Starting phenix.real_space_refine on Wed Feb 4 14:22:31 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9lgd_63062/02_2026/9lgd_63062_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/9lgd_63062/02_2026/9lgd_63062.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.29 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9lgd_63062/02_2026/9lgd_63062.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9lgd_63062/02_2026/9lgd_63062.map" model { file = "/net/cci-nas-00/data/ceres_data/9lgd_63062/02_2026/9lgd_63062_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9lgd_63062/02_2026/9lgd_63062_neut.cif" } resolution = 3.29 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 sd= 0.071 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 Mg 1 5.21 5 S 57 5.16 5 C 7049 2.51 5 N 1805 2.21 5 O 1941 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 39 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 10856 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 10824 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1362, 10824 Classifications: {'peptide': 1362} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 48, 'TRANS': 1313} Chain breaks: 8 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Chain: "A" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 1.98, per 1000 atoms: 0.18 Number of scatterers: 10856 At special positions: 0 Unit cell: (78, 111.28, 145.6, 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 57 16.00 P 3 15.00 Mg 1 11.99 O 1941 8.00 N 1805 7.00 C 7049 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.91 Conformation dependent library (CDL) restraints added in 360.4 milliseconds 2688 Ramachandran restraints generated. 1344 Oldfield, 0 Emsley, 1344 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2580 Finding SS restraints... Secondary structure from input PDB file: 54 helices and 6 sheets defined 69.1% alpha, 5.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.41 Creating SS restraints... Processing helix chain 'A' and resid 17 through 22 removed outlier: 3.654A pdb=" N THR A 21 " --> pdb=" O GLU A 17 " (cutoff:3.500A) Processing helix chain 'A' and resid 30 through 60 removed outlier: 3.959A pdb=" N LEU A 38 " --> pdb=" O GLN A 34 " (cutoff:3.500A) removed outlier: 5.027A pdb=" N VAL A 39 " --> pdb=" O ASN A 35 " (cutoff:3.500A) Proline residue: A 42 - end of helix Proline residue: A 51 - end of helix removed outlier: 3.866A pdb=" N LEU A 55 " --> pdb=" O PRO A 51 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N TYR A 56 " --> pdb=" O PHE A 52 " (cutoff:3.500A) Processing helix chain 'A' and resid 68 through 94 removed outlier: 3.696A pdb=" N LEU A 89 " --> pdb=" O CYS A 85 " (cutoff:3.500A) Processing helix chain 'A' and resid 104 through 130 removed outlier: 3.577A pdb=" N VAL A 108 " --> pdb=" O PRO A 104 " (cutoff:3.500A) Proline residue: A 110 - end of helix Processing helix chain 'A' and resid 137 through 160 Processing helix chain 'A' and resid 171 through 191 removed outlier: 3.544A pdb=" N PHE A 175 " --> pdb=" O ARG A 171 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N PHE A 191 " --> pdb=" O VAL A 187 " (cutoff:3.500A) Processing helix chain 'A' and resid 214 through 221 Processing helix chain 'A' and resid 224 through 234 Processing helix chain 'A' and resid 249 through 268 Proline residue: A 255 - end of helix Processing helix chain 'A' and resid 312 through 322 removed outlier: 3.765A pdb=" N VAL A 316 " --> pdb=" O SER A 312 " (cutoff:3.500A) Processing helix chain 'A' and resid 325 through 340 Processing helix chain 'A' and resid 340 through 354 removed outlier: 4.329A pdb=" N GLU A 344 " --> pdb=" O PHE A 340 " (cutoff:3.500A) Processing helix chain 'A' and resid 359 through 410 removed outlier: 4.086A pdb=" N GLY A 363 " --> pdb=" O PRO A 359 " (cutoff:3.500A) Processing helix chain 'A' and resid 411 through 418 Processing helix chain 'A' and resid 419 through 427 Processing helix chain 'A' and resid 429 through 441 removed outlier: 3.579A pdb=" N THR A 439 " --> pdb=" O MET A 435 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N TYR A 440 " --> pdb=" O ASP A 436 " (cutoff:3.500A) Processing helix chain 'A' and resid 442 through 460 removed outlier: 3.672A pdb=" N SER A 446 " --> pdb=" O ASN A 442 " (cutoff:3.500A) Proline residue: A 448 - end of helix Processing helix chain 'A' and resid 466 through 511 Proline residue: A 478 - end of helix removed outlier: 3.600A pdb=" N THR A 489 " --> pdb=" O MET A 485 " (cutoff:3.500A) removed outlier: 4.390A pdb=" N ALA A 493 " --> pdb=" O THR A 489 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N ASP A 499 " --> pdb=" O MET A 495 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N ASN A 500 " --> pdb=" O LYS A 496 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N ARG A 501 " --> pdb=" O SER A 497 " (cutoff:3.500A) Processing helix chain 'A' and resid 511 through 518 Processing helix chain 'A' and resid 521 through 572 removed outlier: 3.859A pdb=" N LYS A 527 " --> pdb=" O ALA A 523 " (cutoff:3.500A) removed outlier: 4.254A pdb=" N ALA A 530 " --> pdb=" O ASP A 526 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N ILE A 531 " --> pdb=" O LYS A 527 " (cutoff:3.500A) removed outlier: 5.117A pdb=" N GLN A 533 " --> pdb=" O LEU A 529 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N GLU A 534 " --> pdb=" O ALA A 530 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N VAL A 538 " --> pdb=" O GLU A 534 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N LEU A 539 " --> pdb=" O GLU A 535 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N THR A 552 " --> pdb=" O VAL A 548 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N TRP A 553 " --> pdb=" O GLY A 549 " (cutoff:3.500A) Proline residue: A 557 - end of helix removed outlier: 3.678A pdb=" N THR A 570 " --> pdb=" O ALA A 566 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N ASP A 572 " --> pdb=" O TYR A 568 " (cutoff:3.500A) Processing helix chain 'A' and resid 578 through 592 Processing helix chain 'A' and resid 592 through 597 removed outlier: 3.826A pdb=" N LEU A 596 " --> pdb=" O LEU A 592 " (cutoff:3.500A) Processing helix chain 'A' and resid 598 through 621 removed outlier: 3.506A pdb=" N ARG A 615 " --> pdb=" O VAL A 611 " (cutoff:3.500A) Processing helix chain 'A' and resid 683 through 692 removed outlier: 3.941A pdb=" N LEU A 688 " --> pdb=" O LYS A 684 " (cutoff:3.500A) Processing helix chain 'A' and resid 721 through 728 Processing helix chain 'A' and resid 733 through 744 removed outlier: 3.682A pdb=" N ALA A 739 " --> pdb=" O ARG A 735 " (cutoff:3.500A) Processing helix chain 'A' and resid 748 through 753 removed outlier: 4.030A pdb=" N ILE A 752 " --> pdb=" O PRO A 748 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N LEU A 753 " --> pdb=" O ASP A 749 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 748 through 753' Processing helix chain 'A' and resid 769 through 784 removed outlier: 3.500A pdb=" N LYS A 773 " --> pdb=" O SER A 769 " (cutoff:3.500A) removed outlier: 4.165A pdb=" N GLN A 774 " --> pdb=" O GLY A 770 " (cutoff:3.500A) Processing helix chain 'A' and resid 799 through 810 Processing helix chain 'A' and resid 831 through 835 Processing helix chain 'A' and resid 852 through 857 removed outlier: 3.785A pdb=" N ALA A 857 " --> pdb=" O GLN A 853 " (cutoff:3.500A) Processing helix chain 'A' and resid 862 through 869 Processing helix chain 'A' and resid 958 through 970 removed outlier: 4.014A pdb=" N TYR A 962 " --> pdb=" O LYS A 958 " (cutoff:3.500A) Processing helix chain 'A' and resid 971 through 998 removed outlier: 4.338A pdb=" N ILE A 978 " --> pdb=" O SER A 974 " (cutoff:3.500A) Processing helix chain 'A' and resid 1008 through 1058 removed outlier: 3.506A pdb=" N GLN A1012 " --> pdb=" O GLN A1008 " (cutoff:3.500A) Processing helix chain 'A' and resid 1059 through 1066 removed outlier: 3.631A pdb=" N PHE A1063 " --> pdb=" O PRO A1059 " (cutoff:3.500A) Processing helix chain 'A' and resid 1069 through 1084 removed outlier: 4.090A pdb=" N GLU A1078 " --> pdb=" O ARG A1074 " (cutoff:3.500A) removed outlier: 5.300A pdb=" N LEU A1079 " --> pdb=" O PHE A1075 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ASP A1080 " --> pdb=" O SER A1076 " (cutoff:3.500A) Processing helix chain 'A' and resid 1084 through 1111 removed outlier: 3.908A pdb=" N GLN A1088 " --> pdb=" O SER A1084 " (cutoff:3.500A) Processing helix chain 'A' and resid 1117 through 1160 removed outlier: 3.573A pdb=" N TYR A1125 " --> pdb=" O LEU A1121 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N VAL A1128 " --> pdb=" O ILE A1124 " (cutoff:3.500A) removed outlier: 4.246A pdb=" N SER A1135 " --> pdb=" O PHE A1131 " (cutoff:3.500A) removed outlier: 4.559A pdb=" N GLN A1138 " --> pdb=" O ALA A1134 " (cutoff:3.500A) Proline residue: A1149 - end of helix Processing helix chain 'A' and resid 1160 through 1168 Processing helix chain 'A' and resid 1169 through 1220 removed outlier: 3.901A pdb=" N PHE A1173 " --> pdb=" O GLU A1169 " (cutoff:3.500A) Proline residue: A1190 - end of helix removed outlier: 3.528A pdb=" N ASN A1207 " --> pdb=" O GLU A1203 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N LEU A1211 " --> pdb=" O ASN A1207 " (cutoff:3.500A) Processing helix chain 'A' and resid 1230 through 1266 removed outlier: 3.986A pdb=" N SER A1234 " --> pdb=" O GLY A1230 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N THR A1241 " --> pdb=" O LEU A1237 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N TYR A1242 " --> pdb=" O GLN A1238 " (cutoff:3.500A) removed outlier: 4.084A pdb=" N ALA A1259 " --> pdb=" O THR A1255 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N VAL A1260 " --> pdb=" O ASN A1256 " (cutoff:3.500A) removed outlier: 4.197A pdb=" N TYR A1266 " --> pdb=" O ARG A1262 " (cutoff:3.500A) Processing helix chain 'A' and resid 1331 through 1333 No H-bonds generated for 'chain 'A' and resid 1331 through 1333' Processing helix chain 'A' and resid 1334 through 1340 removed outlier: 3.644A pdb=" N PHE A1340 " --> pdb=" O THR A1336 " (cutoff:3.500A) Processing helix chain 'A' and resid 1362 through 1368 Processing helix chain 'A' and resid 1394 through 1405 Processing helix chain 'A' and resid 1407 through 1412 Processing helix chain 'A' and resid 1416 through 1419 Processing helix chain 'A' and resid 1423 through 1427 removed outlier: 3.933A pdb=" N GLU A1427 " --> pdb=" O GLU A1424 " (cutoff:3.500A) Processing helix chain 'A' and resid 1431 through 1446 Processing helix chain 'A' and resid 1460 through 1475 Processing helix chain 'A' and resid 1486 through 1492 removed outlier: 3.836A pdb=" N ILE A1490 " --> pdb=" O ARG A1486 " (cutoff:3.500A) removed outlier: 4.231A pdb=" N ASP A1492 " --> pdb=" O ASN A1488 " (cutoff:3.500A) Processing helix chain 'A' and resid 1509 through 1517 removed outlier: 3.567A pdb=" N ARG A1517 " --> pdb=" O LEU A1513 " (cutoff:3.500A) Processing helix chain 'A' and resid 1518 through 1528 Processing sheet with id=AA1, first strand: chain 'A' and resid 664 through 669 removed outlier: 7.447A pdb=" N ILE A 664 " --> pdb=" O LYS A 647 " (cutoff:3.500A) removed outlier: 4.730A pdb=" N LYS A 647 " --> pdb=" O ILE A 664 " (cutoff:3.500A) removed outlier: 6.402A pdb=" N PHE A 666 " --> pdb=" O THR A 645 " (cutoff:3.500A) removed outlier: 4.428A pdb=" N THR A 645 " --> pdb=" O PHE A 666 " (cutoff:3.500A) removed outlier: 6.722A pdb=" N VAL A 668 " --> pdb=" O SER A 643 " (cutoff:3.500A) removed outlier: 6.830A pdb=" N THR A 650 " --> pdb=" O VAL A 698 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 708 through 711 removed outlier: 6.659A pdb=" N ALA A 709 " --> pdb=" O LEU A 790 " (cutoff:3.500A) removed outlier: 6.525A pdb=" N SER A 842 " --> pdb=" O ILE A 846 " (cutoff:3.500A) removed outlier: 5.468A pdb=" N ILE A 846 " --> pdb=" O SER A 842 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 1312 through 1315 removed outlier: 5.143A pdb=" N ILE A1312 " --> pdb=" O ASP A1296 " (cutoff:3.500A) removed outlier: 5.601A pdb=" N PHE A1294 " --> pdb=" O ILE A1351 " (cutoff:3.500A) removed outlier: 7.259A pdb=" N ILE A1351 " --> pdb=" O PHE A1294 " (cutoff:3.500A) removed outlier: 5.577A pdb=" N ASP A1296 " --> pdb=" O GLU A1349 " (cutoff:3.500A) removed outlier: 4.990A pdb=" N GLU A1349 " --> pdb=" O ASP A1296 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N GLU A1347 " --> pdb=" O GLY A1298 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N ILE A1355 " --> pdb=" O ILE A1352 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 1325 through 1326 removed outlier: 6.325A pdb=" N VAL A1325 " --> pdb=" O LEU A1499 " (cutoff:3.500A) removed outlier: 6.915A pdb=" N VAL A1498 " --> pdb=" O GLN A1505 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N GLN A1505 " --> pdb=" O VAL A1498 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'A' and resid 1370 through 1372 removed outlier: 6.760A pdb=" N ILE A1483 " --> pdb=" O LEU A1450 " (cutoff:3.500A) removed outlier: 5.734A pdb=" N LEU A1452 " --> pdb=" O ILE A1483 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 1381 through 1382 removed outlier: 4.094A pdb=" N GLY A1381 " --> pdb=" O CYS A1422 " (cutoff:3.500A) 662 hydrogen bonds defined for protein. 1968 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: 1.51 Time building geometry restraints manager: 1.14 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 2718 1.33 - 1.45: 2137 1.45 - 1.57: 6143 1.57 - 1.69: 5 1.69 - 1.81: 93 Bond restraints: 11096 Sorted by residual: bond pdb=" CA PRO A 658 " pdb=" C PRO A 658 " ideal model delta sigma weight residual 1.514 1.535 -0.021 5.50e-03 3.31e+04 1.43e+01 bond pdb=" N VAL A1496 " pdb=" CA VAL A1496 " ideal model delta sigma weight residual 1.459 1.503 -0.044 1.25e-02 6.40e+03 1.24e+01 bond pdb=" N VAL A1239 " pdb=" CA VAL A1239 " ideal model delta sigma weight residual 1.461 1.498 -0.037 1.17e-02 7.31e+03 1.00e+01 bond pdb=" N ILE A 115 " pdb=" CA ILE A 115 " ideal model delta sigma weight residual 1.460 1.497 -0.038 1.21e-02 6.83e+03 9.78e+00 bond pdb=" C PRO A 658 " pdb=" O PRO A 658 " ideal model delta sigma weight residual 1.246 1.219 0.027 8.50e-03 1.38e+04 9.76e+00 ... (remaining 11091 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.54: 13949 1.54 - 3.09: 982 3.09 - 4.63: 117 4.63 - 6.17: 15 6.17 - 7.71: 4 Bond angle restraints: 15067 Sorted by residual: angle pdb=" PB ATP A1601 " pdb=" O3B ATP A1601 " pdb=" PG ATP A1601 " ideal model delta sigma weight residual 139.87 132.16 7.71 1.00e+00 1.00e+00 5.95e+01 angle pdb=" PA ATP A1601 " pdb=" O3A ATP A1601 " pdb=" PB ATP A1601 " ideal model delta sigma weight residual 136.83 129.66 7.17 1.00e+00 1.00e+00 5.13e+01 angle pdb=" N GLU A1009 " pdb=" CA GLU A1009 " pdb=" C GLU A1009 " ideal model delta sigma weight residual 112.23 105.56 6.67 1.26e+00 6.30e-01 2.80e+01 angle pdb=" N ASN A 575 " pdb=" CA ASN A 575 " pdb=" C ASN A 575 " ideal model delta sigma weight residual 112.72 107.35 5.37 1.14e+00 7.69e-01 2.21e+01 angle pdb=" CA ASP A 792 " pdb=" C ASP A 792 " pdb=" O ASP A 792 " ideal model delta sigma weight residual 122.37 117.96 4.41 1.15e+00 7.56e-01 1.47e+01 ... (remaining 15062 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.85: 5734 17.85 - 35.70: 662 35.70 - 53.56: 159 53.56 - 71.41: 47 71.41 - 89.26: 7 Dihedral angle restraints: 6609 sinusoidal: 2630 harmonic: 3979 Sorted by residual: dihedral pdb=" CA ASP A1492 " pdb=" CB ASP A1492 " pdb=" CG ASP A1492 " pdb=" OD1 ASP A1492 " ideal model delta sinusoidal sigma weight residual -30.00 -89.07 59.07 1 2.00e+01 2.50e-03 1.17e+01 dihedral pdb=" CB GLU A1078 " pdb=" CG GLU A1078 " pdb=" CD GLU A1078 " pdb=" OE1 GLU A1078 " ideal model delta sinusoidal sigma weight residual 0.00 89.26 -89.26 1 3.00e+01 1.11e-03 1.05e+01 dihedral pdb=" CG ARG A1441 " pdb=" CD ARG A1441 " pdb=" NE ARG A1441 " pdb=" CZ ARG A1441 " ideal model delta sinusoidal sigma weight residual 180.00 136.00 44.00 2 1.50e+01 4.44e-03 1.03e+01 ... (remaining 6606 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.054: 1334 0.054 - 0.107: 300 0.107 - 0.161: 96 0.161 - 0.214: 21 0.214 - 0.268: 2 Chirality restraints: 1753 Sorted by residual: chirality pdb=" CA PHE A1216 " pdb=" N PHE A1216 " pdb=" C PHE A1216 " pdb=" CB PHE A1216 " both_signs ideal model delta sigma weight residual False 2.51 2.78 -0.27 2.00e-01 2.50e+01 1.79e+00 chirality pdb=" CA LYS A1525 " pdb=" N LYS A1525 " pdb=" C LYS A1525 " pdb=" CB LYS A1525 " both_signs ideal model delta sigma weight residual False 2.51 2.75 -0.24 2.00e-01 2.50e+01 1.42e+00 chirality pdb=" CA LEU A 241 " pdb=" N LEU A 241 " pdb=" C LEU A 241 " pdb=" CB LEU A 241 " both_signs ideal model delta sigma weight residual False 2.51 2.72 -0.21 2.00e-01 2.50e+01 1.14e+00 ... (remaining 1750 not shown) Planarity restraints: 1859 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ILE A 350 " -0.021 2.00e-02 2.50e+03 4.10e-02 1.68e+01 pdb=" C ILE A 350 " 0.071 2.00e-02 2.50e+03 pdb=" O ILE A 350 " -0.026 2.00e-02 2.50e+03 pdb=" N ASN A 351 " -0.024 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA TYR A 993 " 0.017 2.00e-02 2.50e+03 3.43e-02 1.18e+01 pdb=" C TYR A 993 " -0.059 2.00e-02 2.50e+03 pdb=" O TYR A 993 " 0.022 2.00e-02 2.50e+03 pdb=" N TRP A 994 " 0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A1147 " 0.274 9.50e-02 1.11e+02 1.23e-01 9.30e+00 pdb=" NE ARG A1147 " -0.018 2.00e-02 2.50e+03 pdb=" CZ ARG A1147 " 0.001 2.00e-02 2.50e+03 pdb=" NH1 ARG A1147 " -0.004 2.00e-02 2.50e+03 pdb=" NH2 ARG A1147 " 0.008 2.00e-02 2.50e+03 ... (remaining 1856 not shown) Histogram of nonbonded interaction distances: 1.89 - 2.49: 29 2.49 - 3.09: 7973 3.09 - 3.69: 16666 3.69 - 4.30: 24066 4.30 - 4.90: 40367 Nonbonded interactions: 89101 Sorted by model distance: nonbonded pdb=" OG SER A 685 " pdb="MG MG A1602 " model vdw 1.887 2.170 nonbonded pdb=" OE1 GLN A 713 " pdb="MG MG A1602 " model vdw 2.010 2.170 nonbonded pdb=" O THR A 703 " pdb=" OG1 THR A 703 " model vdw 2.304 3.040 nonbonded pdb=" OD2 ASP A 336 " pdb=" OG SER A 446 " model vdw 2.313 3.040 nonbonded pdb=" OG SER A1044 " pdb=" OD1 ASP A1083 " model vdw 2.320 3.040 ... (remaining 89096 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=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.020 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: 0.000 Extract box with map and model: 0.160 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 9.460 Find NCS groups from input model: 0.150 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.160 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 13.030 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7620 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 0.044 11096 Z= 0.415 Angle : 0.800 7.715 15067 Z= 0.582 Chirality : 0.054 0.268 1753 Planarity : 0.006 0.123 1859 Dihedral : 16.483 89.260 4029 Min Nonbonded Distance : 1.887 Molprobity Statistics. All-atom Clashscore : 8.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.02 % Favored : 95.98 % Rotamer: Outliers : 0.00 % Allowed : 21.19 % Favored : 78.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.21 (0.23), residues: 1344 helix: 0.65 (0.18), residues: 861 sheet: -3.15 (0.84), residues: 30 loop : -1.38 (0.29), residues: 453 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A1147 TYR 0.016 0.001 TYR A1132 PHE 0.025 0.001 PHE A 175 TRP 0.015 0.001 TRP A 361 HIS 0.005 0.001 HIS A 382 Details of bonding type rmsd covalent geometry : bond 0.00577 (11096) covalent geometry : angle 0.79959 (15067) hydrogen bonds : bond 0.17173 ( 662) hydrogen bonds : angle 6.58910 ( 1968) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2688 Ramachandran restraints generated. 1344 Oldfield, 0 Emsley, 1344 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2688 Ramachandran restraints generated. 1344 Oldfield, 0 Emsley, 1344 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 1195 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 181 time to evaluate : 0.358 Fit side-chains REVERT: A 590 ASN cc_start: 0.7526 (m110) cc_final: 0.7187 (m-40) REVERT: A 975 PHE cc_start: 0.8344 (m-80) cc_final: 0.8114 (m-10) outliers start: 0 outliers final: 0 residues processed: 181 average time/residue: 0.0835 time to fit residues: 22.7334 Evaluate side-chains 154 residues out of total 1195 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 154 time to evaluate : 0.380 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 98 optimal weight: 0.9980 chunk 107 optimal weight: 0.6980 chunk 10 optimal weight: 2.9990 chunk 66 optimal weight: 2.9990 chunk 130 optimal weight: 4.9990 chunk 124 optimal weight: 0.0980 chunk 103 optimal weight: 0.6980 chunk 77 optimal weight: 4.9990 chunk 122 optimal weight: 3.9990 chunk 91 optimal weight: 0.9980 chunk 55 optimal weight: 0.0870 overall best weight: 0.5158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 66 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 125 GLN A 574 ASN A 575 ASN A 731 GLN A1207 ASN ** A1222 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3922 r_free = 0.3922 target = 0.160839 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3482 r_free = 0.3482 target = 0.124063 restraints weight = 13559.180| |-----------------------------------------------------------------------------| r_work (start): 0.3486 rms_B_bonded: 2.13 r_work: 0.3358 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.3208 rms_B_bonded: 4.40 restraints_weight: 0.2500 r_work (final): 0.3208 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7790 moved from start: 0.1172 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 11096 Z= 0.134 Angle : 0.523 5.891 15067 Z= 0.276 Chirality : 0.038 0.140 1753 Planarity : 0.004 0.043 1859 Dihedral : 5.747 86.576 1497 Min Nonbonded Distance : 1.971 Molprobity Statistics. All-atom Clashscore : 7.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.20 % Favored : 96.80 % Rotamer: Outliers : 2.51 % Allowed : 21.36 % Favored : 76.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.79 (0.23), residues: 1344 helix: 1.46 (0.18), residues: 872 sheet: -2.92 (0.83), residues: 28 loop : -1.11 (0.30), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A1014 TYR 0.027 0.001 TYR A1032 PHE 0.015 0.001 PHE A 141 TRP 0.010 0.001 TRP A1197 HIS 0.004 0.001 HIS A 382 Details of bonding type rmsd covalent geometry : bond 0.00292 (11096) covalent geometry : angle 0.52316 (15067) hydrogen bonds : bond 0.04760 ( 662) hydrogen bonds : angle 4.51703 ( 1968) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2688 Ramachandran restraints generated. 1344 Oldfield, 0 Emsley, 1344 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2688 Ramachandran restraints generated. 1344 Oldfield, 0 Emsley, 1344 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 1195 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 149 time to evaluate : 0.397 Fit side-chains REVERT: A 125 GLN cc_start: 0.8087 (mm110) cc_final: 0.7741 (mm-40) REVERT: A 138 MET cc_start: 0.6561 (mmm) cc_final: 0.5978 (mmm) REVERT: A 234 GLN cc_start: 0.7973 (OUTLIER) cc_final: 0.7582 (pt0) REVERT: A 574 ASN cc_start: 0.6855 (OUTLIER) cc_final: 0.6639 (p0) REVERT: A 590 ASN cc_start: 0.7717 (m110) cc_final: 0.7191 (m-40) REVERT: A 959 LEU cc_start: 0.8571 (tp) cc_final: 0.8302 (tt) REVERT: A 1237 LEU cc_start: 0.8416 (tp) cc_final: 0.8194 (tt) REVERT: A 1327 ARG cc_start: 0.7487 (mtt90) cc_final: 0.7248 (mtt-85) REVERT: A 1454 GLU cc_start: 0.7503 (OUTLIER) cc_final: 0.7237 (mp0) REVERT: A 1525 LYS cc_start: 0.8952 (tptp) cc_final: 0.8531 (tppp) outliers start: 30 outliers final: 16 residues processed: 169 average time/residue: 0.0953 time to fit residues: 23.6343 Evaluate side-chains 161 residues out of total 1195 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 142 time to evaluate : 0.410 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 ASN Chi-restraints excluded: chain A residue 134 SER Chi-restraints excluded: chain A residue 186 LEU Chi-restraints excluded: chain A residue 234 GLN Chi-restraints excluded: chain A residue 316 VAL Chi-restraints excluded: chain A residue 443 MET Chi-restraints excluded: chain A residue 505 MET Chi-restraints excluded: chain A residue 514 VAL Chi-restraints excluded: chain A residue 574 ASN Chi-restraints excluded: chain A residue 599 LEU Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 831 TYR Chi-restraints excluded: chain A residue 946 LEU Chi-restraints excluded: chain A residue 1089 VAL Chi-restraints excluded: chain A residue 1105 ILE Chi-restraints excluded: chain A residue 1280 MET Chi-restraints excluded: chain A residue 1355 ILE Chi-restraints excluded: chain A residue 1454 GLU Chi-restraints excluded: chain A residue 1480 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 107 optimal weight: 2.9990 chunk 4 optimal weight: 3.9990 chunk 81 optimal weight: 2.9990 chunk 46 optimal weight: 0.7980 chunk 102 optimal weight: 1.9990 chunk 134 optimal weight: 4.9990 chunk 76 optimal weight: 4.9990 chunk 9 optimal weight: 5.9990 chunk 82 optimal weight: 3.9990 chunk 3 optimal weight: 5.9990 chunk 7 optimal weight: 5.9990 overall best weight: 2.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 731 GLN A 853 GLN A1054 ASN A1070 ASN A1138 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3774 r_free = 0.3774 target = 0.148253 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.113824 restraints weight = 14014.506| |-----------------------------------------------------------------------------| r_work (start): 0.3379 rms_B_bonded: 1.86 r_work: 0.3203 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.3058 rms_B_bonded: 4.01 restraints_weight: 0.2500 r_work (final): 0.3058 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7999 moved from start: 0.2375 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.086 11096 Z= 0.352 Angle : 0.716 9.363 15067 Z= 0.374 Chirality : 0.047 0.231 1753 Planarity : 0.005 0.062 1859 Dihedral : 6.113 66.245 1497 Min Nonbonded Distance : 1.753 Molprobity Statistics. All-atom Clashscore : 8.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.94 % Favored : 96.06 % Rotamer: Outliers : 4.44 % Allowed : 20.35 % Favored : 75.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.33 (0.23), residues: 1344 helix: 1.01 (0.17), residues: 871 sheet: -1.45 (1.91), residues: 10 loop : -1.23 (0.29), residues: 463 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 129 TYR 0.031 0.002 TYR A1032 PHE 0.018 0.002 PHE A1294 TRP 0.020 0.002 TRP A 998 HIS 0.009 0.002 HIS A 985 Details of bonding type rmsd covalent geometry : bond 0.00853 (11096) covalent geometry : angle 0.71598 (15067) hydrogen bonds : bond 0.05751 ( 662) hydrogen bonds : angle 4.70603 ( 1968) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2688 Ramachandran restraints generated. 1344 Oldfield, 0 Emsley, 1344 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2688 Ramachandran restraints generated. 1344 Oldfield, 0 Emsley, 1344 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 1195 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 141 time to evaluate : 0.402 Fit side-chains revert: symmetry clash REVERT: A 23 ASN cc_start: 0.8092 (OUTLIER) cc_final: 0.7474 (m110) REVERT: A 138 MET cc_start: 0.7010 (mmm) cc_final: 0.5887 (mmm) REVERT: A 234 GLN cc_start: 0.8171 (OUTLIER) cc_final: 0.7154 (pm20) REVERT: A 590 ASN cc_start: 0.7928 (m110) cc_final: 0.7474 (m110) REVERT: A 767 ASN cc_start: 0.8273 (t0) cc_final: 0.8044 (t0) REVERT: A 959 LEU cc_start: 0.8726 (tp) cc_final: 0.8470 (tt) REVERT: A 1109 LEU cc_start: 0.7827 (OUTLIER) cc_final: 0.7357 (mp) REVERT: A 1229 VAL cc_start: 0.7061 (m) cc_final: 0.6777 (p) REVERT: A 1244 ASN cc_start: 0.8674 (OUTLIER) cc_final: 0.8413 (t0) REVERT: A 1301 TYR cc_start: 0.8081 (t80) cc_final: 0.7874 (t80) REVERT: A 1302 ARG cc_start: 0.6259 (OUTLIER) cc_final: 0.6051 (ptt180) REVERT: A 1327 ARG cc_start: 0.7905 (mtt180) cc_final: 0.7655 (mtt-85) REVERT: A 1349 GLU cc_start: 0.8392 (OUTLIER) cc_final: 0.8108 (pm20) REVERT: A 1491 MET cc_start: 0.8676 (mmm) cc_final: 0.8392 (mmm) REVERT: A 1525 LYS cc_start: 0.8910 (tptp) cc_final: 0.8535 (tppp) outliers start: 53 outliers final: 34 residues processed: 182 average time/residue: 0.0876 time to fit residues: 23.6897 Evaluate side-chains 175 residues out of total 1195 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 135 time to evaluate : 0.360 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 ASN Chi-restraints excluded: chain A residue 134 SER Chi-restraints excluded: chain A residue 186 LEU Chi-restraints excluded: chain A residue 234 GLN Chi-restraints excluded: chain A residue 248 ASP Chi-restraints excluded: chain A residue 316 VAL Chi-restraints excluded: chain A residue 403 VAL Chi-restraints excluded: chain A residue 514 VAL Chi-restraints excluded: chain A residue 560 VAL Chi-restraints excluded: chain A residue 569 VAL Chi-restraints excluded: chain A residue 591 ILE Chi-restraints excluded: chain A residue 599 LEU Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 650 THR Chi-restraints excluded: chain A residue 720 ILE Chi-restraints excluded: chain A residue 752 ILE Chi-restraints excluded: chain A residue 835 MET Chi-restraints excluded: chain A residue 947 VAL Chi-restraints excluded: chain A residue 995 LEU Chi-restraints excluded: chain A residue 997 LEU Chi-restraints excluded: chain A residue 1011 THR Chi-restraints excluded: chain A residue 1041 ILE Chi-restraints excluded: chain A residue 1089 VAL Chi-restraints excluded: chain A residue 1100 VAL Chi-restraints excluded: chain A residue 1105 ILE Chi-restraints excluded: chain A residue 1109 LEU Chi-restraints excluded: chain A residue 1123 LEU Chi-restraints excluded: chain A residue 1139 LEU Chi-restraints excluded: chain A residue 1244 ASN Chi-restraints excluded: chain A residue 1257 ILE Chi-restraints excluded: chain A residue 1268 GLU Chi-restraints excluded: chain A residue 1272 GLU Chi-restraints excluded: chain A residue 1280 MET Chi-restraints excluded: chain A residue 1302 ARG Chi-restraints excluded: chain A residue 1349 GLU Chi-restraints excluded: chain A residue 1355 ILE Chi-restraints excluded: chain A residue 1357 ILE Chi-restraints excluded: chain A residue 1382 SER Chi-restraints excluded: chain A residue 1480 VAL Chi-restraints excluded: chain A residue 1497 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 119 optimal weight: 0.9990 chunk 39 optimal weight: 0.9990 chunk 40 optimal weight: 0.7980 chunk 95 optimal weight: 0.0470 chunk 118 optimal weight: 0.8980 chunk 46 optimal weight: 0.5980 chunk 10 optimal weight: 7.9990 chunk 105 optimal weight: 0.9990 chunk 125 optimal weight: 1.9990 chunk 74 optimal weight: 0.9990 chunk 44 optimal weight: 0.6980 overall best weight: 0.6078 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 34 GLN A 125 GLN A 731 GLN A1070 ASN A1138 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3818 r_free = 0.3818 target = 0.150866 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3347 r_free = 0.3347 target = 0.111285 restraints weight = 13921.468| |-----------------------------------------------------------------------------| r_work (start): 0.3332 rms_B_bonded: 2.28 r_work: 0.3189 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.3036 rms_B_bonded: 4.81 restraints_weight: 0.2500 r_work (final): 0.3036 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7842 moved from start: 0.2311 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 11096 Z= 0.132 Angle : 0.508 6.198 15067 Z= 0.267 Chirality : 0.039 0.155 1753 Planarity : 0.004 0.056 1859 Dihedral : 5.935 60.609 1497 Min Nonbonded Distance : 1.875 Molprobity Statistics. All-atom Clashscore : 6.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.27 % Favored : 96.73 % Rotamer: Outliers : 3.27 % Allowed : 22.28 % Favored : 74.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.91 (0.23), residues: 1344 helix: 1.51 (0.17), residues: 874 sheet: -2.25 (1.31), residues: 18 loop : -1.06 (0.30), residues: 452 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 867 TYR 0.025 0.001 TYR A1032 PHE 0.020 0.001 PHE A 558 TRP 0.016 0.001 TRP A 944 HIS 0.005 0.001 HIS A 382 Details of bonding type rmsd covalent geometry : bond 0.00299 (11096) covalent geometry : angle 0.50788 (15067) hydrogen bonds : bond 0.04245 ( 662) hydrogen bonds : angle 4.18544 ( 1968) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2688 Ramachandran restraints generated. 1344 Oldfield, 0 Emsley, 1344 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2688 Ramachandran restraints generated. 1344 Oldfield, 0 Emsley, 1344 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 1195 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 146 time to evaluate : 0.351 Fit side-chains revert: symmetry clash REVERT: A 138 MET cc_start: 0.6801 (mmm) cc_final: 0.5770 (mmm) REVERT: A 234 GLN cc_start: 0.7807 (OUTLIER) cc_final: 0.6960 (pm20) REVERT: A 590 ASN cc_start: 0.7861 (m110) cc_final: 0.7387 (m110) REVERT: A 774 GLN cc_start: 0.8197 (OUTLIER) cc_final: 0.7946 (mm110) REVERT: A 959 LEU cc_start: 0.8601 (tp) cc_final: 0.8315 (tt) REVERT: A 1327 ARG cc_start: 0.7888 (mtt180) cc_final: 0.7573 (mmt180) REVERT: A 1349 GLU cc_start: 0.8438 (OUTLIER) cc_final: 0.8175 (pm20) REVERT: A 1464 ASP cc_start: 0.8428 (t0) cc_final: 0.8176 (t0) REVERT: A 1491 MET cc_start: 0.8804 (mmm) cc_final: 0.8568 (mmm) REVERT: A 1525 LYS cc_start: 0.8917 (tptp) cc_final: 0.8513 (tppp) outliers start: 39 outliers final: 21 residues processed: 173 average time/residue: 0.0897 time to fit residues: 23.1081 Evaluate side-chains 164 residues out of total 1195 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 140 time to evaluate : 0.411 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 PHE Chi-restraints excluded: chain A residue 55 LEU Chi-restraints excluded: chain A residue 134 SER Chi-restraints excluded: chain A residue 186 LEU Chi-restraints excluded: chain A residue 234 GLN Chi-restraints excluded: chain A residue 316 VAL Chi-restraints excluded: chain A residue 318 TYR Chi-restraints excluded: chain A residue 550 THR Chi-restraints excluded: chain A residue 591 ILE Chi-restraints excluded: chain A residue 599 LEU Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 774 GLN Chi-restraints excluded: chain A residue 946 LEU Chi-restraints excluded: chain A residue 969 ILE Chi-restraints excluded: chain A residue 986 VAL Chi-restraints excluded: chain A residue 995 LEU Chi-restraints excluded: chain A residue 1089 VAL Chi-restraints excluded: chain A residue 1105 ILE Chi-restraints excluded: chain A residue 1280 MET Chi-restraints excluded: chain A residue 1349 GLU Chi-restraints excluded: chain A residue 1355 ILE Chi-restraints excluded: chain A residue 1357 ILE Chi-restraints excluded: chain A residue 1480 VAL Chi-restraints excluded: chain A residue 1497 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 60 optimal weight: 0.9990 chunk 39 optimal weight: 0.0870 chunk 8 optimal weight: 5.9990 chunk 19 optimal weight: 0.6980 chunk 86 optimal weight: 0.7980 chunk 28 optimal weight: 0.4980 chunk 65 optimal weight: 2.9990 chunk 55 optimal weight: 0.5980 chunk 57 optimal weight: 0.3980 chunk 95 optimal weight: 0.0070 chunk 99 optimal weight: 0.9990 overall best weight: 0.3176 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 125 GLN A 731 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3845 r_free = 0.3845 target = 0.153089 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.113978 restraints weight = 13741.290| |-----------------------------------------------------------------------------| r_work (start): 0.3380 rms_B_bonded: 2.26 r_work: 0.3235 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.3084 rms_B_bonded: 4.81 restraints_weight: 0.2500 r_work (final): 0.3084 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7795 moved from start: 0.2390 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 11096 Z= 0.109 Angle : 0.483 6.960 15067 Z= 0.251 Chirality : 0.038 0.205 1753 Planarity : 0.004 0.052 1859 Dihedral : 5.668 57.447 1497 Min Nonbonded Distance : 1.981 Molprobity Statistics. All-atom Clashscore : 6.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 3.10 % Allowed : 22.11 % Favored : 74.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.26 (0.24), residues: 1344 helix: 1.86 (0.18), residues: 875 sheet: -2.27 (0.94), residues: 28 loop : -1.08 (0.30), residues: 441 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 655 TYR 0.025 0.001 TYR A1032 PHE 0.019 0.001 PHE A 141 TRP 0.024 0.001 TRP A 944 HIS 0.004 0.001 HIS A 382 Details of bonding type rmsd covalent geometry : bond 0.00236 (11096) covalent geometry : angle 0.48258 (15067) hydrogen bonds : bond 0.03710 ( 662) hydrogen bonds : angle 3.88905 ( 1968) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2688 Ramachandran restraints generated. 1344 Oldfield, 0 Emsley, 1344 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2688 Ramachandran restraints generated. 1344 Oldfield, 0 Emsley, 1344 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 1195 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 163 time to evaluate : 0.347 Fit side-chains revert: symmetry clash REVERT: A 138 MET cc_start: 0.6791 (mmm) cc_final: 0.5774 (mmm) REVERT: A 234 GLN cc_start: 0.7774 (OUTLIER) cc_final: 0.7449 (pt0) REVERT: A 590 ASN cc_start: 0.7804 (m110) cc_final: 0.7533 (m110) REVERT: A 959 LEU cc_start: 0.8618 (tp) cc_final: 0.8356 (tt) REVERT: A 1454 GLU cc_start: 0.7428 (OUTLIER) cc_final: 0.7162 (mp0) REVERT: A 1464 ASP cc_start: 0.8401 (t0) cc_final: 0.8187 (t0) REVERT: A 1525 LYS cc_start: 0.8935 (tptp) cc_final: 0.8538 (tppp) outliers start: 37 outliers final: 25 residues processed: 186 average time/residue: 0.0817 time to fit residues: 22.9205 Evaluate side-chains 173 residues out of total 1195 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 146 time to evaluate : 0.382 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 PHE Chi-restraints excluded: chain A residue 55 LEU Chi-restraints excluded: chain A residue 134 SER Chi-restraints excluded: chain A residue 186 LEU Chi-restraints excluded: chain A residue 234 GLN Chi-restraints excluded: chain A residue 316 VAL Chi-restraints excluded: chain A residue 318 TYR Chi-restraints excluded: chain A residue 455 LEU Chi-restraints excluded: chain A residue 485 MET Chi-restraints excluded: chain A residue 599 LEU Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 704 VAL Chi-restraints excluded: chain A residue 720 ILE Chi-restraints excluded: chain A residue 995 LEU Chi-restraints excluded: chain A residue 1032 TYR Chi-restraints excluded: chain A residue 1041 ILE Chi-restraints excluded: chain A residue 1089 VAL Chi-restraints excluded: chain A residue 1123 LEU Chi-restraints excluded: chain A residue 1244 ASN Chi-restraints excluded: chain A residue 1257 ILE Chi-restraints excluded: chain A residue 1268 GLU Chi-restraints excluded: chain A residue 1280 MET Chi-restraints excluded: chain A residue 1355 ILE Chi-restraints excluded: chain A residue 1385 MET Chi-restraints excluded: chain A residue 1454 GLU Chi-restraints excluded: chain A residue 1480 VAL Chi-restraints excluded: chain A residue 1497 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 18 optimal weight: 0.9990 chunk 129 optimal weight: 1.9990 chunk 115 optimal weight: 3.9990 chunk 13 optimal weight: 9.9990 chunk 73 optimal weight: 0.0770 chunk 9 optimal weight: 9.9990 chunk 112 optimal weight: 0.9980 chunk 57 optimal weight: 4.9990 chunk 58 optimal weight: 0.6980 chunk 7 optimal weight: 2.9990 chunk 0 optimal weight: 7.9990 overall best weight: 0.9542 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 125 GLN A 480 ASN A1138 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3807 r_free = 0.3807 target = 0.148931 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3341 r_free = 0.3341 target = 0.109999 restraints weight = 13992.776| |-----------------------------------------------------------------------------| r_work (start): 0.3333 rms_B_bonded: 2.19 r_work: 0.3188 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.3037 rms_B_bonded: 4.71 restraints_weight: 0.2500 r_work (final): 0.3037 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7863 moved from start: 0.2565 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 11096 Z= 0.161 Angle : 0.529 7.014 15067 Z= 0.272 Chirality : 0.039 0.176 1753 Planarity : 0.006 0.172 1859 Dihedral : 5.448 60.654 1497 Min Nonbonded Distance : 1.877 Molprobity Statistics. All-atom Clashscore : 7.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.20 % Favored : 96.80 % Rotamer: Outliers : 3.52 % Allowed : 22.45 % Favored : 74.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.19 (0.23), residues: 1344 helix: 1.82 (0.18), residues: 868 sheet: -2.22 (0.95), residues: 28 loop : -1.09 (0.30), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 655 TYR 0.025 0.001 TYR A1032 PHE 0.010 0.001 PHE A 221 TRP 0.013 0.001 TRP A 944 HIS 0.004 0.001 HIS A 382 Details of bonding type rmsd covalent geometry : bond 0.00387 (11096) covalent geometry : angle 0.52857 (15067) hydrogen bonds : bond 0.04090 ( 662) hydrogen bonds : angle 3.98199 ( 1968) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2688 Ramachandran restraints generated. 1344 Oldfield, 0 Emsley, 1344 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2688 Ramachandran restraints generated. 1344 Oldfield, 0 Emsley, 1344 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 1195 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 143 time to evaluate : 0.417 Fit side-chains REVERT: A 138 MET cc_start: 0.6957 (mmm) cc_final: 0.5886 (mmm) REVERT: A 233 ARG cc_start: 0.8425 (mpt-90) cc_final: 0.8123 (mtt180) REVERT: A 234 GLN cc_start: 0.7825 (OUTLIER) cc_final: 0.7560 (pt0) REVERT: A 590 ASN cc_start: 0.7862 (m110) cc_final: 0.7578 (m110) REVERT: A 956 GLN cc_start: 0.7715 (tt0) cc_final: 0.6823 (pm20) REVERT: A 959 LEU cc_start: 0.8673 (tp) cc_final: 0.8415 (tt) REVERT: A 1027 ILE cc_start: 0.8182 (OUTLIER) cc_final: 0.7954 (mp) REVERT: A 1109 LEU cc_start: 0.8000 (OUTLIER) cc_final: 0.7608 (mp) REVERT: A 1525 LYS cc_start: 0.8958 (tptp) cc_final: 0.8544 (tppp) outliers start: 42 outliers final: 35 residues processed: 174 average time/residue: 0.0773 time to fit residues: 20.4747 Evaluate side-chains 178 residues out of total 1195 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 140 time to evaluate : 0.305 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 PHE Chi-restraints excluded: chain A residue 55 LEU Chi-restraints excluded: chain A residue 134 SER Chi-restraints excluded: chain A residue 186 LEU Chi-restraints excluded: chain A residue 234 GLN Chi-restraints excluded: chain A residue 316 VAL Chi-restraints excluded: chain A residue 318 TYR Chi-restraints excluded: chain A residue 455 LEU Chi-restraints excluded: chain A residue 485 MET Chi-restraints excluded: chain A residue 514 VAL Chi-restraints excluded: chain A residue 550 THR Chi-restraints excluded: chain A residue 569 VAL Chi-restraints excluded: chain A residue 591 ILE Chi-restraints excluded: chain A residue 599 LEU Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 704 VAL Chi-restraints excluded: chain A residue 720 ILE Chi-restraints excluded: chain A residue 831 TYR Chi-restraints excluded: chain A residue 969 ILE Chi-restraints excluded: chain A residue 986 VAL Chi-restraints excluded: chain A residue 995 LEU Chi-restraints excluded: chain A residue 1027 ILE Chi-restraints excluded: chain A residue 1032 TYR Chi-restraints excluded: chain A residue 1041 ILE Chi-restraints excluded: chain A residue 1089 VAL Chi-restraints excluded: chain A residue 1104 CYS Chi-restraints excluded: chain A residue 1109 LEU Chi-restraints excluded: chain A residue 1123 LEU Chi-restraints excluded: chain A residue 1136 SER Chi-restraints excluded: chain A residue 1139 LEU Chi-restraints excluded: chain A residue 1257 ILE Chi-restraints excluded: chain A residue 1268 GLU Chi-restraints excluded: chain A residue 1280 MET Chi-restraints excluded: chain A residue 1355 ILE Chi-restraints excluded: chain A residue 1357 ILE Chi-restraints excluded: chain A residue 1382 SER Chi-restraints excluded: chain A residue 1480 VAL Chi-restraints excluded: chain A residue 1497 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 113 optimal weight: 2.9990 chunk 38 optimal weight: 3.9990 chunk 98 optimal weight: 1.9990 chunk 29 optimal weight: 0.7980 chunk 49 optimal weight: 0.7980 chunk 75 optimal weight: 0.5980 chunk 0 optimal weight: 8.9990 chunk 45 optimal weight: 0.6980 chunk 105 optimal weight: 0.9990 chunk 118 optimal weight: 0.9990 chunk 89 optimal weight: 0.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 125 GLN A1138 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3812 r_free = 0.3812 target = 0.149414 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3350 r_free = 0.3350 target = 0.110670 restraints weight = 13866.704| |-----------------------------------------------------------------------------| r_work (start): 0.3346 rms_B_bonded: 2.18 r_work: 0.3202 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.3053 rms_B_bonded: 4.69 restraints_weight: 0.2500 r_work (final): 0.3053 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7847 moved from start: 0.2633 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 11096 Z= 0.141 Angle : 0.515 6.122 15067 Z= 0.266 Chirality : 0.039 0.166 1753 Planarity : 0.005 0.143 1859 Dihedral : 5.322 70.378 1497 Min Nonbonded Distance : 1.938 Molprobity Statistics. All-atom Clashscore : 6.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 3.52 % Allowed : 22.28 % Favored : 74.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.29 (0.23), residues: 1344 helix: 1.88 (0.18), residues: 868 sheet: -2.21 (1.23), residues: 18 loop : -1.06 (0.29), residues: 458 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 655 TYR 0.025 0.001 TYR A1032 PHE 0.018 0.001 PHE A 141 TRP 0.015 0.001 TRP A 944 HIS 0.004 0.001 HIS A 382 Details of bonding type rmsd covalent geometry : bond 0.00333 (11096) covalent geometry : angle 0.51470 (15067) hydrogen bonds : bond 0.03928 ( 662) hydrogen bonds : angle 3.93050 ( 1968) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2688 Ramachandran restraints generated. 1344 Oldfield, 0 Emsley, 1344 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2688 Ramachandran restraints generated. 1344 Oldfield, 0 Emsley, 1344 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 1195 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 144 time to evaluate : 0.409 Fit side-chains REVERT: A 138 MET cc_start: 0.6881 (mmm) cc_final: 0.5810 (mmm) REVERT: A 216 LEU cc_start: 0.7454 (OUTLIER) cc_final: 0.7156 (tt) REVERT: A 234 GLN cc_start: 0.7783 (OUTLIER) cc_final: 0.7537 (pt0) REVERT: A 590 ASN cc_start: 0.7853 (m110) cc_final: 0.7564 (m110) REVERT: A 959 LEU cc_start: 0.8658 (tp) cc_final: 0.8408 (tt) REVERT: A 1027 ILE cc_start: 0.8177 (OUTLIER) cc_final: 0.7956 (mp) REVERT: A 1109 LEU cc_start: 0.8005 (OUTLIER) cc_final: 0.7634 (mp) REVERT: A 1327 ARG cc_start: 0.7766 (mtt-85) cc_final: 0.7430 (mmt180) REVERT: A 1454 GLU cc_start: 0.7598 (OUTLIER) cc_final: 0.7159 (mp0) REVERT: A 1464 ASP cc_start: 0.8443 (t0) cc_final: 0.8224 (t0) REVERT: A 1525 LYS cc_start: 0.8954 (tptp) cc_final: 0.8536 (tppp) outliers start: 42 outliers final: 32 residues processed: 177 average time/residue: 0.0961 time to fit residues: 25.3792 Evaluate side-chains 181 residues out of total 1195 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 144 time to evaluate : 0.432 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 PHE Chi-restraints excluded: chain A residue 55 LEU Chi-restraints excluded: chain A residue 186 LEU Chi-restraints excluded: chain A residue 216 LEU Chi-restraints excluded: chain A residue 234 GLN Chi-restraints excluded: chain A residue 316 VAL Chi-restraints excluded: chain A residue 318 TYR Chi-restraints excluded: chain A residue 455 LEU Chi-restraints excluded: chain A residue 550 THR Chi-restraints excluded: chain A residue 569 VAL Chi-restraints excluded: chain A residue 591 ILE Chi-restraints excluded: chain A residue 599 LEU Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 704 VAL Chi-restraints excluded: chain A residue 720 ILE Chi-restraints excluded: chain A residue 831 TYR Chi-restraints excluded: chain A residue 969 ILE Chi-restraints excluded: chain A residue 995 LEU Chi-restraints excluded: chain A residue 1011 THR Chi-restraints excluded: chain A residue 1027 ILE Chi-restraints excluded: chain A residue 1032 TYR Chi-restraints excluded: chain A residue 1041 ILE Chi-restraints excluded: chain A residue 1089 VAL Chi-restraints excluded: chain A residue 1104 CYS Chi-restraints excluded: chain A residue 1109 LEU Chi-restraints excluded: chain A residue 1123 LEU Chi-restraints excluded: chain A residue 1136 SER Chi-restraints excluded: chain A residue 1139 LEU Chi-restraints excluded: chain A residue 1257 ILE Chi-restraints excluded: chain A residue 1268 GLU Chi-restraints excluded: chain A residue 1280 MET Chi-restraints excluded: chain A residue 1355 ILE Chi-restraints excluded: chain A residue 1357 ILE Chi-restraints excluded: chain A residue 1382 SER Chi-restraints excluded: chain A residue 1454 GLU Chi-restraints excluded: chain A residue 1480 VAL Chi-restraints excluded: chain A residue 1497 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 32 optimal weight: 0.9980 chunk 87 optimal weight: 1.9990 chunk 30 optimal weight: 0.4980 chunk 105 optimal weight: 1.9990 chunk 40 optimal weight: 1.9990 chunk 2 optimal weight: 5.9990 chunk 62 optimal weight: 1.9990 chunk 12 optimal weight: 6.9990 chunk 107 optimal weight: 0.9990 chunk 75 optimal weight: 1.9990 chunk 113 optimal weight: 0.8980 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 125 GLN A1138 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3812 r_free = 0.3812 target = 0.148229 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.111205 restraints weight = 14315.063| |-----------------------------------------------------------------------------| r_work (start): 0.3366 rms_B_bonded: 2.19 r_work: 0.3213 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.3071 rms_B_bonded: 4.41 restraints_weight: 0.2500 r_work (final): 0.3071 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7913 moved from start: 0.2778 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 11096 Z= 0.173 Angle : 0.550 7.035 15067 Z= 0.282 Chirality : 0.040 0.160 1753 Planarity : 0.004 0.073 1859 Dihedral : 5.390 85.894 1497 Min Nonbonded Distance : 1.900 Molprobity Statistics. All-atom Clashscore : 7.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.35 % Favored : 96.65 % Rotamer: Outliers : 3.77 % Allowed : 22.28 % Favored : 73.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.22 (0.23), residues: 1344 helix: 1.82 (0.18), residues: 871 sheet: -2.20 (1.23), residues: 18 loop : -1.08 (0.29), residues: 455 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG A 130 TYR 0.026 0.001 TYR A1032 PHE 0.018 0.001 PHE A 141 TRP 0.030 0.001 TRP A 242 HIS 0.004 0.001 HIS A 985 Details of bonding type rmsd covalent geometry : bond 0.00418 (11096) covalent geometry : angle 0.55021 (15067) hydrogen bonds : bond 0.04132 ( 662) hydrogen bonds : angle 3.99789 ( 1968) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2688 Ramachandran restraints generated. 1344 Oldfield, 0 Emsley, 1344 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2688 Ramachandran restraints generated. 1344 Oldfield, 0 Emsley, 1344 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 1195 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 146 time to evaluate : 0.359 Fit side-chains revert: symmetry clash REVERT: A 134 SER cc_start: 0.6864 (OUTLIER) cc_final: 0.6640 (p) REVERT: A 138 MET cc_start: 0.7012 (mmm) cc_final: 0.6696 (mmm) REVERT: A 216 LEU cc_start: 0.7497 (OUTLIER) cc_final: 0.7155 (tt) REVERT: A 234 GLN cc_start: 0.7865 (OUTLIER) cc_final: 0.7611 (pt0) REVERT: A 590 ASN cc_start: 0.7837 (m110) cc_final: 0.7528 (m110) REVERT: A 956 GLN cc_start: 0.7689 (tt0) cc_final: 0.6880 (pm20) REVERT: A 959 LEU cc_start: 0.8705 (tp) cc_final: 0.8477 (tt) REVERT: A 1027 ILE cc_start: 0.8255 (OUTLIER) cc_final: 0.8019 (mp) REVERT: A 1109 LEU cc_start: 0.7984 (OUTLIER) cc_final: 0.7576 (mp) REVERT: A 1327 ARG cc_start: 0.7869 (mtt-85) cc_final: 0.7582 (mmt180) REVERT: A 1349 GLU cc_start: 0.8560 (pm20) cc_final: 0.8355 (pm20) REVERT: A 1454 GLU cc_start: 0.7629 (OUTLIER) cc_final: 0.7309 (mp0) REVERT: A 1464 ASP cc_start: 0.8477 (t0) cc_final: 0.8244 (t0) REVERT: A 1507 TRP cc_start: 0.7240 (t-100) cc_final: 0.6883 (t-100) REVERT: A 1525 LYS cc_start: 0.8907 (tptp) cc_final: 0.8543 (tppp) outliers start: 45 outliers final: 35 residues processed: 184 average time/residue: 0.0938 time to fit residues: 25.7436 Evaluate side-chains 180 residues out of total 1195 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 139 time to evaluate : 0.409 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 PHE Chi-restraints excluded: chain A residue 55 LEU Chi-restraints excluded: chain A residue 134 SER Chi-restraints excluded: chain A residue 186 LEU Chi-restraints excluded: chain A residue 216 LEU Chi-restraints excluded: chain A residue 234 GLN Chi-restraints excluded: chain A residue 316 VAL Chi-restraints excluded: chain A residue 318 TYR Chi-restraints excluded: chain A residue 455 LEU Chi-restraints excluded: chain A residue 514 VAL Chi-restraints excluded: chain A residue 550 THR Chi-restraints excluded: chain A residue 556 THR Chi-restraints excluded: chain A residue 569 VAL Chi-restraints excluded: chain A residue 591 ILE Chi-restraints excluded: chain A residue 599 LEU Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 682 CYS Chi-restraints excluded: chain A residue 720 ILE Chi-restraints excluded: chain A residue 831 TYR Chi-restraints excluded: chain A residue 969 ILE Chi-restraints excluded: chain A residue 986 VAL Chi-restraints excluded: chain A residue 995 LEU Chi-restraints excluded: chain A residue 1011 THR Chi-restraints excluded: chain A residue 1027 ILE Chi-restraints excluded: chain A residue 1032 TYR Chi-restraints excluded: chain A residue 1041 ILE Chi-restraints excluded: chain A residue 1089 VAL Chi-restraints excluded: chain A residue 1104 CYS Chi-restraints excluded: chain A residue 1109 LEU Chi-restraints excluded: chain A residue 1123 LEU Chi-restraints excluded: chain A residue 1136 SER Chi-restraints excluded: chain A residue 1139 LEU Chi-restraints excluded: chain A residue 1257 ILE Chi-restraints excluded: chain A residue 1268 GLU Chi-restraints excluded: chain A residue 1280 MET Chi-restraints excluded: chain A residue 1355 ILE Chi-restraints excluded: chain A residue 1357 ILE Chi-restraints excluded: chain A residue 1382 SER Chi-restraints excluded: chain A residue 1454 GLU Chi-restraints excluded: chain A residue 1480 VAL Chi-restraints excluded: chain A residue 1497 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 3 optimal weight: 4.9990 chunk 42 optimal weight: 0.6980 chunk 26 optimal weight: 0.8980 chunk 94 optimal weight: 2.9990 chunk 109 optimal weight: 0.9980 chunk 27 optimal weight: 3.9990 chunk 62 optimal weight: 0.1980 chunk 0 optimal weight: 7.9990 chunk 55 optimal weight: 0.7980 chunk 97 optimal weight: 0.9980 chunk 17 optimal weight: 3.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 125 GLN A1138 GLN A1207 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3823 r_free = 0.3823 target = 0.150434 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.111171 restraints weight = 13737.839| |-----------------------------------------------------------------------------| r_work (start): 0.3347 rms_B_bonded: 2.22 r_work: 0.3200 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.3048 rms_B_bonded: 4.79 restraints_weight: 0.2500 r_work (final): 0.3048 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7850 moved from start: 0.2814 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 11096 Z= 0.138 Angle : 0.541 8.392 15067 Z= 0.277 Chirality : 0.039 0.159 1753 Planarity : 0.004 0.088 1859 Dihedral : 5.382 83.598 1497 Min Nonbonded Distance : 1.945 Molprobity Statistics. All-atom Clashscore : 7.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 3.85 % Allowed : 22.61 % Favored : 73.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.28 (0.24), residues: 1344 helix: 1.89 (0.18), residues: 869 sheet: -2.14 (1.24), residues: 18 loop : -1.10 (0.29), residues: 457 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG A 130 TYR 0.027 0.001 TYR A1032 PHE 0.017 0.001 PHE A1030 TRP 0.029 0.001 TRP A 242 HIS 0.004 0.001 HIS A 382 Details of bonding type rmsd covalent geometry : bond 0.00324 (11096) covalent geometry : angle 0.54087 (15067) hydrogen bonds : bond 0.03924 ( 662) hydrogen bonds : angle 3.95006 ( 1968) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2688 Ramachandran restraints generated. 1344 Oldfield, 0 Emsley, 1344 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2688 Ramachandran restraints generated. 1344 Oldfield, 0 Emsley, 1344 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 1195 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 144 time to evaluate : 0.464 Fit side-chains REVERT: A 134 SER cc_start: 0.7033 (OUTLIER) cc_final: 0.6717 (p) REVERT: A 138 MET cc_start: 0.6907 (mmm) cc_final: 0.6586 (mmm) REVERT: A 216 LEU cc_start: 0.7410 (OUTLIER) cc_final: 0.7074 (tt) REVERT: A 234 GLN cc_start: 0.7764 (OUTLIER) cc_final: 0.7537 (pt0) REVERT: A 590 ASN cc_start: 0.7871 (m110) cc_final: 0.7590 (m110) REVERT: A 956 GLN cc_start: 0.7704 (tt0) cc_final: 0.6803 (pm20) REVERT: A 959 LEU cc_start: 0.8625 (tp) cc_final: 0.8384 (tt) REVERT: A 1027 ILE cc_start: 0.8178 (OUTLIER) cc_final: 0.7957 (mp) REVERT: A 1109 LEU cc_start: 0.7920 (OUTLIER) cc_final: 0.7517 (mp) REVERT: A 1136 SER cc_start: 0.8841 (OUTLIER) cc_final: 0.8617 (m) REVERT: A 1327 ARG cc_start: 0.7863 (mtt-85) cc_final: 0.7562 (mmt180) REVERT: A 1349 GLU cc_start: 0.8559 (pm20) cc_final: 0.8353 (pm20) REVERT: A 1454 GLU cc_start: 0.7546 (OUTLIER) cc_final: 0.7284 (mp0) REVERT: A 1464 ASP cc_start: 0.8461 (t0) cc_final: 0.8218 (t0) REVERT: A 1525 LYS cc_start: 0.8979 (tptp) cc_final: 0.8575 (tppp) outliers start: 46 outliers final: 36 residues processed: 180 average time/residue: 0.0915 time to fit residues: 24.9162 Evaluate side-chains 184 residues out of total 1195 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 141 time to evaluate : 0.370 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 PHE Chi-restraints excluded: chain A residue 55 LEU Chi-restraints excluded: chain A residue 125 GLN Chi-restraints excluded: chain A residue 134 SER Chi-restraints excluded: chain A residue 186 LEU Chi-restraints excluded: chain A residue 216 LEU Chi-restraints excluded: chain A residue 234 GLN Chi-restraints excluded: chain A residue 316 VAL Chi-restraints excluded: chain A residue 318 TYR Chi-restraints excluded: chain A residue 455 LEU Chi-restraints excluded: chain A residue 550 THR Chi-restraints excluded: chain A residue 556 THR Chi-restraints excluded: chain A residue 591 ILE Chi-restraints excluded: chain A residue 599 LEU Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 704 VAL Chi-restraints excluded: chain A residue 720 ILE Chi-restraints excluded: chain A residue 831 TYR Chi-restraints excluded: chain A residue 969 ILE Chi-restraints excluded: chain A residue 986 VAL Chi-restraints excluded: chain A residue 995 LEU Chi-restraints excluded: chain A residue 1011 THR Chi-restraints excluded: chain A residue 1027 ILE Chi-restraints excluded: chain A residue 1032 TYR Chi-restraints excluded: chain A residue 1034 MET Chi-restraints excluded: chain A residue 1041 ILE Chi-restraints excluded: chain A residue 1089 VAL Chi-restraints excluded: chain A residue 1100 VAL Chi-restraints excluded: chain A residue 1104 CYS Chi-restraints excluded: chain A residue 1109 LEU Chi-restraints excluded: chain A residue 1123 LEU Chi-restraints excluded: chain A residue 1136 SER Chi-restraints excluded: chain A residue 1139 LEU Chi-restraints excluded: chain A residue 1257 ILE Chi-restraints excluded: chain A residue 1268 GLU Chi-restraints excluded: chain A residue 1280 MET Chi-restraints excluded: chain A residue 1355 ILE Chi-restraints excluded: chain A residue 1357 ILE Chi-restraints excluded: chain A residue 1382 SER Chi-restraints excluded: chain A residue 1385 MET Chi-restraints excluded: chain A residue 1454 GLU Chi-restraints excluded: chain A residue 1480 VAL Chi-restraints excluded: chain A residue 1497 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 125 optimal weight: 6.9990 chunk 12 optimal weight: 4.9990 chunk 16 optimal weight: 5.9990 chunk 116 optimal weight: 6.9990 chunk 29 optimal weight: 0.6980 chunk 73 optimal weight: 0.0670 chunk 43 optimal weight: 1.9990 chunk 103 optimal weight: 0.6980 chunk 118 optimal weight: 5.9990 chunk 82 optimal weight: 0.5980 chunk 109 optimal weight: 0.9990 overall best weight: 0.6120 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 125 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3823 r_free = 0.3823 target = 0.150232 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3360 r_free = 0.3360 target = 0.111448 restraints weight = 13790.366| |-----------------------------------------------------------------------------| r_work (start): 0.3359 rms_B_bonded: 2.19 r_work: 0.3214 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.3065 rms_B_bonded: 4.71 restraints_weight: 0.2500 r_work (final): 0.3065 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7841 moved from start: 0.2834 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 11096 Z= 0.131 Angle : 0.541 9.485 15067 Z= 0.276 Chirality : 0.038 0.158 1753 Planarity : 0.005 0.094 1859 Dihedral : 5.344 79.369 1497 Min Nonbonded Distance : 1.951 Molprobity Statistics. All-atom Clashscore : 7.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.27 % Favored : 96.73 % Rotamer: Outliers : 3.60 % Allowed : 23.12 % Favored : 73.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.35 (0.24), residues: 1344 helix: 1.96 (0.18), residues: 869 sheet: -2.11 (1.22), residues: 18 loop : -1.12 (0.29), residues: 457 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG A 130 TYR 0.027 0.001 TYR A1032 PHE 0.024 0.001 PHE A 558 TRP 0.032 0.001 TRP A 242 HIS 0.003 0.001 HIS A 382 Details of bonding type rmsd covalent geometry : bond 0.00303 (11096) covalent geometry : angle 0.54110 (15067) hydrogen bonds : bond 0.03857 ( 662) hydrogen bonds : angle 3.91222 ( 1968) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2688 Ramachandran restraints generated. 1344 Oldfield, 0 Emsley, 1344 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2688 Ramachandran restraints generated. 1344 Oldfield, 0 Emsley, 1344 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 1195 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 145 time to evaluate : 0.429 Fit side-chains REVERT: A 134 SER cc_start: 0.7029 (OUTLIER) cc_final: 0.6694 (p) REVERT: A 138 MET cc_start: 0.6892 (mmm) cc_final: 0.6574 (mmm) REVERT: A 216 LEU cc_start: 0.7403 (OUTLIER) cc_final: 0.7069 (tt) REVERT: A 590 ASN cc_start: 0.7874 (m110) cc_final: 0.7613 (m110) REVERT: A 956 GLN cc_start: 0.7708 (tt0) cc_final: 0.6800 (pm20) REVERT: A 959 LEU cc_start: 0.8620 (tp) cc_final: 0.8383 (tt) REVERT: A 1027 ILE cc_start: 0.8180 (OUTLIER) cc_final: 0.7961 (mp) REVERT: A 1109 LEU cc_start: 0.7933 (OUTLIER) cc_final: 0.7536 (mp) REVERT: A 1136 SER cc_start: 0.8824 (OUTLIER) cc_final: 0.8606 (m) REVERT: A 1327 ARG cc_start: 0.7860 (mtt-85) cc_final: 0.7566 (mmt180) REVERT: A 1454 GLU cc_start: 0.7533 (OUTLIER) cc_final: 0.7281 (mp0) REVERT: A 1464 ASP cc_start: 0.8439 (t0) cc_final: 0.8193 (t0) REVERT: A 1491 MET cc_start: 0.8844 (mmm) cc_final: 0.8593 (mmm) REVERT: A 1525 LYS cc_start: 0.8973 (tptp) cc_final: 0.8569 (tppp) outliers start: 43 outliers final: 35 residues processed: 180 average time/residue: 0.0861 time to fit residues: 23.4304 Evaluate side-chains 181 residues out of total 1195 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 140 time to evaluate : 0.738 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 PHE Chi-restraints excluded: chain A residue 55 LEU Chi-restraints excluded: chain A residue 134 SER Chi-restraints excluded: chain A residue 186 LEU Chi-restraints excluded: chain A residue 216 LEU Chi-restraints excluded: chain A residue 316 VAL Chi-restraints excluded: chain A residue 318 TYR Chi-restraints excluded: chain A residue 455 LEU Chi-restraints excluded: chain A residue 550 THR Chi-restraints excluded: chain A residue 556 THR Chi-restraints excluded: chain A residue 591 ILE Chi-restraints excluded: chain A residue 599 LEU Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 704 VAL Chi-restraints excluded: chain A residue 720 ILE Chi-restraints excluded: chain A residue 831 TYR Chi-restraints excluded: chain A residue 969 ILE Chi-restraints excluded: chain A residue 986 VAL Chi-restraints excluded: chain A residue 995 LEU Chi-restraints excluded: chain A residue 1011 THR Chi-restraints excluded: chain A residue 1027 ILE Chi-restraints excluded: chain A residue 1032 TYR Chi-restraints excluded: chain A residue 1034 MET Chi-restraints excluded: chain A residue 1041 ILE Chi-restraints excluded: chain A residue 1089 VAL Chi-restraints excluded: chain A residue 1100 VAL Chi-restraints excluded: chain A residue 1104 CYS Chi-restraints excluded: chain A residue 1109 LEU Chi-restraints excluded: chain A residue 1123 LEU Chi-restraints excluded: chain A residue 1136 SER Chi-restraints excluded: chain A residue 1139 LEU Chi-restraints excluded: chain A residue 1257 ILE Chi-restraints excluded: chain A residue 1268 GLU Chi-restraints excluded: chain A residue 1280 MET Chi-restraints excluded: chain A residue 1355 ILE Chi-restraints excluded: chain A residue 1357 ILE Chi-restraints excluded: chain A residue 1382 SER Chi-restraints excluded: chain A residue 1385 MET Chi-restraints excluded: chain A residue 1454 GLU Chi-restraints excluded: chain A residue 1480 VAL Chi-restraints excluded: chain A residue 1497 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 4 optimal weight: 4.9990 chunk 128 optimal weight: 2.9990 chunk 40 optimal weight: 2.9990 chunk 3 optimal weight: 0.3980 chunk 32 optimal weight: 0.8980 chunk 134 optimal weight: 0.7980 chunk 34 optimal weight: 1.9990 chunk 65 optimal weight: 0.6980 chunk 2 optimal weight: 5.9990 chunk 126 optimal weight: 0.7980 chunk 45 optimal weight: 0.5980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 230 GLN A1138 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3818 r_free = 0.3818 target = 0.149912 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3355 r_free = 0.3355 target = 0.110992 restraints weight = 13872.587| |-----------------------------------------------------------------------------| r_work (start): 0.3361 rms_B_bonded: 2.20 r_work: 0.3215 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.3064 rms_B_bonded: 4.75 restraints_weight: 0.2500 r_work (final): 0.3064 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7842 moved from start: 0.2912 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 11096 Z= 0.133 Angle : 0.538 9.260 15067 Z= 0.275 Chirality : 0.039 0.157 1753 Planarity : 0.004 0.081 1859 Dihedral : 5.299 70.886 1497 Min Nonbonded Distance : 1.943 Molprobity Statistics. All-atom Clashscore : 7.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.20 % Favored : 96.80 % Rotamer: Outliers : 3.60 % Allowed : 22.78 % Favored : 73.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.43 (0.24), residues: 1344 helix: 1.99 (0.18), residues: 875 sheet: -2.01 (1.22), residues: 18 loop : -1.04 (0.30), residues: 451 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG A 130 TYR 0.026 0.001 TYR A1032 PHE 0.024 0.001 PHE A 558 TRP 0.031 0.001 TRP A 242 HIS 0.003 0.001 HIS A 382 Details of bonding type rmsd covalent geometry : bond 0.00309 (11096) covalent geometry : angle 0.53766 (15067) hydrogen bonds : bond 0.03797 ( 662) hydrogen bonds : angle 3.88253 ( 1968) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2799.80 seconds wall clock time: 48 minutes 41.12 seconds (2921.12 seconds total)