Starting phenix.real_space_refine on Sat Sep 12 16:51:21 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7y8t_33685/09_2026/7y8t_33685.cif Found real_map, /net/cci-nas-00/data/ceres_data/7y8t_33685/09_2026/7y8t_33685.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7y8t_33685/09_2026/7y8t_33685.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7y8t_33685/09_2026/7y8t_33685.map" model { file = "/net/cci-nas-00/data/ceres_data/7y8t_33685/09_2026/7y8t_33685.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7y8t_33685/09_2026/7y8t_33685.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/7y8t_33685/09_2026/7y8t_33685.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7y8t_33685/09_2026/7y8t_33685.cif" } resolution = 2.9 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.119 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: 6 Type Number sf(0) Gaussians Zn 4 6.06 5 P 37 5.49 5 S 59 5.16 5 C 10512 2.51 5 N 2904 2.21 5 O 3238 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 42 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 16754 Number of models: 1 Model: "" Number of chains: 4 Chain: "B" Number of atoms: 5504 Number of conformers: 1 Conformer: "" Number of residues, atoms: 680, 5504 Classifications: {'peptide': 680} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 20, 'TRANS': 659} Chain breaks: 1 Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'GLU:plan': 3} Unresolved non-hydrogen planarities: 12 Chain: "A" Number of atoms: 10466 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1298, 10466 Classifications: {'peptide': 1298} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'CIS': 1, 'PTRANS': 62, 'TRANS': 1234} Chain breaks: 4 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "D" Number of atoms: 780 Number of conformers: 1 Conformer: "" Number of residues, atoms: 37, 780 Classifications: {'RNAv2': 37} Modifications used: {'rna2p_pur': 10, 'rna2p_pyr': 10, 'rna3p_pur': 6, 'rna3p_pyr': 11} Link IDs: {'rna2p': 20, 'rna3p': 16} Chain: "A" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Unusual residues: {' ZN': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 9192 SG CYS A 491 61.116 51.816 50.101 1.00 60.93 S ATOM 9260 SG CYS A 501 61.590 51.013 46.403 1.00 33.74 S ATOM 9274 SG CYS A 503 64.546 50.926 48.695 1.00 41.26 S ATOM 9296 SG CYS A 506 62.050 48.215 49.056 1.00 46.83 S ATOM 13400 SG CYS A1018 46.872 70.098 113.423 1.00 55.51 S ATOM 13627 SG CYS A1406 45.677 71.098 109.912 1.00 53.97 S ATOM 13678 SG CYS A1414 48.583 72.871 111.650 1.00 54.56 S ATOM 13695 SG CYS A1417 49.120 69.478 110.266 1.00 50.15 S ATOM 6180 SG CYS A 88 59.864 27.789 24.176 1.00 41.27 S ATOM 6451 SG CYS A 121 58.524 24.987 21.896 1.00 57.46 S ATOM 6497 SG CYS A 127 60.154 24.231 25.302 1.00 39.89 S ATOM 6521 SG CYS A 130 56.771 25.960 25.153 1.00 52.05 S ATOM 11267 SG CYS A 750 55.228 70.995 75.170 1.00 59.37 S ATOM 11280 SG CYS A 752 58.350 70.400 77.167 1.00 42.86 S ATOM 11302 SG CYS A 755 56.481 67.389 75.796 1.00 46.67 S Time building chain proxies: 3.14, per 1000 atoms: 0.19 Number of scatterers: 16754 At special positions: 0 Unit cell: (107.8, 107.8, 167.2, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Zn 4 29.99 S 59 16.00 P 37 15.00 O 3238 8.00 N 2904 7.00 C 10512 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: 1.38 Conformation dependent library (CDL) restraints added in 563.2 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A1801 " pdb="ZN ZN A1801 " - pdb=" SG CYS A 503 " pdb="ZN ZN A1801 " - pdb=" SG CYS A 506 " pdb="ZN ZN A1801 " - pdb=" SG CYS A 491 " pdb="ZN ZN A1801 " - pdb=" SG CYS A 501 " pdb=" ZN A1802 " pdb="ZN ZN A1802 " - pdb=" SG CYS A1414 " pdb="ZN ZN A1802 " - pdb=" SG CYS A1018 " pdb="ZN ZN A1802 " - pdb=" SG CYS A1406 " pdb="ZN ZN A1802 " - pdb=" SG CYS A1417 " pdb=" ZN A1803 " pdb="ZN ZN A1803 " - pdb=" SG CYS A 88 " pdb="ZN ZN A1803 " - pdb=" SG CYS A 130 " pdb="ZN ZN A1803 " - pdb=" SG CYS A 127 " pdb="ZN ZN A1803 " - pdb=" SG CYS A 121 " pdb=" ZN A1804 " pdb="ZN ZN A1804 " - pdb=" ND1 HIS A 747 " pdb="ZN ZN A1804 " - pdb=" SG CYS A 752 " pdb="ZN ZN A1804 " - pdb=" SG CYS A 750 " pdb="ZN ZN A1804 " - pdb=" SG CYS A 755 " Number of angles added : 21 3928 Ramachandran restraints generated. 1964 Oldfield, 0 Emsley, 1964 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3668 Finding SS restraints... Secondary structure from input PDB file: 73 helices and 21 sheets defined 39.2% alpha, 16.1% beta 0 base pairs and 9 stacking pairs defined. Time for finding SS restraints: 1.61 Creating SS restraints... Processing helix chain 'B' and resid 14 through 32 Processing helix chain 'B' and resid 37 through 59 removed outlier: 3.789A pdb=" N LYS B 42 " --> pdb=" O PRO B 38 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N LYS B 43 " --> pdb=" O VAL B 39 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N GLU B 58 " --> pdb=" O GLY B 54 " (cutoff:3.500A) Processing helix chain 'B' and resid 64 through 81 removed outlier: 3.774A pdb=" N PHE B 68 " --> pdb=" O THR B 64 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N ILE B 80 " --> pdb=" O TYR B 76 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N THR B 81 " --> pdb=" O LEU B 77 " (cutoff:3.500A) Processing helix chain 'B' and resid 90 through 110 removed outlier: 4.069A pdb=" N LYS B 94 " --> pdb=" O PRO B 90 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N ARG B 106 " --> pdb=" O GLU B 102 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N ALA B 107 " --> pdb=" O PHE B 103 " (cutoff:3.500A) Processing helix chain 'B' and resid 115 through 136 Processing helix chain 'B' and resid 141 through 155 Processing helix chain 'B' and resid 164 through 177 Processing helix chain 'B' and resid 183 through 190 Processing helix chain 'B' and resid 194 through 205 Processing helix chain 'B' and resid 209 through 223 removed outlier: 3.617A pdb=" N LYS B 218 " --> pdb=" O GLU B 214 " (cutoff:3.500A) Processing helix chain 'B' and resid 224 through 226 No H-bonds generated for 'chain 'B' and resid 224 through 226' Processing helix chain 'B' and resid 230 through 246 removed outlier: 4.261A pdb=" N ASP B 234 " --> pdb=" O HIS B 230 " (cutoff:3.500A) Processing helix chain 'B' and resid 250 through 267 removed outlier: 4.362A pdb=" N ILE B 256 " --> pdb=" O ARG B 252 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N LYS B 267 " --> pdb=" O ARG B 263 " (cutoff:3.500A) Processing helix chain 'B' and resid 282 through 297 Processing helix chain 'B' and resid 303 through 321 Processing helix chain 'B' and resid 327 through 333 removed outlier: 3.664A pdb=" N LYS B 333 " --> pdb=" O SER B 329 " (cutoff:3.500A) Processing helix chain 'B' and resid 339 through 359 removed outlier: 3.572A pdb=" N HIS B 343 " --> pdb=" O ASP B 339 " (cutoff:3.500A) removed outlier: 4.124A pdb=" N PHE B 345 " --> pdb=" O SER B 341 " (cutoff:3.500A) removed outlier: 4.690A pdb=" N LYS B 346 " --> pdb=" O ASN B 342 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N GLY B 359 " --> pdb=" O ALA B 355 " (cutoff:3.500A) Processing helix chain 'B' and resid 435 through 448 Processing helix chain 'B' and resid 454 through 469 removed outlier: 4.006A pdb=" N LEU B 458 " --> pdb=" O ALA B 454 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N VAL B 459 " --> pdb=" O ALA B 455 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N THR B 460 " --> pdb=" O GLU B 456 " (cutoff:3.500A) Processing helix chain 'B' and resid 470 through 474 removed outlier: 3.570A pdb=" N CYS B 474 " --> pdb=" O PHE B 471 " (cutoff:3.500A) Processing helix chain 'B' and resid 491 through 495 removed outlier: 3.760A pdb=" N ARG B 494 " --> pdb=" O PHE B 491 " (cutoff:3.500A) Processing helix chain 'B' and resid 496 through 500 removed outlier: 3.792A pdb=" N SER B 500 " --> pdb=" O LEU B 497 " (cutoff:3.500A) Processing helix chain 'B' and resid 509 through 513 removed outlier: 3.605A pdb=" N ASN B 513 " --> pdb=" O PHE B 510 " (cutoff:3.500A) Processing helix chain 'B' and resid 521 through 525 Processing helix chain 'B' and resid 566 through 571 removed outlier: 3.822A pdb=" N LEU B 570 " --> pdb=" O SER B 566 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N GLU B 571 " --> pdb=" O SER B 567 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 566 through 571' Processing helix chain 'B' and resid 592 through 595 Processing helix chain 'B' and resid 607 through 614 removed outlier: 3.514A pdb=" N LEU B 611 " --> pdb=" O TYR B 607 " (cutoff:3.500A) Processing helix chain 'B' and resid 627 through 631 Processing helix chain 'B' and resid 644 through 651 removed outlier: 3.876A pdb=" N ALA B 648 " --> pdb=" O SER B 644 " (cutoff:3.500A) Processing helix chain 'B' and resid 665 through 679 removed outlier: 3.873A pdb=" N THR B 669 " --> pdb=" O ARG B 665 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N ASN B 679 " --> pdb=" O TRP B 675 " (cutoff:3.500A) Processing helix chain 'B' and resid 683 through 691 removed outlier: 3.793A pdb=" N TRP B 687 " --> pdb=" O LYS B 683 " (cutoff:3.500A) Processing helix chain 'B' and resid 699 through 707 removed outlier: 3.636A pdb=" N PHE B 703 " --> pdb=" O HIS B 699 " (cutoff:3.500A) Processing helix chain 'A' and resid 27 through 31 removed outlier: 3.592A pdb=" N LYS A 30 " --> pdb=" O ASP A 27 " (cutoff:3.500A) Processing helix chain 'A' and resid 33 through 38 Processing helix chain 'A' and resid 59 through 77 removed outlier: 3.920A pdb=" N VAL A 63 " --> pdb=" O THR A 59 " (cutoff:3.500A) Processing helix chain 'A' and resid 127 through 133 Processing helix chain 'A' and resid 216 through 226 removed outlier: 3.571A pdb=" N ALA A 222 " --> pdb=" O LYS A 218 " (cutoff:3.500A) Processing helix chain 'A' and resid 267 through 287 removed outlier: 3.901A pdb=" N ASN A 287 " --> pdb=" O ALA A 283 " (cutoff:3.500A) Processing helix chain 'A' and resid 288 through 291 removed outlier: 6.410A pdb=" N GLU A 291 " --> pdb=" O ASP A 288 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 288 through 291' Processing helix chain 'A' and resid 292 through 302 Processing helix chain 'A' and resid 303 through 307 removed outlier: 4.664A pdb=" N GLY A 307 " --> pdb=" O ARG A 304 " (cutoff:3.500A) Processing helix chain 'A' and resid 308 through 313 Processing helix chain 'A' and resid 338 through 351 Processing helix chain 'A' and resid 354 through 375 Processing helix chain 'A' and resid 434 through 438 removed outlier: 3.658A pdb=" N SER A 438 " --> pdb=" O PRO A 435 " (cutoff:3.500A) Processing helix chain 'A' and resid 471 through 488 removed outlier: 3.562A pdb=" N LEU A 475 " --> pdb=" O PRO A 471 " (cutoff:3.500A) Processing helix chain 'A' and resid 503 through 510 removed outlier: 3.710A pdb=" N GLU A 508 " --> pdb=" O LYS A 504 " (cutoff:3.500A) Processing helix chain 'A' and resid 569 through 579 removed outlier: 3.736A pdb=" N SER A 573 " --> pdb=" O PRO A 569 " (cutoff:3.500A) Processing helix chain 'A' and resid 617 through 625 Processing helix chain 'A' and resid 626 through 628 No H-bonds generated for 'chain 'A' and resid 626 through 628' Processing helix chain 'A' and resid 630 through 636 removed outlier: 3.643A pdb=" N GLU A 636 " --> pdb=" O LYS A 632 " (cutoff:3.500A) Processing helix chain 'A' and resid 638 through 642 removed outlier: 3.934A pdb=" N LEU A 642 " --> pdb=" O GLU A 639 " (cutoff:3.500A) Processing helix chain 'A' and resid 665 through 667 No H-bonds generated for 'chain 'A' and resid 665 through 667' Processing helix chain 'A' and resid 688 through 693 Processing helix chain 'A' and resid 723 through 740 removed outlier: 3.624A pdb=" N PHE A 731 " --> pdb=" O HIS A 727 " (cutoff:3.500A) Processing helix chain 'A' and resid 741 through 744 Processing helix chain 'A' and resid 752 through 759 Processing helix chain 'A' and resid 776 through 780 removed outlier: 3.544A pdb=" N GLU A 779 " --> pdb=" O ASN A 776 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N PHE A 780 " --> pdb=" O GLY A 777 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 776 through 780' Processing helix chain 'A' and resid 833 through 847 Processing helix chain 'A' and resid 855 through 859 removed outlier: 3.683A pdb=" N GLY A 859 " --> pdb=" O GLY A 856 " (cutoff:3.500A) Processing helix chain 'A' and resid 873 through 883 Processing helix chain 'A' and resid 908 through 914 removed outlier: 3.930A pdb=" N LYS A 912 " --> pdb=" O HIS A 908 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N ASP A 914 " --> pdb=" O SER A 910 " (cutoff:3.500A) Processing helix chain 'A' and resid 999 through 1016 removed outlier: 3.880A pdb=" N LEU A1003 " --> pdb=" O PRO A 999 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N HIS A1010 " --> pdb=" O MET A1006 " (cutoff:3.500A) Processing helix chain 'A' and resid 1394 through 1399 removed outlier: 3.524A pdb=" N LEU A1399 " --> pdb=" O LEU A1395 " (cutoff:3.500A) Processing helix chain 'A' and resid 1400 through 1404 removed outlier: 3.514A pdb=" N HIS A1404 " --> pdb=" O LYS A1401 " (cutoff:3.500A) Processing helix chain 'A' and resid 1414 through 1421 Processing helix chain 'A' and resid 1486 through 1494 removed outlier: 4.050A pdb=" N ILE A1490 " --> pdb=" O GLY A1486 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N GLN A1492 " --> pdb=" O ARG A1488 " (cutoff:3.500A) Processing helix chain 'A' and resid 1528 through 1540 removed outlier: 3.512A pdb=" N ASP A1540 " --> pdb=" O LEU A1536 " (cutoff:3.500A) Processing helix chain 'A' and resid 1552 through 1556 Processing helix chain 'A' and resid 1583 through 1602 removed outlier: 4.063A pdb=" N GLU A1589 " --> pdb=" O SER A1585 " (cutoff:3.500A) Processing helix chain 'A' and resid 1615 through 1618 Processing helix chain 'A' and resid 1619 through 1629 removed outlier: 3.512A pdb=" N LYS A1627 " --> pdb=" O ASP A1623 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N LEU A1628 " --> pdb=" O LYS A1624 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N LEU A1629 " --> pdb=" O LEU A1625 " (cutoff:3.500A) Processing helix chain 'A' and resid 1673 through 1682 Processing sheet with id=AA1, first strand: chain 'B' and resid 425 through 431 removed outlier: 3.521A pdb=" N SER B 425 " --> pdb=" O ASP B 420 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N PHE B 431 " --> pdb=" O GLY B 414 " (cutoff:3.500A) removed outlier: 6.661A pdb=" N VAL B 401 " --> pdb=" O LEU B 485 " (cutoff:3.500A) removed outlier: 7.902A pdb=" N VAL B 487 " --> pdb=" O VAL B 401 " (cutoff:3.500A) removed outlier: 6.853A pdb=" N VAL B 403 " --> pdb=" O VAL B 487 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 536 through 540 removed outlier: 6.569A pdb=" N LEU B 580 " --> pdb=" O ILE B 623 " (cutoff:3.500A) removed outlier: 4.783A pdb=" N THR B 660 " --> pdb=" O LEU B 624 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N GLY B 659 " --> pdb=" O ARG B 710 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 585 through 587 removed outlier: 4.247A pdb=" N HIS B 585 " --> pdb=" O LYS B 599 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N ILE B 605 " --> pdb=" O LEU B 598 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 151 through 153 Processing sheet with id=AA5, first strand: chain 'A' and resid 151 through 153 removed outlier: 3.596A pdb=" N LEU A 211 " --> pdb=" O MET A 6 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N MET A 6 " --> pdb=" O LEU A 211 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 20 through 22 removed outlier: 4.394A pdb=" N LEU A 167 " --> pdb=" O GLY A 54 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 81 through 82 Processing sheet with id=AA8, first strand: chain 'A' and resid 110 through 111 removed outlier: 5.937A pdb=" N THR A 110 " --> pdb=" O VAL A 405 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'A' and resid 173 through 181 removed outlier: 4.859A pdb=" N ARG A 180 " --> pdb=" O ASP A 190 " (cutoff:3.500A) removed outlier: 5.323A pdb=" N ASP A 190 " --> pdb=" O ARG A 180 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 512 through 513 removed outlier: 3.691A pdb=" N GLY A 565 " --> pdb=" O LYS A 414 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N ILE A 417 " --> pdb=" O PHE A 610 " (cutoff:3.500A) removed outlier: 4.653A pdb=" N ARG A 421 " --> pdb=" O ASP A 606 " (cutoff:3.500A) removed outlier: 5.700A pdb=" N ASP A 606 " --> pdb=" O ARG A 421 " (cutoff:3.500A) removed outlier: 6.887A pdb=" N LYS A 423 " --> pdb=" O LEU A 604 " (cutoff:3.500A) removed outlier: 5.693A pdb=" N LEU A 604 " --> pdb=" O LYS A 423 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N ALA A 589 " --> pdb=" O PHE A 602 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 512 through 513 removed outlier: 3.691A pdb=" N GLY A 565 " --> pdb=" O LYS A 414 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N ILE A 417 " --> pdb=" O PHE A 610 " (cutoff:3.500A) removed outlier: 4.653A pdb=" N ARG A 421 " --> pdb=" O ASP A 606 " (cutoff:3.500A) removed outlier: 5.700A pdb=" N ASP A 606 " --> pdb=" O ARG A 421 " (cutoff:3.500A) removed outlier: 6.887A pdb=" N LYS A 423 " --> pdb=" O LEU A 604 " (cutoff:3.500A) removed outlier: 5.693A pdb=" N LEU A 604 " --> pdb=" O LYS A 423 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 469 through 470 removed outlier: 3.505A pdb=" N SER A 517 " --> pdb=" O ILE A 470 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 526 through 530 removed outlier: 3.537A pdb=" N GLU A 526 " --> pdb=" O VAL A 550 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 703 through 704 removed outlier: 6.202A pdb=" N PHE A 720 " --> pdb=" O LEU A 774 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 703 through 704 removed outlier: 6.202A pdb=" N PHE A 720 " --> pdb=" O LEU A 774 " (cutoff:3.500A) removed outlier: 7.764A pdb=" N GLN A 673 " --> pdb=" O ILE A 868 " (cutoff:3.500A) removed outlier: 5.286A pdb=" N ILE A 868 " --> pdb=" O GLN A 673 " (cutoff:3.500A) removed outlier: 6.602A pdb=" N THR A 675 " --> pdb=" O ILE A 866 " (cutoff:3.500A) removed outlier: 4.493A pdb=" N ILE A 866 " --> pdb=" O THR A 675 " (cutoff:3.500A) removed outlier: 6.674A pdb=" N GLU A 677 " --> pdb=" O ALA A 864 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 707 through 708 Processing sheet with id=AB8, first strand: chain 'A' and resid 787 through 789 Processing sheet with id=AB9, first strand: chain 'A' and resid 924 through 927 Processing sheet with id=AC1, first strand: chain 'A' and resid 991 through 992 removed outlier: 6.811A pdb=" N LEU A 996 " --> pdb=" O TYR A1436 " (cutoff:3.500A) removed outlier: 7.025A pdb=" N VAL A1517 " --> pdb=" O GLU A1437 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N CYS A 956 " --> pdb=" O PHE A1520 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N PHE A1524 " --> pdb=" O GLY A 952 " (cutoff:3.500A) removed outlier: 5.747A pdb=" N LEU A 950 " --> pdb=" O ASN A1526 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'A' and resid 1429 through 1431 removed outlier: 3.555A pdb=" N CYS A 956 " --> pdb=" O PHE A1520 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N PHE A1524 " --> pdb=" O GLY A 952 " (cutoff:3.500A) removed outlier: 5.747A pdb=" N LEU A 950 " --> pdb=" O ASN A1526 " (cutoff:3.500A) removed outlier: 7.152A pdb=" N SER A 951 " --> pdb=" O THR A1569 " (cutoff:3.500A) removed outlier: 4.534A pdb=" N THR A1569 " --> pdb=" O SER A 951 " (cutoff:3.500A) removed outlier: 6.758A pdb=" N LYS A 953 " --> pdb=" O LEU A1567 " (cutoff:3.500A) removed outlier: 4.612A pdb=" N LEU A1567 " --> pdb=" O LYS A 953 " (cutoff:3.500A) removed outlier: 6.769A pdb=" N ASN A 955 " --> pdb=" O ASP A1565 " (cutoff:3.500A) removed outlier: 5.077A pdb=" N LYS A1571 " --> pdb=" O LYS A1578 " (cutoff:3.500A) removed outlier: 5.628A pdb=" N LYS A1578 " --> pdb=" O LYS A1571 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'A' and resid 1453 through 1455 removed outlier: 3.634A pdb=" N THR A1509 " --> pdb=" O LEU A1454 " (cutoff:3.500A) 613 hydrogen bonds defined for protein. 1722 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 9 stacking parallelities Total time for adding SS restraints: 3.21 Time building geometry restraints manager: 1.73 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.03 - 1.19: 3 1.19 - 1.34: 5374 1.34 - 1.50: 4929 1.50 - 1.66: 6814 1.66 - 1.82: 83 Bond restraints: 17203 Sorted by residual: bond pdb=" C PHE A 104 " pdb=" O PHE A 104 " ideal model delta sigma weight residual 1.236 1.029 0.207 1.20e-02 6.94e+03 2.96e+02 bond pdb=" C LEU A 105 " pdb=" O LEU A 105 " ideal model delta sigma weight residual 1.234 1.074 0.161 1.22e-02 6.72e+03 1.73e+02 bond pdb=" C SER A 103 " pdb=" O SER A 103 " ideal model delta sigma weight residual 1.237 1.124 0.113 1.17e-02 7.31e+03 9.31e+01 bond pdb=" CA SER A 103 " pdb=" CB SER A 103 " ideal model delta sigma weight residual 1.528 1.407 0.122 1.56e-02 4.11e+03 6.08e+01 bond pdb=" CB SER A 103 " pdb=" OG SER A 103 " ideal model delta sigma weight residual 1.417 1.338 0.079 2.00e-02 2.50e+03 1.54e+01 ... (remaining 17198 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.80: 22663 1.80 - 3.59: 569 3.59 - 5.39: 120 5.39 - 7.19: 14 7.19 - 8.99: 8 Bond angle restraints: 23374 Sorted by residual: angle pdb=" CA PHE A 104 " pdb=" C PHE A 104 " pdb=" N LEU A 105 " ideal model delta sigma weight residual 116.29 124.44 -8.15 1.30e+00 5.92e-01 3.93e+01 angle pdb=" CA SER A 103 " pdb=" C SER A 103 " pdb=" O SER A 103 " ideal model delta sigma weight residual 120.55 113.96 6.59 1.06e+00 8.90e-01 3.86e+01 angle pdb=" CA PHE A 104 " pdb=" CB PHE A 104 " pdb=" CG PHE A 104 " ideal model delta sigma weight residual 113.80 119.47 -5.67 1.00e+00 1.00e+00 3.22e+01 angle pdb=" N SER A 103 " pdb=" CA SER A 103 " pdb=" C SER A 103 " ideal model delta sigma weight residual 111.28 116.80 -5.52 1.09e+00 8.42e-01 2.57e+01 angle pdb=" N SER A 103 " pdb=" CA SER A 103 " pdb=" CB SER A 103 " ideal model delta sigma weight residual 110.12 117.36 -7.24 1.47e+00 4.63e-01 2.42e+01 ... (remaining 23369 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 29.47: 9731 29.47 - 58.93: 486 58.93 - 88.40: 57 88.40 - 117.86: 3 117.86 - 147.33: 1 Dihedral angle restraints: 10278 sinusoidal: 4573 harmonic: 5705 Sorted by residual: dihedral pdb=" C4' U D 5 " pdb=" C3' U D 5 " pdb=" C2' U D 5 " pdb=" C1' U D 5 " ideal model delta sinusoidal sigma weight residual 36.34 -37.48 73.82 1 3.10e+00 1.04e-01 7.21e+02 dihedral pdb=" C4' G D -5 " pdb=" C3' G D -5 " pdb=" C2' G D -5 " pdb=" C1' G D -5 " ideal model delta sinusoidal sigma weight residual 36.34 -37.36 73.71 1 3.10e+00 1.04e-01 7.19e+02 dihedral pdb=" C4' C D 15 " pdb=" C3' C D 15 " pdb=" C2' C D 15 " pdb=" C1' C D 15 " ideal model delta sinusoidal sigma weight residual 36.35 -37.00 73.34 1 3.10e+00 1.04e-01 7.13e+02 ... (remaining 10275 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.117: 2414 0.117 - 0.234: 53 0.234 - 0.350: 55 0.350 - 0.467: 0 0.467 - 0.584: 1 Chirality restraints: 2523 Sorted by residual: chirality pdb=" CA SER A 103 " pdb=" N SER A 103 " pdb=" C SER A 103 " pdb=" CB SER A 103 " both_signs ideal model delta sigma weight residual False 2.51 1.93 0.58 2.00e-01 2.50e+01 8.52e+00 chirality pdb=" C3' A D -2 " pdb=" C4' A D -2 " pdb=" O3' A D -2 " pdb=" C2' A D -2 " both_signs ideal model delta sigma weight residual False -2.50 -2.80 0.31 2.00e-01 2.50e+01 2.34e+00 chirality pdb=" C3' U D 5 " pdb=" C4' U D 5 " pdb=" O3' U D 5 " pdb=" C2' U D 5 " both_signs ideal model delta sigma weight residual False -2.50 -2.80 0.30 2.00e-01 2.50e+01 2.23e+00 ... (remaining 2520 not shown) Planarity restraints: 2881 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU A1672 " -0.067 5.00e-02 4.00e+02 1.01e-01 1.62e+01 pdb=" N PRO A1673 " 0.174 5.00e-02 4.00e+02 pdb=" CA PRO A1673 " -0.053 5.00e-02 4.00e+02 pdb=" CD PRO A1673 " -0.054 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA LEU A 105 " 0.018 2.00e-02 2.50e+03 3.71e-02 1.38e+01 pdb=" C LEU A 105 " -0.064 2.00e-02 2.50e+03 pdb=" O LEU A 105 " 0.025 2.00e-02 2.50e+03 pdb=" N ARG A 106 " 0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA TYR B 277 " 0.015 2.00e-02 2.50e+03 2.96e-02 8.75e+00 pdb=" C TYR B 277 " -0.051 2.00e-02 2.50e+03 pdb=" O TYR B 277 " 0.019 2.00e-02 2.50e+03 pdb=" N TRP B 278 " 0.017 2.00e-02 2.50e+03 ... (remaining 2878 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.75: 2113 2.75 - 3.29: 14638 3.29 - 3.83: 25265 3.83 - 4.36: 30246 4.36 - 4.90: 53909 Nonbonded interactions: 126171 Sorted by model distance: nonbonded pdb=" N GLN A1584 " pdb=" OE1 GLN A1584 " model vdw 2.218 3.120 nonbonded pdb=" NH1 ARG A 737 " pdb=" O HIS A 942 " model vdw 2.231 3.120 nonbonded pdb=" N GLU A 948 " pdb=" OE1 GLU A 948 " model vdw 2.237 3.120 nonbonded pdb=" N GLU A1529 " pdb=" OE1 GLU A1529 " model vdw 2.239 3.120 nonbonded pdb=" OG SER B 65 " pdb=" ND2 ASN B 112 " model vdw 2.248 3.120 ... (remaining 126166 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.400 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.260 Check model and map are aligned: 0.040 Set scattering table: 0.020 Process input model: 17.640 Find NCS groups from input model: 0.080 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.690 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.190 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8467 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 : 0.004 0.207 17219 Z= 0.247 Angle : 0.706 8.987 23395 Z= 0.381 Chirality : 0.062 0.584 2523 Planarity : 0.005 0.101 2881 Dihedral : 16.603 147.330 6610 Min Nonbonded Distance : 2.218 Molprobity Statistics. All-atom Clashscore : 4.73 Ramachandran Plot: Outliers : 0.20 % Allowed : 6.01 % Favored : 93.79 % Rotamer: Outliers : 1.21 % Allowed : 15.44 % Favored : 83.35 % Cbeta Deviations : 0.05 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.05 % Twisted Proline : 1.22 % Twisted General : 0.26 % 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 (0.19), residues: 1964 helix: 1.80 (0.21), residues: 627 sheet: -0.15 (0.33), residues: 255 loop : -1.73 (0.17), residues: 1082 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 137 TYR 0.016 0.001 TYR B 277 PHE 0.027 0.002 PHE A 104 TRP 0.016 0.001 TRP A1685 HIS 0.005 0.001 HIS B 493 Details of bonding type rmsd/Z covalent geometry : bond 0.00400 / 0.25 (17203) covalent geometry : angle 0.70214 / 0.38 (23374) hydrogen bonds : bond 0.19474 / 12.71 ( 581) hydrogen bonds : angle 6.12246 / 4.43 ( 1722) metal coordination : bond 0.00396 / 0.22 ( 16) metal coordination : angle 2.60120 / 1.60 ( 21) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3928 Ramachandran restraints generated. 1964 Oldfield, 0 Emsley, 1964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3928 Ramachandran restraints generated. 1964 Oldfield, 0 Emsley, 1964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 1740 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 143 time to evaluate : 0.393 Fit side-chains revert: symmetry clash REVERT: A 271 ASP cc_start: 0.7072 (m-30) cc_final: 0.6798 (m-30) outliers start: 21 outliers final: 19 residues processed: 162 average time/residue: 0.6357 time to fit residues: 113.6938 Evaluate side-chains 156 residues out of total 1740 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 137 time to evaluate : 0.561 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 161 ASP Chi-restraints excluded: chain B residue 319 SER Chi-restraints excluded: chain B residue 452 GLU Chi-restraints excluded: chain B residue 566 SER Chi-restraints excluded: chain B residue 591 SER Chi-restraints excluded: chain B residue 697 LYS Chi-restraints excluded: chain A residue 25 ASP Chi-restraints excluded: chain A residue 52 THR Chi-restraints excluded: chain A residue 94 THR Chi-restraints excluded: chain A residue 308 GLU Chi-restraints excluded: chain A residue 311 ILE Chi-restraints excluded: chain A residue 417 ILE Chi-restraints excluded: chain A residue 548 ILE Chi-restraints excluded: chain A residue 784 GLU Chi-restraints excluded: chain A residue 1468 ILE Chi-restraints excluded: chain A residue 1475 ILE Chi-restraints excluded: chain A residue 1631 VAL Chi-restraints excluded: chain A residue 1634 LEU Chi-restraints excluded: chain A residue 1662 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 98 optimal weight: 4.9990 chunk 194 optimal weight: 9.9990 chunk 107 optimal weight: 2.9990 chunk 10 optimal weight: 0.8980 chunk 66 optimal weight: 0.8980 chunk 130 optimal weight: 1.9990 chunk 124 optimal weight: 0.7980 chunk 103 optimal weight: 3.9990 chunk 77 optimal weight: 0.9990 chunk 122 optimal weight: 0.2980 chunk 91 optimal weight: 3.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 328 HIS A 896 ASN A1544 ASN A1617 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3911 r_free = 0.3911 target = 0.163732 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3533 r_free = 0.3533 target = 0.129509 restraints weight = 19447.539| |-----------------------------------------------------------------------------| r_work (start): 0.3495 rms_B_bonded: 2.34 r_work: 0.3240 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work: 0.3111 rms_B_bonded: 4.85 restraints_weight: 0.2500 r_work (final): 0.3111 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8595 moved from start: 0.0821 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 17219 Z= 0.159 Angle : 0.942 22.321 23395 Z= 0.411 Chirality : 0.096 1.519 2523 Planarity : 0.005 0.065 2881 Dihedral : 12.113 150.779 2620 Min Nonbonded Distance : 2.303 Molprobity Statistics. All-atom Clashscore : 3.12 Ramachandran Plot: Outliers : 0.15 % Allowed : 5.86 % Favored : 93.99 % Rotamer: Outliers : 2.25 % Allowed : 13.82 % Favored : 83.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.05 % Twisted Proline : 1.22 % Twisted General : 0.11 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.40 (0.19), residues: 1964 helix: 1.80 (0.21), residues: 640 sheet: 0.01 (0.33), residues: 256 loop : -1.75 (0.17), residues: 1068 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 737 TYR 0.013 0.001 TYR B 704 PHE 0.015 0.002 PHE B 703 TRP 0.017 0.001 TRP A1685 HIS 0.005 0.001 HIS B 493 Details of bonding type rmsd/Z covalent geometry : bond 0.00336 / 0.16 (17203) covalent geometry : angle 0.93907 / 0.41 (23374) hydrogen bonds : bond 0.04950 / 3.21 ( 581) hydrogen bonds : angle 4.51717 / 3.29 ( 1722) metal coordination : bond 0.00335 / 0.19 ( 16) metal coordination : angle 2.64141 / 1.55 ( 21) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3928 Ramachandran restraints generated. 1964 Oldfield, 0 Emsley, 1964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3928 Ramachandran restraints generated. 1964 Oldfield, 0 Emsley, 1964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 1740 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 149 time to evaluate : 0.622 Fit side-chains revert: symmetry clash REVERT: B 527 GLU cc_start: 0.6984 (mm-30) cc_final: 0.6779 (mm-30) REVERT: B 686 GLU cc_start: 0.7594 (OUTLIER) cc_final: 0.6753 (mp0) REVERT: A 6 MET cc_start: 0.8441 (OUTLIER) cc_final: 0.7635 (ppp) REVERT: A 147 LYS cc_start: 0.8329 (ttmt) cc_final: 0.7791 (ttpp) REVERT: A 240 ILE cc_start: 0.8327 (OUTLIER) cc_final: 0.8069 (mp) REVERT: A 271 ASP cc_start: 0.7295 (m-30) cc_final: 0.6935 (m-30) REVERT: A 286 GLN cc_start: 0.7989 (OUTLIER) cc_final: 0.7623 (tt0) REVERT: A 288 ASP cc_start: 0.7996 (t0) cc_final: 0.7722 (t0) REVERT: A 697 ARG cc_start: 0.7865 (mtm180) cc_final: 0.7663 (mtm180) REVERT: A 1493 LYS cc_start: 0.7509 (mmtt) cc_final: 0.7186 (tppt) REVERT: A 1580 LYS cc_start: 0.7896 (OUTLIER) cc_final: 0.7314 (mptt) REVERT: A 1685 TRP cc_start: 0.6692 (OUTLIER) cc_final: 0.4758 (m100) outliers start: 39 outliers final: 16 residues processed: 175 average time/residue: 0.6380 time to fit residues: 123.4175 Evaluate side-chains 170 residues out of total 1740 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 148 time to evaluate : 0.445 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 452 GLU Chi-restraints excluded: chain B residue 682 TYR Chi-restraints excluded: chain B residue 686 GLU Chi-restraints excluded: chain A residue 6 MET Chi-restraints excluded: chain A residue 56 SER Chi-restraints excluded: chain A residue 120 ILE Chi-restraints excluded: chain A residue 240 ILE Chi-restraints excluded: chain A residue 286 GLN Chi-restraints excluded: chain A residue 328 HIS Chi-restraints excluded: chain A residue 500 LEU Chi-restraints excluded: chain A residue 548 ILE Chi-restraints excluded: chain A residue 616 GLN Chi-restraints excluded: chain A residue 640 SER Chi-restraints excluded: chain A residue 698 ASP Chi-restraints excluded: chain A residue 836 LEU Chi-restraints excluded: chain A residue 866 ILE Chi-restraints excluded: chain A residue 1468 ILE Chi-restraints excluded: chain A residue 1544 ASN Chi-restraints excluded: chain A residue 1580 LYS Chi-restraints excluded: chain A residue 1618 VAL Chi-restraints excluded: chain A residue 1662 THR Chi-restraints excluded: chain A residue 1685 TRP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 35 optimal weight: 0.5980 chunk 75 optimal weight: 2.9990 chunk 76 optimal weight: 0.8980 chunk 48 optimal weight: 0.9990 chunk 88 optimal weight: 0.7980 chunk 129 optimal weight: 1.9990 chunk 24 optimal weight: 0.9980 chunk 159 optimal weight: 0.9980 chunk 10 optimal weight: 1.9990 chunk 86 optimal weight: 2.9990 chunk 154 optimal weight: 0.0170 overall best weight: 0.6618 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 592 ASN A 328 HIS A1544 ASN A1617 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3922 r_free = 0.3922 target = 0.164766 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3546 r_free = 0.3546 target = 0.130730 restraints weight = 19526.424| |-----------------------------------------------------------------------------| r_work (start): 0.3510 rms_B_bonded: 2.21 r_work: 0.3258 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work: 0.3127 rms_B_bonded: 4.86 restraints_weight: 0.2500 r_work (final): 0.3127 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8577 moved from start: 0.1053 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 17219 Z= 0.133 Angle : 0.742 12.805 23395 Z= 0.345 Chirality : 0.068 0.965 2523 Planarity : 0.004 0.060 2881 Dihedral : 12.124 149.485 2592 Min Nonbonded Distance : 2.398 Molprobity Statistics. All-atom Clashscore : 3.25 Ramachandran Plot: Outliers : 0.15 % Allowed : 5.65 % Favored : 94.20 % Rotamer: Outliers : 2.82 % Allowed : 13.82 % Favored : 83.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.05 % Twisted Proline : 0.00 % Twisted General : 0.16 % 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: -0.26 (0.19), residues: 1964 helix: 1.90 (0.21), residues: 645 sheet: 0.02 (0.32), residues: 262 loop : -1.65 (0.18), residues: 1057 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 137 TYR 0.013 0.001 TYR B 704 PHE 0.013 0.001 PHE B 703 TRP 0.017 0.001 TRP A 612 HIS 0.017 0.001 HIS A 328 Details of bonding type rmsd/Z covalent geometry : bond 0.00283 / 0.13 (17203) covalent geometry : angle 0.73925 / 0.35 (23374) hydrogen bonds : bond 0.04397 / 2.84 ( 581) hydrogen bonds : angle 4.25191 / 3.10 ( 1722) metal coordination : bond 0.00303 / 0.17 ( 16) metal coordination : angle 2.35603 / 1.33 ( 21) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3928 Ramachandran restraints generated. 1964 Oldfield, 0 Emsley, 1964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3928 Ramachandran restraints generated. 1964 Oldfield, 0 Emsley, 1964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 201 residues out of total 1740 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 152 time to evaluate : 0.651 Fit side-chains revert: symmetry clash REVERT: B 109 ASN cc_start: 0.6718 (m-40) cc_final: 0.6512 (m-40) REVERT: B 166 ASP cc_start: 0.6610 (p0) cc_final: 0.6409 (p0) REVERT: B 527 GLU cc_start: 0.6964 (mm-30) cc_final: 0.6731 (mm-30) REVERT: B 618 LYS cc_start: 0.7761 (OUTLIER) cc_final: 0.7230 (ttmm) REVERT: B 686 GLU cc_start: 0.7594 (OUTLIER) cc_final: 0.6737 (mp0) REVERT: A 6 MET cc_start: 0.8297 (OUTLIER) cc_final: 0.7561 (ppp) REVERT: A 144 GLU cc_start: 0.8310 (OUTLIER) cc_final: 0.7999 (mt-10) REVERT: A 147 LYS cc_start: 0.8279 (ttmt) cc_final: 0.7759 (ttpp) REVERT: A 240 ILE cc_start: 0.8360 (OUTLIER) cc_final: 0.8080 (mp) REVERT: A 271 ASP cc_start: 0.7340 (m-30) cc_final: 0.6883 (m-30) REVERT: A 286 GLN cc_start: 0.7914 (tp40) cc_final: 0.7548 (tt0) REVERT: A 288 ASP cc_start: 0.7981 (t0) cc_final: 0.7704 (t0) REVERT: A 808 TYR cc_start: 0.7779 (m-80) cc_final: 0.7357 (t80) REVERT: A 842 LEU cc_start: 0.8374 (OUTLIER) cc_final: 0.8155 (mt) REVERT: A 913 GLN cc_start: 0.8415 (OUTLIER) cc_final: 0.7186 (mp10) REVERT: A 1496 GLU cc_start: 0.8350 (OUTLIER) cc_final: 0.8145 (pt0) REVERT: A 1580 LYS cc_start: 0.7862 (OUTLIER) cc_final: 0.7288 (mptt) REVERT: A 1685 TRP cc_start: 0.6619 (OUTLIER) cc_final: 0.4710 (m100) outliers start: 49 outliers final: 16 residues processed: 187 average time/residue: 0.6606 time to fit residues: 136.7223 Evaluate side-chains 167 residues out of total 1740 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 141 time to evaluate : 0.678 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 452 GLU Chi-restraints excluded: chain B residue 587 GLU Chi-restraints excluded: chain B residue 618 LYS Chi-restraints excluded: chain B residue 682 TYR Chi-restraints excluded: chain B residue 686 GLU Chi-restraints excluded: chain A residue 6 MET Chi-restraints excluded: chain A residue 56 SER Chi-restraints excluded: chain A residue 120 ILE Chi-restraints excluded: chain A residue 144 GLU Chi-restraints excluded: chain A residue 240 ILE Chi-restraints excluded: chain A residue 500 LEU Chi-restraints excluded: chain A residue 518 VAL Chi-restraints excluded: chain A residue 640 SER Chi-restraints excluded: chain A residue 836 LEU Chi-restraints excluded: chain A residue 842 LEU Chi-restraints excluded: chain A residue 866 ILE Chi-restraints excluded: chain A residue 913 GLN Chi-restraints excluded: chain A residue 956 CYS Chi-restraints excluded: chain A residue 997 MET Chi-restraints excluded: chain A residue 1458 VAL Chi-restraints excluded: chain A residue 1468 ILE Chi-restraints excluded: chain A residue 1496 GLU Chi-restraints excluded: chain A residue 1580 LYS Chi-restraints excluded: chain A residue 1582 VAL Chi-restraints excluded: chain A residue 1634 LEU Chi-restraints excluded: chain A residue 1685 TRP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 103 optimal weight: 0.9980 chunk 41 optimal weight: 2.9990 chunk 14 optimal weight: 0.0370 chunk 186 optimal weight: 2.9990 chunk 128 optimal weight: 0.0170 chunk 171 optimal weight: 1.9990 chunk 113 optimal weight: 0.2980 chunk 137 optimal weight: 3.9990 chunk 132 optimal weight: 3.9990 chunk 185 optimal weight: 0.9990 chunk 130 optimal weight: 3.9990 overall best weight: 0.4698 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 514 HIS A 328 HIS A1544 ASN A1617 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3946 r_free = 0.3946 target = 0.167099 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3572 r_free = 0.3572 target = 0.132660 restraints weight = 19540.597| |-----------------------------------------------------------------------------| r_work (start): 0.3535 rms_B_bonded: 2.03 r_work: 0.3302 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.3168 rms_B_bonded: 4.74 restraints_weight: 0.2500 r_work (final): 0.3168 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8541 moved from start: 0.1316 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.050 17219 Z= 0.119 Angle : 0.670 10.709 23395 Z= 0.315 Chirality : 0.061 0.721 2523 Planarity : 0.004 0.058 2881 Dihedral : 12.287 153.783 2589 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 3.22 Ramachandran Plot: Outliers : 0.15 % Allowed : 5.45 % Favored : 94.40 % Rotamer: Outliers : 2.65 % Allowed : 14.69 % Favored : 82.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.05 % Twisted Proline : 0.00 % Twisted General : 0.16 % 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: -0.09 (0.19), residues: 1964 helix: 2.02 (0.21), residues: 652 sheet: 0.10 (0.33), residues: 262 loop : -1.55 (0.18), residues: 1050 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 145 TYR 0.011 0.001 TYR B 704 PHE 0.012 0.001 PHE B 491 TRP 0.016 0.001 TRP A 612 HIS 0.005 0.001 HIS B 493 Details of bonding type rmsd/Z covalent geometry : bond 0.00250 / 0.12 (17203) covalent geometry : angle 0.66739 / 0.32 (23374) hydrogen bonds : bond 0.03725 / 2.41 ( 581) hydrogen bonds : angle 4.02803 / 2.94 ( 1722) metal coordination : bond 0.00247 / 0.14 ( 16) metal coordination : angle 2.08977 / 1.24 ( 21) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3928 Ramachandran restraints generated. 1964 Oldfield, 0 Emsley, 1964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3928 Ramachandran restraints generated. 1964 Oldfield, 0 Emsley, 1964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 199 residues out of total 1740 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 153 time to evaluate : 0.520 Fit side-chains revert: symmetry clash REVERT: B 109 ASN cc_start: 0.6848 (m-40) cc_final: 0.6607 (m-40) REVERT: B 277 TYR cc_start: 0.7788 (t80) cc_final: 0.7445 (t80) REVERT: B 527 GLU cc_start: 0.6974 (mm-30) cc_final: 0.6746 (mm-30) REVERT: B 618 LYS cc_start: 0.7635 (OUTLIER) cc_final: 0.7072 (ttmm) REVERT: B 686 GLU cc_start: 0.7613 (OUTLIER) cc_final: 0.6810 (mp0) REVERT: A 6 MET cc_start: 0.8216 (OUTLIER) cc_final: 0.7555 (ppp) REVERT: A 125 GLU cc_start: 0.7608 (pp20) cc_final: 0.7275 (mm-30) REVERT: A 144 GLU cc_start: 0.8214 (OUTLIER) cc_final: 0.7899 (mt-10) REVERT: A 147 LYS cc_start: 0.8185 (ttmt) cc_final: 0.7796 (ttpm) REVERT: A 271 ASP cc_start: 0.7355 (m-30) cc_final: 0.6863 (m-30) REVERT: A 286 GLN cc_start: 0.7883 (tp40) cc_final: 0.7526 (tt0) REVERT: A 288 ASP cc_start: 0.7844 (t0) cc_final: 0.7590 (t0) REVERT: A 808 TYR cc_start: 0.7682 (m-80) cc_final: 0.7300 (t80) REVERT: A 913 GLN cc_start: 0.8441 (OUTLIER) cc_final: 0.7207 (mp10) REVERT: A 932 LYS cc_start: 0.7517 (OUTLIER) cc_final: 0.7288 (tmtt) REVERT: A 1496 GLU cc_start: 0.8383 (OUTLIER) cc_final: 0.8165 (pt0) REVERT: A 1580 LYS cc_start: 0.7727 (OUTLIER) cc_final: 0.7136 (mptt) REVERT: A 1685 TRP cc_start: 0.6559 (OUTLIER) cc_final: 0.4812 (m100) outliers start: 46 outliers final: 12 residues processed: 184 average time/residue: 0.6660 time to fit residues: 135.1798 Evaluate side-chains 161 residues out of total 1740 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 140 time to evaluate : 0.445 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 278 TRP Chi-restraints excluded: chain B residue 452 GLU Chi-restraints excluded: chain B residue 587 GLU Chi-restraints excluded: chain B residue 618 LYS Chi-restraints excluded: chain B residue 682 TYR Chi-restraints excluded: chain B residue 686 GLU Chi-restraints excluded: chain A residue 6 MET Chi-restraints excluded: chain A residue 144 GLU Chi-restraints excluded: chain A residue 500 LEU Chi-restraints excluded: chain A residue 548 ILE Chi-restraints excluded: chain A residue 836 LEU Chi-restraints excluded: chain A residue 866 ILE Chi-restraints excluded: chain A residue 913 GLN Chi-restraints excluded: chain A residue 932 LYS Chi-restraints excluded: chain A residue 956 CYS Chi-restraints excluded: chain A residue 997 MET Chi-restraints excluded: chain A residue 1468 ILE Chi-restraints excluded: chain A residue 1496 GLU Chi-restraints excluded: chain A residue 1580 LYS Chi-restraints excluded: chain A residue 1634 LEU Chi-restraints excluded: chain A residue 1685 TRP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 0 optimal weight: 10.0000 chunk 174 optimal weight: 0.9980 chunk 56 optimal weight: 0.9980 chunk 36 optimal weight: 0.8980 chunk 187 optimal weight: 0.7980 chunk 192 optimal weight: 0.7980 chunk 12 optimal weight: 5.9990 chunk 159 optimal weight: 0.9980 chunk 28 optimal weight: 4.9990 chunk 168 optimal weight: 3.9990 chunk 178 optimal weight: 4.9990 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 215 HIS B 592 ASN B 621 GLN A 328 HIS A1544 ASN A1617 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3913 r_free = 0.3913 target = 0.163842 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3534 r_free = 0.3534 target = 0.129519 restraints weight = 19374.279| |-----------------------------------------------------------------------------| r_work (start): 0.3491 rms_B_bonded: 2.17 r_work: 0.3242 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.3110 rms_B_bonded: 4.73 restraints_weight: 0.2500 r_work (final): 0.3110 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8563 moved from start: 0.1349 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 17219 Z= 0.144 Angle : 0.723 11.065 23395 Z= 0.341 Chirality : 0.066 0.789 2523 Planarity : 0.004 0.057 2881 Dihedral : 12.403 152.743 2589 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 3.22 Ramachandran Plot: Outliers : 0.15 % Allowed : 5.75 % Favored : 94.09 % Rotamer: Outliers : 3.11 % Allowed : 14.92 % Favored : 81.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.05 % Twisted Proline : 0.00 % Twisted General : 0.11 % 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: -0.13 (0.19), residues: 1964 helix: 1.98 (0.21), residues: 652 sheet: 0.19 (0.32), residues: 262 loop : -1.60 (0.18), residues: 1050 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 137 TYR 0.014 0.001 TYR B 704 PHE 0.017 0.002 PHE B 703 TRP 0.017 0.001 TRP A 612 HIS 0.005 0.001 HIS B 493 Details of bonding type rmsd/Z covalent geometry : bond 0.00320 / 0.14 (17203) covalent geometry : angle 0.72031 / 0.34 (23374) hydrogen bonds : bond 0.04523 / 2.93 ( 581) hydrogen bonds : angle 4.08924 / 2.98 ( 1722) metal coordination : bond 0.00371 / 0.24 ( 16) metal coordination : angle 2.25181 / 1.25 ( 21) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3928 Ramachandran restraints generated. 1964 Oldfield, 0 Emsley, 1964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3928 Ramachandran restraints generated. 1964 Oldfield, 0 Emsley, 1964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 1740 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 146 time to evaluate : 0.529 Fit side-chains revert: symmetry clash REVERT: B 109 ASN cc_start: 0.6875 (m-40) cc_final: 0.6616 (m-40) REVERT: B 166 ASP cc_start: 0.6616 (p0) cc_final: 0.6398 (p0) REVERT: B 527 GLU cc_start: 0.7024 (mm-30) cc_final: 0.6755 (mm-30) REVERT: B 618 LYS cc_start: 0.7747 (OUTLIER) cc_final: 0.7204 (ttmm) REVERT: B 686 GLU cc_start: 0.7649 (OUTLIER) cc_final: 0.6819 (mp0) REVERT: A 6 MET cc_start: 0.8338 (OUTLIER) cc_final: 0.7638 (ppp) REVERT: A 125 GLU cc_start: 0.7527 (pp20) cc_final: 0.7237 (mt-10) REVERT: A 144 GLU cc_start: 0.8305 (OUTLIER) cc_final: 0.7983 (mt-10) REVERT: A 147 LYS cc_start: 0.8208 (ttmt) cc_final: 0.7803 (ttpm) REVERT: A 271 ASP cc_start: 0.7351 (m-30) cc_final: 0.6856 (m-30) REVERT: A 286 GLN cc_start: 0.7986 (OUTLIER) cc_final: 0.7584 (tt0) REVERT: A 808 TYR cc_start: 0.7761 (m-80) cc_final: 0.7339 (t80) REVERT: A 913 GLN cc_start: 0.8392 (OUTLIER) cc_final: 0.7146 (mp10) REVERT: A 1496 GLU cc_start: 0.8379 (OUTLIER) cc_final: 0.8177 (pt0) REVERT: A 1580 LYS cc_start: 0.7735 (OUTLIER) cc_final: 0.7145 (mptt) REVERT: A 1682 THR cc_start: 0.8977 (t) cc_final: 0.8381 (m) REVERT: A 1685 TRP cc_start: 0.6584 (OUTLIER) cc_final: 0.4733 (m100) outliers start: 54 outliers final: 20 residues processed: 183 average time/residue: 0.6385 time to fit residues: 129.2314 Evaluate side-chains 171 residues out of total 1740 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 142 time to evaluate : 0.605 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 452 GLU Chi-restraints excluded: chain B residue 587 GLU Chi-restraints excluded: chain B residue 618 LYS Chi-restraints excluded: chain B residue 682 TYR Chi-restraints excluded: chain B residue 686 GLU Chi-restraints excluded: chain A residue 6 MET Chi-restraints excluded: chain A residue 56 SER Chi-restraints excluded: chain A residue 120 ILE Chi-restraints excluded: chain A residue 144 GLU Chi-restraints excluded: chain A residue 286 GLN Chi-restraints excluded: chain A residue 308 GLU Chi-restraints excluded: chain A residue 518 VAL Chi-restraints excluded: chain A residue 548 ILE Chi-restraints excluded: chain A residue 616 GLN Chi-restraints excluded: chain A residue 640 SER Chi-restraints excluded: chain A residue 836 LEU Chi-restraints excluded: chain A residue 866 ILE Chi-restraints excluded: chain A residue 913 GLN Chi-restraints excluded: chain A residue 956 CYS Chi-restraints excluded: chain A residue 997 MET Chi-restraints excluded: chain A residue 1445 THR Chi-restraints excluded: chain A residue 1468 ILE Chi-restraints excluded: chain A residue 1475 ILE Chi-restraints excluded: chain A residue 1496 GLU Chi-restraints excluded: chain A residue 1544 ASN Chi-restraints excluded: chain A residue 1580 LYS Chi-restraints excluded: chain A residue 1634 LEU Chi-restraints excluded: chain A residue 1662 THR Chi-restraints excluded: chain A residue 1685 TRP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 173 optimal weight: 4.9990 chunk 131 optimal weight: 0.6980 chunk 61 optimal weight: 6.9990 chunk 153 optimal weight: 7.9990 chunk 1 optimal weight: 1.9990 chunk 144 optimal weight: 3.9990 chunk 2 optimal weight: 1.9990 chunk 120 optimal weight: 0.9980 chunk 58 optimal weight: 3.9990 chunk 111 optimal weight: 0.8980 chunk 24 optimal weight: 0.5980 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 215 HIS B 592 ASN A 328 HIS A1544 ASN A1617 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3901 r_free = 0.3901 target = 0.162834 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3520 r_free = 0.3520 target = 0.128423 restraints weight = 19241.336| |-----------------------------------------------------------------------------| r_work (start): 0.3481 rms_B_bonded: 2.16 r_work: 0.3220 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work: 0.3088 rms_B_bonded: 4.89 restraints_weight: 0.2500 r_work (final): 0.3088 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8618 moved from start: 0.1404 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 17219 Z= 0.154 Angle : 0.739 11.125 23395 Z= 0.348 Chirality : 0.067 0.810 2523 Planarity : 0.005 0.058 2881 Dihedral : 12.477 151.320 2589 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 3.34 Ramachandran Plot: Outliers : 0.20 % Allowed : 6.16 % Favored : 93.64 % Rotamer: Outliers : 3.11 % Allowed : 15.09 % Favored : 81.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.05 % Twisted Proline : 0.00 % Twisted General : 0.11 % 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: -0.16 (0.19), residues: 1964 helix: 1.93 (0.21), residues: 651 sheet: 0.19 (0.32), residues: 262 loop : -1.60 (0.18), residues: 1051 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 137 TYR 0.014 0.001 TYR A 661 PHE 0.017 0.002 PHE B 703 TRP 0.018 0.001 TRP A1685 HIS 0.005 0.001 HIS B 493 Details of bonding type rmsd/Z covalent geometry : bond 0.00348 / 0.15 (17203) covalent geometry : angle 0.73537 / 0.35 (23374) hydrogen bonds : bond 0.04719 / 3.06 ( 581) hydrogen bonds : angle 4.11738 / 2.99 ( 1722) metal coordination : bond 0.00413 / 0.28 ( 16) metal coordination : angle 2.46582 / 1.35 ( 21) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3928 Ramachandran restraints generated. 1964 Oldfield, 0 Emsley, 1964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3928 Ramachandran restraints generated. 1964 Oldfield, 0 Emsley, 1964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 196 residues out of total 1740 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 142 time to evaluate : 0.564 Fit side-chains revert: symmetry clash REVERT: B 109 ASN cc_start: 0.6884 (m-40) cc_final: 0.6628 (m-40) REVERT: B 166 ASP cc_start: 0.6635 (p0) cc_final: 0.6406 (p0) REVERT: B 527 GLU cc_start: 0.7040 (mm-30) cc_final: 0.6770 (mm-30) REVERT: B 618 LYS cc_start: 0.7800 (OUTLIER) cc_final: 0.7252 (ttmm) REVERT: B 686 GLU cc_start: 0.7728 (OUTLIER) cc_final: 0.6909 (mp0) REVERT: A 6 MET cc_start: 0.8358 (OUTLIER) cc_final: 0.8011 (ppp) REVERT: A 125 GLU cc_start: 0.7604 (pp20) cc_final: 0.7306 (mt-10) REVERT: A 144 GLU cc_start: 0.8359 (OUTLIER) cc_final: 0.8039 (mt-10) REVERT: A 147 LYS cc_start: 0.8301 (ttmt) cc_final: 0.7807 (ttpp) REVERT: A 240 ILE cc_start: 0.8504 (OUTLIER) cc_final: 0.8190 (mp) REVERT: A 271 ASP cc_start: 0.7416 (m-30) cc_final: 0.6921 (m-30) REVERT: A 286 GLN cc_start: 0.8050 (OUTLIER) cc_final: 0.7668 (tt0) REVERT: A 808 TYR cc_start: 0.7678 (m-80) cc_final: 0.7366 (t80) REVERT: A 913 GLN cc_start: 0.8441 (OUTLIER) cc_final: 0.7256 (mp10) REVERT: A 959 GLU cc_start: 0.8849 (OUTLIER) cc_final: 0.8297 (tt0) REVERT: A 1499 GLU cc_start: 0.8213 (tt0) cc_final: 0.8000 (tt0) REVERT: A 1580 LYS cc_start: 0.7796 (OUTLIER) cc_final: 0.7192 (mptt) REVERT: A 1682 THR cc_start: 0.8986 (t) cc_final: 0.8427 (m) REVERT: A 1685 TRP cc_start: 0.6800 (OUTLIER) cc_final: 0.4946 (m100) outliers start: 54 outliers final: 23 residues processed: 180 average time/residue: 0.6222 time to fit residues: 123.9975 Evaluate side-chains 174 residues out of total 1740 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 141 time to evaluate : 0.466 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 153 VAL Chi-restraints excluded: chain B residue 452 GLU Chi-restraints excluded: chain B residue 587 GLU Chi-restraints excluded: chain B residue 618 LYS Chi-restraints excluded: chain B residue 682 TYR Chi-restraints excluded: chain B residue 686 GLU Chi-restraints excluded: chain A residue 6 MET Chi-restraints excluded: chain A residue 56 SER Chi-restraints excluded: chain A residue 120 ILE Chi-restraints excluded: chain A residue 144 GLU Chi-restraints excluded: chain A residue 240 ILE Chi-restraints excluded: chain A residue 286 GLN Chi-restraints excluded: chain A residue 308 GLU Chi-restraints excluded: chain A residue 518 VAL Chi-restraints excluded: chain A residue 548 ILE Chi-restraints excluded: chain A residue 556 THR Chi-restraints excluded: chain A residue 616 GLN Chi-restraints excluded: chain A residue 640 SER Chi-restraints excluded: chain A residue 836 LEU Chi-restraints excluded: chain A residue 866 ILE Chi-restraints excluded: chain A residue 913 GLN Chi-restraints excluded: chain A residue 956 CYS Chi-restraints excluded: chain A residue 959 GLU Chi-restraints excluded: chain A residue 997 MET Chi-restraints excluded: chain A residue 1445 THR Chi-restraints excluded: chain A residue 1458 VAL Chi-restraints excluded: chain A residue 1468 ILE Chi-restraints excluded: chain A residue 1475 ILE Chi-restraints excluded: chain A residue 1580 LYS Chi-restraints excluded: chain A residue 1582 VAL Chi-restraints excluded: chain A residue 1634 LEU Chi-restraints excluded: chain A residue 1662 THR Chi-restraints excluded: chain A residue 1685 TRP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 199 optimal weight: 2.9990 chunk 103 optimal weight: 0.4980 chunk 148 optimal weight: 2.9990 chunk 102 optimal weight: 2.9990 chunk 18 optimal weight: 0.9990 chunk 5 optimal weight: 0.2980 chunk 68 optimal weight: 3.9990 chunk 169 optimal weight: 3.9990 chunk 164 optimal weight: 0.9980 chunk 31 optimal weight: 3.9990 chunk 57 optimal weight: 2.9990 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 328 HIS A1544 ASN A1617 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3891 r_free = 0.3891 target = 0.161774 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3504 r_free = 0.3504 target = 0.127096 restraints weight = 19228.713| |-----------------------------------------------------------------------------| r_work (start): 0.3458 rms_B_bonded: 2.19 r_work: 0.3203 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.3070 rms_B_bonded: 4.83 restraints_weight: 0.2500 r_work (final): 0.3070 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8637 moved from start: 0.1478 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 17219 Z= 0.166 Angle : 0.772 11.388 23395 Z= 0.364 Chirality : 0.070 0.874 2523 Planarity : 0.005 0.059 2881 Dihedral : 12.593 151.843 2589 Min Nonbonded Distance : 2.417 Molprobity Statistics. All-atom Clashscore : 3.12 Ramachandran Plot: Outliers : 0.31 % Allowed : 6.06 % Favored : 93.64 % Rotamer: Outliers : 3.40 % Allowed : 15.32 % Favored : 81.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.05 % Twisted Proline : 0.00 % Twisted General : 0.16 % 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: -0.24 (0.19), residues: 1964 helix: 1.84 (0.21), residues: 650 sheet: 0.16 (0.32), residues: 262 loop : -1.63 (0.17), residues: 1052 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 137 TYR 0.015 0.001 TYR A 661 PHE 0.018 0.002 PHE B 703 TRP 0.020 0.001 TRP A1685 HIS 0.006 0.001 HIS B 493 Details of bonding type rmsd/Z covalent geometry : bond 0.00378 / 0.17 (17203) covalent geometry : angle 0.76840 / 0.36 (23374) hydrogen bonds : bond 0.05061 / 3.29 ( 581) hydrogen bonds : angle 4.18594 / 3.04 ( 1722) metal coordination : bond 0.00419 / 0.27 ( 16) metal coordination : angle 2.56693 / 1.43 ( 21) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3928 Ramachandran restraints generated. 1964 Oldfield, 0 Emsley, 1964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3928 Ramachandran restraints generated. 1964 Oldfield, 0 Emsley, 1964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 1740 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 147 time to evaluate : 0.496 Fit side-chains revert: symmetry clash REVERT: B 109 ASN cc_start: 0.6904 (m-40) cc_final: 0.6669 (m-40) REVERT: B 166 ASP cc_start: 0.6621 (p0) cc_final: 0.6401 (p0) REVERT: B 180 MET cc_start: 0.6974 (tpp) cc_final: 0.6235 (tpp) REVERT: B 527 GLU cc_start: 0.7045 (mm-30) cc_final: 0.6785 (mm-30) REVERT: B 569 ASP cc_start: 0.8234 (m-30) cc_final: 0.7218 (m-30) REVERT: B 618 LYS cc_start: 0.7790 (OUTLIER) cc_final: 0.7237 (ttmm) REVERT: B 686 GLU cc_start: 0.7740 (OUTLIER) cc_final: 0.6939 (mp0) REVERT: A 124 GLU cc_start: 0.8312 (OUTLIER) cc_final: 0.7986 (mp0) REVERT: A 125 GLU cc_start: 0.7676 (pp20) cc_final: 0.7431 (mm-30) REVERT: A 144 GLU cc_start: 0.8386 (OUTLIER) cc_final: 0.8072 (mt-10) REVERT: A 147 LYS cc_start: 0.8436 (ttmt) cc_final: 0.8001 (ttpp) REVERT: A 240 ILE cc_start: 0.8550 (OUTLIER) cc_final: 0.8233 (mp) REVERT: A 271 ASP cc_start: 0.7423 (m-30) cc_final: 0.6934 (m-30) REVERT: A 286 GLN cc_start: 0.8074 (OUTLIER) cc_final: 0.7693 (tt0) REVERT: A 288 ASP cc_start: 0.8075 (t0) cc_final: 0.7804 (t0) REVERT: A 808 TYR cc_start: 0.7678 (m-80) cc_final: 0.7321 (t80) REVERT: A 913 GLN cc_start: 0.8419 (OUTLIER) cc_final: 0.7231 (mp10) REVERT: A 959 GLU cc_start: 0.8841 (OUTLIER) cc_final: 0.8292 (tt0) REVERT: A 1499 GLU cc_start: 0.8218 (tt0) cc_final: 0.8012 (tt0) REVERT: A 1580 LYS cc_start: 0.7781 (OUTLIER) cc_final: 0.7162 (mptt) REVERT: A 1682 THR cc_start: 0.8765 (t) cc_final: 0.8203 (m) REVERT: A 1685 TRP cc_start: 0.7036 (OUTLIER) cc_final: 0.5062 (m100) outliers start: 59 outliers final: 28 residues processed: 190 average time/residue: 0.6163 time to fit residues: 129.6617 Evaluate side-chains 181 residues out of total 1740 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 143 time to evaluate : 0.638 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 153 VAL Chi-restraints excluded: chain B residue 283 VAL Chi-restraints excluded: chain B residue 452 GLU Chi-restraints excluded: chain B residue 587 GLU Chi-restraints excluded: chain B residue 618 LYS Chi-restraints excluded: chain B residue 682 TYR Chi-restraints excluded: chain B residue 686 GLU Chi-restraints excluded: chain A residue 56 SER Chi-restraints excluded: chain A residue 120 ILE Chi-restraints excluded: chain A residue 124 GLU Chi-restraints excluded: chain A residue 144 GLU Chi-restraints excluded: chain A residue 240 ILE Chi-restraints excluded: chain A residue 286 GLN Chi-restraints excluded: chain A residue 308 GLU Chi-restraints excluded: chain A residue 518 VAL Chi-restraints excluded: chain A residue 529 TYR Chi-restraints excluded: chain A residue 548 ILE Chi-restraints excluded: chain A residue 556 THR Chi-restraints excluded: chain A residue 616 GLN Chi-restraints excluded: chain A residue 640 SER Chi-restraints excluded: chain A residue 751 THR Chi-restraints excluded: chain A residue 784 GLU Chi-restraints excluded: chain A residue 836 LEU Chi-restraints excluded: chain A residue 866 ILE Chi-restraints excluded: chain A residue 913 GLN Chi-restraints excluded: chain A residue 956 CYS Chi-restraints excluded: chain A residue 959 GLU Chi-restraints excluded: chain A residue 997 MET Chi-restraints excluded: chain A residue 1445 THR Chi-restraints excluded: chain A residue 1458 VAL Chi-restraints excluded: chain A residue 1468 ILE Chi-restraints excluded: chain A residue 1475 ILE Chi-restraints excluded: chain A residue 1544 ASN Chi-restraints excluded: chain A residue 1580 LYS Chi-restraints excluded: chain A residue 1582 VAL Chi-restraints excluded: chain A residue 1634 LEU Chi-restraints excluded: chain A residue 1662 THR Chi-restraints excluded: chain A residue 1685 TRP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 41 optimal weight: 2.9990 chunk 110 optimal weight: 0.7980 chunk 14 optimal weight: 0.0060 chunk 6 optimal weight: 1.9990 chunk 88 optimal weight: 0.7980 chunk 124 optimal weight: 3.9990 chunk 171 optimal weight: 2.9990 chunk 61 optimal weight: 1.9990 chunk 65 optimal weight: 5.9990 chunk 38 optimal weight: 4.9990 chunk 48 optimal weight: 0.6980 overall best weight: 0.8598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 183 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 328 HIS A1617 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3902 r_free = 0.3902 target = 0.163036 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3519 r_free = 0.3519 target = 0.128413 restraints weight = 19417.860| |-----------------------------------------------------------------------------| r_work (start): 0.3473 rms_B_bonded: 2.22 r_work: 0.3219 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.3089 rms_B_bonded: 4.84 restraints_weight: 0.2500 r_work (final): 0.3089 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8617 moved from start: 0.1526 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 17219 Z= 0.144 Angle : 0.732 10.718 23395 Z= 0.345 Chirality : 0.067 0.826 2523 Planarity : 0.004 0.059 2881 Dihedral : 12.508 151.409 2589 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 3.52 Ramachandran Plot: Outliers : 0.20 % Allowed : 6.01 % Favored : 93.79 % Rotamer: Outliers : 2.48 % Allowed : 16.59 % Favored : 80.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.05 % Twisted Proline : 0.00 % Twisted General : 0.16 % 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: -0.17 (0.19), residues: 1964 helix: 1.97 (0.21), residues: 644 sheet: 0.17 (0.32), residues: 262 loop : -1.61 (0.17), residues: 1058 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 137 TYR 0.013 0.001 TYR B 277 PHE 0.016 0.001 PHE B 254 TRP 0.019 0.001 TRP A1685 HIS 0.005 0.001 HIS B 493 Details of bonding type rmsd/Z covalent geometry : bond 0.00318 / 0.14 (17203) covalent geometry : angle 0.72894 / 0.35 (23374) hydrogen bonds : bond 0.04576 / 2.97 ( 581) hydrogen bonds : angle 4.12067 / 3.00 ( 1722) metal coordination : bond 0.00319 / 0.19 ( 16) metal coordination : angle 2.46534 / 1.37 ( 21) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3928 Ramachandran restraints generated. 1964 Oldfield, 0 Emsley, 1964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3928 Ramachandran restraints generated. 1964 Oldfield, 0 Emsley, 1964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 1740 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 147 time to evaluate : 0.667 Fit side-chains revert: symmetry clash REVERT: B 109 ASN cc_start: 0.6896 (m-40) cc_final: 0.6665 (m-40) REVERT: B 166 ASP cc_start: 0.6612 (p0) cc_final: 0.6390 (p0) REVERT: B 618 LYS cc_start: 0.7794 (OUTLIER) cc_final: 0.7239 (ttmm) REVERT: B 686 GLU cc_start: 0.7729 (OUTLIER) cc_final: 0.6961 (mp0) REVERT: A 124 GLU cc_start: 0.8329 (OUTLIER) cc_final: 0.8004 (mp0) REVERT: A 125 GLU cc_start: 0.7703 (pp20) cc_final: 0.7468 (mm-30) REVERT: A 144 GLU cc_start: 0.8383 (OUTLIER) cc_final: 0.8068 (mt-10) REVERT: A 147 LYS cc_start: 0.8428 (ttmt) cc_final: 0.8001 (ttpp) REVERT: A 271 ASP cc_start: 0.7411 (m-30) cc_final: 0.6920 (m-30) REVERT: A 286 GLN cc_start: 0.8058 (OUTLIER) cc_final: 0.7624 (tt0) REVERT: A 288 ASP cc_start: 0.8092 (t0) cc_final: 0.7805 (t0) REVERT: A 808 TYR cc_start: 0.7721 (m-80) cc_final: 0.7381 (t80) REVERT: A 913 GLN cc_start: 0.8436 (OUTLIER) cc_final: 0.7248 (mp10) REVERT: A 959 GLU cc_start: 0.8816 (OUTLIER) cc_final: 0.8271 (tt0) REVERT: A 1499 GLU cc_start: 0.8219 (tt0) cc_final: 0.8007 (tt0) REVERT: A 1580 LYS cc_start: 0.7708 (OUTLIER) cc_final: 0.7090 (mptt) REVERT: A 1682 THR cc_start: 0.8692 (t) cc_final: 0.8136 (m) REVERT: A 1685 TRP cc_start: 0.6917 (OUTLIER) cc_final: 0.5069 (m100) outliers start: 43 outliers final: 27 residues processed: 181 average time/residue: 0.6903 time to fit residues: 138.8058 Evaluate side-chains 178 residues out of total 1740 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 142 time to evaluate : 0.657 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 153 VAL Chi-restraints excluded: chain B residue 247 SER Chi-restraints excluded: chain B residue 283 VAL Chi-restraints excluded: chain B residue 452 GLU Chi-restraints excluded: chain B residue 587 GLU Chi-restraints excluded: chain B residue 618 LYS Chi-restraints excluded: chain B residue 682 TYR Chi-restraints excluded: chain B residue 686 GLU Chi-restraints excluded: chain A residue 56 SER Chi-restraints excluded: chain A residue 120 ILE Chi-restraints excluded: chain A residue 124 GLU Chi-restraints excluded: chain A residue 144 GLU Chi-restraints excluded: chain A residue 286 GLN Chi-restraints excluded: chain A residue 308 GLU Chi-restraints excluded: chain A residue 518 VAL Chi-restraints excluded: chain A residue 548 ILE Chi-restraints excluded: chain A residue 556 THR Chi-restraints excluded: chain A residue 616 GLN Chi-restraints excluded: chain A residue 640 SER Chi-restraints excluded: chain A residue 751 THR Chi-restraints excluded: chain A residue 836 LEU Chi-restraints excluded: chain A residue 866 ILE Chi-restraints excluded: chain A residue 913 GLN Chi-restraints excluded: chain A residue 956 CYS Chi-restraints excluded: chain A residue 959 GLU Chi-restraints excluded: chain A residue 997 MET Chi-restraints excluded: chain A residue 1445 THR Chi-restraints excluded: chain A residue 1458 VAL Chi-restraints excluded: chain A residue 1459 LEU Chi-restraints excluded: chain A residue 1468 ILE Chi-restraints excluded: chain A residue 1475 ILE Chi-restraints excluded: chain A residue 1580 LYS Chi-restraints excluded: chain A residue 1582 VAL Chi-restraints excluded: chain A residue 1634 LEU Chi-restraints excluded: chain A residue 1662 THR Chi-restraints excluded: chain A residue 1685 TRP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 121 optimal weight: 0.9980 chunk 179 optimal weight: 0.9990 chunk 55 optimal weight: 1.9990 chunk 17 optimal weight: 4.9990 chunk 22 optimal weight: 0.6980 chunk 15 optimal weight: 1.9990 chunk 188 optimal weight: 4.9990 chunk 123 optimal weight: 0.0370 chunk 146 optimal weight: 1.9990 chunk 106 optimal weight: 0.7980 chunk 195 optimal weight: 1.9990 overall best weight: 0.7060 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 343 HIS A 328 HIS A1544 ASN A1617 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3917 r_free = 0.3917 target = 0.164529 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3530 r_free = 0.3530 target = 0.129363 restraints weight = 19313.686| |-----------------------------------------------------------------------------| r_work (start): 0.3496 rms_B_bonded: 2.09 r_work: 0.3279 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.3149 rms_B_bonded: 4.40 restraints_weight: 0.2500 r_work (final): 0.3149 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8550 moved from start: 0.1575 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 17219 Z= 0.132 Angle : 0.707 10.304 23395 Z= 0.334 Chirality : 0.064 0.768 2523 Planarity : 0.004 0.059 2881 Dihedral : 12.336 151.569 2589 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 3.31 Ramachandran Plot: Outliers : 0.15 % Allowed : 5.70 % Favored : 94.14 % Rotamer: Outliers : 2.59 % Allowed : 16.71 % Favored : 80.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.05 % Twisted Proline : 0.00 % Twisted General : 0.21 % 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: -0.07 (0.19), residues: 1964 helix: 2.05 (0.21), residues: 646 sheet: 0.28 (0.33), residues: 257 loop : -1.57 (0.18), residues: 1061 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 137 TYR 0.013 0.001 TYR B 704 PHE 0.016 0.001 PHE B 254 TRP 0.018 0.001 TRP A1685 HIS 0.004 0.001 HIS B 493 Details of bonding type rmsd/Z covalent geometry : bond 0.00287 / 0.13 (17203) covalent geometry : angle 0.70383 / 0.33 (23374) hydrogen bonds : bond 0.04177 / 2.71 ( 581) hydrogen bonds : angle 4.04093 / 2.94 ( 1722) metal coordination : bond 0.00266 / 0.15 ( 16) metal coordination : angle 2.24475 / 1.28 ( 21) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3928 Ramachandran restraints generated. 1964 Oldfield, 0 Emsley, 1964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3928 Ramachandran restraints generated. 1964 Oldfield, 0 Emsley, 1964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 1740 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 148 time to evaluate : 0.647 Fit side-chains revert: symmetry clash REVERT: B 109 ASN cc_start: 0.6861 (m-40) cc_final: 0.6605 (m-40) REVERT: B 618 LYS cc_start: 0.7716 (OUTLIER) cc_final: 0.7109 (ttmm) REVERT: B 686 GLU cc_start: 0.7656 (OUTLIER) cc_final: 0.6881 (mp0) REVERT: A 124 GLU cc_start: 0.8310 (OUTLIER) cc_final: 0.7996 (mp0) REVERT: A 125 GLU cc_start: 0.7645 (pp20) cc_final: 0.7438 (mm-30) REVERT: A 144 GLU cc_start: 0.8314 (OUTLIER) cc_final: 0.7988 (mt-10) REVERT: A 147 LYS cc_start: 0.8248 (ttmt) cc_final: 0.7773 (ttpp) REVERT: A 271 ASP cc_start: 0.7367 (m-30) cc_final: 0.6869 (m-30) REVERT: A 286 GLN cc_start: 0.7988 (tp40) cc_final: 0.7552 (tt0) REVERT: A 288 ASP cc_start: 0.8018 (t0) cc_final: 0.7767 (t0) REVERT: A 808 TYR cc_start: 0.7692 (m-80) cc_final: 0.7352 (t80) REVERT: A 913 GLN cc_start: 0.8355 (OUTLIER) cc_final: 0.7203 (mp10) REVERT: A 1499 GLU cc_start: 0.8210 (tt0) cc_final: 0.7986 (tt0) REVERT: A 1580 LYS cc_start: 0.7562 (OUTLIER) cc_final: 0.6955 (mptt) REVERT: A 1682 THR cc_start: 0.8609 (t) cc_final: 0.8042 (m) REVERT: A 1685 TRP cc_start: 0.6637 (OUTLIER) cc_final: 0.4786 (m100) outliers start: 45 outliers final: 24 residues processed: 182 average time/residue: 0.6964 time to fit residues: 140.3666 Evaluate side-chains 171 residues out of total 1740 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 140 time to evaluate : 0.644 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 153 VAL Chi-restraints excluded: chain B residue 247 SER Chi-restraints excluded: chain B residue 452 GLU Chi-restraints excluded: chain B residue 587 GLU Chi-restraints excluded: chain B residue 618 LYS Chi-restraints excluded: chain B residue 682 TYR Chi-restraints excluded: chain B residue 686 GLU Chi-restraints excluded: chain A residue 56 SER Chi-restraints excluded: chain A residue 120 ILE Chi-restraints excluded: chain A residue 124 GLU Chi-restraints excluded: chain A residue 144 GLU Chi-restraints excluded: chain A residue 308 GLU Chi-restraints excluded: chain A residue 500 LEU Chi-restraints excluded: chain A residue 518 VAL Chi-restraints excluded: chain A residue 548 ILE Chi-restraints excluded: chain A residue 556 THR Chi-restraints excluded: chain A residue 616 GLN Chi-restraints excluded: chain A residue 640 SER Chi-restraints excluded: chain A residue 784 GLU Chi-restraints excluded: chain A residue 836 LEU Chi-restraints excluded: chain A residue 866 ILE Chi-restraints excluded: chain A residue 913 GLN Chi-restraints excluded: chain A residue 956 CYS Chi-restraints excluded: chain A residue 997 MET Chi-restraints excluded: chain A residue 1458 VAL Chi-restraints excluded: chain A residue 1468 ILE Chi-restraints excluded: chain A residue 1475 ILE Chi-restraints excluded: chain A residue 1580 LYS Chi-restraints excluded: chain A residue 1634 LEU Chi-restraints excluded: chain A residue 1662 THR Chi-restraints excluded: chain A residue 1685 TRP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 185 optimal weight: 1.9990 chunk 105 optimal weight: 0.6980 chunk 36 optimal weight: 1.9990 chunk 47 optimal weight: 0.9980 chunk 85 optimal weight: 0.8980 chunk 110 optimal weight: 2.9990 chunk 165 optimal weight: 1.9990 chunk 4 optimal weight: 5.9990 chunk 199 optimal weight: 2.9990 chunk 157 optimal weight: 5.9990 chunk 163 optimal weight: 0.6980 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 183 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 328 HIS A1544 ASN A1617 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3899 r_free = 0.3899 target = 0.162575 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3508 r_free = 0.3508 target = 0.127466 restraints weight = 19133.411| |-----------------------------------------------------------------------------| r_work (start): 0.3462 rms_B_bonded: 2.17 r_work: 0.3220 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.3089 rms_B_bonded: 4.68 restraints_weight: 0.2500 r_work (final): 0.3089 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8621 moved from start: 0.1591 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 17219 Z= 0.157 Angle : 0.750 10.796 23395 Z= 0.355 Chirality : 0.067 0.829 2523 Planarity : 0.005 0.059 2881 Dihedral : 12.431 151.550 2589 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 3.22 Ramachandran Plot: Outliers : 0.31 % Allowed : 6.21 % Favored : 93.48 % Rotamer: Outliers : 2.30 % Allowed : 17.17 % Favored : 80.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.05 % Twisted Proline : 0.00 % Twisted General : 0.21 % 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: -0.12 (0.19), residues: 1964 helix: 1.92 (0.21), residues: 651 sheet: 0.30 (0.32), residues: 276 loop : -1.59 (0.18), residues: 1037 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 137 TYR 0.015 0.001 TYR B 277 PHE 0.018 0.002 PHE B 254 TRP 0.020 0.001 TRP A1685 HIS 0.005 0.001 HIS B 493 Details of bonding type rmsd/Z covalent geometry : bond 0.00356 / 0.16 (17203) covalent geometry : angle 0.74683 / 0.36 (23374) hydrogen bonds : bond 0.04813 / 3.13 ( 581) hydrogen bonds : angle 4.12711 / 3.00 ( 1722) metal coordination : bond 0.00382 / 0.25 ( 16) metal coordination : angle 2.51765 / 1.38 ( 21) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3928 Ramachandran restraints generated. 1964 Oldfield, 0 Emsley, 1964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3928 Ramachandran restraints generated. 1964 Oldfield, 0 Emsley, 1964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 1740 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 143 time to evaluate : 0.673 Fit side-chains revert: symmetry clash REVERT: B 109 ASN cc_start: 0.6898 (m-40) cc_final: 0.6663 (m-40) REVERT: B 166 ASP cc_start: 0.6603 (p0) cc_final: 0.6393 (p0) REVERT: B 618 LYS cc_start: 0.7766 (OUTLIER) cc_final: 0.7216 (ttmm) REVERT: B 686 GLU cc_start: 0.7767 (OUTLIER) cc_final: 0.6961 (mp0) REVERT: A 124 GLU cc_start: 0.8353 (OUTLIER) cc_final: 0.8044 (mp0) REVERT: A 125 GLU cc_start: 0.7695 (pp20) cc_final: 0.7479 (mm-30) REVERT: A 144 GLU cc_start: 0.8371 (OUTLIER) cc_final: 0.8054 (mt-10) REVERT: A 147 LYS cc_start: 0.8392 (ttmt) cc_final: 0.8003 (ttpp) REVERT: A 271 ASP cc_start: 0.7413 (m-30) cc_final: 0.6930 (m-30) REVERT: A 286 GLN cc_start: 0.8051 (tp40) cc_final: 0.7619 (tt0) REVERT: A 288 ASP cc_start: 0.8035 (t0) cc_final: 0.7831 (t0) REVERT: A 808 TYR cc_start: 0.7693 (m-80) cc_final: 0.7324 (t80) REVERT: A 913 GLN cc_start: 0.8390 (OUTLIER) cc_final: 0.7244 (mp10) REVERT: A 1499 GLU cc_start: 0.8239 (tt0) cc_final: 0.8018 (tt0) REVERT: A 1580 LYS cc_start: 0.7610 (OUTLIER) cc_final: 0.7023 (mptt) REVERT: A 1664 LYS cc_start: 0.8525 (mtpt) cc_final: 0.8194 (pttt) REVERT: A 1682 THR cc_start: 0.8704 (t) cc_final: 0.8155 (m) REVERT: A 1685 TRP cc_start: 0.6937 (OUTLIER) cc_final: 0.4982 (m100) outliers start: 40 outliers final: 26 residues processed: 171 average time/residue: 0.7006 time to fit residues: 132.8045 Evaluate side-chains 173 residues out of total 1740 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 140 time to evaluate : 0.661 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 153 VAL Chi-restraints excluded: chain B residue 247 SER Chi-restraints excluded: chain B residue 283 VAL Chi-restraints excluded: chain B residue 452 GLU Chi-restraints excluded: chain B residue 587 GLU Chi-restraints excluded: chain B residue 618 LYS Chi-restraints excluded: chain B residue 682 TYR Chi-restraints excluded: chain B residue 686 GLU Chi-restraints excluded: chain A residue 56 SER Chi-restraints excluded: chain A residue 120 ILE Chi-restraints excluded: chain A residue 124 GLU Chi-restraints excluded: chain A residue 144 GLU Chi-restraints excluded: chain A residue 308 GLU Chi-restraints excluded: chain A residue 500 LEU Chi-restraints excluded: chain A residue 518 VAL Chi-restraints excluded: chain A residue 548 ILE Chi-restraints excluded: chain A residue 556 THR Chi-restraints excluded: chain A residue 616 GLN Chi-restraints excluded: chain A residue 640 SER Chi-restraints excluded: chain A residue 784 GLU Chi-restraints excluded: chain A residue 866 ILE Chi-restraints excluded: chain A residue 913 GLN Chi-restraints excluded: chain A residue 956 CYS Chi-restraints excluded: chain A residue 997 MET Chi-restraints excluded: chain A residue 1445 THR Chi-restraints excluded: chain A residue 1458 VAL Chi-restraints excluded: chain A residue 1468 ILE Chi-restraints excluded: chain A residue 1475 ILE Chi-restraints excluded: chain A residue 1544 ASN Chi-restraints excluded: chain A residue 1580 LYS Chi-restraints excluded: chain A residue 1634 LEU Chi-restraints excluded: chain A residue 1662 THR Chi-restraints excluded: chain A residue 1685 TRP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 152 optimal weight: 0.9980 chunk 193 optimal weight: 0.3980 chunk 154 optimal weight: 4.9990 chunk 123 optimal weight: 3.9990 chunk 67 optimal weight: 3.9990 chunk 164 optimal weight: 2.9990 chunk 119 optimal weight: 0.5980 chunk 1 optimal weight: 0.9980 chunk 188 optimal weight: 0.9990 chunk 24 optimal weight: 0.9990 chunk 166 optimal weight: 2.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 183 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 328 HIS A1617 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3900 r_free = 0.3900 target = 0.162648 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3510 r_free = 0.3510 target = 0.127646 restraints weight = 19110.224| |-----------------------------------------------------------------------------| r_work (start): 0.3465 rms_B_bonded: 2.17 r_work: 0.3220 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.3088 rms_B_bonded: 4.71 restraints_weight: 0.2500 r_work (final): 0.3088 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8621 moved from start: 0.1595 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.189 17219 Z= 0.229 Angle : 0.902 59.199 23395 Z= 0.477 Chirality : 0.067 0.827 2523 Planarity : 0.005 0.059 2881 Dihedral : 12.432 151.567 2589 Min Nonbonded Distance : 2.188 Molprobity Statistics. All-atom Clashscore : 3.58 Ramachandran Plot: Outliers : 0.31 % Allowed : 6.16 % Favored : 93.53 % Rotamer: Outliers : 2.30 % Allowed : 17.22 % Favored : 80.47 % Cbeta Deviations : 0.05 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.05 % Twisted Proline : 0.00 % Twisted General : 0.21 % 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: -0.10 (0.19), residues: 1964 helix: 1.92 (0.21), residues: 651 sheet: 0.29 (0.32), residues: 276 loop : -1.57 (0.18), residues: 1037 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 137 TYR 0.017 0.001 TYR B 277 PHE 0.018 0.002 PHE B 703 TRP 0.020 0.001 TRP A1685 HIS 0.005 0.001 HIS B 493 Details of bonding type rmsd/Z covalent geometry : bond 0.00434 / 0.23 (17203) covalent geometry : angle 0.89902 / 0.48 (23374) hydrogen bonds : bond 0.04776 / 3.10 ( 581) hydrogen bonds : angle 4.12665 / 3.00 ( 1722) metal coordination : bond 0.00367 / 0.24 ( 16) metal coordination : angle 2.52125 / 1.39 ( 21) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5510.98 seconds wall clock time: 94 minutes 42.64 seconds (5682.64 seconds total)