Starting phenix.real_space_refine on Mon Dec 30 01:26:43 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8sg4_40451/12_2024/8sg4_40451.cif Found real_map, /net/cci-nas-00/data/ceres_data/8sg4_40451/12_2024/8sg4_40451.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.11 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8sg4_40451/12_2024/8sg4_40451.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8sg4_40451/12_2024/8sg4_40451.map" model { file = "/net/cci-nas-00/data/ceres_data/8sg4_40451/12_2024/8sg4_40451.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8sg4_40451/12_2024/8sg4_40451.cif" } resolution = 3.11 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.067 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: 4 Type Number sf(0) Gaussians S 53 5.16 5 C 7571 2.51 5 N 1972 2.21 5 O 2119 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/chem_data/mon_lib" Total number of atoms: 11715 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 11715 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 1469, 11703 Classifications: {'peptide': 1469} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PCIS': 2, 'PTRANS': 41, 'TRANS': 1425} Chain breaks: 2 Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 14 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'HIS:plan': 2} Unresolved non-hydrogen planarities: 10 Conformer: "B" Number of residues, atoms: 1469, 11703 Classifications: {'peptide': 1469} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PCIS': 2, 'PTRANS': 41, 'TRANS': 1425} Chain breaks: 2 Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 14 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'HIS:plan': 2} Unresolved non-hydrogen planarities: 10 bond proxies already assigned to first conformer: 11934 Residues with excluded nonbonded symmetry interactions: 1 residue: pdb=" N AARG A1048 " occ=0.50 ... (20 atoms not shown) pdb=" NH2BARG A1048 " occ=0.50 Time building chain proxies: 12.46, per 1000 atoms: 1.06 Number of scatterers: 11715 At special positions: 0 Unit cell: (108.009, 128.328, 133.675, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 53 16.00 O 2119 8.00 N 1972 7.00 C 7571 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.55 Conformation dependent library (CDL) restraints added in 3.7 seconds 2932 Ramachandran restraints generated. 1466 Oldfield, 0 Emsley, 1466 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2786 Finding SS restraints... Secondary structure from input PDB file: 65 helices and 6 sheets defined 72.5% alpha, 7.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.41 Creating SS restraints... Processing helix chain 'A' and resid 4 through 13 removed outlier: 3.784A pdb=" N TRP A 8 " --> pdb=" O ASN A 4 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N ALA A 9 " --> pdb=" O LEU A 5 " (cutoff:3.500A) Processing helix chain 'A' and resid 29 through 36 Processing helix chain 'A' and resid 36 through 58 removed outlier: 3.924A pdb=" N ILE A 50 " --> pdb=" O ILE A 46 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N CYS A 57 " --> pdb=" O LEU A 53 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N LYS A 58 " --> pdb=" O VAL A 54 " (cutoff:3.500A) Processing helix chain 'A' and resid 69 through 92 removed outlier: 3.785A pdb=" N VAL A 73 " --> pdb=" O ASN A 69 " (cutoff:3.500A) Processing helix chain 'A' and resid 94 through 100 removed outlier: 3.547A pdb=" N GLU A 99 " --> pdb=" O LYS A 95 " (cutoff:3.500A) removed outlier: 4.144A pdb=" N ASN A 100 " --> pdb=" O GLU A 96 " (cutoff:3.500A) Processing helix chain 'A' and resid 100 through 128 removed outlier: 4.006A pdb=" N VAL A 104 " --> pdb=" O ASN A 100 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N TRP A 122 " --> pdb=" O LEU A 118 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N ASP A 126 " --> pdb=" O TRP A 122 " (cutoff:3.500A) Processing helix chain 'A' and resid 132 through 161 Processing helix chain 'A' and resid 166 through 189 Processing helix chain 'A' and resid 195 through 202 removed outlier: 3.994A pdb=" N HIS A 199 " --> pdb=" O MET A 195 " (cutoff:3.500A) Processing helix chain 'A' and resid 210 through 215 removed outlier: 3.581A pdb=" N ASP A 213 " --> pdb=" O ASN A 210 " (cutoff:3.500A) Processing helix chain 'A' and resid 216 through 223 Processing helix chain 'A' and resid 226 through 236 Processing helix chain 'A' and resid 251 through 270 Processing helix chain 'A' and resid 274 through 327 removed outlier: 5.953A pdb=" N SER A 285 " --> pdb=" O ARG A 281 " (cutoff:3.500A) removed outlier: 6.798A pdb=" N LYS A 286 " --> pdb=" O THR A 282 " (cutoff:3.500A) removed outlier: 4.319A pdb=" N MET A 287 " --> pdb=" O PHE A 283 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N GLN A 304 " --> pdb=" O LEU A 300 " (cutoff:3.500A) Proline residue: A 305 - end of helix Processing helix chain 'A' and resid 342 through 392 removed outlier: 3.607A pdb=" N PHE A 346 " --> pdb=" O ILE A 342 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N GLN A 365 " --> pdb=" O SER A 361 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N LEU A 390 " --> pdb=" O TYR A 386 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N VAL A 391 " --> pdb=" O GLN A 387 " (cutoff:3.500A) Processing helix chain 'A' and resid 393 through 399 Processing helix chain 'A' and resid 401 through 411 Processing helix chain 'A' and resid 411 through 424 removed outlier: 4.086A pdb=" N THR A 420 " --> pdb=" O LEU A 416 " (cutoff:3.500A) removed outlier: 4.340A pdb=" N GLN A 421 " --> pdb=" O GLN A 417 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N TRP A 422 " --> pdb=" O ASP A 418 " (cutoff:3.500A) removed outlier: 4.402A pdb=" N ASN A 424 " --> pdb=" O THR A 420 " (cutoff:3.500A) Processing helix chain 'A' and resid 424 through 445 Proline residue: A 430 - end of helix Processing helix chain 'A' and resid 447 through 493 removed outlier: 4.249A pdb=" N GLY A 451 " --> pdb=" O SER A 447 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N LEU A 455 " --> pdb=" O GLY A 451 " (cutoff:3.500A) Proline residue: A 460 - end of helix Processing helix chain 'A' and resid 493 through 501 Processing helix chain 'A' and resid 502 through 517 removed outlier: 3.601A pdb=" N LYS A 517 " --> pdb=" O VAL A 513 " (cutoff:3.500A) Processing helix chain 'A' and resid 517 through 555 Proline residue: A 540 - end of helix removed outlier: 3.684A pdb=" N SER A 544 " --> pdb=" O PRO A 540 " (cutoff:3.500A) Processing helix chain 'A' and resid 560 through 579 Proline residue: A 566 - end of helix removed outlier: 3.858A pdb=" N ASN A 572 " --> pdb=" O LEU A 568 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N LEU A 573 " --> pdb=" O THR A 569 " (cutoff:3.500A) Proline residue: A 577 - end of helix Processing helix chain 'A' and resid 580 through 603 Processing helix chain 'A' and resid 668 through 677 removed outlier: 3.736A pdb=" N LEU A 673 " --> pdb=" O LYS A 669 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N MET A 676 " --> pdb=" O LEU A 672 " (cutoff:3.500A) Processing helix chain 'A' and resid 707 through 713 Processing helix chain 'A' and resid 718 through 729 Processing helix chain 'A' and resid 731 through 738 Processing helix chain 'A' and resid 740 through 743 Processing helix chain 'A' and resid 754 through 770 removed outlier: 3.710A pdb=" N ARG A 770 " --> pdb=" O ALA A 766 " (cutoff:3.500A) Processing helix chain 'A' and resid 779 through 783 removed outlier: 3.810A pdb=" N ALA A 782 " --> pdb=" O PRO A 779 " (cutoff:3.500A) Processing helix chain 'A' and resid 784 through 795 Processing helix chain 'A' and resid 800 through 805 removed outlier: 4.364A pdb=" N THR A 804 " --> pdb=" O LEU A 801 " (cutoff:3.500A) Processing helix chain 'A' and resid 813 through 819 removed outlier: 4.065A pdb=" N ILE A 819 " --> pdb=" O SER A 815 " (cutoff:3.500A) Processing helix chain 'A' and resid 836 through 842 Processing helix chain 'A' and resid 846 through 854 Processing helix chain 'A' and resid 900 through 913 Processing helix chain 'A' and resid 923 through 929 removed outlier: 3.534A pdb=" N GLU A 927 " --> pdb=" O ALA A 924 " (cutoff:3.500A) Processing helix chain 'A' and resid 935 through 946 removed outlier: 3.948A pdb=" N TYR A 939 " --> pdb=" O LYS A 935 " (cutoff:3.500A) Processing helix chain 'A' and resid 947 through 983 Processing helix chain 'A' and resid 987 through 1016 Processing helix chain 'A' and resid 1017 through 1035 removed outlier: 3.807A pdb=" N ARG A1035 " --> pdb=" O ASN A1031 " (cutoff:3.500A) Processing helix chain 'A' and resid 1037 through 1044 removed outlier: 3.801A pdb=" N PHE A1041 " --> pdb=" O PRO A1037 " (cutoff:3.500A) Processing helix chain 'A' and resid 1045 through 1063 removed outlier: 3.607A pdb=" N AILE A1049 " --> pdb=" O PRO A1045 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N ASP A1056 " --> pdb=" O ARG A1052 " (cutoff:3.500A) removed outlier: 4.243A pdb=" N ILE A1057 " --> pdb=" O PHE A1053 " (cutoff:3.500A) Processing helix chain 'A' and resid 1063 through 1089 removed outlier: 3.600A pdb=" N ASN A1074 " --> pdb=" O GLN A1070 " (cutoff:3.500A) Processing helix chain 'A' and resid 1092 through 1137 Proline residue: A1098 - end of helix removed outlier: 3.954A pdb=" N SER A1126 " --> pdb=" O SER A1122 " (cutoff:3.500A) Proline residue: A1127 - end of helix Processing helix chain 'A' and resid 1138 through 1146 Processing helix chain 'A' and resid 1147 through 1202 removed outlier: 3.728A pdb=" N ALA A1165 " --> pdb=" O ASN A1161 " (cutoff:3.500A) Proline residue: A1168 - end of helix removed outlier: 4.113A pdb=" N ASN A1173 " --> pdb=" O SER A1169 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N ARG A1174 " --> pdb=" O ILE A1170 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N ARG A1179 " --> pdb=" O TRP A1175 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N GLN A1201 " --> pdb=" O PHE A1197 " (cutoff:3.500A) Processing helix chain 'A' and resid 1205 through 1218 removed outlier: 3.830A pdb=" N VAL A1209 " --> pdb=" O THR A1205 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N GLN A1218 " --> pdb=" O SER A1214 " (cutoff:3.500A) Processing helix chain 'A' and resid 1218 through 1237 removed outlier: 4.381A pdb=" N THR A1222 " --> pdb=" O GLN A1218 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N ASN A1224 " --> pdb=" O THR A1220 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N VAL A1227 " --> pdb=" O LEU A1223 " (cutoff:3.500A) Processing helix chain 'A' and resid 1237 through 1248 Processing helix chain 'A' and resid 1257 through 1261 removed outlier: 4.105A pdb=" N ARG A1261 " --> pdb=" O GLU A1258 " (cutoff:3.500A) Processing helix chain 'A' and resid 1313 through 1320 removed outlier: 3.779A pdb=" N LEU A1317 " --> pdb=" O SER A1313 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N PHE A1320 " --> pdb=" O THR A1316 " (cutoff:3.500A) Processing helix chain 'A' and resid 1341 through 1347 Processing helix chain 'A' and resid 1363 through 1368 Processing helix chain 'A' and resid 1374 through 1385 Processing helix chain 'A' and resid 1387 through 1395 removed outlier: 4.003A pdb=" N SER A1395 " --> pdb=" O VAL A1391 " (cutoff:3.500A) Processing helix chain 'A' and resid 1397 through 1400 Processing helix chain 'A' and resid 1404 through 1408 removed outlier: 3.534A pdb=" N GLY A1408 " --> pdb=" O GLU A1405 " (cutoff:3.500A) Processing helix chain 'A' and resid 1411 through 1426 removed outlier: 3.658A pdb=" N VAL A1426 " --> pdb=" O ARG A1422 " (cutoff:3.500A) Processing helix chain 'A' and resid 1442 through 1455 removed outlier: 3.597A pdb=" N VAL A1447 " --> pdb=" O GLU A1443 " (cutoff:3.500A) Processing helix chain 'A' and resid 1467 through 1471 Processing helix chain 'A' and resid 1490 through 1497 removed outlier: 3.616A pdb=" N ASP A1497 " --> pdb=" O GLN A1493 " (cutoff:3.500A) Processing helix chain 'A' and resid 1500 through 1509 Processing sheet with id=AA1, first strand: chain 'A' and resid 613 through 615 removed outlier: 4.640A pdb=" N ARG A 682 " --> pdb=" O THR A 633 " (cutoff:3.500A) removed outlier: 7.030A pdb=" N THR A 633 " --> pdb=" O ARG A 682 " (cutoff:3.500A) removed outlier: 6.135A pdb=" N LYS A 684 " --> pdb=" O ASP A 631 " (cutoff:3.500A) removed outlier: 6.231A pdb=" N ASP A 631 " --> pdb=" O LYS A 684 " (cutoff:3.500A) removed outlier: 6.900A pdb=" N ALA A 625 " --> pdb=" O HIS A 690 " (cutoff:3.500A) removed outlier: 5.373A pdb=" N ASP A 630 " --> pdb=" O ILE A 649 " (cutoff:3.500A) removed outlier: 7.016A pdb=" N ILE A 649 " --> pdb=" O ASP A 630 " (cutoff:3.500A) removed outlier: 6.674A pdb=" N ALA A 632 " --> pdb=" O LYS A 647 " (cutoff:3.500A) removed outlier: 4.743A pdb=" N LYS A 647 " --> pdb=" O ALA A 632 " (cutoff:3.500A) removed outlier: 6.539A pdb=" N PHE A 634 " --> pdb=" O ALA A 645 " (cutoff:3.500A) removed outlier: 6.997A pdb=" N LYS A 643 " --> pdb=" O TRP A 636 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 693 through 696 removed outlier: 6.601A pdb=" N ALA A 694 " --> pdb=" O LEU A 775 " (cutoff:3.500A) removed outlier: 7.210A pdb=" N ASP A 777 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 6.628A pdb=" N VAL A 696 " --> pdb=" O ASP A 777 " (cutoff:3.500A) removed outlier: 6.362A pdb=" N CYS A 660 " --> pdb=" O ALA A 824 " (cutoff:3.500A) removed outlier: 7.034A pdb=" N LEU A 826 " --> pdb=" O CYS A 660 " (cutoff:3.500A) removed outlier: 5.731A pdb=" N VAL A 662 " --> pdb=" O LEU A 826 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N GLN A 833 " --> pdb=" O LEU A 825 " (cutoff:3.500A) removed outlier: 6.778A pdb=" N ASP A 827 " --> pdb=" O ILE A 831 " (cutoff:3.500A) removed outlier: 4.920A pdb=" N ILE A 831 " --> pdb=" O ASP A 827 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 705 through 706 Processing sheet with id=AA4, first strand: chain 'A' and resid 1287 through 1296 removed outlier: 6.163A pdb=" N VAL A1288 " --> pdb=" O ARG A1280 " (cutoff:3.500A) removed outlier: 7.205A pdb=" N ARG A1280 " --> pdb=" O VAL A1288 " (cutoff:3.500A) removed outlier: 6.793A pdb=" N LYS A1290 " --> pdb=" O SER A1278 " (cutoff:3.500A) removed outlier: 6.605A pdb=" N SER A1278 " --> pdb=" O LYS A1290 " (cutoff:3.500A) removed outlier: 5.062A pdb=" N ILE A1292 " --> pdb=" O ASN A1276 " (cutoff:3.500A) removed outlier: 4.248A pdb=" N TYR A1277 " --> pdb=" O GLU A1327 " (cutoff:3.500A) removed outlier: 6.612A pdb=" N GLU A1327 " --> pdb=" O TYR A1277 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 1350 through 1352 removed outlier: 6.693A pdb=" N LYS A1301 " --> pdb=" O ARG A1476 " (cutoff:3.500A) removed outlier: 8.141A pdb=" N ILE A1478 " --> pdb=" O LYS A1301 " (cutoff:3.500A) removed outlier: 6.623A pdb=" N GLY A1303 " --> pdb=" O ILE A1478 " (cutoff:3.500A) removed outlier: 7.286A pdb=" N LEU A1480 " --> pdb=" O GLY A1303 " (cutoff:3.500A) removed outlier: 6.191A pdb=" N VAL A1305 " --> pdb=" O LEU A1480 " (cutoff:3.500A) removed outlier: 6.616A pdb=" N ASP A1481 " --> pdb=" O VAL A1485 " (cutoff:3.500A) removed outlier: 5.478A pdb=" N VAL A1485 " --> pdb=" O ASP A1481 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 1361 through 1362 778 hydrogen bonds defined for protein. 2271 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: 5.31 Time building geometry restraints manager: 3.08 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 3717 1.34 - 1.46: 2128 1.46 - 1.58: 6029 1.58 - 1.69: 0 1.69 - 1.81: 86 Bond restraints: 11960 Sorted by residual: bond pdb=" N ASP A 325 " pdb=" CA ASP A 325 " ideal model delta sigma weight residual 1.459 1.484 -0.025 1.19e-02 7.06e+03 4.34e+00 bond pdb=" CA ASP A 778 " pdb=" CB ASP A 778 " ideal model delta sigma weight residual 1.522 1.533 -0.011 7.00e-03 2.04e+04 2.43e+00 bond pdb=" C MET A 459 " pdb=" N PRO A 460 " ideal model delta sigma weight residual 1.335 1.352 -0.016 1.36e-02 5.41e+03 1.43e+00 bond pdb=" CA MET A 459 " pdb=" C MET A 459 " ideal model delta sigma weight residual 1.520 1.535 -0.015 1.23e-02 6.61e+03 1.41e+00 bond pdb=" CB VAL A1209 " pdb=" CG2 VAL A1209 " ideal model delta sigma weight residual 1.521 1.483 0.038 3.30e-02 9.18e+02 1.32e+00 ... (remaining 11955 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.46: 15538 1.46 - 2.92: 564 2.92 - 4.39: 82 4.39 - 5.85: 18 5.85 - 7.31: 10 Bond angle restraints: 16212 Sorted by residual: angle pdb=" N ALA A1465 " pdb=" CA ALA A1465 " pdb=" C ALA A1465 " ideal model delta sigma weight residual 109.46 115.33 -5.87 1.66e+00 3.63e-01 1.25e+01 angle pdb=" C ASN A 898 " pdb=" N SER A 899 " pdb=" CA SER A 899 " ideal model delta sigma weight residual 122.35 127.25 -4.90 1.46e+00 4.69e-01 1.13e+01 angle pdb=" N ASP A 325 " pdb=" CA ASP A 325 " pdb=" C ASP A 325 " ideal model delta sigma weight residual 111.07 107.50 3.57 1.07e+00 8.73e-01 1.12e+01 angle pdb=" CA TYR A1105 " pdb=" CB TYR A1105 " pdb=" CG TYR A1105 " ideal model delta sigma weight residual 113.90 119.44 -5.54 1.80e+00 3.09e-01 9.47e+00 angle pdb=" N PHE A 576 " pdb=" CA PHE A 576 " pdb=" C PHE A 576 " ideal model delta sigma weight residual 109.81 116.38 -6.57 2.21e+00 2.05e-01 8.83e+00 ... (remaining 16207 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.57: 6679 17.57 - 35.13: 395 35.13 - 52.70: 65 52.70 - 70.26: 6 70.26 - 87.83: 8 Dihedral angle restraints: 7153 sinusoidal: 2846 harmonic: 4307 Sorted by residual: dihedral pdb=" CA ASP A1061 " pdb=" C ASP A1061 " pdb=" N ALA A1062 " pdb=" CA ALA A1062 " ideal model delta harmonic sigma weight residual -180.00 -160.12 -19.88 0 5.00e+00 4.00e-02 1.58e+01 dihedral pdb=" CA ILE A1471 " pdb=" C ILE A1471 " pdb=" N MET A1472 " pdb=" CA MET A1472 " ideal model delta harmonic sigma weight residual 180.00 -160.60 -19.40 0 5.00e+00 4.00e-02 1.51e+01 dihedral pdb=" CA ARG A 929 " pdb=" C ARG A 929 " pdb=" N GLU A 930 " pdb=" CA GLU A 930 " ideal model delta harmonic sigma weight residual 180.00 161.27 18.73 0 5.00e+00 4.00e-02 1.40e+01 ... (remaining 7150 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.038: 1233 0.038 - 0.077: 482 0.077 - 0.115: 118 0.115 - 0.153: 40 0.153 - 0.192: 6 Chirality restraints: 1879 Sorted by residual: chirality pdb=" CA VAL A 239 " pdb=" N VAL A 239 " pdb=" C VAL A 239 " pdb=" CB VAL A 239 " both_signs ideal model delta sigma weight residual False 2.44 2.63 -0.19 2.00e-01 2.50e+01 9.17e-01 chirality pdb=" CA TYR A 159 " pdb=" N TYR A 159 " pdb=" C TYR A 159 " pdb=" CB TYR A 159 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.16 2.00e-01 2.50e+01 6.75e-01 chirality pdb=" CA PHE A 576 " pdb=" N PHE A 576 " pdb=" C PHE A 576 " pdb=" CB PHE A 576 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.16 2.00e-01 2.50e+01 6.65e-01 ... (remaining 1876 not shown) Planarity restraints: 2027 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA SER A1054 " -0.012 2.00e-02 2.50e+03 2.48e-02 6.13e+00 pdb=" C SER A1054 " 0.043 2.00e-02 2.50e+03 pdb=" O SER A1054 " -0.016 2.00e-02 2.50e+03 pdb=" N ASN A1055 " -0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 597 " -0.195 9.50e-02 1.11e+02 8.80e-02 6.09e+00 pdb=" NE ARG A 597 " 0.018 2.00e-02 2.50e+03 pdb=" CZ ARG A 597 " -0.018 2.00e-02 2.50e+03 pdb=" NH1 ARG A 597 " 0.009 2.00e-02 2.50e+03 pdb=" NH2 ARG A 597 " -0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ARG A1228 " 0.012 2.00e-02 2.50e+03 2.46e-02 6.05e+00 pdb=" C ARG A1228 " -0.043 2.00e-02 2.50e+03 pdb=" O ARG A1228 " 0.016 2.00e-02 2.50e+03 pdb=" N MET A1229 " 0.014 2.00e-02 2.50e+03 ... (remaining 2024 not shown) Histogram of nonbonded interaction distances: 2.30 - 2.82: 3161 2.82 - 3.34: 11811 3.34 - 3.86: 19402 3.86 - 4.38: 22216 4.38 - 4.90: 38821 Nonbonded interactions: 95411 Sorted by model distance: nonbonded pdb=" O VAL A1227 " pdb=" OG1 THR A1230 " model vdw 2.302 3.040 nonbonded pdb=" O TYR A 837 " pdb=" OG1 THR A 841 " model vdw 2.339 3.040 nonbonded pdb=" OD2 ASP A 734 " pdb=" NH2 ARG A 760 " model vdw 2.369 3.120 nonbonded pdb=" OE2 GLU A 605 " pdb=" NH2 ARG A 638 " model vdw 2.372 3.120 nonbonded pdb=" NZ LYS A 655 " pdb=" O THR A 804 " model vdw 2.384 3.120 ... (remaining 95406 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.50 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: 3.130 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.430 Check model and map are aligned: 0.080 Set scattering table: 0.110 Process input model: 38.000 Find NCS groups from input model: 0.160 Set up NCS constraints: 0.080 Set refine NCS operators: 0.010 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:2.670 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 44.680 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7519 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 : 0.004 0.042 11960 Z= 0.226 Angle : 0.656 7.309 16212 Z= 0.371 Chirality : 0.045 0.192 1879 Planarity : 0.006 0.088 2027 Dihedral : 12.028 87.826 4367 Min Nonbonded Distance : 2.302 Molprobity Statistics. All-atom Clashscore : 0.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.91 % Favored : 98.09 % Rotamer: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.65 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.44 (0.21), residues: 1466 helix: 0.71 (0.16), residues: 963 sheet: -0.58 (0.59), residues: 72 loop : -0.26 (0.30), residues: 431 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP A 422 HIS 0.004 0.001 HIS A 157 PHE 0.023 0.002 PHE A 292 TYR 0.023 0.002 TYR A1105 ARG 0.021 0.001 ARG A 906 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2932 Ramachandran restraints generated. 1466 Oldfield, 0 Emsley, 1466 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2932 Ramachandran restraints generated. 1466 Oldfield, 0 Emsley, 1466 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 1291 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 195 time to evaluate : 1.288 Fit side-chains REVERT: A 520 LYS cc_start: 0.7554 (mmtt) cc_final: 0.6579 (mtpt) REVERT: A 521 ASN cc_start: 0.7780 (t0) cc_final: 0.7296 (t0) REVERT: A 657 ASN cc_start: 0.6901 (m110) cc_final: 0.5537 (p0) REVERT: A 670 THR cc_start: 0.8295 (p) cc_final: 0.7934 (t) REVERT: A 698 GLN cc_start: 0.8780 (tt0) cc_final: 0.8079 (tm-30) REVERT: A 717 TYR cc_start: 0.7823 (t80) cc_final: 0.7495 (t80) REVERT: A 744 THR cc_start: 0.8231 (m) cc_final: 0.7971 (p) REVERT: A 777 ASP cc_start: 0.6896 (t0) cc_final: 0.6424 (t0) REVERT: A 789 ARG cc_start: 0.8625 (ttt180) cc_final: 0.8318 (ptm-80) REVERT: A 1149 LYS cc_start: 0.8307 (ttmt) cc_final: 0.8056 (tptt) REVERT: A 1215 TYR cc_start: 0.8904 (m-80) cc_final: 0.7962 (m-80) REVERT: A 1282 ARG cc_start: 0.8209 (mtt180) cc_final: 0.7773 (mtt180) REVERT: A 1285 LEU cc_start: 0.8079 (mt) cc_final: 0.6944 (mt) REVERT: A 1323 ILE cc_start: 0.7616 (mt) cc_final: 0.7236 (pt) REVERT: A 1327 GLU cc_start: 0.7273 (tt0) cc_final: 0.6800 (tt0) REVERT: A 1493 GLN cc_start: 0.7493 (tt0) cc_final: 0.7207 (tm-30) REVERT: A 1505 LEU cc_start: 0.7887 (mt) cc_final: 0.7564 (mt) REVERT: A 1508 GLU cc_start: 0.8045 (mt-10) cc_final: 0.7494 (pt0) outliers start: 0 outliers final: 0 residues processed: 195 average time/residue: 0.3063 time to fit residues: 82.2541 Evaluate side-chains 114 residues out of total 1291 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 114 time to evaluate : 1.502 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 123 optimal weight: 0.8980 chunk 110 optimal weight: 1.9990 chunk 61 optimal weight: 2.9990 chunk 37 optimal weight: 0.6980 chunk 74 optimal weight: 0.7980 chunk 59 optimal weight: 2.9990 chunk 114 optimal weight: 2.9990 chunk 44 optimal weight: 0.8980 chunk 69 optimal weight: 4.9990 chunk 85 optimal weight: 5.9990 chunk 132 optimal weight: 0.8980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 432 GLN A 469 GLN ** A 473 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 648 ASN A 812 ASN A 969 ASN A1371 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7523 moved from start: 0.1312 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 11960 Z= 0.216 Angle : 0.552 6.787 16212 Z= 0.299 Chirality : 0.042 0.224 1879 Planarity : 0.004 0.060 2027 Dihedral : 4.664 21.916 1589 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 3.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.71 % Favored : 98.29 % Rotamer: Outliers : 0.54 % Allowed : 6.58 % Favored : 92.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.65 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.34 (0.22), residues: 1466 helix: 1.44 (0.16), residues: 973 sheet: -0.56 (0.58), residues: 70 loop : 0.03 (0.31), residues: 423 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 422 HIS 0.007 0.001 HIS A1347 PHE 0.017 0.002 PHE A 954 TYR 0.021 0.001 TYR A 237 ARG 0.014 0.001 ARG A 926 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2932 Ramachandran restraints generated. 1466 Oldfield, 0 Emsley, 1466 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2932 Ramachandran restraints generated. 1466 Oldfield, 0 Emsley, 1466 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 1291 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 128 time to evaluate : 1.308 Fit side-chains REVERT: A 120 LEU cc_start: 0.8520 (tp) cc_final: 0.8304 (tp) REVERT: A 520 LYS cc_start: 0.7511 (mmtt) cc_final: 0.6536 (mtpt) REVERT: A 521 ASN cc_start: 0.7784 (t0) cc_final: 0.7519 (t0) REVERT: A 657 ASN cc_start: 0.6989 (m110) cc_final: 0.5508 (p0) REVERT: A 670 THR cc_start: 0.8177 (p) cc_final: 0.7896 (t) REVERT: A 698 GLN cc_start: 0.8843 (tt0) cc_final: 0.8089 (tm-30) REVERT: A 744 THR cc_start: 0.8319 (m) cc_final: 0.8002 (p) REVERT: A 777 ASP cc_start: 0.6985 (t0) cc_final: 0.6420 (t0) REVERT: A 789 ARG cc_start: 0.8644 (ttt180) cc_final: 0.8354 (ptm-80) REVERT: A 967 MET cc_start: 0.8109 (mmm) cc_final: 0.7830 (mmt) REVERT: A 1105 TYR cc_start: 0.7789 (t80) cc_final: 0.7572 (t80) REVERT: A 1149 LYS cc_start: 0.8312 (ttmt) cc_final: 0.8065 (tptt) REVERT: A 1282 ARG cc_start: 0.7845 (mtt180) cc_final: 0.7475 (ptp-110) REVERT: A 1285 LEU cc_start: 0.7262 (mt) cc_final: 0.6926 (mt) REVERT: A 1327 GLU cc_start: 0.7069 (tt0) cc_final: 0.6618 (tt0) REVERT: A 1493 GLN cc_start: 0.7481 (tt0) cc_final: 0.7219 (tm-30) REVERT: A 1505 LEU cc_start: 0.7829 (mt) cc_final: 0.7603 (mp) REVERT: A 1507 MET cc_start: 0.7836 (mmm) cc_final: 0.7411 (tpt) outliers start: 7 outliers final: 4 residues processed: 131 average time/residue: 0.2755 time to fit residues: 51.8484 Evaluate side-chains 114 residues out of total 1291 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 110 time to evaluate : 1.333 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 124 GLU Chi-restraints excluded: chain A residue 448 MET Chi-restraints excluded: chain A residue 1235 THR Chi-restraints excluded: chain A residue 1451 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 73 optimal weight: 1.9990 chunk 41 optimal weight: 0.9980 chunk 110 optimal weight: 1.9990 chunk 90 optimal weight: 1.9990 chunk 36 optimal weight: 0.9980 chunk 132 optimal weight: 0.6980 chunk 143 optimal weight: 1.9990 chunk 118 optimal weight: 2.9990 chunk 131 optimal weight: 0.8980 chunk 45 optimal weight: 1.9990 chunk 106 optimal weight: 1.9990 overall best weight: 1.1182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 432 GLN ** A 473 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 690 HIS A 928 HIS A1371 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7538 moved from start: 0.1606 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 11960 Z= 0.252 Angle : 0.549 7.377 16212 Z= 0.293 Chirality : 0.041 0.170 1879 Planarity : 0.005 0.106 2027 Dihedral : 4.490 22.558 1589 Min Nonbonded Distance : 2.402 Molprobity Statistics. All-atom Clashscore : 3.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % Rotamer: Outliers : 1.01 % Allowed : 6.97 % Favored : 92.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.65 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.45 (0.22), residues: 1466 helix: 1.57 (0.16), residues: 969 sheet: -0.81 (0.55), residues: 72 loop : 0.03 (0.31), residues: 425 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 422 HIS 0.007 0.001 HIS A1347 PHE 0.017 0.002 PHE A 954 TYR 0.022 0.001 TYR A1105 ARG 0.010 0.001 ARG A 926 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2932 Ramachandran restraints generated. 1466 Oldfield, 0 Emsley, 1466 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2932 Ramachandran restraints generated. 1466 Oldfield, 0 Emsley, 1466 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 1291 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 113 time to evaluate : 1.498 Fit side-chains REVERT: A 124 GLU cc_start: 0.8164 (OUTLIER) cc_final: 0.7799 (tm-30) REVERT: A 520 LYS cc_start: 0.7550 (mmtt) cc_final: 0.6570 (mtpt) REVERT: A 521 ASN cc_start: 0.7843 (t0) cc_final: 0.7519 (t0) REVERT: A 657 ASN cc_start: 0.7033 (m110) cc_final: 0.5622 (p0) REVERT: A 698 GLN cc_start: 0.8830 (tt0) cc_final: 0.8152 (tm-30) REVERT: A 744 THR cc_start: 0.8336 (m) cc_final: 0.7739 (p) REVERT: A 777 ASP cc_start: 0.7084 (t0) cc_final: 0.6514 (t0) REVERT: A 789 ARG cc_start: 0.8734 (ttt180) cc_final: 0.8497 (ptm-80) REVERT: A 1058 TYR cc_start: 0.7847 (t80) cc_final: 0.7314 (t80) REVERT: A 1149 LYS cc_start: 0.8318 (ttmt) cc_final: 0.8110 (tptt) REVERT: A 1284 GLU cc_start: 0.7919 (tm-30) cc_final: 0.7343 (pp20) REVERT: A 1285 LEU cc_start: 0.7466 (mt) cc_final: 0.6916 (mt) REVERT: A 1327 GLU cc_start: 0.7117 (tt0) cc_final: 0.6669 (tt0) REVERT: A 1493 GLN cc_start: 0.7459 (tt0) cc_final: 0.7215 (tm-30) REVERT: A 1507 MET cc_start: 0.7824 (mmm) cc_final: 0.7439 (tpt) outliers start: 13 outliers final: 8 residues processed: 121 average time/residue: 0.2679 time to fit residues: 46.6077 Evaluate side-chains 116 residues out of total 1291 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 107 time to evaluate : 1.394 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 124 GLU Chi-restraints excluded: chain A residue 448 MET Chi-restraints excluded: chain A residue 662 VAL Chi-restraints excluded: chain A residue 1019 ILE Chi-restraints excluded: chain A residue 1235 THR Chi-restraints excluded: chain A residue 1350 SER Chi-restraints excluded: chain A residue 1370 ILE Chi-restraints excluded: chain A residue 1451 THR Chi-restraints excluded: chain A residue 1468 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 131 optimal weight: 3.9990 chunk 99 optimal weight: 0.0770 chunk 68 optimal weight: 5.9990 chunk 14 optimal weight: 1.9990 chunk 63 optimal weight: 5.9990 chunk 89 optimal weight: 1.9990 chunk 133 optimal weight: 2.9990 chunk 141 optimal weight: 0.0870 chunk 69 optimal weight: 0.7980 chunk 126 optimal weight: 0.0980 chunk 38 optimal weight: 0.4980 overall best weight: 0.3116 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 432 GLN A 473 GLN A 812 ASN A 974 HIS A1371 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7474 moved from start: 0.1968 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 11960 Z= 0.137 Angle : 0.473 7.149 16212 Z= 0.255 Chirality : 0.039 0.147 1879 Planarity : 0.004 0.063 2027 Dihedral : 4.175 21.614 1589 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 4.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.78 % Favored : 98.22 % Rotamer: Outliers : 0.46 % Allowed : 8.05 % Favored : 91.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.65 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.98 (0.22), residues: 1466 helix: 2.04 (0.16), residues: 971 sheet: -0.79 (0.55), residues: 72 loop : 0.08 (0.31), residues: 423 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 636 HIS 0.005 0.001 HIS A1347 PHE 0.014 0.001 PHE A 954 TYR 0.023 0.001 TYR A1105 ARG 0.003 0.000 ARG A 926 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2932 Ramachandran restraints generated. 1466 Oldfield, 0 Emsley, 1466 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2932 Ramachandran restraints generated. 1466 Oldfield, 0 Emsley, 1466 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 1291 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 124 time to evaluate : 1.473 Fit side-chains REVERT: A 407 ASN cc_start: 0.7936 (t0) cc_final: 0.7316 (t0) REVERT: A 409 MET cc_start: 0.7487 (ttt) cc_final: 0.7274 (ttt) REVERT: A 521 ASN cc_start: 0.7764 (t0) cc_final: 0.7451 (t0) REVERT: A 592 SER cc_start: 0.7239 (t) cc_final: 0.6703 (p) REVERT: A 657 ASN cc_start: 0.7008 (m110) cc_final: 0.5570 (p0) REVERT: A 662 VAL cc_start: 0.7996 (OUTLIER) cc_final: 0.7704 (m) REVERT: A 698 GLN cc_start: 0.8773 (tt0) cc_final: 0.8145 (tm-30) REVERT: A 716 ARG cc_start: 0.7751 (tmt170) cc_final: 0.7473 (tmt170) REVERT: A 721 PHE cc_start: 0.7047 (t80) cc_final: 0.6713 (t80) REVERT: A 740 ASP cc_start: 0.7869 (t0) cc_final: 0.7366 (p0) REVERT: A 777 ASP cc_start: 0.7085 (t0) cc_final: 0.6511 (t0) REVERT: A 789 ARG cc_start: 0.8745 (ttt180) cc_final: 0.8537 (ptm-80) REVERT: A 1058 TYR cc_start: 0.7751 (t80) cc_final: 0.7378 (t80) REVERT: A 1314 SER cc_start: 0.8040 (m) cc_final: 0.7814 (t) REVERT: A 1327 GLU cc_start: 0.6434 (tt0) cc_final: 0.6039 (tt0) REVERT: A 1493 GLN cc_start: 0.7476 (tt0) cc_final: 0.7226 (tm-30) REVERT: A 1507 MET cc_start: 0.7877 (mmm) cc_final: 0.7558 (tpt) outliers start: 6 outliers final: 2 residues processed: 127 average time/residue: 0.2749 time to fit residues: 50.0895 Evaluate side-chains 111 residues out of total 1291 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 108 time to evaluate : 1.393 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 473 GLN Chi-restraints excluded: chain A residue 662 VAL Chi-restraints excluded: chain A residue 1235 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 117 optimal weight: 0.6980 chunk 80 optimal weight: 1.9990 chunk 2 optimal weight: 0.5980 chunk 105 optimal weight: 0.6980 chunk 58 optimal weight: 0.7980 chunk 120 optimal weight: 0.9980 chunk 97 optimal weight: 3.9990 chunk 0 optimal weight: 20.0000 chunk 72 optimal weight: 0.0870 chunk 126 optimal weight: 0.0170 chunk 35 optimal weight: 1.9990 overall best weight: 0.4196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 473 GLN A 537 ASN A1371 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7479 moved from start: 0.2112 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 11960 Z= 0.144 Angle : 0.473 6.549 16212 Z= 0.253 Chirality : 0.039 0.146 1879 Planarity : 0.004 0.050 2027 Dihedral : 4.104 21.206 1589 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 4.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.91 % Favored : 98.09 % Rotamer: Outliers : 0.77 % Allowed : 8.36 % Favored : 90.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.65 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.12 (0.22), residues: 1466 helix: 2.12 (0.16), residues: 974 sheet: -0.75 (0.55), residues: 72 loop : 0.18 (0.32), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 422 HIS 0.007 0.001 HIS A1347 PHE 0.014 0.001 PHE A 954 TYR 0.023 0.001 TYR A1105 ARG 0.003 0.000 ARG A 206 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2932 Ramachandran restraints generated. 1466 Oldfield, 0 Emsley, 1466 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2932 Ramachandran restraints generated. 1466 Oldfield, 0 Emsley, 1466 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 1291 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 117 time to evaluate : 1.315 Fit side-chains REVERT: A 68 ARG cc_start: 0.8043 (OUTLIER) cc_final: 0.7589 (mtt-85) REVERT: A 407 ASN cc_start: 0.8004 (t0) cc_final: 0.7385 (t0) REVERT: A 521 ASN cc_start: 0.7795 (t0) cc_final: 0.7419 (t0) REVERT: A 592 SER cc_start: 0.7197 (t) cc_final: 0.6658 (p) REVERT: A 657 ASN cc_start: 0.7013 (m110) cc_final: 0.5639 (p0) REVERT: A 662 VAL cc_start: 0.8047 (OUTLIER) cc_final: 0.7761 (m) REVERT: A 698 GLN cc_start: 0.8792 (tt0) cc_final: 0.8182 (tm-30) REVERT: A 716 ARG cc_start: 0.7834 (tmt170) cc_final: 0.7549 (tmt170) REVERT: A 740 ASP cc_start: 0.8048 (t0) cc_final: 0.7651 (t0) REVERT: A 744 THR cc_start: 0.8261 (m) cc_final: 0.7988 (m) REVERT: A 789 ARG cc_start: 0.8747 (ttt180) cc_final: 0.8536 (ptm-80) REVERT: A 1058 TYR cc_start: 0.7740 (t80) cc_final: 0.7366 (t80) REVERT: A 1203 THR cc_start: 0.9114 (p) cc_final: 0.8593 (t) REVERT: A 1314 SER cc_start: 0.8030 (m) cc_final: 0.7820 (t) REVERT: A 1327 GLU cc_start: 0.6547 (tt0) cc_final: 0.6130 (tt0) REVERT: A 1493 GLN cc_start: 0.7476 (tt0) cc_final: 0.7227 (tm-30) REVERT: A 1507 MET cc_start: 0.7876 (mmm) cc_final: 0.7512 (tpt) outliers start: 10 outliers final: 6 residues processed: 123 average time/residue: 0.2686 time to fit residues: 47.9877 Evaluate side-chains 116 residues out of total 1291 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 108 time to evaluate : 1.423 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 ARG Chi-restraints excluded: chain A residue 473 GLN Chi-restraints excluded: chain A residue 662 VAL Chi-restraints excluded: chain A residue 675 CYS Chi-restraints excluded: chain A residue 773 THR Chi-restraints excluded: chain A residue 1235 THR Chi-restraints excluded: chain A residue 1370 ILE Chi-restraints excluded: chain A residue 1451 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 47 optimal weight: 1.9990 chunk 127 optimal weight: 2.9990 chunk 27 optimal weight: 1.9990 chunk 82 optimal weight: 0.7980 chunk 34 optimal weight: 0.9990 chunk 141 optimal weight: 0.7980 chunk 117 optimal weight: 0.9980 chunk 65 optimal weight: 10.0000 chunk 11 optimal weight: 2.9990 chunk 46 optimal weight: 0.8980 chunk 74 optimal weight: 8.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 473 GLN A1371 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7507 moved from start: 0.2149 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 11960 Z= 0.210 Angle : 0.494 9.705 16212 Z= 0.262 Chirality : 0.040 0.158 1879 Planarity : 0.004 0.040 2027 Dihedral : 4.105 20.820 1589 Min Nonbonded Distance : 2.596 Molprobity Statistics. All-atom Clashscore : 4.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % Rotamer: Outliers : 0.70 % Allowed : 8.98 % Favored : 90.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.65 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.01 (0.22), residues: 1466 helix: 2.05 (0.16), residues: 972 sheet: -0.81 (0.56), residues: 72 loop : 0.13 (0.32), residues: 422 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 422 HIS 0.006 0.001 HIS A1347 PHE 0.016 0.001 PHE A 954 TYR 0.024 0.001 TYR A1105 ARG 0.005 0.000 ARG A1282 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2932 Ramachandran restraints generated. 1466 Oldfield, 0 Emsley, 1466 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2932 Ramachandran restraints generated. 1466 Oldfield, 0 Emsley, 1466 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 1291 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 111 time to evaluate : 1.400 Fit side-chains REVERT: A 407 ASN cc_start: 0.8084 (t0) cc_final: 0.7469 (t0) REVERT: A 520 LYS cc_start: 0.7517 (mmtt) cc_final: 0.6614 (mtpt) REVERT: A 521 ASN cc_start: 0.7790 (t0) cc_final: 0.7404 (t0) REVERT: A 592 SER cc_start: 0.7223 (t) cc_final: 0.6678 (p) REVERT: A 657 ASN cc_start: 0.7107 (m110) cc_final: 0.5748 (p0) REVERT: A 662 VAL cc_start: 0.7997 (OUTLIER) cc_final: 0.7712 (m) REVERT: A 698 GLN cc_start: 0.8792 (tt0) cc_final: 0.8186 (tm-30) REVERT: A 716 ARG cc_start: 0.7864 (tmt170) cc_final: 0.7589 (tmt170) REVERT: A 740 ASP cc_start: 0.8143 (t0) cc_final: 0.7467 (p0) REVERT: A 789 ARG cc_start: 0.8755 (ttt180) cc_final: 0.8542 (ptm-80) REVERT: A 1058 TYR cc_start: 0.7846 (t80) cc_final: 0.7444 (t80) REVERT: A 1203 THR cc_start: 0.9119 (p) cc_final: 0.8605 (t) REVERT: A 1314 SER cc_start: 0.8085 (m) cc_final: 0.7859 (t) REVERT: A 1327 GLU cc_start: 0.6820 (tt0) cc_final: 0.6395 (tt0) REVERT: A 1394 MET cc_start: 0.5946 (mtp) cc_final: 0.5710 (mtm) REVERT: A 1493 GLN cc_start: 0.7489 (tt0) cc_final: 0.7240 (tm-30) outliers start: 9 outliers final: 5 residues processed: 116 average time/residue: 0.2632 time to fit residues: 44.7339 Evaluate side-chains 114 residues out of total 1291 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 108 time to evaluate : 1.344 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 662 VAL Chi-restraints excluded: chain A residue 675 CYS Chi-restraints excluded: chain A residue 773 THR Chi-restraints excluded: chain A residue 1235 THR Chi-restraints excluded: chain A residue 1370 ILE Chi-restraints excluded: chain A residue 1451 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 136 optimal weight: 4.9990 chunk 15 optimal weight: 1.9990 chunk 80 optimal weight: 0.9990 chunk 103 optimal weight: 0.8980 chunk 79 optimal weight: 5.9990 chunk 118 optimal weight: 1.9990 chunk 78 optimal weight: 3.9990 chunk 140 optimal weight: 0.8980 chunk 88 optimal weight: 0.9980 chunk 85 optimal weight: 5.9990 chunk 64 optimal weight: 2.9990 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 432 GLN A1371 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7537 moved from start: 0.2163 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 11960 Z= 0.252 Angle : 0.523 9.416 16212 Z= 0.275 Chirality : 0.041 0.170 1879 Planarity : 0.004 0.042 2027 Dihedral : 4.166 20.336 1589 Min Nonbonded Distance : 2.590 Molprobity Statistics. All-atom Clashscore : 4.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer: Outliers : 0.77 % Allowed : 8.98 % Favored : 90.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.65 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.81 (0.22), residues: 1466 helix: 1.89 (0.16), residues: 971 sheet: -0.65 (0.62), residues: 63 loop : -0.01 (0.31), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 422 HIS 0.006 0.001 HIS A1347 PHE 0.017 0.001 PHE A 954 TYR 0.030 0.001 TYR A 722 ARG 0.004 0.000 ARG A1282 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2932 Ramachandran restraints generated. 1466 Oldfield, 0 Emsley, 1466 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2932 Ramachandran restraints generated. 1466 Oldfield, 0 Emsley, 1466 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 1291 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 108 time to evaluate : 1.339 Fit side-chains REVERT: A 206 ARG cc_start: 0.7033 (tpt170) cc_final: 0.6817 (tpt170) REVERT: A 407 ASN cc_start: 0.8065 (t0) cc_final: 0.7753 (t0) REVERT: A 520 LYS cc_start: 0.7543 (mmtt) cc_final: 0.6636 (mtpt) REVERT: A 592 SER cc_start: 0.7260 (t) cc_final: 0.6702 (p) REVERT: A 662 VAL cc_start: 0.7914 (OUTLIER) cc_final: 0.7610 (m) REVERT: A 698 GLN cc_start: 0.8806 (tt0) cc_final: 0.8189 (tm-30) REVERT: A 716 ARG cc_start: 0.7928 (tmt170) cc_final: 0.7645 (tmt170) REVERT: A 740 ASP cc_start: 0.8145 (t0) cc_final: 0.7517 (t0) REVERT: A 789 ARG cc_start: 0.8746 (ttt180) cc_final: 0.8509 (ptm-80) REVERT: A 1058 TYR cc_start: 0.7896 (t80) cc_final: 0.7458 (t80) REVERT: A 1327 GLU cc_start: 0.7167 (tt0) cc_final: 0.6749 (tt0) REVERT: A 1394 MET cc_start: 0.6068 (mtp) cc_final: 0.5734 (mtm) REVERT: A 1507 MET cc_start: 0.7787 (mmm) cc_final: 0.7424 (tpt) outliers start: 10 outliers final: 5 residues processed: 113 average time/residue: 0.2563 time to fit residues: 42.9845 Evaluate side-chains 108 residues out of total 1291 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 102 time to evaluate : 1.313 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 662 VAL Chi-restraints excluded: chain A residue 675 CYS Chi-restraints excluded: chain A residue 773 THR Chi-restraints excluded: chain A residue 1235 THR Chi-restraints excluded: chain A residue 1370 ILE Chi-restraints excluded: chain A residue 1451 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 87 optimal weight: 10.0000 chunk 56 optimal weight: 0.7980 chunk 84 optimal weight: 3.9990 chunk 42 optimal weight: 0.6980 chunk 27 optimal weight: 0.7980 chunk 89 optimal weight: 2.9990 chunk 95 optimal weight: 3.9990 chunk 69 optimal weight: 3.9990 chunk 13 optimal weight: 0.9990 chunk 110 optimal weight: 1.9990 chunk 128 optimal weight: 3.9990 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1371 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7534 moved from start: 0.2249 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 11960 Z= 0.232 Angle : 0.512 9.692 16212 Z= 0.271 Chirality : 0.040 0.177 1879 Planarity : 0.004 0.041 2027 Dihedral : 4.136 20.162 1589 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 4.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer: Outliers : 0.62 % Allowed : 9.21 % Favored : 90.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.65 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.80 (0.22), residues: 1466 helix: 1.86 (0.16), residues: 976 sheet: -0.24 (0.70), residues: 52 loop : -0.07 (0.31), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A1379 HIS 0.006 0.001 HIS A1347 PHE 0.017 0.001 PHE A 954 TYR 0.025 0.001 TYR A1105 ARG 0.005 0.000 ARG A1280 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2932 Ramachandran restraints generated. 1466 Oldfield, 0 Emsley, 1466 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2932 Ramachandran restraints generated. 1466 Oldfield, 0 Emsley, 1466 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 1291 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 102 time to evaluate : 1.283 Fit side-chains REVERT: A 407 ASN cc_start: 0.8047 (t0) cc_final: 0.7737 (t0) REVERT: A 520 LYS cc_start: 0.7529 (mmtt) cc_final: 0.6628 (mtpt) REVERT: A 592 SER cc_start: 0.7263 (t) cc_final: 0.6702 (p) REVERT: A 662 VAL cc_start: 0.7916 (OUTLIER) cc_final: 0.7602 (m) REVERT: A 681 PHE cc_start: 0.8580 (m-80) cc_final: 0.8364 (m-80) REVERT: A 698 GLN cc_start: 0.8796 (tt0) cc_final: 0.8190 (tm-30) REVERT: A 721 PHE cc_start: 0.7134 (t80) cc_final: 0.6742 (t80) REVERT: A 789 ARG cc_start: 0.8747 (ttt180) cc_final: 0.8507 (ptm-80) REVERT: A 1058 TYR cc_start: 0.7905 (t80) cc_final: 0.7473 (t80) REVERT: A 1327 GLU cc_start: 0.7156 (tt0) cc_final: 0.6754 (tt0) REVERT: A 1394 MET cc_start: 0.6079 (mtp) cc_final: 0.5769 (mtm) REVERT: A 1507 MET cc_start: 0.7818 (mmm) cc_final: 0.7413 (tpt) outliers start: 8 outliers final: 6 residues processed: 107 average time/residue: 0.2521 time to fit residues: 39.8354 Evaluate side-chains 108 residues out of total 1291 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 101 time to evaluate : 1.281 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 123 ILE Chi-restraints excluded: chain A residue 580 ILE Chi-restraints excluded: chain A residue 662 VAL Chi-restraints excluded: chain A residue 675 CYS Chi-restraints excluded: chain A residue 1235 THR Chi-restraints excluded: chain A residue 1370 ILE Chi-restraints excluded: chain A residue 1451 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 134 optimal weight: 0.0010 chunk 122 optimal weight: 0.9990 chunk 131 optimal weight: 4.9990 chunk 78 optimal weight: 1.9990 chunk 57 optimal weight: 0.9990 chunk 102 optimal weight: 0.8980 chunk 40 optimal weight: 0.7980 chunk 118 optimal weight: 0.6980 chunk 124 optimal weight: 2.9990 chunk 130 optimal weight: 2.9990 chunk 86 optimal weight: 5.9990 overall best weight: 0.6788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1371 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7511 moved from start: 0.2348 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 11960 Z= 0.175 Angle : 0.493 9.348 16212 Z= 0.260 Chirality : 0.039 0.165 1879 Planarity : 0.003 0.040 2027 Dihedral : 4.038 20.290 1589 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 4.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % Rotamer: Outliers : 0.54 % Allowed : 9.21 % Favored : 90.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.65 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.99 (0.22), residues: 1466 helix: 2.03 (0.16), residues: 976 sheet: -0.11 (0.71), residues: 52 loop : -0.07 (0.31), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 422 HIS 0.005 0.001 HIS A1347 PHE 0.015 0.001 PHE A 954 TYR 0.023 0.001 TYR A1105 ARG 0.005 0.000 ARG A1280 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2932 Ramachandran restraints generated. 1466 Oldfield, 0 Emsley, 1466 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2932 Ramachandran restraints generated. 1466 Oldfield, 0 Emsley, 1466 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 1291 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 103 time to evaluate : 1.331 Fit side-chains REVERT: A 407 ASN cc_start: 0.8055 (t0) cc_final: 0.7443 (t0) REVERT: A 592 SER cc_start: 0.7237 (t) cc_final: 0.6680 (p) REVERT: A 662 VAL cc_start: 0.7927 (OUTLIER) cc_final: 0.7631 (m) REVERT: A 681 PHE cc_start: 0.8470 (m-80) cc_final: 0.8263 (m-80) REVERT: A 698 GLN cc_start: 0.8800 (tt0) cc_final: 0.8189 (tm-30) REVERT: A 716 ARG cc_start: 0.7641 (tmt170) cc_final: 0.7273 (tmt170) REVERT: A 721 PHE cc_start: 0.7073 (t80) cc_final: 0.6742 (t80) REVERT: A 789 ARG cc_start: 0.8739 (ttt180) cc_final: 0.8502 (ptm-80) REVERT: A 1058 TYR cc_start: 0.7843 (t80) cc_final: 0.7452 (t80) REVERT: A 1203 THR cc_start: 0.9123 (p) cc_final: 0.8608 (t) REVERT: A 1314 SER cc_start: 0.8072 (m) cc_final: 0.7857 (t) REVERT: A 1327 GLU cc_start: 0.6998 (tt0) cc_final: 0.6603 (tt0) REVERT: A 1394 MET cc_start: 0.6034 (mtp) cc_final: 0.5758 (mtm) REVERT: A 1507 MET cc_start: 0.7786 (mmm) cc_final: 0.7386 (tpt) outliers start: 7 outliers final: 6 residues processed: 108 average time/residue: 0.2578 time to fit residues: 40.8646 Evaluate side-chains 109 residues out of total 1291 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 102 time to evaluate : 1.348 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 123 ILE Chi-restraints excluded: chain A residue 580 ILE Chi-restraints excluded: chain A residue 662 VAL Chi-restraints excluded: chain A residue 675 CYS Chi-restraints excluded: chain A residue 1235 THR Chi-restraints excluded: chain A residue 1370 ILE Chi-restraints excluded: chain A residue 1451 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 138 optimal weight: 0.4980 chunk 84 optimal weight: 3.9990 chunk 65 optimal weight: 5.9990 chunk 96 optimal weight: 0.8980 chunk 145 optimal weight: 2.9990 chunk 133 optimal weight: 0.1980 chunk 115 optimal weight: 0.5980 chunk 12 optimal weight: 0.6980 chunk 89 optimal weight: 0.6980 chunk 71 optimal weight: 0.7980 chunk 92 optimal weight: 0.9990 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1371 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7500 moved from start: 0.2441 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 11960 Z= 0.156 Angle : 0.480 8.984 16212 Z= 0.253 Chirality : 0.039 0.149 1879 Planarity : 0.003 0.041 2027 Dihedral : 3.999 27.236 1589 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 4.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Rotamer: Outliers : 0.62 % Allowed : 9.29 % Favored : 90.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.65 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.10 (0.22), residues: 1466 helix: 2.12 (0.16), residues: 977 sheet: -0.08 (0.71), residues: 52 loop : -0.04 (0.31), residues: 437 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 422 HIS 0.005 0.001 HIS A1347 PHE 0.016 0.001 PHE A 576 TYR 0.022 0.001 TYR A1105 ARG 0.004 0.000 ARG A1280 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2932 Ramachandran restraints generated. 1466 Oldfield, 0 Emsley, 1466 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2932 Ramachandran restraints generated. 1466 Oldfield, 0 Emsley, 1466 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 1291 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 106 time to evaluate : 1.322 Fit side-chains REVERT: A 407 ASN cc_start: 0.8016 (t0) cc_final: 0.7404 (t0) REVERT: A 521 ASN cc_start: 0.7852 (t0) cc_final: 0.7460 (t0) REVERT: A 529 MET cc_start: 0.7963 (mtp) cc_final: 0.7672 (mtt) REVERT: A 662 VAL cc_start: 0.7837 (OUTLIER) cc_final: 0.7566 (m) REVERT: A 698 GLN cc_start: 0.8761 (tt0) cc_final: 0.8141 (tm-30) REVERT: A 716 ARG cc_start: 0.7656 (tmt170) cc_final: 0.7281 (tmt170) REVERT: A 721 PHE cc_start: 0.7058 (t80) cc_final: 0.6755 (t80) REVERT: A 789 ARG cc_start: 0.8734 (ttt180) cc_final: 0.8499 (ptm-80) REVERT: A 982 TYR cc_start: 0.7623 (m-80) cc_final: 0.7356 (m-80) REVERT: A 1058 TYR cc_start: 0.7820 (t80) cc_final: 0.7465 (t80) REVERT: A 1203 THR cc_start: 0.9131 (p) cc_final: 0.8621 (t) REVERT: A 1280 ARG cc_start: 0.7582 (ptp90) cc_final: 0.6686 (ttm110) REVERT: A 1314 SER cc_start: 0.8064 (m) cc_final: 0.7848 (t) REVERT: A 1327 GLU cc_start: 0.6957 (tt0) cc_final: 0.6559 (tt0) REVERT: A 1394 MET cc_start: 0.6236 (mtp) cc_final: 0.5945 (mtm) REVERT: A 1507 MET cc_start: 0.7812 (mmm) cc_final: 0.7403 (tpt) outliers start: 8 outliers final: 6 residues processed: 111 average time/residue: 0.2690 time to fit residues: 43.1634 Evaluate side-chains 104 residues out of total 1291 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 97 time to evaluate : 1.444 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 123 ILE Chi-restraints excluded: chain A residue 662 VAL Chi-restraints excluded: chain A residue 675 CYS Chi-restraints excluded: chain A residue 773 THR Chi-restraints excluded: chain A residue 1235 THR Chi-restraints excluded: chain A residue 1370 ILE Chi-restraints excluded: chain A residue 1451 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 123 optimal weight: 0.9980 chunk 35 optimal weight: 1.9990 chunk 106 optimal weight: 1.9990 chunk 17 optimal weight: 0.7980 chunk 32 optimal weight: 0.1980 chunk 116 optimal weight: 1.9990 chunk 48 optimal weight: 0.8980 chunk 119 optimal weight: 0.6980 chunk 14 optimal weight: 0.9990 chunk 21 optimal weight: 0.4980 chunk 101 optimal weight: 0.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 704 ASN A1218 GLN A1371 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4014 r_free = 0.4014 target = 0.150066 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3558 r_free = 0.3558 target = 0.112372 restraints weight = 32877.887| |-----------------------------------------------------------------------------| r_work (start): 0.3512 rms_B_bonded: 3.63 r_work: 0.3335 rms_B_bonded: 4.32 restraints_weight: 0.5000 r_work (final): 0.3335 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3338 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3338 r_free = 0.3338 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3338 r_free = 0.3338 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3338 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7784 moved from start: 0.2479 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 11960 Z= 0.165 Angle : 0.479 8.877 16212 Z= 0.252 Chirality : 0.039 0.151 1879 Planarity : 0.003 0.042 2027 Dihedral : 3.964 24.376 1589 Min Nonbonded Distance : 2.395 Molprobity Statistics. All-atom Clashscore : 4.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Rotamer: Outliers : 0.70 % Allowed : 9.37 % Favored : 89.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.65 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.06 (0.22), residues: 1466 helix: 2.11 (0.16), residues: 983 sheet: -0.07 (0.72), residues: 52 loop : -0.15 (0.30), residues: 431 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP A1379 HIS 0.005 0.001 HIS A1347 PHE 0.031 0.001 PHE A 576 TYR 0.028 0.001 TYR A 722 ARG 0.004 0.000 ARG A1280 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2536.35 seconds wall clock time: 47 minutes 33.37 seconds (2853.37 seconds total)