Starting phenix.real_space_refine on Fri Mar 6 00:58:40 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7mvy_24058/03_2026/7mvy_24058.cif Found real_map, /net/cci-nas-00/data/ceres_data/7mvy_24058/03_2026/7mvy_24058.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.39 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7mvy_24058/03_2026/7mvy_24058.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7mvy_24058/03_2026/7mvy_24058.map" model { file = "/net/cci-nas-00/data/ceres_data/7mvy_24058/03_2026/7mvy_24058.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7mvy_24058/03_2026/7mvy_24058.cif" } resolution = 2.39 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= 0.002 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: 5 Type Number sf(0) Gaussians S 56 5.16 5 C 8464 2.51 5 N 2276 2.21 5 O 2422 1.98 5 H 13337 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 6 residue(s): 0.01s 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: 26555 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 25701 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1641, 25701 Classifications: {'peptide': 1641} Link IDs: {'PCIS': 1, 'PTRANS': 69, 'TRANS': 1570} Chain breaks: 14 Chain: "B" Number of atoms: 854 Number of conformers: 1 Conformer: "" Number of residues, atoms: 53, 854 Classifications: {'peptide': 53} Link IDs: {'TRANS': 52} Time building chain proxies: 4.35, per 1000 atoms: 0.16 Number of scatterers: 26555 At special positions: 0 Unit cell: (79.704, 109.836, 186.624, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 56 16.00 O 2422 8.00 N 2276 7.00 C 8464 6.00 H 13337 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.22 Conformation dependent library (CDL) restraints added in 944.7 milliseconds 3324 Ramachandran restraints generated. 1662 Oldfield, 0 Emsley, 1662 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3236 Finding SS restraints... Secondary structure from input PDB file: 94 helices and 1 sheets defined 76.1% alpha, 0.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.68 Creating SS restraints... Processing helix chain 'A' and resid 12 through 19 Processing helix chain 'A' and resid 25 through 36 Processing helix chain 'A' and resid 37 through 42 Processing helix chain 'A' and resid 43 through 52 Processing helix chain 'A' and resid 52 through 61 Processing helix chain 'A' and resid 61 through 66 removed outlier: 3.855A pdb=" N VAL A 65 " --> pdb=" O HIS A 61 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N PHE A 66 " --> pdb=" O PRO A 62 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 61 through 66' Processing helix chain 'A' and resid 71 through 80 Processing helix chain 'A' and resid 89 through 103 Processing helix chain 'A' and resid 106 through 120 Processing helix chain 'A' and resid 120 through 127 Processing helix chain 'A' and resid 131 through 142 Processing helix chain 'A' and resid 163 through 172 Processing helix chain 'A' and resid 173 through 205 Processing helix chain 'A' and resid 211 through 226 Processing helix chain 'A' and resid 237 through 242 Processing helix chain 'A' and resid 242 through 260 removed outlier: 4.131A pdb=" N THR A 246 " --> pdb=" O THR A 242 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N TYR A 247 " --> pdb=" O MET A 243 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N LEU A 250 " --> pdb=" O THR A 246 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N GLU A 252 " --> pdb=" O MET A 248 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N ASP A 253 " --> pdb=" O ASN A 249 " (cutoff:3.500A) Processing helix chain 'A' and resid 271 through 299 Processing helix chain 'A' and resid 306 through 321 removed outlier: 3.765A pdb=" N GLU A 312 " --> pdb=" O GLU A 308 " (cutoff:3.500A) Processing helix chain 'A' and resid 323 through 328 Processing helix chain 'A' and resid 332 through 352 Proline residue: A 338 - end of helix Processing helix chain 'A' and resid 352 through 363 Processing helix chain 'A' and resid 371 through 374 Processing helix chain 'A' and resid 375 through 393 removed outlier: 3.530A pdb=" N GLY A 393 " --> pdb=" O ALA A 389 " (cutoff:3.500A) Processing helix chain 'A' and resid 396 through 419 removed outlier: 4.792A pdb=" N VAL A 400 " --> pdb=" O ALA A 396 " (cutoff:3.500A) Processing helix chain 'A' and resid 463 through 471 removed outlier: 4.011A pdb=" N PHE A 467 " --> pdb=" O PRO A 463 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N GLN A 471 " --> pdb=" O PHE A 467 " (cutoff:3.500A) Processing helix chain 'A' and resid 477 through 489 Processing helix chain 'A' and resid 491 through 504 Processing helix chain 'A' and resid 513 through 531 removed outlier: 4.061A pdb=" N LEU A 522 " --> pdb=" O ALA A 518 " (cutoff:3.500A) removed outlier: 4.748A pdb=" N VAL A 523 " --> pdb=" O ARG A 519 " (cutoff:3.500A) removed outlier: 4.164A pdb=" N PHE A 524 " --> pdb=" O ALA A 520 " (cutoff:3.500A) Processing helix chain 'A' and resid 538 through 550 Processing helix chain 'A' and resid 564 through 577 removed outlier: 3.606A pdb=" N ASN A 568 " --> pdb=" O ALA A 564 " (cutoff:3.500A) removed outlier: 4.251A pdb=" N VAL A 570 " --> pdb=" O SER A 566 " (cutoff:3.500A) removed outlier: 4.722A pdb=" N TYR A 571 " --> pdb=" O LEU A 567 " (cutoff:3.500A) removed outlier: 4.510A pdb=" N MET A 574 " --> pdb=" O VAL A 570 " (cutoff:3.500A) removed outlier: 4.542A pdb=" N LEU A 575 " --> pdb=" O TYR A 571 " (cutoff:3.500A) Processing helix chain 'A' and resid 577 through 583 Processing helix chain 'A' and resid 584 through 591 Processing helix chain 'A' and resid 595 through 610 removed outlier: 4.073A pdb=" N PHE A 599 " --> pdb=" O GLU A 595 " (cutoff:3.500A) Processing helix chain 'A' and resid 613 through 617 removed outlier: 3.796A pdb=" N ALA A 617 " --> pdb=" O LYS A 614 " (cutoff:3.500A) Processing helix chain 'A' and resid 618 through 626 Processing helix chain 'A' and resid 635 through 641 removed outlier: 4.158A pdb=" N ARG A 640 " --> pdb=" O ALA A 637 " (cutoff:3.500A) Processing helix chain 'A' and resid 705 through 719 Processing helix chain 'A' and resid 731 through 755 removed outlier: 3.602A pdb=" N THR A 754 " --> pdb=" O SER A 750 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N ALA A 755 " --> pdb=" O LEU A 751 " (cutoff:3.500A) Processing helix chain 'A' and resid 761 through 771 Processing helix chain 'A' and resid 779 through 792 Processing helix chain 'A' and resid 800 through 821 removed outlier: 4.076A pdb=" N ALA A 819 " --> pdb=" O HIS A 815 " (cutoff:3.500A) removed outlier: 4.376A pdb=" N VAL A 820 " --> pdb=" O ALA A 816 " (cutoff:3.500A) Processing helix chain 'A' and resid 821 through 830 removed outlier: 3.588A pdb=" N VAL A 825 " --> pdb=" O CYS A 821 " (cutoff:3.500A) Processing helix chain 'A' and resid 843 through 848 removed outlier: 3.656A pdb=" N ARG A 846 " --> pdb=" O ARG A 843 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N ILE A 847 " --> pdb=" O LEU A 844 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N THR A 848 " --> pdb=" O SER A 845 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 843 through 848' Processing helix chain 'A' and resid 854 through 877 removed outlier: 4.686A pdb=" N LEU A 860 " --> pdb=" O GLU A 856 " (cutoff:3.500A) removed outlier: 4.260A pdb=" N LEU A 861 " --> pdb=" O ARG A 857 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N SER A 863 " --> pdb=" O ASP A 859 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N LYS A 866 " --> pdb=" O SER A 862 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N CYS A 877 " --> pdb=" O ASP A 873 " (cutoff:3.500A) Processing helix chain 'A' and resid 904 through 926 Processing helix chain 'A' and resid 933 through 957 removed outlier: 4.213A pdb=" N ARG A 937 " --> pdb=" O SER A 933 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N ALA A 955 " --> pdb=" O LEU A 951 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N HIS A 956 " --> pdb=" O VAL A 952 " (cutoff:3.500A) Processing helix chain 'A' and resid 960 through 964 removed outlier: 3.641A pdb=" N THR A 963 " --> pdb=" O SER A 960 " (cutoff:3.500A) Processing helix chain 'A' and resid 966 through 979 Processing helix chain 'A' and resid 989 through 1001 Processing helix chain 'A' and resid 1008 through 1035 Processing helix chain 'A' and resid 1042 through 1055 removed outlier: 4.283A pdb=" N HIS A1046 " --> pdb=" O PRO A1042 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N GLN A1049 " --> pdb=" O THR A1045 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N LEU A1053 " --> pdb=" O GLN A1049 " (cutoff:3.500A) Processing helix chain 'A' and resid 1056 through 1060 Processing helix chain 'A' and resid 1061 through 1063 No H-bonds generated for 'chain 'A' and resid 1061 through 1063' Processing helix chain 'A' and resid 1064 through 1081 Processing helix chain 'A' and resid 1091 through 1097 removed outlier: 3.881A pdb=" N TYR A1095 " --> pdb=" O SER A1091 " (cutoff:3.500A) Processing helix chain 'A' and resid 1097 through 1109 Processing helix chain 'A' and resid 1118 through 1134 Processing helix chain 'A' and resid 1137 through 1145 Processing helix chain 'A' and resid 1169 through 1179 removed outlier: 3.816A pdb=" N ALA A1173 " --> pdb=" O SER A1169 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N GLU A1176 " --> pdb=" O ALA A1172 " (cutoff:3.500A) Processing helix chain 'A' and resid 1185 through 1203 removed outlier: 3.835A pdb=" N ALA A1191 " --> pdb=" O GLN A1187 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N TYR A1202 " --> pdb=" O SER A1198 " (cutoff:3.500A) Processing helix chain 'A' and resid 1203 through 1214 removed outlier: 3.888A pdb=" N ALA A1209 " --> pdb=" O TRP A1205 " (cutoff:3.500A) Processing helix chain 'A' and resid 1214 through 1228 removed outlier: 3.804A pdb=" N ASP A1218 " --> pdb=" O LYS A1214 " (cutoff:3.500A) removed outlier: 4.426A pdb=" N LEU A1220 " --> pdb=" O VAL A1216 " (cutoff:3.500A) removed outlier: 4.040A pdb=" N ARG A1221 " --> pdb=" O VAL A1217 " (cutoff:3.500A) Processing helix chain 'A' and resid 1240 through 1266 removed outlier: 3.962A pdb=" N PHE A1244 " --> pdb=" O ALA A1240 " (cutoff:3.500A) Processing helix chain 'A' and resid 1269 through 1277 Processing helix chain 'A' and resid 1280 through 1287 Processing helix chain 'A' and resid 1294 through 1309 removed outlier: 3.674A pdb=" N HIS A1298 " --> pdb=" O ASN A1294 " (cutoff:3.500A) Processing helix chain 'A' and resid 1314 through 1318 removed outlier: 3.575A pdb=" N PHE A1317 " --> pdb=" O VAL A1314 " (cutoff:3.500A) Processing helix chain 'A' and resid 1334 through 1342 removed outlier: 4.521A pdb=" N GLN A1340 " --> pdb=" O GLU A1336 " (cutoff:3.500A) Processing helix chain 'A' and resid 1355 through 1391 removed outlier: 4.014A pdb=" N GLU A1359 " --> pdb=" O GLY A1355 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N LEU A1389 " --> pdb=" O LEU A1385 " (cutoff:3.500A) Processing helix chain 'A' and resid 1396 through 1417 removed outlier: 3.504A pdb=" N PHE A1400 " --> pdb=" O GLU A1396 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N GLN A1416 " --> pdb=" O LEU A1412 " (cutoff:3.500A) Processing helix chain 'A' and resid 1432 through 1447 removed outlier: 4.075A pdb=" N ALA A1436 " --> pdb=" O ARG A1432 " (cutoff:3.500A) Processing helix chain 'A' and resid 1452 through 1466 removed outlier: 3.770A pdb=" N LEU A1456 " --> pdb=" O ASP A1452 " (cutoff:3.500A) removed outlier: 5.081A pdb=" N ALA A1458 " --> pdb=" O THR A1454 " (cutoff:3.500A) removed outlier: 4.289A pdb=" N LEU A1459 " --> pdb=" O HIS A1455 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N VAL A1460 " --> pdb=" O LEU A1456 " (cutoff:3.500A) Processing helix chain 'A' and resid 1475 through 1495 removed outlier: 3.639A pdb=" N PHE A1479 " --> pdb=" O ASP A1475 " (cutoff:3.500A) Processing helix chain 'A' and resid 1507 through 1517 removed outlier: 4.600A pdb=" N THR A1513 " --> pdb=" O GLN A1509 " (cutoff:3.500A) removed outlier: 5.324A pdb=" N ILE A1514 " --> pdb=" O GLN A1510 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N LEU A1515 " --> pdb=" O VAL A1511 " (cutoff:3.500A) Processing helix chain 'A' and resid 1518 through 1531 Processing helix chain 'A' and resid 1544 through 1559 Processing helix chain 'A' and resid 1561 through 1565 Processing helix chain 'A' and resid 1567 through 1577 removed outlier: 4.278A pdb=" N ASN A1573 " --> pdb=" O VAL A1569 " (cutoff:3.500A) removed outlier: 4.192A pdb=" N ILE A1574 " --> pdb=" O GLN A1570 " (cutoff:3.500A) Processing helix chain 'A' and resid 1579 through 1589 removed outlier: 4.123A pdb=" N VAL A1583 " --> pdb=" O ASP A1579 " (cutoff:3.500A) Processing helix chain 'A' and resid 1619 through 1632 Processing helix chain 'A' and resid 1634 through 1643 Processing helix chain 'A' and resid 1643 through 1653 removed outlier: 4.292A pdb=" N LEU A1647 " --> pdb=" O CYS A1643 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N GLY A1648 " --> pdb=" O ASP A1644 " (cutoff:3.500A) removed outlier: 4.173A pdb=" N HIS A1649 " --> pdb=" O GLY A1645 " (cutoff:3.500A) Processing helix chain 'A' and resid 1655 through 1661 removed outlier: 3.803A pdb=" N ARG A1661 " --> pdb=" O GLY A1657 " (cutoff:3.500A) Processing helix chain 'A' and resid 1670 through 1683 Processing helix chain 'A' and resid 1683 through 1695 removed outlier: 3.546A pdb=" N ALA A1694 " --> pdb=" O ASN A1690 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N LEU A1695 " --> pdb=" O ILE A1691 " (cutoff:3.500A) Processing helix chain 'A' and resid 1699 through 1710 Processing helix chain 'A' and resid 1710 through 1721 removed outlier: 4.387A pdb=" N LEU A1714 " --> pdb=" O PHE A1710 " (cutoff:3.500A) removed outlier: 4.365A pdb=" N ILE A1721 " --> pdb=" O SER A1717 " (cutoff:3.500A) Processing helix chain 'A' and resid 1746 through 1766 removed outlier: 3.540A pdb=" N GLU A1750 " --> pdb=" O LEU A1746 " (cutoff:3.500A) Processing helix chain 'A' and resid 1779 through 1789 Processing helix chain 'A' and resid 1794 through 1800 removed outlier: 3.989A pdb=" N ARG A1799 " --> pdb=" O LEU A1796 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N LEU A1800 " --> pdb=" O ARG A1797 " (cutoff:3.500A) Processing helix chain 'A' and resid 1834 through 1850 Processing helix chain 'B' and resid 248 through 254 Processing helix chain 'B' and resid 259 through 264 removed outlier: 3.993A pdb=" N MET B 263 " --> pdb=" O THR B 259 " (cutoff:3.500A) Processing helix chain 'B' and resid 265 through 299 removed outlier: 3.964A pdb=" N GLU B 269 " --> pdb=" O ALA B 265 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N ASP B 276 " --> pdb=" O ALA B 272 " (cutoff:3.500A) removed outlier: 4.147A pdb=" N ALA B 277 " --> pdb=" O ARG B 273 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 630 through 632 removed outlier: 3.743A pdb=" N VAL A 632 " --> pdb=" O ALA A 698 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ALA A 698 " --> pdb=" O VAL A 632 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N ARG A 655 " --> pdb=" O GLU A 643 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N GLU A 643 " --> pdb=" O ARG A 655 " (cutoff:3.500A) 839 hydrogen bonds defined for protein. 2475 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: 6.11 Time building geometry restraints manager: 3.10 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 13313 1.03 - 1.23: 24 1.23 - 1.42: 5554 1.42 - 1.61: 7835 1.61 - 1.81: 88 Bond restraints: 26814 Sorted by residual: bond pdb=" N SER A 531 " pdb=" CA SER A 531 " ideal model delta sigma weight residual 1.456 1.492 -0.035 1.22e-02 6.72e+03 8.35e+00 bond pdb=" N ARG A 530 " pdb=" CA ARG A 530 " ideal model delta sigma weight residual 1.457 1.495 -0.038 1.33e-02 5.65e+03 8.35e+00 bond pdb=" N ARG A 530 " pdb=" H ARG A 530 " ideal model delta sigma weight residual 0.860 0.916 -0.056 2.00e-02 2.50e+03 7.83e+00 bond pdb=" N ALA A 532 " pdb=" H ALA A 532 " ideal model delta sigma weight residual 0.860 0.914 -0.054 2.00e-02 2.50e+03 7.41e+00 bond pdb=" N SER A 531 " pdb=" H SER A 531 " ideal model delta sigma weight residual 0.860 0.913 -0.053 2.00e-02 2.50e+03 7.08e+00 ... (remaining 26809 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.01: 45126 1.01 - 2.02: 3297 2.02 - 3.03: 55 3.03 - 4.04: 41 4.04 - 5.05: 14 Bond angle restraints: 48533 Sorted by residual: angle pdb=" N ALA A 532 " pdb=" CA ALA A 532 " pdb=" C ALA A 532 " ideal model delta sigma weight residual 112.45 108.10 4.35 1.39e+00 5.18e-01 9.81e+00 angle pdb=" N SER A 531 " pdb=" CA SER A 531 " pdb=" C SER A 531 " ideal model delta sigma weight residual 112.88 109.79 3.09 1.29e+00 6.01e-01 5.72e+00 angle pdb=" CA SER A 531 " pdb=" C SER A 531 " pdb=" O SER A 531 " ideal model delta sigma weight residual 119.59 117.03 2.56 1.18e+00 7.18e-01 4.72e+00 angle pdb=" N ILE A1001 " pdb=" CA ILE A1001 " pdb=" C ILE A1001 " ideal model delta sigma weight residual 111.88 109.79 2.09 1.06e+00 8.90e-01 3.87e+00 angle pdb=" N ARG A 530 " pdb=" CA ARG A 530 " pdb=" C ARG A 530 " ideal model delta sigma weight residual 112.89 110.60 2.29 1.24e+00 6.50e-01 3.40e+00 ... (remaining 48528 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.91: 12141 17.91 - 35.81: 258 35.81 - 53.72: 114 53.72 - 71.63: 36 71.63 - 89.54: 1 Dihedral angle restraints: 12550 sinusoidal: 6793 harmonic: 5757 Sorted by residual: dihedral pdb=" N GLU A 67 " pdb=" CA GLU A 67 " pdb=" CB GLU A 67 " pdb=" CG GLU A 67 " ideal model delta sinusoidal sigma weight residual -180.00 -130.46 -49.54 3 1.50e+01 4.44e-03 8.79e+00 dihedral pdb=" CA LEU A1457 " pdb=" CB LEU A1457 " pdb=" CG LEU A1457 " pdb=" CD1 LEU A1457 " ideal model delta sinusoidal sigma weight residual 180.00 140.16 39.84 3 1.50e+01 4.44e-03 7.08e+00 dihedral pdb=" CA LEU A 844 " pdb=" CB LEU A 844 " pdb=" CG LEU A 844 " pdb=" CD1 LEU A 844 " ideal model delta sinusoidal sigma weight residual 180.00 140.18 39.82 3 1.50e+01 4.44e-03 7.07e+00 ... (remaining 12547 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.028: 1620 0.028 - 0.056: 342 0.056 - 0.085: 134 0.085 - 0.113: 47 0.113 - 0.141: 10 Chirality restraints: 2153 Sorted by residual: chirality pdb=" CA ILE A 682 " pdb=" N ILE A 682 " pdb=" C ILE A 682 " pdb=" CB ILE A 682 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.96e-01 chirality pdb=" CA ILE A 681 " pdb=" N ILE A 681 " pdb=" C ILE A 681 " pdb=" CB ILE A 681 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.12 2.00e-01 2.50e+01 3.73e-01 chirality pdb=" CA VAL A1561 " pdb=" N VAL A1561 " pdb=" C VAL A1561 " pdb=" CB VAL A1561 " both_signs ideal model delta sigma weight residual False 2.44 2.56 -0.12 2.00e-01 2.50e+01 3.68e-01 ... (remaining 2150 not shown) Planarity restraints: 3946 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LYS A 529 " -0.010 2.00e-02 2.50e+03 2.03e-02 4.11e+00 pdb=" C LYS A 529 " 0.035 2.00e-02 2.50e+03 pdb=" O LYS A 529 " -0.013 2.00e-02 2.50e+03 pdb=" N ARG A 530 " -0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ALA A 532 " 0.010 2.00e-02 2.50e+03 1.92e-02 3.70e+00 pdb=" N TYR A 533 " -0.033 2.00e-02 2.50e+03 pdb=" CA TYR A 533 " 0.008 2.00e-02 2.50e+03 pdb=" H TYR A 533 " 0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ALA A1700 " 0.032 5.00e-02 4.00e+02 4.80e-02 3.69e+00 pdb=" N PRO A1701 " -0.083 5.00e-02 4.00e+02 pdb=" CA PRO A1701 " 0.025 5.00e-02 4.00e+02 pdb=" CD PRO A1701 " 0.027 5.00e-02 4.00e+02 ... (remaining 3943 not shown) Histogram of nonbonded interaction distances: 1.64 - 2.23: 1863 2.23 - 2.83: 61114 2.83 - 3.42: 69655 3.42 - 4.01: 90016 4.01 - 4.60: 143330 Nonbonded interactions: 365978 Sorted by model distance: nonbonded pdb=" OE1 GLU A1336 " pdb=" H GLU A1336 " model vdw 1.643 2.450 nonbonded pdb=" OE1 GLN A1509 " pdb=" H GLN A1509 " model vdw 1.646 2.450 nonbonded pdb=" OE1 GLU A1669 " pdb=" H GLU A1669 " model vdw 1.650 2.450 nonbonded pdb=" O MET A1659 " pdb="HD21 ASN A1712 " model vdw 1.661 2.450 nonbonded pdb=" HE1 TRP A 638 " pdb=" O SER A 725 " model vdw 1.688 2.450 ... (remaining 365973 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.81 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.700 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: 0.170 Extract box with map and model: 0.400 Check model and map are aligned: 0.080 Set scattering table: 0.070 Process input model: 23.590 Find NCS groups from input model: 0.090 Set up NCS constraints: 0.030 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:6.670 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.800 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6331 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 0.038 13477 Z= 0.101 Angle : 0.392 5.046 18318 Z= 0.220 Chirality : 0.031 0.141 2153 Planarity : 0.002 0.048 2336 Dihedral : 6.612 89.537 4869 Min Nonbonded Distance : 2.209 Molprobity Statistics. All-atom Clashscore : 3.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.72 % Favored : 99.28 % Rotamer: Outliers : 0.00 % Allowed : 1.14 % Favored : 98.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.47 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.54 (0.20), residues: 1662 helix: 0.40 (0.15), residues: 1154 sheet: -1.72 (1.93), residues: 9 loop : -2.05 (0.27), residues: 499 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 291 TYR 0.007 0.000 TYR A1251 PHE 0.005 0.000 PHE A1344 TRP 0.003 0.000 TRP A 313 HIS 0.002 0.000 HIS A 211 Details of bonding type rmsd covalent geometry : bond 0.00168 (13477) covalent geometry : angle 0.39224 (18318) hydrogen bonds : bond 0.12395 ( 839) hydrogen bonds : angle 4.59459 ( 2475) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3324 Ramachandran restraints generated. 1662 Oldfield, 0 Emsley, 1662 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3324 Ramachandran restraints generated. 1662 Oldfield, 0 Emsley, 1662 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 531 is missing expected H atoms. Skipping. Evaluate side-chains 381 residues out of total 1398 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 381 time to evaluate : 0.647 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1479 PHE cc_start: 0.6209 (t80) cc_final: 0.5880 (t80) REVERT: A 1513 THR cc_start: 0.6685 (t) cc_final: 0.6459 (t) REVERT: A 1574 ILE cc_start: 0.7733 (pp) cc_final: 0.7500 (pt) outliers start: 0 outliers final: 1 residues processed: 381 average time/residue: 1.1852 time to fit residues: 496.7460 Evaluate side-chains 207 residues out of total 1398 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 206 time to evaluate : 0.521 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1796 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 169 random chunks: chunk 98 optimal weight: 1.9990 chunk 107 optimal weight: 1.9990 chunk 10 optimal weight: 1.9990 chunk 66 optimal weight: 2.9990 chunk 130 optimal weight: 2.9990 chunk 124 optimal weight: 2.9990 chunk 103 optimal weight: 0.9990 chunk 77 optimal weight: 3.9990 chunk 122 optimal weight: 0.6980 chunk 91 optimal weight: 1.9990 chunk 149 optimal weight: 5.9990 overall best weight: 1.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 259 GLN A 949 HIS A1120 HIS A1465 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4532 r_free = 0.4532 target = 0.167787 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.4155 r_free = 0.4155 target = 0.135592 restraints weight = 65027.172| |-----------------------------------------------------------------------------| r_work (start): 0.4110 rms_B_bonded: 3.09 r_work: 0.3988 rms_B_bonded: 3.32 restraints_weight: 0.5000 r_work (final): 0.3988 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3999 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3999 r_free = 0.3999 target_work(ls_wunit_k1) = 0.126 | | occupancies: max = 1.00 min = 0.81 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3999 r_free = 0.3999 target_work(ls_wunit_k1) = 0.126 | | occupancies: max = 1.00 min = 0.32 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3999 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7214 moved from start: 0.5451 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.075 13477 Z= 0.273 Angle : 0.748 11.965 18318 Z= 0.391 Chirality : 0.040 0.208 2153 Planarity : 0.007 0.086 2336 Dihedral : 3.732 17.081 1828 Min Nonbonded Distance : 2.285 Molprobity Statistics. All-atom Clashscore : 9.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 2.93 % Allowed : 11.59 % Favored : 85.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.47 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.00 (0.20), residues: 1662 helix: 0.61 (0.15), residues: 1168 sheet: 0.39 (2.28), residues: 9 loop : -1.37 (0.28), residues: 485 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A1081 TYR 0.030 0.003 TYR A1008 PHE 0.030 0.003 PHE A 402 TRP 0.026 0.002 TRP A1203 HIS 0.013 0.002 HIS A 125 Details of bonding type rmsd covalent geometry : bond 0.00625 (13477) covalent geometry : angle 0.74845 (18318) hydrogen bonds : bond 0.04381 ( 839) hydrogen bonds : angle 4.33664 ( 2475) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3324 Ramachandran restraints generated. 1662 Oldfield, 0 Emsley, 1662 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3324 Ramachandran restraints generated. 1662 Oldfield, 0 Emsley, 1662 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 531 is missing expected H atoms. Skipping. Evaluate side-chains 266 residues out of total 1398 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 225 time to evaluate : 0.689 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 72 LYS cc_start: 0.8744 (tptt) cc_final: 0.8417 (tppt) REVERT: A 80 SER cc_start: 0.8425 (OUTLIER) cc_final: 0.7922 (p) REVERT: A 243 MET cc_start: 0.8837 (mtm) cc_final: 0.8633 (mtm) REVERT: A 312 GLU cc_start: 0.7380 (tt0) cc_final: 0.7040 (tm-30) REVERT: A 315 GLU cc_start: 0.7827 (pp20) cc_final: 0.7579 (pp20) REVERT: A 542 VAL cc_start: 0.7596 (OUTLIER) cc_final: 0.7359 (t) REVERT: A 549 LEU cc_start: 0.8041 (OUTLIER) cc_final: 0.7828 (mp) REVERT: A 595 GLU cc_start: 0.7862 (mm-30) cc_final: 0.7630 (mt-10) REVERT: A 597 ASN cc_start: 0.8598 (m-40) cc_final: 0.8375 (m-40) REVERT: A 905 GLU cc_start: 0.7693 (OUTLIER) cc_final: 0.7363 (tp30) REVERT: A 1263 MET cc_start: 0.6954 (mtt) cc_final: 0.6736 (mtt) REVERT: A 1408 VAL cc_start: 0.4411 (OUTLIER) cc_final: 0.4194 (t) REVERT: B 247 ASP cc_start: 0.7612 (p0) cc_final: 0.6388 (t0) outliers start: 41 outliers final: 12 residues processed: 255 average time/residue: 1.0411 time to fit residues: 296.0969 Evaluate side-chains 188 residues out of total 1398 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 171 time to evaluate : 0.676 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 VAL Chi-restraints excluded: chain A residue 80 SER Chi-restraints excluded: chain A residue 131 SER Chi-restraints excluded: chain A residue 187 SER Chi-restraints excluded: chain A residue 254 CYS Chi-restraints excluded: chain A residue 542 VAL Chi-restraints excluded: chain A residue 546 LEU Chi-restraints excluded: chain A residue 549 LEU Chi-restraints excluded: chain A residue 566 SER Chi-restraints excluded: chain A residue 905 GLU Chi-restraints excluded: chain A residue 948 MET Chi-restraints excluded: chain A residue 1035 PHE Chi-restraints excluded: chain A residue 1176 GLU Chi-restraints excluded: chain A residue 1408 VAL Chi-restraints excluded: chain A residue 1517 ARG Chi-restraints excluded: chain B residue 248 VAL Chi-restraints excluded: chain B residue 264 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 169 random chunks: chunk 148 optimal weight: 0.6980 chunk 157 optimal weight: 0.8980 chunk 16 optimal weight: 1.9990 chunk 163 optimal weight: 7.9990 chunk 30 optimal weight: 1.9990 chunk 41 optimal weight: 3.9990 chunk 146 optimal weight: 0.5980 chunk 73 optimal weight: 1.9990 chunk 11 optimal weight: 0.9990 chunk 88 optimal weight: 0.4980 chunk 55 optimal weight: 2.9990 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 288 HIS A 409 HIS A1049 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4496 r_free = 0.4496 target = 0.164790 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4123 r_free = 0.4123 target = 0.133187 restraints weight = 64828.408| |-----------------------------------------------------------------------------| r_work (start): 0.4076 rms_B_bonded: 2.96 r_work: 0.3958 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work (final): 0.3958 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3967 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3967 r_free = 0.3967 target_work(ls_wunit_k1) = 0.124 | | occupancies: max = 1.00 min = 0.32 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3967 r_free = 0.3967 target_work(ls_wunit_k1) = 0.124 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3967 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7189 moved from start: 0.6171 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 13477 Z= 0.138 Angle : 0.539 9.084 18318 Z= 0.270 Chirality : 0.034 0.168 2153 Planarity : 0.005 0.088 2336 Dihedral : 3.243 14.746 1826 Min Nonbonded Distance : 2.306 Molprobity Statistics. All-atom Clashscore : 7.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 2.79 % Allowed : 15.52 % Favored : 81.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.47 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.98 (0.21), residues: 1662 helix: 1.38 (0.15), residues: 1161 sheet: -0.14 (1.34), residues: 19 loop : -1.08 (0.29), residues: 482 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A1081 TYR 0.011 0.001 TYR A 247 PHE 0.021 0.002 PHE A1627 TRP 0.013 0.001 TRP A1203 HIS 0.004 0.001 HIS A 704 Details of bonding type rmsd covalent geometry : bond 0.00308 (13477) covalent geometry : angle 0.53907 (18318) hydrogen bonds : bond 0.03587 ( 839) hydrogen bonds : angle 3.88144 ( 2475) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3324 Ramachandran restraints generated. 1662 Oldfield, 0 Emsley, 1662 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3324 Ramachandran restraints generated. 1662 Oldfield, 0 Emsley, 1662 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 531 is missing expected H atoms. Skipping. Evaluate side-chains 216 residues out of total 1398 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 177 time to evaluate : 0.698 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 7 ARG cc_start: 0.8040 (mmm-85) cc_final: 0.7728 (mmm160) REVERT: A 69 LYS cc_start: 0.7928 (mtmt) cc_final: 0.7628 (mtmm) REVERT: A 72 LYS cc_start: 0.8707 (tptt) cc_final: 0.8479 (tppp) REVERT: A 80 SER cc_start: 0.8476 (t) cc_final: 0.7921 (p) REVERT: A 267 GLU cc_start: 0.7368 (pm20) cc_final: 0.6886 (tp30) REVERT: A 269 PHE cc_start: 0.7898 (m-80) cc_final: 0.7677 (m-80) REVERT: A 308 GLU cc_start: 0.8547 (mp0) cc_final: 0.8220 (pp20) REVERT: A 312 GLU cc_start: 0.7259 (tt0) cc_final: 0.6939 (tm-30) REVERT: A 315 GLU cc_start: 0.7755 (pp20) cc_final: 0.7539 (pp20) REVERT: A 495 GLN cc_start: 0.8469 (tt0) cc_final: 0.8069 (tp-100) REVERT: A 522 LEU cc_start: 0.7797 (OUTLIER) cc_final: 0.7135 (mm) REVERT: A 539 ASP cc_start: 0.7668 (m-30) cc_final: 0.7365 (t0) REVERT: A 542 VAL cc_start: 0.7545 (OUTLIER) cc_final: 0.7293 (t) REVERT: A 595 GLU cc_start: 0.7649 (mm-30) cc_final: 0.7311 (mt-10) REVERT: A 597 ASN cc_start: 0.8673 (m-40) cc_final: 0.8414 (m110) REVERT: A 689 ARG cc_start: 0.7472 (ttm170) cc_final: 0.7128 (mtp-110) REVERT: A 1234 MET cc_start: 0.7307 (OUTLIER) cc_final: 0.6943 (tpt) REVERT: A 1314 VAL cc_start: 0.8043 (OUTLIER) cc_final: 0.7830 (t) outliers start: 39 outliers final: 13 residues processed: 202 average time/residue: 1.1303 time to fit residues: 253.3574 Evaluate side-chains 175 residues out of total 1398 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 158 time to evaluate : 0.712 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 187 SER Chi-restraints excluded: chain A residue 319 SER Chi-restraints excluded: chain A residue 355 ARG Chi-restraints excluded: chain A residue 522 LEU Chi-restraints excluded: chain A residue 542 VAL Chi-restraints excluded: chain A residue 546 LEU Chi-restraints excluded: chain A residue 566 SER Chi-restraints excluded: chain A residue 948 MET Chi-restraints excluded: chain A residue 1030 LEU Chi-restraints excluded: chain A residue 1035 PHE Chi-restraints excluded: chain A residue 1088 GLU Chi-restraints excluded: chain A residue 1234 MET Chi-restraints excluded: chain A residue 1314 VAL Chi-restraints excluded: chain A residue 1416 GLN Chi-restraints excluded: chain A residue 1552 THR Chi-restraints excluded: chain A residue 1588 PHE Chi-restraints excluded: chain B residue 248 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 169 random chunks: chunk 150 optimal weight: 9.9990 chunk 147 optimal weight: 0.0570 chunk 131 optimal weight: 0.7980 chunk 47 optimal weight: 2.9990 chunk 139 optimal weight: 4.9990 chunk 27 optimal weight: 1.9990 chunk 112 optimal weight: 2.9990 chunk 144 optimal weight: 3.9990 chunk 16 optimal weight: 0.9980 chunk 71 optimal weight: 2.9990 chunk 128 optimal weight: 2.9990 overall best weight: 1.3702 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 106 ASN A 383 HIS A1378 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4369 r_free = 0.4369 target = 0.154700 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3951 r_free = 0.3951 target = 0.121974 restraints weight = 65015.081| |-----------------------------------------------------------------------------| r_work (start): 0.3907 rms_B_bonded: 2.86 r_work: 0.3787 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work (final): 0.3787 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3797 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3797 r_free = 0.3797 target_work(ls_wunit_k1) = 0.113 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3797 r_free = 0.3797 target_work(ls_wunit_k1) = 0.113 | | occupancies: max = 1.00 min = 0.27 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3797 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7379 moved from start: 0.7540 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 13477 Z= 0.225 Angle : 0.628 9.854 18318 Z= 0.324 Chirality : 0.037 0.213 2153 Planarity : 0.005 0.049 2336 Dihedral : 3.754 21.575 1826 Min Nonbonded Distance : 2.239 Molprobity Statistics. All-atom Clashscore : 9.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.37 % Favored : 96.63 % Rotamer: Outliers : 3.29 % Allowed : 15.52 % Favored : 81.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.47 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.81 (0.21), residues: 1662 helix: 1.22 (0.15), residues: 1170 sheet: -0.53 (1.16), residues: 19 loop : -1.08 (0.29), residues: 473 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 20 TYR 0.022 0.002 TYR A1223 PHE 0.021 0.002 PHE A1208 TRP 0.022 0.002 TRP A1203 HIS 0.009 0.002 HIS A 288 Details of bonding type rmsd covalent geometry : bond 0.00510 (13477) covalent geometry : angle 0.62844 (18318) hydrogen bonds : bond 0.04276 ( 839) hydrogen bonds : angle 4.21647 ( 2475) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3324 Ramachandran restraints generated. 1662 Oldfield, 0 Emsley, 1662 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3324 Ramachandran restraints generated. 1662 Oldfield, 0 Emsley, 1662 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 531 is missing expected H atoms. Skipping. Evaluate side-chains 211 residues out of total 1398 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 165 time to evaluate : 0.585 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 7 ARG cc_start: 0.8108 (mmm-85) cc_final: 0.7789 (mmm160) REVERT: A 72 LYS cc_start: 0.8597 (tptt) cc_final: 0.8254 (tppt) REVERT: A 174 GLU cc_start: 0.7643 (tp30) cc_final: 0.7256 (tp30) REVERT: A 267 GLU cc_start: 0.7843 (pm20) cc_final: 0.7597 (tp30) REVERT: A 315 GLU cc_start: 0.7852 (pp20) cc_final: 0.7622 (pp20) REVERT: A 370 GLU cc_start: 0.7460 (pm20) cc_final: 0.7175 (pm20) REVERT: A 387 THR cc_start: 0.7806 (m) cc_final: 0.7502 (p) REVERT: A 405 SER cc_start: 0.8408 (OUTLIER) cc_final: 0.8082 (p) REVERT: A 485 MET cc_start: 0.7385 (mmp) cc_final: 0.7178 (mmt) REVERT: A 495 GLN cc_start: 0.8524 (tt0) cc_final: 0.8109 (tp-100) REVERT: A 522 LEU cc_start: 0.7900 (OUTLIER) cc_final: 0.7390 (mm) REVERT: A 542 VAL cc_start: 0.7798 (OUTLIER) cc_final: 0.7577 (t) REVERT: A 566 SER cc_start: 0.7888 (OUTLIER) cc_final: 0.7580 (p) REVERT: A 595 GLU cc_start: 0.7886 (mm-30) cc_final: 0.7494 (mt-10) REVERT: A 597 ASN cc_start: 0.8845 (m-40) cc_final: 0.8579 (m-40) REVERT: A 1234 MET cc_start: 0.7558 (OUTLIER) cc_final: 0.7171 (tpt) REVERT: A 1382 TYR cc_start: 0.7519 (m-10) cc_final: 0.7300 (m-10) REVERT: A 1409 GLU cc_start: 0.6411 (OUTLIER) cc_final: 0.5802 (mp0) REVERT: B 268 LEU cc_start: 0.7642 (mt) cc_final: 0.7298 (mt) REVERT: B 269 GLU cc_start: 0.7427 (mp0) cc_final: 0.6911 (pp20) outliers start: 46 outliers final: 18 residues processed: 199 average time/residue: 1.0911 time to fit residues: 241.9619 Evaluate side-chains 170 residues out of total 1398 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 146 time to evaluate : 0.722 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 187 SER Chi-restraints excluded: chain A residue 206 SER Chi-restraints excluded: chain A residue 254 CYS Chi-restraints excluded: chain A residue 319 SER Chi-restraints excluded: chain A residue 374 LEU Chi-restraints excluded: chain A residue 382 ILE Chi-restraints excluded: chain A residue 405 SER Chi-restraints excluded: chain A residue 474 ASP Chi-restraints excluded: chain A residue 522 LEU Chi-restraints excluded: chain A residue 535 ILE Chi-restraints excluded: chain A residue 542 VAL Chi-restraints excluded: chain A residue 566 SER Chi-restraints excluded: chain A residue 700 LEU Chi-restraints excluded: chain A residue 794 LYS Chi-restraints excluded: chain A residue 948 MET Chi-restraints excluded: chain A residue 1030 LEU Chi-restraints excluded: chain A residue 1047 LEU Chi-restraints excluded: chain A residue 1088 GLU Chi-restraints excluded: chain A residue 1234 MET Chi-restraints excluded: chain A residue 1320 THR Chi-restraints excluded: chain A residue 1409 GLU Chi-restraints excluded: chain A residue 1554 ILE Chi-restraints excluded: chain A residue 1588 PHE Chi-restraints excluded: chain B residue 248 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 169 random chunks: chunk 67 optimal weight: 0.9980 chunk 104 optimal weight: 1.9990 chunk 135 optimal weight: 0.3980 chunk 19 optimal weight: 0.8980 chunk 52 optimal weight: 0.3980 chunk 51 optimal weight: 1.9990 chunk 10 optimal weight: 0.9980 chunk 108 optimal weight: 0.9990 chunk 109 optimal weight: 0.5980 chunk 24 optimal weight: 0.9990 chunk 150 optimal weight: 9.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 106 ASN A 259 GLN A 412 HIS A1416 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4382 r_free = 0.4382 target = 0.156038 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3973 r_free = 0.3973 target = 0.123469 restraints weight = 65020.163| |-----------------------------------------------------------------------------| r_work (start): 0.3930 rms_B_bonded: 2.86 r_work: 0.3811 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work (final): 0.3811 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3820 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3820 r_free = 0.3820 target_work(ls_wunit_k1) = 0.114 | | occupancies: max = 1.00 min = 0.27 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3820 r_free = 0.3820 target_work(ls_wunit_k1) = 0.114 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3820 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7343 moved from start: 0.7631 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 13477 Z= 0.133 Angle : 0.542 6.703 18318 Z= 0.274 Chirality : 0.034 0.161 2153 Planarity : 0.004 0.058 2336 Dihedral : 3.512 20.791 1826 Min Nonbonded Distance : 2.285 Molprobity Statistics. All-atom Clashscore : 8.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 2.72 % Allowed : 16.31 % Favored : 80.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.47 % 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: 1.15 (0.21), residues: 1662 helix: 1.51 (0.15), residues: 1180 sheet: -0.46 (1.14), residues: 19 loop : -1.13 (0.29), residues: 463 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 689 TYR 0.011 0.001 TYR A 247 PHE 0.030 0.002 PHE A1208 TRP 0.014 0.001 TRP A1203 HIS 0.009 0.001 HIS A1262 Details of bonding type rmsd covalent geometry : bond 0.00296 (13477) covalent geometry : angle 0.54188 (18318) hydrogen bonds : bond 0.03667 ( 839) hydrogen bonds : angle 3.97491 ( 2475) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3324 Ramachandran restraints generated. 1662 Oldfield, 0 Emsley, 1662 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3324 Ramachandran restraints generated. 1662 Oldfield, 0 Emsley, 1662 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 531 is missing expected H atoms. Skipping. Evaluate side-chains 195 residues out of total 1398 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 157 time to evaluate : 0.742 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 7 ARG cc_start: 0.8079 (mmm-85) cc_final: 0.7755 (mmm160) REVERT: A 80 SER cc_start: 0.8583 (OUTLIER) cc_final: 0.8086 (p) REVERT: A 174 GLU cc_start: 0.7658 (tp30) cc_final: 0.7305 (tp30) REVERT: A 248 MET cc_start: 0.8089 (mtt) cc_final: 0.7858 (mtt) REVERT: A 387 THR cc_start: 0.7748 (m) cc_final: 0.7454 (p) REVERT: A 405 SER cc_start: 0.8453 (m) cc_final: 0.8144 (p) REVERT: A 485 MET cc_start: 0.7341 (mmp) cc_final: 0.7118 (mmt) REVERT: A 495 GLN cc_start: 0.8467 (tt0) cc_final: 0.8103 (tp-100) REVERT: A 522 LEU cc_start: 0.7896 (OUTLIER) cc_final: 0.7290 (mm) REVERT: A 542 VAL cc_start: 0.7748 (OUTLIER) cc_final: 0.7495 (t) REVERT: A 566 SER cc_start: 0.7851 (OUTLIER) cc_final: 0.7569 (p) REVERT: A 595 GLU cc_start: 0.7739 (mm-30) cc_final: 0.7348 (mt-10) REVERT: A 597 ASN cc_start: 0.8838 (m-40) cc_final: 0.8557 (m-40) REVERT: A 1175 MET cc_start: 0.7209 (mpt) cc_final: 0.6460 (mpt) REVERT: A 1382 TYR cc_start: 0.7615 (m-10) cc_final: 0.7343 (m-10) REVERT: A 1409 GLU cc_start: 0.6236 (OUTLIER) cc_final: 0.5645 (mp0) REVERT: B 247 ASP cc_start: 0.7217 (p0) cc_final: 0.5945 (t0) outliers start: 38 outliers final: 18 residues processed: 186 average time/residue: 1.0350 time to fit residues: 215.2592 Evaluate side-chains 165 residues out of total 1398 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 142 time to evaluate : 0.688 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 SER Chi-restraints excluded: chain A residue 201 THR Chi-restraints excluded: chain A residue 206 SER Chi-restraints excluded: chain A residue 252 GLU Chi-restraints excluded: chain A residue 319 SER Chi-restraints excluded: chain A residue 358 GLN Chi-restraints excluded: chain A residue 374 LEU Chi-restraints excluded: chain A residue 522 LEU Chi-restraints excluded: chain A residue 535 ILE Chi-restraints excluded: chain A residue 542 VAL Chi-restraints excluded: chain A residue 566 SER Chi-restraints excluded: chain A residue 660 VAL Chi-restraints excluded: chain A residue 948 MET Chi-restraints excluded: chain A residue 1030 LEU Chi-restraints excluded: chain A residue 1035 PHE Chi-restraints excluded: chain A residue 1047 LEU Chi-restraints excluded: chain A residue 1088 GLU Chi-restraints excluded: chain A residue 1320 THR Chi-restraints excluded: chain A residue 1409 GLU Chi-restraints excluded: chain A residue 1412 LEU Chi-restraints excluded: chain A residue 1552 THR Chi-restraints excluded: chain A residue 1588 PHE Chi-restraints excluded: chain B residue 248 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 169 random chunks: chunk 133 optimal weight: 0.6980 chunk 149 optimal weight: 9.9990 chunk 112 optimal weight: 1.9990 chunk 166 optimal weight: 4.9990 chunk 147 optimal weight: 10.0000 chunk 152 optimal weight: 0.9980 chunk 38 optimal weight: 1.9990 chunk 139 optimal weight: 4.9990 chunk 82 optimal weight: 0.9980 chunk 109 optimal weight: 0.0970 chunk 69 optimal weight: 2.9990 overall best weight: 0.9580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 106 ASN A 259 GLN ** A1049 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1416 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4347 r_free = 0.4347 target = 0.153617 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3945 r_free = 0.3945 target = 0.121525 restraints weight = 65331.392| |-----------------------------------------------------------------------------| r_work (start): 0.3884 rms_B_bonded: 2.79 r_work: 0.3767 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work (final): 0.3767 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3770 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3770 r_free = 0.3770 target_work(ls_wunit_k1) = 0.112 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3770 r_free = 0.3770 target_work(ls_wunit_k1) = 0.112 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3770 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7338 moved from start: 0.7960 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 13477 Z= 0.162 Angle : 0.552 6.531 18318 Z= 0.282 Chirality : 0.035 0.174 2153 Planarity : 0.004 0.058 2336 Dihedral : 3.557 21.123 1826 Min Nonbonded Distance : 2.255 Molprobity Statistics. All-atom Clashscore : 8.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.19 % Favored : 96.81 % Rotamer: Outliers : 3.22 % Allowed : 15.88 % Favored : 80.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.47 % 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: 1.12 (0.21), residues: 1662 helix: 1.51 (0.15), residues: 1182 sheet: -0.63 (1.13), residues: 19 loop : -1.19 (0.29), residues: 461 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 689 TYR 0.015 0.001 TYR A 247 PHE 0.038 0.002 PHE A1208 TRP 0.015 0.001 TRP A1203 HIS 0.009 0.001 HIS A1262 Details of bonding type rmsd covalent geometry : bond 0.00363 (13477) covalent geometry : angle 0.55207 (18318) hydrogen bonds : bond 0.03794 ( 839) hydrogen bonds : angle 4.01247 ( 2475) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3324 Ramachandran restraints generated. 1662 Oldfield, 0 Emsley, 1662 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3324 Ramachandran restraints generated. 1662 Oldfield, 0 Emsley, 1662 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 531 is missing expected H atoms. Skipping. Evaluate side-chains 206 residues out of total 1398 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 161 time to evaluate : 0.707 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 7 ARG cc_start: 0.8102 (mmm-85) cc_final: 0.7760 (mmm160) REVERT: A 80 SER cc_start: 0.8603 (OUTLIER) cc_final: 0.8099 (p) REVERT: A 174 GLU cc_start: 0.7709 (tp30) cc_final: 0.7408 (tp30) REVERT: A 248 MET cc_start: 0.8231 (mtt) cc_final: 0.7966 (mtt) REVERT: A 387 THR cc_start: 0.7724 (m) cc_final: 0.7421 (p) REVERT: A 405 SER cc_start: 0.8468 (OUTLIER) cc_final: 0.8163 (p) REVERT: A 485 MET cc_start: 0.7438 (mmp) cc_final: 0.7083 (mmt) REVERT: A 495 GLN cc_start: 0.8480 (tt0) cc_final: 0.8088 (tp-100) REVERT: A 522 LEU cc_start: 0.7856 (OUTLIER) cc_final: 0.7334 (mm) REVERT: A 566 SER cc_start: 0.7871 (OUTLIER) cc_final: 0.7586 (p) REVERT: A 595 GLU cc_start: 0.7720 (mm-30) cc_final: 0.7331 (mt-10) REVERT: A 597 ASN cc_start: 0.8853 (m-40) cc_final: 0.8598 (m-40) REVERT: A 701 GLU cc_start: 0.8076 (pp20) cc_final: 0.7789 (pp20) REVERT: A 1409 GLU cc_start: 0.6198 (OUTLIER) cc_final: 0.5685 (mp0) REVERT: B 247 ASP cc_start: 0.7180 (p0) cc_final: 0.5922 (t0) REVERT: B 268 LEU cc_start: 0.7694 (mt) cc_final: 0.7359 (mt) REVERT: B 269 GLU cc_start: 0.7510 (mp0) cc_final: 0.6919 (tm-30) outliers start: 45 outliers final: 17 residues processed: 193 average time/residue: 1.0451 time to fit residues: 225.0847 Evaluate side-chains 170 residues out of total 1398 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 148 time to evaluate : 0.662 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 SER Chi-restraints excluded: chain A residue 187 SER Chi-restraints excluded: chain A residue 201 THR Chi-restraints excluded: chain A residue 206 SER Chi-restraints excluded: chain A residue 319 SER Chi-restraints excluded: chain A residue 374 LEU Chi-restraints excluded: chain A residue 405 SER Chi-restraints excluded: chain A residue 474 ASP Chi-restraints excluded: chain A residue 522 LEU Chi-restraints excluded: chain A residue 566 SER Chi-restraints excluded: chain A residue 660 VAL Chi-restraints excluded: chain A residue 700 LEU Chi-restraints excluded: chain A residue 948 MET Chi-restraints excluded: chain A residue 1030 LEU Chi-restraints excluded: chain A residue 1088 GLU Chi-restraints excluded: chain A residue 1139 MET Chi-restraints excluded: chain A residue 1320 THR Chi-restraints excluded: chain A residue 1384 LEU Chi-restraints excluded: chain A residue 1409 GLU Chi-restraints excluded: chain A residue 1552 THR Chi-restraints excluded: chain A residue 1588 PHE Chi-restraints excluded: chain B residue 248 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 169 random chunks: chunk 76 optimal weight: 0.4980 chunk 16 optimal weight: 0.9990 chunk 100 optimal weight: 1.9990 chunk 153 optimal weight: 1.9990 chunk 80 optimal weight: 2.9990 chunk 56 optimal weight: 1.9990 chunk 161 optimal weight: 5.9990 chunk 6 optimal weight: 0.3980 chunk 154 optimal weight: 1.9990 chunk 155 optimal weight: 9.9990 chunk 92 optimal weight: 1.9990 overall best weight: 1.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 106 ASN A 259 GLN A 482 GLN ** A1049 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1416 GLN A1690 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4332 r_free = 0.4332 target = 0.152130 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3913 r_free = 0.3913 target = 0.119661 restraints weight = 65427.790| |-----------------------------------------------------------------------------| r_work (start): 0.3872 rms_B_bonded: 2.80 r_work: 0.3754 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work (final): 0.3754 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3763 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3763 r_free = 0.3763 target_work(ls_wunit_k1) = 0.111 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3763 r_free = 0.3763 target_work(ls_wunit_k1) = 0.111 | | occupancies: max = 1.00 min = 0.24 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3763 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7396 moved from start: 0.8291 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 13477 Z= 0.182 Angle : 0.584 12.802 18318 Z= 0.296 Chirality : 0.035 0.176 2153 Planarity : 0.004 0.059 2336 Dihedral : 3.677 22.453 1826 Min Nonbonded Distance : 2.236 Molprobity Statistics. All-atom Clashscore : 8.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.13 % Favored : 96.87 % Rotamer: Outliers : 2.65 % Allowed : 17.24 % Favored : 80.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.47 % 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: 1.02 (0.21), residues: 1662 helix: 1.42 (0.15), residues: 1183 sheet: -0.66 (1.15), residues: 19 loop : -1.17 (0.29), residues: 460 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 20 TYR 0.025 0.002 TYR A 415 PHE 0.034 0.002 PHE A1208 TRP 0.015 0.001 TRP A1680 HIS 0.015 0.001 HIS A1262 Details of bonding type rmsd covalent geometry : bond 0.00407 (13477) covalent geometry : angle 0.58394 (18318) hydrogen bonds : bond 0.03959 ( 839) hydrogen bonds : angle 4.08589 ( 2475) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3324 Ramachandran restraints generated. 1662 Oldfield, 0 Emsley, 1662 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3324 Ramachandran restraints generated. 1662 Oldfield, 0 Emsley, 1662 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 531 is missing expected H atoms. Skipping. Evaluate side-chains 194 residues out of total 1398 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 157 time to evaluate : 0.680 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 7 ARG cc_start: 0.8086 (mmm-85) cc_final: 0.7742 (mmm160) REVERT: A 20 ARG cc_start: 0.8065 (ttm110) cc_final: 0.7862 (ttm110) REVERT: A 80 SER cc_start: 0.8651 (OUTLIER) cc_final: 0.8174 (p) REVERT: A 174 GLU cc_start: 0.7714 (tp30) cc_final: 0.7446 (tp30) REVERT: A 248 MET cc_start: 0.8297 (mtt) cc_final: 0.7992 (mtt) REVERT: A 252 GLU cc_start: 0.7135 (OUTLIER) cc_final: 0.6920 (mp0) REVERT: A 387 THR cc_start: 0.7815 (m) cc_final: 0.7486 (p) REVERT: A 405 SER cc_start: 0.8472 (OUTLIER) cc_final: 0.8102 (p) REVERT: A 495 GLN cc_start: 0.8467 (tt0) cc_final: 0.8093 (tp-100) REVERT: A 566 SER cc_start: 0.7908 (OUTLIER) cc_final: 0.7639 (p) REVERT: A 595 GLU cc_start: 0.7841 (mm-30) cc_final: 0.7476 (mt-10) REVERT: A 597 ASN cc_start: 0.8875 (m-40) cc_final: 0.8624 (m-40) REVERT: A 701 GLU cc_start: 0.8072 (pp20) cc_final: 0.7755 (pp20) REVERT: A 731 ASP cc_start: 0.7628 (t0) cc_final: 0.7365 (m-30) REVERT: A 1409 GLU cc_start: 0.6103 (OUTLIER) cc_final: 0.5632 (mp0) REVERT: A 1710 PHE cc_start: 0.2228 (m-80) cc_final: 0.1730 (m-10) REVERT: B 247 ASP cc_start: 0.7305 (p0) cc_final: 0.6078 (t0) REVERT: B 268 LEU cc_start: 0.7797 (mt) cc_final: 0.7420 (mt) REVERT: B 269 GLU cc_start: 0.7477 (mp0) cc_final: 0.6838 (tm-30) outliers start: 37 outliers final: 22 residues processed: 184 average time/residue: 1.0684 time to fit residues: 218.9861 Evaluate side-chains 173 residues out of total 1398 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 146 time to evaluate : 0.656 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 LEU Chi-restraints excluded: chain A residue 80 SER Chi-restraints excluded: chain A residue 187 SER Chi-restraints excluded: chain A residue 201 THR Chi-restraints excluded: chain A residue 206 SER Chi-restraints excluded: chain A residue 252 GLU Chi-restraints excluded: chain A residue 319 SER Chi-restraints excluded: chain A residue 405 SER Chi-restraints excluded: chain A residue 474 ASP Chi-restraints excluded: chain A residue 522 LEU Chi-restraints excluded: chain A residue 566 SER Chi-restraints excluded: chain A residue 660 VAL Chi-restraints excluded: chain A residue 700 LEU Chi-restraints excluded: chain A residue 714 LEU Chi-restraints excluded: chain A residue 794 LYS Chi-restraints excluded: chain A residue 796 LEU Chi-restraints excluded: chain A residue 948 MET Chi-restraints excluded: chain A residue 1030 LEU Chi-restraints excluded: chain A residue 1047 LEU Chi-restraints excluded: chain A residue 1139 MET Chi-restraints excluded: chain A residue 1320 THR Chi-restraints excluded: chain A residue 1384 LEU Chi-restraints excluded: chain A residue 1409 GLU Chi-restraints excluded: chain A residue 1552 THR Chi-restraints excluded: chain A residue 1554 ILE Chi-restraints excluded: chain A residue 1588 PHE Chi-restraints excluded: chain B residue 248 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 169 random chunks: chunk 19 optimal weight: 0.9990 chunk 8 optimal weight: 2.9990 chunk 143 optimal weight: 4.9990 chunk 1 optimal weight: 0.9980 chunk 89 optimal weight: 1.9990 chunk 136 optimal weight: 0.6980 chunk 155 optimal weight: 8.9990 chunk 137 optimal weight: 0.8980 chunk 46 optimal weight: 0.9980 chunk 73 optimal weight: 1.9990 chunk 108 optimal weight: 0.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 106 ASN A 259 GLN A 482 GLN A1690 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4333 r_free = 0.4333 target = 0.152240 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3913 r_free = 0.3913 target = 0.119833 restraints weight = 65259.189| |-----------------------------------------------------------------------------| r_work (start): 0.3873 rms_B_bonded: 2.79 r_work: 0.3755 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work (final): 0.3755 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3767 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3767 r_free = 0.3767 target_work(ls_wunit_k1) = 0.111 | | occupancies: max = 1.00 min = 0.24 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3767 r_free = 0.3767 target_work(ls_wunit_k1) = 0.111 | | occupancies: max = 1.00 min = 0.26 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3767 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7385 moved from start: 0.8465 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 13477 Z= 0.155 Angle : 0.561 7.785 18318 Z= 0.283 Chirality : 0.035 0.173 2153 Planarity : 0.004 0.062 2336 Dihedral : 3.626 22.244 1826 Min Nonbonded Distance : 2.270 Molprobity Statistics. All-atom Clashscore : 8.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer: Outliers : 2.93 % Allowed : 17.10 % Favored : 79.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.47 % 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: 1.16 (0.21), residues: 1662 helix: 1.53 (0.15), residues: 1183 sheet: -0.66 (1.12), residues: 19 loop : -1.15 (0.29), residues: 460 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 20 TYR 0.019 0.002 TYR A 415 PHE 0.025 0.002 PHE A1208 TRP 0.019 0.001 TRP A1680 HIS 0.012 0.001 HIS A1262 Details of bonding type rmsd covalent geometry : bond 0.00347 (13477) covalent geometry : angle 0.56129 (18318) hydrogen bonds : bond 0.03803 ( 839) hydrogen bonds : angle 4.04537 ( 2475) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3324 Ramachandran restraints generated. 1662 Oldfield, 0 Emsley, 1662 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3324 Ramachandran restraints generated. 1662 Oldfield, 0 Emsley, 1662 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 531 is missing expected H atoms. Skipping. Evaluate side-chains 196 residues out of total 1398 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 155 time to evaluate : 0.642 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 7 ARG cc_start: 0.8080 (mmm-85) cc_final: 0.7732 (mmm160) REVERT: A 20 ARG cc_start: 0.8093 (ttm110) cc_final: 0.7882 (ttm110) REVERT: A 80 SER cc_start: 0.8663 (OUTLIER) cc_final: 0.8198 (p) REVERT: A 174 GLU cc_start: 0.7737 (tp30) cc_final: 0.7489 (tp30) REVERT: A 248 MET cc_start: 0.8268 (mtt) cc_final: 0.7952 (mtt) REVERT: A 252 GLU cc_start: 0.7086 (OUTLIER) cc_final: 0.6844 (mp0) REVERT: A 387 THR cc_start: 0.7787 (m) cc_final: 0.7452 (p) REVERT: A 405 SER cc_start: 0.8473 (OUTLIER) cc_final: 0.8104 (p) REVERT: A 495 GLN cc_start: 0.8491 (tt0) cc_final: 0.8090 (tp-100) REVERT: A 566 SER cc_start: 0.7859 (OUTLIER) cc_final: 0.7624 (p) REVERT: A 595 GLU cc_start: 0.7736 (mm-30) cc_final: 0.7385 (mt-10) REVERT: A 597 ASN cc_start: 0.8865 (m-40) cc_final: 0.8614 (m-40) REVERT: A 689 ARG cc_start: 0.7501 (mtp-110) cc_final: 0.7267 (mtp-110) REVERT: A 701 GLU cc_start: 0.8076 (pp20) cc_final: 0.7729 (pp20) REVERT: A 731 ASP cc_start: 0.7602 (t0) cc_final: 0.7358 (m-30) REVERT: A 1211 ARG cc_start: 0.5117 (tpt-90) cc_final: 0.4333 (mmm-85) REVERT: A 1409 GLU cc_start: 0.6039 (OUTLIER) cc_final: 0.5568 (mp0) REVERT: A 1627 PHE cc_start: 0.6518 (OUTLIER) cc_final: 0.6270 (m-80) REVERT: A 1710 PHE cc_start: 0.2256 (m-80) cc_final: 0.1765 (m-10) REVERT: B 247 ASP cc_start: 0.7578 (p0) cc_final: 0.6314 (t0) REVERT: B 269 GLU cc_start: 0.7487 (mp0) cc_final: 0.7149 (pp20) outliers start: 41 outliers final: 20 residues processed: 185 average time/residue: 1.0604 time to fit residues: 219.0057 Evaluate side-chains 169 residues out of total 1398 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 143 time to evaluate : 0.416 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 SER Chi-restraints excluded: chain A residue 187 SER Chi-restraints excluded: chain A residue 201 THR Chi-restraints excluded: chain A residue 206 SER Chi-restraints excluded: chain A residue 252 GLU Chi-restraints excluded: chain A residue 319 SER Chi-restraints excluded: chain A residue 374 LEU Chi-restraints excluded: chain A residue 405 SER Chi-restraints excluded: chain A residue 522 LEU Chi-restraints excluded: chain A residue 566 SER Chi-restraints excluded: chain A residue 660 VAL Chi-restraints excluded: chain A residue 714 LEU Chi-restraints excluded: chain A residue 794 LYS Chi-restraints excluded: chain A residue 796 LEU Chi-restraints excluded: chain A residue 948 MET Chi-restraints excluded: chain A residue 1030 LEU Chi-restraints excluded: chain A residue 1047 LEU Chi-restraints excluded: chain A residue 1139 MET Chi-restraints excluded: chain A residue 1320 THR Chi-restraints excluded: chain A residue 1409 GLU Chi-restraints excluded: chain A residue 1438 THR Chi-restraints excluded: chain A residue 1552 THR Chi-restraints excluded: chain A residue 1554 ILE Chi-restraints excluded: chain A residue 1588 PHE Chi-restraints excluded: chain A residue 1627 PHE Chi-restraints excluded: chain B residue 248 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 169 random chunks: chunk 68 optimal weight: 0.9990 chunk 46 optimal weight: 1.9990 chunk 52 optimal weight: 0.8980 chunk 142 optimal weight: 3.9990 chunk 134 optimal weight: 1.9990 chunk 45 optimal weight: 0.9980 chunk 148 optimal weight: 7.9990 chunk 27 optimal weight: 0.5980 chunk 47 optimal weight: 0.1980 chunk 80 optimal weight: 3.9990 chunk 73 optimal weight: 1.9990 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 106 ASN A 259 GLN A 482 GLN A1416 GLN A1690 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4331 r_free = 0.4331 target = 0.152203 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3924 r_free = 0.3924 target = 0.120397 restraints weight = 65204.527| |-----------------------------------------------------------------------------| r_work (start): 0.3880 rms_B_bonded: 2.74 r_work: 0.3761 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work (final): 0.3761 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3771 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3771 r_free = 0.3771 target_work(ls_wunit_k1) = 0.112 | | occupancies: max = 1.00 min = 0.26 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3771 r_free = 0.3771 target_work(ls_wunit_k1) = 0.112 | | occupancies: max = 1.00 min = 0.28 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3771 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7371 moved from start: 0.8581 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 13477 Z= 0.139 Angle : 0.559 8.190 18318 Z= 0.281 Chirality : 0.034 0.146 2153 Planarity : 0.004 0.063 2336 Dihedral : 3.613 21.730 1826 Min Nonbonded Distance : 2.280 Molprobity Statistics. All-atom Clashscore : 8.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.13 % Favored : 96.87 % Rotamer: Outliers : 2.07 % Allowed : 18.60 % Favored : 79.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.47 % 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: 1.23 (0.21), residues: 1662 helix: 1.59 (0.15), residues: 1182 sheet: -0.62 (1.13), residues: 19 loop : -1.14 (0.29), residues: 461 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 20 TYR 0.019 0.002 TYR A 537 PHE 0.027 0.002 PHE A 654 TRP 0.014 0.001 TRP A1680 HIS 0.013 0.001 HIS A1262 Details of bonding type rmsd covalent geometry : bond 0.00313 (13477) covalent geometry : angle 0.55938 (18318) hydrogen bonds : bond 0.03668 ( 839) hydrogen bonds : angle 3.98150 ( 2475) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3324 Ramachandran restraints generated. 1662 Oldfield, 0 Emsley, 1662 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3324 Ramachandran restraints generated. 1662 Oldfield, 0 Emsley, 1662 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 531 is missing expected H atoms. Skipping. Evaluate side-chains 182 residues out of total 1398 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 153 time to evaluate : 0.510 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 7 ARG cc_start: 0.8066 (mmm-85) cc_final: 0.7712 (mmm160) REVERT: A 20 ARG cc_start: 0.8101 (ttm110) cc_final: 0.7897 (ttm110) REVERT: A 80 SER cc_start: 0.8666 (OUTLIER) cc_final: 0.8209 (p) REVERT: A 174 GLU cc_start: 0.7759 (tp30) cc_final: 0.7527 (tp30) REVERT: A 248 MET cc_start: 0.8245 (mtt) cc_final: 0.7921 (mtt) REVERT: A 252 GLU cc_start: 0.7079 (OUTLIER) cc_final: 0.6835 (mp0) REVERT: A 387 THR cc_start: 0.7775 (m) cc_final: 0.7428 (p) REVERT: A 405 SER cc_start: 0.8457 (OUTLIER) cc_final: 0.8093 (p) REVERT: A 495 GLN cc_start: 0.8478 (tt0) cc_final: 0.8078 (tp-100) REVERT: A 566 SER cc_start: 0.7846 (OUTLIER) cc_final: 0.7627 (p) REVERT: A 595 GLU cc_start: 0.7726 (mm-30) cc_final: 0.7246 (mt-10) REVERT: A 597 ASN cc_start: 0.8869 (m-40) cc_final: 0.8614 (m-40) REVERT: A 689 ARG cc_start: 0.7529 (mtp-110) cc_final: 0.7263 (mtp-110) REVERT: A 690 PHE cc_start: 0.7107 (m-80) cc_final: 0.6847 (m-80) REVERT: A 701 GLU cc_start: 0.8084 (pp20) cc_final: 0.7724 (pp20) REVERT: A 731 ASP cc_start: 0.7585 (t0) cc_final: 0.7295 (m-30) REVERT: A 1211 ARG cc_start: 0.4940 (tpt-90) cc_final: 0.4711 (mmm-85) REVERT: A 1409 GLU cc_start: 0.6085 (OUTLIER) cc_final: 0.5662 (mp0) REVERT: A 1627 PHE cc_start: 0.6551 (OUTLIER) cc_final: 0.6333 (m-80) REVERT: A 1710 PHE cc_start: 0.2194 (m-80) cc_final: 0.1739 (m-10) REVERT: B 247 ASP cc_start: 0.7539 (p0) cc_final: 0.6284 (t0) REVERT: B 269 GLU cc_start: 0.7451 (mp0) cc_final: 0.6963 (tm-30) outliers start: 29 outliers final: 17 residues processed: 177 average time/residue: 1.0512 time to fit residues: 207.7074 Evaluate side-chains 165 residues out of total 1398 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 142 time to evaluate : 0.716 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 SER Chi-restraints excluded: chain A residue 187 SER Chi-restraints excluded: chain A residue 206 SER Chi-restraints excluded: chain A residue 252 GLU Chi-restraints excluded: chain A residue 319 SER Chi-restraints excluded: chain A residue 374 LEU Chi-restraints excluded: chain A residue 405 SER Chi-restraints excluded: chain A residue 474 ASP Chi-restraints excluded: chain A residue 566 SER Chi-restraints excluded: chain A residue 660 VAL Chi-restraints excluded: chain A residue 700 LEU Chi-restraints excluded: chain A residue 714 LEU Chi-restraints excluded: chain A residue 794 LYS Chi-restraints excluded: chain A residue 796 LEU Chi-restraints excluded: chain A residue 948 MET Chi-restraints excluded: chain A residue 1030 LEU Chi-restraints excluded: chain A residue 1139 MET Chi-restraints excluded: chain A residue 1320 THR Chi-restraints excluded: chain A residue 1409 GLU Chi-restraints excluded: chain A residue 1552 THR Chi-restraints excluded: chain A residue 1588 PHE Chi-restraints excluded: chain A residue 1627 PHE Chi-restraints excluded: chain B residue 248 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 169 random chunks: chunk 159 optimal weight: 6.9990 chunk 90 optimal weight: 0.9990 chunk 101 optimal weight: 0.9990 chunk 56 optimal weight: 1.9990 chunk 105 optimal weight: 0.8980 chunk 8 optimal weight: 1.9990 chunk 129 optimal weight: 0.9990 chunk 7 optimal weight: 0.9990 chunk 145 optimal weight: 4.9990 chunk 150 optimal weight: 0.7980 chunk 115 optimal weight: 0.9980 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 106 ASN A 259 GLN A 482 GLN A1690 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4318 r_free = 0.4318 target = 0.151005 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3905 r_free = 0.3905 target = 0.119100 restraints weight = 65108.783| |-----------------------------------------------------------------------------| r_work (start): 0.3861 rms_B_bonded: 2.73 r_work: 0.3744 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.3632 rms_B_bonded: 4.99 restraints_weight: 0.2500 r_work (final): 0.3632 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3637 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3637 r_free = 0.3637 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.28 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3637 r_free = 0.3637 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3637 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7472 moved from start: 0.8744 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 13477 Z= 0.159 Angle : 0.566 7.592 18318 Z= 0.286 Chirality : 0.035 0.143 2153 Planarity : 0.004 0.063 2336 Dihedral : 3.650 22.116 1826 Min Nonbonded Distance : 2.239 Molprobity Statistics. All-atom Clashscore : 9.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.37 % Favored : 96.63 % Rotamer: Outliers : 2.36 % Allowed : 18.67 % Favored : 78.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.47 % 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: 1.20 (0.21), residues: 1662 helix: 1.58 (0.15), residues: 1184 sheet: -0.57 (1.14), residues: 19 loop : -1.20 (0.29), residues: 459 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A1018 TYR 0.023 0.002 TYR A 537 PHE 0.019 0.002 PHE B 278 TRP 0.025 0.001 TRP A1680 HIS 0.014 0.001 HIS A1262 Details of bonding type rmsd covalent geometry : bond 0.00359 (13477) covalent geometry : angle 0.56564 (18318) hydrogen bonds : bond 0.03773 ( 839) hydrogen bonds : angle 4.00534 ( 2475) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3324 Ramachandran restraints generated. 1662 Oldfield, 0 Emsley, 1662 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3324 Ramachandran restraints generated. 1662 Oldfield, 0 Emsley, 1662 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 531 is missing expected H atoms. Skipping. Evaluate side-chains 181 residues out of total 1398 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 148 time to evaluate : 0.675 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 7 ARG cc_start: 0.8196 (mmm-85) cc_final: 0.7828 (mmm160) REVERT: A 20 ARG cc_start: 0.8256 (ttm110) cc_final: 0.8022 (ttm110) REVERT: A 80 SER cc_start: 0.8830 (OUTLIER) cc_final: 0.8346 (p) REVERT: A 174 GLU cc_start: 0.7936 (tp30) cc_final: 0.7631 (tp30) REVERT: A 248 MET cc_start: 0.8393 (mtt) cc_final: 0.8108 (mtt) REVERT: A 252 GLU cc_start: 0.7303 (OUTLIER) cc_final: 0.7056 (mp0) REVERT: A 387 THR cc_start: 0.7922 (m) cc_final: 0.7560 (p) REVERT: A 405 SER cc_start: 0.8520 (OUTLIER) cc_final: 0.8208 (p) REVERT: A 495 GLN cc_start: 0.8641 (tt0) cc_final: 0.8137 (tp-100) REVERT: A 499 GLU cc_start: 0.8410 (mt-10) cc_final: 0.8139 (mt-10) REVERT: A 566 SER cc_start: 0.7919 (OUTLIER) cc_final: 0.7700 (p) REVERT: A 595 GLU cc_start: 0.7906 (mm-30) cc_final: 0.7505 (mt-10) REVERT: A 597 ASN cc_start: 0.8985 (m-40) cc_final: 0.8741 (m-40) REVERT: A 689 ARG cc_start: 0.7624 (mtp-110) cc_final: 0.7329 (mtp-110) REVERT: A 701 GLU cc_start: 0.8262 (pp20) cc_final: 0.7903 (pp20) REVERT: A 731 ASP cc_start: 0.7763 (t0) cc_final: 0.7297 (m-30) REVERT: A 1211 ARG cc_start: 0.5237 (tpt-90) cc_final: 0.4663 (mmm-85) REVERT: A 1409 GLU cc_start: 0.6190 (OUTLIER) cc_final: 0.5783 (mp0) REVERT: A 1462 SER cc_start: 0.7583 (m) cc_final: 0.7138 (t) REVERT: A 1627 PHE cc_start: 0.6566 (OUTLIER) cc_final: 0.6250 (m-80) REVERT: A 1710 PHE cc_start: 0.2175 (m-80) cc_final: 0.1708 (m-10) REVERT: B 247 ASP cc_start: 0.7505 (p0) cc_final: 0.6220 (t0) REVERT: B 269 GLU cc_start: 0.7572 (mp0) cc_final: 0.6946 (tm-30) outliers start: 33 outliers final: 18 residues processed: 173 average time/residue: 1.1058 time to fit residues: 212.4391 Evaluate side-chains 165 residues out of total 1398 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 141 time to evaluate : 0.449 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 SER Chi-restraints excluded: chain A residue 187 SER Chi-restraints excluded: chain A residue 201 THR Chi-restraints excluded: chain A residue 206 SER Chi-restraints excluded: chain A residue 252 GLU Chi-restraints excluded: chain A residue 319 SER Chi-restraints excluded: chain A residue 374 LEU Chi-restraints excluded: chain A residue 405 SER Chi-restraints excluded: chain A residue 474 ASP Chi-restraints excluded: chain A residue 522 LEU Chi-restraints excluded: chain A residue 566 SER Chi-restraints excluded: chain A residue 700 LEU Chi-restraints excluded: chain A residue 714 LEU Chi-restraints excluded: chain A residue 794 LYS Chi-restraints excluded: chain A residue 796 LEU Chi-restraints excluded: chain A residue 1030 LEU Chi-restraints excluded: chain A residue 1139 MET Chi-restraints excluded: chain A residue 1320 THR Chi-restraints excluded: chain A residue 1409 GLU Chi-restraints excluded: chain A residue 1438 THR Chi-restraints excluded: chain A residue 1552 THR Chi-restraints excluded: chain A residue 1554 ILE Chi-restraints excluded: chain A residue 1627 PHE Chi-restraints excluded: chain B residue 248 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 169 random chunks: chunk 90 optimal weight: 0.9990 chunk 68 optimal weight: 0.9980 chunk 110 optimal weight: 0.9980 chunk 114 optimal weight: 1.9990 chunk 137 optimal weight: 1.9990 chunk 27 optimal weight: 1.9990 chunk 36 optimal weight: 1.9990 chunk 151 optimal weight: 4.9990 chunk 3 optimal weight: 1.9990 chunk 67 optimal weight: 0.6980 chunk 15 optimal weight: 0.5980 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 259 GLN A 482 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4321 r_free = 0.4321 target = 0.151192 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3902 r_free = 0.3902 target = 0.119061 restraints weight = 64713.198| |-----------------------------------------------------------------------------| r_work (start): 0.3860 rms_B_bonded: 2.74 r_work: 0.3745 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.3632 rms_B_bonded: 4.98 restraints_weight: 0.2500 r_work (final): 0.3632 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3639 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3639 r_free = 0.3639 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3639 r_free = 0.3639 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3639 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7471 moved from start: 0.8820 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 13477 Z= 0.149 Angle : 0.563 7.832 18318 Z= 0.284 Chirality : 0.035 0.149 2153 Planarity : 0.004 0.063 2336 Dihedral : 3.672 21.964 1826 Min Nonbonded Distance : 2.316 Molprobity Statistics. All-atom Clashscore : 9.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.37 % Favored : 96.63 % Rotamer: Outliers : 1.72 % Allowed : 19.67 % Favored : 78.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.47 % 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: 1.25 (0.21), residues: 1662 helix: 1.60 (0.15), residues: 1186 sheet: -0.59 (1.15), residues: 19 loop : -1.16 (0.29), residues: 457 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A1018 TYR 0.024 0.002 TYR A 537 PHE 0.019 0.001 PHE B 278 TRP 0.020 0.001 TRP A1680 HIS 0.015 0.001 HIS A1262 Details of bonding type rmsd covalent geometry : bond 0.00336 (13477) covalent geometry : angle 0.56295 (18318) hydrogen bonds : bond 0.03713 ( 839) hydrogen bonds : angle 3.99160 ( 2475) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 11676.63 seconds wall clock time: 197 minutes 19.50 seconds (11839.50 seconds total)