: 0.8770 (mm-30) cc_final: 0.8321 (mp0) REVERT: A 1097 LYS cc_start: 0.7018 (mttt) cc_final: 0.6616 (mttp) REVERT: A 1166 MET cc_start: 0.4938 (mmm) cc_final: 0.4735 (mmm) REVERT: A 1243 LYS cc_start: 0.5196 (mttt) cc_final: 0.4837 (mptt) outliers start: 15 outliers final: 5 residues processed: 103 average time/residue: 1.2662 time to fit residues: 141.0746 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 : 1.086 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 LYS Chi-restraints excluded: chain A residue 344 SER Chi-restraints excluded: chain A residue 395 ILE 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: 0.5980 chunk 39 optimal weight: 2.9990 chunk 53 optimal weight: 6.9990 chunk 4 optimal weight: 2.9990 chunk 85 optimal weight: 0.6980 chunk 99 optimal weight: 3.9990 chunk 62 optimal weight: 0.5980 chunk 108 optimal weight: 0.9990 chunk 54 optimal weight: 0.9990 chunk 56 optimal weight: 8.9990 chunk 110 optimal weight: 0.3980 overall best weight: 0.6582 ------------------------------------------------------------------------------- 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 = 0.4177 r_free = 0.4177 target = 0.202161 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3666 r_free = 0.3666 target = 0.147760 restraints weight = 9767.344| |-----------------------------------------------------------------------------| r_work (start): 0.3447 rms_B_bonded: 3.87 r_work: 0.2961 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.2807 rms_B_bonded: 4.63 restraints_weight: 0.2500 r_work (final): 0.2807 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7979 moved from start: 0.2582 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 9963 Z= 0.215 Angle : 0.519 8.301 13537 Z= 0.261 Chirality : 0.040 0.190 1585 Planarity : 0.004 0.049 1648 Dihedral : 6.200 57.772 1705 Min Nonbonded Distance : 2.617 Molprobity Statistics. All-atom Clashscore : 5.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.85 % Favored : 98.15 % Rotamer: Outliers : 1.25 % Allowed : 11.61 % Favored : 87.14 % 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: 1.38 (0.24), residues: 1187 helix: 1.31 (0.18), residues: 787 sheet: 0.08 (0.59), residues: 69 loop : 0.40 (0.36), residues: 331 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 733 HIS 0.007 0.001 HIS A 153 PHE 0.024 0.002 PHE A 336 TYR 0.011 0.001 TYR A 881 ARG 0.007 0.000 ARG A 815 *********************** 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 101 residues out of total 1042 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 88 time to evaluate : 0.963 Fit side-chains revert: symmetry clash REVERT: A 36 LYS cc_start: 0.8263 (OUTLIER) cc_final: 0.8018 (mtmt) REVERT: A 52 ARG cc_start: 0.7865 (mtt180) cc_final: 0.7146 (mmt180) REVERT: A 74 ASP cc_start: 0.7393 (t0) cc_final: 0.6732 (t0) REVERT: A 126 MET cc_start: 0.7656 (mmm) cc_final: 0.7215 (mpt) REVERT: A 611 MET cc_start: 0.6670 (ttp) cc_final: 0.5931 (tmt) REVERT: A 803 GLU cc_start: 0.7974 (tp30) cc_final: 0.7754 (mm-30) REVERT: A 909 GLN cc_start: 0.8003 (tt0) cc_final: 0.7480 (tt0) REVERT: A 998 ARG cc_start: 0.7859 (mtm-85) cc_final: 0.6917 (mpt90) REVERT: A 1011 GLU cc_start: 0.7613 (pt0) cc_final: 0.7016 (tp30) REVERT: A 1044 ASP cc_start: 0.6398 (t0) cc_final: 0.5935 (p0) REVERT: A 1093 GLU cc_start: 0.8836 (mm-30) cc_final: 0.8401 (mp0) REVERT: A 1097 LYS cc_start: 0.7283 (mttt) cc_final: 0.6901 (mttp) REVERT: A 1166 MET cc_start: 0.5273 (mmm) cc_final: 0.5042 (mmm) REVERT: A 1243 LYS cc_start: 0.5434 (mttt) cc_final: 0.4993 (mptt) REVERT: A 1253 LYS cc_start: 0.7363 (mmtt) cc_final: 0.7086 (mmpt) outliers start: 13 outliers final: 6 residues processed: 95 average time/residue: 1.3299 time to fit residues: 135.8355 Evaluate side-chains 90 residues out of total 1042 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 83 time to evaluate : 1.025 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 LYS Chi-restraints excluded: chain A residue 202 VAL 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 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: 0.9990 chunk 33 optimal weight: 0.1980 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: 0.9980 chunk 10 optimal weight: 0.5980 chunk 83 optimal weight: 0.5980 chunk 112 optimal weight: 0.7980 overall best weight: 0.5180 ------------------------------------------------------------------------------- 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 = 0.4189 r_free = 0.4189 target = 0.203188 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.122671 restraints weight = 9810.110| |-----------------------------------------------------------------------------| r_work (start): 0.3194 rms_B_bonded: 1.97 r_work: 0.3046 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.2894 rms_B_bonded: 4.02 restraints_weight: 0.2500 r_work (final): 0.2894 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7443 moved from start: 0.2742 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= 0.185 Angle : 0.499 7.426 13537 Z= 0.250 Chirality : 0.040 0.188 1585 Planarity : 0.004 0.047 1648 Dihedral : 6.084 58.596 1705 Min Nonbonded Distance : 2.620 Molprobity Statistics. All-atom Clashscore : 5.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.68 % Favored : 98.32 % Rotamer: Outliers : 1.06 % Allowed : 12.38 % Favored : 86.56 % 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: 1.48 (0.18), residues: 782 sheet: -0.00 (0.54), residues: 80 loop : 0.47 (0.37), residues: 325 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 733 HIS 0.006 0.001 HIS A 153 PHE 0.023 0.001 PHE A1048 TYR 0.011 0.001 TYR A 289 ARG 0.006 0.000 ARG A 815 *********************** 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 102 residues out of total 1042 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 91 time to evaluate : 1.102 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 36 LYS cc_start: 0.7993 (OUTLIER) cc_final: 0.7758 (mtmt) REVERT: A 52 ARG cc_start: 0.7202 (mtt180) cc_final: 0.6355 (mmt180) REVERT: A 74 ASP cc_start: 0.7166 (t0) cc_final: 0.6496 (t0) REVERT: A 126 MET cc_start: 0.7504 (mmm) cc_final: 0.7000 (mpt) REVERT: A 611 MET cc_start: 0.6705 (ttp) cc_final: 0.5919 (tmt) REVERT: A 803 GLU cc_start: 0.7513 (tp30) cc_final: 0.7243 (mm-30) REVERT: A 909 GLN cc_start: 0.7646 (tt0) cc_final: 0.7096 (tt0) REVERT: A 998 ARG cc_start: 0.7489 (mtm-85) cc_final: 0.6374 (mpt90) REVERT: A 1011 GLU cc_start: 0.7018 (pt0) cc_final: 0.6347 (tp30) REVERT: A 1044 ASP cc_start: 0.6238 (t0) cc_final: 0.5649 (p0) REVERT: A 1093 GLU cc_start: 0.8713 (mm-30) cc_final: 0.8293 (mp0) REVERT: A 1097 LYS cc_start: 0.7049 (mttt) cc_final: 0.6774 (mttp) REVERT: A 1243 LYS cc_start: 0.5220 (mttt) cc_final: 0.4858 (mptt) outliers start: 11 outliers final: 7 residues processed: 99 average time/residue: 1.3562 time to fit residues: 144.0987 Evaluate side-chains 95 residues out of total 1042 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 87 time to evaluate : 1.040 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 LYS Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 259 SER 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 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: 0.6980 chunk 55 optimal weight: 10.0000 chunk 33 optimal weight: 0.3980 chunk 40 optimal weight: 2.9990 chunk 99 optimal weight: 0.2980 chunk 11 optimal weight: 0.8980 chunk 87 optimal weight: 0.6980 chunk 49 optimal weight: 5.9990 chunk 82 optimal weight: 1.9990 chunk 32 optimal weight: 0.7980 chunk 44 optimal weight: 3.9990 overall best weight: 0.5780 ------------------------------------------------------------------------------- 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 = 0.4221 r_free = 0.4221 target = 0.206397 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 73)----------------| | r_work = 0.3395 r_free = 0.3395 target = 0.125285 restraints weight = 9932.659| |-----------------------------------------------------------------------------| r_work (start): 0.3179 rms_B_bonded: 1.94 r_work: 0.3032 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.2880 rms_B_bonded: 3.98 restraints_weight: 0.2500 r_work (final): 0.2880 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7439 moved from start: 0.2775 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 9963 Z= 0.198 Angle : 0.509 8.801 13537 Z= 0.256 Chirality : 0.040 0.188 1585 Planarity : 0.004 0.046 1648 Dihedral : 6.105 58.803 1705 Min Nonbonded Distance : 2.621 Molprobity Statistics. All-atom Clashscore : 5.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.94 % Favored : 98.06 % Rotamer: Outliers : 0.96 % Allowed : 13.53 % Favored : 85.51 % 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: 1.56 (0.24), residues: 1187 helix: 1.48 (0.18), residues: 782 sheet: -0.03 (0.54), residues: 80 loop : 0.44 (0.37), residues: 325 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 733 HIS 0.006 0.001 HIS A 153 PHE 0.023 0.001 PHE A 336 TYR 0.015 0.001 TYR A 289 ARG 0.007 0.000 ARG A 815 *********************** 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 99 residues out of total 1042 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 89 time to evaluate : 0.955 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 36 LYS cc_start: 0.7946 (OUTLIER) cc_final: 0.7688 (mtmt) REVERT: A 52 ARG cc_start: 0.7185 (mtt180) cc_final: 0.6330 (mmt180) REVERT: A 74 ASP cc_start: 0.7158 (t0) cc_final: 0.6602 (t0) REVERT: A 126 MET cc_start: 0.7509 (mmm) cc_final: 0.7006 (mpt) REVERT: A 611 MET cc_start: 0.6731 (ttp) cc_final: 0.5930 (tmt) REVERT: A 803 GLU cc_start: 0.7532 (tp30) cc_final: 0.7266 (mm-30) REVERT: A 909 GLN cc_start: 0.7640 (tt0) cc_final: 0.7085 (tt0) REVERT: A 998 ARG cc_start: 0.7506 (mtm-85) cc_final: 0.6375 (mpt90) REVERT: A 1011 GLU cc_start: 0.7003 (pt0) cc_final: 0.6337 (tp30) REVERT: A 1044 ASP cc_start: 0.6270 (t0) cc_final: 0.5707 (p0) REVERT: A 1093 GLU cc_start: 0.8820 (mm-30) cc_final: 0.8315 (mp0) REVERT: A 1097 LYS cc_start: 0.7049 (mttt) cc_final: 0.6743 (mttp) REVERT: A 1169 GLU cc_start: 0.6910 (mt-10) cc_final: 0.6428 (tm-30) REVERT: A 1243 LYS cc_start: 0.5222 (mttt) cc_final: 0.4858 (mptt) outliers start: 10 outliers final: 8 residues processed: 96 average time/residue: 1.3582 time to fit residues: 139.9236 Evaluate side-chains 92 residues out of total 1042 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 83 time to evaluate : 1.018 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 LYS Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 259 SER Chi-restraints excluded: chain A residue 344 SER Chi-restraints excluded: chain A residue 395 ILE Chi-restraints excluded: chain A residue 586 ILE Chi-restraints excluded: chain A residue 826 SER 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: 0.3980 chunk 62 optimal weight: 0.8980 chunk 92 optimal weight: 2.9990 chunk 16 optimal weight: 0.8980 chunk 40 optimal weight: 9.9990 chunk 6 optimal weight: 0.0470 chunk 23 optimal weight: 1.9990 chunk 4 optimal weight: 0.9990 chunk 61 optimal weight: 0.8980 chunk 82 optimal weight: 0.9990 chunk 77 optimal weight: 0.8980 overall best weight: 0.6278 ------------------------------------------------------------------------------- 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 = 0.4218 r_free = 0.4218 target = 0.206063 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.124412 restraints weight = 9907.858| |-----------------------------------------------------------------------------| r_work (start): 0.3168 rms_B_bonded: 1.96 r_work: 0.3019 rms_B_bonded: 2.54 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: 0.7458 moved from start: 0.2823 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 9963 Z= 0.207 Angle : 0.520 9.685 13537 Z= 0.260 Chirality : 0.040 0.189 1585 Planarity : 0.004 0.045 1648 Dihedral : 6.117 59.170 1705 Min Nonbonded Distance : 2.620 Molprobity Statistics. All-atom Clashscore : 5.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.77 % Favored : 98.23 % Rotamer: Outliers : 1.54 % Allowed : 13.15 % 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: 1.52 (0.24), residues: 1187 helix: 1.46 (0.18), residues: 782 sheet: -0.08 (0.54), residues: 80 loop : 0.40 (0.37), residues: 325 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 733 HIS 0.007 0.001 HIS A 153 PHE 0.028 0.002 PHE A1048 TYR 0.017 0.001 TYR A 289 ARG 0.007 0.000 ARG A 815 *********************** 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 102 residues out of total 1042 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 86 time to evaluate : 1.101 Fit side-chains revert: symmetry clash REVERT: A 36 LYS cc_start: 0.7955 (OUTLIER) cc_final: 0.7684 (mtmt) REVERT: A 52 ARG cc_start: 0.7212 (mtt180) cc_final: 0.6340 (mmt180) REVERT: A 74 ASP cc_start: 0.7165 (t0) cc_final: 0.6607 (t0) REVERT: A 126 MET cc_start: 0.7513 (mmm) cc_final: 0.7010 (mpt) REVERT: A 284 ARG cc_start: 0.7002 (OUTLIER) cc_final: 0.6686 (mtt90) REVERT: A 611 MET cc_start: 0.6688 (ttp) cc_final: 0.5911 (tmt) REVERT: A 803 GLU cc_start: 0.7517 (tp30) cc_final: 0.7249 (mm-30) REVERT: A 909 GLN cc_start: 0.7630 (tt0) cc_final: 0.7086 (tt0) REVERT: A 998 ARG cc_start: 0.7532 (mtm-85) cc_final: 0.6381 (mpt90) REVERT: A 1011 GLU cc_start: 0.7033 (pt0) cc_final: 0.6375 (tp30) REVERT: A 1044 ASP cc_start: 0.6296 (t0) cc_final: 0.5785 (p0) REVERT: A 1093 GLU cc_start: 0.8811 (mm-30) cc_final: 0.8319 (mp0) REVERT: A 1097 LYS cc_start: 0.7058 (mttt) cc_final: 0.6760 (mttp) REVERT: A 1169 GLU cc_start: 0.6828 (mt-10) cc_final: 0.6374 (tm-30) REVERT: A 1243 LYS cc_start: 0.5290 (mttt) cc_final: 0.4913 (mptt) outliers start: 16 outliers final: 9 residues processed: 97 average time/residue: 1.3620 time to fit residues: 142.1769 Evaluate side-chains 95 residues out of total 1042 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 84 time to evaluate : 1.075 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 LYS Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 259 SER Chi-restraints excluded: chain A residue 284 ARG Chi-restraints excluded: chain A residue 344 SER Chi-restraints excluded: chain A residue 395 ILE Chi-restraints excluded: chain A residue 586 ILE Chi-restraints excluded: chain A residue 826 SER 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: 5.9990 chunk 30 optimal weight: 1.9990 chunk 38 optimal weight: 0.9980 chunk 69 optimal weight: 1.9990 chunk 101 optimal weight: 0.0000 chunk 87 optimal weight: 0.9980 chunk 66 optimal weight: 0.9980 chunk 71 optimal weight: 0.1980 chunk 77 optimal weight: 0.5980 chunk 9 optimal weight: 1.9990 overall best weight: 0.5584 ------------------------------------------------------------------------------- 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 = 0.4182 r_free = 0.4182 target = 0.202179 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.125554 restraints weight = 9812.463| |-----------------------------------------------------------------------------| r_work (start): 0.3276 rms_B_bonded: 2.36 r_work: 0.3087 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.2933 rms_B_bonded: 4.22 restraints_weight: 0.2500 r_work (final): 0.2933 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7502 moved from start: 0.2875 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= 0.194 Angle : 0.517 10.526 13537 Z= 0.258 Chirality : 0.040 0.198 1585 Planarity : 0.004 0.045 1648 Dihedral : 6.078 59.310 1705 Min Nonbonded Distance : 2.621 Molprobity Statistics. All-atom Clashscore : 5.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.85 % Favored : 98.15 % Rotamer: Outliers : 1.06 % Allowed : 13.63 % 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: 1.58 (0.24), residues: 1187 helix: 1.51 (0.18), residues: 782 sheet: -0.01 (0.54), residues: 80 loop : 0.39 (0.37), residues: 325 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 733 HIS 0.006 0.001 HIS A 153 PHE 0.022 0.001 PHE A 336 TYR 0.025 0.001 TYR A 289 ARG 0.007 0.000 ARG A 815 ********************** 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 98 residues out of total 1042 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 87 time to evaluate : 1.135 Fit side-chains revert: symmetry clash REVERT: A 36 LYS cc_start: 0.8007 (OUTLIER) cc_final: 0.7739 (mtmt) REVERT: A 52 ARG cc_start: 0.7296 (mtt180) cc_final: 0.6420 (mmt180) REVERT: A 74 ASP cc_start: 0.7147 (t0) cc_final: 0.6588 (t0) REVERT: A 126 MET cc_start: 0.7513 (mmm) cc_final: 0.7016 (mpt) REVERT: A 611 MET cc_start: 0.6692 (ttp) cc_final: 0.5890 (tmt) REVERT: A 803 GLU cc_start: 0.7568 (tp30) cc_final: 0.7091 (tp30) REVERT: A 909 GLN cc_start: 0.7688 (tt0) cc_final: 0.7131 (tt0) REVERT: A 998 ARG cc_start: 0.7559 (mtm-85) cc_final: 0.6418 (mpt90) REVERT: A 1011 GLU cc_start: 0.7060 (pt0) cc_final: 0.6391 (tp30) REVERT: A 1044 ASP cc_start: 0.6284 (t0) cc_final: 0.5822 (p0) REVERT: A 1093 GLU cc_start: 0.8823 (mm-30) cc_final: 0.8322 (mp0) REVERT: A 1097 LYS cc_start: 0.7066 (mttt) cc_final: 0.6766 (mttp) REVERT: A 1169 GLU cc_start: 0.6832 (mt-10) cc_final: 0.6373 (tm-30) REVERT: A 1243 LYS cc_start: 0.5308 (mttt) cc_final: 0.4929 (mptt) outliers start: 11 outliers final: 9 residues processed: 94 average time/residue: 1.3397 time to fit residues: 135.2039 Evaluate side-chains 94 residues out of total 1042 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 84 time to evaluate : 1.033 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 LYS Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 259 SER Chi-restraints excluded: chain A residue 344 SER Chi-restraints excluded: chain A residue 395 ILE Chi-restraints excluded: chain A residue 586 ILE Chi-restraints excluded: chain A residue 826 SER 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 34 optimal weight: 0.4980 chunk 45 optimal weight: 4.9990 chunk 98 optimal weight: 0.9990 chunk 1 optimal weight: 0.9990 chunk 112 optimal weight: 1.9990 chunk 76 optimal weight: 0.5980 chunk 101 optimal weight: 3.9990 chunk 55 optimal weight: 0.5980 chunk 46 optimal weight: 0.7980 chunk 81 optimal weight: 0.5980 chunk 96 optimal weight: 10.0000 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 = 0.4218 r_free = 0.4218 target = 0.205951 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.128289 restraints weight = 9786.113| |-----------------------------------------------------------------------------| r_work (start): 0.3241 rms_B_bonded: 2.45 r_work: 0.3053 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.2897 rms_B_bonded: 4.36 restraints_weight: 0.2500 r_work (final): 0.2897 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7606 moved from start: 0.2879 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 9963 Z= 0.206 Angle : 0.523 10.075 13537 Z= 0.261 Chirality : 0.040 0.189 1585 Planarity : 0.004 0.045 1648 Dihedral : 6.100 59.511 1705 Min Nonbonded Distance : 2.620 Molprobity Statistics. All-atom Clashscore : 5.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.02 % Favored : 97.98 % Rotamer: Outliers : 1.06 % Allowed : 13.72 % Favored : 85.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.57 (0.24), residues: 1187 helix: 1.51 (0.18), residues: 782 sheet: -0.01 (0.55), residues: 80 loop : 0.38 (0.37), residues: 325 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 733 HIS 0.007 0.001 HIS A 153 PHE 0.030 0.002 PHE A1048 TYR 0.022 0.001 TYR A 289 ARG 0.007 0.000 ARG A 815 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7412.10 seconds wall clock time: 131 minutes 50.63 seconds (7910.63 seconds total)