Starting phenix.real_space_refine on Sat Jan 18 18:05:36 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8zpv_60355/01_2025/8zpv_60355.cif Found real_map, /net/cci-nas-00/data/ceres_data/8zpv_60355/01_2025/8zpv_60355.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8zpv_60355/01_2025/8zpv_60355.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8zpv_60355/01_2025/8zpv_60355.map" model { file = "/net/cci-nas-00/data/ceres_data/8zpv_60355/01_2025/8zpv_60355.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8zpv_60355/01_2025/8zpv_60355.cif" } resolution = 2.9 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= 0.002 sd= 0.042 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: 5 Type Number sf(0) Gaussians Zn 2 6.06 5 S 74 5.16 5 C 7899 2.51 5 N 2140 2.21 5 O 2325 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 74 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/chem_data/mon_lib" Total number of atoms: 12440 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 10260 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1275, 10260 Classifications: {'peptide': 1275} Link IDs: {'PCIS': 1, 'PTRANS': 47, 'TRANS': 1226} Chain breaks: 3 Chain: "B" Number of atoms: 400 Number of conformers: 1 Conformer: "" Number of residues, atoms: 51, 400 Classifications: {'peptide': 51} Link IDs: {'PTRANS': 1, 'TRANS': 49} Chain: "C" Number of atoms: 425 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 425 Classifications: {'peptide': 54} Link IDs: {'PTRANS': 1, 'TRANS': 52} Chain: "D" Number of atoms: 922 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 922 Classifications: {'peptide': 117} Link IDs: {'PTRANS': 2, 'TRANS': 114} Chain breaks: 1 Chain: "E" Number of atoms: 431 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 431 Classifications: {'peptide': 55} Link IDs: {'PTRANS': 1, 'TRANS': 53} Chain: "A" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 8492 SG CYS A1191 44.469 84.960 26.391 1.00160.50 S ATOM 10070 SG CYS A1428 48.058 85.635 25.185 1.00194.84 S ATOM 10076 SG CYS A1429 46.286 85.240 29.473 1.00198.05 S ATOM 8842 SG CYS A1236 64.542 90.436 34.526 1.00174.18 S ATOM 8865 SG CYS A1239 63.480 94.704 36.057 1.00174.85 S Time building chain proxies: 6.78, per 1000 atoms: 0.55 Number of scatterers: 12440 At special positions: 0 Unit cell: (103.18, 112.823, 167.788, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Zn 2 29.99 S 74 16.00 O 2325 8.00 N 2140 7.00 C 7899 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: 2.85 Conformation dependent library (CDL) restraints added in 1.6 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A2301 " pdb="ZN ZN A2301 " - pdb=" SG CYS A1429 " pdb="ZN ZN A2301 " - pdb=" SG CYS A1428 " pdb="ZN ZN A2301 " - pdb=" SG CYS A1191 " pdb=" ZN A2302 " pdb="ZN ZN A2302 " - pdb=" NE2 HIS A1423 " pdb="ZN ZN A2302 " - pdb=" NE2 HIS A1421 " pdb="ZN ZN A2302 " - pdb=" SG CYS A1239 " pdb="ZN ZN A2302 " - pdb=" SG CYS A1236 " Number of angles added : 2 3068 Ramachandran restraints generated. 1534 Oldfield, 0 Emsley, 1534 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2968 Finding SS restraints... Secondary structure from input PDB file: 75 helices and 9 sheets defined 61.2% alpha, 4.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.28 Creating SS restraints... Processing helix chain 'A' and resid 22 through 34 removed outlier: 4.062A pdb=" N LEU A 26 " --> pdb=" O VAL A 22 " (cutoff:3.500A) Processing helix chain 'A' and resid 43 through 57 removed outlier: 3.892A pdb=" N SER A 47 " --> pdb=" O ASP A 43 " (cutoff:3.500A) Processing helix chain 'A' and resid 60 through 77 Processing helix chain 'A' and resid 79 through 83 Processing helix chain 'A' and resid 91 through 96 Processing helix chain 'A' and resid 104 through 137 removed outlier: 3.507A pdb=" N ASP A 108 " --> pdb=" O THR A 104 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N ASN A 109 " --> pdb=" O SER A 105 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N ILE A 110 " --> pdb=" O LYS A 106 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N ILE A 120 " --> pdb=" O LYS A 116 " (cutoff:3.500A) removed outlier: 4.119A pdb=" N ILE A 121 " --> pdb=" O ALA A 117 " (cutoff:3.500A) removed outlier: 5.484A pdb=" N LYS A 123 " --> pdb=" O ASN A 119 " (cutoff:3.500A) removed outlier: 5.410A pdb=" N LYS A 124 " --> pdb=" O ILE A 120 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N THR A 133 " --> pdb=" O LEU A 129 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N LEU A 136 " --> pdb=" O ILE A 132 " (cutoff:3.500A) Processing helix chain 'A' and resid 147 through 155 Processing helix chain 'A' and resid 156 through 163 Processing helix chain 'A' and resid 166 through 187 removed outlier: 3.615A pdb=" N PHE A 170 " --> pdb=" O TRP A 166 " (cutoff:3.500A) Processing helix chain 'A' and resid 189 through 193 Processing helix chain 'A' and resid 231 through 255 removed outlier: 3.633A pdb=" N CYS A 239 " --> pdb=" O VAL A 235 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N ASP A 240 " --> pdb=" O LEU A 236 " (cutoff:3.500A) Processing helix chain 'A' and resid 260 through 273 removed outlier: 3.988A pdb=" N ARG A 264 " --> pdb=" O PRO A 260 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N ASN A 266 " --> pdb=" O ILE A 262 " (cutoff:3.500A) Processing helix chain 'A' and resid 275 through 280 Processing helix chain 'A' and resid 282 through 288 removed outlier: 3.952A pdb=" N ILE A 286 " --> pdb=" O ARG A 282 " (cutoff:3.500A) Processing helix chain 'A' and resid 289 through 300 removed outlier: 3.795A pdb=" N LEU A 293 " --> pdb=" O MET A 289 " (cutoff:3.500A) Processing helix chain 'A' and resid 304 through 308 removed outlier: 3.927A pdb=" N ARG A 308 " --> pdb=" O ARG A 305 " (cutoff:3.500A) Processing helix chain 'A' and resid 309 through 327 removed outlier: 3.832A pdb=" N HIS A 314 " --> pdb=" O ALA A 310 " (cutoff:3.500A) Processing helix chain 'A' and resid 330 through 346 Processing helix chain 'A' and resid 349 through 354 Processing helix chain 'A' and resid 355 through 362 removed outlier: 3.558A pdb=" N PHE A 359 " --> pdb=" O PHE A 356 " (cutoff:3.500A) removed outlier: 4.863A pdb=" N PHE A 360 " --> pdb=" O PHE A 357 " (cutoff:3.500A) removed outlier: 4.166A pdb=" N ARG A 361 " --> pdb=" O SER A 358 " (cutoff:3.500A) Processing helix chain 'A' and resid 369 through 382 removed outlier: 4.047A pdb=" N ALA A 373 " --> pdb=" O GLU A 369 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N HIS A 380 " --> pdb=" O LYS A 376 " (cutoff:3.500A) Processing helix chain 'A' and resid 388 through 409 removed outlier: 3.810A pdb=" N ILE A 392 " --> pdb=" O GLU A 388 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N ILE A 398 " --> pdb=" O LYS A 394 " (cutoff:3.500A) Processing helix chain 'A' and resid 425 through 435 Processing helix chain 'A' and resid 439 through 446 Processing helix chain 'A' and resid 467 through 472 removed outlier: 3.619A pdb=" N MET A 471 " --> pdb=" O LEU A 467 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N LYS A 472 " --> pdb=" O SER A 468 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 467 through 472' Processing helix chain 'A' and resid 479 through 483 Processing helix chain 'A' and resid 488 through 492 removed outlier: 3.587A pdb=" N LEU A 492 " --> pdb=" O ARG A 489 " (cutoff:3.500A) Processing helix chain 'A' and resid 504 through 512 Processing helix chain 'A' and resid 516 through 526 removed outlier: 3.817A pdb=" N GLU A 522 " --> pdb=" O TYR A 518 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N TYR A 523 " --> pdb=" O ASN A 519 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N VAL A 524 " --> pdb=" O MET A 520 " (cutoff:3.500A) Processing helix chain 'A' and resid 557 through 574 Processing helix chain 'A' and resid 575 through 578 Processing helix chain 'A' and resid 725 through 730 removed outlier: 3.635A pdb=" N ASN A 729 " --> pdb=" O LYS A 725 " (cutoff:3.500A) Processing helix chain 'A' and resid 731 through 747 removed outlier: 4.622A pdb=" N ILE A 737 " --> pdb=" O GLU A 733 " (cutoff:3.500A) removed outlier: 5.539A pdb=" N PHE A 738 " --> pdb=" O SER A 734 " (cutoff:3.500A) Processing helix chain 'A' and resid 754 through 760 Processing helix chain 'A' and resid 780 through 784 removed outlier: 3.818A pdb=" N THR A 784 " --> pdb=" O LEU A 781 " (cutoff:3.500A) Processing helix chain 'A' and resid 802 through 822 Proline residue: A 812 - end of helix Processing helix chain 'A' and resid 847 through 874 removed outlier: 3.695A pdb=" N ARG A 865 " --> pdb=" O LEU A 861 " (cutoff:3.500A) Processing helix chain 'A' and resid 904 through 910 removed outlier: 4.157A pdb=" N SER A 908 " --> pdb=" O GLN A 904 " (cutoff:3.500A) Processing helix chain 'A' and resid 922 through 941 Processing helix chain 'A' and resid 943 through 965 Processing helix chain 'A' and resid 972 through 982 Proline residue: A 978 - end of helix Processing helix chain 'A' and resid 982 through 992 Processing helix chain 'A' and resid 993 through 997 removed outlier: 3.668A pdb=" N ILE A 996 " --> pdb=" O PRO A 993 " (cutoff:3.500A) Processing helix chain 'A' and resid 1003 through 1008 Processing helix chain 'A' and resid 1014 through 1029 Processing helix chain 'A' and resid 1034 through 1042 removed outlier: 3.680A pdb=" N GLN A1038 " --> pdb=" O GLU A1034 " (cutoff:3.500A) Processing helix chain 'A' and resid 1049 through 1056 Processing helix chain 'A' and resid 1067 through 1082 Processing helix chain 'A' and resid 1086 through 1090 Processing helix chain 'A' and resid 1096 through 1110 Processing helix chain 'A' and resid 1115 through 1120 Processing helix chain 'A' and resid 1121 through 1126 Processing helix chain 'A' and resid 1127 through 1138 removed outlier: 3.548A pdb=" N LEU A1137 " --> pdb=" O GLU A1133 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N LEU A1138 " --> pdb=" O ILE A1134 " (cutoff:3.500A) Processing helix chain 'A' and resid 1141 through 1153 removed outlier: 4.144A pdb=" N ARG A1150 " --> pdb=" O ARG A1146 " (cutoff:3.500A) Processing helix chain 'A' and resid 1155 through 1164 removed outlier: 3.824A pdb=" N VAL A1159 " --> pdb=" O GLN A1155 " (cutoff:3.500A) Processing helix chain 'A' and resid 1164 through 1178 Processing helix chain 'A' and resid 1191 through 1204 removed outlier: 3.629A pdb=" N SER A1201 " --> pdb=" O ARG A1197 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N HIS A1202 " --> pdb=" O ALA A1198 " (cutoff:3.500A) Processing helix chain 'A' and resid 1292 through 1309 Processing helix chain 'A' and resid 1311 through 1323 removed outlier: 3.596A pdb=" N TRP A1319 " --> pdb=" O TRP A1315 " (cutoff:3.500A) Processing helix chain 'A' and resid 1393 through 1407 removed outlier: 3.592A pdb=" N LEU A1398 " --> pdb=" O GLN A1394 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N SER A1401 " --> pdb=" O LEU A1397 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N GLY A1405 " --> pdb=" O SER A1401 " (cutoff:3.500A) Processing helix chain 'B' and resid 522 through 539 Processing helix chain 'B' and resid 542 through 548 removed outlier: 4.028A pdb=" N ILE B 546 " --> pdb=" O GLU B 542 " (cutoff:3.500A) Processing helix chain 'B' and resid 550 through 556 removed outlier: 3.525A pdb=" N VAL B 556 " --> pdb=" O SER B 552 " (cutoff:3.500A) Processing helix chain 'B' and resid 557 through 565 Processing helix chain 'C' and resid 520 through 530 removed outlier: 4.088A pdb=" N ASN C 528 " --> pdb=" O ILE C 524 " (cutoff:3.500A) Processing helix chain 'C' and resid 530 through 541 removed outlier: 4.234A pdb=" N ASN C 534 " --> pdb=" O ASP C 530 " (cutoff:3.500A) removed outlier: 5.115A pdb=" N GLU C 538 " --> pdb=" O ASN C 534 " (cutoff:3.500A) Processing helix chain 'C' and resid 543 through 557 removed outlier: 4.933A pdb=" N LYS C 549 " --> pdb=" O LYS C 545 " (cutoff:3.500A) Processing helix chain 'C' and resid 558 through 562 Processing helix chain 'D' and resid 520 through 552 Proline residue: D 544 - end of helix removed outlier: 4.028A pdb=" N LYS D 549 " --> pdb=" O LYS D 545 " (cutoff:3.500A) Processing helix chain 'D' and resid 552 through 565 removed outlier: 3.865A pdb=" N LYS D 559 " --> pdb=" O ARG D 555 " (cutoff:3.500A) removed outlier: 4.439A pdb=" N LEU D 564 " --> pdb=" O THR D 560 " (cutoff:3.500A) Processing helix chain 'D' and resid 657 through 672 Processing helix chain 'D' and resid 674 through 688 Processing helix chain 'D' and resid 690 through 707 Processing helix chain 'E' and resid 520 through 542 removed outlier: 5.037A pdb=" N ASN E 528 " --> pdb=" O ILE E 524 " (cutoff:3.500A) removed outlier: 4.546A pdb=" N MET E 531 " --> pdb=" O ILE E 527 " (cutoff:3.500A) removed outlier: 4.672A pdb=" N GLU E 537 " --> pdb=" O LEU E 533 " (cutoff:3.500A) removed outlier: 5.356A pdb=" N GLU E 538 " --> pdb=" O ASN E 534 " (cutoff:3.500A) removed outlier: 4.657A pdb=" N GLN E 539 " --> pdb=" O HIS E 535 " (cutoff:3.500A) Processing helix chain 'E' and resid 542 through 563 removed outlier: 4.324A pdb=" N ILE E 546 " --> pdb=" O GLU E 542 " (cutoff:3.500A) removed outlier: 4.738A pdb=" N GLU E 551 " --> pdb=" O ILE E 547 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N VAL E 556 " --> pdb=" O SER E 552 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 84 through 85 Processing sheet with id=AA2, first strand: chain 'A' and resid 385 through 386 Processing sheet with id=AA3, first strand: chain 'A' and resid 418 through 419 Processing sheet with id=AA4, first strand: chain 'A' and resid 538 through 541 Processing sheet with id=AA5, first strand: chain 'A' and resid 824 through 827 removed outlier: 4.206A pdb=" N ARG A 824 " --> pdb=" O THR A 839 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N ALA A 837 " --> pdb=" O ALA A 826 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 763 through 765 Processing sheet with id=AA7, first strand: chain 'A' and resid 888 through 891 Processing sheet with id=AA8, first strand: chain 'A' and resid 1113 through 1114 Processing sheet with id=AA9, first strand: chain 'A' and resid 1226 through 1230 removed outlier: 3.505A pdb=" N HIS A1421 " --> pdb=" O ARG A1228 " (cutoff:3.500A) 645 hydrogen bonds defined for protein. 1830 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: 3.76 Time building geometry restraints manager: 3.32 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.05 - 1.20: 15 1.20 - 1.35: 4107 1.35 - 1.51: 3357 1.51 - 1.66: 5057 1.66 - 1.81: 121 Bond restraints: 12657 Sorted by residual: bond pdb=" N PRO A 13 " pdb=" CA PRO A 13 " ideal model delta sigma weight residual 1.467 1.681 -0.214 1.17e-02 7.31e+03 3.36e+02 bond pdb=" C LYS A1175 " pdb=" O LYS A1175 " ideal model delta sigma weight residual 1.237 1.050 0.187 1.17e-02 7.31e+03 2.56e+02 bond pdb=" C LEU A1176 " pdb=" O LEU A1176 " ideal model delta sigma weight residual 1.237 1.055 0.181 1.17e-02 7.31e+03 2.40e+02 bond pdb=" C ILE A1172 " pdb=" O ILE A1172 " ideal model delta sigma weight residual 1.237 1.096 0.141 1.17e-02 7.31e+03 1.46e+02 bond pdb=" C LEU A1171 " pdb=" O LEU A1171 " ideal model delta sigma weight residual 1.237 1.117 0.120 1.17e-02 7.31e+03 1.06e+02 ... (remaining 12652 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.76: 16964 3.76 - 7.51: 109 7.51 - 11.27: 16 11.27 - 15.03: 3 15.03 - 18.78: 2 Bond angle restraints: 17094 Sorted by residual: angle pdb=" C TYR A 12 " pdb=" N PRO A 13 " pdb=" CA PRO A 13 " ideal model delta sigma weight residual 119.93 138.71 -18.78 1.07e+00 8.73e-01 3.08e+02 angle pdb=" N PRO A 13 " pdb=" CA PRO A 13 " pdb=" C PRO A 13 " ideal model delta sigma weight residual 111.26 95.78 15.48 1.63e+00 3.76e-01 9.02e+01 angle pdb=" CA LYS A1175 " pdb=" C LYS A1175 " pdb=" O LYS A1175 " ideal model delta sigma weight residual 120.55 111.73 8.82 1.06e+00 8.90e-01 6.92e+01 angle pdb=" CA PRO A 13 " pdb=" N PRO A 13 " pdb=" CD PRO A 13 " ideal model delta sigma weight residual 112.00 101.55 10.45 1.40e+00 5.10e-01 5.57e+01 angle pdb=" C ASN A1174 " pdb=" CA ASN A1174 " pdb=" CB ASN A1174 " ideal model delta sigma weight residual 110.85 98.25 12.60 1.70e+00 3.46e-01 5.49e+01 ... (remaining 17089 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.76: 6654 17.76 - 35.52: 833 35.52 - 53.29: 209 53.29 - 71.05: 52 71.05 - 88.81: 23 Dihedral angle restraints: 7771 sinusoidal: 3209 harmonic: 4562 Sorted by residual: dihedral pdb=" CA ILE A1238 " pdb=" C ILE A1238 " pdb=" N CYS A1239 " pdb=" CA CYS A1239 " ideal model delta harmonic sigma weight residual -180.00 -130.98 -49.02 0 5.00e+00 4.00e-02 9.61e+01 dihedral pdb=" CA ILE B 536 " pdb=" C ILE B 536 " pdb=" N GLU B 537 " pdb=" CA GLU B 537 " ideal model delta harmonic sigma weight residual 180.00 144.59 35.41 0 5.00e+00 4.00e-02 5.01e+01 dihedral pdb=" CA ILE A 828 " pdb=" C ILE A 828 " pdb=" N VAL A 829 " pdb=" CA VAL A 829 " ideal model delta harmonic sigma weight residual -180.00 -146.66 -33.34 0 5.00e+00 4.00e-02 4.45e+01 ... (remaining 7768 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.131: 1939 0.131 - 0.263: 17 0.263 - 0.394: 4 0.394 - 0.525: 0 0.525 - 0.656: 2 Chirality restraints: 1962 Sorted by residual: chirality pdb=" CA PRO A 13 " pdb=" N PRO A 13 " pdb=" C PRO A 13 " pdb=" CB PRO A 13 " both_signs ideal model delta sigma weight residual False 2.72 3.37 -0.66 2.00e-01 2.50e+01 1.08e+01 chirality pdb=" CA HIS A 16 " pdb=" N HIS A 16 " pdb=" C HIS A 16 " pdb=" CB HIS A 16 " both_signs ideal model delta sigma weight residual False 2.51 1.93 0.58 2.00e-01 2.50e+01 8.50e+00 chirality pdb=" CA ILE A 21 " pdb=" N ILE A 21 " pdb=" C ILE A 21 " pdb=" CB ILE A 21 " both_signs ideal model delta sigma weight residual False 2.43 2.76 -0.33 2.00e-01 2.50e+01 2.70e+00 ... (remaining 1959 not shown) Planarity restraints: 2171 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ILE A1172 " 0.028 2.00e-02 2.50e+03 5.68e-02 3.23e+01 pdb=" C ILE A1172 " -0.098 2.00e-02 2.50e+03 pdb=" O ILE A1172 " 0.037 2.00e-02 2.50e+03 pdb=" N LEU A1173 " 0.034 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU A1173 " 0.025 2.00e-02 2.50e+03 5.09e-02 2.59e+01 pdb=" C LEU A1173 " -0.088 2.00e-02 2.50e+03 pdb=" O LEU A1173 " 0.033 2.00e-02 2.50e+03 pdb=" N ASN A1174 " 0.030 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU A1121 " -0.020 2.00e-02 2.50e+03 4.04e-02 1.63e+01 pdb=" C GLU A1121 " 0.070 2.00e-02 2.50e+03 pdb=" O GLU A1121 " -0.026 2.00e-02 2.50e+03 pdb=" N ILE A1122 " -0.024 2.00e-02 2.50e+03 ... (remaining 2168 not shown) Histogram of nonbonded interaction distances: 2.03 - 2.60: 188 2.60 - 3.18: 11431 3.18 - 3.75: 19054 3.75 - 4.33: 24957 4.33 - 4.90: 41138 Nonbonded interactions: 96768 Sorted by model distance: nonbonded pdb=" O VAL B 556 " pdb=" OG1 THR B 560 " model vdw 2.026 3.040 nonbonded pdb=" O ILE A 145 " pdb=" N ASN A 147 " model vdw 2.087 3.120 nonbonded pdb=" OE1 GLU A1223 " pdb="ZN ZN A2301 " model vdw 2.129 2.230 nonbonded pdb=" N GLU A 14 " pdb=" OE1 GLU A 14 " model vdw 2.160 3.120 nonbonded pdb=" O GLU A 522 " pdb=" OG SER A 526 " model vdw 2.175 3.040 ... (remaining 96763 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'B' selection = (chain 'C' and resid 519 through 569) selection = (chain 'E' and resid 519 through 569) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.370 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: 0.030 Extract box with map and model: 0.470 Check model and map are aligned: 0.090 Set scattering table: 0.110 Process input model: 30.420 Find NCS groups from input model: 0.170 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:12.270 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 45.980 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7262 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 : 0.007 0.214 12657 Z= 0.494 Angle : 0.830 18.785 17094 Z= 0.507 Chirality : 0.052 0.656 1962 Planarity : 0.004 0.057 2171 Dihedral : 17.498 88.812 4803 Min Nonbonded Distance : 2.026 Molprobity Statistics. All-atom Clashscore : 14.13 Ramachandran Plot: Outliers : 0.13 % Allowed : 8.21 % Favored : 91.66 % Rotamer: Outliers : 10.22 % Allowed : 24.45 % Favored : 65.33 % Cbeta Deviations : 0.27 % Peptide Plane: Cis-proline : 1.92 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.34 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.61 (0.20), residues: 1534 helix: -0.78 (0.17), residues: 828 sheet: -1.82 (0.53), residues: 79 loop : -3.04 (0.22), residues: 627 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 754 HIS 0.009 0.001 HIS A 16 PHE 0.012 0.001 PHE A 553 TYR 0.013 0.001 TYR A 389 ARG 0.009 0.000 ARG A1181 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3068 Ramachandran restraints generated. 1534 Oldfield, 0 Emsley, 1534 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3068 Ramachandran restraints generated. 1534 Oldfield, 0 Emsley, 1534 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 515 residues out of total 1399 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 143 poor density : 372 time to evaluate : 1.218 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 17 LEU cc_start: 0.6325 (OUTLIER) cc_final: 0.5578 (tm) REVERT: A 144 GLU cc_start: 0.5606 (OUTLIER) cc_final: 0.5143 (pm20) REVERT: A 146 ILE cc_start: 0.7010 (OUTLIER) cc_final: 0.5898 (mt) REVERT: A 148 ILE cc_start: 0.5033 (OUTLIER) cc_final: 0.4632 (pp) REVERT: A 291 GLU cc_start: 0.8157 (pm20) cc_final: 0.7494 (mp0) REVERT: A 544 LYS cc_start: 0.7813 (mttm) cc_final: 0.6565 (mttm) REVERT: A 556 MET cc_start: 0.6452 (mtm) cc_final: 0.6156 (mtp) REVERT: A 577 LYS cc_start: 0.8459 (mttt) cc_final: 0.8045 (mppt) REVERT: A 801 TYR cc_start: 0.8099 (m-10) cc_final: 0.7326 (m-10) REVERT: A 1123 LEU cc_start: 0.9004 (tt) cc_final: 0.8619 (tm) REVERT: A 1243 ASN cc_start: 0.7819 (t0) cc_final: 0.7342 (t0) REVERT: A 1313 GLU cc_start: 0.9115 (mm-30) cc_final: 0.8710 (mm-30) REVERT: A 1420 TYR cc_start: 0.8541 (t80) cc_final: 0.8280 (t80) REVERT: A 1424 VAL cc_start: 0.8104 (p) cc_final: 0.7721 (p) REVERT: B 532 ARG cc_start: 0.6278 (tmm160) cc_final: 0.5826 (mmm160) REVERT: C 531 MET cc_start: 0.7863 (mpp) cc_final: 0.7632 (ttt) REVERT: D 674 ASP cc_start: 0.4080 (OUTLIER) cc_final: 0.3432 (m-30) REVERT: D 678 ARG cc_start: 0.8342 (ttp-110) cc_final: 0.8024 (ttp-110) REVERT: E 561 ASN cc_start: 0.8483 (t0) cc_final: 0.8280 (t0) outliers start: 143 outliers final: 24 residues processed: 482 average time/residue: 0.9367 time to fit residues: 505.0324 Evaluate side-chains 247 residues out of total 1399 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 218 time to evaluate : 1.358 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 ASP Chi-restraints excluded: chain A residue 17 LEU Chi-restraints excluded: chain A residue 141 ARG Chi-restraints excluded: chain A residue 144 GLU Chi-restraints excluded: chain A residue 146 ILE Chi-restraints excluded: chain A residue 148 ILE Chi-restraints excluded: chain A residue 439 THR Chi-restraints excluded: chain A residue 451 CYS Chi-restraints excluded: chain A residue 486 VAL Chi-restraints excluded: chain A residue 495 THR Chi-restraints excluded: chain A residue 498 LYS Chi-restraints excluded: chain A residue 500 THR Chi-restraints excluded: chain A residue 721 THR Chi-restraints excluded: chain A residue 850 VAL Chi-restraints excluded: chain A residue 886 THR Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain A residue 945 ASN Chi-restraints excluded: chain A residue 1141 THR Chi-restraints excluded: chain A residue 1149 LEU Chi-restraints excluded: chain A residue 1188 SER Chi-restraints excluded: chain A residue 1192 SER Chi-restraints excluded: chain A residue 1440 ASP Chi-restraints excluded: chain B residue 522 ASN Chi-restraints excluded: chain B residue 538 GLU Chi-restraints excluded: chain B residue 549 LYS Chi-restraints excluded: chain B residue 556 VAL Chi-restraints excluded: chain D residue 555 ARG Chi-restraints excluded: chain D residue 674 ASP Chi-restraints excluded: chain D residue 676 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 129 optimal weight: 4.9990 chunk 115 optimal weight: 6.9990 chunk 64 optimal weight: 6.9990 chunk 39 optimal weight: 2.9990 chunk 78 optimal weight: 0.3980 chunk 61 optimal weight: 1.9990 chunk 119 optimal weight: 0.4980 chunk 46 optimal weight: 10.0000 chunk 72 optimal weight: 0.6980 chunk 89 optimal weight: 0.8980 chunk 138 optimal weight: 9.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 55 HIS A 135 ASN A 331 GLN A1038 GLN A1165 HIS A1169 GLN ** A1189 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1256 GLN A1259 GLN A1394 GLN A1417 ASN ** B 528 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 539 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 561 ASN D 690 ASN E 534 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3503 r_free = 0.3503 target = 0.085926 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2983 r_free = 0.2983 target = 0.059956 restraints weight = 37037.396| |-----------------------------------------------------------------------------| r_work (start): 0.2926 rms_B_bonded: 4.04 r_work: 0.2782 rms_B_bonded: 4.63 restraints_weight: 0.5000 r_work (final): 0.2782 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7709 moved from start: 0.3745 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.079 12657 Z= 0.246 Angle : 0.788 12.310 17094 Z= 0.404 Chirality : 0.047 0.184 1962 Planarity : 0.004 0.047 2171 Dihedral : 7.481 50.577 1733 Min Nonbonded Distance : 2.371 Molprobity Statistics. All-atom Clashscore : 11.73 Ramachandran Plot: Outliers : 0.07 % Allowed : 7.11 % Favored : 92.83 % Rotamer: Outliers : 7.29 % Allowed : 31.31 % Favored : 61.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.92 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.34 % 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: -1.35 (0.21), residues: 1534 helix: 0.16 (0.18), residues: 830 sheet: -1.30 (0.50), residues: 94 loop : -2.33 (0.25), residues: 610 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP A1319 HIS 0.010 0.001 HIS A 55 PHE 0.022 0.001 PHE A 553 TYR 0.019 0.002 TYR A 732 ARG 0.018 0.001 ARG E 532 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3068 Ramachandran restraints generated. 1534 Oldfield, 0 Emsley, 1534 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3068 Ramachandran restraints generated. 1534 Oldfield, 0 Emsley, 1534 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 341 residues out of total 1399 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 102 poor density : 239 time to evaluate : 1.363 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 146 ILE cc_start: 0.6437 (OUTLIER) cc_final: 0.6033 (mt) REVERT: A 202 ARG cc_start: 0.8880 (ttm170) cc_final: 0.8623 (tpp80) REVERT: A 291 GLU cc_start: 0.8675 (OUTLIER) cc_final: 0.8165 (mp0) REVERT: A 471 MET cc_start: 0.9131 (mmp) cc_final: 0.8745 (mmp) REVERT: A 577 LYS cc_start: 0.8840 (mttt) cc_final: 0.8547 (mtmm) REVERT: A 1026 MET cc_start: 0.8177 (OUTLIER) cc_final: 0.7969 (mtt) REVERT: A 1123 LEU cc_start: 0.8866 (tt) cc_final: 0.8430 (tm) REVERT: A 1243 ASN cc_start: 0.8025 (t0) cc_final: 0.7482 (t0) REVERT: A 1424 VAL cc_start: 0.7702 (p) cc_final: 0.7369 (p) REVERT: C 530 ASP cc_start: 0.7792 (p0) cc_final: 0.7410 (p0) REVERT: D 575 MET cc_start: 0.7980 (mpp) cc_final: 0.7772 (mpp) REVERT: D 577 MET cc_start: 0.8244 (tmm) cc_final: 0.7988 (tmm) REVERT: D 686 ASN cc_start: 0.8493 (m-40) cc_final: 0.8214 (m110) outliers start: 102 outliers final: 39 residues processed: 309 average time/residue: 1.0595 time to fit residues: 361.8318 Evaluate side-chains 237 residues out of total 1399 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 195 time to evaluate : 1.334 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 99 THR Chi-restraints excluded: chain A residue 132 ILE Chi-restraints excluded: chain A residue 141 ARG Chi-restraints excluded: chain A residue 146 ILE Chi-restraints excluded: chain A residue 291 GLU Chi-restraints excluded: chain A residue 293 LEU Chi-restraints excluded: chain A residue 297 LEU Chi-restraints excluded: chain A residue 320 HIS Chi-restraints excluded: chain A residue 344 ILE Chi-restraints excluded: chain A residue 358 SER Chi-restraints excluded: chain A residue 425 SER Chi-restraints excluded: chain A residue 439 THR Chi-restraints excluded: chain A residue 464 ASP Chi-restraints excluded: chain A residue 495 THR Chi-restraints excluded: chain A residue 498 LYS Chi-restraints excluded: chain A residue 552 LEU Chi-restraints excluded: chain A residue 728 LEU Chi-restraints excluded: chain A residue 839 THR Chi-restraints excluded: chain A residue 842 VAL Chi-restraints excluded: chain A residue 850 VAL Chi-restraints excluded: chain A residue 886 THR Chi-restraints excluded: chain A residue 901 VAL Chi-restraints excluded: chain A residue 903 SER Chi-restraints excluded: chain A residue 919 LEU Chi-restraints excluded: chain A residue 946 VAL Chi-restraints excluded: chain A residue 1026 MET Chi-restraints excluded: chain A residue 1080 ILE Chi-restraints excluded: chain A residue 1088 MET Chi-restraints excluded: chain A residue 1149 LEU Chi-restraints excluded: chain A residue 1162 LEU Chi-restraints excluded: chain A residue 1251 VAL Chi-restraints excluded: chain A residue 1336 ILE Chi-restraints excluded: chain A residue 1339 VAL Chi-restraints excluded: chain A residue 1440 ASP Chi-restraints excluded: chain B residue 549 LYS Chi-restraints excluded: chain B residue 556 VAL Chi-restraints excluded: chain D residue 564 LEU Chi-restraints excluded: chain D residue 567 ILE Chi-restraints excluded: chain D residue 658 ASP Chi-restraints excluded: chain D residue 685 LEU Chi-restraints excluded: chain E residue 545 LYS Chi-restraints excluded: chain E residue 559 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 148 optimal weight: 10.0000 chunk 146 optimal weight: 8.9990 chunk 107 optimal weight: 0.0870 chunk 15 optimal weight: 4.9990 chunk 137 optimal weight: 9.9990 chunk 106 optimal weight: 0.8980 chunk 44 optimal weight: 4.9990 chunk 118 optimal weight: 8.9990 chunk 2 optimal weight: 3.9990 chunk 119 optimal weight: 6.9990 chunk 55 optimal weight: 0.8980 overall best weight: 2.1762 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 16 HIS A 55 HIS A 92 ASN A 331 GLN ** A 951 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1189 ASN A1259 GLN A1324 GLN ** B 528 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 539 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 522 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3490 r_free = 0.3490 target = 0.084371 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.2950 r_free = 0.2950 target = 0.057947 restraints weight = 37284.931| |-----------------------------------------------------------------------------| r_work (start): 0.2903 rms_B_bonded: 4.01 r_work: 0.2756 rms_B_bonded: 4.65 restraints_weight: 0.5000 r_work (final): 0.2756 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8261 moved from start: 0.7095 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.109 12657 Z= 0.346 Angle : 0.844 13.436 17094 Z= 0.440 Chirality : 0.049 0.234 1962 Planarity : 0.005 0.046 2171 Dihedral : 6.821 47.215 1699 Min Nonbonded Distance : 2.302 Molprobity Statistics. All-atom Clashscore : 12.33 Ramachandran Plot: Outliers : 0.07 % Allowed : 7.95 % Favored : 91.98 % Rotamer: Outliers : 8.65 % Allowed : 29.38 % Favored : 61.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.92 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.27 % 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: -1.06 (0.22), residues: 1534 helix: 0.38 (0.18), residues: 819 sheet: -1.19 (0.51), residues: 89 loop : -2.10 (0.25), residues: 626 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A1248 HIS 0.009 0.001 HIS A 55 PHE 0.029 0.002 PHE A 553 TYR 0.012 0.001 TYR A 284 ARG 0.014 0.001 ARG A1180 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3068 Ramachandran restraints generated. 1534 Oldfield, 0 Emsley, 1534 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3068 Ramachandran restraints generated. 1534 Oldfield, 0 Emsley, 1534 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 299 residues out of total 1399 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 121 poor density : 178 time to evaluate : 1.382 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 43 ASP cc_start: 0.8398 (t0) cc_final: 0.8131 (t0) REVERT: A 146 ILE cc_start: 0.7210 (OUTLIER) cc_final: 0.6761 (mt) REVERT: A 282 ARG cc_start: 0.9318 (OUTLIER) cc_final: 0.9034 (mtp180) REVERT: A 289 MET cc_start: 0.9376 (OUTLIER) cc_final: 0.9163 (ttp) REVERT: A 291 GLU cc_start: 0.8916 (OUTLIER) cc_final: 0.8514 (mp0) REVERT: A 380 HIS cc_start: 0.8763 (OUTLIER) cc_final: 0.8555 (t-90) REVERT: A 577 LYS cc_start: 0.9379 (mttt) cc_final: 0.9051 (mtmm) REVERT: A 712 PHE cc_start: 0.8279 (m-80) cc_final: 0.8003 (m-80) REVERT: A 893 LYS cc_start: 0.9499 (mmmm) cc_final: 0.9125 (mppt) REVERT: A 1123 LEU cc_start: 0.8898 (tt) cc_final: 0.8551 (tm) REVERT: A 1133 GLU cc_start: 0.8768 (pp20) cc_final: 0.8514 (pp20) REVERT: A 1245 MET cc_start: 0.8483 (OUTLIER) cc_final: 0.8219 (mmm) REVERT: C 531 MET cc_start: 0.7569 (mpt) cc_final: 0.7134 (ttm) REVERT: C 555 ARG cc_start: 0.8122 (mmp-170) cc_final: 0.7861 (mmm160) REVERT: C 570 HIS cc_start: 0.7808 (OUTLIER) cc_final: 0.7365 (m90) REVERT: D 577 MET cc_start: 0.8461 (tmm) cc_final: 0.8228 (tmm) REVERT: D 665 LYS cc_start: 0.9348 (mtpp) cc_final: 0.9007 (tttm) REVERT: D 686 ASN cc_start: 0.8618 (m-40) cc_final: 0.8384 (m110) REVERT: E 555 ARG cc_start: 0.9081 (mmm160) cc_final: 0.8860 (mmm160) outliers start: 121 outliers final: 40 residues processed: 265 average time/residue: 1.1699 time to fit residues: 340.3951 Evaluate side-chains 205 residues out of total 1399 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 158 time to evaluate : 1.356 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 HIS Chi-restraints excluded: chain A residue 99 THR Chi-restraints excluded: chain A residue 132 ILE Chi-restraints excluded: chain A residue 133 THR Chi-restraints excluded: chain A residue 146 ILE Chi-restraints excluded: chain A residue 148 ILE Chi-restraints excluded: chain A residue 150 GLU Chi-restraints excluded: chain A residue 214 LEU Chi-restraints excluded: chain A residue 235 VAL Chi-restraints excluded: chain A residue 282 ARG Chi-restraints excluded: chain A residue 289 MET Chi-restraints excluded: chain A residue 291 GLU Chi-restraints excluded: chain A residue 377 VAL Chi-restraints excluded: chain A residue 380 HIS Chi-restraints excluded: chain A residue 381 MET Chi-restraints excluded: chain A residue 404 ILE Chi-restraints excluded: chain A residue 425 SER Chi-restraints excluded: chain A residue 439 THR Chi-restraints excluded: chain A residue 461 LEU Chi-restraints excluded: chain A residue 495 THR Chi-restraints excluded: chain A residue 498 LYS Chi-restraints excluded: chain A residue 537 VAL Chi-restraints excluded: chain A residue 728 LEU Chi-restraints excluded: chain A residue 734 SER Chi-restraints excluded: chain A residue 839 THR Chi-restraints excluded: chain A residue 850 VAL Chi-restraints excluded: chain A residue 903 SER Chi-restraints excluded: chain A residue 919 LEU Chi-restraints excluded: chain A residue 946 VAL Chi-restraints excluded: chain A residue 1004 LEU Chi-restraints excluded: chain A residue 1033 THR Chi-restraints excluded: chain A residue 1149 LEU Chi-restraints excluded: chain A residue 1245 MET Chi-restraints excluded: chain A residue 1339 VAL Chi-restraints excluded: chain A residue 1429 CYS Chi-restraints excluded: chain A residue 1433 VAL Chi-restraints excluded: chain A residue 1440 ASP Chi-restraints excluded: chain B residue 549 LYS Chi-restraints excluded: chain B residue 550 LEU Chi-restraints excluded: chain B residue 556 VAL Chi-restraints excluded: chain C residue 529 LEU Chi-restraints excluded: chain C residue 570 HIS Chi-restraints excluded: chain D residue 555 ARG Chi-restraints excluded: chain D residue 564 LEU Chi-restraints excluded: chain D residue 671 HIS Chi-restraints excluded: chain D residue 685 LEU Chi-restraints excluded: chain E residue 531 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 93 optimal weight: 1.9990 chunk 28 optimal weight: 0.9990 chunk 114 optimal weight: 2.9990 chunk 15 optimal weight: 5.9990 chunk 95 optimal weight: 5.9990 chunk 20 optimal weight: 3.9990 chunk 118 optimal weight: 7.9990 chunk 105 optimal weight: 0.6980 chunk 5 optimal weight: 1.9990 chunk 57 optimal weight: 6.9990 chunk 17 optimal weight: 0.6980 overall best weight: 1.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 16 HIS A 331 GLN A 951 ASN A1120 HIS A1202 HIS A1394 GLN ** B 528 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 539 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 539 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3497 r_free = 0.3497 target = 0.084773 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.2949 r_free = 0.2949 target = 0.057925 restraints weight = 36836.913| |-----------------------------------------------------------------------------| r_work (start): 0.2895 rms_B_bonded: 3.98 r_work: 0.2750 rms_B_bonded: 4.62 restraints_weight: 0.5000 r_work (final): 0.2750 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8330 moved from start: 0.7847 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 12657 Z= 0.220 Angle : 0.748 11.521 17094 Z= 0.385 Chirality : 0.046 0.211 1962 Planarity : 0.004 0.045 2171 Dihedral : 6.381 46.868 1694 Min Nonbonded Distance : 2.387 Molprobity Statistics. All-atom Clashscore : 10.54 Ramachandran Plot: Outliers : 0.07 % Allowed : 6.45 % Favored : 93.48 % Rotamer: Outliers : 5.58 % Allowed : 31.67 % Favored : 62.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.92 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.27 % 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: -0.48 (0.22), residues: 1534 helix: 0.85 (0.19), residues: 814 sheet: -0.36 (0.56), residues: 79 loop : -1.89 (0.25), residues: 641 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A1319 HIS 0.037 0.002 HIS A 16 PHE 0.037 0.001 PHE A 553 TYR 0.012 0.001 TYR A 284 ARG 0.010 0.000 ARG D 532 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3068 Ramachandran restraints generated. 1534 Oldfield, 0 Emsley, 1534 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3068 Ramachandran restraints generated. 1534 Oldfield, 0 Emsley, 1534 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 241 residues out of total 1399 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 163 time to evaluate : 1.512 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 282 ARG cc_start: 0.9325 (OUTLIER) cc_final: 0.9002 (mtp180) REVERT: A 291 GLU cc_start: 0.8978 (OUTLIER) cc_final: 0.8601 (mp0) REVERT: A 577 LYS cc_start: 0.9468 (mttt) cc_final: 0.9249 (mtmm) REVERT: A 712 PHE cc_start: 0.8466 (m-80) cc_final: 0.8196 (m-80) REVERT: A 893 LYS cc_start: 0.9544 (mmmm) cc_final: 0.9233 (mppt) REVERT: A 939 GLU cc_start: 0.8701 (tp30) cc_final: 0.8499 (tp30) REVERT: A 1123 LEU cc_start: 0.8828 (tt) cc_final: 0.8509 (tm) REVERT: A 1414 ASP cc_start: 0.7796 (OUTLIER) cc_final: 0.6831 (t0) REVERT: B 541 LYS cc_start: 0.9114 (pptt) cc_final: 0.8802 (mttp) REVERT: C 531 MET cc_start: 0.7539 (mpt) cc_final: 0.7077 (ttm) REVERT: C 570 HIS cc_start: 0.7840 (OUTLIER) cc_final: 0.7396 (m90) REVERT: D 577 MET cc_start: 0.8614 (OUTLIER) cc_final: 0.8367 (tpp) REVERT: D 665 LYS cc_start: 0.9405 (mtpp) cc_final: 0.9124 (tttm) outliers start: 78 outliers final: 30 residues processed: 219 average time/residue: 1.2436 time to fit residues: 298.1727 Evaluate side-chains 175 residues out of total 1399 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 140 time to evaluate : 1.488 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 99 THR Chi-restraints excluded: chain A residue 132 ILE Chi-restraints excluded: chain A residue 214 LEU Chi-restraints excluded: chain A residue 235 VAL Chi-restraints excluded: chain A residue 282 ARG Chi-restraints excluded: chain A residue 291 GLU Chi-restraints excluded: chain A residue 381 MET Chi-restraints excluded: chain A residue 425 SER Chi-restraints excluded: chain A residue 439 THR Chi-restraints excluded: chain A residue 495 THR Chi-restraints excluded: chain A residue 498 LYS Chi-restraints excluded: chain A residue 537 VAL Chi-restraints excluded: chain A residue 839 THR Chi-restraints excluded: chain A residue 917 GLU Chi-restraints excluded: chain A residue 946 VAL Chi-restraints excluded: chain A residue 1004 LEU Chi-restraints excluded: chain A residue 1083 ASN Chi-restraints excluded: chain A residue 1149 LEU Chi-restraints excluded: chain A residue 1239 CYS Chi-restraints excluded: chain A residue 1339 VAL Chi-restraints excluded: chain A residue 1414 ASP Chi-restraints excluded: chain A residue 1433 VAL Chi-restraints excluded: chain A residue 1440 ASP Chi-restraints excluded: chain B residue 549 LYS Chi-restraints excluded: chain B residue 556 VAL Chi-restraints excluded: chain C residue 529 LEU Chi-restraints excluded: chain C residue 533 LEU Chi-restraints excluded: chain C residue 570 HIS Chi-restraints excluded: chain D residue 564 LEU Chi-restraints excluded: chain D residue 577 MET Chi-restraints excluded: chain D residue 685 LEU Chi-restraints excluded: chain E residue 520 VAL Chi-restraints excluded: chain E residue 531 MET Chi-restraints excluded: chain E residue 559 LYS Chi-restraints excluded: chain E residue 564 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 144 optimal weight: 0.6980 chunk 68 optimal weight: 1.9990 chunk 92 optimal weight: 6.9990 chunk 13 optimal weight: 3.9990 chunk 32 optimal weight: 2.9990 chunk 15 optimal weight: 4.9990 chunk 67 optimal weight: 0.9990 chunk 118 optimal weight: 0.9980 chunk 61 optimal weight: 0.9990 chunk 41 optimal weight: 9.9990 chunk 108 optimal weight: 5.9990 overall best weight: 1.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 331 GLN A1259 GLN ** B 539 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 539 GLN E 528 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3497 r_free = 0.3497 target = 0.084668 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.2945 r_free = 0.2945 target = 0.057690 restraints weight = 36590.272| |-----------------------------------------------------------------------------| r_work (start): 0.2890 rms_B_bonded: 3.97 r_work: 0.2743 rms_B_bonded: 4.63 restraints_weight: 0.5000 r_work (final): 0.2743 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8376 moved from start: 0.8546 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 12657 Z= 0.214 Angle : 0.728 11.481 17094 Z= 0.372 Chirality : 0.045 0.230 1962 Planarity : 0.004 0.054 2171 Dihedral : 5.992 46.302 1691 Min Nonbonded Distance : 2.356 Molprobity Statistics. All-atom Clashscore : 10.18 Ramachandran Plot: Outliers : 0.07 % Allowed : 7.56 % Favored : 92.37 % Rotamer: Outliers : 6.15 % Allowed : 31.45 % Favored : 62.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.92 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.27 % 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: -0.19 (0.23), residues: 1534 helix: 1.05 (0.19), residues: 814 sheet: -0.22 (0.57), residues: 84 loop : -1.71 (0.26), residues: 636 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 754 HIS 0.011 0.001 HIS D 535 PHE 0.038 0.001 PHE A 553 TYR 0.012 0.001 TYR A 284 ARG 0.010 0.001 ARG A1295 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3068 Ramachandran restraints generated. 1534 Oldfield, 0 Emsley, 1534 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3068 Ramachandran restraints generated. 1534 Oldfield, 0 Emsley, 1534 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 240 residues out of total 1399 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 154 time to evaluate : 1.546 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 282 ARG cc_start: 0.9231 (OUTLIER) cc_final: 0.8907 (mtp180) REVERT: A 289 MET cc_start: 0.9341 (OUTLIER) cc_final: 0.9115 (ttm) REVERT: A 291 GLU cc_start: 0.9037 (OUTLIER) cc_final: 0.8702 (mp0) REVERT: A 425 SER cc_start: 0.8683 (OUTLIER) cc_final: 0.8147 (p) REVERT: A 577 LYS cc_start: 0.9543 (mttt) cc_final: 0.9200 (mtmm) REVERT: A 893 LYS cc_start: 0.9579 (mmmm) cc_final: 0.9227 (mttp) REVERT: A 939 GLU cc_start: 0.8752 (tp30) cc_final: 0.8490 (tp30) REVERT: A 1133 GLU cc_start: 0.8834 (pp20) cc_final: 0.8609 (pp20) REVERT: A 1134 ILE cc_start: 0.8344 (OUTLIER) cc_final: 0.8128 (mp) REVERT: A 1295 ARG cc_start: 0.9231 (tpp80) cc_final: 0.8809 (ttm110) REVERT: A 1414 ASP cc_start: 0.8036 (OUTLIER) cc_final: 0.7039 (t0) REVERT: C 531 MET cc_start: 0.7725 (mpt) cc_final: 0.7333 (ttm) REVERT: C 570 HIS cc_start: 0.7695 (OUTLIER) cc_final: 0.7415 (m90) REVERT: D 541 LYS cc_start: 0.9056 (mtmm) cc_final: 0.8854 (mtmm) REVERT: D 577 MET cc_start: 0.8584 (OUTLIER) cc_final: 0.8368 (tpp) REVERT: D 665 LYS cc_start: 0.9431 (mtpp) cc_final: 0.9166 (tttt) REVERT: D 695 GLN cc_start: 0.9118 (pp30) cc_final: 0.8794 (tp-100) outliers start: 86 outliers final: 37 residues processed: 221 average time/residue: 1.2498 time to fit residues: 301.2333 Evaluate side-chains 180 residues out of total 1399 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 135 time to evaluate : 1.679 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 HIS Chi-restraints excluded: chain A residue 84 MET Chi-restraints excluded: chain A residue 99 THR Chi-restraints excluded: chain A residue 133 THR Chi-restraints excluded: chain A residue 214 LEU Chi-restraints excluded: chain A residue 235 VAL Chi-restraints excluded: chain A residue 282 ARG Chi-restraints excluded: chain A residue 289 MET Chi-restraints excluded: chain A residue 291 GLU Chi-restraints excluded: chain A residue 358 SER Chi-restraints excluded: chain A residue 381 MET Chi-restraints excluded: chain A residue 387 LEU Chi-restraints excluded: chain A residue 425 SER Chi-restraints excluded: chain A residue 439 THR Chi-restraints excluded: chain A residue 461 LEU Chi-restraints excluded: chain A residue 495 THR Chi-restraints excluded: chain A residue 498 LYS Chi-restraints excluded: chain A residue 537 VAL Chi-restraints excluded: chain A residue 728 LEU Chi-restraints excluded: chain A residue 839 THR Chi-restraints excluded: chain A residue 850 VAL Chi-restraints excluded: chain A residue 883 ILE Chi-restraints excluded: chain A residue 917 GLU Chi-restraints excluded: chain A residue 919 LEU Chi-restraints excluded: chain A residue 946 VAL Chi-restraints excluded: chain A residue 1134 ILE Chi-restraints excluded: chain A residue 1149 LEU Chi-restraints excluded: chain A residue 1239 CYS Chi-restraints excluded: chain A residue 1414 ASP Chi-restraints excluded: chain A residue 1429 CYS Chi-restraints excluded: chain A residue 1433 VAL Chi-restraints excluded: chain A residue 1440 ASP Chi-restraints excluded: chain B residue 549 LYS Chi-restraints excluded: chain B residue 556 VAL Chi-restraints excluded: chain C residue 529 LEU Chi-restraints excluded: chain C residue 570 HIS Chi-restraints excluded: chain D residue 555 ARG Chi-restraints excluded: chain D residue 564 LEU Chi-restraints excluded: chain D residue 577 MET Chi-restraints excluded: chain D residue 660 SER Chi-restraints excluded: chain D residue 685 LEU Chi-restraints excluded: chain E residue 520 VAL Chi-restraints excluded: chain E residue 531 MET Chi-restraints excluded: chain E residue 559 LYS Chi-restraints excluded: chain E residue 564 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 37 optimal weight: 6.9990 chunk 60 optimal weight: 3.9990 chunk 73 optimal weight: 0.9980 chunk 126 optimal weight: 0.7980 chunk 6 optimal weight: 3.9990 chunk 104 optimal weight: 6.9990 chunk 119 optimal weight: 6.9990 chunk 139 optimal weight: 9.9990 chunk 22 optimal weight: 0.7980 chunk 105 optimal weight: 3.9990 chunk 83 optimal weight: 5.9990 overall best weight: 2.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 331 GLN ** B 535 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 528 ASN D 548 ASN D 671 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3444 r_free = 0.3444 target = 0.081945 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2872 r_free = 0.2872 target = 0.054876 restraints weight = 37363.236| |-----------------------------------------------------------------------------| r_work (start): 0.2826 rms_B_bonded: 3.99 r_work: 0.2676 rms_B_bonded: 4.63 restraints_weight: 0.5000 r_work (final): 0.2676 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8477 moved from start: 0.9377 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.084 12657 Z= 0.302 Angle : 0.787 12.285 17094 Z= 0.404 Chirality : 0.048 0.302 1962 Planarity : 0.004 0.044 2171 Dihedral : 6.139 46.828 1691 Min Nonbonded Distance : 2.339 Molprobity Statistics. All-atom Clashscore : 10.26 Ramachandran Plot: Outliers : 0.13 % Allowed : 7.37 % Favored : 92.50 % Rotamer: Outliers : 6.00 % Allowed : 31.59 % Favored : 62.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.92 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.20 % 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: -0.17 (0.23), residues: 1534 helix: 1.03 (0.19), residues: 819 sheet: -0.19 (0.57), residues: 84 loop : -1.66 (0.26), residues: 631 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 915 HIS 0.009 0.001 HIS A1421 PHE 0.013 0.001 PHE A1379 TYR 0.015 0.001 TYR A 284 ARG 0.011 0.001 ARG E 555 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3068 Ramachandran restraints generated. 1534 Oldfield, 0 Emsley, 1534 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3068 Ramachandran restraints generated. 1534 Oldfield, 0 Emsley, 1534 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 240 residues out of total 1399 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 156 time to evaluate : 1.496 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 144 GLU cc_start: 0.6597 (OUTLIER) cc_final: 0.6156 (pt0) REVERT: A 282 ARG cc_start: 0.9239 (OUTLIER) cc_final: 0.8934 (mtp180) REVERT: A 289 MET cc_start: 0.9312 (OUTLIER) cc_final: 0.9088 (ttm) REVERT: A 291 GLU cc_start: 0.9102 (OUTLIER) cc_final: 0.8818 (mp0) REVERT: A 331 GLN cc_start: 0.7888 (OUTLIER) cc_final: 0.7636 (tm-30) REVERT: A 419 TYR cc_start: 0.8266 (t80) cc_final: 0.8006 (t80) REVERT: A 425 SER cc_start: 0.8975 (OUTLIER) cc_final: 0.8470 (p) REVERT: A 577 LYS cc_start: 0.9669 (mttt) cc_final: 0.9354 (mtmm) REVERT: A 886 THR cc_start: 0.9106 (OUTLIER) cc_final: 0.8889 (t) REVERT: A 893 LYS cc_start: 0.9582 (mmmm) cc_final: 0.9271 (mttp) REVERT: A 1414 ASP cc_start: 0.8258 (OUTLIER) cc_final: 0.7204 (t0) REVERT: A 1442 GLU cc_start: 0.8729 (OUTLIER) cc_final: 0.8237 (pp20) REVERT: C 570 HIS cc_start: 0.7847 (OUTLIER) cc_final: 0.7564 (m90) REVERT: D 577 MET cc_start: 0.8663 (OUTLIER) cc_final: 0.8407 (tpp) REVERT: D 665 LYS cc_start: 0.9445 (mtpp) cc_final: 0.9192 (tttt) REVERT: D 693 GLU cc_start: 0.9017 (mp0) cc_final: 0.8789 (mp0) REVERT: E 555 ARG cc_start: 0.9101 (mmm160) cc_final: 0.8890 (mmm160) outliers start: 84 outliers final: 37 residues processed: 223 average time/residue: 1.3333 time to fit residues: 323.9407 Evaluate side-chains 183 residues out of total 1399 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 135 time to evaluate : 1.519 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 99 THR Chi-restraints excluded: chain A residue 144 GLU Chi-restraints excluded: chain A residue 148 ILE Chi-restraints excluded: chain A residue 214 LEU Chi-restraints excluded: chain A residue 282 ARG Chi-restraints excluded: chain A residue 289 MET Chi-restraints excluded: chain A residue 291 GLU Chi-restraints excluded: chain A residue 331 GLN Chi-restraints excluded: chain A residue 358 SER Chi-restraints excluded: chain A residue 387 LEU Chi-restraints excluded: chain A residue 425 SER Chi-restraints excluded: chain A residue 439 THR Chi-restraints excluded: chain A residue 472 LYS Chi-restraints excluded: chain A residue 495 THR Chi-restraints excluded: chain A residue 498 LYS Chi-restraints excluded: chain A residue 537 VAL Chi-restraints excluded: chain A residue 553 PHE Chi-restraints excluded: chain A residue 728 LEU Chi-restraints excluded: chain A residue 755 MET Chi-restraints excluded: chain A residue 829 VAL Chi-restraints excluded: chain A residue 839 THR Chi-restraints excluded: chain A residue 850 VAL Chi-restraints excluded: chain A residue 883 ILE Chi-restraints excluded: chain A residue 886 THR Chi-restraints excluded: chain A residue 903 SER Chi-restraints excluded: chain A residue 917 GLU Chi-restraints excluded: chain A residue 919 LEU Chi-restraints excluded: chain A residue 946 VAL Chi-restraints excluded: chain A residue 1004 LEU Chi-restraints excluded: chain A residue 1033 THR Chi-restraints excluded: chain A residue 1239 CYS Chi-restraints excluded: chain A residue 1339 VAL Chi-restraints excluded: chain A residue 1414 ASP Chi-restraints excluded: chain A residue 1429 CYS Chi-restraints excluded: chain A residue 1433 VAL Chi-restraints excluded: chain A residue 1440 ASP Chi-restraints excluded: chain A residue 1442 GLU Chi-restraints excluded: chain B residue 549 LYS Chi-restraints excluded: chain B residue 556 VAL Chi-restraints excluded: chain C residue 529 LEU Chi-restraints excluded: chain C residue 570 HIS Chi-restraints excluded: chain D residue 564 LEU Chi-restraints excluded: chain D residue 577 MET Chi-restraints excluded: chain D residue 578 ILE Chi-restraints excluded: chain E residue 520 VAL Chi-restraints excluded: chain E residue 531 MET Chi-restraints excluded: chain E residue 559 LYS Chi-restraints excluded: chain E residue 564 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 5 optimal weight: 2.9990 chunk 17 optimal weight: 4.9990 chunk 76 optimal weight: 3.9990 chunk 127 optimal weight: 8.9990 chunk 32 optimal weight: 4.9990 chunk 113 optimal weight: 9.9990 chunk 19 optimal weight: 4.9990 chunk 96 optimal weight: 6.9990 chunk 47 optimal weight: 0.9990 chunk 131 optimal weight: 6.9990 chunk 114 optimal weight: 0.6980 overall best weight: 2.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 535 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 690 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3422 r_free = 0.3422 target = 0.080961 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.2843 r_free = 0.2843 target = 0.053849 restraints weight = 37032.610| |-----------------------------------------------------------------------------| r_work (start): 0.2799 rms_B_bonded: 3.99 r_work: 0.2647 rms_B_bonded: 4.62 restraints_weight: 0.5000 r_work (final): 0.2647 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8521 moved from start: 0.9778 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 12657 Z= 0.354 Angle : 0.815 11.163 17094 Z= 0.418 Chirality : 0.048 0.217 1962 Planarity : 0.005 0.086 2171 Dihedral : 6.145 47.501 1689 Min Nonbonded Distance : 2.331 Molprobity Statistics. All-atom Clashscore : 11.65 Ramachandran Plot: Outliers : 0.13 % Allowed : 7.56 % Favored : 92.31 % Rotamer: Outliers : 5.79 % Allowed : 32.95 % Favored : 61.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.92 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.20 % 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: -0.14 (0.23), residues: 1534 helix: 1.10 (0.19), residues: 813 sheet: 0.21 (0.60), residues: 74 loop : -1.73 (0.25), residues: 647 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 915 HIS 0.009 0.001 HIS A1421 PHE 0.026 0.001 PHE A 553 TYR 0.014 0.001 TYR A 284 ARG 0.007 0.000 ARG D 532 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3068 Ramachandran restraints generated. 1534 Oldfield, 0 Emsley, 1534 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3068 Ramachandran restraints generated. 1534 Oldfield, 0 Emsley, 1534 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 219 residues out of total 1399 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 138 time to evaluate : 1.284 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 144 GLU cc_start: 0.6413 (OUTLIER) cc_final: 0.5466 (pm20) REVERT: A 282 ARG cc_start: 0.9165 (OUTLIER) cc_final: 0.8935 (mtp180) REVERT: A 289 MET cc_start: 0.9297 (OUTLIER) cc_final: 0.9045 (ttm) REVERT: A 291 GLU cc_start: 0.9120 (OUTLIER) cc_final: 0.8830 (mp0) REVERT: A 425 SER cc_start: 0.9074 (OUTLIER) cc_final: 0.8598 (p) REVERT: A 577 LYS cc_start: 0.9717 (mttt) cc_final: 0.9404 (mtmm) REVERT: A 886 THR cc_start: 0.9154 (OUTLIER) cc_final: 0.8944 (t) REVERT: A 893 LYS cc_start: 0.9579 (mmmm) cc_final: 0.9265 (mttp) REVERT: A 1414 ASP cc_start: 0.8255 (OUTLIER) cc_final: 0.7190 (t0) REVERT: A 1442 GLU cc_start: 0.8670 (OUTLIER) cc_final: 0.8242 (pp20) REVERT: C 531 MET cc_start: 0.8005 (mpm) cc_final: 0.7601 (ttm) REVERT: C 570 HIS cc_start: 0.7947 (OUTLIER) cc_final: 0.7552 (m90) REVERT: D 662 ASP cc_start: 0.9218 (m-30) cc_final: 0.8752 (m-30) REVERT: D 678 ARG cc_start: 0.8592 (ttp-110) cc_final: 0.8202 (ttm-80) outliers start: 81 outliers final: 41 residues processed: 206 average time/residue: 1.3555 time to fit residues: 303.9583 Evaluate side-chains 185 residues out of total 1399 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 135 time to evaluate : 1.415 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 84 MET Chi-restraints excluded: chain A residue 99 THR Chi-restraints excluded: chain A residue 144 GLU Chi-restraints excluded: chain A residue 148 ILE Chi-restraints excluded: chain A residue 214 LEU Chi-restraints excluded: chain A residue 282 ARG Chi-restraints excluded: chain A residue 289 MET Chi-restraints excluded: chain A residue 291 GLU Chi-restraints excluded: chain A residue 358 SER Chi-restraints excluded: chain A residue 387 LEU Chi-restraints excluded: chain A residue 425 SER Chi-restraints excluded: chain A residue 439 THR Chi-restraints excluded: chain A residue 451 CYS Chi-restraints excluded: chain A residue 461 LEU Chi-restraints excluded: chain A residue 472 LYS Chi-restraints excluded: chain A residue 477 SER Chi-restraints excluded: chain A residue 495 THR Chi-restraints excluded: chain A residue 498 LYS Chi-restraints excluded: chain A residue 537 VAL Chi-restraints excluded: chain A residue 552 LEU Chi-restraints excluded: chain A residue 728 LEU Chi-restraints excluded: chain A residue 748 LEU Chi-restraints excluded: chain A residue 755 MET Chi-restraints excluded: chain A residue 829 VAL Chi-restraints excluded: chain A residue 839 THR Chi-restraints excluded: chain A residue 850 VAL Chi-restraints excluded: chain A residue 883 ILE Chi-restraints excluded: chain A residue 886 THR Chi-restraints excluded: chain A residue 903 SER Chi-restraints excluded: chain A residue 917 GLU Chi-restraints excluded: chain A residue 946 VAL Chi-restraints excluded: chain A residue 1004 LEU Chi-restraints excluded: chain A residue 1033 THR Chi-restraints excluded: chain A residue 1149 LEU Chi-restraints excluded: chain A residue 1239 CYS Chi-restraints excluded: chain A residue 1339 VAL Chi-restraints excluded: chain A residue 1414 ASP Chi-restraints excluded: chain A residue 1433 VAL Chi-restraints excluded: chain A residue 1440 ASP Chi-restraints excluded: chain A residue 1442 GLU Chi-restraints excluded: chain B residue 549 LYS Chi-restraints excluded: chain B residue 556 VAL Chi-restraints excluded: chain C residue 529 LEU Chi-restraints excluded: chain C residue 570 HIS Chi-restraints excluded: chain D residue 564 LEU Chi-restraints excluded: chain D residue 659 SER Chi-restraints excluded: chain E residue 520 VAL Chi-restraints excluded: chain E residue 531 MET Chi-restraints excluded: chain E residue 559 LYS Chi-restraints excluded: chain E residue 564 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 2 optimal weight: 3.9990 chunk 125 optimal weight: 3.9990 chunk 106 optimal weight: 0.9990 chunk 14 optimal weight: 0.9990 chunk 19 optimal weight: 2.9990 chunk 49 optimal weight: 4.9990 chunk 135 optimal weight: 0.8980 chunk 34 optimal weight: 0.8980 chunk 59 optimal weight: 2.9990 chunk 20 optimal weight: 0.8980 chunk 17 optimal weight: 0.8980 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 528 ASN ** D 548 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3467 r_free = 0.3467 target = 0.083238 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2903 r_free = 0.2903 target = 0.056159 restraints weight = 37039.299| |-----------------------------------------------------------------------------| r_work (start): 0.2855 rms_B_bonded: 4.01 r_work: 0.2707 rms_B_bonded: 4.63 restraints_weight: 0.5000 r_work (final): 0.2707 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8481 moved from start: 0.9943 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 12657 Z= 0.210 Angle : 0.788 12.570 17094 Z= 0.396 Chirality : 0.046 0.177 1962 Planarity : 0.004 0.064 2171 Dihedral : 5.897 46.508 1689 Min Nonbonded Distance : 2.348 Molprobity Statistics. All-atom Clashscore : 10.58 Ramachandran Plot: Outliers : 0.13 % Allowed : 6.84 % Favored : 93.02 % Rotamer: Outliers : 4.15 % Allowed : 34.38 % Favored : 61.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.92 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.20 % 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: -0.02 (0.23), residues: 1534 helix: 1.16 (0.19), residues: 817 sheet: 0.44 (0.60), residues: 74 loop : -1.66 (0.26), residues: 643 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 754 HIS 0.008 0.001 HIS A1421 PHE 0.033 0.001 PHE A 553 TYR 0.022 0.001 TYR A 419 ARG 0.007 0.000 ARG D 532 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3068 Ramachandran restraints generated. 1534 Oldfield, 0 Emsley, 1534 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3068 Ramachandran restraints generated. 1534 Oldfield, 0 Emsley, 1534 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 1399 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 148 time to evaluate : 1.379 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 144 GLU cc_start: 0.6094 (OUTLIER) cc_final: 0.5292 (pm20) REVERT: A 291 GLU cc_start: 0.9114 (OUTLIER) cc_final: 0.8846 (mp0) REVERT: A 425 SER cc_start: 0.9030 (OUTLIER) cc_final: 0.8558 (p) REVERT: A 577 LYS cc_start: 0.9711 (mttt) cc_final: 0.9423 (mtmm) REVERT: A 799 GLU cc_start: 0.8969 (tp30) cc_final: 0.8630 (tp30) REVERT: A 893 LYS cc_start: 0.9559 (mmmm) cc_final: 0.9273 (mttp) REVERT: A 1414 ASP cc_start: 0.8194 (OUTLIER) cc_final: 0.7153 (t0) REVERT: A 1442 GLU cc_start: 0.8632 (OUTLIER) cc_final: 0.8237 (pp20) REVERT: C 531 MET cc_start: 0.8063 (mpm) cc_final: 0.7710 (ttm) REVERT: C 542 GLU cc_start: 0.9059 (pm20) cc_final: 0.8775 (pm20) REVERT: C 570 HIS cc_start: 0.7825 (OUTLIER) cc_final: 0.7595 (m90) REVERT: D 662 ASP cc_start: 0.9240 (m-30) cc_final: 0.8771 (m-30) REVERT: D 678 ARG cc_start: 0.8613 (ttp-110) cc_final: 0.8210 (ttm-80) outliers start: 58 outliers final: 32 residues processed: 194 average time/residue: 1.2901 time to fit residues: 273.1475 Evaluate side-chains 173 residues out of total 1399 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 135 time to evaluate : 1.352 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 84 MET Chi-restraints excluded: chain A residue 99 THR Chi-restraints excluded: chain A residue 144 GLU Chi-restraints excluded: chain A residue 214 LEU Chi-restraints excluded: chain A residue 291 GLU Chi-restraints excluded: chain A residue 358 SER Chi-restraints excluded: chain A residue 425 SER Chi-restraints excluded: chain A residue 439 THR Chi-restraints excluded: chain A residue 461 LEU Chi-restraints excluded: chain A residue 495 THR Chi-restraints excluded: chain A residue 498 LYS Chi-restraints excluded: chain A residue 537 VAL Chi-restraints excluded: chain A residue 728 LEU Chi-restraints excluded: chain A residue 829 VAL Chi-restraints excluded: chain A residue 839 THR Chi-restraints excluded: chain A residue 850 VAL Chi-restraints excluded: chain A residue 917 GLU Chi-restraints excluded: chain A residue 946 VAL Chi-restraints excluded: chain A residue 1004 LEU Chi-restraints excluded: chain A residue 1033 THR Chi-restraints excluded: chain A residue 1239 CYS Chi-restraints excluded: chain A residue 1339 VAL Chi-restraints excluded: chain A residue 1414 ASP Chi-restraints excluded: chain A residue 1433 VAL Chi-restraints excluded: chain A residue 1440 ASP Chi-restraints excluded: chain A residue 1442 GLU Chi-restraints excluded: chain B residue 549 LYS Chi-restraints excluded: chain B residue 556 VAL Chi-restraints excluded: chain C residue 529 LEU Chi-restraints excluded: chain C residue 570 HIS Chi-restraints excluded: chain D residue 556 VAL Chi-restraints excluded: chain D residue 564 LEU Chi-restraints excluded: chain D residue 573 SER Chi-restraints excluded: chain D residue 685 LEU Chi-restraints excluded: chain E residue 520 VAL Chi-restraints excluded: chain E residue 531 MET Chi-restraints excluded: chain E residue 559 LYS Chi-restraints excluded: chain E residue 564 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 139 optimal weight: 0.0570 chunk 146 optimal weight: 6.9990 chunk 76 optimal weight: 5.9990 chunk 24 optimal weight: 2.9990 chunk 51 optimal weight: 2.9990 chunk 43 optimal weight: 0.9980 chunk 125 optimal weight: 7.9990 chunk 106 optimal weight: 0.9980 chunk 83 optimal weight: 5.9990 chunk 103 optimal weight: 3.9990 chunk 55 optimal weight: 0.9990 overall best weight: 1.2102 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 535 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.083071 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2905 r_free = 0.2905 target = 0.056222 restraints weight = 36351.020| |-----------------------------------------------------------------------------| r_work (start): 0.2855 rms_B_bonded: 3.95 r_work: 0.2706 rms_B_bonded: 4.59 restraints_weight: 0.5000 r_work (final): 0.2706 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8470 moved from start: 1.0115 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 12657 Z= 0.227 Angle : 0.794 12.699 17094 Z= 0.398 Chirality : 0.046 0.300 1962 Planarity : 0.004 0.057 2171 Dihedral : 5.813 45.984 1689 Min Nonbonded Distance : 2.309 Molprobity Statistics. All-atom Clashscore : 10.62 Ramachandran Plot: Outliers : 0.13 % Allowed : 7.30 % Favored : 92.57 % Rotamer: Outliers : 4.00 % Allowed : 34.52 % Favored : 61.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.92 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.20 % 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: 0.05 (0.23), residues: 1534 helix: 1.21 (0.19), residues: 815 sheet: 0.53 (0.60), residues: 74 loop : -1.61 (0.26), residues: 645 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 754 HIS 0.008 0.001 HIS A1421 PHE 0.041 0.001 PHE A 553 TYR 0.014 0.001 TYR A 389 ARG 0.006 0.000 ARG D 532 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3068 Ramachandran restraints generated. 1534 Oldfield, 0 Emsley, 1534 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3068 Ramachandran restraints generated. 1534 Oldfield, 0 Emsley, 1534 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 199 residues out of total 1399 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 143 time to evaluate : 1.463 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 144 GLU cc_start: 0.6110 (OUTLIER) cc_final: 0.5367 (pm20) REVERT: A 291 GLU cc_start: 0.9097 (OUTLIER) cc_final: 0.8838 (mp0) REVERT: A 425 SER cc_start: 0.9069 (OUTLIER) cc_final: 0.8633 (p) REVERT: A 577 LYS cc_start: 0.9710 (mttt) cc_final: 0.9405 (mtmm) REVERT: A 725 LYS cc_start: 0.9059 (mtmm) cc_final: 0.8688 (mppt) REVERT: A 799 GLU cc_start: 0.8963 (tp30) cc_final: 0.8631 (tp30) REVERT: A 893 LYS cc_start: 0.9542 (mmmm) cc_final: 0.9269 (mttp) REVERT: A 1133 GLU cc_start: 0.9425 (tt0) cc_final: 0.9071 (mt-10) REVERT: A 1414 ASP cc_start: 0.8235 (OUTLIER) cc_final: 0.7222 (t0) REVERT: A 1442 GLU cc_start: 0.8569 (OUTLIER) cc_final: 0.8221 (pp20) REVERT: C 531 MET cc_start: 0.8017 (mpm) cc_final: 0.7636 (ttm) REVERT: C 542 GLU cc_start: 0.9088 (pm20) cc_final: 0.8709 (pm20) REVERT: C 546 ILE cc_start: 0.8632 (pp) cc_final: 0.8378 (mp) REVERT: C 570 HIS cc_start: 0.7796 (OUTLIER) cc_final: 0.7575 (m90) REVERT: D 655 MET cc_start: 0.2910 (mpt) cc_final: 0.2213 (mpt) REVERT: D 662 ASP cc_start: 0.9273 (m-30) cc_final: 0.8826 (m-30) REVERT: D 678 ARG cc_start: 0.8650 (ttp-110) cc_final: 0.8256 (ttm-80) REVERT: E 541 LYS cc_start: 0.9311 (mmmt) cc_final: 0.8980 (mmmt) REVERT: E 549 LYS cc_start: 0.9151 (ptmm) cc_final: 0.8833 (pptt) outliers start: 56 outliers final: 35 residues processed: 190 average time/residue: 1.3224 time to fit residues: 274.4949 Evaluate side-chains 179 residues out of total 1399 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 138 time to evaluate : 1.623 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 99 THR Chi-restraints excluded: chain A residue 144 GLU Chi-restraints excluded: chain A residue 214 LEU Chi-restraints excluded: chain A residue 291 GLU Chi-restraints excluded: chain A residue 358 SER Chi-restraints excluded: chain A residue 425 SER Chi-restraints excluded: chain A residue 439 THR Chi-restraints excluded: chain A residue 451 CYS Chi-restraints excluded: chain A residue 461 LEU Chi-restraints excluded: chain A residue 472 LYS Chi-restraints excluded: chain A residue 495 THR Chi-restraints excluded: chain A residue 498 LYS Chi-restraints excluded: chain A residue 537 VAL Chi-restraints excluded: chain A residue 728 LEU Chi-restraints excluded: chain A residue 829 VAL Chi-restraints excluded: chain A residue 839 THR Chi-restraints excluded: chain A residue 850 VAL Chi-restraints excluded: chain A residue 883 ILE Chi-restraints excluded: chain A residue 917 GLU Chi-restraints excluded: chain A residue 946 VAL Chi-restraints excluded: chain A residue 1004 LEU Chi-restraints excluded: chain A residue 1033 THR Chi-restraints excluded: chain A residue 1155 GLN Chi-restraints excluded: chain A residue 1239 CYS Chi-restraints excluded: chain A residue 1339 VAL Chi-restraints excluded: chain A residue 1414 ASP Chi-restraints excluded: chain A residue 1429 CYS Chi-restraints excluded: chain A residue 1433 VAL Chi-restraints excluded: chain A residue 1440 ASP Chi-restraints excluded: chain A residue 1442 GLU Chi-restraints excluded: chain B residue 549 LYS Chi-restraints excluded: chain B residue 556 VAL Chi-restraints excluded: chain C residue 570 HIS Chi-restraints excluded: chain D residue 564 LEU Chi-restraints excluded: chain D residue 573 SER Chi-restraints excluded: chain D residue 685 LEU Chi-restraints excluded: chain E residue 520 VAL Chi-restraints excluded: chain E residue 531 MET Chi-restraints excluded: chain E residue 543 ILE Chi-restraints excluded: chain E residue 559 LYS Chi-restraints excluded: chain E residue 564 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 57 optimal weight: 0.6980 chunk 39 optimal weight: 0.9990 chunk 35 optimal weight: 2.9990 chunk 85 optimal weight: 3.9990 chunk 32 optimal weight: 0.2980 chunk 44 optimal weight: 5.9990 chunk 10 optimal weight: 0.9990 chunk 109 optimal weight: 6.9990 chunk 126 optimal weight: 7.9990 chunk 144 optimal weight: 0.8980 chunk 56 optimal weight: 4.9990 overall best weight: 0.7784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 548 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3482 r_free = 0.3482 target = 0.084035 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2926 r_free = 0.2926 target = 0.057097 restraints weight = 36138.486| |-----------------------------------------------------------------------------| r_work (start): 0.2875 rms_B_bonded: 3.97 r_work: 0.2727 rms_B_bonded: 4.62 restraints_weight: 0.5000 r_work (final): 0.2727 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8447 moved from start: 1.0190 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 12657 Z= 0.205 Angle : 0.824 14.163 17094 Z= 0.410 Chirality : 0.047 0.367 1962 Planarity : 0.005 0.076 2171 Dihedral : 5.786 45.297 1689 Min Nonbonded Distance : 2.303 Molprobity Statistics. All-atom Clashscore : 11.13 Ramachandran Plot: Outliers : 0.07 % Allowed : 6.84 % Favored : 93.09 % Rotamer: Outliers : 3.36 % Allowed : 35.17 % Favored : 61.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.92 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.20 % 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: 0.11 (0.23), residues: 1534 helix: 1.25 (0.19), residues: 815 sheet: 0.10 (0.57), residues: 84 loop : -1.54 (0.26), residues: 635 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A1204 HIS 0.007 0.001 HIS A1421 PHE 0.010 0.001 PHE A 889 TYR 0.017 0.001 TYR A 419 ARG 0.017 0.000 ARG E 555 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3068 Ramachandran restraints generated. 1534 Oldfield, 0 Emsley, 1534 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3068 Ramachandran restraints generated. 1534 Oldfield, 0 Emsley, 1534 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 1399 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 150 time to evaluate : 1.435 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 144 GLU cc_start: 0.5955 (OUTLIER) cc_final: 0.5380 (pm20) REVERT: A 291 GLU cc_start: 0.9088 (OUTLIER) cc_final: 0.8827 (mp0) REVERT: A 425 SER cc_start: 0.9061 (OUTLIER) cc_final: 0.8641 (p) REVERT: A 577 LYS cc_start: 0.9712 (mttt) cc_final: 0.9431 (mtmm) REVERT: A 799 GLU cc_start: 0.8952 (tp30) cc_final: 0.8622 (tp30) REVERT: A 893 LYS cc_start: 0.9540 (mmmm) cc_final: 0.9273 (mttp) REVERT: A 1133 GLU cc_start: 0.9408 (tt0) cc_final: 0.9077 (mt-10) REVERT: A 1295 ARG cc_start: 0.9128 (tpp80) cc_final: 0.8682 (ttm170) REVERT: A 1414 ASP cc_start: 0.8186 (OUTLIER) cc_final: 0.7176 (t0) REVERT: A 1442 GLU cc_start: 0.8513 (OUTLIER) cc_final: 0.8189 (pp20) REVERT: C 531 MET cc_start: 0.7943 (mpm) cc_final: 0.7550 (ttm) REVERT: C 542 GLU cc_start: 0.9115 (pm20) cc_final: 0.8780 (pm20) REVERT: C 546 ILE cc_start: 0.8550 (pp) cc_final: 0.8272 (mp) REVERT: D 678 ARG cc_start: 0.8601 (ttp-110) cc_final: 0.8197 (ttm-80) REVERT: D 699 ASN cc_start: 0.9193 (m-40) cc_final: 0.8822 (m110) REVERT: E 549 LYS cc_start: 0.9177 (ptmm) cc_final: 0.8884 (pptt) outliers start: 47 outliers final: 29 residues processed: 189 average time/residue: 1.3489 time to fit residues: 276.8734 Evaluate side-chains 179 residues out of total 1399 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 145 time to evaluate : 4.302 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 99 THR Chi-restraints excluded: chain A residue 144 GLU Chi-restraints excluded: chain A residue 214 LEU Chi-restraints excluded: chain A residue 291 GLU Chi-restraints excluded: chain A residue 319 MET Chi-restraints excluded: chain A residue 358 SER Chi-restraints excluded: chain A residue 425 SER Chi-restraints excluded: chain A residue 439 THR Chi-restraints excluded: chain A residue 451 CYS Chi-restraints excluded: chain A residue 461 LEU Chi-restraints excluded: chain A residue 472 LYS Chi-restraints excluded: chain A residue 495 THR Chi-restraints excluded: chain A residue 498 LYS Chi-restraints excluded: chain A residue 537 VAL Chi-restraints excluded: chain A residue 728 LEU Chi-restraints excluded: chain A residue 829 VAL Chi-restraints excluded: chain A residue 850 VAL Chi-restraints excluded: chain A residue 946 VAL Chi-restraints excluded: chain A residue 1004 LEU Chi-restraints excluded: chain A residue 1033 THR Chi-restraints excluded: chain A residue 1155 GLN Chi-restraints excluded: chain A residue 1239 CYS Chi-restraints excluded: chain A residue 1414 ASP Chi-restraints excluded: chain A residue 1429 CYS Chi-restraints excluded: chain A residue 1433 VAL Chi-restraints excluded: chain A residue 1440 ASP Chi-restraints excluded: chain A residue 1442 GLU Chi-restraints excluded: chain B residue 549 LYS Chi-restraints excluded: chain B residue 556 VAL Chi-restraints excluded: chain D residue 564 LEU Chi-restraints excluded: chain D residue 685 LEU Chi-restraints excluded: chain E residue 520 VAL Chi-restraints excluded: chain E residue 531 MET Chi-restraints excluded: chain E residue 564 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 1 optimal weight: 0.8980 chunk 16 optimal weight: 1.9990 chunk 143 optimal weight: 0.9980 chunk 70 optimal weight: 0.6980 chunk 91 optimal weight: 6.9990 chunk 33 optimal weight: 0.9990 chunk 17 optimal weight: 0.9980 chunk 105 optimal weight: 0.4980 chunk 126 optimal weight: 6.9990 chunk 99 optimal weight: 2.9990 chunk 147 optimal weight: 0.8980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 331 GLN ** B 535 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 548 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3487 r_free = 0.3487 target = 0.084252 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2932 r_free = 0.2932 target = 0.057290 restraints weight = 36706.487| |-----------------------------------------------------------------------------| r_work (start): 0.2885 rms_B_bonded: 3.98 r_work: 0.2737 rms_B_bonded: 4.62 restraints_weight: 0.5000 r_work (final): 0.2737 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8437 moved from start: 1.0302 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 12657 Z= 0.210 Angle : 0.829 14.078 17094 Z= 0.410 Chirality : 0.047 0.374 1962 Planarity : 0.004 0.054 2171 Dihedral : 5.702 44.884 1689 Min Nonbonded Distance : 2.280 Molprobity Statistics. All-atom Clashscore : 11.01 Ramachandran Plot: Outliers : 0.07 % Allowed : 7.04 % Favored : 92.89 % Rotamer: Outliers : 2.93 % Allowed : 35.38 % Favored : 61.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.92 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.20 % 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: 0.13 (0.23), residues: 1534 helix: 1.28 (0.19), residues: 814 sheet: 0.06 (0.57), residues: 84 loop : -1.52 (0.26), residues: 636 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A1204 HIS 0.007 0.001 HIS A1421 PHE 0.039 0.001 PHE A 553 TYR 0.014 0.001 TYR A 389 ARG 0.013 0.000 ARG E 555 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10097.82 seconds wall clock time: 181 minutes 1.39 seconds (10861.39 seconds total)