Starting phenix.real_space_refine on Thu Mar 5 12:03:34 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7m68_23690/03_2026/7m68_23690.cif Found real_map, /net/cci-nas-00/data/ceres_data/7m68_23690/03_2026/7m68_23690.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.04 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7m68_23690/03_2026/7m68_23690.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7m68_23690/03_2026/7m68_23690.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7m68_23690/03_2026/7m68_23690.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7m68_23690/03_2026/7m68_23690.map" } resolution = 4.04 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= -0.001 sd= 0.907 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: 6 Type Number sf(0) Gaussians P 3 5.49 5 S 46 5.16 5 C 7024 2.51 5 N 1833 2.21 5 O 1981 1.98 5 H 10933 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 21820 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 21820 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1390, 21820 Classifications: {'peptide': 1390} Link IDs: {'PTRANS': 37, 'TRANS': 1352} Chain breaks: 4 Unresolved non-hydrogen bonds: 222 Unresolved non-hydrogen angles: 280 Unresolved non-hydrogen dihedrals: 191 Unresolved non-hydrogen chiralities: 15 Planarities with less than four sites: {'PHE:plan': 3, 'ARG:plan': 4, 'GLU:plan': 5, 'TYR:plan': 4, 'TRP:plan': 1, 'HIS:plan': 1, 'GLN:plan1': 4, 'ASN:plan1': 3, 'ASP:plan': 1, 'TPO:plan-1': 1} Unresolved non-hydrogen planarities: 129 Time building chain proxies: 3.28, per 1000 atoms: 0.15 Number of scatterers: 21820 At special positions: 0 Unit cell: (131.968, 117.534, 103.1, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 46 16.00 P 3 15.00 O 1981 8.00 N 1833 7.00 C 7024 6.00 H 10933 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS A 946 " - pdb=" SG CYS A1017 " distance=2.05 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.06 Conformation dependent library (CDL) restraints added in 503.9 milliseconds 2742 Ramachandran restraints generated. 1371 Oldfield, 0 Emsley, 1371 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2632 Finding SS restraints... Secondary structure from input PDB file: 53 helices and 5 sheets defined 71.4% alpha, 6.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.34 Creating SS restraints... Processing helix chain 'A' and resid 29 through 61 removed outlier: 3.671A pdb=" N GLY A 49 " --> pdb=" O MET A 45 " (cutoff:3.500A) removed outlier: 4.466A pdb=" N LEU A 53 " --> pdb=" O GLY A 49 " (cutoff:3.500A) Processing helix chain 'A' and resid 71 through 96 removed outlier: 3.752A pdb=" N ARG A 75 " --> pdb=" O ILE A 71 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N ILE A 93 " --> pdb=" O ALA A 89 " (cutoff:3.500A) removed outlier: 4.209A pdb=" N SER A 94 " --> pdb=" O SER A 90 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N LYS A 95 " --> pdb=" O LEU A 91 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N GLU A 96 " --> pdb=" O ASN A 92 " (cutoff:3.500A) Processing helix chain 'A' and resid 101 through 124 removed outlier: 3.832A pdb=" N SER A 105 " --> pdb=" O PHE A 101 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N LEU A 118 " --> pdb=" O LEU A 114 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N HIS A 121 " --> pdb=" O ALA A 117 " (cutoff:3.500A) removed outlier: 4.085A pdb=" N GLU A 124 " --> pdb=" O LEU A 120 " (cutoff:3.500A) Processing helix chain 'A' and resid 134 through 160 Processing helix chain 'A' and resid 169 through 189 removed outlier: 3.691A pdb=" N PHE A 175 " --> pdb=" O ILE A 171 " (cutoff:3.500A) Processing helix chain 'A' and resid 197 through 202 removed outlier: 3.589A pdb=" N ILE A 200 " --> pdb=" O HIS A 197 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N HIS A 201 " --> pdb=" O GLN A 198 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N GLN A 202 " --> pdb=" O HIS A 199 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 197 through 202' Processing helix chain 'A' and resid 210 through 214 removed outlier: 3.870A pdb=" N ASP A 213 " --> pdb=" O ASN A 210 " (cutoff:3.500A) Processing helix chain 'A' and resid 216 through 223 removed outlier: 3.642A pdb=" N THR A 222 " --> pdb=" O PHE A 218 " (cutoff:3.500A) Processing helix chain 'A' and resid 223 through 236 Processing helix chain 'A' and resid 251 through 269 removed outlier: 3.697A pdb=" N LEU A 255 " --> pdb=" O SER A 251 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N ASN A 262 " --> pdb=" O LYS A 258 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N GLN A 269 " --> pdb=" O ASN A 265 " (cutoff:3.500A) Processing helix chain 'A' and resid 273 through 302 removed outlier: 5.703A pdb=" N SER A 285 " --> pdb=" O ARG A 281 " (cutoff:3.500A) removed outlier: 7.167A pdb=" N LYS A 286 " --> pdb=" O THR A 282 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N MET A 287 " --> pdb=" O PHE A 283 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N PHE A 302 " --> pdb=" O ASP A 298 " (cutoff:3.500A) Processing helix chain 'A' and resid 302 through 328 removed outlier: 3.739A pdb=" N GLN A 306 " --> pdb=" O PHE A 302 " (cutoff:3.500A) Processing helix chain 'A' and resid 342 through 391 removed outlier: 3.735A pdb=" N ALA A 383 " --> pdb=" O SER A 379 " (cutoff:3.500A) Processing helix chain 'A' and resid 393 through 399 Processing helix chain 'A' and resid 401 through 423 removed outlier: 4.358A pdb=" N VAL A 413 " --> pdb=" O MET A 409 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N GLN A 414 " --> pdb=" O SER A 410 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N GLN A 421 " --> pdb=" O GLN A 417 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N TRP A 422 " --> pdb=" O ASP A 418 " (cutoff:3.500A) Processing helix chain 'A' and resid 424 through 444 Proline residue: A 430 - end of helix Processing helix chain 'A' and resid 449 through 493 Proline residue: A 460 - end of helix removed outlier: 3.987A pdb=" N ASN A 493 " --> pdb=" O GLU A 489 " (cutoff:3.500A) Processing helix chain 'A' and resid 493 through 501 Processing helix chain 'A' and resid 502 through 538 removed outlier: 3.717A pdb=" N TYR A 506 " --> pdb=" O TRP A 502 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N ASN A 516 " --> pdb=" O GLU A 512 " (cutoff:3.500A) Processing helix chain 'A' and resid 539 through 555 removed outlier: 4.193A pdb=" N ALA A 549 " --> pdb=" O CYS A 545 " (cutoff:3.500A) removed outlier: 4.079A pdb=" N VAL A 552 " --> pdb=" O PHE A 548 " (cutoff:3.500A) removed outlier: 4.570A pdb=" N TYR A 553 " --> pdb=" O ALA A 549 " (cutoff:3.500A) Processing helix chain 'A' and resid 563 through 604 removed outlier: 4.497A pdb=" N PHE A 576 " --> pdb=" O ASN A 572 " (cutoff:3.500A) Proline residue: A 577 - end of helix Proline residue: A 582 - end of helix removed outlier: 4.191A pdb=" N LEU A 585 " --> pdb=" O ILE A 581 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N ASN A 586 " --> pdb=" O PRO A 582 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N SER A 587 " --> pdb=" O MET A 583 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N SER A 592 " --> pdb=" O PHE A 588 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N VAL A 593 " --> pdb=" O ILE A 589 " (cutoff:3.500A) Processing helix chain 'A' and resid 608 through 612 removed outlier: 4.144A pdb=" N SER A 611 " --> pdb=" O GLN A 608 " (cutoff:3.500A) removed outlier: 4.511A pdb=" N VAL A 612 " --> pdb=" O PRO A 609 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 608 through 612' Processing helix chain 'A' and resid 668 through 677 Processing helix chain 'A' and resid 706 through 712 Processing helix chain 'A' and resid 718 through 729 Processing helix chain 'A' and resid 731 through 737 Processing helix chain 'A' and resid 754 through 769 Processing helix chain 'A' and resid 779 through 783 removed outlier: 4.155A pdb=" N ALA A 782 " --> pdb=" O PRO A 779 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N VAL A 783 " --> pdb=" O LEU A 780 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 779 through 783' Processing helix chain 'A' and resid 784 through 796 removed outlier: 3.504A pdb=" N HIS A 790 " --> pdb=" O HIS A 786 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N GLU A 793 " --> pdb=" O ARG A 789 " (cutoff:3.500A) Processing helix chain 'A' and resid 813 through 820 Processing helix chain 'A' and resid 836 through 843 removed outlier: 3.512A pdb=" N LYS A 842 " --> pdb=" O ASP A 838 " (cutoff:3.500A) removed outlier: 4.283A pdb=" N ASP A 843 " --> pdb=" O GLU A 839 " (cutoff:3.500A) Processing helix chain 'A' and resid 845 through 850 Processing helix chain 'A' and resid 918 through 928 removed outlier: 4.441A pdb=" N ASN A 922 " --> pdb=" O GLY A 918 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N ILE A 923 " --> pdb=" O ASP A 919 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N ARG A 926 " --> pdb=" O ASN A 922 " (cutoff:3.500A) Processing helix chain 'A' and resid 936 through 946 Processing helix chain 'A' and resid 947 through 982 Processing helix chain 'A' and resid 987 through 1035 removed outlier: 3.683A pdb=" N LEU A1013 " --> pdb=" O GLN A1009 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N TRP A1014 " --> pdb=" O THR A1010 " (cutoff:3.500A) removed outlier: 4.101A pdb=" N ILE A1019 " --> pdb=" O VAL A1015 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N HIS A1020 " --> pdb=" O PHE A1016 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N ARG A1035 " --> pdb=" O ASN A1031 " (cutoff:3.500A) Processing helix chain 'A' and resid 1037 through 1044 Processing helix chain 'A' and resid 1045 through 1089 removed outlier: 3.704A pdb=" N ILE A1049 " --> pdb=" O PRO A1045 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N ILE A1057 " --> pdb=" O PHE A1053 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N TYR A1058 " --> pdb=" O SER A1054 " (cutoff:3.500A) removed outlier: 4.132A pdb=" N LEU A1064 " --> pdb=" O VAL A1060 " (cutoff:3.500A) removed outlier: 4.589A pdb=" N GLY A1065 " --> pdb=" O ASP A1061 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N SER A1069 " --> pdb=" O GLY A1065 " (cutoff:3.500A) Processing helix chain 'A' and resid 1092 through 1138 Proline residue: A1098 - end of helix removed outlier: 4.608A pdb=" N GLU A1116 " --> pdb=" O ARG A1112 " (cutoff:3.500A) removed outlier: 4.402A pdb=" N SER A1126 " --> pdb=" O SER A1122 " (cutoff:3.500A) Proline residue: A1127 - end of helix Processing helix chain 'A' and resid 1138 through 1146 Processing helix chain 'A' and resid 1147 through 1165 Processing helix chain 'A' and resid 1166 through 1202 Processing helix chain 'A' and resid 1205 through 1217 Processing helix chain 'A' and resid 1218 through 1248 removed outlier: 3.919A pdb=" N THR A1222 " --> pdb=" O GLN A1218 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N ARG A1228 " --> pdb=" O ASN A1224 " (cutoff:3.500A) Processing helix chain 'A' and resid 1311 through 1321 removed outlier: 3.847A pdb=" N LEU A1315 " --> pdb=" O GLY A1311 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N THR A1316 " --> pdb=" O LYS A1312 " (cutoff:3.500A) Processing helix chain 'A' and resid 1337 through 1341 removed outlier: 3.863A pdb=" N GLY A1341 " --> pdb=" O ILE A1337 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1337 through 1341' Processing helix chain 'A' and resid 1342 through 1348 Processing helix chain 'A' and resid 1362 through 1368 Processing helix chain 'A' and resid 1375 through 1386 Processing helix chain 'A' and resid 1387 through 1394 removed outlier: 3.887A pdb=" N VAL A1391 " --> pdb=" O LEU A1387 " (cutoff:3.500A) Processing helix chain 'A' and resid 1411 through 1426 Processing helix chain 'A' and resid 1442 through 1455 Processing helix chain 'A' and resid 1467 through 1474 Processing sheet with id=AA1, first strand: chain 'A' and resid 613 through 615 removed outlier: 7.451A pdb=" N ILE A 628 " --> pdb=" O GLN A 652 " (cutoff:3.500A) removed outlier: 5.303A pdb=" N GLN A 652 " --> pdb=" O ILE A 628 " (cutoff:3.500A) removed outlier: 7.576A pdb=" N ASP A 630 " --> pdb=" O ASN A 650 " (cutoff:3.500A) removed outlier: 6.454A pdb=" N ASN A 650 " --> pdb=" O ASP A 630 " (cutoff:3.500A) removed outlier: 5.480A pdb=" N ALA A 632 " --> pdb=" O ASN A 648 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 613 through 615 removed outlier: 6.704A pdb=" N LEU A 635 " --> pdb=" O ARG A 682 " (cutoff:3.500A) removed outlier: 5.618A pdb=" N ARG A 682 " --> pdb=" O LEU A 635 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 693 through 696 removed outlier: 6.448A pdb=" N ALA A 694 " --> pdb=" O LEU A 775 " (cutoff:3.500A) removed outlier: 8.268A pdb=" N ASP A 777 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 7.333A pdb=" N VAL A 696 " --> pdb=" O ASP A 777 " (cutoff:3.500A) removed outlier: 6.508A pdb=" N TYR A 774 " --> pdb=" O VAL A 808 " (cutoff:3.500A) removed outlier: 7.987A pdb=" N ALA A 810 " --> pdb=" O TYR A 774 " (cutoff:3.500A) removed outlier: 7.015A pdb=" N LEU A 776 " --> pdb=" O ALA A 810 " (cutoff:3.500A) removed outlier: 6.135A pdb=" N THR A 659 " --> pdb=" O LEU A 809 " (cutoff:3.500A) removed outlier: 6.752A pdb=" N LEU A 658 " --> pdb=" O SER A 822 " (cutoff:3.500A) removed outlier: 8.285A pdb=" N ALA A 824 " --> pdb=" O LEU A 658 " (cutoff:3.500A) removed outlier: 6.652A pdb=" N CYS A 660 " --> pdb=" O ALA A 824 " (cutoff:3.500A) removed outlier: 7.220A pdb=" N LEU A 826 " --> pdb=" O CYS A 660 " (cutoff:3.500A) removed outlier: 5.793A pdb=" N VAL A 662 " --> pdb=" O LEU A 826 " (cutoff:3.500A) removed outlier: 7.314A pdb=" N ILE A 823 " --> pdb=" O GLN A 834 " (cutoff:3.500A) removed outlier: 4.863A pdb=" N GLN A 834 " --> pdb=" O ILE A 823 " (cutoff:3.500A) removed outlier: 7.172A pdb=" N LEU A 825 " --> pdb=" O THR A 832 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 1293 through 1296 removed outlier: 3.864A pdb=" N THR A1279 " --> pdb=" O GLU A1327 " (cutoff:3.500A) removed outlier: 6.463A pdb=" N GLU A1327 " --> pdb=" O THR A1279 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 1350 through 1351 removed outlier: 6.954A pdb=" N SER A1350 " --> pdb=" O VAL A1432 " (cutoff:3.500A) removed outlier: 8.685A pdb=" N ASP A1434 " --> pdb=" O SER A1350 " (cutoff:3.500A) removed outlier: 6.513A pdb=" N LEU A1431 " --> pdb=" O LEU A1462 " (cutoff:3.500A) removed outlier: 7.861A pdb=" N ILE A1464 " --> pdb=" O LEU A1431 " (cutoff:3.500A) removed outlier: 6.466A pdb=" N LEU A1433 " --> pdb=" O ILE A1464 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N GLY A1303 " --> pdb=" O ARG A1476 " (cutoff:3.500A) 727 hydrogen bonds defined for protein. 2160 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 4.51 Time building geometry restraints manager: 2.76 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.04: 10914 1.04 - 1.25: 1574 1.25 - 1.45: 3231 1.45 - 1.66: 6242 1.66 - 1.87: 75 Bond restraints: 22036 Sorted by residual: bond pdb=" CG2 TPO A 911 " pdb="HG21 TPO A 911 " ideal model delta sigma weight residual 0.970 1.090 -0.120 2.00e-02 2.50e+03 3.62e+01 bond pdb=" CB TPO A 911 " pdb=" HB TPO A 911 " ideal model delta sigma weight residual 0.970 1.090 -0.120 2.00e-02 2.50e+03 3.60e+01 bond pdb=" CG2 TPO A 911 " pdb="HG23 TPO A 911 " ideal model delta sigma weight residual 0.970 1.089 -0.119 2.00e-02 2.50e+03 3.53e+01 bond pdb=" CG2 TPO A 911 " pdb="HG22 TPO A 911 " ideal model delta sigma weight residual 0.970 1.089 -0.119 2.00e-02 2.50e+03 3.51e+01 bond pdb=" OG1 TPO A 911 " pdb=" P TPO A 911 " ideal model delta sigma weight residual 1.717 1.611 0.106 2.00e-02 2.50e+03 2.81e+01 ... (remaining 22031 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.04: 38862 2.04 - 4.08: 898 4.08 - 6.12: 70 6.12 - 8.16: 5 8.16 - 10.20: 3 Bond angle restraints: 39838 Sorted by residual: angle pdb=" CB TPO A 911 " pdb=" OG1 TPO A 911 " pdb=" P TPO A 911 " ideal model delta sigma weight residual 119.31 109.18 10.13 3.00e+00 1.11e-01 1.14e+01 angle pdb=" OG1 TPO A 911 " pdb=" P TPO A 911 " pdb=" O1P TPO A 911 " ideal model delta sigma weight residual 100.43 109.65 -9.22 3.00e+00 1.11e-01 9.45e+00 angle pdb=" C LEU A 559 " pdb=" N THR A 560 " pdb=" CA THR A 560 " ideal model delta sigma weight residual 122.61 127.34 -4.73 1.56e+00 4.11e-01 9.19e+00 angle pdb=" CA ARG A 638 " pdb=" CB ARG A 638 " pdb=" CG ARG A 638 " ideal model delta sigma weight residual 114.10 120.07 -5.97 2.00e+00 2.50e-01 8.92e+00 angle pdb=" CA LEU A 135 " pdb=" CB LEU A 135 " pdb=" CG LEU A 135 " ideal model delta sigma weight residual 116.30 126.50 -10.20 3.50e+00 8.16e-02 8.49e+00 ... (remaining 39833 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.08: 9218 17.08 - 34.16: 824 34.16 - 51.24: 191 51.24 - 68.32: 88 68.32 - 85.40: 12 Dihedral angle restraints: 10333 sinusoidal: 5531 harmonic: 4802 Sorted by residual: dihedral pdb=" CA SER A 846 " pdb=" C SER A 846 " pdb=" N PRO A 847 " pdb=" CA PRO A 847 " ideal model delta harmonic sigma weight residual 180.00 -156.05 -23.95 0 5.00e+00 4.00e-02 2.30e+01 dihedral pdb=" CA ILE A1352 " pdb=" C ILE A1352 " pdb=" N PRO A1353 " pdb=" CA PRO A1353 " ideal model delta harmonic sigma weight residual -180.00 -156.45 -23.55 0 5.00e+00 4.00e-02 2.22e+01 dihedral pdb=" CA CYS A 546 " pdb=" C CYS A 546 " pdb=" N THR A 547 " pdb=" CA THR A 547 " ideal model delta harmonic sigma weight residual 180.00 -160.29 -19.71 0 5.00e+00 4.00e-02 1.55e+01 ... (remaining 10330 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.036: 1240 0.036 - 0.072: 368 0.072 - 0.109: 123 0.109 - 0.145: 36 0.145 - 0.181: 5 Chirality restraints: 1772 Sorted by residual: chirality pdb=" CA VAL A 624 " pdb=" N VAL A 624 " pdb=" C VAL A 624 " pdb=" CB VAL A 624 " both_signs ideal model delta sigma weight residual False 2.44 2.62 -0.18 2.00e-01 2.50e+01 8.19e-01 chirality pdb=" CA ILE A 626 " pdb=" N ILE A 626 " pdb=" C ILE A 626 " pdb=" CB ILE A 626 " both_signs ideal model delta sigma weight residual False 2.43 2.60 -0.17 2.00e-01 2.50e+01 7.28e-01 chirality pdb=" CA ILE A1352 " pdb=" N ILE A1352 " pdb=" C ILE A1352 " pdb=" CB ILE A1352 " both_signs ideal model delta sigma weight residual False 2.43 2.59 -0.16 2.00e-01 2.50e+01 6.50e-01 ... (remaining 1769 not shown) Planarity restraints: 3225 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PHE A 576 " 0.048 5.00e-02 4.00e+02 7.31e-02 8.55e+00 pdb=" N PRO A 577 " -0.126 5.00e-02 4.00e+02 pdb=" CA PRO A 577 " 0.038 5.00e-02 4.00e+02 pdb=" CD PRO A 577 " 0.040 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLN A 304 " -0.043 5.00e-02 4.00e+02 6.57e-02 6.91e+00 pdb=" N PRO A 305 " 0.114 5.00e-02 4.00e+02 pdb=" CA PRO A 305 " -0.034 5.00e-02 4.00e+02 pdb=" CD PRO A 305 " -0.037 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER A1126 " -0.036 5.00e-02 4.00e+02 5.37e-02 4.62e+00 pdb=" N PRO A1127 " 0.093 5.00e-02 4.00e+02 pdb=" CA PRO A1127 " -0.027 5.00e-02 4.00e+02 pdb=" CD PRO A1127 " -0.030 5.00e-02 4.00e+02 ... (remaining 3222 not shown) Histogram of nonbonded interaction distances: 1.74 - 2.31: 4473 2.31 - 2.89: 48808 2.89 - 3.46: 54469 3.46 - 4.03: 69269 4.03 - 4.60: 106027 Nonbonded interactions: 283046 Sorted by model distance: nonbonded pdb=" O LEU A 802 " pdb=" HZ3 LYS A 807 " model vdw 1.743 2.450 nonbonded pdb=" O GLY A 797 " pdb=" H GLY A 800 " model vdw 1.763 2.450 nonbonded pdb=" O VAL A1447 " pdb=" HG1 THR A1451 " model vdw 1.768 2.450 nonbonded pdb=" O ALA A 278 " pdb=" HG1 THR A 282 " model vdw 1.779 2.450 nonbonded pdb=" O ILE A1097 " pdb=" HG SER A1100 " model vdw 1.780 2.450 ... (remaining 283041 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.58 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue 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: 1.790 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: 0.130 Extract box with map and model: 0.280 Check model and map are aligned: 0.060 Set scattering table: 0.050 Process input model: 18.330 Find NCS groups from input model: 0.190 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:1.330 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.200 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7210 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.106 11104 Z= 0.226 Angle : 0.751 10.200 15069 Z= 0.399 Chirality : 0.042 0.181 1772 Planarity : 0.005 0.073 1879 Dihedral : 13.487 85.370 3985 Min Nonbonded Distance : 2.358 Molprobity Statistics. All-atom Clashscore : 1.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.76 % Favored : 94.24 % Rotamer: Outliers : 0.60 % Allowed : 9.52 % Favored : 89.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.08 (0.22), residues: 1371 helix: 1.01 (0.16), residues: 925 sheet: -0.93 (0.61), residues: 54 loop : -2.53 (0.29), residues: 392 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 765 TYR 0.027 0.002 TYR A 991 PHE 0.032 0.002 PHE A 548 TRP 0.011 0.001 TRP A1014 HIS 0.005 0.001 HIS A 364 Details of bonding type rmsd covalent geometry : bond 0.00502 (11103) covalent geometry : angle 0.74939 (15067) SS BOND : bond 0.01407 ( 1) SS BOND : angle 4.79312 ( 2) hydrogen bonds : bond 0.11560 ( 722) hydrogen bonds : angle 5.25771 ( 2160) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2742 Ramachandran restraints generated. 1371 Oldfield, 0 Emsley, 1371 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2742 Ramachandran restraints generated. 1371 Oldfield, 0 Emsley, 1371 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 40 is missing expected H atoms. Skipping. Residue MET 76 is missing expected H atoms. Skipping. Residue VAL 86 is missing expected H atoms. Skipping. Residue LYS 95 is missing expected H atoms. Skipping. Residue VAL 104 is missing expected H atoms. Skipping. Residue TYR 107 is missing expected H atoms. Skipping. Residue LEU 112 is missing expected H atoms. Skipping. Residue VAL 116 is missing expected H atoms. Skipping. Residue LEU 118 is missing expected H atoms. Skipping. Residue TYR 159 is missing expected H atoms. Skipping. Residue ILE 162 is missing expected H atoms. Skipping. Residue TYR 164 is missing expected H atoms. Skipping. Residue THR 179 is missing expected H atoms. Skipping. Residue LYS 192 is missing expected H atoms. Skipping. Residue ILE 200 is missing expected H atoms. Skipping. Residue LEU 497 is missing expected H atoms. Skipping. Residue LEU 525 is missing expected H atoms. Skipping. Residue MET 529 is missing expected H atoms. Skipping. Residue THR 633 is missing expected H atoms. Skipping. Residue LEU 635 is missing expected H atoms. Skipping. Residue LYS 654 is missing expected H atoms. Skipping. Residue LYS 655 is missing expected H atoms. Skipping. Residue ILE 661 is missing expected H atoms. Skipping. Residue LEU 802 is missing expected H atoms. Skipping. Residue LYS 933 is missing expected H atoms. Skipping. Residue MET 962 is missing expected H atoms. Skipping. Residue SER 980 is missing expected H atoms. Skipping. Residue TYR 1281 is missing expected H atoms. Skipping. Residue ILE 1304 is missing expected H atoms. Skipping. Residue SER 1395 is missing expected H atoms. Skipping. Residue LYS 1457 is missing expected H atoms. Skipping. Evaluate side-chains 373 residues out of total 1219 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 366 time to evaluate : 0.456 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: 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: 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 27 ASP cc_start: 0.8713 (t0) cc_final: 0.8397 (t0) REVERT: A 81 LEU cc_start: 0.9231 (tt) cc_final: 0.9022 (tt) REVERT: A 142 GLU cc_start: 0.8582 (tp30) cc_final: 0.7924 (tt0) REVERT: A 245 LYS cc_start: 0.8489 (mttt) cc_final: 0.8171 (mttt) REVERT: A 453 ILE cc_start: 0.8420 (mt) cc_final: 0.8141 (tp) REVERT: A 532 THR cc_start: 0.8144 (m) cc_final: 0.7911 (p) REVERT: A 574 LEU cc_start: 0.8815 (tt) cc_final: 0.8504 (tt) REVERT: A 583 MET cc_start: 0.8932 (tmm) cc_final: 0.8564 (tmm) REVERT: A 967 MET cc_start: 0.8270 (mmp) cc_final: 0.8001 (mmt) REVERT: A 1059 LYS cc_start: 0.7617 (mmtt) cc_final: 0.7415 (ttpt) REVERT: A 1107 GLN cc_start: 0.8650 (tm-30) cc_final: 0.8073 (tm-30) REVERT: A 1178 TYR cc_start: 0.8354 (t80) cc_final: 0.7983 (t80) REVERT: A 1194 LEU cc_start: 0.8513 (tp) cc_final: 0.8231 (mp) REVERT: A 1234 GLU cc_start: 0.8690 (tm-30) cc_final: 0.8163 (tm-30) outliers start: 7 outliers final: 4 residues processed: 372 average time/residue: 0.2065 time to fit residues: 111.1662 Evaluate side-chains 239 residues out of total 1219 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 235 time to evaluate : 0.583 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 98 optimal weight: 0.9980 chunk 107 optimal weight: 2.9990 chunk 10 optimal weight: 10.0000 chunk 66 optimal weight: 8.9990 chunk 130 optimal weight: 8.9990 chunk 124 optimal weight: 10.0000 chunk 103 optimal weight: 0.9990 chunk 77 optimal weight: 9.9990 chunk 122 optimal weight: 9.9990 chunk 91 optimal weight: 9.9990 chunk 55 optimal weight: 9.9990 overall best weight: 4.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 369 ASN A 424 ASN A 704 ASN A 790 HIS A1155 ASN A1236 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4029 r_free = 0.4029 target = 0.142755 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3694 r_free = 0.3694 target = 0.117612 restraints weight = 77105.893| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3765 r_free = 0.3765 target = 0.122696 restraints weight = 31208.440| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3808 r_free = 0.3808 target = 0.125780 restraints weight = 16682.737| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3835 r_free = 0.3835 target = 0.127737 restraints weight = 10876.016| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3849 r_free = 0.3849 target = 0.128842 restraints weight = 8190.354| |-----------------------------------------------------------------------------| r_work (final): 0.3847 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3847 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3847 r_free = 0.3847 target_work(ls_wunit_k1) = 0.130 | | occupancies: max = 1.00 min = 0.58 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3847 r_free = 0.3847 target_work(ls_wunit_k1) = 0.130 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3847 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7231 moved from start: 0.3012 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 11104 Z= 0.194 Angle : 0.572 4.878 15069 Z= 0.327 Chirality : 0.038 0.164 1772 Planarity : 0.004 0.060 1879 Dihedral : 5.220 80.209 1498 Min Nonbonded Distance : 2.363 Molprobity Statistics. All-atom Clashscore : 6.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.89 % Favored : 95.11 % Rotamer: Outliers : 0.09 % Allowed : 2.49 % Favored : 97.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.64 (0.23), residues: 1371 helix: 1.63 (0.17), residues: 920 sheet: -0.85 (0.63), residues: 55 loop : -2.38 (0.29), residues: 396 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 597 TYR 0.017 0.001 TYR A 991 PHE 0.020 0.002 PHE A1016 TRP 0.008 0.001 TRP A1175 HIS 0.014 0.001 HIS A 790 Details of bonding type rmsd covalent geometry : bond 0.00403 (11103) covalent geometry : angle 0.57091 (15067) SS BOND : bond 0.01911 ( 1) SS BOND : angle 2.93829 ( 2) hydrogen bonds : bond 0.04828 ( 722) hydrogen bonds : angle 4.82641 ( 2160) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2742 Ramachandran restraints generated. 1371 Oldfield, 0 Emsley, 1371 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2742 Ramachandran restraints generated. 1371 Oldfield, 0 Emsley, 1371 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 40 is missing expected H atoms. Skipping. Residue MET 76 is missing expected H atoms. Skipping. Residue VAL 86 is missing expected H atoms. Skipping. Residue LYS 95 is missing expected H atoms. Skipping. Residue VAL 104 is missing expected H atoms. Skipping. Residue TYR 107 is missing expected H atoms. Skipping. Residue LEU 112 is missing expected H atoms. Skipping. Residue VAL 116 is missing expected H atoms. Skipping. Residue LEU 118 is missing expected H atoms. Skipping. Residue TYR 159 is missing expected H atoms. Skipping. Residue ILE 162 is missing expected H atoms. Skipping. Residue TYR 164 is missing expected H atoms. Skipping. Residue THR 179 is missing expected H atoms. Skipping. Residue LYS 192 is missing expected H atoms. Skipping. Residue ILE 200 is missing expected H atoms. Skipping. Residue LEU 497 is missing expected H atoms. Skipping. Residue LEU 525 is missing expected H atoms. Skipping. Residue MET 529 is missing expected H atoms. Skipping. Residue THR 633 is missing expected H atoms. Skipping. Residue LEU 635 is missing expected H atoms. Skipping. Residue LYS 654 is missing expected H atoms. Skipping. Residue LYS 655 is missing expected H atoms. Skipping. Residue ILE 661 is missing expected H atoms. Skipping. Residue LEU 802 is missing expected H atoms. Skipping. Residue LYS 933 is missing expected H atoms. Skipping. Residue MET 962 is missing expected H atoms. Skipping. Residue SER 980 is missing expected H atoms. Skipping. Residue TYR 1281 is missing expected H atoms. Skipping. Residue ILE 1304 is missing expected H atoms. Skipping. Residue SER 1395 is missing expected H atoms. Skipping. Residue LYS 1457 is missing expected H atoms. Skipping. Evaluate side-chains 270 residues out of total 1219 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 269 time to evaluate : 0.487 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: 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: 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 142 GLU cc_start: 0.8569 (tp30) cc_final: 0.7942 (tt0) REVERT: A 219 SER cc_start: 0.8637 (t) cc_final: 0.8297 (p) REVERT: A 226 MET cc_start: 0.7900 (mmm) cc_final: 0.7696 (mmm) REVERT: A 245 LYS cc_start: 0.8389 (mttt) cc_final: 0.8138 (mttt) REVERT: A 298 ASP cc_start: 0.8432 (m-30) cc_final: 0.7916 (m-30) REVERT: A 532 THR cc_start: 0.8351 (m) cc_final: 0.8130 (p) REVERT: A 583 MET cc_start: 0.8949 (tmm) cc_final: 0.8435 (tmm) REVERT: A 698 GLN cc_start: 0.9384 (pm20) cc_final: 0.9048 (pm20) REVERT: A 1178 TYR cc_start: 0.8331 (t80) cc_final: 0.7710 (t80) REVERT: A 1234 GLU cc_start: 0.8714 (tm-30) cc_final: 0.8138 (tm-30) REVERT: A 1379 TRP cc_start: 0.6885 (t-100) cc_final: 0.6334 (t60) outliers start: 1 outliers final: 1 residues processed: 270 average time/residue: 0.1867 time to fit residues: 76.3118 Evaluate side-chains 213 residues out of total 1219 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 212 time to evaluate : 0.568 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 130 optimal weight: 20.0000 chunk 127 optimal weight: 8.9990 chunk 43 optimal weight: 10.0000 chunk 53 optimal weight: 8.9990 chunk 2 optimal weight: 9.9990 chunk 3 optimal weight: 7.9990 chunk 6 optimal weight: 7.9990 chunk 63 optimal weight: 10.0000 chunk 15 optimal weight: 10.0000 chunk 116 optimal weight: 3.9990 chunk 72 optimal weight: 10.0000 overall best weight: 7.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 121 HIS A 369 ASN ** A 424 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 648 ASN A1055 ASN A1070 GLN A1435 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3969 r_free = 0.3969 target = 0.138009 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3620 r_free = 0.3620 target = 0.112663 restraints weight = 78799.680| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3690 r_free = 0.3690 target = 0.117409 restraints weight = 32605.892| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3730 r_free = 0.3730 target = 0.120294 restraints weight = 17832.856| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3755 r_free = 0.3755 target = 0.122076 restraints weight = 11892.809| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3768 r_free = 0.3768 target = 0.123112 restraints weight = 9184.787| |-----------------------------------------------------------------------------| r_work (final): 0.3785 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3785 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3785 r_free = 0.3785 target_work(ls_wunit_k1) = 0.125 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3785 r_free = 0.3785 target_work(ls_wunit_k1) = 0.125 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3785 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7381 moved from start: 0.3926 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.050 11104 Z= 0.272 Angle : 0.643 8.729 15069 Z= 0.368 Chirality : 0.039 0.168 1772 Planarity : 0.004 0.068 1879 Dihedral : 5.307 76.638 1498 Min Nonbonded Distance : 2.339 Molprobity Statistics. All-atom Clashscore : 8.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.93 % Favored : 93.07 % Rotamer: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.06 (0.22), residues: 1371 helix: 1.01 (0.17), residues: 922 sheet: -0.99 (0.61), residues: 64 loop : -2.49 (0.30), residues: 385 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A1228 TYR 0.022 0.002 TYR A 991 PHE 0.048 0.002 PHE A 996 TRP 0.010 0.001 TRP A 427 HIS 0.008 0.001 HIS A 364 Details of bonding type rmsd covalent geometry : bond 0.00555 (11103) covalent geometry : angle 0.64124 (15067) SS BOND : bond 0.00917 ( 1) SS BOND : angle 3.65164 ( 2) hydrogen bonds : bond 0.05253 ( 722) hydrogen bonds : angle 5.22457 ( 2160) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2742 Ramachandran restraints generated. 1371 Oldfield, 0 Emsley, 1371 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2742 Ramachandran restraints generated. 1371 Oldfield, 0 Emsley, 1371 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 40 is missing expected H atoms. Skipping. Residue MET 76 is missing expected H atoms. Skipping. Residue VAL 86 is missing expected H atoms. Skipping. Residue LYS 95 is missing expected H atoms. Skipping. Residue VAL 104 is missing expected H atoms. Skipping. Residue TYR 107 is missing expected H atoms. Skipping. Residue LEU 112 is missing expected H atoms. Skipping. Residue VAL 116 is missing expected H atoms. Skipping. Residue LEU 118 is missing expected H atoms. Skipping. Residue TYR 159 is missing expected H atoms. Skipping. Residue ILE 162 is missing expected H atoms. Skipping. Residue TYR 164 is missing expected H atoms. Skipping. Residue THR 179 is missing expected H atoms. Skipping. Residue LYS 192 is missing expected H atoms. Skipping. Residue ILE 200 is missing expected H atoms. Skipping. Residue LEU 497 is missing expected H atoms. Skipping. Residue LEU 525 is missing expected H atoms. Skipping. Residue MET 529 is missing expected H atoms. Skipping. Residue THR 633 is missing expected H atoms. Skipping. Residue LEU 635 is missing expected H atoms. Skipping. Residue LYS 654 is missing expected H atoms. Skipping. Residue LYS 655 is missing expected H atoms. Skipping. Residue ILE 661 is missing expected H atoms. Skipping. Residue LEU 802 is missing expected H atoms. Skipping. Residue LYS 933 is missing expected H atoms. Skipping. Residue MET 962 is missing expected H atoms. Skipping. Residue SER 980 is missing expected H atoms. Skipping. Residue TYR 1281 is missing expected H atoms. Skipping. Residue ILE 1304 is missing expected H atoms. Skipping. Residue SER 1395 is missing expected H atoms. Skipping. Residue LYS 1457 is missing expected H atoms. Skipping. Evaluate side-chains 252 residues out of total 1219 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 252 time to evaluate : 0.563 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: 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 27 ASP cc_start: 0.8915 (t70) cc_final: 0.8591 (t0) REVERT: A 142 GLU cc_start: 0.8526 (tp30) cc_final: 0.7948 (tt0) REVERT: A 245 LYS cc_start: 0.8547 (mttt) cc_final: 0.8293 (mttt) REVERT: A 298 ASP cc_start: 0.8568 (m-30) cc_final: 0.8147 (m-30) REVERT: A 532 THR cc_start: 0.8489 (m) cc_final: 0.8285 (p) REVERT: A 579 MET cc_start: 0.5529 (tpt) cc_final: 0.5326 (tpt) REVERT: A 583 MET cc_start: 0.8924 (tmm) cc_final: 0.8488 (tmm) REVERT: A 698 GLN cc_start: 0.9442 (pm20) cc_final: 0.8873 (pm20) REVERT: A 967 MET cc_start: 0.7830 (mmt) cc_final: 0.7299 (mpp) REVERT: A 1234 GLU cc_start: 0.8751 (tm-30) cc_final: 0.8272 (tm-30) REVERT: A 1472 MET cc_start: 0.5714 (mmm) cc_final: 0.5483 (mmm) outliers start: 0 outliers final: 0 residues processed: 252 average time/residue: 0.1760 time to fit residues: 68.8667 Evaluate side-chains 201 residues out of total 1219 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 201 time to evaluate : 0.547 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 102 optimal weight: 7.9990 chunk 48 optimal weight: 7.9990 chunk 15 optimal weight: 9.9990 chunk 108 optimal weight: 0.7980 chunk 123 optimal weight: 6.9990 chunk 24 optimal weight: 0.9980 chunk 59 optimal weight: 10.0000 chunk 84 optimal weight: 20.0000 chunk 90 optimal weight: 4.9990 chunk 111 optimal weight: 2.9990 chunk 64 optimal weight: 3.9990 overall best weight: 2.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 424 ASN A 928 HIS A1055 ASN A1435 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4006 r_free = 0.4006 target = 0.140847 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3676 r_free = 0.3676 target = 0.116119 restraints weight = 78513.610| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3743 r_free = 0.3743 target = 0.120814 restraints weight = 33260.432| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3783 r_free = 0.3783 target = 0.123690 restraints weight = 18409.898| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3805 r_free = 0.3805 target = 0.125487 restraints weight = 12346.715| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3822 r_free = 0.3822 target = 0.126693 restraints weight = 9518.203| |-----------------------------------------------------------------------------| r_work (final): 0.3822 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3821 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3821 r_free = 0.3821 target_work(ls_wunit_k1) = 0.127 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3821 r_free = 0.3821 target_work(ls_wunit_k1) = 0.127 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3821 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7250 moved from start: 0.3982 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 11104 Z= 0.131 Angle : 0.512 5.613 15069 Z= 0.289 Chirality : 0.037 0.154 1772 Planarity : 0.004 0.064 1879 Dihedral : 5.045 77.456 1498 Min Nonbonded Distance : 2.400 Molprobity Statistics. All-atom Clashscore : 6.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.13 % Favored : 93.87 % Rotamer: Outliers : 0.00 % Allowed : 2.06 % Favored : 97.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.35 (0.23), residues: 1371 helix: 1.37 (0.17), residues: 923 sheet: -0.96 (0.61), residues: 63 loop : -2.42 (0.30), residues: 385 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 207 TYR 0.027 0.002 TYR A1109 PHE 0.046 0.002 PHE A 996 TRP 0.010 0.001 TRP A 277 HIS 0.004 0.001 HIS A 928 Details of bonding type rmsd covalent geometry : bond 0.00267 (11103) covalent geometry : angle 0.51114 (15067) SS BOND : bond 0.00449 ( 1) SS BOND : angle 1.96802 ( 2) hydrogen bonds : bond 0.04819 ( 722) hydrogen bonds : angle 4.70110 ( 2160) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2742 Ramachandran restraints generated. 1371 Oldfield, 0 Emsley, 1371 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2742 Ramachandran restraints generated. 1371 Oldfield, 0 Emsley, 1371 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 40 is missing expected H atoms. Skipping. Residue MET 76 is missing expected H atoms. Skipping. Residue VAL 86 is missing expected H atoms. Skipping. Residue LYS 95 is missing expected H atoms. Skipping. Residue VAL 104 is missing expected H atoms. Skipping. Residue TYR 107 is missing expected H atoms. Skipping. Residue LEU 112 is missing expected H atoms. Skipping. Residue VAL 116 is missing expected H atoms. Skipping. Residue LEU 118 is missing expected H atoms. Skipping. Residue TYR 159 is missing expected H atoms. Skipping. Residue ILE 162 is missing expected H atoms. Skipping. Residue TYR 164 is missing expected H atoms. Skipping. Residue THR 179 is missing expected H atoms. Skipping. Residue LYS 192 is missing expected H atoms. Skipping. Residue ILE 200 is missing expected H atoms. Skipping. Residue LEU 497 is missing expected H atoms. Skipping. Residue LEU 525 is missing expected H atoms. Skipping. Residue MET 529 is missing expected H atoms. Skipping. Residue THR 633 is missing expected H atoms. Skipping. Residue LEU 635 is missing expected H atoms. Skipping. Residue LYS 654 is missing expected H atoms. Skipping. Residue LYS 655 is missing expected H atoms. Skipping. Residue ILE 661 is missing expected H atoms. Skipping. Residue LEU 802 is missing expected H atoms. Skipping. Residue LYS 933 is missing expected H atoms. Skipping. Residue MET 962 is missing expected H atoms. Skipping. Residue SER 980 is missing expected H atoms. Skipping. Residue TYR 1281 is missing expected H atoms. Skipping. Residue ILE 1304 is missing expected H atoms. Skipping. Residue SER 1395 is missing expected H atoms. Skipping. Residue LYS 1457 is missing expected H atoms. Skipping. Evaluate side-chains 265 residues out of total 1219 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 265 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: 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: 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: symmetry clash revert: symmetry clash REVERT: A 27 ASP cc_start: 0.8867 (t70) cc_final: 0.8457 (t0) REVERT: A 142 GLU cc_start: 0.8471 (tp30) cc_final: 0.8198 (mm-30) REVERT: A 245 LYS cc_start: 0.8369 (mttt) cc_final: 0.8115 (mttt) REVERT: A 298 ASP cc_start: 0.8473 (m-30) cc_final: 0.8060 (m-30) REVERT: A 502 TRP cc_start: 0.7721 (m-10) cc_final: 0.7499 (m-10) REVERT: A 532 THR cc_start: 0.8419 (m) cc_final: 0.8212 (p) REVERT: A 583 MET cc_start: 0.8881 (tmm) cc_final: 0.8306 (tmm) REVERT: A 698 GLN cc_start: 0.9422 (pm20) cc_final: 0.8850 (pm20) REVERT: A 967 MET cc_start: 0.7747 (mmt) cc_final: 0.7103 (mmt) REVERT: A 1029 MET cc_start: 0.7544 (tpt) cc_final: 0.7196 (tpt) REVERT: A 1178 TYR cc_start: 0.8355 (t80) cc_final: 0.8029 (t80) REVERT: A 1234 GLU cc_start: 0.8678 (tm-30) cc_final: 0.8199 (tm-30) REVERT: A 1373 TYR cc_start: 0.7137 (t80) cc_final: 0.6800 (t80) REVERT: A 1473 ASP cc_start: 0.8504 (t0) cc_final: 0.7958 (p0) outliers start: 0 outliers final: 0 residues processed: 265 average time/residue: 0.1873 time to fit residues: 74.6953 Evaluate side-chains 212 residues out of total 1219 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 212 time to evaluate : 0.501 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 104 optimal weight: 0.7980 chunk 29 optimal weight: 5.9990 chunk 136 optimal weight: 9.9990 chunk 62 optimal weight: 20.0000 chunk 95 optimal weight: 10.0000 chunk 23 optimal weight: 6.9990 chunk 54 optimal weight: 2.9990 chunk 41 optimal weight: 10.0000 chunk 42 optimal weight: 0.9990 chunk 79 optimal weight: 9.9990 chunk 6 optimal weight: 10.0000 overall best weight: 3.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 210 ASN A 424 ASN A1055 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3994 r_free = 0.3994 target = 0.139996 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3656 r_free = 0.3656 target = 0.114941 restraints weight = 77521.385| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3725 r_free = 0.3725 target = 0.119776 restraints weight = 32058.141| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3767 r_free = 0.3767 target = 0.122822 restraints weight = 17514.528| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3791 r_free = 0.3791 target = 0.124699 restraints weight = 11538.531| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 42)----------------| | r_work = 0.3810 r_free = 0.3810 target = 0.125943 restraints weight = 8832.574| |-----------------------------------------------------------------------------| r_work (final): 0.3816 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3817 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3817 r_free = 0.3817 target_work(ls_wunit_k1) = 0.127 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3817 r_free = 0.3817 target_work(ls_wunit_k1) = 0.127 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3817 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7291 moved from start: 0.4194 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 11104 Z= 0.152 Angle : 0.525 5.335 15069 Z= 0.295 Chirality : 0.037 0.160 1772 Planarity : 0.004 0.063 1879 Dihedral : 4.962 77.203 1498 Min Nonbonded Distance : 2.291 Molprobity Statistics. All-atom Clashscore : 7.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.00 % Favored : 93.00 % Rotamer: Outliers : 0.09 % Allowed : 1.29 % Favored : 98.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.47 (0.23), residues: 1371 helix: 1.47 (0.17), residues: 923 sheet: -0.91 (0.61), residues: 64 loop : -2.41 (0.30), residues: 384 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A1228 TYR 0.022 0.001 TYR A 991 PHE 0.053 0.002 PHE A 996 TRP 0.011 0.001 TRP A 636 HIS 0.003 0.001 HIS A 297 Details of bonding type rmsd covalent geometry : bond 0.00315 (11103) covalent geometry : angle 0.52370 (15067) SS BOND : bond 0.01076 ( 1) SS BOND : angle 2.56489 ( 2) hydrogen bonds : bond 0.04699 ( 722) hydrogen bonds : angle 4.70575 ( 2160) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2742 Ramachandran restraints generated. 1371 Oldfield, 0 Emsley, 1371 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2742 Ramachandran restraints generated. 1371 Oldfield, 0 Emsley, 1371 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 40 is missing expected H atoms. Skipping. Residue MET 76 is missing expected H atoms. Skipping. Residue VAL 86 is missing expected H atoms. Skipping. Residue LYS 95 is missing expected H atoms. Skipping. Residue VAL 104 is missing expected H atoms. Skipping. Residue TYR 107 is missing expected H atoms. Skipping. Residue LEU 112 is missing expected H atoms. Skipping. Residue VAL 116 is missing expected H atoms. Skipping. Residue LEU 118 is missing expected H atoms. Skipping. Residue TYR 159 is missing expected H atoms. Skipping. Residue ILE 162 is missing expected H atoms. Skipping. Residue TYR 164 is missing expected H atoms. Skipping. Residue THR 179 is missing expected H atoms. Skipping. Residue LYS 192 is missing expected H atoms. Skipping. Residue ILE 200 is missing expected H atoms. Skipping. Residue LEU 497 is missing expected H atoms. Skipping. Residue LEU 525 is missing expected H atoms. Skipping. Residue MET 529 is missing expected H atoms. Skipping. Residue THR 633 is missing expected H atoms. Skipping. Residue LEU 635 is missing expected H atoms. Skipping. Residue LYS 654 is missing expected H atoms. Skipping. Residue LYS 655 is missing expected H atoms. Skipping. Residue ILE 661 is missing expected H atoms. Skipping. Residue LEU 802 is missing expected H atoms. Skipping. Residue LYS 933 is missing expected H atoms. Skipping. Residue MET 962 is missing expected H atoms. Skipping. Residue SER 980 is missing expected H atoms. Skipping. Residue TYR 1281 is missing expected H atoms. Skipping. Residue ILE 1304 is missing expected H atoms. Skipping. Residue SER 1395 is missing expected H atoms. Skipping. Residue LYS 1457 is missing expected H atoms. Skipping. Evaluate side-chains 276 residues out of total 1219 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 275 time to evaluate : 0.559 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: 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: 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 27 ASP cc_start: 0.8928 (t70) cc_final: 0.8532 (t0) REVERT: A 142 GLU cc_start: 0.8502 (tp30) cc_final: 0.8037 (mm-30) REVERT: A 298 ASP cc_start: 0.8428 (m-30) cc_final: 0.8090 (m-30) REVERT: A 583 MET cc_start: 0.8874 (tmm) cc_final: 0.8382 (tmm) REVERT: A 698 GLN cc_start: 0.9436 (pm20) cc_final: 0.8849 (pm20) REVERT: A 967 MET cc_start: 0.7852 (mmt) cc_final: 0.7366 (mmt) REVERT: A 1178 TYR cc_start: 0.8411 (t80) cc_final: 0.8089 (t80) REVERT: A 1234 GLU cc_start: 0.8669 (tm-30) cc_final: 0.8195 (tm-30) REVERT: A 1473 ASP cc_start: 0.8415 (t0) cc_final: 0.7914 (p0) outliers start: 1 outliers final: 0 residues processed: 276 average time/residue: 0.1814 time to fit residues: 76.1921 Evaluate side-chains 214 residues out of total 1219 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 214 time to evaluate : 0.563 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 14 optimal weight: 10.0000 chunk 119 optimal weight: 9.9990 chunk 45 optimal weight: 4.9990 chunk 31 optimal weight: 4.9990 chunk 8 optimal weight: 10.0000 chunk 100 optimal weight: 8.9990 chunk 56 optimal weight: 5.9990 chunk 33 optimal weight: 5.9990 chunk 21 optimal weight: 8.9990 chunk 77 optimal weight: 7.9990 chunk 90 optimal weight: 10.0000 overall best weight: 5.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 210 ASN A 424 ASN ** A1366 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1390 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 = 0.3964 r_free = 0.3964 target = 0.138425 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3620 r_free = 0.3620 target = 0.113524 restraints weight = 79357.503| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3690 r_free = 0.3690 target = 0.118279 restraints weight = 33083.281| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3732 r_free = 0.3732 target = 0.121212 restraints weight = 18129.218| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3754 r_free = 0.3754 target = 0.122943 restraints weight = 12011.918| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3773 r_free = 0.3773 target = 0.124182 restraints weight = 9271.072| |-----------------------------------------------------------------------------| r_work (final): 0.3784 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3784 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3784 r_free = 0.3784 target_work(ls_wunit_k1) = 0.125 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3784 r_free = 0.3784 target_work(ls_wunit_k1) = 0.125 | | occupancies: max = 1.00 min = 0.30 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3784 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7388 moved from start: 0.4490 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 11104 Z= 0.219 Angle : 0.574 6.967 15069 Z= 0.330 Chirality : 0.038 0.166 1772 Planarity : 0.004 0.064 1879 Dihedral : 5.073 75.448 1498 Min Nonbonded Distance : 2.221 Molprobity Statistics. All-atom Clashscore : 8.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.95 % Favored : 92.05 % Rotamer: Outliers : 0.09 % Allowed : 1.20 % Favored : 98.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.20 (0.23), residues: 1371 helix: 1.23 (0.17), residues: 922 sheet: -0.93 (0.62), residues: 64 loop : -2.44 (0.30), residues: 385 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 638 TYR 0.022 0.002 TYR A 991 PHE 0.052 0.002 PHE A 996 TRP 0.009 0.001 TRP A 277 HIS 0.004 0.001 HIS A1390 Details of bonding type rmsd covalent geometry : bond 0.00448 (11103) covalent geometry : angle 0.57341 (15067) SS BOND : bond 0.00440 ( 1) SS BOND : angle 2.26411 ( 2) hydrogen bonds : bond 0.04950 ( 722) hydrogen bonds : angle 5.00375 ( 2160) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2742 Ramachandran restraints generated. 1371 Oldfield, 0 Emsley, 1371 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2742 Ramachandran restraints generated. 1371 Oldfield, 0 Emsley, 1371 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 40 is missing expected H atoms. Skipping. Residue MET 76 is missing expected H atoms. Skipping. Residue VAL 86 is missing expected H atoms. Skipping. Residue LYS 95 is missing expected H atoms. Skipping. Residue VAL 104 is missing expected H atoms. Skipping. Residue TYR 107 is missing expected H atoms. Skipping. Residue LEU 112 is missing expected H atoms. Skipping. Residue VAL 116 is missing expected H atoms. Skipping. Residue LEU 118 is missing expected H atoms. Skipping. Residue TYR 159 is missing expected H atoms. Skipping. Residue ILE 162 is missing expected H atoms. Skipping. Residue TYR 164 is missing expected H atoms. Skipping. Residue THR 179 is missing expected H atoms. Skipping. Residue LYS 192 is missing expected H atoms. Skipping. Residue ILE 200 is missing expected H atoms. Skipping. Residue LEU 497 is missing expected H atoms. Skipping. Residue LEU 525 is missing expected H atoms. Skipping. Residue MET 529 is missing expected H atoms. Skipping. Residue THR 633 is missing expected H atoms. Skipping. Residue LEU 635 is missing expected H atoms. Skipping. Residue LYS 654 is missing expected H atoms. Skipping. Residue LYS 655 is missing expected H atoms. Skipping. Residue ILE 661 is missing expected H atoms. Skipping. Residue LEU 802 is missing expected H atoms. Skipping. Residue LYS 933 is missing expected H atoms. Skipping. Residue MET 962 is missing expected H atoms. Skipping. Residue SER 980 is missing expected H atoms. Skipping. Residue TYR 1281 is missing expected H atoms. Skipping. Residue ILE 1304 is missing expected H atoms. Skipping. Residue SER 1395 is missing expected H atoms. Skipping. Residue LYS 1457 is missing expected H atoms. Skipping. Evaluate side-chains 262 residues out of total 1219 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 261 time to evaluate : 0.523 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: 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 27 ASP cc_start: 0.9015 (t70) cc_final: 0.8678 (t0) REVERT: A 138 TYR cc_start: 0.8326 (t80) cc_final: 0.7422 (t80) REVERT: A 142 GLU cc_start: 0.8555 (tp30) cc_final: 0.8030 (tp30) REVERT: A 298 ASP cc_start: 0.8454 (m-30) cc_final: 0.8142 (m-30) REVERT: A 583 MET cc_start: 0.8846 (tmm) cc_final: 0.8346 (tmm) REVERT: A 698 GLN cc_start: 0.9442 (pm20) cc_final: 0.8789 (pm20) REVERT: A 967 MET cc_start: 0.7932 (mmt) cc_final: 0.7535 (mmt) REVERT: A 1029 MET cc_start: 0.7802 (tpt) cc_final: 0.7364 (tpt) REVERT: A 1234 GLU cc_start: 0.8699 (tm-30) cc_final: 0.8250 (tm-30) outliers start: 1 outliers final: 0 residues processed: 262 average time/residue: 0.1861 time to fit residues: 74.6257 Evaluate side-chains 210 residues out of total 1219 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 210 time to evaluate : 0.604 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 28 optimal weight: 5.9990 chunk 128 optimal weight: 8.9990 chunk 64 optimal weight: 10.0000 chunk 87 optimal weight: 8.9990 chunk 109 optimal weight: 4.9990 chunk 22 optimal weight: 3.9990 chunk 91 optimal weight: 7.9990 chunk 114 optimal weight: 0.7980 chunk 17 optimal weight: 6.9990 chunk 62 optimal weight: 20.0000 chunk 77 optimal weight: 5.9990 overall best weight: 4.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 210 ASN A 424 ASN ** A1366 ASN ** 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 = 0.3956 r_free = 0.3956 target = 0.138491 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3616 r_free = 0.3616 target = 0.113815 restraints weight = 79162.362| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3686 r_free = 0.3686 target = 0.118639 restraints weight = 32569.425| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3728 r_free = 0.3728 target = 0.121614 restraints weight = 17673.656| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3754 r_free = 0.3754 target = 0.123549 restraints weight = 11638.730| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3767 r_free = 0.3767 target = 0.124632 restraints weight = 8778.004| |-----------------------------------------------------------------------------| r_work (final): 0.3781 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3776 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3776 r_free = 0.3776 target_work(ls_wunit_k1) = 0.125 | | occupancies: max = 1.00 min = 0.30 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3776 r_free = 0.3776 target_work(ls_wunit_k1) = 0.125 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.3776 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7344 moved from start: 0.4607 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 11104 Z= 0.167 Angle : 0.535 5.525 15069 Z= 0.303 Chirality : 0.037 0.157 1772 Planarity : 0.004 0.064 1879 Dihedral : 4.997 75.052 1498 Min Nonbonded Distance : 2.257 Molprobity Statistics. All-atom Clashscore : 8.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.44 % Favored : 92.56 % Rotamer: Outliers : 0.09 % Allowed : 0.94 % Favored : 98.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.31 (0.23), residues: 1371 helix: 1.29 (0.17), residues: 921 sheet: -0.80 (0.64), residues: 62 loop : -2.34 (0.30), residues: 388 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 207 TYR 0.022 0.002 TYR A 991 PHE 0.052 0.002 PHE A 996 TRP 0.010 0.001 TRP A 277 HIS 0.003 0.001 HIS A 297 Details of bonding type rmsd covalent geometry : bond 0.00343 (11103) covalent geometry : angle 0.53461 (15067) SS BOND : bond 0.00321 ( 1) SS BOND : angle 1.65542 ( 2) hydrogen bonds : bond 0.04804 ( 722) hydrogen bonds : angle 4.79722 ( 2160) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2742 Ramachandran restraints generated. 1371 Oldfield, 0 Emsley, 1371 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2742 Ramachandran restraints generated. 1371 Oldfield, 0 Emsley, 1371 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 40 is missing expected H atoms. Skipping. Residue MET 76 is missing expected H atoms. Skipping. Residue VAL 86 is missing expected H atoms. Skipping. Residue LYS 95 is missing expected H atoms. Skipping. Residue VAL 104 is missing expected H atoms. Skipping. Residue TYR 107 is missing expected H atoms. Skipping. Residue LEU 112 is missing expected H atoms. Skipping. Residue VAL 116 is missing expected H atoms. Skipping. Residue LEU 118 is missing expected H atoms. Skipping. Residue TYR 159 is missing expected H atoms. Skipping. Residue ILE 162 is missing expected H atoms. Skipping. Residue TYR 164 is missing expected H atoms. Skipping. Residue THR 179 is missing expected H atoms. Skipping. Residue LYS 192 is missing expected H atoms. Skipping. Residue ILE 200 is missing expected H atoms. Skipping. Residue LEU 497 is missing expected H atoms. Skipping. Residue LEU 525 is missing expected H atoms. Skipping. Residue MET 529 is missing expected H atoms. Skipping. Residue THR 633 is missing expected H atoms. Skipping. Residue LEU 635 is missing expected H atoms. Skipping. Residue LYS 654 is missing expected H atoms. Skipping. Residue LYS 655 is missing expected H atoms. Skipping. Residue ILE 661 is missing expected H atoms. Skipping. Residue LEU 802 is missing expected H atoms. Skipping. Residue LYS 933 is missing expected H atoms. Skipping. Residue MET 962 is missing expected H atoms. Skipping. Residue SER 980 is missing expected H atoms. Skipping. Residue TYR 1281 is missing expected H atoms. Skipping. Residue ILE 1304 is missing expected H atoms. Skipping. Residue SER 1395 is missing expected H atoms. Skipping. Residue LYS 1457 is missing expected H atoms. Skipping. Evaluate side-chains 266 residues out of total 1219 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 265 time to evaluate : 0.544 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: 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: 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 27 ASP cc_start: 0.9026 (t70) cc_final: 0.8694 (t0) REVERT: A 138 TYR cc_start: 0.8383 (t80) cc_final: 0.7486 (t80) REVERT: A 142 GLU cc_start: 0.8558 (tp30) cc_final: 0.8012 (tp30) REVERT: A 298 ASP cc_start: 0.8334 (m-30) cc_final: 0.8098 (m-30) REVERT: A 418 ASP cc_start: 0.8903 (t0) cc_final: 0.8693 (t70) REVERT: A 583 MET cc_start: 0.8809 (tmm) cc_final: 0.8434 (tmm) REVERT: A 698 GLN cc_start: 0.9486 (pm20) cc_final: 0.8865 (pm20) REVERT: A 967 MET cc_start: 0.7923 (mmt) cc_final: 0.7346 (mmt) REVERT: A 1004 LEU cc_start: 0.9037 (tt) cc_final: 0.8818 (tt) REVERT: A 1029 MET cc_start: 0.7718 (tpt) cc_final: 0.7349 (tpt) REVERT: A 1178 TYR cc_start: 0.8530 (t80) cc_final: 0.8133 (t80) REVERT: A 1234 GLU cc_start: 0.8609 (tm-30) cc_final: 0.8090 (tm-30) outliers start: 1 outliers final: 0 residues processed: 266 average time/residue: 0.1823 time to fit residues: 73.8706 Evaluate side-chains 209 residues out of total 1219 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 209 time to evaluate : 0.473 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 62 optimal weight: 7.9990 chunk 98 optimal weight: 8.9990 chunk 19 optimal weight: 4.9990 chunk 4 optimal weight: 10.0000 chunk 68 optimal weight: 6.9990 chunk 11 optimal weight: 4.9990 chunk 107 optimal weight: 0.9990 chunk 86 optimal weight: 1.9990 chunk 135 optimal weight: 3.9990 chunk 137 optimal weight: 5.9990 chunk 78 optimal weight: 7.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 210 ASN A 424 ASN ** A1366 ASN ** 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 = 0.3971 r_free = 0.3971 target = 0.139604 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3633 r_free = 0.3633 target = 0.114951 restraints weight = 78601.625| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3702 r_free = 0.3702 target = 0.119696 restraints weight = 33581.746| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3743 r_free = 0.3743 target = 0.122690 restraints weight = 18571.162| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.3770 r_free = 0.3770 target = 0.124551 restraints weight = 12334.179| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3783 r_free = 0.3783 target = 0.125613 restraints weight = 9462.024| |-----------------------------------------------------------------------------| r_work (final): 0.3785 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3788 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3788 r_free = 0.3788 target_work(ls_wunit_k1) = 0.126 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3788 r_free = 0.3788 target_work(ls_wunit_k1) = 0.126 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.3788 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7267 moved from start: 0.4704 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 11104 Z= 0.146 Angle : 0.526 6.479 15069 Z= 0.294 Chirality : 0.037 0.158 1772 Planarity : 0.005 0.158 1879 Dihedral : 4.949 74.783 1498 Min Nonbonded Distance : 2.258 Molprobity Statistics. All-atom Clashscore : 8.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.37 % Favored : 92.63 % Rotamer: Outliers : 0.09 % Allowed : 1.29 % Favored : 98.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.44 (0.23), residues: 1371 helix: 1.40 (0.17), residues: 921 sheet: -0.84 (0.62), residues: 62 loop : -2.30 (0.31), residues: 388 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A1143 TYR 0.023 0.001 TYR A 991 PHE 0.049 0.001 PHE A 996 TRP 0.011 0.001 TRP A 225 HIS 0.002 0.001 HIS A1390 Details of bonding type rmsd covalent geometry : bond 0.00297 (11103) covalent geometry : angle 0.52539 (15067) SS BOND : bond 0.00299 ( 1) SS BOND : angle 1.48510 ( 2) hydrogen bonds : bond 0.04694 ( 722) hydrogen bonds : angle 4.70768 ( 2160) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2742 Ramachandran restraints generated. 1371 Oldfield, 0 Emsley, 1371 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2742 Ramachandran restraints generated. 1371 Oldfield, 0 Emsley, 1371 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 40 is missing expected H atoms. Skipping. Residue MET 76 is missing expected H atoms. Skipping. Residue VAL 86 is missing expected H atoms. Skipping. Residue LYS 95 is missing expected H atoms. Skipping. Residue VAL 104 is missing expected H atoms. Skipping. Residue TYR 107 is missing expected H atoms. Skipping. Residue LEU 112 is missing expected H atoms. Skipping. Residue VAL 116 is missing expected H atoms. Skipping. Residue LEU 118 is missing expected H atoms. Skipping. Residue TYR 159 is missing expected H atoms. Skipping. Residue ILE 162 is missing expected H atoms. Skipping. Residue TYR 164 is missing expected H atoms. Skipping. Residue THR 179 is missing expected H atoms. Skipping. Residue LYS 192 is missing expected H atoms. Skipping. Residue ILE 200 is missing expected H atoms. Skipping. Residue LEU 497 is missing expected H atoms. Skipping. Residue LEU 525 is missing expected H atoms. Skipping. Residue MET 529 is missing expected H atoms. Skipping. Residue THR 633 is missing expected H atoms. Skipping. Residue LEU 635 is missing expected H atoms. Skipping. Residue LYS 654 is missing expected H atoms. Skipping. Residue LYS 655 is missing expected H atoms. Skipping. Residue ILE 661 is missing expected H atoms. Skipping. Residue LEU 802 is missing expected H atoms. Skipping. Residue LYS 933 is missing expected H atoms. Skipping. Residue MET 962 is missing expected H atoms. Skipping. Residue SER 980 is missing expected H atoms. Skipping. Residue TYR 1281 is missing expected H atoms. Skipping. Residue ILE 1304 is missing expected H atoms. Skipping. Residue SER 1395 is missing expected H atoms. Skipping. Residue LYS 1457 is missing expected H atoms. Skipping. Evaluate side-chains 262 residues out of total 1219 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 261 time to evaluate : 0.582 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: 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: 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 27 ASP cc_start: 0.9022 (t70) cc_final: 0.8634 (t0) REVERT: A 138 TYR cc_start: 0.8379 (t80) cc_final: 0.7512 (t80) REVERT: A 142 GLU cc_start: 0.8530 (tp30) cc_final: 0.7993 (tp30) REVERT: A 180 CYS cc_start: 0.8973 (m) cc_final: 0.8503 (m) REVERT: A 298 ASP cc_start: 0.8411 (m-30) cc_final: 0.8103 (m-30) REVERT: A 418 ASP cc_start: 0.8920 (t0) cc_final: 0.8709 (t70) REVERT: A 583 MET cc_start: 0.8756 (tmm) cc_final: 0.8360 (tmm) REVERT: A 698 GLN cc_start: 0.9486 (pm20) cc_final: 0.8895 (pm20) REVERT: A 850 LYS cc_start: 0.8140 (ptpt) cc_final: 0.7611 (tmtt) REVERT: A 967 MET cc_start: 0.7783 (mmt) cc_final: 0.7356 (mmt) REVERT: A 1178 TYR cc_start: 0.8386 (t80) cc_final: 0.8093 (t80) REVERT: A 1234 GLU cc_start: 0.8659 (tm-30) cc_final: 0.8145 (tm-30) REVERT: A 1243 ILE cc_start: 0.9232 (tp) cc_final: 0.8915 (tp) REVERT: A 1473 ASP cc_start: 0.8474 (t0) cc_final: 0.8109 (p0) outliers start: 1 outliers final: 0 residues processed: 262 average time/residue: 0.1887 time to fit residues: 75.0201 Evaluate side-chains 214 residues out of total 1219 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 214 time to evaluate : 0.522 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 33 optimal weight: 6.9990 chunk 50 optimal weight: 5.9990 chunk 29 optimal weight: 0.7980 chunk 3 optimal weight: 6.9990 chunk 19 optimal weight: 5.9990 chunk 122 optimal weight: 10.0000 chunk 23 optimal weight: 6.9990 chunk 112 optimal weight: 2.9990 chunk 111 optimal weight: 4.9990 chunk 121 optimal weight: 8.9990 chunk 99 optimal weight: 7.9990 overall best weight: 4.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 210 ASN A 424 ASN ** A1366 ASN ** 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 = 0.3971 r_free = 0.3971 target = 0.139593 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3633 r_free = 0.3633 target = 0.114883 restraints weight = 78630.329| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3700 r_free = 0.3700 target = 0.119572 restraints weight = 33131.918| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3740 r_free = 0.3740 target = 0.122452 restraints weight = 18344.245| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3762 r_free = 0.3762 target = 0.124204 restraints weight = 12281.575| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3778 r_free = 0.3778 target = 0.125409 restraints weight = 9523.272| |-----------------------------------------------------------------------------| r_work (final): 0.3785 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3784 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3784 r_free = 0.3784 target_work(ls_wunit_k1) = 0.125 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3784 r_free = 0.3784 target_work(ls_wunit_k1) = 0.125 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.3784 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7285 moved from start: 0.4863 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 11104 Z= 0.165 Angle : 0.541 5.672 15069 Z= 0.305 Chirality : 0.037 0.162 1772 Planarity : 0.004 0.107 1879 Dihedral : 4.941 73.957 1498 Min Nonbonded Distance : 2.250 Molprobity Statistics. All-atom Clashscore : 8.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.73 % Favored : 92.27 % Rotamer: Outliers : 0.09 % Allowed : 0.77 % Favored : 99.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.38 (0.23), residues: 1371 helix: 1.38 (0.17), residues: 920 sheet: -0.90 (0.63), residues: 62 loop : -2.35 (0.31), residues: 389 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A1143 TYR 0.023 0.002 TYR A 991 PHE 0.050 0.002 PHE A 996 TRP 0.013 0.001 TRP A1175 HIS 0.003 0.001 HIS A1390 Details of bonding type rmsd covalent geometry : bond 0.00338 (11103) covalent geometry : angle 0.54130 (15067) SS BOND : bond 0.00238 ( 1) SS BOND : angle 1.32513 ( 2) hydrogen bonds : bond 0.04716 ( 722) hydrogen bonds : angle 4.76300 ( 2160) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2742 Ramachandran restraints generated. 1371 Oldfield, 0 Emsley, 1371 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2742 Ramachandran restraints generated. 1371 Oldfield, 0 Emsley, 1371 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 40 is missing expected H atoms. Skipping. Residue MET 76 is missing expected H atoms. Skipping. Residue VAL 86 is missing expected H atoms. Skipping. Residue LYS 95 is missing expected H atoms. Skipping. Residue VAL 104 is missing expected H atoms. Skipping. Residue TYR 107 is missing expected H atoms. Skipping. Residue LEU 112 is missing expected H atoms. Skipping. Residue VAL 116 is missing expected H atoms. Skipping. Residue LEU 118 is missing expected H atoms. Skipping. Residue TYR 159 is missing expected H atoms. Skipping. Residue ILE 162 is missing expected H atoms. Skipping. Residue TYR 164 is missing expected H atoms. Skipping. Residue THR 179 is missing expected H atoms. Skipping. Residue LYS 192 is missing expected H atoms. Skipping. Residue ILE 200 is missing expected H atoms. Skipping. Residue LEU 497 is missing expected H atoms. Skipping. Residue LEU 525 is missing expected H atoms. Skipping. Residue MET 529 is missing expected H atoms. Skipping. Residue THR 633 is missing expected H atoms. Skipping. Residue LEU 635 is missing expected H atoms. Skipping. Residue LYS 654 is missing expected H atoms. Skipping. Residue LYS 655 is missing expected H atoms. Skipping. Residue ILE 661 is missing expected H atoms. Skipping. Residue LEU 802 is missing expected H atoms. Skipping. Residue LYS 933 is missing expected H atoms. Skipping. Residue MET 962 is missing expected H atoms. Skipping. Residue SER 980 is missing expected H atoms. Skipping. Residue TYR 1281 is missing expected H atoms. Skipping. Residue ILE 1304 is missing expected H atoms. Skipping. Residue SER 1395 is missing expected H atoms. Skipping. Residue LYS 1457 is missing expected H atoms. Skipping. Evaluate side-chains 266 residues out of total 1219 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 265 time to evaluate : 0.560 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: 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 27 ASP cc_start: 0.8998 (t70) cc_final: 0.8610 (t0) REVERT: A 138 TYR cc_start: 0.8300 (t80) cc_final: 0.7457 (t80) REVERT: A 142 GLU cc_start: 0.8537 (tp30) cc_final: 0.8011 (tp30) REVERT: A 180 CYS cc_start: 0.8978 (m) cc_final: 0.8578 (m) REVERT: A 298 ASP cc_start: 0.8413 (m-30) cc_final: 0.8123 (m-30) REVERT: A 418 ASP cc_start: 0.8981 (t0) cc_final: 0.8770 (t70) REVERT: A 583 MET cc_start: 0.8743 (tmm) cc_final: 0.8346 (tmm) REVERT: A 698 GLN cc_start: 0.9512 (pm20) cc_final: 0.9062 (pm20) REVERT: A 850 LYS cc_start: 0.8177 (ptpt) cc_final: 0.7674 (tmtt) REVERT: A 967 MET cc_start: 0.7879 (mmt) cc_final: 0.7308 (mmt) REVERT: A 1178 TYR cc_start: 0.8366 (t80) cc_final: 0.8009 (t80) REVERT: A 1234 GLU cc_start: 0.8687 (tm-30) cc_final: 0.8170 (tm-30) REVERT: A 1243 ILE cc_start: 0.9192 (tp) cc_final: 0.8972 (tp) REVERT: A 1346 ARG cc_start: 0.7770 (mtt180) cc_final: 0.6508 (ttp-110) REVERT: A 1379 TRP cc_start: 0.6770 (t-100) cc_final: 0.6112 (t60) REVERT: A 1473 ASP cc_start: 0.8469 (t0) cc_final: 0.8087 (p0) outliers start: 1 outliers final: 0 residues processed: 266 average time/residue: 0.1920 time to fit residues: 77.4811 Evaluate side-chains 213 residues out of total 1219 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 213 time to evaluate : 0.494 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 23 optimal weight: 6.9990 chunk 106 optimal weight: 5.9990 chunk 1 optimal weight: 10.0000 chunk 97 optimal weight: 3.9990 chunk 68 optimal weight: 3.9990 chunk 77 optimal weight: 6.9990 chunk 136 optimal weight: 5.9990 chunk 138 optimal weight: 2.9990 chunk 130 optimal weight: 5.9990 chunk 37 optimal weight: 1.9990 chunk 114 optimal weight: 0.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 210 ASN A 424 ASN ** A1366 ASN ** 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 = 0.3980 r_free = 0.3980 target = 0.140348 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3643 r_free = 0.3643 target = 0.115629 restraints weight = 79389.371| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3712 r_free = 0.3712 target = 0.120412 restraints weight = 33775.152| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3753 r_free = 0.3753 target = 0.123358 restraints weight = 18728.437| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3776 r_free = 0.3776 target = 0.125157 restraints weight = 12540.207| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 47)----------------| | r_work = 0.3795 r_free = 0.3795 target = 0.126448 restraints weight = 9663.636| |-----------------------------------------------------------------------------| r_work (final): 0.3797 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3794 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3794 r_free = 0.3794 target_work(ls_wunit_k1) = 0.126 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3794 r_free = 0.3794 target_work(ls_wunit_k1) = 0.126 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.3794 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7245 moved from start: 0.4866 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 11104 Z= 0.130 Angle : 0.512 6.967 15069 Z= 0.286 Chirality : 0.037 0.156 1772 Planarity : 0.004 0.062 1879 Dihedral : 4.870 74.004 1498 Min Nonbonded Distance : 2.278 Molprobity Statistics. All-atom Clashscore : 7.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.86 % Favored : 93.14 % Rotamer: Outliers : 0.09 % Allowed : 0.17 % Favored : 99.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.57 (0.23), residues: 1371 helix: 1.52 (0.17), residues: 921 sheet: -0.93 (0.60), residues: 67 loop : -2.28 (0.31), residues: 383 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A1143 TYR 0.022 0.001 TYR A 991 PHE 0.047 0.001 PHE A 996 TRP 0.044 0.002 TRP A 139 HIS 0.003 0.001 HIS A 364 Details of bonding type rmsd covalent geometry : bond 0.00267 (11103) covalent geometry : angle 0.51171 (15067) SS BOND : bond 0.00276 ( 1) SS BOND : angle 1.35608 ( 2) hydrogen bonds : bond 0.04577 ( 722) hydrogen bonds : angle 4.57632 ( 2160) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2742 Ramachandran restraints generated. 1371 Oldfield, 0 Emsley, 1371 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2742 Ramachandran restraints generated. 1371 Oldfield, 0 Emsley, 1371 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 40 is missing expected H atoms. Skipping. Residue MET 76 is missing expected H atoms. Skipping. Residue VAL 86 is missing expected H atoms. Skipping. Residue LYS 95 is missing expected H atoms. Skipping. Residue VAL 104 is missing expected H atoms. Skipping. Residue TYR 107 is missing expected H atoms. Skipping. Residue LEU 112 is missing expected H atoms. Skipping. Residue VAL 116 is missing expected H atoms. Skipping. Residue LEU 118 is missing expected H atoms. Skipping. Residue TYR 159 is missing expected H atoms. Skipping. Residue ILE 162 is missing expected H atoms. Skipping. Residue TYR 164 is missing expected H atoms. Skipping. Residue THR 179 is missing expected H atoms. Skipping. Residue LYS 192 is missing expected H atoms. Skipping. Residue ILE 200 is missing expected H atoms. Skipping. Residue LEU 497 is missing expected H atoms. Skipping. Residue LEU 525 is missing expected H atoms. Skipping. Residue MET 529 is missing expected H atoms. Skipping. Residue THR 633 is missing expected H atoms. Skipping. Residue LEU 635 is missing expected H atoms. Skipping. Residue LYS 654 is missing expected H atoms. Skipping. Residue LYS 655 is missing expected H atoms. Skipping. Residue ILE 661 is missing expected H atoms. Skipping. Residue LEU 802 is missing expected H atoms. Skipping. Residue LYS 933 is missing expected H atoms. Skipping. Residue MET 962 is missing expected H atoms. Skipping. Residue SER 980 is missing expected H atoms. Skipping. Residue TYR 1281 is missing expected H atoms. Skipping. Residue ILE 1304 is missing expected H atoms. Skipping. Residue SER 1395 is missing expected H atoms. Skipping. Residue LYS 1457 is missing expected H atoms. Skipping. Evaluate side-chains 265 residues out of total 1219 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 264 time to evaluate : 0.614 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: 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 27 ASP cc_start: 0.8992 (t70) cc_final: 0.8586 (t0) REVERT: A 138 TYR cc_start: 0.8330 (t80) cc_final: 0.7837 (t80) REVERT: A 142 GLU cc_start: 0.8453 (tp30) cc_final: 0.7974 (tt0) REVERT: A 180 CYS cc_start: 0.8957 (m) cc_final: 0.8670 (m) REVERT: A 298 ASP cc_start: 0.8376 (m-30) cc_final: 0.8067 (m-30) REVERT: A 418 ASP cc_start: 0.8933 (t0) cc_final: 0.8726 (t70) REVERT: A 583 MET cc_start: 0.8706 (tmm) cc_final: 0.8369 (tmm) REVERT: A 698 GLN cc_start: 0.9499 (pm20) cc_final: 0.8927 (pm20) REVERT: A 850 LYS cc_start: 0.8140 (ptpt) cc_final: 0.7646 (tmtt) REVERT: A 967 MET cc_start: 0.7835 (mmt) cc_final: 0.7266 (mmt) REVERT: A 1178 TYR cc_start: 0.8342 (t80) cc_final: 0.7982 (t80) REVERT: A 1234 GLU cc_start: 0.8686 (tm-30) cc_final: 0.8211 (tm-30) REVERT: A 1346 ARG cc_start: 0.7767 (mtt180) cc_final: 0.6032 (ttm170) REVERT: A 1379 TRP cc_start: 0.6751 (t-100) cc_final: 0.6124 (t60) REVERT: A 1473 ASP cc_start: 0.8453 (t0) cc_final: 0.7968 (p0) outliers start: 1 outliers final: 0 residues processed: 265 average time/residue: 0.1689 time to fit residues: 69.5711 Evaluate side-chains 212 residues out of total 1219 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 212 time to evaluate : 0.578 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 57 optimal weight: 6.9990 chunk 106 optimal weight: 10.0000 chunk 52 optimal weight: 0.9990 chunk 41 optimal weight: 5.9990 chunk 68 optimal weight: 3.9990 chunk 61 optimal weight: 7.9990 chunk 130 optimal weight: 7.9990 chunk 9 optimal weight: 10.0000 chunk 55 optimal weight: 3.9990 chunk 62 optimal weight: 10.0000 chunk 19 optimal weight: 6.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 210 ASN A 424 ASN A1291 HIS ** A1366 ASN ** 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 = 0.3963 r_free = 0.3963 target = 0.139037 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3623 r_free = 0.3623 target = 0.114408 restraints weight = 79459.865| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3691 r_free = 0.3691 target = 0.119085 restraints weight = 33948.693| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3731 r_free = 0.3731 target = 0.121995 restraints weight = 18899.875| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.3757 r_free = 0.3757 target = 0.123802 restraints weight = 12635.546| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.3770 r_free = 0.3770 target = 0.124891 restraints weight = 9752.957| |-----------------------------------------------------------------------------| r_work (final): 0.3769 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3766 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3766 r_free = 0.3766 target_work(ls_wunit_k1) = 0.124 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3766 r_free = 0.3766 target_work(ls_wunit_k1) = 0.124 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.3766 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7326 moved from start: 0.4988 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 11104 Z= 0.173 Angle : 0.552 7.146 15069 Z= 0.310 Chirality : 0.037 0.152 1772 Planarity : 0.004 0.063 1879 Dihedral : 4.898 73.305 1498 Min Nonbonded Distance : 2.251 Molprobity Statistics. All-atom Clashscore : 8.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.66 % Favored : 92.34 % Rotamer: Outliers : 0.09 % Allowed : 0.51 % Favored : 99.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.45 (0.23), residues: 1371 helix: 1.43 (0.17), residues: 920 sheet: -0.97 (0.59), residues: 67 loop : -2.32 (0.31), residues: 384 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A1143 TYR 0.022 0.002 TYR A 991 PHE 0.044 0.002 PHE A 996 TRP 0.026 0.001 TRP A 139 HIS 0.003 0.001 HIS A1291 Details of bonding type rmsd covalent geometry : bond 0.00357 (11103) covalent geometry : angle 0.55160 (15067) SS BOND : bond 0.00292 ( 1) SS BOND : angle 1.34610 ( 2) hydrogen bonds : bond 0.04656 ( 722) hydrogen bonds : angle 4.74499 ( 2160) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3402.96 seconds wall clock time: 58 minutes 36.98 seconds (3516.98 seconds total)