Starting phenix.real_space_refine on Thu Feb 5 04:49:01 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9n0q_48790/02_2026/9n0q_48790.cif Found real_map, /net/cci-nas-00/data/ceres_data/9n0q_48790/02_2026/9n0q_48790.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.09 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9n0q_48790/02_2026/9n0q_48790.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9n0q_48790/02_2026/9n0q_48790.map" model { file = "/net/cci-nas-00/data/ceres_data/9n0q_48790/02_2026/9n0q_48790.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9n0q_48790/02_2026/9n0q_48790.cif" } resolution = 3.09 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= 0.002 sd= 0.026 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 Zn 2 6.06 5 S 105 5.16 5 C 9377 2.51 5 N 2504 2.21 5 O 2680 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 2 residue(s): 0.01s 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: 14668 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 12989 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1648, 12989 Classifications: {'peptide': 1648} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 88, 'TRANS': 1559} Chain breaks: 3 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "B" Number of atoms: 507 Number of conformers: 1 Conformer: "" Number of residues, atoms: 66, 507 Classifications: {'peptide': 66} Link IDs: {'PTRANS': 5, 'TRANS': 60} Chain: "C" Number of atoms: 390 Number of conformers: 1 Conformer: "" Number of residues, atoms: 49, 390 Classifications: {'peptide': 49} Link IDs: {'TRANS': 48} Chain: "D" Number of atoms: 390 Number of conformers: 1 Conformer: "" Number of residues, atoms: 49, 390 Classifications: {'peptide': 49} Link IDs: {'TRANS': 48} Chain: "E" Number of atoms: 390 Number of conformers: 1 Conformer: "" Number of residues, atoms: 49, 390 Classifications: {'peptide': 49} Link IDs: {'TRANS': 48} Chain: "A" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 7697 SG CYS A 993 35.934 105.843 84.113 1.00 46.42 S ATOM 9128 SG CYS A1210 38.122 106.309 85.990 1.00 64.79 S ATOM 9150 SG CYS A1213 38.141 103.434 84.124 1.00 38.84 S ATOM 11445 SG CYS A1511 52.119 83.431 112.751 1.00114.88 S ATOM 12006 SG CYS A1586 54.022 80.118 113.373 1.00130.00 S Time building chain proxies: 3.08, per 1000 atoms: 0.21 Number of scatterers: 14668 At special positions: 0 Unit cell: (94.288, 130.808, 144.088, 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) Zn 2 29.99 S 105 16.00 O 2680 8.00 N 2504 7.00 C 9377 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.04 Conformation dependent library (CDL) restraints added in 540.9 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A1801 " pdb="ZN ZN A1801 " - pdb=" SG CYS A1213 " pdb="ZN ZN A1801 " - pdb=" SG CYS A1210 " pdb="ZN ZN A1801 " - pdb=" SG CYS A 993 " pdb=" ZN A1802 " pdb="ZN ZN A1802 " - pdb=" SG CYS A1511 " pdb="ZN ZN A1802 " - pdb=" SG CYS A1586 " pdb="ZN ZN A1802 " - pdb=" NE2 HIS A1485 " 3690 Ramachandran restraints generated. 1845 Oldfield, 0 Emsley, 1845 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3536 Finding SS restraints... Secondary structure from input PDB file: 89 helices and 8 sheets defined 59.6% alpha, 5.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.60 Creating SS restraints... Processing helix chain 'A' and resid 33 through 41 Processing helix chain 'A' and resid 45 through 53 removed outlier: 3.507A pdb=" N VAL A 49 " --> pdb=" O LEU A 45 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N ARG A 50 " --> pdb=" O PRO A 46 " (cutoff:3.500A) Processing helix chain 'A' and resid 61 through 63 No H-bonds generated for 'chain 'A' and resid 61 through 63' Processing helix chain 'A' and resid 64 through 70 removed outlier: 3.727A pdb=" N LEU A 68 " --> pdb=" O ASP A 64 " (cutoff:3.500A) Processing helix chain 'A' and resid 81 through 99 Processing helix chain 'A' and resid 104 through 118 removed outlier: 3.746A pdb=" N TYR A 109 " --> pdb=" O THR A 105 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N SER A 110 " --> pdb=" O LYS A 106 " (cutoff:3.500A) Processing helix chain 'A' and resid 118 through 139 Processing helix chain 'A' and resid 176 through 202 Processing helix chain 'A' and resid 208 through 221 Processing helix chain 'A' and resid 225 through 249 removed outlier: 4.944A pdb=" N SER A 237 " --> pdb=" O ILE A 233 " (cutoff:3.500A) Proline residue: A 238 - end of helix Processing helix chain 'A' and resid 255 through 259 removed outlier: 3.748A pdb=" N VAL A 259 " --> pdb=" O PHE A 256 " (cutoff:3.500A) Processing helix chain 'A' and resid 261 through 266 Processing helix chain 'A' and resid 266 through 280 Processing helix chain 'A' and resid 280 through 289 removed outlier: 3.555A pdb=" N SER A 289 " --> pdb=" O LEU A 285 " (cutoff:3.500A) Processing helix chain 'A' and resid 300 through 312 Processing helix chain 'A' and resid 318 through 346 removed outlier: 3.523A pdb=" N SER A 324 " --> pdb=" O GLN A 320 " (cutoff:3.500A) Processing helix chain 'A' and resid 358 through 368 removed outlier: 3.521A pdb=" N LYS A 362 " --> pdb=" O ASP A 358 " (cutoff:3.500A) Processing helix chain 'A' and resid 378 through 382 removed outlier: 3.530A pdb=" N ALA A 382 " --> pdb=" O GLN A 379 " (cutoff:3.500A) Processing helix chain 'A' and resid 397 through 402 removed outlier: 3.660A pdb=" N ILE A 401 " --> pdb=" O ASP A 397 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N VAL A 402 " --> pdb=" O PHE A 398 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 397 through 402' Processing helix chain 'A' and resid 410 through 417 removed outlier: 3.819A pdb=" N TRP A 414 " --> pdb=" O ARG A 411 " (cutoff:3.500A) removed outlier: 4.628A pdb=" N VAL A 415 " --> pdb=" O ARG A 412 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N PHE A 416 " --> pdb=" O ASP A 413 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N GLU A 417 " --> pdb=" O TRP A 414 " (cutoff:3.500A) Processing helix chain 'A' and resid 419 through 428 removed outlier: 3.514A pdb=" N PHE A 423 " --> pdb=" O ASN A 419 " (cutoff:3.500A) Processing helix chain 'A' and resid 442 through 449 Processing helix chain 'A' and resid 454 through 465 Proline residue: A 461 - end of helix Processing helix chain 'A' and resid 468 through 471 Processing helix chain 'A' and resid 495 through 512 removed outlier: 3.501A pdb=" N VAL A 512 " --> pdb=" O LEU A 508 " (cutoff:3.500A) Processing helix chain 'A' and resid 516 through 524 removed outlier: 3.781A pdb=" N THR A 522 " --> pdb=" O THR A 518 " (cutoff:3.500A) Processing helix chain 'A' and resid 524 through 539 Processing helix chain 'A' and resid 553 through 558 removed outlier: 3.745A pdb=" N PHE A 558 " --> pdb=" O TRP A 554 " (cutoff:3.500A) Processing helix chain 'A' and resid 559 through 574 removed outlier: 3.520A pdb=" N GLN A 563 " --> pdb=" O ARG A 559 " (cutoff:3.500A) Proline residue: A 565 - end of helix Processing helix chain 'A' and resid 581 through 586 removed outlier: 4.016A pdb=" N THR A 585 " --> pdb=" O ARG A 581 " (cutoff:3.500A) Processing helix chain 'A' and resid 587 through 589 No H-bonds generated for 'chain 'A' and resid 587 through 589' Processing helix chain 'A' and resid 627 through 645 Processing helix chain 'A' and resid 670 through 689 removed outlier: 3.820A pdb=" N ALA A 689 " --> pdb=" O HIS A 685 " (cutoff:3.500A) Processing helix chain 'A' and resid 694 through 698 removed outlier: 3.599A pdb=" N CYS A 698 " --> pdb=" O VAL A 695 " (cutoff:3.500A) Processing helix chain 'A' and resid 720 through 726 removed outlier: 3.504A pdb=" N SER A 726 " --> pdb=" O LEU A 722 " (cutoff:3.500A) Processing helix chain 'A' and resid 738 through 756 removed outlier: 3.575A pdb=" N LYS A 742 " --> pdb=" O ASN A 738 " (cutoff:3.500A) Processing helix chain 'A' and resid 759 through 779 removed outlier: 3.727A pdb=" N GLU A 778 " --> pdb=" O GLU A 774 " (cutoff:3.500A) Processing helix chain 'A' and resid 780 through 785 Processing helix chain 'A' and resid 786 through 795 Processing helix chain 'A' and resid 797 through 801 removed outlier: 3.623A pdb=" N ILE A 800 " --> pdb=" O GLY A 797 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N GLY A 801 " --> pdb=" O PRO A 798 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 797 through 801' Processing helix chain 'A' and resid 805 through 809 removed outlier: 3.787A pdb=" N THR A 808 " --> pdb=" O THR A 805 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N LEU A 809 " --> pdb=" O PRO A 806 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 805 through 809' Processing helix chain 'A' and resid 819 through 834 removed outlier: 4.546A pdb=" N PHE A 823 " --> pdb=" O ASP A 819 " (cutoff:3.500A) Processing helix chain 'A' and resid 838 through 847 removed outlier: 3.561A pdb=" N VAL A 842 " --> pdb=" O THR A 838 " (cutoff:3.500A) Processing helix chain 'A' and resid 855 through 862 removed outlier: 3.922A pdb=" N LEU A 859 " --> pdb=" O ASP A 855 " (cutoff:3.500A) Processing helix chain 'A' and resid 880 through 890 Processing helix chain 'A' and resid 902 through 915 Processing helix chain 'A' and resid 921 through 930 Processing helix chain 'A' and resid 932 through 946 removed outlier: 3.680A pdb=" N TYR A 936 " --> pdb=" O SER A 932 " (cutoff:3.500A) Processing helix chain 'A' and resid 950 through 957 Processing helix chain 'A' and resid 960 through 979 removed outlier: 3.975A pdb=" N LEU A 964 " --> pdb=" O GLU A 960 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N VAL A 967 " --> pdb=" O ALA A 963 " (cutoff:3.500A) Processing helix chain 'A' and resid 986 through 991 removed outlier: 4.062A pdb=" N GLU A 991 " --> pdb=" O PRO A 988 " (cutoff:3.500A) Processing helix chain 'A' and resid 993 through 1007 Processing helix chain 'A' and resid 1017 through 1021 Processing helix chain 'A' and resid 1032 through 1036 removed outlier: 3.738A pdb=" N LEU A1036 " --> pdb=" O GLU A1033 " (cutoff:3.500A) Processing helix chain 'A' and resid 1084 through 1100 removed outlier: 3.952A pdb=" N LYS A1088 " --> pdb=" O ALA A1084 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N ARG A1100 " --> pdb=" O TRP A1096 " (cutoff:3.500A) Processing helix chain 'A' and resid 1104 through 1118 Processing helix chain 'A' and resid 1153 through 1156 Processing helix chain 'A' and resid 1178 through 1196 removed outlier: 3.500A pdb=" N VAL A1182 " --> pdb=" O HIS A1178 " (cutoff:3.500A) Processing helix chain 'A' and resid 1210 through 1214 removed outlier: 3.585A pdb=" N CYS A1213 " --> pdb=" O CYS A1210 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N PHE A1214 " --> pdb=" O LYS A1211 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1210 through 1214' Processing helix chain 'A' and resid 1255 through 1277 removed outlier: 3.892A pdb=" N SER A1259 " --> pdb=" O ASP A1255 " (cutoff:3.500A) Processing helix chain 'A' and resid 1279 through 1284 removed outlier: 3.896A pdb=" N MET A1284 " --> pdb=" O GLY A1280 " (cutoff:3.500A) Processing helix chain 'A' and resid 1297 through 1303 Processing helix chain 'A' and resid 1305 through 1320 removed outlier: 3.554A pdb=" N ARG A1320 " --> pdb=" O LEU A1316 " (cutoff:3.500A) Processing helix chain 'A' and resid 1322 through 1335 Processing helix chain 'A' and resid 1338 through 1348 Processing helix chain 'A' and resid 1351 through 1357 removed outlier: 3.870A pdb=" N CYS A1357 " --> pdb=" O LEU A1353 " (cutoff:3.500A) Processing helix chain 'A' and resid 1357 through 1364 removed outlier: 4.061A pdb=" N ARG A1362 " --> pdb=" O ALA A1358 " (cutoff:3.500A) Processing helix chain 'A' and resid 1371 through 1381 Processing helix chain 'A' and resid 1381 through 1386 removed outlier: 4.160A pdb=" N ILE A1385 " --> pdb=" O LEU A1381 " (cutoff:3.500A) Processing helix chain 'A' and resid 1398 through 1403 removed outlier: 3.594A pdb=" N HIS A1402 " --> pdb=" O ASN A1398 " (cutoff:3.500A) Processing helix chain 'A' and resid 1408 through 1420 removed outlier: 5.602A pdb=" N SER A1418 " --> pdb=" O ALA A1414 " (cutoff:3.500A) removed outlier: 4.394A pdb=" N VAL A1419 " --> pdb=" O ALA A1415 " (cutoff:3.500A) removed outlier: 4.390A pdb=" N GLY A1420 " --> pdb=" O ALA A1416 " (cutoff:3.500A) Processing helix chain 'A' and resid 1450 through 1464 removed outlier: 3.920A pdb=" N SER A1454 " --> pdb=" O SER A1450 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N LEU A1457 " --> pdb=" O GLN A1453 " (cutoff:3.500A) Processing helix chain 'A' and resid 1476 through 1486 removed outlier: 3.554A pdb=" N ALA A1480 " --> pdb=" O ASP A1476 " (cutoff:3.500A) Processing helix chain 'A' and resid 1499 through 1509 removed outlier: 3.569A pdb=" N MET A1508 " --> pdb=" O ARG A1504 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N ASP A1509 " --> pdb=" O LEU A1505 " (cutoff:3.500A) Processing helix chain 'A' and resid 1519 through 1525 Processing helix chain 'A' and resid 1590 through 1594 removed outlier: 3.659A pdb=" N TYR A1594 " --> pdb=" O ARG A1591 " (cutoff:3.500A) Processing helix chain 'A' and resid 1597 through 1616 removed outlier: 3.566A pdb=" N TYR A1608 " --> pdb=" O LEU A1604 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N LEU A1616 " --> pdb=" O MET A1612 " (cutoff:3.500A) Processing helix chain 'A' and resid 1623 through 1641 removed outlier: 4.171A pdb=" N ILE A1639 " --> pdb=" O VAL A1635 " (cutoff:3.500A) removed outlier: 4.752A pdb=" N GLY A1641 " --> pdb=" O GLN A1637 " (cutoff:3.500A) Processing helix chain 'A' and resid 1683 through 1689 removed outlier: 3.631A pdb=" N LEU A1687 " --> pdb=" O SER A1683 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N ASP A1689 " --> pdb=" O ALA A1685 " (cutoff:3.500A) Processing helix chain 'A' and resid 1701 through 1709 Processing helix chain 'B' and resid 119 through 126 Processing helix chain 'B' and resid 127 through 168 removed outlier: 3.761A pdb=" N LYS B 158 " --> pdb=" O LEU B 154 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N VAL B 168 " --> pdb=" O ALA B 164 " (cutoff:3.500A) Processing helix chain 'C' and resid 119 through 125 Processing helix chain 'C' and resid 127 through 165 removed outlier: 3.785A pdb=" N SER C 165 " --> pdb=" O LEU C 161 " (cutoff:3.500A) Processing helix chain 'D' and resid 119 through 125 Processing helix chain 'D' and resid 127 through 160 removed outlier: 3.659A pdb=" N ARG D 132 " --> pdb=" O SER D 128 " (cutoff:3.500A) Processing helix chain 'D' and resid 161 through 166 Processing helix chain 'E' and resid 119 through 126 removed outlier: 3.771A pdb=" N ASP E 126 " --> pdb=" O ALA E 122 " (cutoff:3.500A) Processing helix chain 'E' and resid 127 through 166 removed outlier: 3.513A pdb=" N ILE E 131 " --> pdb=" O HIS E 127 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N LEU E 141 " --> pdb=" O ASN E 137 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N LYS E 158 " --> pdb=" O LEU E 154 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 58 through 60 removed outlier: 4.487A pdb=" N LEU A 173 " --> pdb=" O LEU A 60 " (cutoff:3.500A) removed outlier: 4.774A pdb=" N PHE A 158 " --> pdb=" O GLY A 147 " (cutoff:3.500A) removed outlier: 5.495A pdb=" N GLY A 147 " --> pdb=" O PHE A 158 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 351 through 353 Processing sheet with id=AA3, first strand: chain 'A' and resid 407 through 408 removed outlier: 3.796A pdb=" N THR A 494 " --> pdb=" O LEU A 473 " (cutoff:3.500A) removed outlier: 7.727A pdb=" N LEU A 473 " --> pdb=" O THR A 494 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 650 through 655 removed outlier: 3.654A pdb=" N ASN A 658 " --> pdb=" O GLN A 655 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 704 through 707 Processing sheet with id=AA6, first strand: chain 'A' and resid 1022 through 1026 removed outlier: 3.579A pdb=" N LEU A1205 " --> pdb=" O HIS A1025 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 1490 through 1493 removed outlier: 3.743A pdb=" N ILE A1471 " --> pdb=" O ILE A1492 " (cutoff:3.500A) removed outlier: 8.501A pdb=" N ILE A1534 " --> pdb=" O VAL A1468 " (cutoff:3.500A) removed outlier: 6.682A pdb=" N TYR A1470 " --> pdb=" O ILE A1534 " (cutoff:3.500A) removed outlier: 6.918A pdb=" N THR A1533 " --> pdb=" O ILE A1543 " (cutoff:3.500A) removed outlier: 8.684A pdb=" N LEU A1545 " --> pdb=" O THR A1533 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 1659 through 1662 755 hydrogen bonds defined for protein. 2205 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: 2.56 Time building geometry restraints manager: 1.46 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: 4699 1.34 - 1.47: 3321 1.47 - 1.59: 6791 1.59 - 1.71: 0 1.71 - 1.83: 165 Bond restraints: 14976 Sorted by residual: bond pdb=" C ARG A1623 " pdb=" N PRO A1624 " ideal model delta sigma weight residual 1.334 1.404 -0.070 2.34e-02 1.83e+03 8.90e+00 bond pdb=" C GLY A 147 " pdb=" N PRO A 148 " ideal model delta sigma weight residual 1.332 1.357 -0.025 1.12e-02 7.97e+03 4.94e+00 bond pdb=" CA ILE A 455 " pdb=" CB ILE A 455 " ideal model delta sigma weight residual 1.537 1.565 -0.028 1.29e-02 6.01e+03 4.79e+00 bond pdb=" CA PRO A 75 " pdb=" C PRO A 75 " ideal model delta sigma weight residual 1.517 1.532 -0.015 6.70e-03 2.23e+04 4.72e+00 bond pdb=" CA ILE A 262 " pdb=" C ILE A 262 " ideal model delta sigma weight residual 1.520 1.538 -0.019 8.80e-03 1.29e+04 4.42e+00 ... (remaining 14971 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.28: 19689 2.28 - 4.56: 520 4.56 - 6.84: 75 6.84 - 9.12: 24 9.12 - 11.40: 7 Bond angle restraints: 20315 Sorted by residual: angle pdb=" C THR A1242 " pdb=" N VAL A1243 " pdb=" CA VAL A1243 " ideal model delta sigma weight residual 120.24 123.66 -3.42 6.30e-01 2.52e+00 2.94e+01 angle pdb=" C SER A 948 " pdb=" N THR A 949 " pdb=" CA THR A 949 " ideal model delta sigma weight residual 121.54 129.66 -8.12 1.91e+00 2.74e-01 1.81e+01 angle pdb=" C PHE A1433 " pdb=" N THR A1434 " pdb=" CA THR A1434 " ideal model delta sigma weight residual 121.54 129.38 -7.84 1.91e+00 2.74e-01 1.69e+01 angle pdb=" C SER A 731 " pdb=" N THR A 732 " pdb=" CA THR A 732 " ideal model delta sigma weight residual 122.46 128.15 -5.69 1.41e+00 5.03e-01 1.63e+01 angle pdb=" C SER A 893 " pdb=" N ARG A 894 " pdb=" CA ARG A 894 " ideal model delta sigma weight residual 121.54 129.24 -7.70 1.91e+00 2.74e-01 1.62e+01 ... (remaining 20310 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.07: 8431 17.07 - 34.15: 568 34.15 - 51.22: 83 51.22 - 68.30: 15 68.30 - 85.37: 7 Dihedral angle restraints: 9104 sinusoidal: 3651 harmonic: 5453 Sorted by residual: dihedral pdb=" CA GLU A 875 " pdb=" C GLU A 875 " pdb=" N ARG A 876 " pdb=" CA ARG A 876 " ideal model delta harmonic sigma weight residual 180.00 151.78 28.22 0 5.00e+00 4.00e-02 3.19e+01 dihedral pdb=" CA MET A 918 " pdb=" C MET A 918 " pdb=" N PRO A 919 " pdb=" CA PRO A 919 " ideal model delta harmonic sigma weight residual 180.00 154.05 25.95 0 5.00e+00 4.00e-02 2.69e+01 dihedral pdb=" CA VAL A1649 " pdb=" C VAL A1649 " pdb=" N TYR A1650 " pdb=" CA TYR A1650 " ideal model delta harmonic sigma weight residual 180.00 155.11 24.89 0 5.00e+00 4.00e-02 2.48e+01 ... (remaining 9101 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.076: 1994 0.076 - 0.152: 332 0.152 - 0.227: 29 0.227 - 0.303: 0 0.303 - 0.379: 1 Chirality restraints: 2356 Sorted by residual: chirality pdb=" CB ILE A1237 " pdb=" CA ILE A1237 " pdb=" CG1 ILE A1237 " pdb=" CG2 ILE A1237 " both_signs ideal model delta sigma weight residual False 2.64 2.27 0.38 2.00e-01 2.50e+01 3.59e+00 chirality pdb=" CG LEU C 141 " pdb=" CB LEU C 141 " pdb=" CD1 LEU C 141 " pdb=" CD2 LEU C 141 " both_signs ideal model delta sigma weight residual False -2.59 -2.37 -0.22 2.00e-01 2.50e+01 1.25e+00 chirality pdb=" CG LEU A1510 " pdb=" CB LEU A1510 " pdb=" CD1 LEU A1510 " pdb=" CD2 LEU A1510 " both_signs ideal model delta sigma weight residual False -2.59 -2.38 -0.21 2.00e-01 2.50e+01 1.09e+00 ... (remaining 2353 not shown) Planarity restraints: 2561 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP A 348 " -0.016 2.00e-02 2.50e+03 2.41e-02 1.45e+01 pdb=" CG TRP A 348 " 0.058 2.00e-02 2.50e+03 pdb=" CD1 TRP A 348 " -0.044 2.00e-02 2.50e+03 pdb=" CD2 TRP A 348 " 0.002 2.00e-02 2.50e+03 pdb=" NE1 TRP A 348 " 0.007 2.00e-02 2.50e+03 pdb=" CE2 TRP A 348 " 0.007 2.00e-02 2.50e+03 pdb=" CE3 TRP A 348 " -0.002 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 348 " 0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 348 " -0.013 2.00e-02 2.50e+03 pdb=" CH2 TRP A 348 " -0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LEU A 354 " 0.053 5.00e-02 4.00e+02 8.10e-02 1.05e+01 pdb=" N PRO A 355 " -0.140 5.00e-02 4.00e+02 pdb=" CA PRO A 355 " 0.043 5.00e-02 4.00e+02 pdb=" CD PRO A 355 " 0.044 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA A1358 " -0.051 5.00e-02 4.00e+02 7.70e-02 9.48e+00 pdb=" N PRO A1359 " 0.133 5.00e-02 4.00e+02 pdb=" CA PRO A1359 " -0.039 5.00e-02 4.00e+02 pdb=" CD PRO A1359 " -0.043 5.00e-02 4.00e+02 ... (remaining 2558 not shown) Histogram of nonbonded interaction distances: 1.96 - 2.55: 45 2.55 - 3.14: 10746 3.14 - 3.73: 22608 3.73 - 4.31: 30870 4.31 - 4.90: 51445 Nonbonded interactions: 115714 Sorted by model distance: nonbonded pdb=" OD1 ASP A1509 " pdb="ZN ZN A1802 " model vdw 1.964 2.230 nonbonded pdb=" OE2 GLU A1020 " pdb="ZN ZN A1801 " model vdw 1.985 2.230 nonbonded pdb=" OD2 ASP A1509 " pdb="ZN ZN A1802 " model vdw 2.010 2.230 nonbonded pdb=" CG ASP A1509 " pdb="ZN ZN A1802 " model vdw 2.212 2.460 nonbonded pdb=" O LEU A 285 " pdb=" OG SER A 289 " model vdw 2.271 3.040 ... (remaining 115709 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 Found NCS groups: ncs_group { reference = chain 'C' selection = chain 'D' selection = chain 'E' } 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: 3.630 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: 0.320 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 15.010 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:1.170 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.350 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7167 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 : 0.005 0.071 14982 Z= 0.234 Angle : 0.908 11.402 20315 Z= 0.481 Chirality : 0.055 0.379 2356 Planarity : 0.009 0.081 2561 Dihedral : 11.873 85.374 5568 Min Nonbonded Distance : 1.964 Molprobity Statistics. All-atom Clashscore : 3.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.44 % Favored : 95.56 % Rotamer: Outliers : 0.00 % Allowed : 0.12 % Favored : 99.88 % 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: -2.07 (0.17), residues: 1845 helix: -1.04 (0.14), residues: 1000 sheet: 0.09 (0.57), residues: 92 loop : -1.91 (0.20), residues: 753 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A 879 TYR 0.036 0.002 TYR A 109 PHE 0.022 0.003 PHE A 814 TRP 0.058 0.004 TRP A 348 HIS 0.013 0.002 HIS A 191 Details of bonding type rmsd covalent geometry : bond 0.00474 (14976) covalent geometry : angle 0.90832 (20315) hydrogen bonds : bond 0.15542 ( 755) hydrogen bonds : angle 6.28868 ( 2205) metal coordination : bond 0.01634 ( 6) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3690 Ramachandran restraints generated. 1845 Oldfield, 0 Emsley, 1845 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3690 Ramachandran restraints generated. 1845 Oldfield, 0 Emsley, 1845 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 302 residues out of total 1638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 302 time to evaluate : 0.583 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 20 ILE cc_start: 0.7314 (pt) cc_final: 0.7048 (mm) REVERT: A 22 ARG cc_start: 0.7744 (ptp90) cc_final: 0.7346 (ptt-90) REVERT: A 117 THR cc_start: 0.8382 (m) cc_final: 0.8113 (p) REVERT: A 212 ILE cc_start: 0.8454 (mm) cc_final: 0.8165 (mm) REVERT: A 391 ASP cc_start: 0.7716 (t0) cc_final: 0.7429 (m-30) REVERT: A 477 VAL cc_start: 0.8098 (t) cc_final: 0.7864 (m) REVERT: A 503 VAL cc_start: 0.6480 (t) cc_final: 0.5530 (p) REVERT: A 505 GLU cc_start: 0.7295 (mt-10) cc_final: 0.7004 (mt-10) REVERT: A 511 GLU cc_start: 0.6714 (mp0) cc_final: 0.6483 (mp0) REVERT: A 575 ASN cc_start: 0.7949 (t0) cc_final: 0.7548 (t0) REVERT: A 609 VAL cc_start: 0.8649 (t) cc_final: 0.8324 (p) REVERT: A 621 THR cc_start: 0.8379 (t) cc_final: 0.8150 (m) REVERT: A 665 LYS cc_start: 0.7957 (tttm) cc_final: 0.7438 (ttpp) REVERT: A 676 GLU cc_start: 0.7307 (mt-10) cc_final: 0.6726 (mt-10) REVERT: A 710 LYS cc_start: 0.7398 (ttmt) cc_final: 0.7176 (ttpt) REVERT: A 718 VAL cc_start: 0.8315 (t) cc_final: 0.8017 (m) REVERT: A 722 LEU cc_start: 0.8494 (mt) cc_final: 0.8254 (mp) REVERT: A 745 CYS cc_start: 0.7492 (p) cc_final: 0.7289 (t) REVERT: A 747 THR cc_start: 0.8661 (m) cc_final: 0.8051 (p) REVERT: A 889 SER cc_start: 0.6204 (m) cc_final: 0.6004 (t) REVERT: A 1176 THR cc_start: 0.7464 (p) cc_final: 0.7233 (t) REVERT: A 1409 MET cc_start: 0.6408 (tpt) cc_final: 0.6157 (tpt) REVERT: A 1605 MET cc_start: 0.7456 (ttm) cc_final: 0.7051 (ttm) REVERT: C 152 MET cc_start: 0.7485 (mmt) cc_final: 0.6913 (mpp) REVERT: D 149 MET cc_start: 0.7204 (tpt) cc_final: 0.6616 (tpt) REVERT: E 149 MET cc_start: 0.7698 (ttm) cc_final: 0.7483 (ttm) REVERT: E 152 MET cc_start: 0.7911 (ttt) cc_final: 0.7500 (ttt) outliers start: 0 outliers final: 0 residues processed: 302 average time/residue: 0.1340 time to fit residues: 57.6553 Evaluate side-chains 250 residues out of total 1638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 250 time to evaluate : 0.533 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 98 optimal weight: 0.6980 chunk 107 optimal weight: 1.9990 chunk 10 optimal weight: 0.6980 chunk 66 optimal weight: 1.9990 chunk 130 optimal weight: 5.9990 chunk 124 optimal weight: 7.9990 chunk 103 optimal weight: 0.9980 chunk 77 optimal weight: 0.9980 chunk 122 optimal weight: 20.0000 chunk 91 optimal weight: 1.9990 chunk 149 optimal weight: 9.9990 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 48 HIS A 137 GLN A 664 HIS A 692 ASN A1291 ASN A1323 GLN ** A1431 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1455 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4260 r_free = 0.4260 target = 0.186228 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3727 r_free = 0.3727 target = 0.143158 restraints weight = 21292.456| |-----------------------------------------------------------------------------| r_work (start): 0.3692 rms_B_bonded: 2.42 r_work: 0.3561 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.3403 rms_B_bonded: 4.68 restraints_weight: 0.2500 r_work (final): 0.3403 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7316 moved from start: 0.1881 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 14982 Z= 0.192 Angle : 0.642 9.823 20315 Z= 0.336 Chirality : 0.045 0.166 2356 Planarity : 0.006 0.059 2561 Dihedral : 4.819 24.832 2025 Min Nonbonded Distance : 1.998 Molprobity Statistics. All-atom Clashscore : 6.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.90 % Favored : 96.10 % Rotamer: Outliers : 1.22 % Allowed : 6.29 % Favored : 92.49 % 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: -0.66 (0.19), residues: 1845 helix: 0.42 (0.16), residues: 1015 sheet: 0.15 (0.54), residues: 98 loop : -1.72 (0.21), residues: 732 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 70 TYR 0.028 0.002 TYR A 109 PHE 0.023 0.002 PHE A 230 TRP 0.038 0.002 TRP A 203 HIS 0.013 0.002 HIS A1181 Details of bonding type rmsd covalent geometry : bond 0.00443 (14976) covalent geometry : angle 0.64157 (20315) hydrogen bonds : bond 0.05788 ( 755) hydrogen bonds : angle 4.49726 ( 2205) metal coordination : bond 0.01077 ( 6) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3690 Ramachandran restraints generated. 1845 Oldfield, 0 Emsley, 1845 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3690 Ramachandran restraints generated. 1845 Oldfield, 0 Emsley, 1845 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 284 residues out of total 1638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 264 time to evaluate : 0.564 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 117 THR cc_start: 0.8273 (m) cc_final: 0.7899 (p) REVERT: A 212 ILE cc_start: 0.8401 (mm) cc_final: 0.8136 (mm) REVERT: A 308 GLN cc_start: 0.7749 (tp40) cc_final: 0.7533 (tp40) REVERT: A 490 PHE cc_start: 0.7122 (p90) cc_final: 0.6906 (p90) REVERT: A 505 GLU cc_start: 0.7529 (mt-10) cc_final: 0.7311 (mt-10) REVERT: A 609 VAL cc_start: 0.8680 (t) cc_final: 0.8342 (p) REVERT: A 665 LYS cc_start: 0.8004 (tttm) cc_final: 0.7497 (ttpp) REVERT: A 676 GLU cc_start: 0.7251 (mt-10) cc_final: 0.6993 (mt-10) REVERT: A 696 GLU cc_start: 0.7411 (OUTLIER) cc_final: 0.7189 (mp0) REVERT: A 718 VAL cc_start: 0.8362 (t) cc_final: 0.8146 (m) REVERT: A 746 LEU cc_start: 0.8476 (tp) cc_final: 0.8201 (tt) REVERT: A 860 VAL cc_start: 0.8093 (m) cc_final: 0.7806 (t) REVERT: A 913 ASP cc_start: 0.7544 (t0) cc_final: 0.7337 (t70) REVERT: A 1054 THR cc_start: 0.6743 (p) cc_final: 0.6536 (p) REVERT: A 1194 ILE cc_start: 0.7843 (mm) cc_final: 0.7621 (mt) REVERT: A 1409 MET cc_start: 0.6453 (tpt) cc_final: 0.6197 (tpt) REVERT: A 1605 MET cc_start: 0.7640 (ttm) cc_final: 0.7372 (ttm) REVERT: C 156 MET cc_start: 0.6737 (mmm) cc_final: 0.6511 (tmm) REVERT: D 148 MET cc_start: 0.5929 (ttt) cc_final: 0.5516 (ttt) REVERT: D 152 MET cc_start: 0.7095 (mmm) cc_final: 0.6800 (mmm) REVERT: E 152 MET cc_start: 0.7831 (ttt) cc_final: 0.7570 (tpp) REVERT: E 156 MET cc_start: 0.7023 (ttp) cc_final: 0.6767 (ttp) outliers start: 20 outliers final: 15 residues processed: 271 average time/residue: 0.1333 time to fit residues: 51.3463 Evaluate side-chains 265 residues out of total 1638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 249 time to evaluate : 0.552 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 395 ASP Chi-restraints excluded: chain A residue 494 THR Chi-restraints excluded: chain A residue 518 THR Chi-restraints excluded: chain A residue 552 SER Chi-restraints excluded: chain A residue 696 GLU Chi-restraints excluded: chain A residue 701 SER Chi-restraints excluded: chain A residue 724 GLN Chi-restraints excluded: chain A residue 750 CYS Chi-restraints excluded: chain A residue 779 LEU Chi-restraints excluded: chain A residue 931 LEU Chi-restraints excluded: chain A residue 940 ILE Chi-restraints excluded: chain A residue 964 LEU Chi-restraints excluded: chain A residue 966 SER Chi-restraints excluded: chain A residue 1018 VAL Chi-restraints excluded: chain A residue 1090 THR Chi-restraints excluded: chain A residue 1577 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 85 optimal weight: 0.7980 chunk 175 optimal weight: 8.9990 chunk 111 optimal weight: 2.9990 chunk 84 optimal weight: 0.7980 chunk 176 optimal weight: 1.9990 chunk 164 optimal weight: 50.0000 chunk 116 optimal weight: 2.9990 chunk 83 optimal weight: 2.9990 chunk 166 optimal weight: 5.9990 chunk 130 optimal weight: 6.9990 chunk 3 optimal weight: 2.9990 overall best weight: 1.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 137 GLN A 575 ASN ** A1023 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1431 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4211 r_free = 0.4211 target = 0.181784 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3652 r_free = 0.3652 target = 0.138256 restraints weight = 21382.474| |-----------------------------------------------------------------------------| r_work (start): 0.3630 rms_B_bonded: 2.40 r_work: 0.3490 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.3330 rms_B_bonded: 4.62 restraints_weight: 0.2500 r_work (final): 0.3330 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7442 moved from start: 0.3004 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.082 14982 Z= 0.304 Angle : 0.730 9.162 20315 Z= 0.384 Chirality : 0.050 0.207 2356 Planarity : 0.007 0.059 2561 Dihedral : 5.083 24.211 2025 Min Nonbonded Distance : 1.925 Molprobity Statistics. All-atom Clashscore : 7.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.20 % Favored : 94.80 % Rotamer: Outliers : 2.38 % Allowed : 9.10 % Favored : 88.52 % 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: -0.69 (0.19), residues: 1845 helix: 0.56 (0.16), residues: 1019 sheet: -0.56 (0.50), residues: 113 loop : -1.95 (0.21), residues: 713 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 923 TYR 0.031 0.003 TYR A 109 PHE 0.031 0.003 PHE A1160 TRP 0.044 0.003 TRP A 203 HIS 0.024 0.002 HIS A1181 Details of bonding type rmsd covalent geometry : bond 0.00722 (14976) covalent geometry : angle 0.72967 (20315) hydrogen bonds : bond 0.06696 ( 755) hydrogen bonds : angle 4.54914 ( 2205) metal coordination : bond 0.01695 ( 6) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3690 Ramachandran restraints generated. 1845 Oldfield, 0 Emsley, 1845 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3690 Ramachandran restraints generated. 1845 Oldfield, 0 Emsley, 1845 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 318 residues out of total 1638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 279 time to evaluate : 0.572 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 24 ASP cc_start: 0.7985 (m-30) cc_final: 0.7753 (m-30) REVERT: A 89 GLU cc_start: 0.7870 (mt-10) cc_final: 0.7603 (mt-10) REVERT: A 117 THR cc_start: 0.8411 (m) cc_final: 0.8109 (p) REVERT: A 126 GLU cc_start: 0.7217 (mt-10) cc_final: 0.6880 (mt-10) REVERT: A 149 LYS cc_start: 0.8447 (mmtm) cc_final: 0.8217 (mmtm) REVERT: A 212 ILE cc_start: 0.8506 (mm) cc_final: 0.8302 (mm) REVERT: A 308 GLN cc_start: 0.7779 (tp40) cc_final: 0.7510 (tp40) REVERT: A 359 LYS cc_start: 0.7964 (ttpp) cc_final: 0.7727 (tttm) REVERT: A 417 GLU cc_start: 0.7643 (mm-30) cc_final: 0.7366 (mm-30) REVERT: A 451 ARG cc_start: 0.7785 (mtp85) cc_final: 0.7005 (mtp85) REVERT: A 561 GLU cc_start: 0.7626 (mp0) cc_final: 0.6801 (pm20) REVERT: A 633 ILE cc_start: 0.7836 (mt) cc_final: 0.7635 (mt) REVERT: A 665 LYS cc_start: 0.8091 (tttm) cc_final: 0.7780 (ttpt) REVERT: A 676 GLU cc_start: 0.7361 (mt-10) cc_final: 0.7104 (mt-10) REVERT: A 787 GLU cc_start: 0.8107 (tt0) cc_final: 0.7523 (tt0) REVERT: A 860 VAL cc_start: 0.8366 (m) cc_final: 0.8044 (t) REVERT: A 938 LEU cc_start: 0.7744 (mm) cc_final: 0.7467 (mp) REVERT: A 1409 MET cc_start: 0.6449 (tpt) cc_final: 0.6228 (tpt) REVERT: E 152 MET cc_start: 0.8044 (ttt) cc_final: 0.7565 (tpp) outliers start: 39 outliers final: 21 residues processed: 299 average time/residue: 0.1219 time to fit residues: 52.8447 Evaluate side-chains 290 residues out of total 1638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 269 time to evaluate : 0.468 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 VAL Chi-restraints excluded: chain A residue 408 ILE Chi-restraints excluded: chain A residue 518 THR Chi-restraints excluded: chain A residue 536 SER Chi-restraints excluded: chain A residue 537 HIS Chi-restraints excluded: chain A residue 696 GLU Chi-restraints excluded: chain A residue 701 SER Chi-restraints excluded: chain A residue 750 CYS Chi-restraints excluded: chain A residue 779 LEU Chi-restraints excluded: chain A residue 931 LEU Chi-restraints excluded: chain A residue 940 ILE Chi-restraints excluded: chain A residue 964 LEU Chi-restraints excluded: chain A residue 966 SER Chi-restraints excluded: chain A residue 1018 VAL Chi-restraints excluded: chain A residue 1034 LEU Chi-restraints excluded: chain A residue 1042 CYS Chi-restraints excluded: chain A residue 1153 ILE Chi-restraints excluded: chain A residue 1164 TYR Chi-restraints excluded: chain A residue 1284 MET Chi-restraints excluded: chain A residue 1430 THR Chi-restraints excluded: chain C residue 149 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 44 optimal weight: 0.6980 chunk 15 optimal weight: 0.9980 chunk 109 optimal weight: 0.8980 chunk 57 optimal weight: 0.7980 chunk 121 optimal weight: 9.9990 chunk 22 optimal weight: 0.6980 chunk 69 optimal weight: 1.9990 chunk 93 optimal weight: 8.9990 chunk 11 optimal weight: 0.5980 chunk 160 optimal weight: 1.9990 chunk 27 optimal weight: 0.6980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 137 GLN A 226 HIS A 575 ASN A 738 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4242 r_free = 0.4242 target = 0.184221 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3682 r_free = 0.3682 target = 0.140643 restraints weight = 21281.423| |-----------------------------------------------------------------------------| r_work (start): 0.3661 rms_B_bonded: 2.53 r_work: 0.3531 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.3370 rms_B_bonded: 4.73 restraints_weight: 0.2500 r_work (final): 0.3370 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7401 moved from start: 0.3127 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 14982 Z= 0.143 Angle : 0.556 5.950 20315 Z= 0.290 Chirality : 0.042 0.151 2356 Planarity : 0.005 0.056 2561 Dihedral : 4.611 21.229 2025 Min Nonbonded Distance : 2.306 Molprobity Statistics. All-atom Clashscore : 6.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.23 % Favored : 95.77 % Rotamer: Outliers : 1.71 % Allowed : 11.61 % Favored : 86.68 % 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: -0.03 (0.20), residues: 1845 helix: 1.18 (0.17), residues: 1007 sheet: -0.34 (0.51), residues: 112 loop : -1.72 (0.21), residues: 726 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 923 TYR 0.020 0.002 TYR A 109 PHE 0.021 0.001 PHE A 230 TRP 0.033 0.002 TRP A 203 HIS 0.008 0.001 HIS A 226 Details of bonding type rmsd covalent geometry : bond 0.00326 (14976) covalent geometry : angle 0.55563 (20315) hydrogen bonds : bond 0.04870 ( 755) hydrogen bonds : angle 4.12825 ( 2205) metal coordination : bond 0.00496 ( 6) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3690 Ramachandran restraints generated. 1845 Oldfield, 0 Emsley, 1845 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3690 Ramachandran restraints generated. 1845 Oldfield, 0 Emsley, 1845 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 296 residues out of total 1638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 268 time to evaluate : 0.394 Fit side-chains revert: symmetry clash REVERT: A 24 ASP cc_start: 0.7917 (m-30) cc_final: 0.7698 (m-30) REVERT: A 126 GLU cc_start: 0.7121 (mt-10) cc_final: 0.6895 (mt-10) REVERT: A 212 ILE cc_start: 0.8466 (mm) cc_final: 0.8250 (mm) REVERT: A 359 LYS cc_start: 0.7763 (ttpp) cc_final: 0.7536 (tttm) REVERT: A 451 ARG cc_start: 0.7769 (mtp85) cc_final: 0.6950 (mtp85) REVERT: A 511 GLU cc_start: 0.7167 (mp0) cc_final: 0.6889 (mp0) REVERT: A 561 GLU cc_start: 0.7570 (mp0) cc_final: 0.6796 (pm20) REVERT: A 665 LYS cc_start: 0.8047 (tttm) cc_final: 0.7624 (ttpp) REVERT: A 676 GLU cc_start: 0.7338 (mt-10) cc_final: 0.7093 (mt-10) REVERT: A 722 LEU cc_start: 0.8493 (mt) cc_final: 0.8273 (mp) REVERT: A 860 VAL cc_start: 0.8325 (m) cc_final: 0.8018 (t) REVERT: A 987 GLN cc_start: 0.8014 (tp40) cc_final: 0.7707 (tp-100) REVERT: A 1191 ASP cc_start: 0.7822 (t70) cc_final: 0.7612 (t70) REVERT: A 1409 MET cc_start: 0.6415 (tpt) cc_final: 0.6168 (tpt) REVERT: A 1577 MET cc_start: 0.4201 (ttp) cc_final: 0.3971 (tmm) REVERT: B 152 MET cc_start: 0.7855 (tpt) cc_final: 0.7336 (tpt) REVERT: C 155 MET cc_start: 0.6584 (ttt) cc_final: 0.5738 (mtt) REVERT: C 156 MET cc_start: 0.6910 (mmm) cc_final: 0.6602 (tmm) REVERT: D 145 MET cc_start: 0.6816 (tpp) cc_final: 0.5758 (mpp) outliers start: 28 outliers final: 17 residues processed: 280 average time/residue: 0.1199 time to fit residues: 48.3143 Evaluate side-chains 274 residues out of total 1638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 257 time to evaluate : 0.551 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 259 VAL Chi-restraints excluded: chain A residue 363 ASN Chi-restraints excluded: chain A residue 408 ILE Chi-restraints excluded: chain A residue 471 ASP Chi-restraints excluded: chain A residue 537 HIS Chi-restraints excluded: chain A residue 614 THR Chi-restraints excluded: chain A residue 701 SER Chi-restraints excluded: chain A residue 778 GLU Chi-restraints excluded: chain A residue 931 LEU Chi-restraints excluded: chain A residue 964 LEU Chi-restraints excluded: chain A residue 1018 VAL Chi-restraints excluded: chain A residue 1042 CYS Chi-restraints excluded: chain A residue 1090 THR Chi-restraints excluded: chain A residue 1098 LYS Chi-restraints excluded: chain A residue 1153 ILE Chi-restraints excluded: chain A residue 1332 MET Chi-restraints excluded: chain C residue 149 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 180 optimal weight: 5.9990 chunk 163 optimal weight: 0.0980 chunk 99 optimal weight: 0.6980 chunk 93 optimal weight: 5.9990 chunk 25 optimal weight: 0.7980 chunk 144 optimal weight: 2.9990 chunk 152 optimal weight: 0.6980 chunk 169 optimal weight: 0.7980 chunk 39 optimal weight: 0.2980 chunk 164 optimal weight: 50.0000 chunk 123 optimal weight: 4.9990 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 137 GLN A 575 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4245 r_free = 0.4245 target = 0.184546 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3689 r_free = 0.3689 target = 0.140986 restraints weight = 21163.792| |-----------------------------------------------------------------------------| r_work (start): 0.3677 rms_B_bonded: 2.51 r_work: 0.3545 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.3384 rms_B_bonded: 4.72 restraints_weight: 0.2500 r_work (final): 0.3384 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7387 moved from start: 0.3279 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 14982 Z= 0.126 Angle : 0.544 6.314 20315 Z= 0.279 Chirality : 0.041 0.147 2356 Planarity : 0.005 0.057 2561 Dihedral : 4.403 19.447 2025 Min Nonbonded Distance : 2.101 Molprobity Statistics. All-atom Clashscore : 7.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.23 % Favored : 95.77 % Rotamer: Outliers : 1.41 % Allowed : 13.32 % Favored : 85.28 % 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: 0.30 (0.20), residues: 1845 helix: 1.45 (0.17), residues: 1013 sheet: -0.23 (0.51), residues: 112 loop : -1.61 (0.22), residues: 720 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A1048 TYR 0.020 0.001 TYR A 500 PHE 0.020 0.001 PHE A 230 TRP 0.028 0.001 TRP A1235 HIS 0.007 0.001 HIS A 226 Details of bonding type rmsd covalent geometry : bond 0.00282 (14976) covalent geometry : angle 0.54351 (20315) hydrogen bonds : bond 0.04439 ( 755) hydrogen bonds : angle 3.96241 ( 2205) metal coordination : bond 0.00423 ( 6) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3690 Ramachandran restraints generated. 1845 Oldfield, 0 Emsley, 1845 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3690 Ramachandran restraints generated. 1845 Oldfield, 0 Emsley, 1845 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 291 residues out of total 1638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 268 time to evaluate : 0.534 Fit side-chains revert: symmetry clash REVERT: A 24 ASP cc_start: 0.7893 (m-30) cc_final: 0.7682 (m-30) REVERT: A 126 GLU cc_start: 0.7136 (mt-10) cc_final: 0.6885 (mt-10) REVERT: A 149 LYS cc_start: 0.8331 (mmtm) cc_final: 0.8040 (mmtt) REVERT: A 359 LYS cc_start: 0.7701 (ttpp) cc_final: 0.7475 (tttm) REVERT: A 418 TYR cc_start: 0.8040 (m-80) cc_final: 0.7795 (m-80) REVERT: A 451 ARG cc_start: 0.7729 (mtp85) cc_final: 0.6899 (mtp85) REVERT: A 511 GLU cc_start: 0.7171 (mp0) cc_final: 0.6892 (mp0) REVERT: A 561 GLU cc_start: 0.7562 (mp0) cc_final: 0.7173 (mp0) REVERT: A 665 LYS cc_start: 0.8055 (tttm) cc_final: 0.7730 (ttpt) REVERT: A 722 LEU cc_start: 0.8503 (mt) cc_final: 0.8277 (mp) REVERT: A 860 VAL cc_start: 0.8324 (m) cc_final: 0.8049 (t) REVERT: A 1191 ASP cc_start: 0.7799 (t70) cc_final: 0.7571 (t70) REVERT: A 1409 MET cc_start: 0.6540 (tpt) cc_final: 0.6239 (tpt) REVERT: C 156 MET cc_start: 0.6638 (mmm) cc_final: 0.6217 (tmm) outliers start: 23 outliers final: 14 residues processed: 279 average time/residue: 0.1321 time to fit residues: 52.9659 Evaluate side-chains 272 residues out of total 1638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 258 time to evaluate : 0.351 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 259 VAL Chi-restraints excluded: chain A residue 408 ILE Chi-restraints excluded: chain A residue 471 ASP Chi-restraints excluded: chain A residue 537 HIS Chi-restraints excluded: chain A residue 701 SER Chi-restraints excluded: chain A residue 750 CYS Chi-restraints excluded: chain A residue 778 GLU Chi-restraints excluded: chain A residue 779 LEU Chi-restraints excluded: chain A residue 964 LEU Chi-restraints excluded: chain A residue 1018 VAL Chi-restraints excluded: chain A residue 1042 CYS Chi-restraints excluded: chain A residue 1098 LYS Chi-restraints excluded: chain A residue 1332 MET Chi-restraints excluded: chain C residue 149 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 60 optimal weight: 3.9990 chunk 39 optimal weight: 0.4980 chunk 44 optimal weight: 1.9990 chunk 65 optimal weight: 1.9990 chunk 87 optimal weight: 0.7980 chunk 13 optimal weight: 0.9980 chunk 55 optimal weight: 0.6980 chunk 74 optimal weight: 0.8980 chunk 138 optimal weight: 0.9990 chunk 110 optimal weight: 2.9990 chunk 3 optimal weight: 3.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 575 ASN A 738 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4235 r_free = 0.4235 target = 0.182503 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3691 r_free = 0.3691 target = 0.140040 restraints weight = 21237.284| |-----------------------------------------------------------------------------| r_work (start): 0.3659 rms_B_bonded: 2.37 r_work: 0.3518 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.3360 rms_B_bonded: 4.66 restraints_weight: 0.2500 r_work (final): 0.3360 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7390 moved from start: 0.3486 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 14982 Z= 0.153 Angle : 0.565 10.430 20315 Z= 0.288 Chirality : 0.042 0.160 2356 Planarity : 0.005 0.057 2561 Dihedral : 4.383 19.811 2025 Min Nonbonded Distance : 2.012 Molprobity Statistics. All-atom Clashscore : 7.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.39 % Favored : 95.61 % Rotamer: Outliers : 1.89 % Allowed : 13.44 % Favored : 84.67 % 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: 0.40 (0.20), residues: 1845 helix: 1.58 (0.17), residues: 1004 sheet: -0.16 (0.52), residues: 112 loop : -1.59 (0.22), residues: 729 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 923 TYR 0.023 0.001 TYR A 109 PHE 0.020 0.002 PHE A 230 TRP 0.028 0.002 TRP A1235 HIS 0.008 0.001 HIS A 226 Details of bonding type rmsd covalent geometry : bond 0.00358 (14976) covalent geometry : angle 0.56546 (20315) hydrogen bonds : bond 0.04675 ( 755) hydrogen bonds : angle 3.96411 ( 2205) metal coordination : bond 0.00659 ( 6) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3690 Ramachandran restraints generated. 1845 Oldfield, 0 Emsley, 1845 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3690 Ramachandran restraints generated. 1845 Oldfield, 0 Emsley, 1845 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 290 residues out of total 1638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 259 time to evaluate : 0.538 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 24 ASP cc_start: 0.7908 (m-30) cc_final: 0.7683 (m-30) REVERT: A 70 ARG cc_start: 0.8165 (OUTLIER) cc_final: 0.7818 (ptp-170) REVERT: A 126 GLU cc_start: 0.7166 (mt-10) cc_final: 0.6908 (mt-10) REVERT: A 149 LYS cc_start: 0.8421 (mmtm) cc_final: 0.8126 (mmtt) REVERT: A 359 LYS cc_start: 0.7767 (ttpp) cc_final: 0.7543 (tttm) REVERT: A 451 ARG cc_start: 0.7746 (mtp85) cc_final: 0.6913 (mtp85) REVERT: A 561 GLU cc_start: 0.7609 (mp0) cc_final: 0.7210 (mp0) REVERT: A 609 VAL cc_start: 0.8576 (t) cc_final: 0.8251 (p) REVERT: A 665 LYS cc_start: 0.8071 (tttm) cc_final: 0.7739 (ttpt) REVERT: A 722 LEU cc_start: 0.8497 (mt) cc_final: 0.8287 (mp) REVERT: A 860 VAL cc_start: 0.8300 (m) cc_final: 0.8031 (t) REVERT: A 1191 ASP cc_start: 0.7780 (t70) cc_final: 0.7528 (t70) REVERT: A 1409 MET cc_start: 0.6528 (tpt) cc_final: 0.6197 (tpt) REVERT: C 156 MET cc_start: 0.6665 (mmm) cc_final: 0.6268 (tmm) REVERT: D 148 MET cc_start: 0.6145 (ttm) cc_final: 0.5872 (ttm) REVERT: D 155 MET cc_start: 0.7655 (ppp) cc_final: 0.7451 (ppp) outliers start: 31 outliers final: 21 residues processed: 274 average time/residue: 0.1332 time to fit residues: 51.9694 Evaluate side-chains 276 residues out of total 1638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 254 time to evaluate : 0.368 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 ARG Chi-restraints excluded: chain A residue 73 VAL Chi-restraints excluded: chain A residue 259 VAL Chi-restraints excluded: chain A residue 408 ILE Chi-restraints excluded: chain A residue 471 ASP Chi-restraints excluded: chain A residue 536 SER Chi-restraints excluded: chain A residue 537 HIS Chi-restraints excluded: chain A residue 552 SER Chi-restraints excluded: chain A residue 614 THR Chi-restraints excluded: chain A residue 701 SER Chi-restraints excluded: chain A residue 750 CYS Chi-restraints excluded: chain A residue 778 GLU Chi-restraints excluded: chain A residue 796 VAL Chi-restraints excluded: chain A residue 931 LEU Chi-restraints excluded: chain A residue 951 VAL Chi-restraints excluded: chain A residue 964 LEU Chi-restraints excluded: chain A residue 1018 VAL Chi-restraints excluded: chain A residue 1042 CYS Chi-restraints excluded: chain A residue 1046 THR Chi-restraints excluded: chain A residue 1090 THR Chi-restraints excluded: chain A residue 1153 ILE Chi-restraints excluded: chain A residue 1332 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 84 optimal weight: 0.3980 chunk 53 optimal weight: 1.9990 chunk 69 optimal weight: 0.9980 chunk 111 optimal weight: 3.9990 chunk 3 optimal weight: 5.9990 chunk 148 optimal weight: 0.0050 chunk 0 optimal weight: 2.9990 chunk 97 optimal weight: 0.3980 chunk 82 optimal weight: 0.5980 chunk 115 optimal weight: 0.9990 chunk 71 optimal weight: 0.4980 overall best weight: 0.3794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 575 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4251 r_free = 0.4251 target = 0.183966 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3704 r_free = 0.3704 target = 0.141434 restraints weight = 21150.847| |-----------------------------------------------------------------------------| r_work (start): 0.3686 rms_B_bonded: 2.41 r_work: 0.3554 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.3396 rms_B_bonded: 4.65 restraints_weight: 0.2500 r_work (final): 0.3396 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7358 moved from start: 0.3581 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 14982 Z= 0.113 Angle : 0.527 7.324 20315 Z= 0.268 Chirality : 0.040 0.142 2356 Planarity : 0.004 0.058 2561 Dihedral : 4.195 18.832 2025 Min Nonbonded Distance : 2.421 Molprobity Statistics. All-atom Clashscore : 7.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.90 % Favored : 96.10 % Rotamer: Outliers : 1.77 % Allowed : 14.11 % Favored : 84.12 % 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: 0.63 (0.20), residues: 1845 helix: 1.77 (0.17), residues: 1004 sheet: 0.15 (0.58), residues: 92 loop : -1.50 (0.22), residues: 749 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A1048 TYR 0.021 0.001 TYR A 500 PHE 0.020 0.001 PHE A 230 TRP 0.032 0.001 TRP A1235 HIS 0.005 0.001 HIS A 226 Details of bonding type rmsd covalent geometry : bond 0.00253 (14976) covalent geometry : angle 0.52749 (20315) hydrogen bonds : bond 0.04038 ( 755) hydrogen bonds : angle 3.80698 ( 2205) metal coordination : bond 0.00274 ( 6) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3690 Ramachandran restraints generated. 1845 Oldfield, 0 Emsley, 1845 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3690 Ramachandran restraints generated. 1845 Oldfield, 0 Emsley, 1845 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 284 residues out of total 1638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 255 time to evaluate : 0.524 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 70 ARG cc_start: 0.8061 (OUTLIER) cc_final: 0.7761 (ptm160) REVERT: A 126 GLU cc_start: 0.7157 (mt-10) cc_final: 0.6901 (mt-10) REVERT: A 149 LYS cc_start: 0.8401 (mmtm) cc_final: 0.8112 (mmtt) REVERT: A 359 LYS cc_start: 0.7659 (ttpp) cc_final: 0.7428 (tttm) REVERT: A 418 TYR cc_start: 0.7882 (m-80) cc_final: 0.7666 (m-80) REVERT: A 561 GLU cc_start: 0.7601 (mp0) cc_final: 0.7318 (mp0) REVERT: A 609 VAL cc_start: 0.8574 (t) cc_final: 0.8261 (p) REVERT: A 665 LYS cc_start: 0.8035 (tttm) cc_final: 0.7683 (ttpt) REVERT: A 722 LEU cc_start: 0.8486 (mt) cc_final: 0.8282 (mp) REVERT: A 860 VAL cc_start: 0.8262 (m) cc_final: 0.7979 (t) REVERT: A 1191 ASP cc_start: 0.7776 (t70) cc_final: 0.7461 (t70) REVERT: A 1409 MET cc_start: 0.6508 (tpt) cc_final: 0.6157 (tpt) REVERT: A 1577 MET cc_start: 0.4503 (OUTLIER) cc_final: 0.3919 (ppp) REVERT: B 148 MET cc_start: 0.7422 (mtp) cc_final: 0.7221 (mtp) REVERT: C 156 MET cc_start: 0.6519 (mmm) cc_final: 0.6122 (tmm) REVERT: D 148 MET cc_start: 0.6115 (ttm) cc_final: 0.5771 (ttm) REVERT: D 155 MET cc_start: 0.7510 (ppp) cc_final: 0.7143 (ppp) outliers start: 29 outliers final: 19 residues processed: 271 average time/residue: 0.1279 time to fit residues: 49.6068 Evaluate side-chains 267 residues out of total 1638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 246 time to evaluate : 0.573 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 ARG Chi-restraints excluded: chain A residue 73 VAL Chi-restraints excluded: chain A residue 236 ILE Chi-restraints excluded: chain A residue 471 ASP Chi-restraints excluded: chain A residue 482 GLU Chi-restraints excluded: chain A residue 536 SER Chi-restraints excluded: chain A residue 537 HIS Chi-restraints excluded: chain A residue 552 SER Chi-restraints excluded: chain A residue 701 SER Chi-restraints excluded: chain A residue 750 CYS Chi-restraints excluded: chain A residue 778 GLU Chi-restraints excluded: chain A residue 796 VAL Chi-restraints excluded: chain A residue 913 ASP Chi-restraints excluded: chain A residue 951 VAL Chi-restraints excluded: chain A residue 964 LEU Chi-restraints excluded: chain A residue 1018 VAL Chi-restraints excluded: chain A residue 1042 CYS Chi-restraints excluded: chain A residue 1090 THR Chi-restraints excluded: chain A residue 1332 MET Chi-restraints excluded: chain A residue 1567 LEU Chi-restraints excluded: chain A residue 1577 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 58 optimal weight: 2.9990 chunk 80 optimal weight: 0.7980 chunk 157 optimal weight: 8.9990 chunk 141 optimal weight: 0.5980 chunk 83 optimal weight: 1.9990 chunk 25 optimal weight: 0.6980 chunk 34 optimal weight: 2.9990 chunk 103 optimal weight: 2.9990 chunk 33 optimal weight: 0.5980 chunk 59 optimal weight: 3.9990 chunk 65 optimal weight: 2.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 575 ASN A1044 GLN A1455 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4232 r_free = 0.4232 target = 0.182281 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3680 r_free = 0.3680 target = 0.139424 restraints weight = 21192.950| |-----------------------------------------------------------------------------| r_work (start): 0.3636 rms_B_bonded: 2.29 r_work: 0.3495 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.3338 rms_B_bonded: 4.61 restraints_weight: 0.2500 r_work (final): 0.3338 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7402 moved from start: 0.3761 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 14982 Z= 0.169 Angle : 0.576 8.486 20315 Z= 0.294 Chirality : 0.043 0.179 2356 Planarity : 0.005 0.061 2561 Dihedral : 4.323 19.385 2025 Min Nonbonded Distance : 1.999 Molprobity Statistics. All-atom Clashscore : 7.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.66 % Favored : 95.34 % Rotamer: Outliers : 2.02 % Allowed : 14.54 % Favored : 83.45 % 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: 0.49 (0.20), residues: 1845 helix: 1.69 (0.17), residues: 999 sheet: -0.26 (0.51), residues: 119 loop : -1.58 (0.22), residues: 727 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A1048 TYR 0.025 0.002 TYR A 109 PHE 0.025 0.002 PHE A1168 TRP 0.032 0.002 TRP A1235 HIS 0.009 0.001 HIS A 178 Details of bonding type rmsd covalent geometry : bond 0.00401 (14976) covalent geometry : angle 0.57593 (20315) hydrogen bonds : bond 0.04769 ( 755) hydrogen bonds : angle 3.94160 ( 2205) metal coordination : bond 0.00714 ( 6) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3690 Ramachandran restraints generated. 1845 Oldfield, 0 Emsley, 1845 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3690 Ramachandran restraints generated. 1845 Oldfield, 0 Emsley, 1845 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 297 residues out of total 1638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 264 time to evaluate : 0.537 Fit side-chains revert: symmetry clash REVERT: A 70 ARG cc_start: 0.8186 (OUTLIER) cc_final: 0.7919 (ptp-170) REVERT: A 126 GLU cc_start: 0.7165 (mt-10) cc_final: 0.6864 (mt-10) REVERT: A 149 LYS cc_start: 0.8459 (mmtm) cc_final: 0.8142 (mmtt) REVERT: A 299 ILE cc_start: 0.8137 (mt) cc_final: 0.7936 (mm) REVERT: A 359 LYS cc_start: 0.7777 (ttpp) cc_final: 0.7570 (tttm) REVERT: A 418 TYR cc_start: 0.8030 (m-80) cc_final: 0.7827 (m-80) REVERT: A 561 GLU cc_start: 0.7664 (mp0) cc_final: 0.7365 (mp0) REVERT: A 609 VAL cc_start: 0.8604 (t) cc_final: 0.8274 (p) REVERT: A 665 LYS cc_start: 0.8064 (tttm) cc_final: 0.7734 (ttpt) REVERT: A 1191 ASP cc_start: 0.7732 (OUTLIER) cc_final: 0.7431 (t70) REVERT: A 1409 MET cc_start: 0.6526 (tpt) cc_final: 0.6133 (tpt) REVERT: C 156 MET cc_start: 0.6805 (mmm) cc_final: 0.6440 (tmm) REVERT: D 148 MET cc_start: 0.6131 (ttm) cc_final: 0.5706 (ttm) outliers start: 33 outliers final: 23 residues processed: 280 average time/residue: 0.1271 time to fit residues: 50.7126 Evaluate side-chains 289 residues out of total 1638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 264 time to evaluate : 0.521 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 ARG Chi-restraints excluded: chain A residue 73 VAL Chi-restraints excluded: chain A residue 408 ILE Chi-restraints excluded: chain A residue 471 ASP Chi-restraints excluded: chain A residue 482 GLU Chi-restraints excluded: chain A residue 536 SER Chi-restraints excluded: chain A residue 552 SER Chi-restraints excluded: chain A residue 614 THR Chi-restraints excluded: chain A residue 701 SER Chi-restraints excluded: chain A residue 750 CYS Chi-restraints excluded: chain A residue 778 GLU Chi-restraints excluded: chain A residue 796 VAL Chi-restraints excluded: chain A residue 913 ASP Chi-restraints excluded: chain A residue 931 LEU Chi-restraints excluded: chain A residue 951 VAL Chi-restraints excluded: chain A residue 964 LEU Chi-restraints excluded: chain A residue 970 LYS Chi-restraints excluded: chain A residue 1018 VAL Chi-restraints excluded: chain A residue 1034 LEU Chi-restraints excluded: chain A residue 1042 CYS Chi-restraints excluded: chain A residue 1090 THR Chi-restraints excluded: chain A residue 1153 ILE Chi-restraints excluded: chain A residue 1191 ASP Chi-restraints excluded: chain A residue 1332 MET Chi-restraints excluded: chain A residue 1567 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 116 optimal weight: 1.9990 chunk 49 optimal weight: 0.9980 chunk 127 optimal weight: 0.8980 chunk 45 optimal weight: 0.8980 chunk 122 optimal weight: 6.9990 chunk 14 optimal weight: 0.9980 chunk 70 optimal weight: 0.7980 chunk 143 optimal weight: 0.0370 chunk 57 optimal weight: 0.7980 chunk 98 optimal weight: 0.7980 chunk 68 optimal weight: 2.9990 overall best weight: 0.6658 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 575 ASN A 738 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4237 r_free = 0.4237 target = 0.182706 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3682 r_free = 0.3682 target = 0.139573 restraints weight = 21210.024| |-----------------------------------------------------------------------------| r_work (start): 0.3648 rms_B_bonded: 2.39 r_work: 0.3516 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.3357 rms_B_bonded: 4.67 restraints_weight: 0.2500 r_work (final): 0.3357 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7399 moved from start: 0.3854 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 14982 Z= 0.139 Angle : 0.556 8.118 20315 Z= 0.283 Chirality : 0.042 0.173 2356 Planarity : 0.005 0.061 2561 Dihedral : 4.278 19.226 2025 Min Nonbonded Distance : 2.012 Molprobity Statistics. All-atom Clashscore : 7.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.01 % Favored : 95.99 % Rotamer: Outliers : 1.83 % Allowed : 15.15 % Favored : 83.02 % 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: 0.55 (0.20), residues: 1845 helix: 1.75 (0.17), residues: 1005 sheet: -0.13 (0.53), residues: 112 loop : -1.59 (0.22), residues: 728 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A1048 TYR 0.022 0.001 TYR A 500 PHE 0.026 0.001 PHE A1168 TRP 0.055 0.002 TRP A1235 HIS 0.006 0.001 HIS A 226 Details of bonding type rmsd covalent geometry : bond 0.00323 (14976) covalent geometry : angle 0.55553 (20315) hydrogen bonds : bond 0.04383 ( 755) hydrogen bonds : angle 3.85314 ( 2205) metal coordination : bond 0.00509 ( 6) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3690 Ramachandran restraints generated. 1845 Oldfield, 0 Emsley, 1845 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3690 Ramachandran restraints generated. 1845 Oldfield, 0 Emsley, 1845 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 287 residues out of total 1638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 257 time to evaluate : 0.520 Fit side-chains revert: symmetry clash REVERT: A 70 ARG cc_start: 0.8134 (OUTLIER) cc_final: 0.7897 (ptp-170) REVERT: A 126 GLU cc_start: 0.7136 (mt-10) cc_final: 0.6843 (mt-10) REVERT: A 149 LYS cc_start: 0.8436 (mmtm) cc_final: 0.8125 (mmtt) REVERT: A 299 ILE cc_start: 0.8144 (mt) cc_final: 0.7934 (mm) REVERT: A 359 LYS cc_start: 0.7755 (ttpp) cc_final: 0.7541 (tttm) REVERT: A 418 TYR cc_start: 0.7973 (m-80) cc_final: 0.7635 (m-10) REVERT: A 511 GLU cc_start: 0.7087 (mp0) cc_final: 0.6807 (mp0) REVERT: A 561 GLU cc_start: 0.7649 (mp0) cc_final: 0.7346 (mp0) REVERT: A 609 VAL cc_start: 0.8595 (t) cc_final: 0.8258 (p) REVERT: A 665 LYS cc_start: 0.8053 (tttm) cc_final: 0.7718 (ttpt) REVERT: A 835 THR cc_start: 0.8190 (m) cc_final: 0.7859 (p) REVERT: A 860 VAL cc_start: 0.8303 (m) cc_final: 0.7995 (t) REVERT: A 1191 ASP cc_start: 0.7759 (OUTLIER) cc_final: 0.7441 (t70) REVERT: A 1409 MET cc_start: 0.6487 (tpt) cc_final: 0.6093 (tpt) REVERT: C 145 MET cc_start: 0.6481 (mmm) cc_final: 0.6230 (mmm) REVERT: D 148 MET cc_start: 0.6022 (ttm) cc_final: 0.5598 (ttm) outliers start: 30 outliers final: 22 residues processed: 272 average time/residue: 0.1289 time to fit residues: 50.8285 Evaluate side-chains 280 residues out of total 1638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 256 time to evaluate : 0.571 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 ARG Chi-restraints excluded: chain A residue 73 VAL Chi-restraints excluded: chain A residue 408 ILE Chi-restraints excluded: chain A residue 471 ASP Chi-restraints excluded: chain A residue 482 GLU Chi-restraints excluded: chain A residue 536 SER Chi-restraints excluded: chain A residue 537 HIS Chi-restraints excluded: chain A residue 552 SER Chi-restraints excluded: chain A residue 614 THR Chi-restraints excluded: chain A residue 701 SER Chi-restraints excluded: chain A residue 750 CYS Chi-restraints excluded: chain A residue 778 GLU Chi-restraints excluded: chain A residue 796 VAL Chi-restraints excluded: chain A residue 913 ASP Chi-restraints excluded: chain A residue 931 LEU Chi-restraints excluded: chain A residue 951 VAL Chi-restraints excluded: chain A residue 964 LEU Chi-restraints excluded: chain A residue 1018 VAL Chi-restraints excluded: chain A residue 1042 CYS Chi-restraints excluded: chain A residue 1090 THR Chi-restraints excluded: chain A residue 1153 ILE Chi-restraints excluded: chain A residue 1191 ASP Chi-restraints excluded: chain A residue 1332 MET Chi-restraints excluded: chain A residue 1567 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 112 optimal weight: 0.9980 chunk 72 optimal weight: 0.7980 chunk 93 optimal weight: 0.9990 chunk 142 optimal weight: 5.9990 chunk 25 optimal weight: 1.9990 chunk 117 optimal weight: 0.9990 chunk 54 optimal weight: 0.5980 chunk 37 optimal weight: 3.9990 chunk 73 optimal weight: 2.9990 chunk 20 optimal weight: 1.9990 chunk 180 optimal weight: 5.9990 overall best weight: 0.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 575 ASN A 692 ASN A 867 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4226 r_free = 0.4226 target = 0.181799 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3679 r_free = 0.3679 target = 0.139304 restraints weight = 21262.479| |-----------------------------------------------------------------------------| r_work (start): 0.3643 rms_B_bonded: 2.35 r_work: 0.3501 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.3338 rms_B_bonded: 4.65 restraints_weight: 0.2500 r_work (final): 0.3338 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7399 moved from start: 0.3953 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 14982 Z= 0.164 Angle : 0.581 8.010 20315 Z= 0.297 Chirality : 0.043 0.196 2356 Planarity : 0.005 0.062 2561 Dihedral : 4.347 19.135 2025 Min Nonbonded Distance : 1.982 Molprobity Statistics. All-atom Clashscore : 7.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.61 % Favored : 95.39 % Rotamer: Outliers : 1.71 % Allowed : 15.03 % Favored : 83.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 0.52 (0.20), residues: 1845 helix: 1.70 (0.17), residues: 1004 sheet: -0.17 (0.53), residues: 112 loop : -1.58 (0.22), residues: 729 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A1048 TYR 0.023 0.002 TYR A 109 PHE 0.025 0.002 PHE A1168 TRP 0.053 0.002 TRP A1235 HIS 0.008 0.001 HIS A 226 Details of bonding type rmsd covalent geometry : bond 0.00387 (14976) covalent geometry : angle 0.58129 (20315) hydrogen bonds : bond 0.04681 ( 755) hydrogen bonds : angle 3.91994 ( 2205) metal coordination : bond 0.00697 ( 6) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3690 Ramachandran restraints generated. 1845 Oldfield, 0 Emsley, 1845 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3690 Ramachandran restraints generated. 1845 Oldfield, 0 Emsley, 1845 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 286 residues out of total 1638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 258 time to evaluate : 0.595 Fit side-chains revert: symmetry clash REVERT: A 70 ARG cc_start: 0.8168 (OUTLIER) cc_final: 0.7912 (ptp-170) REVERT: A 126 GLU cc_start: 0.7244 (mt-10) cc_final: 0.6948 (mt-10) REVERT: A 137 GLN cc_start: 0.8406 (mt0) cc_final: 0.8149 (mt0) REVERT: A 154 MET cc_start: 0.8292 (ttp) cc_final: 0.7913 (ttm) REVERT: A 299 ILE cc_start: 0.8148 (mt) cc_final: 0.7942 (mm) REVERT: A 359 LYS cc_start: 0.7764 (ttpp) cc_final: 0.7537 (tttm) REVERT: A 408 ILE cc_start: 0.7980 (OUTLIER) cc_final: 0.7403 (tt) REVERT: A 427 TYR cc_start: 0.8129 (m-80) cc_final: 0.7666 (m-80) REVERT: A 561 GLU cc_start: 0.7668 (mp0) cc_final: 0.7340 (mp0) REVERT: A 609 VAL cc_start: 0.8559 (t) cc_final: 0.8216 (p) REVERT: A 665 LYS cc_start: 0.8060 (tttm) cc_final: 0.7703 (ttpt) REVERT: A 860 VAL cc_start: 0.8256 (m) cc_final: 0.7960 (t) REVERT: A 1191 ASP cc_start: 0.7764 (OUTLIER) cc_final: 0.7464 (t70) REVERT: A 1409 MET cc_start: 0.6504 (tpt) cc_final: 0.6080 (tpt) REVERT: C 145 MET cc_start: 0.6426 (mmm) cc_final: 0.6116 (mmm) REVERT: C 149 MET cc_start: 0.5985 (OUTLIER) cc_final: 0.5555 (ttp) REVERT: D 148 MET cc_start: 0.6053 (ttm) cc_final: 0.5585 (ttm) REVERT: D 156 MET cc_start: 0.6950 (mtm) cc_final: 0.6673 (ttm) outliers start: 28 outliers final: 21 residues processed: 272 average time/residue: 0.1332 time to fit residues: 52.3378 Evaluate side-chains 279 residues out of total 1638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 254 time to evaluate : 0.453 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 ARG Chi-restraints excluded: chain A residue 73 VAL Chi-restraints excluded: chain A residue 408 ILE Chi-restraints excluded: chain A residue 482 GLU Chi-restraints excluded: chain A residue 536 SER Chi-restraints excluded: chain A residue 552 SER Chi-restraints excluded: chain A residue 614 THR Chi-restraints excluded: chain A residue 701 SER Chi-restraints excluded: chain A residue 750 CYS Chi-restraints excluded: chain A residue 778 GLU Chi-restraints excluded: chain A residue 796 VAL Chi-restraints excluded: chain A residue 913 ASP Chi-restraints excluded: chain A residue 928 LEU Chi-restraints excluded: chain A residue 931 LEU Chi-restraints excluded: chain A residue 951 VAL Chi-restraints excluded: chain A residue 964 LEU Chi-restraints excluded: chain A residue 1018 VAL Chi-restraints excluded: chain A residue 1034 LEU Chi-restraints excluded: chain A residue 1042 CYS Chi-restraints excluded: chain A residue 1090 THR Chi-restraints excluded: chain A residue 1153 ILE Chi-restraints excluded: chain A residue 1191 ASP Chi-restraints excluded: chain A residue 1332 MET Chi-restraints excluded: chain A residue 1567 LEU Chi-restraints excluded: chain C residue 149 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 104 optimal weight: 2.9990 chunk 40 optimal weight: 2.9990 chunk 13 optimal weight: 0.9980 chunk 83 optimal weight: 1.9990 chunk 20 optimal weight: 1.9990 chunk 165 optimal weight: 4.9990 chunk 44 optimal weight: 0.6980 chunk 25 optimal weight: 0.5980 chunk 121 optimal weight: 0.9990 chunk 169 optimal weight: 0.9980 chunk 62 optimal weight: 0.9990 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 575 ASN A 738 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4224 r_free = 0.4224 target = 0.181709 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3681 r_free = 0.3681 target = 0.139395 restraints weight = 21111.578| |-----------------------------------------------------------------------------| r_work (start): 0.3645 rms_B_bonded: 2.26 r_work: 0.3506 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.3347 rms_B_bonded: 4.51 restraints_weight: 0.2500 r_work (final): 0.3347 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7390 moved from start: 0.4058 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 14982 Z= 0.161 Angle : 0.582 9.428 20315 Z= 0.296 Chirality : 0.043 0.286 2356 Planarity : 0.005 0.063 2561 Dihedral : 4.359 22.464 2025 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 7.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.28 % Favored : 95.72 % Rotamer: Outliers : 1.71 % Allowed : 15.21 % Favored : 83.08 % 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: 0.50 (0.20), residues: 1845 helix: 1.68 (0.17), residues: 1008 sheet: -0.23 (0.53), residues: 112 loop : -1.59 (0.23), residues: 725 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A1048 TYR 0.023 0.002 TYR A 109 PHE 0.024 0.002 PHE A1168 TRP 0.042 0.002 TRP A1235 HIS 0.008 0.001 HIS A 226 Details of bonding type rmsd covalent geometry : bond 0.00380 (14976) covalent geometry : angle 0.58190 (20315) hydrogen bonds : bond 0.04654 ( 755) hydrogen bonds : angle 3.93167 ( 2205) metal coordination : bond 0.00602 ( 6) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4805.11 seconds wall clock time: 82 minutes 43.48 seconds (4963.48 seconds total)