Starting phenix.real_space_refine on Wed Mar 4 10:20:34 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7wo9_32643/03_2026/7wo9_32643.cif Found real_map, /net/cci-nas-00/data/ceres_data/7wo9_32643/03_2026/7wo9_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 { model { file = "/net/cci-nas-00/data/ceres_data/7wo9_32643/03_2026/7wo9_32643.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7wo9_32643/03_2026/7wo9_32643.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7wo9_32643/03_2026/7wo9_32643.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7wo9_32643/03_2026/7wo9_32643.map" } resolution = 2.81 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 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): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 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: 2.74, per 1000 atoms: 0.22 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: 0.99 Conformation dependent library (CDL) restraints added in 622.5 milliseconds 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: 0.54 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: 2.58 Time building geometry restraints manager: 1.35 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: 10.530 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: 0.370 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 12.510 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:8.500 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.070 ------------------------------------------------------------------------------- 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.49 (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 ARG 0.006 0.000 ARG A1313 TYR 0.019 0.001 TYR A 323 PHE 0.028 0.001 PHE A1285 TRP 0.072 0.002 TRP A1495 HIS 0.002 0.001 HIS A 729 Details of bonding type rmsd covalent geometry : bond 0.00231 (12977) covalent geometry : angle 0.50404 (17579) hydrogen bonds : bond 0.14670 ( 782) hydrogen bonds : angle 4.92984 ( 2295) *********************** 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 : 0.465 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 105 average time/residue: 0.5020 time to fit residues: 58.2533 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 : 0.452 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 98 optimal weight: 0.9980 chunk 107 optimal weight: 6.9990 chunk 10 optimal weight: 0.9980 chunk 66 optimal weight: 1.9990 chunk 130 optimal weight: 20.0000 chunk 124 optimal weight: 0.0970 chunk 103 optimal weight: 6.9990 chunk 77 optimal weight: 0.0570 chunk 122 optimal weight: 0.9980 chunk 91 optimal weight: 0.5980 chunk 149 optimal weight: 8.9990 overall best weight: 0.5496 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 363 ASN A 388 ASN A 729 HIS A 788 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4618 r_free = 0.4618 target = 0.235645 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.4215 r_free = 0.4215 target = 0.186613 restraints weight = 13781.267| |-----------------------------------------------------------------------------| r_work (start): 0.4176 rms_B_bonded: 1.37 r_work: 0.3881 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.3755 rms_B_bonded: 3.82 restraints_weight: 0.2500 r_work (final): 0.3755 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7747 moved from start: 0.0858 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= 0.114 Angle : 0.500 7.457 17579 Z= 0.258 Chirality : 0.037 0.147 2108 Planarity : 0.004 0.071 2189 Dihedral : 3.852 27.998 1656 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 4.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.40 % Favored : 95.60 % Rotamer: Outliers : 0.74 % Allowed : 5.84 % Favored : 93.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.73 (0.22), residues: 1569 helix: 1.89 (0.16), residues: 1081 sheet: 0.53 (0.91), residues: 37 loop : -0.61 (0.31), residues: 451 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 333 TYR 0.018 0.001 TYR A1260 PHE 0.023 0.001 PHE A1605 TRP 0.041 0.002 TRP A1495 HIS 0.005 0.001 HIS A 729 Details of bonding type rmsd covalent geometry : bond 0.00244 (12977) covalent geometry : angle 0.50007 (17579) hydrogen bonds : bond 0.04553 ( 782) hydrogen bonds : angle 3.90708 ( 2295) *********************** 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 93 residues out of total 1489 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 82 time to evaluate : 0.425 Fit side-chains revert: symmetry clash REVERT: A 589 GLU cc_start: 0.7435 (OUTLIER) cc_final: 0.6839 (mm-30) REVERT: A 1170 ASP cc_start: 0.7298 (OUTLIER) cc_final: 0.7081 (t70) outliers start: 11 outliers final: 4 residues processed: 88 average time/residue: 0.5492 time to fit residues: 53.3121 Evaluate side-chains 77 residues out of total 1489 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 71 time to evaluate : 0.472 ------------------------------------------------------------------------------- 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 1006 ASP 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 62 optimal weight: 0.2980 chunk 91 optimal weight: 0.8980 chunk 4 optimal weight: 0.9990 chunk 34 optimal weight: 0.5980 chunk 55 optimal weight: 0.5980 chunk 18 optimal weight: 0.0970 chunk 89 optimal weight: 0.9980 chunk 109 optimal weight: 0.6980 chunk 43 optimal weight: 2.9990 chunk 49 optimal weight: 2.9990 chunk 20 optimal weight: 0.6980 overall best weight: 0.4578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 246 ASN A 388 ASN A 729 HIS A1492 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4624 r_free = 0.4624 target = 0.236070 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.4223 r_free = 0.4223 target = 0.187392 restraints weight = 13800.568| |-----------------------------------------------------------------------------| r_work (start): 0.4185 rms_B_bonded: 1.35 r_work: 0.3891 rms_B_bonded: 2.26 restraints_weight: 0.5000 r_work: 0.3762 rms_B_bonded: 3.81 restraints_weight: 0.2500 r_work (final): 0.3762 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7735 moved from start: 0.1066 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 12977 Z= 0.102 Angle : 0.473 7.500 17579 Z= 0.244 Chirality : 0.036 0.139 2108 Planarity : 0.003 0.060 2189 Dihedral : 3.787 28.107 1656 Min Nonbonded Distance : 2.568 Molprobity Statistics. All-atom Clashscore : 4.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.95 % Favored : 96.05 % Rotamer: Outliers : 0.67 % Allowed : 8.19 % Favored : 91.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.86 (0.22), residues: 1569 helix: 2.03 (0.16), residues: 1084 sheet: 0.50 (0.93), residues: 37 loop : -0.69 (0.30), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 333 TYR 0.017 0.001 TYR A1260 PHE 0.020 0.001 PHE A1605 TRP 0.031 0.001 TRP A1495 HIS 0.003 0.001 HIS A1429 Details of bonding type rmsd covalent geometry : bond 0.00217 (12977) covalent geometry : angle 0.47274 (17579) hydrogen bonds : bond 0.04014 ( 782) hydrogen bonds : angle 3.72323 ( 2295) *********************** 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 85 residues out of total 1489 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 75 time to evaluate : 0.523 Fit side-chains revert: symmetry clash REVERT: A 589 GLU cc_start: 0.7446 (OUTLIER) cc_final: 0.6860 (mm-30) outliers start: 10 outliers final: 5 residues processed: 82 average time/residue: 0.5255 time to fit residues: 47.7728 Evaluate side-chains 77 residues out of total 1489 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 71 time to evaluate : 0.507 ------------------------------------------------------------------------------- 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 1006 ASP Chi-restraints excluded: chain A residue 1128 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 7 optimal weight: 8.9990 chunk 12 optimal weight: 0.7980 chunk 20 optimal weight: 0.6980 chunk 10 optimal weight: 4.9990 chunk 102 optimal weight: 0.8980 chunk 69 optimal weight: 2.9990 chunk 134 optimal weight: 0.0970 chunk 103 optimal weight: 0.9980 chunk 152 optimal weight: 1.9990 chunk 25 optimal weight: 4.9990 chunk 85 optimal weight: 0.4980 overall best weight: 0.5978 ------------------------------------------------------------------------------- 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 = 0.4616 r_free = 0.4616 target = 0.235091 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.4210 r_free = 0.4210 target = 0.186174 restraints weight = 13778.429| |-----------------------------------------------------------------------------| r_work (start): 0.4172 rms_B_bonded: 1.42 r_work: 0.3869 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.3737 rms_B_bonded: 3.98 restraints_weight: 0.2500 r_work (final): 0.3737 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7768 moved from start: 0.1223 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 12977 Z= 0.109 Angle : 0.475 7.423 17579 Z= 0.246 Chirality : 0.037 0.134 2108 Planarity : 0.003 0.057 2189 Dihedral : 3.783 28.068 1656 Min Nonbonded Distance : 2.612 Molprobity Statistics. All-atom Clashscore : 4.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.33 % Favored : 95.67 % Rotamer: Outliers : 1.21 % Allowed : 9.60 % Favored : 89.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.88 (0.22), residues: 1569 helix: 2.07 (0.16), residues: 1085 sheet: 0.45 (0.93), residues: 37 loop : -0.78 (0.30), residues: 447 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 333 TYR 0.011 0.001 TYR A1251 PHE 0.022 0.001 PHE A 102 TRP 0.025 0.001 TRP A1495 HIS 0.003 0.001 HIS A 318 Details of bonding type rmsd covalent geometry : bond 0.00241 (12977) covalent geometry : angle 0.47535 (17579) hydrogen bonds : bond 0.04171 ( 782) hydrogen bonds : angle 3.67841 ( 2295) *********************** 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 91 residues out of total 1489 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 73 time to evaluate : 0.467 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 589 GLU cc_start: 0.7528 (OUTLIER) cc_final: 0.6937 (mm-30) REVERT: A 1053 LEU cc_start: 0.6557 (OUTLIER) cc_final: 0.5973 (mt) REVERT: A 1313 ARG cc_start: 0.7000 (OUTLIER) cc_final: 0.6322 (mtp85) outliers start: 18 outliers final: 8 residues processed: 86 average time/residue: 0.4991 time to fit residues: 47.5286 Evaluate side-chains 80 residues out of total 1489 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 69 time to evaluate : 0.444 ------------------------------------------------------------------------------- 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 360 GLN Chi-restraints excluded: chain A residue 589 GLU Chi-restraints excluded: chain A residue 794 ILE Chi-restraints excluded: chain A residue 837 ASP Chi-restraints excluded: chain A residue 1006 ASP Chi-restraints excluded: chain A residue 1053 LEU Chi-restraints excluded: chain A residue 1128 LEU 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 18 optimal weight: 0.9990 chunk 17 optimal weight: 0.5980 chunk 24 optimal weight: 0.9990 chunk 31 optimal weight: 0.0070 chunk 36 optimal weight: 2.9990 chunk 20 optimal weight: 0.9980 chunk 83 optimal weight: 0.7980 chunk 27 optimal weight: 2.9990 chunk 111 optimal weight: 0.0670 chunk 97 optimal weight: 8.9990 chunk 110 optimal weight: 1.9990 overall best weight: 0.4936 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4622 r_free = 0.4622 target = 0.235893 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.4209 r_free = 0.4209 target = 0.185609 restraints weight = 13813.869| |-----------------------------------------------------------------------------| r_work (start): 0.4240 rms_B_bonded: 1.38 r_work: 0.3942 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.3809 rms_B_bonded: 4.44 restraints_weight: 0.2500 r_work (final): 0.3809 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7774 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 : 0.002 0.042 12977 Z= 0.102 Angle : 0.466 7.374 17579 Z= 0.241 Chirality : 0.036 0.163 2108 Planarity : 0.003 0.037 2189 Dihedral : 3.745 28.028 1656 Min Nonbonded Distance : 2.621 Molprobity Statistics. All-atom Clashscore : 4.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.14 % Favored : 95.86 % Rotamer: Outliers : 1.07 % Allowed : 10.75 % Favored : 88.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.98 (0.22), residues: 1569 helix: 2.16 (0.16), residues: 1084 sheet: 0.47 (0.94), residues: 37 loop : -0.75 (0.30), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 333 TYR 0.021 0.001 TYR A1260 PHE 0.021 0.001 PHE A1605 TRP 0.022 0.001 TRP A1495 HIS 0.003 0.001 HIS A1429 Details of bonding type rmsd covalent geometry : bond 0.00220 (12977) covalent geometry : angle 0.46636 (17579) hydrogen bonds : bond 0.03901 ( 782) hydrogen bonds : angle 3.62244 ( 2295) *********************** 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 88 residues out of total 1489 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 72 time to evaluate : 0.496 Fit side-chains revert: symmetry clash REVERT: A 589 GLU cc_start: 0.7596 (OUTLIER) cc_final: 0.7014 (mm-30) REVERT: A 1053 LEU cc_start: 0.6627 (OUTLIER) cc_final: 0.6039 (mt) REVERT: A 1313 ARG cc_start: 0.7061 (OUTLIER) cc_final: 0.6417 (mtp85) REVERT: A 1374 GLN cc_start: 0.2599 (OUTLIER) cc_final: 0.1578 (tt0) outliers start: 16 outliers final: 9 residues processed: 83 average time/residue: 0.5289 time to fit residues: 48.6501 Evaluate side-chains 80 residues out of total 1489 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 67 time to evaluate : 0.490 ------------------------------------------------------------------------------- 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 360 GLN Chi-restraints excluded: chain A residue 589 GLU 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 1128 LEU 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 122 optimal weight: 0.9990 chunk 63 optimal weight: 0.9990 chunk 22 optimal weight: 0.0970 chunk 83 optimal weight: 0.7980 chunk 33 optimal weight: 0.6980 chunk 146 optimal weight: 6.9990 chunk 147 optimal weight: 6.9990 chunk 61 optimal weight: 0.7980 chunk 40 optimal weight: 3.9990 chunk 52 optimal weight: 3.9990 chunk 99 optimal weight: 1.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 729 HIS A1102 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4539 r_free = 0.4539 target = 0.229535 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.4151 r_free = 0.4151 target = 0.185881 restraints weight = 12868.209| |-----------------------------------------------------------------------------| r_work (start): 0.4136 rms_B_bonded: 1.29 r_work: 0.3708 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.3485 rms_B_bonded: 4.17 restraints_weight: 0.2500 r_work (final): 0.3485 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7829 moved from start: 0.1408 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 12977 Z= 0.114 Angle : 0.482 7.242 17579 Z= 0.249 Chirality : 0.037 0.135 2108 Planarity : 0.003 0.038 2189 Dihedral : 3.785 27.906 1656 Min Nonbonded Distance : 2.582 Molprobity Statistics. All-atom Clashscore : 4.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.53 % Favored : 95.47 % Rotamer: Outliers : 1.14 % Allowed : 11.69 % Favored : 87.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.90 (0.22), residues: 1569 helix: 2.10 (0.16), residues: 1083 sheet: 0.52 (0.95), residues: 37 loop : -0.80 (0.30), residues: 449 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 333 TYR 0.020 0.001 TYR A1260 PHE 0.019 0.001 PHE A1605 TRP 0.021 0.001 TRP A1495 HIS 0.003 0.001 HIS A 318 Details of bonding type rmsd covalent geometry : bond 0.00256 (12977) covalent geometry : angle 0.48151 (17579) hydrogen bonds : bond 0.04289 ( 782) hydrogen bonds : angle 3.65844 ( 2295) *********************** 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 90 residues out of total 1489 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 73 time to evaluate : 0.475 Fit side-chains revert: symmetry clash REVERT: A 589 GLU cc_start: 0.7613 (OUTLIER) cc_final: 0.7023 (mm-30) REVERT: A 1053 LEU cc_start: 0.6603 (OUTLIER) cc_final: 0.5943 (mt) REVERT: A 1313 ARG cc_start: 0.6902 (OUTLIER) cc_final: 0.6390 (mtp85) REVERT: A 1374 GLN cc_start: 0.2584 (OUTLIER) cc_final: 0.1686 (tt0) outliers start: 17 outliers final: 11 residues processed: 86 average time/residue: 0.5170 time to fit residues: 49.2483 Evaluate side-chains 83 residues out of total 1489 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 68 time to evaluate : 0.372 ------------------------------------------------------------------------------- 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 272 ILE Chi-restraints excluded: chain A residue 323 TYR Chi-restraints excluded: chain A residue 360 GLN Chi-restraints excluded: chain A residue 589 GLU Chi-restraints excluded: chain A residue 693 MET Chi-restraints excluded: chain A residue 728 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 1128 LEU Chi-restraints excluded: chain A residue 1313 ARG Chi-restraints excluded: chain A residue 1374 GLN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 111 optimal weight: 1.9990 chunk 154 optimal weight: 4.9990 chunk 119 optimal weight: 0.6980 chunk 146 optimal weight: 7.9990 chunk 144 optimal weight: 10.0000 chunk 43 optimal weight: 0.9990 chunk 14 optimal weight: 8.9990 chunk 78 optimal weight: 0.4980 chunk 22 optimal weight: 0.6980 chunk 64 optimal weight: 0.3980 chunk 121 optimal weight: 4.9990 overall best weight: 0.6582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 729 HIS A1153 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4540 r_free = 0.4540 target = 0.229638 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4157 r_free = 0.4157 target = 0.186602 restraints weight = 12964.664| |-----------------------------------------------------------------------------| r_work (start): 0.4133 rms_B_bonded: 1.25 r_work: 0.3703 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.3435 rms_B_bonded: 4.88 restraints_weight: 0.2500 r_work (final): 0.3435 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7868 moved from start: 0.1457 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 12977 Z= 0.113 Angle : 0.482 7.153 17579 Z= 0.250 Chirality : 0.037 0.135 2108 Planarity : 0.003 0.038 2189 Dihedral : 3.790 27.839 1656 Min Nonbonded Distance : 2.558 Molprobity Statistics. All-atom Clashscore : 4.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.40 % Favored : 95.60 % Rotamer: Outliers : 1.41 % Allowed : 12.09 % Favored : 86.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.91 (0.22), residues: 1569 helix: 2.10 (0.16), residues: 1083 sheet: 0.50 (0.96), residues: 37 loop : -0.77 (0.31), residues: 449 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 333 TYR 0.019 0.001 TYR A1260 PHE 0.020 0.001 PHE A 102 TRP 0.020 0.001 TRP A1495 HIS 0.003 0.001 HIS A 318 Details of bonding type rmsd covalent geometry : bond 0.00254 (12977) covalent geometry : angle 0.48211 (17579) hydrogen bonds : bond 0.04210 ( 782) hydrogen bonds : angle 3.65623 ( 2295) *********************** 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: 21 poor density : 68 time to evaluate : 0.420 Fit side-chains revert: symmetry clash REVERT: A 589 GLU cc_start: 0.7711 (OUTLIER) cc_final: 0.7130 (mm-30) REVERT: A 1053 LEU cc_start: 0.6709 (OUTLIER) cc_final: 0.6015 (mt) REVERT: A 1313 ARG cc_start: 0.6998 (OUTLIER) cc_final: 0.6439 (mtp85) REVERT: A 1374 GLN cc_start: 0.2653 (OUTLIER) cc_final: 0.1610 (tt0) outliers start: 21 outliers final: 11 residues processed: 84 average time/residue: 0.4888 time to fit residues: 45.4706 Evaluate side-chains 81 residues out of total 1489 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 66 time to evaluate : 0.450 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 VAL Chi-restraints excluded: chain A residue 215 GLN Chi-restraints excluded: chain A residue 272 ILE Chi-restraints excluded: chain A residue 323 TYR Chi-restraints excluded: chain A residue 360 GLN Chi-restraints excluded: chain A residue 589 GLU 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 1128 LEU 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 32 optimal weight: 0.7980 chunk 13 optimal weight: 0.7980 chunk 96 optimal weight: 1.9990 chunk 8 optimal weight: 0.6980 chunk 115 optimal weight: 0.6980 chunk 82 optimal weight: 2.9990 chunk 0 optimal weight: 3.9990 chunk 88 optimal weight: 0.0020 chunk 91 optimal weight: 0.9980 chunk 157 optimal weight: 6.9990 chunk 55 optimal weight: 0.7980 overall best weight: 0.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 729 HIS A1153 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4542 r_free = 0.4542 target = 0.229809 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.4165 r_free = 0.4165 target = 0.187410 restraints weight = 12913.739| |-----------------------------------------------------------------------------| r_work (start): 0.4153 rms_B_bonded: 1.21 r_work: 0.3745 rms_B_bonded: 2.14 restraints_weight: 0.5000 r_work: 0.3505 rms_B_bonded: 3.97 restraints_weight: 0.2500 r_work (final): 0.3505 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7816 moved from start: 0.1495 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 12977 Z= 0.110 Angle : 0.494 8.585 17579 Z= 0.253 Chirality : 0.037 0.141 2108 Planarity : 0.003 0.037 2189 Dihedral : 3.770 27.814 1656 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 4.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.27 % Favored : 95.73 % Rotamer: Outliers : 1.21 % Allowed : 12.36 % Favored : 86.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.92 (0.22), residues: 1569 helix: 2.11 (0.16), residues: 1083 sheet: 0.50 (0.96), residues: 37 loop : -0.75 (0.31), residues: 449 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 333 TYR 0.019 0.001 TYR A1260 PHE 0.018 0.001 PHE A1605 TRP 0.020 0.001 TRP A1495 HIS 0.003 0.001 HIS A 318 Details of bonding type rmsd covalent geometry : bond 0.00244 (12977) covalent geometry : angle 0.49386 (17579) hydrogen bonds : bond 0.04135 ( 782) hydrogen bonds : angle 3.66295 ( 2295) *********************** 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 87 residues out of total 1489 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 69 time to evaluate : 0.464 Fit side-chains revert: symmetry clash REVERT: A 589 GLU cc_start: 0.7567 (OUTLIER) cc_final: 0.6954 (mm-30) REVERT: A 1053 LEU cc_start: 0.6571 (OUTLIER) cc_final: 0.5920 (mt) REVERT: A 1313 ARG cc_start: 0.6784 (OUTLIER) cc_final: 0.6299 (mtp85) REVERT: A 1374 GLN cc_start: 0.2680 (OUTLIER) cc_final: 0.1873 (tt0) outliers start: 18 outliers final: 12 residues processed: 81 average time/residue: 0.4919 time to fit residues: 44.2966 Evaluate side-chains 82 residues out of total 1489 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 66 time to evaluate : 0.412 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 VAL Chi-restraints excluded: chain A residue 215 GLN Chi-restraints excluded: chain A residue 272 ILE Chi-restraints excluded: chain A residue 323 TYR Chi-restraints excluded: chain A residue 360 GLN Chi-restraints excluded: chain A residue 589 GLU Chi-restraints excluded: chain A residue 602 VAL 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 1128 LEU 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 153 optimal weight: 4.9990 chunk 5 optimal weight: 2.9990 chunk 27 optimal weight: 2.9990 chunk 79 optimal weight: 1.9990 chunk 102 optimal weight: 0.7980 chunk 61 optimal weight: 0.9980 chunk 126 optimal weight: 0.9990 chunk 55 optimal weight: 0.7980 chunk 70 optimal weight: 0.4980 chunk 97 optimal weight: 0.8980 chunk 35 optimal weight: 0.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 729 HIS A1093 ASN A1153 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4533 r_free = 0.4533 target = 0.228676 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.4153 r_free = 0.4153 target = 0.186183 restraints weight = 13006.646| |-----------------------------------------------------------------------------| r_work (start): 0.4139 rms_B_bonded: 1.24 r_work: 0.3719 rms_B_bonded: 2.18 restraints_weight: 0.5000 r_work: 0.3480 rms_B_bonded: 4.00 restraints_weight: 0.2500 r_work (final): 0.3480 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7840 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 0.043 12977 Z= 0.124 Angle : 0.514 8.542 17579 Z= 0.263 Chirality : 0.038 0.147 2108 Planarity : 0.003 0.039 2189 Dihedral : 3.840 27.678 1656 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 4.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.59 % Favored : 95.41 % Rotamer: Outliers : 1.14 % Allowed : 12.56 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.84 (0.22), residues: 1569 helix: 2.04 (0.16), residues: 1081 sheet: 0.48 (0.96), residues: 37 loop : -0.74 (0.30), residues: 451 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 333 TYR 0.018 0.001 TYR A1260 PHE 0.018 0.001 PHE A1605 TRP 0.020 0.001 TRP A1495 HIS 0.003 0.001 HIS A 318 Details of bonding type rmsd covalent geometry : bond 0.00286 (12977) covalent geometry : angle 0.51377 (17579) hydrogen bonds : bond 0.04567 ( 782) hydrogen bonds : angle 3.72334 ( 2295) *********************** 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 86 residues out of total 1489 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 69 time to evaluate : 0.481 Fit side-chains revert: symmetry clash REVERT: A 589 GLU cc_start: 0.7627 (OUTLIER) cc_final: 0.7004 (mm-30) REVERT: A 1053 LEU cc_start: 0.6639 (OUTLIER) cc_final: 0.5960 (mt) REVERT: A 1313 ARG cc_start: 0.6860 (OUTLIER) cc_final: 0.6361 (mtp85) REVERT: A 1374 GLN cc_start: 0.2680 (OUTLIER) cc_final: 0.1816 (tt0) outliers start: 17 outliers final: 12 residues processed: 81 average time/residue: 0.4614 time to fit residues: 41.8162 Evaluate side-chains 83 residues out of total 1489 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 67 time to evaluate : 0.445 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 VAL Chi-restraints excluded: chain A residue 215 GLN Chi-restraints excluded: chain A residue 272 ILE Chi-restraints excluded: chain A residue 323 TYR Chi-restraints excluded: chain A residue 360 GLN Chi-restraints excluded: chain A residue 589 GLU Chi-restraints excluded: chain A residue 602 VAL 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 1128 LEU 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 62 optimal weight: 2.9990 chunk 68 optimal weight: 0.8980 chunk 17 optimal weight: 0.9990 chunk 18 optimal weight: 0.4980 chunk 118 optimal weight: 2.9990 chunk 89 optimal weight: 1.9990 chunk 46 optimal weight: 5.9990 chunk 32 optimal weight: 0.9990 chunk 116 optimal weight: 3.9990 chunk 124 optimal weight: 0.0670 chunk 12 optimal weight: 0.6980 overall best weight: 0.6320 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 729 HIS A1151 ASN A1153 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4540 r_free = 0.4540 target = 0.229511 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.4162 r_free = 0.4162 target = 0.187111 restraints weight = 13054.236| |-----------------------------------------------------------------------------| r_work (start): 0.4149 rms_B_bonded: 1.24 r_work: 0.3732 rms_B_bonded: 2.19 restraints_weight: 0.5000 r_work: 0.3494 rms_B_bonded: 4.04 restraints_weight: 0.2500 r_work (final): 0.3494 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7825 moved from start: 0.1580 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 12977 Z= 0.113 Angle : 0.504 9.645 17579 Z= 0.258 Chirality : 0.037 0.133 2108 Planarity : 0.003 0.038 2189 Dihedral : 3.799 27.698 1656 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 4.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.46 % Favored : 95.54 % Rotamer: Outliers : 1.07 % Allowed : 12.76 % Favored : 86.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.89 (0.22), residues: 1569 helix: 2.09 (0.16), residues: 1081 sheet: 0.49 (0.96), residues: 37 loop : -0.75 (0.30), residues: 451 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 333 TYR 0.017 0.001 TYR A1260 PHE 0.018 0.001 PHE A1605 TRP 0.020 0.001 TRP A1495 HIS 0.003 0.001 HIS A 318 Details of bonding type rmsd covalent geometry : bond 0.00255 (12977) covalent geometry : angle 0.50420 (17579) hydrogen bonds : bond 0.04205 ( 782) hydrogen bonds : angle 3.67634 ( 2295) ********************** 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 81 residues out of total 1489 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 65 time to evaluate : 0.340 Fit side-chains revert: symmetry clash REVERT: A 589 GLU cc_start: 0.7603 (OUTLIER) cc_final: 0.6986 (mm-30) REVERT: A 1053 LEU cc_start: 0.6610 (OUTLIER) cc_final: 0.5927 (mt) REVERT: A 1313 ARG cc_start: 0.6876 (OUTLIER) cc_final: 0.6389 (mtp85) REVERT: A 1374 GLN cc_start: 0.2657 (OUTLIER) cc_final: 0.1835 (tt0) outliers start: 16 outliers final: 12 residues processed: 76 average time/residue: 0.4800 time to fit residues: 40.8476 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 : 0.549 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 VAL Chi-restraints excluded: chain A residue 215 GLN Chi-restraints excluded: chain A residue 272 ILE Chi-restraints excluded: chain A residue 323 TYR Chi-restraints excluded: chain A residue 360 GLN Chi-restraints excluded: chain A residue 589 GLU Chi-restraints excluded: chain A residue 602 VAL 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 1128 LEU 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 156 optimal weight: 6.9990 chunk 48 optimal weight: 8.9990 chunk 2 optimal weight: 0.9990 chunk 73 optimal weight: 0.8980 chunk 95 optimal weight: 0.8980 chunk 144 optimal weight: 9.9990 chunk 46 optimal weight: 7.9990 chunk 75 optimal weight: 0.5980 chunk 11 optimal weight: 0.6980 chunk 64 optimal weight: 0.9990 chunk 52 optimal weight: 1.9990 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 A1153 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4532 r_free = 0.4532 target = 0.228517 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.4149 r_free = 0.4149 target = 0.185742 restraints weight = 12905.951| |-----------------------------------------------------------------------------| r_work (start): 0.4139 rms_B_bonded: 1.21 r_work: 0.3724 rms_B_bonded: 2.15 restraints_weight: 0.5000 r_work: 0.3492 rms_B_bonded: 3.86 restraints_weight: 0.2500 r_work (final): 0.3492 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7824 moved from start: 0.1628 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 12977 Z= 0.127 Angle : 0.521 9.230 17579 Z= 0.266 Chirality : 0.038 0.134 2108 Planarity : 0.003 0.040 2189 Dihedral : 3.846 27.620 1656 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 4.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.53 % Favored : 95.47 % Rotamer: Outliers : 1.21 % Allowed : 12.69 % Favored : 86.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.80 (0.22), residues: 1569 helix: 2.00 (0.16), residues: 1081 sheet: 0.46 (0.95), residues: 37 loop : -0.76 (0.30), residues: 451 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 333 TYR 0.018 0.001 TYR A1260 PHE 0.018 0.001 PHE A1605 TRP 0.020 0.001 TRP A1495 HIS 0.004 0.001 HIS A 318 Details of bonding type rmsd covalent geometry : bond 0.00295 (12977) covalent geometry : angle 0.52095 (17579) hydrogen bonds : bond 0.04576 ( 782) hydrogen bonds : angle 3.72147 ( 2295) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4445.20 seconds wall clock time: 76 minutes 32.82 seconds (4592.82 seconds total)