Starting phenix.real_space_refine on Thu Feb 5 04:47:47 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9n0r_48791/02_2026/9n0r_48791.cif Found real_map, /net/cci-nas-00/data/ceres_data/9n0r_48791/02_2026/9n0r_48791.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.71 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9n0r_48791/02_2026/9n0r_48791.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9n0r_48791/02_2026/9n0r_48791.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9n0r_48791/02_2026/9n0r_48791.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9n0r_48791/02_2026/9n0r_48791.map" } resolution = 2.71 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 56.627 41.063 94.923 1.00 38.25 S ATOM 9128 SG CYS A1210 54.043 41.308 96.865 1.00 37.11 S ATOM 9150 SG CYS A1213 54.163 43.218 93.755 1.00 40.32 S ATOM 11445 SG CYS A1511 40.897 73.714 111.369 1.00 88.58 S ATOM 12006 SG CYS A1586 38.893 76.961 110.684 1.00 95.69 S Time building chain proxies: 3.27, per 1000 atoms: 0.22 Number of scatterers: 14668 At special positions: 0 Unit cell: (92.96, 131.472, 145.416, 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: 1.46 Conformation dependent library (CDL) restraints added in 654.0 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 A 993 " pdb="ZN ZN A1801 " - pdb=" SG CYS A1210 " 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 59.9% alpha, 5.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.61 Creating SS restraints... Processing helix chain 'A' and resid 33 through 41 Processing helix chain 'A' and resid 45 through 54 removed outlier: 3.639A pdb=" N ARG A 50 " --> pdb=" O PRO A 46 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N GLN A 54 " --> pdb=" O ARG A 50 " (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: 3.621A 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: 3.652A pdb=" N TYR A 109 " --> pdb=" O THR A 105 " (cutoff:3.500A) Processing helix chain 'A' and resid 118 through 139 Processing helix chain 'A' and resid 176 through 202 removed outlier: 3.546A pdb=" N LEU A 202 " --> pdb=" O VAL A 198 " (cutoff:3.500A) Processing helix chain 'A' and resid 208 through 221 Processing helix chain 'A' and resid 225 through 249 removed outlier: 5.094A 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: 3.542A 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: 3.559A 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: 3.504A pdb=" N SER A 324 " --> pdb=" O GLN A 320 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ILE A 332 " --> pdb=" O THR A 328 " (cutoff:3.500A) Processing helix chain 'A' and resid 358 through 368 Processing helix chain 'A' and resid 378 through 382 removed outlier: 3.509A pdb=" N ALA A 382 " --> pdb=" O GLN A 379 " (cutoff:3.500A) Processing helix chain 'A' and resid 397 through 402 removed outlier: 3.745A pdb=" N ILE A 401 " --> pdb=" O ASP A 397 " (cutoff:3.500A) removed outlier: 3.812A 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: 3.833A pdb=" N TRP A 414 " --> pdb=" O ARG A 411 " (cutoff:3.500A) removed outlier: 4.540A pdb=" N VAL A 415 " --> pdb=" O ARG A 412 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N PHE A 416 " --> pdb=" O ASP A 413 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N GLU A 417 " --> pdb=" O TRP A 414 " (cutoff:3.500A) Processing helix chain 'A' and resid 419 through 428 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 511 Processing helix chain 'A' and resid 516 through 524 removed outlier: 3.877A pdb=" N THR A 522 " --> pdb=" O THR A 518 " (cutoff:3.500A) Processing helix chain 'A' and resid 524 through 542 removed outlier: 4.701A pdb=" N THR A 540 " --> pdb=" O SER A 536 " (cutoff:3.500A) removed outlier: 4.252A pdb=" N LYS A 541 " --> pdb=" O HIS A 537 " (cutoff:3.500A) Processing helix chain 'A' and resid 553 through 558 removed outlier: 3.832A pdb=" N PHE A 558 " --> pdb=" O TRP A 554 " (cutoff:3.500A) Processing helix chain 'A' and resid 559 through 574 removed outlier: 3.586A 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: 3.971A 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: 3.825A pdb=" N ALA A 689 " --> pdb=" O HIS A 685 " (cutoff:3.500A) Processing helix chain 'A' and resid 694 through 698 removed outlier: 3.834A pdb=" N CYS A 698 " --> pdb=" O VAL A 695 " (cutoff:3.500A) Processing helix chain 'A' and resid 720 through 726 removed outlier: 3.505A pdb=" N SER A 726 " --> pdb=" O LEU A 722 " (cutoff:3.500A) Processing helix chain 'A' and resid 738 through 756 removed outlier: 3.625A pdb=" N LYS A 742 " --> pdb=" O ASN A 738 " (cutoff:3.500A) Processing helix chain 'A' and resid 759 through 779 removed outlier: 3.768A 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: 3.556A pdb=" N ILE A 800 " --> pdb=" O GLY A 797 " (cutoff:3.500A) removed outlier: 3.622A 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: 3.861A pdb=" N THR A 808 " --> pdb=" O THR A 805 " (cutoff:3.500A) removed outlier: 3.697A 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: 4.584A pdb=" N PHE A 823 " --> pdb=" O ASP A 819 " (cutoff:3.500A) Processing helix chain 'A' and resid 838 through 847 removed outlier: 3.524A pdb=" N VAL A 842 " --> pdb=" O THR A 838 " (cutoff:3.500A) Processing helix chain 'A' and resid 855 through 862 removed outlier: 3.853A 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 931 removed outlier: 3.673A pdb=" N LEU A 931 " --> pdb=" O ALA A 927 " (cutoff:3.500A) Processing helix chain 'A' and resid 932 through 946 removed outlier: 3.713A 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: 3.915A pdb=" N LEU A 964 " --> pdb=" O GLU A 960 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N VAL A 967 " --> pdb=" O ALA A 963 " (cutoff:3.500A) Processing helix chain 'A' and resid 987 through 991 removed outlier: 4.048A 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: 3.785A pdb=" N LEU A1036 " --> pdb=" O GLU A1033 " (cutoff:3.500A) Processing helix chain 'A' and resid 1084 through 1100 removed outlier: 4.113A pdb=" N LYS A1088 " --> pdb=" O ALA A1084 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N HIS A1094 " --> pdb=" O THR A1090 " (cutoff:3.500A) removed outlier: 4.126A 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 1151 through 1156 removed outlier: 3.650A pdb=" N THR A1156 " --> pdb=" O ASN A1152 " (cutoff:3.500A) Processing helix chain 'A' and resid 1178 through 1196 Processing helix chain 'A' and resid 1210 through 1214 removed outlier: 3.555A pdb=" N CYS A1213 " --> pdb=" O CYS A1210 " (cutoff:3.500A) removed outlier: 3.651A 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 1278 removed outlier: 3.883A pdb=" N SER A1259 " --> pdb=" O ASP A1255 " (cutoff:3.500A) Processing helix chain 'A' and resid 1279 through 1284 removed outlier: 3.771A 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 1304 through 1320 removed outlier: 4.114A pdb=" N VAL A1308 " --> pdb=" O PRO A1304 " (cutoff:3.500A) removed outlier: 3.594A 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: 3.657A pdb=" N CYS A1357 " --> pdb=" O LEU A1353 " (cutoff:3.500A) Processing helix chain 'A' and resid 1357 through 1364 removed outlier: 4.107A 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: 4.085A pdb=" N ILE A1385 " --> pdb=" O LEU A1381 " (cutoff:3.500A) Processing helix chain 'A' and resid 1398 through 1403 removed outlier: 3.539A pdb=" N HIS A1402 " --> pdb=" O ASN A1398 " (cutoff:3.500A) Processing helix chain 'A' and resid 1408 through 1420 removed outlier: 3.722A pdb=" N LYS A1417 " --> pdb=" O ILE A1413 " (cutoff:3.500A) removed outlier: 5.028A pdb=" N SER A1418 " --> pdb=" O ALA A1414 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N VAL A1419 " --> pdb=" O ALA A1415 " (cutoff:3.500A) removed outlier: 4.382A pdb=" N GLY A1420 " --> pdb=" O ALA A1416 " (cutoff:3.500A) Processing helix chain 'A' and resid 1450 through 1464 removed outlier: 4.039A pdb=" N SER A1454 " --> pdb=" O SER A1450 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N LEU A1457 " --> pdb=" O GLN A1453 " (cutoff:3.500A) Processing helix chain 'A' and resid 1476 through 1486 Processing helix chain 'A' and resid 1499 through 1509 removed outlier: 3.564A pdb=" N MET A1508 " --> pdb=" O ARG A1504 " (cutoff:3.500A) removed outlier: 4.005A 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: 3.554A pdb=" N TYR A1594 " --> pdb=" O ARG A1591 " (cutoff:3.500A) Processing helix chain 'A' and resid 1597 through 1616 removed outlier: 3.530A pdb=" N TYR A1608 " --> pdb=" O LEU A1604 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N LEU A1616 " --> pdb=" O MET A1612 " (cutoff:3.500A) Processing helix chain 'A' and resid 1623 through 1638 Processing helix chain 'A' and resid 1683 through 1689 removed outlier: 3.525A pdb=" N LEU A1687 " --> pdb=" O SER A1683 " (cutoff:3.500A) removed outlier: 3.616A 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: 3.863A pdb=" N LYS B 158 " --> pdb=" O LEU B 154 " (cutoff:3.500A) removed outlier: 3.578A 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: 3.701A pdb=" N SER C 165 " --> pdb=" O LEU C 161 " (cutoff:3.500A) Processing helix chain 'D' and resid 119 through 126 Processing helix chain 'D' and resid 127 through 160 removed outlier: 3.676A pdb=" N ARG D 132 " --> pdb=" O SER D 128 " (cutoff:3.500A) Processing helix chain 'D' and resid 160 through 166 removed outlier: 3.971A pdb=" N ALA D 164 " --> pdb=" O ASP D 160 " (cutoff:3.500A) Processing helix chain 'E' and resid 119 through 126 removed outlier: 3.712A pdb=" N ASP E 126 " --> pdb=" O ALA E 122 " (cutoff:3.500A) Processing helix chain 'E' and resid 127 through 166 removed outlier: 3.575A pdb=" N ILE E 131 " --> pdb=" O HIS E 127 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N LEU E 141 " --> pdb=" O ASN E 137 " (cutoff:3.500A) removed outlier: 3.670A 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: 4.507A pdb=" N LEU A 173 " --> pdb=" O LEU A 60 " (cutoff:3.500A) removed outlier: 4.836A pdb=" N PHE A 158 " --> pdb=" O GLY A 147 " (cutoff:3.500A) removed outlier: 5.565A 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: 3.876A pdb=" N THR A 494 " --> pdb=" O LEU A 473 " (cutoff:3.500A) removed outlier: 7.774A 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 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 Processing sheet with id=AA7, first strand: chain 'A' and resid 1490 through 1493 removed outlier: 6.366A pdb=" N LEU A1469 " --> pdb=" O ILE A1492 " (cutoff:3.500A) removed outlier: 8.471A pdb=" N ILE A1534 " --> pdb=" O VAL A1468 " (cutoff:3.500A) removed outlier: 6.699A pdb=" N TYR A1470 " --> pdb=" O ILE A1534 " (cutoff:3.500A) removed outlier: 6.968A pdb=" N THR A1533 " --> pdb=" O ILE A1543 " (cutoff:3.500A) removed outlier: 8.705A pdb=" N LEU A1545 " --> pdb=" O THR A1533 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 1658 through 1662 758 hydrogen bonds defined for protein. 2217 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: 2.96 Time building geometry restraints manager: 1.93 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: 4573 1.34 - 1.46: 3227 1.46 - 1.58: 7011 1.58 - 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 8.99e+00 bond pdb=" CA ILE A1593 " pdb=" CB ILE A1593 " ideal model delta sigma weight residual 1.531 1.554 -0.023 1.11e-02 8.12e+03 4.20e+00 bond pdb=" CB ARG A1436 " pdb=" CG ARG A1436 " ideal model delta sigma weight residual 1.520 1.577 -0.057 3.00e-02 1.11e+03 3.62e+00 bond pdb=" CA ILE A 455 " pdb=" C ILE A 455 " ideal model delta sigma weight residual 1.520 1.536 -0.017 8.80e-03 1.29e+04 3.60e+00 bond pdb=" C ILE A 262 " pdb=" N PRO A 263 " ideal model delta sigma weight residual 1.335 1.358 -0.023 1.28e-02 6.10e+03 3.20e+00 ... (remaining 14971 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.38: 19673 2.38 - 4.76: 528 4.76 - 7.14: 91 7.14 - 9.52: 17 9.52 - 11.90: 6 Bond angle restraints: 20315 Sorted by residual: angle pdb=" N ILE A 895 " pdb=" CA ILE A 895 " pdb=" C ILE A 895 " ideal model delta sigma weight residual 112.12 105.70 6.42 8.40e-01 1.42e+00 5.85e+01 angle pdb=" C ASN A 454 " pdb=" N ILE A 455 " pdb=" CA ILE A 455 " ideal model delta sigma weight residual 120.24 123.85 -3.61 6.30e-01 2.52e+00 3.28e+01 angle pdb=" C SER A 893 " pdb=" N ARG A 894 " pdb=" CA ARG A 894 " ideal model delta sigma weight residual 121.54 129.81 -8.27 1.91e+00 2.74e-01 1.87e+01 angle pdb=" CA ARG A1436 " pdb=" CB ARG A1436 " pdb=" CG ARG A1436 " ideal model delta sigma weight residual 114.10 122.74 -8.64 2.00e+00 2.50e-01 1.87e+01 angle pdb=" N GLY A1535 " pdb=" CA GLY A1535 " pdb=" C GLY A1535 " ideal model delta sigma weight residual 112.34 121.13 -8.79 2.04e+00 2.40e-01 1.86e+01 ... (remaining 20310 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.06: 8422 17.06 - 34.12: 576 34.12 - 51.19: 84 51.19 - 68.25: 15 68.25 - 85.31: 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 180.00 151.60 28.40 0 5.00e+00 4.00e-02 3.23e+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 180.00 152.43 27.57 0 5.00e+00 4.00e-02 3.04e+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 180.00 153.66 26.34 0 5.00e+00 4.00e-02 2.78e+01 ... (remaining 9101 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.089: 2106 0.089 - 0.178: 237 0.178 - 0.267: 12 0.267 - 0.356: 0 0.356 - 0.445: 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 2.20 0.45 2.00e-01 2.50e+01 4.96e+00 chirality pdb=" CG LEU C 162 " pdb=" CB LEU C 162 " pdb=" CD1 LEU C 162 " pdb=" CD2 LEU C 162 " both_signs ideal model delta sigma weight residual False -2.59 -2.33 -0.25 2.00e-01 2.50e+01 1.62e+00 chirality pdb=" CB VAL A 860 " pdb=" CA VAL A 860 " pdb=" CG1 VAL A 860 " pdb=" CG2 VAL A 860 " both_signs ideal model delta sigma weight residual False -2.63 -2.41 -0.22 2.00e-01 2.50e+01 1.21e+00 ... (remaining 2353 not shown) Planarity restraints: 2561 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP A 348 " 0.020 2.00e-02 2.50e+03 3.11e-02 2.42e+01 pdb=" CG TRP A 348 " -0.076 2.00e-02 2.50e+03 pdb=" CD1 TRP A 348 " 0.055 2.00e-02 2.50e+03 pdb=" CD2 TRP A 348 " -0.004 2.00e-02 2.50e+03 pdb=" NE1 TRP A 348 " -0.005 2.00e-02 2.50e+03 pdb=" CE2 TRP A 348 " -0.009 2.00e-02 2.50e+03 pdb=" CE3 TRP A 348 " 0.007 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 348 " -0.004 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 348 " 0.016 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 " 0.054 5.00e-02 4.00e+02 8.17e-02 1.07e+01 pdb=" N PRO A 355 " -0.141 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 " 0.054 5.00e-02 4.00e+02 8.10e-02 1.05e+01 pdb=" N PRO A1359 " -0.140 5.00e-02 4.00e+02 pdb=" CA PRO A1359 " 0.041 5.00e-02 4.00e+02 pdb=" CD PRO A1359 " 0.046 5.00e-02 4.00e+02 ... (remaining 2558 not shown) Histogram of nonbonded interaction distances: 1.92 - 2.52: 38 2.52 - 3.11: 10146 3.11 - 3.71: 22275 3.71 - 4.30: 31810 4.30 - 4.90: 52229 Nonbonded interactions: 116498 Sorted by model distance: nonbonded pdb=" OD1 ASP A1509 " pdb="ZN ZN A1802 " model vdw 1.921 2.230 nonbonded pdb=" OE2 GLU A1020 " pdb="ZN ZN A1801 " model vdw 2.010 2.230 nonbonded pdb=" OD2 ASP A1509 " pdb="ZN ZN A1802 " model vdw 2.058 2.230 nonbonded pdb=" CG ASP A1509 " pdb="ZN ZN A1802 " model vdw 2.197 2.460 nonbonded pdb=" OG SER A1444 " pdb=" OE1 GLN A1455 " model vdw 2.315 3.040 ... (remaining 116493 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: 3.850 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: 0.000 Extract box with map and model: 0.380 Check model and map are aligned: 0.040 Set scattering table: 0.050 Process input model: 17.320 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: 0.010 Load rotamer database and sin/cos tables:6.730 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.500 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7679 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 0.073 14982 Z= 0.246 Angle : 0.954 11.902 20315 Z= 0.510 Chirality : 0.056 0.445 2356 Planarity : 0.010 0.082 2561 Dihedral : 11.906 85.311 5568 Min Nonbonded Distance : 1.921 Molprobity Statistics. All-atom Clashscore : 3.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.72 % Favored : 95.28 % 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: -1.87 (0.17), residues: 1845 helix: -0.90 (0.14), residues: 1008 sheet: 0.38 (0.54), residues: 98 loop : -1.82 (0.20), residues: 739 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG A 876 TYR 0.048 0.003 TYR A 109 PHE 0.025 0.003 PHE A 489 TRP 0.076 0.004 TRP A 348 HIS 0.019 0.002 HIS A 191 Details of bonding type rmsd covalent geometry : bond 0.00519 (14976) covalent geometry : angle 0.95363 (20315) hydrogen bonds : bond 0.15392 ( 758) hydrogen bonds : angle 6.22718 ( 2217) metal coordination : bond 0.01646 ( 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 320 residues out of total 1638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 320 time to evaluate : 0.574 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 379 GLN cc_start: 0.8116 (mp10) cc_final: 0.7914 (mp10) REVERT: A 424 TRP cc_start: 0.8408 (t-100) cc_final: 0.8184 (t-100) REVERT: A 425 LYS cc_start: 0.8172 (mmtp) cc_final: 0.7963 (mmtp) REVERT: A 470 GLU cc_start: 0.7812 (mp0) cc_final: 0.7464 (mp0) REVERT: A 518 THR cc_start: 0.8470 (m) cc_final: 0.8247 (t) REVERT: A 669 GLN cc_start: 0.8490 (mt0) cc_final: 0.8256 (mt0) REVERT: A 702 ASP cc_start: 0.7798 (p0) cc_final: 0.7497 (p0) REVERT: A 724 GLN cc_start: 0.8147 (mt0) cc_final: 0.7931 (mt0) REVERT: A 746 LEU cc_start: 0.8490 (tp) cc_final: 0.8240 (tt) REVERT: A 921 ARG cc_start: 0.8489 (mtt-85) cc_final: 0.8261 (mtt-85) REVERT: A 970 LYS cc_start: 0.8606 (tttm) cc_final: 0.8402 (ttmt) REVERT: A 1222 PHE cc_start: 0.8018 (p90) cc_final: 0.7599 (p90) REVERT: A 1332 MET cc_start: 0.6864 (ptm) cc_final: 0.6468 (ptm) REVERT: A 1470 TYR cc_start: 0.6369 (m-10) cc_final: 0.5947 (m-10) REVERT: A 1490 THR cc_start: 0.7663 (m) cc_final: 0.7248 (p) REVERT: B 149 MET cc_start: 0.7894 (tpt) cc_final: 0.7648 (tpt) REVERT: D 149 MET cc_start: 0.7145 (tpt) cc_final: 0.6882 (tpt) outliers start: 0 outliers final: 0 residues processed: 320 average time/residue: 0.6181 time to fit residues: 215.5930 Evaluate side-chains 264 residues out of total 1638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 264 time to evaluate : 0.545 ------------------------------------------------------------------------------- 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: 0.7980 chunk 107 optimal weight: 1.9990 chunk 10 optimal weight: 0.5980 chunk 66 optimal weight: 0.7980 chunk 130 optimal weight: 10.0000 chunk 124 optimal weight: 4.9990 chunk 103 optimal weight: 2.9990 chunk 77 optimal weight: 0.5980 chunk 122 optimal weight: 40.0000 chunk 91 optimal weight: 0.9990 chunk 149 optimal weight: 8.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 48 HIS A 205 GLN ** A 308 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 345 ASN A 572 GLN A 575 ASN A 908 GLN A 975 GLN A1025 HIS A1094 HIS A1455 GLN ** A1555 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4122 r_free = 0.4122 target = 0.170881 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3529 r_free = 0.3529 target = 0.124441 restraints weight = 19289.406| |-----------------------------------------------------------------------------| r_work (start): 0.3507 rms_B_bonded: 1.65 r_work: 0.3386 rms_B_bonded: 2.08 restraints_weight: 0.5000 r_work: 0.3250 rms_B_bonded: 3.47 restraints_weight: 0.2500 r_work (final): 0.3250 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7752 moved from start: 0.1654 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 14982 Z= 0.162 Angle : 0.610 7.340 20315 Z= 0.320 Chirality : 0.042 0.173 2356 Planarity : 0.006 0.060 2561 Dihedral : 4.967 25.999 2025 Min Nonbonded Distance : 1.874 Molprobity Statistics. All-atom Clashscore : 7.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.28 % Favored : 95.72 % Rotamer: Outliers : 2.02 % Allowed : 6.96 % Favored : 91.02 % 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: -0.47 (0.19), residues: 1845 helix: 0.54 (0.16), residues: 1031 sheet: 0.41 (0.54), residues: 98 loop : -1.67 (0.21), residues: 716 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 22 TYR 0.032 0.002 TYR A 109 PHE 0.022 0.002 PHE A 230 TRP 0.042 0.002 TRP A 203 HIS 0.028 0.002 HIS A1555 Details of bonding type rmsd covalent geometry : bond 0.00374 (14976) covalent geometry : angle 0.60977 (20315) hydrogen bonds : bond 0.05946 ( 758) hydrogen bonds : angle 4.60617 ( 2217) metal coordination : bond 0.01007 ( 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 307 residues out of total 1638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 274 time to evaluate : 0.457 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 117 THR cc_start: 0.8363 (m) cc_final: 0.8068 (p) REVERT: A 470 GLU cc_start: 0.7767 (mp0) cc_final: 0.7465 (mp0) REVERT: A 518 THR cc_start: 0.8468 (m) cc_final: 0.8187 (t) REVERT: A 746 LEU cc_start: 0.8442 (tp) cc_final: 0.8195 (tt) REVERT: A 972 SER cc_start: 0.8686 (t) cc_final: 0.8409 (m) REVERT: A 986 MET cc_start: 0.8380 (OUTLIER) cc_final: 0.8139 (mtp) REVERT: A 1222 PHE cc_start: 0.8053 (p90) cc_final: 0.7686 (p90) REVERT: A 1300 MET cc_start: 0.6753 (mmm) cc_final: 0.6393 (mmm) REVERT: A 1332 MET cc_start: 0.6873 (ptm) cc_final: 0.6412 (ptm) REVERT: A 1459 MET cc_start: 0.7384 (mmt) cc_final: 0.6724 (mmt) REVERT: A 1577 MET cc_start: 0.6049 (OUTLIER) cc_final: 0.5721 (mmp) REVERT: B 149 MET cc_start: 0.7906 (tpt) cc_final: 0.7613 (tpt) outliers start: 33 outliers final: 12 residues processed: 285 average time/residue: 0.6498 time to fit residues: 201.3477 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 : 0.575 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 SER Chi-restraints excluded: chain A residue 103 HIS Chi-restraints excluded: chain A residue 161 SER Chi-restraints excluded: chain A residue 266 CYS Chi-restraints excluded: chain A residue 447 LEU Chi-restraints excluded: chain A residue 695 VAL Chi-restraints excluded: chain A residue 716 VAL Chi-restraints excluded: chain A residue 840 SER Chi-restraints excluded: chain A residue 966 SER Chi-restraints excluded: chain A residue 986 MET Chi-restraints excluded: chain A residue 1013 VAL Chi-restraints excluded: chain A residue 1209 SER Chi-restraints excluded: chain A residue 1454 SER 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: 0.8980 chunk 175 optimal weight: 6.9990 chunk 111 optimal weight: 0.0670 chunk 84 optimal weight: 0.8980 chunk 176 optimal weight: 0.8980 chunk 164 optimal weight: 40.0000 chunk 116 optimal weight: 0.2980 chunk 83 optimal weight: 0.6980 chunk 166 optimal weight: 2.9990 chunk 130 optimal weight: 5.9990 chunk 3 optimal weight: 0.0980 overall best weight: 0.4118 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 308 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 572 GLN A 724 GLN A 829 GLN A 908 GLN A 975 GLN A1025 HIS ** A1555 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4143 r_free = 0.4143 target = 0.172901 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3543 r_free = 0.3543 target = 0.125645 restraints weight = 19292.984| |-----------------------------------------------------------------------------| r_work (start): 0.3526 rms_B_bonded: 1.69 r_work: 0.3396 rms_B_bonded: 2.17 restraints_weight: 0.5000 r_work: 0.3254 rms_B_bonded: 3.61 restraints_weight: 0.2500 r_work (final): 0.3254 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7752 moved from start: 0.2024 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 14982 Z= 0.122 Angle : 0.546 9.550 20315 Z= 0.283 Chirality : 0.040 0.142 2356 Planarity : 0.005 0.058 2561 Dihedral : 4.583 23.810 2025 Min Nonbonded Distance : 1.975 Molprobity Statistics. All-atom Clashscore : 6.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.96 % Favored : 96.04 % Rotamer: Outliers : 1.95 % Allowed : 10.26 % Favored : 87.78 % 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: 0.20 (0.20), residues: 1845 helix: 1.24 (0.17), residues: 1021 sheet: 0.58 (0.55), residues: 98 loop : -1.60 (0.21), residues: 726 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A1055 TYR 0.027 0.001 TYR A 109 PHE 0.017 0.001 PHE A 230 TRP 0.036 0.001 TRP A 203 HIS 0.013 0.001 HIS A1555 Details of bonding type rmsd covalent geometry : bond 0.00265 (14976) covalent geometry : angle 0.54571 (20315) hydrogen bonds : bond 0.04850 ( 758) hydrogen bonds : angle 4.27605 ( 2217) metal coordination : bond 0.00505 ( 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 304 residues out of total 1638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 272 time to evaluate : 0.584 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 470 GLU cc_start: 0.7830 (mp0) cc_final: 0.7567 (mp0) REVERT: A 518 THR cc_start: 0.8453 (m) cc_final: 0.8193 (t) REVERT: A 746 LEU cc_start: 0.8504 (tp) cc_final: 0.8209 (tt) REVERT: A 925 MET cc_start: 0.8412 (mtp) cc_final: 0.8129 (mtp) REVERT: A 972 SER cc_start: 0.8731 (t) cc_final: 0.8434 (m) REVERT: A 1049 SER cc_start: 0.8615 (p) cc_final: 0.8323 (t) REVERT: A 1222 PHE cc_start: 0.8047 (p90) cc_final: 0.7845 (p90) REVERT: A 1300 MET cc_start: 0.6671 (mmm) cc_final: 0.6331 (mmm) REVERT: A 1332 MET cc_start: 0.6885 (ptm) cc_final: 0.6397 (ptm) REVERT: A 1459 MET cc_start: 0.7408 (mmt) cc_final: 0.6780 (mmt) REVERT: A 1577 MET cc_start: 0.6199 (OUTLIER) cc_final: 0.5718 (mmp) REVERT: B 149 MET cc_start: 0.7863 (tpt) cc_final: 0.7538 (tpt) REVERT: B 155 MET cc_start: 0.8163 (OUTLIER) cc_final: 0.7945 (mtp) REVERT: C 156 MET cc_start: 0.7378 (OUTLIER) cc_final: 0.6282 (tmm) outliers start: 32 outliers final: 11 residues processed: 283 average time/residue: 0.6393 time to fit residues: 197.1412 Evaluate side-chains 276 residues out of total 1638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 262 time to evaluate : 0.547 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 SER Chi-restraints excluded: chain A residue 112 VAL Chi-restraints excluded: chain A residue 525 SER Chi-restraints excluded: chain A residue 534 ARG Chi-restraints excluded: chain A residue 695 VAL Chi-restraints excluded: chain A residue 716 VAL Chi-restraints excluded: chain A residue 840 SER Chi-restraints excluded: chain A residue 966 SER Chi-restraints excluded: chain A residue 1013 VAL Chi-restraints excluded: chain A residue 1174 ASP Chi-restraints excluded: chain A residue 1454 SER Chi-restraints excluded: chain A residue 1577 MET Chi-restraints excluded: chain B residue 155 MET Chi-restraints excluded: chain C residue 156 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 44 optimal weight: 1.9990 chunk 15 optimal weight: 2.9990 chunk 109 optimal weight: 0.7980 chunk 57 optimal weight: 0.2980 chunk 121 optimal weight: 7.9990 chunk 22 optimal weight: 1.9990 chunk 69 optimal weight: 0.9980 chunk 93 optimal weight: 0.7980 chunk 11 optimal weight: 0.9990 chunk 160 optimal weight: 9.9990 chunk 27 optimal weight: 0.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 205 GLN A 572 GLN A 829 GLN A 908 GLN A 975 GLN ** A1439 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4122 r_free = 0.4122 target = 0.170933 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3506 r_free = 0.3506 target = 0.122974 restraints weight = 19127.910| |-----------------------------------------------------------------------------| r_work (start): 0.3486 rms_B_bonded: 1.71 r_work: 0.3357 rms_B_bonded: 2.17 restraints_weight: 0.5000 r_work: 0.3215 rms_B_bonded: 3.62 restraints_weight: 0.2500 r_work (final): 0.3215 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7781 moved from start: 0.2297 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 14982 Z= 0.152 Angle : 0.561 10.121 20315 Z= 0.290 Chirality : 0.041 0.145 2356 Planarity : 0.005 0.058 2561 Dihedral : 4.521 21.980 2025 Min Nonbonded Distance : 1.990 Molprobity Statistics. All-atom Clashscore : 7.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.44 % Favored : 95.56 % Rotamer: Outliers : 2.44 % Allowed : 11.79 % Favored : 85.77 % 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: 0.35 (0.20), residues: 1845 helix: 1.40 (0.17), residues: 1025 sheet: 0.43 (0.54), residues: 100 loop : -1.57 (0.22), residues: 720 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 58 TYR 0.027 0.002 TYR A 109 PHE 0.022 0.001 PHE A 230 TRP 0.034 0.002 TRP A 203 HIS 0.012 0.001 HIS A1181 Details of bonding type rmsd covalent geometry : bond 0.00359 (14976) covalent geometry : angle 0.56127 (20315) hydrogen bonds : bond 0.05265 ( 758) hydrogen bonds : angle 4.20974 ( 2217) metal coordination : bond 0.00666 ( 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 300 residues out of total 1638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 260 time to evaluate : 0.401 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 470 GLU cc_start: 0.7883 (mp0) cc_final: 0.7633 (mp0) REVERT: A 518 THR cc_start: 0.8467 (m) cc_final: 0.8139 (t) REVERT: A 746 LEU cc_start: 0.8543 (tp) cc_final: 0.8248 (tt) REVERT: A 965 GLU cc_start: 0.8007 (tt0) cc_final: 0.7588 (tp30) REVERT: A 972 SER cc_start: 0.8704 (t) cc_final: 0.8422 (m) REVERT: A 1049 SER cc_start: 0.8571 (p) cc_final: 0.8310 (t) REVERT: A 1300 MET cc_start: 0.6649 (mmm) cc_final: 0.6289 (mmm) REVERT: A 1459 MET cc_start: 0.7397 (mmt) cc_final: 0.6802 (mmt) REVERT: A 1577 MET cc_start: 0.6185 (OUTLIER) cc_final: 0.5732 (mmp) REVERT: B 149 MET cc_start: 0.7866 (tpt) cc_final: 0.7499 (tpt) REVERT: B 155 MET cc_start: 0.8209 (OUTLIER) cc_final: 0.7996 (mtp) REVERT: C 156 MET cc_start: 0.7343 (OUTLIER) cc_final: 0.6318 (tmm) REVERT: D 149 MET cc_start: 0.7355 (tpt) cc_final: 0.7141 (tpt) outliers start: 40 outliers final: 18 residues processed: 273 average time/residue: 0.6197 time to fit residues: 184.0574 Evaluate side-chains 283 residues out of total 1638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 262 time to evaluate : 0.477 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 103 HIS Chi-restraints excluded: chain A residue 104 MET Chi-restraints excluded: chain A residue 112 VAL Chi-restraints excluded: chain A residue 250 VAL Chi-restraints excluded: chain A residue 266 CYS Chi-restraints excluded: chain A residue 525 SER Chi-restraints excluded: chain A residue 534 ARG Chi-restraints excluded: chain A residue 695 VAL Chi-restraints excluded: chain A residue 716 VAL Chi-restraints excluded: chain A residue 840 SER Chi-restraints excluded: chain A residue 934 VAL Chi-restraints excluded: chain A residue 966 SER Chi-restraints excluded: chain A residue 968 ARG Chi-restraints excluded: chain A residue 1013 VAL Chi-restraints excluded: chain A residue 1174 ASP Chi-restraints excluded: chain A residue 1454 SER Chi-restraints excluded: chain A residue 1577 MET Chi-restraints excluded: chain B residue 145 MET Chi-restraints excluded: chain B residue 155 MET Chi-restraints excluded: chain C residue 156 MET Chi-restraints excluded: chain E residue 148 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 180 optimal weight: 3.9990 chunk 163 optimal weight: 4.9990 chunk 99 optimal weight: 0.9980 chunk 93 optimal weight: 5.9990 chunk 25 optimal weight: 0.5980 chunk 144 optimal weight: 0.3980 chunk 152 optimal weight: 0.5980 chunk 169 optimal weight: 0.7980 chunk 39 optimal weight: 0.7980 chunk 164 optimal weight: 40.0000 chunk 123 optimal weight: 10.0000 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 908 GLN A 975 GLN ** A1439 HIS ** 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 = 0.4127 r_free = 0.4127 target = 0.171324 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3510 r_free = 0.3510 target = 0.123258 restraints weight = 19011.035| |-----------------------------------------------------------------------------| r_work (start): 0.3492 rms_B_bonded: 1.71 r_work: 0.3363 rms_B_bonded: 2.17 restraints_weight: 0.5000 r_work: 0.3220 rms_B_bonded: 3.60 restraints_weight: 0.2500 r_work (final): 0.3220 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7773 moved from start: 0.2493 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= 0.136 Angle : 0.542 9.699 20315 Z= 0.280 Chirality : 0.041 0.142 2356 Planarity : 0.005 0.058 2561 Dihedral : 4.397 20.912 2025 Min Nonbonded Distance : 2.015 Molprobity Statistics. All-atom Clashscore : 6.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.01 % Favored : 95.99 % Rotamer: Outliers : 2.38 % Allowed : 12.34 % 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: 0.59 (0.20), residues: 1845 helix: 1.66 (0.17), residues: 1019 sheet: 0.42 (0.55), residues: 98 loop : -1.52 (0.22), residues: 728 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG A1055 TYR 0.024 0.002 TYR A 109 PHE 0.022 0.001 PHE A1222 TRP 0.028 0.001 TRP A 203 HIS 0.010 0.001 HIS A1181 Details of bonding type rmsd covalent geometry : bond 0.00317 (14976) covalent geometry : angle 0.54206 (20315) hydrogen bonds : bond 0.04870 ( 758) hydrogen bonds : angle 4.10718 ( 2217) metal coordination : bond 0.00604 ( 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 304 residues out of total 1638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 265 time to evaluate : 0.405 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 462 PHE cc_start: 0.8318 (m-80) cc_final: 0.8049 (m-80) REVERT: A 624 GLU cc_start: 0.7754 (OUTLIER) cc_final: 0.7435 (tp30) REVERT: A 965 GLU cc_start: 0.8015 (tt0) cc_final: 0.7549 (tp30) REVERT: A 972 SER cc_start: 0.8708 (t) cc_final: 0.8419 (m) REVERT: A 1049 SER cc_start: 0.8569 (p) cc_final: 0.8283 (t) REVERT: A 1300 MET cc_start: 0.6673 (mmm) cc_final: 0.6307 (mmm) REVERT: A 1345 MET cc_start: 0.7665 (tpt) cc_final: 0.7448 (tpp) REVERT: A 1459 MET cc_start: 0.7380 (mmt) cc_final: 0.6783 (mmt) REVERT: A 1577 MET cc_start: 0.6193 (OUTLIER) cc_final: 0.5705 (mmp) REVERT: B 149 MET cc_start: 0.7804 (tpt) cc_final: 0.7438 (tpt) REVERT: B 152 MET cc_start: 0.8185 (tpp) cc_final: 0.7964 (tpt) REVERT: C 156 MET cc_start: 0.7327 (OUTLIER) cc_final: 0.6358 (tmm) REVERT: D 145 MET cc_start: 0.7560 (mtp) cc_final: 0.7201 (mtt) REVERT: D 149 MET cc_start: 0.7308 (tpt) cc_final: 0.7070 (tpt) outliers start: 39 outliers final: 18 residues processed: 276 average time/residue: 0.6149 time to fit residues: 184.8136 Evaluate side-chains 279 residues out of total 1638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 258 time to evaluate : 0.563 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 SER Chi-restraints excluded: chain A residue 103 HIS Chi-restraints excluded: chain A residue 112 VAL Chi-restraints excluded: chain A residue 250 VAL Chi-restraints excluded: chain A residue 258 SER Chi-restraints excluded: chain A residue 266 CYS Chi-restraints excluded: chain A residue 525 SER Chi-restraints excluded: chain A residue 534 ARG Chi-restraints excluded: chain A residue 624 GLU Chi-restraints excluded: chain A residue 695 VAL Chi-restraints excluded: chain A residue 716 VAL Chi-restraints excluded: chain A residue 786 ASP Chi-restraints excluded: chain A residue 840 SER Chi-restraints excluded: chain A residue 934 VAL Chi-restraints excluded: chain A residue 966 SER Chi-restraints excluded: chain A residue 968 ARG Chi-restraints excluded: chain A residue 1013 VAL Chi-restraints excluded: chain A residue 1454 SER Chi-restraints excluded: chain A residue 1577 MET Chi-restraints excluded: chain C residue 156 MET Chi-restraints excluded: chain E residue 148 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 60 optimal weight: 2.9990 chunk 39 optimal weight: 1.9990 chunk 44 optimal weight: 0.9990 chunk 65 optimal weight: 0.3980 chunk 87 optimal weight: 5.9990 chunk 13 optimal weight: 2.9990 chunk 55 optimal weight: 1.9990 chunk 74 optimal weight: 0.5980 chunk 138 optimal weight: 9.9990 chunk 110 optimal weight: 1.9990 chunk 3 optimal weight: 2.9990 overall best weight: 1.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 103 HIS A 664 HIS A 908 GLN A 975 GLN A1025 HIS ** A1439 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4104 r_free = 0.4104 target = 0.169432 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3479 r_free = 0.3479 target = 0.121301 restraints weight = 18907.881| |-----------------------------------------------------------------------------| r_work (start): 0.3463 rms_B_bonded: 1.66 r_work: 0.3334 rms_B_bonded: 2.11 restraints_weight: 0.5000 r_work: 0.3193 rms_B_bonded: 3.51 restraints_weight: 0.2500 r_work (final): 0.3193 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7816 moved from start: 0.2672 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 14982 Z= 0.205 Angle : 0.607 10.742 20315 Z= 0.310 Chirality : 0.044 0.213 2356 Planarity : 0.005 0.059 2561 Dihedral : 4.563 20.815 2025 Min Nonbonded Distance : 1.954 Molprobity Statistics. All-atom Clashscore : 7.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.55 % Favored : 95.45 % Rotamer: Outliers : 2.50 % Allowed : 12.58 % Favored : 84.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.46 (0.20), residues: 1845 helix: 1.55 (0.17), residues: 1019 sheet: 0.24 (0.54), residues: 100 loop : -1.55 (0.22), residues: 726 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A1055 TYR 0.027 0.002 TYR A 109 PHE 0.026 0.002 PHE A 230 TRP 0.023 0.002 TRP A 203 HIS 0.013 0.001 HIS A1181 Details of bonding type rmsd covalent geometry : bond 0.00505 (14976) covalent geometry : angle 0.60739 (20315) hydrogen bonds : bond 0.05844 ( 758) hydrogen bonds : angle 4.24310 ( 2217) metal coordination : bond 0.00852 ( 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 310 residues out of total 1638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 269 time to evaluate : 0.595 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 294 TRP cc_start: 0.8323 (OUTLIER) cc_final: 0.7642 (m100) REVERT: A 624 GLU cc_start: 0.7750 (OUTLIER) cc_final: 0.7430 (tp30) REVERT: A 965 GLU cc_start: 0.8056 (tt0) cc_final: 0.7658 (tp30) REVERT: A 972 SER cc_start: 0.8708 (t) cc_final: 0.8478 (m) REVERT: A 1049 SER cc_start: 0.8585 (p) cc_final: 0.8293 (t) REVERT: A 1300 MET cc_start: 0.6603 (mmm) cc_final: 0.6214 (mmm) REVERT: A 1332 MET cc_start: 0.6878 (ptm) cc_final: 0.6246 (ptm) REVERT: A 1345 MET cc_start: 0.7688 (tpt) cc_final: 0.7444 (tpp) REVERT: A 1459 MET cc_start: 0.7373 (mmt) cc_final: 0.6771 (mmt) REVERT: A 1577 MET cc_start: 0.6182 (OUTLIER) cc_final: 0.5735 (mmp) REVERT: B 149 MET cc_start: 0.7789 (tpt) cc_final: 0.7378 (tpt) REVERT: C 156 MET cc_start: 0.7384 (OUTLIER) cc_final: 0.6475 (tmm) REVERT: D 145 MET cc_start: 0.7658 (mtp) cc_final: 0.7330 (mtt) REVERT: D 149 MET cc_start: 0.7329 (tpt) cc_final: 0.7122 (tpt) outliers start: 41 outliers final: 20 residues processed: 282 average time/residue: 0.5753 time to fit residues: 177.5694 Evaluate side-chains 286 residues out of total 1638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 262 time to evaluate : 0.450 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 103 HIS Chi-restraints excluded: chain A residue 104 MET Chi-restraints excluded: chain A residue 112 VAL Chi-restraints excluded: chain A residue 250 VAL Chi-restraints excluded: chain A residue 258 SER Chi-restraints excluded: chain A residue 266 CYS Chi-restraints excluded: chain A residue 294 TRP Chi-restraints excluded: chain A residue 479 LYS Chi-restraints excluded: chain A residue 525 SER Chi-restraints excluded: chain A residue 534 ARG Chi-restraints excluded: chain A residue 624 GLU Chi-restraints excluded: chain A residue 695 VAL Chi-restraints excluded: chain A residue 716 VAL Chi-restraints excluded: chain A residue 786 ASP Chi-restraints excluded: chain A residue 796 VAL Chi-restraints excluded: chain A residue 840 SER Chi-restraints excluded: chain A residue 934 VAL Chi-restraints excluded: chain A residue 966 SER Chi-restraints excluded: chain A residue 968 ARG Chi-restraints excluded: chain A residue 1013 VAL Chi-restraints excluded: chain A residue 1209 SER Chi-restraints excluded: chain A residue 1454 SER Chi-restraints excluded: chain A residue 1577 MET Chi-restraints excluded: chain C residue 156 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 84 optimal weight: 0.6980 chunk 53 optimal weight: 0.9990 chunk 69 optimal weight: 0.9990 chunk 111 optimal weight: 0.9990 chunk 3 optimal weight: 2.9990 chunk 148 optimal weight: 0.9990 chunk 0 optimal weight: 2.9990 chunk 97 optimal weight: 0.8980 chunk 82 optimal weight: 0.7980 chunk 115 optimal weight: 0.5980 chunk 71 optimal weight: 4.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 908 GLN A1023 HIS A1025 HIS A1044 GLN A1291 ASN ** A1439 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1455 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4111 r_free = 0.4111 target = 0.170041 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3492 r_free = 0.3492 target = 0.122033 restraints weight = 18874.936| |-----------------------------------------------------------------------------| r_work (start): 0.3474 rms_B_bonded: 1.67 r_work: 0.3351 rms_B_bonded: 2.10 restraints_weight: 0.5000 r_work: 0.3213 rms_B_bonded: 3.49 restraints_weight: 0.2500 r_work (final): 0.3213 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7790 moved from start: 0.2758 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 14982 Z= 0.157 Angle : 0.575 9.818 20315 Z= 0.294 Chirality : 0.042 0.150 2356 Planarity : 0.005 0.059 2561 Dihedral : 4.450 20.254 2025 Min Nonbonded Distance : 1.993 Molprobity Statistics. All-atom Clashscore : 7.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.44 % Favored : 95.56 % Rotamer: Outliers : 2.57 % Allowed : 13.19 % Favored : 84.24 % 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: 0.59 (0.20), residues: 1845 helix: 1.64 (0.17), residues: 1025 sheet: 0.28 (0.54), residues: 98 loop : -1.49 (0.22), residues: 722 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG A1055 TYR 0.022 0.002 TYR A 109 PHE 0.022 0.001 PHE A 230 TRP 0.020 0.001 TRP A 638 HIS 0.012 0.001 HIS A 103 Details of bonding type rmsd covalent geometry : bond 0.00375 (14976) covalent geometry : angle 0.57534 (20315) hydrogen bonds : bond 0.05243 ( 758) hydrogen bonds : angle 4.14501 ( 2217) metal coordination : bond 0.00601 ( 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 302 residues out of total 1638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 260 time to evaluate : 0.388 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 624 GLU cc_start: 0.7709 (OUTLIER) cc_final: 0.7362 (tp30) REVERT: A 745 CYS cc_start: 0.8670 (t) cc_final: 0.8407 (m) REVERT: A 965 GLU cc_start: 0.8030 (tt0) cc_final: 0.7673 (tp30) REVERT: A 972 SER cc_start: 0.8711 (t) cc_final: 0.8468 (m) REVERT: A 1049 SER cc_start: 0.8568 (p) cc_final: 0.8281 (t) REVERT: A 1055 ARG cc_start: 0.7565 (ttm110) cc_final: 0.7263 (ttm-80) REVERT: A 1300 MET cc_start: 0.6690 (mmm) cc_final: 0.6304 (mmm) REVERT: A 1332 MET cc_start: 0.6845 (ptm) cc_final: 0.6215 (ptm) REVERT: A 1345 MET cc_start: 0.7731 (tpt) cc_final: 0.7486 (tpp) REVERT: A 1459 MET cc_start: 0.7382 (mmt) cc_final: 0.6796 (mmt) REVERT: A 1577 MET cc_start: 0.6096 (OUTLIER) cc_final: 0.5709 (mmp) REVERT: B 149 MET cc_start: 0.7778 (tpt) cc_final: 0.7351 (tpt) REVERT: C 156 MET cc_start: 0.7372 (OUTLIER) cc_final: 0.6530 (tmm) REVERT: D 145 MET cc_start: 0.7678 (mtp) cc_final: 0.7332 (mtt) REVERT: D 149 MET cc_start: 0.7345 (tpt) cc_final: 0.7142 (tpt) outliers start: 42 outliers final: 21 residues processed: 275 average time/residue: 0.6206 time to fit residues: 186.3245 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 : 0.496 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 103 HIS Chi-restraints excluded: chain A residue 112 VAL Chi-restraints excluded: chain A residue 161 SER Chi-restraints excluded: chain A residue 250 VAL Chi-restraints excluded: chain A residue 258 SER Chi-restraints excluded: chain A residue 266 CYS Chi-restraints excluded: chain A residue 479 LYS Chi-restraints excluded: chain A residue 525 SER Chi-restraints excluded: chain A residue 534 ARG Chi-restraints excluded: chain A residue 624 GLU Chi-restraints excluded: chain A residue 695 VAL Chi-restraints excluded: chain A residue 716 VAL Chi-restraints excluded: chain A residue 786 ASP Chi-restraints excluded: chain A residue 796 VAL Chi-restraints excluded: chain A residue 840 SER Chi-restraints excluded: chain A residue 934 VAL Chi-restraints excluded: chain A residue 966 SER Chi-restraints excluded: chain A residue 968 ARG Chi-restraints excluded: chain A residue 1013 VAL Chi-restraints excluded: chain A residue 1209 SER Chi-restraints excluded: chain A residue 1454 SER Chi-restraints excluded: chain A residue 1577 MET Chi-restraints excluded: chain C residue 156 MET Chi-restraints excluded: chain E residue 148 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 58 optimal weight: 1.9990 chunk 80 optimal weight: 0.5980 chunk 157 optimal weight: 0.0170 chunk 141 optimal weight: 0.8980 chunk 83 optimal weight: 0.9980 chunk 25 optimal weight: 0.7980 chunk 34 optimal weight: 2.9990 chunk 103 optimal weight: 2.9990 chunk 33 optimal weight: 1.9990 chunk 59 optimal weight: 0.2980 chunk 65 optimal weight: 0.6980 overall best weight: 0.4818 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 103 HIS A 908 GLN ** A1439 HIS ** 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 = 0.4126 r_free = 0.4126 target = 0.171316 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.123563 restraints weight = 19115.389| |-----------------------------------------------------------------------------| r_work (start): 0.3494 rms_B_bonded: 1.68 r_work: 0.3372 rms_B_bonded: 2.12 restraints_weight: 0.5000 r_work: 0.3234 rms_B_bonded: 3.53 restraints_weight: 0.2500 r_work (final): 0.3234 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7770 moved from start: 0.2841 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= 0.123 Angle : 0.541 9.174 20315 Z= 0.276 Chirality : 0.040 0.141 2356 Planarity : 0.005 0.061 2561 Dihedral : 4.252 19.305 2025 Min Nonbonded Distance : 2.072 Molprobity Statistics. All-atom Clashscore : 7.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.34 % Favored : 95.66 % Rotamer: Outliers : 2.38 % Allowed : 13.87 % Favored : 83.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 0.76 (0.20), residues: 1845 helix: 1.78 (0.17), residues: 1029 sheet: 0.29 (0.54), residues: 100 loop : -1.42 (0.23), residues: 716 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A1055 TYR 0.021 0.001 TYR A 109 PHE 0.018 0.001 PHE A 230 TRP 0.021 0.001 TRP A 638 HIS 0.008 0.001 HIS A 226 Details of bonding type rmsd covalent geometry : bond 0.00278 (14976) covalent geometry : angle 0.54064 (20315) hydrogen bonds : bond 0.04549 ( 758) hydrogen bonds : angle 4.02798 ( 2217) metal coordination : bond 0.00427 ( 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 300 residues out of total 1638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 261 time to evaluate : 0.352 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 203 TRP cc_start: 0.7458 (OUTLIER) cc_final: 0.6669 (t60) REVERT: A 462 PHE cc_start: 0.8283 (m-80) cc_final: 0.8024 (m-80) REVERT: A 624 GLU cc_start: 0.7665 (OUTLIER) cc_final: 0.7317 (tp30) REVERT: A 965 GLU cc_start: 0.8006 (tt0) cc_final: 0.7663 (tp30) REVERT: A 972 SER cc_start: 0.8717 (t) cc_final: 0.8471 (m) REVERT: A 1049 SER cc_start: 0.8583 (p) cc_final: 0.8297 (t) REVERT: A 1300 MET cc_start: 0.6636 (mmm) cc_final: 0.6245 (mmm) REVERT: A 1332 MET cc_start: 0.6842 (ptm) cc_final: 0.6219 (ptm) REVERT: A 1345 MET cc_start: 0.7713 (tpt) cc_final: 0.7457 (tpp) REVERT: A 1459 MET cc_start: 0.7381 (mmt) cc_final: 0.6812 (mmt) REVERT: A 1577 MET cc_start: 0.6021 (OUTLIER) cc_final: 0.5682 (mmp) REVERT: B 149 MET cc_start: 0.7796 (tpt) cc_final: 0.7362 (tpt) REVERT: C 156 MET cc_start: 0.7411 (OUTLIER) cc_final: 0.6624 (tmm) REVERT: D 145 MET cc_start: 0.7667 (mtp) cc_final: 0.7318 (mtt) outliers start: 39 outliers final: 20 residues processed: 280 average time/residue: 0.5724 time to fit residues: 175.1705 Evaluate side-chains 278 residues out of total 1638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 254 time to evaluate : 0.423 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 SER Chi-restraints excluded: chain A residue 103 HIS Chi-restraints excluded: chain A residue 112 VAL Chi-restraints excluded: chain A residue 161 SER Chi-restraints excluded: chain A residue 203 TRP Chi-restraints excluded: chain A residue 250 VAL Chi-restraints excluded: chain A residue 258 SER Chi-restraints excluded: chain A residue 266 CYS Chi-restraints excluded: chain A residue 391 ASP Chi-restraints excluded: chain A residue 479 LYS Chi-restraints excluded: chain A residue 525 SER Chi-restraints excluded: chain A residue 534 ARG Chi-restraints excluded: chain A residue 624 GLU Chi-restraints excluded: chain A residue 695 VAL Chi-restraints excluded: chain A residue 716 VAL Chi-restraints excluded: chain A residue 796 VAL Chi-restraints excluded: chain A residue 840 SER Chi-restraints excluded: chain A residue 934 VAL Chi-restraints excluded: chain A residue 966 SER Chi-restraints excluded: chain A residue 968 ARG Chi-restraints excluded: chain A residue 1013 VAL Chi-restraints excluded: chain A residue 1033 GLU Chi-restraints excluded: chain A residue 1577 MET Chi-restraints excluded: chain C residue 156 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 116 optimal weight: 2.9990 chunk 49 optimal weight: 0.6980 chunk 127 optimal weight: 8.9990 chunk 45 optimal weight: 2.9990 chunk 122 optimal weight: 0.1980 chunk 14 optimal weight: 0.3980 chunk 70 optimal weight: 0.5980 chunk 143 optimal weight: 0.9990 chunk 57 optimal weight: 0.7980 chunk 98 optimal weight: 0.9990 chunk 68 optimal weight: 1.9990 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 103 HIS A 908 GLN ** A1439 HIS ** 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 = 0.4126 r_free = 0.4126 target = 0.171257 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3511 r_free = 0.3511 target = 0.123434 restraints weight = 19095.720| |-----------------------------------------------------------------------------| r_work (start): 0.3492 rms_B_bonded: 1.69 r_work: 0.3366 rms_B_bonded: 2.13 restraints_weight: 0.5000 r_work: 0.3224 rms_B_bonded: 3.55 restraints_weight: 0.2500 r_work (final): 0.3224 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7780 moved from start: 0.2905 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 14982 Z= 0.129 Angle : 0.550 10.114 20315 Z= 0.279 Chirality : 0.041 0.155 2356 Planarity : 0.005 0.061 2561 Dihedral : 4.209 19.696 2025 Min Nonbonded Distance : 2.059 Molprobity Statistics. All-atom Clashscore : 7.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.50 % Favored : 95.50 % 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: 0.82 (0.20), residues: 1845 helix: 1.82 (0.17), residues: 1029 sheet: 0.36 (0.55), residues: 100 loop : -1.39 (0.23), residues: 716 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A 58 TYR 0.023 0.001 TYR A 109 PHE 0.021 0.001 PHE A1222 TRP 0.021 0.001 TRP A 638 HIS 0.011 0.001 HIS A 103 Details of bonding type rmsd covalent geometry : bond 0.00299 (14976) covalent geometry : angle 0.54954 (20315) hydrogen bonds : bond 0.04592 ( 758) hydrogen bonds : angle 4.01122 ( 2217) metal coordination : bond 0.00455 ( 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 : 0.482 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 203 TRP cc_start: 0.7450 (OUTLIER) cc_final: 0.6674 (t60) REVERT: A 294 TRP cc_start: 0.8167 (OUTLIER) cc_final: 0.7435 (m100) REVERT: A 462 PHE cc_start: 0.8285 (m-80) cc_final: 0.8023 (m-80) REVERT: A 624 GLU cc_start: 0.7695 (OUTLIER) cc_final: 0.7361 (tp30) REVERT: A 745 CYS cc_start: 0.8669 (t) cc_final: 0.8389 (m) REVERT: A 965 GLU cc_start: 0.8033 (tt0) cc_final: 0.7672 (tp30) REVERT: A 972 SER cc_start: 0.8720 (t) cc_final: 0.8475 (m) REVERT: A 1049 SER cc_start: 0.8564 (p) cc_final: 0.8290 (t) REVERT: A 1300 MET cc_start: 0.6589 (mmm) cc_final: 0.6202 (mmm) REVERT: A 1332 MET cc_start: 0.6842 (ptm) cc_final: 0.6218 (ptm) REVERT: A 1345 MET cc_start: 0.7673 (tpt) cc_final: 0.7428 (tpp) REVERT: A 1459 MET cc_start: 0.7403 (mmt) cc_final: 0.6846 (mmt) REVERT: A 1577 MET cc_start: 0.6037 (OUTLIER) cc_final: 0.5773 (mmp) REVERT: B 149 MET cc_start: 0.7763 (tpt) cc_final: 0.7361 (tpt) REVERT: C 156 MET cc_start: 0.7380 (OUTLIER) cc_final: 0.6614 (tmm) REVERT: D 145 MET cc_start: 0.7623 (mtp) cc_final: 0.7290 (mtt) outliers start: 30 outliers final: 19 residues processed: 269 average time/residue: 0.6482 time to fit residues: 189.8096 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 : 0.499 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 SER Chi-restraints excluded: chain A residue 112 VAL Chi-restraints excluded: chain A residue 161 SER Chi-restraints excluded: chain A residue 203 TRP Chi-restraints excluded: chain A residue 250 VAL Chi-restraints excluded: chain A residue 294 TRP Chi-restraints excluded: chain A residue 391 ASP Chi-restraints excluded: chain A residue 479 LYS Chi-restraints excluded: chain A residue 525 SER Chi-restraints excluded: chain A residue 534 ARG Chi-restraints excluded: chain A residue 624 GLU Chi-restraints excluded: chain A residue 695 VAL Chi-restraints excluded: chain A residue 716 VAL Chi-restraints excluded: chain A residue 796 VAL Chi-restraints excluded: chain A residue 840 SER Chi-restraints excluded: chain A residue 934 VAL Chi-restraints excluded: chain A residue 940 ILE Chi-restraints excluded: chain A residue 966 SER Chi-restraints excluded: chain A residue 968 ARG Chi-restraints excluded: chain A residue 1013 VAL Chi-restraints excluded: chain A residue 1033 GLU Chi-restraints excluded: chain A residue 1209 SER Chi-restraints excluded: chain A residue 1577 MET Chi-restraints excluded: chain C residue 156 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 112 optimal weight: 0.5980 chunk 72 optimal weight: 0.9990 chunk 93 optimal weight: 6.9990 chunk 142 optimal weight: 0.9990 chunk 25 optimal weight: 0.8980 chunk 117 optimal weight: 1.9990 chunk 54 optimal weight: 0.8980 chunk 37 optimal weight: 0.8980 chunk 73 optimal weight: 3.9990 chunk 20 optimal weight: 0.5980 chunk 180 optimal weight: 4.9990 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 103 HIS A 908 GLN A 933 ASN ** A1439 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4116 r_free = 0.4116 target = 0.170454 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3495 r_free = 0.3495 target = 0.122408 restraints weight = 19036.780| |-----------------------------------------------------------------------------| r_work (start): 0.3478 rms_B_bonded: 1.69 r_work: 0.3352 rms_B_bonded: 2.13 restraints_weight: 0.5000 r_work: 0.3209 rms_B_bonded: 3.55 restraints_weight: 0.2500 r_work (final): 0.3209 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7797 moved from start: 0.2960 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 14982 Z= 0.154 Angle : 0.576 10.821 20315 Z= 0.292 Chirality : 0.042 0.164 2356 Planarity : 0.005 0.061 2561 Dihedral : 4.289 19.940 2025 Min Nonbonded Distance : 2.012 Molprobity Statistics. All-atom Clashscore : 7.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.82 % Favored : 95.18 % Rotamer: Outliers : 1.89 % Allowed : 15.15 % Favored : 82.96 % 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: 0.76 (0.20), residues: 1845 helix: 1.76 (0.17), residues: 1029 sheet: 0.37 (0.55), residues: 100 loop : -1.42 (0.23), residues: 716 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.000 ARG A1055 TYR 0.026 0.002 TYR A 578 PHE 0.022 0.001 PHE A 230 TRP 0.020 0.001 TRP A 638 HIS 0.010 0.001 HIS A1181 Details of bonding type rmsd covalent geometry : bond 0.00372 (14976) covalent geometry : angle 0.57628 (20315) hydrogen bonds : bond 0.04992 ( 758) hydrogen bonds : angle 4.07587 ( 2217) metal coordination : bond 0.00584 ( 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 287 residues out of total 1638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 256 time to evaluate : 0.585 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 203 TRP cc_start: 0.7518 (OUTLIER) cc_final: 0.6752 (t60) REVERT: A 462 PHE cc_start: 0.8272 (m-80) cc_final: 0.8049 (m-80) REVERT: A 523 MET cc_start: 0.7565 (mtt) cc_final: 0.7285 (mtt) REVERT: A 626 MET cc_start: 0.7406 (OUTLIER) cc_final: 0.6895 (mtp) REVERT: A 745 CYS cc_start: 0.8651 (t) cc_final: 0.8429 (m) REVERT: A 965 GLU cc_start: 0.8046 (tt0) cc_final: 0.7689 (tp30) REVERT: A 972 SER cc_start: 0.8719 (t) cc_final: 0.8482 (m) REVERT: A 1049 SER cc_start: 0.8592 (p) cc_final: 0.8310 (t) REVERT: A 1300 MET cc_start: 0.6550 (mmm) cc_final: 0.6146 (mmm) REVERT: A 1332 MET cc_start: 0.6837 (ptm) cc_final: 0.6215 (ptm) REVERT: A 1345 MET cc_start: 0.7686 (tpt) cc_final: 0.7440 (tpp) REVERT: A 1459 MET cc_start: 0.7376 (mmt) cc_final: 0.6811 (mmt) REVERT: A 1577 MET cc_start: 0.6046 (OUTLIER) cc_final: 0.5773 (mmp) REVERT: B 149 MET cc_start: 0.7775 (tpt) cc_final: 0.7397 (tpt) REVERT: C 156 MET cc_start: 0.7383 (OUTLIER) cc_final: 0.7095 (tmm) REVERT: D 145 MET cc_start: 0.7634 (mtp) cc_final: 0.7299 (mtt) outliers start: 31 outliers final: 18 residues processed: 269 average time/residue: 0.6884 time to fit residues: 201.6405 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 : 0.391 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 SER Chi-restraints excluded: chain A residue 112 VAL Chi-restraints excluded: chain A residue 161 SER Chi-restraints excluded: chain A residue 203 TRP Chi-restraints excluded: chain A residue 266 CYS Chi-restraints excluded: chain A residue 391 ASP Chi-restraints excluded: chain A residue 479 LYS Chi-restraints excluded: chain A residue 534 ARG Chi-restraints excluded: chain A residue 626 MET Chi-restraints excluded: chain A residue 695 VAL Chi-restraints excluded: chain A residue 716 VAL Chi-restraints excluded: chain A residue 796 VAL Chi-restraints excluded: chain A residue 840 SER Chi-restraints excluded: chain A residue 934 VAL Chi-restraints excluded: chain A residue 940 ILE Chi-restraints excluded: chain A residue 966 SER Chi-restraints excluded: chain A residue 968 ARG Chi-restraints excluded: chain A residue 1013 VAL Chi-restraints excluded: chain A residue 1033 GLU Chi-restraints excluded: chain A residue 1209 SER Chi-restraints excluded: chain A residue 1577 MET Chi-restraints excluded: chain C residue 156 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 104 optimal weight: 1.9990 chunk 40 optimal weight: 1.9990 chunk 13 optimal weight: 1.9990 chunk 83 optimal weight: 0.9990 chunk 20 optimal weight: 0.3980 chunk 165 optimal weight: 4.9990 chunk 44 optimal weight: 0.9980 chunk 25 optimal weight: 0.0970 chunk 121 optimal weight: 0.7980 chunk 169 optimal weight: 0.8980 chunk 62 optimal weight: 0.9980 overall best weight: 0.6378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 103 HIS A 493 GLN A 908 GLN A 933 ASN A1023 HIS ** A1439 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4108 r_free = 0.4108 target = 0.170290 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.123084 restraints weight = 19120.777| |-----------------------------------------------------------------------------| r_work (start): 0.3482 rms_B_bonded: 1.70 r_work: 0.3361 rms_B_bonded: 2.11 restraints_weight: 0.5000 r_work: 0.3223 rms_B_bonded: 3.52 restraints_weight: 0.2500 r_work (final): 0.3223 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7776 moved from start: 0.3028 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 14982 Z= 0.139 Angle : 0.566 10.416 20315 Z= 0.286 Chirality : 0.041 0.187 2356 Planarity : 0.005 0.062 2561 Dihedral : 4.231 19.984 2025 Min Nonbonded Distance : 2.027 Molprobity Statistics. All-atom Clashscore : 7.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.72 % Favored : 95.28 % Rotamer: Outliers : 1.77 % Allowed : 15.33 % Favored : 82.90 % 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: 0.79 (0.20), residues: 1845 helix: 1.79 (0.17), residues: 1029 sheet: 0.36 (0.54), residues: 100 loop : -1.41 (0.23), residues: 716 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 58 TYR 0.025 0.002 TYR A1164 PHE 0.020 0.001 PHE A1222 TRP 0.020 0.001 TRP A 638 HIS 0.008 0.001 HIS A1181 Details of bonding type rmsd covalent geometry : bond 0.00329 (14976) covalent geometry : angle 0.56569 (20315) hydrogen bonds : bond 0.04724 ( 758) hydrogen bonds : angle 4.02747 ( 2217) metal coordination : bond 0.00462 ( 6) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6245.52 seconds wall clock time: 106 minutes 55.61 seconds (6415.61 seconds total)