Starting phenix.real_space_refine on Sun Sep 29 10:17:16 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7m69_23691/09_2024/7m69_23691.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7m69_23691/09_2024/7m69_23691.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.42 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7m69_23691/09_2024/7m69_23691.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7m69_23691/09_2024/7m69_23691.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7m69_23691/09_2024/7m69_23691.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7m69_23691/09_2024/7m69_23691.cif" } resolution = 3.42 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.758 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 47 5.16 5 C 7028 2.51 5 N 1824 2.21 5 O 1981 1.98 5 H 10912 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 21795 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 21795 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1390, 21795 Classifications: {'peptide': 1390} Link IDs: {'PTRANS': 37, 'TRANS': 1352} Chain breaks: 4 Unresolved non-hydrogen bonds: 225 Unresolved non-hydrogen angles: 283 Unresolved non-hydrogen dihedrals: 192 Unresolved non-hydrogen chiralities: 13 Planarities with less than four sites: {'GLN:plan1': 4, 'TPO:plan-1': 1, 'TYR:plan': 4, 'ASN:plan1': 4, 'TRP:plan': 1, 'ASP:plan': 1, 'HIS:plan': 1, 'PHE:plan': 2, 'GLU:plan': 5, 'ARG:plan': 7} Unresolved non-hydrogen planarities: 141 Time building chain proxies: 10.86, per 1000 atoms: 0.50 Number of scatterers: 21795 At special positions: 0 Unit cell: (129.906, 123.72, 107.224, 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 47 16.00 P 3 15.00 O 1981 8.00 N 1824 7.00 C 7028 6.00 H 10912 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=2.02 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: 5.31 Conformation dependent library (CDL) restraints added in 1.8 seconds 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: 52 helices and 6 sheets defined 70.4% alpha, 5.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.70 Creating SS restraints... Processing helix chain 'A' and resid 29 through 60 removed outlier: 4.902A pdb=" N LEU A 53 " --> pdb=" O GLY A 49 " (cutoff:3.500A) removed outlier: 5.233A pdb=" N VAL A 54 " --> pdb=" O ILE A 50 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ASN A 55 " --> pdb=" O ARG A 51 " (cutoff:3.500A) removed outlier: 4.345A pdb=" N LYS A 60 " --> pdb=" O LEU A 56 " (cutoff:3.500A) Processing helix chain 'A' and resid 71 through 95 removed outlier: 3.566A pdb=" N ILE A 93 " --> pdb=" O ALA A 89 " (cutoff:3.500A) removed outlier: 4.123A pdb=" N SER A 94 " --> pdb=" O SER A 90 " (cutoff:3.500A) Processing helix chain 'A' and resid 96 through 98 No H-bonds generated for 'chain 'A' and resid 96 through 98' Processing helix chain 'A' and resid 101 through 124 removed outlier: 3.779A pdb=" N LEU A 118 " --> pdb=" O LEU A 114 " (cutoff:3.500A) removed outlier: 3.622A 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: 3.565A pdb=" N PHE A 175 " --> pdb=" O ILE A 171 " (cutoff:3.500A) Processing helix chain 'A' and resid 197 through 201 removed outlier: 3.685A pdb=" N HIS A 201 " --> pdb=" O GLN A 198 " (cutoff:3.500A) Processing helix chain 'A' and resid 216 through 223 removed outlier: 3.808A pdb=" N THR A 222 " --> pdb=" O PHE A 218 " (cutoff:3.500A) Processing helix chain 'A' and resid 226 through 236 Processing helix chain 'A' and resid 251 through 269 removed outlier: 3.705A pdb=" N LEU A 255 " --> pdb=" O SER A 251 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N ASN A 262 " --> pdb=" O LYS A 258 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N GLN A 269 " --> pdb=" O ASN A 265 " (cutoff:3.500A) Processing helix chain 'A' and resid 273 through 284 Processing helix chain 'A' and resid 284 through 328 removed outlier: 3.663A pdb=" N LEU A 288 " --> pdb=" O GLY A 284 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N LEU A 289 " --> pdb=" O SER A 285 " (cutoff:3.500A) Proline residue: A 305 - end of helix Processing helix chain 'A' and resid 342 through 392 removed outlier: 3.679A pdb=" N ALA A 383 " --> pdb=" O SER A 379 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N TYR A 386 " --> pdb=" O THR A 382 " (cutoff:3.500A) Processing helix chain 'A' and resid 393 through 400 Processing helix chain 'A' and resid 401 through 411 removed outlier: 3.564A pdb=" N ILE A 405 " --> pdb=" O SER A 401 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N MET A 409 " --> pdb=" O ILE A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 411 through 445 removed outlier: 3.884A pdb=" N GLN A 421 " --> pdb=" O GLN A 417 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N TRP A 422 " --> pdb=" O ASP A 418 " (cutoff:3.500A) removed outlier: 5.344A pdb=" N ASN A 424 " --> pdb=" O THR A 420 " (cutoff:3.500A) removed outlier: 4.958A pdb=" N LEU A 425 " --> pdb=" O GLN A 421 " (cutoff:3.500A) Proline residue: A 430 - end of helix removed outlier: 3.653A pdb=" N GLY A 445 " --> pdb=" O TYR A 441 " (cutoff:3.500A) Processing helix chain 'A' and resid 449 through 493 Proline residue: A 460 - end of helix removed outlier: 3.679A pdb=" N ARG A 467 " --> pdb=" O SER A 463 " (cutoff:3.500A) removed outlier: 3.821A 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 503 through 555 removed outlier: 4.337A pdb=" N CYS A 527 " --> pdb=" O THR A 523 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N SER A 533 " --> pdb=" O MET A 529 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N PHE A 534 " --> pdb=" O ALA A 530 " (cutoff:3.500A) Proline residue: A 540 - end of helix Processing helix chain 'A' and resid 563 through 603 removed outlier: 3.666A pdb=" N SER A 575 " --> pdb=" O PHE A 571 " (cutoff:3.500A) removed outlier: 4.502A pdb=" N PHE A 576 " --> pdb=" O ASN A 572 " (cutoff:3.500A) Proline residue: A 577 - end of helix removed outlier: 3.545A pdb=" N ILE A 580 " --> pdb=" O PHE A 576 " (cutoff:3.500A) Proline residue: A 582 - end of helix removed outlier: 3.746A pdb=" N LEU A 585 " --> pdb=" O ILE A 581 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N ASN A 586 " --> pdb=" O PRO A 582 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N SER A 587 " --> pdb=" O MET A 583 " (cutoff:3.500A) Processing helix chain 'A' and resid 668 through 678 Processing helix chain 'A' and resid 706 through 713 Processing helix chain 'A' and resid 718 through 729 Processing helix chain 'A' and resid 731 through 737 removed outlier: 4.001A pdb=" N LEU A 735 " --> pdb=" O LEU A 731 " (cutoff:3.500A) Processing helix chain 'A' and resid 754 through 769 Processing helix chain 'A' and resid 784 through 797 removed outlier: 4.024A 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: 3.522A pdb=" N ASP A 843 " --> pdb=" O GLU A 839 " (cutoff:3.500A) Processing helix chain 'A' and resid 920 through 929 Processing helix chain 'A' and resid 936 through 946 Processing helix chain 'A' and resid 947 through 982 removed outlier: 3.758A pdb=" N VAL A 951 " --> pdb=" O ASN A 947 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N CYS A 952 " --> pdb=" O PRO A 948 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N VAL A 953 " --> pdb=" O LYS A 949 " (cutoff:3.500A) Processing helix chain 'A' and resid 987 through 1016 removed outlier: 4.064A pdb=" N TRP A1014 " --> pdb=" O THR A1010 " (cutoff:3.500A) Processing helix chain 'A' and resid 1016 through 1035 removed outlier: 3.758A 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 1088 removed outlier: 3.656A pdb=" N ILE A1049 " --> pdb=" O PRO A1045 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N ILE A1057 " --> pdb=" O PHE A1053 " (cutoff:3.500A) removed outlier: 4.358A pdb=" N ALA A1062 " --> pdb=" O TYR A1058 " (cutoff:3.500A) removed outlier: 4.527A pdb=" N LEU A1064 " --> pdb=" O VAL A1060 " (cutoff:3.500A) removed outlier: 5.351A pdb=" N GLY A1065 " --> pdb=" O ASP A1061 " (cutoff:3.500A) Processing helix chain 'A' and resid 1089 through 1091 No H-bonds generated for 'chain 'A' and resid 1089 through 1091' Processing helix chain 'A' and resid 1092 through 1124 Proline residue: A1098 - end of helix removed outlier: 4.025A pdb=" N ARG A1115 " --> pdb=" O LEU A1111 " (cutoff:3.500A) removed outlier: 4.337A pdb=" N GLU A1116 " --> pdb=" O ARG A1112 " (cutoff:3.500A) Processing helix chain 'A' and resid 1125 through 1138 removed outlier: 3.883A pdb=" N TYR A1129 " --> pdb=" O ARG A1125 " (cutoff:3.500A) Processing helix chain 'A' and resid 1138 through 1146 Processing helix chain 'A' and resid 1147 through 1202 Proline residue: A1168 - end of helix Processing helix chain 'A' and resid 1205 through 1217 removed outlier: 3.694A pdb=" N VAL A1209 " --> pdb=" O THR A1205 " (cutoff:3.500A) Processing helix chain 'A' and resid 1218 through 1247 removed outlier: 3.843A pdb=" N THR A1222 " --> pdb=" O GLN A1218 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N ASN A1224 " --> pdb=" O THR A1220 " (cutoff:3.500A) removed outlier: 4.206A pdb=" N VAL A1238 " --> pdb=" O GLU A1234 " (cutoff:3.500A) removed outlier: 4.653A pdb=" N SER A1239 " --> pdb=" O THR A1235 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N VAL A1240 " --> pdb=" O ASN A1236 " (cutoff:3.500A) Processing helix chain 'A' and resid 1311 through 1321 removed outlier: 3.838A pdb=" N LEU A1315 " --> pdb=" O GLY A1311 " (cutoff:3.500A) removed outlier: 4.324A pdb=" N THR A1316 " --> pdb=" O LYS A1312 " (cutoff:3.500A) Processing helix chain 'A' and resid 1337 through 1341 removed outlier: 3.873A 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 1363 through 1368 Processing helix chain 'A' and resid 1375 through 1386 Processing helix chain 'A' and resid 1387 through 1394 removed outlier: 3.588A pdb=" N VAL A1391 " --> pdb=" O LEU A1387 " (cutoff:3.500A) Processing helix chain 'A' and resid 1404 through 1408 removed outlier: 4.249A pdb=" N GLY A1408 " --> pdb=" O GLU A1405 " (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 removed outlier: 3.808A pdb=" N SER A1474 " --> pdb=" O THR A1470 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 613 through 615 removed outlier: 5.793A pdb=" N GLN A 613 " --> pdb=" O VAL A 689 " (cutoff:3.500A) removed outlier: 6.490A pdb=" N ALA A 625 " --> pdb=" O HIS A 690 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 645 through 649 removed outlier: 5.653A pdb=" N ALA A 632 " --> pdb=" O ASN A 648 " (cutoff:3.500A) removed outlier: 6.302A pdb=" N LEU A 635 " --> pdb=" O ARG A 682 " (cutoff:3.500A) removed outlier: 4.778A 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: 6.453A pdb=" N ALA A 694 " --> pdb=" O LEU A 775 " (cutoff:3.500A) removed outlier: 8.117A pdb=" N ASP A 777 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 7.210A pdb=" N VAL A 696 " --> pdb=" O ASP A 777 " (cutoff:3.500A) removed outlier: 6.432A pdb=" N TYR A 774 " --> pdb=" O VAL A 808 " (cutoff:3.500A) removed outlier: 8.120A pdb=" N ALA A 810 " --> pdb=" O TYR A 774 " (cutoff:3.500A) removed outlier: 6.870A pdb=" N LEU A 776 " --> pdb=" O ALA A 810 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N ILE A 823 " --> pdb=" O GLY A 835 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N GLN A 833 " --> pdb=" O LEU A 825 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 1294 through 1296 Processing sheet with id=AA5, first strand: chain 'A' and resid 1349 through 1353 removed outlier: 6.223A pdb=" N LEU A1431 " --> pdb=" O LEU A1462 " (cutoff:3.500A) removed outlier: 8.127A pdb=" N ILE A1464 " --> pdb=" O LEU A1431 " (cutoff:3.500A) removed outlier: 6.545A pdb=" N LEU A1433 " --> pdb=" O ILE A1464 " (cutoff:3.500A) removed outlier: 6.784A pdb=" N LYS A1301 " --> pdb=" O ARG A1476 " (cutoff:3.500A) removed outlier: 7.763A pdb=" N ILE A1478 " --> pdb=" O LYS A1301 " (cutoff:3.500A) removed outlier: 5.953A pdb=" N GLY A1303 " --> pdb=" O ILE A1478 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 1361 through 1362 removed outlier: 3.789A pdb=" N GLY A1361 " --> pdb=" O LEU A1403 " (cutoff:3.500A) 724 hydrogen bonds defined for protein. 2151 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: 8.09 Time building geometry restraints manager: 6.46 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: 10893 1.04 - 1.23: 416 1.23 - 1.43: 4244 1.43 - 1.63: 6382 1.63 - 1.83: 77 Bond restraints: 22012 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 3.63e+01 bond pdb=" CG2 TPO A 911 " pdb="HG23 TPO A 911 " ideal model delta sigma weight residual 0.970 1.090 -0.120 2.00e-02 2.50e+03 3.58e+01 bond pdb=" CB TPO A 911 " pdb=" HB 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 3.52e+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 22007 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.01: 38451 2.01 - 4.03: 1202 4.03 - 6.04: 120 6.04 - 8.06: 14 8.06 - 10.07: 6 Bond angle restraints: 39793 Sorted by residual: angle pdb=" N HIS A 790 " pdb=" CA HIS A 790 " pdb=" C HIS A 790 " ideal model delta sigma weight residual 111.28 105.90 5.38 1.09e+00 8.42e-01 2.44e+01 angle pdb=" N ASN A 799 " pdb=" CA ASN A 799 " pdb=" C ASN A 799 " ideal model delta sigma weight residual 112.26 106.12 6.14 1.32e+00 5.74e-01 2.16e+01 angle pdb=" N PRO A 798 " pdb=" CA PRO A 798 " pdb=" C PRO A 798 " ideal model delta sigma weight residual 113.53 107.42 6.11 1.39e+00 5.18e-01 1.93e+01 angle pdb=" CA THR A1018 " pdb=" C THR A1018 " pdb=" O THR A1018 " ideal model delta sigma weight residual 121.00 116.49 4.51 1.05e+00 9.07e-01 1.84e+01 angle pdb=" CA HIS A 794 " pdb=" C HIS A 794 " pdb=" O HIS A 794 " ideal model delta sigma weight residual 120.55 116.17 4.38 1.06e+00 8.90e-01 1.71e+01 ... (remaining 39788 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.91: 9315 17.91 - 35.82: 749 35.82 - 53.73: 184 53.73 - 71.64: 71 71.64 - 89.55: 11 Dihedral angle restraints: 10330 sinusoidal: 5522 harmonic: 4808 Sorted by residual: dihedral pdb=" CB CYS A 946 " pdb=" SG CYS A 946 " pdb=" SG CYS A1017 " pdb=" CB CYS A1017 " ideal model delta sinusoidal sigma weight residual 93.00 147.92 -54.92 1 1.00e+01 1.00e-02 4.08e+01 dihedral pdb=" CA TRP A 636 " pdb=" C TRP A 636 " pdb=" N GLN A 637 " pdb=" CA GLN A 637 " ideal model delta harmonic sigma weight residual -180.00 -155.39 -24.61 0 5.00e+00 4.00e-02 2.42e+01 dihedral pdb=" CA THR A 603 " pdb=" C THR A 603 " pdb=" N ASN A 604 " pdb=" CA ASN A 604 " ideal model delta harmonic sigma weight residual 180.00 156.24 23.76 0 5.00e+00 4.00e-02 2.26e+01 ... (remaining 10327 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.038: 1251 0.038 - 0.076: 352 0.076 - 0.114: 119 0.114 - 0.151: 41 0.151 - 0.189: 11 Chirality restraints: 1774 Sorted by residual: chirality pdb=" CB VAL A 618 " pdb=" CA VAL A 618 " pdb=" CG1 VAL A 618 " pdb=" CG2 VAL A 618 " both_signs ideal model delta sigma weight residual False -2.63 -2.44 -0.19 2.00e-01 2.50e+01 8.95e-01 chirality pdb=" CA THR A1018 " pdb=" N THR A1018 " pdb=" C THR A1018 " pdb=" CB THR A1018 " both_signs ideal model delta sigma weight residual False 2.53 2.34 0.19 2.00e-01 2.50e+01 8.71e-01 chirality pdb=" CA VAL A 699 " pdb=" N VAL A 699 " pdb=" C VAL A 699 " pdb=" CB VAL A 699 " both_signs ideal model delta sigma weight residual False 2.44 2.61 -0.17 2.00e-01 2.50e+01 7.31e-01 ... (remaining 1771 not shown) Planarity restraints: 3223 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LEU A 802 " 0.016 2.00e-02 2.50e+03 3.22e-02 1.04e+01 pdb=" C LEU A 802 " -0.056 2.00e-02 2.50e+03 pdb=" O LEU A 802 " 0.020 2.00e-02 2.50e+03 pdb=" N HIS A 803 " 0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA A 632 " -0.015 2.00e-02 2.50e+03 2.99e-02 8.95e+00 pdb=" C ALA A 632 " 0.052 2.00e-02 2.50e+03 pdb=" O ALA A 632 " -0.020 2.00e-02 2.50e+03 pdb=" N THR A 633 " -0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU A 646 " -0.014 2.00e-02 2.50e+03 2.92e-02 8.54e+00 pdb=" C LEU A 646 " 0.051 2.00e-02 2.50e+03 pdb=" O LEU A 646 " -0.019 2.00e-02 2.50e+03 pdb=" N LYS A 647 " -0.017 2.00e-02 2.50e+03 ... (remaining 3220 not shown) Histogram of nonbonded interaction distances: 1.75 - 2.32: 4525 2.32 - 2.89: 48864 2.89 - 3.46: 55002 3.46 - 4.03: 69718 4.03 - 4.60: 107289 Nonbonded interactions: 285398 Sorted by model distance: nonbonded pdb=" H GLY A 622 " pdb=" O LYS A 655 " model vdw 1.747 2.450 nonbonded pdb=" HH TYR A1110 " pdb=" OD1 ASN A1173 " model vdw 1.765 2.450 nonbonded pdb=" O ALA A 396 " pdb=" HG SER A 400 " model vdw 1.783 2.450 nonbonded pdb=" O VAL A 543 " pdb=" HG1 THR A 547 " model vdw 1.783 2.450 nonbonded pdb=" O GLY A 705 " pdb=" H VAL A 746 " model vdw 1.785 2.450 ... (remaining 285393 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.630 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: 0.360 Extract box with map and model: 0.780 Check model and map are aligned: 0.150 Set scattering table: 0.190 Process input model: 45.800 Find NCS groups from input model: 0.150 Set up NCS constraints: 0.060 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:2.700 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 51.830 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7136 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 : 0.006 0.106 11100 Z= 0.363 Angle : 0.867 10.075 15064 Z= 0.482 Chirality : 0.044 0.189 1774 Planarity : 0.005 0.050 1876 Dihedral : 13.253 89.553 3979 Min Nonbonded Distance : 2.304 Molprobity Statistics. All-atom Clashscore : 0.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.11 % Favored : 94.89 % Rotamer: Outliers : 1.29 % Allowed : 7.97 % Favored : 90.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.08 (0.21), residues: 1371 helix: 0.87 (0.16), residues: 909 sheet: -0.56 (0.51), residues: 76 loop : -2.15 (0.28), residues: 386 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 225 HIS 0.010 0.001 HIS A 803 PHE 0.016 0.002 PHE A 634 TYR 0.038 0.002 TYR A 991 ARG 0.005 0.001 ARG A 765 *********************** 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 ILE 46 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 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 LYS 192 is missing expected H atoms. Skipping. Residue ILE 200 is missing expected H atoms. Skipping. Residue MET 458 is missing expected H atoms. Skipping. Residue LEU 497 is missing expected H atoms. Skipping. Residue LYS 517 is missing expected H atoms. Skipping. Residue LEU 522 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 MET 739 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 LEU 1417 is missing expected H atoms. Skipping. Residue LYS 1457 is missing expected H atoms. Skipping. Evaluate side-chains 415 residues out of total 1219 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 400 time to evaluate : 1.720 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 146 ASN cc_start: 0.8305 (m110) cc_final: 0.7895 (m110) REVERT: A 176 GLN cc_start: 0.8622 (tt0) cc_final: 0.8343 (tt0) REVERT: A 226 MET cc_start: 0.8326 (mmm) cc_final: 0.7657 (mmm) REVERT: A 467 ARG cc_start: 0.8213 (tpt170) cc_final: 0.7410 (mtp180) REVERT: A 485 ARG cc_start: 0.8289 (ttp80) cc_final: 0.7411 (mmp80) REVERT: A 486 VAL cc_start: 0.8746 (t) cc_final: 0.8206 (p) REVERT: A 504 LYS cc_start: 0.8687 (ttpp) cc_final: 0.8276 (tptt) REVERT: A 718 ASP cc_start: 0.7909 (t0) cc_final: 0.7421 (m-30) REVERT: A 735 LEU cc_start: 0.8350 (mp) cc_final: 0.8064 (tp) REVERT: A 789 ARG cc_start: 0.8744 (ttt180) cc_final: 0.8268 (ttp80) REVERT: A 962 MET cc_start: 0.8787 (tpp) cc_final: 0.8364 (tpp) REVERT: A 966 VAL cc_start: 0.9529 (t) cc_final: 0.9322 (m) REVERT: A 1029 MET cc_start: 0.8704 (tpt) cc_final: 0.8414 (tpp) REVERT: A 1048 ARG cc_start: 0.7803 (ttt180) cc_final: 0.7308 (ttm110) REVERT: A 1107 GLN cc_start: 0.8716 (OUTLIER) cc_final: 0.8515 (tm-30) REVERT: A 1108 GLN cc_start: 0.8389 (tp40) cc_final: 0.8062 (tp-100) REVERT: A 1319 LEU cc_start: 0.8751 (tp) cc_final: 0.8499 (tp) REVERT: A 1386 HIS cc_start: 0.7332 (t-90) cc_final: 0.6936 (m-70) REVERT: A 1390 HIS cc_start: 0.7108 (t70) cc_final: 0.6424 (t70) REVERT: A 1394 MET cc_start: 0.4952 (mtt) cc_final: 0.4655 (mpp) REVERT: A 1482 ASN cc_start: 0.6964 (m110) cc_final: 0.6551 (t0) outliers start: 15 outliers final: 2 residues processed: 411 average time/residue: 0.5048 time to fit residues: 293.4102 Evaluate side-chains 284 residues out of total 1219 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 281 time to evaluate : 1.619 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 157 HIS Chi-restraints excluded: chain A residue 807 LYS Chi-restraints excluded: chain A residue 1107 GLN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 117 optimal weight: 9.9990 chunk 105 optimal weight: 4.9990 chunk 58 optimal weight: 5.9990 chunk 35 optimal weight: 8.9990 chunk 71 optimal weight: 8.9990 chunk 56 optimal weight: 4.9990 chunk 108 optimal weight: 5.9990 chunk 42 optimal weight: 7.9990 chunk 66 optimal weight: 2.9990 chunk 81 optimal weight: 6.9990 chunk 126 optimal weight: 30.0000 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 969 ASN A1027 ASN A1466 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7354 moved from start: 0.3321 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 11100 Z= 0.325 Angle : 0.631 6.621 15064 Z= 0.350 Chirality : 0.038 0.180 1774 Planarity : 0.004 0.043 1876 Dihedral : 6.063 79.416 1504 Min Nonbonded Distance : 2.311 Molprobity Statistics. All-atom Clashscore : 8.89 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.38 % Favored : 95.55 % Rotamer: Outliers : 2.91 % Allowed : 16.37 % Favored : 80.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.69 (0.22), residues: 1371 helix: 1.52 (0.17), residues: 911 sheet: -0.55 (0.51), residues: 77 loop : -1.97 (0.29), residues: 383 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A 225 HIS 0.010 0.001 HIS A 803 PHE 0.021 0.002 PHE A 541 TYR 0.015 0.002 TYR A 506 ARG 0.003 0.000 ARG A1143 *********************** 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 ILE 46 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 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 LYS 192 is missing expected H atoms. Skipping. Residue ILE 200 is missing expected H atoms. Skipping. Residue MET 458 is missing expected H atoms. Skipping. Residue LEU 497 is missing expected H atoms. Skipping. Residue LYS 517 is missing expected H atoms. Skipping. Residue LEU 522 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 MET 739 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 LEU 1417 is missing expected H atoms. Skipping. Residue LYS 1457 is missing expected H atoms. Skipping. Evaluate side-chains 306 residues out of total 1219 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 272 time to evaluate : 1.709 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 467 ARG cc_start: 0.8241 (tpt170) cc_final: 0.7377 (mtp180) REVERT: A 485 ARG cc_start: 0.8353 (ttp80) cc_final: 0.7610 (mmp80) REVERT: A 504 LYS cc_start: 0.8878 (ttpp) cc_final: 0.8498 (tptp) REVERT: A 718 ASP cc_start: 0.7890 (t0) cc_final: 0.7309 (m-30) REVERT: A 735 LEU cc_start: 0.8337 (mp) cc_final: 0.8105 (tp) REVERT: A 789 ARG cc_start: 0.8742 (ttt180) cc_final: 0.8316 (tmt-80) REVERT: A 813 LYS cc_start: 0.8827 (tptm) cc_final: 0.8495 (tppt) REVERT: A 1029 MET cc_start: 0.8797 (tpt) cc_final: 0.8415 (tpp) REVERT: A 1038 MET cc_start: 0.8634 (mmm) cc_final: 0.8412 (mmm) REVERT: A 1048 ARG cc_start: 0.8182 (ttt180) cc_final: 0.7668 (ttm110) REVERT: A 1107 GLN cc_start: 0.8765 (OUTLIER) cc_final: 0.8558 (tm-30) REVERT: A 1110 TYR cc_start: 0.8903 (t80) cc_final: 0.8615 (t80) REVERT: A 1390 HIS cc_start: 0.7002 (t70) cc_final: 0.6768 (t-90) REVERT: A 1473 ASP cc_start: 0.8075 (t70) cc_final: 0.7538 (m-30) REVERT: A 1482 ASN cc_start: 0.6961 (m110) cc_final: 0.6573 (t0) outliers start: 34 outliers final: 25 residues processed: 290 average time/residue: 0.4567 time to fit residues: 191.7092 Evaluate side-chains 272 residues out of total 1219 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 246 time to evaluate : 1.750 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 135 LEU Chi-restraints excluded: chain A residue 157 HIS Chi-restraints excluded: chain A residue 158 THR Chi-restraints excluded: chain A residue 185 LEU Chi-restraints excluded: chain A residue 191 LYS Chi-restraints excluded: chain A residue 264 GLU Chi-restraints excluded: chain A residue 282 THR Chi-restraints excluded: chain A residue 303 THR Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain A residue 435 ILE Chi-restraints excluded: chain A residue 595 ILE Chi-restraints excluded: chain A residue 662 VAL Chi-restraints excluded: chain A residue 765 ARG Chi-restraints excluded: chain A residue 801 LEU Chi-restraints excluded: chain A residue 807 LYS Chi-restraints excluded: chain A residue 994 ILE Chi-restraints excluded: chain A residue 1064 LEU Chi-restraints excluded: chain A residue 1107 GLN Chi-restraints excluded: chain A residue 1113 THR Chi-restraints excluded: chain A residue 1126 SER Chi-restraints excluded: chain A residue 1231 VAL Chi-restraints excluded: chain A residue 1235 THR Chi-restraints excluded: chain A residue 1342 LEU Chi-restraints excluded: chain A residue 1349 LEU Chi-restraints excluded: chain A residue 1420 LEU Chi-restraints excluded: chain A residue 1452 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 70 optimal weight: 9.9990 chunk 39 optimal weight: 4.9990 chunk 105 optimal weight: 8.9990 chunk 85 optimal weight: 2.9990 chunk 34 optimal weight: 3.9990 chunk 126 optimal weight: 20.0000 chunk 136 optimal weight: 7.9990 chunk 112 optimal weight: 0.9980 chunk 125 optimal weight: 5.9990 chunk 43 optimal weight: 9.9990 chunk 101 optimal weight: 0.8980 overall best weight: 2.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1390 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7345 moved from start: 0.3774 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 11100 Z= 0.202 Angle : 0.569 8.192 15064 Z= 0.307 Chirality : 0.037 0.178 1774 Planarity : 0.004 0.040 1876 Dihedral : 5.889 78.484 1504 Min Nonbonded Distance : 2.292 Molprobity Statistics. All-atom Clashscore : 8.98 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.81 % Favored : 95.11 % Rotamer: Outliers : 2.31 % Allowed : 19.19 % Favored : 78.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.93 (0.23), residues: 1371 helix: 1.67 (0.17), residues: 918 sheet: -0.47 (0.51), residues: 77 loop : -1.85 (0.31), residues: 376 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 422 HIS 0.008 0.001 HIS A1390 PHE 0.020 0.001 PHE A 634 TYR 0.012 0.001 TYR A1105 ARG 0.007 0.000 ARG A 485 *********************** 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 ILE 46 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 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 LYS 192 is missing expected H atoms. Skipping. Residue ILE 200 is missing expected H atoms. Skipping. Residue MET 458 is missing expected H atoms. Skipping. Residue LEU 497 is missing expected H atoms. Skipping. Residue LYS 517 is missing expected H atoms. Skipping. Residue LEU 522 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 MET 739 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 LEU 1417 is missing expected H atoms. Skipping. Residue LYS 1457 is missing expected H atoms. Skipping. Evaluate side-chains 286 residues out of total 1219 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 259 time to evaluate : 1.602 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 467 ARG cc_start: 0.8293 (tpt170) cc_final: 0.7371 (mtp180) REVERT: A 485 ARG cc_start: 0.8288 (ttp80) cc_final: 0.7502 (mmp80) REVERT: A 504 LYS cc_start: 0.8908 (ttpp) cc_final: 0.8514 (tptt) REVERT: A 718 ASP cc_start: 0.7891 (t0) cc_final: 0.7310 (m-30) REVERT: A 735 LEU cc_start: 0.8188 (mp) cc_final: 0.7969 (tp) REVERT: A 789 ARG cc_start: 0.8665 (ttt180) cc_final: 0.8247 (tmt-80) REVERT: A 813 LYS cc_start: 0.8764 (tptm) cc_final: 0.8461 (tppt) REVERT: A 1029 MET cc_start: 0.8738 (tpt) cc_final: 0.8424 (tpp) REVERT: A 1048 ARG cc_start: 0.8140 (ttt180) cc_final: 0.7595 (ttm110) REVERT: A 1107 GLN cc_start: 0.8737 (OUTLIER) cc_final: 0.8532 (tm-30) REVERT: A 1110 TYR cc_start: 0.8862 (t80) cc_final: 0.8590 (t80) REVERT: A 1292 ILE cc_start: 0.8295 (pt) cc_final: 0.7915 (mp) REVERT: A 1386 HIS cc_start: 0.8201 (t-90) cc_final: 0.7118 (m-70) REVERT: A 1405 GLU cc_start: 0.7770 (mt-10) cc_final: 0.7367 (mt-10) REVERT: A 1473 ASP cc_start: 0.8038 (t70) cc_final: 0.7535 (m-30) REVERT: A 1482 ASN cc_start: 0.6994 (m110) cc_final: 0.6587 (t0) outliers start: 27 outliers final: 24 residues processed: 273 average time/residue: 0.4895 time to fit residues: 194.6685 Evaluate side-chains 274 residues out of total 1219 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 249 time to evaluate : 1.663 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 135 LEU Chi-restraints excluded: chain A residue 157 HIS Chi-restraints excluded: chain A residue 158 THR Chi-restraints excluded: chain A residue 170 PHE Chi-restraints excluded: chain A residue 264 GLU Chi-restraints excluded: chain A residue 303 THR Chi-restraints excluded: chain A residue 379 SER Chi-restraints excluded: chain A residue 595 ILE Chi-restraints excluded: chain A residue 662 VAL Chi-restraints excluded: chain A residue 673 LEU Chi-restraints excluded: chain A residue 765 ARG Chi-restraints excluded: chain A residue 801 LEU Chi-restraints excluded: chain A residue 807 LYS Chi-restraints excluded: chain A residue 994 ILE Chi-restraints excluded: chain A residue 1061 ASP Chi-restraints excluded: chain A residue 1073 VAL Chi-restraints excluded: chain A residue 1083 THR Chi-restraints excluded: chain A residue 1107 GLN Chi-restraints excluded: chain A residue 1186 ILE Chi-restraints excluded: chain A residue 1213 LEU Chi-restraints excluded: chain A residue 1231 VAL Chi-restraints excluded: chain A residue 1235 THR Chi-restraints excluded: chain A residue 1274 PHE Chi-restraints excluded: chain A residue 1349 LEU Chi-restraints excluded: chain A residue 1420 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 124 optimal weight: 9.9990 chunk 95 optimal weight: 5.9990 chunk 65 optimal weight: 0.5980 chunk 13 optimal weight: 2.9990 chunk 60 optimal weight: 0.0980 chunk 84 optimal weight: 10.0000 chunk 126 optimal weight: 30.0000 chunk 134 optimal weight: 20.0000 chunk 66 optimal weight: 6.9990 chunk 120 optimal weight: 5.9990 chunk 36 optimal weight: 10.0000 overall best weight: 3.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 476 GLN ** A1390 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7370 moved from start: 0.4162 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 11100 Z= 0.214 Angle : 0.555 6.548 15064 Z= 0.301 Chirality : 0.036 0.180 1774 Planarity : 0.004 0.038 1876 Dihedral : 5.809 77.151 1504 Min Nonbonded Distance : 2.292 Molprobity Statistics. All-atom Clashscore : 8.61 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.96 % Favored : 94.97 % Rotamer: Outliers : 3.17 % Allowed : 19.11 % Favored : 77.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.02 (0.23), residues: 1371 helix: 1.73 (0.17), residues: 919 sheet: -0.33 (0.51), residues: 77 loop : -1.84 (0.31), residues: 375 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 225 HIS 0.008 0.001 HIS A 803 PHE 0.016 0.001 PHE A 115 TYR 0.015 0.001 TYR A1024 ARG 0.002 0.000 ARG A1179 *********************** 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 ILE 46 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 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 LYS 192 is missing expected H atoms. Skipping. Residue ILE 200 is missing expected H atoms. Skipping. Residue MET 458 is missing expected H atoms. Skipping. Residue LEU 497 is missing expected H atoms. Skipping. Residue LYS 517 is missing expected H atoms. Skipping. Residue LEU 522 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 MET 739 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 LEU 1417 is missing expected H atoms. Skipping. Residue LYS 1457 is missing expected H atoms. Skipping. Evaluate side-chains 282 residues out of total 1219 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 245 time to evaluate : 1.685 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 467 ARG cc_start: 0.8326 (tpt170) cc_final: 0.7389 (mtp180) REVERT: A 485 ARG cc_start: 0.8313 (ttp80) cc_final: 0.7465 (mmp80) REVERT: A 504 LYS cc_start: 0.8950 (ttpp) cc_final: 0.8559 (tptt) REVERT: A 718 ASP cc_start: 0.7945 (t0) cc_final: 0.7328 (m-30) REVERT: A 735 LEU cc_start: 0.8251 (mp) cc_final: 0.8035 (tp) REVERT: A 789 ARG cc_start: 0.8675 (ttt180) cc_final: 0.8191 (tmt-80) REVERT: A 813 LYS cc_start: 0.8679 (tptm) cc_final: 0.8320 (tppt) REVERT: A 1029 MET cc_start: 0.8775 (tpt) cc_final: 0.8430 (tpp) REVERT: A 1048 ARG cc_start: 0.8142 (ttt180) cc_final: 0.7609 (ttm110) REVERT: A 1110 TYR cc_start: 0.8861 (t80) cc_final: 0.8521 (t80) REVERT: A 1292 ILE cc_start: 0.8355 (pt) cc_final: 0.7954 (mp) REVERT: A 1405 GLU cc_start: 0.7852 (mt-10) cc_final: 0.7310 (mt-10) REVERT: A 1473 ASP cc_start: 0.8055 (t70) cc_final: 0.7533 (m-30) REVERT: A 1482 ASN cc_start: 0.6989 (m110) cc_final: 0.6596 (t0) outliers start: 37 outliers final: 27 residues processed: 262 average time/residue: 0.4618 time to fit residues: 175.5495 Evaluate side-chains 262 residues out of total 1219 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 235 time to evaluate : 1.641 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 135 LEU Chi-restraints excluded: chain A residue 157 HIS Chi-restraints excluded: chain A residue 158 THR Chi-restraints excluded: chain A residue 170 PHE Chi-restraints excluded: chain A residue 264 GLU Chi-restraints excluded: chain A residue 303 THR Chi-restraints excluded: chain A residue 361 SER Chi-restraints excluded: chain A residue 379 SER Chi-restraints excluded: chain A residue 595 ILE Chi-restraints excluded: chain A residue 662 VAL Chi-restraints excluded: chain A residue 673 LEU Chi-restraints excluded: chain A residue 765 ARG Chi-restraints excluded: chain A residue 801 LEU Chi-restraints excluded: chain A residue 802 LEU Chi-restraints excluded: chain A residue 807 LYS Chi-restraints excluded: chain A residue 994 ILE Chi-restraints excluded: chain A residue 1061 ASP Chi-restraints excluded: chain A residue 1073 VAL Chi-restraints excluded: chain A residue 1083 THR Chi-restraints excluded: chain A residue 1113 THR Chi-restraints excluded: chain A residue 1186 ILE Chi-restraints excluded: chain A residue 1213 LEU Chi-restraints excluded: chain A residue 1231 VAL Chi-restraints excluded: chain A residue 1235 THR Chi-restraints excluded: chain A residue 1394 MET Chi-restraints excluded: chain A residue 1420 LEU Chi-restraints excluded: chain A residue 1452 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 111 optimal weight: 1.9990 chunk 76 optimal weight: 8.9990 chunk 1 optimal weight: 10.0000 chunk 100 optimal weight: 8.9990 chunk 55 optimal weight: 4.9990 chunk 114 optimal weight: 4.9990 chunk 92 optimal weight: 2.9990 chunk 0 optimal weight: 6.9990 chunk 68 optimal weight: 0.8980 chunk 120 optimal weight: 8.9990 chunk 33 optimal weight: 3.9990 overall best weight: 2.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 535 GLN ** A1390 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7374 moved from start: 0.4370 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 11100 Z= 0.204 Angle : 0.544 7.293 15064 Z= 0.295 Chirality : 0.036 0.177 1774 Planarity : 0.003 0.038 1876 Dihedral : 5.347 71.054 1501 Min Nonbonded Distance : 2.305 Molprobity Statistics. All-atom Clashscore : 8.29 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.32 % Favored : 94.60 % Rotamer: Outliers : 3.00 % Allowed : 19.28 % Favored : 77.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.11 (0.23), residues: 1371 helix: 1.80 (0.17), residues: 920 sheet: -0.35 (0.51), residues: 77 loop : -1.79 (0.31), residues: 374 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A1014 HIS 0.006 0.001 HIS A 803 PHE 0.015 0.001 PHE A 115 TYR 0.013 0.001 TYR A1105 ARG 0.003 0.000 ARG A 682 *********************** 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 ILE 46 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 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 LYS 192 is missing expected H atoms. Skipping. Residue ILE 200 is missing expected H atoms. Skipping. Residue MET 458 is missing expected H atoms. Skipping. Residue LEU 497 is missing expected H atoms. Skipping. Residue LYS 517 is missing expected H atoms. Skipping. Residue LEU 522 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 MET 739 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 LEU 1417 is missing expected H atoms. Skipping. Residue LYS 1457 is missing expected H atoms. Skipping. Evaluate side-chains 283 residues out of total 1219 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 248 time to evaluate : 1.636 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: A 467 ARG cc_start: 0.8344 (tpt170) cc_final: 0.7379 (mtp180) REVERT: A 485 ARG cc_start: 0.8353 (ttp80) cc_final: 0.7479 (mmp80) REVERT: A 504 LYS cc_start: 0.8976 (ttpp) cc_final: 0.8595 (tptt) REVERT: A 718 ASP cc_start: 0.7991 (t0) cc_final: 0.7361 (m-30) REVERT: A 735 LEU cc_start: 0.8257 (mp) cc_final: 0.8041 (tp) REVERT: A 789 ARG cc_start: 0.8657 (ttt180) cc_final: 0.8182 (tmt-80) REVERT: A 813 LYS cc_start: 0.8633 (tptm) cc_final: 0.8296 (tppt) REVERT: A 1029 MET cc_start: 0.8774 (tpt) cc_final: 0.8417 (tpp) REVERT: A 1048 ARG cc_start: 0.8132 (ttt180) cc_final: 0.7631 (ttm110) REVERT: A 1110 TYR cc_start: 0.8856 (t80) cc_final: 0.8575 (t80) REVERT: A 1292 ILE cc_start: 0.8365 (pt) cc_final: 0.7986 (mp) REVERT: A 1405 GLU cc_start: 0.7874 (mt-10) cc_final: 0.7315 (mt-10) REVERT: A 1473 ASP cc_start: 0.8046 (t70) cc_final: 0.7535 (m-30) REVERT: A 1482 ASN cc_start: 0.6972 (m110) cc_final: 0.6541 (t0) outliers start: 35 outliers final: 28 residues processed: 265 average time/residue: 0.4699 time to fit residues: 180.0401 Evaluate side-chains 264 residues out of total 1219 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 236 time to evaluate : 1.625 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 135 LEU Chi-restraints excluded: chain A residue 157 HIS Chi-restraints excluded: chain A residue 158 THR Chi-restraints excluded: chain A residue 170 PHE Chi-restraints excluded: chain A residue 264 GLU Chi-restraints excluded: chain A residue 303 THR Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain A residue 361 SER Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 379 SER Chi-restraints excluded: chain A residue 563 LEU Chi-restraints excluded: chain A residue 595 ILE Chi-restraints excluded: chain A residue 662 VAL Chi-restraints excluded: chain A residue 673 LEU Chi-restraints excluded: chain A residue 765 ARG Chi-restraints excluded: chain A residue 801 LEU Chi-restraints excluded: chain A residue 994 ILE Chi-restraints excluded: chain A residue 1023 LYS Chi-restraints excluded: chain A residue 1073 VAL Chi-restraints excluded: chain A residue 1083 THR Chi-restraints excluded: chain A residue 1113 THR Chi-restraints excluded: chain A residue 1186 ILE Chi-restraints excluded: chain A residue 1213 LEU Chi-restraints excluded: chain A residue 1235 THR Chi-restraints excluded: chain A residue 1274 PHE Chi-restraints excluded: chain A residue 1349 LEU Chi-restraints excluded: chain A residue 1394 MET Chi-restraints excluded: chain A residue 1420 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 45 optimal weight: 9.9990 chunk 120 optimal weight: 4.9990 chunk 26 optimal weight: 3.9990 chunk 78 optimal weight: 10.0000 chunk 33 optimal weight: 2.9990 chunk 134 optimal weight: 9.9990 chunk 111 optimal weight: 3.9990 chunk 62 optimal weight: 4.9990 chunk 11 optimal weight: 5.9990 chunk 44 optimal weight: 10.0000 chunk 70 optimal weight: 9.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 167 GLN ** A1390 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7408 moved from start: 0.4609 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 11100 Z= 0.258 Angle : 0.565 6.442 15064 Z= 0.309 Chirality : 0.037 0.175 1774 Planarity : 0.004 0.043 1876 Dihedral : 5.320 71.658 1497 Min Nonbonded Distance : 2.269 Molprobity Statistics. All-atom Clashscore : 9.35 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.54 % Favored : 94.38 % Rotamer: Outliers : 3.34 % Allowed : 19.45 % Favored : 77.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.94 (0.23), residues: 1371 helix: 1.66 (0.17), residues: 926 sheet: -0.34 (0.51), residues: 77 loop : -1.89 (0.32), residues: 368 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A1014 HIS 0.007 0.001 HIS A 803 PHE 0.015 0.001 PHE A 996 TYR 0.015 0.001 TYR A1105 ARG 0.002 0.000 ARG A1179 *********************** 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 ILE 46 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 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 LYS 192 is missing expected H atoms. Skipping. Residue ILE 200 is missing expected H atoms. Skipping. Residue MET 458 is missing expected H atoms. Skipping. Residue LEU 497 is missing expected H atoms. Skipping. Residue LYS 517 is missing expected H atoms. Skipping. Residue LEU 522 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 MET 739 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 LEU 1417 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 fitting. rotamer outliers: 39 poor density : 237 time to evaluate : 1.630 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: A 442 LYS cc_start: 0.8568 (mmmt) cc_final: 0.8366 (mmtp) REVERT: A 467 ARG cc_start: 0.8409 (tpt170) cc_final: 0.7404 (mtm180) REVERT: A 485 ARG cc_start: 0.8394 (ttp80) cc_final: 0.7566 (mmp80) REVERT: A 504 LYS cc_start: 0.9056 (ttpp) cc_final: 0.8679 (tptt) REVERT: A 718 ASP cc_start: 0.8030 (t0) cc_final: 0.7301 (m-30) REVERT: A 789 ARG cc_start: 0.8673 (ttt180) cc_final: 0.8216 (tmt-80) REVERT: A 813 LYS cc_start: 0.8668 (tptm) cc_final: 0.8329 (tppt) REVERT: A 1029 MET cc_start: 0.8820 (tpt) cc_final: 0.8439 (tpp) REVERT: A 1048 ARG cc_start: 0.8143 (ttt180) cc_final: 0.7682 (ttm110) REVERT: A 1110 TYR cc_start: 0.8877 (t80) cc_final: 0.8538 (t80) REVERT: A 1292 ILE cc_start: 0.8378 (pt) cc_final: 0.7992 (mp) REVERT: A 1322 MET cc_start: 0.8068 (mmm) cc_final: 0.7756 (mmm) REVERT: A 1473 ASP cc_start: 0.8081 (t70) cc_final: 0.7558 (m-30) REVERT: A 1482 ASN cc_start: 0.6903 (m110) cc_final: 0.6524 (t0) outliers start: 39 outliers final: 34 residues processed: 255 average time/residue: 0.4698 time to fit residues: 174.4576 Evaluate side-chains 261 residues out of total 1219 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 227 time to evaluate : 1.536 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 135 LEU Chi-restraints excluded: chain A residue 157 HIS Chi-restraints excluded: chain A residue 158 THR Chi-restraints excluded: chain A residue 170 PHE Chi-restraints excluded: chain A residue 217 ILE Chi-restraints excluded: chain A residue 264 GLU Chi-restraints excluded: chain A residue 303 THR Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain A residue 361 SER Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 379 SER Chi-restraints excluded: chain A residue 563 LEU Chi-restraints excluded: chain A residue 595 ILE Chi-restraints excluded: chain A residue 662 VAL Chi-restraints excluded: chain A residue 673 LEU Chi-restraints excluded: chain A residue 676 MET Chi-restraints excluded: chain A residue 765 ARG Chi-restraints excluded: chain A residue 801 LEU Chi-restraints excluded: chain A residue 817 LEU Chi-restraints excluded: chain A residue 994 ILE Chi-restraints excluded: chain A residue 1061 ASP Chi-restraints excluded: chain A residue 1073 VAL Chi-restraints excluded: chain A residue 1083 THR Chi-restraints excluded: chain A residue 1101 VAL Chi-restraints excluded: chain A residue 1113 THR Chi-restraints excluded: chain A residue 1186 ILE Chi-restraints excluded: chain A residue 1213 LEU Chi-restraints excluded: chain A residue 1231 VAL Chi-restraints excluded: chain A residue 1235 THR Chi-restraints excluded: chain A residue 1274 PHE Chi-restraints excluded: chain A residue 1349 LEU Chi-restraints excluded: chain A residue 1394 MET Chi-restraints excluded: chain A residue 1420 LEU Chi-restraints excluded: chain A residue 1452 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 129 optimal weight: 9.9990 chunk 15 optimal weight: 0.7980 chunk 76 optimal weight: 4.9990 chunk 98 optimal weight: 6.9990 chunk 113 optimal weight: 5.9990 chunk 75 optimal weight: 4.9990 chunk 133 optimal weight: 7.9990 chunk 83 optimal weight: 10.0000 chunk 81 optimal weight: 0.6980 chunk 61 optimal weight: 0.9990 chunk 82 optimal weight: 10.0000 overall best weight: 2.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1390 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7388 moved from start: 0.4761 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 11100 Z= 0.188 Angle : 0.545 5.947 15064 Z= 0.293 Chirality : 0.036 0.174 1774 Planarity : 0.003 0.041 1876 Dihedral : 5.228 70.822 1497 Min Nonbonded Distance : 2.252 Molprobity Statistics. All-atom Clashscore : 9.16 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.76 % Favored : 94.16 % Rotamer: Outliers : 3.00 % Allowed : 20.14 % Favored : 76.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.10 (0.23), residues: 1371 helix: 1.77 (0.17), residues: 926 sheet: -0.18 (0.51), residues: 77 loop : -1.84 (0.32), residues: 368 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A1014 HIS 0.005 0.001 HIS A 803 PHE 0.014 0.001 PHE A 115 TYR 0.014 0.001 TYR A1105 ARG 0.002 0.000 ARG A 485 *********************** 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 ILE 46 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 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 LYS 192 is missing expected H atoms. Skipping. Residue ILE 200 is missing expected H atoms. Skipping. Residue MET 458 is missing expected H atoms. Skipping. Residue LEU 497 is missing expected H atoms. Skipping. Residue LYS 517 is missing expected H atoms. Skipping. Residue LEU 522 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 MET 739 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 LEU 1417 is missing expected H atoms. Skipping. Residue LYS 1457 is missing expected H atoms. Skipping. Evaluate side-chains 271 residues out of total 1219 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 236 time to evaluate : 1.626 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: A 226 MET cc_start: 0.8649 (mmm) cc_final: 0.8366 (mmm) REVERT: A 442 LYS cc_start: 0.8577 (mmmt) cc_final: 0.8373 (mmtp) REVERT: A 467 ARG cc_start: 0.8382 (tpt170) cc_final: 0.7383 (mtm180) REVERT: A 485 ARG cc_start: 0.8372 (ttp80) cc_final: 0.7598 (mmp80) REVERT: A 504 LYS cc_start: 0.9026 (ttpp) cc_final: 0.8633 (tptt) REVERT: A 718 ASP cc_start: 0.8019 (t0) cc_final: 0.7309 (m-30) REVERT: A 789 ARG cc_start: 0.8637 (ttt180) cc_final: 0.8171 (tmt-80) REVERT: A 813 LYS cc_start: 0.8656 (tptm) cc_final: 0.8323 (tppt) REVERT: A 1048 ARG cc_start: 0.8138 (ttt180) cc_final: 0.7711 (ttm110) REVERT: A 1110 TYR cc_start: 0.8833 (t80) cc_final: 0.8508 (t80) REVERT: A 1292 ILE cc_start: 0.8333 (pt) cc_final: 0.7962 (mp) REVERT: A 1473 ASP cc_start: 0.8060 (t70) cc_final: 0.7555 (m-30) REVERT: A 1482 ASN cc_start: 0.6901 (m110) cc_final: 0.6520 (t0) outliers start: 35 outliers final: 34 residues processed: 248 average time/residue: 0.4604 time to fit residues: 164.2813 Evaluate side-chains 266 residues out of total 1219 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 232 time to evaluate : 1.551 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 135 LEU Chi-restraints excluded: chain A residue 157 HIS Chi-restraints excluded: chain A residue 158 THR Chi-restraints excluded: chain A residue 170 PHE Chi-restraints excluded: chain A residue 217 ILE Chi-restraints excluded: chain A residue 264 GLU Chi-restraints excluded: chain A residue 303 THR Chi-restraints excluded: chain A residue 361 SER Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 370 VAL Chi-restraints excluded: chain A residue 379 SER Chi-restraints excluded: chain A residue 563 LEU Chi-restraints excluded: chain A residue 595 ILE Chi-restraints excluded: chain A residue 662 VAL Chi-restraints excluded: chain A residue 673 LEU Chi-restraints excluded: chain A residue 676 MET Chi-restraints excluded: chain A residue 739 MET Chi-restraints excluded: chain A residue 765 ARG Chi-restraints excluded: chain A residue 801 LEU Chi-restraints excluded: chain A residue 817 LEU Chi-restraints excluded: chain A residue 994 ILE Chi-restraints excluded: chain A residue 1039 THR Chi-restraints excluded: chain A residue 1061 ASP Chi-restraints excluded: chain A residue 1073 VAL Chi-restraints excluded: chain A residue 1083 THR Chi-restraints excluded: chain A residue 1101 VAL Chi-restraints excluded: chain A residue 1113 THR Chi-restraints excluded: chain A residue 1186 ILE Chi-restraints excluded: chain A residue 1213 LEU Chi-restraints excluded: chain A residue 1231 VAL Chi-restraints excluded: chain A residue 1274 PHE Chi-restraints excluded: chain A residue 1349 LEU Chi-restraints excluded: chain A residue 1394 MET Chi-restraints excluded: chain A residue 1420 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 53 optimal weight: 5.9990 chunk 80 optimal weight: 0.0070 chunk 40 optimal weight: 1.9990 chunk 26 optimal weight: 3.9990 chunk 25 optimal weight: 0.9980 chunk 85 optimal weight: 7.9990 chunk 91 optimal weight: 8.9990 chunk 66 optimal weight: 2.9990 chunk 12 optimal weight: 5.9990 chunk 105 optimal weight: 3.9990 chunk 121 optimal weight: 20.0000 overall best weight: 2.0004 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1390 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7375 moved from start: 0.4823 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 11100 Z= 0.170 Angle : 0.531 5.969 15064 Z= 0.285 Chirality : 0.036 0.175 1774 Planarity : 0.003 0.040 1876 Dihedral : 5.122 69.407 1497 Min Nonbonded Distance : 2.219 Molprobity Statistics. All-atom Clashscore : 8.93 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.69 % Favored : 94.24 % Rotamer: Outliers : 2.66 % Allowed : 20.82 % Favored : 76.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.24 (0.23), residues: 1371 helix: 1.87 (0.17), residues: 928 sheet: -0.13 (0.55), residues: 71 loop : -1.74 (0.32), residues: 372 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A1014 HIS 0.005 0.001 HIS A 803 PHE 0.013 0.001 PHE A 115 TYR 0.012 0.001 TYR A1105 ARG 0.004 0.000 ARG A1346 *********************** 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 ILE 46 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 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 LYS 192 is missing expected H atoms. Skipping. Residue ILE 200 is missing expected H atoms. Skipping. Residue MET 458 is missing expected H atoms. Skipping. Residue LEU 497 is missing expected H atoms. Skipping. Residue LYS 517 is missing expected H atoms. Skipping. Residue LEU 522 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 MET 739 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 LEU 1417 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 fitting. rotamer outliers: 31 poor density : 239 time to evaluate : 1.628 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: A 226 MET cc_start: 0.8646 (mmm) cc_final: 0.8392 (mmm) REVERT: A 412 ASP cc_start: 0.8060 (m-30) cc_final: 0.7746 (m-30) REVERT: A 442 LYS cc_start: 0.8558 (mmmt) cc_final: 0.8116 (tttt) REVERT: A 467 ARG cc_start: 0.8386 (tpt170) cc_final: 0.7387 (mtp180) REVERT: A 485 ARG cc_start: 0.8310 (ttp80) cc_final: 0.7542 (mmp80) REVERT: A 504 LYS cc_start: 0.8979 (ttpp) cc_final: 0.8554 (tptt) REVERT: A 516 ASN cc_start: 0.7041 (t0) cc_final: 0.6829 (t0) REVERT: A 718 ASP cc_start: 0.8033 (t0) cc_final: 0.7328 (m-30) REVERT: A 789 ARG cc_start: 0.8587 (ttt180) cc_final: 0.8137 (tmt-80) REVERT: A 813 LYS cc_start: 0.8598 (tptm) cc_final: 0.8275 (tppt) REVERT: A 971 TRP cc_start: 0.6788 (m-10) cc_final: 0.6377 (m-10) REVERT: A 1029 MET cc_start: 0.8443 (tpp) cc_final: 0.8213 (tpp) REVERT: A 1048 ARG cc_start: 0.8137 (ttt180) cc_final: 0.7667 (ttm110) REVERT: A 1110 TYR cc_start: 0.8853 (t80) cc_final: 0.8568 (t80) REVERT: A 1292 ILE cc_start: 0.8325 (pt) cc_final: 0.7982 (mp) REVERT: A 1461 ILE cc_start: 0.7702 (pp) cc_final: 0.7347 (mp) REVERT: A 1473 ASP cc_start: 0.8047 (t70) cc_final: 0.7523 (m-30) REVERT: A 1482 ASN cc_start: 0.6901 (m110) cc_final: 0.6520 (t0) outliers start: 31 outliers final: 30 residues processed: 250 average time/residue: 0.4737 time to fit residues: 171.9383 Evaluate side-chains 262 residues out of total 1219 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 232 time to evaluate : 1.641 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 135 LEU Chi-restraints excluded: chain A residue 157 HIS Chi-restraints excluded: chain A residue 158 THR Chi-restraints excluded: chain A residue 170 PHE Chi-restraints excluded: chain A residue 217 ILE Chi-restraints excluded: chain A residue 264 GLU Chi-restraints excluded: chain A residue 303 THR Chi-restraints excluded: chain A residue 370 VAL Chi-restraints excluded: chain A residue 379 SER Chi-restraints excluded: chain A residue 595 ILE Chi-restraints excluded: chain A residue 662 VAL Chi-restraints excluded: chain A residue 673 LEU Chi-restraints excluded: chain A residue 676 MET Chi-restraints excluded: chain A residue 739 MET Chi-restraints excluded: chain A residue 765 ARG Chi-restraints excluded: chain A residue 801 LEU Chi-restraints excluded: chain A residue 802 LEU Chi-restraints excluded: chain A residue 817 LEU Chi-restraints excluded: chain A residue 994 ILE Chi-restraints excluded: chain A residue 1039 THR Chi-restraints excluded: chain A residue 1061 ASP Chi-restraints excluded: chain A residue 1073 VAL Chi-restraints excluded: chain A residue 1083 THR Chi-restraints excluded: chain A residue 1186 ILE Chi-restraints excluded: chain A residue 1213 LEU Chi-restraints excluded: chain A residue 1231 VAL Chi-restraints excluded: chain A residue 1274 PHE Chi-restraints excluded: chain A residue 1349 LEU Chi-restraints excluded: chain A residue 1394 MET Chi-restraints excluded: chain A residue 1420 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 128 optimal weight: 4.9990 chunk 117 optimal weight: 9.9990 chunk 124 optimal weight: 20.0000 chunk 75 optimal weight: 0.8980 chunk 54 optimal weight: 0.8980 chunk 98 optimal weight: 6.9990 chunk 38 optimal weight: 0.8980 chunk 112 optimal weight: 0.6980 chunk 118 optimal weight: 20.0000 chunk 81 optimal weight: 5.9990 chunk 132 optimal weight: 8.9990 overall best weight: 1.6782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1390 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7366 moved from start: 0.4902 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 11100 Z= 0.160 Angle : 0.528 6.187 15064 Z= 0.283 Chirality : 0.036 0.173 1774 Planarity : 0.003 0.040 1876 Dihedral : 5.048 68.411 1497 Min Nonbonded Distance : 2.213 Molprobity Statistics. All-atom Clashscore : 8.66 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.54 % Favored : 94.38 % Rotamer: Outliers : 2.31 % Allowed : 21.59 % Favored : 76.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.37 (0.23), residues: 1371 helix: 1.97 (0.17), residues: 927 sheet: -0.00 (0.55), residues: 71 loop : -1.70 (0.33), residues: 373 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A1014 HIS 0.005 0.001 HIS A 803 PHE 0.038 0.001 PHE A1320 TYR 0.018 0.001 TYR A 500 ARG 0.006 0.000 ARG A 682 *********************** 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 ILE 46 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 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 LYS 192 is missing expected H atoms. Skipping. Residue ILE 200 is missing expected H atoms. Skipping. Residue MET 458 is missing expected H atoms. Skipping. Residue LEU 497 is missing expected H atoms. Skipping. Residue LYS 517 is missing expected H atoms. Skipping. Residue LEU 522 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 MET 739 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 LEU 1417 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 fitting. rotamer outliers: 27 poor density : 238 time to evaluate : 1.545 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: A 226 MET cc_start: 0.8633 (mmm) cc_final: 0.8391 (mmm) REVERT: A 412 ASP cc_start: 0.8002 (m-30) cc_final: 0.7671 (m-30) REVERT: A 442 LYS cc_start: 0.8556 (mmmt) cc_final: 0.8107 (tttt) REVERT: A 466 MET cc_start: 0.7646 (ppp) cc_final: 0.7387 (ppp) REVERT: A 467 ARG cc_start: 0.8407 (tpt170) cc_final: 0.7391 (mtp180) REVERT: A 485 ARG cc_start: 0.8365 (ttp80) cc_final: 0.7567 (mmp80) REVERT: A 504 LYS cc_start: 0.8966 (ttpp) cc_final: 0.8521 (tptt) REVERT: A 516 ASN cc_start: 0.7091 (t0) cc_final: 0.6872 (t0) REVERT: A 718 ASP cc_start: 0.8035 (t0) cc_final: 0.7359 (m-30) REVERT: A 789 ARG cc_start: 0.8566 (ttt180) cc_final: 0.8107 (tmt-80) REVERT: A 813 LYS cc_start: 0.8593 (tptm) cc_final: 0.8282 (tppt) REVERT: A 962 MET cc_start: 0.8580 (tpp) cc_final: 0.8268 (tpp) REVERT: A 971 TRP cc_start: 0.6742 (m-10) cc_final: 0.6342 (m-10) REVERT: A 1029 MET cc_start: 0.8437 (tpp) cc_final: 0.8215 (tpp) REVERT: A 1048 ARG cc_start: 0.8110 (ttt180) cc_final: 0.7686 (ttm110) REVERT: A 1110 TYR cc_start: 0.8834 (t80) cc_final: 0.8499 (t80) REVERT: A 1292 ILE cc_start: 0.8316 (pt) cc_final: 0.7934 (mp) REVERT: A 1405 GLU cc_start: 0.7976 (mt-10) cc_final: 0.7342 (mt-10) REVERT: A 1473 ASP cc_start: 0.8034 (t70) cc_final: 0.7523 (m-30) REVERT: A 1482 ASN cc_start: 0.6897 (m110) cc_final: 0.6517 (t0) outliers start: 27 outliers final: 26 residues processed: 247 average time/residue: 0.4969 time to fit residues: 182.1679 Evaluate side-chains 260 residues out of total 1219 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 234 time to evaluate : 1.490 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 135 LEU Chi-restraints excluded: chain A residue 157 HIS Chi-restraints excluded: chain A residue 217 ILE Chi-restraints excluded: chain A residue 264 GLU Chi-restraints excluded: chain A residue 303 THR Chi-restraints excluded: chain A residue 370 VAL Chi-restraints excluded: chain A residue 379 SER Chi-restraints excluded: chain A residue 595 ILE Chi-restraints excluded: chain A residue 662 VAL Chi-restraints excluded: chain A residue 673 LEU Chi-restraints excluded: chain A residue 676 MET Chi-restraints excluded: chain A residue 739 MET Chi-restraints excluded: chain A residue 765 ARG Chi-restraints excluded: chain A residue 801 LEU Chi-restraints excluded: chain A residue 817 LEU Chi-restraints excluded: chain A residue 994 ILE Chi-restraints excluded: chain A residue 1061 ASP Chi-restraints excluded: chain A residue 1073 VAL Chi-restraints excluded: chain A residue 1083 THR Chi-restraints excluded: chain A residue 1186 ILE Chi-restraints excluded: chain A residue 1213 LEU Chi-restraints excluded: chain A residue 1231 VAL Chi-restraints excluded: chain A residue 1274 PHE Chi-restraints excluded: chain A residue 1349 LEU Chi-restraints excluded: chain A residue 1394 MET Chi-restraints excluded: chain A residue 1420 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 80 optimal weight: 6.9990 chunk 62 optimal weight: 7.9990 chunk 91 optimal weight: 0.9980 chunk 138 optimal weight: 20.0000 chunk 127 optimal weight: 0.6980 chunk 110 optimal weight: 5.9990 chunk 11 optimal weight: 6.9990 chunk 85 optimal weight: 6.9990 chunk 67 optimal weight: 5.9990 chunk 87 optimal weight: 1.9990 chunk 117 optimal weight: 5.9990 overall best weight: 3.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1390 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7398 moved from start: 0.5050 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 11100 Z= 0.213 Angle : 0.551 5.946 15064 Z= 0.301 Chirality : 0.037 0.208 1774 Planarity : 0.003 0.042 1876 Dihedral : 5.111 69.350 1497 Min Nonbonded Distance : 2.161 Molprobity Statistics. All-atom Clashscore : 9.35 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.69 % Favored : 94.24 % Rotamer: Outliers : 2.74 % Allowed : 21.42 % Favored : 75.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.24 (0.23), residues: 1371 helix: 1.85 (0.17), residues: 927 sheet: -0.05 (0.55), residues: 75 loop : -1.72 (0.33), residues: 369 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A1014 HIS 0.006 0.001 HIS A 803 PHE 0.031 0.001 PHE A1320 TYR 0.015 0.001 TYR A1105 ARG 0.003 0.000 ARG A1179 ********************** 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 ILE 46 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 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 LYS 192 is missing expected H atoms. Skipping. Residue ILE 200 is missing expected H atoms. Skipping. Residue MET 458 is missing expected H atoms. Skipping. Residue LEU 497 is missing expected H atoms. Skipping. Residue LYS 517 is missing expected H atoms. Skipping. Residue LEU 522 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 MET 739 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 LEU 1417 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 fitting. rotamer outliers: 32 poor density : 234 time to evaluate : 1.687 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: A 412 ASP cc_start: 0.8062 (m-30) cc_final: 0.7739 (m-30) REVERT: A 442 LYS cc_start: 0.8627 (mmmt) cc_final: 0.8123 (tttt) REVERT: A 466 MET cc_start: 0.7619 (ppp) cc_final: 0.7365 (ppp) REVERT: A 467 ARG cc_start: 0.8453 (tpt170) cc_final: 0.7425 (mtm180) REVERT: A 485 ARG cc_start: 0.8316 (ttp80) cc_final: 0.7568 (mmp80) REVERT: A 495 LYS cc_start: 0.9541 (pttm) cc_final: 0.9324 (ptpp) REVERT: A 504 LYS cc_start: 0.8983 (ttpp) cc_final: 0.8544 (tptt) REVERT: A 516 ASN cc_start: 0.7093 (t0) cc_final: 0.6890 (t0) REVERT: A 718 ASP cc_start: 0.8091 (t0) cc_final: 0.7348 (m-30) REVERT: A 789 ARG cc_start: 0.8613 (ttt180) cc_final: 0.8169 (tmt-80) REVERT: A 813 LYS cc_start: 0.8640 (tptm) cc_final: 0.8325 (tppt) REVERT: A 1029 MET cc_start: 0.8428 (tpp) cc_final: 0.8205 (tpp) REVERT: A 1048 ARG cc_start: 0.8174 (ttt180) cc_final: 0.7756 (ttm110) REVERT: A 1110 TYR cc_start: 0.8890 (t80) cc_final: 0.8549 (t80) REVERT: A 1292 ILE cc_start: 0.8354 (pt) cc_final: 0.7997 (mp) REVERT: A 1482 ASN cc_start: 0.6937 (m110) cc_final: 0.6564 (t0) outliers start: 32 outliers final: 30 residues processed: 246 average time/residue: 0.4709 time to fit residues: 168.6422 Evaluate side-chains 261 residues out of total 1219 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 231 time to evaluate : 1.610 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 135 LEU Chi-restraints excluded: chain A residue 157 HIS Chi-restraints excluded: chain A residue 191 LYS Chi-restraints excluded: chain A residue 217 ILE Chi-restraints excluded: chain A residue 264 GLU Chi-restraints excluded: chain A residue 303 THR Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 370 VAL Chi-restraints excluded: chain A residue 379 SER Chi-restraints excluded: chain A residue 595 ILE Chi-restraints excluded: chain A residue 662 VAL Chi-restraints excluded: chain A residue 673 LEU Chi-restraints excluded: chain A residue 676 MET Chi-restraints excluded: chain A residue 739 MET Chi-restraints excluded: chain A residue 765 ARG Chi-restraints excluded: chain A residue 801 LEU Chi-restraints excluded: chain A residue 817 LEU Chi-restraints excluded: chain A residue 994 ILE Chi-restraints excluded: chain A residue 1013 LEU Chi-restraints excluded: chain A residue 1061 ASP Chi-restraints excluded: chain A residue 1073 VAL Chi-restraints excluded: chain A residue 1083 THR Chi-restraints excluded: chain A residue 1186 ILE Chi-restraints excluded: chain A residue 1213 LEU Chi-restraints excluded: chain A residue 1231 VAL Chi-restraints excluded: chain A residue 1274 PHE Chi-restraints excluded: chain A residue 1320 PHE Chi-restraints excluded: chain A residue 1349 LEU Chi-restraints excluded: chain A residue 1420 LEU Chi-restraints excluded: chain A residue 1477 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 33 optimal weight: 4.9990 chunk 101 optimal weight: 4.9990 chunk 16 optimal weight: 5.9990 chunk 30 optimal weight: 9.9990 chunk 110 optimal weight: 3.9990 chunk 46 optimal weight: 0.9990 chunk 113 optimal weight: 3.9990 chunk 13 optimal weight: 8.9990 chunk 20 optimal weight: 5.9990 chunk 96 optimal weight: 9.9990 chunk 6 optimal weight: 5.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4199 r_free = 0.4199 target = 0.146063 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3865 r_free = 0.3865 target = 0.118741 restraints weight = 81060.791| |-----------------------------------------------------------------------------| r_work (start): 0.3807 rms_B_bonded: 4.18 r_work: 0.3669 rms_B_bonded: 4.17 restraints_weight: 0.5000 r_work (final): 0.3669 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3687 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3687 r_free = 0.3687 target_work(ls_wunit_k1) = 0.108 | | occupancies: max = 1.00 min = 0.58 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3686 r_free = 0.3686 target_work(ls_wunit_k1) = 0.108 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3686 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7397 moved from start: 0.5189 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 11100 Z= 0.239 Angle : 0.565 6.935 15064 Z= 0.308 Chirality : 0.037 0.210 1774 Planarity : 0.003 0.043 1876 Dihedral : 5.156 69.939 1497 Min Nonbonded Distance : 2.144 Molprobity Statistics. All-atom Clashscore : 9.48 Ramachandran Plot: Outliers : 0.07 % Allowed : 6.05 % Favored : 93.87 % Rotamer: Outliers : 2.66 % Allowed : 21.59 % Favored : 75.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.17 (0.23), residues: 1371 helix: 1.78 (0.17), residues: 928 sheet: -0.04 (0.55), residues: 75 loop : -1.71 (0.33), residues: 368 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A1014 HIS 0.006 0.001 HIS A 803 PHE 0.032 0.001 PHE A1320 TYR 0.017 0.001 TYR A 500 ARG 0.002 0.000 ARG A1179 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5035.84 seconds wall clock time: 88 minutes 26.00 seconds (5306.00 seconds total)