Starting phenix.real_space_refine on Wed Feb 4 18:45:03 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9utu_64501/02_2026/9utu_64501_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/9utu_64501/02_2026/9utu_64501.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.72 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9utu_64501/02_2026/9utu_64501_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9utu_64501/02_2026/9utu_64501_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9utu_64501/02_2026/9utu_64501.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9utu_64501/02_2026/9utu_64501.map" } resolution = 2.72 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 sd= 0.037 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 Mg 1 5.21 5 S 75 5.16 5 C 7834 2.51 5 N 2002 2.21 5 O 2075 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 27 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 11987 Number of models: 1 Model: "" Number of chains: 3 Chain: "B" Number of atoms: 11474 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1406, 11474 Classifications: {'peptide': 1406} Link IDs: {'PTRANS': 64, 'TRANS': 1341} Chain breaks: 11 Chain: "C" Number of atoms: 512 Number of conformers: 1 Conformer: "" Number of residues, atoms: 64, 512 Classifications: {'peptide': 64} Link IDs: {'PTRANS': 7, 'TRANS': 56} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 7934 SG CYS B1244 35.746 51.731 49.729 1.00 48.83 S Time building chain proxies: 2.53, per 1000 atoms: 0.21 Number of scatterers: 11987 At special positions: 0 Unit cell: (96.8, 115.5, 136.4, 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 75 16.00 Mg 1 11.99 O 2075 8.00 N 2002 7.00 C 7834 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS B1328 " - pdb=" SG CYS B1345 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.80 Conformation dependent library (CDL) restraints added in 508.5 milliseconds 2888 Ramachandran restraints generated. 1444 Oldfield, 0 Emsley, 1444 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2798 Finding SS restraints... Secondary structure from input PDB file: 82 helices and 4 sheets defined 70.1% alpha, 3.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.58 Creating SS restraints... Processing helix chain 'B' and resid 148 through 153 Processing helix chain 'B' and resid 160 through 176 removed outlier: 3.924A pdb=" N ASP B 166 " --> pdb=" O GLU B 162 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N ILE B 167 " --> pdb=" O GLN B 163 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N PHE B 168 " --> pdb=" O ILE B 164 " (cutoff:3.500A) Processing helix chain 'B' and resid 178 through 197 removed outlier: 3.614A pdb=" N ASN B 184 " --> pdb=" O ASP B 180 " (cutoff:3.500A) Processing helix chain 'B' and resid 201 through 214 Processing helix chain 'B' and resid 219 through 229 removed outlier: 3.744A pdb=" N LYS B 223 " --> pdb=" O ALA B 219 " (cutoff:3.500A) Processing helix chain 'B' and resid 232 through 242 Processing helix chain 'B' and resid 242 through 247 Processing helix chain 'B' and resid 281 through 294 Processing helix chain 'B' and resid 297 through 314 removed outlier: 3.742A pdb=" N GLU B 314 " --> pdb=" O LEU B 310 " (cutoff:3.500A) Processing helix chain 'B' and resid 315 through 320 removed outlier: 3.595A pdb=" N ARG B 319 " --> pdb=" O ASN B 316 " (cutoff:3.500A) Processing helix chain 'B' and resid 321 through 337 removed outlier: 3.618A pdb=" N LEU B 325 " --> pdb=" O THR B 321 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N ASP B 337 " --> pdb=" O LEU B 333 " (cutoff:3.500A) Processing helix chain 'B' and resid 338 through 344 Processing helix chain 'B' and resid 351 through 357 Processing helix chain 'B' and resid 357 through 368 removed outlier: 4.272A pdb=" N ILE B 361 " --> pdb=" O VAL B 357 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N GLN B 368 " --> pdb=" O PHE B 364 " (cutoff:3.500A) Processing helix chain 'B' and resid 383 through 387 removed outlier: 3.621A pdb=" N ILE B 387 " --> pdb=" O HIS B 384 " (cutoff:3.500A) Processing helix chain 'B' and resid 389 through 395 removed outlier: 3.622A pdb=" N LEU B 393 " --> pdb=" O GLY B 389 " (cutoff:3.500A) Processing helix chain 'B' and resid 396 through 398 No H-bonds generated for 'chain 'B' and resid 396 through 398' Processing helix chain 'B' and resid 399 through 404 removed outlier: 3.610A pdb=" N ALA B 404 " --> pdb=" O PRO B 400 " (cutoff:3.500A) Processing helix chain 'B' and resid 413 through 417 Processing helix chain 'B' and resid 425 through 429 removed outlier: 3.959A pdb=" N VAL B 429 " --> pdb=" O LEU B 426 " (cutoff:3.500A) Processing helix chain 'B' and resid 430 through 434 removed outlier: 3.731A pdb=" N ASP B 433 " --> pdb=" O VAL B 430 " (cutoff:3.500A) Processing helix chain 'B' and resid 443 through 452 removed outlier: 3.703A pdb=" N HIS B 447 " --> pdb=" O ARG B 443 " (cutoff:3.500A) Processing helix chain 'B' and resid 452 through 470 removed outlier: 4.221A pdb=" N TRP B 456 " --> pdb=" O PHE B 452 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N VAL B 457 " --> pdb=" O ASN B 453 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N MET B 458 " --> pdb=" O ARG B 454 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N SER B 461 " --> pdb=" O VAL B 457 " (cutoff:3.500A) removed outlier: 4.351A pdb=" N ILE B 462 " --> pdb=" O MET B 458 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N ASN B 470 " --> pdb=" O TYR B 466 " (cutoff:3.500A) Processing helix chain 'B' and resid 471 through 476 removed outlier: 3.797A pdb=" N PHE B 474 " --> pdb=" O SER B 471 " (cutoff:3.500A) Processing helix chain 'B' and resid 488 through 497 Processing helix chain 'B' and resid 498 through 515 removed outlier: 3.518A pdb=" N VAL B 502 " --> pdb=" O LEU B 498 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N TRP B 515 " --> pdb=" O THR B 511 " (cutoff:3.500A) Processing helix chain 'B' and resid 526 through 551 removed outlier: 3.922A pdb=" N ARG B 530 " --> pdb=" O GLN B 526 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N TRP B 533 " --> pdb=" O SER B 529 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N PHE B 534 " --> pdb=" O ARG B 530 " (cutoff:3.500A) Proline residue: B 545 - end of helix Processing helix chain 'B' and resid 552 through 557 removed outlier: 3.657A pdb=" N VAL B 557 " --> pdb=" O ASP B 553 " (cutoff:3.500A) Processing helix chain 'B' and resid 559 through 583 removed outlier: 3.622A pdb=" N HIS B 563 " --> pdb=" O SER B 559 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N PHE B 571 " --> pdb=" O ALA B 567 " (cutoff:3.500A) Processing helix chain 'B' and resid 589 through 594 removed outlier: 3.844A pdb=" N MET B 593 " --> pdb=" O PHE B 589 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N LYS B 594 " --> pdb=" O THR B 590 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 589 through 594' Processing helix chain 'B' and resid 603 through 608 Processing helix chain 'B' and resid 615 through 644 removed outlier: 3.846A pdb=" N TRP B 619 " --> pdb=" O GLY B 615 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N TYR B 622 " --> pdb=" O ARG B 618 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N TRP B 625 " --> pdb=" O SER B 621 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N TYR B 637 " --> pdb=" O TYR B 633 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N TYR B 638 " --> pdb=" O SER B 634 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N PHE B 639 " --> pdb=" O GLU B 635 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N LEU B 642 " --> pdb=" O TYR B 638 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N LEU B 644 " --> pdb=" O LEU B 640 " (cutoff:3.500A) Processing helix chain 'B' and resid 644 through 652 Processing helix chain 'B' and resid 666 through 671 removed outlier: 3.908A pdb=" N VAL B 671 " --> pdb=" O VAL B 667 " (cutoff:3.500A) Processing helix chain 'B' and resid 671 through 688 Processing helix chain 'B' and resid 690 through 712 removed outlier: 3.910A pdb=" N LEU B 694 " --> pdb=" O LEU B 690 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N SER B 708 " --> pdb=" O SER B 704 " (cutoff:3.500A) removed outlier: 4.301A pdb=" N PHE B 709 " --> pdb=" O VAL B 705 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N TYR B 710 " --> pdb=" O GLY B 706 " (cutoff:3.500A) Processing helix chain 'B' and resid 719 through 724 Processing helix chain 'B' and resid 725 through 734 Processing helix chain 'B' and resid 745 through 764 removed outlier: 3.655A pdb=" N LEU B 749 " --> pdb=" O LYS B 745 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N GLN B 752 " --> pdb=" O VAL B 748 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N VAL B 753 " --> pdb=" O LEU B 749 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N ALA B 756 " --> pdb=" O GLN B 752 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N GLU B 764 " --> pdb=" O SER B 760 " (cutoff:3.500A) Processing helix chain 'B' and resid 768 through 773 removed outlier: 3.570A pdb=" N VAL B 772 " --> pdb=" O ALA B 768 " (cutoff:3.500A) removed outlier: 4.119A pdb=" N GLN B 773 " --> pdb=" O ILE B 769 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 768 through 773' Processing helix chain 'B' and resid 786 through 790 removed outlier: 4.126A pdb=" N LEU B 790 " --> pdb=" O LYS B 787 " (cutoff:3.500A) Processing helix chain 'B' and resid 815 through 826 Processing helix chain 'B' and resid 856 through 862 Processing helix chain 'B' and resid 872 through 880 Processing helix chain 'B' and resid 880 through 895 removed outlier: 3.693A pdb=" N LYS B 892 " --> pdb=" O VAL B 888 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N ILE B 893 " --> pdb=" O LYS B 889 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N LEU B 894 " --> pdb=" O ASP B 890 " (cutoff:3.500A) Processing helix chain 'B' and resid 932 through 946 removed outlier: 3.649A pdb=" N ARG B 946 " --> pdb=" O TRP B 942 " (cutoff:3.500A) Processing helix chain 'B' and resid 949 through 958 removed outlier: 3.685A pdb=" N THR B 953 " --> pdb=" O THR B 949 " (cutoff:3.500A) Processing helix chain 'B' and resid 958 through 972 removed outlier: 4.145A pdb=" N ARG B 962 " --> pdb=" O MET B 958 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N ASN B 972 " --> pdb=" O TYR B 968 " (cutoff:3.500A) Processing helix chain 'B' and resid 972 through 978 removed outlier: 4.248A pdb=" N VAL B 976 " --> pdb=" O ASN B 972 " (cutoff:3.500A) Processing helix chain 'B' and resid 982 through 997 removed outlier: 3.607A pdb=" N ARG B 996 " --> pdb=" O LYS B 992 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N LYS B 997 " --> pdb=" O MET B 993 " (cutoff:3.500A) Processing helix chain 'B' and resid 1006 through 1010 removed outlier: 3.989A pdb=" N PHE B1010 " --> pdb=" O LEU B1007 " (cutoff:3.500A) Processing helix chain 'B' and resid 1011 through 1025 removed outlier: 3.674A pdb=" N PHE B1020 " --> pdb=" O GLU B1016 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N LEU B1021 " --> pdb=" O ASN B1017 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N LEU B1022 " --> pdb=" O ALA B1018 " (cutoff:3.500A) Processing helix chain 'B' and resid 1082 through 1090 removed outlier: 3.825A pdb=" N HIS B1088 " --> pdb=" O ASP B1084 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N ALA B1089 " --> pdb=" O ASN B1085 " (cutoff:3.500A) Processing helix chain 'B' and resid 1091 through 1093 No H-bonds generated for 'chain 'B' and resid 1091 through 1093' Processing helix chain 'B' and resid 1108 through 1113 Processing helix chain 'B' and resid 1114 through 1120 removed outlier: 3.555A pdb=" N ALA B1120 " --> pdb=" O ARG B1116 " (cutoff:3.500A) Processing helix chain 'B' and resid 1121 through 1123 No H-bonds generated for 'chain 'B' and resid 1121 through 1123' Processing helix chain 'B' and resid 1138 through 1142 Processing helix chain 'B' and resid 1201 through 1206 removed outlier: 3.697A pdb=" N THR B1206 " --> pdb=" O THR B1202 " (cutoff:3.500A) Processing helix chain 'B' and resid 1222 through 1233 Processing helix chain 'B' and resid 1272 through 1282 removed outlier: 3.625A pdb=" N TYR B1276 " --> pdb=" O SER B1272 " (cutoff:3.500A) Processing helix chain 'B' and resid 1283 through 1292 Processing helix chain 'B' and resid 1294 through 1325 removed outlier: 4.439A pdb=" N HIS B1298 " --> pdb=" O HIS B1294 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N GLN B1305 " --> pdb=" O ASN B1301 " (cutoff:3.500A) Processing helix chain 'B' and resid 1348 through 1378 removed outlier: 3.598A pdb=" N VAL B1355 " --> pdb=" O ALA B1351 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N ARG B1356 " --> pdb=" O VAL B1352 " (cutoff:3.500A) Proline residue: B1372 - end of helix Processing helix chain 'B' and resid 1437 through 1446 removed outlier: 3.569A pdb=" N PHE B1445 " --> pdb=" O LEU B1441 " (cutoff:3.500A) Processing helix chain 'B' and resid 1450 through 1467 removed outlier: 3.748A pdb=" N HIS B1467 " --> pdb=" O GLY B1463 " (cutoff:3.500A) Processing helix chain 'B' and resid 1471 through 1489 removed outlier: 4.089A pdb=" N PHE B1475 " --> pdb=" O PRO B1471 " (cutoff:3.500A) Proline residue: B1486 - end of helix removed outlier: 3.948A pdb=" N PHE B1489 " --> pdb=" O ALA B1485 " (cutoff:3.500A) Processing helix chain 'B' and resid 1495 through 1511 Processing helix chain 'B' and resid 1556 through 1563 removed outlier: 3.652A pdb=" N LEU B1560 " --> pdb=" O HIS B1556 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N MET B1562 " --> pdb=" O THR B1558 " (cutoff:3.500A) Processing helix chain 'B' and resid 1565 through 1584 removed outlier: 3.934A pdb=" N ILE B1582 " --> pdb=" O ALA B1578 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N ASN B1583 " --> pdb=" O PHE B1579 " (cutoff:3.500A) Processing helix chain 'B' and resid 1598 through 1623 removed outlier: 3.587A pdb=" N ILE B1602 " --> pdb=" O SER B1598 " (cutoff:3.500A) Proline residue: B1609 - end of helix Processing helix chain 'B' and resid 1627 through 1635 removed outlier: 4.259A pdb=" N PHE B1631 " --> pdb=" O SER B1627 " (cutoff:3.500A) Processing helix chain 'B' and resid 1638 through 1663 removed outlier: 3.529A pdb=" N MET B1642 " --> pdb=" O THR B1638 " (cutoff:3.500A) Processing helix chain 'B' and resid 1670 through 1696 removed outlier: 4.426A pdb=" N ILE B1674 " --> pdb=" O VAL B1670 " (cutoff:3.500A) removed outlier: 4.314A pdb=" N GLY B1675 " --> pdb=" O ARG B1671 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N THR B1696 " --> pdb=" O ALA B1692 " (cutoff:3.500A) Processing helix chain 'B' and resid 1723 through 1753 removed outlier: 3.811A pdb=" N ILE B1735 " --> pdb=" O THR B1731 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N HIS B1748 " --> pdb=" O PHE B1744 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N CYS B1753 " --> pdb=" O VAL B1749 " (cutoff:3.500A) Processing helix chain 'B' and resid 1754 through 1760 removed outlier: 3.679A pdb=" N ILE B1758 " --> pdb=" O GLN B1754 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N ILE B1760 " --> pdb=" O PRO B1756 " (cutoff:3.500A) Processing helix chain 'B' and resid 1762 through 1774 removed outlier: 3.650A pdb=" N MET B1770 " --> pdb=" O PHE B1766 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N LEU B1771 " --> pdb=" O HIS B1767 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N PHE B1772 " --> pdb=" O SER B1768 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N TRP B1773 " --> pdb=" O ILE B1769 " (cutoff:3.500A) Processing helix chain 'B' and resid 1786 through 1825 removed outlier: 3.584A pdb=" N THR B1790 " --> pdb=" O SER B1786 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N ILE B1815 " --> pdb=" O PHE B1811 " (cutoff:3.500A) Proline residue: B1818 - end of helix removed outlier: 3.871A pdb=" N ALA B1823 " --> pdb=" O ALA B1819 " (cutoff:3.500A) Processing helix chain 'C' and resid 83 through 87 removed outlier: 4.096A pdb=" N GLN C 87 " --> pdb=" O VAL C 84 " (cutoff:3.500A) Processing helix chain 'C' and resid 104 through 117 removed outlier: 3.502A pdb=" N THR C 108 " --> pdb=" O ARG C 104 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N VAL C 116 " --> pdb=" O PHE C 112 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N SER C 117 " --> pdb=" O GLU C 113 " (cutoff:3.500A) Processing helix chain 'C' and resid 119 through 124 removed outlier: 4.271A pdb=" N ALA C 123 " --> pdb=" O ASP C 119 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N GLN C 124 " --> pdb=" O PRO C 120 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 119 through 124' Processing helix chain 'C' and resid 127 through 132 Processing sheet with id=AA1, first strand: chain 'B' and resid 370 through 373 Processing sheet with id=AA2, first strand: chain 'B' and resid 998 through 999 removed outlier: 3.723A pdb=" N VAL B 844 " --> pdb=" O LYS B 999 " (cutoff:3.500A) removed outlier: 7.728A pdb=" N SER B1003 " --> pdb=" O VAL B 844 " (cutoff:3.500A) removed outlier: 6.965A pdb=" N THR B 846 " --> pdb=" O SER B1003 " (cutoff:3.500A) removed outlier: 4.480A pdb=" N LEU B1033 " --> pdb=" O MET B1004 " (cutoff:3.500A) removed outlier: 4.604A pdb=" N ILE B1047 " --> pdb=" O LEU B1072 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N PHE B1068 " --> pdb=" O LEU B1051 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 998 through 999 removed outlier: 3.723A pdb=" N VAL B 844 " --> pdb=" O LYS B 999 " (cutoff:3.500A) removed outlier: 6.784A pdb=" N THR B 843 " --> pdb=" O GLN B1099 " (cutoff:3.500A) removed outlier: 7.074A pdb=" N ALA B1149 " --> pdb=" O ASN B1200 " (cutoff:3.500A) removed outlier: 7.648A pdb=" N LYS B1237 " --> pdb=" O ALA B1149 " (cutoff:3.500A) removed outlier: 4.355A pdb=" N VAL B1151 " --> pdb=" O LYS B1237 " (cutoff:3.500A) removed outlier: 6.589A pdb=" N CYS B1239 " --> pdb=" O VAL B1151 " (cutoff:3.500A) removed outlier: 4.934A pdb=" N ALA B1153 " --> pdb=" O CYS B1239 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 1105 through 1106 removed outlier: 3.745A pdb=" N GLY B1245 " --> pdb=" O ASP B1106 " (cutoff:3.500A) 619 hydrogen bonds defined for protein. 1803 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.21 Time building geometry restraints manager: 1.13 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 3401 1.34 - 1.46: 2242 1.46 - 1.58: 6552 1.58 - 1.70: 0 1.70 - 1.82: 118 Bond restraints: 12313 Sorted by residual: bond pdb=" N GLU B1044 " pdb=" CA GLU B1044 " ideal model delta sigma weight residual 1.454 1.487 -0.034 1.14e-02 7.69e+03 8.66e+00 bond pdb=" N GLU B1043 " pdb=" CA GLU B1043 " ideal model delta sigma weight residual 1.454 1.489 -0.035 1.27e-02 6.20e+03 7.51e+00 bond pdb=" N GLU B1041 " pdb=" CA GLU B1041 " ideal model delta sigma weight residual 1.455 1.488 -0.033 1.27e-02 6.20e+03 6.80e+00 bond pdb=" N THR B1040 " pdb=" CA THR B1040 " ideal model delta sigma weight residual 1.454 1.487 -0.033 1.31e-02 5.83e+03 6.35e+00 bond pdb=" N GLN C 87 " pdb=" CA GLN C 87 " ideal model delta sigma weight residual 1.454 1.485 -0.031 1.29e-02 6.01e+03 5.66e+00 ... (remaining 12308 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.66: 16372 1.66 - 3.33: 277 3.33 - 4.99: 56 4.99 - 6.65: 5 6.65 - 8.31: 2 Bond angle restraints: 16712 Sorted by residual: angle pdb=" C GLN B 779 " pdb=" N VAL B 780 " pdb=" CA VAL B 780 " ideal model delta sigma weight residual 120.33 124.62 -4.29 8.00e-01 1.56e+00 2.87e+01 angle pdb=" C VAL B1371 " pdb=" CA VAL B1371 " pdb=" CB VAL B1371 " ideal model delta sigma weight residual 113.70 110.41 3.29 9.50e-01 1.11e+00 1.20e+01 angle pdb=" C ASP B1592 " pdb=" N ASP B1593 " pdb=" CA ASP B1593 " ideal model delta sigma weight residual 121.54 127.76 -6.22 1.91e+00 2.74e-01 1.06e+01 angle pdb=" C VAL B 780 " pdb=" CA VAL B 780 " pdb=" CB VAL B 780 " ideal model delta sigma weight residual 114.00 109.78 4.22 1.31e+00 5.83e-01 1.04e+01 angle pdb=" CA GLU B1041 " pdb=" C GLU B1041 " pdb=" O GLU B1041 " ideal model delta sigma weight residual 121.56 118.11 3.45 1.09e+00 8.42e-01 1.00e+01 ... (remaining 16707 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.93: 6590 17.93 - 35.86: 513 35.86 - 53.79: 111 53.79 - 71.72: 30 71.72 - 89.66: 15 Dihedral angle restraints: 7259 sinusoidal: 2934 harmonic: 4325 Sorted by residual: dihedral pdb=" CB CYS B1328 " pdb=" SG CYS B1328 " pdb=" SG CYS B1345 " pdb=" CB CYS B1345 " ideal model delta sinusoidal sigma weight residual -86.00 -131.49 45.49 1 1.00e+01 1.00e-02 2.87e+01 dihedral pdb=" CA ILE B 214 " pdb=" C ILE B 214 " pdb=" N GLY B 215 " pdb=" CA GLY B 215 " ideal model delta harmonic sigma weight residual -180.00 -161.62 -18.38 0 5.00e+00 4.00e-02 1.35e+01 dihedral pdb=" CG ARG B 520 " pdb=" CD ARG B 520 " pdb=" NE ARG B 520 " pdb=" CZ ARG B 520 " ideal model delta sinusoidal sigma weight residual 90.00 40.98 49.02 2 1.50e+01 4.44e-03 1.22e+01 ... (remaining 7256 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.041: 1332 0.041 - 0.081: 393 0.081 - 0.122: 111 0.122 - 0.163: 4 0.163 - 0.203: 1 Chirality restraints: 1841 Sorted by residual: chirality pdb=" CA LEU B1039 " pdb=" N LEU B1039 " pdb=" C LEU B1039 " pdb=" CB LEU B1039 " both_signs ideal model delta sigma weight residual False 2.51 2.71 -0.20 2.00e-01 2.50e+01 1.03e+00 chirality pdb=" CA ASP B1593 " pdb=" N ASP B1593 " pdb=" C ASP B1593 " pdb=" CB ASP B1593 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.16 2.00e-01 2.50e+01 6.59e-01 chirality pdb=" CA ASP B 484 " pdb=" N ASP B 484 " pdb=" C ASP B 484 " pdb=" CB ASP B 484 " both_signs ideal model delta sigma weight residual False 2.51 2.36 0.15 2.00e-01 2.50e+01 5.65e-01 ... (remaining 1838 not shown) Planarity restraints: 2095 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLU B 832 " 0.032 5.00e-02 4.00e+02 4.79e-02 3.67e+00 pdb=" N PRO B 833 " -0.083 5.00e-02 4.00e+02 pdb=" CA PRO B 833 " 0.025 5.00e-02 4.00e+02 pdb=" CD PRO B 833 " 0.026 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLN B1725 " -0.031 5.00e-02 4.00e+02 4.60e-02 3.39e+00 pdb=" N PRO B1726 " 0.080 5.00e-02 4.00e+02 pdb=" CA PRO B1726 " -0.023 5.00e-02 4.00e+02 pdb=" CD PRO B1726 " -0.026 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY B1628 " -0.029 5.00e-02 4.00e+02 4.35e-02 3.03e+00 pdb=" N PRO B1629 " 0.075 5.00e-02 4.00e+02 pdb=" CA PRO B1629 " -0.022 5.00e-02 4.00e+02 pdb=" CD PRO B1629 " -0.024 5.00e-02 4.00e+02 ... (remaining 2092 not shown) Histogram of nonbonded interaction distances: 2.18 - 2.72: 350 2.72 - 3.27: 12067 3.27 - 3.81: 17984 3.81 - 4.36: 20990 4.36 - 4.90: 37608 Nonbonded interactions: 88999 Sorted by model distance: nonbonded pdb=" NZ LYS B1246 " pdb="MG MG B1901 " model vdw 2.178 2.250 nonbonded pdb=" O PRO B 472 " pdb=" OG1 THR B 476 " model vdw 2.245 3.040 nonbonded pdb=" O LYS B1067 " pdb=" NH2 ARG C 99 " model vdw 2.252 3.120 nonbonded pdb=" OG1 THR B 843 " pdb=" O ARG B1094 " model vdw 2.289 3.040 nonbonded pdb=" O THR B1606 " pdb=" NE2 GLN B1683 " model vdw 2.308 3.120 ... (remaining 88994 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=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.760 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.210 Check model and map are aligned: 0.020 Set scattering table: 0.040 Process input model: 11.360 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:7.150 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.620 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7923 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 : 0.003 0.035 12314 Z= 0.150 Angle : 0.568 8.314 16714 Z= 0.331 Chirality : 0.041 0.203 1841 Planarity : 0.004 0.048 2095 Dihedral : 14.393 89.655 4458 Min Nonbonded Distance : 2.178 Molprobity Statistics. All-atom Clashscore : 3.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer: Outliers : 0.39 % Allowed : 0.08 % Favored : 99.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.45 (0.22), residues: 1444 helix: 1.95 (0.18), residues: 815 sheet: 0.85 (0.86), residues: 31 loop : -0.41 (0.25), residues: 598 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG B 520 TYR 0.016 0.001 TYR B 875 PHE 0.012 0.001 PHE B1010 TRP 0.023 0.001 TRP B1662 HIS 0.003 0.001 HIS B1088 Details of bonding type rmsd covalent geometry : bond 0.00275 (12313) covalent geometry : angle 0.56789 (16712) SS BOND : bond 0.00290 ( 1) SS BOND : angle 1.09608 ( 2) hydrogen bonds : bond 0.17749 ( 618) hydrogen bonds : angle 4.90854 ( 1803) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2888 Ramachandran restraints generated. 1444 Oldfield, 0 Emsley, 1444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2888 Ramachandran restraints generated. 1444 Oldfield, 0 Emsley, 1444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 1292 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 158 time to evaluate : 0.552 Fit side-chains revert: symmetry clash REVERT: B 938 ARG cc_start: 0.7920 (mtt180) cc_final: 0.7662 (ttm110) REVERT: B 1269 GLN cc_start: 0.7724 (tp40) cc_final: 0.7304 (tp-100) REVERT: B 1562 MET cc_start: 0.7885 (ppp) cc_final: 0.7635 (ppp) REVERT: B 1733 LYS cc_start: 0.7895 (mptt) cc_final: 0.7565 (tppp) outliers start: 5 outliers final: 1 residues processed: 161 average time/residue: 0.6429 time to fit residues: 112.0649 Evaluate side-chains 133 residues out of total 1292 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 132 time to evaluate : 0.478 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 1043 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 98 optimal weight: 0.7980 chunk 107 optimal weight: 0.4980 chunk 10 optimal weight: 0.0980 chunk 66 optimal weight: 1.9990 chunk 130 optimal weight: 4.9990 chunk 124 optimal weight: 5.9990 chunk 103 optimal weight: 5.9990 chunk 77 optimal weight: 1.9990 chunk 122 optimal weight: 7.9990 chunk 91 optimal weight: 2.9990 chunk 55 optimal weight: 2.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 240 ASN B1748 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4043 r_free = 0.4043 target = 0.164558 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.107876 restraints weight = 17048.232| |-----------------------------------------------------------------------------| r_work (start): 0.3357 rms_B_bonded: 3.01 r_work: 0.3223 rms_B_bonded: 3.57 restraints_weight: 0.5000 r_work (final): 0.3223 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7610 moved from start: 0.1012 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 12314 Z= 0.139 Angle : 0.536 8.870 16714 Z= 0.284 Chirality : 0.042 0.236 1841 Planarity : 0.005 0.051 2095 Dihedral : 4.111 25.532 1620 Min Nonbonded Distance : 2.106 Molprobity Statistics. All-atom Clashscore : 2.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.94 % Favored : 98.06 % Rotamer: Outliers : 0.93 % Allowed : 7.51 % Favored : 91.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.63 (0.22), residues: 1444 helix: 2.06 (0.18), residues: 829 sheet: 0.99 (0.85), residues: 31 loop : -0.34 (0.26), residues: 584 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B1671 TYR 0.013 0.001 TYR B1800 PHE 0.012 0.001 PHE C 139 TRP 0.014 0.001 TRP B1662 HIS 0.005 0.001 HIS B1088 Details of bonding type rmsd covalent geometry : bond 0.00300 (12313) covalent geometry : angle 0.53613 (16712) SS BOND : bond 0.00253 ( 1) SS BOND : angle 0.74533 ( 2) hydrogen bonds : bond 0.06037 ( 618) hydrogen bonds : angle 3.99182 ( 1803) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2888 Ramachandran restraints generated. 1444 Oldfield, 0 Emsley, 1444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2888 Ramachandran restraints generated. 1444 Oldfield, 0 Emsley, 1444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 1292 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 139 time to evaluate : 0.495 Fit side-chains REVERT: B 384 HIS cc_start: 0.8056 (OUTLIER) cc_final: 0.7787 (t70) REVERT: B 938 ARG cc_start: 0.8034 (mtt180) cc_final: 0.7589 (ttm110) REVERT: B 1269 GLN cc_start: 0.8103 (tp40) cc_final: 0.7512 (tp-100) REVERT: B 1562 MET cc_start: 0.8308 (ppp) cc_final: 0.7671 (ppp) REVERT: B 1621 MET cc_start: 0.1997 (ppp) cc_final: 0.1334 (ptt) REVERT: B 1733 LYS cc_start: 0.7586 (mptt) cc_final: 0.7259 (tppp) REVERT: C 91 GLN cc_start: 0.7676 (mm-40) cc_final: 0.7424 (mm-40) outliers start: 12 outliers final: 8 residues processed: 144 average time/residue: 0.5704 time to fit residues: 89.3383 Evaluate side-chains 137 residues out of total 1292 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 128 time to evaluate : 0.448 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 180 ASP Chi-restraints excluded: chain B residue 384 HIS Chi-restraints excluded: chain B residue 391 ASP Chi-restraints excluded: chain B residue 702 ILE Chi-restraints excluded: chain B residue 761 MET Chi-restraints excluded: chain B residue 1058 ILE Chi-restraints excluded: chain B residue 1316 VAL Chi-restraints excluded: chain B residue 1759 ILE Chi-restraints excluded: chain C residue 89 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 41 optimal weight: 4.9990 chunk 70 optimal weight: 1.9990 chunk 21 optimal weight: 3.9990 chunk 82 optimal weight: 5.9990 chunk 14 optimal weight: 2.9990 chunk 42 optimal weight: 0.9980 chunk 45 optimal weight: 3.9990 chunk 109 optimal weight: 5.9990 chunk 87 optimal weight: 1.9990 chunk 85 optimal weight: 0.7980 chunk 2 optimal weight: 0.7980 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 240 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4030 r_free = 0.4030 target = 0.163234 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.106324 restraints weight = 17255.346| |-----------------------------------------------------------------------------| r_work (start): 0.3357 rms_B_bonded: 3.05 r_work: 0.3223 rms_B_bonded: 3.57 restraints_weight: 0.5000 r_work (final): 0.3223 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7665 moved from start: 0.1283 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 12314 Z= 0.145 Angle : 0.540 10.936 16714 Z= 0.282 Chirality : 0.042 0.169 1841 Planarity : 0.005 0.046 2095 Dihedral : 4.067 17.759 1617 Min Nonbonded Distance : 2.064 Molprobity Statistics. All-atom Clashscore : 2.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.66 % Favored : 98.34 % Rotamer: Outliers : 1.78 % Allowed : 9.52 % Favored : 88.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.56 (0.22), residues: 1444 helix: 2.06 (0.18), residues: 829 sheet: 0.96 (0.84), residues: 31 loop : -0.46 (0.26), residues: 584 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B1357 TYR 0.016 0.001 TYR B1503 PHE 0.013 0.001 PHE C 139 TRP 0.011 0.001 TRP B 456 HIS 0.006 0.001 HIS B1088 Details of bonding type rmsd covalent geometry : bond 0.00332 (12313) covalent geometry : angle 0.53993 (16712) SS BOND : bond 0.00242 ( 1) SS BOND : angle 0.61472 ( 2) hydrogen bonds : bond 0.05804 ( 618) hydrogen bonds : angle 3.85438 ( 1803) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2888 Ramachandran restraints generated. 1444 Oldfield, 0 Emsley, 1444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2888 Ramachandran restraints generated. 1444 Oldfield, 0 Emsley, 1444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 1292 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 140 time to evaluate : 0.459 Fit side-chains REVERT: B 384 HIS cc_start: 0.8063 (OUTLIER) cc_final: 0.7790 (t70) REVERT: B 938 ARG cc_start: 0.8055 (mtt180) cc_final: 0.7610 (ttm110) REVERT: B 948 GLN cc_start: 0.8677 (mm-40) cc_final: 0.8354 (mm-40) REVERT: B 1269 GLN cc_start: 0.8173 (tp40) cc_final: 0.7488 (tp-100) REVERT: B 1562 MET cc_start: 0.8258 (ppp) cc_final: 0.7608 (ppp) REVERT: B 1621 MET cc_start: 0.2054 (OUTLIER) cc_final: 0.1355 (ptt) REVERT: B 1733 LYS cc_start: 0.7609 (mptt) cc_final: 0.7262 (tppp) REVERT: C 91 GLN cc_start: 0.7657 (mm-40) cc_final: 0.7391 (mm-40) outliers start: 23 outliers final: 11 residues processed: 152 average time/residue: 0.5041 time to fit residues: 83.5113 Evaluate side-chains 144 residues out of total 1292 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 131 time to evaluate : 0.543 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 180 ASP Chi-restraints excluded: chain B residue 384 HIS Chi-restraints excluded: chain B residue 391 ASP Chi-restraints excluded: chain B residue 430 VAL Chi-restraints excluded: chain B residue 547 ILE Chi-restraints excluded: chain B residue 597 THR Chi-restraints excluded: chain B residue 667 VAL Chi-restraints excluded: chain B residue 702 ILE Chi-restraints excluded: chain B residue 761 MET Chi-restraints excluded: chain B residue 1058 ILE Chi-restraints excluded: chain B residue 1144 THR Chi-restraints excluded: chain B residue 1316 VAL Chi-restraints excluded: chain B residue 1621 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 142 optimal weight: 0.7980 chunk 28 optimal weight: 0.4980 chunk 97 optimal weight: 0.9990 chunk 39 optimal weight: 0.8980 chunk 113 optimal weight: 4.9990 chunk 29 optimal weight: 0.0370 chunk 25 optimal weight: 0.9990 chunk 63 optimal weight: 1.9990 chunk 115 optimal weight: 3.9990 chunk 99 optimal weight: 1.9990 chunk 52 optimal weight: 1.9990 overall best weight: 0.6460 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 240 ASN B1104 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4050 r_free = 0.4050 target = 0.165335 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.108712 restraints weight = 17093.034| |-----------------------------------------------------------------------------| r_work (start): 0.3399 rms_B_bonded: 3.05 r_work: 0.3267 rms_B_bonded: 3.57 restraints_weight: 0.5000 r_work (final): 0.3267 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7593 moved from start: 0.1456 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 12314 Z= 0.108 Angle : 0.500 11.628 16714 Z= 0.258 Chirality : 0.040 0.165 1841 Planarity : 0.004 0.043 2095 Dihedral : 3.900 17.372 1617 Min Nonbonded Distance : 2.125 Molprobity Statistics. All-atom Clashscore : 3.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.66 % Favored : 98.34 % Rotamer: Outliers : 1.47 % Allowed : 11.30 % Favored : 87.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.68 (0.22), residues: 1444 helix: 2.15 (0.18), residues: 833 sheet: 0.96 (0.86), residues: 31 loop : -0.41 (0.26), residues: 580 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 520 TYR 0.013 0.001 TYR B1804 PHE 0.008 0.001 PHE B1658 TRP 0.011 0.001 TRP B 445 HIS 0.003 0.000 HIS B1088 Details of bonding type rmsd covalent geometry : bond 0.00223 (12313) covalent geometry : angle 0.49982 (16712) SS BOND : bond 0.00167 ( 1) SS BOND : angle 0.56159 ( 2) hydrogen bonds : bond 0.04628 ( 618) hydrogen bonds : angle 3.71146 ( 1803) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2888 Ramachandran restraints generated. 1444 Oldfield, 0 Emsley, 1444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2888 Ramachandran restraints generated. 1444 Oldfield, 0 Emsley, 1444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 1292 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 142 time to evaluate : 0.421 Fit side-chains REVERT: B 384 HIS cc_start: 0.8056 (OUTLIER) cc_final: 0.7807 (t70) REVERT: B 520 ARG cc_start: 0.8045 (mtt90) cc_final: 0.7706 (mpt-90) REVERT: B 563 HIS cc_start: 0.6439 (OUTLIER) cc_final: 0.6188 (t-90) REVERT: B 938 ARG cc_start: 0.8037 (mtt180) cc_final: 0.7576 (ttm110) REVERT: B 948 GLN cc_start: 0.8602 (mm-40) cc_final: 0.8355 (mm110) REVERT: B 1269 GLN cc_start: 0.8167 (tp40) cc_final: 0.7497 (tp-100) REVERT: B 1501 LEU cc_start: 0.8131 (OUTLIER) cc_final: 0.7898 (mm) REVERT: B 1562 MET cc_start: 0.8198 (ppp) cc_final: 0.7563 (ppp) REVERT: B 1621 MET cc_start: 0.1876 (OUTLIER) cc_final: 0.1239 (ptt) REVERT: B 1733 LYS cc_start: 0.7613 (mptt) cc_final: 0.7245 (tppp) REVERT: C 91 GLN cc_start: 0.7620 (mm-40) cc_final: 0.7331 (mm-40) outliers start: 19 outliers final: 8 residues processed: 152 average time/residue: 0.5753 time to fit residues: 95.2412 Evaluate side-chains 144 residues out of total 1292 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 132 time to evaluate : 0.456 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 180 ASP Chi-restraints excluded: chain B residue 384 HIS Chi-restraints excluded: chain B residue 430 VAL Chi-restraints excluded: chain B residue 550 PHE Chi-restraints excluded: chain B residue 563 HIS Chi-restraints excluded: chain B residue 667 VAL Chi-restraints excluded: chain B residue 702 ILE Chi-restraints excluded: chain B residue 846 THR Chi-restraints excluded: chain B residue 978 MET Chi-restraints excluded: chain B residue 1501 LEU Chi-restraints excluded: chain B residue 1621 MET Chi-restraints excluded: chain C residue 89 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 7 optimal weight: 3.9990 chunk 143 optimal weight: 4.9990 chunk 53 optimal weight: 8.9990 chunk 27 optimal weight: 1.9990 chunk 109 optimal weight: 5.9990 chunk 126 optimal weight: 0.1980 chunk 142 optimal weight: 1.9990 chunk 56 optimal weight: 1.9990 chunk 50 optimal weight: 2.9990 chunk 64 optimal weight: 6.9990 chunk 108 optimal weight: 0.0020 overall best weight: 1.2394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 240 ASN B 563 HIS B1104 ASN B1243 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4040 r_free = 0.4040 target = 0.163831 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.107023 restraints weight = 17141.834| |-----------------------------------------------------------------------------| r_work (start): 0.3361 rms_B_bonded: 3.03 r_work: 0.3230 rms_B_bonded: 3.55 restraints_weight: 0.5000 r_work (final): 0.3230 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7625 moved from start: 0.1571 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 12314 Z= 0.139 Angle : 0.528 8.437 16714 Z= 0.274 Chirality : 0.041 0.162 1841 Planarity : 0.005 0.045 2095 Dihedral : 3.944 17.090 1617 Min Nonbonded Distance : 2.058 Molprobity Statistics. All-atom Clashscore : 2.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.66 % Favored : 98.34 % Rotamer: Outliers : 2.24 % Allowed : 11.46 % Favored : 86.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.60 (0.23), residues: 1444 helix: 2.10 (0.18), residues: 835 sheet: 0.76 (0.76), residues: 41 loop : -0.49 (0.26), residues: 568 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 520 TYR 0.014 0.001 TYR B1804 PHE 0.012 0.001 PHE B 821 TRP 0.012 0.001 TRP B 445 HIS 0.005 0.001 HIS B1088 Details of bonding type rmsd covalent geometry : bond 0.00322 (12313) covalent geometry : angle 0.52755 (16712) SS BOND : bond 0.00251 ( 1) SS BOND : angle 0.53330 ( 2) hydrogen bonds : bond 0.05371 ( 618) hydrogen bonds : angle 3.70071 ( 1803) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2888 Ramachandran restraints generated. 1444 Oldfield, 0 Emsley, 1444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2888 Ramachandran restraints generated. 1444 Oldfield, 0 Emsley, 1444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 1292 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 132 time to evaluate : 0.426 Fit side-chains REVERT: B 384 HIS cc_start: 0.8058 (OUTLIER) cc_final: 0.7777 (t70) REVERT: B 520 ARG cc_start: 0.8121 (mtt90) cc_final: 0.7771 (mpt-90) REVERT: B 938 ARG cc_start: 0.8028 (mtt180) cc_final: 0.7568 (ttm110) REVERT: B 948 GLN cc_start: 0.8662 (mm-40) cc_final: 0.8375 (mm110) REVERT: B 1269 GLN cc_start: 0.8181 (tp40) cc_final: 0.7537 (tp-100) REVERT: B 1501 LEU cc_start: 0.8060 (OUTLIER) cc_final: 0.7802 (mm) REVERT: B 1562 MET cc_start: 0.8223 (ppp) cc_final: 0.7595 (ppp) REVERT: B 1621 MET cc_start: 0.1859 (OUTLIER) cc_final: 0.1219 (ptm) outliers start: 29 outliers final: 16 residues processed: 145 average time/residue: 0.5460 time to fit residues: 86.7962 Evaluate side-chains 147 residues out of total 1292 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 128 time to evaluate : 0.422 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 180 ASP Chi-restraints excluded: chain B residue 384 HIS Chi-restraints excluded: chain B residue 391 ASP Chi-restraints excluded: chain B residue 430 VAL Chi-restraints excluded: chain B residue 563 HIS Chi-restraints excluded: chain B residue 597 THR Chi-restraints excluded: chain B residue 667 VAL Chi-restraints excluded: chain B residue 702 ILE Chi-restraints excluded: chain B residue 761 MET Chi-restraints excluded: chain B residue 846 THR Chi-restraints excluded: chain B residue 1144 THR Chi-restraints excluded: chain B residue 1316 VAL Chi-restraints excluded: chain B residue 1459 MET Chi-restraints excluded: chain B residue 1501 LEU Chi-restraints excluded: chain B residue 1621 MET Chi-restraints excluded: chain B residue 1753 CYS Chi-restraints excluded: chain B residue 1759 ILE Chi-restraints excluded: chain C residue 89 ILE Chi-restraints excluded: chain C residue 130 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 26 optimal weight: 0.9990 chunk 51 optimal weight: 0.0470 chunk 63 optimal weight: 2.9990 chunk 47 optimal weight: 3.9990 chunk 142 optimal weight: 0.9990 chunk 75 optimal weight: 0.7980 chunk 79 optimal weight: 0.9990 chunk 92 optimal weight: 5.9990 chunk 109 optimal weight: 10.0000 chunk 105 optimal weight: 0.7980 chunk 17 optimal weight: 0.8980 overall best weight: 0.7080 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 240 ASN B1104 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4053 r_free = 0.4053 target = 0.165134 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.108557 restraints weight = 17088.738| |-----------------------------------------------------------------------------| r_work (start): 0.3388 rms_B_bonded: 3.04 r_work: 0.3256 rms_B_bonded: 3.56 restraints_weight: 0.5000 r_work (final): 0.3256 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7606 moved from start: 0.1682 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 12314 Z= 0.111 Angle : 0.510 9.777 16714 Z= 0.262 Chirality : 0.040 0.161 1841 Planarity : 0.004 0.041 2095 Dihedral : 3.869 16.862 1617 Min Nonbonded Distance : 2.096 Molprobity Statistics. All-atom Clashscore : 2.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.80 % Favored : 98.20 % Rotamer: Outliers : 1.86 % Allowed : 12.23 % Favored : 85.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.68 (0.23), residues: 1444 helix: 2.14 (0.18), residues: 836 sheet: 0.82 (0.77), residues: 41 loop : -0.41 (0.26), residues: 567 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 520 TYR 0.012 0.001 TYR B1292 PHE 0.009 0.001 PHE B1658 TRP 0.012 0.001 TRP B 445 HIS 0.011 0.001 HIS B 563 Details of bonding type rmsd covalent geometry : bond 0.00238 (12313) covalent geometry : angle 0.50969 (16712) SS BOND : bond 0.00158 ( 1) SS BOND : angle 0.44556 ( 2) hydrogen bonds : bond 0.04680 ( 618) hydrogen bonds : angle 3.63052 ( 1803) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2888 Ramachandran restraints generated. 1444 Oldfield, 0 Emsley, 1444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2888 Ramachandran restraints generated. 1444 Oldfield, 0 Emsley, 1444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 1292 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 133 time to evaluate : 0.314 Fit side-chains REVERT: B 384 HIS cc_start: 0.8056 (OUTLIER) cc_final: 0.7803 (t70) REVERT: B 520 ARG cc_start: 0.8099 (mtt90) cc_final: 0.7831 (mpt-90) REVERT: B 526 GLN cc_start: 0.7318 (tm-30) cc_final: 0.7118 (pp30) REVERT: B 938 ARG cc_start: 0.8014 (mtt180) cc_final: 0.7569 (ttm110) REVERT: B 948 GLN cc_start: 0.8639 (mm-40) cc_final: 0.8380 (mm110) REVERT: B 1269 GLN cc_start: 0.8194 (tp40) cc_final: 0.7570 (tp-100) REVERT: B 1501 LEU cc_start: 0.8042 (OUTLIER) cc_final: 0.7828 (mm) REVERT: B 1562 MET cc_start: 0.8246 (ppp) cc_final: 0.7656 (ppp) REVERT: B 1621 MET cc_start: 0.1713 (OUTLIER) cc_final: 0.1396 (ptm) outliers start: 24 outliers final: 15 residues processed: 145 average time/residue: 0.4945 time to fit residues: 78.5499 Evaluate side-chains 147 residues out of total 1292 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 129 time to evaluate : 0.296 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 180 ASP Chi-restraints excluded: chain B residue 384 HIS Chi-restraints excluded: chain B residue 430 VAL Chi-restraints excluded: chain B residue 550 PHE Chi-restraints excluded: chain B residue 563 HIS Chi-restraints excluded: chain B residue 597 THR Chi-restraints excluded: chain B residue 667 VAL Chi-restraints excluded: chain B residue 702 ILE Chi-restraints excluded: chain B residue 761 MET Chi-restraints excluded: chain B residue 846 THR Chi-restraints excluded: chain B residue 1144 THR Chi-restraints excluded: chain B residue 1459 MET Chi-restraints excluded: chain B residue 1501 LEU Chi-restraints excluded: chain B residue 1557 ARG Chi-restraints excluded: chain B residue 1621 MET Chi-restraints excluded: chain B residue 1759 ILE Chi-restraints excluded: chain C residue 89 ILE Chi-restraints excluded: chain C residue 130 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 92 optimal weight: 4.9990 chunk 48 optimal weight: 6.9990 chunk 3 optimal weight: 3.9990 chunk 119 optimal weight: 6.9990 chunk 25 optimal weight: 0.5980 chunk 99 optimal weight: 2.9990 chunk 57 optimal weight: 0.9980 chunk 118 optimal weight: 0.7980 chunk 54 optimal weight: 0.9980 chunk 135 optimal weight: 9.9990 chunk 13 optimal weight: 2.9990 overall best weight: 1.2782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 240 ASN B 563 HIS B1104 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4035 r_free = 0.4035 target = 0.163525 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.106597 restraints weight = 17115.565| |-----------------------------------------------------------------------------| r_work (start): 0.3363 rms_B_bonded: 3.03 r_work: 0.3232 rms_B_bonded: 3.54 restraints_weight: 0.5000 r_work (final): 0.3232 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7636 moved from start: 0.1760 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 12314 Z= 0.139 Angle : 0.537 10.106 16714 Z= 0.276 Chirality : 0.041 0.266 1841 Planarity : 0.004 0.041 2095 Dihedral : 3.930 17.588 1617 Min Nonbonded Distance : 2.053 Molprobity Statistics. All-atom Clashscore : 2.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.87 % Favored : 98.13 % Rotamer: Outliers : 1.93 % Allowed : 12.62 % Favored : 85.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 1.60 (0.22), residues: 1444 helix: 2.09 (0.18), residues: 833 sheet: 0.81 (0.76), residues: 41 loop : -0.47 (0.26), residues: 570 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B1671 TYR 0.014 0.001 TYR B1804 PHE 0.013 0.001 PHE B1658 TRP 0.010 0.001 TRP B 456 HIS 0.005 0.001 HIS B1088 Details of bonding type rmsd covalent geometry : bond 0.00321 (12313) covalent geometry : angle 0.53726 (16712) SS BOND : bond 0.00225 ( 1) SS BOND : angle 0.61958 ( 2) hydrogen bonds : bond 0.05345 ( 618) hydrogen bonds : angle 3.64997 ( 1803) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2888 Ramachandran restraints generated. 1444 Oldfield, 0 Emsley, 1444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2888 Ramachandran restraints generated. 1444 Oldfield, 0 Emsley, 1444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 1292 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 131 time to evaluate : 0.394 Fit side-chains REVERT: B 384 HIS cc_start: 0.8064 (OUTLIER) cc_final: 0.7778 (t70) REVERT: B 520 ARG cc_start: 0.8149 (mtt90) cc_final: 0.7811 (mpt-90) REVERT: B 526 GLN cc_start: 0.7389 (tm-30) cc_final: 0.7147 (pp30) REVERT: B 938 ARG cc_start: 0.8036 (mtt180) cc_final: 0.7601 (ttm110) REVERT: B 948 GLN cc_start: 0.8689 (mm-40) cc_final: 0.8375 (mm-40) REVERT: B 1269 GLN cc_start: 0.8213 (tp40) cc_final: 0.7557 (tp-100) REVERT: B 1501 LEU cc_start: 0.8053 (OUTLIER) cc_final: 0.7834 (mm) REVERT: B 1562 MET cc_start: 0.8216 (ppp) cc_final: 0.7652 (ppp) REVERT: B 1621 MET cc_start: 0.1712 (OUTLIER) cc_final: 0.1383 (ptm) outliers start: 25 outliers final: 16 residues processed: 143 average time/residue: 0.5475 time to fit residues: 85.3034 Evaluate side-chains 148 residues out of total 1292 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 129 time to evaluate : 0.449 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 180 ASP Chi-restraints excluded: chain B residue 384 HIS Chi-restraints excluded: chain B residue 391 ASP Chi-restraints excluded: chain B residue 430 VAL Chi-restraints excluded: chain B residue 563 HIS Chi-restraints excluded: chain B residue 597 THR Chi-restraints excluded: chain B residue 667 VAL Chi-restraints excluded: chain B residue 702 ILE Chi-restraints excluded: chain B residue 761 MET Chi-restraints excluded: chain B residue 846 THR Chi-restraints excluded: chain B residue 1144 THR Chi-restraints excluded: chain B residue 1459 MET Chi-restraints excluded: chain B residue 1501 LEU Chi-restraints excluded: chain B residue 1507 ILE Chi-restraints excluded: chain B residue 1557 ARG Chi-restraints excluded: chain B residue 1621 MET Chi-restraints excluded: chain B residue 1759 ILE Chi-restraints excluded: chain C residue 89 ILE Chi-restraints excluded: chain C residue 130 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 101 optimal weight: 3.9990 chunk 73 optimal weight: 0.9990 chunk 141 optimal weight: 0.0370 chunk 113 optimal weight: 3.9990 chunk 24 optimal weight: 1.9990 chunk 26 optimal weight: 0.9990 chunk 35 optimal weight: 1.9990 chunk 98 optimal weight: 0.9990 chunk 44 optimal weight: 0.6980 chunk 142 optimal weight: 2.9990 chunk 84 optimal weight: 2.9990 overall best weight: 0.7464 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 240 ASN B1688 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4049 r_free = 0.4049 target = 0.164847 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.108146 restraints weight = 17078.138| |-----------------------------------------------------------------------------| r_work (start): 0.3382 rms_B_bonded: 3.03 r_work: 0.3252 rms_B_bonded: 3.55 restraints_weight: 0.5000 r_work (final): 0.3252 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7610 moved from start: 0.1830 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 12314 Z= 0.113 Angle : 0.517 10.404 16714 Z= 0.264 Chirality : 0.040 0.242 1841 Planarity : 0.004 0.041 2095 Dihedral : 3.864 16.868 1617 Min Nonbonded Distance : 2.084 Molprobity Statistics. All-atom Clashscore : 2.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.80 % Favored : 98.20 % Rotamer: Outliers : 1.93 % Allowed : 13.00 % Favored : 85.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.68 (0.23), residues: 1444 helix: 2.14 (0.18), residues: 835 sheet: 0.87 (0.77), residues: 41 loop : -0.42 (0.26), residues: 568 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B1357 TYR 0.013 0.001 TYR B1804 PHE 0.010 0.001 PHE B1500 TRP 0.012 0.001 TRP B 445 HIS 0.008 0.001 HIS B1688 Details of bonding type rmsd covalent geometry : bond 0.00245 (12313) covalent geometry : angle 0.51692 (16712) SS BOND : bond 0.00185 ( 1) SS BOND : angle 0.64024 ( 2) hydrogen bonds : bond 0.04718 ( 618) hydrogen bonds : angle 3.59755 ( 1803) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2888 Ramachandran restraints generated. 1444 Oldfield, 0 Emsley, 1444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2888 Ramachandran restraints generated. 1444 Oldfield, 0 Emsley, 1444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 1292 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 134 time to evaluate : 0.347 Fit side-chains REVERT: B 384 HIS cc_start: 0.8142 (OUTLIER) cc_final: 0.7863 (t70) REVERT: B 520 ARG cc_start: 0.8137 (mtt90) cc_final: 0.7802 (mpt-90) REVERT: B 526 GLN cc_start: 0.7415 (tm-30) cc_final: 0.7165 (pp30) REVERT: B 938 ARG cc_start: 0.8025 (mtt180) cc_final: 0.7600 (ttm110) REVERT: B 948 GLN cc_start: 0.8659 (mm-40) cc_final: 0.8367 (mm110) REVERT: B 1269 GLN cc_start: 0.8203 (tp40) cc_final: 0.7550 (tp-100) REVERT: B 1501 LEU cc_start: 0.8030 (OUTLIER) cc_final: 0.7806 (mm) REVERT: B 1562 MET cc_start: 0.8236 (ppp) cc_final: 0.7644 (ppp) REVERT: B 1621 MET cc_start: 0.1828 (OUTLIER) cc_final: 0.1484 (ptm) outliers start: 25 outliers final: 17 residues processed: 146 average time/residue: 0.5875 time to fit residues: 92.9321 Evaluate side-chains 147 residues out of total 1292 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 127 time to evaluate : 0.341 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 180 ASP Chi-restraints excluded: chain B residue 384 HIS Chi-restraints excluded: chain B residue 391 ASP Chi-restraints excluded: chain B residue 430 VAL Chi-restraints excluded: chain B residue 550 PHE Chi-restraints excluded: chain B residue 597 THR Chi-restraints excluded: chain B residue 667 VAL Chi-restraints excluded: chain B residue 702 ILE Chi-restraints excluded: chain B residue 761 MET Chi-restraints excluded: chain B residue 846 THR Chi-restraints excluded: chain B residue 1144 THR Chi-restraints excluded: chain B residue 1316 VAL Chi-restraints excluded: chain B residue 1459 MET Chi-restraints excluded: chain B residue 1501 LEU Chi-restraints excluded: chain B residue 1507 ILE Chi-restraints excluded: chain B residue 1557 ARG Chi-restraints excluded: chain B residue 1621 MET Chi-restraints excluded: chain B residue 1759 ILE Chi-restraints excluded: chain C residue 89 ILE Chi-restraints excluded: chain C residue 130 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 95 optimal weight: 2.9990 chunk 27 optimal weight: 1.9990 chunk 124 optimal weight: 5.9990 chunk 13 optimal weight: 3.9990 chunk 75 optimal weight: 0.6980 chunk 63 optimal weight: 0.9980 chunk 78 optimal weight: 1.9990 chunk 72 optimal weight: 0.9990 chunk 47 optimal weight: 0.7980 chunk 111 optimal weight: 2.9990 chunk 145 optimal weight: 0.9980 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 240 ASN B 563 HIS B1104 ASN B1688 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4049 r_free = 0.4049 target = 0.164743 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.108051 restraints weight = 16952.514| |-----------------------------------------------------------------------------| r_work (start): 0.3369 rms_B_bonded: 3.02 r_work: 0.3239 rms_B_bonded: 3.54 restraints_weight: 0.5000 r_work (final): 0.3239 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7609 moved from start: 0.1883 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 12314 Z= 0.118 Angle : 0.526 9.031 16714 Z= 0.270 Chirality : 0.041 0.239 1841 Planarity : 0.004 0.041 2095 Dihedral : 3.852 16.753 1617 Min Nonbonded Distance : 2.075 Molprobity Statistics. All-atom Clashscore : 3.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % Rotamer: Outliers : 1.78 % Allowed : 13.31 % Favored : 84.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.68 (0.23), residues: 1444 helix: 2.13 (0.18), residues: 836 sheet: 1.01 (0.87), residues: 31 loop : -0.40 (0.26), residues: 577 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B1357 TYR 0.012 0.001 TYR B1804 PHE 0.011 0.001 PHE B1500 TRP 0.011 0.001 TRP B 445 HIS 0.007 0.001 HIS B1688 Details of bonding type rmsd covalent geometry : bond 0.00263 (12313) covalent geometry : angle 0.52638 (16712) SS BOND : bond 0.00187 ( 1) SS BOND : angle 0.68105 ( 2) hydrogen bonds : bond 0.04730 ( 618) hydrogen bonds : angle 3.58102 ( 1803) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2888 Ramachandran restraints generated. 1444 Oldfield, 0 Emsley, 1444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2888 Ramachandran restraints generated. 1444 Oldfield, 0 Emsley, 1444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 1292 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 131 time to evaluate : 0.509 Fit side-chains REVERT: B 384 HIS cc_start: 0.8138 (OUTLIER) cc_final: 0.7854 (t70) REVERT: B 520 ARG cc_start: 0.8142 (mtt90) cc_final: 0.7797 (mpt-90) REVERT: B 938 ARG cc_start: 0.8017 (mtt180) cc_final: 0.7597 (ttm110) REVERT: B 948 GLN cc_start: 0.8665 (mm-40) cc_final: 0.8367 (mm110) REVERT: B 1269 GLN cc_start: 0.8207 (tp40) cc_final: 0.7554 (tp-100) REVERT: B 1501 LEU cc_start: 0.8084 (OUTLIER) cc_final: 0.7870 (mm) REVERT: B 1562 MET cc_start: 0.8204 (ppp) cc_final: 0.7619 (ppp) REVERT: B 1621 MET cc_start: 0.1796 (OUTLIER) cc_final: 0.1416 (ptm) outliers start: 23 outliers final: 11 residues processed: 143 average time/residue: 0.5811 time to fit residues: 90.3366 Evaluate side-chains 141 residues out of total 1292 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 127 time to evaluate : 0.457 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 180 ASP Chi-restraints excluded: chain B residue 384 HIS Chi-restraints excluded: chain B residue 391 ASP Chi-restraints excluded: chain B residue 430 VAL Chi-restraints excluded: chain B residue 597 THR Chi-restraints excluded: chain B residue 667 VAL Chi-restraints excluded: chain B residue 702 ILE Chi-restraints excluded: chain B residue 846 THR Chi-restraints excluded: chain B residue 1144 THR Chi-restraints excluded: chain B residue 1316 VAL Chi-restraints excluded: chain B residue 1501 LEU Chi-restraints excluded: chain B residue 1621 MET Chi-restraints excluded: chain C residue 89 ILE Chi-restraints excluded: chain C residue 130 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 37 optimal weight: 9.9990 chunk 77 optimal weight: 3.9990 chunk 60 optimal weight: 3.9990 chunk 83 optimal weight: 0.7980 chunk 130 optimal weight: 5.9990 chunk 19 optimal weight: 2.9990 chunk 25 optimal weight: 0.0970 chunk 16 optimal weight: 0.8980 chunk 112 optimal weight: 2.9990 chunk 28 optimal weight: 0.5980 chunk 101 optimal weight: 0.9980 overall best weight: 0.6778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 240 ASN B1104 ASN B1688 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4058 r_free = 0.4058 target = 0.165776 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.109227 restraints weight = 17034.159| |-----------------------------------------------------------------------------| r_work (start): 0.3394 rms_B_bonded: 3.03 r_work: 0.3265 rms_B_bonded: 3.54 restraints_weight: 0.5000 r_work (final): 0.3265 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7592 moved from start: 0.1960 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 12314 Z= 0.107 Angle : 0.510 11.965 16714 Z= 0.260 Chirality : 0.040 0.269 1841 Planarity : 0.004 0.041 2095 Dihedral : 3.792 16.835 1617 Min Nonbonded Distance : 2.093 Molprobity Statistics. All-atom Clashscore : 3.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.80 % Favored : 98.20 % Rotamer: Outliers : 1.39 % Allowed : 14.01 % Favored : 84.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.73 (0.23), residues: 1444 helix: 2.16 (0.18), residues: 839 sheet: 1.08 (0.87), residues: 31 loop : -0.36 (0.26), residues: 574 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B1357 TYR 0.012 0.001 TYR B1804 PHE 0.009 0.001 PHE B1500 TRP 0.012 0.001 TRP B 445 HIS 0.004 0.001 HIS B1688 Details of bonding type rmsd covalent geometry : bond 0.00231 (12313) covalent geometry : angle 0.50953 (16712) SS BOND : bond 0.00174 ( 1) SS BOND : angle 0.74047 ( 2) hydrogen bonds : bond 0.04325 ( 618) hydrogen bonds : angle 3.54867 ( 1803) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2888 Ramachandran restraints generated. 1444 Oldfield, 0 Emsley, 1444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2888 Ramachandran restraints generated. 1444 Oldfield, 0 Emsley, 1444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 1292 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 132 time to evaluate : 0.323 Fit side-chains REVERT: B 384 HIS cc_start: 0.8126 (OUTLIER) cc_final: 0.7869 (t70) REVERT: B 520 ARG cc_start: 0.8107 (mtt90) cc_final: 0.7775 (mpt-90) REVERT: B 656 MET cc_start: 0.5540 (ppp) cc_final: 0.4971 (pp-130) REVERT: B 938 ARG cc_start: 0.8035 (mtt180) cc_final: 0.7584 (ttm110) REVERT: B 948 GLN cc_start: 0.8651 (mm-40) cc_final: 0.8360 (mm110) REVERT: B 1057 GLU cc_start: 0.8301 (tt0) cc_final: 0.8018 (tt0) REVERT: B 1269 GLN cc_start: 0.8261 (tp40) cc_final: 0.7615 (tp-100) REVERT: B 1501 LEU cc_start: 0.8025 (OUTLIER) cc_final: 0.7805 (mm) REVERT: B 1562 MET cc_start: 0.8190 (ppp) cc_final: 0.7604 (ppp) REVERT: B 1621 MET cc_start: 0.1747 (OUTLIER) cc_final: 0.1349 (ptm) REVERT: C 91 GLN cc_start: 0.7819 (mm-40) cc_final: 0.7536 (mm-40) outliers start: 18 outliers final: 12 residues processed: 142 average time/residue: 0.5904 time to fit residues: 91.0480 Evaluate side-chains 141 residues out of total 1292 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 126 time to evaluate : 0.452 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 180 ASP Chi-restraints excluded: chain B residue 384 HIS Chi-restraints excluded: chain B residue 391 ASP Chi-restraints excluded: chain B residue 430 VAL Chi-restraints excluded: chain B residue 597 THR Chi-restraints excluded: chain B residue 667 VAL Chi-restraints excluded: chain B residue 702 ILE Chi-restraints excluded: chain B residue 846 THR Chi-restraints excluded: chain B residue 1144 THR Chi-restraints excluded: chain B residue 1316 VAL Chi-restraints excluded: chain B residue 1501 LEU Chi-restraints excluded: chain B residue 1621 MET Chi-restraints excluded: chain B residue 1750 ILE Chi-restraints excluded: chain C residue 89 ILE Chi-restraints excluded: chain C residue 130 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 33 optimal weight: 0.6980 chunk 88 optimal weight: 0.1980 chunk 70 optimal weight: 0.9980 chunk 67 optimal weight: 7.9990 chunk 57 optimal weight: 0.5980 chunk 109 optimal weight: 0.9980 chunk 11 optimal weight: 4.9990 chunk 72 optimal weight: 0.8980 chunk 122 optimal weight: 8.9990 chunk 79 optimal weight: 3.9990 chunk 145 optimal weight: 0.6980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 240 ASN B1104 ASN B1688 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4061 r_free = 0.4061 target = 0.166208 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.109522 restraints weight = 16988.880| |-----------------------------------------------------------------------------| r_work (start): 0.3387 rms_B_bonded: 3.03 r_work: 0.3258 rms_B_bonded: 3.56 restraints_weight: 0.5000 r_work (final): 0.3258 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7585 moved from start: 0.2013 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 12314 Z= 0.104 Angle : 0.501 10.705 16714 Z= 0.256 Chirality : 0.040 0.257 1841 Planarity : 0.004 0.042 2095 Dihedral : 3.719 16.820 1617 Min Nonbonded Distance : 2.090 Molprobity Statistics. All-atom Clashscore : 3.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.80 % Favored : 98.20 % Rotamer: Outliers : 1.47 % Allowed : 14.01 % Favored : 84.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.77 (0.23), residues: 1444 helix: 2.19 (0.18), residues: 839 sheet: 1.12 (0.88), residues: 31 loop : -0.34 (0.26), residues: 574 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B1357 TYR 0.013 0.001 TYR B1804 PHE 0.010 0.001 PHE B1500 TRP 0.013 0.001 TRP B 445 HIS 0.007 0.001 HIS B1688 Details of bonding type rmsd covalent geometry : bond 0.00223 (12313) covalent geometry : angle 0.50091 (16712) SS BOND : bond 0.00125 ( 1) SS BOND : angle 0.75124 ( 2) hydrogen bonds : bond 0.04160 ( 618) hydrogen bonds : angle 3.50712 ( 1803) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4333.65 seconds wall clock time: 74 minutes 23.52 seconds (4463.52 seconds total)