Starting phenix.real_space_refine on Wed Jun 11 13:33:11 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7wo9_32643/06_2025/7wo9_32643.cif Found real_map, /net/cci-nas-00/data/ceres_data/7wo9_32643/06_2025/7wo9_32643.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.81 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7wo9_32643/06_2025/7wo9_32643.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7wo9_32643/06_2025/7wo9_32643.map" model { file = "/net/cci-nas-00/data/ceres_data/7wo9_32643/06_2025/7wo9_32643.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7wo9_32643/06_2025/7wo9_32643.cif" } resolution = 2.81 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= 0.046 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 29 5.16 5 C 8262 2.51 5 N 2036 2.21 5 O 2416 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 2 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 12743 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 12743 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1581, 12743 Classifications: {'peptide': 1581} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 44, 'TRANS': 1536} Chain breaks: 5 Time building chain proxies: 9.59, per 1000 atoms: 0.75 Number of scatterers: 12743 At special positions: 0 Unit cell: (78.156, 106.212, 187.708, 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 29 16.00 O 2416 8.00 N 2036 7.00 C 8262 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: 3.28 Conformation dependent library (CDL) restraints added in 1.7 seconds 3138 Ramachandran restraints generated. 1569 Oldfield, 0 Emsley, 1569 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3086 Finding SS restraints... Secondary structure from input PDB file: 91 helices and 3 sheets defined 75.1% alpha, 1.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.62 Creating SS restraints... Processing helix chain 'A' and resid 14 through 25 Processing helix chain 'A' and resid 26 through 27 No H-bonds generated for 'chain 'A' and resid 26 through 27' Processing helix chain 'A' and resid 28 through 32 Processing helix chain 'A' and resid 33 through 47 Processing helix chain 'A' and resid 70 through 80 Processing helix chain 'A' and resid 86 through 92 Processing helix chain 'A' and resid 94 through 119 removed outlier: 3.854A pdb=" N LEU A 110 " --> pdb=" O ARG A 106 " (cutoff:3.500A) Processing helix chain 'A' and resid 120 through 122 No H-bonds generated for 'chain 'A' and resid 120 through 122' Processing helix chain 'A' and resid 123 through 132 removed outlier: 3.555A pdb=" N PHE A 129 " --> pdb=" O GLU A 125 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N ILE A 130 " --> pdb=" O THR A 126 " (cutoff:3.500A) Processing helix chain 'A' and resid 133 through 151 Processing helix chain 'A' and resid 155 through 162 Processing helix chain 'A' and resid 167 through 199 Processing helix chain 'A' and resid 205 through 219 removed outlier: 4.009A pdb=" N GLN A 217 " --> pdb=" O PHE A 213 " (cutoff:3.500A) Processing helix chain 'A' and resid 219 through 229 Processing helix chain 'A' and resid 247 through 273 removed outlier: 4.983A pdb=" N LEU A 253 " --> pdb=" O ASP A 249 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N SER A 254 " --> pdb=" O LEU A 250 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N SER A 259 " --> pdb=" O GLU A 255 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N ARG A 260 " --> pdb=" O THR A 256 " (cutoff:3.500A) Processing helix chain 'A' and resid 286 through 291 Processing helix chain 'A' and resid 293 through 308 Processing helix chain 'A' and resid 318 through 336 removed outlier: 3.609A pdb=" N HIS A 322 " --> pdb=" O HIS A 318 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N PHE A 327 " --> pdb=" O TYR A 323 " (cutoff:3.500A) Processing helix chain 'A' and resid 345 through 356 removed outlier: 4.399A pdb=" N PHE A 349 " --> pdb=" O ASP A 345 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N ALA A 350 " --> pdb=" O ILE A 346 " (cutoff:3.500A) Processing helix chain 'A' and resid 357 through 369 Processing helix chain 'A' and resid 372 through 387 removed outlier: 4.219A pdb=" N THR A 376 " --> pdb=" O ASP A 372 " (cutoff:3.500A) Processing helix chain 'A' and resid 388 through 390 No H-bonds generated for 'chain 'A' and resid 388 through 390' Processing helix chain 'A' and resid 393 through 405 removed outlier: 3.618A pdb=" N SER A 405 " --> pdb=" O ALA A 401 " (cutoff:3.500A) Processing helix chain 'A' and resid 408 through 417 Processing helix chain 'A' and resid 418 through 431 removed outlier: 3.578A pdb=" N ILE A 427 " --> pdb=" O LYS A 423 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N ILE A 428 " --> pdb=" O LYS A 424 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N LYS A 431 " --> pdb=" O ILE A 427 " (cutoff:3.500A) Processing helix chain 'A' and resid 438 through 446 Processing helix chain 'A' and resid 449 through 459 removed outlier: 4.414A pdb=" N ASP A 459 " --> pdb=" O PHE A 455 " (cutoff:3.500A) Processing helix chain 'A' and resid 469 through 473 removed outlier: 3.787A pdb=" N ASP A 472 " --> pdb=" O SER A 469 " (cutoff:3.500A) Processing helix chain 'A' and resid 560 through 579 removed outlier: 3.922A pdb=" N LEU A 564 " --> pdb=" O ASN A 560 " (cutoff:3.500A) Processing helix chain 'A' and resid 584 through 602 Processing helix chain 'A' and resid 607 through 619 removed outlier: 3.506A pdb=" N SER A 619 " --> pdb=" O LEU A 615 " (cutoff:3.500A) Processing helix chain 'A' and resid 633 through 649 removed outlier: 3.630A pdb=" N VAL A 637 " --> pdb=" O SER A 633 " (cutoff:3.500A) Processing helix chain 'A' and resid 650 through 665 removed outlier: 3.634A pdb=" N THR A 665 " --> pdb=" O MET A 661 " (cutoff:3.500A) Processing helix chain 'A' and resid 668 through 679 removed outlier: 3.846A pdb=" N VAL A 672 " --> pdb=" O TYR A 668 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N SER A 674 " --> pdb=" O HIS A 670 " (cutoff:3.500A) Processing helix chain 'A' and resid 689 through 698 Processing helix chain 'A' and resid 698 through 703 Processing helix chain 'A' and resid 705 through 723 Processing helix chain 'A' and resid 731 through 751 removed outlier: 3.596A pdb=" N LYS A 735 " --> pdb=" O SER A 731 " (cutoff:3.500A) Processing helix chain 'A' and resid 752 through 756 Processing helix chain 'A' and resid 760 through 784 removed outlier: 4.089A pdb=" N LYS A 764 " --> pdb=" O ASN A 760 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N PHE A 765 " --> pdb=" O PHE A 761 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N HIS A 770 " --> pdb=" O GLU A 766 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N TYR A 776 " --> pdb=" O THR A 772 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N ASP A 777 " --> pdb=" O LEU A 773 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N VAL A 782 " --> pdb=" O VAL A 778 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N THR A 784 " --> pdb=" O HIS A 780 " (cutoff:3.500A) Processing helix chain 'A' and resid 795 through 807 Processing helix chain 'A' and resid 814 through 825 removed outlier: 4.090A pdb=" N ASN A 818 " --> pdb=" O ASP A 814 " (cutoff:3.500A) Processing helix chain 'A' and resid 826 through 828 No H-bonds generated for 'chain 'A' and resid 826 through 828' Processing helix chain 'A' and resid 829 through 836 Processing helix chain 'A' and resid 842 through 864 Processing helix chain 'A' and resid 871 through 880 removed outlier: 3.628A pdb=" N LYS A 875 " --> pdb=" O SER A 871 " (cutoff:3.500A) Processing helix chain 'A' and resid 881 through 889 removed outlier: 3.520A pdb=" N ASP A 886 " --> pdb=" O SER A 882 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N VAL A 887 " --> pdb=" O LYS A 883 " (cutoff:3.500A) Processing helix chain 'A' and resid 896 through 910 removed outlier: 3.675A pdb=" N ILE A 900 " --> pdb=" O PHE A 896 " (cutoff:3.500A) Processing helix chain 'A' and resid 918 through 924 Processing helix chain 'A' and resid 924 through 940 removed outlier: 3.648A pdb=" N MET A 929 " --> pdb=" O GLU A 925 " (cutoff:3.500A) Processing helix chain 'A' and resid 945 through 962 Processing helix chain 'A' and resid 964 through 974 Processing helix chain 'A' and resid 979 through 983 Processing helix chain 'A' and resid 989 through 992 Processing helix chain 'A' and resid 993 through 1003 removed outlier: 4.062A pdb=" N VAL A 997 " --> pdb=" O SER A 993 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N LEU A1003 " --> pdb=" O GLN A 999 " (cutoff:3.500A) Processing helix chain 'A' and resid 1009 through 1026 removed outlier: 3.986A pdb=" N THR A1026 " --> pdb=" O TYR A1022 " (cutoff:3.500A) Processing helix chain 'A' and resid 1037 through 1050 Processing helix chain 'A' and resid 1051 through 1054 Processing helix chain 'A' and resid 1061 through 1089 removed outlier: 3.546A pdb=" N ARG A1077 " --> pdb=" O LYS A1073 " (cutoff:3.500A) Processing helix chain 'A' and resid 1093 through 1101 Processing helix chain 'A' and resid 1104 through 1110 removed outlier: 3.748A pdb=" N LEU A1108 " --> pdb=" O ASP A1104 " (cutoff:3.500A) Processing helix chain 'A' and resid 1111 through 1114 removed outlier: 3.668A pdb=" N GLN A1114 " --> pdb=" O HIS A1111 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1111 through 1114' Processing helix chain 'A' and resid 1119 through 1134 removed outlier: 3.781A pdb=" N ASN A1127 " --> pdb=" O HIS A1123 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N LYS A1131 " --> pdb=" O ASN A1127 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N GLU A1132 " --> pdb=" O LEU A1128 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N LYS A1133 " --> pdb=" O LYS A1129 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N TRP A1134 " --> pdb=" O PHE A1130 " (cutoff:3.500A) Processing helix chain 'A' and resid 1138 through 1143 Processing helix chain 'A' and resid 1159 through 1167 Processing helix chain 'A' and resid 1170 through 1175 Processing helix chain 'A' and resid 1182 through 1218 removed outlier: 3.549A pdb=" N LEU A1192 " --> pdb=" O THR A1188 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N LEU A1194 " --> pdb=" O ALA A1190 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N GLN A1195 " --> pdb=" O SER A1191 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N ARG A1217 " --> pdb=" O THR A1213 " (cutoff:3.500A) Processing helix chain 'A' and resid 1223 through 1239 removed outlier: 4.067A pdb=" N VAL A1227 " --> pdb=" O ASN A1223 " (cutoff:3.500A) Processing helix chain 'A' and resid 1248 through 1268 removed outlier: 3.783A pdb=" N PHE A1265 " --> pdb=" O ILE A1261 " (cutoff:3.500A) removed outlier: 4.364A pdb=" N LYS A1266 " --> pdb=" O LEU A1262 " (cutoff:3.500A) removed outlier: 4.222A pdb=" N LEU A1267 " --> pdb=" O TYR A1263 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N SER A1268 " --> pdb=" O SER A1264 " (cutoff:3.500A) Processing helix chain 'A' and resid 1273 through 1289 removed outlier: 3.792A pdb=" N ILE A1277 " --> pdb=" O LYS A1273 " (cutoff:3.500A) Processing helix chain 'A' and resid 1298 through 1304 removed outlier: 4.068A pdb=" N SER A1302 " --> pdb=" O ASN A1298 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N LEU A1303 " --> pdb=" O ILE A1299 " (cutoff:3.500A) Processing helix chain 'A' and resid 1305 through 1307 No H-bonds generated for 'chain 'A' and resid 1305 through 1307' Processing helix chain 'A' and resid 1308 through 1319 Processing helix chain 'A' and resid 1328 through 1360 removed outlier: 3.924A pdb=" N LYS A1346 " --> pdb=" O LEU A1342 " (cutoff:3.500A) Processing helix chain 'A' and resid 1379 through 1384 removed outlier: 3.702A pdb=" N ASP A1384 " --> pdb=" O ASP A1380 " (cutoff:3.500A) Processing helix chain 'A' and resid 1387 through 1397 Processing helix chain 'A' and resid 1401 through 1416 Processing helix chain 'A' and resid 1418 through 1431 Processing helix chain 'A' and resid 1439 through 1452 removed outlier: 4.027A pdb=" N THR A1443 " --> pdb=" O LEU A1439 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N LEU A1444 " --> pdb=" O GLY A1440 " (cutoff:3.500A) removed outlier: 4.257A pdb=" N THR A1445 " --> pdb=" O GLN A1441 " (cutoff:3.500A) Processing helix chain 'A' and resid 1453 through 1462 removed outlier: 3.543A pdb=" N ASN A1462 " --> pdb=" O ALA A1458 " (cutoff:3.500A) Processing helix chain 'A' and resid 1464 through 1471 removed outlier: 3.698A pdb=" N VAL A1468 " --> pdb=" O GLY A1464 " (cutoff:3.500A) Processing helix chain 'A' and resid 1472 through 1480 Processing helix chain 'A' and resid 1488 through 1510 Processing helix chain 'A' and resid 1514 through 1525 Processing helix chain 'A' and resid 1525 through 1539 removed outlier: 3.727A pdb=" N ILE A1529 " --> pdb=" O PHE A1525 " (cutoff:3.500A) Processing helix chain 'A' and resid 1544 through 1558 Processing helix chain 'A' and resid 1559 through 1564 removed outlier: 3.686A pdb=" N LEU A1564 " --> pdb=" O MET A1560 " (cutoff:3.500A) Processing helix chain 'A' and resid 1591 through 1606 removed outlier: 3.760A pdb=" N LYS A1595 " --> pdb=" O SER A1591 " (cutoff:3.500A) Processing helix chain 'A' and resid 1608 through 1616 Processing helix chain 'A' and resid 1620 through 1629 Processing helix chain 'A' and resid 1632 through 1655 Processing sheet with id=AA1, first strand: chain 'A' and resid 275 through 276 Processing sheet with id=AA2, first strand: chain 'A' and resid 460 through 466 removed outlier: 5.492A pdb=" N TYR A 557 " --> pdb=" O SER A 462 " (cutoff:3.500A) removed outlier: 5.269A pdb=" N ALA A 464 " --> pdb=" O PHE A 555 " (cutoff:3.500A) removed outlier: 7.157A pdb=" N PHE A 555 " --> pdb=" O ALA A 464 " (cutoff:3.500A) removed outlier: 5.421A pdb=" N THR A 466 " --> pdb=" O ILE A 553 " (cutoff:3.500A) removed outlier: 7.235A pdb=" N ILE A 553 " --> pdb=" O THR A 466 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N LEU A 556 " --> pdb=" O LYS A 525 " (cutoff:3.500A) removed outlier: 5.928A pdb=" N LYS A 525 " --> pdb=" O LEU A 556 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 503 through 505 782 hydrogen bonds defined for protein. 2295 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: 5.04 Time building geometry restraints manager: 3.91 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 4003 1.34 - 1.46: 1874 1.46 - 1.57: 7054 1.57 - 1.69: 0 1.69 - 1.81: 46 Bond restraints: 12977 Sorted by residual: bond pdb=" N LEU A 583 " pdb=" CA LEU A 583 " ideal model delta sigma weight residual 1.456 1.489 -0.034 1.25e-02 6.40e+03 7.20e+00 bond pdb=" N ASP A 584 " pdb=" CA ASP A 584 " ideal model delta sigma weight residual 1.456 1.487 -0.031 1.23e-02 6.61e+03 6.35e+00 bond pdb=" N ASP A 585 " pdb=" CA ASP A 585 " ideal model delta sigma weight residual 1.459 1.489 -0.030 1.19e-02 7.06e+03 6.27e+00 bond pdb=" N LYS A 716 " pdb=" CA LYS A 716 " ideal model delta sigma weight residual 1.459 1.489 -0.030 1.21e-02 6.83e+03 6.10e+00 bond pdb=" N LEU A 773 " pdb=" CA LEU A 773 " ideal model delta sigma weight residual 1.457 1.488 -0.031 1.29e-02 6.01e+03 5.90e+00 ... (remaining 12972 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.50: 17254 1.50 - 3.00: 251 3.00 - 4.50: 45 4.50 - 6.01: 24 6.01 - 7.51: 5 Bond angle restraints: 17579 Sorted by residual: angle pdb=" CA VAL A1398 " pdb=" C VAL A1398 " pdb=" O VAL A1398 " ideal model delta sigma weight residual 120.78 116.80 3.98 1.25e+00 6.40e-01 1.01e+01 angle pdb=" OG1 THR A1028 " pdb=" CB THR A1028 " pdb=" CG2 THR A1028 " ideal model delta sigma weight residual 109.30 103.23 6.07 2.00e+00 2.50e-01 9.22e+00 angle pdb=" CA TRP A1495 " pdb=" CB TRP A1495 " pdb=" CG TRP A1495 " ideal model delta sigma weight residual 113.60 119.25 -5.65 1.90e+00 2.77e-01 8.84e+00 angle pdb=" C THR A1417 " pdb=" N LEU A1418 " pdb=" CA LEU A1418 " ideal model delta sigma weight residual 121.54 127.16 -5.62 1.91e+00 2.74e-01 8.67e+00 angle pdb=" C GLN A1558 " pdb=" N LYS A1559 " pdb=" CA LYS A1559 " ideal model delta sigma weight residual 121.54 127.07 -5.53 1.91e+00 2.74e-01 8.37e+00 ... (remaining 17574 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.00: 7100 18.00 - 36.00: 671 36.00 - 54.00: 88 54.00 - 72.00: 16 72.00 - 90.00: 9 Dihedral angle restraints: 7884 sinusoidal: 3176 harmonic: 4708 Sorted by residual: dihedral pdb=" CB GLU A1185 " pdb=" CG GLU A1185 " pdb=" CD GLU A1185 " pdb=" OE1 GLU A1185 " ideal model delta sinusoidal sigma weight residual 0.00 -90.00 90.00 1 3.00e+01 1.11e-03 1.07e+01 dihedral pdb=" CB GLU A 510 " pdb=" CG GLU A 510 " pdb=" CD GLU A 510 " pdb=" OE1 GLU A 510 " ideal model delta sinusoidal sigma weight residual 0.00 89.13 -89.13 1 3.00e+01 1.11e-03 1.05e+01 dihedral pdb=" CA ASP A 153 " pdb=" CB ASP A 153 " pdb=" CG ASP A 153 " pdb=" OD1 ASP A 153 " ideal model delta sinusoidal sigma weight residual -30.00 -85.27 55.27 1 2.00e+01 2.50e-03 1.03e+01 ... (remaining 7881 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.034: 1462 0.034 - 0.068: 496 0.068 - 0.101: 113 0.101 - 0.135: 32 0.135 - 0.169: 5 Chirality restraints: 2108 Sorted by residual: chirality pdb=" CB THR A1028 " pdb=" CA THR A1028 " pdb=" OG1 THR A1028 " pdb=" CG2 THR A1028 " both_signs ideal model delta sigma weight residual False 2.55 2.72 -0.17 2.00e-01 2.50e+01 7.15e-01 chirality pdb=" CA ILE A 785 " pdb=" N ILE A 785 " pdb=" C ILE A 785 " pdb=" CB ILE A 785 " both_signs ideal model delta sigma weight residual False 2.43 2.59 -0.15 2.00e-01 2.50e+01 5.90e-01 chirality pdb=" CA LEU A 583 " pdb=" N LEU A 583 " pdb=" C LEU A 583 " pdb=" CB LEU A 583 " both_signs ideal model delta sigma weight residual False 2.51 2.65 -0.14 2.00e-01 2.50e+01 5.15e-01 ... (remaining 2105 not shown) Planarity restraints: 2189 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP A1495 " 0.028 2.00e-02 2.50e+03 2.64e-02 1.74e+01 pdb=" CG TRP A1495 " -0.072 2.00e-02 2.50e+03 pdb=" CD1 TRP A1495 " 0.030 2.00e-02 2.50e+03 pdb=" CD2 TRP A1495 " -0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP A1495 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 TRP A1495 " -0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP A1495 " 0.011 2.00e-02 2.50e+03 pdb=" CZ2 TRP A1495 " 0.003 2.00e-02 2.50e+03 pdb=" CZ3 TRP A1495 " 0.000 2.00e-02 2.50e+03 pdb=" CH2 TRP A1495 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ARG A1309 " -0.066 5.00e-02 4.00e+02 9.84e-02 1.55e+01 pdb=" N PRO A1310 " 0.170 5.00e-02 4.00e+02 pdb=" CA PRO A1310 " -0.050 5.00e-02 4.00e+02 pdb=" CD PRO A1310 " -0.054 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO A 507 " 0.043 5.00e-02 4.00e+02 6.51e-02 6.78e+00 pdb=" N PRO A 508 " -0.113 5.00e-02 4.00e+02 pdb=" CA PRO A 508 " 0.034 5.00e-02 4.00e+02 pdb=" CD PRO A 508 " 0.036 5.00e-02 4.00e+02 ... (remaining 2186 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.76: 2133 2.76 - 3.30: 12699 3.30 - 3.83: 20740 3.83 - 4.37: 23748 4.37 - 4.90: 41866 Nonbonded interactions: 101186 Sorted by model distance: nonbonded pdb=" O HIS A 780 " pdb=" OG1 THR A 784 " model vdw 2.227 3.040 nonbonded pdb=" NH1 ARG A 333 " pdb=" O PHE A 341 " model vdw 2.241 3.120 nonbonded pdb=" O ALA A1428 " pdb=" NH2 ARG A1432 " model vdw 2.253 3.120 nonbonded pdb=" O LEU A1589 " pdb=" NZ LYS A1595 " model vdw 2.269 3.120 nonbonded pdb=" OG SER A 826 " pdb=" OH TYR A 844 " model vdw 2.290 3.040 ... (remaining 101181 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: 8.170 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: 0.580 Check model and map are aligned: 0.080 Set scattering table: 0.120 Process input model: 34.880 Find NCS groups from input model: 0.160 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:13.200 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 57.260 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7510 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 : 0.002 0.042 12977 Z= 0.126 Angle : 0.504 7.507 17579 Z= 0.270 Chirality : 0.037 0.169 2108 Planarity : 0.004 0.098 2189 Dihedral : 13.974 89.997 4798 Min Nonbonded Distance : 2.227 Molprobity Statistics. All-atom Clashscore : 5.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.21 % Favored : 95.79 % Rotamer: Outliers : 0.00 % Allowed : 0.27 % Favored : 99.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.49 (0.22), residues: 1569 helix: 1.68 (0.16), residues: 1079 sheet: 0.54 (0.91), residues: 36 loop : -0.62 (0.30), residues: 454 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.072 0.002 TRP A1495 HIS 0.002 0.001 HIS A 729 PHE 0.028 0.001 PHE A1285 TYR 0.019 0.001 TYR A 323 ARG 0.006 0.000 ARG A1313 Details of bonding type rmsd hydrogen bonds : bond 0.14670 ( 782) hydrogen bonds : angle 4.92984 ( 2295) covalent geometry : bond 0.00231 (12977) covalent geometry : angle 0.50404 (17579) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3138 Ramachandran restraints generated. 1569 Oldfield, 0 Emsley, 1569 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3138 Ramachandran restraints generated. 1569 Oldfield, 0 Emsley, 1569 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 1489 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 105 time to evaluate : 1.360 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 105 average time/residue: 1.1227 time to fit residues: 132.1583 Evaluate side-chains 71 residues out of total 1489 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 71 time to evaluate : 1.460 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 133 optimal weight: 2.9990 chunk 119 optimal weight: 3.9990 chunk 66 optimal weight: 1.9990 chunk 40 optimal weight: 2.9990 chunk 80 optimal weight: 3.9990 chunk 63 optimal weight: 4.9990 chunk 123 optimal weight: 0.9990 chunk 47 optimal weight: 20.0000 chunk 75 optimal weight: 0.9980 chunk 92 optimal weight: 0.0970 chunk 143 optimal weight: 6.9990 overall best weight: 1.4184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 246 ASN A 363 ASN A 388 ASN A 729 HIS A 788 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4585 r_free = 0.4585 target = 0.231789 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.4170 r_free = 0.4170 target = 0.182465 restraints weight = 13653.819| |-----------------------------------------------------------------------------| r_work (start): 0.4127 rms_B_bonded: 1.37 r_work: 0.3795 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.3648 rms_B_bonded: 4.26 restraints_weight: 0.2500 r_work (final): 0.3648 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7874 moved from start: 0.1059 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 12977 Z= 0.183 Angle : 0.581 7.668 17579 Z= 0.301 Chirality : 0.040 0.180 2108 Planarity : 0.004 0.075 2189 Dihedral : 4.100 27.789 1656 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 5.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.91 % Favored : 95.09 % Rotamer: Outliers : 1.01 % Allowed : 6.25 % Favored : 92.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.30 (0.22), residues: 1569 helix: 1.57 (0.16), residues: 1076 sheet: 0.51 (0.90), residues: 37 loop : -0.77 (0.30), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.002 TRP A1495 HIS 0.006 0.001 HIS A 318 PHE 0.023 0.002 PHE A1605 TYR 0.026 0.002 TYR A1260 ARG 0.006 0.001 ARG A 333 Details of bonding type rmsd hydrogen bonds : bond 0.05914 ( 782) hydrogen bonds : angle 4.11589 ( 2295) covalent geometry : bond 0.00439 (12977) covalent geometry : angle 0.58122 (17579) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3138 Ramachandran restraints generated. 1569 Oldfield, 0 Emsley, 1569 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3138 Ramachandran restraints generated. 1569 Oldfield, 0 Emsley, 1569 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 1489 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 77 time to evaluate : 1.411 Fit side-chains revert: symmetry clash REVERT: A 589 GLU cc_start: 0.7696 (OUTLIER) cc_final: 0.7084 (mm-30) REVERT: A 1170 ASP cc_start: 0.7428 (OUTLIER) cc_final: 0.7171 (t70) outliers start: 15 outliers final: 6 residues processed: 87 average time/residue: 1.1561 time to fit residues: 112.0568 Evaluate side-chains 79 residues out of total 1489 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 71 time to evaluate : 1.367 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 LYS Chi-restraints excluded: chain A residue 215 GLN Chi-restraints excluded: chain A residue 323 TYR Chi-restraints excluded: chain A residue 589 GLU Chi-restraints excluded: chain A residue 794 ILE Chi-restraints excluded: chain A residue 1006 ASP Chi-restraints excluded: chain A residue 1152 GLU Chi-restraints excluded: chain A residue 1170 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 148 optimal weight: 30.0000 chunk 4 optimal weight: 0.8980 chunk 116 optimal weight: 2.9990 chunk 155 optimal weight: 20.0000 chunk 5 optimal weight: 7.9990 chunk 16 optimal weight: 0.6980 chunk 69 optimal weight: 2.9990 chunk 6 optimal weight: 0.3980 chunk 118 optimal weight: 0.0980 chunk 42 optimal weight: 0.9990 chunk 61 optimal weight: 0.8980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 360 GLN A 729 HIS A1151 ASN A1492 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4609 r_free = 0.4609 target = 0.234382 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.4207 r_free = 0.4207 target = 0.186192 restraints weight = 13798.300| |-----------------------------------------------------------------------------| r_work (start): 0.4169 rms_B_bonded: 1.37 r_work: 0.3855 rms_B_bonded: 2.26 restraints_weight: 0.5000 r_work: 0.3715 rms_B_bonded: 3.80 restraints_weight: 0.2500 r_work (final): 0.3715 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7778 moved from start: 0.1146 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.049 12977 Z= 0.112 Angle : 0.486 7.716 17579 Z= 0.253 Chirality : 0.037 0.144 2108 Planarity : 0.004 0.062 2189 Dihedral : 3.939 27.919 1656 Min Nonbonded Distance : 2.586 Molprobity Statistics. All-atom Clashscore : 4.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.33 % Favored : 95.67 % Rotamer: Outliers : 0.74 % Allowed : 9.00 % Favored : 90.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.61 (0.22), residues: 1569 helix: 1.87 (0.16), residues: 1078 sheet: 0.45 (0.93), residues: 37 loop : -0.84 (0.30), residues: 454 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.001 TRP A1495 HIS 0.004 0.001 HIS A 729 PHE 0.021 0.001 PHE A1605 TYR 0.018 0.001 TYR A1260 ARG 0.005 0.000 ARG A 333 Details of bonding type rmsd hydrogen bonds : bond 0.04440 ( 782) hydrogen bonds : angle 3.82468 ( 2295) covalent geometry : bond 0.00247 (12977) covalent geometry : angle 0.48569 (17579) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3138 Ramachandran restraints generated. 1569 Oldfield, 0 Emsley, 1569 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3138 Ramachandran restraints generated. 1569 Oldfield, 0 Emsley, 1569 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 1489 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 72 time to evaluate : 1.444 Fit side-chains revert: symmetry clash REVERT: A 589 GLU cc_start: 0.7613 (OUTLIER) cc_final: 0.6980 (mm-30) REVERT: A 1170 ASP cc_start: 0.7442 (OUTLIER) cc_final: 0.7221 (t70) REVERT: A 1213 THR cc_start: 0.8134 (t) cc_final: 0.7924 (p) outliers start: 11 outliers final: 6 residues processed: 79 average time/residue: 1.1200 time to fit residues: 99.2989 Evaluate side-chains 76 residues out of total 1489 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 68 time to evaluate : 1.494 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 LYS Chi-restraints excluded: chain A residue 215 GLN Chi-restraints excluded: chain A residue 323 TYR Chi-restraints excluded: chain A residue 589 GLU Chi-restraints excluded: chain A residue 856 THR Chi-restraints excluded: chain A residue 1006 ASP Chi-restraints excluded: chain A residue 1152 GLU Chi-restraints excluded: chain A residue 1170 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 139 optimal weight: 5.9990 chunk 3 optimal weight: 0.9990 chunk 148 optimal weight: 0.7980 chunk 85 optimal weight: 1.9990 chunk 23 optimal weight: 1.9990 chunk 10 optimal weight: 0.9980 chunk 109 optimal weight: 0.5980 chunk 22 optimal weight: 0.9990 chunk 12 optimal weight: 0.6980 chunk 17 optimal weight: 0.9990 chunk 132 optimal weight: 7.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 729 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4600 r_free = 0.4600 target = 0.233394 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.4188 r_free = 0.4188 target = 0.184164 restraints weight = 13578.010| |-----------------------------------------------------------------------------| r_work (start): 0.4144 rms_B_bonded: 1.35 r_work: 0.3830 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work: 0.3690 rms_B_bonded: 3.77 restraints_weight: 0.2500 r_work (final): 0.3690 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7809 moved from start: 0.1277 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 12977 Z= 0.126 Angle : 0.499 7.597 17579 Z= 0.259 Chirality : 0.037 0.141 2108 Planarity : 0.004 0.059 2189 Dihedral : 3.932 27.925 1656 Min Nonbonded Distance : 2.612 Molprobity Statistics. All-atom Clashscore : 4.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.84 % Favored : 95.16 % Rotamer: Outliers : 1.21 % Allowed : 10.34 % Favored : 88.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.60 (0.22), residues: 1569 helix: 1.87 (0.16), residues: 1081 sheet: 0.37 (0.93), residues: 37 loop : -0.86 (0.30), residues: 451 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP A1495 HIS 0.004 0.001 HIS A 318 PHE 0.020 0.001 PHE A1605 TYR 0.021 0.001 TYR A1260 ARG 0.005 0.000 ARG A 333 Details of bonding type rmsd hydrogen bonds : bond 0.04708 ( 782) hydrogen bonds : angle 3.79693 ( 2295) covalent geometry : bond 0.00291 (12977) covalent geometry : angle 0.49867 (17579) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3138 Ramachandran restraints generated. 1569 Oldfield, 0 Emsley, 1569 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3138 Ramachandran restraints generated. 1569 Oldfield, 0 Emsley, 1569 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 1489 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 74 time to evaluate : 1.378 Fit side-chains REVERT: A 589 GLU cc_start: 0.7645 (OUTLIER) cc_final: 0.7022 (mm-30) REVERT: A 1053 LEU cc_start: 0.6576 (OUTLIER) cc_final: 0.5960 (mt) REVERT: A 1170 ASP cc_start: 0.7465 (OUTLIER) cc_final: 0.7228 (t70) REVERT: A 1213 THR cc_start: 0.8204 (t) cc_final: 0.7978 (p) REVERT: A 1313 ARG cc_start: 0.6999 (OUTLIER) cc_final: 0.6391 (mtp85) outliers start: 18 outliers final: 7 residues processed: 86 average time/residue: 1.0171 time to fit residues: 98.7099 Evaluate side-chains 78 residues out of total 1489 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 67 time to evaluate : 1.374 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 LYS Chi-restraints excluded: chain A residue 215 GLN Chi-restraints excluded: chain A residue 323 TYR Chi-restraints excluded: chain A residue 589 GLU Chi-restraints excluded: chain A residue 602 VAL Chi-restraints excluded: chain A residue 794 ILE Chi-restraints excluded: chain A residue 856 THR Chi-restraints excluded: chain A residue 1006 ASP Chi-restraints excluded: chain A residue 1053 LEU Chi-restraints excluded: chain A residue 1170 ASP Chi-restraints excluded: chain A residue 1313 ARG Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 28 optimal weight: 0.0570 chunk 136 optimal weight: 0.9990 chunk 4 optimal weight: 0.9990 chunk 20 optimal weight: 0.6980 chunk 22 optimal weight: 2.9990 chunk 83 optimal weight: 0.0050 chunk 15 optimal weight: 0.9990 chunk 105 optimal weight: 0.6980 chunk 114 optimal weight: 1.9990 chunk 128 optimal weight: 0.8980 chunk 81 optimal weight: 5.9990 overall best weight: 0.4712 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1102 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4616 r_free = 0.4616 target = 0.235233 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.4215 r_free = 0.4215 target = 0.186892 restraints weight = 13714.837| |-----------------------------------------------------------------------------| r_work (start): 0.4178 rms_B_bonded: 1.42 r_work: 0.3866 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.3736 rms_B_bonded: 3.93 restraints_weight: 0.2500 r_work (final): 0.3736 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7757 moved from start: 0.1333 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 12977 Z= 0.101 Angle : 0.463 7.531 17579 Z= 0.241 Chirality : 0.036 0.173 2108 Planarity : 0.003 0.039 2189 Dihedral : 3.816 27.974 1656 Min Nonbonded Distance : 2.624 Molprobity Statistics. All-atom Clashscore : 4.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.40 % Favored : 95.60 % Rotamer: Outliers : 0.94 % Allowed : 11.48 % Favored : 87.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.86 (0.22), residues: 1569 helix: 2.08 (0.16), residues: 1079 sheet: 0.42 (0.94), residues: 37 loop : -0.80 (0.30), residues: 453 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP A1495 HIS 0.003 0.001 HIS A1429 PHE 0.022 0.001 PHE A1605 TYR 0.016 0.001 TYR A1260 ARG 0.004 0.000 ARG A 333 Details of bonding type rmsd hydrogen bonds : bond 0.03918 ( 782) hydrogen bonds : angle 3.65625 ( 2295) covalent geometry : bond 0.00216 (12977) covalent geometry : angle 0.46308 (17579) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3138 Ramachandran restraints generated. 1569 Oldfield, 0 Emsley, 1569 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3138 Ramachandran restraints generated. 1569 Oldfield, 0 Emsley, 1569 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 1489 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 75 time to evaluate : 1.410 Fit side-chains revert: symmetry clash REVERT: A 1053 LEU cc_start: 0.6632 (OUTLIER) cc_final: 0.6023 (mt) REVERT: A 1213 THR cc_start: 0.8044 (t) cc_final: 0.7815 (p) REVERT: A 1313 ARG cc_start: 0.7044 (OUTLIER) cc_final: 0.6435 (mtp85) REVERT: A 1374 GLN cc_start: 0.2568 (OUTLIER) cc_final: 0.1548 (tt0) outliers start: 14 outliers final: 8 residues processed: 85 average time/residue: 1.1770 time to fit residues: 112.5038 Evaluate side-chains 78 residues out of total 1489 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 67 time to evaluate : 1.835 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 VAL Chi-restraints excluded: chain A residue 35 LYS Chi-restraints excluded: chain A residue 215 GLN Chi-restraints excluded: chain A residue 323 TYR Chi-restraints excluded: chain A residue 693 MET Chi-restraints excluded: chain A residue 856 THR Chi-restraints excluded: chain A residue 1006 ASP Chi-restraints excluded: chain A residue 1053 LEU Chi-restraints excluded: chain A residue 1152 GLU Chi-restraints excluded: chain A residue 1313 ARG Chi-restraints excluded: chain A residue 1374 GLN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 138 optimal weight: 9.9990 chunk 89 optimal weight: 1.9990 chunk 92 optimal weight: 0.0030 chunk 133 optimal weight: 3.9990 chunk 149 optimal weight: 7.9990 chunk 142 optimal weight: 30.0000 chunk 30 optimal weight: 2.9990 chunk 54 optimal weight: 0.8980 chunk 39 optimal weight: 4.9990 chunk 75 optimal weight: 3.9990 chunk 56 optimal weight: 1.9990 overall best weight: 1.5796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 729 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4580 r_free = 0.4580 target = 0.230948 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.4137 r_free = 0.4137 target = 0.178300 restraints weight = 13866.486| |-----------------------------------------------------------------------------| r_work (start): 0.4078 rms_B_bonded: 1.38 r_work: 0.3760 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.3624 rms_B_bonded: 3.84 restraints_weight: 0.2500 r_work (final): 0.3624 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7871 moved from start: 0.1566 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 12977 Z= 0.189 Angle : 0.574 7.280 17579 Z= 0.298 Chirality : 0.041 0.176 2108 Planarity : 0.004 0.044 2189 Dihedral : 4.130 27.621 1656 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 4.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.10 % Favored : 94.90 % Rotamer: Outliers : 1.41 % Allowed : 12.29 % Favored : 86.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.34 (0.21), residues: 1569 helix: 1.65 (0.16), residues: 1077 sheet: 0.32 (0.94), residues: 37 loop : -0.89 (0.30), residues: 455 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP A1495 HIS 0.006 0.001 HIS A 318 PHE 0.021 0.002 PHE A 102 TYR 0.017 0.002 TYR A1260 ARG 0.004 0.000 ARG A 333 Details of bonding type rmsd hydrogen bonds : bond 0.05966 ( 782) hydrogen bonds : angle 3.95321 ( 2295) covalent geometry : bond 0.00466 (12977) covalent geometry : angle 0.57360 (17579) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3138 Ramachandran restraints generated. 1569 Oldfield, 0 Emsley, 1569 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3138 Ramachandran restraints generated. 1569 Oldfield, 0 Emsley, 1569 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 1489 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 71 time to evaluate : 1.385 Fit side-chains REVERT: A 589 GLU cc_start: 0.7740 (OUTLIER) cc_final: 0.7145 (mm-30) REVERT: A 1170 ASP cc_start: 0.7543 (OUTLIER) cc_final: 0.7243 (t70) REVERT: A 1213 THR cc_start: 0.8276 (t) cc_final: 0.8054 (p) REVERT: A 1313 ARG cc_start: 0.7119 (OUTLIER) cc_final: 0.6541 (mtp85) outliers start: 21 outliers final: 11 residues processed: 88 average time/residue: 1.1004 time to fit residues: 108.0961 Evaluate side-chains 84 residues out of total 1489 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 70 time to evaluate : 1.376 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 VAL Chi-restraints excluded: chain A residue 35 LYS Chi-restraints excluded: chain A residue 215 GLN Chi-restraints excluded: chain A residue 323 TYR Chi-restraints excluded: chain A residue 589 GLU Chi-restraints excluded: chain A residue 602 VAL Chi-restraints excluded: chain A residue 728 ILE Chi-restraints excluded: chain A residue 794 ILE Chi-restraints excluded: chain A residue 856 THR Chi-restraints excluded: chain A residue 1006 ASP Chi-restraints excluded: chain A residue 1053 LEU Chi-restraints excluded: chain A residue 1170 ASP Chi-restraints excluded: chain A residue 1181 THR Chi-restraints excluded: chain A residue 1313 ARG Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 32 optimal weight: 1.9990 chunk 153 optimal weight: 4.9990 chunk 149 optimal weight: 3.9990 chunk 142 optimal weight: 40.0000 chunk 83 optimal weight: 0.1980 chunk 69 optimal weight: 2.9990 chunk 42 optimal weight: 0.9980 chunk 92 optimal weight: 0.1980 chunk 77 optimal weight: 0.9990 chunk 6 optimal weight: 5.9990 chunk 60 optimal weight: 0.6980 overall best weight: 0.6182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 729 HIS A1151 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4604 r_free = 0.4604 target = 0.233917 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.4191 r_free = 0.4191 target = 0.184196 restraints weight = 13659.182| |-----------------------------------------------------------------------------| r_work (start): 0.4148 rms_B_bonded: 1.45 r_work: 0.3832 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.3695 rms_B_bonded: 3.94 restraints_weight: 0.2500 r_work (final): 0.3695 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7807 moved from start: 0.1510 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 12977 Z= 0.112 Angle : 0.485 7.344 17579 Z= 0.254 Chirality : 0.037 0.155 2108 Planarity : 0.003 0.041 2189 Dihedral : 3.934 27.666 1656 Min Nonbonded Distance : 2.557 Molprobity Statistics. All-atom Clashscore : 4.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.46 % Favored : 95.54 % Rotamer: Outliers : 1.34 % Allowed : 12.83 % Favored : 85.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.64 (0.22), residues: 1569 helix: 1.92 (0.16), residues: 1078 sheet: 0.27 (0.94), residues: 37 loop : -0.87 (0.30), residues: 454 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP A1495 HIS 0.004 0.001 HIS A 729 PHE 0.019 0.001 PHE A1605 TYR 0.012 0.001 TYR A1260 ARG 0.003 0.000 ARG A 333 Details of bonding type rmsd hydrogen bonds : bond 0.04338 ( 782) hydrogen bonds : angle 3.74351 ( 2295) covalent geometry : bond 0.00250 (12977) covalent geometry : angle 0.48546 (17579) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3138 Ramachandran restraints generated. 1569 Oldfield, 0 Emsley, 1569 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3138 Ramachandran restraints generated. 1569 Oldfield, 0 Emsley, 1569 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 1489 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 69 time to evaluate : 1.393 Fit side-chains REVERT: A 215 GLN cc_start: 0.7339 (OUTLIER) cc_final: 0.7134 (mt0) REVERT: A 589 GLU cc_start: 0.7654 (OUTLIER) cc_final: 0.7078 (mm-30) REVERT: A 1053 LEU cc_start: 0.6512 (OUTLIER) cc_final: 0.5848 (mt) REVERT: A 1170 ASP cc_start: 0.7452 (OUTLIER) cc_final: 0.7156 (t70) REVERT: A 1213 THR cc_start: 0.8069 (t) cc_final: 0.7858 (p) REVERT: A 1313 ARG cc_start: 0.7037 (OUTLIER) cc_final: 0.6504 (mtp85) REVERT: A 1374 GLN cc_start: 0.2627 (OUTLIER) cc_final: 0.1695 (tt0) outliers start: 20 outliers final: 7 residues processed: 88 average time/residue: 1.0918 time to fit residues: 108.0880 Evaluate side-chains 78 residues out of total 1489 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 65 time to evaluate : 1.362 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 VAL Chi-restraints excluded: chain A residue 35 LYS Chi-restraints excluded: chain A residue 215 GLN Chi-restraints excluded: chain A residue 323 TYR Chi-restraints excluded: chain A residue 589 GLU Chi-restraints excluded: chain A residue 602 VAL Chi-restraints excluded: chain A residue 856 THR Chi-restraints excluded: chain A residue 1006 ASP Chi-restraints excluded: chain A residue 1053 LEU Chi-restraints excluded: chain A residue 1170 ASP Chi-restraints excluded: chain A residue 1181 THR Chi-restraints excluded: chain A residue 1313 ARG Chi-restraints excluded: chain A residue 1374 GLN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 155 optimal weight: 6.9990 chunk 91 optimal weight: 3.9990 chunk 110 optimal weight: 0.9980 chunk 121 optimal weight: 8.9990 chunk 62 optimal weight: 0.4980 chunk 33 optimal weight: 0.9980 chunk 46 optimal weight: 1.9990 chunk 150 optimal weight: 30.0000 chunk 44 optimal weight: 0.2980 chunk 137 optimal weight: 5.9990 chunk 136 optimal weight: 2.9990 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 729 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4593 r_free = 0.4593 target = 0.232709 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.4178 r_free = 0.4178 target = 0.183057 restraints weight = 13744.127| |-----------------------------------------------------------------------------| r_work (start): 0.4131 rms_B_bonded: 1.40 r_work: 0.3803 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.3660 rms_B_bonded: 3.94 restraints_weight: 0.2500 r_work (final): 0.3660 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7842 moved from start: 0.1568 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 12977 Z= 0.137 Angle : 0.528 8.944 17579 Z= 0.273 Chirality : 0.038 0.151 2108 Planarity : 0.003 0.041 2189 Dihedral : 3.969 27.654 1656 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 4.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.65 % Favored : 95.35 % Rotamer: Outliers : 1.28 % Allowed : 13.30 % Favored : 85.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.55 (0.22), residues: 1569 helix: 1.83 (0.16), residues: 1079 sheet: 0.26 (0.94), residues: 37 loop : -0.86 (0.30), residues: 453 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP A1495 HIS 0.004 0.001 HIS A 318 PHE 0.019 0.001 PHE A1605 TYR 0.017 0.001 TYR A1260 ARG 0.003 0.000 ARG A 333 Details of bonding type rmsd hydrogen bonds : bond 0.04897 ( 782) hydrogen bonds : angle 3.81468 ( 2295) covalent geometry : bond 0.00325 (12977) covalent geometry : angle 0.52817 (17579) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3138 Ramachandran restraints generated. 1569 Oldfield, 0 Emsley, 1569 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3138 Ramachandran restraints generated. 1569 Oldfield, 0 Emsley, 1569 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 1489 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 69 time to evaluate : 1.366 Fit side-chains REVERT: A 1053 LEU cc_start: 0.6525 (OUTLIER) cc_final: 0.5842 (mt) REVERT: A 1170 ASP cc_start: 0.7489 (OUTLIER) cc_final: 0.7179 (t70) REVERT: A 1213 THR cc_start: 0.8168 (t) cc_final: 0.7954 (p) REVERT: A 1313 ARG cc_start: 0.7062 (OUTLIER) cc_final: 0.6545 (mtp85) REVERT: A 1374 GLN cc_start: 0.2661 (OUTLIER) cc_final: 0.1799 (tt0) outliers start: 19 outliers final: 11 residues processed: 83 average time/residue: 1.0388 time to fit residues: 97.3859 Evaluate side-chains 82 residues out of total 1489 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 67 time to evaluate : 1.492 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 VAL Chi-restraints excluded: chain A residue 35 LYS Chi-restraints excluded: chain A residue 294 THR Chi-restraints excluded: chain A residue 323 TYR Chi-restraints excluded: chain A residue 602 VAL Chi-restraints excluded: chain A residue 608 ILE Chi-restraints excluded: chain A residue 693 MET Chi-restraints excluded: chain A residue 794 ILE Chi-restraints excluded: chain A residue 856 THR Chi-restraints excluded: chain A residue 1006 ASP Chi-restraints excluded: chain A residue 1053 LEU Chi-restraints excluded: chain A residue 1170 ASP Chi-restraints excluded: chain A residue 1181 THR Chi-restraints excluded: chain A residue 1313 ARG Chi-restraints excluded: chain A residue 1374 GLN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 48 optimal weight: 9.9990 chunk 34 optimal weight: 0.8980 chunk 98 optimal weight: 0.9990 chunk 106 optimal weight: 0.9990 chunk 133 optimal weight: 0.9980 chunk 96 optimal weight: 1.9990 chunk 146 optimal weight: 5.9990 chunk 29 optimal weight: 0.5980 chunk 82 optimal weight: 1.9990 chunk 126 optimal weight: 0.6980 chunk 56 optimal weight: 0.9980 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 729 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4529 r_free = 0.4529 target = 0.228245 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4148 r_free = 0.4148 target = 0.185724 restraints weight = 12979.514| |-----------------------------------------------------------------------------| r_work (start): 0.4135 rms_B_bonded: 1.20 r_work: 0.3721 rms_B_bonded: 2.13 restraints_weight: 0.5000 r_work: 0.3469 rms_B_bonded: 4.00 restraints_weight: 0.2500 r_work (final): 0.3469 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7858 moved from start: 0.1595 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 12977 Z= 0.128 Angle : 0.518 8.962 17579 Z= 0.267 Chirality : 0.038 0.133 2108 Planarity : 0.003 0.041 2189 Dihedral : 3.954 27.648 1656 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 4.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.65 % Favored : 95.35 % Rotamer: Outliers : 1.21 % Allowed : 13.36 % Favored : 85.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.59 (0.22), residues: 1569 helix: 1.85 (0.16), residues: 1080 sheet: 0.27 (0.94), residues: 37 loop : -0.84 (0.30), residues: 452 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP A1495 HIS 0.004 0.001 HIS A 318 PHE 0.019 0.001 PHE A1605 TYR 0.016 0.001 TYR A1260 ARG 0.003 0.000 ARG A 333 Details of bonding type rmsd hydrogen bonds : bond 0.04694 ( 782) hydrogen bonds : angle 3.78468 ( 2295) covalent geometry : bond 0.00297 (12977) covalent geometry : angle 0.51781 (17579) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3138 Ramachandran restraints generated. 1569 Oldfield, 0 Emsley, 1569 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3138 Ramachandran restraints generated. 1569 Oldfield, 0 Emsley, 1569 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 1489 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 66 time to evaluate : 1.523 Fit side-chains REVERT: A 1053 LEU cc_start: 0.6585 (OUTLIER) cc_final: 0.5854 (mt) REVERT: A 1170 ASP cc_start: 0.7530 (OUTLIER) cc_final: 0.7259 (t70) REVERT: A 1213 THR cc_start: 0.8154 (t) cc_final: 0.7938 (p) REVERT: A 1313 ARG cc_start: 0.6867 (OUTLIER) cc_final: 0.6395 (mtp85) REVERT: A 1374 GLN cc_start: 0.2627 (OUTLIER) cc_final: 0.1826 (tt0) outliers start: 18 outliers final: 12 residues processed: 79 average time/residue: 1.0083 time to fit residues: 90.4837 Evaluate side-chains 81 residues out of total 1489 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 65 time to evaluate : 1.383 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 VAL Chi-restraints excluded: chain A residue 35 LYS Chi-restraints excluded: chain A residue 294 THR Chi-restraints excluded: chain A residue 323 TYR Chi-restraints excluded: chain A residue 602 VAL Chi-restraints excluded: chain A residue 608 ILE Chi-restraints excluded: chain A residue 693 MET Chi-restraints excluded: chain A residue 728 ILE Chi-restraints excluded: chain A residue 794 ILE Chi-restraints excluded: chain A residue 856 THR Chi-restraints excluded: chain A residue 1006 ASP Chi-restraints excluded: chain A residue 1053 LEU Chi-restraints excluded: chain A residue 1170 ASP Chi-restraints excluded: chain A residue 1181 THR Chi-restraints excluded: chain A residue 1313 ARG Chi-restraints excluded: chain A residue 1374 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 151 optimal weight: 0.0050 chunk 53 optimal weight: 0.5980 chunk 13 optimal weight: 0.5980 chunk 142 optimal weight: 0.0050 chunk 30 optimal weight: 0.9980 chunk 67 optimal weight: 0.9990 chunk 69 optimal weight: 2.9990 chunk 81 optimal weight: 2.9990 chunk 49 optimal weight: 3.9990 chunk 103 optimal weight: 0.3980 chunk 111 optimal weight: 0.4980 overall best weight: 0.3008 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 729 HIS A1093 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4557 r_free = 0.4557 target = 0.231511 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.4177 r_free = 0.4177 target = 0.188614 restraints weight = 12966.880| |-----------------------------------------------------------------------------| r_work (start): 0.4163 rms_B_bonded: 1.21 r_work: 0.3765 rms_B_bonded: 2.17 restraints_weight: 0.5000 r_work: 0.3530 rms_B_bonded: 4.01 restraints_weight: 0.2500 r_work (final): 0.3530 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7782 moved from start: 0.1597 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 12977 Z= 0.097 Angle : 0.476 9.000 17579 Z= 0.245 Chirality : 0.036 0.134 2108 Planarity : 0.003 0.038 2189 Dihedral : 3.755 27.897 1656 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 5.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.08 % Favored : 95.92 % Rotamer: Outliers : 0.87 % Allowed : 13.70 % Favored : 85.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.92 (0.22), residues: 1569 helix: 2.12 (0.16), residues: 1080 sheet: 0.36 (0.95), residues: 37 loop : -0.76 (0.30), residues: 452 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP A1495 HIS 0.003 0.001 HIS A1429 PHE 0.028 0.001 PHE A 102 TYR 0.011 0.001 TYR A 252 ARG 0.003 0.000 ARG A 333 Details of bonding type rmsd hydrogen bonds : bond 0.03510 ( 782) hydrogen bonds : angle 3.61260 ( 2295) covalent geometry : bond 0.00201 (12977) covalent geometry : angle 0.47630 (17579) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3138 Ramachandran restraints generated. 1569 Oldfield, 0 Emsley, 1569 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3138 Ramachandran restraints generated. 1569 Oldfield, 0 Emsley, 1569 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 1489 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 74 time to evaluate : 1.487 Fit side-chains REVERT: A 1053 LEU cc_start: 0.6573 (OUTLIER) cc_final: 0.5918 (mt) REVERT: A 1170 ASP cc_start: 0.7482 (OUTLIER) cc_final: 0.7258 (t70) REVERT: A 1313 ARG cc_start: 0.6806 (OUTLIER) cc_final: 0.6331 (mtp85) REVERT: A 1374 GLN cc_start: 0.2665 (OUTLIER) cc_final: 0.1870 (tt0) outliers start: 13 outliers final: 6 residues processed: 83 average time/residue: 1.0696 time to fit residues: 100.2539 Evaluate side-chains 77 residues out of total 1489 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 67 time to evaluate : 1.517 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 VAL Chi-restraints excluded: chain A residue 294 THR Chi-restraints excluded: chain A residue 608 ILE Chi-restraints excluded: chain A residue 693 MET Chi-restraints excluded: chain A residue 728 ILE Chi-restraints excluded: chain A residue 1006 ASP Chi-restraints excluded: chain A residue 1053 LEU Chi-restraints excluded: chain A residue 1170 ASP Chi-restraints excluded: chain A residue 1313 ARG Chi-restraints excluded: chain A residue 1374 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 150 optimal weight: 0.9990 chunk 39 optimal weight: 0.0770 chunk 62 optimal weight: 0.0970 chunk 35 optimal weight: 0.9980 chunk 89 optimal weight: 1.9990 chunk 133 optimal weight: 4.9990 chunk 113 optimal weight: 0.9990 chunk 111 optimal weight: 0.0970 chunk 14 optimal weight: 6.9990 chunk 120 optimal weight: 0.8980 chunk 29 optimal weight: 0.7980 overall best weight: 0.3934 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 210 ASN A 729 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4548 r_free = 0.4548 target = 0.230545 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.4173 r_free = 0.4173 target = 0.188281 restraints weight = 12962.295| |-----------------------------------------------------------------------------| r_work (start): 0.4164 rms_B_bonded: 1.26 r_work: 0.3750 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.3505 rms_B_bonded: 4.14 restraints_weight: 0.2500 r_work (final): 0.3505 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7805 moved from start: 0.1623 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.053 12977 Z= 0.101 Angle : 0.488 8.881 17579 Z= 0.250 Chirality : 0.036 0.135 2108 Planarity : 0.003 0.038 2189 Dihedral : 3.710 27.934 1656 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 4.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.21 % Favored : 95.79 % Rotamer: Outliers : 0.87 % Allowed : 13.97 % Favored : 85.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.97 (0.22), residues: 1569 helix: 2.15 (0.16), residues: 1082 sheet: 0.41 (0.95), residues: 37 loop : -0.74 (0.30), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A1495 HIS 0.003 0.001 HIS A1429 PHE 0.020 0.001 PHE A 102 TYR 0.013 0.001 TYR A1251 ARG 0.008 0.000 ARG A 333 Details of bonding type rmsd hydrogen bonds : bond 0.03724 ( 782) hydrogen bonds : angle 3.59494 ( 2295) covalent geometry : bond 0.00218 (12977) covalent geometry : angle 0.48819 (17579) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10018.77 seconds wall clock time: 172 minutes 14.47 seconds (10334.47 seconds total)