Starting phenix.real_space_refine on Thu Sep 18 00:35:57 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8zpv_60355/09_2025/8zpv_60355.cif Found real_map, /net/cci-nas-00/data/ceres_data/8zpv_60355/09_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_60355/09_2025/8zpv_60355.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8zpv_60355/09_2025/8zpv_60355.map" model { file = "/net/cci-nas-00/data/ceres_data/8zpv_60355/09_2025/8zpv_60355.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8zpv_60355/09_2025/8zpv_60355.cif" } resolution = 2.9 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/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: 3.41, per 1000 atoms: 0.27 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: 1.12 Conformation dependent library (CDL) restraints added in 744.8 milliseconds Enol-peptide restraints added in 1.2 microseconds 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: 0.47 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: 2.29 Time building geometry restraints manager: 1.45 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: 1.410 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.230 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 15.120 Find NCS groups from input model: 0.080 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:8.010 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.980 ------------------------------------------------------------------------------- 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 12664 Z= 0.461 Angle : 0.893 40.237 17096 Z= 0.512 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.61 (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 ARG 0.009 0.000 ARG A1181 TYR 0.013 0.001 TYR A 389 PHE 0.012 0.001 PHE A 553 TRP 0.010 0.001 TRP A 754 HIS 0.009 0.001 HIS A 16 Details of bonding type rmsd covalent geometry : bond 0.00721 (12657) covalent geometry : angle 0.83027 (17094) hydrogen bonds : bond 0.13912 ( 645) hydrogen bonds : angle 5.48875 ( 1830) metal coordination : bond 0.08475 ( 7) metal coordination : angle 30.48527 ( 2) *********************** 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 : 0.514 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: 0.5695 (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: 0.7508 (mp0) REVERT: A 544 LYS cc_start: 0.7813 (mttm) cc_final: 0.6600 (mttp) REVERT: A 556 MET cc_start: 0.6452 (mtm) cc_final: 0.6155 (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: 0.7334 (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: 0.7825 (p) REVERT: B 532 ARG cc_start: 0.6278 (tmm160) cc_final: 0.5794 (mmm160) REVERT: C 531 MET cc_start: 0.7863 (mpp) cc_final: 0.7631 (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: 0.8279 (t0) outliers start: 143 outliers final: 24 residues processed: 482 average time/residue: 0.4535 time to fit residues: 243.2506 Evaluate side-chains 250 residues out of total 1399 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 221 time to evaluate : 0.493 ------------------------------------------------------------------------------- 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 98 optimal weight: 5.9990 chunk 107 optimal weight: 1.9990 chunk 10 optimal weight: 0.7980 chunk 66 optimal weight: 3.9990 chunk 130 optimal weight: 0.6980 chunk 124 optimal weight: 0.8980 chunk 103 optimal weight: 0.8980 chunk 77 optimal weight: 2.9990 chunk 122 optimal weight: 0.7980 chunk 91 optimal weight: 5.9990 chunk 149 optimal weight: 10.0000 overall best weight: 0.8180 ------------------------------------------------------------------------------- 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 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 539 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 534 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3516 r_free = 0.3516 target = 0.086498 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3001 r_free = 0.3001 target = 0.060587 restraints weight = 37192.842| |-----------------------------------------------------------------------------| r_work (start): 0.2950 rms_B_bonded: 4.05 r_work: 0.2804 rms_B_bonded: 4.68 restraints_weight: 0.5000 r_work (final): 0.2804 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7721 moved from start: 0.3793 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 12664 Z= 0.177 Angle : 0.808 12.488 17096 Z= 0.413 Chirality : 0.047 0.208 1962 Planarity : 0.005 0.048 2171 Dihedral : 7.470 50.967 1733 Min Nonbonded Distance : 2.377 Molprobity Statistics. All-atom Clashscore : 11.17 Ramachandran Plot: Outliers : 0.07 % Allowed : 7.24 % Favored : 92.70 % Rotamer: Outliers : 7.51 % Allowed : 30.74 % Favored : 61.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.92 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.34 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.25 (0.22), residues: 1534 helix: 0.23 (0.18), residues: 829 sheet: -0.99 (0.54), residues: 84 loop : -2.29 (0.25), residues: 621 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG E 532 TYR 0.021 0.002 TYR A 732 PHE 0.024 0.001 PHE A 553 TRP 0.021 0.001 TRP A1319 HIS 0.010 0.002 HIS A 55 Details of bonding type rmsd covalent geometry : bond 0.00376 (12657) covalent geometry : angle 0.80840 (17094) hydrogen bonds : bond 0.04761 ( 645) hydrogen bonds : angle 4.72309 ( 1830) metal coordination : bond 0.01518 ( 7) metal coordination : angle 1.10095 ( 2) *********************** 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 351 residues out of total 1399 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 105 poor density : 246 time to evaluate : 0.542 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: 0.6513 (OUTLIER) cc_final: 0.5993 (mt) REVERT: A 202 ARG cc_start: 0.8868 (ttm170) cc_final: 0.8628 (tpp80) REVERT: A 291 GLU cc_start: 0.8702 (OUTLIER) cc_final: 0.8185 (mp0) REVERT: A 471 MET cc_start: 0.9158 (mmp) cc_final: 0.8850 (mmp) REVERT: A 577 LYS cc_start: 0.8836 (mttt) cc_final: 0.8555 (mtmm) REVERT: A 712 PHE cc_start: 0.7937 (m-10) cc_final: 0.7735 (m-80) REVERT: A 1123 LEU cc_start: 0.8833 (tt) cc_final: 0.8381 (tm) REVERT: A 1243 ASN cc_start: 0.8028 (t0) cc_final: 0.7466 (t0) REVERT: A 1424 VAL cc_start: 0.7787 (p) cc_final: 0.7475 (p) REVERT: B 543 ILE cc_start: 0.8497 (mp) cc_final: 0.8131 (mm) REVERT: C 531 MET cc_start: 0.7898 (mpp) cc_final: 0.7581 (ttt) REVERT: D 526 LEU cc_start: 0.6235 (mm) cc_final: 0.5810 (pp) REVERT: D 575 MET cc_start: 0.8073 (mpp) cc_final: 0.7792 (mpp) REVERT: D 577 MET cc_start: 0.8321 (tmm) cc_final: 0.8067 (tmm) REVERT: D 686 ASN cc_start: 0.8516 (m-40) cc_final: 0.8219 (m110) outliers start: 105 outliers final: 35 residues processed: 316 average time/residue: 0.5078 time to fit residues: 177.0101 Evaluate side-chains 243 residues out of total 1399 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 206 time to evaluate : 0.511 ------------------------------------------------------------------------------- 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 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 537 VAL Chi-restraints excluded: chain A residue 552 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 946 VAL 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 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 538 GLU Chi-restraints excluded: chain D residue 564 LEU Chi-restraints excluded: chain D residue 567 ILE Chi-restraints excluded: chain D residue 685 LEU 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 104 optimal weight: 7.9990 chunk 13 optimal weight: 0.8980 chunk 16 optimal weight: 1.9990 chunk 81 optimal weight: 0.7980 chunk 85 optimal weight: 3.9990 chunk 78 optimal weight: 0.8980 chunk 42 optimal weight: 5.9990 chunk 32 optimal weight: 2.9990 chunk 7 optimal weight: 5.9990 chunk 61 optimal weight: 0.4980 chunk 23 optimal weight: 1.9990 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 55 HIS A 92 ASN A 331 GLN A1259 GLN A1324 GLN D 539 GLN E 522 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.086691 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3007 r_free = 0.3007 target = 0.060258 restraints weight = 37336.088| |-----------------------------------------------------------------------------| r_work (start): 0.2919 rms_B_bonded: 4.03 r_work: 0.2773 rms_B_bonded: 4.65 restraints_weight: 0.5000 r_work (final): 0.2773 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8018 moved from start: 0.5576 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 12664 Z= 0.188 Angle : 0.774 11.437 17096 Z= 0.399 Chirality : 0.047 0.243 1962 Planarity : 0.005 0.047 2171 Dihedral : 6.254 49.860 1695 Min Nonbonded Distance : 2.339 Molprobity Statistics. All-atom Clashscore : 11.37 Ramachandran Plot: Outliers : 0.07 % Allowed : 7.04 % Favored : 92.89 % Rotamer: Outliers : 6.93 % Allowed : 29.88 % Favored : 63.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.92 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.27 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.77 (0.22), residues: 1534 helix: 0.59 (0.19), residues: 828 sheet: -0.43 (0.58), residues: 74 loop : -2.06 (0.25), residues: 632 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A1180 TYR 0.011 0.001 TYR A 389 PHE 0.028 0.001 PHE A 553 TRP 0.010 0.001 TRP A1248 HIS 0.009 0.001 HIS A 55 Details of bonding type rmsd covalent geometry : bond 0.00370 (12657) covalent geometry : angle 0.77343 (17094) hydrogen bonds : bond 0.04735 ( 645) hydrogen bonds : angle 4.56661 ( 1830) metal coordination : bond 0.00816 ( 7) metal coordination : angle 3.07330 ( 2) *********************** 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 304 residues out of total 1399 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 97 poor density : 207 time to evaluate : 0.499 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 14 GLU cc_start: 0.8681 (OUTLIER) cc_final: 0.8472 (pm20) REVERT: A 43 ASP cc_start: 0.8181 (t0) cc_final: 0.7828 (OUTLIER) REVERT: A 146 ILE cc_start: 0.6768 (OUTLIER) cc_final: 0.6214 (mt) REVERT: A 282 ARG cc_start: 0.9252 (OUTLIER) cc_final: 0.8783 (ttp80) REVERT: A 291 GLU cc_start: 0.8765 (OUTLIER) cc_final: 0.8330 (mp0) REVERT: A 392 ILE cc_start: 0.8742 (OUTLIER) cc_final: 0.8534 (pp) REVERT: A 577 LYS cc_start: 0.9057 (mttt) cc_final: 0.8682 (mtmm) REVERT: A 712 PHE cc_start: 0.8104 (m-10) cc_final: 0.7884 (m-80) REVERT: A 824 ARG cc_start: 0.7503 (mpp-170) cc_final: 0.7277 (mpp-170) REVERT: A 893 LYS cc_start: 0.9274 (mmmm) cc_final: 0.8884 (mppt) REVERT: A 1133 GLU cc_start: 0.8680 (pp20) cc_final: 0.8449 (pp20) REVERT: A 1243 ASN cc_start: 0.8127 (t0) cc_final: 0.7496 (t0) REVERT: C 530 ASP cc_start: 0.7873 (p0) cc_final: 0.7641 (p0) REVERT: C 555 ARG cc_start: 0.7746 (mmp-170) cc_final: 0.7539 (mmm160) REVERT: D 575 MET cc_start: 0.8102 (mpp) cc_final: 0.7882 (mpp) REVERT: D 678 ARG cc_start: 0.8197 (ttp-110) cc_final: 0.7922 (ttm-80) REVERT: D 686 ASN cc_start: 0.8533 (m-40) cc_final: 0.8245 (m110) REVERT: E 555 ARG cc_start: 0.9091 (mmm160) cc_final: 0.8812 (mmm160) outliers start: 97 outliers final: 32 residues processed: 273 average time/residue: 0.5240 time to fit residues: 156.7654 Evaluate side-chains 221 residues out of total 1399 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 185 time to evaluate : 0.511 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 GLU Chi-restraints excluded: chain A residue 99 THR 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 235 VAL Chi-restraints excluded: chain A residue 282 ARG Chi-restraints excluded: chain A residue 291 GLU Chi-restraints excluded: chain A residue 297 LEU Chi-restraints excluded: chain A residue 377 VAL Chi-restraints excluded: chain A residue 392 ILE 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 842 VAL Chi-restraints excluded: chain A residue 850 VAL Chi-restraints excluded: chain A residue 919 LEU Chi-restraints excluded: chain A residue 946 VAL Chi-restraints excluded: chain A residue 1055 SER Chi-restraints excluded: chain A residue 1149 LEU Chi-restraints excluded: chain A residue 1429 CYS 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 D residue 532 ARG Chi-restraints excluded: chain D residue 555 ARG 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 Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 48 optimal weight: 0.0670 chunk 1 optimal weight: 0.7980 chunk 22 optimal weight: 0.9990 chunk 41 optimal weight: 4.9990 chunk 20 optimal weight: 0.8980 chunk 52 optimal weight: 2.9990 chunk 29 optimal weight: 3.9990 chunk 97 optimal weight: 5.9990 chunk 108 optimal weight: 5.9990 chunk 17 optimal weight: 0.7980 chunk 150 optimal weight: 0.9980 overall best weight: 0.7118 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 55 HIS A 331 GLN A1259 GLN ** B 535 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.087449 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3028 r_free = 0.3028 target = 0.061122 restraints weight = 36968.771| |-----------------------------------------------------------------------------| r_work (start): 0.2977 rms_B_bonded: 3.98 r_work: 0.2833 rms_B_bonded: 4.64 restraints_weight: 0.5000 r_work (final): 0.2833 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8215 moved from start: 0.6401 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 12664 Z= 0.135 Angle : 0.741 11.174 17096 Z= 0.375 Chirality : 0.046 0.276 1962 Planarity : 0.004 0.046 2171 Dihedral : 6.088 47.520 1694 Min Nonbonded Distance : 2.366 Molprobity Statistics. All-atom Clashscore : 10.58 Ramachandran Plot: Outliers : 0.07 % Allowed : 6.52 % Favored : 93.42 % Rotamer: Outliers : 6.00 % Allowed : 31.31 % Favored : 62.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.92 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.27 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.42 (0.22), residues: 1534 helix: 0.89 (0.19), residues: 810 sheet: -0.08 (0.58), residues: 74 loop : -1.86 (0.25), residues: 650 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 669 TYR 0.010 0.001 TYR A 284 PHE 0.031 0.001 PHE A 553 TRP 0.008 0.001 TRP A1248 HIS 0.007 0.001 HIS A1421 Details of bonding type rmsd covalent geometry : bond 0.00289 (12657) covalent geometry : angle 0.74095 (17094) hydrogen bonds : bond 0.04154 ( 645) hydrogen bonds : angle 4.44005 ( 1830) metal coordination : bond 0.00505 ( 7) metal coordination : angle 2.19873 ( 2) *********************** 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 282 residues out of total 1399 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 198 time to evaluate : 0.540 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 14 GLU cc_start: 0.8744 (OUTLIER) cc_final: 0.8527 (pm20) REVERT: A 43 ASP cc_start: 0.8208 (t0) cc_final: 0.7908 (OUTLIER) REVERT: A 146 ILE cc_start: 0.6991 (OUTLIER) cc_final: 0.6578 (mt) REVERT: A 289 MET cc_start: 0.9347 (OUTLIER) cc_final: 0.9099 (ttp) REVERT: A 291 GLU cc_start: 0.8907 (OUTLIER) cc_final: 0.8523 (mp0) REVERT: A 471 MET cc_start: 0.9267 (mmp) cc_final: 0.8941 (mmp) REVERT: A 577 LYS cc_start: 0.9170 (mttt) cc_final: 0.8894 (mtmm) REVERT: A 712 PHE cc_start: 0.8178 (m-10) cc_final: 0.7926 (m-80) REVERT: A 893 LYS cc_start: 0.9375 (mmmm) cc_final: 0.9056 (mppt) REVERT: A 1414 ASP cc_start: 0.7424 (OUTLIER) cc_final: 0.6577 (t0) REVERT: A 1440 ASP cc_start: 0.7466 (OUTLIER) cc_final: 0.7256 (p0) REVERT: C 531 MET cc_start: 0.7565 (mpt) cc_final: 0.7129 (ttm) REVERT: C 570 HIS cc_start: 0.7454 (OUTLIER) cc_final: 0.7163 (m90) REVERT: D 542 GLU cc_start: 0.9166 (mm-30) cc_final: 0.8928 (mm-30) REVERT: D 665 LYS cc_start: 0.9218 (mtpp) cc_final: 0.8923 (tttm) REVERT: D 678 ARG cc_start: 0.8261 (ttp-110) cc_final: 0.7911 (ttm-80) outliers start: 84 outliers final: 29 residues processed: 252 average time/residue: 0.5819 time to fit residues: 159.8658 Evaluate side-chains 212 residues out of total 1399 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 177 time to evaluate : 0.502 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 GLU Chi-restraints excluded: chain A residue 99 THR Chi-restraints excluded: chain A residue 146 ILE Chi-restraints excluded: chain A residue 180 MET Chi-restraints excluded: chain A residue 289 MET Chi-restraints excluded: chain A residue 291 GLU 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 552 LEU Chi-restraints excluded: chain A residue 829 VAL 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 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 1251 VAL 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 1440 ASP 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 538 GLU 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 83 optimal weight: 0.8980 chunk 108 optimal weight: 6.9990 chunk 20 optimal weight: 2.9990 chunk 35 optimal weight: 1.9990 chunk 13 optimal weight: 0.4980 chunk 10 optimal weight: 4.9990 chunk 33 optimal weight: 0.8980 chunk 15 optimal weight: 3.9990 chunk 24 optimal weight: 0.8980 chunk 60 optimal weight: 0.9990 chunk 75 optimal weight: 0.7980 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 A1202 HIS A1259 GLN A1394 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.087318 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3020 r_free = 0.3020 target = 0.060839 restraints weight = 36743.780| |-----------------------------------------------------------------------------| r_work (start): 0.2967 rms_B_bonded: 3.92 r_work: 0.2824 rms_B_bonded: 4.60 restraints_weight: 0.5000 r_work (final): 0.2824 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8296 moved from start: 0.7156 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.069 12664 Z= 0.139 Angle : 0.736 10.901 17096 Z= 0.375 Chirality : 0.046 0.281 1962 Planarity : 0.004 0.054 2171 Dihedral : 5.919 48.598 1694 Min Nonbonded Distance : 2.402 Molprobity Statistics. All-atom Clashscore : 9.74 Ramachandran Plot: Outliers : 0.13 % Allowed : 7.11 % Favored : 92.76 % Rotamer: Outliers : 5.93 % Allowed : 31.74 % Favored : 62.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.92 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.20 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.17 (0.22), residues: 1534 helix: 1.00 (0.19), residues: 825 sheet: 0.26 (0.60), residues: 74 loop : -1.70 (0.26), residues: 635 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.001 ARG D 532 TYR 0.021 0.001 TYR A 389 PHE 0.038 0.001 PHE A 553 TRP 0.006 0.001 TRP A 915 HIS 0.007 0.001 HIS A1421 Details of bonding type rmsd covalent geometry : bond 0.00308 (12657) covalent geometry : angle 0.73541 (17094) hydrogen bonds : bond 0.04259 ( 645) hydrogen bonds : angle 4.43852 ( 1830) metal coordination : bond 0.00669 ( 7) metal coordination : angle 2.24939 ( 2) *********************** 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 270 residues out of total 1399 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 187 time to evaluate : 0.769 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: symmetry clash REVERT: A 14 GLU cc_start: 0.8692 (OUTLIER) cc_final: 0.8485 (pm20) REVERT: A 43 ASP cc_start: 0.8304 (t0) cc_final: 0.7986 (OUTLIER) REVERT: A 146 ILE cc_start: 0.7156 (OUTLIER) cc_final: 0.6737 (mt) REVERT: A 291 GLU cc_start: 0.8962 (OUTLIER) cc_final: 0.8597 (mp0) REVERT: A 431 LEU cc_start: 0.9475 (OUTLIER) cc_final: 0.9248 (mm) REVERT: A 577 LYS cc_start: 0.9307 (mttt) cc_final: 0.9015 (mtmm) REVERT: A 893 LYS cc_start: 0.9453 (mmmm) cc_final: 0.9187 (mppt) REVERT: A 903 SER cc_start: 0.9367 (OUTLIER) cc_final: 0.9029 (p) REVERT: A 1225 MET cc_start: 0.8414 (mmt) cc_final: 0.8152 (mmm) REVERT: A 1414 ASP cc_start: 0.7424 (OUTLIER) cc_final: 0.6475 (t0) REVERT: A 1440 ASP cc_start: 0.7260 (OUTLIER) cc_final: 0.7032 (p0) REVERT: A 1442 GLU cc_start: 0.8840 (OUTLIER) cc_final: 0.8349 (pp20) REVERT: C 531 MET cc_start: 0.7667 (mpt) cc_final: 0.7198 (ttm) REVERT: C 570 HIS cc_start: 0.7444 (OUTLIER) cc_final: 0.7219 (m90) REVERT: D 660 SER cc_start: 0.8432 (m) cc_final: 0.8189 (m) REVERT: D 686 ASN cc_start: 0.8630 (m-40) cc_final: 0.8357 (m110) outliers start: 83 outliers final: 40 residues processed: 243 average time/residue: 0.5694 time to fit residues: 151.6932 Evaluate side-chains 213 residues out of total 1399 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 165 time to evaluate : 0.504 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 GLU Chi-restraints excluded: chain A residue 99 THR 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 201 MET Chi-restraints excluded: chain A residue 289 MET Chi-restraints excluded: chain A residue 291 GLU Chi-restraints excluded: chain A residue 384 ASP Chi-restraints excluded: chain A residue 425 SER Chi-restraints excluded: chain A residue 431 LEU Chi-restraints excluded: chain A residue 439 THR Chi-restraints excluded: chain A residue 461 LEU 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 537 VAL Chi-restraints excluded: chain A residue 553 PHE Chi-restraints excluded: chain A residue 566 ILE 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 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 1149 LEU Chi-restraints excluded: chain A residue 1239 CYS Chi-restraints excluded: chain A residue 1251 VAL Chi-restraints excluded: chain A residue 1253 ARG Chi-restraints excluded: chain A residue 1414 ASP Chi-restraints excluded: chain A residue 1429 CYS 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 533 LEU Chi-restraints excluded: chain C residue 570 HIS Chi-restraints excluded: chain D residue 538 GLU Chi-restraints excluded: chain D residue 555 ARG Chi-restraints excluded: chain D residue 564 LEU Chi-restraints excluded: chain D residue 567 ILE Chi-restraints excluded: chain D residue 677 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 22 optimal weight: 1.9990 chunk 43 optimal weight: 0.9980 chunk 144 optimal weight: 0.9980 chunk 35 optimal weight: 0.1980 chunk 68 optimal weight: 5.9990 chunk 95 optimal weight: 4.9990 chunk 0 optimal weight: 7.9990 chunk 36 optimal weight: 0.9990 chunk 94 optimal weight: 2.9990 chunk 75 optimal weight: 0.7980 chunk 135 optimal weight: 2.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 331 GLN A 951 ASN A1256 GLN E 528 ASN ** E 535 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.087120 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3008 r_free = 0.3008 target = 0.060211 restraints weight = 37018.550| |-----------------------------------------------------------------------------| r_work (start): 0.2956 rms_B_bonded: 4.00 r_work: 0.2811 rms_B_bonded: 4.67 restraints_weight: 0.5000 r_work (final): 0.2811 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8286 moved from start: 0.7564 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 12664 Z= 0.138 Angle : 0.753 12.841 17096 Z= 0.379 Chirality : 0.045 0.186 1962 Planarity : 0.004 0.054 2171 Dihedral : 5.903 50.286 1694 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 9.82 Ramachandran Plot: Outliers : 0.13 % Allowed : 7.11 % Favored : 92.76 % Rotamer: Outliers : 5.15 % Allowed : 33.31 % Favored : 61.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.92 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.20 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.01 (0.23), residues: 1534 helix: 1.17 (0.19), residues: 817 sheet: 0.44 (0.61), residues: 74 loop : -1.65 (0.26), residues: 643 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG E 555 TYR 0.019 0.001 TYR A 389 PHE 0.027 0.001 PHE A 553 TRP 0.007 0.001 TRP A 915 HIS 0.016 0.001 HIS E 535 Details of bonding type rmsd covalent geometry : bond 0.00309 (12657) covalent geometry : angle 0.75246 (17094) hydrogen bonds : bond 0.04148 ( 645) hydrogen bonds : angle 4.36736 ( 1830) metal coordination : bond 0.00647 ( 7) metal coordination : angle 2.31093 ( 2) *********************** 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 253 residues out of total 1399 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 181 time to evaluate : 0.542 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 14 GLU cc_start: 0.8693 (OUTLIER) cc_final: 0.8482 (pm20) REVERT: A 144 GLU cc_start: 0.5927 (OUTLIER) cc_final: 0.4215 (pm20) REVERT: A 146 ILE cc_start: 0.7306 (OUTLIER) cc_final: 0.6881 (mt) REVERT: A 289 MET cc_start: 0.9348 (OUTLIER) cc_final: 0.8897 (ttp) REVERT: A 291 GLU cc_start: 0.8965 (OUTLIER) cc_final: 0.8572 (mp0) REVERT: A 577 LYS cc_start: 0.9364 (mttt) cc_final: 0.9057 (mtmm) REVERT: A 893 LYS cc_start: 0.9542 (mmmm) cc_final: 0.9240 (mppt) REVERT: A 1088 MET cc_start: 0.7596 (mmm) cc_final: 0.7260 (mtt) REVERT: A 1225 MET cc_start: 0.8192 (mmt) cc_final: 0.7838 (mmm) REVERT: A 1262 ARG cc_start: 0.8448 (pmm-80) cc_final: 0.7991 (ptp-170) REVERT: A 1414 ASP cc_start: 0.7622 (OUTLIER) cc_final: 0.6631 (t0) REVERT: A 1440 ASP cc_start: 0.7291 (OUTLIER) cc_final: 0.7073 (p0) REVERT: A 1442 GLU cc_start: 0.8794 (OUTLIER) cc_final: 0.8348 (pp20) REVERT: C 531 MET cc_start: 0.7662 (mpt) cc_final: 0.7256 (ttm) REVERT: C 570 HIS cc_start: 0.7567 (OUTLIER) cc_final: 0.7346 (m90) REVERT: D 678 ARG cc_start: 0.8268 (ttp-110) cc_final: 0.8038 (ttp-110) REVERT: D 686 ASN cc_start: 0.8640 (m-40) cc_final: 0.8395 (m110) outliers start: 72 outliers final: 35 residues processed: 231 average time/residue: 0.6120 time to fit residues: 153.9200 Evaluate side-chains 211 residues out of total 1399 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 167 time to evaluate : 0.501 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 GLU Chi-restraints excluded: chain A residue 99 THR Chi-restraints excluded: chain A residue 133 THR Chi-restraints excluded: chain A residue 144 GLU Chi-restraints excluded: chain A residue 146 ILE Chi-restraints excluded: chain A residue 201 MET Chi-restraints excluded: chain A residue 235 VAL Chi-restraints excluded: chain A residue 289 MET Chi-restraints excluded: chain A residue 291 GLU 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 537 VAL Chi-restraints excluded: chain A residue 552 LEU Chi-restraints excluded: chain A residue 566 ILE 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 842 VAL 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 1239 CYS Chi-restraints excluded: chain A residue 1253 ARG Chi-restraints excluded: chain A residue 1363 LEU Chi-restraints excluded: chain A residue 1414 ASP Chi-restraints excluded: chain A residue 1429 CYS 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 538 GLU Chi-restraints excluded: chain D residue 564 LEU Chi-restraints excluded: chain D residue 567 ILE Chi-restraints excluded: chain D residue 677 LEU Chi-restraints excluded: chain D residue 685 LEU Chi-restraints excluded: chain D residue 703 ASP 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 91 optimal weight: 7.9990 chunk 77 optimal weight: 3.9990 chunk 32 optimal weight: 3.9990 chunk 144 optimal weight: 1.9990 chunk 101 optimal weight: 9.9990 chunk 132 optimal weight: 1.9990 chunk 128 optimal weight: 5.9990 chunk 68 optimal weight: 2.9990 chunk 66 optimal weight: 4.9990 chunk 39 optimal weight: 2.9990 chunk 93 optimal weight: 0.9990 overall best weight: 2.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 331 GLN A1256 GLN ** E 535 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3455 r_free = 0.3455 target = 0.082537 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2883 r_free = 0.2883 target = 0.055269 restraints weight = 36875.240| |-----------------------------------------------------------------------------| r_work (start): 0.2837 rms_B_bonded: 4.00 r_work: 0.2686 rms_B_bonded: 4.64 restraints_weight: 0.5000 r_work (final): 0.2686 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8468 moved from start: 0.9275 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 12664 Z= 0.219 Angle : 0.834 10.864 17096 Z= 0.429 Chirality : 0.049 0.233 1962 Planarity : 0.005 0.100 2171 Dihedral : 6.263 53.035 1691 Min Nonbonded Distance : 2.329 Molprobity Statistics. All-atom Clashscore : 11.13 Ramachandran Plot: Outliers : 0.13 % Allowed : 7.69 % Favored : 92.18 % Rotamer: Outliers : 6.22 % Allowed : 33.17 % Favored : 60.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.92 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.20 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.19 (0.23), residues: 1534 helix: 1.02 (0.19), residues: 820 sheet: -0.26 (0.55), residues: 89 loop : -1.69 (0.26), residues: 625 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG D 532 TYR 0.020 0.002 TYR A 389 PHE 0.015 0.002 PHE A 458 TRP 0.017 0.001 TRP A 915 HIS 0.011 0.001 HIS E 535 Details of bonding type rmsd covalent geometry : bond 0.00504 (12657) covalent geometry : angle 0.83368 (17094) hydrogen bonds : bond 0.06156 ( 645) hydrogen bonds : angle 4.71203 ( 1830) metal coordination : bond 0.00837 ( 7) metal coordination : angle 2.07923 ( 2) *********************** 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 250 residues out of total 1399 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 163 time to evaluate : 0.525 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: 0.6289 (OUTLIER) cc_final: 0.5571 (pt0) REVERT: A 291 GLU cc_start: 0.9058 (OUTLIER) cc_final: 0.8712 (mp0) REVERT: A 425 SER cc_start: 0.8991 (OUTLIER) cc_final: 0.8497 (p) REVERT: A 520 MET cc_start: 0.9169 (OUTLIER) cc_final: 0.8955 (tpp) REVERT: A 555 LYS cc_start: 0.8985 (OUTLIER) cc_final: 0.8770 (mtpp) REVERT: A 577 LYS cc_start: 0.9652 (mttt) cc_final: 0.9339 (mtmm) REVERT: A 893 LYS cc_start: 0.9587 (mmmm) cc_final: 0.9263 (mttp) REVERT: A 1392 TYR cc_start: 0.8245 (OUTLIER) cc_final: 0.7976 (t80) REVERT: A 1393 GLN cc_start: 0.8772 (mm110) cc_final: 0.8453 (mt0) REVERT: A 1414 ASP cc_start: 0.8172 (OUTLIER) cc_final: 0.7135 (t0) REVERT: A 1442 GLU cc_start: 0.8729 (OUTLIER) cc_final: 0.8287 (pp20) REVERT: C 531 MET cc_start: 0.7755 (mpt) cc_final: 0.7377 (ttm) REVERT: D 554 ASP cc_start: 0.9154 (p0) cc_final: 0.8333 (p0) REVERT: D 655 MET cc_start: 0.1252 (mpt) cc_final: 0.0987 (mpt) REVERT: D 674 ASP cc_start: 0.6013 (m-30) cc_final: 0.5295 (m-30) REVERT: D 678 ARG cc_start: 0.8526 (ttp-110) cc_final: 0.8104 (ttm-80) REVERT: D 686 ASN cc_start: 0.8629 (m-40) cc_final: 0.8312 (m110) REVERT: D 692 GLU cc_start: 0.9198 (pm20) cc_final: 0.8982 (pm20) REVERT: D 693 GLU cc_start: 0.8583 (pm20) cc_final: 0.8380 (pm20) REVERT: D 695 GLN cc_start: 0.9118 (pp30) cc_final: 0.8892 (tp-100) REVERT: D 696 GLU cc_start: 0.9779 (tp30) cc_final: 0.9570 (tp30) REVERT: E 542 GLU cc_start: 0.9057 (pm20) cc_final: 0.8571 (pm20) outliers start: 87 outliers final: 36 residues processed: 227 average time/residue: 0.6294 time to fit residues: 155.1748 Evaluate side-chains 194 residues out of total 1399 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 150 time to evaluate : 0.507 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 99 THR Chi-restraints excluded: chain A residue 133 THR Chi-restraints excluded: chain A residue 144 GLU Chi-restraints excluded: chain A residue 148 ILE Chi-restraints excluded: chain A residue 235 VAL Chi-restraints excluded: chain A residue 291 GLU Chi-restraints excluded: chain A residue 300 LEU Chi-restraints excluded: chain A residue 345 LEU Chi-restraints excluded: chain A residue 384 ASP 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 472 LYS Chi-restraints excluded: chain A residue 495 THR Chi-restraints excluded: chain A residue 498 LYS Chi-restraints excluded: chain A residue 520 MET Chi-restraints excluded: chain A residue 537 VAL Chi-restraints excluded: chain A residue 555 LYS 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 842 VAL Chi-restraints excluded: chain A residue 850 VAL 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 1149 LEU Chi-restraints excluded: chain A residue 1239 CYS Chi-restraints excluded: chain A residue 1363 LEU Chi-restraints excluded: chain A residue 1392 TYR Chi-restraints excluded: chain A residue 1414 ASP Chi-restraints excluded: chain A residue 1429 CYS 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 538 GLU 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 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 125 optimal weight: 2.9990 chunk 23 optimal weight: 0.8980 chunk 3 optimal weight: 3.9990 chunk 126 optimal weight: 7.9990 chunk 106 optimal weight: 0.9990 chunk 78 optimal weight: 1.9990 chunk 37 optimal weight: 4.9990 chunk 122 optimal weight: 0.0020 chunk 41 optimal weight: 6.9990 chunk 121 optimal weight: 6.9990 chunk 46 optimal weight: 10.0000 overall best weight: 1.3794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 331 GLN ** 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 = 0.3478 r_free = 0.3478 target = 0.083796 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2917 r_free = 0.2917 target = 0.056550 restraints weight = 36811.097| |-----------------------------------------------------------------------------| r_work (start): 0.2870 rms_B_bonded: 4.03 r_work: 0.2722 rms_B_bonded: 4.66 restraints_weight: 0.5000 r_work (final): 0.2722 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8441 moved from start: 0.9537 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 12664 Z= 0.159 Angle : 0.824 13.954 17096 Z= 0.409 Chirality : 0.047 0.269 1962 Planarity : 0.004 0.081 2171 Dihedral : 5.867 45.751 1689 Min Nonbonded Distance : 2.343 Molprobity Statistics. All-atom Clashscore : 10.54 Ramachandran Plot: Outliers : 0.13 % Allowed : 6.84 % Favored : 93.02 % Rotamer: Outliers : 4.15 % Allowed : 35.03 % Favored : 60.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.92 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.20 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.01 (0.23), residues: 1534 helix: 1.18 (0.19), residues: 815 sheet: 0.02 (0.57), residues: 84 loop : -1.63 (0.26), residues: 635 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG E 532 TYR 0.014 0.001 TYR A 389 PHE 0.043 0.001 PHE A 553 TRP 0.006 0.001 TRP A1204 HIS 0.009 0.001 HIS E 535 Details of bonding type rmsd covalent geometry : bond 0.00368 (12657) covalent geometry : angle 0.82390 (17094) hydrogen bonds : bond 0.04906 ( 645) hydrogen bonds : angle 4.52480 ( 1830) metal coordination : bond 0.00672 ( 7) metal coordination : angle 2.12340 ( 2) *********************** 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 214 residues out of total 1399 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 156 time to evaluate : 0.375 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: 0.6027 (OUTLIER) cc_final: 0.4926 (pm20) REVERT: A 289 MET cc_start: 0.9233 (OUTLIER) cc_final: 0.9010 (ttm) REVERT: A 291 GLU cc_start: 0.9086 (OUTLIER) cc_final: 0.8783 (mp0) REVERT: A 425 SER cc_start: 0.8943 (OUTLIER) cc_final: 0.8449 (p) REVERT: A 520 MET cc_start: 0.9173 (OUTLIER) cc_final: 0.8956 (tpp) REVERT: A 577 LYS cc_start: 0.9666 (mttt) cc_final: 0.9352 (mtmm) REVERT: A 893 LYS cc_start: 0.9571 (mmmm) cc_final: 0.9258 (mttp) REVERT: A 1392 TYR cc_start: 0.8289 (t80) cc_final: 0.8054 (t80) REVERT: A 1393 GLN cc_start: 0.8742 (mm110) cc_final: 0.8470 (mt0) REVERT: A 1414 ASP cc_start: 0.8092 (OUTLIER) cc_final: 0.7056 (t0) REVERT: A 1442 GLU cc_start: 0.8692 (OUTLIER) cc_final: 0.8280 (pp20) REVERT: C 531 MET cc_start: 0.7804 (mpt) cc_final: 0.7357 (ttm) REVERT: D 537 GLU cc_start: 0.8426 (pp20) cc_final: 0.8051 (pp20) REVERT: D 674 ASP cc_start: 0.6057 (m-30) cc_final: 0.5380 (m-30) REVERT: D 678 ARG cc_start: 0.8519 (ttp-110) cc_final: 0.8085 (ttm-80) REVERT: E 542 GLU cc_start: 0.8932 (pm20) cc_final: 0.8718 (pm20) REVERT: E 555 ARG cc_start: 0.9044 (mmm160) cc_final: 0.8766 (mmm160) outliers start: 58 outliers final: 28 residues processed: 204 average time/residue: 0.6343 time to fit residues: 140.0668 Evaluate side-chains 172 residues out of total 1399 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 137 time to evaluate : 0.500 ------------------------------------------------------------------------------- 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 133 THR Chi-restraints excluded: chain A residue 144 GLU Chi-restraints excluded: chain A residue 235 VAL Chi-restraints excluded: chain A residue 289 MET Chi-restraints excluded: chain A residue 291 GLU 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 520 MET 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 829 VAL 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 903 SER Chi-restraints excluded: chain A residue 917 GLU Chi-restraints excluded: chain A residue 946 VAL Chi-restraints excluded: chain A residue 1239 CYS Chi-restraints excluded: chain A residue 1339 VAL Chi-restraints excluded: chain A residue 1363 LEU Chi-restraints excluded: chain A residue 1414 ASP 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 99 optimal weight: 5.9990 chunk 58 optimal weight: 2.9990 chunk 152 optimal weight: 9.9990 chunk 20 optimal weight: 0.8980 chunk 107 optimal weight: 4.9990 chunk 73 optimal weight: 0.9980 chunk 75 optimal weight: 0.9990 chunk 84 optimal weight: 0.8980 chunk 147 optimal weight: 1.9990 chunk 17 optimal weight: 0.8980 chunk 34 optimal weight: 0.9980 overall best weight: 0.9380 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3489 r_free = 0.3489 target = 0.084483 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2937 r_free = 0.2937 target = 0.057379 restraints weight = 36689.797| |-----------------------------------------------------------------------------| r_work (start): 0.2889 rms_B_bonded: 4.00 r_work: 0.2742 rms_B_bonded: 4.65 restraints_weight: 0.5000 r_work (final): 0.2742 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8424 moved from start: 0.9693 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 12664 Z= 0.154 Angle : 0.842 13.287 17096 Z= 0.417 Chirality : 0.046 0.178 1962 Planarity : 0.005 0.081 2171 Dihedral : 5.824 44.847 1689 Min Nonbonded Distance : 2.341 Molprobity Statistics. All-atom Clashscore : 11.17 Ramachandran Plot: Outliers : 0.07 % Allowed : 7.04 % Favored : 92.89 % Rotamer: Outliers : 3.72 % Allowed : 35.67 % Favored : 60.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.92 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.20 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.06 (0.23), residues: 1534 helix: 1.22 (0.19), residues: 816 sheet: 0.13 (0.60), residues: 84 loop : -1.59 (0.26), residues: 634 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A1082 TYR 0.011 0.001 TYR A 389 PHE 0.051 0.001 PHE A 553 TRP 0.010 0.001 TRP A 806 HIS 0.009 0.001 HIS E 535 Details of bonding type rmsd covalent geometry : bond 0.00349 (12657) covalent geometry : angle 0.84146 (17094) hydrogen bonds : bond 0.04632 ( 645) hydrogen bonds : angle 4.50330 ( 1830) metal coordination : bond 0.00615 ( 7) metal coordination : angle 2.29925 ( 2) *********************** 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: 52 poor density : 147 time to evaluate : 0.503 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: 0.6042 (OUTLIER) cc_final: 0.5242 (pm20) REVERT: A 289 MET cc_start: 0.9240 (OUTLIER) cc_final: 0.9008 (ttm) REVERT: A 291 GLU cc_start: 0.9089 (OUTLIER) cc_final: 0.8797 (mp0) REVERT: A 419 TYR cc_start: 0.8338 (t80) cc_final: 0.8039 (t80) REVERT: A 425 SER cc_start: 0.8941 (OUTLIER) cc_final: 0.8466 (p) REVERT: A 520 MET cc_start: 0.9184 (OUTLIER) cc_final: 0.8978 (tpp) REVERT: A 577 LYS cc_start: 0.9677 (mttt) cc_final: 0.9418 (mtmm) REVERT: A 893 LYS cc_start: 0.9566 (mmmm) cc_final: 0.9274 (mttp) REVERT: A 1392 TYR cc_start: 0.8259 (OUTLIER) cc_final: 0.8023 (t80) REVERT: A 1393 GLN cc_start: 0.8711 (mm110) cc_final: 0.8444 (mt0) REVERT: A 1414 ASP cc_start: 0.8071 (OUTLIER) cc_final: 0.7064 (t0) REVERT: A 1442 GLU cc_start: 0.8646 (OUTLIER) cc_final: 0.8282 (pp20) REVERT: C 531 MET cc_start: 0.7801 (mpt) cc_final: 0.7368 (ttm) REVERT: D 674 ASP cc_start: 0.6110 (m-30) cc_final: 0.5453 (m-30) REVERT: D 678 ARG cc_start: 0.8596 (ttp-110) cc_final: 0.8036 (ttm-80) REVERT: E 555 ARG cc_start: 0.9058 (mmm160) cc_final: 0.8771 (mmm160) outliers start: 52 outliers final: 30 residues processed: 187 average time/residue: 0.6430 time to fit residues: 130.5883 Evaluate side-chains 174 residues out of total 1399 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 136 time to evaluate : 0.576 ------------------------------------------------------------------------------- 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 133 THR Chi-restraints excluded: chain A residue 144 GLU Chi-restraints excluded: chain A residue 151 CYS Chi-restraints excluded: chain A residue 289 MET Chi-restraints excluded: chain A residue 291 GLU 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 520 MET 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 834 GLU 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 903 SER Chi-restraints excluded: chain A residue 917 GLU Chi-restraints excluded: chain A residue 946 VAL Chi-restraints excluded: chain A residue 1134 ILE Chi-restraints excluded: chain A residue 1239 CYS Chi-restraints excluded: chain A residue 1339 VAL Chi-restraints excluded: chain A residue 1392 TYR Chi-restraints excluded: chain A residue 1414 ASP 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 564 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 65 optimal weight: 4.9990 chunk 59 optimal weight: 2.9990 chunk 60 optimal weight: 0.9980 chunk 52 optimal weight: 3.9990 chunk 132 optimal weight: 9.9990 chunk 95 optimal weight: 0.0770 chunk 43 optimal weight: 0.8980 chunk 148 optimal weight: 20.0000 chunk 126 optimal weight: 9.9990 chunk 115 optimal weight: 5.9990 chunk 87 optimal weight: 0.1980 overall best weight: 1.0340 ------------------------------------------------------------------------------- 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 = 0.3492 r_free = 0.3492 target = 0.084621 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2942 r_free = 0.2942 target = 0.057623 restraints weight = 36523.363| |-----------------------------------------------------------------------------| r_work (start): 0.2894 rms_B_bonded: 3.98 r_work: 0.2745 rms_B_bonded: 4.61 restraints_weight: 0.5000 r_work (final): 0.2745 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8433 moved from start: 0.9922 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 12664 Z= 0.156 Angle : 0.872 16.224 17096 Z= 0.429 Chirality : 0.047 0.342 1962 Planarity : 0.005 0.087 2171 Dihedral : 5.790 44.671 1689 Min Nonbonded Distance : 2.310 Molprobity Statistics. All-atom Clashscore : 11.29 Ramachandran Plot: Outliers : 0.07 % Allowed : 7.11 % Favored : 92.83 % Rotamer: Outliers : 3.22 % Allowed : 36.38 % Favored : 60.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.92 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.20 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.12 (0.23), residues: 1534 helix: 1.25 (0.19), residues: 817 sheet: 0.27 (0.60), residues: 84 loop : -1.56 (0.26), residues: 633 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 551 TYR 0.011 0.001 TYR A 284 PHE 0.010 0.001 PHE A 889 TRP 0.007 0.001 TRP A 806 HIS 0.010 0.001 HIS E 535 Details of bonding type rmsd covalent geometry : bond 0.00358 (12657) covalent geometry : angle 0.87139 (17094) hydrogen bonds : bond 0.04528 ( 645) hydrogen bonds : angle 4.51365 ( 1830) metal coordination : bond 0.00482 ( 7) metal coordination : angle 2.23840 ( 2) ********************** 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 193 residues out of total 1399 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 148 time to evaluate : 0.504 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 144 GLU cc_start: 0.5970 (OUTLIER) cc_final: 0.5294 (pm20) REVERT: A 291 GLU cc_start: 0.9089 (OUTLIER) cc_final: 0.8812 (mp0) REVERT: A 419 TYR cc_start: 0.8357 (t80) cc_final: 0.8124 (t80) REVERT: A 425 SER cc_start: 0.9019 (OUTLIER) cc_final: 0.8581 (p) REVERT: A 577 LYS cc_start: 0.9689 (mttt) cc_final: 0.9426 (mtmm) REVERT: A 893 LYS cc_start: 0.9554 (mmmm) cc_final: 0.9277 (mttp) REVERT: A 1392 TYR cc_start: 0.8311 (OUTLIER) cc_final: 0.8103 (t80) REVERT: A 1393 GLN cc_start: 0.8683 (mm110) cc_final: 0.8434 (mt0) REVERT: A 1414 ASP cc_start: 0.8120 (OUTLIER) cc_final: 0.7094 (t0) REVERT: A 1442 GLU cc_start: 0.8599 (OUTLIER) cc_final: 0.8281 (pp20) REVERT: C 531 MET cc_start: 0.7818 (mpt) cc_final: 0.7279 (ttm) REVERT: C 542 GLU cc_start: 0.9030 (pm20) cc_final: 0.8755 (pm20) REVERT: D 674 ASP cc_start: 0.6168 (m-30) cc_final: 0.5504 (m-30) REVERT: D 678 ARG cc_start: 0.8582 (ttp-110) cc_final: 0.8281 (ttm-80) outliers start: 45 outliers final: 27 residues processed: 181 average time/residue: 0.6374 time to fit residues: 124.9089 Evaluate side-chains 171 residues out of total 1399 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 138 time to evaluate : 0.690 ------------------------------------------------------------------------------- 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 133 THR Chi-restraints excluded: chain A residue 144 GLU Chi-restraints excluded: chain A residue 151 CYS Chi-restraints excluded: chain A residue 291 GLU 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 842 VAL Chi-restraints excluded: chain A residue 850 VAL Chi-restraints excluded: chain A residue 946 VAL Chi-restraints excluded: chain A residue 1239 CYS Chi-restraints excluded: chain A residue 1339 VAL Chi-restraints excluded: chain A residue 1392 TYR Chi-restraints excluded: chain A residue 1414 ASP 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 564 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 16 optimal weight: 0.7980 chunk 143 optimal weight: 4.9990 chunk 147 optimal weight: 4.9990 chunk 93 optimal weight: 4.9990 chunk 85 optimal weight: 4.9990 chunk 39 optimal weight: 4.9990 chunk 60 optimal weight: 0.7980 chunk 34 optimal weight: 0.9980 chunk 73 optimal weight: 3.9990 chunk 68 optimal weight: 0.4980 chunk 123 optimal weight: 4.9990 overall best weight: 1.4182 ------------------------------------------------------------------------------- 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 671 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3476 r_free = 0.3476 target = 0.083850 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2927 r_free = 0.2927 target = 0.057180 restraints weight = 36250.357| |-----------------------------------------------------------------------------| r_work (start): 0.2881 rms_B_bonded: 3.92 r_work: 0.2731 rms_B_bonded: 4.62 restraints_weight: 0.5000 r_work (final): 0.2731 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8491 moved from start: 1.0142 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 12664 Z= 0.169 Angle : 0.882 16.381 17096 Z= 0.434 Chirality : 0.048 0.376 1962 Planarity : 0.005 0.081 2171 Dihedral : 5.803 44.427 1689 Min Nonbonded Distance : 2.277 Molprobity Statistics. All-atom Clashscore : 11.57 Ramachandran Plot: Outliers : 0.07 % Allowed : 6.98 % Favored : 92.96 % Rotamer: Outliers : 2.93 % Allowed : 36.53 % Favored : 60.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.92 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.20 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.10 (0.23), residues: 1534 helix: 1.20 (0.19), residues: 821 sheet: 0.12 (0.58), residues: 89 loop : -1.52 (0.26), residues: 624 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 551 TYR 0.011 0.001 TYR A 284 PHE 0.038 0.001 PHE A 553 TRP 0.008 0.001 TRP A 806 HIS 0.009 0.001 HIS E 535 Details of bonding type rmsd covalent geometry : bond 0.00399 (12657) covalent geometry : angle 0.88221 (17094) hydrogen bonds : bond 0.04839 ( 645) hydrogen bonds : angle 4.54558 ( 1830) metal coordination : bond 0.00514 ( 7) metal coordination : angle 2.06708 ( 2) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5248.77 seconds wall clock time: 90 minutes 14.23 seconds (5414.23 seconds total)